title: mut_vitc_pu1

extract_protocol:
Frozen cell pellets (10e7 cells) were cross-linked by formaldehyde (1% final concentration) and washed by PBS. Cells were lysed and chromatin was Covaris E-220 Sonicator (Covaris). Chromatin fragments were incubated with protein G and A Sepharose beads (GE Healthcare) for two hours at 4oC to eliminate non-specific binding. Unbound chromatin fragments were separated from the beads and incubated with PU.1 antibody (SCBT; sc-22805) at 4oC overnight in IP buffer (10mM Tris-HCl pH 7.5, 2mM EDTA, 90mM NaCl, 0.1% Triton X-100, 0.1% Deoxycholate, 0.1% SDS). After incubation, IPs were washed twice with ChIP wash buffer (20mM Tris-HCl pH 8.0, 2mM EDTA, 150mM NaCl, 1% Triton X-100, 0.1% SDS) and once with final ChIP wash buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% SDS). IPs were eluted in elution buffer (1% SDS, 100mM Sodium Bicarbonate) and incubated at 68oC for 2 hours to reverse crosslinks. DNA fragments were stripped from histones and purified using QIAquick PCR Purification Kit (Qiagen) and subjected to 8 cycles of paired-end indexing PCR. Illumina sequencing  libraries were generated as previously described. Libraries were PCR amplified and sequenced on the Illumina NextSeq 500 platform following the manufacturer’s protocols (Illumina, Hayward CA.)
Genomic DNA/RNA was extracted using the Qiagen AllPrep Mini Kit according to the manufacturer's instructions.

value: Anti-PU.1; SCBT; sc-22805


title: mut_unt_pu1

status: Public on Jul 01 2017

type: SRA

city: Vancouver

first: Martin

last: Hirst

state: British Columbia

address: 2125 East Mall

department: Department of Microbiology & Immunology

country: Canada

institute: University of British Columbia

library_source: genomic

data_processing:
Base-calling was performed using RTA v2 on the NextSeq 500 platform
Alignment to mm10 was performed by bwa (bwa-mem) version 0.7.6a and 20 million reads were randomly subsampled from each library using   SAMtools (v0.1.2)
Wig tracks were generated from bam through in-house tools using ChIP-Seq mode with SAMtools (v0.1.16) flags "-F 1028 -q 5"
A custom java program (bamToWig) was used to generate wig files for downstream analysis and visualization. Reads with BWA mapping quality scores <5 were discarded and reads that aligned to the same genomic coordinate were counted only once in the profile generation.
Peaks were called using MACS2 (V2.1.0.2) on narrow mode with q<1e-5
Chastity failed reads were flagged using in-house tools
Duplicate reads were marked using Picard Tools' MarkDuplicates.jar (version 1.71)
Wig tracks were generated from bam through in-house tools using ChIP-Seq mode with SAMtools (v0.1.16) flags "-F 1028 -q 5"
Genome_build: mm10
Supplementary_files_format_and_content: mut_iMR_medip.bed: regions gaining methylation in untreated IDH1mut compared to untreated IDH1wt from meDIP-seq data
Supplementary_files_format_and_content: deMR_medip.bed: regions losing methylation upon vitamin C treatment in IDH1mut from meDIP-seq data
Supplementary_files_format_and_content: iMR_medip.bed: regions gaining methylation upon vitamin C treatment in IDH1mut from meDIP-seq data
Supplementary_files_format_and_content: iHR_medip.bed: regions gaining hydroxy-methylation upon vitamin C treatment in IDH1mut from hmeDIP-seq data
Supplementary_files_format_and_content: H3K4me1_unt.bed: peak coordinates, -log10(q) and peak width for H3K4me1 untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K4me1_vitc.bed: peak coordinates, -log10(q) and peak width for H3K4me1 vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K4me3_unt.bed: peak coordinates, -log10(q) and peak width for H3K4me3 untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K4me3_vitc.bed: peak coordinates, -log10(q) and peak width for H3K4me3 vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K27ac_unt.bed: peak coordinates, -log10(q) and peak width for H3K27ac untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K27ac_vitc.bed: peak coordinates, -log10(q) and peak width for H3K27ac vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: pu1_unt.bed: peak coordinates, -log10(q) and peak width for pu1 untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: pu1_vitc.bed: peak coordinates, -log10(q) and peak width for pu1 vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: runx1_unt.bed: peak coordinates, -log10(q) and peak width for runx1 untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: runx1_vitc.bed: peak coordinates, -log10(q) and peak width for runx1 vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: mut_unt_RNAseq_pc_rpkm: rpkm values for IDH1mut untreated RNA-seq where columns are as described (http://www.epigenomes.ca/data/CEMT/analysis/readme/file_formats.html)
Supplementary_files_format_and_content: mut_vitc_RNAseq_pc_rpkm: rpkm values for IDH1mut vitaminC RNA-seq where columns are as described (http://www.epigenomes.ca/data/CEMT/analysis/readme/file_formats.html)
Supplementary_files_format_and_content: vitc_downregulated_genes.txt: For genes down-regulated by vitamin C; Gene Name and Ensembl id (mm10 v71)
Supplementary_files_format_and_content: vitc_upregulated_genes.txt: For genes up-regulated by vitamin C; Gene Name and Ensembl id (mm10 v71)
Supplementary_files_format_and_content: iMR_wgbs.bed: regions gaining methylation upon vitamin C treatment in IDH1mut from WGBS data
Supplementary_files_format_and_content: deMR_wgbs.bed: regions losing methylation upon vitamin C treatment in IDH1mut from WGBS data
Supplementary_files_format_and_content: ctrl_unt.q5.F1028.PET.wig: wt_unt_meDIPSeq wig file
Supplementary_files_format_and_content: ctrl_vitc.q5.F1028.PET.wig: wt_vitc_meDIPSeq wig file
Supplementary_files_format_and_content: mut_unt.q5.F1028.PET.wig: mut_unt_meDIPSeq wig file
Supplementary_files_format_and_content: mut_vitc.q5.F1028.PET.wig: mut_vitc_meDIPSeq wig file
Supplementary_files_format_and_content: muthmedip_unt.q5.F1028.PET.wig: mut_unt_hmeDIPSeq wig file
Supplementary_files_format_and_content: muthmedip_vitc.q5.F1028.PET.wig: mut_vitc_hmeDIPSeq wig file
Supplementary_files_format_and_content: H3K4me1_unt.q5.F1028.PET.wig: mut_unt_H3K4me1 wig file
Supplementary_files_format_and_content: H3K4me1_vitc.q5.F1028.PET.wig: mut_vitc_H3K4me1 wig file
Supplementary_files_format_and_content: H3K4me3_unt.q5.F1028.PET.wig: mut_unt_H3K4me3 wig file
Supplementary_files_format_and_content: H3K4me3_vitc.q5.F1028.PET.wig: mut_vitc_H3K4me3 wig file
Supplementary_files_format_and_content: H3K27ac_unt.q5.F1028.PET.wig: mut_unt_H3K27ac wig file
Supplementary_files_format_and_content: H3K27ac_vitc.q5.F1028.PET.wig: mut_vitc_H3K27ac wig file
Supplementary_files_format_and_content: input_unt.q5.F1028.PET.wig: mut_unt_hchip_input wig file
Supplementary_files_format_and_content: input_vitc.q5.F1028.PET.wig: mut_vitc_hchip_input wig file
Supplementary_files_format_and_content: pu1_unt.q5.F1028.PET.wig: mut_unt_pu1 wig file
Supplementary_files_format_and_content: pu1_vitc.q5.F1028.PET.wig: mut_vitc_pu1 wig file
Supplementary_files_format_and_content: runx1_unt.q5.F1028.PET.wig: mut_unt_runx1 wig file
Supplementary_files_format_and_content: runx1_vitc.q5.F1028.PET.wig: mut_vitc_runx1 wig file
Supplementary_files_format_and_content: Input-untreated_tfchip.q5.F1028.PET.wig: mut_unt_tfchip_input wig file
Supplementary_files_format_and_content: Input-VitC_tfchip.q5.F1028.PET.wig: mut_vitc_tfchip_input wig file
Supplementary_files_format_and_content: IDH1mut-VitC-1.q0.F516.neg.wig: IDH1mut_rnaSeq untreated negative strand wig file
Supplementary_files_format_and_content: IDH1mut-VitC-1.q0.F516.pos.wig: IDH1mut_rnaSeq untreated positive strand wig file
Supplementary_files_format_and_content: IDH1mut-untreated-1.q0.F516.neg.wig: IDH1mut_rnaSeq vitamin C treated negative strand wig file
Supplementary_files_format_and_content: IDH1mut-untreated-1.q0.F516.pos.wig: IDH1mut_rnaSeq vitamin C treated positive strand wig file

molecule: genomic DNA

organism: Mus musculus

source_name: HOXA9 IDH1 R132H

growth_protocol: Cells were plated at a density of 5x105 cells/ml in 4mL DMEM medium (Stem Cell Technologies, Vancouver, Canada) supplemented with 10% heat inactivated fetal bovine serum (Life Technologies) and 6 ng/ml murine IL-3, 10 ng/ml human IL-6, and 20 ng/ml murine SCF (Peprotech, Hamburg, Germany).

treatment_protocol: For vitamin C treated samples, daily addition (0h, 24h, 48h) of vitamin C to a final concentration of 0.345mM before harvesting at 72h after the first treatment

tag: cell type

value: HOXA9 immortalized bone marrow

tag: treatment

value: Untreated

tag: vector genotype

value: IDH1 R132H

tag: chip antibody


title: Hela snoRD50a ASO replicate 2

city: guangzhou

first: chengguo

last: yao

address: No. 74 zhongshan 2rd road

department: school of medicine

country: China

institute: sysu

library_source: transcriptomic

data_processing:
Reads were trimed and mapped to hg19 allowing up 2 mismatches. Normalized iCLIP signals within mRNA PAS sites (-150 nt to 150 nt relative to cleavage sites) were compared between control and snoRD50a KD cells.
Genome_build: hg19
Supplementary_files_format_and_content: reads counts

molecule: total RNA

organism: Homo sapiens

source_name: Hela snoRD50a ASO

growth_protocol: Hela cells were grown using standard DEME medium plus 10% FBS under 5% CO2 condition

extract_protocol:
RNAs were recovered by Fip1 antibodies
Recovered RNAs were ligated onto an 3' adaptor, RT reactions were carried out for converting RNAs to cDNA, cDNAs were further circularized, digested, and PCR amplified. PCR product were sent for sequencing.
Single-end sequencing (SE50) was performed on an Illumina platform

treatment_protocol: Hela cells no treatment or, NC ASO, snoRD50a ASOs treated, the concentration is 50 nM, we used RNAi max for ASO transfection, and harvest cells 2 days after transfection.

