title: single cell from LSK-SLAM-13.34 [LIB021528_GEN00057108_S53_R1]

city: Baltimore

first: Yuqi

last: Tan

address: 733 North Broadway, MRB 653

institute: Johns Hopkins University

data_processing:
We only use R1 from the pair-end sequence reads. Sequence reads were trimmed to a final length of 40 bases using Trimming software Cutadapt (Martin, 2011).
Salmon (Patro et al., 2017) was used to quasi-map trimmed reads to the reference transcriptome (ENSEMBL (Zerbino et al., 2018) GRCh38.80), including 6511 non-coding RNAs (scaRNAs, lincRNAs, snRNAs, and snoRNAs), to estimate transcript abundances. The number of reads mapping to the transcriptome ranged from 7.7 to 12.0 million. Read counts per gene were derived by summing the counts per transcript across all transcripts associated with the gene
For quality control measures, 0.1% of reads were randomly sampled from each FASTQ and directly aligned to ENSEMBL GRC Release 80 (ftp://ftp.ensembl.org/pub/release-80/gtf/) reference genomes using HISAT2 (Kim et al., 2015) to determine percentage alignment to H. Sapiens, M. Musculus, S. Cerevisiae, E. Coli, and D. Rerio genomes, as well as overlaps with genomic features (including rRNA, mtRNA, protein-coding regions), ambiguous and non-unique alignments, and unaligned reads.
Genome_build: GRCm38
Supplementary_files_format_and_content: comma delimited files containing metadata and count matrix for all samples

source_name: Fetal liver (FL)

extract_protocol:
Embryos were harvested from the uterus and dissected in cold dissecting buffer (Dulbecco’s phosphate buffered saline with 10% fetal bovine serum and antibiotics). Dissected tissues were dissociated in 0.125% collagenase type I (Sigma-Aldrich) and 1 U Dispase (Stemcell Technologies) at 37°C for 30 min. The samples were reduced to single cell suspension by mechanical trituration, washed with dissecting media, and passed through 40mm cell strainer. FACS was used to enrich single cell population of interest
Cells were lysed and single cell libraries prepared by the C1 System using the SMARTer Ultra Low RNA Kit (Clontech) and protocols provided by Fluidigm.

value: embryonic tissue

tag: strain


title: single cell from LSK-SLAM-13.35 [LIB021528_GEN00057129_S74_R1]

status: Public on Apr 17 2020

type: SRA

state: MD

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue


title: single cell from LSK-SLAM-13.32 [LIB021528_GEN00057147_S92_R1]


title: RNA-seq_Runx1Evi1_NoDox_HP_Rep1

city: Birmingham

first: Peter

last: Keane

address: Vincent Drive

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

data_processing:
Raw paired-end sequencing data were processed to remove low quality sequences and adaptors with Trimmomatic v0.32.
The processed reads were then aligned to the mouse genome (version mm10) using Hisat2 v2.1.0 with default parameters
Gene expression was measured as Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values with Stringtie v1.3.3 using gene models from RefSeq as the reference transcriptome.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file containing gene name (column 1) and FPKM value (column 2)

source_name: A2lox.cre mESC

growth_protocol: RUNX1-EVI1 from the pME18s-RUNX1-EVI1 plasmid was cloned into the p2lox-targeting vector. A2lox ESCs were transduced with 20 µg of p2lox-RUNX-EVI1 using the 4D-Nucleofector (Lonza) with the mouse ES program, with the P3 primary cell kit. Individual colonies were expanded on mouse embryonic feeder cells in ES cell medium, comprising DMEM (Sigma D6546), 15% FCS (Sigma ES-009), 100 units/ml penicillin, 100 µg/ml streptomycin, 1 mM sodium pyruvate, 1mM L-glutamine, 0.15 mM monothioglycerol, 1x non-essential amino acids and  103 U/ml leukaemia inhibitory factor (ESGRO, Millipore) following 7 days of 300 µg/ml neomycin selection.

extract_protocol:
RNA was isolated from sorted cells using the NucleoSpin RNA kit (Macherey-Nagel).
RNA-seq libraries were prepared from two biological replicates using the True-Seq stranded total RNA kit (Illumina) and sequenced paired-end in a pool of 12 indexed libraries using a Next-Seq 500 high output kit v2 150 cycles (Illumina) at the Genomics Birmingham sequencing facility.

treatment_protocol: ESCs were passaged twice onto gelatine-coated tissue culture plastic without MEFs, on the second passage DMEM was substituted for IMDM (Sigma I3390). Cells were then plated into bacterial-grade dishes at a density of 2.5x104 cells/ml with IMDM, 15% FCS (Gibco), 100 units/ml penicillin, 100 µg/ml streptomycin, 1 mM sodium pyruvate, 1mM L-glutamine, 0.15 mM monothioglycerol, 0.18 mg/ml hTransferrin (Roche), 50 µg/ml ascorbic acid. After 3.25 days the resulting embryoid bodies were dispersed using TrypLE express (Gibco) to single cells and FLK1+ cells were purified by magnetic cells sorting, using biotin-conjugated CD309 antibody (eBioscience), anti-biotin microbeads (Miltenyi Biotec) and LS columns (Miltenyi Biotec). These FLK1+ cells were then cultured in gelatin-coated flasks – 1.4x106 cells in a T150 flask – in IMDM, 10% FCS (Gibco), 20% D4T condition media, 100 units/ml penicillin, 100 µg/ml streptomycin, 1 mM sodium pyruvate, 1mM L-glutamine, 0.45 mM monothioglycerol, 0.18 mg/ml hTransferrin (Roche), 25 µg/ml ascorbic acid, 5 ng/ml mVEGF (Peprotech) and 10 ng/ml mIL-6 (Peprotech). After 1 day 0.5 µg/ml doxycycline was added where appropriate and cells were cultured for a further 18 hours

