Reanalysis of TSA-Seq mapping to determine genomic coordinates for speckles-associated domains.

In this reanalysis, 9 GSM series were reanalyzed to obtain the genomic coordinates of speckles-associated domains. Reanalysis of the following samples in GSE81553: BioProject accession: PRJNA321975 GEO Sample SRA Runs BioSample Title ========== ======== ========= ===== GSM2157129 SRR3538915 SAMN05007004 No Primary Control_for_SON TSA-Seq GSM2157131 SRR3538917 SAMN05007006 SON TSA-Seq Condition 1 (TSA only) GSM2157132 SRR3538918 SAMN05007007 SON TSA-Seq Condition 1 (TSA only) Second pull down GSM2157134 SRR3538920 SAMN05007009 SON TSA-Seq Condition 2 (TSA+Sucrose) GSM2157136 SRR3538922 SAMN05007011 SON TSA-Seq Condition 1 (TSA only) Replicate GSM2157138 SRR3538924 SAMN05007013 SON TSA-Seq Condition 2 (TSA+Sucrose) Replicate GSM2157140 SRR3538926 SAMN05007015 SON TSA-Seq Condition 3 (TSA+Sucrose+DTT) GSM2157142 SRR3538928 SAMN05007017 Lamin A/C TSA-Seq Condition 2 (TSA+Sucrose) GSM2157144 SRR3538930 SAMN05007019 Lamin B TSA-Seq Condition 2 (TSA+Sucrose) *data processing step Raw files were downloaded from NCBI, and reanalysis was done using the method described in the original article (PMID: 30154186). The raw sequence reads were aligned against the UCSC hg19 human genome by bowtie2 version 2.3.4.3. Aligned files were sorted in BAM format, and SAMtools version 1.3.1 removed duplicates without any parameter except input. The number of TSA mapped reads was normalized in 20 kb to the total number of mapped reads for a sample. The TSA enrichment score was calculated as the fold change (log2 ratio) between the pulldown sample and the corresponding input for a sliding window of 100 bp in size. For normalization, the parameters were: N =20000, r=100 and l=100. The Python script tsatools_normalisation was used. The SRR3538919 was used as control for SRR3538917 and SRR3538918; SRR3538916, SRR3538921, SRR3538923, SRR3538925, SRR3538927, SRR3538929, SRR3538931 were used as input for the SRR3538920, SRR3538922, SRR3538924, SRR3538926, SRR3538928, and SRR3538930 respectively. UCSC tool wig2bed was used to make bedfile. TSA-Seq score of top 5% percentile as speckles-associated domain. wig and bed data. The SRR3538917_95P.txt contains coordinates of Speckles-associated domains or SPADs and was used in publications ( PMIDs:32665593 and 35203306).