tag: cell line

value: HeLa

tag: genotype/variation

value: snoRD50a KD

tag: rip antibody

value: Fip1 (Bethyl Laboratory, Catolog# A301-462A, Lot# A301-462A-1)


title: Hela replicate 2

source_name: Hela

value: control (untreated)


title: Hela replicate 1


title: mut_vitc_tfchip_input

data_processing:
Base-calling was performed using RTA v2 on the NextSeq 500 platform
Alignment to mm10 was performed by bwa (bwa-mem) version 0.7.6a and 20 million reads were randomly subsampled from each library using
Wig tracks were generated from bam through in-house tools using ChIP-Seq mode with SAMtools (v0.1.16) flags "-F 1028 -q 5"
A custom java program (bamToWig) was used to generate wig files for downstream analysis and visualization. Reads with BWA mapping quality scores <5 were discarded and reads that aligned to the same genomic coordinate were counted only once in the profile generation.
Peaks were called using MACS2 (V2.1.0.2) on narrow mode with q<1e-5 using the input as a control
Chastity failed reads were flagged using in-house tools
Duplicate reads were marked using Picard Tools' MarkDuplicates.jar (version 1.71)
Wig tracks were generated from bam through in-house tools using ChIP-Seq mode with SAMtools (v0.1.16) flags "-F 1028 -q 5"
Genome_build: mm10
Supplementary_files_format_and_content: mut_iMR_medip.bed: regions gaining methylation in untreated IDH1mut compared to untreated IDH1wt from meDIP-seq data
Supplementary_files_format_and_content: deMR_medip.bed: regions losing methylation upon vitamin C treatment in IDH1mut from meDIP-seq data
Supplementary_files_format_and_content: iMR_medip.bed: regions gaining methylation upon vitamin C treatment in IDH1mut from meDIP-seq data
Supplementary_files_format_and_content: iHR_medip.bed: regions gaining hydroxy-methylation upon vitamin C treatment in IDH1mut from hmeDIP-seq data
Supplementary_files_format_and_content: H3K4me1_unt.bed: peak coordinates, -log10(q) and peak width for H3K4me1 untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K4me1_vitc.bed: peak coordinates, -log10(q) and peak width for H3K4me1 vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K4me3_unt.bed: peak coordinates, -log10(q) and peak width for H3K4me3 untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K4me3_vitc.bed: peak coordinates, -log10(q) and peak width for H3K4me3 vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K27ac_unt.bed: peak coordinates, -log10(q) and peak width for H3K27ac untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K27ac_vitc.bed: peak coordinates, -log10(q) and peak width for H3K27ac vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: pu1_unt.bed: peak coordinates, -log10(q) and peak width for pu1 untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: pu1_vitc.bed: peak coordinates, -log10(q) and peak width for pu1 vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: runx1_unt.bed: peak coordinates, -log10(q) and peak width for runx1 untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: runx1_vitc.bed: peak coordinates, -log10(q) and peak width for runx1 vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: mut_unt_RNAseq_pc_rpkm: rpkm values for IDH1mut untreated RNA-seq where columns are as described (http://www.epigenomes.ca/data/CEMT/analysis/readme/file_formats.html)
Supplementary_files_format_and_content: mut_vitc_RNAseq_pc_rpkm: rpkm values for IDH1mut vitaminC RNA-seq where columns are as described (http://www.epigenomes.ca/data/CEMT/analysis/readme/file_formats.html)
Supplementary_files_format_and_content: vitc_downregulated_genes.txt: For genes down-regulated by vitamin C; Gene Name and Ensembl id (mm10 v71)
Supplementary_files_format_and_content: vitc_upregulated_genes.txt: For genes up-regulated by vitamin C; Gene Name and Ensembl id (mm10 v71)
Supplementary_files_format_and_content: iMR_wgbs.bed: regions gaining methylation upon vitamin C treatment in IDH1mut from WGBS data
Supplementary_files_format_and_content: deMR_wgbs.bed: regions losing methylation upon vitamin C treatment in IDH1mut from WGBS data
Supplementary_files_format_and_content: ctrl_unt.q5.F1028.PET.wig: wt_unt_meDIPSeq wig file
Supplementary_files_format_and_content: ctrl_vitc.q5.F1028.PET.wig: wt_vitc_meDIPSeq wig file
Supplementary_files_format_and_content: mut_unt.q5.F1028.PET.wig: mut_unt_meDIPSeq wig file
Supplementary_files_format_and_content: mut_vitc.q5.F1028.PET.wig: mut_vitc_meDIPSeq wig file
Supplementary_files_format_and_content: muthmedip_unt.q5.F1028.PET.wig: mut_unt_hmeDIPSeq wig file
Supplementary_files_format_and_content: muthmedip_vitc.q5.F1028.PET.wig: mut_vitc_hmeDIPSeq wig file
Supplementary_files_format_and_content: H3K4me1_unt.q5.F1028.PET.wig: mut_unt_H3K4me1 wig file
Supplementary_files_format_and_content: H3K4me1_vitc.q5.F1028.PET.wig: mut_vitc_H3K4me1 wig file
Supplementary_files_format_and_content: H3K4me3_unt.q5.F1028.PET.wig: mut_unt_H3K4me3 wig file
Supplementary_files_format_and_content: H3K4me3_vitc.q5.F1028.PET.wig: mut_vitc_H3K4me3 wig file
Supplementary_files_format_and_content: H3K27ac_unt.q5.F1028.PET.wig: mut_unt_H3K27ac wig file
Supplementary_files_format_and_content: H3K27ac_vitc.q5.F1028.PET.wig: mut_vitc_H3K27ac wig file
Supplementary_files_format_and_content: input_unt.q5.F1028.PET.wig: mut_unt_hchip_input wig file
Supplementary_files_format_and_content: input_vitc.q5.F1028.PET.wig: mut_vitc_hchip_input wig file
Supplementary_files_format_and_content: pu1_unt.q5.F1028.PET.wig: mut_unt_pu1 wig file
Supplementary_files_format_and_content: pu1_vitc.q5.F1028.PET.wig: mut_vitc_pu1 wig file
Supplementary_files_format_and_content: runx1_unt.q5.F1028.PET.wig: mut_unt_runx1 wig file
Supplementary_files_format_and_content: runx1_vitc.q5.F1028.PET.wig: mut_vitc_runx1 wig file
Supplementary_files_format_and_content: Input-untreated_tfchip.q5.F1028.PET.wig: mut_unt_tfchip_input wig file
Supplementary_files_format_and_content: Input-VitC_tfchip.q5.F1028.PET.wig: mut_vitc_tfchip_input wig file
Supplementary_files_format_and_content: IDH1mut-VitC-1.q0.F516.neg.wig: IDH1mut_rnaSeq untreated negative strand wig file
Supplementary_files_format_and_content: IDH1mut-VitC-1.q0.F516.pos.wig: IDH1mut_rnaSeq untreated positive strand wig file
Supplementary_files_format_and_content: IDH1mut-untreated-1.q0.F516.neg.wig: IDH1mut_rnaSeq vitamin C treated negative strand wig file
Supplementary_files_format_and_content: IDH1mut-untreated-1.q0.F516.pos.wig: IDH1mut_rnaSeq vitamin C treated positive strand wig file

extract_protocol:
Frozen cell pellets (10e7 cells) were cross-linked by formaldehyde (1% final concentration) and washed by PBS. Cells were lysed and chromatin was Covaris E-220 Sonicator (Covaris). Chromatin fragments were incubated with protein G and A Sepharose beads (GE Healthcare) for two hours at 4oC to eliminate non-specific binding. Unbound chromatin fragments were separated from the beads and incubated with no antibody at 4oC overnight in IP buffer (10mM Tris-HCl pH 7.5, 2mM EDTA, 90mM NaCl, 0.1% Triton X-100, 0.1% Deoxycholate, 0.1% SDS). After incubation, IPs were washed twice with ChIP wash buffer (20mM Tris-HCl pH 8.0, 2mM EDTA, 150mM NaCl, 1% Triton X-100, 0.1% SDS) and once with final ChIP wash buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% SDS). IPs were eluted in elution buffer (1% SDS, 100mM Sodium Bicarbonate) and incubated at 68oC for 2 hours to reverse crosslinks. DNA fragments were stripped from histones and purified using QIAquick PCR Purification Kit (Qiagen) and subjected to 8 cycles of paired-end indexing PCR. Illumina sequencing  libraries were generated as previously described. Libraries were PCR amplified and sequenced on the Illumina NextSeq 500 platform following the manufacturer’s protocols (Illumina, Hayward CA.)
Genomic DNA/RNA was extracted using the Qiagen AllPrep Mini Kit according to the manufacturer's instructions.

value: Vitamin C


title: transfection of snoRD50a ASO-2, replicate 2

data_processing:
Library strategy: PAS-Seq
Raw reads were trimmed, mapped to human genome (hg19), allowing up to 2 mismatches  using Bowtie2 with the settings “bowtie2 -p 28 -N 1 -k 1”. A poly(A) junction is  where the 3’ end of the read maps. Internal priming was removed as  described previously (reference 37 [Shepard, P. J., E. A. Choi, et al. Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq. RNA. 2011; 17: 761-772]). Mapped PAS-seq reads were clustered, normalized  as described previously (reference 8 [Yao, C., J. Biesinger, et al. Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation. Proc Natl Acad Sci U S A. 2012£»109:18773-18778]). For APA analysis, same procedures  were followed as described previously (reference 8). For gene expression analysis in  Figure 5B, all the normalized PAS-seq reads (RPM) for a gene were summed  to stand for the expression level of this gene, and DESeq2 package was used  to analyzed the gene expression change
Genome_build: hg19
Supplementary_files_format_and_content: Excel files containing APA analysis and gene expression analysis

source_name: transfection of snoRD50a ASO-2

extract_protocol:
total RNA were extracted by Trizol reagents (Life technology), 15 ug total RNAs were fragemented by fragment buffer (Ambion) for 10 mins in 75'c. RNAs were precipitated by ethanol overnight for library construction.
Fragmented mRNA transcripts were converted into cDNA with a primer that contains an oligo(dT) sequence, two primer binding sites for nested PCR and two BamHI restriction enzyme sites. This specifically designed primer ensures this library is strand-specific. cDNAs were size-fractionated, purified, and further subject to circularization and linearization. A limited number of PCR cycles were used to amplify the linearized cDNAs.
SE100 were performed to sequence the library pool.

treatment_protocol: Cells were transfected with NC or snoRD50a ASOs before analysis


title: Hela NC ASO replicate 2

source_name: Hela NC ASO

value: control (NC ASO)


title: Hela snoRD50a ASO replicate 1


title: transfection of snoRD50a ASO-1, replicate 1

source_name: transfection of snoRD50a ASO-1


title: transfection of snoRD50a ASO-1, replicate 2


title: transfection of snoRD50a ASO-2, replicate 1


title: transfection of NC ASO (negative ASO), replicate 1

source_name: transfection of NC ASO (negative ASO)

value: control ( NC ASO)


title: transfection of NC ASO (negative ASO), replicate 2


title: SVL-m RIP-seq

description: RNA-biotin based pull down assay with Hela Nuclear Extract

data_processing:
Raw reads were trimmed by Trimmomatic (V0.32), and mapped to the human  genome (hg19), allowing up to two mismatches using OSA (Omicsoft  Sequence Aligner, version 7.0.1.20). Expression level estimation was reported  as TPM (Transcripts Per Kilobase Million) value for each sample. Stringent  cut-off parameters (Average TPM>200, fold change>5) was applied to select  highly reliable changes
Genome_build: hg19
Supplementary_files_format_and_content: TPMs, differentially expressed genes

molecule: nuclear RNA

source_name: Hela cells

extract_protocol:
RNA substrates were made by in vitro transcription using SP6 or T7 RNA polymerase and DNA templates ,and biotinylated at 3’ end using a biotinylation Kit. Biotinylated RNAs were first bound to the streptavidin beads, and then incubated with Hela NE in the polyadenylation condition for 20 minutes, after biotin-streptavidine binding, washing, pull-down sample were heated in 1XSSC buffer for elution, as suggested by the manual of the Dynalbeads M280. The eluted samples were further subject to RNA purification for RNA-seq.
Strand-specific RNA-seq libraries were prepared following the described protocol (Hunt, A. G, 2015) with the RNA-biotin based pull-down sample, and single-end squenceing (SE50) was carried out in Illumina Genome Analyzer II platform.
SE50 was applied to sequence the library pool.

treatment_protocol: Hela nuclear extracts were prepared using standard protocol described previously (The BARD1-CstF-50 interaction links mRNA 3' endformation to DNA damage and tumor suppression. Cell.2001;104: 743-753)

tag: rna substrate

value: Mutant SVL


title: SVL RIP-seq

value: SVL


title: Hela NC ASO replicate 1


title: UnrelatedSet1_GM10839

city: Ann Arbor

first: Isabel

middle: Xiaorong

last: Wang

state: Michigan

address: 210 washtenaw ave

department: Pediatrics&Genetics

country: USA

institute: HHMI/University of Michigan

data_processing:
Low-quality bases as designated by CASAVA (v1.8) were trimmed from the 3' end of reads.
Reads were aligned using GSNAP (v2012-04-10). (Read length + 2)/12 – 2 or fewer mismatches were tolerated. Alignments to novel exon-exon junctions and known junctions as defined by RefSeq (downloaded March 7, 2011) and Gencode (v3c) were allowed. A list of SNPs in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) was used to allow for SNP-tolerant alignments.
Variants were called with Samtools (v0.1.16)
Genome_build: hg18

source_name: cultured B-cells

growth_protocol: Cultured B-cell lines were obtained from Coriell (Camden, NJ, USA). The B-cells were grown to a density of 5x105 cells/mL in RPMI 1640 supplemented with 15% fetal bovine serum, 100 units/mL penicillin and 100 μg/mL streptomycin, and 2 mmol/L L-glutamine.

