title: FCS-H3K36me3-spikeIn-13617

first: Hendrik

last: Marks

address: Geert Grooteplein 26/28

department: Molecular Biology

institute: Radboud University Nijmegen, RIMLS

description: ChIP targeting H3K36me3 modification using antibody H3K36me3 (Diagenode pAb-192-050)

data_processing:
For RNA-Seq and ChIP-Seq, Initial data processing and base calling was performed using the Illumina Analysis Pipeline. Initial data processing and base calling of Bisulfite-seq/WGBS was performed as in (Farlik et al., 2015).
For RNA-Seq, strand specific RNA-seq reads were aligned to the mm9 reference genome and counted using STAR v2.5.2b with parameters --quantMode GeneCounts --outSAMmapqUnique 255 --outSAMmultNmax 1 --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16
For ChIP-Seq, reads were mapped to a merged mm9 and dm3 genome using bowtie2 2.0.2 with parameters --very-sensitive --end-to-end. Duplicate and unmapped reads were removed. The data mapped to dm3 and mm9 genomes were split into separate files.
For RNA-Seq, only uniquely mapping tags (mapq=255) were kept. Bigwigs were generated using bam2bw (https://bitbucket.org/simonvh/bam2bw.git) v1.25 with parameters –e 150 –c –p.
For ChIP-Seq, Only uniquely mapping tags (mapq >=30) were kept for quantification. Bigwigs were generated using bam2bw (https://bitbucket.org/simonvh/bam2bw.git) v1.25 with parameter –e 180 and custom scaling factor -s set to account for the relative abundance of the dm3 spike-in chromatin.
Data processing and data analysis of Bisulfite-seq/WGBS data was performed as in Habibi et al. (2013)
Genome_build: mm9 + dm3
Supplementary_files_format_and_content: bigWig files are directly compatible with the UCSC genome browser.

source_name: Embryonic Stem Cells (ESCs)

growth_protocol: E14 ESCs (129/Ola background) were maintained in Dulbecco’s Modified Eagle Medium (DMEM) containing 15% fetal bovine serum, 5µM beta mercaptoethanol (BME) (Sigma) and Leukemia inhibitory factor (LIF; 1000U/ml) (Millipore), referred to as serum ESCs, or in serum-free N2B27 (or Ndiff) supplemented with PD0325901 (1 µM), CH99021 (3 µM) and LIF (1000U/ml), referred to as 2i ESCs. Serum+2i cells were grown in Serum medium supplemented with PD0325901 (1 µM) and CH99021 (3 µM). The Eed-/- and Suz12-/- ESCs originate from the lab of Anton Wutz (Schoeftner et al., 2006 and Wutz & Jaenisch, 2000) and Kristian Helin (Pasini et al., 2007), respectively

extract_protocol:
For RNA-Seq, total RNA was isolated using a RNeasy mini kit (Invitrogen) according to manufacturer’s instructions with on-column DNAseI treatment. Ribosomal RNA was depleted using Ribo-Zero Gold rRNGA Removal Kit (Illumina) according to manufacturer protocol starting from 5µg RNA. The resulting 180uL of rRNA depleted RNA was purified by mixing 18uL 3 M Sodium Acetate and 2 uL of 20 mg/mL glycogen, then adding 3x volumes of ice-cold 100% ethanol and incubation at -20°C for 1 hour. Samples were centrifuged at 10.000g for 30 minutes. After removal of supernatant, RNA pellet was washed in 500uL ice-cold 70% ethanol and centrifuged at 10.000g. Supernatant was removed and RNA was eluted in 40uL nuclease free H2O. rRNA depleted RNA was fragmented to ~200bp size using 10uL of a 5x 200mM Tris-acetate, 500 mM Potassium Acetate, 150 mM Magnesium Acetate, pH 8.2 solution at 95°C for 200 seconds, then incubated on ice for 10 minutes before repeating the ethanol purification procedure. First strand cDNA synthesis was performed using SuperScript III RT enzyme (Life Technologies), purified using Qiaquick MinElute Column (Qiagen). For ChIP-Seq, chromatin extracts were prepared by on-plate cell crosslinking in 1% PFA for 8 minutes. Crosslinking was quenched using 125 mM freshly dissolved Glycine final concentration. Fixed cells were washed in PBS twice, then collected by scraping. Pellets were lysed and sonicated in 50 mM Tris pH 8.0, 1% SDS and fresh protease inhibitor cocktail (Roche) at a density of 15 million cells per mL. The cells were sonicated in a Diagenode Bioruptor Pico for 8-10 30-second cycles. Proper sonication was verified using agarose gel size checks after decrosslinking and the eluted DNA was quantified using Qubit HS. 25ug DNA equivalent mouse chromatin was ChIPped using 4ug H3K27me3 (Millipore 04-779) or 2ug H3K36me3 (Diagenode pAb-192-050) antibody. Spike-in normalization was performed by adding 50ng Drosophila Melanogaster material (Active Motif 53083) and 2ug Drosophila-specific H2Av antibody (Active Motif 61686) to the mouse chromatin. ChIPs were diluted 9-fold using IP buffer (1% Triton X100, 1.2mM EDTA, 16.7mM Tris pH8.0, 167mM NaCl) and incubated overnight at 4°C while rotating. Subsequently, a mixture of 10uL Protein A and 10uL protein G (thermo) was blocked twice in IP buffer with 0.15% SDS and added to the ChIP. ChIPs with beads were left to incubate for 1 hour and precipitated using a magnetic rack. Chromatin was washed once (2mM EDTA, 20mM Tris pH8.0, 1% Triton, 0.1% SDS, 150mM NaCl), twice (2mM EDTA, 20mM Tris pH8.0, 1% Triton, 0.1% SDS, 500mM NaCl) and twice (1mM EDTA, 10 mM Tris pH8,0). Specific ChIPped DNA was eluted using 200mM NaCl, 1%SDS, 20mM Tris pH8.0 by shaking at 65°C for one hour, addition of and 1:100 10mg/mL Proteinase K and shaking at 55°C for one hour, then shaking at 65°C for at least four hours. The DNA was purified using Qiagen Minelute according to manufacturer instructions. For Bisulfite-seq, genomic DNA was extracted using the Wizard genomic DNA isolation kit (Promega). 200ng of purified genomic DNA was digested with Proteinase K before proceeding with sample processing for WGBS.
For RNA-Seq, second strand synthesis was performed using incorporation of dUNTP’s. Libraries were generated using Kapa Hyper Prep kit (KAPA Biosystems) according to manufacturer’s protocol with modification of dUNTP cleavage before amplification. Libraries were size selected using Agencourt Ampure XP beads (Beckman Coulter). For ChIP-Seq, libraries were generated using Kapa Hyper Prep on 5ng DNA according to manufacturer instructions and size selected using Ampure XP beads. DNA was quantified using Qubit HS and DNA fragment sizes checked using Agilent Bioanalyzer HS. For WGBS, sample prep, paired-end sequencing and further analysis of Bisulfite-seq/WGBS was performed as in (Farlik et al., 2015).

treatment_protocol: ESCs were adapted to defined media containing 2i between 14 and 28 days; Treatment with 5-azacytidine (Sigma) was performed for 6 days at a final concentration of 1 µM. 5-azacytidine was refreshed every day.

tag: antibody

value: ESCs

value: Maintained in serum-containing medium


title: FCS-H3K27me3-rep2-spikeIn-13616

status: Public on Nov 24 2018

type: SRA

city: Nijmegen

country: Netherlands

description: ChIP targeting H3K27me3 modification using antibody H3K27me3 (Millipore 04-779)

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell type

tag: cell line

tag: genotype/variation

value: wild type

tag: strain background

tag: treatment


title: 2iFCS-H3K27me3-rep1-spikeIn-13618

value: Adapted to Serum medium containing 2i for 14 days


title: 2iFCS-H3K27me3-rep2-spikeIn-13619


title: FCS-input-spikeIn-13621


title: 2i-input-spikeIn-13620

value: Adapted to defined media containing 2i >14 days


title: 2i-H3K27me3-rep2-spikeIn-13613


title: 2iFCS-input-spikeIn-13622


title: 2i-H3K27me3-rep1-spikeIn-13612


title: GM12878cisRep2

city: Chapel Hill

first: Yanyan

last: Yang

state: NC

address: 120 Mason Farm Road

department: Biochemistry & Biophysics

country: USA

institute: University of North Carolina  at Chapel Hill

description: Replicate 2

data_processing:
Library strategy: XR-seq
Adaptor trimming
Filtering reads based on length
Random sampling
Alignment
Read filtering based on nucleotide composition
Strand separation
Gene coverage count
Remove mismatches and gaps and duplicates
Genome_build: rDNA and DHFR
Supplementary_files_format_and_content: wig files

organism: Homo sapiens

source_name: human lymphocyte cells

growth_protocol: NHF1, CSB, XPC, GM12878 and wild-type mouse skin fibroblast cells were grown in DMEM (Life Technologies, Gaithersburg, MD) supplemented with 10% fetal bovine serum (Gemini, Woodland, CA). Cells were maintained in an incubator at 37°C under 5% CO2.

extract_protocol:
Cells were lysed gently and small molecular weight DNA, consisting mostly of excised 26-27 mers, was separated from chromosomal high molecular weight DNA by centrifugation.
Briefly, the excised oligomers are immunoprecipitated with anti-TFIIH (anti-XPB and anti-p62) antibodies because the excision product is released in a relatively stable complex with TFIIH, which also protects the excision product from degradation by non-specific nucleases. This is followed by extraction of the excised oligomers and ligation to adaptors and a second immunoprecipitation with anti-CPD antibodies. Then photolyase repairs the CPD damage. This is followed by PCR amplification with index primers and NGS sequencing on HiSeq platform.

treatment_protocol: Cells were grown to about 80% confluence in 150mm dishes. Media was removed, cells were washed with PBS, irradiated with 20 J/m2 of UV, and then warm, fresh media was added and cells were incubated for 3hr at 37°C (MSF), 1hr at 37°C (NHF1, XPC, CSB). GM12878 were treated with cisplatin 2hr at 37°C. Cells were then harvested and processed using the XR-seq procedure.

value: B lymphocytes

value: cisplatin


title: FCS-H3K27me3-rep1-spikeIn-13615


title: GM12878cisRep1

description: Replicate 1


title: S-3

city: Hefei

first: Yang

last: Zhao

address: changjiang road 130

country: China

institute: Anhui Agricultural University

library_source: transcriptomic

data_processing:
Raw reads were filtered to obtained clean reads
Clean reads were aligned to the reference genome with HISat software (v2.0.1)
Gene expression level was measured using HTSeq software (V0.6.1)
The significantly differentially expressed genes were identified using the DESeq R package (1.10.1) with fold changes ≥2 and FDR ≤ 0.05
Genome_build: maize B73 reference genome (RefGen_v3)
Supplementary_files_format_and_content: xls file include fpkm values for the 18 samples

molecule: total RNA

organism: Zea mays

source_name: leaves

growth_protocol: Seedlings were grown in a greenhouse at 28 °C/23 °C (day/night) with a 16-h light/8-h dark photoperiod

extract_protocol:
Total RNA was extracted using TRIzol reagent,1 μg of total RNA with RNA Integrity Number (RIN) values above 7 was used for library construction
The cDNA library preparations were constructed using a NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

treatment_protocol: 42 °C/35 °C (day/night) for two days

tag: developmental stage

value: seedlings

tag: tissue

value: leaves

tag: genotype

value: maternal line

value: Heat treatment for 2 days


title: 2C Sal

status: Public on Nov 25 2018

type: RNA

city: Valhalla

first: Bistra

last: Nankova

state: NY

address: 95 Grassland Rd

institute: New York Medical College

description: gene expression data from saline treated control animal

hyb_protocol: Following fragmentation in the presence of heat and Mg2+ the biotynilated cRNA was hybridized to Clariom_S_Mouse array. The array was washed and stained with streptavidin phycoerythtin (SAPE) using fluidics.

scan_protocol: The arrays were scanned using GeneChip Scanner 3000

data_processing: The data were normalized by RMA and quantile normalization using Partecl Genomics Suite 6.6. Quality control was performed by PCA. Differentially expressed genes were selected with adjusted p value (Benjamini-Hochberg Procedure) ≤ 0.05 and fold change ≥ 1.5. DEGs between selected pairs was tested using Limma R package.

label: biotin

source_name: saline 90 min

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Total RNA was isolated from dissected aadrenal medullae using RNeasy kit according to the manufacturer’s procedure (Qiagen,Hilden, Germany) with DNAse on column treatment. RNA quality and quantity was assessed using a NanoDrop® Spectrophotometer ND-2000c (ThermoFisher, Waltham, MA). Genome-wide transcriptome profiling (3 individual samples per experimental group) was performed at Yale Center for Genome Analysis, New Haven, CT.

treatment_protocol: All treatments (intraperitoneal injection of regular human insulin Humulin at a dose of 2IU/kg or same volume of saline were performed after 3 hrs fasting period (water ad libitum). The animals were sacrificed 90 min after injection. The adrenal medullae were dissected and immediately frozen until further analyses.

value: adrenal medulla

tag: strain

tag: Sex

value: male

tag: gut microbiota status

value: normally colonized


title: HT1080_INH_4h_1_3

city: Kraków

first: Andrzej

last: Mazan

address: Bobrzyńskiego 14

country: Poland

institute: Selvita S.A.

