title: ATAC-seq; XaWT Xi[delta]Xist cells; siBRG1; Rep2

extract_protocol:
50,000 cells were washed briefly in cold PBS and permeabilized with cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) containing proteinase inhibitor cocktail (Roche). Nuclei were resuspended in 1X TD Buffer (Illumina FC-121-1030), and 2.5uL of Tn5 Transposase (Illumina FC-121-1030) were added. Transposition reaction was performed at 37C for 30 min, and DNA was purified using a Qiagen MinElute Kit.
DNA libraries were amplified for a total of 8 cycles. Libraries were assessed for quality control on the BioAnalyzer 2100 (Aglient) to ensure nucleosomal phasing and complexity. Sequencing was performed on the HiSeq 2500 (Illumina), using 50 bp paired-end reads. Sequencing Nextera adpters: F: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, R: GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG

treatment_protocol: siRNA BRG1 transfection


title: Aldh1_2_TCACTGA_TRAP_RF

status: Public on Jan 14 2019

type: SRA

city: St Louis

first: Joseph

middle: D

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

country: USA

institute: Washington University

library_source: transcriptomic

data_processing:
Quality check using using FastQC (version 0.11.2)
Trim low-quality bases from the ends of reads and to remove adapter sequences using Trimmomatic (version 0.32). Only fragments 25-35 nt in length were retained for subsequent analysis
Reads aligning to the mouse rRNA were removed using STAR (version 2.3.1z8)
Surviving reads were then aligned to non-degenerate mouse transcriptome using Bowtie2 (version 2.2.2), retaining both uniquely mapped and multi-mapped reads
For Readthrough identification: In order to count reads aligning to non-overlapping regions for readthrough analysis in culture (deposited in GSE77076) and TRAP-RF data, we used the BEDTools intersect command. Then, similar to prior work (Dunn et al 2013), we removed reads aligning to the following positions: 12 nts after the start codon; 15 nts before and 9 nts after the first stop codon, and 15 nts after the second stop codon. This resulted in four remaining transcriptomic regions: 5’UTR, CDS, readthrough region, and distal 3’UTR. Reads were counted in each of these regions using the uniq Unix utility. Readthrough analysis was performed in R. Transcripts were filtered based on CDS counts as follows: in culture RF, transcripts with ≥ 320 CDS counts across all samples were retained, and in TRAP RF, transcripts with ≥ 128 CDS counts across replicates in either the Aldh1l1 or Snap25 samples were retained. Subsequently, to avoid false positive identification of readthrough events because of alternative splicing, if a gene was annotated as having multiple isoforms with stop codons at different genomic locations, only the transcript with the downstream-most stop codon was retained. Using edgeR, counts were normalized to RPKM, and readthrough rate was defined for each transcript as the ratio of readthrough region RPKM to coding sequence RPKM. Next, for readthrough identification in culture RF and brain TRAP-RF datasets, transcripts with ≥ 32 readthrough region counts across samples were retained. In each dataset, surviving transcripts with ≥ 1% readthrough rate in at least 2 samples were retained for readthrough analysis. Genes with ≥ 100% readthrough or with RPKM(distal 3’UTR) ≥ RPKM(readthrough region), for any transcript isoform or in any sample, were labeled false positives and eliminated.
Genome_build: Ensembl 75 (mouse) transcriptome with degenerate sequences removed
Supplementary_files_format_and_content: txt files with counts of certain transcript region for each sample [For annotation on transcript region: "a": 5' untranslated region [5'UTR]; "b": Coding Sequence[CDS]; "c": readthrough region; "d": distal 3'UTR]

molecule: total RNA

organism: Mus musculus

source_name: brain

extract_protocol:
TRAP-RF-in-vivo: P21 Snap25::eGFP-RpL10a, Aldh1l1:: eGFP-RpL10a, along with their eGFP-negative littermates were euthanized, and their brains frozen in liquid nitrogen and stored at -80C until use. Two brains were pooled per sample, and replicate experiments were done. TRAP was  performed as described (Heiman et al 2008) with a few modifications. Briefly, the brains were homogenized in ice in a buffer (20 mM pH 7.4 HEPES, 150 mM KCl, 5 mM MgCl2, 0.5 mM dithiothreitol, 100 μg/ml CHX, Turbo DNAse, protease inhibitors, and RNase inhibitors). The lysates were cleared by centrifuging at 2000 xg for 10 m at 40C and then treated with DHPC (to 30mM, Avanti) and NP-40 (to 1%, Ipgal-ca630, Sigma) for 5 min in ice. Lysates were then further cleared by centrifuging at 20,000 xg for 15 m at 40C and then mixed with protein L-coated magnetic beads (Invitrogen), previously conjugated with a mix of two monoclonal anti-GFP antibodies  (Doyle et al 2008), and incubated with rotation for 4 h at 4°C. Beads were washed 5 times with a high-salt buffer (20 mM pH7.4 HEPES, 350 mM KCl, 5 mM MgCl2, 1% NP-40, 0.5 mM dithiothreitol, and 100 μg/ml CHX) and then resuspended in normal-salt buffer (150 mM KCl, otherwise as above). To couple to RF, on-bead RNA digestion was performed with RNAse I (Invitrogen) for 1 h with end-to-end rotation, followed by washing three times with normal-salt buffer. Small ribosomal subunits with the mRNA fragments were eluted with ribosome dissociation buffer as described (20 mM pH7.3 Tris-HCl, 250 mM NaCl, 0.5% Triton X-100, 50mM EDTA) (Gonzalez et al 2014). RNA was extracted with phenol-chloroform, quality-tested with Agilent BioAnalyzer, and then subjected to dephosphorylation and subsequent library preparation as described for RF (Ingolia et al 2011). Briefly, the cell lysates were treated with RNAseI and subjected to sucrose-cushion ultracentrifugation for pelleting monosomes. mRNA fragments were isolated from the monosomes, size-selected in a polyacrylamide, ligated to cloning linkers, and converted to cDNAs.
The cDNAs were then circularized, depleted of rRNAs, PCRed and size-selected and finally deep-sequenced on Illumina Hiseq 2000 (50 bp, single end).

tag: footpring method

value: TRAP RF

tag: condition

value: in vivo

value: astrocyte

tag: strain

tag: age

tag: molecule

value: ribomsome protected RNA fragment


title: HeyA8_80h_1

city: Bethesda

first: Markus

last: Hafner

state: MD

address: 50 South Drive

department: NIAMS

institute: NIH

data_processing:
Illumina HiSeq 3000 platform was used for sequencing
Basecalling was done using bcl2fastq V2.17.1
The reads were aligned to the hg19 genome using TopHat
The miRNA normalized counts was generated as in Farazi et al., Cancer research 2011 (GEO accession number GSE28884)
Genome_build: hg19
Supplementary_files_format_and_content: format: xlsx content: Normalized counts

organism: Homo sapiens

growth_protocol: HeyA8 cells are cultured in RPMI1640 medium supplemented with 10% FBS and 1% L-Glutamine. HCT116 cell lines were cultured in McCoy's 5A medium, supplemented with 10% FBS and 1% L-Glutamine.

extract_protocol:
AGO1-4 were pulled down from whole cell lysate (Hauptmann et al., 2015 PNAS).  The RNA was isolated using Trizol.
Preadenylated, barcoded 3´adapter oligonucleotide was ligated followed by ligation of a 5´adapter. Ligation products were reverse transcribed and amplified by PCR.

treatment_protocol: cells were treated where indicated with Doxorubicin (doxo) for 20h, 40h or 80h

tag: cells

value: treated with 80hr of Doxorubicin

tag: passages

tag: pull down

value: Pull down with Pan-AGO peptide (Hauptmann et al., 2015 PNAS


title: H2228

city: La Jolla

first: Sheng

last: Zhong

state: California

address: 9500 Gilman Drive MC 0412

department: Bioengineering

institute: University of California, San Diego

data_processing:
Alignment STAR (v2.5.4b) with default parameters
Called for fusion candidates with STAR-Fusion (v0.8.0) using default parameters
Expression data was calculated with Cufflinks (v2.2.1)
Genome_build: hg38
Supplementary_files_format_and_content: gene fpkm, isoform fpkm, STAR-fusion candidates

source_name: non-small cell lung cancer cell line

extract_protocol:
Lung cancer biopsies were obtained flash frozen in dry ice, and RNA was harvested using Trizol reagent. RNA quality and quantity was analyzed using High Sensitivity D1000 ScreenTape.
Libraries were prepared according to Illumina's instructions accompanying the TruSight RNA Pan-Cancer Panel (Part# RS-303-1002).

tag: tissue

value: non-small cell lung cancer cell line

tag: patient diagnosis

tag: tumor stage

tag: gender


title: 22RV-1_PTEN, BRG1-KD

city: Shanghai

first: Ni

last: Li

state: Shanghai

address: 320 Yueyang Road, Shanghai, 200025 P.R. China

country: China

institute: Institute of Health Sciences, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences

description: PTEN, BRG1-KD

data_processing:
Raw reads were subjected to quality control (QC) to determine if a resequencing step is needed.
After QC, raw reads were filtered into clean reads which will be aligned to the reference sequences.Filtering steps are as follows:1) Remove reads with adaptors;2) Remove reads in which unknown bases are more than 10%;3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose  sequencing quality  is no more than 5).
Use  Bowtie2  to map clean reads to reference gene and use  BWA to reference genome.
RSEM  was used to computed maximum likelihood abundance estimates. FPKM  method is used in calculated expression level.
Use NOISeq to screen differentially expressed genes.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data were txt format and all gene FPKM of each sample were contained in each txt file.

source_name: cell line

growth_protocol: RPMI1640 supplied with 10% fetal bovine serum.

extract_protocol:
RNA was harvested using Trizol reagent followed by RNeasy Mini kit (Qiagen) cleanup. Total RNA was subjected to Hiseq RNA-Seq, performed by BGI Tech Solutions Co., Ltd. Transcriptome reads from RNA-Seq experiments were mapped to the reference genome (hg19) by using BWA/Bowtie tool. Genes expression level is quantified by a software package called RSEM.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell type