tag: cell type

value: Hematpoietic progenitor

tag: construct

value: doxycycline inducible RUNX1-EVI1

tag: dox status

value: NoDox


title: RNA-seq_Runx1Evi1_NoDox_HE1_Rep1

value: Hemogenic endothelial 1


title: single cell from LSK-SLAM-13.30 [LIB021528_GEN00057143_S88_R1]


title: single cell from LSK-SLAM-13.31 [LIB021528_GEN00057146_S91_R1]


title: single cell from LSK-SLAM-13.28 [LIB021528_GEN00057141_S86_R1]


title: single cell from LSK-SLAM-13.29 [LIB021528_GEN00057142_S87_R1]


title: single cell from LSK-SLAM-13.33 [LIB021528_GEN00057151_S96_R1]


title: AMs, S, DGM-01160_am

type: RNA

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing:
CEL files were imported into Partek Genomics Suite using Robust Multi-Array (RMA) normalization. HG-U133 Plus 2.0 probesets were filtered on 1938 probesets that correpsond with Mita Carta 2.0 genes. Statistical comparisons for microarray data were calculated using Partek software and age corrected analysis of covariance (ANCOVA) with a p<0.05 following Benjamini-Hochberg correction considered significant.
The 1938 Mito Carta 2.0 probesets are represented in Series supplementary file 88AM_RMA.csv.

label: biotin

organism: Homo sapiens

source_name: alveolar macrophages obtained from bronchoalveolar lavage

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: phenotype

value: S

tag: age

tag: gender

value: F

tag: ethnicity

value: His

tag: pack-yrs


title: AMs, S, DGM-00977_am

value: M

value: alveolar macrophages obtained from bronchoalveolar lavage


title: Runx1Evi1_NoDox_Prog_DHS

library_source: genomic

data_processing:
Library strategy: DNaseI-seq
Raw single-end reads from DNaseI-seq experiments were processed with Trimmomatic v0.32.
The processed reads were aligned to the mouse genome (version mm10) using Bowtie2 v2.2.39 with the option --very-sensitive-local.
The resulting alignments were filtered to remove potentially PCR duplicated reads using the MarkDuplicates function in Picard v2.10.5
Peaks corresponding to regions of open chromatin were identified using MACS2 v2.1.1 with the options -g mm --keep-dup all -B --trackline --nomodel --shift -100 --extsize 200.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files of read pileups generated by MACS v2.1.1

molecule: genomic DNA

extract_protocol:
DNaseI was performed as previously described [Bert et al., 2007. PMID:17283044]. 3x10^5 sorted cells were added directly to DNaseI (Worthington Biochemical Corporation) used between 6 and 13 U/ml for 3 minutes at 22°C. The reaction was terminated by addition of SDS to 0.5% and cell lysates treated with 0.5 mg/ml proteinase K overnight at 45°C overnight then 0.2 mg/ml RNaseA for 1 hour at 37°C. DNA was isolated by phenol/chloroform extraction and level of DNaseI digestion was assessed using qRT-PCR for the active TBP promoter compared to an inactive region of chromosome 1 to ensure comparable digestion points were used.
DNaseI fragments were size selected on an agarose gel to between 50 and 250 bp then used to generate a library using the KAPA hyper prep kit, according to the manufacturer’s instructions.  These were then further size selected to obtain fragments between 200 and 300 bp and sequenced single-end in a pool of 12 indexed libraries using a Next-Seq 500 high output kit v2 75 cycles (Illumina) at the Genomics Birmingham sequencing facility.

value: Hematopoietic progenitor

value: doxycycline inducible RUNX1-EVI1 construct


title: single cell from LSK-SLAM-13.26 [LIB021528_GEN00057139_S84_R1]


title: single cell from LSK-SLAM-13.25 [LIB021528_GEN00057137_S82_R1]


title: single cell from LSK-SLAM-13.27 [LIB021528_GEN00057140_S85_R1]


title: single cell from LSK-SLAM-13.24 [LIB021528_GEN00057136_S81_R1]


title: AMs, S, DGM-00413_am


title: AMs, S, DGM-00613_am

value: Eur


title: AMs, S, DGM-00641_am


title: single cell from LSK-SLAM-13.22 [LIB021528_GEN00057132_S77_R1]


title: AMs, S, DGM-00583_am


title: AMs, S, DGM-01011_am


title: single cell from LSK-SLAM-13.21 [LIB021528_GEN00057127_S72_R1]


title: AMs, S, DGM-00216_am


title: AMs, S, DGM-00300_am


title: AMs, S, DGM-01135_am


title: AMs, S, DGM-00515_am


title: single cell from LSK-SLAM-13.20 [LIB021528_GEN00057126_S71_R1]


title: single cell from LSK-SLAM-13.23 [LIB021528_GEN00057133_S78_R1]


title: single cell from LSK-SLAM-13.18 [LIB021528_GEN00057122_S67_R1]


title: AMs, S, DGM-00206_am


title: single cell from LSK-SLAM-13.17 [LIB021528_GEN00057121_S66_R1]


title: single cell from LSK-SLAM-13.16 [LIB021528_GEN00057120_S65_R1]