data_processing:
Raw reads were processed by Torrent Suite analysis pipeline and mapped to human genome assembly hg19 AmpliSeqTranscriptome version 1 by TMAP.
Reads corresponding to each gene were counted using HTSeq framework v. 0.10.0 (PMID: 25260700)
Normalization and differential expression were conducted by DESeq2 v. 1.20.0 (PMID:25516281), using default parameters and options.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include counts for each Sample

source_name: human fibrosarcoma

growth_protocol: HT-1080 (0.6 mln) cells were seeded on 6cm dishes in 3ml of MEM+NEAA+10%FBS and incubated overnight at 37ºC, 5% CO2

extract_protocol:
RNA was isolated with RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions and RNA integrity was assessed using Agilent RNA 6000 Nano Kit on Agilent 2100 Bioanalyzer.
RNA was subjected to library preparation using Ion AmpliSeq Transcriptome Human Gene Expression Panel, according to manufacturer's protocol. Briefly, RNA was reverse transcribed and cDNA subjected to multiplex PCR reaction to amplify parts of targeted transcripts. Amplicons were then partially digested at primer sequences followed by adapters ligation to amplicons and purification on AMPure® XP beads. Resulting library was  quantified on Bioanalyzer 2100 and diluted to ~100 pM prior to template preparation. Up to eight barcoded libraries were subjected to automated template preparation with Ion PI™ Hi-Q™ Chef Kit on the Ion Chef Instrument. Barcoded RNA-Seq libraries samples were sequenced on a PI chip.

treatment_protocol: After the treatment (4 hours) cells medium was removed, cells were washed with PBS and scrapped. Pellet was collected and frozen for RNA-seq study.

value: fibrosarcoma

tag: time point

value: 4 hours


title: HT1080_DMSO_4h_2_3

value: 0.1% DMSO


title: HT1080_INH_4h_1_2


title: HT1080_INH_24h_3_3

treatment_protocol: After the treatment (24 hours) cells medium was removed, cells were washed with PBS and scrapped. Pellet was collected and frozen for RNA-seq study.

value: 24 hours


title: HT1080_DMSO_4h_2_1


title: HT1080_DMSO_24h_4_1


title: HT1080_INH_4h_1_1


title: HT1080_DMSO_4h_2_2


title: HT1080_INH_24h_3_1


title: S-2


title: 2i-H3K36me3-spikeIn-13614

value: ESCs


title: HT1080_DMSO_24h_4_3


title: S-1


title: HT1080_DMSO_24h_4_2


title: R-1

value: paternal line


title: HT1080_INH_24h_3_2


title: R-3


title: R-2


title: SARB 35 3

city: Erlangen

first: Benardina

last: Ndreshkjana

address: Universitätsstraße 22

department: Experimental Tumor Pathology

country: Germany

institute: Uniklinikum Erlangen

description:
20160919_206971480318_01_12.RCC
SAMPLE 15

hyb_protocol: For the hybridization setup pre-heat a thermal cycler to 65°C, remove Reporter CodeSet, Capture ProbeSet, and RNA samples from the freezer and thaw at room temperature. Invert or flick the tubes several times to mix well and briefly spin down reagents. Create a hybridization master mix by adding 70 µl of hybridization buffer to the tube containing the Reporter CodeSet. Add 8 µl of master mix to each of the 12 tubes and then ad 5 µl of sample to each tube. Invert the Capture ProbeSet tube to mix and spin down the contents. Add 2 µl of Capture ProbeSet to each tube immediately before placing at 65 °C. Briefly spin down and immediately place the tubes in the pre-heated 65 °C thermal cycler. Incubate reactions for 16 h. Ramp reactions down to 4 °C and follow Prep Station.

scan_protocol: After the hybridization step the samples were transfered to the Prep Station which processes samples to prepare them for data collection on the Digital Analyzer. All consumable components and reagents required for sample processing on the Prep Station are provided in the nCounter Master Kit and must be loaded onto the Prep Station The Prep Station can process up to 12 lanes per run in approximately 2.5 - 3 h and the instrument transfers the liquid, performs the magnetic bead separations and immobilization of molecular labels on the sample cartidge surface. Then the Cartidge is transfere into nCounter Digital Analyzer which is a multi-channel epifluorescence scanner specifically configured for use with NanoString’s nCounter Cartridges.

data_processing:
The number of the images taken corresponds to the number of reporters counted. Images were processed internally were each line gives one Reportet Code Count (RCC) file which contains the counts for that lane. The RCC files were then downloaded from the digital analyzer and were imported into nSolver for quality control and analysis. Data processing was performed using nSolver Analysis Software 3.0. All samples were normalized using the geometric mean of the housekeeping genes. The geometric mean of negative controls and positive control normalization was performed as well. Fold change data were then exported from nSolver into excel.
Provided data include: Normalized counts, Raw data counts and Fold Change data obtained by nSolver Analysis Software 3.0 which includes the analysis for all the 15 samples. In the fold change data the three replicates from each sample were grouped together and the fold changes were created by Ratio of each treatment versus the untreated control sample

source_name: HCT116 Sarb 35 3

label_protocol: 50 ng of total RNA (contained in 5 µl) of each sample was labeled with the Reporter CodeSet & Capture ProbeSet included in the following kit: nCounter PanCancer Pathways Panel (XT_PGX_HuV1_CancerPath_CSO XT-CSO-PATH1-12)

growth_protocol: HCT116 cells were let grown in RPMI medium, supplemented wit 10% FBS and 1% P/S.

extract_protocol: The collection of cell pellet was performed on ice and the cells were scraped from the plates and the respective supernatants with the cells were transferred to a 50-ml tube, washed with ice cold PBS and the remaining cells were scraped and centrifuged for 5 min, 5000 rpm at 4° C. The supernatants were then discarded and the cells were washed with 1 ml cold PBS, transferred to 1.5 ml tube and centrifuged another time with the same settings. The supernatants were then discarded, the pellets were freeze in liquid nitrogen and stored at -80° C. RNA was isolated using QIAzol® Lysis Reagent (Qiagen) in combination with RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocols. cDNA synthesis was performed with the QuantiTect Reverse Transcription Kit (Qiagen)

treatment_protocol: After 24 h of adherence the cells were washed with PBS and treated with 40 µM of TQ, 15 µM of 5-FU, 35 µM of Combi (35 µM TQ + 35 µM 5-FU) and 35 µM of SARB hybrid, or left untreated. The cells were collected after 24 h of treatment.


title: SARB 35 2

description:
20160919_206971480318_01_11.RCC
SAMPLE 14

source_name: HCT116 Sarb 35 2


title: F1-3

value: An'nong 591 F1


title: SARB 35 1

description:
20160919_206971480318_01_10.RCC
SAMPLE 13

source_name: HCT116 Sarb 35 1


title: Combi 35 3

description:
20170210_207181720718_HCEC TNF30 HCEC C3 HCT116_03.RCC
SAMPLE 12


title: F1-2


title: Combi 35 1

description:
20170706_207065740518_HCT116 HCEC_01.RCC
SAMPLE 10


title: CS-1

value: control


title: CS-3


title: CS-2


title: F1-1


title: CR-2


title: AM580_2

city: Hong Kong

first: Jasper

middle: Fuk-Woo

last: Chan

state: Hong Kong

address: Block T, 122 Pokfield Road

department: Microbiology

country: Hong Kong

institute: The University of Hong Kong

data_processing:
BGISeq-500 reads were trimmed and clipped for quality control.
Read quality was checked for each sample using FastQC v0.10.1.
High-quality reads were then imported into TopHat v2.0.8 for alignment into BAM files.
BAM files were imported into Cufflinks v2.0.2 for FPKM count and DEG analysis.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM of all genes in all conditions in xls format

source_name: Calu-3 cells

growth_protocol: Cells are maintained in DMME medium supplemented with 10% heat-inactivated Fetal Bovine Serum (FBS) (Gibco), 50 units/ml penicillin and 50 µg/ml streptomycin (P/S) (Invitrogen)

extract_protocol:
Cell lysate were collected and cellular RNA were extracted using Rneasy mini rna extraction kit (qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Calu-3 cells were mock infected or infected with MERS-CoV at 2 MOI and incubated in DMEM medium. At 24hpi, total cellular RNAs  were collected.

value: lung adenocarcinoma

tag: passage


title: Virus_2


title: AM580_1


title: 5-FU 15 1

description:
20160919_206971480318_01_07.RCC
SAMPLE 7


title: AM580_3


title: 5-FU 15 2

description:
20160919_206971480318_01_08.RCC
SAMPLE 8


title: TQ 40 3

description:
20160919_206971480318_01_06.RCC
SAMPLE 6


title: 5-FU 15 3

description:
20160919_206971480318_01_09.RCC
SAMPLE 9


title: Ctr 3

description:
20170706_207065740518_HCT116 HCEC_03.RCC
SAMPLE 3

source_name: HCT116 Ctr 3


title: TQ 40 2

description:
20160919_206971480318_01_05.RCC
SAMPLE 5


title: TQ 40 1

description:
20160919_206971480318_01_04.RCC
SAMPLE 4


title: Virus_3


title: CR-3


title: Eed_ko_2i_rep2_S33166

value: Eed-/-

value: Adapted to defined media containing 2i >14 days


title: Ctr 1

description:
20160919_206971480318_01_01.RCC
SAMPLE 1

source_name: HCT116 Ctr 1


title: Virus_1


title: Combi 35 2

description:
20170210_207181720718_HCEC TNF30 HCEC C3 HCT116_02.RCC
SAMPLE 11


title: CR-1

value: seedlings

value: leaves


title: Suz12_ko_2i_rep2_S33168

value: Suz12 KO


title: CF1-3


title: Mock_3


title: Suz12_ko_2i_rep1_S33167


title: Mock_2


title: CF1-2


title: 74_110H8 48h

status: Public on Nov 23 2018

city: Sherbrooke

first: Sherif

last: Abou Elela

state: Québec

address: 3201, rue Jean-Mignault

department: Microbiologie et Infectiologie

country: Canada

institute: Université de Sherbrooke

data_processing:
TrimmomaticPE: Started with arguments: -phred33 R1.fastq.gz R2.fastq.gz R1TRIMpaired.fastq.gz R1TRIMunpaired.fastq.gz R2TRIMpaired.fastq.gz R2TRIMunpaired.fastq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
alignment bowtie2 -x SacCer3 -1 R1TRIMpaired.fastq.gz  -2 R2TRIMpaired.fastq.gz  -S TRIM.sam
htseq-count -s yes -t exon TRIM.sam  > TRIM.csv
TUXEDO suite for FPKM
DESeq2 for LOG2FC
Genome_build: SacCer3
Supplementary_files_format_and_content: comma-separated-value (csv) files holding the name of every gene and their abundance value (raw counts , fpkm for each dataset) and LOG2FC for comparison

organism: Saccharomyces cerevisiae

source_name: ysf3Δi strain #2

growth_protocol:
grown to stationary phase in synthetic minimal media
Cells grown in SD supplemented with histine, leucine, uracil, lysine and 2% of D-glucose

extract_protocol:
Total RNA ribodepleted, fragmented (200nt)
Total RNA was isolated from cells grown in log or stationary phases using a commercial kit (Omega Bio-Tek) and DNase treatment (Qiagen) was performed.
RNA libraries were prepared for sequencing using standard Illumina protocols (ScriptSeqV2 RNA-Seq)

value: ysf3-intron deletion

value: BY background


title: Ctr 2

description:
20170706_207065740518_HCT116 HCEC_02.RCC
SAMPLE 2

source_name: HCT116 Ctr 2


title: 74_110H6 log

source_name: ysf3Δi strain #1

growth_protocol:
grown to log phase in synthetic minimal media
Cells grown in SD supplemented with histine, leucine, uracil, lysine and 2% of D-glucose


title: Mock_1


title: 74_110H8 log


title: Eed_ko_2i_rep1_S33165


title: 74_110H6 48h


title: CF1-1


title: 72_121C5 48h

source_name: mms2Δi strain #2

value: mms2-intron deletion


title: WT_10H2 log

source_name: wild type strain #1

value: wild type


title: RAD21 – 1h 110 mM NaCl + 1h isotonic - IP rep2

city: Barcelona

first: Francesc

last: Posas

address: Carrar Baldiri Reixac 10

country: Spain

institute: Cell Signaling Group, IRB Barcelona

description: SEQUENCING_CORE: CRG

data_processing:
CTCF and RAD21 ChIP-sequencing reads were mapped against hg38 using bowtie2 v2.2.6 (settings: --very-sensitive). For RAD21, Illumina sequencing adapters were trimmed with cutadapt (settings: --quality-base 33 -q 28,28) and only the first mate was used for downstream analyses. Narrow CTCF and RAD21 peaks were called using MACS2 callpeak (-g hs -B --SPMR) supplying the corresponding input DNA as background control. Differential binding of CTCF and RAD21 was assessed by DiffBind v2.4.6 using minOverlap=2 to count reads in binding site intervals, DBA_REPLICATE as  blocking factor and the DESeq2 implementation (DBA_DESEQ2) for hypothesis testing. All motif analyses were performed using HOMER's findMotifsGenome.pl (v4.9.1).
Pol II ChIP-sequencing reads were mapped against hg38 using bowtie2 v2.2.6 (settings: --very-sensitive). Broad Pol II peaks were called using MACS2 callpeak (-g hs -B --SPMR --broad --broad-cutoff 0.1 -p 0.01) supplying the corresponding input DNA as background control.
Genome_build: hg38
Supplementary_files_format_and_content: MACS2 narrow peak calls for CTCF and RAD21 samples in narrowPeak format as well as MACS2 broad peak calls for PolII samples in broadPeak format are provided.

source_name: T47D whole cell

growth_protocol: T47D were routinely grown in their optimal medium according the ATCC recommendations.