extract_protocol: RNA-seq libraries were prepared following Illumina's recommendations. Briefly, cells were harvested 24 hours after addition of fresh medium, and total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). Poly-A mRNA was isolated and fragmented. First strand cDNA was prepared using reverse transcriptase and random hexamers. After second strand cDNA synthesis, ends were repaired and a single ‘A’ base was added followed by adapter sequences. Library fragments were selected for an average size of 200 to 260 base pairs, PCR amplified, and then sequenced using Illumina next-generation sequencing technology.

tag: sample

tag: family

tag: relation

value: mother

tag: protocol

value: non-directional


title: UnrelatedSet1_GM12877

value: father


title: siMAF_rep1

city: New York

first: Lionel

middle: B.

last: Ivashkiv

state: NY

address: 535 East 70th Street

institute: Hospital for Special Surgery

description:
mRNA-seq
Processed data file: siCtrl_siMAF_RPKM_table.txt

data_processing:
FastQC was used to evaluate quality of sequenced reads (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Contaminated adaptor portions of sequenced reads were trimmed using the Trim Galore program (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore).
Sequenced reads were mapped to reference human genome (hg19 assembly) using STAR aligner (2.5.2b, Dobin et al., 2013 Bioinformatics) with default parameters.
Cufflinks version 2.2.1 (Trapnell et al., 2012 Nat Protoc) was used to estimate the abundance (RPKM) of transcripts.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: AdGFP_AdMAF_RPKM_table.txt: Tab-delimited text file includes RPKM values.
Supplementary_files_format_and_content: Resting_IFNg_RPKM_table.txt: Tab-delimited text file includes RPKM values.
Supplementary_files_format_and_content: siCtrl_siMAF_RPKM_table.txt: Tab-delimited text file includes RPKM values.

source_name: Primary human monocyte-derived macrophages, siMAF

growth_protocol: Peripheral blood mononuclear cells were obtained from the blood of healthy donors by density gradient centrifugation using Ficoll (Invitrogen) and a protocol approved by the Hospital for Special Surgery Institutional Review Board. CD14+ human monocytes were purified from PBMCs by positive selection using anti-CD14 magnetic beads as recommended by the manufacturer (Miltenyi Biotec). Monocytes were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (Invitrogen) supplemented with 10% heat-inactivated defined FBS (HyClone), penicillin/streptomycin (Invitrogen), L-glutamine (Invitrogen), and 10 ng/mL human macrophage colony-stimulating factor (M-CSF; Peprotech).

extract_protocol:
RNA extraction kit from QIAGEN, according to company's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with or without IFN-γ (100U/ml) for 48 hours.

tag: disease state

value: healthy

tag: tissue

value: peripheral blood

value: primary human monocyte-derived macrophages

tag: sirna

value: siMAF


title: Family1420Set_GM10839


title: siMAF_rep2


title: Family1420Set_GM10838


title: siCtrl_rep1

source_name: Primary human monocyte-derived macrophages, siCtrl

value: siCtrl


title: IFN-γ_rep2

description:
Stranded-specific total RNA-seq
Processed data file: Resting_IFNg_RPKM_table.txt

source_name: Primary human monocyte-derived macrophages, IFN-γ

value: IFN-γ


title: AdMAF_untreated_rep2

description:
mRNA-seq
Processed data file: AdGFP_AdMAF_RPKM_table.txt

source_name: Primary human monocyte-derived macrophages, AdMAF, untreated

tag: adenovirus

value: AdMAF


title: AdMAF_IFN-γ_rep1

source_name: Primary human monocyte-derived macrophages, AdMAF, IFN-γ

value: IFN-gamma


title: siCtrl_rep2


title: AdGFP_untreated_rep2

source_name: Primary human monocyte-derived macrophages, AdGFP, untreated

value: AdGFP


title: IFN-γ_rep1


title: AdMAF_untreated_rep1


title: SMC1_Resting_rep2

data_processing:
FastQC was used to evaluate quality of sequenced reads (http://www.bioinformatics.babraham.ac.uk/project/fastqc). Contaminated adaptor portions of sequenced reads were trimmed using the Trim Galore program (http://www.bioinformatics.babraham.ac.uk/project/trim_galore).
Sequenced reads were mapped to reference human genome (hg19 assembly) using Bowtie2 (version 2.2.5, Langmead et al., 2012 Nat Methods) with default parameters.
HOMER (version 4.7.2, Heinz et al., 2010) was used to identify peaks of ChIP-seq enrichment over background. A false discovery rate (FDR) threshold of 0.001 was used for all data sets.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Bed files.

source_name: Primary human monocyte-derived macrophages, untreated, SMC1 ChIP

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Preparation Kit.

value: anti-SMC1 (Bethyl Laboratories A300-055A)


title: AdMAF_IFN-γ_rep2


title: AdGFP_IFN-γ_rep1

source_name: Primary human monocyte-derived macrophages, AdGFP, IFN-γ


title: PU.1_Resting_rep2

source_name: Primary human monocyte-derived macrophages, untreated, PU.1 ChIP

value: anti-PU.1 (Santa Cruz sc-352)


title: PU.1_Resting_rep1


title: SMC1_IFN-γ

source_name: Primary human monocyte-derived macrophages, IFN-γ, SMC1 ChIP


title: SMC1_Resting_rep1


title: AdGFP_untreated_rep1


title: PU.1_IFN-γ_rep2

source_name: Primary human monocyte-derived macrophages, IFN-γ, PU.1 ChIP


title: PU.1_IFN-γ_rep1


title: MAF_Resting

source_name: Primary human monocyte-derived macrophages, untreated, MAF ChIP

value: anti-MAF (Santa Cruz sc-7866)


title: Untreated_rep2

source_name: Primary human monocyte-derived macrophages, untreated


title: Untreated_rep1


title: MAF_IFN-γ

source_name: Primary human monocyte-derived macrophages, IFN-γ, MAF ChIP


title: Pol2_IFN-γ

source_name: Primary human monocyte-derived macrophages, IFN-γ, Pol2 ChIP

value: anti-Pol2 (Covance MMS-126R)


title: H3K4me3_Resting

source_name: Primary human monocyte-derived macrophages, untreated, H3K4me3 ChIP

value: anti-H3K4me3 (Abcam ab8580)


title: C/EBPB_Resting_rep1

source_name: Primary human monocyte-derived macrophages, untreated, C/EBPB ChIP

value: anti-C/EBPB (Santa Cruz sc-150)


title: ATAC_IFN-γ_rep2

extract_protocol:
Nuclei were pelleted by centrifugation for 5 min at 500g, 4°C.
Assay for transposase-accessible chromatin using sequencing (ATAC-seq) protocol developed by Buenrostro et al., 2013; single end protocol.


title: H3K4me3_IFN-γ

source_name: Primary human monocyte-derived macrophages, IFN-γ, H3K4me3 ChIP


title: AdGFP_IFN-γ_rep2


title: C/EBPB_IFN-γ_rep2

source_name: Primary human monocyte-derived macrophages, IFN-γ, C/EBPB ChIP


title: C/EBPB_IFN-γ_rep1


title: C/EBPB_Resting_rep2


title: MCF7_HG

city: Naples

first: Valerio

last: Costa

state: Italy

address: Via P. Castellino, 111

department: Institute of Genetics and Biophysics

country: Italy

institute: National Research Council

description: Barcode: TGACCA

data_processing:
Quality assessment and mapping: Reads' quality was assessed using “FastQC” and TopHat software (version 2.0.10; Kim et al, 2013) was used to map the reads against the RefSeq human transcripts and reference human genome (UCSC hg19 release) with default parameters. RefSeq annotation was downloaded from UCSC Genome Browser (http://genome.ucsc.edu) and only the protein-coding gene annotation coordinates were used.
Files' conversion: SAMTools and BEDTools were used to convert file formats (.sam/.bam/.bed). Coverage files in bedgraph format were produced using the GenomeCoverage option of BEDTools.
Filtering and normalization: Filtering of low-coverage genes (Proportion test method), normalization (upper quartile method), quantification of gene expression (SummerizeOverlaps option in R language).
Analysis of differential expression: Uniquely mapping reads were used for further analyses. The analysis of differential expression (NoiSeq method) were carried out using “RNASeqGUI” (Russo and Angelini, 2014). A posterior probability threshold of 0.8 was used to select differentially expressed genes (DEGs).
Pathway analysis: Pathway analysis was performed using PANTHER (Protein ANalysis THrough Evolutionary Relationships; http://www.pantherdb.org).
Genome_build: hg19
Supplementary_files_format_and_content: [MCF7_HGtoLG.txt] Normalized (FQUA) gene expression counts of MCF7 grown in HG and then shifted to LG
[MCF7_HG.txt] Normalized (FQUA) gene expression counts of MCF7 grown in HG (control cells)
[Raw_counts_MCF7_HGtoLG.txt] raw read counts
[Raw_counts_MCF7_HG.txt] raw read counts

source_name: MCF7 cell line

growth_protocol: MCF7 human breast cancer cells (ERa+, PR+, HER2-) were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 2 mM glutamine, 100 units/ml penicillin and 100 units/ml streptomycin. At 48 hours before the induction of the experiments, the cells were shifted to phenol red free DMEM supplemented with 10% Charcoal Stripped (C/S) FBS, 2 mM glutamine, 100 units/ml penicillin and 100 units/ml streptomycin. Cultures were maintained in a humidified atmosphere of 95% air and 5% CO2 at 37°C.

extract_protocol:
Total RNA was isolated from cells using TRIzol solution (Life Technologies, Carlsbad, CA, USA) according to the manufacturer's instructions. All RNA samples were quantified by measuring the absorbance at 260 nm and 280 nm (NanoDrop spectrophotometer, Life Technologies, Carlsbad, CA, USA). The integrity of RNA samples was further analyzed by using the digital electrophoresis system Experion with the “RNA StdSens Kit” (Biorad, Hercules, CA, USA), following the manufacturer's instructions. The run and result analysis were performed by the Experion software. RNA samples with a RNA Quality Indicator (RQI) value ≥ 9 were considered good for the further analysis.
Paired-end cDNA libraries were prepared for sequencing on the Illumina Hi-Seq 2000 platform using “TruSeq RNA Sample Preparation kit” (Illumina) according to manufacturer's protocol42. The yield and the size distribution of purified cDNA libraries were assessed using “Qubit dsDNA HS (High Sensitivity) Assay Kit” on Qubit Fluorometer (Life Technologies, Carlsbad, CA, USA) and “Experion DNA 1K Analysis Kit” (Biorad, Hercules, CA, USA) on the Experion system (Biorad, Hercules, CA, USA), respectively. Peak median values were determined at approximately 200-260 bp. Sample concentration and peak median values were used to calculate molar concentration of cDNA libraries prior to sequencing on the Illumina HiSeq 2000

treatment_protocol: MCF7 were cultured in 5.5 mM glucose (Low Glucose; LG), corresponding to normal fasting glucose levels in humans, or in 25 mM glucose (High Glucose; HG) corresponding to the regular culture condition for this cell line but resembling hyperglycaemia in humans.