title: single cell from LSK-SLAM-13.15 [LIB021528_GEN00057119_S64_R1]


title: single cell from LSK-SLAM-13.14 [LIB021528_GEN00057118_S63_R1]


title: single cell from LSK-SLAM-13.11 [LIB021528_GEN00057114_S59_R1]


title: single cell from LSK-SLAM-13.13 [LIB021528_GEN00057117_S62_R1]


title: AMs, S, DGM-00065_am


title: single cell from LSK-SLAM-13.10 [LIB021528_GEN00057113_S58_R1]


title: single cell from LSK-SLAM-13.12 [LIB021528_GEN00057116_S61_R1]


title: single cell from LSK-SLAM-13.9 [LIB021528_GEN00057111_S56_R1]


title: AMs, S, DGM-01127_am


title: single cell from LSK-SLAM-13.8 [LIB021528_GEN00057110_S55_R1]


title: AMs, S, DGM-00626_am


title: AMs, S, DGM-00552_am


title: AMs, S, DGM-00752_am

value: Afr


title: single cell from LSK-SLAM-13.19 [LIB021528_GEN00057123_S68_R1]


title: AMs, S, DGM-00878_am


title: AMs, S, DGM-00013_am


title: single cell from LSK-SLAM-13.7 [LIB021528_GEN00057109_S54_R1]


title: AMs, S, DGM-00612_am


title: AMs, S, DGM-00798_am


title: AMs, S, DGM-00051_am


title: AMs, S, DGM-00914_am


title: AMs, S, DGM-00784_am


title: single cell from PL-11.40 [LIB021528_GEN00057101_S46_R1]

source_name: Placenta (PL)


title: AMs, S, DGM-00743_am


title: AMs, S, DGM-00321_am


title: single cell from PL-11.38 [LIB021528_GEN00057099_S44_R1]


title: AMs, S, DGM-00447_am


title: AMs, S, DGM-00278_am


title: AMs, S, DGM-00474_am


title: AMs, S, DGM-00567_am


title: AMs, S, DGM-00205_am


title: single cell from PL-11.37 [LIB021528_GEN00057098_S43_R1]


title: single cell from PL-11.36 [LIB021528_GEN00057094_S39_R1]


title: single cell from PL-11.35 [LIB021528_GEN00057089_S34_R1]


title: single cell from LSK-SLAM-13.6 [LIB021528_GEN00057107_S52_R1]


title: single cell from PL-11.33 [LIB021528_GEN00057086_S31_R1]


title: single cell from PL-11.32 [LIB021528_GEN00057084_S29_R1]


title: single cell from LSK-SLAM-13.5 [LIB021528_GEN00057104_S49_R1]


title: single cell from PL-11.31 [LIB021528_GEN00057082_S27_R1]


title: single cell from PL-11.39 [LIB021528_GEN00057100_S45_R1]


title: single cell from PL-11.29 [LIB021528_GEN00057078_S23_R1]


title: AMs, S, DGM-00224_am


title: AMs, S, DGM-00708_am


title: AMs, S, DGM-00732_am


title: single cell from PL-11.34 [LIB021528_GEN00057088_S33_R1]


title: AMs, S, DGM-00127_am


title: single cell from PL-11.27 [LIB021528_GEN00057069_S14_R1]


title: AMs, S, DGM-00004_am


title: single cell from PL-11.26 [LIB021528_GEN00057068_S13_R1]


title: single cell from PL-11.28 [LIB021528_GEN00057074_S19_R1]


title: single cell from PL-11.25 [LIB021528_GEN00057063_S8_R1]


title: AMs, NS, DGM-00080_am

value: NS


title: AMs, NS, DGM-00066_am


title: AMs, NS, DGM-00774_am


title: single cell from PL-11.30 [LIB021528_GEN00057081_S26_R1]


title: AMs, S, DGM-00537_am


title: single cell from PL-11.23 [LIB021528_GEN00057058_S3_R1]


title: AMs, S, DGM-00815_am


title: AMs, S, DGM-00273_am


title: AMs, S, DGM-01089_am


title: single cell from PL-11.22 [LIB021528_GEN00057102_S47_R1]


title: AMs, NS, DGM-00069_am


title: AMs, NS, DGM-00052_am


title: AMs, S, DGM-01107_am


title: AMs, S, DGM-00599_am


title: AMs, NS, DGM-00030_am


title: single cell from PL-11.20 [LIB021528_GEN00057080_S25_R1]


title: single cell from PL-11.21 [LIB021528_GEN00057096_S41_R1]


title: single cell from PL-11.19 [LIB021528_GEN00057077_S22_R1]


title: single cell from PL-11.18 [LIB021528_GEN00057067_S12_R1]


title: AMs, NS, DGM-00078_am


title: single cell from PL-11.16 [LIB021528_GEN00057060_S5_R1]


title: AMs, NS, DGM-00082_am


title: single cell from PL-11.15 [LIB021528_GEN00057056_S1_R1]


title: single cell from PL-11.14 [LIB021528_GEN00057103_S48_R1]


title: AMs, NS, DGM-00936_am


title: AMs, NS, DGM-00249_am


title: single cell from PL-11.13 [LIB021528_GEN00057097_S42_R1]


title: single cell from PL-11.12 [LIB021528_GEN00057092_S37_R1]


title: single cell from PL-11.11 [LIB021528_GEN00057091_S36_R1]


title: single cell from PL-11.17 [LIB021528_GEN00057065_S10_R1]


title: single cell from PL-11.9 [LIB021528_GEN00057076_S21_R1]


