title: PRC1CPM_TAM_eaXInput_rep3

city: Oxford

first: Nadezda

middle: A

last: Fursova

address: South Parks Rd

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

description:
Input for AEBP2 and EPOP cChIP-seq
mESC_PRC1CPM_TAM_eaXInput_MERGED.bw

data_processing:
For calibrated ChIP-seq, paired-end reads were aligned to the concatenated mouse and spike-in genome sequences (mm10+dm6 for native cChIP-seq, and mm10+hg19 for cross-linked cChIP-seq) using Bowtie 2 (Langmead and Salzberg, 2012) with the “--no-mixed” and “--no-discordant” options. Only uniquely mapped reads after removal of PCR duplicates with Sambamba (Tarasov et al., 2015) were used for downstream analysis.
For visualisation of cChIP-seq data and annotation of genomic regions with read counts, uniquely aligned mouse reads were normalised using dm6 or hg19 spike-in as described previously (Fursova et al., 2019). Briefly, mm10 reads were randomly subsampled based on the total number of spike-in (dm6 or hg19) reads in each sample. To account for any minor variations in spike-in cell mixing between replicates, we used the ratio of spike-in/mouse total read counts in the corresponding Input samples to correct the subsampling factors. After normalisation, read densities for individual biological replicates were compared across RING1B peaks using multiBamSummary and plotCorrelation from deepTools (Ramirez et al., 2014). For each experimental condition, biological replicates correlated well (Pearson correlation coefficient > 0.95) and were merged for downstream analysis.
For comparative box plot analysis, RING1B-bound sites were annotated with read counts from merged spike-in normalised replicates using multiBamSummary from deeptools ( “--outRawCounts”).
To identify genomic regions bound by RING1B, SUZ12 and PCGF2, we carried out peak calling using MACS2 (“BAMPE” and “--broad” options specified), with corresponding Input samples used as a control. For RING1B and SUZ12, peaks were called using merged biological replicates from untreated PRC1CPM and PRC1CKO cells for RING1B and SUZ12 cChIP-seq respectively, and only peaks identified in both cell lines were selected. For PCGF2, individual replicates from untreated PRC1CPM ESC were used, and only peaks identified in all biological replicates were taken forward. For all peak sets, peaks overlapping with a custom-build set of blacklisted genomic regions were discarded to remove sequencing artefacts. For RING1B-bound regions, RING1B cChIP-seq in PRC1CKO ESCs was used to filter out peaks which showed no significant loss of RING1B signal following tamoxifen treatment (p-adj < 0.05 and > 2-fold).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files showing the genome coverage for merged spike-in normalised biological replicates were generated using the pileup function from MACS2. Differential tracks of log2 fold changes in genome coverage following tamoxifen treatment were obtained using bigwigCompare function from deeptools suite.
Supplementary_files_format_and_content: bed files containing RING1B-, SUZ12- and PCGF2- bound genomic intervals, identified using MACS2 ("--broad" and "BAMPE" options) from biological replicates

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, tamoxifen-treated (72hr OHT), gDNA-seq

growth_protocol: Mouse embryonic stem cells were grown on gelatin-coated plates at 37°C and 5% CO2, in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), 1x non-essential amino acids (Life Technologies), 0.5 mM beta-mercaptoethanol (Life Technologies), and 10 ng/mL leukemia inhibitory factor. Human HEK293T cells used for calibrated ChIP-seq were grown at 37°C and 5% CO2, in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), and 0.5 mM beta-mercaptoethanol (Life Technologies). Drosophila S2 (SG4) cells were grown adhesively at 25°C in Schneider’s Drosophila Medium (Life Technologies), supplemented with 1x penicillin-streptomycin solution (Life Technologies) and 10% heat-inactivated fetal bovine serum (Labtech).

extract_protocol:
For RING1B, SUZ12, JARID2, PCL2, AEBP2, EPOP, PCGF2, PCGF1 and PCGF6, cChIP-seq was performed as described previously (Fursova et al., 2019). Briefly, 5 x 10^7 mouse ESCs (untreated or following 72 hours OHT treatment) were mixed with 2 x 10^6 human HEK293T cells. Cells were resuspended in 10 ml phosphate buffered saline (PBS) and crosslinked at 25°C with 2 mM DSG (Thermo Scientific) for 45 minutes, and then with 1% formaldehyde (methanol-free, Thermo Scientific) for a further 15 minutes. Reactions were quenched with 125 mM glycine. Crosslinked cells were incubated in lysis buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton-X100) for 10 minutes at 4˚C. Released nuclei were washed (10 mM Tris-HCl pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) for 5 minutes at 4˚C. Chromatin was then resuspended in 1 ml of sonication buffer (10 mM Tris-HCl pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na deoxycholate, 0.5% N-lauroylsarcosine) and sonicated for 30 minutes using a BioRuptor Pico (Diagenode), shearing genomic DNA to an average size of 0.5 kb. Following sonication, TritonX-100 was added to a final concentration of 1%. For ChIP, sonicated chromatin was diluted 10-fold in ChIP dilution buffer (1% Triton-X100, 1 mM EDTA, 20 mM Tris-HCl pH 8, 150 mM NaCl) and pre-cleared for 1 hour using Protein A agarose beads (Repligen) blocked with 1 mg/ml BSA and 1 mg/ml yeast tRNA. For each ChIP reaction, 1ml of diluted and pre-cleared chromatin was incubated overnight with the appropriate antibody, anti-RING1B (CST, D22F2, 3 ul), anti-SUZ12 (CST, D39F6, 3 ul), anti-PCGF1 (in-house, 5 ul), anti-PCGF2 (Santa Cruz, sc-10744, 3 ul), anti-JARID2 (CST D6M9X, 3 ul), anti-PCL2 (GenWay GWB-FA7207, 2 ul), anti-AEBP2 (CST #D7C6X, 10 ul), anti-PCL2 (Active motif #61753, 5 ul), or anti-PCGF6 (3 ul). Antibody-bound chromatin was captured using blocked protein A agarose for 1 hour at 4°C and collected by centrifugation. ChIP washes were performed as described previously (Farcas et al., 2012). ChIP DNA was eluted in elution buffer (1% SDS, 0.1 M NaHCO3) and cross-links were reversed overnight at 65oC with 200 mM NaCl and 2 ul RNase A (Sigma). A matched input sample (10% of original ChIP reaction) was identically treated. The following day, ChIP samples and Inputs were incubated with Proteinase K (Sigma) for 1.5 hours at 56oC and purified using ChIP DNA Clean and Concentrator Kit (Zymo Research). Native cChIP-seq for H2AK119ub1, H3K27me3, and H3K4me3 was performed as described previously (Fursova et al., 2019). Briefly, 5 x 10^7 mouse ESCs (both untreated and following 72 hours OHT treatment) were mixed with 2 x 10^7 Drosophila SG4 cells in PBS. Mixed cells were pelleted and nuclei were released by resuspending in ice cold lysis buffer (10mM Tris-HCl pH 8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 5 mM N-ethylmaleimide). Nuclei were then washed, and resuspended in 1 ml of MNase digestion buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.25 M sucrose, 3 mM CaCl2, 10 mM N-ethylmaleimide, 1x protease inhibitor cocktail (Roche)). Each sample was incubated with 200 units of MNase (Fermentas) at 37°C for 5 min, followed by the addition of 4 mM EDTA to halt MNase digestion. Following centrifugation at 1500 g for 5 min at 4°C, the supernatant (S1) was retained. The remaining pellet was incubated with 300 µl of nucleosome release buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2 mM EDTA, 1x protease inhibitor cocktail (Roche), 10 mM N-ethylmaleimide) at 4°C for 1 h, passed five times through a 27G needle using a 1 ml syringe, and spun at 1500 g for 5 min at 4°C. The second supernatant (S2) was collected and combined with corresponding S1 sample from above. A small amount of S1/S2 DNA was purified and visualized on a 1.5% agarose gel to confirm digestion to mostly mono-nucleosomes. For ChIP experiments, S1/S2 nucleosomes were diluted 10-fold in native ChIP incubation buffer (70 mM NaCl, 10 mM Tris pH 7.5, 2 mM MgCl2, 2 mM EDTA, 0.1% Triton, 1x protease inhibitor cocktail (Roche), 10 mM N-ethylmaleimide (NEM)), and 1 ml aliquots were made. Each ChIP reaction was then incubated overnight at 4oC with 5 ul of anti-H2AK119ub1 (CST D27C4), 5 ul of anti-H3K27me3 (in-house), or 3 ul anti-H3K4me3 (in-house) antibody. Antibody-bound nucleosomes were captured using protein A agarose (Repligen) beads, pre-blocked in native ChIP incubation buffer supplemented with 1 mg/ml BSA and 1 mg/ml yeast tRNA, for 1 hour at 4°C and collected by centrifugation. Immunoprecipitated material was washed four times with Native ChIP wash buffer (20 mM Tris pH 7.5, 2 mM EDTA, 125 mM NaCl, 0.1% Triton-X100) and once with Tris-EDTA buffer (10 mM Tris pH 8, 1 mM EDTA). ChIP DNA was eluted using 100 ul of elution buffer (1% SDS, 0.1 M NaHCO3), and then purified using ChIP DNA Clean and Concentrator Kit (Zymo Research). For each individual ChIP sample, DNA from a matched Input control (corresponding to 10% of original ChIP reaction) was also purified.
cChIP-seq libraries for both ChIP and Input samples were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina, following manufacturer’s guidelines. Samples were indexed using NEBNext Multiplex Oligos. The average size and concentration of all libraries was analysed using the 2100 Bioanalyzer High Sensitivity DNA Kit (Agilent) followed by qPCR using SensiMix SYBR (Bioline, UK) and KAPA Illumina DNA standards (Roche). Libraries were sequenced as 40 bp paired-end reads on Illumina NextSeq 500 platform.

treatment_protocol: To induce conditional removal of PRC1 or PRC1 catalytic activity in PRC1CKO and PRC1CPM ESC lines, cells were treated with 800 nM 4-hydroxytamoxifen (TAM) for 72 hours.

tag: clone

tag: replicate

tag: treatment agent

value: tamoxifen (OHT)

tag: treatment time point

value: 72 hr

tag: spike-in reference organism

value: Homo sapiens

tag: spike-in cell line

tag: ChIP

tag: antibody


title: PRC1CPM_UNT_eaXInput_rep3

status: Public on Jan 08 2020

type: SRA

description:
Input for AEBP2 and EPOP cChIP-seq
mESC_PRC1CPM_UNT_eaXInput_MERGED.bw

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control, gDNA-seq

tag: cell line

tag: genotype

tag: strain

value: 0 hr


title: PRC1CPM_UNT_eaXInput_rep2


title: PRC1CPM_TAM_eaXInput_rep1


title: PRC1CPM_UNT_eaXInput_rep1


title: 873 G1E-ER4+E2

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

country: USA

institute: Pennsylvania State University

data_processing:
Illumina's bcl2fastq2 to generate fastq files
Custom script to trim reads to 30nts
Map reads with Bowtie 0.12.8 with parameters -y -v 2 -p 7 --best --strata -k 1 --sam-nohead --sam
Samtools v1.6 to filter chrM and unmapped reads
Fseq v1.85 to generate wiggles.  Use parameters -v -of wig -f 0
Homer v36 to call peaks.  Use parameter -style dnase.
Custom script to format peaks in bed format and bedtools to remove blacklist regions
UCSC's wigToBigWig to convert wiggle track
Genome_build: mm10
Supplementary_files_format_and_content: bigWig, signal from Fseq
Supplementary_files_format_and_content: bed, peaks from Homer

source_name: cell line

extract_protocol:
Approximately 50,000 cells were collected by centrifugation at 600 xg for 10 min at 4 °C. Cells were washed once with cold 1x PBS and centrifuged as above. Cells were lysed by gently pipetting to resuspend cell pellet in cold lysis buffer (10 mM Tris–HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and centrifuged as above.
Cells were suspended in the following mix: 25 μl 2X Tagment DNA buffer (Illumina cat# FC-121-1030), 3 μl Tn5 Transposase (Illumina cat#FC-121-1030), 22 μl nuclease-free H2O and incubated for 30 min at 37 °C. Reactions were terminated by adding 5 μl of 1% SDS solution and purified using SPRIselect beads. Following purification, library fragments were amplified using NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers 1 and 2 using the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s, and 72 °C for 1 min.  Libraries were amplified for a total of 17–19 cycles and then purified using AMPure XP beads (Beckman Coulter cat #A63881).

tag: cell type

value: G1E clone rescued by expression of an E2-dependent GATA1-ER hybrid protein


title: Organoid Ngn3-RFP positive single cell transcriptomes, ISX-9 treated

city: London

first: Patricia

last: Fonseca Pedro

state: I am not in the U.S. or Canada

address: Hodgkin Building, 2nd Floor, Newcomen Street

institute: King's College London

description: Sample 2

library_source: transcriptomic

data_processing:
The DNA library was paired-end sequenced on an Illumina Nextseq™ 500, high output, with a 1x75 bp Illumina kit (R1: 26 cycles, index read: 6 cycles, R2: 60 cycles). During sequencing, Read 1 was assigned 26 base pairs and was used for identification of the Illumina library barcode, cel barcode and UMI. R2 was assigned 60 base pairs and used to map to the reference transcriptome of Hg19 with BWA (Anders and Huber, 2010). Data was demultiplexed as described in Grün et al. 2014. Single-cell transcriptomics analysis was done using the RaceID3 algorithm, following an adapted version of the RaceID manual (https://cran.r-project.org/web/packages/RaceID/vignettes/RaceID.html).
Genome_build: hg19
Supplementary_files_format_and_content: ReadCounts.tsv

molecule: total RNA

source_name: Murine small intestine (Jejunum + Ileum) epithelium organoids

extract_protocol:
Samples were processed by Single Cell Discoveries B.V. according the SORT-seq method (Muraro et al., 2016). Ngn3-RFP-positive cells were sorted into 384-well plates with 5 μl of vapor-lock (QIAGEN) containing 100-200 nl of RT primers (consisting of a 24 bp polyT stretch, a 4bp random molecular barcode (UMI), a cell-specific 8bp barcode, the 5′ Illumina TruSeq small RNA kit adaptor and a T7 promoter), dNTPs and and mRNA ERCC Spike-Ins (Agilent). Plate was spun and frozen at −80°C. Cells were then lysed by 5 min at 65°C.
mRNA of each cell was reverse transcribed, converted to double-stranded cDNA, pooled and in vitro transcribed for linear following the CEL-Seq 2 protocol (Hashimshony et al., 2016). Illumina sequencing libraries were then prepared with the TruSeq small RNA primers (Illumina) and sequenced paired-end at 75 bp read length the Illumina NextSeq.