value: breast cancer cell line MCF7

tag: growth protocol

value: grown in high glucose


title: ATAC_IFN-γ_rep1

source_name: Primary human monocyte-derived macrophages, IFN-γ

value: healthy

tag: cell type


title: CD14+ NIG ZIKV Infected

city: Reno

first: Subhash

middle: C

last: Verma

state: NV

address: 1664 N Virginia Street, MS 320

department: Microbiology and Immunology

institute: University of Nevada, Reno

description: RNA-seq analysis

data_processing:
The libraries were run on Illumina Hi-seq instrument and Illumina software was used for peak calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Sequence were imported into CLC Henomic Workbech 7.0 with NCBI/Sanger or Illumia pipeline 1.8 and later option.
Reads were mapped to the human genome database sequence to calculate the RPKM values of cellular gene using CLC Workbench
Relative expressions were calculated with reference of mock infected control cells
Genome_build: NCBI genome build of human genome, Homo sapiens (hg19) sequence

source_name: purified human CD14+ cells

growth_protocol: CD14+ cells were grown in RPMI with 10% FBS

extract_protocol:
Total RNA was extracted from the mock infected control and ZIKV infected cells
The libraries were constructed using TrueSeq RNA sample preparation kit v2 from Illumina.

treatment_protocol: Cells were infected with ZIKV virus and allowed to grow for 12h

tag: infection

value: NIG ZIKV infected cells for 12h


title: ATAC_Resting_rep1

value: peripheral blood

value: primary human monocyte-derived macrophages

tag: treatment


title: PF151

city: Cambridge

first: Guangan

last: Hu

state: MA

address: 500 Main Street

department: Koch Institute

institute: MIT

data_processing:
Illumina software used for basecalling.
Paired sequences were aligned to the human genome using Tophat2
Raw counts of each gene for each sample were calculated by HTseq program
Raw counts of each sample normaized with TMM in calcNormFactors() of edgeR, values log2-transformed
Differentially expressed genes between paired samples before and after treatment were performed using the program edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include cpount values for each Sample PF118, PF119, PF128, PF131, PF149, PF151, PF154 and PF155

source_name: pleural macrophages

growth_protocol: Pleural macrophages were purified from freshly isolated PEMCs using human CD14 MicroBeads. Macrophages were futher purified by seeding in culture plates with complete RPMI, incubating at 37°C for 20 minutes and washing off the unattached cells.

extract_protocol:
TRIzol
SMARTer Universal Low Input RNA Kit

tag: patient

value: patient 3

tag: antibiotic treatment

value: after


title: CD14+ mock infected control

description: RNA-seq analysis

value: Mock infected control cells


title: PF149

value: before


title: CD14+ PR ZIKV Infected

description: RNA-seq analysis

value: PR ZIKV infected cells for 12h


title: PF155

value: patient 4


title: PF131

value: patient 2


title: PF128


title: PF119

value: patient 1


title: PF118


title: Pol2_Resting

source_name: Primary human monocyte-derived macrophages, untreated, Pol2 ChIP

tag: chip antibody

value: anti-Pol2 (Covance MMS-126R)


title: ATAC_Resting_rep2


title: BC064

city: Worcester

first: Yu

last: Liu

address: AS5-1018, 368 Plantation Street

department: Program in Systems Biology

institute: University of Massachusetts Medical School

data_processing:
The fastq files were obtained using Illumina CASAVA v1.8
The quality of fastq reads was examined by FASTQC and low quality 5' nucleotides were removed before mapping
The fastq read were mapped on human geneome (hg19) using Tophat 1.4.1
The read counts were calculated using customed R scripts to calculate transcript union reads per million reads (truRPMs)
Genome_build: hg19
Supplementary_files_format_and_content: all_truRPMs.txt: coding gene expression of all the samples in the cohort

source_name: FFPE bladder tumor block

extract_protocol:
The viable tumor regions were first marked by a pathologist and the total RNAs were then extracted from the tumor regions
The sequencing libraries were constructed using RiboZero and Illumina TruSeq RNA preparation kit following the kit instructions. For FFPE samples, the RNA fragmentation step was removed because FFPE RNAs are fragments.

value: Bladder

tag: tumor grade (2004 who)

value: High grade

tag: tumor stage


title: BC054

value: Low grade

value: pTa


title: BC053


title: BC061


title: BC063


title: BC059


title: PF154


title: BC060


title: MCF7_HG→LG

description: Barcode: GCCAAT

tag: cell line

value: breast cancer cell line MCF7

value: grown in high glucose and then shifted in low glucose


title: BC055


title: BC048


title: BC049


title: BC046


title: BC044


title: BC050


title: BC043


title: BC052


title: BC051


title: BC041


title: BC038


title: BC040

value: pTx


title: BC042


title: BC045


title: BC035


title: BC039


title: BC034


title: BC033


title: BC047


title: BC031


title: BC032


title: BC025


title: BC028


title: BC026


title: BC024


title: BC023


title: BC016


title: BC021


title: BC029


title: BC030


title: BC022


title: BC015


title: BC017


title: BC013


title: BC019


title: BC010


title: BC020


title: BC009


title: BC008


title: BC012


title: BC027


title: BC011


title: BC036


title: BC007


title: BC014


title: BC006


title: BC004


title: BC005


title: BC003


title: BC002


title: BC001


title: Family1420Set_GM12007

source_name: cultured B-cells

tag: sample

tag: family

value: son

value: non-directional


title: Family1362Set_GM11996

tag: relation

tag: protocol


title: Family1420Set_GM12002

value: daughter


title: Family1420Set_GM11999


title: Family1420Set_GM11998


title: Family1420Set_GM12000


title: Family1420Set_GM11997


title: Family1362Set_GM11995

value: maternal grandmother


title: Family1362Set_GM11988


title: Family1362Set_GM11991


title: Family1362Set_GM11990


title: Family1362Set_GM11993

value: paternal grandmother


title: Family1362Set_GM11994

value: maternal grandfather


title: Family1362Set_GM11984


title: Family1362Set_GM11989


title: Family1362Set_GM11985


title: Family1362Set_GM11992

value: paternal grandfather


title: Family1362Set_GM11987


title: Family1362Set_GM11983


title: Family1362Set_GM11986


title: Family1362Set_GM10860

value: father


title: TwinSet_GM14582

value: twin brother


title: Family1362Set_GM11982


title: Family1362Set_GM10861

value: mother


title: TwinSet_GM14581

value: proband


title: BC037

tag: tissue

value: Bladder


title: Family1420Set_GM12001


title: TwinSet_GM14569


title: TwinSet_GM14568


title: TwinSet_GM14521

value: twin sister


title: TwinSet_GM14468


title: TwinSet_GM14506


title: TwinSet_GM14467


title: TwinSet_GM14520


title: TwinSet_GM14507


title: TwinSet_GM14453


title: insituHiC_9837_M_CK-KO_neuronal

first: Eddie

last: Loh

address: 1425 Madison Avenue

department: Department of Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description:
insituHiC_9837_M_CK-KO_neuronal_20000.HiCPro.interaction.txt
insituHiC_20000.HiCPro.bed

data_processing:
Library strategy: HiC-Seq
RNA-seq: The sequenced RNAseq data were aligned to the Mouse (mm10) reference genome using Tophat2 short-read aligner. Reads were counted using HTSeq against the Gencode vM4 Mouse annotation. Genes were filtered based on the criteria that all replicates in either condition must have at least 5 reads per gene. On the resulting filtered transcript, a pairwise differential analysis between Setdb1 conditional mutant vs control cortex was performed using the voom-limma R package, which converts counts into precision weighted log2 counts per million and determines differentially expressed genes using a linear model. Significantly differentially expressed genes were identified using a cutoff of Benjamini-Hochberg adjusted p-value less than 0.05.
ChIP-seq: The sequenced ChIP-seq data was first checked for quality using the various metrics generated by FastQC (v0.11.2). Raw sequencing reads were then aligned to the Mouse (mm10) reference genome using default settings of Bowtie (v2.2.0). Uniquely mapped reads were retained and the alignments were subsequently filtered using the SAMtools package (v0.1.19) to remove duplicate reads. Differential analysis between mutant and control samples was performed using diffReps with window size 1000 bp and moving step size 500 bp, and FDR<5% as significance cutoff.
insituHiC: The processing of the raw 2x125bp read pair in-situ HiC FASTQ files was performed using the HiC-Pro analysis pipeline. In brief, HiC-Pro performs four major tasks: aligning short reads, filtering for valid pairs, binning, and normalizing contact matrices. HiC-Pro implements the truncation-based alignment strategy using Bowtie v2.2.318, mapping full reads end-to-end or the 5’ portion of reads preceding a GATCGATC ligation site that results from restriction enzyme digestion with MboI followed by end ligation. Invalid interactions such as same-strand, dangling-end, self-cycle, and single-end pairs are not retained. Binning was performed in 20kb non-overlapping, adjacent windows across the genome and resulting interaction matrices were obtained.
Genome_build: mm10
Supplementary_files_format_and_content: text files of differential expression genes (RNAseq), differential binding regions (ChIPseq) and interaction counts (insituHiC)
Supplementary_files_format_and_content: ChIPseq_CTCF_neuron_KO_vs_WT_1kb_001b.annotated.txt: text file of differential binding regions
Supplementary_files_format_and_content: ChIPseq_H3K27ac_neuron_KO_vs_WT_1kb_001a.annotated.txt: text file of differential binding regions
Supplementary_files_format_and_content: ChIPseq_H3K9me3_neuron_KO_vs_WT_1kb_001a.annotated.txt: text file of differential binding regions
Supplementary_files_format_and_content: RNAseq_Setdb1-CK-KO_KO_vs_WT_gencode_vM4.txt: text file of differential expression genes
Supplementary_files_format_and_content: insituHiC_432_M_WT_neuronal_20000.HiCPro.interaction.txt: text file of interaction raw counts
Supplementary_files_format_and_content: insituHiC_513_M_CK-KO_neuronal_20000.HiCPro.interaction.txt: text file of interaction raw counts
Supplementary_files_format_and_content: insituHiC_9836_M_WT_neuronal_20000.HiCPro.interaction.txt: text file of interaction raw counts
Supplementary_files_format_and_content: insituHiC_9837_M_CK-KO_neuronal_20000.HiCPro.interaction.txt: text file of interaction raw counts
Supplementary_files_format_and_content: insituHiC_20000.HiCPro.bed: bed file of interaction bins

source_name: adult mouse cortex

extract_protocol:
Nuclei were extracted from mouse brain tissue with 1% formaline fixation, collected by FACS, digested with MboI, biotinylation of the strand ends and in nuclei re-ligated, followed by reverse-crosslinking, DNA precipitation, sonication and Biotin pull-down.
standard library preparation for Illumina sequencing

tag: age

value: adult

tag: gender

value: M

tag: genotype

value: CK-KO

value: neuronal


title: insituHiC_513_M_CK-KO_neuronal

description:
insituHiC_513_M_CK-KO_neuronal_20000.HiCPro.interaction.txt
insituHiC_20000.HiCPro.bed

