title: EAC RNA-Seq #1

city: San Antonio

first: Chin-Hsing Annie

state: TX

address: One UTSA Circle

department: Biology

institute: University of Texas at San Antonio

data_processing:
Basecalls performed with Illumina RTA version 1.12.4.2
Raw read counts were normalized with DESeq
Reads were aligned to the hg19 genome with Tophat.
Cuffdiff v2.1.1 was applied to analyze the differential gene expression between EAC and control (SQ) using a log2(fold change) of 1.0 as a cut-off for gene experssion.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited cuffdiff output file includes sample gene FPKMs and gene-level differential expression.

source_name: EAC primary specimen

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen/Life Technologies #15596-026).
Libraries were prepared according to instructions forIllumina RNA-Seq library preparation kit with Ribozero.

value: esophagus

tag: region

value: epithelium

tag: developmental stage

value: adult


title: BMMacs_DHX58_KO_48h_-_3_L4.LB6_1

status: Public on Feb 01 2019

type: SRA

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

country: USA

institute: University of Minnesota

description: mRNA isolated from Macrophages

library_source: transcriptomic

data_processing:
Constructed libraries were sequenced on an NextSeq 500 Illumina platform, producing 2x75nt stranded paired end reads (52 Gb). Image analysis, base calling, and error estimation were performed using Illumina Analysis Pipeline (version 2.8).
Quality control of the primary sequencing data was performed using FastQC (version 0.11.3) and included adapter trimming using cutadapt (version 1.8.3).
Reads were aligned using STAR (version 2.4.2)
Genome_build: Mus_musculus UCSC build mm10
Supplementary_files_format_and_content: We mapped reads to the mouse reference genome ( Mus_musculus, UCSC , mm10) from Illumina's igenomes using STAR. After mapping, we assigned aligned read counts from BAM files to exons and genes using the python package HT-Seq.  HT-Seq provided the most accurate way of aligning read counts to overlapping exons. Reads that mapped to multiple positions were removed.

molecule: polyA RNA

organism: Mus musculus

source_name: Bone marrow derived Macrophages from C57BI/6 mice with DHX58 knocked out and WNV infected at 48 hours

growth_protocol: Primary human astrocytes were maintained on collagen-coated tissue culture plates in a complete astrocyte medium (ScienCell Laboratories) in 2% FBS.

extract_protocol:
mRNA was isolated using the QIAGEN miRNeasy Kit.
Illumina Truseq
Library quality was evaluated using the Qubit® 3.0 Fluorometer and the Agilent 2100 Bioanalyzer instrument. Constructed libraries were sequenced on an NextSeq 500 Illumina platform, producing 2x75nt stranded paired end reads (52 Gb). Image analysis, base calling, and error estimation were performed using Illumina Analysis Pipeline (version 2.8).

treatment_protocol: Primary human astrocytes were treated for 4 hours with 10U/ml recombinant human IFN-β or a PBS vehicle. Cells were then lysed in buffer RLT (Qiagen).

tag: cell type

value: Bone marrow derived macrophages

tag: gene knockout

tag: infection

value: WNV

tag: timepoint


title: in vivo RBC_1

city: Boston

first: Brian

last: Lin

state: MA

address: 136 Harrison Avenue

department: DMCB

institute: Tufts University

data_processing:
STAR mapper version 2.5.2b
cuffquant, part of cufflinks 2.2.1
cuffnorm, part of cufflinks 2.2.1
Genome_build: MM9
Supplementary_files_format_and_content: csv of FPKM values from output of cuffnorm

molecule: total RNA

source_name: Respiratory basal cells

extract_protocol:
Zymo quick-RNA microprep, cat# R1050 was used for both in vitro samples, and microdissected respiratory basal cells
RNA was prepped using standard Illumina library construction methods

tag: passages

tag: facs

value: TdTomato+

tag: mouse strain


title: EAC RNA-Seq #2

organism: Homo sapiens

tag: tissue


title: in vitro HBC_2

source_name: Olfactory epithelium horizontal basal cells

value: wildtype


title: Control Esophageal Total H3 ChIP-Seq #2

library_source: genomic

data_processing:
Basecalls performed with Illumina RTA version 1.12.4.2
Unique paired-end reads were aligned to UCSC hg38 using Bowtie version 1.0.1 and the following parameters:  bowtie -n 2 -m 1 -e 70 --best --sam --chunkmbs 256 --phred33-quals --maxins 1000 hg38 -1 R1.fastq -2 R2.fastq
Normalized peaks were generated using MACS2 version 2.1.0.20140616 using the following parameters:  macs2 callpeak -t sample.bam -c input.bam -f BAMPE -g 2.7e9
Peaks were associated to the nearest transcription start site using BEDOPS closest-features with --closest option and Gencode v21 human annotation.
Genome_build: GRCh38
Supplementary_files_format_and_content: narrowPeak files containing ChIP-Seq peak calls generated from MACS2

molecule: genomic DNA

source_name: squamous-lined epithelia esophageal primary tissue

extract_protocol:
Esophageal adenocarcinoma specimens from two patients (both poorly differentiated) and normal human esophageal tissues were crosslinked in 1.1% formaldehyde before chromatin shearing using the Diagenode Bioruptor. The resulting sheared 200-500 bp chromatin fragments were incubated with H3K9me3 (Millipore #07-473) or H3K27me3 (Millipore #07-449) antibody-conjugated Protein A Dynabeads (Life Technology #10002D) overnight. For normalization, an aliquot of sheared chromatin fragments were incubated with antibody against unmodified H3 antibody-conjugated Protein A Dynabeads.
Libraries were prepared according to instructions for Illumina Library Kit, Illumina TruSeq v2 (Cat#15026486)

tag: chip antibody

value: Millipore #05-499


title: Control Esophageal Total H3 ChIP-Seq #1


title: EAC H3K9me3 ChIP-Seq #1

value: Millipore #07-442; Active Motif #39162


title: EAC H3K9me3 ChIP-Seq #2


title: ISL2-2

city: Peiking

first: haibo

last: Han

address: 52 Fucheng Road, Haidian District

department: Department of Cell Biology

country: China

institute: Peking University School of Oncology

data_processing:
Basecalls performed using CASAVA version 1.4
aligned to the hg19 genome assembly using BWA .
Uniquely mapped reads with mapping quality >=20 were retrieved for downstream analysis.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: Exel files include RPKM values for each Sample

source_name: Huh7 cells

extract_protocol:
Total RNA was harvested using Qiagen Kit.1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The Huh7 cells were transfected by ISL1 Lentivirus and blank lentivirus as control.

tag: cell line


title: EAC H3K27me3 ChIP-Seq #2

value: Millipore #07-449; Active Motif #39158


title: D316A-Tg CHOW [10_WATsc_D316A-Tg_S22]

city: London

first: David

last: Carling

address: Imperial College London, Hammersmith Hospital Campus, DuCane Road

country: United Kingdom

institute: MRC London Institute of Medical Sciences (LMS)

description:
10_WATsc_D316A-Tg_S22
bcl2fastq 2.20.0.422

data_processing:
The sequencing data was demultiplexed using Illumina bcl2fastq
The quality of the reads was assessed thanks to FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
The reads were then processed and mapped to the human genome mm10 using the Bcbio-nextgen framework version 0.9.0 (https://github.com/chapmanb/bcbio-nextgen). The aligner used was STAR 2.4.1.
The identification of the differentially expressed genes between D316A and WT samples was performed using DESeq2 in R.
Genome_build: mm10
Supplementary_files_format_and_content: Each processed data files is tab separated. It reports the raw counts obtained for each samples. CHOW and HFD diet are reported separately.

source_name: subcutaneous white adipose tissue

extract_protocol:
Animals were euthanized under Schedule 1 of the Animals (Scientific Procedures) Act 1986. Subcutaneous white adipose was retrieved from the inguinal region near the flank, the lymph node removed and the tissue flash-frozen in liquid nitrogen. RNA extraction was performed using Trizol Reagent and isolated using Qiagen RNeasy Mini Kits as per manufacturers instructions. Total RNA quantification was performed using a NanoDrop spectrophotometer. RNA integrity was assessed, with a minimum RIN of 7 permitted for sequencing (Maryam Clausen, contributer).
Illumina TruSeq stranded mRNA-seq protocol

tag: strain

value: subcutaneous white adipose tissue

tag: age

value: 16 weeks

tag: diet

value: CHOW

tag: genotype

value: D316A Transgenic (gain-of-function D316A-Tg)


title: Control-2


title: ISL1-1


title: Control RNA-Seq


title: Control-1


title: HG_METFORMIN_REP2

city: Melbourne

first: Assam

last: El-Osta

address: 75 Commercial Road

country: Australia

institute: Baker Heart and Diabetes Institute

data_processing:
Illumina pipeline 1.4  was used for base calling
Artefacts were filtered using fastx_artefacts_filter
Reads were aligned to the hg19 Ref-seq transcriptome using bwa 0.5.9 with default parameters
Transcript abundance was extracted out of the aligned file and collated into singe tabular format
Genome_build: hg19 Refseq transcriptome
Supplementary_files_format_and_content: tabular count abundance measurements

growth_protocol: Primary HAECs (human aortic endothelial cells), purchased from Lonza (Walkersville, MD, USA), were cultured in EBM-2 medium (Lonza) containing EGM-2 growth factors and supplements (Lonza) and 2% fetal bovine serum (Gibco).

extract_protocol:
After the incubation, total RNA was isolated using TRIZOL. Genomic DNA contamination was removed by DNAse treatment (Qiagen).
mRNA-Seq libraries were prepared according to Illumina mRNA-Seq library preparation kit (cat # RS-100-0801). Briefly, 8 µg of total RNA was taken for mRNA isolation using poly-T oligo-attached magnetic beads. Poly-A mRNA was fragmented with the presence of divalent cations under elevated temperatures. The mRNA fragments were reverse transcribed via SuperScript II (Invitrogen) with random primers. The second strand was synthesized with addition of RNaseH and DNA Pol I. Double stranded complementary DNA (dscDNAs) were end-repaired, followed by 3’ adenylation and ligation to universal adapters. The ligated cDNA library was separated on a 2.0% agarose gel. Library cDNA fragments in the range of 200 bp ± 10 bp were isolated by gel purification (Qiagen) and amplified with 15 cycles of PCR

treatment_protocol: HAEC were incubated for 64 hours with DMSO (control), metformin (2 mM), D-glucose (30 mM) or metformin and D-glucose (2 mM and 30 mM respectively). Media with freshly prepared DMSO/metformin/D-glucose was replaced every 12 hours.

tag: disease

value: healthy

tag: stimulated with

value: 2mM metformin and 30mM D-glucose for 64hrs


title: HG_METFORMIN_REP3

value: Primary HAECs (human aortic endothelial cells)


title: HG_DMSO_REP1

value: DMSO and D-glucose (30 mM) for 64hrs


title: ISL1-chip-seq

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using BWA.
Uniquely mapped reads with mapping quality >=20 were retrieved for downstream analysis.
Peaks were called using MACS2.
Genome_build: hg19

extract_protocol:
Cell lysates were clarified from sonicated nuclei and ISL1-DNA complexes were isolated with ISL1 antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: The Huh7 cells were transfected by ISL1 Lentivirus.

tag: come from

value: ATCC

value: ISL1(Abcam ab20670 )

tag: cell ine


title: NG_METFORMIN_REP3

tag: cell type

value: metformin (2 mM) for 64 hrs


title: HG_METFORMIN_REP1


title: HG_DMSO_REP3


title: HG_DMSO_REP2


title: NG_METFORMIN_REP1


title: NG_DMSO_REP3

value: DMSO (control) for 64hrs


title: NG_DMSO_REP2


title: NG_DMSO_REP1


title: EAC H3K27me3 ChIP-Seq #1

value: esophagus

tag: region

value: epithelium

tag: developmental stage

value: adult


title: pqsA.1T

city: Braunschweig

first: Denitsa

last: Eckweiler

state: Lower Saxony

address: Spielmannstr. 7

department: Institute of Microbiology

country: Germany

institute: Technische Universität Braunschweig

description: PA14 pqsA::Mar2xT7 extracted from tumors from four mice pooled before RNA extraction and divided into two technical replicas for sequencing

data_processing:
RNA-seq reads were mapped to the PA14 genome using the Stampy aligner with default settings.
Differential expression was estimated using the R library edgeR excluding rRNA/tRNA genes and making use of the biological or technical replicates for each condition
Quality control of the samples is provided as supplementary information
Genome_build: gi|116048575|ref|NC_008463.1|
Supplementary_files_format_and_content: The processed files in TXT format include Genes, log2FC, uncorrected P-value and corrected P-value (Padj). The P-values are presented in the Phred-scale (-10*log10(actual P-value))

organism: Pseudomonas aeruginosa

source_name: pqsA_murine tumor cells  (pqsA_t)

growth_protocol: Mice bearing tumors of approximately 4–6 mm diameter in size were intravenously injected with 5×106 CFU of P. Aeruginosa strain suspended in PBS

extract_protocol:
Using Rneasy kit (Qiagen) plus Qiashredder columns.
Customized protocol (Dötsch et al., PloS ONE, 2012). Briefly, eukariotic RNA was depleted using MICROBEnrich Kit (both for tumor samples and control sampels), subsequently bacterial rRNA was depleted using MICROBExpress kit with the Pseudomonas module (Ambion) and fragmented by sonication using Covaris Adaptive Acoustics device (Covaris). Upon ligation of barcoded adapters, reverse transcription with SuperScript II kit (Invitrogen) followed. Amplification was done by PCR using Illumina platform compatible primers. Established cDNA library was normalized by double strand specific nuclease treatment (Evrogen) according DSN Normalization Sample Preparation Guide from Illumina.

