This folder contains processed raw data for Yip et al., "Antisense oligonucleotide-mediated perturbation of long non-coding RNA reveals functional features in stem cells and across cell types".

Exosome_sensitivity_iPSC.tsv.gz:
Rownames: geneID (FANTOM CAT geneID)
Colnames:
exo_sensitivity: Exosome sensitivity calculated by (TPMExosome_suppressed - TPMControl) / TPMExosome_suppressed, where TPMExosome_suppressed is from the mean TPM value of iPSC with EXOSC3 KD by siRNA (2 libraries) and TPMControl is from the mean TPM value of iPSC transfected with control siRNA (2 libraries)
exo_deplete_avg_cpm: Mean TPM value of iPSC with EXOSC3 KD by siRNA (2 libraries)
control_avg_cpm:  Mean TPM value of iPSC transfected with control siRNA (2 libraries)
log2FC: Fold change in log2 scale by edgeR
log2CPM: Average TPM of all 4 libraries in log2 scale by edgeR
PValue: p-value by edgeR
FDR: false discovery rate by edgeR

Fractionation_tpm_RNAseq.tsv.gz:
Matrix showing the TPM values of each of the 6 libraries by RNA-seq
Rownames: geneID (FANTOM CAT geneID)
Colnames: 6 libraries: iPSC.chromatin_rep1, iPSC.chromatin_rep2, iPSC.nuclear_rep1, iPSC.nuclear_rep2, iPSC.cytoplasmic_rep1, iPSC.cytoplasmic_rep2

HTCAGE_n761_batchremoved_TMM_cpm.tsv.gz:
Matrix showing the normalized CPM values with batch effect correction of each of the 761 libraries by HTCAGE
Rownames: geneID (FANTOM CAT geneID)
Colnames: 761 libraries with or without knockdown of lncRNAs or positive-control genes

HiC_sig.pair_n390_TPM01mRNA.tsv.gz:
The lncRNA_mRNA pairs with significant Hi-C connection(FDR < 0.05), if multiple Hi-C contacts (10 kb bin) found in a pair, only the one with lowest FDR was shown
Colnames:
label: [geneIG of lncRNA]_[geneID of mRNA] pairs with Hi-C connection at any point along their gene body
readCount: Number of read of an interaction (10 kb bin), a representative interaction having the lowest q-value was shown
pvalue: p-value of an interaction (10 kb bin), a representative interaction having the lowest q-value was shown
qvalue: False discovery rate of an interaction (10 kb bin), a representative interaction having the lowest q-value was shown
min.distance: The minimum genomic distance between the lncRNA and the mRNA
TAD: The lncRNA and the mRNA within the same TAD or not (TAD defined by the same Hi-C data using 50 kb bin)
lncRNA.geneID: geneID of the lncRNA (limited to 390 lncRNAs in the assay)
mRNA.geneID: geneID of the mRNA (limited to those have >0.1 TPM in the assayed iPS line)

RADICL.sig.pair_n390_TPM01mRNA.tsv.gz
The lncRNA_mRNA pairs with significant RADICL connection(FDR < 0.05), if multiple RADICL contacts (25 kb bin) found in a pair, only the one with lowest FDR was shown
Colnames:
label: [geneIG of lncRNA]_[geneID of mRNA] pairs with RADICL connection at any point along their gene body
RNA.geneID: geneID of the RNA side (limited to 390 lncRNAs in the assay)
DNA.geneID: geneID of the DNA side (limited to those hitting a mRNA gene with >0.1 TPM in the assayed iPS line)
RNA.chr: Chromatin of the RNA side
DNA.chr: Chromatin of the DNA side
DNA_bin_ID: the ID of the DNA bin (25 kb bin)
gene_bin_reads: Number of read of an interaction, a representative interaction having the lowest q-value was shown
binom_prob: p-value of an interaction, a representative interaction having the lowest q-value was shown
binom_fdr: False discovery rate of an interaction, a representative interaction having the lowest q-value was shown
RNA.HGNC: HGNC ID of the RNA
DNA.HGNC: HGNC ID of the DNA
group: Groups by genomic distance between the RNA and the DNA

iPSC_ref_raw_count_nantiCAGE.tsv.gz
Matrix showing the CTSS raw count of each of the 2 libraries by nanti-CAGE, the libraries are from biological replicates of the same untreated iPSC
Rownames: geneID (FANTOM CAT geneID)
Colnames: 2 libraries: ACC.lib1, CAC.lib2

iPSC_ref_tpm_RNAseq.tsv.gz
Matrix showing the TPM values of each of the 3 libraries by RNA-seq, the libraries are from biological replicates of the same untreated iPSC
Rownames: geneID (FANTOM CAT geneID)
Colnames: 3 libraries: GTGAAA.lib1, CTTGTA.lib2, GCCAAT.lib3

MARA.table.all.target.tsv.gz
MARA.motif: motif name
MARA.pvalue: p-value derived from MARA
MARA.FDR: adjusted. p-value derived from MARA
MARA.activity: activity derived from MARA
target.gapmerID: ASO ID of the lncRNA targets
target.geneID: gene ID of the lncRNA targets
target.HGNC: gene symbol of the lncRNA targets, use HGNC if available

GSEA.table.all.target.tsv.gz
GSEA.pathway: pathway names
GSEA.NES: NES derived from fgsea
GSEA.padj: adjusted p-value derived from fgsea
GSEA.Zscore: across sample Z-Score calculated from NES of fgsea 
target.gapmerID: ASO ID of the lncRNA targets
target.geneID: gene ID of the lncRNA targets
target.HGNC: gene symbol of the lncRNA targets, use HGNC if available

EdgeR.table.all.target.tsv.gz
DEG.geneID: gene ID of the gene with CAGE signal
DEG.HGNC: gene symbol of the gene with CAGE signal, use HGNC if available
EdgeR.log2FC: log2 fold change values derived from edgeR
EdgeR.log2CPM: log2 CPM values derived from edgeR
EdgeR.pvalue: p-value derived from edgeR
EdgeR.FDR: adjusted p-value derived from edgeR
EdgeR.Zscore: across sample Z-Score calculated from log2 fold change of edgeR 
target.gapmerID: ASO ID of the lncRNA targets
target.geneID: gene ID of the lncRNA targets
target.HGNC: gene symbol of the lncRNA targets, use HGNC if available