value: prostate cancer

tag: morphology

value: epithelial

tag: genotype/variation

value: PTEN, BRG1-KD


title: ATAC-seq; XaWT Xi[delta]Xist cells; siCTL; Rep1

city: Boston

first: Jeannie

middle: T

last: Lee

state: MA

address: 185 Cambridge Street

department: Molecular Biology

institute: Harvard University / MGH

library_source: genomic

data_processing:
Base-calling was performed with Illumina real time analysis (RTA) basecaller v1.17.21.3
For ATAC-seq: Adaptor sequences were trimmed with Trim Galore! V0.4.1 (stringency 12 and allowed error rate 0.2). Identical genomic sequences (PCR duplicates) were removed by custom program prior to alignment. To account for the M. mus (mus) / M. castaneus (cas) hybrid character of mouse dermal fibroblast lines that were employed in a ChIP-seq studies, reads were first aligned to custom mus/129 and cas genomes, and then mapped back to the reference mm10 genome. All alignments were performed by utilizing bowtie2 (v2.2.7) in paired-end mode. Post-processing of alignments was performed with custom scripts using SAMtools, and BEDtools (v2.25.0). These included accounting, alignment file-type conversion, extracting and reads sorting (SAMtools), and obtaining wig coverage files (SAMtools depth). To increase available read depth, we pooled together two biological replicates of ATAC-seq performed in wild-type cells, and separately pooled two biological replicates of ATAC-seq performed in XaWT Xi[delta]Xist cells. We also pooled two ATAC-seq biological replicates performed in a second XaWT Xi[delta]Xist cell line that served us as an independent biological system showing highly concordant results with those obtained by our main cell system. In each of these cases, pooled replicates were highly correlated to each other (r2 > 0.9), indicating strong data reproducibility. For visualizing ATAC-seq binding signal, we generated fragments per million (fpm)-normalized bigWig files from the raw ATAC read counts for all reads (comp), mus-specific (mus), and cas-specific reads, separately. Uniquely aligned wig files were scaled to total number of fragments per million in each library (determined by SAMtools flagstat combining reads ‘‘with itself and mate mapped’’ and ‘‘singletons’’). ATAC-seq tag density bigWig files were viewed in Integrative Genomics Viewer (IGV). To quantify reproducibility between two biological replicates of ATAC-seq generated in WT cells (or XaWT Xi[delta]Xist cells), we first counted per each two replicates the number of uniquely aligned neutral/cas/mus (comp) reads, per sample, and performed random downsampling without replacement of the larger sample in order to equalize reads number within two replicates (in general, all of our replicate samples had very similar numbers of reads also prior to downsampling). Next, we called MACS2 peaks (by employing –BAMPE (paired-end mode), and pvalue=0.005) in individual replicates. Peak sets called in individual replicates were then combined, and overlapping peaks were merged to form a union peak set. By applying Homer suit’s makeTagDirectory and annotatePeaks algorithms we obtained a read count matrix of two biological replicates over union peak set, and normalized these values per each library’s reads size by using edgeR. Log2 of ATAC-seq peaks’ signal within autosomes was plotted (≥10 reads per peak), and Pearson correlation coefficient of two biological replicates was calculated. In both cell lines, WT and XaWT Xi[delta]Xist, correlation coefficients of biological replicates of ATAC-seq were high (r2>0.94, 0.95, respectively), indicating strong data reproducibility. Similarly, high correlation coefficients were also obtained when comparing two biological replicates of ATAC-seq performed in WT cells treated with siControl, or with siBRG1 (r2 >0.92, 0.9, respectively), and in XaWT Xi[delta]Xist cells treated with siControl, or with siBRG1 (r2 >0.96, in both).
For ChIP-seq: Adaptor sequences were trimmed with Trim Galore! V0.4.1 (stringency 12 and allowed error rate 0.2). Identical genomic sequences (PCR duplicates) were removed by custom program prior to alignment. To account for the M. mus (mus) / M. castaneus (cas) hybrid character of mouse dermal fibroblast lines that were employed in a ATAC-seq and ChIP-seq studies, reads were first aligned to custom mus/129 and cas genomes, and then mapped back to the reference mm10 genome. All alignments were performed by utilizing novoalign (v3.00.02) in paired-end mode (Novocraft Technology, Selangor, Malaysia). Post-processing of alignments was performed with custom scripts using SAMtools v0.1.18, and BEDtools (v2.25.0). These included accounting, alignment file-type conversion, extracting and reads sorting (SAMtools), and obtaining wig coverage files (SAMtools depth).  In each of these cases, pooled replicates were highly correlated to each other (r2 > 0.91), indicating strong data reproducibility (for details about calculation of correlation coefficients between two replicates see the following section). For visualizing ChIP binding signal, we generated fragments per million (fpm)-normalized bigWig files from the raw ChIP read counts for all reads (comp), mus-specific (mus), and cas-specific reads separately. Uniquely aligned wig files were scaled to total number of fragments per million in each library (determined by SAMtools flagstat combining reads ‘‘with itself and mate mapped’’ and ‘‘singletons’’). ChIP-seq tag density bigWig files were viewed in Integrative Genomics Viewer (IGV). To quantify reproducibility between two biological replicates of BRG1 ChIP-seq generated in WT cells (or XaWT Xi[delta]Xist cells), we first called MACS2 peaks (by employing –BAMPE (paired-end mode), qvalue=0.005, and –bdg) in individual replicates, by contrasting each sample (uniquely aligned comp reads) against its corresponding control sample (prepared in the same cell line). Fold-enrichment signal (FE; IP sample’s signal over its corresponding Input sample’s signal) was calculated per each sample by executing MACS2 bdgcmp using –method FE. Peak sets called in individual replicates were then pooled, and overlapping peaks were merged to form a union peak set. By applying Homer suit’s makeTagDirectory and annotatePeaks algorithms we obtained a read counts matrix of two biological replicates over union peak set, and normalized these values per each library’s reads size using edgeR. Log2 fold-enrichment peak signal was plotted, and Pearson correlation coefficient of two biological replicates was calculated. In both cell lines, WT and XaWT Xi[delta]Xist, BRG1 ChIP-seq correlation coefficients of biological replicates were high (r2 >0.97, 0.91, respectively), indicating strong data reproducibility.
Genome_build: mm10

molecule: genomic DNA

source_name: Dermal female fibroblasts (XaWT Xi[delta]Xist). Genetic manipulation: Post XCI deletion of Xist on inactive X-chromosome

growth_protocol: Differentiated mouse fibroblast cells were cultured in regular fibroblast medium, 1% Pen/Strep, high-glucose DMEM+GlutaMax with 10% FBS

treatment_protocol: siRNA Control transfection

value: CAST/Ei x 129/Sv/Jae

value: Differentiated dermal female fibroblast cells

tag: Sex

value: Female


title: ATAC-seq; XaWT Xi[delta]Xist cells; siBRG1; Rep1


title: 22RV-1_PTEN-KD

description: PTEN-KD

value: PTEN-KD


title: HeyA8_40h_1

value: treated with 40hr of Doxorubicin


title: HCT116_Ctrl_1

value: control cells


title: HeyA8_20h_2

value: treated with 20hr of Doxorubicin


title: 22RV-1_control

description: control

value: control


title: HeyA8_20h_1


title: HeyA8_40h_2


title: ATAC-seq; WT cells; siCHD4; Rep1

source_name: Dermal female fibroblasts (WT)

treatment_protocol: siRNA CHD4 transfection


title: ATAC-seq; WT cells; siSNF2H; Rep1

treatment_protocol: siRNA SNF2H transfection


title: HeyA8_Ctrl_2


title: ATAC-seq; WT cells; siBRG1; Rep1


title: ATAC-seq; WT cells; siBRG1; Rep2


title: dLsd1RNAi_4

city: Beijing

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

institute: NIBS

data_processing:
Illumina Casava1.8 software used for basecalling.
RNAseq sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to BDGP6 genome and Transposon elements sequence using STAR 2.5.2b with default parameters.
RPM (reads per million) was calculated for each transposon element.
Genome_build: Ensemble Drosophila melanogaster BDGP6
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample, and the distribution of abundance for small RNA samples.

organism: Drosophila melanogaster

extract_protocol:
RNA and library was prepared by following the manufacturer’s instructions
Libraries were prepared for sequencing using standard Illumina protocols

value: dLsd1 RNAi

value: adult stage 5-7 days old

value: ovary


title: dLsd1RNAi_3


title: Nerve

city: Vienna

first: Andreas

last: Bergthaler

address: Lazarettgasse 14 AKH BT25.3

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

data_processing:
The DNA methylation (RRBS) data were analyzed using the RefFreeDMA pipeline and methylation calling related to the scaffold assembly status of the published Tasmanian Devil reference genome sarHar1.
A custom ad-hoc reference genome was deduced directly from the RRBS sequencing reads and used for read mapping and methylation calling.
Based on the thus produced DNA methylation profiles, differential DNA methylation analysis was performed as part of the RefFreeDMA pipeline.
Gene annotations were transferred by mapping the deduced genome fragments to the published scaffold-level Tasmanian Devil genome sarHar1, downloaded from the UCSC genome browser. A gene annotation file was produced by joining the UCSC transcript annotation file with the Ensembl v86 transcript annotation file of sarHar1 based on the common Ensembl transcript identifiers.
Gene promoters were defined as the region between 5000 bases downstream and 2500 bases upstream of the transcription start site.
Genome_build: custom ad-hoc reference genome generated by the RefFreeDMA library: toSelf_filtered_0.08mm_final_concat.fa. This genome is provided with the submission.
Supplementary_files_format_and_content: tab-delimited text file containing the percentage of methylation in promoters of annotated genes. For promoter methylation analysis we focused on a total of 69754 CpGs that are also covered in at least 80% of the samples (coverage between 8 to 200 reads). Individual CpGs are averaged across the promoter region.
Supplementary_files_format_and_content: fasta file of the Tasmanian devil ad-hoc reference genome build from the RRBS reads

organism: Sarcophilus harrisii

source_name: peripheral nerve tissue

growth_protocol: Devil Facial Tumor cell strain 1 were grown in RPMI (Gibco 21875-034) supplemented with 10% Fetal bovine serum (PAA A15-101), 1% Pen Strep Glutamine (Gibco 10378-016) and 50 µM 2-Mercaptoethanol (Sigma M-3148). Fibroblasts were grown in Advanced DMEM (Gibco 12491-015) supplemented with 10% Fetal bovine serum (PAA A15-101), 1% Pen Strep Glutamine (Gibco 10378-016). Cells were grown at 35°C in 5% CO2 and lifted with either PBS containing 1mM EDTA or 0.05% Trypsin-EDTA (Gibco 25300-054).

extract_protocol:
DNA methylation profiling by RRBS was performed using 100 ng of genomic DNA isolated from RNA-later preserved tissue samples through the Allprep DNA/RNA Mini kit (QIAGEN).
DNA was digested using the restriction enzymes MspI and TaqI in combination in order to increase genome-wide coverage. Restriction enzyme digestion was followed by fragment end repair, A-tailing, and adapter ligation. The amount of effective library was determined by qPCR, and samples were multiplexed in pools of 13 with similar qPCR Ct values.
The pools were then subjected to bisulfite conversion followed by library enrichment by PCR. Enrichment cycles were determined using qPCR and ranged from 9 to 13 (median: 11). After confirming adequate fragment size distributions on Bioanalyzer High Sensitivity DNA chips (Agilent), libraries were sequenced on Illumina HiSeq 3000/4000 machines in a 50 base pair single-read setup.

value: peripheral nerve tissue


title: ATAC-seq; WT cells; siCTL; Rep2


title: DFTD

value: cell line


title: dLsd1RNAi_2


title: ATAC-seq; WT cells; siCTL; Rep1


title: dLsd1RNAi_1


title: ATAC-seq; XaWT Xi[delta]Xist #2 cells; Rep2

description:
ATAC_Xidel2.merged.comp.bw
ATAC_Xidel2.merged.mus.bw
ATAC_Xidel2.merged.cas.bw

source_name: Dermal female fibroblasts (XaWT Xi[delta]Xist) 2nd cell line. Genetic manipulation: Post XCI deletion of Xist on inactive X-chromosome


title: Tumor_Kempton_2

source_name: tumor

value: tumor

tag: animal

value: Kempton


title: H6_1 [RNA]

first: Su-Ren

last: Chen

address: 1Beichen West Road, Chaoyang District

department: State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
SOAPnuke: v1.5.2, -l 15 -q 0.2 -n 0.05
HISAT2: v2.0.4, --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000
Bowtie2: v2.2.5, -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
RSEM: v1.2.12, default
DEGseq: Fold Change >= 2 and Adjusted Pvalue <= 0.001
Genome_build: mm10
Supplementary_files_format_and_content: Including RPKM values for each sample

source_name: Mouse testicular peritubular myoid (PTM) cells

growth_protocol: The isolated PTM cells were cultured in DMEM/F12 containing 10% fetal bovine serum (FBS) at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from the NC, H1, and H6 PTM cells using TRNzol (Tiangen, Beijing, China).
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: Cell culture dishes of peritubular myoid cells were placed in 42℃ sterile water bath for 30 min and then put back in cell culture incubator. Cells were collected 1 hour and 6 hours after heat treatment.