title: single cell from PL-11.10 [LIB021528_GEN00057090_S35_R1]


title: AMs, NS, DGM-00757_am


title: AMs, NS, DGM-00696_am


title: AMs, NS, DGM-00904_am


title: AMs, NS, DGM-00123_am


title: single cell from PL-11.6 [LIB021528_GEN00057066_S11_R1]


title: single cell from PL-11.5 [LIB021528_GEN00057059_S4_R1]


title: AMs, NS, DGM-00041_am


title: single cell from PL-11.7 [LIB021528_GEN00057070_S15_R1]


title: AMs, NS, DGM-00661_am


title: AMs, NS, DGM-00465_am


title: single cellf from YS [LIB019717_GEN00050518_S66_R1]

source_name: yolk sac (YS)


title: single cellf from YS [LIB019717_GEN00050512_S61_R1]


title: single cell from PL-11.8 [LIB021528_GEN00057075_S20_R1]


title: single cellf from YS [LIB019717_GEN00050502_S54_R1]


title: AMs, NS, DGM-00035_am


title: AMs, NS, DGM-00029_am


title: AMs, NS, DGM-00529_am


title: AMs, COPDs, DGM-10135_am

value: COPDs


title: AMs, NS, DGM-00795_am


title: single cell from PL-11.24 [LIB021528_GEN00057061_S6_R1]


title: AMs, NS, DGM-00897_am


title: AMs, NS, DGM-00084_am


title: AMs, COPDs, DGM-00683_am


title: AMs, COPDs, DGM-10133_am


title: AMs, COPDs, DGM-10132_am


title: AMs, COPDs, DGM-00512_am


title: single cellf from YS [LIB019717_GEN00050536_S83_R1]


title: AMs, COPDs, DGM-10144_am


title: single cellf from YS [LIB019717_GEN00050533_S80_R1]


title: single cellf from YS [LIB019717_GEN00050530_S77_R1]


title: AMs, COPDs, DGM-01357_am


title: single cellf from YS [LIB019717_GEN00050534_S81_R1]


title: single cellf from YS [LIB019717_GEN00050531_S78_R1]


title: AMs, COPDs, DGM-01275_am


title: single cellf from YS [LIB019717_GEN00050528_S75_R1]


title: single cellf from YS [LIB019717_GEN00050527_S74_R1]


title: single cellf from YS [LIB019717_GEN00050529_S76_R1]


title: single cellf from YS [LIB019717_GEN00050526_S73_R1]


title: AMs, COPDs, DGM-00420_am


title: single cellf from YS [LIB019717_GEN00050535_S82_R1]


title: single cellf from YS [LIB019717_GEN00050525_S72_R1]


title: AMs, COPDs, DGM-00313_am


title: AMs, COPDs, DGM-10131_am


title: AMs, COPDs, DGM-00760_am


title: AMs, COPDs, DGM-00197_am


title: single cellf from YS [LIB019717_GEN00050524_S71_R1]


title: single cellf from YS [LIB019717_GEN00050523_S70_R1]


title: AMs, COPDs, DGM-00028_am


title: AMs, COPDs, DGM-00061_am


title: AMs, COPDs, DGM-00167_am


title: AMs, COPDs, DGM-00740_am


title: single cellf from YS [LIB019717_GEN00050520_S68_R1]


title: single cellf from YS [LIB019717_GEN00050519_S67_R1]


title: AMs, COPDs, DGM-00262_am


title: HeLa Enriched chromatin-associated RNA, rep A

city: Aarhus

first: Ulf Andersson

middle: Vang

last: Ørom

address: C F Mollers Alle 3

country: Denmark

institute: Aarhus University

description: HeLa enrichment rep A

data_processing:
Reads were mapped to GRCh37/hg19 using STAR version 2.4.2a. The SAM alignement files were converted to sorted BAM using samtools. BAM files were converted to BED using bedtools bamtobed. Only uniquely mapped reads (score 255) were kept. BED files were converted to strand-specific WIG using 'bedtools genomecov -bg -g hg19.chrom.sizes' and WIG files were converted to bigWIG using wigToBigWig from the UCSC utilities.
Genome_build: hg19
Supplementary_files_format_and_content: RPKM

source_name: HeLa cells

extract_protocol: Cells were cultured in complete DMEM. RNA was isolated with TRIzol and depleted for rRNA. Library construction was done for an Illumina HiSeq2500. Targets were enriched with the custom enrichment probe library.

tag: cell line

value: HeLa


title: Enriched chromatin-associated RNA,  rep B

description: HeLa enrichment rep B


title: single cellf from YS [LIB019717_GEN00050522_S69_R1]

value: embryonic tissue


title: MCF-7_GII_TCDD_5

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

data_processing:
Data were processed with the pipeline described at the following address: https://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/tree/master
Briefly, samples demultiplexing was performed with a python script. It transforms the raw paired-end fastq files into a single-end fastq file for each sample. Alignment on refseq reference transcriptome was performed using bwa. Aligned reads are parsed and UMI are counted for each gene in each sample to create an expression matrix. The expression matrix was normalized and rlog-transformed using the DESeq2 library.
Genome_build: hg19
Supplementary_files_format_and_content: the tab-delimited matrix files include UMI counts and normalized rlog transformed data for each sample.

