GEO data

[ManuSetty]

Thanks for this great resource!

I have a question about the GEO submission metadata. Some of the samples are associated with multiple antibodies in the annotation - could you please provide information on how to map the reads onto the specific antibody?

An example screenshot:

How do I figure out the antibody source of each read in these samples ?

[cxzhu]

Hi @ManuSetty, Thank you for your interest in our data! You can find the sample barcode annotation (tissue region, antibodies, rep#) in Extended Dat Fig. 2a, and the "Nuclei_metaData.xls" file associated with the RNA count matrix file in GEO.

[ManuSetty]

Thanks for the quick clarification @cxzhu !

[ManuSetty]

Another quick question: Can you please provide the prefix and sample correspondence used to generate the Cell_ID in the "Nuclei_metaData.xls". Thanks!

[cxzhu]

Hi @ManuSetty,

Here is the prefix list: Sub_Lib#	Prefix
H3K4me1H3K27ac#01	01
H3K4me1H3K27ac#02	02
H3K4me1H3K27ac#03	03
H3K4me1H3K27ac#04	04
H3K4me1H3K27ac#05	05
H3K4me1H3K27ac#06	06
H3K4me1H3K27ac#07	07
H3K4me1H3K27ac#08	08
H3K4me1H3K27ac#09	09
H3K4me1H3K27ac#10	10
H3K4me1H3K27ac#11	11
H3K4me1H3K27ac#12	12
H3K4me1H3K27ac#13	13
H3K4me1H3K27ac#14	14
H3K4me1H3K27ac#15	15
H3K4me1H3K27ac#16	16
H3K27me3H3K9me3#01	21
H3K27me3H3K9me3#02	22
H3K27me3H3K9me3#03	23
H3K27me3H3K9me3#04	24
H3K27me3H3K9me3#05	25
H3K27me3H3K9me3#06	26
H3K27me3H3K9me3#07	27
H3K27me3H3K9me3#08	28
H3K27me3H3K9me3#09	29
H3K27me3H3K9me3#10	30
H3K27me3H3K9me3#11	31
H3K27me3H3K9me3#12	32
H3K4me3_#01	41
H3K4me3_#02	42
H3K4me3_#03	43
H3K4me3_#04	44
H3K4me3_#05	45
H3K4me3_#06	46
H3K4me3_#07	47
H3K4me3_#08	48
Paired-seq_#01	51
Paired-seq_#02	52
Paired-seq_#03	53
Paired-seq_#04	54
Paired-seq_#05	55
Paired-seq_#06	56

[ManuSetty]

Perfect - thanks @cxzhu !