Question about data

[lilac-moon]

hello. My name is Sohee Kim. I'm looking at your data with interest, but I have a question. In RIS conditions, there are d0, d3-6, and d9 in the columns of TPM data, d1-d9, IR_d1-d9 in RIS_raw_counts.txt, d2, d3-9_IR in RIS_column_data.txt, There are also d2_no_xray and d3-9_xray data sequencing raw data in GEO. I would like to know the exact time points of the RIS condition, and I am curious if 'no-xray control' also has a time points.

[dghendrickson]

Hi Sohee, thanks for your interest. The column names in github and in source data are the same, I just changed the name of "d2" to "d0" for ease of interpretation so readers would not think that d2 had been exposed to radiation. "d2" is the second day after plating and about ~.5 day before radiation. There are no "no_xray " time points. I hope this helps - Dave

On Mon, Sep 25, 2023 at 11:20 PM lilac-moon @.***> wrote:

hello. My name is Sohee Kim. I'm looking at your data with interest, but I have a question. In RIS conditions, there are d0, d3-6, and d9 in the columns of TPM data, d1-d9, IR_d1-d9 in RIS_raw_counts.txt, d2, d3-9_IR in RIS_column_data.txt, There are also d2_no_xray and d3-9_xray data sequencing raw data in GEO. I would like to know the exact time points of the RIS condition, and I am curious if 'no-xray control' also has a time points.

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[lilac-moon]

Thanks for your answer. I just don't know what columns in RIS_raw_counts.txt are. There are d(1-9)_A, B, C and d(1_9)_IR_A, B, C. what it meas?

[dghendrickson]

It is there by accident and not used in paper, if its not in the RIS_column_data.txt, you can ignore it.

On Wed, Sep 27, 2023 at 12:14 AM lilac-moon @.***> wrote:

Thanks for your answer. I just don't know what d1_A-C, d2_A-C, d3_A-C .. columns are in RIS_raw_counts.txt.

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[WJPina]

hello, I'm interested in your scRNA-seq results, however, the raw counts matrix in H5AD data file downloaded from GSE175533 is absent which makes it difficult to reproduce somes resultes in your paper accoding to your source codes. I will be so grateful if you can provide me the raw counts matrix of 8 scRNA-seq samples. bests

[dghendrickson]

How are you trying to access it R or python?

On Sat, Sep 28, 2024, 2:40 AM Pina @.***> wrote:

hello, I'm interested in your scRNA-seq results, however, the raw counts matrix in H5AD data file downloaded from GSE175533 is absent which makes it difficult to reproduce somes resultes in your paper accoding to your source codes. 20240928173920.png (view on web) https://github.com/user-attachments/assets/7568d868-b643-4bde-bdee-0ba7b82a6a3f I will be so grateful if you can provide me the raw counts matrix of 8 scRNA-seq samples. bests

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[WJPina]

Sorry for late reply. I used codes in the figure below where I downloaded GSE175533_sceasy_hay.h5ad file from GEO and read it by scanpy in Python. However, as you can see, the X matrix is normalized and the adata.raw is NoneType. I don't know how I can access the raw counts matrix which is used to perform DESeq2. Looking forward to your reply. Bests.

------------------ 原始邮件 ------------------ 发件人: "dghendrickson/hayflick" @.>; 发送时间: 2024年9月28日(星期六) 晚上7:57 @.>; @.**@.>; 主题: Re: [dghendrickson/hayflick] Question about data (Issue #1)

How are you trying to access it R or python?

On Sat, Sep 28, 2024, 2:40 AM Pina @.***> wrote:

> hello, > I'm interested in your scRNA-seq results, however, the raw counts matrix > in H5AD data file downloaded from GSE175533 is absent which makes it > difficult to reproduce somes resultes in your paper accoding to your source > codes. > 20240928173920.png (view on web) > <https://github.com/user-attachments/assets/7568d868-b643-4bde-bdee-0ba7b82a6a3f&gt; > I will be so grateful if you can provide me the raw counts matrix of 8 > scRNA-seq samples. > bests > > — > Reply to this email directly, view it on GitHub > <https://github.com/dghendrickson/hayflick/issues/1#issuecomment-2380583556&gt;, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/ALKURAWVEN4JVJZJ5NQ5EBTZYZ2RXAVCNFSM6AAAAABPAPDFTOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGOBQGU4DGNJVGY&gt; > . > You are receiving this because you commented.Message ID: > @.***> >

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