extract_protocol:
Cells were cross-linked in 1% formaldehyde for 10 min, quenched with glycine for 5 min and harvested in 2 mL of PBS with protease inhibitors. The cells were then lysed, first in cell lysis buffer (5 mM Pipes pH 8, 85 mM KCl, 0.5% Nonidet P-40) and then in nuclei lysis buffer (50 mM Tris–HCl pH 8.1, 1% SDS, 10 mM EDTA), after which sonication was performed (15x30 sec, intervals of 30 sec). Subsequently DNA was immunoprecipitated with the indicated antibody O/N at 4 ºC with IP buffer (16.7 mM Tris–HCl pH 8, 167 mM NaCl, 1.2 mM EDTA, 0.01% SDS, 1.1% TritonX100). Pre-blocked beads (50 uL magnetic (Dynabeads from Invitrogen) or 50 uL of Agarose (Diagenode) beads) were incubated with samples for 1 h at 4 ºC, and were then washed with 2x low salt (20 mM Tris–HCl pH 8, 0.1% SDS, 1% Triton x100, 2 mM EDTA, 150 mM NaCl), 2x high salt (20 mM Tris–HCl pH 8, 0.1% SDS, 1% Triton X100, 2 mM EDTA, 500 mM NaCl), 2x LiCl (10 mM Tris–HCl pH 8, 250 mM LiCl, 1% Nonidet-P40; 1% Na deoxycholate; 1 mM EDTA) and 2x TE (10 mM Tris pH 8, 1 mM EDTA). Beads were eluted with 1% SDS, 0.1 M NaHCO3 for 10 min at 65 ºC and were then de-crosslinked O/N at 65 ºC with NaCl (200 mM). The following day, RNAse A digestions were performed for 2 h at 37 ºC and proteinase K digestions were performed for 1 h at 45 ºC. Finally, DNA was extracted using phenol /chloroform /isoamyl precipitation and was eluted in 30 uL of water. CTCF and Pol II ChIP-seq were performed using Protein A Agarose Beads (Diagenode #C03020002). RAD21 ChIP-seq was performed using Invitrogen M-280 sheep anti-rabbit IgG #112.03D magnetic beads.
TruSeq ChIP Library Preparation Kit according to manufacturer specifications.

treatment_protocol: For the experiments cells were grown 48 hours in medium without phenol red complemented with 10% charchoal-dextran treated Fetal Bovine Serum (which corresponds to steroid depleted condition). After further synchronization in G0/G1 by overnight culture in medium without phenol red in absence of FBS, cells were harvested (steroid depleted (-H) condition). In the case of stress treatments, cells were further treated for the times indicated with 110 mM NaCl or shifted to isotonic condition for 60 min (recovery).

tag: chip antibody

tag: replicate

value: untreated

value: 110 mM NaCl

value: 60 min + 60 min


title: 72_121C3 log

source_name: mms2Δi strain #1


title: 72_121C5 log


title: 72_121C3 48h


title: WT_10H3 48h

source_name: wild type strain #2


title: WT_10H2 48h


title: RAD21 – 1h 110 mM NaCl - IP rep2

description: SEQUENCING_CORE: CRG

value: 60 min


title: WT_10H3 log


title: RAD21 – no stress - IP rep2

description: SEQUENCING_CORE: CRG


title: RAD21 – 1h 110 mM NaCl - IP rep1

description: SEQUENCING_CORE: CRG


title: RAD21 – no stress - IP rep1

description: SEQUENCING_CORE: CRG


title: CD4+ T cells #6

city: Leiden

last: Li

address: Albinusdreef 2

institute: LUMC

data_processing:
cellranger version 1.3.1 mkfastq
cellranger version 1.3.1 count
Genome_build: GRCh38
Supplementary_files_format_and_content: Count table in H5 format.  Barcode list and gene list in tsv format.  Matrix in mtx format.

extract_protocol:
A single-cell suspension was prepared following the 10X Genomics single cell sample preparation protocol.
Droplet-based single-cell partitioning and single-cell RNA-Seq libraries were generated using the Chromium Single-Cell 3′ Reagent v2 Kit (10X Genomics, Pleasanton, CA) as per the manufacturer’s protocol.
R2 contains the biological information.  R1 has 16bp of 10x barcode and 10bp of UMI.  I1 contains the sample index barcode (8bp).

treatment_protocol: Single, live, CD3+CD8a–TCRγδ–CD4+/– T-cells from the intestines of fetus #6 were sorted using a FACSAria III flow cytometer (BD Biosciences). Post-sort purity was 96.5%.

value: fetus

tag: gestational week

value: intestine

value: CD4+ T

tag: molecule subtype

value: nuclear RNA


title: RAD21 – 1h 110 mM NaCl + 1h isotonic - IP rep1

description: SEQUENCING_CORE: CRG


title: H3K27Ac_HUVEC_siERG+siFLI1_Rep1

city: Kumamoto

first: Nao

last: Nagai

address: 2-2-1 Honjo, Chuo-ku

country: Japan

institute: Kumamoto University

data_processing:
Basecalling and demultiplexing were performed using CASAVA1.8.2 (Illumina).
ChIP-seq reads were aligned to the hg19 reference genome using ELAND (Illumina).
Peak-calling was performed with MACS with the default settings.
bigWig files were converted from Wig files using the wigToBigWig program.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

growth_protocol: HUVECs were cultured in EGM-2 (Lonza) supplemented with 5% fetal bovine serum.

extract_protocol:
Whole cell lysate was sonicated and subsequently incubated with the antibody to isolate DNA.
Libraries were prepared using KAPA Hyper Prep Kit (for illumina) (KAPA)

treatment_protocol: siRNAs were transfected with RNAiMAX Transfection Reagent (Thermo Fisher Scientific) following the manufacturer’s instructions.

tag: cell type

value: HUVEC

tag: stimulation

value: siERG+siFLI1, day7

value: H3K27Ac (MBL, MABI0309)


title: FLI1_HUVEC_Rep1

value: FLI1 (Santa Cruz, sc-356)


title: H3K4me3_HUVEC_siERG+siFLI1_Rep1

value: H3K4me3 (MBL, MABI0304)


title: ERG_HUVEC_Rep1

value: ERG (Abcam, ab136152)


title: RAD21 – input

description: SEQUENCING_CORE: CRG

tag: cell line


title: H3K27Ac_HUVEC_siControl_Rep1

value: siControl, day7


title: H3K4me3_HUVEC_siControl_Rep1


title: SS2_15_0049_P21

city: Lund

first: Kristian

last: Pietras

address: Medicon Village, Building 404:A3

department: Laboratory Medicine

country: Sweden

institute: Lund University

data_processing:
Single-end 43 bp long reads were aligned at ESCG to mm10 mouse genome.
RefSeq annotation was used for gene expression quantification, which resulted in 24490 endogenous gene counts and 92 spike-in counts
The expression values were computed as reads per kilobase of gene model and million mappable reads (RPKMs) to normalize for varying sequencing depths across sequenced cells and the gene lengths.
The expression values were computed per gene as described in Ramsköld et al. (2009 PLoS Comp Biol), using uniquely aligned reads and correcting for the uniquely alignable positions using MULTo (Storvall et al. 2013 PLoS ONE).
Genome_build: mm10

source_name: Mammary tumor fibroblast

extract_protocol:
Breast tumors and mammary fat pads of FVB/N-Tg(MMTVPyVT)634Mul/J mice were collected after heart perfusion with PBS. Tumors were minced and digested in 10 ml FACS buffer PBS, 5% Cell dissociation buffer (Gibco), 0.2 % BSA containing 25 mg Collagenase II, 25 mg Collagenase IV, 5 mg DNAse, 15 min stirring at 37 °C. The digested cell suspension was strained through a 100 µm cell strainer with the plunger of a plastic syringe. After spinning down for 3 minutes at 300 x g, red blood cells were lysed using RBL buffer containing 0.15 M ammonium chloride and 10 mM sodium EDTA in ddH2O for 30 seconds. Red blood cell lysis was stopped with ice cold FACS buffer. Cells were counted after additional straining through a 70 µm mesh cells and centrifugation at 300 x g for 3 minutes. Fc regions on cells were blocked with 2 µl Fc-block in 50µl FACS buffer per 10^6 cells for 10 min on ice. The cells were incubated in staining cocktail containing anti-CD31-APC (1 µl/10^6 cells) anti-CD45-APC (1 µl/10^6 cells), anti-CSPG4-AF647 (0.4 µl/10^6 cells) and anti-CD326-APC (5 µl/10^6 cells) in FACS buffer for 30 minutes on ice. 4’-6’-diamidino-2-phenylindole (DAPI) was added to the cell suspension before sorting for alive EpCAM-, NG2-, CD31-, CD45- cells.
The library were constructed following the Smart-Seq2 protocol (Picelli et al. Nature Methods 2013).

tag: age

value: 14 weeks

tag: marker genes

value: Mammary tumor fibroblast

value: cancer-associated fibroblasts (CAFs)