tag: treatment

value: heat 6hr after

tag: passage

value: Primary


title: H6_3 [RNA]

value: Mouse testicular peritubular myoid (PTM) cells

tag: strain


title: H6_2 [RNA]


title: terminator-lacI-HP1a_uas-ova_H3K4me2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to BDGP6 genome using Bowtie v1.1.2 with -v 3 -m 1 parameters.
Peaks were called using MACS version 1.4.2 with default parameters.
Genome_build: Ensemble Drosophila melanogaster BDGP6.
Supplementary_files_format_and_content: bigwig files were generated using Homer package.

source_name: ovary

extract_protocol:
Drosophila DamID was carried out according to iDamIDseq based on a method from Gutierrez-Triana JA et al.2016
Libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

tag: age

tag: chip antibody

value: H3K4me2 (Abcam, ab7766)


title: ATAC-seq; XaWT Xi[delta]Xist #2 cells; Rep1

value: CAST/Ei x 129/Sv/Jae

tag: cells

value: Differentiated dermal female fibroblast cells

value: Female


title: Tumor_Kepmtpn_3


title: H1_3 [RNA]

value: heat 1hr after


title: terminator-lacI-HP1a_H3K4me2


title: HeyA8_Ctrl_1

value: control cells

tag: passages

tag: pull down

value: Pull down with Pan-AGO peptide (Hauptmann et al., 2015 PNAS


title: Tumor_Kempton_1

tag: tissue


title: Skin_Kempton

source_name: skin

value: skin


title: ATAC-seq; XaWT Xi[delta]Xist cells; Rep1

description:
AccessibilityClass_Monoallelic.bed
AccessibilityClass_Biallelic.bed
AccessibilityClass_XiRestored.bed
ATAC_Xidel.merged.comp.bw
ATAC_Xidel.merged.mus.bw
ATAC_Xidel.merged.cas.bw


title: Tumor_Cradle_1

value: Cradle Mt


title: ATAC-seq; WT cells; Rep2

description:
AccessibilityClass_Monoallelic.bed
AccessibilityClass_Biallelic.bed
AccessibilityClass_XiRestored.bed
ATAC_WT.merged.comp.bw
ATAC_WT.merged.mus.bw
ATAC_WT.merged.cas.bw


title: NC_3 [RNA]


title: ATAC-seq; WT cells; Rep1


title: Tumor_Cradle_2


title: NC_1 [RNA]


title: Spleen_Kempton

source_name: spleen

value: spleen


title: NC 3

data_processing:
SOAPnuke: v1.5.2, -l 15 -q 0.2 -n 0.05
HISAT2: v2.0.4, --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000
Bowtie2: v2.2.5, -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
RSEM: v1.2.12, default
DEGseq: Fold Change >= 2 and Adjusted Pvalue <= 0.001
Genome_build: hg38
Supplementary_files_format_and_content: Including RPKM values for each sample

growth_protocol: The human EOC cell line SKOV3 44 (ATCC®HTB-77TM) was purchased from American Type Culture Collection (ATCC, VA, USA). Cells were cultured in McCoy’s 5a medium (Invitrogen, Beijing, China) containing 10% fetal bovine serum (Invitrogen), 1% penicillin/stretomycin (Invitrogen) at 37 °C with 5% CO2.

extract_protocol:
Total RNA was extracted from the CD83-OV, CD83-KD, and CD83-NC SKOV3 cells using TRNzol (Tiangen, Beijing, China).
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: To generate human CD83 stable overexpression or knockdown SKOV3 cell line, LV5-full length CD83 lentivirus (CD83-OV) or triple LV3-CD83-shRNA lentivirus (CD83-KD) (LV3-CD83-258, 5’-GCTCCGAAGATGTGGACTTGC-3’; LV3-CD83-486, 5’-GGACATACAGGTGCACTCTGC-3’; LV3-CD83-679, 5’-GCTACAGAGTATCTTCCCAGA-3’) was synthesized and constructed by GenePharma (Shanghai, China), respectively. LV5 or LV3 lentivirus, containing GFP and puromycin resistant site, was served as negative control (NC). Polybrene (4 μg/ml) was used to increase the lentivirus infection efficiency. Stable infected cell lines (GFP+) could be obtained by two rounds of 1 μg/ml puromycin selection.

value: control

tag: cell line


title: ATAC-seq; XaWT Xi[delta]Xist cells; Rep2


title: 22RV-1_BRG1-KD

value: prostate cancer

value: epithelial


title: Spleen_Cradle


title: NC_2 [RNA]


title: Skin_Cradle


title: NC 2


title: H1_1 [RNA]


title: HeyA8_80h_2

value: treated with 80hr of Doxorubicin


title: KD 3

value: CD83 stable knockdown


title: NC 1


title: Tumor_Wisedale_2

value: tumor

value: Wisedale


title: Tumor_Wisedale_1


title: terminator-lacO-GFP_H3K4me2

value: lacO--terminator-GFP

value: adult stage 5-7 days old

value: ovary

value: H3K4me2 (Abcam, ab7766)


title: Skin_Wisedale


title: KD 2


title: H1_2 [RNA]

value: heat 1hr after

value: Mouse testicular peritubular myoid (PTM) cells

value: Primary


title: KD 1


title: Tumor_Narawntapu_2

value: Narawntapu


title: OV 3

value: CD83 stable overexpression


title: Skin_Narawntapu

value: skin


title: Spleen_Narawntapu

value: spleen


title: Tumor_Narawntapu_1


title: Mut_3

city: San Antonio

first: Bernard

last: Arulanandam

state: Texas

address: 1 UTSA Cir

department: Biology

institute: University of Texas at San Antonio

data_processing:
The sequencing reads were preprocessed by the Trim Galore program with default parameters to remove adapters and low-quality sequences
The reads were then aligned to Acinetobacter baumannii strain CI79 reference genome ASM51663v2 using HISAT2 with default settings
The reads were counted using the featureCounts program
After eliminating genes with low expression (< 1 counts per million (CPM) in more than three samples across the dataset), the raw expression value was normalized using the calcNormFactors function implemented in the edgeR program
Differentially expressed genes (DEGs) were then determined by quasi-likelihood F-test using glmQLFit function implemented in the edgeR package. Genes with FDR-adjusted P-value (≤0.05) and fold change ≥2 (or ≤-2) were considered to be differentially expressed in this study
Heatmaps and the volcano plot were generated using R functions.
Genome_build: GenBank assembly accession: GCA_000516635.2
Supplementary_files_format_and_content: csv files show raw counts and statistics for each sample

organism: Acinetobacter baumannii

source_name: ∆trxA

growth_protocol: Bacteria were grown to mid-log phase

extract_protocol:
RNA isolation using a PureLink RNA Mini Kit (Ambion). RNA was then enriched for mRNA by removing rRNA from the total RNA using a MICROBExpress Kit (Ambion)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: thioredoxin-A knockout

tag: growth phase

value: Mid-log


title: Strain3

description:
TD_RNAseqCounts.txt
S14
HiSeq 3000 and HiSeq 4000 instrument model

data_processing:
Base calls provided by the Illumina Realtime Analysis software were converted into BAM format using Illumina2bam and demultiplexed using BamIndexDecoder.
aired-end reads were trimmed for adaptor sequences and filtered with the trimmomatic tool.
Trimmed reads were aligned on the version 7.0 of the Tasmanian Devil with the STAR aligner.
Counting of reads on annotated transcripts (Sarcophilus_harrisii.DEVIL7.0.90.gtf from Ensembl) was performed with featurecounts on fragments.
The DESeq2 Biconductor library has been used for counts normalization and differential analysis between the transcriptomes of the four DFTD and fibroblast cell lines
Genome_build: version 7.0 of the Tasmanian Devil Ensembl genome
Supplementary_files_format_and_content: tab-delimited text file of normalised DESeq2 counts on the 5 cell lines

source_name: DFTD cell line

growth_protocol: Devil Facial Tumor cell strains 1-4 were grown in RPMI (Gibco 21875-034) supplemented with 10% Fetal bovine serum (PAA A15-101), 1% Pen Strep Glutamine (Gibco 10378-016) and 50 µM 2-Mercaptoethanol (Sigma M-3148). Fibroblasts were grown in Advanced DMEM (Gibco 12491-015) supplemented with 10% Fetal bovine serum (PAA A15-101), 1% Pen Strep Glutamine (Gibco 10378-016). Cells were grown at 35°C in 5% CO2 and lifted with either PBS containing 1mM EDTA or 0.05% Trypsin-EDTA (Gibco 25300-054).

extract_protocol:
For expression analysis from cell lines, total RNA was isolated from approximately 1 x 106 cells using QIAzol lysis reagent according to the manufacturer’s instructions (Qiagen).
RNA-seq libraries were prepared with TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer).
The 5 libraries were pooled, diluted and sequenced on Illumina HiSeq 3000/4000 using 75 bp paired-end chemistry.

tag: sample type

value: DFTD cell line


title: Mut_2


title: Mut_1


title: Ci79_1

source_name: WT

value: WT


title: Strain4

description:
TD_RNAseqCounts.txt
S20
HiSeq 3000 and HiSeq 4000 instrument model


title: Fibroblast

description:
TD_RNAseqCounts.txt
S27
HiSeq 3000 and HiSeq 4000 instrument model

source_name: Fibroblast

value: Fibroblast


title: siNXF1_RNAseq_rep1_TotalRNA

city: Newark

first: Bin

last: Tian

state: NJ

address: 205 South Orange Ave.

department: Department of Microbiology, Biochemistry and Molecular Genetics

institute: Rutgers New Jersey Medical School

description: Analysis of gene expression and splicing under siNXF1

data_processing:
Adpter trimming performed using Cutadapt
3'READs reads were aligned to hg19 using bowtie2. Reads with a mapping quality score (MAPQ) >=10 were kept for further analysis. Reads with >=2 non-genomic 5’Ts after alignment were called polyA site supporting (PASS) reads. pAs within 24 nt of each other were clustered. pAs with less than 5 PASS reads in all the samples were first trimmed.
RNAseq of nacent RNA reads were aligned to hg19 using STAR. Only mapped reads without any soft clipping at the 5’ end of read were used for further analysis. The genomic position corresponding to the 5’ end of each read was identified by a Python script using the HTSeq software package (Anders et al., 2015). The 5’ positions of the remaining reads were used to reflect Pol II positions, the reads mapped to the same region were uniqued
ChIP-seq reads reads were mapped to the hg19 genome assembly using BWA-MEM (0.7.15). The reads mapped to the same region were uniqued, and the unique reads count of each position was then normorlized to one million (UPM).
Raw reads from RNA-seq of total RNA were first mapped to the hg19 genome assembly using STAR (v2.5.2) (Dobin et al., 2013) with default parameters. The read count of the coding sequence (CDS) of each gene was summed and then normalized by the median ratio method in DESeq (Dobin et al., 2013). Only genes with more than five reads in all samples were used for further gene expression analysis.  Alternative splicing (AS) was analyzed using rMATS (v4.0.2) (Shen et al., 2014) with default parameters. Significant AS events were those with a delta PSI >5% and P-value <0.05. Only AS events with at least five reads mapped on splice junctions were used for further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include reads count for each pAs/pol2/nascent RNA loci/gene

source_name: cervical cancer cells

growth_protocol: HeLa cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (Biochrom).

extract_protocol: See extract_protocols.xls linked at the foot of the GSE117701 record.

treatment_protocol: For untreated samples, cells were cultured in normal medium; Sodium Arsenite treatment: 250 µM. For RNAi, siRNAs were transfected with Lipofectamine® RNAiMAX (Invitrogen) following the manufacture’s procedure.