treatment_protocol: (Bielecki et al.. PLoS One 2011) Three days post-infection (p.i.) mice were necrotized and infected tumors prepared for stabilization of bacterial RNA in the following way: the tumors were removed and excised into 2–4 pieces, put onto nylon filters for cell culture (70 µm pore size) and suspended in 2 ml of RNAproctect Bacteria Reagent in 2 cm petri dishes. The tumors from 4 mice were spent through the membrane with a sterile spatula. The resulting pooled mixture in the RNAprotect reagent was collected and centrifuged for 5 min at maximum speed 16,000 x g. The pellet was immediately frozen at −70°C for further RNA extraction

tag: strain background

tag: genotype/variation

value: transposon mutant of pqsA; pqsA::Mar2xT7

tag: sample type

value: tumor cells  collected from mice infected with PA14 pqsA transposon mutants


title: pqsA_OD2-1

description: PA14 pqsA::Mar2xT7 OD2 exponential growth two out of four biological replicas pooled

source_name: pqsA_exponential growth (pqsA_e)

growth_protocol: LB medium at 37°C and 180 r.p.m. until OD600=2.0.

treatment_protocol: Cells from 2 pooled cultures were harvested by addition of the same volume of RNA-protect buffer (Qiagen) and centrifugation.

value: exponential growth_planktonic culture


title: pqsA_OD5.5-2

description: PA14 pqsA::Mar2xT7 OD5.5 stationary growth two out of four biological replicas pooled

source_name: pqsA_stationary growth (pqsA_s)

growth_protocol: LB medium at 37°C and 180 r.p.m. until OD600=5.5.

value: stationary growth_planktonic culture


title: pqsA_OD2-2


title: PA14_OD5.5-2

description: PA14 OD5.5 stationary growth two out of four biological replicas pooled

source_name: PA14_stationary growth (PA14_s)

value: wild type


title: PA14.1T

description: PA14 extracted from tumors from four mice pooled before RNA extraction and divided into two technical replicas for sequencing

source_name: WT_murine tumor cells (PA14_t)

value: tumor cells  collected from mice infected with PA14 wild type


title: PA14_OD5.5-1


title: PA14_OD2-2

description: PA14 OD2 exponential growth two out of four biological replicas pooled

source_name: PA14_exponential growth (PA14_e)


title: PA14.2T


title: pqsA.2T


title: NG_METFORMIN_REP2

value: healthy

tag: passages


title: E145_EC_brain_AO1

status: Public on Jan 31 2019

city: Stockholm

first: Julianna

middle: MV

last: Kele-Olovsson

address: Nanna Svartz väg 2

department: Physiology and Pharmacology

country: Sweden

institute: LICR ltd and Karolinska Institutet

description: E14.5 brain endothelial cells overexpressing Axin1 biol repl 1

data_processing:
Alignment by Bowtie to genome and transcriptome and merged to genome coordinates
Selection of uniquely aligned reads
Expression values and read counts by rpkmforgenes.py using RefSeq annotation
Differential expression by DESeq
Genome_build: mm9
Supplementary_files_format_and_content: Excel 97-2004 .xls file with p-values and RPKM values

source_name: Brain endothelial cells

extract_protocol:
TRAP (Hupe et al. Nucleic Acids Research 2013 doi:10.1093/nar/gkt995)
TruSeq RNA Sample prep kit v2 kit (Illumina)

treatment_protocol: Tamoxifen at E12.5 to mother

value: Brain endothelial cells

tag: genetic modification

value: R26 Axin1 IresLacZ overexpression

value: embryonic day E14.5


title: E145_EC-Brain1

description: E14.5 brain endothelial cells biol repl 1

value: Wt


title: E145_EC-Brain3

description: E14.5 brain endothelial cells biol repl 3


title: E145_EC-Brain2

description: E14.5 brain endothelial cells biol repl 2


title: E145_EC_brain_AO2

description: E14.5 brain endothelial cells overexpressing Axin1 biol repl 2


title: pqsA_OD5.5-1


title: CAY7065gray-2

city: Providence

first: Richard

last: Bennett

state: RI

address: 171 Meeting St

department: Molecular Microbiology and Immunology

institute: Brown University

description: cell at OD=1 in log-phase

data_processing:
Reads were aligned to the C. albicans SC5314 A21 genome and assigned to individual A21 genome features (http://candidagenome.org/download/gff) using STAR v2.5
Transcript abundance measurements were calculated using HTseq (version 0.8.0) as transcripts per million (TPM)
Genome_build: SC5314 A21 genome

organism: Candida albicans

source_name: Candida albicans intermediate cells

growth_protocol: Cells were grown in SCD overnight, diluted in fresh SCD to an OD600 of 0.1 and harvested in exponential growth at an OD600 of 1.0

extract_protocol:
The MasterPure Yeast RNA Purification Kit (Epicentre) was used to purify RNA. RNA was treated with Turbo DNaseI (Ambion).
PolyA RNA was isolated and used to construct strand-specific libraries using the dUTP second strand marking method using the Illumina TruSeq Stranded library preparation kit.

tag: cell state

value: intermediate


title: SN78-1

description: cell at OD=1 in log-phase

source_name: Candida albicans white cells

value: white


title: CAY7064white-3

description: cell at OD=1 in log-phase


title: SN78-3

description: cell at OD=1 in log-phase


title: RB731opaque-2

description: cell at OD=1 in log-phase

source_name: Candida albicans opaque cells

value: opaque


title: RB731opaque-3

description: cell at OD=1 in log-phase


title: SN78-2

description: cell at OD=1 in log-phase


title: CAY7065gray-1

description: cell at OD=1 in log-phase


title: CAY7064white-2

description: cell at OD=1 in log-phase


title: CAY7065gray-3

description: cell at OD=1 in log-phase


title: CAY7059opaque-3

description: cell at OD=1 in log-phase


title: CAY7064white-1

description: cell at OD=1 in log-phase


title: CAY7059opaque-2

description: cell at OD=1 in log-phase


title: CAY7059opaque-1

description: cell at OD=1 in log-phase


title: E145_EC_brain_AO3

description: E14.5 brain endothelial cells overexpressing Axin1 biol repl 3

tag: strain


title: PA14_OD2-1


title: CAY7057white-2

description: cell at OD=1 in log-phase


title: CAY7058gray-2

description: cell at OD=1 in log-phase


title: CAY7058gray-1

description: cell at OD=1 in log-phase


title: CAY7058gray-3

description: cell at OD=1 in log-phase


title: CAY7023opaque-2

description: cell at OD=1 in log-phase


title: CAY7023opaque-3

description: cell at OD=1 in log-phase


title: RB731opaque-1

description: cell at OD=1 in log-phase


title: CAY7023opaque-1

description: cell at OD=1 in log-phase


title: CAY7022gray-2

description: cell at OD=1 in log-phase


title: CAY7022gray-3

description: cell at OD=1 in log-phase


title: CAY7021white-1

description: cell at OD=1 in log-phase


title: RB717white-2

description: cell at OD=1 in log-phase


title: RB717white-1

description: cell at OD=1 in log-phase


title: RB717white-3

description: cell at OD=1 in log-phase


title: Hsp20 KO, rep1

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

description:
Sample name: FGC7
Processed data file: countsTable.txt

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8.
fastq sequences were aligned to mm10 using Tophat.
Number of read counts was calculated for each Entrez gene.
Differential expression analysis was performed using DESeq.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: countsTable.txt: Tab-delimited text file includes raw counts with genes in rows and samples in columns.

source_name: inguinal white adipose tissue, Hsp20 KO

growth_protocol: Standard housing protocol, nonfasted mice.

extract_protocol:
Standard protocol of the RNeasy Lipid Tissue Mini Kit (Qiagen, Cat.# 74804).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/background

value: Hsp20 KO

tag: age

value: 12 weeks

tag: tissue

value: inguinal white adipose


title: WT, rep1

description:
Sample name: FGC1
Processed data file: countsTable.txt

source_name: inguinal white adipose tissue, WT

value: WT


title: CAY7057white-1

description: cell at OD=1 in log-phase


title: WT, rep2

description:
Sample name: FGC2
Processed data file: countsTable.txt


title: Hsp20 KO, rep2

description:
Sample name: FGC8
Processed data file: countsTable.txt


title: Hsp20 KO, rep3

description:
Sample name: FGC9
Processed data file: countsTable.txt


title: WT, rep3

description:
Sample name: FGC3
Processed data file: countsTable.txt


title: apc8-1 small RNA-seq

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

institute: Yunnan Agricultural University

description: small RNA

data_processing:
The sequencing reads were filtered to remove reads with more than 5 nucleotides with sequencing scores smaller than 20.
3'-adaptor sequences were removed to extract small RNAs.
Redundant sequences were eliminated, and unique small RNAs were counted.
Unique small RNAs were mapped back to the A. thaliana reference genome using SOAP2.
Custom programs were then used to calculate the normalized abundance (RPTM, Reads Per Ten Million sequencing tags) of siRNAs.
Genome_build: TAIR10
Supplementary_files_format_and_content: sequence and count value separated by tab

organism: Arabidopsis thaliana

source_name: inflorescences

growth_protocol: Plants were grown in soil in long-day conditions.

extract_protocol:
Total RNA was isolated from selected tissues using TRIzol reagent with the manufacture's protocol.
Small RNA libraries were prepared by following the Illumina's protocol.

treatment_protocol: no treatment

value: inflorescences


title: Col-0 small RNA-seq

description: small RNA

value: wt


title: pol-iv small RNA-seq

description: small RNA

value: pol-iv


title: D16(serum)

city: Warsaw

first: Marcin

last: Tabaka

address: Kasprzaka 44/52

country: Poland

institute: International Centre for Translational Eye Research

data_processing:
Reads were aligned to the UCSC mm10 transcriptome (using RNA-Seq genome-aligner  STAR), and a matrix of UMI counts was obtained using CELLRANGER from the 10X Genomics pipeline  (v1.1.0) with default parameters
All cells with less than 1000 UMIs detected per cell in total and all  genes that were expressed in less than 50 cells were discarded, leaving 65,781 cells and 16,339  genes for further analysis. The elements of expression matrix were normalized by dividing UMI count  by the total UMI counts detected in a cell, multiplied by 10,000, and log-transformed after adding a pseudocount of 1.
Genome_build: mm10
Supplementary_files_format_and_content: txt file contains normalized and log-transformed expression matrix

source_name: 2nd MEFs

growth_protocol: For the reprogramming assay, 20,000 low passage MEFs (no greater than 3-4 passages from isolation) were seeded in a 6-well plate. These cells were cultured at 37°C and 5% CO2 in reprogramming medium containing KnockOut DMEM (GIBCO), 10% knockout serum replacement (KSR, GIBCO), 10% fetalbovine serum (FBS, GIBCO), 1% GlutaMAX (Invitrogen), 1% nonessential amino acids (NEAA, Invitrogen), 0.055 mM 2-mercaptoethanol (Sigma), 1% penicillin-streptomycin (Invitrogen) and 1,000 U/ml leukemia inhibitory factor (LIF, Millipore). Day 0 medium was supplemented with 2g/mL doxycycline Phase-1(Dox) to induce the polycistronic OKSM expression cassette. Medium was refreshed every other day. At day 8, doxycycline was withdrawn, and cells were transferred to either serum-free 2i medium containing 3 M CHIR99021, 1 M PD0325901, and LIF (Phase-2(2i)) (25) or maintained in reprogramming medium (Phase-2(serum)). Fresh medium was added every other day until the final time point on day 16. Oct4-EGFP positive iPSC colonies should start to appear on day 10, indicative of successful reprogramming of the endogenous Oct4 locus.