title: SS2_15_0049_P20


title: SS2_15_0049_P19


title: SS2_15_0049_P18


title: SS2_15_0049_P22


title: SS2_15_0049_P17


title: SS2_15_0049_P15


title: SS2_15_0049_P14


title: SS2_15_0049_P12


title: SS2_15_0049_P11


title: SS2_15_0049_P10


title: SS2_15_0049_P9


title: SS2_15_0049_P8


title: SS2_15_0049_P16


title: SS2_15_0049_P7


title: SS2_15_0049_P6


title: SS2_15_0049_P5


title: SS2_15_0049_P4


title: SS2_15_0049_P24


title: SS2_15_0049_P23


title: SS2_15_0049_P3


title: SS2_15_0049_O24


title: SS2_15_0049_O20


title: SS2_15_0049_O22


title: SS2_15_0049_P1


title: SS2_15_0049_P2


title: SS2_15_0049_P13


title: SS2_15_0049_O23


title: SS2_15_0049_O21


title: SS2_15_0049_O18


title: SS2_15_0049_O15


title: SS2_15_0049_O16


title: SS2_15_0049_O17


title: SS2_15_0049_O13


title: SS2_15_0049_O12


title: SS2_15_0049_O11


title: SS2_15_0049_O9


title: SS2_15_0049_O10


title: SS2_15_0049_O8


title: SS2_15_0049_O2


title: SS2_15_0049_O4


title: SS2_15_0049_O3


title: SS2_15_0049_O1


title: SS2_15_0049_N24


title: SS2_15_0049_O6


title: SS2_15_0049_O19


title: SS2_15_0049_N23


title: SS2_15_0049_N22


title: SS2_15_0049_N21


title: SS2_15_0049_O14


title: SS2_15_0049_N18


title: SS2_15_0049_N17


title: SS2_15_0049_N14


title: SS2_15_0049_N16


title: SS2_15_0049_N13


title: SS2_15_0049_N10


title: SS2_15_0049_N19


title: SS2_15_0049_N15


title: SS2_15_0049_O5


title: SS2_15_0049_N9


title: SS2_15_0049_N11


title: SS2_15_0049_N7


title: SS2_15_0049_O7


title: SS2_15_0049_N4


title: SS2_15_0049_N12


title: SS2_15_0049_N8


title: SS2_15_0049_N6


title: SS2_15_0049_N1


title: SS2_15_0049_M24


title: SS2_15_0049_N3


title: SS2_15_0049_M23


title: SS2_15_0049_N2


title: SS2_15_0049_M21


title: SS2_15_0049_M20


title: SS2_15_0049_M19


title: SS2_15_0049_M17


title: SS2_15_0049_M15


title: SS2_15_0049_M14


title: SS2_15_0049_M16


title: SS2_15_0049_M13


title: SS2_15_0049_N20


title: SS2_15_0049_M9


title: SS2_15_0049_M10


title: SS2_15_0049_N5


title: SS2_15_0049_M11


title: SS2_15_0049_M8


title: SS2_15_0049_M3


title: SS2_15_0049_M7


title: SS2_15_0049_M6


title: SS2_15_0049_M5


title: SS2_15_0049_L24


title: SS2_15_0049_M1


title: SS2_15_0049_M4


title: SS2_15_0049_L20


title: SS2_15_0049_L18


title: SS2_15_0049_L23


title: SS2_15_0049_L21


title: SS2_15_0049_M12


title: SS2_15_0049_L17


title: SS2_15_0049_M2


title: SS2_15_0049_L12


title: SS2_15_0049_L14


title: SS2_15_0049_M22


title: SS2_15_0049_M18


title: SS2_15_0049_L16


title: SS2_15_0049_L15


title: SS2_15_0049_L13


title: SS2_15_0049_L10


title: SS2_15_0049_L11


title: SS2_15_0049_L8


title: SS2_15_0049_L7


title: SS2_15_0049_L9


title: SS2_15_0049_L5


title: SS2_15_0049_L6


title: SS2_15_0049_L19


title: SS2_15_0049_L3


title: SS2_15_0049_L4


title: SS2_15_0049_K23


title: SS2_15_0049_K22


title: SS2_15_0049_L2


title: SS2_15_0049_K24


title: SS2_15_0049_K20


title: SS2_15_0049_K17


title: SS2_15_0049_L22


title: SS2_15_0049_K18


title: SS2_15_0049_K21


title: SS2_15_0049_K11


title: SS2_15_0049_K12


title: SS2_15_0049_K13


title: SS2_15_0049_K7


title: SS2_15_0049_K10


title: SS2_15_0049_K9


title: SS2_15_0049_K8


title: SS2_15_0049_K6


title: SS2_15_0049_K16


title: SS2_15_0049_L1


title: SS2_15_0049_K5


title: SS2_15_0049_K2


title: SS2_15_0049_K19


title: SS2_15_0049_J23


title: SS2_15_0049_K3


title: SS2_15_0049_J22


title: SS2_15_0049_K4


title: SS2_15_0049_K1


title: SS2_15_0049_J24


title: SS2_15_0049_J16


title: SS2_15_0049_J19


title: SS2_15_0049_K15


title: SS2_15_0049_J20


title: SS2_15_0049_J15


title: SS2_15_0049_J14


title: SS2_15_0049_K14


title: SS2_15_0049_J17


title: SS2_15_0049_J12


title: SS2_15_0049_J21


title: SS2_15_0049_J11


title: SS2_15_0049_J10


title: SS2_15_0049_J9


title: SS2_15_0049_J13


title: SS2_15_0049_J6


title: SS2_15_0049_J8


title: SS2_15_0049_J7


title: SS2_15_0049_J18


title: SS2_15_0049_J4


title: SS2_15_0049_J5


title: SS2_15_0049_J3


title: SS2_15_0049_I21


title: SS2_15_0049_I18


title: SS2_15_0049_J1


title: SS2_15_0049_I24


title: SS2_15_0049_I17


title: SS2_15_0049_I19


title: SS2_15_0049_I15


title: SS2_15_0049_I10


title: SS2_15_0049_I20


title: SS2_15_0049_I16


title: SS2_15_0049_I14


title: SS2_15_0049_I11


title: SS2_15_0049_I8


title: SS2_15_0049_I9


title: SS2_15_0049_I7


title: SS2_15_0049_J2


title: SS2_15_0049_I12


title: SS2_15_0049_I6


title: SS2_15_0049_I22


title: SS2_15_0049_I5


title: SS2_15_0049_I23


title: SS2_15_0049_I3


title: SS2_15_0049_I1


title: SS2_15_0049_I4


title: SS2_15_0049_H23


title: SS2_15_0049_I2


title: SS2_15_0049_H21


title: SS2_15_0049_H18


title: SS2_15_0049_H22


title: SS2_15_0049_H24


title: SS2_15_0049_H20


title: SS2_15_0049_H14


title: SS2_15_0049_H19


title: SS2_15_0049_H17


title: SS2_15_0049_H15


title: SS2_15_0049_I13


title: SS2_15_0049_H12


title: SS2_15_0049_H13


title: SS2_15_0049_H10


title: SS2_15_0049_H9


title: SS2_15_0049_H8


title: SS2_15_0049_H6


title: SS2_15_0049_H5


title: SS2_15_0049_H2


title: SS2_15_0049_H7


title: SS2_15_0049_H4


title: SS2_15_0049_H1


title: SS2_15_0049_G24


title: SS2_15_0049_H3


title: SS2_15_0049_G22


title: SS2_15_0049_H16


title: SS2_15_0049_G23


title: SS2_15_0049_G21


title: SS2_15_0049_G20


title: SS2_15_0049_G19


title: SS2_15_0049_H11


title: SS2_15_0049_G16


title: SS2_15_0049_G15


title: SS2_15_0049_G17


title: SS2_15_0049_G18


title: SS2_15_0049_G13


title: SS2_15_0049_G9


title: SS2_15_0049_G7


title: SS2_15_0049_G12


title: SS2_15_0049_G8


title: SS2_15_0049_G6


title: SS2_15_0049_G11


title: SS2_15_0049_G5


title: SS2_15_0049_G3


title: SS2_15_0049_G2


title: SS2_15_0049_G1


title: SS2_15_0049_F24


title: SS2_15_0049_F23


title: SS2_15_0049_F22


title: SS2_15_0049_F19


title: SS2_15_0049_F21


title: SS2_15_0049_F16


title: SS2_15_0049_F17


title: SS2_15_0049_F18


title: SS2_15_0049_G14


title: SS2_15_0049_F15


title: SS2_15_0049_G10


title: SS2_15_0049_F12


title: SS2_15_0049_F9


title: SS2_15_0049_F14


title: SS2_15_0049_F10


title: SS2_15_0049_F11


title: SS2_15_0049_F7


title: SS2_15_0049_F13


title: SS2_15_0049_F8


title: SS2_15_0049_F6


title: SS2_15_0049_F5


title: SS2_15_0049_F3


title: SS2_15_0049_F4


title: SS2_15_0049_G4


title: SS2_15_0049_F2


title: SS2_15_0049_E23


title: SS2_15_0049_F20


title: SS2_15_0049_E24


title: SS2_15_0049_E22


title: SS2_15_0049_E21


title: SS2_15_0049_E19


title: SS2_15_0049_E18


title: SS2_15_0049_E17


title: SS2_15_0049_E15


title: SS2_15_0049_E16


title: SS2_15_0049_E13


title: SS2_15_0049_E11


title: SS2_15_0049_E10


title: SS2_15_0049_E8


title: SS2_15_0049_E12


title: SS2_15_0049_E9


title: SS2_15_0049_E14


title: SS2_15_0049_E5


title: SS2_15_0049_E3


title: SS2_15_0049_E4


title: SS2_15_0049_E7


title: SS2_15_0049_E6


title: SS2_15_0049_E2


title: SS2_15_0049_D24


title: SS2_15_0049_E1


title: SS2_15_0049_D23


title: SS2_15_0049_D22


title: SS2_15_0049_D21


title: SS2_15_0049_F1


title: SS2_15_0049_E20


title: SS2_15_0049_D19


title: SS2_15_0049_D17


title: SS2_15_0049_D18


title: SS2_15_0049_D20


title: SS2_15_0049_D16


title: SS2_15_0049_D15


title: SS2_15_0049_D13


title: SS2_15_0049_D11


title: SS2_15_0049_D14


title: SS2_15_0049_D9


title: SS2_15_0049_D10


title: SS2_15_0049_D8


title: SS2_15_0049_D6


title: SS2_15_0049_D4


title: SS2_15_0049_D2


title: SS2_15_0049_C24


title: SS2_15_0049_C20


title: SS2_15_0049_D3


title: SS2_15_0049_C22


title: SS2_15_0049_D5


title: SS2_15_0049_C21


title: SS2_15_0049_D1


title: SS2_15_0049_C23


title: SS2_15_0049_C15


title: SS2_15_0049_C11


title: SS2_15_0049_C13


title: SS2_15_0049_C14


title: SS2_15_0049_C18


title: SS2_15_0049_C19


title: SS2_15_0049_C12


title: SS2_15_0049_C17


title: SS2_15_0049_C10


title: SS2_15_0049_C16


title: SS2_15_0049_D12


title: SS2_15_0049_D7


title: SS2_15_0049_C9


title: SS2_15_0049_C8


title: SS2_15_0049_C6


title: SS2_15_0049_C4


title: SS2_15_0049_C5


title: SS2_15_0049_B24


title: SS2_15_0049_C1


title: SS2_15_0049_B22


title: SS2_15_0049_B23


title: SS2_15_0049_B19


title: SS2_15_0049_B17


title: SS2_15_0049_B18


title: SS2_15_0049_B21


title: SS2_15_0049_B16


title: SS2_15_0049_B15


title: SS2_15_0049_B10


title: SS2_15_0049_B9


title: SS2_15_0049_B8


title: SS2_15_0049_B12


title: SS2_15_0049_B13


title: SS2_15_0049_C3


title: SS2_15_0049_B14


title: SS2_15_0049_B7


title: SS2_15_0049_B2


title: SS2_15_0049_B3


title: SS2_15_0049_B4


title: SS2_15_0049_C2


title: SS2_15_0049_B11


title: SS2_15_0049_A24


title: SS2_15_0049_B5


title: SS2_15_0049_B20


title: SS2_15_0049_A22


title: SS2_15_0049_A21


title: SS2_15_0049_A20


title: SS2_15_0049_B6


title: SS2_15_0049_C7


title: SS2_15_0049_A18


title: SS2_15_0049_A17


title: SS2_15_0049_A15


title: SS2_15_0049_A14


title: SS2_15_0049_A11


title: SS2_15_0049_A12


title: SS2_15_0049_A13


title: SS2_15_0049_A10


title: SS2_15_0049_B1


title: SS2_15_0049_A9


title: SS2_15_0049_A5


title: SS2_15_0049_A6


title: SS2_15_0049_A8


title: SS2_15_0049_A7


title: SS2_15_0048_P24


title: SS2_15_0049_A1


title: SS2_15_0049_A2


title: SS2_15_0048_P22


title: SS2_15_0049_A4


title: SS2_15_0048_P23


title: SS2_15_0049_A19


title: SS2_15_0048_P20


title: SS2_15_0048_P18


title: SS2_15_0048_P21


title: SS2_15_0048_P17


title: SS2_15_0048_P19


title: SS2_15_0049_A16


title: SS2_15_0048_P16


title: SS2_15_0048_P14


title: SS2_15_0048_P15


title: SS2_15_0048_P13


title: SS2_15_0049_A3


title: SS2_15_0048_P12


title: SS2_15_0048_P8


title: SS2_15_0048_P9


title: SS2_15_0048_P4


title: SS2_15_0048_P6


title: SS2_15_0048_P7


title: SS2_15_0048_P3


title: SS2_15_0048_P2


title: SS2_15_0048_P1


title: SS2_15_0048_O23


title: SS2_15_0048_O22


title: SS2_15_0048_O20


title: SS2_15_0048_O21


title: SS2_15_0048_O24


title: SS2_15_0048_O18


title: SS2_15_0048_O19


title: SS2_15_0048_O16


title: SS2_15_0048_O15


title: SS2_15_0048_O14


title: SS2_15_0048_O13


title: SS2_15_0048_O12


title: SS2_15_0048_P10


title: SS2_15_0048_P11


title: SS2_15_0048_O9


title: SS2_15_0048_O10


title: SS2_15_0048_O11


title: SS2_15_0048_O8


title: SS2_15_0048_O7


title: SS2_15_0049_A23


title: SS2_15_0048_O6


title: SS2_15_0048_O4


title: SS2_15_0048_O2


title: SS2_15_0048_O5


title: SS2_15_0048_O3


title: SS2_15_0048_O1


title: SS2_15_0048_N20


title: SS2_15_0048_N24


title: SS2_15_0048_N22


title: SS2_15_0048_N23


title: SS2_15_0048_N21


title: SS2_15_0048_P5


title: SS2_15_0048_N16


title: SS2_15_0048_N13


title: SS2_15_0048_N14


title: SS2_15_0048_N11


title: SS2_15_0048_O17


title: SS2_15_0048_N18


title: SS2_15_0048_N12


title: SS2_15_0048_N19


title: SS2_15_0048_N10


title: SS2_15_0048_N15


title: SS2_15_0048_N9


title: SS2_15_0048_N8


title: SS2_15_0048_M23


title: SS2_15_0048_N5


title: SS2_15_0048_N3


title: SS2_15_0048_N1


title: SS2_15_0048_N4


title: SS2_15_0048_N17


title: SS2_15_0048_M24


title: SS2_15_0048_M22


title: SS2_15_0048_N6


title: SS2_15_0048_M20


title: SS2_15_0048_M21


title: SS2_15_0048_M19


title: SS2_15_0048_M17


title: SS2_15_0048_M15


title: SS2_15_0048_M14


title: SS2_15_0048_M18


title: SS2_15_0048_M16


title: SS2_15_0048_M10


title: SS2_15_0048_M11


title: SS2_15_0048_M12


title: SS2_15_0048_M9


title: SS2_15_0048_M8


title: SS2_15_0048_N2


title: SS2_15_0048_M6


title: SS2_15_0048_M7


title: SS2_15_0048_M13


title: SS2_15_0048_M5


title: SS2_15_0048_M4


title: SS2_15_0048_M3


title: SS2_15_0048_N7


title: SS2_15_0048_M2


title: SS2_15_0048_M1


title: SS2_15_0048_L24


title: SS2_15_0048_L21


title: SS2_15_0048_L18


title: SS2_15_0048_L20


title: SS2_15_0048_L17


title: SS2_15_0048_L19


title: SS2_15_0048_L14


title: SS2_15_0048_L15


title: SS2_15_0048_L12


title: SS2_15_0048_L10


title: SS2_15_0048_L13


title: SS2_15_0048_L11


title: SS2_15_0048_L8


title: SS2_15_0048_L7


title: SS2_15_0048_L6


title: SS2_15_0048_L3


title: SS2_15_0048_L5


title: SS2_15_0048_L1


title: SS2_15_0048_L4


title: SS2_15_0048_K24


title: SS2_15_0048_L22


title: SS2_15_0048_K23


title: SS2_15_0048_K21


title: SS2_15_0048_K20


title: SS2_15_0048_K19


title: SS2_15_0048_K18


title: SS2_15_0048_K17


title: SS2_15_0048_L16


title: SS2_15_0048_K15


title: SS2_15_0048_K14


title: SS2_15_0048_K16


title: SS2_15_0048_K11


title: SS2_15_0048_K10


title: SS2_15_0048_K9


title: SS2_15_0048_K12


title: SS2_15_0048_K8


title: SS2_15_0048_L2


title: SS2_15_0048_K7


title: SS2_15_0048_K6


title: SS2_15_0048_K5


