search

ebi-ait / hca-ebi-wrangler-central

This repo is for tracking work related to wrangling datasets for the HCA, associated tasks and for maintaining related documentation.
https://ebi-ait.github.io/hca-ebi-wrangler-central/
Apache License 2.0
7 stars 2 forks source link

Peng He - ImmuneLung #597

Closed ESapenaVentura closed 10 months ago

ESapenaVentura commented 2 years ago

Project short name:

ImmuneLung

Primary Wrangler:

@ESapenaVentura

Secondary Wrangler:

TBD

Associated files

Key Events

ESapenaVentura commented 2 years ago

Organoid data: https://www.biorxiv.org/content/10.1101/2021.06.30.450501v1?rss=1&utm_source=dlvr.it&utm_medium=twitter

MightyAx commented 2 years ago

Organiod data is due to be split out and finished by the 15th February.

ESapenaVentura commented 2 years ago

This will be used for the Immune Lung dataset

Current status:

Wkt8 commented 2 years ago

Rough publication date (Peng) for late March, but he wants accessions ASAP.

ofanobilbao commented 2 years ago

@ESapenaVentura any news/progress on this?

gabsie commented 2 years ago

This dataset went live but was meant to go live late November. Enrique will try and help.

ESapenaVentura commented 2 years ago

Managed to retract the dataset

Wkt8 commented 2 years ago

ArrayExpress did ad-hoc annotation on the dataset, this was wrong in one of the samples. Enrique has created a ticket in the ArrayExpress helpdesk.

We should think about how much active support we give as opposed to pointing people at the ArrayExpress / service helpdesk.

ofanobilbao commented 1 year ago

Might be now public as https://www.cell.com/cell-stem-cell/fulltext/S1934-5909(22)00460-X?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS193459092200460X%3Fshowall%3Dtrue

idazucchi commented 11 months ago
  1. check if the publication matches the project
  2. update ingest and close ticket
idazucchi commented 10 months ago

@arschat to check with Peng if this is the same dataset and if it can be pushed to the DCP?

arschat commented 10 months ago

Asked Peng if the biorxiv manuscript has being submitted and data & metadata have being made public yet.

Project in ingest does not have a submission, but there is a filled spreadsheet in the drive folder. The fastq files and donor HDBR accessions mentioned in the spreadsheets, is wrangled in the #1160 which is still on hold due to more organoid data about to be submitted in AE and then in DCP.

The Cell Stem Cell publication has this accession E-MTAB-11435 of primary data, and uses data from E-MTAB-11278 which was wrangled in #274 . Both the biorxiv and the Cell Stem Cell publication reference the GSE178529 which includes only bulk RNA-seq and bulk ATAC-seq data as well as DamID-seq (no single cell sequencing data).

arschat commented 10 months ago

Peng verified that the biorxiv manuscript is the one that is now published in Cell Stem Cell.

arschat commented 10 months ago

The action here is to wrangle E-MTAB-11435 and GSE178529. I updated ingest with this information but it is down-prioritized since it is not a bionetworks dataset, HCA publication.

Therefore ticket is closed