Multigene curations ready to go live

[beamilon]

I have curated multi-gene displays for all datasets in the following profiles (very few have issues and I am keeping track of them and will create tickets later):

• Adult
• Aging
• Central auditory system
• Chick
• Development
• Ear (diverse variety)
• Hair cell
• Hair cell and supporting cell transcriptomics and epigenomics, Mouse (Segil 2021)
• Hair cell reprogramming - transcriptomics and epigenetics (Segil)
• Hearing (default)
• Human disease
• Lateral wall
• Mouse models
• Mouse models 2
• Neuron

[jorvis]

OK, and what user were you logged in as when you made these curations?

[beamilon]

Curator

[beamilon]

@jorvis: some datasets seem to have escaped the transfer of owner for multigene display. If it is just because you are still implementing them, SORRY.

• P7-adult, mouse, RNA-seq, medial geniculate and primary auditory cortex (A1) (Hackett)
• P25-30, mouse, microarray, IHC vs OHC (He)
• in vitro, chick, RNA-seq, utricle, response to Streptomycin (Lovett)
• E6.5, chicken, RNA-seq, proximal, middle, distal sections of basilar papilla (Corwin)
• E10.5, mouse, microarray, otic vesicle, periotic tissue, and non-otic tissue (Heller)
• P3, 8 wko, mouse, microarray, cochlear sensory epithelium (Zine)
• P2, mouse, scRNA-seq, cochlea (Hertzano/Ament)
• P7, Mouse, cochlea, scRNAseq (Hertzano/Ament)
• P7, mouse, scRNA-seq, utricle (Hertzano/Ament)
• P2, mouse, scRNA-seq, utricle (Hertzano/Ament)
• P1, mouse, scRNA-seq, cochlea, hair cells, supporting cells, and non sensory cells (Kelley)
• P1, mouse, scRNA-seq, utricle, hair cells, supporting cells, and transitional epithelial cells (Kelley)
• P1, P12, P100, mouse, scRNA-seq, utricular hair cells (Kelley)
• RNAseq, Deiters' cells,pillar cells, Inner Hair Cells and Outer Hair Cells (He)
• P2, mouse, sc-qRT-PCR, cochlea (Heller)
• E16-P7, mouse, RNA-seq, hair cells vs rest of tissue (Chen)
• E16.5, P0, mouse, RNA-seq, cochlear and vestibular sensory epithelium (Avraham)
• E18.5-P0, mouse, RNA-seq, IHC vs OHC and INSM1 control vs KO OHC (Garcia-Añoveros)
• P8, mouse, scRNA-seq, hair cells, Anc80-Ikzf2 transduced and control (Hertzano)
• P3, P7, P13 and P60, mouse, microarray, Alpha9 nAChR WT and KO Cochleae (Vetter)
• E18.5, P15, P90, mouse, microarray, IGF1 WT and Mutant vestibular organs (Milo)
• 9 wko, mouse, scRNA-seq, cochlea, spiral ganglion neurons (Decibel Tx)

[beamilon]

@jorvis, I added multigene display to these additional datasets.

• Outer Hair Cell Response to PTS-inducing noise (PrestinCre;RiboTag;CBA mice), RiboTag RNA-seq
• Supporting Cell Response to PTS-inducing noise (Sox2Cre;RiboTag;CBA mice), RiboTag RNA-seq
• Spiral Ganglion Neurons (SGN) Response to PTS-inducing noise (scRNA-seq), UMAP display
• Spiral Ganglion Neurons (SGN) Response to PTS-inducing noise (scRNA-seq), violin plot display
• Lateral Wall Response to PTS-inducing noise (scRNA-seq), UMAP display
• Lateral Wall Response to PTS-inducing noise (scRNA-seq), violin plot display
• CD45+ Cochlear Immune Cells Response to PTS-inducing noise, scRNA-seq, UMAP display
• CD45+ Cochlear Immune Cells Response to PTS-inducing noise, scRNA-seq, violin plot display
• Lateral Wall Immune Cells Response to PTS-inducing noise, scRNA-seq, UMAP display
• Lateral Wall Immune Cells Response to PTS-inducing noise, scRNA-seq, violin plot display
• Supporting Cell and Hair Cells Specific Transcriptional Responses to Heat Shock in the Mouse Utricle Epithelium (Cunningham)
• 4-8 weeks, mouse, RNA-seq, utricle, heat shock (Cunningham)
• P1, mouse, RNA-seq, cochlea, hair cells, Gentamicin-induced gene expression changes (Segil)
• 6-7wks, mouse, RNA-seq, cochleae post 2h of 120dB noise exposure (Nishizaki)
• P60, mouse, RNA-seq, cochlea exposed to ambient (70dB), loud (94dB) and very loud (105dB) noise (Savas)
• Post-hatched 1-day-old, chicken, RNA-seq, basilar papillae treated with streptomycin (Nakagawa)
• P3-5, mouse, microarray, organ of Corti (OC) and spiral ganglion (SG) treated with kainate (KA) for 2h and 5h, 24h and 72h post culture vs Control (CTRL) (Stankovic)
• Mouse, RNA-seq, HEI-OC1 cells exposed to cisplatin vs untreated controls (Hati)

[jorvis]

I haven't done anything here yet. Are these datasets all within the same profiles as mentioned initially?