title: SS2_15_0048_K3


title: SS2_15_0048_K4


title: SS2_15_0048_K2


title: SS2_15_0048_J24


title: SS2_15_0048_K22


title: SS2_15_0048_J19


title: SS2_15_0048_J20


title: SS2_15_0048_J23


title: SS2_15_0048_J21


title: SS2_15_0048_J18


title: SS2_15_0048_J17


title: SS2_15_0048_J22


title: SS2_15_0048_J16


title: SS2_15_0048_J14


title: SS2_15_0048_J15


title: SS2_15_0048_K1


title: SS2_15_0048_J7


title: SS2_15_0048_J8


title: SS2_15_0048_I24


title: SS2_15_0048_J6


title: SS2_15_0048_J1


title: SS2_15_0048_J5


title: SS2_15_0048_I23


title: SS2_15_0048_J10


title: SS2_15_0048_J9


title: SS2_15_0048_J11


title: SS2_15_0048_J4


title: SS2_15_0048_J3


title: SS2_15_0048_J2


title: SS2_15_0048_I21


title: SS2_15_0048_J12


title: SS2_15_0048_J13


title: SS2_15_0048_I18


title: SS2_15_0048_I12


title: SS2_15_0048_I14


title: SS2_15_0048_I17


title: SS2_15_0048_I19


title: SS2_15_0048_I20


title: SS2_15_0048_I13


title: SS2_15_0048_I15


title: SS2_15_0048_I11


title: SS2_15_0048_I16


title: SS2_15_0048_I3


title: SS2_15_0048_I1


title: SS2_15_0048_I2


title: SS2_15_0048_I8


title: SS2_15_0048_I4


title: SS2_15_0048_I10


title: SS2_15_0048_I6


title: SS2_15_0048_I7


title: SS2_15_0048_H23


title: SS2_15_0048_I5


title: SS2_15_0048_H24


title: SS2_15_0048_I22


title: SS2_15_0048_H22


title: SS2_15_0048_H20


title: SS2_15_0048_H19


title: SS2_15_0048_H18


title: SS2_15_0048_H17


title: SS2_15_0048_I9


title: SS2_15_0048_H16


title: SS2_15_0048_H15


title: SS2_15_0048_H13


title: SS2_15_0048_H14


title: SS2_15_0048_H12


title: SS2_15_0048_H11


title: SS2_15_0048_H10


title: SS2_15_0048_H9


title: SS2_15_0048_H7


title: SS2_15_0048_H8


title: SS2_15_0048_H6


title: SS2_15_0048_H4


title: SS2_15_0048_H3


title: SS2_15_0048_H21


title: SS2_15_0048_H2


title: SS2_15_0048_H1


title: SS2_15_0048_H5


title: SS2_15_0048_G23


title: SS2_15_0048_G22


title: SS2_15_0048_G20


title: SS2_15_0048_G18


title: SS2_15_0048_G19


title: SS2_15_0048_G21


title: SS2_15_0048_G17


title: SS2_15_0048_G15


title: SS2_15_0048_G14


title: SS2_15_0048_G16


title: SS2_15_0048_G11


title: SS2_15_0048_G12


title: SS2_15_0048_G10


title: SS2_15_0048_G13


title: SS2_15_0048_G9


title: SS2_15_0048_G8


title: SS2_15_0048_G6


title: SS2_15_0048_G3


title: SS2_15_0048_G5


title: SS2_15_0048_F23


title: SS2_15_0048_F24


title: SS2_15_0048_F22


title: SS2_15_0048_G2


title: SS2_15_0048_G1


title: SS2_15_0048_G24


title: SS2_15_0048_F20


title: SS2_15_0048_F17


title: SS2_15_0048_F15


title: SS2_15_0048_F19


title: SS2_15_0048_F18


title: SS2_15_0048_F16


title: SS2_15_0048_F14


title: SS2_15_0048_F13


title: SS2_15_0048_F11


title: SS2_15_0048_F10


title: SS2_15_0048_F9


title: SS2_15_0048_F8


title: SS2_15_0048_F7


title: SS2_15_0048_G7


title: SS2_15_0048_F12


title: SS2_15_0048_G4


title: SS2_15_0048_F6


title: SS2_15_0048_F21


title: SS2_15_0048_F4


title: SS2_15_0048_F3


title: SS2_15_0048_E24


title: SS2_15_0048_F2


title: SS2_15_0048_E23


title: SS2_15_0048_E21


title: SS2_15_0048_E22


title: SS2_15_0048_E18


title: SS2_15_0048_E15


title: SS2_15_0048_E16


title: SS2_15_0048_E19


title: SS2_15_0048_E17


title: SS2_15_0048_E14


title: SS2_15_0048_E11


title: SS2_15_0048_E13


title: SS2_15_0048_E9


title: SS2_15_0048_E8


title: SS2_15_0048_F5


title: SS2_15_0048_E6


title: SS2_15_0048_E7


title: SS2_15_0048_F1


title: SS2_15_0048_E4


title: SS2_15_0048_E5


title: SS2_15_0048_E3


title: SS2_15_0048_E20


title: SS2_15_0048_E2


title: SS2_15_0048_D23


title: SS2_15_0048_L9


title: SS2_15_0048_D21


title: SS2_15_0048_D20


title: SS2_15_0048_K13


title: SS2_15_0048_D19


title: SS2_15_0048_D18


title: SS2_15_0048_E12


title: SS2_15_0048_D22


title: SS2_15_0048_L23


title: SS2_15_0048_E10


title: SS2_15_0048_D14


title: SS2_15_0048_D17


title: SS2_15_0048_D15


title: SS2_15_0048_D12


title: SS2_15_0048_D13


title: SS2_15_0048_D10


title: SS2_15_0048_D9


title: SS2_15_0048_D16


title: SS2_15_0048_D8


title: SS2_15_0048_D24


title: SS2_15_0048_E1


title: SS2_15_0048_D3


title: SS2_15_0048_D5


title: SS2_15_0048_D4


title: SS2_15_0048_D6


title: SS2_15_0048_D7


title: SS2_15_0048_D1


title: SS2_15_0048_D2


title: SS2_15_0048_C24


title: SS2_15_0048_C23


title: SS2_15_0048_C22


title: SS2_15_0048_C20


title: SS2_15_0048_C21


title: SS2_15_0048_C15


title: SS2_15_0048_C14


title: SS2_15_0048_C16


title: SS2_15_0048_C18


title: SS2_15_0048_C17


title: SS2_15_0048_C13


title: SS2_15_0048_C12


title: SS2_15_0048_D11


title: SS2_15_0048_C10


title: SS2_15_0048_C7


title: SS2_15_0048_C6


title: SS2_15_0048_C8


title: SS2_15_0048_C5


title: SS2_15_0048_C9


title: SS2_15_0048_C4


title: SS2_15_0048_B24


title: SS2_15_0048_B23


title: SS2_15_0048_C3


title: SS2_15_0048_B21


title: SS2_15_0048_B22


title: SS2_15_0048_B20


title: SS2_15_0048_C1


title: SS2_15_0048_B19


title: SS2_15_0048_B18


title: SS2_15_0048_B17


title: SS2_15_0048_C19


title: SS2_15_0048_C11


title: SS2_15_0048_B15


title: SS2_15_0048_B13


title: SS2_15_0048_B14


title: SS2_15_0048_B11


title: SS2_15_0048_B8


title: SS2_15_0048_B10


title: SS2_15_0048_B9


title: SS2_15_0048_B7


title: SS2_15_0048_B4


title: SS2_15_0048_B5


title: SS2_15_0048_B3


title: SS2_15_0048_B2


title: SS2_15_0048_B1


title: SS2_15_0048_A22


title: SS2_15_0048_A23


title: SS2_15_0048_A21


title: SS2_15_0048_A19


title: SS2_15_0048_A18


title: SS2_15_0048_A15


title: SS2_15_0048_A17


title: SS2_15_0048_A12


title: SS2_15_0048_B16


title: SS2_15_0048_B12


title: SS2_15_0048_A14


title: SS2_15_0048_A13


title: SS2_15_0048_B6


title: LeeHS201712_XENLAtx_kdm3aMO_4

city: Ulsan

first: Taejoon

last: Kwon

address: 50 Unist-gil

department: Department of Biomedical Engineering

country: South Korea

institute: Ulsan National Institute of Science and Technology

data_processing:
Mapped paired-reads to primary transcripts with bwa mem (0.7.10)
Filtered out reads mapped on multiple targets (i.e. reads mapped on both species)
Count reads per transcripts, and transferred it to human orthologs (humanized)
Genome_build: X. laevis JGIv18 primary transcripts (available at http://www.xenbase.org)
Supplementary_files_format_and_content: Read counts for each samples based on Xenopus transcripts

molecule: polyA RNA

organism: Xenopus laevis

growth_protocol: Embryos at NF stage 32 were collected.

extract_protocol:
The extraction of total RNA was done by lysing the embryos in Isol-RNA lysis reagent (5 Prime, Hamburg, Germany)
RNA sequencing library was constructed according to manufacturer’s instructions (Illumina, San Diego, CA, USA) using polyA enrichment.

treatment_protocol: For morphants, we injected kdm5c MO and kdm3a MO on two-cell stage embryo.

tag: developmental stage

value: NF stage 32

value: kdm3a MO

value: whole embryo


title: LeeHS201707_XENLAtx_kdm5cMO_2

tag: injected with

value: kdm5c MO

tag: tissue


title: SS2_15_0048_A9

tag: strain


title: SS2_15_0048_A10


title: SS2_15_0048_A8


title: SS2_15_0048_A11


title: LeeHS201712_XENLAtx_kdm3aMO_3


title: LeeHS201707_XENLAtx_kdm5cMO_1


title: LeeHS201707_XENLAtx_ctrl_2


title: SS2_15_0048_A5


title: SS2_15_0048_A20


title: SS2_15_0048_A7


title: SS2_15_0048_A6


title: SS2_15_0048_A4


title: SS2_15_0048_A3


title: SS2_15_0048_A16


title: SS2_15_0048_A24


title: SS2_15_0048_A1


title: SS2_15_0048_A2


title: CD_rosuvastatin_rep6

city: Kuopio

first: Henri

last: Niskanen

department: A.I. Virtanen Institute

country: Finland

institute: University of Eastern Finland

description: Rosuvastatin sample-Chow diet - replicate 6

data_processing:
Libraries were sequenced for 50 cycles on an Illumina HiSeq 2000 according to the manufacturer’s instructions.
RNA-Seq results were trimmed to remove 3' A-stretches originating from the library preparation and poor quality reads were filtered out (minimum 97% of bp over quality cutoff 10). Reads aligning to rRNA (abundant sequences as annotated by iGenomes) and blacklisted regions (unusually low or high mappability, defined by ENCODE) were excluded from analysis.
Reads were aligned to the mm9 genome using Tophat.
Data analysis was performed using HOMER and the detailed instructions for analysis can be found at http://homer.salk.edu/homer/
Genome_build: mm9
Supplementary_files_format_and_content: Gene expression values (RPKM, log2 fold changes and FDRs) and UCSC bedGraphs are provided

source_name: mouse liver tissue

extract_protocol:
RNA was extracted from mouse livers using Trizol reagent  and ribosomal DNA was removed by RiboZero Gold Kit (Ilumina)
The RNA was base-hydrolyzed, dephosphorylated with PNK and purified using RNA Clean & Concentrator kit (Zymo). Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers containing Illumina adapter sequences. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified using ChIP DNA Clean & Concentrator kit. The recovered cDNA was RNaseH treated and circularized (CircLigase) and amplified for 10 cycles. The final product was ran on 10% TBE gel, gel purified (180-350 bp) and cleaned-up using ChIP DNA clean & Concentrator Kit.

treatment_protocol: At age of 4 months chow diet animals were fed with regular chow diet containing either placebo or Rosuvastatin for 12 weeks. Western diet animals were fed 2 months prior to treatment with western diet. Afterwards they were fed for 12 weeks with western diet containing either placebo or rosuvastatin.

value: liver

tag: genotype

value: IGF-II/LDLR-/-, ApoB 100/100

value: biological replicate #6

tag: agent

value: Rosuvastatin

tag: diet

value: Chow diet


title: CD_rosuvastatin_rep5

description: Rosuvastatin sample-Chow diet - replicate 5

value: biological replicate #5


title: Cnot6l_MII_1 [polysome RNA-seq]

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequencing reads were mapped to the mouse genome (mm9) with TopHat v2.0.11 coupled with Bowtie v2.1.0. The mapped reads were subjected to Cufflinks v2.2.1 with the reference annotation (UCSC gene models) to calculate the FPKM values of each gene.
Genome_build: mm9
Supplementary_files_format_and_content: the processed data files contain the FPKM values of each gene (gene id, chromosome, strand, TSS, TES, description, FPKM value)

growth_protocol: Oocytes at the GV stage were harvested in M2 medium (M7167; Sigma-Aldrich) and cultured in mini-drops of M16 medium (M7292; Sigma-Aldrich) covered with mineral oil (M5310; Sigma-Aldrich) at 37ºC in a 5% CO2 atmosphere. In some experiments, U0126 (20 μM) was added to the culture media to inhibit ERK1/2 activation. Zygotes were harvested from fertilized females 24 h after the hCG injection, and cultured in KSOM medium (Millipore).

extract_protocol:
Polysome-bound RNAs were purified with RNeasy Mini kit (Qiagen, 74106)
RNA-seq libraries were constructed from 500 pg of pre-amplified cDNA using a DNA library preparation kit (TruePrep DNA Library Prep Kit V2 for Illumina, Vazyme) which is based on Tn5 transposase.

tag: strain background

tag: genotype/variation

value: post natal day 21

tag: tissue/cell type

value: oocyte in vitro 16h

value: polysome bounded mRNA


title: Cnot6l_GV_1 [polysome RNA-seq]

value: oocyte PMSG48h


title: Cnot6l_GV_2 [polysome RNA-seq]


title: Cnot6l_MI_2 [polysome RNA-seq]

value: oocyte in vitro 8h


title: Cnot6l_MI_1 [polysome RNA-seq]


title: Cnot6l_MII_2 [polysome RNA-seq]


title: CD_rosuvastatin_rep4

description: Rosuvastatin sample-Chow diet - replicate 4

tag: replicate

value: biological replicate #4


title: WT_MII_2 [polysome RNA-seq]

value: wild type

tag: molecule subtype


title: CD_rosuvastatin_rep3

description: Rosuvastatin sample-Chow diet - replicate 3

value: biological replicate #3


title: CD_rosuvastatin_rep2

description: Rosuvastatin sample-Chow diet - replicate 2

value: biological replicate #2


title: WT_MI_2 [polysome RNA-seq]


title: LeeHS201707_XENLAtx_ctrl_1

value: NF stage 32

value: whole embryo


title: WT_MI_1 [polysome RNA-seq]


title: CD_rosuvastatin_rep1

description: Rosuvastatin sample-Chow diet - replicate 1

value: liver

value: biological replicate #1


title: HUVEC_siFLI1_day7

description: Gene expression data from HUVECs treated with siFLI1 for 7 days

hyb_protocol: Following fragmentation, 10 microgram of cRNA were hybridized for 16 hour at 45 degrees C. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChip was scanned using the Affymetrix GeneChip scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: HUVECs treated with siFLI1, day7

label_protocol: Biotinylated cRNA were prepared using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics)