tag: cell type


title: ChIPseq_CTCF_1646_F_CK-KO_neuronal

description: ChIPseq_CTCF_neuronal_KOvsWT_1kb_001_annotated.txt

data_processing:
RNA-seq: The sequenced RNAseq data were aligned to the Mouse (mm10) reference genome using Tophat2 short-read aligner. Reads were counted using HTSeq against the Gencode vM4 Mouse annotation. Genes were filtered based on the criteria that all replicates in either condition must have at least 5 reads per gene. On the resulting filtered transcript, a pairwise differential analysis between Setdb1 conditional mutant vs control cortex was performed using the voom-limma R package, which converts counts into precision weighted log2 counts per million and determines differentially expressed genes using a linear model. Significantly differentially expressed genes were identified using a cutoff of Benjamini-Hochberg adjusted p-value less than 0.05.
ChIP-seq: The sequenced ChIP-seq data was first checked for quality using the various metrics generated by FastQC (v0.11.2). Raw sequencing reads were then aligned to the Mouse (mm10) reference genome using default settings of Bowtie (v2.2.0). Uniquely mapped reads were retained and the alignments were subsequently filtered using the SAMtools package (v0.1.19) to remove duplicate reads. Differential analysis between mutant and control samples was performed using diffReps with window size 1000 bp and moving step size 500 bp, and FDR<5% as significance cutoff.
insituHiC: The processing of the raw 2x125bp read pair in-situ HiC FASTQ files was performed using the HiC-Pro analysis pipeline. In brief, HiC-Pro performs four major tasks: aligning short reads, filtering for valid pairs, binning, and normalizing contact matrices. HiC-Pro implements the truncation-based alignment strategy using Bowtie v2.2.318, mapping full reads end-to-end or the 5’ portion of reads preceding a GATCGATC ligation site that results from restriction enzyme digestion with MboI followed by end ligation. Invalid interactions such as same-strand, dangling-end, self-cycle, and single-end pairs are not retained. Binning was performed in 20kb non-overlapping, adjacent windows across the genome and resulting interaction matrices were obtained.
Genome_build: mm10
Supplementary_files_format_and_content: text files of differential expression genes (RNAseq), differential binding regions (ChIPseq) and interaction counts (insituHiC)
Supplementary_files_format_and_content: ChIPseq_CTCF_neuron_KO_vs_WT_1kb_001b.annotated.txt: text file of differential binding regions
Supplementary_files_format_and_content: ChIPseq_H3K27ac_neuron_KO_vs_WT_1kb_001a.annotated.txt: text file of differential binding regions
Supplementary_files_format_and_content: ChIPseq_H3K9me3_neuron_KO_vs_WT_1kb_001a.annotated.txt: text file of differential binding regions
Supplementary_files_format_and_content: RNAseq_Setdb1-CK-KO_KO_vs_WT_gencode_vM4.txt: text file of differential expression genes
Supplementary_files_format_and_content: insituHiC_432_M_WT_neuronal_20000.HiCPro.interaction.txt: text file of interaction raw counts
Supplementary_files_format_and_content: insituHiC_513_M_CK-KO_neuronal_20000.HiCPro.interaction.txt: text file of interaction raw counts
Supplementary_files_format_and_content: insituHiC_9836_M_WT_neuronal_20000.HiCPro.interaction.txt: text file of interaction raw counts
Supplementary_files_format_and_content: insituHiC_9837_M_CK-KO_neuronal_20000.HiCPro.interaction.txt: text file of interaction raw counts
Supplementary_files_format_and_content: insituHiC_20000.HiCPro.bed: bed file of interaction bins

extract_protocol:
Nuclei were extracted from mouse brain tissue with or without formaline fixation. Neuronal nuclei were collected by FACS. Cromatin was fragmented by Mnase digestion (histone ChIP) or sonication (CTCF ChIP), and immunoprecipitated by different antibodies.
ChIP DNA was end repaired (End-it DNA Repair kit; Epicentre) and A tailed (Klenow Exo-minus; Epicentre). Adaptors (Illumina) were ligated to the ChIP-DNA (Fast-Link kit; Epicentre) and then PCR amplified using Illumina TruSeq ChIP Library Prep Kit. Library DNA with expected size (NChIP, ~275bp; XChIP, 350bp to 500bp) was selected by Pippin.

tag: antibody

value: CTCF

value: F


title: ChIPseq_CTCF_Input_WT_neuronal

value: F/M

value: WT


title: ChIPseq_CTCF_1586_F_WT_neuronal


title: TwinSet_GM14447

value: non-directional


title: ChIPseq_CTCF_1415_F_CK-KO_neuronal


title: ChIPseq_CTCF_1413_F_WT_neuronal


title: insituHiC_9836_M_WT_neuronal

description:
insituHiC_9836_M_WT_neuronal_20000.HiCPro.interaction.txt
insituHiC_20000.HiCPro.bed


title: TwinSet_GM14433


title: TwinSet_GM14432


title: TwinSet_GM14409


title: ChIPseq_H3K27ac_Input_KO_neuronal

description: ChIPseq_H3K27ac_neuronal_KOvsWT_1kb_001_annotated.txt


title: TwinSet_GM14452


title: ChIPseq_CTCF_1383_M_WT_neuronal


title: ChIPseq_CTCF_1385_M_CK-KO_neuronal


title: ChIPseq_H3K27ac_Input_WT_neuronal


title: ChIPseq_CTCF_1584_F_CK-KO_neuronal


title: TwinSet_GM14408


title: insituHiC_432_M_WT_neuronal

description:
insituHiC_432_M_WT_neuronal_20000.HiCPro.interaction.txt
insituHiC_20000.HiCPro.bed


title: ChIPseq_CTCF_1648_F_WT_neuronal


title: ChIPseq_CTCF_Input_KO_neuronal


title: TwinSet_GM14448


title: ChIPseq_H3K27ac_2065_M_WT_neuronal


title: TwinSet_GM14382


title: ChIPseq_H3K27ac_2058_M_WT_neuronal


title: ChIPseq_H3K27ac_1788_M_WT_neuronal


title: TwinSet_GM14381


title: ChIPseq_H3K9me3_Input_CK-KO_neuronal

description: ChIPseq_H3K9me3_neuronal_KOvsWT_1kb_001_annotated.txt


title: ChIPseq_H3K27ac_1787_M_KO_neuronal


title: ChIPseq_H3K9me3_2494_M_WT_neuronal


title: UnrelatedSet1_GM12750

value: maternal grandfather


title: ChIPseq_H3K9me3_2471_F_WT_neuronal


title: UnrelatedSet1_GM12716

value: paternal grandfather


title: ChIPseq_H3K9me3_2473_F_CK-KO_neuronal


title: Control, replicate 3

city: Paris

first: Frédérique

last: Peronnet

address: 9, quai saint-Bernard

department: UMR7622-Developmental biology

country: France

institute: CNRS-SU

data_processing:
Quality checking with fastqc
Filtering with fastq_quality_filter (fastx-Toolkit suite). Parameters: p 90, q 20
Alignement to the Drosophila melanogaster genome (dm6, r6.07) using TopHat 2 (v2.0.10) (default parameters)
Recovery of reads with Tophat mapping quality = 50 (unique alignment)
Assignment of unique reads to Ensembl BDGP5 v77 assembly by the "summerizeOverlaps" function of the "GenomicAlignments" R package (v1.2.2). Parameters: Union mode
Normalization and differential analysis by DESeq 2 (v1.6.3)
Genome_build: dm6, r6.07
Supplementary_files_format_and_content: Raw and DESeq2 normalized count data for gene features are provided as a matrices for the whole series

organism: Drosophila melanogaster

source_name: Third instar female larvae wing imaginal disc

growth_protocol: Flies were raised on standard yeast-cornmeal medium at 25°C.

extract_protocol:
Wing imaginal discs from da-Gal4/UAS-CycGΔP and da-Gal4/+ third instar female larvae were dissected, and total RNAs were extracted as previously described except that 150 discs homogenized by pipetting were used for each extraction (Coléno-Costes et al., 2012). Three biological replicates were generated for each genotype. Library preparation and Illumina sequencing were performed at the Ecole Normale Supérieure Genomic Platform (Paris, France). Messenger (polyA+) RNAs were purified from 1 µg of total RNA using oligo(dT).
Libraries were prepared using the strand specific RNA-Seq library preparation TruSeq Stranded mRNA kit (Illumina).
Multiplex by 6 on 2 flowcell lanes; 50 bp single read sequencing on a HiSeq 1500 device (Illumina). Mean of 38.1 ± 4.8 million reads.

treatment_protocol: No treatment.

value: Wing imaginal disc

value: Third instar larvae


title: ChIPseq_H3K9me3_2474_F_WT_neuronal


title: ChIPseq_H3K9me3_2493_M_CK-KO_neuronal


title: UnrelatedSet1_GM12004

value: paternal grandmother


title: ChIPseq_H3K9me3_2472_F_CK-KO_neuronal


title: RNAseq_2351_F_CK-KO

description: RNAseq_Setdb1-CK-KO_KOvsWT_gencode_vM4.txt

source_name: adult mouse prefrontal cortex

extract_protocol:
Total RNA was prepared with RNeasy Lipid Tissue Mini kit (Qiagen; catalog #74804) with on-column DNase1 treatment.
RNAseq library was generated using Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Mouse

value: brain homogenate


title: ChIPseq_H3K27ac_2066_M_KO_neuronal


title: Control, replicate 2


title: RNAseq_2350_F_WT


title: UnrelatedSet1_GM11995

value: maternal grandmother


title: ChIPseq_H3K27ac_2060_M_KO_neuronal


title: UnrelatedSet1_GM11994


title: RNAseq_2314_F_CK-KO


title: RNAseq_2313_F_WT


title: UnrelatedSet1_GM11993


title: Control, replicate 1


title: CycGΔP overexpressed in imaginal wing discs, replicate 3

value: UAS-CycG^deltaP, da-Gal4/+


title: UnrelatedSet1_GM12878

value: mother


title: ChIPseq_H3K9me3_Input_WT_neuronal

value: adult


title: UnrelatedSet1_GM12717


title: UnrelatedSet1_GM11992


title: CycGΔP overexpressed in imaginal wing discs, replicate 1


title: CycGΔP overexpressed in imaginal wing discs, replicate 2


title: DiscoverySet_GM12750

value: directional


title: Galactose fed flies-Rep2_RNA seq

city: Singapore

first: Jahnavi

last: Suresh

state: Singapore

address: 14 Medical Drive

department: Science

country: Singapore

institute: Yale-NUS college

data_processing:
Index of the reference genome was built using Bowtie v2.2.3 and
paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
Read numbers were counted using HTSeq v0.6.1 and then FPKM of each gene was calculated based on the length of the gene and read count mapped to this gene.
Differential expression analysis of two conditions with two biological replicates per condition was performed using bio conductor R package DESeq2.
Genome_build: BDGP6.81
Supplementary_files_format_and_content: counts

source_name: whole flies

growth_protocol: Flies were fed with the food containing two different sugars namely Glucose and alactose

extract_protocol:
Total RNA samples were extracted from whole flies using Zymo RNA extraction kit (#R1054S) as per manufacturee's instructions
Sequencing libraries were generated using NEBNext Ultra RNA library prep kit for Illumina following manufacturer’s protocol and index codes were added to each sample. Briefly, mRNA was purified from total RNA using poly-A captured and then fragmented. First strand cDNA synthesis was performed using random hexamers and M-MuLV reverse transcriptase (RNase H). Second strand cDNA synthesis was subsequently performed using DNA polymerase 1 and RNase H. Overhangs were blunted, 3’ends were adenylated and adaptors with hairpin loop structures were lygated and subjected to hybridization. Library fragments were purified with AMpure XP system in order to select 150~200 bp fragments in length. PCR amplification was carried out with size selected fragments with Phusion high fedility DNA polymerase, universal primers and index primer. Finally, PCR products were purified and library quality was assessed on the Bio analyzer (Agilent).

value: whole flies

tag: age of flies

value: 5 day old

tag: strain

value: Oregon

tag: diet

value: Galactose fed


title: Galactose fed flies-Rep1_RNA seq


title: Glu_IP_ChIP-seq

data_processing:
FastQC is used to check the quality of reads before and after trimming
Peak calling was done with MACS2.
Fold enrichment value is calculated by MACS2. The transcription start site (TSS) of each peak is identified by Peak annotator component of Peak Analyzer.
The peaks with fold enrichment changing more than 2 fold are considered as differentially expressed genes.
Genome_build: DM86
Supplementary_files_format_and_content: bigwig files containing ChIP-seq peaks

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody using Easy Magna Chip kit (Catalog # 17¬10085 & # 17¬10086, Millipore
Sequencing libraries were generated using library Preparation Kit (NEB) following manufacturer’s recommendations and index codes were added to each sample. Briefly, the DNA sample was fragmented by sonication to a size of 75~100bp, and then DNA fragments were end polished, A-tailed, and ligated with the full-length adapter for Illumina sequencing with further PCR amplification.