source_name: Breast adenocarcinoma cell

extract_protocol:
RNA was extracted using an RNeasy mini kit (Qiagen) according to the manufacturer’s instructions
a 3’Digital Gene Expression (DGE) library was constructed using a modified SCRB-Seq protocol with barcoded poly-dT RT primers and a hybrid Nextera/TruSeq sequencing strategy

value: Breast adenocarcinoma cell

tag: treatment

value: GII+TCDD


title: MCF-7_GI_TCDD_5

value: GI+TCDD


title: MCF-7_GII_5

value: GII


title: single cellf from YS [LIB019717_GEN00050508_S57_R1]


title: single cellf from YS [LIB019717_GEN00050507_S56_R1]


title: single cellf from YS [LIB019717_GEN00050513_S62_R1]


title: single cellf from YS [LIB019717_GEN00050516_S64_R1]


title: AMs, COPDs, DGM-10130_am


title: AMs, COPDs, DGM-00050_am


title: MCF-7_GI_5

value: GI


title: AMs, COPDs, DGM-10406_am


title: MCF-7_TCDD_5

value: TCDD


title: single cellf from YS [LIB019717_GEN00050501_S53_R1]


title: single cell from AUV [LIB019717_GEN00050471_S29_R1]

source_name: aorta and umbilical and vitelline arteries (AUV)


title: MCF-7_GII_TCDD_4


title: MCF-7_Ctrl_5

value: Control


title: MCF-7_GI_TCDD_4


title: single cellf from YS [LIB019717_GEN00050495_S52_R1]


title: single cell from AUV [LIB019717_GEN00050455_S13_R1]


title: MCF-7_GII_4


title: MCF-7_TCDD_4


title: single cell from AUV [LIB019717_GEN00050483_S41_R1]


title: MCF-7_GI_4


title: single cell from AUV [LIB019717_GEN00050485_S43_R1]


title: MCF-7_Ctrl_4


title: single cell from AUV [LIB019717_GEN00050484_S42_R1]


title: single cell from AUV [LIB019717_GEN00050482_S40_R1]


title: MCF-7_GII_TCDD_3


title: single cell from AUV [LIB019717_GEN00050480_S38_R1]


title: single cell from AUV [LIB019717_GEN00050479_S37_R1]


title: MCF-7_GI_TCDD_3


title: MCF-7_GII_3


title: single cellf from YS [LIB019717_GEN00050494_S51_R1]


title: MCF-7_GI_3


title: MCF-7_Ctrl_3


title: MCF-7_GII_TCDD_2


title: MCF-7_TCDD_3


title: single cell from AUV [LIB019717_GEN00050470_S28_R1]


title: single cell from AUV [LIB019717_GEN00050477_S35_R1]


title: single cell from AUV [LIB019717_GEN00050475_S33_R1]


title: single cell from AUV [LIB019717_GEN00050476_S34_R1]


title: single cell from AUV [LIB019717_GEN00050468_S26_R1]


title: single cell from AUV [LIB019717_GEN00050466_S24_R1]


title: MCF-7_GII_2


title: single cell from AUV [LIB019717_GEN00050465_S23_R1]


title: single cell from AUV [LIB019717_GEN00050463_S21_R1]


title: single cell from AUV [LIB019717_GEN00050467_S25_R1]


title: MCF-7_GI_2


title: MCF-7_TCDD_2


title: MCF-7_GII_TCDD_1


title: MCF-7_Ctrl_2


title: single cell from AUV [LIB019717_GEN00050462_S20_R1]


title: single cell from AUV [LIB019717_GEN00050461_S19_R1]


title: MCF-7_GI_1


title: MCF-7_GI_TCDD_1


title: single cell from AUV [LIB019717_GEN00050458_S16_R1]


title: single cell from AUV [LIB019717_GEN00050473_S31_R1]


title: EmuMyc_CHD9#KO3

city: Amsterdam

first: Anton

last: Berns

state: Amsterdam

address: Plesmanlann 121

department: Division of Molecular Genetics

country: Netherlands

institute: NKI

description:
Enlarged lymph nodes from moribund Emu-Myc control, Chd9+/- and Chd9-/- mice were isolated and snap-frozen
4774_12_KO4

data_processing:
Illumina Casava1.7 software used for basecalling.
Tophat version: 2.1, HTSeq count (v0.5.3), DESeq2
Genome_build: mm9 (MEFs, ESCs), mm10 (ED15 brain and liver; EmuMyc  lymphomas), hg37 (K562 and SNB19 cells)
Supplementary_files_format_and_content: tab-delimited text files include raw read count values for each Sample

source_name: lymph node

extract_protocol:
Total RNA was extracted using Trizol, prepared using TruSeq protocol, and standard sample preparation protocols and RNA-seq was performed on a HiSeq2000 machine (Illumina) at the NKI Genomics Core Facility.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Chd9; EmuMyc

value: lymph node

value: moribund animal

tag: genotype


title: MCF-7_TCDD_1


title: EmuMyc_CHD9#KO2

description:
Enlarged lymph nodes from moribund Emu-Myc control, Chd9+/- and Chd9-/- mice were isolated and snap-frozen
4774_11_KO3


title: MCF-7_GI_TCDD_2


title: single cell from AUV [LIB019717_GEN00050456_S14_R1]


title: MCF-7_Ctrl_1


title: AMs, NS, DGM-00044_am

value: M

value: alveolar macrophages obtained from bronchoalveolar lavage


title: EmuMyc_CHD9#HET3

description:
Enlarged lymph nodes from moribund Emu-Myc control, Chd9+/- and Chd9-/- mice were isolated and snap-frozen
4772_8_HET4