tag: cell type

value: HeLa

tag: protocol

value: RNA-seq

tag: molecule subtype

value: total RNA


title: Strain1

description:
TD_RNAseqCounts.txt
S2
HiSeq 3000 and HiSeq 4000 instrument model


title: PTEN-KD_ATAC-Seq

data_processing:
Raw sequence reads were initially processed by FastQC for quality control.
Adapter sequences and poor quality reads were removed by using Cutadapt.
Quality filtered reads were mapped to hg19/GRCh37 reference genome using BWA(0.7.10), and only uniquely mapped reads were kept.
Sam files were converted to Bam format using Samtools and used for peak calling.
MACS2 was used to call peaks and an initial threshold q-value of 0.01 was set as cutoff.
Genome_build: hg19
Supplementary_files_format_and_content: The number of fragments in each bin is stored in a bigWig file.

extract_protocol:
Harvest and count 50,000 cells individually. Centrifuge to discard the supernatant, and immediately continue to transposition reaction according to standard protocols. Purify and PCR amplify transposed DNA. Qiagen MinElute PCR purification Kit purify DNA.
libraries were constructed following the NEB kit

value: prostate cancer

tag: genotype/variation

value: PTEN knockdown


title: genomic-DNA-IP_NSL3

status: Public on Jan 13 2019

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing: The paired-end gDNA-seq reads were aligned using STAR (version 2.5.1b) against the Drosophila melanogaster reference genome (version dm3, UCSC) and processed as outlined in the MNase-seq read mapping section. Peak calling of the gDNA pulled down by GFP, MCRS2, NSL1 and NSL3 was performed as outlined in the ChIP-seq peak calling section using 50 base pair bins. As control served the input to the pull down experiments. After the identification of enriched bins, we merged directly adjacent bins and determined the maximal bin within the so-derived regions. The coordinates of these maximal bins per enriched region were referred to as peak center.

source_name: cultured fruit fly cells

growth_protocol: S2 cells were cultured in Schneider’s medium (Gibco) supplemented with 10% FCS and 0.05% Pluronic F-68 (Sigma-Aldrich). The cultures were maintained on shaking incubators at 27 ºC, at a speed of 80 rpm. The cells were kept at a density of 1-16 million/ml.

extract_protocol: Genomic DIP–seq experiments. The pellet from 1 × 108 S2 cells was suspended in 1 ml of lysis buffer (10 mM Tris pH 8, 25 mM EDTA, 100 mM NaCl, 0.1% SDS) and treated with protease K overnight at 55 °C. The DNA is tested with Bradford assay and protein gel to ensure that no proteins remain. DNA is sonicated with Covaris sonicator (power 175 W, duty factor 10%, cycles per burst 200, 250 s) to obtain fragment size average of 200-bp. DNA was purified with the DNA Clean & Concentrator (Zymo).  Proteins were purified using FLAG bead slurry (sigma). The beads were incubated with the extracts for 2 hours followed by 4 washes in HEMGT buffer (25 mM HEPES, pH 7.9, 12.5 mM MgCl2, 150 mM KCl, 10% glycerol). DIP-seq experiment was performed with 1μg of genomic DNA and 1.5 μg of FLAG-NSL3 or FLAG-GFP at 4 °C for 2 hours in 500 μl of DIP buffer (2 mM Tris-HCl pH 7.5, 100 mM KCl, 2 mM MgCl2, 10% glycerol, 10 μM ZnCl2). The FLAG bead was washed six times with 1ml of DIP buffer. Elution was performed with 3X FLAG peptide (100μg/ml, overnight) or digestion with proteinase K (1 h at 56 °C), DNA was purified with the DNA Clean & Concentrator (Zymo). The sequencing was performed using the Illumina HiSeq platform with a 75-bp paired-end kit.

treatment_protocol:
For ChIP-Seq and gDIP experiments, following antibodies are used : Anti-ISWI, anti-BRM and anti-Mi-2 (from Dr. Peter Verrijzer), anti-CHD3 antibody (from Dr. Alexander Brehm), anti-NURF38 (from Dr. Paul Badenhorst) are used for western blot analysis. Anti-NSL complex antibodies (S. Mendjan et al., Mol Cell 2006, and Raja et al. Mol Cell. 2010) and anti-NURF301 (Novus Biologicals, Cat. no. 40360002)
For knockdown experiments, 2 ml of S2 cells at 1 million cells per ml was plated in 6-well dishes and left to attach for 1 hour. 10 ug of purified double stranded RNA was diluted with Schneider’s medium. The RNA transfection was performed using Lipofectamine RNAiMAX Reagent (Invitrogen), according to manufacturers instructions. The double stranded RNAs were mixed with the transfection reagent and kept at room temperature for 15 minutes before the mixture was added to the cells. The cells were harvested after 4 days and cell numbers were counted.

tag: source developmental stage

value: embryonic cell line (S2)

tag: Sex

value: Male


title: genomic-DNA-IP_MCRS2

data_processing:
Library strategy: DIP-seq
The paired-end gDNA-seq reads were aligned using STAR (version 2.5.1b) against the Drosophila melanogaster reference genome (version dm3, UCSC) and processed as outlined in the MNase-seq read mapping section. Peak calling of the gDNA pulled down by GFP, MCRS2, NSL1 and NSL3 was performed as outlined in the ChIP-seq peak calling section using 50 base pair bins. As control served the input to the pull down experiments. After the identification of enriched bins, we merged directly adjacent bins and determined the maximal bin within the so-derived regions. The coordinates of these maximal bins per enriched region were referred to as peak center.

tag: passage


title: siCntl_RNAseq_rep1_TotalRNA

tag: treatment

value: Untreated


title: genomic-DNA-IP_GFP


title: genomic-DNA-IP_Input


title: OV 1

tag: genotype


title: OV 2


title: Spleen_Wisedale

tag: animal

value: Wisedale


title: RNAseq_NSL1_rep3

description: LamHo_RNAseq_DESeq2.counts_normalized.tsv

data_processing: The paired-end RNA-seq reads were aligned using STAR (version 2.5.1b) against the Drosophila melanogaster reference genome (version dm3, UCSC) plus the Saccharomyces cerevisiae genome (release R64-1-1, ENSEMBL) including the corresponding gene annotations from both species. Standard RNA-seq analyses are not able to detect global shifts in gene expression. We expected that a NSL1 knockdown may lead to a global downregulation of almost every expressed gene. In such a scenario, genes that are un- or only mildly affect by the NSL1 knockdown would appear upregulated. To mitigate this problem, we spiked yeast RNA into the RNA preparations according to the cell number, which had been estimated by qPCR. The yeast RNA serves as external control to normalize the RNA-seq data, because the abundance of yeast RNAs remains unchanged. Thus, after mapping to the combined Drosophila and yeast reference genomes, we obtained the read counts for the 16 yeast chromosomes. And used these counts to calculate size factors using the DESeq2 function estimateSizeFactorsForMatrix using triplicates for control, MOF, NSL1 and NURF knockdowns.  For each condition and replicate we counted reads mapping to annotated exon ranges per gene, where overlapping exons were merged. We counted only the first mate to retain the strand information. A preliminary principal component analysis on the rlog transformed counts revealed that two samples, one control and one NSL1 sample, were outliers, i.e. did not cluster with their respective conditions. These were removed prior to any downstream analysis.

molecule: polyA RNA

extract_protocol: RNA was extracted using direct-zol (Zymo) according to the manufacturer's protocol. DNase-I treatment was carried out to eliminate genomic DNA contamination. cDNA was made and analyzed by paired end poly(A) RNA sequencing.


title: RNAseq_NSL1_rep2


title: RNAseq_NSL1_rep1


title: RNAseq_GST_rep3


title: RNAseq_GST_rep2


title: RNAseq_GST_rep1


title: Strain2

description:
TD_RNAseqCounts.txt
S8
HiSeq 3000 and HiSeq 4000 instrument model


title: Ci79_3


title: Ci79_2


title: PTEN_BRG1-KD_ATAC-Seq

value: PTEN and BRG1 knockdown


title: genomic-DNA-IP_NSL1


title: MNase_exp2_NURF301_rep2_320U

data_processing: MNase-seq analysis step. The paired-end reads were aligned using Bowtie2 (version 2.0.5; ) or with STAR (version 2.5.1b; ) against the Drosophila melanogaster reference genome (version dm3, UCSC). Default parameters were used, except for the STAR alignment, where we set the option alignIntronMax to 1. In case of Bowtie2 resulting BAM files were sorted using samtools , while this step was omitted for STAR alignments as they were already sorted. The sorted BAM files were indexed using samtools. To get an unbiased estimate of the nucleosome signal we counted the 5’ starting positions of the reads separated by their orientation, i.e. plus- and minus-strand alignments. This results in two vectors and with components and, where indicates the position and corresponds to the counts for plus-strand reads and for minus-strand reads. For all positions where we calculated , while for positions where. For a well-positioned nucleosome at its dyad position we expect many more plus-strand reads than minus- strand reads at its left border at position and vice versa many more minus strand reads than plus-strand reads at its right border at position. To account for the inprecise mapping of the nucleosome borders by MNase-seq, we defined a function for and zero otherwise. This function was convolved against the vector to obtain the nucleosome signal at the nucleosome dyad position. This nucleosome signal is between -74 and +74, where a negative value indicates depletion and positive signal enrichment. Note, that this procedure yields a normalized nucleosome signal, which is independent on library size.

extract_protocol: 50 million S2 cells were harvested and washed with PBS. Cells were counted very carefully to ensure that the same number of cells was collected for each sample. The cells were resuspended in 1 ml of crosslinking solution (50 mM HEPES, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) and 37% formaldehyde was added to a final concentration of 1%. The tube was rotated at room temperature for 10 minutes and the reaction was quenched with 2.5 M glycine at a final concentration of 125 mM. The cells were spun down immediately after addition of glycine and the solution was replaced with fresh PBS that contained 125 mM glycine. The cells were resuspended and rotated at room temperature for 5 minutes. The cells were pelleted into equal aliquots by centrifugation with 2000 rpm for 5 minutes.  Cells were permeabilized with NP-40. The chromatin was digested with various amount of MNase at 25 ºC for 10 minutes. Digested chromatin was then analyzed on an agarose gel to reveal the digestion pattern. We aimed to achieve a slightly under-digested condition with di- and tri-nucleosomes still visible. In addition, the digestion pattern of each sample needed to be exactly the same. After the optimal amount of MNase was determined for each individual experiment, a new aliquot of the cells was again digested with MNase at 25 ºC for 10 minutes. The reaction was stopped by addition of EDTA, NaCl and SDS to an end concentration of 20 mM, 150 mM and 1% respectively. The samples were placed on ice during handling to ensure that the MNase digestion was halted completely. The chromatin was then de-crosslinked overnight at 65 ºC overnight in TE buffer. The sample was treated with RNaseA (0.2 mg/ml) for 30 minutes at 37 ºC, and with Proteinase K (0.05 mg/ml) for 2 hours at 50 ºC. Finally, DNA was purified using Minelute columns (Qiagen) and eluted in nuclease-free water. The eluted DNA was then analyzed with the E-Gel Pre-cast Agarose Gels system (Invitrogen). Bands at positions corresponding to 150 bp, 300 bp, 450 bp, represented mono- di and tri-nucleosomes, respectively. The 150 bp fragment was purified from the E-gel according to manufacturers’ specifications and used to generate the library for the Illumina paired-end sequencing. To minimize the effect of PCR artefacts, only 3 cycles of PCR were performed in the library generation procedure.