treatment_protocol: Sample 1 was exposed to DMSO for 48h (Control). Sample 2 was exposed to ISX-9 for 48h.

value: Neurog3-RFP hom

tag: tissue

value: intestine

value: sorted Ngn3-RFP-positive cells

tag: method

value: CEL-Seq2 384 primer

tag: treatment


title: Organoid Ngn3-RFP positive single cell transcriptomes, DMSO treated

description: Sample 1

value: DMSO


title: PRC1CPM_TAM_EPOP_rep3

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, tamoxifen-treated (72hr OHT), EPOP ChIP-seq

value: EPOP

value: Active motif (# 61753)


title: PRC1CPM_UNT_EPOP_rep3

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control, EPOP ChIP-seq


title: PRC1CPM_TAM_EPOP_rep1


title: PRC1CPM_TAM_EPOP_rep2


title: PRC1CPM_UNT_EPOP_rep1


title: PRC1CPM_UNT_EPOP_rep2


title: PRC1CPM_TAM_AEBP2_rep1

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, tamoxifen-treated (72hr OHT), AEBP2 ChIP-seq

value: Cell Signalling Technology (# D7C6X)


title: PRC1CPM_TAM_AEBP2_rep3


title: PRC1CPM_UNT_AEBP2_rep3

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control, AEBP2 ChIP-seq


title: Young_GDHD_TMNP

city: Singapore

first: Hassen

last: Kared

address: 8A Biomedical Grove - Immunos Building - Level 3

country: Singapore

institute: Singapore Immunology Network (SIgN) - A*STAR

description:
RHT2460
read_count_bulk.txt
rpkm_bulk.txt

data_processing:
The paired-end reads were mapped to Human GRCh38 reference genome version 25 using STAR alignment tool.
The number of reads mapped to each gene was counted using feature Counts and the human reference genome to obtain the read count table.
RPKM (Reads Per Kilobase of transcript per Million mapped reads) values were computed using edgeR R package by filtering the genes that have zeros total count and by normalizing the count with TMM algorithm.
Genome_build: GRCh38 version 25
Supplementary_files_format_and_content: tab-delimited text files include read count values and RPKM values for the 36 samples from bulk data

organism: Homo sapiens

source_name: TMNP

extract_protocol:
Total RNA was extracted following the double extraction protocol: RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction (TRIzol, Thermo Fisher Scientific, Waltham, MA, USA) followed by a Qiagen RNeasy Micro clean-up procedure (Qiagen, Hilden, Germany). All human RNAs were analyzed on Agilent Bioanalyzer for quality assessment with RNA Integrity Number (RIN) range from 6.2 to 9.6 and median RIN 8.9 (Agilent, Santa Clara, CA, USA)
cDNA libraries were prepared using 1ng of total RNA and 0.5ul of a 1:50,000 dilution of ERCC RNA Spike in Controls (Ambion Thermo Fisher Scientific, Waltham, MA, USA) using SMARTSeq v2 protocol (Picelli et al., 2014) except for the following modifications: 1. Use of 20µM TSO, 2. Use of 250pg of cDNA with 1/5 reaction of Illumina Nextera XT kit (Illumina, San Diego, CA, USA). The length distribution of the cDNA libraries was monitored using DNA High Sensitivity Reagent Kit on the Perkin Elmer Labchip (Perkin Elmer, Waltham, MA, USA). All samples were subjected to an indexed PE sequencing run of 2x51 cycles on an Illumina HiSeq 2000 (16 samples/lane).

tag: donorid

value: GDHD

tag: batch

value: TMNP

tag: developmental stage

value: Young


title: PRC1CPM_UNT_AEBP2_rep1

tag: clone

tag: replicate


title: PRC1CPM_UNT_AEBP2_rep2

tag: treatment agent

tag: treatment time point


title: EIU2w-5

city: Bristol

first: Oliver

middle: H

last: Bell

state: Bristol

address: Office F38, Biomedical Sciences Building, University Walk

institute: University of Bristol

data_processing:
BASE-CALLING: NextSeq Control Software v2.0 (NCS) and Real-Time Analysis Software v2 (RTA).
CONVERSION TO FASTQ FILES: using bcl2fastq2 v2.20
MAIN DATA PROCESSING: The data was processed through an analysis pipeline using the Partek Flow (Build version 6.0.17.0614; Partek Inc., St. Louis, MO) software with the following task nodes (non-default parameters are specified in brackets): Trim adapters (inputting Nextera XT Index Kit v2 adapter sequences (24)), Trim bases (From 3’ end, 1 base), Trim bases (from 3’ end with minimum quality score (Phred) of 30), Align reads using STAR (2.5.3a using mm10 as the reference index), Quantify to transcriptome (Partek E/M using mm10 – Ensembl Transcripts release 89 as the reference index)
DATA NORMALISATION AND DIFFERENTIAL GENE EXPRESSION ANALYSIS (DGEA) ANALYSIS: The Partek Flow data output was further analysed using Partek Genomics Suite (PGS) (Version 6.6, Build 6.16.0812). PGS normalises data using the reads per kilobase million (RPKM) approach and performs differential gene expression analysis using an ANOVA model; a gene is considered differentially-expressed (DEG) if it has an FDR step-up p value ≤0.05 and a fold-change ≥±2.
PATHWAY ANALYSIS: The data was subsequently analysed for enrichment of GO terms and the KEGG pathways; a pathway is considered significantly-enriched if the enrichment score is ≥3 (equivalent to a p value ≤0.05). The fold-change and p-values of all genes were then imported into Ingenuity Pathway Analysis (IPA) version 01-13 (Qiagen Bioinformatics, Aarhus, Denmark) and analysed according to the manual. Pathways were considered significantly altered if they had a p value ≤0.05 and a z-score (directionality score) ≥±2. PGS and IPA were both used to generate figures.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data (Gene_RPKMs.txt) provided as a tab-delimited file of the normalised gene reads (RPKM) for each sample.
Supplementary_files_format_and_content: Processed data (4h.txt and 18h.txt) provided as a tab-delimited file of the results of DIFFERENTIAL GENE EXPRESSION ANALYSIS (DGEA), including the DIFFERENTIALLY-EXPRESSED GENES (DEGs) at 4- and 18 hours endotoxin-induced uveitis (EIU) compared to naive controls (notably the p values and fold-changes).

molecule: polyA RNA

source_name: Retinal Microglia

extract_protocol:
Retinal single cell suspensions were re-suspended in 200 µL FACS buffer containing DRAQ7 (DR77524; Biostatus, Shepshed, UK). Live microglial cells (tdTomatohi DRAQ7-) were immediately sorted using a BD Influx Cell Sorter. Retinal samples were prepared in small batches in order to maintain cell viability and ensure high quality RNA.  Cells were sorted into 0.2 mL endonuclease-free tubes containing 0.05 µL RNase inhibitor, 0.95 µL lysis buffer, and a variable amount of nuclease-free water depending on the number of cells collected: 9.5-(x/850*3) µL, where x is the number of cells isolated, using components of the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio USA, Inc., Mountain View, CA). Samples were sorted in a constrained randomised order in blocks; blocks were made as small as possible and consisted of a balance of every experimental group to ensure that time- or order-dependent (batch) effects of sorting were mitigated.   cDNA generated using SMART Seq v4 Ultra Low Input RNA Kit. cDNA isolated using Agencourt AMPure XP DNA beads. cDNA quantified by Agilent Bioanalyser.
Nextera XT DNA Kit -- as per recommendations, used 150 pg as input amount.

value: Retinal Microglia

value: Cx3cr1CreER:R26-tdTomato (C57BL/6)

tag: experimental group

value: Endotoxin-Induced Uveitis (EIU) by lipopolysaccharide (LPS) 2 weeks post-injection (resolution)

value: Heterozygote

tag: gender

value: Male

tag: eye (left or right)

value: Right

tag: experiment 1 or 2


title: EIU2w-7

tag: genotype

value: Left


title: EIU2w-4

tag: strain


title: EIU2w-3


title: PRC1CPM_TAM_eaXInput_rep2

tag: cell line

value: tamoxifen (OHT)

value: 72 hr

tag: spike-in reference organism

value: Homo sapiens

tag: spike-in cell line

tag: ChIP

tag: antibody


title: EIU2w-2

tag: tissue


title: EIU18h-5

value: Endotoxin-Induced Uveitis (EIU) by lipopolysaccharide (LPS) 18 hours post-injection (peak cellular infiltrate)


title: EIU2w-6


title: EIU18h-4


title: EIU18h-2


title: EIU18h-3


title: EIU2w-1


title: EIU18h-1


title: EIU4h-6

value: Endotoxin-Induced Uveitis (EIU) by lipopolysaccharide (LPS) 4 hours post-injection (early)


title: EIU4h-5


title: EIU4h-4


title: EIU4h-3


title: EIU4h-1


title: Naive-10

value: naive


title: EIU4h-2


title: Young_CM8K_RTE

description:
RHT2446
read_count_bulk.txt
rpkm_bulk.txt

source_name: RTE

tag: donorid

tag: batch

tag: cell type

value: RTE

tag: developmental stage


title: PRC1CPM_TAM_AEBP2_rep2

tag: clone

tag: replicate

tag: treatment agent

tag: treatment time point

value: Cell Signalling Technology (# D7C6X)


title: Naive-8

tag: experimental group

tag: gender

tag: eye (left or right)

tag: experiment 1 or 2


title: Naive-7

tag: strain

tag: genotype


title: Naive-5


title: Naive-4


title: Naive-1


title: Naive-3


title: Naive-6


title: RING1AKORING1Bfl_UNT_NativeInput_rep2

description: RING1AKORING1Bfl_UNT_NativeInput_MERGED.bw

source_name: Mouse embryonic stem cells with Drosophila spike-in, untreated control, gDNA-seq

tag: cell line

value: 3 hr

tag: spike-in reference organism

value: Drosophila melanogaster

tag: spike-in cell line

tag: ChIP


title: RING1AKORING1Bfl_UNT_H3K4me3_rep2

source_name: Mouse embryonic stem cells with Drosophila spike-in, untreated control, H3K4me3 ChIP-seq

value: 1 hr

tag: antibody

value: In house (Farcas et al., 2012)


title: RING1AKORING1Bfl_UNT_NativeInput_rep1

value: 2 hr


title: RING1AKORING1Bfl_UNT_H3K4me3_rep1

value: 0 hr


title: PRC1CPM_TAM_suz12.XInput_rep3


title: PRC1CPM_UNT_suz12.XInput_rep3


title: PRC1CPM_TAM_suz12.XInput_rep1


title: PRC1CPM_UNT_suz12.XInput_rep2


title: Naive-9

tag: tissue

value: Retinal Microglia

value: Cx3cr1CreER:R26-tdTomato (C57BL/6)

value: Heterozygote

value: Male


title: PRC1CPM_UNT_suz12.XInput_rep1


title: PRC1CPM_TAM_SUZ12_rep2

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, tamoxifen-treated (72hr OHT), SUZ12 ChIP-seq

value: tamoxifen (OHT)

value: 72 hr

value: Cell Signaling Technology(# D39F6)


title: PRC1CPM_TAM_SUZ12_rep3

value: Homo sapiens


title: PRC1CPM_UNT_SUZ12_rep3

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control, SUZ12 ChIP-seq


title: PRC1CPM_UNT_ring1b.jarid2.pcl2.XInput_rep1

description: mESC_PRC1CPM_UNT_ring1b.jarid2.pcl2.XInput_MERGED.bw


title: PRC1CPM_TAM_SUZ12_rep1


title: PRC1CPM_TAM_PCL2_rep3

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, tamoxifen-treated (72hr OHT), PCL2 ChIP-seq

value: GenWay (# GWB-FA7207)


title: PRC1CPM_TAM_ring1b.jarid2.pcl2.XInput_rep2

description: mESC_PRC1CPM_TAM_ring1b.jarid2.pcl2.XInput_MERGED.bw


title: PRC1CPM_UNT_SUZ12_rep2


title: PRC1CPM_TAM_ring1b.jarid2.pcl2.XInput_rep3


title: PRC1CPM_TAM_ring1b.jarid2.pcl2.XInput_rep1


title: Naive-2

value: naive

value: Right


title: PRC1CPM_UNT_ring1b.jarid2.pcl2.XInput_rep2


title: PRC1CPM_UNT_ring1b.jarid2.pcl2.XInput_rep3


title: PRC1CPM_UNT_SUZ12_rep1


title: PRC1CPM_TAM_suz12.XInput_rep2


title: PRC1CPM_TAM_PCL2_rep2


title: PRC1CPM_TAM_PCL2_rep1


title: PRC1CPM_UNT_PCL2_rep3

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control, PCL2 ChIP-seq


title: PRC1CPM_UNT_PCL2_rep1


title: PRC1CPM_UNT_PCL2_rep2


title: PRC1CPM_TAM_JARID2_rep3

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, tamoxifen-treated (72hr OHT), JARID2 ChIP-seq