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

tag: cell

value: HUVEC

value: siFLI1, day7


title: HUVEC_siERG_day7

description: Gene expression data from HUVECs treated with siERG for 7 days

source_name: HUVECs treated with siERG, day7

tag: stimulation

value: siERG, day7


title: HUVEC_siERG+siFLI1_day3

description: Gene expression data from HUVECs treated with siERG and FLI1 for 3 days

source_name: HUVECs treated with siERG and siFLI1, day3

value: siERG+siFLI1, day3


title: HUVEC_siControl_day7

description: Gene expression data from HUVECs treated with siControl for 7 days

source_name: HUVECs treated with siControl, day7

value: siControl, day7


title: HUVEC_siERG+siFLI1_day7

description: Gene expression data from HUVECs treated with siERG and FLI1 for 7 days

source_name: HUVECs treated with siERG and siFLI1, day7

value: siERG+siFLI1, day7


title: HUVEC_siFLI1_day3

description: Gene expression data from HUVECs treated with siFLI1 for 3 days

source_name: HUVECs treated with siFLI1, day3

value: siFLI1, day3


title: WT_MII_1 [polysome RNA-seq]

value: post natal day 21

value: oocyte in vitro 16h

value: polysome bounded mRNA


title: Pol II – 1h 110 mM NaCl - input rep2

description: SEQUENCING_CORE: CRG

tag: cell line

tag: chip antibody

value: untreated

tag: treatment

value: 110 mM NaCl

value: 60 min


title: HUVEC_siControl_day3

description: Gene expression data from HUVECs treated with siControl for 3 days

source_name: HUVECs treated with siControl, day3

value: siControl, day3


title: CD_placebo_rep5

description: Placebo sample-Chow diet - replicate 5

value: IGF-II/LDLR-/-, ApoB 100/100

value: biological replicate #5

value: Placebo

value: Chow diet


title: CD_placebo_rep4

description: Placebo sample-Chow diet - replicate 4

value: liver

value: biological replicate #4


title: Pol II – 1h 110 mM NaCl - input rep1

description: SEQUENCING_CORE: CRG


title: WT_GV_2 [polysome RNA-seq]

value: wild type

tag: age

value: oocyte PMSG48h


title: WT_GV_1 [polysome RNA-seq]


title: Pol II – no stress - input rep2

description: SEQUENCING_CORE: CRG


title: Pol II – no stress - input rep1

description: SEQUENCING_CORE: CRG


title: CD_placebo_rep3

description: Placebo sample-Chow diet - replicate 3

value: biological replicate #3


title: CD_placebo_rep2

description: Placebo sample-Chow diet - replicate 2

value: biological replicate #2


title: Btg4_Zyg_2

extract_protocol:
Total RNA was isolated from 100 oocytes at indicated stages using the RNeasy Mini kit (Qiagen, 74106). RNA-Seq libraries were prepared using Smart-Seq2 protocol with slightly modification
RNA-seq libraries were constructed from 500 pg of pre-amplified cDNA using a DNA library preparation kit (TruePrep DNA Library Prep Kit V2 for Illumina, Vazyme) which based on Tn5 transposase

value: post natal day 21

tag: cell type

value: embryo; zygote


title: Pol II – 1h 110 mM NaCl - IP rep2

description: SEQUENCING_CORE: CRG

value: Pol II (Millipore 05-623)


title: CL1-5_Stable-expreesing FAM198B gene_rep2

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

description: Gene expression data from CL1-5 stable-expressing an pcDNA3.1-FAM198B-V5 vector

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 450C on Affymetrix Human Genome U133 plus 2.0 GeneChip on Affymetrix Hybridization Oven 645, 60 RPM, then washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The expression data were analyzed by GeneSpring GX 13.0 (Silicon Genetics, Redwood City, CA). The Affymetrix CEL files were transformed by GC-RMA algorithm, and each probe set was summarized using the median of the corresponding probes.

source_name: lung cancer cell, CL1-5 stable-expressing FAM198B vector

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)(Santa Clara, CA, USA, http://www.affymetrix.com).

growth_protocol: The human lung cancer cell line, CL1-5, was grown in DMEM media supplemented with 10% FBS and  incubated at 37°C in a humidified 20% O2 and 5% CO2 environment.

treatment_protocol: CL1-5 cells were individually transfected with pcDNA3.1-V5 mock control vector and FAM198B-V5. The stable-expressing cells were maintained in complete media with 1 mg/ml neomycin.

tag: tumor type

value: lung adenocacinoma

tag: ethnicity

value: Asian

value: 64 years

tag: gender

value: male


title: CL1-5_Stable-expressing mock control vector_rep1

description: Gene expression data from CL1-5 stable-expressing an pcDNA3.1-V5 mock control vector

source_name: lung cancer cell, CL1-5 stable-expressing an mock control vector


title: CD_placebo_rep1

description: Placebo sample-Chow diet - replicate 1

tag: strain

tag: tissue

tag: genotype

value: IGF-II/LDLR-/-, ApoB 100/100

value: biological replicate #1

tag: agent


title: CL1-5_Stable-expressing mock control vector_rep3


title: CL1-5_Stable-expreesing FAM198B gene_rep1


title: CL1-5_Stable-expreesing FAM198B gene_rep3


title: HUVEC_siERG_day3

description: Gene expression data from HUVECs treated with siERG for 3 days

source_name: HUVECs treated with siERG, day3

value: HUVEC

value: siERG, day3


title: Btg4_MII_2

tag: strain background

tag: genotype/variation

value: oocyte in vitro 16h


title: CL1-5_Stable-expressing mock control vector_rep2


title: Pol II – no stress - IP rep2

description: SEQUENCING_CORE: CRG

tag: replicate

value: untreated


title: Pol II - no stress - IP rep1

description: SEQUENCING_CORE: CRG


title: CTCF – 1h 110 mM NaCl - input rep2

description: SEQUENCING_CORE: CRG

value: 110 mM NaCl

value: 60 min


title: CTCF – 30min 110 mM NaCl - input rep1

description: SEQUENCING_CORE: CRG

value: 30 min


title: Btg4_MII_1


title: CTCF – 7.5min 110 mM NaCl - input rep2

description: SEQUENCING_CORE: CRG

value: 7.5 min


title: HFD_rosuvastatin_rep5

description: Rosuvastatin sample-Western Diet - replicate 5

value: liver

value: biological replicate #5

value: Rosuvastatin

tag: diet

value: Western Diet


title: Btg4_MI_2

value: post natal day 21

value: oocyte in vitro 8h


title: Btg4_MI_1


title: HFD_rosuvastatin_rep4

description: Rosuvastatin sample-Western Diet - replicate 4

value: biological replicate #4


title: CTCF – 1h 110 mM NaCl - input rep1

description: SEQUENCING_CORE: CRG


title: Btg4_Zyg_1

value: embryo; zygote


title: CTCF – no stress - input rep2

description: SEQUENCING_CORE: CRG


title: CTCF – no stress - input rep1

description: SEQUENCING_CORE: CRG


title: CTCF – 1h 110 mM NaCl - IP rep2

description: SEQUENCING_CORE: CRG


title: CTCF – 7.5min 110 mM NaCl - input rep1

description: SEQUENCING_CORE: CRG


title: HFD_rosuvastatin_rep3

description: Rosuvastatin sample-Western Diet - replicate 3

value: IGF-II/LDLR-/-, ApoB 100/100

value: biological replicate #3


title: Pol II – 1h 110 mM NaCl - IP rep1

description: SEQUENCING_CORE: CRG

value: Pol II (Millipore 05-623)


title: HFD_rosuvastatin_rep2

description: Rosuvastatin sample-Western Diet - replicate 2

value: biological replicate #2


title: Btg4_GV_1

value: oocyte PMSG48h


title: HFD_rosuvastatin_rep1

description: Rosuvastatin sample-Western Diet - replicate 1

value: biological replicate #1


title: CTCF – 30min 110 mM NaCl - IP rep2

description: SEQUENCING_CORE: CRG

value: untreated

value: 110 mM NaCl


title: CTCF – 7.5min 110 mM NaCl - IP rep2

description: SEQUENCING_CORE: CRG

value: 7.5 min


title: RAD21 – 1h 110 mM NaCl + 1h isotonic + triptolide pre-treatment

description:
SEQUENCING_CORE: CRG
IP

data_processing:
CTCF and RAD21 ChIP-sequencing reads were mapped against hg38 using bowtie2 v2.2.6 (settings: --very-sensitive). Illumina sequencing adapters were trimmed with cutadapt (settings: --quality-base 33 -q 28,28). Narrow CTCF and RAD21 peaks were called using MACS2 callpeak (-g hs -B --SPMR) supplying a previously sequenced input DNA as background control.
Genome_build: hg38
Supplementary_files_format_and_content: MACS2 narrow peak calls for CTCF and RAD21 samples in narrowPeak format are provided.

value: replicate 1

value: 500 nM triptolide

value: 60 min + 60 min


title: HFD_placebo_rep4

description: Placebo sample-Western Diet - replicate 4

value: liver

value: Placebo

value: Western Diet


title: RAD21 – 1h 110 mM NaCl + 1h isotonic

description:
SEQUENCING_CORE: CRG
IP


title: CTCF – no stress - IP rep2

description: SEQUENCING_CORE: CRG


title: Btg4_GV_2

value: post natal day 21


title: Cnot6l_Zyg_2

value: embryo; zygote


title: RAD21 – 1h 110 mM NaCl

description:
SEQUENCING_CORE: CRG
IP

value: 60 min


title: HFD_placebo_rep3

description: Placebo sample-Western Diet - replicate 3

value: IGF-II/LDLR-/-, ApoB 100/100

value: biological replicate #3


title: RAD21 – no stress + triptolide

description:
SEQUENCING_CORE: CRG
IP


title: Cnot6l_MII_1

value: oocyte in vitro 16h


title: HFD_placebo_rep2

description: Placebo sample-Western Diet - replicate 2

value: biological replicate #2


title: Cnot6l_MII_2


title: Cnot6l_MI_2

value: oocyte in vitro 8h


title: CTCF – 1h 110 mM NaCl - IP rep1

description: SEQUENCING_CORE: CRG

value: untreated


title: HFD_placebo_rep1

description: Placebo sample-Western Diet - replicate 1

value: biological replicate #1


title: CTCF – 7.5min 110 mM NaCl - IP rep1

description: SEQUENCING_CORE: CRG

value: 110 mM NaCl

value: 7.5 min


title: Cnot6l_MI_1


title: CTCF - no stress - IP rep1

description: SEQUENCING_CORE: CRG


title: RAD21 – no stress

description:
SEQUENCING_CORE: CRG
IP

value: replicate 1


title: CTCF – 1h 110 mM NaCl + 1h isotonic + triptolide pre-treatment

description:
SEQUENCING_CORE: CRG
IP

value: 500 nM triptolide

value: 60 min + 60 min


title: HiC – 1h 110 mM NaCl + recovery + triptolide (batch 3)

description:
SEQUENCING_CORE: CRG
FPR_27

data_processing:
RNA-sequencing reads were mapped to the hg38 genome using TopHat2 v2.1.0 (settings: --max-multihits 1 --library-type fr-firststrand --b2-very-sensitive –no-coverage-search). Quantification was performed with featureCounts v1.5.1 (-s 2 -p) using the GENCODE v24 annotation. Differential expression testing was performed using DESeq2 v1.14.1
HiC sequencing reads: all steps inidicated in https://github.com/4DGenome/pipelines/tree/master/hic-16.05
Genome_build: hg38
Supplementary_files_format_and_content: DESeq2_raw_counts_NaCl.tsv contains raw read counts of RNA-seq samples obtained via featureCounts after alignment. Each column represents one sample in lexicographical order.
Supplementary_files_format_and_content: TSV files containing raw HiC contact matrices for each sample with 50kb resolution (*_raw_50kb.tsv.gz) as well as TSV files containing the eigenvectors calculated for each sample with 100kb resolution (*_ev_100kb.tsv.gz).

extract_protocol:
HiC: in situ Hi-C was performed according previously described protocol (Rao et al., 2014) with some modifications (Le Dily et al., 2017). RNA-seq: RNA from control or NaCl-treated T47D cells was extracted at the indicated times using the RNeasy Plus Mini Kit (Invitrogen #74134).
HiC: Paired-end libraries were generated with Truseq adaptors (Illumina) according previously published Hi-C protocols (Rao et al., 2014). RNA-seq: stranded polyA selected libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina, RS-122-2101) according to the manufacturer’s standard protocol.

treatment_protocol: For the experiments cells were grown 48 hours in medium without phenol red complemented with 10% charchoal-dextran treated Fetal Bovine Serum (which corresponds to steroid depleted condition). After further synchronization in. G0/G1 by overnight culture in medium without phenol red in absence of FBS, cells were harvested (steroid depleted (-H) condition). In the case of stress treatments, cells were further treated for the times indicated with 110 mM NaCl

tag: batch

value: triptolide

value: 180 min

value: 110 mM NaCl + recovery


title: HFD_rosuvastatin_rep6

description: Rosuvastatin sample-Western Diet - replicate 6

value: liver

value: biological replicate #6

value: Rosuvastatin

value: Western Diet


title: HiC – 1h 110 mM NaCl + recovery (batch 3)

description:
SEQUENCING_CORE: CRG
FPR_26

tag: cell line


title: CTCF – 1h 110 mM NaCl + 1h isotonic

description:
SEQUENCING_CORE: CRG
IP

tag: chip antibody


title: Cnot6l_GV_2

value: post natal day 21

value: oocyte PMSG48h


title: Cnot6l_GV_1


title: Cnot6l_Zyg_1

value: embryo; zygote


title: RAD21 – 1h 110 mM NaCl + triptolide

description:
SEQUENCING_CORE: CRG
IP

value: untreated

tag: treatment

value: 60 min


title: CTCF – 1h 110 mM NaCl + triptolide

description:
SEQUENCING_CORE: CRG
IP

value: 110 mM NaCl


title: WT_Zyg_2

value: wild type

tag: age


title: HiC – 1h 110 mM NaCl (batch 3)

description:
SEQUENCING_CORE: CRG
FPR_24


title: HiC – no stress + triptolide (batch 3)

description:
SEQUENCING_CORE: CRG
FPR_22


title: CTCF – 1h 110 mM NaCl

description:
SEQUENCING_CORE: CRG
IP

value: replicate 1


title: WT_Zyg_1

tag: cell type


title: CTCF – no stress + triptolide pre-treatment

description:
SEQUENCING_CORE: CRG
IP


title: WT_MII_2

value: oocyte in vitro 16h


title: HiC – 1h 110 mM NaCl (batch 2)

description:
SEQUENCING_CORE: CRG
FPR11_18430


title: WT_MII_1


title: HiC – no stress (batch 3)

description:
SEQUENCING_CORE: CRG
FPR_21


title: H3K27Ac_HUVEC_siERG+siFLI1_Rep2

value: HUVEC

tag: stimulation

value: siERG+siFLI1, day7

value: H3K27Ac (MBL, MABI0309)