title: MNase_exp2_NURF301_rep1_320U


title: MNase_exp2_NSL1_rep2_80U


title: MNase_exp2_NURF301_rep1_1280U


title: MNase_exp2_NURF301_rep1_80U


title: MNase_exp2_NSL1_rep2_320U


title: MNase_exp2_NSL1_rep1_80U


title: MNase_exp2_NSL1_rep2_1280U


title: MNase_exp2_NURF301_rep2_1280U


title: MNase_exp2_NSL1_rep1_320U


title: MNase_exp2_INO80_rep2_80U


title: MNase_exp2_INO80_rep2_1280U


title: MNase_exp2_INO80_rep2_320U


title: MNase_exp2_INO80_rep1_80U


title: MNase_exp2_INO80_rep1_1280U


title: MNase_exp2_NURF301_rep2_80U


title: MNase_exp2_INO80_rep1_320U


title: MNase_exp2_GST_rep2_80U


title: MNase_exp2_GST_rep2_1280U


title: MNase_exp2_GST_rep1_80U


title: MNase_exp2_GST_rep1_320U


title: MNase_exp2_NSL1_rep1_1280U


title: MNase_exp1_NSL1_rep2


title: MNase_exp2_GST_rep1_1280U


title: MNase_exp1_GST_rep2


title: CR-ZT18-2

city: CLEVELAND

first: Roman

last: Kondratov

state: Ohio

address: 2399 euclid avenue, bges dept, sr289

department: Biomedical Sciences

institute: CLEVELAND STATE UNIVERSITY

description: Animals were Calorie restricted

data_processing:
Quality check was done using FastQc
Adapter removal by AfterQc
Readcounts by HTSeq
Differential expression by Deseq2
Genome_build: GRCm38.p5 Release M15
Supplementary_files_format_and_content: Txt file

source_name: Liver after 30% calorie restricted diet for three months

extract_protocol: Poly A tail selection, Non stranded

tag: strain

value: Liver

tag: age

value: Polysome associated RNA

tag: timepoint

value: 18 hours


title: CR-ZT10-2

description: Animals were Calorie restricted

tag: tissue

value: 10 hours


title: CR-ZT22-2

description: Animals were Calorie restricted

value: 22 hours


title: CR-ZT10-1B

description: Animals were Calorie restricted


title: CR-ZT6-2

description: Animals were Calorie restricted

value: 6 hours


title: CR-ZT14-2

description: Animals were Calorie restricted

value: 14 hours


title: CRZT22-1

description: Animals were Calorie restricted


title: CR-ZT14-1

description: Animals were Calorie restricted


title: CR-ZT2-1

description: Animals were Calorie restricted

value: 2 hours


title: CR-ZT18-1

description: Animals were Calorie restricted


title: MNase_exp1_NSL1_rep1


title: CR-ZT6-1

description: Animals were Calorie restricted


title: MNase-ChIP_NURF301_Digestion2_rep1

data_processing:
Library strategy: Mnase-ChIP
MNase-seq analysis step. The paired-end reads were aligned using Bowtie2 (version 2.0.5; ) or with STAR (version 2.5.1b; ) against the Drosophila melanogaster reference genome (version dm3, UCSC). Default parameters were used, except for the STAR alignment, where we set the option alignIntronMax to 1. In case of Bowtie2 resulting BAM files were sorted using samtools , while this step was omitted for STAR alignments as they were already sorted. The sorted BAM files were indexed using samtools. To get an unbiased estimate of the nucleosome signal we counted the 5’ starting positions of the reads separated by their orientation, i.e. plus- and minus-strand alignments. This results in two vectors and with components and, where indicates the position and corresponds to the counts for plus-strand reads and for minus-strand reads. For all positions where we calculated , while for positions where. For a well-positioned nucleosome at its dyad position we expect many more plus-strand reads than minus- strand reads at its left border at position and vice versa many more minus strand reads than plus-strand reads at its right border at position. To account for the inprecise mapping of the nucleosome borders by MNase-seq, we defined a function for and zero otherwise. This function was convolved against the vector to obtain the nucleosome signal at the nucleosome dyad position. This nucleosome signal is between -74 and +74, where a negative value indicates depletion and positive signal enrichment. Note, that this procedure yields a normalized nucleosome signal, which is independent on library size.
The ChIP-seq reads were aligned either with Bowtie2 or STAR and processed as outlined in the MNase-seq read mapping section. Peaks were called using the Bioconductor package normR. Reads/fragments were counted using the Bioconductor package bamsignals. For single-end ChIP libraries the fragment size was estimated by convolving the vector of counts of minus strand reads against the corresponding vector of plus strand reads. The fragment size was determined by choosing the distance for which was maximal. For paired-end ChIP and input libraries we counted the number of fragment midpoints falling into non-overlapping 200 base pair bins along the genome. For single-end ChIP and input libraries the 5’ positions of the reads were shifted by half the fragment size to the right for plus strand and to the left for minus strand reads. For each ChIP experiment a normR analysis was performed using the function enrichR, where the count vectors for the ChIP and the corresponding input control served as input. Normalized log2 Chip over control were calculated by where corresponds to the number of ChIP fragments/reads in a bin of size , x to the number of control fragments/reads in the same bin. to the average number of ChIP fragments/reads in 200 base pair bins that had a qvalue > 0.1 divided by 200 and multiplied by , and to the average number of control fragments/reads in 200 base pair bins that had a qvalue > 0.1 divided by 200 and multiplied by.

extract_protocol: 50 million S2 cells were harvested and washed with PBS. The cell was resuspended in 1ml of crosslinking solution (50 mM HEPES, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), 37% formaldehyde was added to a final concentration of 1.8%. The tube was rotated at room temperature for 10 minutes and the reaction was quenched with 2.5 M glycine at a final concentration of 125 mM. The cells were spun down immediately after addition of glycine, and the solution was replaced with fresh PBS with 125 mM glycine. For NSL1 and NURF301 MNase-ChIP-seq, we used MNase for chromatin shearing. Cells were washed as above described and suspended in MNase digestion buffer. A small aliquot of the samples is used to determine the optimal MNase concentration (20-200 U/ml tested) to obtain the desired fragment size. Digestion is performed in room temperature for 20 minutes and finally quenched by addition of 1 mM EDTA and 2X RIPA buffer.


title: MNase_exp1_GST_rep1


title: MNase-ChIP_NURF301_Digestion2_rep2


title: CR-ZT2-2

description: Animals were Calorie restricted


title: MNase_exp2_GST_rep2_320U


title: AL-ZT14-2

description: Animals were fed Ad libitum

source_name: Liver from control animal fed Ad libitum


title: ALZT18-2

description: Animals were fed Ad libitum


title: AL-ZT22-2C

description: Animals were fed Ad libitum


title: MNase-ChIP_NURF301_Digestion1_rep1


title: AL-ZT22-2d

description: Animals were fed Ad libitum


title: MNase-ChIP_NURF301_Digestion1_rep2


title: AL-ZT18-1

description: Animals were fed Ad libitum


title: AL-ZT14-1

description: Animals were fed Ad libitum


title: MNase-ChIP_NSL1_Digestion2_rep1


title: MNase-ChIP_NSL1_Digestion1_rep1


title: AL-ZT10-2

description: Animals were fed Ad libitum


title: MNase-ChIP_Input_Digestion2


title: MNase-ChIP_Input_Digestion1


title: AL-ZT6-2

description: Animals were fed Ad libitum


title: AL-ZT10-1

description: Animals were fed Ad libitum


title: AL-ZT6-1

description: Animals were fed Ad libitum


title: MAPCap_NSL1_rep3

data_processing: MapCap paired-end reads were mapped as outlined in the RNA-seq read mapping section. Prior to mapping the corresponding unique molecular identifier (UMI) was added to the read name to preserve it for downstream analysis. The MapCap approach aims at identifying 5’ cap positions at single base pair resolution. Due to the limited input material, an amplification of the library via PCR is necessary. UMI was added to each fragment, such that PCR artifacts can be filtered out. To use the UMI information the UMIs were extracted from the read name and appended as RX tag to the tag section of the BAM record by a custom perl script. PCR duplicates were removed using the Picard function MarkDuplicates by setting the options REMOVE_DUPLICATES=true and BARCODE_TAG=RX. The paired-end MapCap reads can be used to assign a putative 5’ cap position to the corresponding gene. This can be achieved by mapping the second mate to the annotated exons and assigning the 5’ cap position to the corresponding gene. We used a custom perl script to perform these assignments whose output denotes the gene, chromosome, position, strand and count of 5 caps, which we will refer to as transcriptional start sites (TSSs). We constructed a union of all TSSs by requiring at least 2 reads per TSS and sample (control, MOF, NSL1 and NURF knockdowns in triplicates) using a custom perl script whose output denotes the gene, chromosome, position, strand and counts for all samples. To each gene we assigned one TSS, which had the maximal number of summed counts in the three control knockdown samples. From the identity of these TSSs we derived a count matrix, which served as input to a DESeq2 analysis as outlined in the RNA-seq/DESeq2 analysis section.

extract_protocol: Protein G magnetic Dynabeads (Invitrogen) were prepared with IPP buffer (50 mM Tris-HCl pH 7.4, 150 mM NaCl, 0.1% NP-40). 2.5 μg of anti-m7G antibody (SYSY, catalog nr: 201 011) were incubated with the beads for at least 1 hour in 4ºC. The beads were finally washed twice with IPP buffer. RNA extractions were carried out with the Direct-zol Miniprep kit (Zymo Research). Abundant small RNAs (< 200 nt) were removed using the RNA Clean and Concentrator Kit (Zymo Research) and eluted in 100 μl TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). RNA fragmentation was performed using the Covaris E220 Focused-ultrasonicator (Duty cycle: 10%, Intensity: 5, Power: 175 W, Cycles/Burst: 200, time: 140 s). After sonication, the capped RNA was captured with the antibody-coupled Protein G magnetic beads for 1 to 2 hours in 4 ºC. Then, the beads were washed 3 times with IPP buffer. RNA 3' ends were repaired using PNK. Custom-made, barcoded adapters were ligated to the RNA using T4 RNA Ligase 1 for 1 h at 25 °C. Excess adapters were washed away with IPP buffer and RNA was purified by column purification. Isolated RNA was reverse-transcribed and treated with RNase H. cDNA was column-purified and circularized with CircLigase for 2–16 hours. Circularized cDNA was directly PCR amplified, the amplified library was finally cleaned up using Ampure beads.


title: MAPCap_NSL1_rep2


title: MNase-ChIP_NSL1_Digestion2_rep2


title: MAPCap_GST_rep2


title: MAPCap_GST_rep3


title: MAPCap_GST_rep1


title: AL-ZT2-2

description: Animals were fed Ad libitum


title: AL-ZT2-1

description: Animals were fed Ad libitum


title: single-cell-RNAseq_GST

data_processing: 10x genomics data was processed using the vendor provided pipeline. See https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/bam for information on barcodes and UMIs. We used the cellranger Rkit to obtain matrices with cells in the columns and genes in the rows, using barcodes.tsv and genes.tsv files corresponding to each condition. For each condition (GST-control and NSL1 knockdown) we retained only cells that had more than 2,000 nonzero genes. Next, we selected genes that had nonzero entries in more than 50% of the remaining cells. The filtering resulted in 3,258 cells for the control and 588 for the NSL1 knockdown and in total 1,787 genes. scRNA-seq data was normalized using BASiCS. As input served unique molecular identifier counts for each gene and cell in the control and NSL1 knockdown experiment. To control for technical variability ERCC spike ins were used. We retained only cells that had more than 2,000 nonzero genes and had more than 10 ERCC spike in reads. Thereafter, we selected genes whose mean count was larger than 1 and ERCC spike ins that had at least one nonzero entry. Because there were many more control cells than NSL1 KD cells, we subsampled the control to the same number of cells as in the NSL1 knockdown (560). We repeated this 32 times. After running the BASiCS algorithm, we detected differential variability using the BASiCS_TestDE function. The assignment as a gene that changed variability required that all 32 subsamples flagged the gene as having an increased variability upon NSL1 KD.