value: Cell Signalling Technology (# D6M9X)


title: PRC1CPM_TAM_JARID2_rep1


title: PRC1CPM_UNT_JARID2_rep1

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control, JARID2 ChIP-seq


title: PRC1CPM_UNT_JARID2_rep2


title: PRC1CPM_TAM_RING1B_rep3

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, tamoxifen-treated (72hr OHT), RING1B ChIP-seq

value: Cell Signaling Technology(# D22F2)


title: PRC1CPM_UNT_JARID2_rep3


title: PRC1CPM_TAM_RING1B_rep2


title: PRC1CPM_TAM_JARID2_rep2


title: PRC1CPM_UNT_RING1B_rep3

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control, RING1B ChIP-seq


title: PRC1CPM_TAM_RING1B_rep1


title: PRC1CPM_UNT_RING1B_rep2


title: PRC1CPM_TAM_PCGF6_rep2

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, tamoxifen-treated (72hr OHT), PCGF6 ChIP-seq

value: LifeSpan BioSciences (# LS-C482495)


title: PRC1CPM_TAM_pcgf.XInput_rep1

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, tamoxifen-treated (72hr OHT), gDNA-seq


title: PRC1CPM_UNT_pcgf.XInput_rep2

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control, gDNA-seq


title: PRC1CPM_UNT_RING1B_rep1


title: PRC1CPM_UNT_pcgf.XInput_rep3


title: PRC1CPM_UNT_PCGF6_rep2

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control, PCGF6 ChIP-seq


title: PRC1CPM_TAM_PCGF6_rep1


title: PRC1CPM_TAM_PCGF6_rep3


title: PRC1CPM_TAM_pcgf.XInput_rep3


title: PRC1CPM_UNT_PCGF6_rep1


title: PRC1CPM_UNT_PCGF6_rep3


title: PRC1CPM_TAM_PCGF2_rep2

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, tamoxifen-treated (72hr OHT), PCGF2 ChIP-seq

value: Santa Cruz (# sc-10744)


title: PRC1CPM_TAM_PCGF2_rep1


title: PRC1CPM_TAM_PCGF2_rep3


title: PRC1CPM_UNT_PCGF2_rep3

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control, PCGF2 ChIP-seq


title: PRC1CPM_UNT_PCGF2_rep2


title: PRC1CPM_UNT_PCGF2_rep1


title: PRC1CPM_TAM_pcgf.XInput_rep2


title: PRC1CPM_TAM_PCGF1_rep3

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, tamoxifen-treated (72hr OHT), PCGF1 ChIP-seq

value: In house (Blackledge et al., 2014)


title: PRC1CPM_UNT_pcgf.XInput_rep1

value: 0 hr


title: PRC1CPM_TAM_PCGF1_rep2


title: PRC1CPM_UNT_PCGF1_rep3

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control, PCGF1 ChIP-seq


title: PRC1CPM_UNT_PCGF1_rep1


title: PRC1CPM_UNT_PCGF1_rep2


title: PRC1CKO_TAM_SUZ12_rep3


title: PRC1CPM_TAM_PCGF1_rep1


title: PRC1CKO_TAM_SUZ12_rep2


title: PRC1CKO_TAM_SUZ12_rep1


title: PRC1CKO_UNT_SUZ12_rep3


title: RING1B_I53A_NativeInput_rep2

source_name: Mouse embryonic stem cells with Drosophila spike-in, mutated version of RING1B (I53A), gDNA-seq

value: Drosophila melanogaster


title: RING1B_WT_NativeInput_rep2

source_name: Mouse embryonic stem cells with Drosophila spike-in, wild-type RING1B, gDNA-seq


title: PRC1CKO_UNT_SUZ12_rep1

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control, SUZ12 ChIP-seq


title: RING1B_WT_NativeInput_rep1


title: RING1B_I53A.D56K_NativeInput_rep2

description: mESC_RING1B_I53A.D56K_NativeInput_MERGED.bw

source_name: Mouse embryonic stem cells with Drosophila spike-in, mutated version of RING1B (I53A and D56K), gDNA-seq


title: RING1B_I53A.D56K_H2AK119ub1_rep2

description: mESC_RING1B_I53A.D56K_H2AK119ub_MERGED.bw

source_name: Mouse embryonic stem cells with Drosophila spike-in, mutated version of RING1B (I53A and D56K), H2AK119ub1 ChIP-seq

value: Cell Signaling Technology(#D27C4 )


title: RING1B_I53A_H2AK119ub1_rep1

source_name: Mouse embryonic stem cells with Drosophila spike-in, mutated version of RING1B (I53A), H2AK119ub1 ChIP-seq


title: RING1B_I53A.D56K_NativeInput_rep1


title: RING1B_I53A.D56K_H2AK119ub1_rep1


title: RING1B_WT_H2AK119ub1_rep2

source_name: Mouse embryonic stem cells with Drosophila spike-in, wild-type RING1B, H2AK119ub1 ChIP-seq


title: PRC1CPM_TAM_NativeInput_rep3

source_name: Mouse embryonic stem cells with Drosophila spike-in, tamoxifen-treated (72hr OHT), gDNA-seq


title: RING1B_WT_H2AK119ub1_rep1


title: PRC1CPM_TAM_NativeInput_rep2


title: PRC1CPM_TAM_NativeInput_rep1


title: PRC1CPM_UNT_NativeInput_rep2

source_name: Mouse embryonic stem cells with Drosophila spike-in, untreated control, gDNA-seq


title: PRC1CPM_UNT_NativeInput_rep3


title: PRC1CPM_UNT_NativeInput_rep1


title: RING1B_I53A_NativeInput_rep1


title: PRC1CKO_UNT_SUZ12_rep2


title: RING1B_I53A_H2AK119ub1_rep2


title: PRC1CPM_TAM_H3K27me3_rep3

source_name: Mouse embryonic stem cells with Drosophila spike-in, tamoxifen-treated (72hr OHT), H3K27me3 ChIP-seq

value: In house (Rose, 2016)


title: PRC1CPM_TAM_H3K27me3_rep2


title: PRC1CPM_TAM_H3K27me3_rep1


title: PRC1CPM_TAM_H2AK119ub1_rep3

source_name: Mouse embryonic stem cells with Drosophila spike-in, tamoxifen-treated (72hr OHT), H2AK119ub1 ChIP-seq


title: PRC1CPM_UNT_H3K27me3_rep2

source_name: Mouse embryonic stem cells with Drosophila spike-in, untreated control, H3K27me3 ChIP-seq


title: PRC1CPM_UNT_H3K27me3_rep1


title: PRC1CPM_UNT_H3K27me3_rep3


title: PRC1CPM_TAM_H2AK119ub1_rep2


title: PRC1CPM_UNT_H2AK119ub1_rep2

source_name: Mouse embryonic stem cells with Drosophila spike-in, untreated control, H2AK119ub1 ChIP-seq


title: Control_151022

city: Seattle

first: Julia Yue

last: Cui

state: WA

address: 4225 Roosevelt Way NE

department: Department of Environmental and Occupational Health Sciences

institute: University of Washington

data_processing:
Hierarchical Indexing for Spliced Alignment of Transcripts (HISAT) was used to align the RNA-Seq reads
Samtools was used to sort the bam files
DESeq2 was used to obtain normalized abundance measures

source_name: HepaRG

growth_protocol: The HepaRG cells were seeded at 2.6 × 104 cells/cm2 in six-well plates and grown in William’s medium E supplemented with growth medium supplement (Catalog #ADD711, Triangle Research Labs, NC), GlutaMAX-I (1X), 100 IU/ml penicillin, and 100 μg/ml streptomycin. The cells were cultured in differentiation medium for another 2 weeks.  The medium was renewed every 2 to 3 days.  Prior to the treatment, the cell medium was changed to induction medium (Williams’ medium E with induction supplement (HPRG740, Life Technologies, Carlsbad, CA) for 24 h..

extract_protocol:
RNA from these treated cells was isolated using RNA-Bee reagent (1 ml/well, Tel-Test Inc., Friendswood, Texas, Catalog No.) per manufacturers’ instructions
The library construction and sequencing were conducted using a similar method as described before (Li et. al., 2018). The cDNA libraries were constructed from total RNA samples using an Illumina TruSeq Stranded mRNA kit (Illumina, San Diego, CA).

treatment_protocol: The fully differentiated HepaRG cells were then treated with vehicle control (0.1% DMSO), CITCO (1 µM, Sigma-Aldrich), RIF (10 µM, Sigma-Aldrich), BDE-47 (25 µM, Chem Service Inc., West Chester, PA, Catalog No.), or BDE-99 (25 µM, AccuStandard Inc., New Haven, CT, Catalog No.) in triplicates for 24 hours

value: Liver derived cell line

tag: cell type

value: HepaRG

tag: passages


title: Control_151021


title: PRC1CPM_UNT_H2AK119ub1_rep1

tag: clone

tag: replicate


title: PRC1CPM_UNT_H2AK119ub1_rep3

tag: treatment agent

tag: treatment time point


title: Control_151020


title: PRC1CPM_TAM_H2AK119ub1_rep1

value: tamoxifen (OHT)

value: 72 hr


title: TIR1_AUX_CaptureC_rep2

description:
Cdh11_id3045509_Tir1_AUX_bg.bed_bg_sorted.bw
Ctdspl_id3399202_Tir1_AUX_bg.bed_bg_sorted.bw
Dlx2_id648162_Tir1_AUX_bg.bed_bg_sorted.bw
Dmbx1_id1596177_Tir1_AUX_bg.bed_bg_sorted.bw
Eomes_id3398229_Tir1_AUX_bg.bed_bg_sorted.bw
Fgf9_id4743707_Tir1_AUX_bg.bed_bg_sorted.bw
Fli1_id3186524_Tir1_AUX_bg.bed_bg_sorted.bw
Gata5_id916656_Tir1_AUX_bg.bed_bg_sorted.bw
Hcrtr1_id1632351_Tir1_AUX_bg.bed_bg_sorted.bw
Hoxb1_id3958722_Tir1_AUX_bg.bed_bg_sorted.bw
Hoxb2_id3958685_Tir1_AUX_bg.bed_bg_sorted.bw
Hoxb3_id3958676_Tir1_AUX_bg.bed_bg_sorted.bw
Hoxb5_id3958568_Tir1_AUX_bg.bed_bg_sorted.bw
Hoxd10_id655429_Tir1_AUX_bg.bed_bg_sorted.bw
Igfbp5_id174464_Tir1_AUX_bg.bed_bg_sorted.bw
Isl1_id4592795_Tir1_AUX_bg.bed_bg_sorted.bw
Islr2_id3250762_Tir1_AUX_bg.bed_bg_sorted.bw
Nkx2-1_id4153981_Tir1_AUX_bg.bed_bg_sorted.bw
Nkx2-2_id834429_Tir1_AUX_bg.bed_bg_sorted.bw
Nlgn1_id982921_Tir1_AUX_bg.bed_bg_sorted.bw
Nptx1_id4015617_Tir1_AUX_bg.bed_bg_sorted.bw
Pax7_id1656305_Tir1_AUX_bg.bed_bg_sorted.bw
Sp5_id645627_Tir1_AUX_bg.bed_bg_sorted.bw
Zfp503_id4652828_Tir1_AUX_bg.bed_bg_sorted.bw

data_processing:
Library strategy: CaptureC
For CaptureC, paired-end reads were aligned and filtered for HiC artefacts using HiCUP (Wingett S, et al. (2015)) and Bowtie2 (Langmead and Salzberg, 2012) with fragment filter set to 100-800bp. Read counts of reads aligning to captured gene promoters and interaction scores (=significant interactions) were then called  by CHiCAGO (Cairns et al., 2016).
For visualisation of CaptureC data weighted pooled read counts from chicago data files were normalized to total read count aligning to captured gene promoters in the sample and further to the number of promoters in the respective capture experiment. Bigwig files were generated from these normalized read counts.
For comparative boxplot analysis interactions called by chicago (score >= 5) across all samples were aggregated and interactions with a distance of less than 10 DpnII fragments were merged to a single interaction peak. For each interaction peak we then quantified mean normalized read count and chicago score of all overlapping DpnII fragments.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files showing the genome coverage of normalized read counts from merged biological replicates for each sample and each promoter were generated from CHiCAGO data object.
Supplementary_files_format_and_content: a text file with a list of bait Polycomb target sites used for CaptureC, detailing the genomic coordinates and sequences of oligonucleotides used to generate the capture probes
Supplementary_files_format_and_content: a text file containing genomic coordinates of interaction peaks which were annotated with normalisied read counts from merged biological replicates

source_name: Mouse embryonic stem cells , no degron control, auxin treated (6h),  CaptureC