extract_protocol:
We collected a total of 66,000 cells from twelve time points over a period of 16 days in two different culture conditions. Single or duplicate samples were collected at day 0 (before and after Dox addition), 2, 4, 6, and 8 in Phase-1(Dox); day 9, 10, 11, 12, 16 in Phase-2(2i); and day 10, 12, 16 in Phase-2(serum). Cells were also collected from established iPSCs cell lines reprogrammed from the same MEFs, maintained either in Phase-2(2i) conditions or in Phase-2(serum) medium. For all time points, selected wells were trypsinized for 5 mins followed by inactivation of trypsin by addition of MEF medium. Cells were subsequently spun down and washed with 1X PBS supplemented with 0.1% bovine serum albumin. The cells were then passed through a 40 micron filter to remove cell debris and large clumps. Cell count was determined using Neubauer chamber hemocytometer to a final concentration of 1000 cells/ul.
Single-cell RNA-Seq libraries were generated from each time point using the 10X Genomics Chromium Controller Instrument (10X Genomics, Pleasanton, CA) and ChromiumTM Single Cell 3’ Reagent Kits v1 (PN-120230, PN-120231, PN-120232) according to manufacturer’s instructions. Reverse transcription and sample indexing was performed using the C1000 Touch Thermal cycler with 96-Deep Well Reaction Module. Briefly, the suspended cells were loaded on a Chromium controller Single-Cell Instrument to first generate single-cell Gel Bead-In-Emulsions (GEMs). After breaking the GEMs, the barcoded cDNA was then purified and amplified. The amplified barcoded cDNA was fragmented, Atailed and ligated with adaptors. Finally, PCR amplification was performed to enable sample indexing and enrichment of the 3’ RNA-Seq libraries. The final libraries were quantified using Thermo Fisher Qubit dsDNA HS Assay kit (Q32851) and the fragment size distribution of the libraries were determined using the Agilent 2100 BioAnalyzer High Sensitivity DNA kit (5067-4626). Pooled libraries were then sequenced using Illumina Sequencing By Synthesis (SBS) chemistry.

tag: cell types

value: 2nd MEFs (OKSM)

tag: time point


title: D10-2(2i)


title: iPSCs (2i)

source_name: iPSCs

value: iPSCs (OKSM)

tag: time point:


title: D12(serum)


title: D12-2(2i)


title: D16(2i)


title: D11(2i)


title: CAY7021white-3

description: cell at OD=1 in log-phase


title: D10(serum)


title: nrpe1-12-1 lncRNA-seq

description: lncRNA

data_processing:
TopHat (v2.0.13) was used to aligned the obtained reads to the genome of Arabidopsis (TAIR10).
Cufflinks (v2.2.1) was used to obtain the genes and transcripts and genes with the TAIR10 annotation.
Cuffmerge (v1.0.0) was used to merge the assembled genes and transcripts from individual libraries.
CuffCompare (v2.2.1) was used to compare the merged genes and transcripts to the annotated genes and transcripts in the TAIR10 database.
Cuffquant (v2.2.1) was used to quantify the expression levels (FPKM) values of genes and transcripts.
Cuffnorm (v2.2.1) was used to normalize the FPKM values of genes and transcripts.
Genome_build: TAIR10
Supplementary_files_format_and_content: FPKM values of genes

source_name: seedlings

growth_protocol: Plants were grown in MS plate 16/8 hr ligh/dark cycle, 22 degree. For all experiments, 14-day-old seedlings were used.

extract_protocol:
Total RNA were extracted with Trizol (Amion).
RNA libraries were prepared for sequencing using standard Illumina protocols with only ribosomal RNA removal.

value: seedling


title: apc8-1-2 lncRNA-seq

description: lncRNA


title: D10-1(2i)


title: D9-2(2i)


title: D9-1(2i)


title: Col-0-2 lncRNA-seq

description: lncRNA


title: apc8-1-1 lncRNA-seq

description: lncRNA


title: D8-2


title: nrpe1-12-2 lncRNA-seq

description: lncRNA


title: D6-1


title: D8-1


title: Col-0-1 lncRNA-seq

description: lncRNA


title: D12-1(2i)


title: D2-2


title: NES KO 3 4d

city: Solna

first: Florian

middle: Andreas

last: Schober

address: Solnavägen 9

department: Department of Medical Biochemistry and Biophysics (MBB)

institute: Karolinska Institutet

data_processing:
RNA quality was confirmed using a Bioanalyzer 2100 (Agilent). Samples with a minimum RNA integrity number (RIN) of 8.5 were used. Clustering was done by 'cBot' and samples were sequenced on HiSeq2500 (HiSeq Control Software 2.2.58/RTA 1.18.64) with a 2x126 setup using 'HiSeq SBS Kit v4' chemistry. The Bcl to FastQ conversion was performed using bcl2fastq from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+.
The reads were mapped using Tophat2 to the human reference assembly, version GRCh38.
Data analysis was performed with R (v3.3.2) (R Core Team(2013)). Mapped RNAseq count files were cleaned by removing all genes with raw counts of less than 3 per one million counts. Data were then normalised on the total amount of reads per sample using DESeq 2 (v1.14.1).
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file including normalized counts per gene as Ensemble Gene ID for each sample .

source_name: NES cells, KO, 4d

growth_protocol: NES cells (passage 15 to 50) were cultured on 100 μg/ml poly-ornithine / 2 μg/ml laminin-coated culture dishes (both (Sigma-Aldrich)), in DMEM/F-12 Glutamax (Thermo Fisher Scientific) media containing 17 mM glucose, 100 units/ml penicillin-streptomycin (Thermo Fisher Scientific), N-2 (1:100) (Thermo Fisher Scientific), B27 (1:1000) (Thermo Fisher Scientific), 10 ng/μl bFGF (Thermo Fisher Scientific) and 10 ng/μl EGF (Peprotech) at 37° in a 5% CO2 atmosphere. Three-forths of the media was exchanged daily. Cells were trypsinised using TrypLE Express 1x (Thermo Fisher Scientific).

extract_protocol:
Total RNA was extracted using TRIzol (Thermo Fisher Scientific), followed by DNase-treatment using TURBO DNA-free kit (Thermo Fisher Scientific).
The library method used was Illumina TruSeq Stranded mRNA, Poly-A selection (200 ng used for each library)

treatment_protocol: Neuronal differentiation was induced by removing the growth factors bFGF and EGF from the media and increasing the B27 concentration to 1:100.

tag: genotype

value: Neuroephithelial stem cells

tag: differentiation status

value: differentiating


title: miRNAs from spent media of flight cells, Standard medium, biological replicate 3

city: Milan

first: Silvia

last: Bradamante

address: Via Golgi 19

country: Italy

institute: CNR-ISTM, Institute of Molecular Science and Technology

description:
FMSM_2_Exhmed_2
miRNA

data_processing:
Pre-processing: Sequencing adapters removal performed with Trimmomatic (v0.32)
Pre-processing: reads in the size range of 18-50 nucleotides were selected and used for downstream analysis
Mapping: mapped against mature miRNAs in the mirBase (version 21) using BWA tool (command bwa aln; v0.7.5a)
Feature count: miRNAs expression counts were obtained with samtools (z1.2)
Differential expression analysis: differential expression analysis was performed using the edgeR (Bioconductor version 2.13). Counts were normalized and differential expression was inferred using the negative binomial distribution and a shrinkage estimator for the distribution variance of the counts.
Genome_build: mirBase: r21 mature RNA
Supplementary_files_format_and_content: raw count of reads mapping to different miRNAs for each sample

source_name: hBMSCs on board the ISS cultured in standard medium

growth_protocol:
Standard Medium (SM): DMEM (Dulbecco’s Modified Eagle’s medium) supplemented with 12.5 mM HEPES, 10 U/mL heparin, 200 mM glutamine, 500 μg/mL streptomycin sulphate, 600 μg/mL penicillin.
Osteogenic Medium (OM): SM added with 0.1 M ascorbic acid, 10 mM b-glycerophosphate, and 10-8 M 1,25(OH)2D3 (Vit D3).

extract_protocol:
We used the exoRNeasy Serum/Plasma Midi Kit for miRNAs extraction from exosomes
The presence and the integrity of small RNA was assessed using an Agilent Bioanalyzer
HiSeq Rapid SBS kit v2

tag: cell type

value: bone marrow mesenchymal stem cells

tag: location

value: on board the ISS

tag: medium

value: standard

tag: rna fraction

value: miRNAs from exosomes (from spent media)


title: D2-1


title: D4-1


title: NES KO 3 0d

source_name: NES cells, KO, 0d

value: undifferentiated


title: miRNAs from spent media of ground cells, Osteogenic medium, biological replicate 3

description:
GMOM_3_Exhmed_2
miRNA

source_name: hBMSCs on ground cultured in osteogenic medium

value: ground

value: osteogenic


title: NES KO 2 0d


title: miRNAs from spent media of flight cells, Osteogenic medium, biological replicate 2

description:
FMOM_2_Exhmed_1
miRNA

source_name: hBMSCs on board the ISS cultured in osteogenic medium


title: miRNAs from spent media of flight cells, Osteogenic medium, biological replicate 1

description:
FMOM_2_Exhmed_0
miRNA


title: miRNAs from spent media of flight cells, Standard medium, biological replicate 2

description:
FMSM_2_Exhmed_1
miRNA


title: miRNAs from spent media of flight cells, Osteogenic medium, biological replicate 3

description:
FMOM_2_Exhmed_2
miRNA


title: NES KO 1 4d


title: NES KO 1 0d


title: D0


title: CAY7022gray-1

description: cell at OD=1 in log-phase

tag: strain background

value: intermediate, DATA is removed due to contaminants


title: miRNAs from spent media of ground cells, Osteogenic medium, biological replicate 1

description:
GMOM_3_Exhmed_0
miRNA


title: NES control 3 4d

source_name: NES cells, control, 4d

value: wildtype


title: D6-2


title: D4-2


title: NES control 1 4d


title: 11H020

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

data_processing:
Basecalls performed using CASAVA 1.8
Sequenced reads were mapped to the reference genome using CASAVA 1.8
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CASAVA 1.8
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample. Columns are: Chromosome, Start location, Stop location, Gene, RPKM, base count.

source_name: normal tissue

extract_protocol:
TriZol + RNeasy mini Kit (Qiagen, #74106)
TruSeq RNA Sample Preparation (Illumina)