title: HepG2_GII_TCDD_5

source_name: Liver hepatocellular carcinoma cell

value: Liver hepatocellular carcinoma cell


title: EmuMyc_CHD9#HET2

description:
Enlarged lymph nodes from moribund Emu-Myc control, Chd9+/- and Chd9-/- mice were isolated and snap-frozen
4774_6_HET2


title: HepG2_GI_TCDD_5


title: AMs, COPDs, DGM-01355_am

value: Afr


title: EmuMyc_CHD9#HET1

description:
Enlarged lymph nodes from moribund Emu-Myc control, Chd9+/- and Chd9-/- mice were isolated and snap-frozen
4774_5_HET1


title: HepG2_GII_5


title: MCF-7_GII_1


title: single cell from AUV [LIB019717_GEN00050460_S18_R1]


title: EmuMyc_CHD9#WT3

description:
Enlarged lymph nodes from moribund Emu-Myc control, Chd9+/- and Chd9-/- mice were isolated and snap-frozen
4774_4_WT4

value: wild type


title: EmuMyc_CHD9#WT2

description:
Enlarged lymph nodes from moribund Emu-Myc control, Chd9+/- and Chd9-/- mice were isolated and snap-frozen
4774_3_WT3


title: HepG2_GI_5


title: EmuMyc_CHD9#WT1

description:
Enlarged lymph nodes from moribund Emu-Myc control, Chd9+/- and Chd9-/- mice were isolated and snap-frozen
4774_1_WT1


title: single cell from AUV [LIB019717_GEN00050450_S8_R1]


title: single cell from AUV [LIB019717_GEN00050449_S7_R1]


title: CHD9#WT1_E15_BRAIN

description:
Embryonic (E15) brain and liver were isolated from littermates and snap-frozen.
3122_3_ED15_5_7_WT_brain

source_name: brain E15

value: embryonic brain


title: CHD9#WT2_E15_BRAIN

description:
Embryonic (E15) brain and liver were isolated from littermates and snap-frozen.
3122_1_ED15_5_9_WT_brain


title: EmuMyc_CHD9#KO1

description:
Enlarged lymph nodes from moribund Emu-Myc control, Chd9+/- and Chd9-/- mice were isolated and snap-frozen
4774_10_KO2


title: HepG2_TCDD_5


title: single cell from AUV [LIB019717_GEN00050446_S4_R1]

value: embryonic tissue


title: CHD9#KO2_E15_BRAIN

description:
Embryonic (E15) brain and liver were isolated from littermates and snap-frozen.
3122_5_ED15_5_6_KO_brain


title: single cell from AUV [LIB019717_GEN00050454_S12_R1]


title: HepG2_Ctrl_5


title: single cell from AUV [LIB019717_GEN00050452_S10_R1]


title: single cell from AUV [LIB019717_GEN00050453_S11_R1]


title: HepG2_GII_TCDD_4


title: single cell from AUV [LIB019717_GEN00050444_S3_R1]


title: CHD9#KO2_E15_LIVER

description:
Embryonic (E15) brain and liver were isolated from littermates and snap-frozen.
3122_8_ED15_5_9_KO_liver

source_name: liver E15

value: embryonic liver


title: CHD9#KO1_E15_BRAIN

description:
Embryonic (E15) brain and liver were isolated from littermates and snap-frozen.
3122_7_ED15_5_3_KO_brain


title: single cell from AUV [LIB019717_GEN00050443_S2_R1]


title: CHD9#KO1_E15_LIVER

description:
Embryonic (E15) brain and liver were isolated from littermates and snap-frozen.
3122_6_ED15_5_7_KO_liver


title: single cell from AUV [LIB019717_GEN00050442_S1_R1]


title: HepG2_GI_TCDD_4


title: HepG2_GII_4


title: CHD9#WT3_MEF

description:
Mouse embryonic fibroblasts (MEFs) were isolated from the Chd9+/-x Chd9+/- cross at day 13.5 post coitum and cultured using standard methods. Briefly, Heads and organs of embryonic day 13.5 embryos were removed, and the remaining fetal tissue was minced, rinsed in PBS, and incubated for 1 h in 0.5 ml of 0.1% trypsin/EDTA solution at 37°C. Subsequently, the cell aggregates were dissociated in DMEM supplemented with 10% FBS (GIBCO) and 1% penicillin-streptomycin (GIBCO). After removal of large clumps, the cells were plated in a 175-cm2 flask. After 2–3 days, confluent cultures were frozen down and considered as being passage 1.
2498_7_B_WT

source_name: MEF

value: primary mouse embryonic fibroblasts

value: early passage


title: CHD9#WT2_MEF

description:
Mouse embryonic fibroblasts (MEFs) were isolated from the Chd9+/-x Chd9+/- cross at day 13.5 post coitum and cultured using standard methods. Briefly, Heads and organs of embryonic day 13.5 embryos were removed, and the remaining fetal tissue was minced, rinsed in PBS, and incubated for 1 h in 0.5 ml of 0.1% trypsin/EDTA solution at 37°C. Subsequently, the cell aggregates were dissociated in DMEM supplemented with 10% FBS (GIBCO) and 1% penicillin-streptomycin (GIBCO). After removal of large clumps, the cells were plated in a 175-cm2 flask. After 2–3 days, confluent cultures were frozen down and considered as being passage 1.
2498_6_B_WT