extract_protocol:
CaptureC libraries were prepared as described previously (Hughes et al., Nature Genetics 2014). Briefly, 10 Million mouse ES cells were trypsinized, collected in 50ml falcon tubes in 9.3ml media and crosslinked with 1.25ml 16% formaldehyde for 10min at room temperature. Cells were quenched with 1.5M glycine, washed with PBS and lysed for 20 minutes at 4oC lysis buffer (10mM Tris pH 8, 10mM NaCl, 0.2% NP-40, supplemented with complete proteinase inhibitors) prior to snap freezing in 1ml lysis buffer at -80oC.
Lysates were then thawed on ice, pelleted and resuspended in 650µl 1x DpnII buffer (NEB). Three 1.5ml tubes with 200µl lysate each were treated in parallel with SDS (0.28% final concentration, 1hr, 37 oC, interval shaking 500rpm, 30sec on/30sec off), quenched with trypsin (1.67% final concentration, 1hr, 37 oC, interval shaking 500rpm, 30sec on/30sec off) and subjected to a 24 hour digestion with 3x10µl DpnII (homemade, 37 oC, interval shaking 500rpm, 30sec on/30sec off). Each chromatin aliquot was independently ligated with 8 µl T4 Ligase (240 U) in a volume of 1440µl (20 hours, 16oC). Following this, the nuclei containing ligated chromatin were pelleted to remove any non-nuclear chromatin, reverse-crosslinked and the ligated DNA was phenol-chloroform purified. The sample was resupended in 300µl water and sonicated 13x (Pico Bioruptor, 30sec on, 30sec off) or until a fragment size of approximately 200bp was reached. Fragments were size selected using AmpureX beads (Beckman Coulter: A63881, selection ratios: 0.85x / 0.4x). 2x 1-5µg of DNA were adaptor ligated and indexed using the NEBNext DNA library Prep Reagent Set (New England Biolabs: E6040S/L) and NEBNext Multiplex Oligos for Illumina Primer sets 1 (New England: E7335S/L) and 2 (New England: E7500S/L). The libraries were amplified 7x using Herculase II Fusion Polymerase kit (Agilent: 600677). Libraries were hybridized in teh following way: Probes were designed using the online tool by the Hughes lab (CapSequm: http://apps.molbiol.ox.ac.uk/CaptureC/cgi-bin/CapSequm.cgi) to be either 120bp (Sox2) or 70bp long each, two probes for each promoter of interest. The probes were pooled at a 2.9nM each and the samples were multiplexed by mass prior to hybridization. Hybridization was carried out using the Nimblegen SeqCap system (Roche, Nimblegen SeqCap EZ HE-oligo kit A # 06777287001, Nimblegen SeqCap EZ HE-oligo kit B # 06777317001, Nimblegen SeqCap EZ Accessory kit v2 # 07145594001, Nimblegen SeqCap EZ Hybridisation and wash kit # 05634261001) according to Roche protocol for 72 hours followed by a 24 hours hybridization (double Capture). The captured libraries were sequenced on Illumina NextSeq 500 as 81 bp paired-end reads.

treatment_protocol: To induce conditional removal of PRC1 catalytic activity in PRC1CPM ESC line, cells were treated with 800 nM 4-hydroxytamoxifen (TAM) for 72 hours. To induce degradation of RING1B in PRC1DEG cell line, cells were treated with 0.5 mM IAA (auxin) for 6 hours.

value: auxin (AUX)

value: 6 hr


title: BDE99_151029


title: PRC1DEG_AUX_CaptureC_rep3

description:
Cdh11_id3045509_Ring1b_AUX_bg.bed_bg_sorted.bw
Ctdspl_id3399202_Ring1b_AUX_bg.bed_bg_sorted.bw
Dlx2_id648162_Ring1b_AUX_bg.bed_bg_sorted.bw
Dmbx1_id1596177_Ring1b_AUX_bg.bed_bg_sorted.bw
Eomes_id3398229_Ring1b_AUX_bg.bed_bg_sorted.bw
Fgf9_id4743707_Ring1b_AUX_bg.bed_bg_sorted.bw
Fli1_id3186524_Ring1b_AUX_bg.bed_bg_sorted.bw
Gata5_id916656_Ring1b_AUX_bg.bed_bg_sorted.bw
Hcrtr1_id1632351_Ring1b_AUX_bg.bed_bg_sorted.bw
Hoxb1_id3958722_Ring1b_AUX_bg.bed_bg_sorted.bw
Hoxb2_id3958685_Ring1b_AUX_bg.bed_bg_sorted.bw
Hoxb3_id3958676_Ring1b_AUX_bg.bed_bg_sorted.bw
Hoxb5_id3958568_Ring1b_AUX_bg.bed_bg_sorted.bw
Hoxd10_id655429_Ring1b_AUX_bg.bed_bg_sorted.bw
Igfbp5_id174464_Ring1b_AUX_bg.bed_bg_sorted.bw
Isl1_id4592795_Ring1b_AUX_bg.bed_bg_sorted.bw
Islr2_id3250762_Ring1b_AUX_bg.bed_bg_sorted.bw
Nkx2-1_id4153981_Ring1b_AUX_bg.bed_bg_sorted.bw
Nkx2-2_id834429_Ring1b_AUX_bg.bed_bg_sorted.bw
Nlgn1_id982921_Ring1b_AUX_bg.bed_bg_sorted.bw
Nptx1_id4015617_Ring1b_AUX_bg.bed_bg_sorted.bw
Pax7_id1656305_Ring1b_AUX_bg.bed_bg_sorted.bw
Sp5_id645627_Ring1b_AUX_bg.bed_bg_sorted.bw
Zfp503_id4652828_Ring1b_AUX_bg.bed_bg_sorted.bw

source_name: Mouse embryonic stem cells , with degron, auxin treated (6h),  CaptureC

value: Tir1; Ring1a-/-; Ring1bAID


title: PRC1DEG_AUX_CaptureC_rep2


title: TIR1_AUX_CaptureC_rep1


title: TIR1_AUX_CaptureC_rep3


title: PRC1DEG_AUX_CaptureC_rep1


title: BDE99_151027


title: BDE47_151032


title: PRC1CPM_TAM_CaptureC_rep2

description:
Cdh11_id3045509_CPM_TAM_bg.bed_bg_sorted.bw
Ctdspl_id3399202_CPM_TAM_bg.bed_bg_sorted.bw
Dlx2_id648162_CPM_TAM_bg.bed_bg_sorted.bw
Dmbx1_id1596177_CPM_TAM_bg.bed_bg_sorted.bw
Eomes_id3398229_CPM_TAM_bg.bed_bg_sorted.bw
Fgf9_id4743707_CPM_TAM_bg.bed_bg_sorted.bw
Fli1_id3186524_CPM_TAM_bg.bed_bg_sorted.bw
Gata5_id916656_CPM_TAM_bg.bed_bg_sorted.bw
Hcrtr1_id1632351_CPM_TAM_bg.bed_bg_sorted.bw
Hoxb1_id3958722_CPM_TAM_bg.bed_bg_sorted.bw
Hoxb2_id3958685_CPM_TAM_bg.bed_bg_sorted.bw
Hoxb3_id3958676_CPM_TAM_bg.bed_bg_sorted.bw
Hoxb5_id3958568_CPM_TAM_bg.bed_bg_sorted.bw
Hoxd10_id655429_CPM_TAM_bg.bed_bg_sorted.bw
Igfbp5_id174464_CPM_TAM_bg.bed_bg_sorted.bw
Isl1_id4592795_CPM_TAM_bg.bed_bg_sorted.bw
Islr2_id3250762_CPM_TAM_bg.bed_bg_sorted.bw
Nkx2-1_id4153981_CPM_TAM_bg.bed_bg_sorted.bw
Nkx2-2_id834429_CPM_TAM_bg.bed_bg_sorted.bw
Nlgn1_id982921_CPM_TAM_bg.bed_bg_sorted.bw
Nptx1_id4015617_CPM_TAM_bg.bed_bg_sorted.bw
Pax7_id1656305_CPM_TAM_bg.bed_bg_sorted.bw
Sp5_id645627_CPM_TAM_bg.bed_bg_sorted.bw
Zfp503_id4652828_CPM_TAM_bg.bed_bg_sorted.bw

source_name: Mouse embryonic stem cells , tamoxifen-treated (72hr OHT), CaptureC


title: PRC1CPM_TAM_CaptureC_rep1


title: PRC1CPM_UNT_CaptureC_rep3

description:
Cdh11_id3045509_CPM_UNT_bg.bed_bg_sorted.bw
Ctdspl_id3399202_CPM_UNT_bg.bed_bg_sorted.bw
Dlx2_id648162_CPM_UNT_bg.bed_bg_sorted.bw
Dmbx1_id1596177_CPM_UNT_bg.bed_bg_sorted.bw
Eomes_id3398229_CPM_UNT_bg.bed_bg_sorted.bw
Fgf9_id4743707_CPM_UNT_bg.bed_bg_sorted.bw
Fli1_id3186524_CPM_UNT_bg.bed_bg_sorted.bw
Gata5_id916656_CPM_UNT_bg.bed_bg_sorted.bw
Hcrtr1_id1632351_CPM_UNT_bg.bed_bg_sorted.bw
Hoxb1_id3958722_CPM_UNT_bg.bed_bg_sorted.bw
Hoxb2_id3958685_CPM_UNT_bg.bed_bg_sorted.bw
Hoxb3_id3958676_CPM_UNT_bg.bed_bg_sorted.bw
Hoxb5_id3958568_CPM_UNT_bg.bed_bg_sorted.bw
Hoxd10_id655429_CPM_UNT_bg.bed_bg_sorted.bw
Igfbp5_id174464_CPM_UNT_bg.bed_bg_sorted.bw
Isl1_id4592795_CPM_UNT_bg.bed_bg_sorted.bw
Islr2_id3250762_CPM_UNT_bg.bed_bg_sorted.bw
Nkx2-1_id4153981_CPM_UNT_bg.bed_bg_sorted.bw
Nkx2-2_id834429_CPM_UNT_bg.bed_bg_sorted.bw
Nlgn1_id982921_CPM_UNT_bg.bed_bg_sorted.bw
Nptx1_id4015617_CPM_UNT_bg.bed_bg_sorted.bw
Pax7_id1656305_CPM_UNT_bg.bed_bg_sorted.bw
Sp5_id645627_CPM_UNT_bg.bed_bg_sorted.bw
Zfp503_id4652828_CPM_UNT_bg.bed_bg_sorted.bw

source_name: Mouse embryonic stem cells , untreated control, CaptureC


title: BDE47_151031


title: PRC1CPM_UNT_CaptureC_rep2


title: BDE47_151030


title: RIF_151024


title: BDE99_151028


title: RIF_151023


title: TW2_pos_animal4_scRNA-seq

city: Dallas

first: Yi-Li

last: Min

state: Texas

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: UT Southwestern Medical Center

data_processing:
convert 10x BAM sequenc file into fastq file with cellranger mkfastq
Aligment to mm10 genome with cellranger count
Genome_build: mm10
Supplementary_files_format_and_content: h5 count matrix

extract_protocol:
FACS
10x single cell genomics

treatment_protocol: 10 days post TMX treatment

value: Heart non-CMs

tag: age

value: 9 weeks

value: Tw2-CreERT2; R26-tdTO


title: TW2_pos_animal3_scRNA-seq


title: TW2_pos_animal1_scRNA-seq


title: PRC1CPM_TAM_CaptureC_rep3


title: CITCO_151025


title: TW2_pos_animal2_scRNA-seq


title: CITCO_151026


title: NAc_mRNA_TAL5

city: Worcester

first: Alper

last: Kucukural

state: MA

address: 364 Plantation Street

department: Program in Molecular Medicine

institute: UMass Medical School

data_processing:
miRNA Mapping: The 3¢-adapter sequence was removed using Cutadapt (version 1.11) with ‘–overlap’ option 7bp. Reads between 15-27 nucleotides long were mapped to mm10 using Bowtie (version 1.1.2) allowing for no mismatches. miRNA reads ±5 nucleotides from the mature, annotated 5¢ start position were counted. Reads mapping to multiple locations on a single mature miRNA were recorded as a single count, and reads mapped to multiple mature miRNAs were apportioned by the number of the aligned mature miRNAs.
mRNA Mapping: Reads were mapped to the mm10 reference genome using STAR (version 2.5.3a) and mapped reads were quantified with RSEM (version 1.3.0)
Differential Expression analysis: Samples were normalized using RUV-Seq (version 1.8.0) removing unwanted variables including batch effects. Differential expression analysis was performed using DESeq2 (version 1.14.1).
Genome_build: mm10
Supplementary_files_format_and_content: xlsx tables

source_name: Nucleus accumbens tissue punch

extract_protocol:
The IPN and MHb were dissected by a single midline circular tissue punch (0.75 mm diameter). Punches from 4 animals were pooled for each sample and total RNA was isolated using a miRVANA miRNA isolation kit (Ambion). Small RNAs (18-30 nt) were separated from the sample by denaturing gel electrophoresis. The small RNA pool was used to generate miRNA-Seq libraries and the remaining RNAs (> 30 nt) were used to generate stranded mRNA-Seq libraries.
Small RNA libraries were synthesized using a modified protocol for Illumina TruSeq Small RNA Cloning (April 2014, www.zamorlab.umassmed.edu/protocols/). mRNA-Seq libraries were synthesized using the TruSeq Stranded mRNA Library Prep kit (Illumina) according to manufacturer’s instructions. All libraries were gel-purified, assessed by Fragment Analyzer (Advanced Analytical, AATI) and their concentrations were quantified using KAPA Library Quantification Kits (KAPA Biosystems).
miRNA-Seq libraries were pooled and single-end (75 cycles) sequencing was performed. mRNA-Seq libraries were pooled and paired-end (76 cycles x 2) sequencing was performed.

treatment_protocol: Male C5BL/6J mice were treated with nicotine tartrate (NIC, 200 g/ml nicotine base) or equivalent tartaric acid (TA) in their drinking water with saccharine (3 g/L) to increase palatability starting at 6 weeks of age. After 6 weeks, mice in spontaneous withdrawal groups had nicotine bottles replaced with tartaric acid solution for a withdrawal period of 48 hours (NAWD) or 4 weeks (NLWD). An additional age-matched control group for NLWD was treated with TA solution for 10 weeks (TAL).