value: bone marrow

tag: gender

value: F


title: NES KO 2 4d


title: NES control 3 0d

source_name: NES cells, control, 0d


title: NES control 2 4d


title: 07H140


title: NES control 2 0d


title: NES control 1 0d


title: S224E Hi-C^2, rep1

first: Andrea

middle: June

last: Kriz

address: 185 Cambridge St

department: Molecular Biology

institute: Massachusetts General Hospital, Harvard Medical School

data_processing:
ChIP-seq: BWA was used to align reads against the mm9 reference genome (68). Alignments were filtered for uniquely mapped reads and duplicates were removed. Input-normalized coverage tracks were generated using SPP (Kharchenko et al., 2008).  To identify prospective CTCF binding sites, we resolved regions of ChIP-Seq tag enrichment. Tag counts were analyzed in a 1 Kb window over the chromosome length with a 200bp step and estimated statistical significance of enrichment of ChIP vs input using negative binomial distribution, with the estimate of the mean based on the tag counts in input, and the size parameter(s) selected based on manual inspection of resulting peak calls. Regions of significant enrichment were generated by merging adjacent significantly enriched windows separated by 1 Kb or less. Broad regions of enrichment were called using SPP (Kharchenko et al., 2008). Genomic location of the resultant 50,749 CTCF and 912 CTCF Ser224-P peaks (z=6) was categorized using CEAS according to RefGene annotation of introns, exons, and UTRs (Shin et al., 2012).  CTCF and CTCF Ser224-P data was visualized using IGV with ENCODE mESC CTCF ChIP-seq (GSM723015) and RNA-seq (GSM723776) data plotted for reference.  Motif search of the ChIP-seq peak datasets (z=6) and logo generation was performed using MEME-ChIP with default parameters (http://meme-suite.org/)
RNA-seq: RNA-seq reads were trimmed using cutadapt with the options -e 0.2 -q 20 -a AGATCGGAAGAGC -m 20 --overlap 12. Trimmed reads were aligned to the mm9 reference genome using TopHat2 as previously described. PCR duplicates were removed and HOMER used to tabulate unique reads mapping to exons of each gene. DESeq2 was then used to identify differentially expressed (DE) genes. DE genes were counted as those with adjusted p-value < 0.01. Only genes with at least one count in one of the four samples were included in the analysis.    For visualizing RNA-seq reads overlapping codon 224 of CTCF, RNA-seq reads were aligned to the CTCF S224E transgene sequence using the same parameters as above and an index of the CTCF S224E transgene sequence generated using bowtie2 with the default parameters. The resulting bam file of aligned reads was then visualized on IGV.    Overrepresentation analysis of upregulated and downregulated DE genes was done using the PANTHER Classification System (http://www.pantherdb.org). Gene symbols for downregulated or upregulated DE genes used as input lists and the gene symbols of all expressed genes (i.e., all genes used in DESeq2 analysis) were used as the reference list.     Metagene plots of ChIP-seq over DE upregulated, downregulated and all genes were generated via CEAS using bigwig files of reads from CTCF or CTCF Ser224-P ChIP-seq (Kharchenko et al., 2008).
Hi-C^2: Reads were trimmed using cutadapt with the options --adapter=GATCGATC (MboI ligation junction) and --minimum-length=20. Reads of each pair were individually mapped to the mus and cas reference genomes using novoalign and merged into non-allelic Hi-C summary files and filtered using HOMER. To avoid computational complexities arising from normalization of sparse, non-enriched regions in the Hi-C contact map, only Hi-C interactions falling within the capture region were analyzed further. For each capture, a custom script was used to pull out the filtered Hi-C interactions falling within the target region from the HOMER tag directories. Hi-C contact maps of the capture regions were then generated from these HOMER tags using the ‘pre’ command of Juicer tools. The resulting Hi-C contact maps in .hic format were visualized and normalized with the ‘Coverage (Sqrt)’ option in Juicebox . Insulation scores were computed for Hi-C2 datasets as previously described (Crane et al. 2015, Giorgetti et al. 2016) with a few modifications. Briefly, 25kb resolution ‘Coverage (Sqrt)’ normalized Hi-C2 interaction matrices were extracted from Juicebox using the ‘dump’ function of Juicer tools and converted to the cworld matrix format using custom shell and R scripts. Insulation scores were then computed from the cworld matrices using the ‘matrix2insulation.pl’ cworld script and the parameters ‘-v --is 125000 --ids 75000 –im sum’ and manually normalized using the total number of reads falling in the capture region, rather than total number of reads on the chromosome. TAD scores were then calculated from the insulation scores using the ‘insulation2tads.pl’ cworld script with default parameters and the Mecp2 TAD boundaries manually defined as the bins chrX:71200000-71225000 and chrX:71650000-71675000.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq: Input-normalized bigWig files (bw)
Supplementary_files_format_and_content: RNA-seq: bigWig files (bw) of fpm values. Raw exonic read counts in each RNA-seq library are summarized in 'counts' .txt files
Supplementary_files_format_and_content: Hi-C^2: Compressed Hi-C matrix (.hic) files for filtered Hi-C reads in the capture region (chrX:70,370,161-71,832,975 ). File can be loaded onto Juicebox to view either raw or normalized Hi-C interaction matrices at 5kb to 2.5Mb resolutions.

source_name: mESC

growth_protocol: ES cells were grown on γ-irradiated MEF feeders in ES medium (1% Pen/Strep, high-glucose DMEM+GlutaMAX, LIF) with 15% FBS.

extract_protocol:
ChIP-seq: Harvested cells were crosslinked for 5 minutes in 1% formaldehyde.  Crosslinking was quenched by the addition of glycine to 125mM.  Fixed cells were PBS washed and cell pellets were frozen at -80C. Approximately 2x10^7 cells were used per ChIP. Pellets were resuspended in Lysis buffer 1 (25mM HEPES pH 7.5, 25mM EDTA, 0.5% SDS).  Chromatin was sheared in a Qsonica Q800R for 20 minutes at 40% power 30sec on 30sec off at 4C to ~150bp.  After centrifuging away debris, 4 volumes of Lysis buffer 2 (25mM HEPES pH 7.5, 187.5mM NaCl, 1.25% Triton X-100, 0.625% sodium deoxycholate, 6.25% glycerol, 12.5mM sodium pyrophosphate, 12.5mM B-glycerophosphate, 6.25mM NaF, 1.25mM Na3VO4) were added with protease inhibitors (1mM PMSF, 1ug/mL pepstatin, and 1 ug/mL leupeptin).  Sepharose 4B (Sigma-Aldrich) was washed with ChIP Wash Buffer 1 (25mM HEPES pH 7.5, 150mM NaCl, 1% Triton X-100, 0.5% sodium deoxycholate, 5% glycerol, 5mM EDTA, 10mM sodium pyrophosphate, 10mM B-glycerophosphate, 5mM NaF, 1mM Na3VO4, protease inhibitors) and used to preclear the chromatin samples.  25μL/IP Protein G Dynabeads (ThermoFisher) were blocked in ChIP Wash Buffer 1 100ug/mL Acyclovir, 100ug/mL Zalcitabine, 5% Gly-Gly (Sigma-Aldrich). Beads were then washed with ChIP Wash Buffer 1.  Precleared chromatin, 2ug of anti-CTCF or anti-CTCF Ser224-P antibodies (Table 1), and blocked Protein G Dynabeads were incubated together overnight at 4C with rotation.  10% of the precleared chromatin input was also saved.  IP samples were washed with ChIP Wash Buffer 1, then with ChIP Wash Buffer 2 (25mM HEPES pH 7.5, 300mM NaCl, 1% Triton X-100, 0.5% sodium deoxycholate, 5% glycerol, 5mM EDTA, 10mM sodium pyrophosphate, 10mM B-glycerophosphate, 5mM NaF, 1mM Na3VO4, protease inhibitors) and then with TENG (50mM Tris-HCl pH 8.0, 1mM EDTA, 50mM NaCl, 5% glycerol, protease inhibitors).  IPs were incubated for 30minutes at 37C in TENG with 200ug/mL RNase A. 10% Input samples were also treated with 200ug/mL RNase A.  IPs were washed with ChIP Wash Buffer 2 and then TENG.  IPs were then eluted at 65C in Elution Buffer (50mM Tris-HCl pH7.5, 10mM EDTA, 1% SDS).  An equal volume of TE (Tris-HCl pH 8.0, 1mM EDTA) was added to the eluate with 40ug Proteinase K and incubated for 2hrs at 45C.   The input samples were similarly protease treated in parallel.  Both IP and input cross-links were reversed at 65C overnight and then phenol/chloroform/isoamyl alcohol extracted.  The aqueous phase was further chloroform extracted and then alcohol precipitated.  The DNA was suspended in TE.
RNA-seq: RNA was purified by TRIzol (Thermo Fisher) extraction via manufacturer’s instructions. Polyadenylated mRNA was the selected from total cell RNA using oligo(dT) beads (New England BioLabs).
Hi-C^2: In-situ Hi-C was performed as described in Rao et al. (2014): 3-5 million cells were crosslinked with 1% formaldehyde for 10min. Crosslinked cell pellets were lysed with 300uL ice-cold HiC lysis buffer (10mM Tris HCl pH 8, 10mM NaCl, 0.2% Igepal CA630) with protease inhibitors (Roche). Cell suspension was incubated for 30min at 4C with rotation, then pelleted at 2500xg for 5min. Pelleted nuclei were then washed with 500ul ice-cold HiC lysis buffer and resuspended in 50uL 0.5% SDS solution and incubated at 62C for 10min. 145ul H2O and 25ul 10% Triton X-100 were added to quench SDS and nuclei incubated at 37C for 15min. 26.1ul of 10X NEB Buffer 2 and 100U of MboI restriction enzyme were added and nuclei digested overnight at 37C with rotation. MboI was then heat activated at 62C for 20min, then nuclei cooled to room temperature. To fill in MboI fragment overhangs and mark DNA ends with biotin, 50ul of fill-in master mix was added (37.5ul 0.4mM biotin-14-dATP, 1.5ul 10mM dCTP, 1.5ul 10mM dGTP, 1.5ul 10mM dTTP, 8ul 5U/ul DNA Polymerase I, Large (Klenow) Fragment) and mixed by pipetting. Nuclei were then incubated at 37C for 1h with rotation. To ligate biotinylated DNA ends together, 900ul ligation master mix was added (649ul H2O, 120ul 10X NEB T4 ligase buffer, 100ul 10% Triton X-100, 6ul of 20mg/ml BSA, 25ul of 400U/ul T4 DNA ligase). Reaction was mixed by inverting and incubated at room temperature for 4h with rotation. Reaction was then centrifuged at 1700xg for 5min at room temperature. Pelleted nuclei were resuspended in 750ul TES buffer (1mM EDTA, 10mM Tris-HCl pH 8, 0.5% SDS), 50ul Proteinase K (20mg/ml) added and incubated at 55C for 1h with rotation. To reverse crosslinks, 88.9ul 3M NaCl was added and crosslinks reversed by incubated overnight at 65C with shaking (Eppendorf thermomixer, 950rpm). Samples were cooled to room temperature and DNA extracted with phase-lock gel tubes (5Prime). RNA was digested from purifying DNA by adding 2ul RNAse A (20mg/ml) and incubating at 37C for 1h. DNA was then extracted with phase-lock gel tubes (5Prime) and resuspended in 130ul 1X Tris buffer (10mM Tris-HCl, pH 8). To ensure complete resuspension, DNA was then incubated at 37C for 15min. DNA was then sonicated to a size of 300-500bp using a Covaris with the following parameters: 140W, 10% duty cycle, 200 bursts/cycle, 100s. Samples were then size selected to 300-500bp using AMPure XP beads and eluted in 300ul 1X Tris buffer. To pulldown biotinylated ligation products, 30ul (per sample) of MyOne Streptavidin C1 beads were washed with 400ul of 1X Tween washing buffer (5mM Tris-HCl pH 7.5, 0.5mM EDTA, 1M NaCl, 0.05% Tween 20) and resuspended in 300ul 2X binding buffer (10mM Tris-HCl pH 7.5, 1mM EDTA, 2M NaCl). Beads were then added to purified DNA and sample incubated at room temperature for 15min with rotation. Beads were washed twice with 600ul 1X Tween Washing buffer. Subsequent library preparation steps were then done directly on beads. HYbrid Capture Hi-C (Hi-C^2) probes were designed and hybridization to in-situ Hi-C libraries carried out as described previously (Sanborn et al., 2015). Probe sets were designed to enrich interactions in the region of interest: chrX:70,370,161-71,832,975 (mm9). Briefly, 120 bp probes were designed around the MboI restriction sites in the regions of interest and custom synthesized pools of single stranded oligodeoxynucleotides ordered from CustomArray, Inc. (Bothell, WA). Single stranded DNA oligos were amplified and biotinylated in a MAXIScript T7 transcription reaction (Ambion). The resulting biotinylated RNA probes were hybridized to 250-300 ng of in situ Hi-C libraries for 24 hours at 65C. DNA hybridized to the RNA probes was pulled down by streptavidin beads (Dynabeads MyOne Streptavidin C1, Life Technologies), washed, and eluted.
Libraries were constructed using the NEBNext ChIP-seq Library Preparation Kit with no modifications to the protocol. We used 12-18 cycles of PCR amplification, depending on library concentration measured by qPCR.

treatment_protocol: Tet-on CTCF S224E mESCs were grown for six days with or without  1ug/mL doxycycline (RNA-seq). Tet-on CTCF, CTCF S224A, and CTCF S224E mESCs were grown for two days with or without 1ug/mL doxycycline (Hi-C^2).

value: ES cell (F1-2.1)

value: CAST/Ei x 129/Sv/Jae

value: Tet-on CTCF S224E

tag: treatment

tag: chip antibody


title: S224E Dox Hi-C^2, rep1

tag: strain

value: Doxycycline (1ug/mL), 2 days


title: WT Dox Hi-C^2, rep1

value: Tet-on CTCF (wild-type)


title: Elf1-AF hESC H3K9me3 rep2

city: Seattle

last: Hawkins

state: WA

address: 1959 NE Pacific St, HSB K226

department: Division of Medical Genetics, Department of Genome Sciences

institute: University of Washington

data_processing:
ChIP-seq and Dnase-HiC reads were aligned using Bowtie2
ChIP-seq peaks were identified using MACS v1.4
HiC processing was done using HiTC Bioconductor package, TADs and boundaries were identified using TopDom