[beamilon]

The first list yes. The second list are datasets in NIHL, cell type-specific transcriptomics, mouse cochlea (Hertzano 2021) and in Noise/Damage/Protection.

[beamilon]

More curations done today:

• P0, mouse, RNA-seq, epithelial vs neuronal, mesenchymal and vascular endothelial (Hertzano)
• 8-10 weeks-old, mouse, microarray, middle ear epithelium (MEE) in vitro air-liquid interface (ALI) culture for 7 days (Bingle)
• RNASEQ, schwannoma cells exposed to electromagnetic field (EMF)
• embryonic stem cell line, microarray, induction of hair cells (Henrique)
• human, RNA-seq, dermal fibroblasts transdifferentiated towards the otic lineage (Schimmang)
• P1, P4, mouse, RNA-seq, cochlea, with and without Wnt activation (Dabdoub)
• P1-2, mouse, RNA-seq, LGR5+ progenitors after neomycin injury (Chai)
• 4-6wks, mouse, scRNA-seq, utricle Atoh1-transduced supporting cells (Groves)
• P7, mouse, RNA-seq, cochlea, Notch1 conditional KO with and without b-catenin overexpression (Li)
• Hair cell induction from mESCs, 9 days in culture, RNA-seq, derived from control, Barhl1-mutants or mouse mutant for the Atoh1-bound Barhl1-enhancer (B-Ebox) (Huang)
• Adult, human, RNA-seq, vestibular sensory epithelia (Forge)
• Microarray, synaptic regeneration, cochlear hair cells and neurons (Stankovic's lab)

[jorvis]

OK. I'll tackle these tonight.

[beamilon]

Here are more. I will try to finish tomorrow

• Dying Tall and Short HCs, chicken (Heller)
• Dying Tall HCs, chicken - violin plot (Heller)
• Dying Tall HCs, chicken - trajectory colored by expression (Heller)
• Dying Tall HCs, chicken - trajectory colored by cell type (Heller)
• Dying Short HCs, chicken - violin plot (Heller)
• Dying Short HCs, chicken - trajectory colored by expression (Heller)
• Dying Short HCs, chicken - trajectory colored by cell type (Heller)
• Molecular anatomy of the chicken utricle (P7) - Trajectory Striola I, Violin Display,entrezID
• Molecular anatomy of the chicken utricle(P7)- Trajectory Striola I, Gene Expression,entrezID
• Molecular anatomy of the chicken utricle (P7) - Trajectory Striola I,States,entrezID
• Molecular anatomy of the chicken utricle (P7)- Trajectory Striola II, Violin Display,entrezID
• Molecular anatomy of the chicken utricle (P7) - Trajectory Striola II,Gene Expression,entrezID
• Molecular anatomy of the chicken utricle (P7) - Trajectory Striola II,States,entrezID
• Molecular anatomy of the chicken utricle(P7)-Trajectory Extrastriola, Violin Display,entrezID
• Molecular anatomy of the chicken utricle(P7)-Trajectory Extrastriola, Gene Expression,entrezID
• Molecular anatomy of the chicken utricle(P7)-Trajectory Extrastriola, States,entrezID
• scRNAseq, Atoh1+Ikzf2 overexpression in adult supporting cells, published UMAP (Liu, 2021)
• scRNAseq, Atoh1+Ikzf2 overexpression in adult supporting cells, published violin plot(Liu, 2021)

[beamilon]

Last datasets for now:

• scRNA-Seq of all principal neonatal cochlear cell groups,cell type,svg (Heller)
• scRNA-Seq of all principal neonatal cochlear cell groups,gate (Heller)
• scRNA-Seq of all principal neonatal cochlear cell groups,CellTrails (Heller)
• scRNA-Seq of all principal neonatal cochlear cell groups,cell type,color_code (Heller)
• scRNA-Seq of all principal neonatal cochlear cell groups,violin,version2 (Heller)
• P2, mouse, scRNA-seq, Organ of Corti Clustering (Waldhaus)
• mouse, scRNA-seq, Organ of Corti Violin Plots (Waldhaus)
• P2, mouse, scATAC-seq, Organ of Corti Transcription Factor Motif Accessibility (Waldhaus)
• Mouse, scRNAseq,postnatal mouse utricle,SWNE plot(Jan)
• 4dpf, zebrafish, microarray, hair cell, mantle cell and skin (Hudspeth)
• 5dpf, zebrafish, RNA-seq, hair cell (IP) and whole larvae input (IN) (Hertzano)
• Neuromast Regeneration,scRNAseq--All Time Points, line plot
• Neuromast Regeneration,scRNAseq--control
• Neuromast Regeneration,scRNAseq--0min
• Neuromast Regeneration,scRNAseq--0.5hr
• Neuromast Regeneration,scRNAseq--1hr
• Neuromast Regeneration,scRNAseq--3hr
• Neuromast Regeneration,scRNAseq--5hr
• Neuromast Regeneration,scRNAseq--10hr