title: MB69_ACACGC Salmonella large bowel CD45+ CD11c- CD11b- lymphocytes

city: Corvallis

first: Andrey

last: Morgun

state: OR

address: 1601 SW Jefferson Way

institute: Oregon State University

data_processing:
De-multiplexed sequencing reads were generated using Illumina bcl2fastq (released version 2.18.0.12) allowing no mismatches in the index read.
Sequences were processed to remove adapter, polyA and low-quality bases by BBTools (https://jgi.doe.gov/data-and-tools/bbtools/)
Reads were aligned to mouse genome and transcriptome using Tophat (v2.1.1)
Number of reads per million for mouse genes were counted using HTSeq (v 0.6.0) and quantile normalized
Genome_build: ENSEMBL NCBIM37
Supplementary_files_format_and_content: comma-delimited text files include quantile normalized counts per million values for each Sample

extract_protocol:
Samples for each population were prepared by pooling cells sorted from 5 mice. In total 5 samples were prepared, representing 5 independent cell sorting experiment.
The cDNA libraries were prepared using the QuantSeq 3’mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria) as per the manufacturer’s instructions.

treatment_protocol: Total RNA was isolated from cell populations sorted from LB of control mice and mice infected with Salmonella enterica (SL1344) (Day 5).

tag: infection

value: Salmonella

value: large bowel

value: CD45+ CD11c- CD11b- lymphocytes

tag: experiment

value: E


title: HepG2_GI_4

value: GI


title: MB68_TCGTTC Salmonella large bowel CD45+ CD11c- CD11b- lymphocytes

value: D


title: HepG2_TCDD_4

value: TCDD


title: D0 Control 1: hAECs_ Day 0_ Control 1

city: Tsukuba

first: Farhana

last: Ferdousi

state: Ibaraki

address: Tennodai 1-1-1

country: Japan

institute: University of Tsukuba

description: Gene expression data from untreated control hAECs on day 0

hyb_protocol: Following fragmentation, 250 ng of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array (HG-219). GeneChips were washed and stained in the Gene Atlas Fluidics Station 400

scan_protocol: GeneChips were scanned using the GeneAtlas Imaging Station

data_processing:
The raw data were normalized using Expression Console Software provided by the Affymetrix following robust multichip average (RMA) algorithm (http://www.affymetrix.com). Subsequent analysis of the gene expression data was carried out in the freely available Transcriptome Analysis Console (TAC) version 4 (Thermofisher inc.). Further analysis was conducted using an online data mining tool DAVID (Database for Annotation, Visualization and Integrated Discovery, ver. 6.8). We used 'Functional Annotation' tool of DAVID to identify the most relevant biological terms, including gene ontology (GO) terms, biological pathways, tissue expression, and disease associations (Huang da et al., 2009). We also performed gene set enrichment analysis (GSEA) [https://www.gsea-msigdb.org/gsea/index.jsp]. We prepared heat maps in online visualization tool Morpheus (https://software.broadinstitute.org/morpheus/).
Signal intensity of all the samples deraived from Expression Console (2nd sheet). For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, we used freely available Transcriptome Analysis Console software (CHP files).

source_name: Untreated control hAECs on day0, biological rep 1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 9.4 ug total RNA

growth_protocol: AECs were isolated from delivered term placenta and were maintained in Placenta Epithelial Cell Basal Medium (PromoCell, Cat. # C-26140) in 2D culture plate. Finally, 3D spheroids were formed by seeding 1×106 AECs in Placenta Basal Epithelial Cell Medium into each well of the 24-well plate.

extract_protocol: For RNA extraction, Isogen (Nippon Gene Co. Ltd., Toyama, Japan) was added and the cell suspensions were centrifuged for 5 minutes at 500 g and the pellet was stored at -80oC until use.

treatment_protocol: After the initial 24 hour culture, the medium was changed with 20 μM of isorhamnetin every 48 hours for the treatment samples. Control samples were maintained in Placental basal medium that was also changed every 48 hours. Finally, we collected the treatment and control samples from 10- and 20-day cultures. Day 0 control samples were collected after the initial treatment.

value: amnion epithelial cells


title: D10 Control 2: hAECs_ Day 10_ Control 2

description: Gene expression data from untreated control hAECs on day 10

source_name: Untreated control hAECs on day10, biological rep 2


title: CHD9#WT1_MEF

description:
Mouse embryonic fibroblasts (MEFs) were isolated from the Chd9+/-x Chd9+/- cross at day 13.5 post coitum and cultured using standard methods. Briefly, Heads and organs of embryonic day 13.5 embryos were removed, and the remaining fetal tissue was minced, rinsed in PBS, and incubated for 1 h in 0.5 ml of 0.1% trypsin/EDTA solution at 37°C. Subsequently, the cell aggregates were dissociated in DMEM supplemented with 10% FBS (GIBCO) and 1% penicillin-streptomycin (GIBCO). After removal of large clumps, the cells were plated in a 175-cm2 flask. After 2–3 days, confluent cultures were frozen down and considered as being passage 1.
2498_5_B_WT


title: HepG2_Ctrl_4

value: Control


title: D10 Control 3: hAECs_ Day 10_ Control 3

source_name: Untreated control hAECs on day10, biological rep 3


title: single cellf from YS [LIB019717_GEN00050492_S49_R1]


title: D0 Control 2: hAECs_ Day 0_ Control 2

source_name: Untreated control hAECs on day0, biological rep 2


title: CHD9#KO4_MEF

description:
Mouse embryonic fibroblasts (MEFs) were isolated from the Chd9+/-x Chd9+/- cross at day 13.5 post coitum and cultured using standard methods. Briefly, Heads and organs of embryonic day 13.5 embryos were removed, and the remaining fetal tissue was minced, rinsed in PBS, and incubated for 1 h in 0.5 ml of 0.1% trypsin/EDTA solution at 37°C. Subsequently, the cell aggregates were dissociated in DMEM supplemented with 10% FBS (GIBCO) and 1% penicillin-streptomycin (GIBCO). After removal of large clumps, the cells were plated in a 175-cm2 flask. After 2–3 days, confluent cultures were frozen down and considered as being passage 1.
2498_4_B_KO