Genome_build: hg19

source_name: Primed human embryonic stem cells

growth_protocol: As outlined in Sperber et al., 2015

extract_protocol: ChIP-seq as outlined in Hawkins et al., 2013; DNase-HiC similar to Deng et al., 2015

tag: developmental stage

value: primed

value: embryonic stem cell

tag: growth condition

value: Activin, FGF

value: Diagenode anti-H3K9me3, cat C15410056


title: Elf1-AF hESC H3K9me3 rep1


title: S224A Dox Hi-C^2, rep1

value: Tet-on CTCF S224A


title: Elf1-AF hESC H3K4me3 rep2

value: Active Motif anti-H3K4me3, cat 39159


title: Elf1-AF hESC Input rep2


title: Elf1-AF hESC H3K4me3 rep1


title: Elf1-AF hESC H3K4me1 rep2

value: Diagenode anti-H3K4me1, cat C154100037


title: Elf1-AF hESC H3K4me1 rep1


title: miRNAs from spent media of ground cells, Osteogenic medium, biological replicate 2

description:
GMOM_3_Exhmed_1
miRNA

value: bone marrow mesenchymal stem cells

value: ground

value: osteogenic

value: miRNAs from exosomes (from spent media)


title: Elf1-AF hESC H3K27ac rep2

value: Active Motif anti-H3K27ac, cat 39133


title: Elf1-AF hESC H3K27ac rep1


title: Naïve hESC Input rep1

source_name: Naïve human embryonic stem cells

value: naive

value: GSKi + MEKi (2i), Lif, IGF1, FGF


title: Naïve hESC H3K9me3 rep2


title: Naïve hESC Input rep2


title: Naïve hESC H3K9me3 rep1


title: Naïve hESC H3K4me3 rep2


title: Naïve hESC H3K4me1 rep2


title: 09H007

tag: tissue

value: bone marrow

value: F

tag: age


title: Naïve hESC H3K4me3 rep1


title: S224A Hi-C^2, rep1

value: ES cell (F1-2.1)

value: CAST/Ei x 129/Sv/Jae


title: Elf1-AF hESC Input rep1

value: primed

value: embryonic stem cell


title: WT Hi-C^2, rep1

value: Tet-on CTCF (wild-type)


title: Naïve hESC H3K4me1 rep1


title: Naïve hESC H3K27me3 rep2

value: Active Motif anti-H3K27me3, cat 39155


title: Elf1-AF hESC H3K27me3 rep2

value: Activin, FGF


title: Naïve hESC H3K27ac rep2


title: Naïve hESC H3K27ac rep1


title: Elf1-AF hESC H3K27me3 rep1


title: 129_Cast_MEF_Biological_Rep2_Technical_Rep2

city: Durham

first: Rasim

last: Barutcu

state: NC

address: 6 Davis Drive

institute: ScitoVation

data_processing:
Hi-C mapping, filtering, correction and binning was performed with the HiC-Pro software v2.7.8.  The reads were mapped to the mm9 mouse reference genome.  For allele-specific Hi-C analysis, a high quality SNP list for the 129 and CastEiJ genomes was generated by using the mm9 annotation from the Mouse Sanger Database, using the HiC-Pro “extract_snps.py” tool.  Next, 129/CastEiJ SNP-masked mm9 reference genome was generated using the bedtools “maskfasta” tool.  Then, allele-specific Hi-C data was analyzed using the HiC-Pro “ALLELE_SPECIFIC_SNP” configuration option.    There was a high correlation among the Hi-C biological replicates, indicating the high quality and reproducibility of the datasets. Therefore, we pooled all biological replicates for each condition and mapped, filtered, corrected and binned them as a single Hi-C dataset, and used the pooled datasets for all subsequent analyses.
Genome_build: mm9

extract_protocol: Hi-C libraries were generated with an in-dilution Hi-C protocol (Beleghzal et al, 2016), using the HindIII restriction enzyme.  Briefly, ~25 million cells were crosslinked with 1 % formaldehyde for 10 minutes at room temperature. After quenching the formaldehyde with glycine, the nuclei were isolated, and the DNA was digested with HindIII, end-labelled with biotin-14-dCTP, and in-dilution ligation was performed. Following phenol-chloroform extraction, the biotin was removed from non-ligated ends, and the DNA was sheared by using a Covaris S220 instrument. After A-tailing and adapter ligation, paired-end sequencing was performed on a HiSeq instrument. Hi-C libraries were prepared in two biological replicates from mEFs prepared from two distinct mouse embryos.

value: 129xCast Hybrid Background

value: Mouse Embryonic Fibroblasts


title: 129_Cast_MEF_Biological_Rep1_Technical_Rep1


title: 129_Cast_MEF_Biological_Rep2_Technical_Rep1


title: 129_Cast_MEF_Biological_Rep1_Technical_Rep2


title: 129_Cast_MEF_Biological_Rep2_Technical_Rep3


title: Smchd1KD4

city: East Lansing

first: Uros

last: Midic

state: MI

address: 474 S. Shaw Lane

department: Animal Sciences

institute: Michigan State University

data_processing:
Illumina Real Time Analysis (RTA) v1.18.6
TopHat 2.1.1 alignment to NCBI GRCm38.p4 (Mus Musculus) assemblies
Trimming 8 bases from 5' end of unaligned reads (from first alignment); alignment of trimmed reads
Merging accepted_hits.bam from three alignment step (samtools merge)
Cuffdiff 2.2.1 comparison of 5 control (scrambled siRNA) libraries and 5 SMCHD1 knockout (SMCHD1 siRNA) libraries
Genome_build: GRCm38.p4 (Mus Musculus)
Supplementary_files_format_and_content: gene_exp.diff file produced by Cuffdiff; FPKMs.fpkm file contains FPKM values extracted from genes.read_group_tracking files produced by Cuffdiff

source_name: Morula

growth_protocol: Embryos were obtained by superovulation of 8-16 week old female mice (C57BL/6 x DBA/2)F1 (B6D2F1), The Jackson Laboratory, Bar Harbor, ME), mated to males of the same genotype.  Oocytes were isolated at the second meiotic metaphase (MII) stage, and embryos were isolated in M2 medium (Hogan et al., 1994) (Millipore, Billerica, MA) at the 1-cell stage.  Cumulus cells were removed using hyaluronidase (Sigma-Aldrich, St. Louis, MO) as described (Chung et al., 2003). Embryos were cultured in KSOM medium (Erbach et al., 1994) in humidified atmospheres containing 5% O2 and 5% CO2 at 37C.

extract_protocol:
RNA was extracted from pools of 35 morula stage embryos (93 h post-hCG injection) that had been injected with either scrambled control (5 pools) or Smchd1 siRNA (5 pools).  Each pool of embryos was an independent biological replicate. RNA was extracted using the PicoPure RNA Isolation kit (Life Technologies, Grand Island, NY) with DNAse digestion to remove any contaminating DNA.
Aliquots of approximately half of each sample were processed through the Ovation RNA-Seq System v2 using the Ribo-SPIATM Technology (Nugen, San Carlos, CA). This was followed by fragmentation to 300 bp using a Covaris sonicator followed by a brief S1 nuclease digestion as described ((Head et al., 2011).  After purification and end repair, the cDNA was processed through the Ovation Ultralow DR Multiplex Systems 1-8 and 9-16 for end repair, barcoding and final library production. Barcoded libraries were pooled, loaded on flowcells and sequenced with Illumina HISeq 2500 in rapid run mode to generate 50 nt single end reads. The samples were loaded at 65% of optimal loading concentration, along with PhiX Control library (Illumina) added at 10% of loading concentration to increase read sequence complexity.

treatment_protocol: The cytoplasm of zygotes was microinjected with approximately 10 pl of 100 uM Smchd1 siRNA or control scrambled siRNA.  In some cases a piezo pipette driver was used to facilitate penetration of the cell membrane.  siRNAs were obtained from GE Dharmacon (#L-040501-01-0005, Lafayette, CO).  The Smchd1 siRNA was a mixture of four oligonucleotides:  GAAAUGAACUAAAAGCGU, GAAGGAGAAGGACGAGUUA, CUGUGAAAGAUGUCCGCUA, and CUAACAAGGUGGGAGCAUA.

value: Smchd1 siRNA knockout


title: Smchd1KD3


title: Smchd1KD2


title: 10wEE_DG_7_mm_smallrna

city: Goettingen

first: Eva

last: Benito Garagorri

state: Niedersachsen

address: Von Siebold Strasse 3A

department: Epigenetics of Aging

institute: DZNE Goettingen

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were first trimmed for adaptor contamination with cutadapt using the following options: -m 15 -M 32; Mapping was done to mm10 with STAR with the following options: --outFilterMismatchNmax 0.05; --outFilterMatchNmin 15; --alignIntronMax 1; counting was done with htseq on miRbase in the "intersection non-empty" mode
miRNA counts were generated using htseq over miRbase in the "intersection non-empty" mode
Genome_build: mm10
Supplementary_files_format_and_content: txt file containing miRNA reads

source_name: animals kept in environmental enrichment for 10 weeks

extract_protocol:
CA and DG were microdissected under a microscope and snap-frozen in liquid nitrogen. RNA was extracted with Tri reagent (Sigma) and treated with DNAse I (Life Technologies) according to manufacturer's instructions.
Libraries were prepared using Illumina's TruSeq standard protocols starting from 1µg total RNA

value: 20 weeks

value: DG hippocampal subregion


title: 10wEE_DG_6_mm_smallrna


title: 10wEE_DG_5_mm_smallrna


title: Control_siRNA5

value: Scrambled siRNA (control)


title: 10wEE_DG_3_mm_smallrna


title: Control_siRNA4


title: 10wEE_DG_4_mm_smallrna


title: 10wEE_DG_2_mm_smallrna


title: 10wEE_DG_1_mm_smallrna


title: Naïve hESC H3K27me3 rep1

value: naive


title: Control_siRNA3


title: Smchd1KD5


title: Control_siRNA2


title: 10wHC_DG_6_mm_smallrna

source_name: animals kept in home cage for 10 weeks


title: 10wHC_DG_5_mm_smallrna


title: 10wEE_DG_8_mm_smallrna


title: 129_Cast_MEF_Biological_Rep1_Technical_Rep3


title: 10wHC_DG_1_mm_smallrna


title: 10wHC_DG_2_mm_smallrna


title: 2wEE_DG_5_mm_smallrna

source_name: animals kept in environmental enrichment for 2 weeks


title: 2wEE_DG_4_mm_smallrna


title: 10wHC_DG_4_mm_smallrna


title: Smchd1KD1


title: 10wHC_DG_3_mm_smallrna


title: 2wEE_DG_3_mm_smallrna


title: 2wHC_DG_5_mm_smallrna

source_name: animals kept in home cage for 2 weeks


title: 2wHC_DG_6_mm_smallrna


title: 2wEE_DG_1_mm_smallrna


title: 2wEE_DG_2_mm_smallrna


title: 2wHC_DG_3_mm_smallrna


title: 2wHC_DG_2_mm_smallrna


title: 10wEE_CA_7_mm_smallrna

value: CA hippocampal subregion


title: 2wHC_DG_4_mm_smallrna


title: 10wEE_CA_4_mm_smallrna


title: 10wEE_CA_6_mm_smallrna


title: Control_siRNA1


title: 10wEE_CA_8_mm_smallrna


title: 2wHC_DG_1_mm_smallrna


title: 10wEE_CA_5_mm_smallrna


title: 10wEE_CA_1_mm_smallrna


title: 10wHC_CA_6_mm_smallrna


title: 10wEE_CA_2_mm_smallrna


title: 10wHC_CA_4_mm_smallrna


title: 10wHC_CA_5_mm_smallrna


title: 10wEE_CA_3_mm_smallrna


title: 10wHC_CA_2_mm_smallrna


title: 10wHC_CA_3_mm_smallrna


title: 2wEE_CA_7_mm_smallrna


title: 2wEE_CA_6_mm_smallrna


title: 10wHC_CA_1_mm_smallrna


title: 2wEE_CA_5_mm_smallrna


title: 2wEE_CA_3_mm_smallrna


title: 2wHC_CA_6_mm_smallrna


title: 2wEE_CA_1_mm_smallrna


title: 2wEE_CA_2_mm_smallrna


title: 2wHC_CA_5_mm_smallrna


title: 2wHC_CA_3_mm_smallrna


title: 2wHC_CA_4_mm_smallrna


title: 2wHC_CA_2_mm_smallrna


title: miRNAs from spent media of flight cells, Standard medium, biological replicate 1

description:
FMSM_2_Exhmed_0
miRNA

value: bone marrow mesenchymal stem cells

value: on board the ISS

value: standard

value: miRNAs from exosomes (from spent media)


title: 2wHC_CA_1_mm_smallrna


title: mRNAseq_16wkHFD_replicate1

city: Bethesda

first: Anthony

middle: Robert

last: Soltis

state: MD

address: 4301 Jones Bridge Road

department: Anatomy, Physiology and Genetics

institute: Uniformed Services University

description:
mRNA_16wkHFD_allTimes_allReps_gene_raw_read_counts.txt
mRNA_16wkHFD_allTimes_allReps_gene_CQN_DESeq2_normalized_read_counts.txt

data_processing:
Raw sequencing reads were aligned to known mouse RefSeq gene transcripts obtained from the UCSC table browser (accessed on January 25, 2012) and the mouse genome (build mm9) with the splice junction-aware short-read alignment tool TopHat (version 1.4.0). We restricted TopHat to only align to known transcript splice junctions. Gene-level read counts were quantified using the python package HTSeq. We used the Bioconductor package conditional quantile normalization (CQN, version 1.6.0) to remove systematic biases due to GC-content and gene length coverage and used DESeq2 (version 1.0.18) to perform differential expression analyses. We considered a gene to be differentially expressed if it possessed an absolute log2 fold-change between conditions ≥ 0.5, an FDR-adjusted p-value (q-value) ≤ 0.05, and was expressed in at least one tested condition (i.e. ≥ 0.1 FPKM).
Genome_build: mm9
Supplementary_files_format_and_content: *_raw_read_counts.txt files were generated with the HTSeq count python program using BAM files against mouse RefSeq gene models (included in *.gtf file) with, column 1 containing gene names and the remaining containing read count values for each labeled condition; *_normalized_read_counts.txt files contain conditional quantile normalization (CQN) and DESeq2 normalized counts for all samples in the same format as the raw read count files

extract_protocol:
All livers were removed using clamps cooled in liquid nitrogen. Frozen liver were then pulverized using a CryoPREP impactor (Covaris).
We extracted total RNA from the pulverized frozen livers of mice using the miRNeasy Mini kit (Qiagen). We prepared mRNA-Seq libraries using the TruSeq RNA Sample Prep Kit v1 (Illumina) and size-selected using 2% agarose gel electrophoresis for 180 +/- 25 base-pairs of insert. We multiplexed mRNA-Seq libraries and paired-end sequenced samples for 40-50 base-pairs on an Illumina Hi-Seq 2000 machine.