value: Nucleus accumbens tissue punch

tag: condition

value: Long tartaric acid control


title: IPN_mRNA_NAWD5

source_name: Interpeduncular nucleus  tissue punch

value: Interpeduncular nucleus  tissue punch

value: Acute nicotine withdrawal


title: IPN_mRNA_TA5

value: Chronic tartaric acid control


title: RNA-seq_s-s41

city: Beijing

first: Jiangping

last: Song

address: 167A Beilishi Road, Xi Cheng District

department: Department of Cardiac Surgery

country: China

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

description:
name in processed data file:
Sample 30

data_processing:
For RNA-seq analysis, sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38.p11 annotation using HISAT2 (version 2.1.0) .The Fragments Per Kilobase of transcript per Million mapped reads (FPKM) value of the  transcripts was calculated based on StringTie (version 1.3.4) with default parameters.
For small RNA-seq dataset, the reads were first subjected to adapter removal through the Cutadapt program. The known mature miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs according to the miRNA sequence database miRbase  (Release 22).
Genome_build: RNA-seq: GRCh38.p11; SmallRNA-seq: miRBase (Release 22)
Supplementary_files_format_and_content: Merged file: tab-delimited text files include FPKM values for RNAseq and read counts for small RNA-seq for each Sample.

source_name: Healthy donor

extract_protocol:
The total RNA was extracted with the Trizol protocol from the frozen LV samples. RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA) and RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). Only RNA samples with a total amount of at least 6μg and RNA integrity number (RIN) of at least 6.9 (range: 6.9 to 8.5, mean±SD: 7.9±0.4) were used for subsequent library construction and sequencing.
For RNA, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. Briefly, fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPs with dTTP were replaced by dUTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37° C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina Hiseq 2500 platform and 150 bp paired-end reads were generated.
For small RNA, sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, NEB 3' SR Adaptor was directly, and specifically ligated to 3' end of miRNA, siRNA and piRNA. After the 3' ligation reaction, the SR RT Primer hybridized to the excess of 3' SR Adaptor (that remained free after the 3' ligation reaction) and transformed the single-stranded DNA adaptor into a double-stranded DNA molecule. This step is important to prevent adaptor-dimer formation, besides, dsDNAs are not substrates for ligation mediated by T4 RNA Ligase 1 and therefore do not ligate to the 5´ SR Adaptor in the subsequent ligation step. 5´ends adapter was ligated to 5´ends of miRNAs, siRNA and piRNA. Then first strand cDNA was synthesized using M-MuLV Reverse Transcriptase (RNase H–). PCR amplification was performed using LongAmp Taq 2X Master Mix, SR Primer for Illumina and index (X) primer. PCR products were purified on an 8% polyacrylamide gel (100V, 80 min). DNA fragments corresponding to 140~160 bp (the length of small noncoding RNA plus the 3' and 5' adaptors) were recovered and dissolved in 8 μL elution buffer. At last, library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq SR Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2500 platform and 50 bp single-end reads were generated.

treatment_protocol: All the HF patients received standard medication treatment without mitral valve modeling

value: left ventricular heart tissue

tag: diagnosis

value: Not available

tag: Sex

value: M

tag: nyha

tag: smoking history

tag: ph

tag: lvef (%)

tag: total amount (ug)

tag: rin


title: IPN_mRNA_Nic5

tag: strain

tag: tissue

value: Chronic nicotine


title: RNA-seq_s-s39

description:
name in processed data file:
Sample 29


title: NAc_mRNA_TAL4


title: RNA-seq_s-s5

description:
name in processed data file:
Sample 25


title: RNA-seq_s-s6

description:
name in processed data file:
Sample 26


title: RNA-seq_s-s37

description:
name in processed data file:
Sample 27


title: RNA-seq_s-s4

description:
name in processed data file:
Sample 24


title: NAc_mRNA_TAL2


title: NAc_mRNA_TAL1


title: RNA-seq_s-s3

description:
name in processed data file:
Sample 23


title: PRC1CPM_UNT_CaptureC_rep1

tag: cell line

tag: genotype

value: 0 hr


title: NAc_mRNA_NLWD5

value: Long nicotine withdrawal


title: RNA-seq_s-s2

description:
name in processed data file:
Sample 22


title: NAc_mRNA_NLWD4


title: RNA-seq_s-s38

description:
name in processed data file:
Sample 28


title: RNA-seq_s-s29

description:
name in processed data file:
Sample 21

source_name: Heart failure

value: Mcd

value: Ⅳ

value: Y


title: RNA-seq_s-s28

description:
name in processed data file:
Sample 20

value: Ⅲ

value: N


title: RNA-seq_s-s27

description:
name in processed data file:
Sample 19


title: NAc_mRNA_NLWD3


title: NAc_mRNA_NLWD2


title: RNA-seq_s-s25

description:
name in processed data file:
Sample 17

value: DCM

value: F


title: RNA-seq_s-s24

description:
name in processed data file:
Sample 16


title: NAc_mRNA_TA5

value: Nucleus accumbens tissue punch


title: NAc_mRNA_TA4


title: RNA-seq_s-s26

description:
name in processed data file:
Sample 18

value: Ⅱ


title: NAc_mRNA_TA3


title: NAc_mRNA_TA2


title: NAc_mRNA_Nic5


title: NAc_mRNA_Nic4


title: RNA-seq_s-s21

description:
name in processed data file:
Sample 14


title: RNA-seq_s-s19

description:
name in processed data file:
Sample 12


title: RNA-seq_s-s17

description:
name in processed data file:
Sample 11


title: RNA-seq_s-s20

description:
name in processed data file:
Sample 13


title: NAc_mRNA_TAL3

value: Long tartaric acid control


title: RNA-seq_s-s16

description:
name in processed data file:
Sample 10


title: RNA-seq_s-s15

description:
name in processed data file:
Sample 9


title: RNA-seq_s-s14

description:
name in processed data file:
Sample 8


title: NAc_mRNA_Nic2


title: NAc_mRNA_Nic1


title: RNA-seq_s-s13

description:
name in processed data file:
Sample 7


title: NAc_mRNA_NLWD1


title: NAc_mRNA_NAWD4

value: Acute nicotine withdrawal


title: RNA-seq_s-s12

description:
name in processed data file:
Sample 6

value: left ventricular heart tissue


title: RNA-seq_s-s22

description:
name in processed data file:
Sample 15


title: RNA-seq_s-s10

description:
name in processed data file:
Sample 4


title: NAc_mRNA_NAWD1


title: RNA-seq_s-s9

description:
name in processed data file:
Sample 3


title: NAc_mRNA_TA1

value: Chronic tartaric acid control


title: MHb_mRNA_TAL4

source_name: Medial habenula tissue punch

value: Medial habenula tissue punch


title: RNA-seq_s-s8

description:
name in processed data file:
Sample 2

value: M


title: miRNA-seq_s-s41

description:
name in processed data file:
Sample 30

value: Not available


title: MHb_mRNA_TAL3


title: NAc_mRNA_Nic3

value: Chronic nicotine


title: MHb_mRNA_TAL2


title: miRNA-seq_s-s39

description:
name in processed data file:
Sample 29


title: MHb_mRNA_NLWD5

value: Long nicotine withdrawal


title: miRNA-seq_s-s37

description:
name in processed data file:
Sample 27


title: miRNA-seq_s-s38

description:
name in processed data file:
Sample 28


title: MHb_mRNA_NLWD4


title: RNA-seq_s-s11

description:
name in processed data file:
Sample 5

value: Ⅳ


title: miRNA-seq_s-s6

description:
name in processed data file:
Sample 26


title: MHb_mRNA_NLWD2


title: NAc_mRNA_NAWD3


title: NAc_mRNA_NAWD2


title: MHb_mRNA_NLWD3


title: miRNA-seq_s-s4

description:
name in processed data file:
Sample 24


title: miRNA-seq_s-s2

description:
name in processed data file:
Sample 22


title: miRNA-seq_s-s5

description:
name in processed data file:
Sample 25


title: MHb_mRNA_TA4


title: miRNA-seq_s-s3

description:
name in processed data file:
Sample 23


title: MHb_mRNA_NLWD1


title: MHb_mRNA_TA3


title: RNA-seq_s-s7

description:
name in processed data file:
Sample 1


title: MHb_mRNA_TAL5


title: MHb_mRNA_TA2


title: miRNA-seq_s-s29

description:
name in processed data file:
Sample 21

value: Mcd

value: Y


title: miRNA-seq_s-s28

description:
name in processed data file:
Sample 20

value: Ⅲ

value: N


title: MHb_mRNA_TAL1


title: MHb_mRNA_TA1


title: miRNA-seq_s-s27

description:
name in processed data file:
Sample 19


title: MHb_mRNA_Nic4


title: miRNA-seq_s-s26

description:
name in processed data file:
Sample 18

value: DCM


title: MHb_mRNA_Nic3


title: miRNA-seq_s-s24

description:
name in processed data file:
Sample 16


title: MHb_mRNA_Nic2


title: miRNA-seq_s-s25

description:
name in processed data file:
Sample 17

value: F


title: miRNA-seq_s-s22

description:
name in processed data file:
Sample 15


title: miRNA-seq_s-s21

description:
name in processed data file:
Sample 14


title: MHb_mRNA_NAWD4


title: MHb_mRNA_Nic1


title: miRNA-seq_s-s20

description:
name in processed data file:
Sample 13


title: miRNA-seq_s-s19

description:
name in processed data file:
Sample 12


title: miRNA-seq_s-s17

description:
name in processed data file:
Sample 11

value: Ⅱ


title: miRNA-seq_s-s16

description:
name in processed data file:
Sample 10


title: MHb_mRNA_NAWD3


title: miRNA-seq_s-s15

description:
name in processed data file:
Sample 9


title: IPN_mRNA_TA4

value: Interpeduncular nucleus  tissue punch


title: MHb_mRNA_NAWD2

value: Acute nicotine withdrawal


title: MHb_mRNA_NAWD1


title: miRNA-seq_s-s13

description:
name in processed data file:
Sample 7

value: left ventricular heart tissue


title: IPN_mRNA_TA2

value: Chronic tartaric acid control


title: IPN_mRNA_TA3


title: miRNA-seq_s-s12

description:
name in processed data file:
Sample 6


title: IPN_mRNA_TA1


title: miRNA-seq_s-s14

description:
name in processed data file:
Sample 8


title: IPN_mRNA_Nic3


title: IPN_mRNA_Nic2


title: miRNA-seq_s-s11

description:
name in processed data file:
Sample 5


title: miRNA-seq_s-s10

description:
name in processed data file:
Sample 4


title: IPN_mRNA_NAWD4


title: miRNA-seq_s-s9

description:
name in processed data file:
Sample 3


title: miRNA-seq_s-s7

description:
name in processed data file:
Sample 1


title: IPN_mRNA_NAWD3


title: IPN_mRNA_NAWD2


title: G50T2_CardiogenicShock

city: Milano

first: Matteo

last: Barcella

address: Via Olgettina 60

country: Italy

institute: SR-TIGET

description:
Ribo and Globin depleted library
processed data file: rawcounts_CS_SS.xlsx

data_processing:
Basecalls performed using CASAVA version 1.8.2
Trimming performed with Trimmomatic v0.35, with following parameters: MINLEN:40, AVGQUAL:25 and TRAILING:15
Trimmed reads aligned to GRCh38 using STAR v.2.5.2b using as reference transcript the gencode (v.25) primary assembly gene transfer file (GTF).
Gene counting performed on files including only uniquely mapped fragments using featurecounts v1.5.1 with custom parameters: --minOverlap 5; only both reads, no multimapping.
Genome_build: GRCh38
Supplementary_files_format_and_content: excel file including raw counts for each sample (columns) across 58096 genes (rows) [counts matrix]

source_name: CardiogenicShock_T2_whole blood

extract_protocol:
Peripheral blood was collected in EDTA tubes at T1,T2 and T3 and stored at -20°C after adding 400µl of 2X Denaturing solution (Ambion, USA).Total RNA was extracted from 800 µl of blood with MirVana Paris Kit and treated with Turbo DNA-free Kit (Ambion, USA). RNA Quality was assessed on Agilent Bioanalyzer with the RNA 6000 Nano Kit (Agilent, Santa Clara, CA) and samples were considered suitable for processing if RNA Integrity Number was greater than 7.5
Sequencing libraries were prepared with the TruSeq Stranded Total RNA with Ribo-Zero Globin Kit (Illumina, San Diego, CA) using 800 ng of total RNA