tag: chip antibody

value: Glucose fed


title: Gal_IP_ChIP-seq


title: Glu_In_ChIP-seq


title: Gal_IN_ChIP-seq


title: RAL360-1

city: Irvine

first: Grace

middle: Yuh Chwen

last: Lee

state: CA

address: UCI

institute: University of California, Irvine

data_processing:
raw reads were pre-processed with trim-galore to remove adatoprs and low quality bases
processed reads were mapped to reference genomes with TopHat
read counts for each gene were generated by htseq-count
Genome_build: D. melanogaster release 6 (fly base), D.simulans release 2 (fly base)
Supplementary_files_format_and_content: read counts for the exons of each gene

source_name: embryos

growth_protocol: Flies were reared on standard medium at 25C, 12hr/12hr light and dark cycle

extract_protocol:
Embryos were collected on standard apple juice plate. Before collection, pre-collection for 1hr was performed. Embryos were then collected for 4 hours and aged for 4 hours in 25C. ChIP was performed following standrad modEncode protocol.
Illumina TreSeq

tag: Stage

value: 4-8hr embryo


title: RAL360-2


title: RAL315-2


title: BC187

city: Guangzhou

first: Jian-Rong

last: Yang

address: No. 74, Zhongshan 2nd Road

institute: Sun Yat-sen University

data_processing:
All raw read sequences generated by RNA-seq were first processed by cutadapt to trim any remaining adaptor sequences
The trimmed reads were then aligned to the genome of the corresponding strains by tophat under the default parameter set except that a maximal intron size of 10 kb was allowed because the largest annotated intron in S. cerevisiae is 9349 bp
Alignment results were fed to cufflinks for quantification of known transcripts in S. cerevisiae, S. paradoxus, and S. mikatae.
Some ORFs are further filtered when they have no reliable one-to-one orthologs between the three species, giving rise to a final list of expression level for 4325 ORFs in the 9 species
Genome_build: S.cerevisiae (SGD R64.1.1), S. paradoxus and S.mikatae from [Scannell DR, et al. (2011) The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus. G3 (Bethesda) 1:11-25.]
Supplementary_files_format_and_content: Tab-delimited text files. Containing ORF names (represented by the S.cerevisiae ORF ID) and expression level (RPKM) in each strain.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

growth_protocol: Each of the nine yeast strains was streaked to form single colonies from frozen glycerol stocks held at -80°C onto YPD plates (1% yeast extract, 2% peptone, 2% glucose, 2% agar).  After 48 hours of growth at 30°C, a single colony was picked and inoculated into 5 ml of the synthetic oak exudate medium (1% sucrose, 0.5% fructose, 0.5% glucose, 0.1% yeast extract, and 0.15% peptone).  Strains were grown for 24 hours at 30°C before dilution into fresh synthetic oak exudate medium to an OD660 of 0.1.  Cultures were grown at 30°C until OD660 = 0.5 (mid-log phase), at which point cells were harvested by centrifugation.

extract_protocol:
Extraction of mRNA was carried out using MicroPoly(A)Purist Kit (Ambion) and 200 ng of the resulting mRNA sample was fragmented (Fragmentation Buffer, NEB) before ethanol precipitation.
First strand cDNA synthesis was performed using random hexamer priming (Superscript II, Invitrogen), followed by second strand cDNA synthesis (Invitrogen) as recommended by the manufacturer.  End repair, A-tailing, and ligation of the Illumina adapters necessary for sequencing were then carried out using the NEBnext mRNA sample preparation kit (NEB).  Libraries were then size-selected by agarose gel electrophoresis followed by gel extraction such that libraries consisted of fragments containing inserts of approximately 250 bp in length.  Polymerase-chain-reaction amplification was performed for 15 cycles using NEBnext mRNA sample preparation kit

tag: location isolated

value: Napa Valley, CA, USA

tag: source

value: Barrel fermentation

tag: ecological environment

value: Wine


title: Y9

value: Indonesia

value: Ragi (similar to sake)

value: Distillery


title: YJM145

value: USA

value: Lung of an AIDS patient

value: Clinical


title: DBVPG6040

value: Netherlands

value: Fermenting fruit juice

value: Fruit juice


title: UnrelatedSet1_GM07000

tag: sample

tag: family

value: paternal grandmother

value: non-directional


title: RAL315-1


title: RAL360-INPUT3

data_processing:
raw reads were pre-processed with trim-galore to remove adatoprs and low quality bases
processed reads were mapped to reference genomes with bwa
reads with mapping quality score smaller than 30 were filtered using samtools
fold enrichment (IP with respect to matching INPUT) tracks were generated using MAC2
Genome_build: D. melanogaster release 6 (fly base), D.simulans release 2 (fly base)
Supplementary_files_format_and_content: bigWig

extract_protocol:
Embryos were collected on standard apple juice plate. Before collection, pre-collection for 1hr was performed. Embryos were then collected for 4 hours and aged for 4 hours in 25C. ChIP was performed following standrad modEncode protocol.
Library was prepared using NuGen  Ovation Ultralow Library Systems V2


title: YPS606_rep1

description: The YPS606 replicate samples (GSM2150322 and GSM2150323) were analyzed together. Therefore there is a single processed data file for YPS606 isolate, located on GSM2150322).

value: Woodland, PA, USA

value: Oak tree

value: Wild


title: DiscoverySet_GM12004

extract_protocol: RNA-seq libraries were prepared following Illumina's recommendations. Briefly, cells were harvested 24 hours after addition of fresh medium, and total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). Poly-A mRNA was isolated and fragmented. First strand cDNA was prepared using reverse transcriptase and random hexamers. After second strand cDNA synthesis, ends were repaired and a single ‘A’ base was added followed by adapter sequences. Library fragments were selected for an average size of 200 to 260 base pairs, PCR amplified, and then sequenced using Illumina next-generation sequencing technology.

tag: relation

tag: protocol

value: directional


title: YPS606_rep2


title: RAL360-IP3

description: Processed data file is generated by contrasting IP to corresponding INPUT

value: 4-8hr embryo


title: DBVPG1788

value: Turku, Finland

value: Soil


title: Zheng 58

city: Beijing

first: Yong-Xin

address: No.1 Beichenxi Road, Chaoyang District

department: State Key Laboratory of Plant Genomics

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

data_processing:
Base-call using Illumina's RTA package.
Quality access by FastQC.
Adapter sequences were trimmed by fastx.
Summary fastq to reads and counts by Perl script.
sRNAs were aligned to maize genome v2 by psRobot 1.2
Genome_build: AGPv2
Supplementary_files_format_and_content: text file include reads and counts of each sRNA

organism: Zea mays

source_name: embryo from the seeds

extract_protocol:
Total RNA from the all samples was extracted with TRIzol reagent (Invitrogen, 15596-026) following the manufacturer’s protocol.
Small RNA libraies were constructed by TruSeq Small RNA Sample Prep Kit (Illumina) following the manufacturer’s instructions. Briefly, 1 µg total RNA or purified small RNA was ligated with 3’ and 5’ adaptors and used as a template for RT-PCR. After PCR amplification, 6 µL of each sample were pooled and separated on a 6% polyacrylamide Gel. Gel slices corresponding to ~18-26 nt small RNAs were recovered.

tag: cultivar

value: Zheng 58

tag: tissue

value: whole embryo

tag: treatment

value: 24 hours soaked seeds at 26°C


title: Change 7-2

value: Change 7-2


title: Lingdan 20

value: Lingdan 20


title: Zhengdan 958

value: Zhengdan 958


title: Glucose fed flies-Rep2_RNA seq

tag: cell type

value: whole flies

value: 5 day old

value: Oregon

value: Glucose fed


title: RAL360-INPUT2


title: 9058


title: RAL360-IP2


title: Glucose fed flies-Rep1_RNA seq


title: RAL360-INPUT1


title: RAL315-INPUT1


title: RAL315-INPUT2


title: RAL315-IP2


title: RAL315-IP1


title: Hi-C male 2 [Sample 4]

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

data_processing:
Paired-end reads were mapped separately to the reference genome (BDGP 5.74) using bowtie2 (2.0.2) with "-local" settings. Hi-C data processing and analysis steps were carried out using the Homer software package (Heinz et al., 2010). Paired-end tag directories were generated by pooling technical (sequencing) replicates. Reads were extensively filtered with the recommended parameters, i.e. "-tbp 1 -removePEbg -fragLength 500 -restrictionSite GATC -both -removeSelfLigation -removeSpikes 10000 5". Background models, coverage-normalized ("-simpleNorm") as well as coverage- and distance-normalized correlation matrices ("-corr") were created using various resolutions ("-res") and smoothing ("-superRes") windows, from which 10 kb resolution with 50 kb smoothing was chosen for downstream analysis. The genome was divided into two compartments based on principal component analysis of the correlation matrix ("runHiCpca.pl"), where H4K16ac regions (peaks) served as a seed to define the sign of the PC1 values (processed data file).
Genome_build: BDGP 5.74
Supplementary_files_format_and_content: Bedgraph format. Hi-C PC1 values; 4C-seq, ChIP-seq and RNA-seq signals.

source_name: embryo

extract_protocol: Hi-C methods. Embryo sorting (female/male) was based on a Y chromosomal GFP reporter (y[1]w[67c23]/Dp(1;Y)y[+],P{w[+mC]=ActGFP}SH1) described in (Hayashi, 2010). The flies were raised in standard cornmeal yeast extract media at 25°C. Embryos were collected in 0.03% Triton X-100, 0.4% NaCl 16-18 hr after egg laying, then de-chorionated for 5 min in fresh bleach. ~3000 GFP+ (male) and GFP- (female) embryos each were sorted with a Union Biometra COPAS Large Particle Sorter, and then processed for Hi-C as in (Sexton et al., 2012).

value: embryo

tag: strain/background

tag: age

tag: gender

value: male


title: Hi-C female 1 [Sample 1]

value: female


title: Dsim-Ref-INPUT3

organism: Drosophila simulans


title: Hi-C female 2 [Sample 2]


title: Dsim-ref-1


title: Dsim-ref-2


title: Dsim-Ref-IP3


title: Dsim-Ref-IP2


title: Dsim-Ref-INPUT1


title: Dsim-Ref-IP1


title: RAL360-IP1


title: Dsim-Ref-INPUT2


title: R. norvegicus replicate 1

city: Salt Lake City

first: Robert

middle: B

last: Weiss

state: UT

department: Human Genetics

institute: University of Utah

description:
Sample 13
PolyA RNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Paired-end reads were quality filtered and trimmed using Trimmomatic (Bolger et al. 2014).
The subsequent overlapping paired-end reads were merged using FLASH (Mago_ and Salzberg 2011).
The coding transcripts from the M7 release of the GENCODE mouse genome annotation (gencode.vM7.pc_transcripts.fa) were formatted as a nucleotide database and Illumina reads were aligned using a fast version of the Smith-Waterman algorithm implemented in cross_match (Gordon et al. 1998) with a -minscore parameter of 50 and a -masklevel parameter of 101 to allow reads to align to multiple transcripts.
Total read counts were generated from read alignments per CDS region using custom Perl scripts that collapsed transcript level alignments (ENSMUST identifiers) to gene level alignments (ENSMUSG identifiers).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include raw read counts for each Sample.