treatment_protocol: We fed mice a standard chow diet (Prolab Isopro RMH 3000, Purina) or a high-fat diet (S3282, Bioserve) for 6 or 16 weeks. HFD feeding was initiated when mice were 8 weeks of age for the 16 week time point or at 18 weeks of age for the 6 week time point. All mice were sacrificed at 24 weeks of age following overnight starvation. Some mice were administered 1 U/kg of insulin (Novolin R, Novo Nordisk) diluted in PBS via intraperitoneal injection. These mice were sacrificed at variable times post insulin injection. Other mice were treated with metformin (Sigma, PHR1084), initiated at 8 or 18 weeks, dissolved in drinking water to attain a dose of 270 mg/kg/day lean body mass by dilution of a freshly prepared 10 mg/ml stock solution.

value: liver

tag: diet

value: 16 week high-fat diet

value: 24 weeks

value: wild type

value: No insulin/metformin treatment


title: mRNAseq_16wkHFD_replicate2


title: mRNAseq_16wkHFD_replicate3


title: mRNAseq_CD_replicate3

description:
mRNA_CD_allTimes_allReps_gene_raw_read_counts.txt
mRNA_CD_allTimes_allReps_gene_CQN_DESeq2_normalized_read_counts.txt

value: chow diet


title: mRNAseq_16wkHFD_0_Ins_metformin_replicate3

description: mRNA_16wkHFD_0_Ins_metformin_allReps_gene_raw_read_counts.txt

value: Metformin treatment


title: mRNAseq_CD_replicate1


title: mRNAseq_CD_replicate2


title: mRNAseq_16wkHFD_0_Ins_metformin_replicate1


title: mRNAseq_16wkHFD_120m_Ins_replicate1

value: 120 min intraperitoneal insulin


title: mRNAseq_16wkHFD_0_Ins_metformin_replicate2


title: mRNAseq_16wkHFD_120m_Ins_replicate2


title: mRNAseq_16wkHFD_60m_Ins_replicate2

value: 60 min intraperitoneal insulin


title: mRNAseq_16wkHFD_30m_Ins_replicate6

value: 30 min intraperitoneal insulin


title: mRNAseq_16wkHFD_60m_Ins_replicate3


title: mRNAseq_16wkHFD_30m_Ins_replicate5


title: 2wEE_CA_4_mm_smallrna

value: 20 weeks


title: mRNAseq_16wkHFD_60m_Ins_replicate1


title: mRNAseq_16wkHFD_30m_Ins_replicate3


title: mRNAseq_16wkHFD_30m_Ins_replicate2


title: mRNAseq_6wkHFD_0_Ins_metformin_replicate2

description: mRNA_6wkHFD_0_Ins_metformin_allReps_gene_raw_read_counts.txt

value: 6 week high-fat diet


title: mRNAseq_16wkHFD_15m_Ins_replicate2

value: 15 min intraperitoneal insulin


title: mRNAseq_6wkHFD_0_Ins_metformin_replicate3


title: mRNAseq_16wkHFD_15m_Ins_replicate1


title: mRNAseq_6wkHFD_0_Ins_replicate3

description: mRNA_6wkHFD_0_Ins_allReps_gene_raw_read_counts.txt


title: mRNAseq_16wkHFD_30m_Ins_replicate4


title: mRNAseq_16wkHFD_120m_Ins_replicate3


title: mRNAseq_6wkHFD_0_Ins_replicate2


title: mRNAseq_CD_0_Ins_metformin_replicate3

description: mRNA_CD_0_Ins_metformin_allReps_gene_raw_read_counts.txt


title: mRNAseq_CD_120m_Ins_replicate2


title: mRNAseq_CD_120m_Ins_replicate3


title: mRNAseq_6wkHFD_0_Ins_replicate1


title: mRNAseq_16wkHFD_15m_Ins_replicate3


title: mRNAseq_CD_120m_Ins_replicate1


title: mRNAseq_CD_60m_Ins_replicate3


title: mRNAseq_CD_30m_Ins_replicate1


title: mRNAseq_CD_30m_Ins_replicate2


title: mRNAseq_CD_60m_Ins_replicate2


title: mRNAseq_CD_15m_Ins_replicate3


title: mRNAseq_CD_15m_Ins_replicate2


title: mRNAseq_CD_30m_Ins_replicate3


title: mRNAseq_CD_15m_Ins_replicate1


title: mRNAseq_CD_60m_Ins_replicate1


title: mRNAseq_6wkHFD_0_Ins_metformin_replicate1


title: P21_R3

city: Oxford

first: Esther

last: Becker

address: Sherrington Road

institute: University of Oxford

data_processing:
Trimmed for SMARTer adapter sequences with Cutadapt v1.2.1
Aligned with GSNAP 2012-07-20
Merge BAM files across sequencing lanes
Uniquely aligning reads counted with HTSeq 0.5.3p9
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: txt files of HTSeq count outputs over Ensembl 72 GRCm38.p1 gene models

source_name: Purkinje cells

extract_protocol:
Purkinje cells were laser microdissected, flash frozen on dry ice, and RNA was harvested using the RNeasy Micro Kit (Qiagen).
cDNA libraries were prepared using the SMARTer Ultra Low RNA Kit for Illumina sequencing (Clontech), followe by NEBNext DNA Library Prep Master Mix Set for Illumina (New England Biolabs).

value: cerebellum - Purkinje cells

tag: developmenttal timepoint

value: postnatal day P21


title: P14_R1

value: postnatal day P14


title: P14_R2


title: P21_R1


title: P14_R3


title: P8_R1

value: postnatal day P8


title: P8_R3


title: mRNAseq_CD_0_Ins_metformin_replicate2

value: liver

tag: genotype


title: P8_R2


title: P4_R2

value: postnatal day P4


title: P0_R3

value: postnatal day P0


title: P4_R1


title: P4_R3


title: P0_R1


title: mRNA from flight cells, Standard medium, biological replicate 3_RNA-seq

data_processing:
Pre processing: Sickle trimmer was used to remove low quality ends of the raw reads (using a quality threshold of 20, with option –q 20) and to remove short reads (using a minimum length threshold of 30, with option –l 30); Adapters were removed using CUTADAPT
Mapping: Reads were firstly aligned to reference genome  with TopHat2 (v2.1.1); unmapped reads were re-aligned with Bowtie2 (v2.2.9)  in local mode. Alignments were joined with picard tools (v1.119)
Feature count: Gene count data were obtained with htsseq-count command in HTSeq framework (v0.6.0)
Differential expression analysis: performed using the edgeR (v3.16.5) package in R. After library normalization, the genewise exact tests for differences in the mean between the two groups of negative-binomially distributed counts was calculated with command exactTest. Significantly differentially expressed genes (DE-genes) between the two conditions (FMOM vs FMSM), without adjustment for multiple testing, were identified and exported for further analysis.
Genome_build: ENSEMBLE GRCh38.p5 Human Genome assembly
Supplementary_files_format_and_content: text file with mRNA count data.

extract_protocol:
Samples were preserved in RNAlater; resuspended by scraping in Trizol (Thermo Fisher Scientific) for total RNA extraction. 100ng of total RNA were used to purify mRNA and to synthesize cDNA in one tube (Thermo Fisher Scientific -Dynabeads mRNA DIRECT Micro Kit), using RCC RNA Spike-In Control Mixes (Thermo Fisher Scientific) as a control.
Ion Total RNA-Seq Kit v2 to construct the whole transcriptome libraries, using oligo-dT primers.

value: bone marrow mesenchymal stem cells

value: standard


title: mRNA from flight cells, Osteogenic medium, biological replicate 1_RNA-seq

value: osteogenic


title: P0_R2


title: mRNA from flight cells, Standard medium, biological replicate 1_RNA-seq


title: Naïve DNase-HiC rep2

first: David

data_processing:
Library strategy: HiC-seq
ChIP-seq and Dnase-HiC reads were aligned using Bowtie2
ChIP-seq peaks were identified using MACS v1.4
HiC processing was done using HiTC Bioconductor package, TADs and boundaries were identified using TopDom

Genome_build: hg19

value: naive

value: embryonic stem cell

value: GSKi + MEKi (2i), Lif, IGF1, FGF


title: Day50_+CHIR_differentiated lung_cells_replicate_3

status: Public on Jan 30 2019

city: New York

first: Hans-Willem

last: Snoeck

state: NY

address: 650 W. 168th Street, BB816

department: Medicine

institute: Columbia University Medical Center

description:
CFKDCI_3
Barcode: TAGCTT
raw_counts_ensembl.txt
raw_counts_table.txt

data_processing:
We used RTA (Illumina) for base calling and bcl2fastq2 (version 2.17) for converting BCL to fastq format, coupled with adaptor trimming.
We mapped the reads to a reference genome (Human: NCBI/build37.2) using STAR(2.5.2b) and featureCounts(v1.5.0-p3)
We test for differentially expressed genes under various conditions using DEseq
Genome_build: NCBI/build37.2
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each sample

source_name: Day50_+CHIR_differentiated lung_cells

extract_protocol:
RLT buffer and RNeasy Micro Kit (Qiagen, Valencia, CA).
Libraries were generated using Illumina TruSeq RNA prep kit after poly-A pull-down to enrich mRNAs from total RNA samples

treatment_protocol: ES cell-derived Lung Epithelial cells generated by directed differentiation of RUES 2 Embryonic Stem Cell line to first definitive endoderm,then anterior foregut endoderm followed by specification for the lung field according to established protocols (Huang, SX. et al. Nature Protocols (2015)).  Maturation of the lung progenitors was achieved after treatment with dexamethasone, c-AMP and IBMX in the presence or absence of CHIR9921.

tag: cell line

value: RUES2 Human Embryonic Stem Cells

value: Lung progenitors

tag: time

value: Day 50

value: +CHIR


title: Naïve DNase-HiC rep1

tag: cell type


title: P21_R2

value: cerebellum - Purkinje cells


title: Day50_-CHIR_differentiated lung_cells_replicate_2

description:
FKDCI_2
Barcode: ACTTGA
raw_counts_ensembl.txt
raw_counts_table.txt

source_name: Day50_-CHIR_differentiated lung_cells

value: -CHIR


title: Day50_-CHIR_differentiated lung_cells_replicate_3

description:
FKDCI_3
Barcode: GGCTAC
raw_counts_ensembl.txt
raw_counts_table.txt


title: Day50_+CHIR_differentiated lung_cells_replicate_2

description:
CFKDCI_2
Barcode: CAGATC
raw_counts_ensembl.txt
raw_counts_table.txt


title: Day50_+CHIR_differentiated lung_cells_replicate_1

description:
CFKDCI_1
Barcode: TGACCA
raw_counts_ensembl.txt
raw_counts_table.txt


title: Day50_-CHIR_differentiated lung_cells_replicate_1

description:
FKDCI_1
Barcode: ACAGTG
raw_counts_ensembl.txt
raw_counts_table.txt


title: Day25_lung_progenitors_replicate_3

description:
D25_3
Barcode: TTAGGC
raw_counts_ensembl.txt

value: Day 25


title: Day25_lung_progenitors_replicate_2

description:
D25_2
Barcode: CGATGT
raw_counts_ensembl.txt


title: Day25_lung_progenitors_replicate_1

description:
D25_1
Barcode: ATCACG
raw_counts_ensembl.txt


title: E14-serum_1

city: Basel

first: Ilya

middle: M.