tag: patient

tag: timepoint

tag: clinical classification

value: CS

value: Whole blood


title: G50T3_CardiogenicShock

source_name: CardiogenicShock_T3_whole blood


title: IPN_mRNA_TAL4

value: Long tartaric acid control


title: IPN_mRNA_NAWD1


title: IPN_mRNA_TAL3


title: G48T1_CardiogenicShock

source_name: CardiogenicShock_T1_whole blood


title: G48T2_CardiogenicShock


title: G50T1_CardiogenicShock


title: IPN_mRNA_TAL1


title: IPN_mRNA_Nic4

value: Chronic nicotine


title: G46T3_CardiogenicShock


title: G48T3_CardiogenicShock


title: IPN_mRNA_NLWD5

value: Long nicotine withdrawal


title: IPN_mRNA_NLWD2


title: NAc_miRNA_TAL5

value: Nucleus accumbens tissue punch


title: NAc_miRNA_TAL4


title: G46T1_CardiogenicShock


title: NAc_miRNA_TAL3


title: miRNA-seq_s-s8

description:
name in processed data file:
Sample 2

value: M

tag: age

value: Ⅳ


title: NAc_miRNA_TAL2

tag: condition


title: G32T2_CardiogenicShock


title: G32T1_CardiogenicShock


title: G24T3_CardiogenicShock


title: NAc_miRNA_NLWD5


title: NAc_miRNA_TAL1


title: G24T2_CardiogenicShock


title: G24T1_CardiogenicShock


title: NAc_miRNA_NLWD3


title: NAc_miRNA_NLWD4


title: G16T2_CardiogenicShock


title: G14T1_CardiogenicShock


title: NAc_miRNA_TA4


title: NAc_miRNA_TA3


title: G46T2_CardiogenicShock


title: NAc_miRNA_NLWD1


title: G16T1_CardiogenicShock


title: G14T2_CardiogenicShock


title: NAc_miRNA_TA2


title: NAc_miRNA_TA5


title: G10T3_CardiogenicShock


title: G16T3_CardiogenicShock


title: G32T3_CardiogenicShock


title: G14T3_CardiogenicShock


title: NAc_miRNA_TA1


title: NAc_miRNA_Nic5


title: NAc_miRNA_Nic4


title: G10T2_CardiogenicShock


title: G10T1_CardiogenicShock


title: NAc_miRNA_Nic2


title: NAc_miRNA_Nic1


title: E31T2_CardiogenicShock


title: E31T1_CardiogenicShock


title: NAc_miRNA_NLWD2


title: E25T3_CardiogenicShock


title: E25T2_CardiogenicShock


title: NAc_miRNA_NAWD6


title: G49T3_SepticShock

source_name: SepticShock_T3_whole blood

value: SS


title: NAc_miRNA_NAWD5


title: NAc_miRNA_NAWD4


title: E25T1_CardiogenicShock


title: G49T1_SepticShock [re-analysis]

source_name: SepticShock_T1_whole blood


title: G47T3_SepticShock


title: NAc_miRNA_NAWD3


title: MHb_miRNA_TAL5

value: Medial habenula tissue punch


title: MHb_miRNA_TAL3


title: MHb_miRNA_TAL4


title: G49T2_SepticShock [re-analysis]

source_name: SepticShock_T2_whole blood


title: E31T3_CardiogenicShock


title: G47T2_SepticShock [re-analysis]


title: NAc_miRNA_NAWD1


title: G45T3_SepticShock


title: G47T1_SepticShock [re-analysis]


title: NAc_miRNA_Nic3


title: IPN_mRNA_Nic1


title: MHb_miRNA_TAL2


title: G45T2_SepticShock [re-analysis]


title: MHb_miRNA_TAL1


title: G45T1_SepticShock [re-analysis]


title: MHb_miRNA_NLWD3


title: MHb_miRNA_NLWD5


title: MHb_miRNA_NLWD4


title: G44T2_SepticShock [re-analysis]


title: G44T1_SepticShock [re-analysis]


title: MHb_miRNA_NLWD2


title: G43T3_SepticShock


title: MHb_miRNA_TA5


title: MHb_miRNA_TA3


title: MHb_miRNA_TA4


title: MHb_miRNA_TA2


title: G43T2_SepticShock [re-analysis]


title: G35T3_SepticShock


title: MHb_miRNA_TA1


title: G42T3_SepticShock


title: MHb_miRNA_Nic2


title: MHb_miRNA_Nic3


title: G33T3_SepticShock


title: G42T2_SepticShock [re-analysis]


title: G35T1_SepticShock [re-analysis]


title: MHb_miRNA_Nic4


title: G43T1_SepticShock [re-analysis]


title: MHb_miRNA_Nic1


title: G42T1_SepticShock [re-analysis]


title: G35T2_SepticShock [re-analysis]


title: G44T3_SepticShock


title: MHb_miRNA_Nic5


title: MHb_miRNA_NAWD5


title: MHb_miRNA_NAWD4


title: G33T2_SepticShock [re-analysis]


title: MHb_miRNA_NLWD1


title: G33T1_SepticShock [re-analysis]


title: G29T3_SepticShock


title: MHb_miRNA_NAWD3


title: G29T2_SepticShock [re-analysis]


title: MHb_miRNA_NAWD2


title: MHb_miRNA_NAWD1


title: IPN_miRNA_TAL5


title: IPN_miRNA_TAL4


title: G26T2_SepticShock


title: IPN_miRNA_TAL1


title: IPN_miRNA_TAL2


title: IPN_miRNA_TAL3


title: G26T3_SepticShock


title: IPN_miRNA_NLWD3


title: G12T2_SepticShock [re-analysis]


title: IPN_miRNA_NLWD2


title: G26T1_SepticShock


title: G28T1_SepticShock [re-analysis]


title: IPN_miRNA_NLWD1


title: G11T3_SepticShock


title: G12T3_SepticShock


title: IPN_miRNA_NLWD5


title: G28T2_SepticShock [re-analysis]


title: IPN_miRNA_NLWD4


title: IPN_miRNA_TA5


title: G11T2_SepticShock [re-analysis]


title: G11T1_SepticShock [re-analysis]


title: E41T3_SepticShock


title: G29T1_SepticShock [re-analysis]


title: G28T3_SepticShock


title: IPN_miRNA_TA2


title: E41T1_SepticShock [re-analysis]


title: IPN_miRNA_TA1


title: E40T3_SepticShock


title: IPN_miRNA_NIC5


title: E32T3_SepticShock


title: E40T1_SepticShock [re-analysis]


title: IPN_miRNA_NIC2


title: IPN_miRNA_NIC3


title: G12T1_SepticShock [re-analysis]


title: IPN_miRNA_TA4


title: E32T1_SepticShock [re-analysis]


title: E40T2_SepticShock [re-analysis]


title: E17T2_SepticShock [re-analysis]


title: E17T3_SepticShock


title: E32T2_SepticShock [re-analysis]


title: IPN_miRNA_NAWD1


title: E16T3_SepticShock


title: IPN_miRNA_NAWD2


title: IPN_miRNA_NAWD3


title: IPN_miRNA_NAWD5


title: E41T2_SepticShock [re-analysis]


title: E16T2_SepticShock [re-analysis]


title: E16T1_SepticShock [re-analysis]


title: Tumor GNP cell 6496-b_cul

city: Charlottesville

first: Kevin

middle: A.

last: Janes

state: VA

address: Box 800759 Health System

department: Department of Biomedical Engineering

institute: University of Virginia

data_processing:
Adaptor Trimming by bioconductor
Initial quality assessment of sequencing reads using FastQC
Genome alignment with STAR
Genome_build: mm10
Supplementary_files_format_and_content: counts

extract_protocol:
The laser capture microdissection (LCM) experiment was designed and modified according to previous studies (Janes et al., 2010; Wang and Janes, 2013). Briefly, tumor brains were removed and slowly lowered into liquid nitrogen-cooled methyl-butane. Keep fully submerged for 1 minute then store at -80ºC. Tumor tissue was cut at 8 μm thickness on a cryostat and sections were collected on positively-charged slides. Slides were fixed in 100% ethanol for 5 minutes at room temperature and then transferred into 100% xylene for 5 minutes at room temperature. Slide was then air-dried for 5 minutes. Laser capture microdissection of individual cells was performed on an ArcturusXT LCM system (Applied Biosystems) with an infrared laser using CapSure HS LCM caps after optimization of laser power and duration.
Reamplified cDNA (~500 bp 3’ ends) was tagmented with the Nextera XT kit (Illumina)

tag: cell type

value: Tumor GNP cell

tag: rna extraction methods

value: Laser capture microdissection


title: E07T3_SepticShock


title: IPN_miRNA_NIC4


title: E17T1_SepticShock [re-analysis]


title: Tumor GNP cell 5980_cul


title: IPN_miRNA_NAWD4


title: E07T1_SepticShock [re-analysis]


title: Tumor GNP cell 679_cul

source_name: 679 cul


title: Tumor-derived astrocyte 6494_YA

value: Tumor-derived astrocyte


title: Tumor-derived astrocyte 6636_YA


title: IPN_miRNA_NIC1

value: Interpeduncular nucleus  tissue punch


title: Normal astrocyte 6281_AD

value: Normal astrocyte


title: Aged rep9

city: Cambridge

first: Laura

last: Woods

address: Babraham Hall

institute: The Babraham Institute

description: Sample 19

data_processing:
Raw FastQ data were trimmed with Trim Galore (v0.3.8, default parameters;  www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and mapped to the Homo sapiens GRCh38 genome assembly using TopHat v2.0.12. Raw counts for DESeq2 analysis were generated at mRNA level using SeqMonk software (www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw counts RNA-Seq data files are tab-delimited and contain the following  columns: (1) Gene ID; (2) Chromosome; (3) Start; (4) End; (5) Strand; (6) Description; (7-40) Raw Counts for each sample

source_name: Human endometrium

extract_protocol:
Biopsies were timed between 5-13 days post-LH surge according to home ovulation tests.  Endometrial biopsies were obtained using a Wallach Endocell® endometrial sampler.  The device was introduced into the uterus until resistance from the fundus was felt. The piston was withdrawn to generate negative pressure and the device rotated through 360° as it was gradually withdrawn from the fundus to the cervical ostium.
Total RNA was extracted using the Allprep DNA/RNA Mini kit (Qiagen 80204).
mRNA was isolated from total DNA-free RNA (350ng) using the Dynabeads mRNA purification kit (Life Technologies 61006). Indexed, strand specific libraries were prepared using the ScriptSeq v2 RNA-Seq Library Preparation kit (Epicentre SSV21106) according to the manufacturer's instructions. Libraries were quantified/assessed using both the KAPA Library Quantification Kit (KAPA Biosystems KK4824) and Bioanalyzer 2100 system (Agilent). Indexed libraries were pooled and sequenced with a 100bp single-end protocol on an Illumina HiSeq2500 sequencer.

tag: ID

tag: age (years)

tag: day of cycle


title: Aged rep10

description: Sample 20


title: Tumor-derived astrocyte 6409_YA


title: Tumor-derived astrocyte 6637_YA


title: Aged rep4

description: Sample 14


title: Aged rep5

description: Sample 15


title: Aged rep7

description: Sample 17


title: Aged rep6

description: Sample 16


title: Normal astrocyte 6284_AD


title: Normal astrocyte 5171_AD


title: Aged rep2

description: Sample 12


title: HUVEC_Input_n3_FM [ChIP-seq]

city: Frankfurt

first: David

last: John

state: Hessen

address: Theodor-Stern-Kai 7

country: Germany

institute: Institute for Cardiovascular Regeneration

description: Input in full medium

data_processing:
Chip-Seq: The samples were sequenced on  Illumina NextSeq hardware and assessed for quality using FastQC (Andrews S. 2010,  FastQC: a quality control tool for high throughput sequence data. Available online at:  http://www.bioinformatics.babraham.ac.uk/projects/fastqc) or used for qRT-PCR analysis  with the primers described before. Reads were trimmed using fastx-trimmer  (http://hannonlab.cshl.edu/fastx_toolkit/). Trimmed sequences were mapped to the  GRCH38 version of the human genome with STAR 2.4.2a 4 using only unique alignments  to exclude reads with unclear placing. PCR duplicates were removed using Picard 1.136  (Picard: A set of tools (in Java) for working with next generation sequencing data in the  BAM format; http://broadinstitute.github.io/picard/) to avoid PCR artefacts leading to  multiple copies of the same original fragment. Peaks were called using homer findPeaks  version 4.0311 with parameter –region to combine close peaks. The minimum distance and size of peaks for H3K9me3 were set to -size 2000 and –minDist 10000
Data were filtered using the following specifications:
RNA:SEQ: Base calling and FASTQ were done with  Illumina's HiSeq Control Software version 1.5.15.1 (RTA v1.13.18 and bclfastq v1.8.3).  Sequenced reads were mapped to the mouse reference genome with TopHat version  2.0.5, and differentially expressed genes were assessed by use of Cuffdiff, a part of the  Cufflinks version 2.1.1 package.
Cellular suspensions were loaded on a 10X Chromium Controller (10X Genomics) according to manufacturer’s protocol based on the 10X Genomics proprietary technology13. HUVEC study and murine scRNA-seq libraries were prepared using Chromium Single Cell 3′ v2 Reagent Kit and Chromium Single Cell 3′ v3 Reagent Kit, respectively (10X Genomics), according to manufacturer’s protocols. Briefly, the initial step consisted in performing an emulsion where individual cells were isolated into droplets together with gel beads coated with unique primers bearing 10X cell barcodes, UMI (unique molecular identifiers) and poly(dT) sequences. Reverse transcription reactions were engaged to generate barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads MyOne Silane Beads (Thermo Fisher Scientific). Bulk cDNA was amplified using a Biometra Thermocycler Professional Basic Gradient with 96-Well Sample Block (98°C for 3 minutes; cycled 14×: 98°C for 15 s, 67°C for 20 s, and 72°C for 1 minute; 72°C for 1 minute; held at 4°C). Amplified cDNA product was cleaned with the SPRIselect Reagent Kit (Beckman Coulter). Indexed sequencing libraries were constructed using the reagents from the Chromium Single Cell 3′ v2 and Chromium Single Cell 3′ v3 Reagent Kits as follows: fragmentation, end repair and A-tailing; size selection with SPRIselect; adaptor ligation; post-ligation cleanup with SPRIselect; sample index PCR and cleanup with SPRI select beads. Library quantification and quality assessment was performed using Bioanalyzer Agilent 2100 using a High Sensitivity DNA chip (Agilent Genomics). Indexed libraries were equimolarly pooled and sequenced using paired-end 26x98bp as sequencing mode by GenomeScan (Leiden, Netherlands). Single-cell RNA-seq outputs were processed using the Cell Ranger (10X Genomics) suite versions 2.1.1 (in vitro HUVEC samples) or 3.0.1 (in vivo 3d AMI samples). HUVEC in vitro data has been mapped to the GRCh38 (version 1.2.0) reference genome by using the “count” function. Subsequently, individual processed datasets have been merged with “aggregate”. Secondary analysis was conducted using the Seurat 2.3.4 package in R.14 We filtered the data for cells expressing at least 200 genes. Moreover, we aimed to avoid doublets by removing cells with high unique molecular identifier (UMI) counts (> 90000) and high number of genes (> 8000). We also accounted for possible dead cells and removed cells with high mitochondrial content (> 10 % of total UMI). The remaining matrix was log-normalized and scaled. After detecting variable genes, a principal component analysis (PCA) using 10 dimensions was applied. Clustering of the cells was then performed by Seurat’s FindCluster function with 0.6 resolution. We used t-distributed stochastic neighbor embedding (t-SNE) to visualize cell clusters.15 We applied a generic threshold of 2.5 to the scaled value of all candidate genes to separate high and low or no expressing cells. Accordingly, in vivo 3d AMI data we mapped against the mm10 (version 3.0.0) reference genome using Cell Ranger “count”. In Seurat 2.3.4 we applied similar filters for removing cells with high and low UMI counts but removed the upper 5 % and lower 1 % of all cells per individual sample. High mitochondrial content cells (>10 %) were removed similarly. We only kept genes that showed at least in 2 cells an UMI count of more than 1. We merged the data and counted cells expressing at least 1 UMI for Cdh5 and Pecam1 (ECs) as well as Cdh5, Pecam1 and two mesenchymal markers (EndMT cells) between the libraries.
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene_expression.tsv was generatedby cuffdiff and assembled by cummerbund; ChIP-seq bed files