title: CTCF – no stress

description:
SEQUENCING_CORE: CRG
IP


title: WT_MI_2

value: oocyte in vitro 8h


title: HiC – 1h 110 mM NaCl (batch 1)

description:
SEQUENCING_CORE: CRG
FPR3_16867


title: HiC – no stress (batch 2)

description:
SEQUENCING_CORE: CRG
FPR9_18428


title: WT_MI_1


title: HiC – no stress (batch 1)

description:
SEQUENCING_CORE: CRG
FPR1_16865


title: H3K4me3_HUVEC_siERG+siFLI1_Rep2

value: H3K4me3 (MBL, MABI0304)


title: HiC – 1h 110 mM NaCl + triptolide (batch 3)

description:
SEQUENCING_CORE: CRG
FPR_25

value: triptolide

value: 180 min


title: WT_GV_2


title: WT_GV_1


title: SS2_15_0048_C2

value: 14 weeks

tag: marker genes

value: Mammary tumor fibroblast

value: cancer-associated fibroblasts (CAFs)


title: RNA-seq – 6h 110 mM NaCl (batch 2)

description:
SEQUENCING_CORE: CRG
DESeq2_raw_counts_NaCl.tsv
RAF14_10819_TGACCA

value: 360 min


title: FLI1_HUVEC_Rep2

value: FLI1 (Abcam, ab15289)


title: ERG_HUVEC_Rep2

value: ERG (Abcam, ab136152)


title: RNA-seq – 6h 110 mM NaCl (batch 1)

description:
SEQUENCING_CORE: CRG
DESeq2_raw_counts_NaCl.tsv
RAF13_10818_CGATGT

value: untreated

value: 110 mM NaCl


title: RNA-seq – 3h 110 mM NaCl (batch 2)

description:
SEQUENCING_CORE: CRG
DESeq2_raw_counts_NaCl.tsv
RAF10_10815_GCCAAT


title: K562_ATAC_no_lysis_buffer

city: Berlin

first: Aslihan

last: Karabacak

address: Robert-Rössle-Straße 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

data_processing:
Adapter sequences were trimmed from the 3’ end of the reads. Trimmed reads were aligned to the hg19 build of the human genome, using bowtie2 (Langmead and Salzberg, 2012) with parameter -X set to 1500, to allow correct alignment of paired-end fragments up to 1500 base pairs. Only reads that aligned uniquely to a single location were retained, by filtering out the multimappers marked with the XS:i flag in the sam file. PCR duplicates were removed using Picard (http://broadinstitute.github.io/picard/). Further processing was performed to filter out contigs as well as the Y and mitochondrial chromosomes, and retain only reads that aligned concordantly as a pair within the expected fragment length range (38-1500 bp). Signal bedGraph files were generated with the SignalGenerator.sh script from JAMM (Ibrahim et al., 2014), with the parameters -f 1 and -n depth. BedGraph files were converted to the binary bigWig format.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files contain library depth normalized signal in 10 base pair bins genome-wide. These are the binary versions of bedGraph files which contain 4 columns: chromosome, start, end, signal.

extract_protocol: ATAC-seq was performed on 50000 cells, following the published protocol (Buenrostro et al., 2013) but increasing transposition time from 30 minutes to 1 hour. The centrifugation in lysis buffer step was omitted, and the cell pellets were taken directly to the transposition reaction.


title: RNA-seq – 3h 110 mM NaCl (batch 1)

description:
SEQUENCING_CORE: CRG
DESeq2_raw_counts_NaCl.tsv
RAF09_10814_ACAGTG


title: H3K27Ac_HUVEC_siControl_Rep2

value: siControl, day7


title: K562_ATAC_5_minute_lysis

extract_protocol: ATAC-seq was performed on 50000 cells, following the published protocol (Buenrostro et al., 2013) but increasing transposition time from 30 minutes to 1 hour. Cell lysis was performed via a 5 minute centrifugation in lysis buffer, as opposed to the 10 minutes described in the original protocol (Buenrostro et al., 2013).


title: RNA-seq – 1h 110 mM NaCl (batch 2)

description:
SEQUENCING_CORE: CRG
DESeq2_raw_counts_NaCl.tsv
RAF06_10811_GTCCGC

value: 60 min


title: RNA-seq – 1h 110 mM NaCl (batch 1)

description:
SEQUENCING_CORE: CRG
DESeq2_raw_counts_NaCl.tsv
RAF05_10810_ACTGAT


title: RNA-seq – no stress (batch 1)

description:
SEQUENCING_CORE: CRG
DESeq2_raw_counts_NaCl.tsv
RAF01_10806_ATCACG


title: HEK293_ATAC_low_depth_bio2_tech1

extract_protocol: ATAC-seq was performed on 100000 cells, following the published protocol (Buenrostro et al., 2013) but increasing transposition time from 30 minutes to 1 hour. In addition, the centrifugation in lysis buffer step was omitted, and the cell pellets were taken directly to the transposition reaction.


title: RNA-seq – no stress (batch 2)

description:
SEQUENCING_CORE: CRG
DESeq2_raw_counts_NaCl.tsv
RAF02_10807_ACTTGA


title: HEK293_ATAC_low_depth_bio2_tech2


title: HEK293_DNase

data_processing:
The reads were trimmed to the first 20 bases. Trimmed reads were aligned to the hg19 build of the human genome, using the Burrows-Wheeler aligner (BWA) (Li and Durbin, 2009), tolerating up to two mismatches. Sequences aligning to more than four locations were discarded. Further processing was performed to filter out unwanted chromosomes and alpha satellites. In order to remove PCR artifacts, reads that piled up (>=10 reads) at a single base were discarded, if they constituted at least 70 percent of all reads in the surrounding 30 base pair window. Signal bedGraph files were generated with the SignalGenerator.sh script from JAMM (Ibrahim et al., 2014), with the parameters -f 1 and -n depth. BedGraph files were converted to the binary bigWig format.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files contain library depth normalized signal in 10 base pair bins genome-wide. These are the binary versions of bedGraph files which contain 4 columns: chromosome, start, end, signal.

extract_protocol: DNase-seq was conducted on 50 million cells as previously described (Song and Crawford, 2010), with the minor modification of using 5’ phosphorylated oligo 1b. Samples digested with 12U, 4U and 1.2U total DNase I were pooled.


title: HEK293_ATAC_low_depth_bio1_tech2


title: HEK293_ATAC_low_depth_bio1_tech1


title: ESP3

city: Columbia

first: Sathesh

middle: K

last: Sivasankaran

state: MO

address: Bond Life Sciences Center Suite 106, 1201 Rollins Street

institute: University of Missouri

description: Early Stationary Phase

data_processing:
Segemehl V0.18 used for mapping
Read counts were calculated custom made perl script.
reads were normalised using VOOM approach from Limma package in R
Differential gene expression was calculated using Limma in R
Mapped reads were transformed into graphical "GR" files for visualisation uding IGB
Genome_build: Cronobacter sakazakii SP291; NC_020260.1
Supplementary_files_format_and_content: tab-delimited text files include VOOM transformed values for each Sample.

organism: Cronobacter sakazakii

source_name: Control

extract_protocol:
Cells were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina HiSeq2500 RNA Sample Prep Kit was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: status

value: Early Stationary Phase


title: HEK293_ATAC_medium_depth_bio1_tech2


title: K562_ATAC_10_minute_lysis

extract_protocol: ATAC-seq was performed on 50000 cells, following the published protocol (Buenrostro et al., 2013) but increasing transposition time from 30 minutes to 1 hour. Cell lysis was performed via a 10 minute centrifugation in lysis buffer, as described in the original protocol (Buenrostro et al., 2013).


title: HEK293_ATAC_medium_depth_bio1_tech1


title: K562_DNase


title: HEK293_ATAC_high_depth_bio2_tech1


title: HEK293_ATAC_medium_depth_bio2_tech1


title: polyRNA_IFNg_rep1

city: Villejuif

first: Caroline

last: Robert

state: ILE-DE-FRANCE

address: 114 rue Edouard Vaillant, Bâtiment de Médecine Moléculaire

country: France

institute: Institut Gustave Roussy

description: Gene expression data from polysomal associated RNA from A375 treated 24h with Interferon-gamma

hyb_protocol: Accoding to Affymetrix protocol

scan_protocol: Accoding to Affymetrix protocol

data_processing: The data were analyzed with  Affymetrix default analysis settings and global scaling as normalization method.

source_name: polysomal RNA, A375, IFNg, 24h

label_protocol: Accoding to Affymetrix protocol

growth_protocol: A375 melanoma cells were cultured according to the ATCC protocol

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

treatment_protocol: One day after spliting A375 cells were treated for 2 hours with DMSO or silvestrol, 24 hourswith Interferon-gamma

tag: tumor type

value: melanoma cells

tag: fraction

value: polysomal associated RNA

tag: time point

value: Interferon-gamma


title: HEK293_ATAC_high_depth_bio2_tech2


title: polyRNA_IFNg+silves_rep2

description: Gene expression data from polysomal associated RNA from A375 treated 24h with Interferon-gamma and 2h with silvestrol

source_name: polysomal RNA, A375, IFNg 24h, silves, 2h

tag: agent

value: Interferon-gamma and 2h silvestrol


title: 7312A-2

first: Hanchu

last: Xiong

address: Jiefang Road NO.88

institute: Cancer Institute, Second Affiliated Hospital, College of Medicine, Zhejiang University

description: Gene expression data from HEK293T cells transfected with Vpx 7312A expression vector

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Samples were analyzed with Affymetrix software.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

value: fibroblast


title: DMS3

description: desiccation after ESP

source_name: Treated

tag: strain

value: desiccation after ESP (Early Stationary Phase)


title: 7312A-3

source_name: HEK293T cells transfected with Vpx 7312A expression vector


title: ESP1

description: Early Stationary Phase


title: 7312A-1


title: HEK293_ATAC_high_depth_bio1_tech2


title: totRNA_IFNg+silves_rep1

description: Gene expression data from total RNA from A375 treated 24h with Interferon-gamma and 2h with silvestrol

source_name: total RNA, A375, IFNg 24h, silves, 2h

value: total RNA


title: polyRNA_DMSO_rep1

description: Gene expression data from polysomal associated RNA from A375 treated 2h with DMSO

source_name: polysomal RNA, A375,DMSO, 2h

value: DMSO


title: polyRNA_IFNg_rep2


title: polyRNA_DMSO_rep2


title: totRNA_IFNg_rep2

description: Gene expression data from total RNA from A375 treated 24h with Interferon-gamma

source_name: total RNA, A375, IFNg, 24h


title: totRNA_IFNg+silves_rep2


title: totRNA_IFNg_rep1


title: HEK293_ATAC_high_depth_bio1_tech1


title: polyRNA_IFNg+silves_rep1


title: HN120-MCRDH-H3K4me3

status: Public on Nov 22 2018

city: Singapore

first: Vibhor

last: Kumar

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

description: HS002-SR-R00208_AC9A1YACXX.CHH25656-GATCAG_S60_L008

data_processing:
Basecalls performed using gis-rpd pipelines/chromatin-profiling/chipseq/ pipline https://github.com/gis-rpd/pipelines/tree/master/chromatin-profiling/chipseq
ChIP-seq reads were aligned to the hg19 genome assembly
We employed Dfilter to call ChIP peaks in the naïve, drug-resistant and drug-holiday H3K4me3 and H3K27ac ChIP-seq libraries relative to input controls.
Genome_build: hg19
Supplementary_files_format_and_content: .wig files were generated using Dfilter.

source_name: HN120 PCRDH HNSCC

growth_protocol: Tumors were minced prior to enzymatic dissociation using 4 mg/ml Collagenase type IV (Thermo Fisher, cat. no. 17104019) in DMEM/F12, at 37 °C for 2 hours. Cells were washed using cyclical treatment of pelleting and resuspension in phosphate buffered saline (Thermo Fisher, cat. no 14190235) for 3 cycles. The final cell suspensions were strained through 70 µm cell strainers (Falcon, cat. no. 352350), prior to pelleting and resuspension in RPMI (Thermo Fisher, cat. no 61870036), supplemented with 10% fetal bovine serum (Biowest, cat. no S181B), and 1% penicillin-streptomycin (Thermo Fisher, cat. no. 15140122). Cells were kept in a humidified atmosphere of 5% CO2 at 37°C. Cell line identity was authenticated by comparing the short tandem repeat (STR) profile (Indexx BioResearch) of each cell line to its original tumor.

extract_protocol:
For chromatin prepration one million cell were cross-linked (10% FBS/DMEM containing 1.5% PFA) for 30 min. Followed by addition of 1/20 volume of 2.5M glycine, next these cells were incubated on ice for 5 min. Crosslinked cellular material was re-dissolved in buffer contacting 10 mM Tris-HCl, pH8, 1 mM EDTA, 0.5 mM EGTA, 1X protease inhibitor cocktail (Roche) followed by sonication for 10-12 cycles (30 sec on/off). Chromatin was pulled by incubation with H3K4me3 or H3K427ac antibody-coupled dynabeads and 150 μl of ChIP buffer (433 mM NaCl, 0.43% sodium deoxycholate, 4.3% Triton X-100). The 1/10 of chromatin mixture was separated for input control. The beads were washed 5x with RIPA buffer and incubated in 100 μl of elution buffer (50 mM Tris-HCl, pH8, 1% SDS, 10 mM EDTA) at 65°C for 20 min with brief vortexing followed by recovery of immunoprecipitated chromatin. The immunoprecipitated chromatin and input samples were de-crosslinked by incubation at 65°C overnight and subsequent incubation with 0.2 μg/μl of RNase A at 37°C for 1 hr and with 0.2 μg/μl of proteinase K at 55°C for 2 hr. The DNA was extracted by phenol/chloroform/isoamylalcohol (49:49:2) and ethanol precipitated in presence of 40 μg of glycogen. After washing with 70% ethanol, pellets were resuspended in 10 mM Tris-HCl, pH8.
Multiplexed ChIP-seq libraries were generated using NEBNext ChIP-seq library Prep kit (NEB) following the instructions from the manufacturer. The sequencing was performed on Illumina HiSeq-2500. We employed Dfilter to call ChIP peaks in the naïve, drug-resistant and drug-holiday H3K4me3 and H3K27ac ChIP-seq libraries relative to input controls.