last: Flyamer

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
Fastq files were generated by the sequencing facilities (Wellcome Trust Clinical Research Facility for test sequencing on NextSeq 550, BGI for deep sequencing on HiSeq 4000).
Reads were processed using distiller (https://github.com/mirnylab/distiller-nf) on the high-performance computing cluster of the University of Edinburgh (Eddie3). Mapping was performed to the mm9 genome build. Hi-C pairs with exactly matching coordinates were removed as PCR or optical duplicates (pcr_dups_max_mismatch_bp: 0). Only read pairs with both mapq>30 were retained. The output statistics information and multiresolution Cooler files were used in downstream analyses.
For pileup analysis, we took all regions of interest in the Hi-C maps, e.g. all cis interactions between CGIs bound or not bound by RING1B, and averaged a 15×15 window centered on them at 5 Kb resolution (10 Kb for the Du et al data, and comparison with it). For each of those windows 10 control windows were obtained by randomly shifting the position of the original window between 100 kb and 1 Mb along the diagonal of the map. All control windows were averaged, and were used to normalise the pile-up to remove the distance-dependency of interactions. Then, the final matrix was divided by the average value of its top-left and bottom-right 3×3 corners, to normalize the local background. Values of enrichment are the enrichment of interactions in the center pixel of the matrix, after all described normalization procedures. The code used to perform this analysis is available here: https://github.com/Phlya/CoolPUp
genome build: mm9
processed data files format and content: We provide 4 processed files for each biological sample, and three for combined data for each condition. They are (i) a gzip-compressed .pairs file (https://pairtools.readthedocs.io/en/latest/index.html, except W are called C, and U are called L), according to an older .pairtools format convention), (ii) 5 kb resolution .cool files (https://github.com/mirnylab/cooler), (iii) 10 kb resolution .cool files, and (iv) multiresolution .cool files storing data in resolution 1*2^n kb, which can be used in HiGlass (https://github.com/hms-dbmi/higlass) for interactive visualization.

source_name: Mouse ES cells

growth_protocol: Cells were maintained at 37°C with 5% CO2 and passaged every 2-3 days. Serum cells were maintained in either GMEM (Gibco) supplemented with 15% foetal calf serum, 0.1mM nonessential amino acids (SIGMA), 1mM sodium Pyruvate (Sigma) 1% Penicillin/Streptomycin, 2mM L-glutamine, 0.1mM β-mercaptoethanol (Thermo Fisher), and ESGRO LIF (Millipore) at 1000U/mL. Cells were grown on 0.2% gelatin (Sigma). 2i culture conditions include 50% DMEM/F12 (Gibco), 50% Neurobasal media (Gibco), 0.5% N2 supplement, 1% B27 & RA (Gibco), 7.5% BSA (Gibco), 1% Penicilllin/Streptomycin, 2mM L-glutamine, Monothioglycerol 1.5 x 10-4M (Sigma), 1000U/ml ESGRO LIF (Millipore), 1uM PD0325901 (MEK inhibitor, Stemgent) and 3Um CHIR99021 (GSK3 inhibitor, Stemgent). mESCs were passaged every 2-3 days using trypsin/EDTA (Sigma). 2i conversions were carried out for 14 days.

extract_protocol:
Hi-C was performed largely as described (Rao et. el., 2014) with minor modifications. Briefly, ES cells were crosslinked in 1% formaldehyde for 10 minutes, snap-frozen in 2-5 mln aliquots and stored at -80°C. After permeabilization in lysis buffer (0.2% Igepal, 10 mM Tris-HCl pH 8.0, 10 mM NaCl, 1x Halt Protease inhibitor cocktail) nuclei were isolated in 0.3% SDS in NEBuffer 3 at 62° for 10 minutes. SDS was quenched with 1% Triton X-100 at 37° for 1 h, then the nuclei were pelleted and resuspended in 250 ul DpnII buffer with 600 U DpnII. After overnight digestion, 200 more units were added for 2 hours. Then the ends were filled-in using Klenow, d(G/C/T)TPs and biotin-14-dATP for 1.5 hrs at 37°. After ligation at room temperature for 4 hrs the nuclei were spun down, resuspended in 200 ul mQ and digested with proteinase K for 30 min at 55° in presence of 1% SDS. Then the cross-links were reversed at 65° overnight after addition of NaCl to a final concentration of 1.85 M. In the morning, after ethanol precipitation and a wash with 70-80% Ethanol, DNA was resuspended in 500 ul of sonication buffer (50 mM Tris pH 8.0, 0.1%SDS, 10 mM EDTA), incubated on ice for 15 min and then sheared using a probe sonicator to fragment size of 200-700 bp. Then the DNA was concentrated on Amicon filter units, bound to MyOne T1 Streptavidin beads and used for Illumina library preparation. Small aliquots were taken before and after DpnII treatment, and before sonication to confirm efficient DNA digestion and ligation by running them on 1% agarose gel. Samples were first test-sequenced on NextSeq 550 (WTCRF, Edinburgh) to check library quality, and then selected libraries were sequenced deeply on HiSeq 4000 (BGI).
In house Illumina library protocol from Rao et. al., 2014.

tag: culture condition

value: Serum+LIF

tag: biologial replicate


title: E14-2i_1


title: E14-2i_2


title: mRNA from flight cells, Standard medium, biological replicate 2_RNA-seq

source_name: hBMSCs on board the ISS cultured in standard medium

tag: medium


title: Lymphoid_GR6

status: Public on Jan 29 2019

city: Boston

first: Edroaldo

last: Lummertz da Rocha

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Boston Children's Hospital

description: MLL-AF9 transformed mouse HSPCs cultured under lymphoid conditions

data_processing:
RNA-seq reads were trimmed for adaptor sequence using Trimmomatic and aligned to mouse genome mm10 using Bowtie/Tophat
Counts were generated using featureCounts
Normalization was performed with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file containing gene expression counts

source_name: Lymphoid, hematopoietic stem and progenitor cells (HSPCs)

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen) per the manufacturer’s protocol.  Purified RNA was subjected to polyA selection using the NEBNext Polyadenylated mRNA Magnetic Isolation Module and subsequently used for library preparation with the NEBNext Ultra RNA Library Prep Kit (both from New England Biolabs). Libraries were analyzed on a Tapestation (Agilent) for quality control, quantified using the Qubit dsDNA HS Assay (Invitrogen) and equimolar pools were sequenced on HiSeq 2500 using 100-bp single-end protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: MLL-AF9 transformed HSPCs

tag: culture conditions

value: pro-lymphoid


title: neo10ccl5_d

description: leukemia treated with ccl5

source_name: neo10ccl5, primary neonatal murine leukemia

value: primary neonatal murine leukemia

tag: treatment

tag: sample type

value: primary neonatal leukemia transplant


title: neo10ccl5_c

description: leukemia treated with ccl5


title: negative_2f

description: leukemia under control conditions

source_name: negative, primary neonatal murine leukemia

value: control


title: Lymphoid_GR5


title: negative_1e

description: leukemia under control conditions

source_name: neo_control, primary neonatal murine leukemia


title: negative_3b

description: leukemia under control conditions

source_name: neo10ctrl, primary neonatal murine leukemia


title: neo30ccl5_a

description: leukemia treated with ccl5

source_name: neo30ccl5, primary neonatal murine leukemia

value: tertiary neonatal leukemia transplant


title: Myeloid_GR4

description: MLL-AF9 transformed mouse HSPCs cultured under myeloid conditions

source_name: Myeloid, hematopoietic stem and progenitor cells (HSPCs)

value: pro-myeloid


title: mRNAseq_16wkHFD_30m_Ins_replicate1

description:
mRNA_16wkHFD_allTimes_allReps_gene_raw_read_counts.txt
mRNA_16wkHFD_allTimes_allReps_gene_CQN_DESeq2_normalized_read_counts.txt

tag: strain

value: liver

value: 16 week high-fat diet

value: 24 weeks

value: wild type

value: 30 min intraperitoneal insulin


title: Lymphoid_GR1


title: Myeloid_GR2


title: E14-serum_2


title: RNA-seq G_homo_rep3

city: Nagoya

first: Hiroshi

middle: I.

last: Suzuki

address: 65 Tsurumai-cho, Showa-ku

department: DIvision of Molecular Oncology, Graduate School of Medicine

country: Japan

institute: Nagoya University

data_processing:
RNA-seq samples were analyzed by Illumina NextSeq 500.
Sequenced reads were aligned to the mm9 reference genome assembly and gene counts were quantified using STAR (v2.5.1b)
Genome_build: mm9
Supplementary_files_format_and_content: Summary txt file includes normalized FPKM gene counts.

source_name: primary chondrocytes

growth_protocol: Mouse primary rib chondrocytes were isolated from the frontal part of the lib cage of 7 day-old mice and cultured in standard culture conditions.

extract_protocol:
Total RNA was extracted using Direct-zol RNA MiniPrep kit (Zymo Research).
DNA libraries were generated using TruSeq Stranded mRNA sample preparation kit and analyzed by NextSeq.

value: chondrocytes

tag: genotype and drug

value: miR-140 G/G


title: RNA-seq G_homo_rep1


title: RNA-seq G_hetero_rep2

value: miR-140 WT/G hetero


title: RNA-seq G_hetero_rep3


title: RNA-seq KO_rep2

value: miR-140 KO


title: RNA-seq WT_rep3

value: miR-140 WT


title: RNA-seq G_hetero_rep1


title: RNA-seq WT_rep2


title: RNA-seq G_homo_rep2


title: SmallRNA-seq KO_rep3

data_processing:
Small RNA-seq samples were analyzed by Illumina HiSeq 2000
Obtained sequences were processed for adaptor removal and size exclusion of sequences < 15 nt with Cutadapt.
Filtered reads were mapped to mm9 genome assembly with bowtie 1.0.1, allowing two mismatches, and further analyzed as previously described using miRBase v21 (Langmead et al., 2009; Zamudio et al., 2014).
Genome_build: mm9
Supplementary_files_format_and_content: Summary txt file includes miRNA expression values normalized to non-miRNA small RNA reads.

extract_protocol:
Total RNA was extracted using Direct-zol RNA MiniPrep kit (Zymo Research).
Small RNA libraries was prepared with the NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs) and analyzed by Illumina HiSeq 2000.


title: RNA-seq WT_rep1


title: SmallRNA-seq G_homo_rep3


title: SmallRNA-seq KO_rep1


title: SmallRNA-seq KO_rep2


title: SmallRNA-seq G_homo_rep1


title: SmallRNA-seq G_hetero_rep2


title: SmallRNA-seq G_homo_rep2


title: SmallRNA-seq WT_rep3


title: SmallRNA-seq G_hetero_rep1


title: RNA-seq KO_rep1


title: RNA-seq KO_rep3


title: iPS HNF4a ChIP

status: Public on Jan 28 2019

city: Charleston

first: Stephen

middle: A

last: Duncan

state: SC

address: 173 Ashley Avenue, BSB 6th Floor, Room 657A

department: Regenerative Medicine and Cell Biology

institute: Medical University South Carolina

data_processing:
Samples were sequenced on Illumina HiSeq 2000
Alignment to the human genome NCBI 37/hg19 was performed using Bowtie 2
Model Based Analysis of ChIP-Seq (MACS) was used for peak-calling with a two-sided and p-value cut off (<10–e5) to reduce identifying false-positive peaks
PeakAnalyzer was used to annotate the peaks with nearest Ensemble genes
Genome_build: NCBI 37/hg19
Supplementary_files_format_and_content: Bed files comprises of peaks with nearest genes

source_name: Day 8 cells

growth_protocol: iPS cells were maintained as detailed in Mallanna et al 2013

extract_protocol: On Day 8, Cells were fixed with 1% PFA for 10 min, quenched with glycine, collected and frozen at -80C.  Cell pellets were lysed (85mM KCl; 5mM PIPES;0.5% NP40), nuclei were collected and chromatin was sonicated on a S220 Focused-ultrasonicator (Covaris) to a mean size of 300-500 bp.

treatment_protocol: iPS cells were differentiated for 8 days following the hepatocyte differentiaiton protocol as detailed in Mallanna et al 2013

value: iPS cells


title: SmallRNA-seq WT_rep1


title: Kc167_mock_input_6

first: Cameron

last: Palmer

address: 50 South Drive

department: National Institute of Diabetes and Digestive and Kidney Diseases

institute: National Institutes of Health

description:
ib37_mock_input
Processed data file: mock_clamp-abcam.narrowPeak

data_processing:
Reads were trimmed using cutadapt v1.8.1 with arguments --quality-cutoff 20 -a AGATCGGAAGAGC --minimum-length 25 --overlap 10
Trimmed reads were mapped with bowtie2 v2.2.9 with default arguments to the dm6 assembly.
Multimappers were removed from aligned reads with samtools v1.2 vew command with argument -q 20.
Duplicates were removed from mapped, uniquely-mapping reads with picard MarkDuplicates v2.9.2.
Macs2 v2.1.0.20150731 was used to call peaks by providing replicate Ips and inputs as multiple BAMs, effectively calling peaks on pooled samples, and using additional arguments -f BAM --gsize=dm
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: narrowPeak files of called peaks as output from macs2 peak-calling.