source_name: Input in full medium

growth_protocol: Experiments were performed using human umbilical vein endothelial cells (HUVEC) purchased from Lonza. Cells were cultured in endothelial basal medium without phenol red (#C-22215, PromoCell), supplemented with hydrocortisone (#CC-4035C, Lonza), ascorbic acid (#CC-4116C, Lonza), bovine brain extract (BBE) (#CC-4092C, Lonza), epidermal growth factor (EGF) (#CC-4017, Lonza), 10% fetal bovine serum (FBS) (#CC-4101, Lonza) and GA-1000 (Gentamicin+Amphotericin-B, CC-4081C, Lonza) or for EndMT without EGF and BBE.

extract_protocol:
Total RNA was isolated using Qiazol Lysis Reagent (#79306; Qiagen) and miRNeasy-kit (#217004; Qiagen) with additional DNase I (#79254; Qiagen) digestion according to the manufacturer’s protocol. 1 μg of RNA from each sample was reverse-transcribed using random hexamer primed single-strand cDNA (10 min at 25 °C, 15 min at 42 °C, 5 min at 99 °C) by MMLV Reverse Transcriptase (#N8080018; Life technologies) as previously described. (Boeckel et al., 2011). For qPCR, cDNA was amplified using Fast SYBR Green Mastermix (#4385612 Life Technologies) on a ViiA7- Realtime qPCR System (Life Technologies). Expression level of mRNAs were normalized to RPLP0 which served as a housekeeping gene using the 2‑ΔCt method.
900ng of total RNA was used as input for whole transcriptome RNA-seq library preparation (TruSeq® Stranded Total RNA, Illumina) following low throughput protocol. Sequencing was performed on Illumina Nextseq 500 (Illumina) using V2 chemistry and 75bp single-end setup.

treatment_protocol: 4 x 10^5 HUVEC were seeded in a 60 mm cell culture dish, cells were cultivated either full medium (FM) or in differentiation media (DM).  After 24 h of cultivation, cells were treated with 10 ng/ml TGF-β2 (#302-B2, R&D System). After additional 48 h of incubation, the treatment was repeated. 96h later, RNA was isolated.

tag: genotype/variation

value: Wild-type

tag: passages

tag: treatment

value: full medium (FM)

tag: chip antibody

value: IgG

tag: chip antibody cat. #

tag: chip antibody lot nr.


title: HUVEC_Input_n3_DM [ChIP-seq]

description: Input in differentiation medium

source_name: Input in differentiation medium

value: human umbilical vein endothelial cells (HUVEC)

value: differentiation media (DM)


title: Normal astrocyte 5173_AD

tag: strain


title: Young rep6

description: Sample 6


title: Young rep8

description: Sample 8


title: Young rep9

description: Sample 9


title: Young rep7

description: Sample 7


title: HUVEC_Input_n2_DM [ChIP-seq]

description: Input in differentiation medium


title: HUVEC_Input_n1_DM [ChIP-seq]

description: Input in differentiation medium


title: Young rep4

description: Sample 4


title: HUVEC_H3K9_n3_DM [ChIP-seq]

description: H3K9me3 in differentiation medium

source_name: H3K9me3 in differentiation medium

value: C15410193 (Diagenode)


title: Young rep2

description: Sample 2


title: Young rep3

description: Sample 3


title: Young rep5

description: Sample 5


title: HUVEC_H3K9_n2_FM [ChIP-seq]

description: H3K9me3 in full medium

source_name: H3K9me3 in full medium


title: HUVEC_H3K9_n1_DM [ChIP-seq]

description: H3K9me3 in differentiation medium


title: HUVEC_H3K9_n2_DM [ChIP-seq]

description: H3K9me3 in differentiation medium


title: HUVEC_FM_n4 [RNA-seq]

description:
cultivated under full medium
processed data file: Gene_expression.tsv

source_name: cultivated under full medium


title: HUVEC_H3K9_n1_FM [ChIP-seq]

description: H3K9me3 in full medium


title: Young rep10

description: Sample 10


title: HUVEC_FM_n3 [RNA-seq]


title: Aged rep8

description: Sample 18


title: HUVEC_Input_n1_FM [ChIP-seq]

description: Input in full medium


title: At WT drought rep3

city: Wuhan

first: Zhulong

last: Chan

state: Hubei Province

address: No. 1, Shizishan St, Nanhu

department: College of Horticulture and Forestry Sciences

institute: Huazhong Agricultural University

data_processing:
Index of the Arabidopsis genome was built and paired-end clean reads were aligned to the Arabidopsis genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the read numbers mapped to each gene, and the FPKM of each gene was calculated based on the length of the gene and read counts mapped to this gene.
Differential expression analysis of two conditions/groups was performed using the DESeq2 R package (1.16.1).
The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate.

organism: Arabidopsis thaliana

source_name: leaf

extract_protocol:
The rosette leaves of were collected for RAN isolation following the standard Qiagen RNeasy mini kit protocol. RNA purity and integrity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) and RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA), respectively.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: leaf

tag: treatment time

value: 10 days after drought

tag: genotype

value: WT


title: Aged rep1

description: Sample 11


title: HUVEC_H3K9_n3_FM [ChIP-seq]

description: H3K9me3 in full medium


title: At WT drought rep2


title: HUVEC_FM_n2 [RNA-seq]


title: At WT drought rep1


title: MtPHD6 drought rep3


title: Young rep1

description: Sample 1


title: HUVEC_FM_n1 [RNA-seq]


title: MtPHD6 drought rep1


title: At WT control rep3


title: HUVEC_DM_n3 [RNA-seq]

description:
cultivated under differentiation medium
processed data file: Gene_expression.tsv

source_name: cultivated under differentiation medium


title: At WT control rep2


title: HUVEC_DM_n2 [RNA-seq]


title: MtPHD6 control rep3


title: At WT control rep1


title: ChIP-seq_VCaP_H2AK119ub_siNON_EtOH_rep2

city: Kuopio

first: Einari

last: Niskanen

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

description: ChIP-seq sample

data_processing:
The quality of raw reads was analyzed by FastQC and FASTX-toolkit was used for preprocessing raw reads (removal of artifacts, trimming reads, quality filtering and collapsing identical reads).
For ChIP-seq, reads were aligned against human genome hg19 with Bowtie software (version 0.12.9) with the command line: -v 1 -k 1 -m 1 -f -S --best hg19. Peak calling was done in HOMER (version 4.10.3) using findPeaks command and approppriate input as a control. Two replicates were compared with each other using bedTools (intersectBed) and only those binding sites found in both replicates were used for further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: For ChIP-seq, the genomic intervals of BCOR binding sites that were common to two replicates are given in bed format. For AR and H2AK119ub, signal tracks are given in tdf format.

source_name: VCaP cells

growth_protocol: VCaP cells were maintained in DMEM (Gibco, Invitrogen, 41965-039) supplemented with 10% Defined FBS (Hyclone, SH30070.03), 100U/ml penicillin and 100 ug/ml streptomycin. Before hormone treatments, cells were kept on DMEM supplemented with 2.5% charcoal-treated FBS (steroid-depleted medium).

extract_protocol:
For ChIP-seq, VCaP cells were silenced using siRNA transfection for three days when indicate, grown on steroid-depleted medium for two days and treated for 1h with R1881 (10mM) or equal volume of vehicle (ethanol). Samples were fixed for 10 min. in room temperature with 1% (v/v) formaldehyde, fragmented to 200-400bp fragments by sonication (Bioruptor, Diagenode) and chromatin immunoprecipitation was done using rabbit polyclonal anti-BCOR antibody (A310-672A, Bethyl Laboratories), rabbit antiserum against AR or anti-H2AK119ub antibody (#8240, Cell Signaling Technology). Two biological replicates of each condition were sequenced using Illumina HiSeq 2000 or NextSeq500 at EMBL GeneCore (Heidelberg, Germany).
Library preparation was done using NEBNext Ultra II kit (New England Biolabs) and sequenced using Illumina HiSeq 2000 or NextSeq 500 at EMBL GeneCore (Heidelberg, Germany).

treatment_protocol: See samples.

tag: cell line

value: VCaP

tag: treatment 1

value: siNON transfection, 72h

tag: treatment 2

value: steroid-depleted medium, 24h

tag: treatment 3

value: ethanol, 1h

value: rabbit monoclonal anti-H2AK119ub antibody (Cell Signaling Technology, 8240)


title: ChIP-seq_VCaP_H2AK119ub_siNON_R1881_rep2

description: ChIP-seq sample


title: IPN_miRNA_TA3

source_name: Interpeduncular nucleus  tissue punch

tag: condition

value: Chronic tartaric acid control


title: ChIP-seq_VCaP_H2AK119ub_siNON_R1881_rep1

description: ChIP-seq sample


title: E07T2_SepticShock [re-analysis]

tag: patient

tag: timepoint

tag: clinical classification

value: SS

value: Whole blood


title: ChIP-seq_VCaP_H2AK119ub_siNON_EtOH_rep1

description: ChIP-seq sample


title: MtPHD6 control rep1


title: Tumor GNP cell 6493_cul

tag: cell type

value: Tumor GNP cell

tag: rna extraction methods

value: Laser capture microdissection


title: ChIP-seq_VCaP_H2AK119ub_siBCOR_R1881_rep1

description: ChIP-seq sample

value: siBCOR transfection, 72h

tag: chip antibody


title: ChIP-seq_VCaP_H2AK119ub_siBCOR_EtOH_rep2

description: ChIP-seq sample


title: ChIP-seq_VCaP_AR_siNON-R1881_rep2

description: ChIP-seq sample

value: rabbit antiserum against AR


title: ChIP-seq_VCaP_H2AK119ub_siBCOR_EtOH_rep1

description: ChIP-seq sample


title: HUVEC_DM_n4 [RNA-seq]

tag: genotype/variation

value: Wild-type

value: human umbilical vein endothelial cells (HUVEC)

tag: passages

tag: treatment

value: differentiation media (DM)


title: HUVEC_DM_n1  [RNA-seq]


title: Aged rep3

description: Sample 13

tag: ID

tag: age (years)

tag: day of cycle


title: MtPHD6 drought rep2

tag: tissue

value: leaf

tag: treatment time

value: 10 days after drought

tag: genotype


title: ChIP-seq_VCaP_AR_siNON-R1881_rep1

description: ChIP-seq sample

tag: cell line

value: VCaP

tag: treatment 1

tag: treatment 2

tag: treatment 3


title: MtPHD6 control rep2


title: ChIP-seq_VCaP_H2AK119ub_siBCOR_R1881_rep2

description: ChIP-seq sample


title: ChIP-seq_VCaP_AR_siNON-EtOH_rep1

description: ChIP-seq sample

value: siNON transfection, 72h


title: ChIP-seq_VCaP_AR_siBCOR-R1881_rep1

description: ChIP-seq sample

value: steroid-depleted medium, 24h


title: ChIP-seq_VCaP_AR_siBCOR-EtOH_rep2

description: ChIP-seq sample

value: ethanol, 1h


title: ChIP-seq_VCaP_AR_siBCOR-R1881_rep3

description: ChIP-seq sample


title: HUVEC_Input_n2_FM [ChIP-seq]

description: Input in full medium

value: full medium (FM)

value: IgG

tag: chip antibody cat. #

tag: chip antibody lot nr.