organism: Rattus norvegicus

source_name: foregut tissue

extract_protocol:
We collected a small section of the fornix ventricularis of the stomach (or the fundus of the stomach), which was immediately rinsed in ice-cold physiological saline buffer and placed in RNAlater solution. After 24 hours, the RNAlater solution was removed and tissues were frozen at -80°C. Total RNA from each animal was isolated from frozen tissue samples using Qiagen RNeasy kit according to manufacturer instructions (Valencia, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Sprague Dawley

value: fornix ventricularis of the stomach

tag: sex type

value: virgin female


title: R. norvegicus replicate 2

description:
Sample 14
PolyA RNA


title: R. norvegicus replicate 3

description:
Sample 15
PolyA RNA


title: SK-N-SH batch2, doxo 100nM 1, RNA-seq

city: Zurich

first: Valentina

last: Boeva

address: Universitatstrasse 6

department: Computer Science

country: Switzerland

institute: ETH Zurich

data_processing:
ChIP-seq: Alignment with Bowtie2, default options
ChIP-seq: Quality filtering: Q > 20; duplicates kept
ChIP-seq: Peak calling with HMCan v1.30
ChIP-seq: Renormalization of wig profiles among all H3K27ac samples with an in-house R script
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files correspond to renormalized signal; score in .bed files correspond to the likelihood of a region to be enriched in H3K27ac or to be a binding site of a TF
RNA-seq:TopHat2 v2.0.643 with the following parameters: global alignment, no mismatch in the 22 bp seed, up to three mismatches in the read, library type fr-firststrand
Genome_build: hg19/GRCh37

source_name: SK-N-SH batch2, doxo 100nM 1

growth_protocol:
ChIP-seq: Neuroblastoma cell lines were cultured at 37°C with 5% CO2 in a humidified atmosphere in RPMI (GE Healthcare, for CLB cell lines, SH-EP, GICAN and NB69), in IMDM (Gibco) for NB-EBc1 (according to the provided conditions) or DMEM (GE Healthcare, for other cell lines), with 10%, 15% or 20% FCS (Eurobio) and 100 μg/ml penicillin/streptomycin (Gibco). Primary hNCC lines were grown as previously described under bioethical approval PFS14-011 from the French Biomedical Agency for the use of human embryonic material to S. Zaffran. Briefly, cells were grown in Glutamax DMEM:F12 [Gibco] supplemented with 12% FCS (Eurobio), 100 μg/ml penicillin/streptomycin, 10 mM HEPES, 100 ng/ml hydrocortisone, 10 μg/ml transferrin, 400 pg/ml 3,3,5-thio-iodo-thyronine, 10 pg/ml glucagon, 100 pg/ml epidermal growth factor, 1 ng/ml insulin and 200 pg/ml fibroblast growth factor 2 (all products supplied by Sigma-Aldrich except EGF and FGF2 from Gibco).
RNA-seq: Neuroblastoma cell lines were cultured at 37°C with 5% CO2 in a humidified atmosphere in RPMI (GE Healthcare, for CLB cell lines, SH-EP, GICAN and NB69), in IMDM (Gibco) for NB-EBc1 (according to the provided conditions) or DMEM (GE Healthcare, for other cell lines), with 10%, 15% or 20% FCS (Eurobio) and 100 μg/ml penicillin/streptomycin (Gibco). Primary hNCC lines were grown as previously described under bioethical approval PFS14-011 from the French Biomedical Agency for the use of human embryonic material to S. Zaffran. Briefly, cells were grown in Glutamax DMEM:F12 [Gibco] supplemented with 12% FCS (Eurobio), 100 μg/ml penicillin/streptomycin, 10 mM HEPES, 100 ng/ml hydrocortisone, 10 μg/ml transferrin, 400 pg/ml 3,3,5-thio-iodo-thyronine, 10 pg/ml glucagon, 100 pg/ml epidermal growth factor, 1 ng/ml insulin and 200 pg/ml fibroblast growth factor 2 (all products supplied by Sigma-Aldrich except EGF and FGF2 from Gibco).

extract_protocol:
ChIP-seq: Chromatin preparation and ChIP were performed with Ideal ChIP-seq kit for histones or transcription factors according to the supplier's protocol (Diagenode )
ChIP-seq: llumina sequencing libraries were prepared from ChIP and input DNAs using the TruSeq ChIP library preparation kit according to the manufacturer’s protocol. Briefly, DNA were subjected to consecutive steps of end-repair, dA-tailing and ligation to TruSeq indexed Illumina adapters. Size-selection was performed only for the H3K27ac ChIP (100 – 600 bp). After a final amplification step, the resulting DNA libraries were quantified using a qPCR method (KAPA library quantification kit) and sequenced on the Illumina HiSeq2500 instrument (rapid run mode; single reads 100 nts).
RNA-seq: Total RNA was extracted from fresh cells or frozen tumors using TRIzol® Reagent (Invitrogen), or AllPrep DNA/RNA Mini Kit (Qiagen) or NucleoSpin RNA kit (Macherey-Nagel; for the SK-N-SH cell line treated with chemotherapy). All samples were subjected to quality control on a Bioanalyzer instrument and only RNA with RIN (RNA Integrity Number) > 6 were used for sequencing.
RNA-seq: RNA sequencing libraries were prepared from 1 µg of total RNA using the Illumina TruSeq Stranded mRNA Library preparation kit which allows performing a strand-specific sequencing. A first step of polyA selection using magnetic beads is done to focus sequencing on polyadenylated transcripts. After fragmentation, cDNA synthesis was performed and resulting fragments were used for dA-tailing and then ligated to the TruSeq indexed adapters. PCR amplification is finally achieved to create the final cDNA library. After qPCR quantification, sequencing was carried out using 2 x 50 cycles (paired-end reads 50 nts) for all samples (except SH-EP, 2 x 100; Pair1-Relapse and Pair3-Relapse, 2 x 75; Pair2-Relapse, 2 x 150). Sequencing was performed with the Illumina HiSeq2500 instrument (high output mode).

treatment_protocol:
RNA-seq: Cells were not treated unless it is specified
RNA-seq: Treatment of cell lines with chemotherapy: SK-N-SH cells were plated in 6-well plates and then treated with cisplatin (7.5 µM) or doxorubicin (100 nM) for 7 days, medium and drugs were changed every 2 days. RNAs were extracted using NucleoSpin RNA kit (Macherey-Nagel).
RNA-seq: Doxycycline-inducible shRNA systems: PHOX2B-specific short hairpin RNAs sh1783 (5’-CCGGTGGAAGGCAGAAACCATTAAA- CTCGAGTTTAATGGTTTCTGCCTTCCATTTTTG-3’) and sh1437 (5’-CCGGAGTAATCG- CGCTAAGAATAAACTCGAGTTTATTCTTAGCGCGATTACTTTTTTG-3’) were selected from Sigma Mission shRNA library and cloned into the pLKO-Tet-On all-in-one system46 (Addgene). Lentiviral particles were produced in HEK293T cells and CLB-GA cells were infected as previously described4. SH-SY5Y cells were incubated with viral particules for 48 hours without polybrene. Selection with puromycin (Invitrogen) at 400 ng/ml or 1 µg/ml, respectively, was performed 24 h after infection and maintained during all culture experiments, for CLB-GA and SH-SY5Y cells, respectively. PHOX2B knockdown efficacy was assessed by Western blot 24 h/48 h/96 h after the addition of doxycycline (100 ng/ml or 1 μg/ml). For colony formation assays, 6x104 transduced cells were plated at day 0 in 6-well dishes and stained with crystal violet at day 11.

value: Neuroblastoma cell line

value: doxorubicin


title: WT2

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
fastq seqences were aligned to mm9 using Tophat
number of read counts was calculated for each Entrez gene
differential expression analysis was performed using Deseq
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns

source_name: wild-type FVB/N mouse heart

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: FVB/N

value: heart

tag: genotype

value: wild type


title: WT4


title: KO3

source_name: AE3-null FVB/N mouse heart


title: Hi-C male 1 [Sample 3]


title: KO4


title: KO1


title: SK-N-SH batch 2, Ctrl 2, RNA-seq

source_name: SK-N-SH batch 2, Ctrl 2

value: DMSO


title: SK-N-SH batch 2, Ctrl 1, RNA-seq

source_name: SK-N-SH batch 2, Ctrl 1


title: SK-N-SH batch 2, RNA-seq

source_name: SK-N-SH batch 2


title: NB69, RNA-seq


title: NB-EBc1, RNA-seq


title: SK-N-SH batch 1, RNA-seq

source_name: SK-N-SH batch 1


title: KO2


title: CLB-GA_shPHOX2B_dox_J13, RNA-seq

value: Doxycycline-inducible shRNA


title: CHP-212, RNA-seq


title: WT3


title: WT1


title: SH-EP, RNA-seq

source_name: SH-EP


title: CLB-GA_shPHOX2B_dox_J5, RNA-seq


title: CLB-GA_shPHOX2B_dox_J2, RNA-seq


title: CLB-GA_shPHOX2B_dox_J0, RNA-seq


title: SK-N-SH batch2, cisPt 7-5uM 2, RNA-seq

source_name: SK-N-SH batch2, cisPt 7-5uM 2

value: cisplatin


title: CLB-MA, RNA-seq

source_name: CLB-MA


title: hNCC rep2, RNA-seq

source_name: hNCC rep2


title: CLB-GA, RNA-seq

source_name: CLB-GA


title: TR-14, RNA-seq


title: hNCC rep1, RNA-seq

source_name: hNCC rep1


title: CLB-BER-Lud, RNA-seq

source_name: CLB-BER-Lud


title: SH-SY5Y, RNA-seq


title: SK-N-FI, RNA-seq

source_name: SK-N-FI


title: SK-N-DZ, RNA-seq

source_name: SK-N-DZ


title: SJNB12, RNA-seq


title: GICAN, RNA-seq

source_name: GICAN


title: N206, RNA-seq


title: IMR32, RNA-seq


title: LAN-1, RNA-seq


title: SK-N-BE(2)-C, RNA-seq


title: GIMEN, RNA-seq

source_name: GIMEN


title: CLB-CAR, RNA-seq

source_name: CLB-CAR


title: SJNB6, RNA-seq


title: CLB-GA HAND2, ChIP-seq

tag: chip antibody

value: sc-9409 (goat polyclonal)


title: CLB-GA PHOX2B, ChIP-seq

value: sc-376997X (mouse monoclonal)


title: CLB-GA GATA3, ChIP-seq

value: sc-22206X (goat polyclonal)


title: SJNB8, RNA-seq


title: hNCC rep1 Input, ChIP-seq

value: neural crest line


title: hNCC rep2 Input, ChIP-seq


title: hNCC rep1 H3K27ac, ChIP-seq

value: ab4729 (rabbit polyclonal, Abcam)


title: hNCC rep2 H3K27ac, ChIP-seq


title: NB-EBc1 H3K27ac, ChIP-seq


title: SK-N-SH H3K27ac, ChIP-seq

source_name: SK-N-SH


title: NB-EBc1 Input, ChIP-seq


title: Yuyu 22

source_name: embryo from the seeds

value: Yuyu 22

value: whole embryo

value: 24 hours soaked seeds at 26°C


title: SK-N-SH Input, ChIP-seq


title: Cerebellum Diestrus3

city: Tallahassee

first: Cynthia

last: Vied

state: Florida

address: 1115 W. Call St

department: Translational Science Laboratory

institute: Florida State University

data_processing:
Sequences from Illumina adapters were trimmed using Trimmomatic (version 0.32) using the TruSeq3-SE.fa adapter sequence file provided with the program. A minimum length of 50 bases (MINLEN:50) was chosen as a cutoff for each read and 2 seed mismatches were allowed. All reads between 50 and 100 bases were included in further analyses.
The trimmed sequencing reads were aligned to the mouse genome (genome release GRCm38) using Tophat (2.0.8, --read-mismatches and --read-edit-dist set to 6). A General Transfer Format (GTF) file was used with Tophat (--GTF option) for the purpose of gene annotation (Mus_musculus.GRCm38.68.gtf).
Following mapping reads were futher processed (filtered, sorted and indexed) with Samtools and only reads that mapped to a single gene were used for further analysis.
The uniquely mapped reads were used to generate counts for each annotated gene using easyRNASeq (from Bioconductor version 1.4.0, geneModels summarization)
Differential expression analysis of count tables for pairwise comparisons of estrous cycle stages (proestrus to estrus, estrus to metestrus, metestrus to diestrus, diestrus to proestrus, proestrus to metestrus, estrus to diestrus) within each brain region was performed using the default settings of DESeq (1.12.1, Benjamini-Hochberg FDR correction).
Cufflinks (2.1.1, --no-effective-length-correction, --max-bundle-length 10000000 --GTF Mus_musculus.GRCm38.68.gtf) was used to generate FPKM (fragments per kilobase per million reads) normalized values.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Microsoft Excel Worksheet (.xlsx). Contains unnormalized counts generated by easyRNASeq. The raw counts were used by DESeq for differential expression analysis.

source_name: Cerebellum

growth_protocol: Adult female C57BL/6J mice were purchased from the Jackson Laboratory (Bar Harbor, ME).  Mice were group housed and kept on a 12 hour light:dark cycle.  Food and water were provided ad libitum.  After delivery, the animals were acclimated for two weeks before being euthanized by rapid decapitation at 90-92 days of age.