treatment_protocol: Drug-resistant cells were obtained by contineous culture of cells with cisplatin.

value: Metastatic Cisplatin Resistant Drug Holiday (MCRDH) cells

tag: passages

tag: source

value: drug-holiday model

value: H3K4me3 (04-745, Millipore)


title: HN120-MCR-H2K27ac

description: HS002-SR-R00208_AC9A1YACXX.CHH25649-CTTGTA_S53_L8.final

source_name: HN120 cis-platin resistant metastatic HNSCC

value: Metastatic Cisplatin Resistant (MCR) cells

value: Cisplatin-reistant model


title: DMS2

description: desiccation after ESP


title: HN120-Met-H3K27ac

description: HS004-SR-R00143_BC5E7KANXX.CHC469-GCCAAT_S20_L5.final

source_name: HN120 Metastatic HNSCC

value: Lymph node metastatic cells

value: patient derived primary culture


title: HN120-MCRDH-H3K27ac

description: HS002-SR-R00208_AC9A1YACXX.CHH25653-GCCAAT_S57_L8.final

source_name: HN120 MCRDH HNSCC


title: HN120-PCRDH-H3K27ac

description: HS002-SR-R00209_BC9A25ACXX.CHH25657-CTTGTA_S1_L001

value: Primary Cisplatin Resistant Drug Holiday (PCRDH) cells


title: HN120-PCR-H3K4me3

description: HS004-SR-R00143_BC5E7KANXX.CHH20687-CTTGTA_S34_L8.final

source_name: HN120 cis-platin resistant primary HNSCC

value: Primary Cisplatin Resistant (PCR) cells


title: HN120-MCR-H3K4me3

description: HS002-SR-R00208_AC9A1YACXX.CHH25652-ACAGTG_S56_L008


title: HN120-Met-H3K4me3

description: HS004-SR-R00143_BC5E7KANXX.CHC468-ACAGTG_S19_L005


title: HN120-MCR-Input

description: HS002-SR-R00208_AC9A1YACXX.CHH24486-CTTGTA_S42_L006


title: HN120-PCRDH-Input

description: HS002-SR-R00208_AC9A1YACXX.CHH24488-TGACCA_S44_L006


title: HN120-PCR-Input

description: HS004-SR-R00143_BC5E7KANXX.CHH20689-TGACCA_S36_L008


title: totRNA_DMSO_rep1

description: Gene expression data from total RNA from A375 treated 2h with DMSO

source_name: total RNA, A375,DMSO, 2h

value: melanoma cells


title: HN120-Met-Input

description: HS004-SR-R00143_BC5E7KANXX.CHC470-CAGATC_S21_L005


title: HN120-Pri-H3K27ac

description: HS002-SR-R00209_BC9A25ACXX.CHH25675-CGATGT_S19_L4

source_name: HN120 primary HNSCC

value: Primary cells


title: HN120-Pri-Input

description: HS004-SR-R00143_BC5E7KANXX.CHC467-TGACCA_S18_L005


title: RHC6653 (scRNA-seq)

first: Yiqun Elaine

last: Cao

address: 8 College Road

institute: Duke-NUS Medical School

description: Resistant

data_processing:
Basecalls performed using gis-rpd pipelines/bcl2fastq/ https://github.com/gis-rpd/pipelines/tree/master/bcl2fastq
Single-cell RNA-seq reads were aligned to the hg19 genome assembly
Data were filtered using the RaceID algoritham https://github.com/dgrun/RaceID
Genome_build: hg19
Supplementary_files_format_and_content: good_Data_TPM.txt -- Raw TPM values of 1302 cells for downstream analysis
Supplementary_files_format_and_content: good_Data_cellinfo.txt -- Detailed information of 1302 cells for downstream analysis

extract_protocol:
The C1 Single-Cell Auto Prep IFC (Fluidigm) system was employed for single-cell RNA-seq. Single cells were captured, followed by reverse transcription and cDNA pre-amplification in the C1-Chips using the SMARTer PCR cDNA Synthesis kit (Clontech) and the Advantage 2 PCR kit (Clontech).
The mRNA and cDNA was harvested in C1 system followed by barcoding in 96 well plate. We employed Nextra XT Library Prep kit (Illumina) for library tegmentation. The tegmented single-cell libraries were amplified by 12-14 round of PCR cycle.

treatment_protocol: Drug resistant cells were maintained in cisplatin

tag: disease state

value: oral squamous cell carcinoma (OSCC)

value: Metastatic

tag: response to cisplatin

value: Resistant


title: HN120-Pri-H3K4me3

description: HS004-SR-R00143_BC5E7KANXX.CHC465-CTTGTA_S16_L005


title: RHC6652 (scRNA-seq)

description: Resistant


title: H3K4me3_HUVEC_siControl_Rep2

extract_protocol:
Whole cell lysate was sonicated and subsequently incubated with the antibody to isolate DNA.
Libraries were prepared using KAPA Hyper Prep Kit (for illumina) (KAPA)

value: HUVEC

value: siControl, day7

value: H3K4me3 (MBL, MABI0304)


title: totRNA_DMSO_rep2

tag: cell line

value: total RNA

value: DMSO


title: RHC6651 (scRNA-seq)

description: Resistant


title: RHC6650 (scRNA-seq)

description: Resistant


title: RHC6647 (scRNA-seq)

description: Resistant


title: HN120-MCRDH-Input

description: HS002-SR-R00208_AC9A1YACXX.CHH24487-CGATGT_S43_L006

value: Metastatic Cisplatin Resistant Drug Holiday (MCRDH) cells

value: drug-holiday model

tag: chip antibody


title: RHC6648 (scRNA-seq)

description: Resistant


title: HN120-PCRDH-H3K4me3

description: HS002-SR-R00209_BC9A25ACXX.CHH25660-ACAGTG_S4_L001

value: H3K4me3 (04-745, Millipore)


title: RHC6649 (scRNA-seq)

description: Resistant


title: ESP2

description: Early Stationary Phase

value: Early Stationary Phase


title: RHC6645 (scRNA-seq)

description: Resistant


title: RHC6644 (scRNA-seq)

description: Resistant


title: RHC6643 (scRNA-seq)

description: Resistant


title: RHC6641 (scRNA-seq)

description: Resistant


title: RHC6640 (scRNA-seq)

description: Resistant


title: RHC6642 (scRNA-seq)

description: Resistant


title: RHC6636 (scRNA-seq)

description: Resistant


title: RHC6638 (scRNA-seq)

description: Resistant


title: RHC6637 (scRNA-seq)

description: Resistant


title: RHC6635 (scRNA-seq)

description: Resistant


title: RHC6639 (scRNA-seq)

description: Resistant


title: RHC6633 (scRNA-seq)

description: Resistant


title: RHC6634 (scRNA-seq)

description: Resistant


title: RHC6630 (scRNA-seq)

description: Resistant


title: RHC6632 (scRNA-seq)

description: Resistant


title: RHC6631 (scRNA-seq)

description: Resistant


title: RHC6629 (scRNA-seq)

description: Resistant


title: RHC6628 (scRNA-seq)

description: Resistant


title: RHC6627 (scRNA-seq)

description: Resistant


title: RHC6646 (scRNA-seq)

description: Resistant


title: RHC6624 (scRNA-seq)

description: Resistant


title: RHC6625 (scRNA-seq)

description: Resistant


title: RHC6622 (scRNA-seq)

description: Resistant


title: RHC6623 (scRNA-seq)

description: Resistant


title: RHC6619 (scRNA-seq)

description: Resistant


title: RHC6621 (scRNA-seq)

description: Resistant


title: RHC6618 (scRNA-seq)

description: Resistant


title: RHC6620 (scRNA-seq)

description: Resistant


title: RHC6616 (scRNA-seq)

description: Resistant


title: RHC6617 (scRNA-seq)

description: Resistant


title: RHC6626 (scRNA-seq)

description: Resistant


title: RHC6615 (scRNA-seq)

description: Resistant


title: RHC6613 (scRNA-seq)

description: Resistant


title: RHC6612 (scRNA-seq)

description: Resistant


title: RHC6611 (scRNA-seq)

description: Resistant


title: RHC6607 (scRNA-seq)

description: Resistant


title: RHC6610 (scRNA-seq)

description: Resistant


title: RHC6608 (scRNA-seq)

description: Resistant


title: RHC6601 (scRNA-seq)

description: Resistant


title: RHC6604 (scRNA-seq)

description: Resistant


title: RHC6602 (scRNA-seq)

description: Resistant


title: RHC6599 (scRNA-seq)

description: Resistant


title: RHC6603 (scRNA-seq)

description: Resistant


title: RHC6600 (scRNA-seq)

description: Resistant


title: RHC6598 (scRNA-seq)

description: Resistant


title: RHC6596 (scRNA-seq)

description: Resistant


title: RHC6593 (scRNA-seq)

description: Resistant


title: RHC6597 (scRNA-seq)

description: Resistant


title: RHC6595 (scRNA-seq)

description: Resistant


title: RHC6586 (scRNA-seq)

description: Resistant


title: RHC6589 (scRNA-seq)

description: Resistant


title: RHC6588 (scRNA-seq)

description: Resistant


title: RHC6614 (scRNA-seq)

description: Resistant


title: RHC6587 (scRNA-seq)

description: Resistant


title: RHC6594 (scRNA-seq)

description: Resistant


title: RHC6590 (scRNA-seq)

description: Resistant


title: RHC6606 (scRNA-seq)

description: Resistant


title: RHC6609 (scRNA-seq)

description: Resistant


title: RHC6583 (scRNA-seq)

description: Resistant


title: RHC6605 (scRNA-seq)

description: Resistant


title: RHC6581 (scRNA-seq)

description: Resistant


title: RHC6580 (scRNA-seq)

description: Resistant


title: RHC6591 (scRNA-seq)

description: Resistant


title: RHC6592 (scRNA-seq)

description: Resistant


title: RHC6578 (scRNA-seq)

description: Resistant


title: RHC6575 (scRNA-seq)

description: Resistant


title: RHC6576 (scRNA-seq)

description: Resistant


title: RHC6577 (scRNA-seq)

description: Resistant


title: RHC6579 (scRNA-seq)

description: Resistant


title: RHC6585 (scRNA-seq)

description: Resistant


title: RHC6571 (scRNA-seq)

description: Resistant


title: RHC6574 (scRNA-seq)

description: Resistant


title: RHC6568 (scRNA-seq)

description: Resistant


title: RHC6569 (scRNA-seq)

description: Resistant


title: RHC6566 (scRNA-seq)

description: Resistant


title: RHC6573 (scRNA-seq)

description: Resistant


title: RHC6570 (scRNA-seq)

description: Resistant


title: RHC6584 (scRNA-seq)

description: Resistant


title: RHC6563 (scRNA-seq)

description: Resistant


title: RHC6572 (scRNA-seq)

description: Resistant


title: RHC6565 (scRNA-seq)

description: Resistant


title: RHC6564 (scRNA-seq)

description: Resistant


title: RHC6582 (scRNA-seq)

description: Resistant


title: RHC6562 (scRNA-seq)

description: Resistant


title: RHC6567 (scRNA-seq)

description: Resistant


title: RHC6560 (scRNA-seq)

description: Resistant


title: RHC6558 (scRNA-seq)

description: Resistant


title: DMS1

description: desiccation after ESP

value: desiccation after ESP (Early Stationary Phase)


title: RHC6561 (scRNA-seq)

description: Resistant


title: RHH2558 (scRNA-seq)

description: Resistant

value: Primary


title: RHH2556 (scRNA-seq)

description: Resistant


title: RHH2557 (scRNA-seq)

description: Resistant


title: RHH2559 (scRNA-seq)

description: Resistant


title: RHH2555 (scRNA-seq)

description: Resistant


title: RHC6559 (scRNA-seq)

description: Resistant


title: RHH2553 (scRNA-seq)

description: Resistant


title: RHH2550 (scRNA-seq)

description: Resistant


title: RHH2548 (scRNA-seq)

description: Resistant


title: RHH2547 (scRNA-seq)

description: Resistant


title: RHH2549 (scRNA-seq)

description: Resistant


title: RHH2545 (scRNA-seq)

description: Resistant


title: RHH2544 (scRNA-seq)

description: Resistant


title: RHH2543 (scRNA-seq)

description: Resistant


title: RHH2546 (scRNA-seq)

description: Resistant


title: RHH2542 (scRNA-seq)

description: Resistant


title: RHH2541 (scRNA-seq)

description: Resistant


title: RHH2540 (scRNA-seq)

description: Resistant


title: RHH2539 (scRNA-seq)

description: Resistant


title: RHH2537 (scRNA-seq)

description: Resistant


title: RHH2536 (scRNA-seq)

description: Resistant


title: RHH2538 (scRNA-seq)

description: Resistant


title: RHH2535 (scRNA-seq)

description: Resistant


title: RHH2534 (scRNA-seq)

description: Resistant


title: RHH2554 (scRNA-seq)

description: Resistant


title: RHH2533 (scRNA-seq)

description: Resistant


title: RHH2530 (scRNA-seq)

description: Resistant


title: RHH2529 (scRNA-seq)

description: Resistant


title: RHH2531 (scRNA-seq)

description: Resistant


title: RHH2551 (scRNA-seq)

description: Resistant


title: RHH2532 (scRNA-seq)

description: Resistant


title: RHH2528 (scRNA-seq)

description: Resistant


title: RHH2527 (scRNA-seq)

description: Resistant


title: RHH2525 (scRNA-seq)

description: Resistant


title: RHH2526 (scRNA-seq)

description: Resistant


title: RHH2524 (scRNA-seq)

description: Resistant


title: RHH2523 (scRNA-seq)

description: Resistant


title: RHH2521 (scRNA-seq)

description: Resistant


title: RHH2552 (scRNA-seq)

description: Resistant


title: RHH2522 (scRNA-seq)

description: Resistant