organism: Drosophila melanogaster

source_name: Kc167 cells, mock, input

growth_protocol: Kc167 cells-derived from Drosophila embryo were routinely maintained in CCM3 (Thermo Scientific HyClone, Logan, UT). The cells were maintained in monolayer at 25°C.

extract_protocol:
ChIP-seq was performed as described previously (Matzat et al., 2012).
ChIP antibodies: clamp: Rabbit anti-CLAMP antibody (sdix, Cat no# 4988.00.02); clamp-abcam: Rabbit anti-CLAMP antibody (made through Abcam by Erica N. Larschan, Brown University); suhw: Guinea pig serum against Su(Hw) (Moshkovich and Lei, 2010 PMID: 21852534); mod: Rabbit serum against Mod(mdg4)2.2 (Van Bortle et al., 2012, PMID: 22722341); cp190: Rabbit serum against CP190 (Pai et al. 2004, PMID: 15574329).
ChIP-seq library was prepared as described previously (Matzat et al., 2012).

treatment_protocol: 10 million Kc167 cells were transfected with 5 ug of dsRNA (DRSC 29935) against Clamp by using Amexa cell line Nucleofector kit V (Lonza) and incubated 6 days at 25°C to obtain significant knockdown of Clamp.

value: mock

tag: chip antibody


title: Kc167_mock_input_8

description:
ib39_mock_input
Processed data file: mock_clamp.narrowPeak


title: Kc167_dsclamp_clamp-abcam_10

description:
ib46_dsclamp_clamp-abcam
Processed data file: dsclamp_clamp-abcam.narrowPeak

source_name: Kc167 cells, dsCLAMP, clamp-abcam ChIP

value: dsCLAMP

value: clamp-abcam


title: Kc167_dsclamp_clamp-abcam_11

description:
ib47_dsclamp_clamp-abcam
Processed data file: dsclamp_clamp-abcam.narrowPeak


title: Kc167_dsclamp_input_10

description:
ib52_dsclamp_input
Processed data file: dsclamp_clamp-abcam.narrowPeak

source_name: Kc167 cells, dsCLAMP, input


title: Kc167_mock_input_0

description:
ib41_mock_input
Processed data file: mock_suhw.narrowPeak


title: Kc167_dsclamp_input_11

description:
ib53_dsclamp_input
Processed data file: dsclamp_clamp-abcam.narrowPeak


title: Kc167_mock_input_9

description:
ib40_mock_input
Processed data file: mock_cp190.narrowPeak


title: Kc167_mock_cp190_9

description:
ib34_mock_cp190
Processed data file: mock_cp190.narrowPeak

source_name: Kc167 cells, mock, cp190 ChIP


title: Kc167_mock_input_5

description:
ib36_mock_input
Processed data file: mock_mod.narrowPeak


title: Kc167_mock_input_7

description:
ib38_mock_input
Processed data file: mock_clamp-abcam.narrowPeak


title: Kc167_mock_clamp-abcam_6

description:
ib31_mock_clamp-abcam
Processed data file: mock_clamp-abcam.narrowPeak

source_name: Kc167 cells, mock, clamp-abcam ChIP


title: Kc167_mock_mod_5

description:
ib30_mock_mod
Processed data file: mock_mod.narrowPeak

source_name: Kc167 cells, mock, mod ChIP

value: mod


title: Kc167_mock_clamp-abcam_7

description:
ib32_mock_clamp-abcam
Processed data file: mock_clamp-abcam.narrowPeak


title: Kc167_mock_input_1

description:
ib14_mock_input
Processed data file: mock_suhw.narrowPeak


title: iPS Input

tag: tissue


title: Kc167_mock_input_2

description:
ib15_mock_input
Processed data file: mock_mod.narrowPeak


title: Kc167_mock_clamp_3

description:
ib08_mock_clamp
Processed data file: mock_clamp.narrowPeak

source_name: Kc167 cells, mock, clamp ChIP

value: clamp


title: Kc167_mock_mod_2

description:
ib07_mock_mod
Processed data file: mock_mod.narrowPeak


title: SmallRNA-seq G_hetero_rep3


title: Kc167_mock_cp190_4

description:
ib29_mock_cp190
Processed data file: mock_cp190.narrowPeak


title: Kc167_mock_input_4

description:
ib35_mock_input
Processed data file: mock_cp190.narrowPeak


title: Kc167_mock_input_3

description:
ib16_mock_input
Processed data file: mock_clamp.narrowPeak


title: SmallRNA-seq WT_rep2


title: Kc167_mock_suhw_1

description:
ib06_mock_suhw
Processed data file: mock_suhw.narrowPeak

source_name: Kc167 cells, mock, suhw ChIP

value: suhw


title: Kc167_mock_clamp_8

description:
ib33_mock_clamp
Processed data file: mock_clamp.narrowPeak


title: Myeloid_GR3

description: MLL-AF9 transformed mouse HSPCs cultured under myeloid conditions

value: MLL-AF9 transformed HSPCs

value: pro-myeloid


title: DEXTGFbeta_2

status: Public on Jan 27 2019

city: Belfast

first: Guillermo

last: López-Campos

state: Northern Ireland

address: 97 Lisburn road

department: Centre for Experimental Medicine

institute: Queen's University of Belfast

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to UCSC hg38 whole genome using Rsubread v1.22 with parameters Type =0 nthreads= 16 nTrim5 13 nTrim3=3
Counts were calculated using FeatureCounts function within the Rssubread package
Genome_build: UCSC hg38
Supplementary_files_format_and_content: A single tab delimited file contains the raw counts for the 18 samples analysed

source_name: BEAS-2B cell line

growth_protocol: Human A549 lung adenocarcinoma cells (ATCC, Manassas, VA, USA) were grown in phenol red-free Dulbecco's modified Eagle's media (DMEM) containing 5% vv−1 heat-inactivated fetal calf serum (FCS), 15 mM HEPES, 0.2% vv−1 sodium bicarbonate, 2 mM L-glutamine, 1% vv−1 non-essential amino acids, 1% vv−1 sodium pyruvate, 5 IU·mL−1 penicillin and 50 µg·mL−1 streptomycin and maintained at 37°C in a humidified 5% CO2/95% air atmosphere

extract_protocol:
Total RNA was extracted using RNeasy miniprep kit (Qiagen)
RNA-Seq libraries were prepared from 500ng total RNA (RIN>8 according to Agilent Bioanalyzer 2100) using NEBNext Ultra RNA library prep kit for Illumina (#E7530) with NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490).

treatment_protocol: Human BEAS-2B bronchial epithelial cells (ATCC, Manassas, VA, USA) were seeded at a density of 25,000 cells/cm2 in 24 well tissue culture plates and allowed to adhere overnight in complete growth medium (LHC-9 media containing 2% v/v heat-inactivated fetal calf serum, 2 mM L-glutamine, 50 IU/mL penicillin and 50 µg/mL streptomycin). Cells were then starved in serum- and steroid-free medium (RPMI medium containing 0.25% bovine serum albumin, 2 mM L-glutamine, 1% v/v sodium pyruvate and 1% v/v non-essential amino acids, 15 mM HEPES, 0.2% v/v sodium bicarbonate, 50 IU/mL penicillin and 50 µg/mL streptomycin) for 24 h prior to treatment with TGF-β1 (40 pM) for 24 h then dexamethasone (30 nM) stimulation for a further 4 h.

value: BEAS-2B bronchial epithelial cells

value: Dexamethasone and TGF-beta1


title: TGF-Beta_1


title: Dex_2

value: Dexamethasone


title: Kc167_mock_suhw_0

description:
ib02_mock_suhw
Processed data file: mock_suhw.narrowPeak


title: TGF-Beta_2


title: DEXTGFbeta_3


title: control_3


title: control_1


title: Dex_3


title: ATAC-seq for patient CLL9 before Ibrutinib treatment

status: Public on Jan 26 2019

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

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

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL9 before Ibrutinib treatment

data_processing:
Illumina Casava1.7 software was used for basecalling.
Sequenced reads were trimmed for adaptor and Nextera sequences
Reads were mapped to hg19 whole genome using bowtie2 v2.2.4 with the –very-sensitive parameter
Duplicate reads were marked and removed with picard tools version 1.118
Read were extended to the average fragment size and bigWig files containing counts of reads per basepair created
Peaks for ATAC-seq samples were called with MACS2 version 2.1.1.20160309 using the “–nomodel” and “–extsize 147” parameters
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files contain counts of reads per basepair; narrowPeak files contain peaks called by MACS2

source_name: Primary peripheral blood mononucleated cells (PBMC) from chronic lymphocytic leukemia patient

extract_protocol:
Heparinized peripheral blood was obtained from CLL patients after signed informed consent. Peripheral blood mononuclear cells (PBMCs) were isolated using Ficoll-Hypaque (GE Healthcare, Uppsala, Sweden) centrifugation. Patients were screened for CLL characteristic chromosomal aberrations including deletions on 13q14, 11q22, and 17p13 and for trisomy 12 by FISH analysis. The IGHV and TP53 mutational status was determined by sequencing (LGC Genomics, Berlin, DE). PBMCs from CLL patients were cryopreserved in RPMI 1640 supplemented with 40% FCS and 10 % DMSO.
~10^5 cells were pelleted by centrifuging for 5 min at 4 °C at 300 x g. After centrifugation, the pellet was carefully resuspended in the transposase reaction mix (12.5 ml 2xTD buffer, 2 ml TDE1 (Illumina) and 10.25 ml nuclease-free water, 0.25 µl 5% Digitonin (Sigma)) for 30 min at 37 °C. Following DNA purification with the MinElute kit eluting in 11 µl, 1 µl of the eluted DNA was used in a quantitative PCR (qPCR) reaction to estimate the optimum number of amplification cycles. Library amplification was followed by SPRI size selection to exclude fragments larger than 1,200 bp. DNA concentration was measured with a Qubit fluorometer (Life Technologies). Library amplification was performed using custom Nextera primers. The libraries were sequenced by the Biomedical Sequencing Facility at CeMM using the Illumina HiSeq3000/4000 platform and the 25-bp paired-end configuration.

tag: patient id

tag: library

value: ATAC-seq

value: CLL

tag: processing batch

tag: clinical centre

value: Vienna General Hospital

tag: clinical status

value: disease

tag: disease

tag: timepoint name

tag: patient gender

value: M

tag: patient years at diagnosis

tag: patient years at sample collection

tag: disease at diagnosis

tag: hospital

tag: patient leukocyte count (10e3/ul)

tag: sample lymphocyte percentage

tag: blood monocyte percentage

tag: blood granulocyte percentage

tag: blood hemoglobin

tag: blood platelets

tag: sample viability percentage

tag: sample viable cd3+ percentage

tag: sample viable cd14+ percentage

tag: sample viable cd19+ percentage

tag: sample viable cd19+cd5+ percentage

tag: sample viable cd19+cd5- percentage

tag: sample viable cd19-cd5+ percentage

tag: sample clone number

tag: sample v-locus

tag: sample d-locus

tag: sample j-locus

tag: sample ighv mutation percentage

tag: sample ighv homology

tag: sample ighv mutation status

value: TRUE

tag: sample del11q percentage

tag: sample del13q percentage

tag: sample del17p percentage

tag: sample tri12 percentage

tag: sample days since ibrutinib treatment


title: ATAC-seq for patient CLL5 before Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL5 before Ibrutinib treatment

tag: patient id

tag: library

tag: cell type

tag: processing batch

tag: clinical centre

tag: sample type

tag: clinical status

tag: disease

tag: timepoint name

tag: patient gender

tag: patient years at diagnosis

tag: patient years at sample collection

tag: disease at diagnosis

tag: hospital

tag: patient leukocyte count (10e3/ul)

tag: sample lymphocyte percentage

tag: blood monocyte percentage

tag: blood granulocyte percentage

tag: blood hemoglobin

tag: blood platelets

tag: sample viability percentage

tag: sample viable cd3+ percentage

tag: sample viable cd14+ percentage

tag: sample cd38+ percentage in viable cd19+cd5+

value: FALSE

tag: patient preliminary response evaluation

value: PR


title: ATAC-seq for patient CLL6 before Ibrutinib treatment

description: ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL6 before Ibrutinib treatment

tag: patient id

tag: library

tag: cell type

tag: processing batch

tag: clinical centre

tag: sample type

tag: clinical status

tag: disease

tag: timepoint name

value: F

tag: sample viable cd19+ percentage

tag: sample viable cd19+cd5+ percentage

tag: sample viable cd19+cd5- percentage

tag: sample viable cd19-cd5+ percentage

tag: sample clone number

tag: sample del11q percentage

tag: sample del13q percentage

tag: sample del17p percentage

tag: sample tri12 percentage

tag: sample tp53 mutation

tag: sample tp53 mutation description

tag: sample days since ibrutinib treatment

value: SD