extract_protocol:
The hypothalamus (from both sides of the brain), hippocampus (from both sides of the brain), neocortex (from both sides of the brain), and cerebellum were dissected and rapidly frozen in liquid nitrogen and stored at -80 degrees. Total RNA was extracted from the entire hypothalamus, hippocampus, neocortex, and cerebellum from each animal using TRI Reagent (Sigma-Aldrich) according to manufacturer’s directions.
Hippocampus RNA-Seq samples (termed libraries) were prepared using the protocols of Mortazavi et al. (2008) and Chang et al. (2011) as described in Vied et al. (2016).  Hypothalamus, neocortex, and cerebellum RNA-Seq libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England BioLabs Inc., catalog # E7530S/L).  ERCC ExFold RNA Spike-In Mixes (Ambion, Austin, TX; catalog No. 4456739) were added to each library just after mRNA isolation according to manufacturer’s suggestions as described in Vied et al. (2016).  RNA-Seq sample quality was examined using Agilent High Sensitivity DNA Bioanalyzer Chips (Agilent Technologies 5067-4626) and quantified by KAPA Library Quantification Kits for Illumina sequencing platforms (KAPA Biosystems KK4824).  Three libraries were genereated for each stage of the estrous cycle (proestrus, estrus, metestrus, diestrus).  Barcodes were added to each library in order to combine multiple libraries in one sequencing lane. We multiplexed 6-9 libraries at a concentration of 12 pM and those were sequenced on an Illumina HiSeq 2500.

tag: Sex

value: Female

value: 92 Days

value: Cerebellum

tag: Stage

value: Diestrus


title: SJNB1, RNA-seq

value: Neuroblastoma cell line


title: NB69 Input, ChIP-seq


title: Cerebellum Diestrus2


title: Cerebellum Diestrus1

value: 90 Days


title: NB69 H3K27ac, ChIP-seq


title: Cerebellum Metestrus3

value: 91 Days

value: Metestrus


title: GICAN Input, ChIP-seq


title: GICAN H3K27ac, ChIP-seq


title: CHP212 Input, ChIP-seq


title: Zong 3

value: Zong 3


title: 87-1


title: Cerebellum Metestrus2


title: SK-N-AS, RNA-seq

source_name: SK-N-AS


title: Cerebellum Metestrus1


title: Cerebellum Estrus2

value: Estrus


title: TR14 Input, ChIP-seq


title: Cerebellum Estrus3


title: CHP212 H3K27ac, ChIP-seq


title: TR14 H3K27ac, ChIP-seq


title: Cerebellum Estrus1


title: Cerebellum Proestrus2

value: Proestrus


title: Cerebellum Proestrus3


title: SK-N-DZ Input, ChIP-seq


title: SK-N-FI H3K27ac, ChIP-seq


title: SK-N-DZ H3K27ac, ChIP-seq


title: SK-N-FI Input, ChIP-seq


title: Cerebellum Proestrus1


title: Neocortex Diestrus3

source_name: Neocortex

value: Neocortex


title: Neocortex Metestrus3


title: SK-N-AS Input, ChIP-seq


title: SK-N-BE(2)-C H3K27ac, ChIP-seq


title: Neocortex Diestrus1


title: Neocortex Diestrus2


title: Neocortex Estrus2


title: SK-N-BE(2)-C Input, ChIP-seq


title: Neocortex Metestrus1


title: Neocortex Estrus1


title: Neocortex Metestrus2


title: SJNB6 H3K27ac, ChIP-seq


title: SJNB8 H3K27ac, ChIP-seq


title: Neocortex Proestrus3


title: SJNB1 Input, ChIP-seq


title: Neocortex Proestrus2


title: CLB-PE, RNA-seq

source_name: CLB-PE


title: Neocortex Proestrus1


title: SJNB12 Input, ChIP-seq


title: SK-N-AS H3K27ac, ChIP-seq


title: Hippocampus Diestrus3

source_name: Hippocampus

value: Hippocampus


title: SH-SY5Y Input, ChIP-seq


title: SJNB6 Input, ChIP-seq


title: Hippocampus Diestrus1


title: SJNB12 H3K27ac, ChIP-seq

value: ab4729 (rabbit polyclonal, Abcam)


title: Hippocampus Metestrus3


title: N206 Input, ChIP-seq


title: SH-EP Input, ChIP-seq

source_name: SH-EP


title: SJNB8 Input, ChIP-seq


title: Hippocampus Metestrus1


title: SH-EP H3K27ac, ChIP-seq


title: N206 H3K27ac, ChIP-seq


title: Hippocampus Estrus2


title: Hippocampus Diestrus2


title: Hippocampus Estrus1


title: Hippocampus Estrus3


title: Hippocampus Metestrus2


title: LAN1 H3K27ac, ChIP-seq


title: IMR32 Input, ChIP-seq


title: Hippocampus Proestrus3


title: SJNB1 H3K27ac, ChIP-seq


title: Hippocampus Proestrus2


title: GIMEN Input, ChIP-seq


title: Hippocampus Proestrus1


title: Hypothalamus Diestrus3

source_name: Hypothalamus

value: Hypothalamus


title: IMR32 H3K27ac, ChIP-seq


title: SH-SY5Y H3K27ac, ChIP-seq


title: Hypothalamus Diestrus1


title: Hypothalamus Metestrus3


title: LAN1 Input, ChIP-seq


title: Hypothalamus Diestrus2


title: Hypothalamus Metestrus1


title: Hypothalamus Estrus3


title: Hypothalamus Metestrus2


title: CLB-MA Input, ChIP-seq

source_name: CLB-MA


title: CLB-MA H3K27ac, ChIP-seq


title: CLB-PE H3K27ac, ChIP-seq


title: Hypothalamus Estrus2


title: CLB-PE Input, ChIP-seq


title: Hypothalamus Proestrus2


title: CLB-GA rep 2 Input, ChIP-seq

source_name: CLB-GA rep 2


title: CLB-GA rep 2 H3K27ac, ChIP-seq


title: Hypothalamus Proestrus3


title: Hypothalamus Estrus1


title: CLB-GA rep 1 Input, ChIP-seq

source_name: CLB-GA rep 1


title: CLB-CAR Input, ChIP-seq


title: CLB-CAR H3K27ac, ChIP-seq


title: CLB-GA rep 1 H3K27ac, ChIP-seq


title: Hypothalamus Proestrus1


title: CLB-BER-Lud Input, ChIP-seq

source_name: CLB-BER-Lud


title: cocx_exo_mnase_1

city: Philadelphia

last: Qiu

state: PA

address: 421 Curie Blvd

department: Radiation Oncology

institute: University of Pennsylvania

data_processing:
Basecalls performed using Illumina CASAVA software.
Raw reads were trimmed for adaptor sequence using cutadapt v1.9 (parameter -q 10 -m 30 -O 4)
Trimmed reads were mapped to consensus rRNA sequences and RN7SL1 using bowtie2 v2.2.4 to remove rRNA reads and get more accurate count of 7SL RNA (parameter --fr --no-mixed --no-discordant)
Reads were then aligned with STAR v2.4.0k to GRCm38/mm10 reference genome (parameter --outFilterMultimapNmax 100 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.06)
Non primary alignment and QC failed reads were removed with samtools (parameter -F 772)
Aligned and filtered reads were counted against GENCODE annotation v21  and RepeatMasker features (UCSC genome browser) using Subread v1.4.6 (parameter -s 2 -minReadOverlap 10)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited txt file including raw read count for gene features and repeatmasker features.

source_name: MRC5 and 1833 (breast cancer) co-culture

growth_protocol: All human breast cancer and/or stromal cell lines were cultured at 37oC in DMEM supplemented with 10% exosome depleted FBS, 100U/ml penicillin and 100µg/ml streptomycin.  For co-culutre experiment, stroma cells and breast cancer cells were mixed at 1:1.

extract_protocol:
Exosomes were isolated from conditioned media collected at 48-72 hours by serial high speed ultracentrifugation, or using 10% final concentration of polyethylene-glycol and low speed centrifugation. Exosome RNA or cellular RNA was extracted with TRIzol.
Library was prepared by using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB).  Fragmentation step was skipped for exosome RNA.

treatment_protocol: Either whole cells or whole exosomes were incubated at 37oC for 30 minutes in MNase Buffer (25mM Tris-HCl, 2.5mM CaCl2, 50mM NaCl, 1X PBS), with or without MNase and with or without 0.1% Triton X-100.

tag: cell line

value: MRC5 and 1833

tag: culture

value: co-culture

tag: fraction

value: exosome RNA

value: micrococcal nuclease only


title: cocx_exo_mnase_2


title: GCLiPP resting CD8 experiment 2

city: San Francisco

first: Adam

middle: Jacob

last: Litterman

address: 513 Parnassus Avenue, UCSF Box 0414, HSE-201

institute: UCSF

description:
RBP crosslinked RNA
biotinylated lystae, oligo-dT selection, streptavidin bead capture, Rnase T1 digestion, linker ligation, reverse transcription, cDNA amplification
Mouse_T_cells_combined_GCLiPP_positive_strand.bw
Mouse_T_cells_combined_GCLiPP_negative_strand.bw
Mouse_CD8_T_cells_GCLiPP_positive_strand.bw
Mouse_CD8_T_cells_GCLiPP_negative_strand.bw
Mouse_GCLiPP_peaks.bed

data_processing:
For GCLiPP raw reads were demultiplexed by a custom script and linker trimmed with fastx_trimmer
Linker dimer reads were discarded and one uniquely aligning read with a given di-nucleotide randomer in the 3' RNA linker was kept for further analysis to remove PCR duplicates
GCliPP reads were aligned to mm10 using bowtie2
Peaks were called with in house perl scripts that convolved a normal distribution against observed read distribution at each nucleotide and looked of local maxima of correlation
RNAseq was aligned to mm10 with STAR
Genome_build: mm10
Supplementary_files_format_and_content: bigwig, reads per million at each location in the genome; bed, location of called peaks and voids of GCLiPP read density; csv, per gene expression data from RNAseq

source_name: CD8 T cells

growth_protocol: Mouse T cells were grown on plates coated with anti-CD3 and anti-CD28 antibodies and the indicated cytokines for 5 days

extract_protocol:
Cells were lysed by re-suspension in PXL buffer without SDS. Cell debris were pelleted and supernatants were biotinylated with EZ-Link-NHS-SS-Biotin. Poly-A RNA was enriched by pulldown with oligo-dT beads. RNPs were captured with M-280 Streptavidin dynabeads and RNAs were digested with RNAse T1
Linkers were ligated on while RNPs were immobilized on M-280 beads and released by proteinase K digestion, size selected by TBE-Urea PAGE gel, gel extracted, reverse transcribed and used for cDNA amplification

treatment_protocol: Four hours before harvest cells were re-plated in fresh medium (resting) or re-stimulated with PMA/Ionomycin (stimulated). Cells were crosslinked with 8000 mJ high energy (254 nM) UV light

tag: culture conditions

tag: restimulation


title: cocx_exo_triton_2

value: 0.1% Triton X-100 and micrococcal nuclease


title: GCLiPP stimulated CD8 experiment 1

value: PMA/Ionomycin


title: cocx_exo_triton_1


title: GCLiPP stimulated CD8 experiment 2


title: cocx_cell_mnase_2

value: cellular RNA


title: cocx_exo_ctrl_1

value: no treatment


title: GCLiPP resting Th2 experiment 3

description:
RBP crosslinked RNA
biotinylated lystae, oligo-dT selection, streptavidin bead capture, Rnase T1 digestion, linker ligation, reverse transcription, cDNA amplification
Mouse_T_cells_combined_GCLiPP_positive_strand.bw
Mouse_T_cells_combined_GCLiPP_negative_strand.bw
Mouse_Th2_T_cells_GCLiPP_positive_strand.bw
Mouse_Th2_T_cells_GCLiPP_negative_strand.bw
Mouse_GCLiPP_peaks.bed

source_name: CD4 T cells

value: IL-4, anti-Ifn-gamma, IL-2


title: GCLiPP stimulated Th2 experiment 3


title: cocx_exo_ctrl_2


title: GCLiPP stimulated Th2 experiment 2


title: cocx_cell_mnase_1


title: GCLiPP stimulated Th2 experiment 1