[jorvis]

This is ready and has run on the Adult profile as a test. When I added your expanded list of datasets though there was at least one instance where there were more than one dataset title with the exact same title. Example:

mysql> select id, date_added, marked_for_removal from dataset where title = 'Spiral Ganglion Neurons (SGN) Response to PTS
-inducing noise (scRNA-seq), violin plot display';
+--------------------------------------+---------------------+--------------------+
| id                                   | date_added          | marked_for_removal |
+--------------------------------------+---------------------+--------------------+
| 11f16f75-bfdd-0397-c9c1-e4cf35db5287 | 2021-01-31 22:58:37 |                  0 |
| 482cb81f-4816-e4e3-a3fe-514707b847d8 | 2021-01-28 03:54:28 |                  0 |
+--------------------------------------+---------------------+--------------------+

We can talk and resolve this tomorrow.

[beamilon]

Some datasets have several windows with different displays in the single gene search. The dataset is the same but the title is slightly different like the one below. Is this the problem? I took advantage of the multiple windows to create different multigene displays. Spiral Ganglion Neurons (SGN) Response to PTS-inducing noise (scRNA-seq), UMAP display Spiral Ganglion Neurons (SGN) Response to PTS-inducing noise (scRNA-seq), violin plot display

[jorvis]

No, it's totally fine to have the display variations in the title as you've shown just there. The ones which are causing an error are those where the titles are absolutely identical. Here are those datasets owned by curator and how many times that title is found. There is even one which is loaded 9 times.

mysql> select title, count(title) from dataset where marked_for_removal = 0 and owner_id = 499 group by title having count(title) > 1;
+-----------------------------------------------------------------------------------------------+--------------+
| title                                                                                         | count(title) |
+-----------------------------------------------------------------------------------------------+--------------+
| scRNAseq, Atoh1+Ikzf2 overexpression in adult supporting cells, published UMAP (Liu, 2021)    |            2 |
| P2, mouse, scATAC-seq, organ of Corti apex and base (Waldhaus)                                |            2 |
| P1, mouse, scRNA-seq, cochlear epithelium,subset50,demo1 (Kelley)                             |            9 |
| Spiral Ganglion Neurons (SGN) Response to PTS-inducing noise (scRNA-seq), violin plot display |            2 |
| Elena upload test                                                                             |            2 |
| CD45+ Cochlear Immune Cells Response to PTS-inducing noise, scRNA-seq, violin plot display    |            2 |
| Lateral Wall Response to PTS-inducing noise (scRNA-seq), violin plot display                  |            2 |
| Lateral Wall Immune Cells Response to PTS-inducing noise, scRNA-seq, violin plot display      |            2 |
+-----------------------------------------------------------------------------------------------+--------------+

[beamilon]

I see. I will check with Ronna because I am sure that some of the duplicates can be removed but we need to make sure that even though the title is the same, the data within them are exactly the same.

[jorvis]

All of the datasets within the profiles initially posted in this ticket have been updated.

Can do the rest when we work out the duplication issue.

[beamilon]

I started looking at the duplicates.

• For scRNAseq, Atoh1+Ikzf2 overexpression in adult supporting cells, published UMAP (Liu, 2021), the correct one was uploaded on Thu Nov 11 2021.
• P2, mouse, scATAC-seq, organ of Corti apex and base (Waldhaus) is a private dataset and it is not in the profile so it doesn't matter for the moment.
• P1, mouse, scRNA-seq, cochlear epithelium,subset50,demo1 (Kelley) seems to be a demo and was not in the profile I curated.
• Same for Spiral Ganglion Neurons (SGN) Response to PTS-inducing noise (scRNA-seq), violin plot display Elena upload test, it is not a version that is in the profile.
• I still need to look at the last three.

[beamilon]

All the needed datasets have multiple displays now. So I think this ticket can be closed.

[beamilon]

I added a display for P0, mouse, RNA-seq, hair cells vs epithelial non-hair cells (Hertzano) So ticket not ready to be closed I guess.

[beamilon]

I think that these 2 datasets were not transferred as default. They are in curator but not in my account 4dpf, zebrafish, microarray, hair cell, mantle cell and skin (Hudspeth) 5dpf, zebrafish, RNA-seq, hair cell (IP) and whole larvae input (IN) (Hertzano)

Now that the following dataset has been fixed, I created a multigene display 4dpf, zebrafish, RNA-seq, TU-tagged hair cells mRNA and whole larvae input (Nicolson)