title: YPS1009 Dis12 SSD1-GFP IP Rep2

city: Madison

first: Audrey

last: Gasch

state: WI

address: 425G Henry mall

department: Genetics

institute: University of Wisconsin

description:
Gasch 1015
ripSeq_03272019_HTSeq_results.txt

data_processing:
Reads trimmed w/ Trimmomatic-0.30
Read alignment done w/ BWA mem Version: 0.7.12-r1039
Reas sorting and indexing w/ Samtools 1.2 (htslib 1.2.1)
Gene counts generated w/ HTSeq version 0.6.0
RPKM Calculated w/ Gasch Laboratory python script
Genome_build: SGD S288C R58-1-1 w/ YPS1009 snps subsitution
Supplementary_files_format_and_content: HTSeq count tables w/ gene counts for each sample

organism: Saccharomyces cerevisiae

source_name: YPS1009_Chr12 SSD1-GFP

growth_protocol: All strains were grown 7+ generations in YPD to OD600 0.3-0.6 except noted samples grown 3 generations in YPD to OD600 0.3-0.6 to minimize loss of aneuploidy

extract_protocol:
RNA was extracted with hot phenol protocol; RNA was rRNA-depleted with Illumina's Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat)
cDNA library was prepared with Illumina's TruSeq Total RNA Stranded Kit

tag: hapoid or diploid

value: Haploid

tag: euploid or aneuploid

value: Aneuploid


title: PANC1_VITD

city: Boston

middle: T

last: Ting

address: 149 E 13th street

department: Cancer Center

institute: Massachusetts General Hospital

data_processing:
Reads aligned to HG38
Deduplicated BAM files used with HTSeq-Count to create count tables
Data was analyzed with DESeq2 for differential expresison analysis
Genome_build: GRCH38
Supplementary_files_format_and_content: Raw and normalized read counts in Text format

source_name: pancreatic ductal adenocarcinoma cell line

growth_protocol: PDAC cell lines were plated in 6-well ultra low attachment plates in RPMI base media with 20 ul/ml B27, 20 ng/ml EGF, 20 ng/ml bFGF and 100 U/mL Penicillin and 100 mg/mL Streptomycin. Tumor spheres were grown for 5 days in the presence of 1,25-dihydroxyvitaminD3 or vehicle control prior to harvesting for RNA isolation.

extract_protocol:
After 5 days of culture, cells were harvested for RNA isolation using miRNEasy Mini Kit (Qiagen) including the optional on column DNAse treatment (Qiagen) per manufacturer's protocol.
To generate libraries for total RNA sequencing the Illumina Smarter Stranded Total RNA-Seq kit v2 (Cat No#634413) was used according to the manufacturer's instructions. Pooled libraries were sequenced on an Illumina NextSeq 500 sequencer.

treatment_protocol: Cells were treated with 10nM 1a,25-dihydroxyvitaminD3 or DMSO for vehicle control on D1 and D3 of culture

value: Calcitriol

tag: culture condition

value: 3D tumorsphere


title: PANC1_VEH

value: DMSO


title: YPS1009 Euploid SSD1-GFP IP Rep2

description:
Gasch 1014
ripSeq_03272019_HTSeq_results.txt

source_name: YPS1009_Euploid SSD1-GFP

value: Euploid


title: ChIP-seq_VCaP_AR_siNON-EtOH_rep2

description: ChIP-seq sample

tag: chip antibody

value: rabbit antiserum against AR


title: MIAPACA2_VITD

tag: treatment


title: YPS1009 Dis12 mock IP Rep2

description:
Gasch 1013
ripSeq_03272019_HTSeq_results.txt

source_name: YPS1009_Chr12 SSD1 untagged


title: MIAPACA2_VEH


title: HPAFII_VITD


title: NHEK_18hr_IL27_1

type: RNA

city: Chapel Hill

last: Corcoran

state: NC

address: 125 Mason Farm Rd

institute: University of North Carolina at Chapel Hill

description: Gene expression data from the human NHEK cell line, stimulated with IL27

hyb_protocol: Hybridization targets were prepared from total RNA using a MessageAmp Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX, USA), hybridized to GeneChip™ Human U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA, USA) in an Affymetrix GeneChip hybridization Oven 645, washed in Affymetrix GeneChip Fluidics Station 450, and scanned with Affymetrix GeneChip Scanner 7G according to standard Affymetrix GeneChip hybridization, wash, and stain protocols.

scan_protocol: Affymetrix scanning protocol according to manufacturer, Affymetrix GeneChip Command Console Scan Control 3.2.3.1515 and Expression Console version 1.2.0.20

data_processing: The data was analyzed using the 'affy' bioconductor package in the R statistical programming environment.

label: biotin

label_protocol: Ambion MessageAmp Premier labeling

growth_protocol: Normal human keratinocytes were grown to subconfluency before treatment with IL-27. Human THP-1 cells (cell line) were pretreated with PMA to induce macrophage-like phenotype

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions

treatment_protocol: Cells were treated with 100ng/ml recombinant human IL-27 for 18hrs.

tag: cell type

value: primiary human epidermal keratinocytes (NHEK)

value: IL-27 (100ng/ml) for 18hrs


title: HPAFII_VEH


title: THP1_18hr_IL27_1

description: Gene expression data from the human THP1 cell line, stimulated with IL27

value: human monocytic cell line


title: NHEK_NoStim_3

description: Gene expression data from the human NHEK cell line, control sample

value: vehicle control (Non-stimulated)


title: YPS1009 Euploid mock IP Rep2

description:
Gasch 1012
ripSeq_03272019_HTSeq_results.txt

source_name: YPS1009_Euploid SSD1 untagged


title: YPS1009 Dis12 SSD1-GFP input Rep2

description:
Gasch 1011
ripSeq_03272019_HTSeq_results.txt


title: CAPAN2_VITD


title: NHEK_18hr_IL27_2


title: YPS1009 Euploid SSD1-GFP input Rep2

description:
Gasch 1010
ripSeq_03272019_HTSeq_results.txt


title: THP1_NoStim_3

description: Gene expression data from the human THP1 cell line, control sample


title: NHEK_NoStim_2


title: THP1_18hr_IL27_3


title: CAPAN2_VEH


title: THP1_NoStim_1


title: YPS1009 Dis12 mock input Rep2

description:
Gasch 1009
ripSeq_03272019_HTSeq_results.txt


title: NHEK_18hr_IL27_3


title: PDAC9_VITD_3

source_name: primary pancreatic ductal adenocarcinoma cell line


title: YPS1009 Euploid mock input Rep2

description:
Gasch 1008
ripSeq_03272019_HTSeq_results.txt


title: NHEK_NoStim_1


title: THP1_NoStim_2


title: HUVEC FM control, rep 3

description:
N3_day3_VM_SCR
Scrambled condition FM medium

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
Gene-expression analysis was performed using the GeneChip Human Exon 1.0 ST array (#900651 Affymetrix) following the supplier’s instructions. Data was analyzed by using the Exon Array Analyzer (EAA) Web interface (http://eaa.mpi-bn.mpg.de/).
probe group file: HuEx-1_0-st-v2.pgf
meta-probeset file: HuEx-1_0-st-v2.mps

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA was isolated using Qiazol Lysis Reagent (#79306; Qiagen) and miRNeasy-kit (#217004; Qiagen) with additional DNase I (#79254; Qiagen) digestion according to the manufacturer’s protocol. 1 μg of RNA from each sample was reverse-transcribed using random hexamer primed single-strand cDNA (10 min at 25 °C, 15 min at 42 °C, 5 min at 99 °C) by MMLV Reverse Transcriptase (#N8080018; Life technologies) as previously described. (Boeckel et al., 2011) For qPCR, cDNA was amplified using Fast SYBR Green Mastermix (#4385612 Life Technologies) on a ViiA7- Realtime qPCR System (Life Technologies). Expression level of mRNAs were normalized to RPLP0 which served as a housekeeping gene using the 2‑ΔCt method.

value: human umbilical vein endothelial cells (HUVEC)

tag: genotype/variation

value: Wild-type

tag: age

value: 3 days


title: PDAC9_VEH_3


title: HUVEC FM siJMJD2B, rep3

description:
N3_day3_VM_SiJMJD2B
JMJD2B knockdown FM medium

value: JMJD2B knockdown


title: THP1_18hr_IL27_2


title: YPS1009 Dis12 SSD1-GFP IP Rep1

description:
Gasch 1007
ripSeq_03082019_HTSeq_results.txt


title: YPS1009 Euploid SSD1-GFP IP Rep1

description:
Gasch 1006
ripSeq_03082019_HTSeq_results.txt


title: HUVEC DM siJMJD2B, rep3

description:
N3_day3_DM_SiJMJD2B
JMJD2B knockdown DM medium

value: differentiation media (DM)


title: HUVEC DM control, rep 3

description:
N3_day3_DM_SCR
Scrambled condition DM medium


title: HUVEC FM control, rep 2

description:
N2_day3_VM_SCR
Scrambled condition FM medium

value: full medium (FM)


title: PDAC9_VITD_2


title: PDAC9_VEH_2


title: HUVEC DM siJMJD2B, rep2

description:
N2_day3_DM_SiJMJD2B
JMJD2B knockdown DM medium


title: HUVEC FM siJMJD2B, rep2

description:
N2_day3_VM_SiJMJD2B
JMJD2B knockdown FM medium


title: YPS1009 Dis12 mock IP Rep1

description:
Gasch 1005
ripSeq_03082019_HTSeq_results.txt

value: Haploid


title: PDAC9_VITD_1


title: YPS1009 Euploid mock IP Rep1

description:
Gasch 1004
ripSeq_03082019_HTSeq_results.txt


title: HUVEC FM control, rep 1

description:
N1_day3_VM_SCR
Scrambled condition FM medium


title: HUVEC DM control, rep 2

description:
N2_day3_DM_SCR
Scrambled condition DM medium


title: PDAC8_VITD_3


title: HUVEC FM siJMJD2B, rep1

description:
N1_day3_VM_SiJMJD2B
JMJD2B knockdown FM medium


title: PDAC9_VEH_1


title: YPS1009 Dis12 SSD1-GFP input Rep1

description:
Gasch 1003
ripSeq_03082019_HTSeq_results.txt

value: Aneuploid


title: IMJCKO6: Nrl-KO replicate 6 ncRNA-seq

city: Chicago

first: Ivan

last: Moskowitz

state: IL

address: 900 E 57th St

department: Pediatrics, Pathology, and Human Genetics

institute: University of Chicago

description: Poly A depleted RNA

data_processing:
Fastq files were aligned to UCSC genome build mm9 using TopHat (version 2.0.10). 168 million and 174 million reads were successfully mapped. RABT assembly was performed by Cufflinks (version 2.2.1, with parameters –g --frag-bias-correct --multi-read-correct --upper-quartile-norm). Analysis of differential expression was performed using Cuffdiff from the Cufflinks package
Genome_build: mm10
Supplementary_files_format_and_content: Significant results in Excel file (mm10)
Supplementary_files_format_and_content: bigWig pooled by genotype and seperated by strand

source_name: Retina

extract_protocol: Libraries were quantitated using the Agilent Bio‐analyzer (model 2100) and pooled in equimolar amounts. The pooled libraries were sequenced with 50-bp stranded single-end reads on the HiSEQ4000 in Rapid Run Mode following the manufacturer's protocols (2013).

tag: tissue

value: retina

value: post natal day 21

value: Nrl knock-out


title: YPS1009 Euploid SSD1-GFP input Rep1

description:
Gasch 1002
ripSeq_03082019_HTSeq_results.txt

value: Euploid


title: PDAC8_VEH_3

value: DMSO

value: 3D tumorsphere


title: IMJCKO5: Nrl-KO replicate 5 ncRNA-seq

description: Poly A depleted RNA


title: YPS1009 Dis12 mock input Rep1

description:
Gasch 1001
ripSeq_03082019_HTSeq_results.txt


title: HUVEC DM siJMJD2B, rep1

description:
N1_day3_DM_SiJMJD2B
JMJD2B knockdown DM medium


title: PDAC8_VITD_2

value: Calcitriol


title: IMJCKO3: Nrl-KO replicate 3 ncRNA-seq

description: Poly A depleted RNA


title: PDAC8_VEH_2


title: YPS1009 Euploid mock input Rep1

description:
Gasch 1000
ripSeq_03082019_HTSeq_results.txt


title: YPS1009 Dis12 ssd1Δ Rep2

description:
Gasch 876
08302017_HTSeq_results.txt


title: IMJCKO2: Nrl-KO replicate 2 ncRNA-seq

description: Poly A depleted RNA


title: YPS1009 Euploid ssd1Δ Rep2

description:
Gasch 875
08302017_HTSeq_results.txt


title: IMJCKO1: Nrl-KO replicate 1 ncRNA-seq

description: Poly A depleted RNA


title: YPS1009 Dis12 Wild-type Rep2

description:
Gasch 874
08302017_HTSeq_results.txt


title: IMJCWT5: Wild-type replicate 5 ncRNA-seq

description: Poly A depleted RNA

value: wild-type


title: PDAC8_VEH_1


title: PDAC6_VITD_3


title: YPS1009 Euploid Wild-type Rep2

description:
Gasch 873
08302017_HTSeq_results.txt


title: PDAC6_VEH_3


title: IMJCWT2: Wild-type replicate 2 ncRNA-seq

description: Poly A depleted RNA


title: YPS1009 Dis12 Wild-type Rep1

description:
Gasch 870
08302017_HTSeq_results.txt


title: YPS1009 Euploid ssd1Δ Rep1

description:
Gasch 871
08302017_HTSeq_results.txt


title: IMJCWT1: Wild-type replicate 1 ncRNA-seq

description: Poly A depleted RNA


title: PDAC6_VITD_2


title: IMJCWT3: Wild-type replicate 3 ncRNA-seq

description: Poly A depleted RNA


title: IMJCKO4: Nrl-KO replicate 4 ncRNA-seq

description: Poly A depleted RNA