extract_protocol: dsRNA-mediated RNAi is performed as described above. Single cells in the control and NSL1 KD samples were carefully diluted, re-suspended and filtered to obtain single cell suspension. The cells are then captured using the 10x genomics Chromium Single Cell 3' Library and Gel Bead Kit v2, 4 rxns (10x Genomics, 120267) according to the manufacturer's instructions (Single Cell 3' Reagent Kits v2 User Guide, CG00052). Sample was loaded to a different lane on a chip (Chromium Single Cell A Chip Kit, 16 rxns, 1000009). After generation of nanoliter-scale Gel bead-in-EMulsions (GEMs), RNA contained in the GEMs were reverse transcribed in a Thermal Cycler (Bio Rad) ( 53°C for 45 min, 85°C for 5 min, hold at 4°C). Then, the single-strand cDNA was isolated and amplified. Finally, the amplified cDNA was fragmented, end-repaired, A-tailed and indexed using the Chromium i7 Multiplex Kit 96 rxns (120262). The clean-up steps during the library generation was performed with Ampure beads. These libraries were sequenced using the Illumina HiSeq platform with a 75-bp paired-end kit. Alignment and initial processing of sequencing data were performed with CellRanger package using the default settings. The package was used to demultiplex the data, generate FASTQ files, align the sequencing reads to the dm3 reference genome, filter cell and UMI (unique molecular identifier) barcodes.


title: single-cell-RNAseq_NSL1


title: biotin-CTCF_OE_biotin_ChIPSeq

status: Public on Jan 12 2019

first: Dipanjan

last: Chowdhury

address: 4 Blackfan Circle

institute: Dana-Farber Cancer Institute

description:
biotin ChIP
biotin-CTCF_sorted_control_lambda.bw
biotin-CTCF_treat_pileup.bw

data_processing:
Before alignment, reads were qualified by FastQC (v0.11.2). TrimGalore (v0.4.4) was used to trim adaptor and low-quality reads if necessary.
Trimmed reads were aligned to hg19 human genome assembly using Bowtie27 (v2.2.5) with parameters “--very-sensitive --end-to-end”.
Proper paired and high quality mapped reads (MAPQ>30) were selected with samtools (v1.2). PCR duplicates were removed by picard tools(v1.90).
reads were then subjected to MACS2 (v2.1.0.20150731).
Peaks with q value less than 0.01 were kept for subsequent analysis. Signal tracks for each sample were generated using the MACS2 pileup function and were normalized to 1 million reads. Bigwig files were generated using the bedGraphToBigWig command for visualization. ChIP signal subtracted with input was used to draw heatmap and profile. Peak annotation was performed using annotatePeaks function from homer. Stringent overlap was done using bedtools (v2.25.0) after peaks width was adjusted to 200 bp region around peak summit. Differential peaks were called by macs2 bdgdiff function with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: peaks, bigWig for biotin ChIP-Seq in biotin-CTCF and biotin-CTCF-s overexpressed HeLa-S3 cells

source_name: Hela S3 cells

growth_protocol: HeLa-S3  cells were cultured in DMEM (Hyclone) supplemented with 10% fetal bovine serum. Cultured cells were maintained at 37°C in a 5% CO2 incubator.

extract_protocol:
For biotin ChIP-seq experiments, cells stably expressed biotin-alone or biotin-CTCF or biotin-CTCF-s were expanded and crosslinked with 1% formaldehyde. Crosslinked cells were sonicated and diluted 10-fold with ChIP dilution buffer, and then incubated with M280 streptavidin dynabeads at 4°C for overnight.
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were crosslinked with 1% formaldehyde for 10 minutes, then quenched with 0.125M glycine for 5 minutes.

tag: cell line

value: Hela S3 cells

value: stably expressed biotin tag alone

tag: antibody


title: biotin-CTCF-s_OE_biotin_ChIPSeq

description:
biotin ChIP
biotin-CTCF-s_sorted_control_lambda.bw
biotin-CTCF-s_treat_pileup.bw


title: MAPCap_NSL1_rep1


title: CTCF-s_OE_CTCF-HiChIP_rep2

description: CTCF-s_OE_CTCF-HiChIP_combine_allValidPairs.hic

data_processing:
Library strategy: HiChIP-seq
HiChIP paired-end reads were first subjected to Trim Galore to remove adaptors.
Trimmed reads were aligned to the hg19 genome using the HiC-Pro software with default settings except that reads were assigned to MboI restriction fragments.
Valid reads generated by HiC-Pro were transformed to .hic format for juice tools with KR normalization using hicpro2juicebox function, then contact domains were identified using juice tools arrowhead function with 10kb resolution.
Genome_build: hg19
Supplementary_files_format_and_content: hic format for CTCF-mediated chromatin looping in Control and CTCF-s OE cells

extract_protocol:
Long-range contacts were generated and ChIP was performed. Libraries were prepared using the Tn5 transposase.
Nextera

value: stably expressed FLAG tag-CTCF-s

value: CTCF(Active motif, 61311)


title: MNase-ChIP_NSL1_Digestion1_rep2

value: embryonic cell line (S2)


title: Control_CTCF-HiChIP_rep1

description: Control_CTCF-HiChIP_combine_allValidPairs.hic

value: stably expressed FLAG tag alone


title: CTCF-s_OE_CTCF-HiChIP_rep1


title: biotin_alone_biotin_ChIPSeq

description: biotin ChIP


title: Control_CTCF-HiChIP_rep2


title: mSCLC_SMC_R716T2S

type: RNA

first: yujuan

last: jin

address: Yueyang Road 320#

institute: Shanghai Institutes for Biological Sciences, CAS

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: Primary cell lines from mouse small cell lung carcinoma model, SMCs

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Mouse SCLC cell lines were derived from SCLC tumors excised from Rb1L/L, Trp53L/L mice. Briefly, the tumor samples were washed three times by phosphate-buffered saline (PBS), then dissected by shears in 100 ml 1% BSA. Then, the mixture was transferred to RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 100 IU/ml of penicillin, and 100 mg/ml of streptomycin at 37℃ and 5% CO2.

extract_protocol: Total RNA of primary cells were isolated by TRIzol reagent (Life Technologies) according to the manufacturer’s instructions. RNA was checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

value: Lung tumor

value: mSCLC

value: SMC

tag: pair

tag: gender

value: female


title: mSCLC_SMC_R1611_S

tag: cell type


title: mSCLC_SMC_R1563S

value: male


title: shboth#2.RNA-Seq

data_processing:
Before alignment, reads were qualified by FastQC (v0.11.2). TrimGalore (v0.4.4) was used to trim adaptor and low-quality reads if necessary.
Trimmed reads were aligned to hg19 human genome assembly using Bowtie27 (v2.2.5) with parameters “--very-sensitive --end-to-end”.
Proper paired and high quality mapped reads (MAPQ>30) were selected with samtools (v1.2). PCR duplicates were removed by picard tools(v1.90).
reads were then subjected to MACS2 (v2.1.0.20150731).
Peaks with q value less than 0.01 were kept for subsequent analysis. Signal tracks for each sample were generated using the MACS2 pileup function and were normalized to 1 million reads. Bigwig files were generated using the bedGraphToBigWig command for visualization. ChIP signal subtracted with input was used to draw heatmap and profile. Peak annotation was performed using annotatePeaks function from homer. Stringent overlap was done using bedtools (v2.25.0) after peaks width was adjusted to 200 bp region around peak summit. Differential peaks were called by macs2 bdgdiff function with default parameters. *control_lambda.bw files include input signal while *treat_pileup.bw represents ChIP signal.
For RNA-Seq analysis, raw reads were aligned to a Bowtie2 (v2.2.5) indexed human genome (hg19 sourced from UCSC) using STAR (v2.5.2a).
Gene expression levels were quantified as read counts generated by RSEM (v1.2.22) with default settings.
Raw tag counts were normalized for GC content using EDASeq (v2.8.0).
Differential transcript expression was called using DESeq2 (v1.10.1).
Genome_build: hg19
Supplementary_files_format_and_content: peaks, bigWig for ChIP-Seq and tsv for RNA-Seq

extract_protocol:
ChIP was performed as previously described (Huang et al.,2013). Briefly, crosslinked cells was sonicated and incubated with protein A and protein G dynabeads (1:1 mix) and the indicated antibodies. Antibody bound DNA was subsequently washed with low salt wash buffer, high salt wash buffer, LiCl wash buffer once, respectively, and then TE wash buffer twice. ChIPed DNA was reverse-crosslinked and purified for DNA library construction followed by sequencing or ChIP-qPCR analysis.
ChIP-Seq and RNA-Seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For loss or gain function of CTCF and CTCF-s, lentivirus was generated in 293T cells, After 48hrs of lentivirus production, harvested the virus and filtered with 0.45 μM filter (Millipore), and infected Hela S3 cells twice, after removing virus for 1 day, screened infected cells with 4 μg/ml of puromycine for at least one weak.

value: stable knockdown both CTCF and CTCF-s


title: shboth#1.RNA-Seq


title: mSCLC_non-SMC_R1611N

source_name: Primary cell lines from mouse small cell lung carcinoma model, non-SMCs

value: non-SMC


title: mSCLC_non-SMC_R716T2N


title: shCTCF-s_rep1.RNA-Seq

value: stable knockdown CTCF-s


title: CtrlshRNA_rep2.RNA-Seq

value: stably expressed CtrlshRNAs


title: shCTCF#2.RNA-Seq

value: stable knockdown CTCF


title: shCTCF#1.RNA-Seq


title: mSCLC_non-SMC_R1563N


title: FLAG-CTCF-s_rep2.RNA-Seq


title: FLAG-CTCF-s_rep1.RNA-Seq


title: CtrlshRNA_rep1.RNA-Seq


title: FLAG-CTCF_rep2.RNA-Seq

value: stably expressed FLAG tag-CTCF


title: FLAG-CTCF-s_FLAG_ChIPSeq

value: Hela S3 cells

tag: chip antibody

value: FLAG-M2 beads(Sigma, M8823)


title: FLAG_rep2.RNA-Seq

tag: genotype/variation


title: FLAG-CTCF_rep1.RNA-Seq


title: FLAG-CTCF_FLAG_ChIPSeq


title: FLAG_rep1.RNA-Seq


title: shCTCF-s_rep2.RNA-Seq


title: Diff-B

city: Stanford

first: Virginia

middle: D.

last: Winn

state: CA

address: 300 Pasteur Drive, Boswell A364

department: OB-GYN/Reproductive, Perinatal and Stem Cell Biology Research

institute: Stanford University

description:
Illumina MiSeq v3
processed data file: Abundances_Diff.txt
processed data file: StemvsDiff_all_with_type.1384366250358.tsv

data_processing:
Data quality check of the input sequence was first performed using FastQC.
Bowtie2 was then used to map the spike-in DNA before the trimming (ea-utils and cutadapt) and filtering (PRINSEQ) steps.
FastQC was re-run to analyze the trimmed reads, allowing a before and after comparison.
Sequence reads were merged using SeqPrep then mapped to the reference genome using Bowtie, followed by generation of a mapping rate summary.
Using the open-source software BEDTools and SAMtools, read alignment and read coverage tracks were generated and deployed to the customized UCSC genome browser.
Quantitation and alignment to miRBase.
Abundance determination and Abundance levels for ncRNAs (miRNAs, tRNAs, rRNAs, lincRNAs, piRNAs, and snoRNAs), antisense transcripts, coding genes and repeat elements (LTR, LINE, SINE, and tandem repeats) were determined.
A summary of reads overlapping each of these annotations in the reference genome was created using SAMtools.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Abundances_Day14.5.txt: Abundances for Day14.5 samples (tab-delimited text).
Supplementary_files_format_and_content: Abundances_Diff.txt: Abundances for Diff samples (tab-delimited text).
Supplementary_files_format_and_content: Abundances_NP.txt: Abundances for NP samples (tab-delimited text).
Supplementary_files_format_and_content: Abundances_Stem.txt: Abundances for Stem samples (tab-delimited text).
Supplementary_files_format_and_content: Differences in expression of ncRNA were calculated and differential expression analysis was performed in R using DESeq; adjusted P-values were calculated using Benjamini-Hochberg procedure. Differential expression results are provided for each comparison: 1) NP vs. Day 14.5 (NPvsDay14.5_all_with_type.1384366252915.tsv) and 2) Stem vs Diff (StemvsDiff_all_with_type.1384366250358.tsv).

source_name: Extracellular vesicles - trophoblast syncytial differentiation in vitro culture conditioned media

growth_protocol: Murine TSCs derived from C57BL/6 mice were maintained on CellStart-CTS coated plastic plates in RPMI-1640 with L-glutamine (Hyclone SH30027) supplemented with 1% penicillin/streptomycin (Hyclone SV30010), 1% sodium pyruvate (Gibco 11360), 85.8 µM β-mercaptoethanol (Bio-Rad 161-0710), 1 μg/ml heparin (Sigma H3149), 25 ng/ml fibroblast growth factor 4 (FGF4) (Sigma F8424) to maintain stemness (STEM; samples 1-6). TSCs cultured on plastic in the absence of FGF4 or heparin at normal oxygen tension (O2, 21%) result in fused, multinuclear syncytial-like cultures (SynT).

extract_protocol:
RNA was purified from ExoE-EV using SeraMir RNA kits (System Biosciences).
RNA-Seq libraries were constructed using modified Illumina adapter methods using the XMIR exosome RNA-Seq Sample Preparation Kit (System Biosciences) and indexed with separate bar codes for multiplex sequencing on an Illumina MiSeq v3 instrument using a 2 x 75 bp paired end run setting.

treatment_protocol: Gestational day (GD) 0.5. Pregnant female mice were sacrificed on GD 14.5. Age-matched, non-pregnant females (NP) were sacrificed in conjunction with each pregnant female. At time of sacrifice (by carbon dioxide asphyxiation followed by bilateral pneumothorax), blood was collected via cardiac puncture. Serum was prepared from the whole blood using venous blood collection serum separator tubes (BD Vacutainer #367986) per manufacturer’s instructions. Serum was stored at -80°C.

tag: strain/background

tag: sample origin

value: ExoQuick TC isolated extracellular vesicles from conditioned media

tag: differentiation protocol

value: Syncytial differentiation (SynT)


title: Diff-A


title: Diff-C


title: Day14.5-A

description:
Illumina MiSeq v3
processed data file: Abundances_Day14.5.txt
processed data file: NPvsDay14.5_all_with_type.1384366252915.tsv

source_name: Extracellular vesicles - GD14.5 pregnant mouse sera

value: ExoQuick isolated extracellular vesicles from mouse sera

tag: pregnancy status


title: Stem-B

description:
Illumina MiSeq v3
processed data file: Abundances_Stem.txt
processed data file: StemvsDiff_all_with_type.1384366250358.tsv

source_name: Extracellular vesicles - trophoblast stem in vitro culture conditioned media

value: Stem


title: Day14.5-C


title: NP-C

description:
Illumina MiSeq v3
processed data file: Abundances_NP.txt
processed data file: NPvsDay14.5_all_with_type.1384366252915.tsv

source_name: Extracellular vesicles - nonpregnant mouse sera

value: Non pregnant


title: Stem-C


title: NP-A


title: Day14.5-B


title: Stem-A


title: NP-B


title: FLAG_FLAG_ChIPSeq

value: stably expressed FLAG tag alone


title: T4_untreated 3

first: Jean-Bosco

last: Tagne

address: 72 East Concord

department: Medicine/Pulmonary

institute: Boston University

data_processing:
Standard Illumina pipeline was used to create the fastq files.
FASTQ files were aligned to mm9 genome using tophat.
HTSeq count was used to generate counts from the BAM/alignment file which are being submitted as processed output.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *_tophat_mm9_sorted.count.txt: Tab-delimited text files with counts for genes generated using HTSeq count.

source_name: metastatic mouse lung cancer cell line

growth_protocol: Primary non-metastatic and metastatic tumor cells, KW-634, 821-LN and 821-T4, were grown in RPMI + GlutaMAX -1 (1X) (Gibco for Life Technologies REF: 61870-036).

extract_protocol:
Total RNA, isolated from each of the three independently samples untreated and treated KW, LN and T4 cancer Kras cell lines.
Libraries were prepared according to Illumina's instructions accompanying the RNA-Seq Kit.
Each sequencing run used a 40 or 80 cycle v4 High Output Sequencing Kit, and corresponding High Output Flow Cell. Illumina libraries were quantified using qRT-PCR. The library was sequenced on the Illumina HiSeq at the Whitehead Institute Genome Technology Core. The location of each barcode was recorded, and this allowed for the post-sequencing identification of each population.

treatment_protocol: The cells were grown in culture medium to reach 40-50% confluency before treatment with 10 µl of 50 nM Nano-miR-200c, miR-200c, empty Nano Control (same composition as the suspension or vehicle with no miRs), antago-miR or control untreated plates before harvesting after 48 hours to study the effect of our treatment.

value: Derived lung cancer cell line

tag: metastaticity

value: metastatic

tag: passages

value: 5 to 8

value: Kras

tag: treatment

value: Untreated


title: T4_treated 2

tag: strain

value: Treated


title: T4_treated 3


title: T4_untreated 2


title: T4_treated 1


title: Baseline male: biological replicate 1

city: Oviedo

first: Guillermo

middle: M

last: Albaiceta

address: Avenida de Roma s/n

country: Spain

institute: Instituto de Investigación Sanitaria del Principado de Asturias

hyb_protocol: Labeled RNA were hybridized to a Mouse Gene 2.0 ST Array. Washing and staining was done ina a GeneChip Fluidics Station 450 (Affymetrix)

scan_protocol: Scanning was performed using GeneChip Scanner 7G (Affymetrix)

data_processing: Data were analyzed (Background correction and normalization using the RMA algorithm) using the oligo and limma packages from Bioconductor, in the R platform.

label: Biotin

source_name: lung homogenate

label_protocol: 100 ng of total RNA were amplified and labeled with biotin using the WT Plus Reagent kit (Affymetrix), following manufacturer's instructions

growth_protocol: Lung tissue from 10 week old mice

extract_protocol: RNA was extracted using Trizol and purified using the RNAeasy minikit (Quiagen)

treatment_protocol: baseline were intact mice. The ventilation was performed using positive inspiratory pressure of 15cmH2O ZEEP, 100 breaths/min, inspiratory:expiratory ratio 1:1, inpired oxygen fraction 0.21, during 2.5 hours

value: Male

tag: conditions

value: Baseline


title: Baseline female: biological replicate 3

value: Female


title: Ventilated male: biological replicate 3

value: Ventilation


title: Ventilated female: biological replicate 2


title: Ventilated female: biological replicate 3


title: Ventilated female: biological replicate 1


title: Ventilated male: biological replicate 2


title: T4_untreated 1


title: Ventilated male: biological replicate 1


title: LN_untreated 3


title: KW_untreated 2

source_name: non-metastatic mouse lung cancer cell line

value: non-metastatic


title: LN_treated 2


title: KW_treated 3


title: KW_untreated 3


title: LN_treated 1


title: KW_treated 2


title: LN_untreated 2


title: KW_treated 1


title: LN_treated 3


title: KW_untreated 1


title: LN_untreated 1


title: Baseline male: biological replicate 2


title: Baseline female: biological replicate 2


title: Baseline female: biological replicate 1


title: Baseline male: biological replicate 3


title: MYBB_r1881_G3- rep.2

city: Campinas

first: Rafaela

last: Rosa-Ribeiro

address: Charles Darwin st, s/n

country: Brazil

institute: State University of Campinas

data_processing:
The sequencing file were aligned using the Bowtie2 with the hg_38 genome
The MACS2 software was used to determine peak enrichment in the CHIP samples, as compared to the input, using the callpeaks function and considering a 200 shift size and a p-value = 0.01
summit.bed file was used to visualize peaks along the chromosomes using the IGV browser
Genome_build: hg38
Supplementary_files_format_and_content: summit.bed/ output of peaks called by MACS2 used to other analysis decribed in the manuscript.

source_name: LNCaP Cells

growth_protocol: LNCaP cells were cultured   in RPMI-1640,  plus 1% antibiotic and antifungic and 10% fetal bovine serum. When cells've gotten 60-70% confluence the medium was changed to RPMI-1640 containing charcoal-treated 0.5% fetal calf serum plus 1% antibiotic and antifungic for 24h.

extract_protocol:
Cells (107) were cross-linking was achieved using 1% methanol-free formaldehyde in RPMI 1640 for 10 min at room temperature. Cells were ressupended in 1% SDS in TE-PMSF buffer and sonicated (Bioruptor; Diagenode, Seraing, Belgium) at 4oC for 15 cycles (30 s ON/30 s OFF).Immunoprecipitation was done with 5ug anti-phosphoT487-BMYB (ab76009, ABCAM) or without any antibody (Input) and 20 uL of protein G coupled to magnetic beads (Thermo-Fisher) in 100 uL total volume, incubated overnight at 4oC. The cross-linking reversal was done with 0.5 mg proteinase K and reversion buffer for 30 min at 65oC.
To produce the libraries were used the TrueSeq DNA kit (Illumina; San Diego, CA, USA), according to the manufacturer´s instructions. The sequencing in a HiSeq2000 equipment. 50 bp fragments were sequenced by the single-end method, with the standart 7 bps index reading and V3 chemistry.

treatment_protocol: Cells were treated with 1 nM R1881 in DMSO, or with DMSO (vehicle) alone, for 6, 12 or 24 h.

tag: passage

value: passage 05 to 10

tag: confluence

value: 70% of confluence

value: androgen r1881


title: MYBB_r1881_G2- rep.1

tag: antibody

value: 5ug anti-phosphoT487-BMYB (ab76009, ABCAM)


title: Input_dmso_G3- rep.2

value: vehicle DMSO


title: MYBB_dsmo_G2- rep.1


title: Input_dmso_G2- rep.1


title: Input_r1881_G2- rep.1


title: LPO3 - input

city: Edinburgh

first: Marcus

middle: James

last: Lyall

state: Lothian

address: The Queen's Medical Research Institute, 47 Little France Crescent

department: University/British Heart Foundation Centre for Cardiovascular Science

country: United Kingdom

institute: University of Edinburgh

description: mapped reads (mm10) were binned across 150bp windows.

data_processing:
Reads mapped to hg19 human build
Data binned into 150bp windows across the genome
Data converted into hg19 build and into a wiggle (.bedgraph) file
data normalised by read count
enriched (5hmC) datasets normalised to mean input dataset to generate enrichment over background dataset
Genome_build: hg19
Supplementary_files_format_and_content: .bedgraph file

growth_protocol: Female H9 ESCs were maintained in mTeSR1 (Stem Cell Technologies, Cambridge UK) on matrigel (Corning, Tewksbury, USA) and differentiated into hepatocyte-like cells as previously described (Szkolnicka D, Curr Protoc Stem Cell Biol 2014;30:1G 5 1-12.)

extract_protocol:
Sheared gDNA was enriched using antibodies against 5hmC (Active Motif , cat# 39769) prior to enrichment through magnetic IgG beads. Following a series of buffer washes the DNA is then released through proteinase K digestion of the antibody and the DNA is subsequently cleaned up using Qiagen QIAquick PCR purification kits (Qiagen) and eluting in 20ul purified water. Enriched DNA was then subjected to 18 cycles of whole genome amplification using using an enhanced amplification kit optimised for next generational sequencing (Sigma-Aldrich SeqPlex DNA Amplification Kit).
Individual libraries were generated from 100ng each of 5mc enriched and input DNA for each sample, using the Ion XpressPlus Fragment Library Kit (life Technologies™). The DNA was end repaired, purified and then ligated to Ion-compatible barcoded adapters (Ion Xpress™ Barcode Adapters 1–96: Life Technologies™), followed by nick-repair to complete the linkage between adapters and DNA inserts. The adapter-ligated library was then amplified (10 cycles) and finally size-selected using two rounds of AMPure XP bead capture to size‐select fragments approximately 100–250 bp in length. An equimolar pool of barcoded libraries was prepared at 100pM; each pool contained an meDIP enriched and corresponding input sample. 8pM of the pooled library was added into an emulsion PCR based template reaction; in this reaction the fragments generated during the library prep were attached to Ion sphere particles (ISPs) and clonally amplified. This process was carried out using the Ion One Touch 2 system and the Ion P1 Template OT2 200 Kit.

treatment_protocol: At day 20 of differentiation, cells were exposed to Sodium L-Lactate (L7022, Sigma, Gillingham, UK) 10mM, Sodium Pyruvate 1mM (Sigma, Dorset, UK) and Octanoic Acid (C2875, Sigma, Gillingham, UK) 2mM for 48 before harvesting.

value: hESC derived hepatocytes

value: female

tag: cell line

value: LPO treated

value: 5-hmC - Active Motif (cat# 39769)


title: LPO3

tag: gender


title: LPO2 - input

tag: cell type


title: LPO2


title: MYBB_dsmo_G3- rep.2


title: control3 - input

value: vehicle


title: LPO1 - input


title: control2 - input


title: control3


title: control1


title: LPO1


title: control2


title: CTCF-s_OE_RAD21_ChIPSeq

description:
CTCF-s_OE_RAD21_ChIPSeq_control_lambda.bw
CTCF-s_OE_RAD21_ChIPSeq_peaks.narrowPeak
CTCF-s_OE_RAD21_ChIPSeq_treat_pileup.bw

data_processing:
Before alignment, reads were qualified by FastQC (v0.11.2). TrimGalore (v0.4.4) was used to trim adaptor and low-quality reads if necessary.
Trimmed reads were aligned to hg19 human genome assembly using Bowtie27 (v2.2.5) with parameters “--very-sensitive --end-to-end”.
Proper paired and high quality mapped reads (MAPQ>30) were selected with samtools (v1.2). PCR duplicates were removed by picard tools(v1.90).
reads were then subjected to MACS2 (v2.1.0.20150731).
Peaks with q value less than 0.01 were kept for subsequent analysis. Signal tracks for each sample were generated using the MACS2 pileup function and were normalized to 1 million reads. Bigwig files were generated using the bedGraphToBigWig command for visualization. ChIP signal subtracted with input was used to draw heatmap and profile. Peak annotation was performed using annotatePeaks function from homer. Stringent overlap was done using bedtools (v2.25.0) after peaks width was adjusted to 200 bp region around peak summit. Differential peaks were called by macs2 bdgdiff function with default parameters. *control_lambda.bw files include input signal while *treat_pileup.bw represents ChIP signal.
Genome_build: hg19
Supplementary_files_format_and_content: peaks, bigWig for ChIP-Seq and hic format for CTCF-mediated chromatin looping in Control and CTCF-s OE cells

extract_protocol:
ChIP was performed as previously described(Huang et al.,2013). Briefly, crosslinked cells was sonicated and incubated with protein A and protein G dynabeads (1:1 mix) and the indicated antibodies. Antibody bound DNA was subsequently washed with low salt wash buffer, high salt wash buffer, LiCl wash buffer once, respectively, and then TE wash buffer twice. ChIPed DNA was reverse-crosslinked and purified for DNA library construction followed by sequencing  analysis.
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols.

value: Hela S3 cells

value: stably expressed FLAG tag-CTCF-s


title: control1 - input


title: BINPV_ChIPseq

city: San Francisco

first: Melanie

last: Ott

address: 1650 Owens Street, 5th Floor

department: Virology and Immunology

institute: Gladstone Institutes

description: Replicate 2

data_processing:
FastQC was used to detect quality control and determine read length for alignment
Skewer Version 0.1.124 was used to remove barcodes with default parameters and -m function
Bowtie Version 1.1.2 was used for aligning reads using the default paramters and the -a -l 55 -n 2 -m 1 functions
MACS2 Version 2.1.0.20150731 was used for peak calling, normalization and genreation of bedgraph pileup files. Callpeak function was used with -B -SPMR to generate normalized bedgraph files.
bedGraphToBigWig Version 4 was used to convert bedgraph files to bigwigs
Genome_build: mm10
Supplementary_files_format_and_content: BigWig Files created from immunoprecipitated samples or created from input samples

source_name: Embryonic Fibroblasts

growth_protocol: NIH3T3 cells were grown in 10% Bovine Calf Serum supplemented with L-Glutamine and Pen/Strep at 1x concentration. Cells were not treated with shRNAs, treated with scrambled shRNAs or RPRD1B shRNAs (indicated in sample section), and selected appropriately with puromycin for at 1 week.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes, thoroughly washed with DPBS, and resuspended in ChIP lysis buffer #1 (10mM Tris pH 7.4, 10mM NaCl, 0.5% NP-40, 1x HALT, 30nM Panobinostat and 5μM Nicotinamide). After sitting on ice for 10 minutes, cells were briefly vortexed and nuclei were pelleted. Nuclei were treated with MNase (NEB, M0247S) for 25 minutes at RT, pelleted and resuspended on ice in ChIP lysis buffer #2 (50mM Tris HCl pH 8.0, 10mM EDTA, 0.5% SDS, 1x HALT, 30nM Panobinostat and 5μM Nicotinamide). Chromatin was further sheared by sonication using the Sonic Dismembrator 500 (ThermoFisher Scientific) and preserved at -80oC until immunoprecipitation. 20-40ug chromatin was used for each IP
2ng of immunoprecipitated DNA from each reaction was used to create libraries using the Ovation Ultra-Low Library prep kit (Nugen, 0344-32) following manufacturer recommendations and libraries were deep sequenced on the HIseq 4000 or NextSeq 500 using single-end 50bp or single-end 75bp sequencing, respectively.

treatment_protocol: Naïve NIH3T3, RPRD1B or Scrambled shRNA selected NIH3T3 cells were treated for 2 hours with complete DMEM containing KDAC inhibitors (30nM Panobinostat, 5uM Nicotinamide) or vehicle controls.

value: Vehicle

tag: background

value: Naïve NIH3T3 Cells


title: AINPV_ChIPseq

description: Replicate 1


title: BINPK_ChIPseq

description: Replicate 2

value: KDAC inhibitor


title: Control_RAD21_ChIPSeq

description:
Control_RAD21_ChIPSeq_control_lambda.bw
Control_RAD21_ChIPSeq_peaks.narrowPeak
Control_RAD21_ChIPSeq_treat_pileup.bw

tag: genotype/variation

value: stably expressed FLAG tag alone


title: xpo1-4_MethylC-Seq

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

description: treated with bisulfite

data_processing:
MethylC-Seq:Reads were mapped to TAIR10 using BRAT-BW v2.0.1 with parameters -m 2 -i 0 -a 1000. Copy-duplicates were remove using remove-dupl command of BRAT-BW. acgt-count command of BRAT-BW was used to count mapped Cs and Ts at each cytosine of forward and reverse strands of the reference
Genome_build: TAIR10
Supplementary_files_format_and_content: For MethylC-Seq: The wig files give methylation level for all Cs(three contexts) with depth >= 4. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position (unconverted_C / ( converted_C+ unconverted_C ) ).

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Seeds were stratified at 4°C for 2 d and germinated at 22°C in a standard growth chamber with a 16-h/8-h light/dark cycle.

extract_protocol: 2-week-old xpo1a-4 seedlings were used for whole genomic bisulfite sequencing. DNA was extracted and sent to BGI (Shenzhen, China) for bisulfite treatment, library preparation and Illumina sequencing.


title: Input_r1881_G3- rep.2


title: CTCF-s_OE_Input

tag: chip antibody


title: AINPK_ChIPseq

description: Replicate 1


title: CTCF-s_OE_CTCF_ChIPSeq

value: CTCF(Active motif, 61311)


title: Control_CTCF_ChIPSeq


title: AK7acK_ChIPseq

description: Replicate 1

value: Pol II (K7ac) - Custom, Polyclonal


title: AK7acV_ChIPseq

description: Replicate 1


title: PCOS-IR miRNA

city: Hefei

first: Bo

last: Xu

state: Anhui

address: Lujiang road 17

institute: The First Affiliated Hospital of University of Science and Technology of China

description:
All these subjects performed ICSI-ET cycles
Expression_miRNA, All_Differentially_Expressed_miRNA

data_processing:
Illumina Casava1.7 software used for basecalling.
the adaptor sequences and low quality reads were removed and then the clean reads were mapped on the reference human genome using the SOAP2 program
These mapped reads were aligned against miRbase, and grouped as miRNAs.
The expression values of miRNAs were normalized based on the absolute number of mappable reads (Normalized counts are displayed by Reads per Million, RPM) to then detect differentially expression profile
Genome_build: GRCh38
Supplementary_files_format_and_content: XSLX files include RPKM values of mRNA for each Sample, miRNA information and Read Counts of miRNA for each Sample

source_name: granulosa cells

extract_protocol:
The small RNA and mRNA sequencing of cumulus granulosa cells from PCOS-IR and PCOS-control patients were performed at KangCheng-Shanghai. For miRNA sequencing, total RNA were extracted using TRIzol reagent (Invitrogen) and then pooled equally and then dispersed by 15% (w/v) denaturing PAGE.The small RNA fragments of about 18–28 nt were isolated by gel extraction and performed RNA purification. After small RNA library construction, these RNAs were sequentially sequenced by the Illumina NextSeq 500 (Illumina, San Diego, CA, USA) according to Illumina’s protocol. For mRNA sequencing, total RNA were extracted and analyized by NanoDrop ND-1000. The mRNA enriched from total RNA was using NEB Next® Poly(A) mRNA Magnetic Isolation Module and then performed mRNA library construction by KAPA Stranded RNA-Seq Library Prep Kit (Illumina). The mRNA sequencing was also using the Illumina NextSeq 500 (Illumina, San Diego, CA, USA) according to Illumina’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cumulus–oocyte complexes were retrieved and washed in multiple dishes with washing medium. Then, the cumulus granulosa cells were collected in fertilisation medium (William A. Cook Australia Pty. Ltd., Queensland, Australia) using two disposable needles and two 1-ml plastic disposable syringes without hyaluronidase

tag: diseaset state

value: polycystic ovary syndrome

tag: homa index

tag: insulin resistance

value: with


title: PCOS-IR mRNA


title: PCOS-control mRNA

value: without


title: PCOS-control miRNA


title: A8WG16V_ChIPseq

description: Replicate 1

value: Pol II (8WG16) - Abcam, ab817


title: Control_Input


title: A8WG16K_ChIPseq

description: Replicate 1