title: MB66_AAGTGG Salmonella large bowel CD45+ CD11c- CD11b- lymphocytes

value: B


title: CHD9#KO3_MEF

description:
Mouse embryonic fibroblasts (MEFs) were isolated from the Chd9+/-x Chd9+/- cross at day 13.5 post coitum and cultured using standard methods. Briefly, Heads and organs of embryonic day 13.5 embryos were removed, and the remaining fetal tissue was minced, rinsed in PBS, and incubated for 1 h in 0.5 ml of 0.1% trypsin/EDTA solution at 37°C. Subsequently, the cell aggregates were dissociated in DMEM supplemented with 10% FBS (GIBCO) and 1% penicillin-streptomycin (GIBCO). After removal of large clumps, the cells were plated in a 175-cm2 flask. After 2–3 days, confluent cultures were frozen down and considered as being passage 1.
2498_3_A_KO


title: HepG2_GI_TCDD_3

value: Liver hepatocellular carcinoma cell

value: GI+TCDD


title: MB64_CGATCT Salmonella large bowel CD45- stromal cells

value: CD45- stromal cells


title: CHD9#KO2_MEF

description:
Mouse embryonic fibroblasts (MEFs) were isolated from the Chd9+/-x Chd9+/- cross at day 13.5 post coitum and cultured using standard methods. Briefly, Heads and organs of embryonic day 13.5 embryos were removed, and the remaining fetal tissue was minced, rinsed in PBS, and incubated for 1 h in 0.5 ml of 0.1% trypsin/EDTA solution at 37°C. Subsequently, the cell aggregates were dissociated in DMEM supplemented with 10% FBS (GIBCO) and 1% penicillin-streptomycin (GIBCO). After removal of large clumps, the cells were plated in a 175-cm2 flask. After 2–3 days, confluent cultures were frozen down and considered as being passage 1.
2498_2_A_KO


title: CHD9#KO1_MEF

description:
Mouse embryonic fibroblasts (MEFs) were isolated from the Chd9+/-x Chd9+/- cross at day 13.5 post coitum and cultured using standard methods. Briefly, Heads and organs of embryonic day 13.5 embryos were removed, and the remaining fetal tissue was minced, rinsed in PBS, and incubated for 1 h in 0.5 ml of 0.1% trypsin/EDTA solution at 37°C. Subsequently, the cell aggregates were dissociated in DMEM supplemented with 10% FBS (GIBCO) and 1% penicillin-streptomycin (GIBCO). After removal of large clumps, the cells were plated in a 175-cm2 flask. After 2–3 days, confluent cultures were frozen down and considered as being passage 1.
2498_1_A_KO


title: MB67_TGCACG Salmonella large bowel CD45+ CD11c- CD11b- lymphocytes

value: C


title: HepG2_GI_3


title: MB63_GCGAAT Salmonella large bowel CD45- stromal cells


title: CHD9#WT3_ES

description:
ESCs were cultured on 0.1% gelatin-coated plates in N2B27 medium (DMEM/F12 from Gibco, Neurobasal medium, N2 supplement and B27 supplement from Invitrogen) with LIF (Chemicon) and 2i, i.e. 1 μM PD0325901 (Axon Medchem) and 3 μM CHIR99021 (Axon MedChem). ESCs were split between 1:4 and 1:8 every 2–3 days and dissociated with Accutase (Sigma). Cells were cultured at 37°C in 5% CO2. Three wild-type control and three Chd9 knockout derived ESC lines were used. For all the experiments early passage MEFs and ESCs were used.
2418_1_WT

source_name: ES

value: derived embryonic stem cells

value: wild type


title: D20 Control 1: hAECs_ Day 20_ Control 1

description: Gene expression data from untreated control hAECs on day 20

source_name: Untreated control hAECs on day20, biological rep 1


title: HepG2_TCDD_3


title: MB62_AGAATC Salmonella large bowel CD45- stromal cells


title: HepG2_GII_TCDD_3

value: GII+TCDD


title: D10 Iso 3: hAECs_ Day 10_isorhamnetin 3

description: Gene expression data from isorhamnetin treated hAECs on day 10

source_name: hAECs treated with isorhamnetin for 10 days, biological rep 3


title: CHD9#WT2_ES

description:
ESCs were cultured on 0.1% gelatin-coated plates in N2B27 medium (DMEM/F12 from Gibco, Neurobasal medium, N2 supplement and B27 supplement from Invitrogen) with LIF (Chemicon) and 2i, i.e. 1 μM PD0325901 (Axon Medchem) and 3 μM CHIR99021 (Axon MedChem). ESCs were split between 1:4 and 1:8 every 2–3 days and dissociated with Accutase (Sigma). Cells were cultured at 37°C in 5% CO2. Three wild-type control and three Chd9 knockout derived ESC lines were used. For all the experiments early passage MEFs and ESCs were used.
1977_12_WT

value: early passage


title: CHD9#WT1_ES

description:
ESCs were cultured on 0.1% gelatin-coated plates in N2B27 medium (DMEM/F12 from Gibco, Neurobasal medium, N2 supplement and B27 supplement from Invitrogen) with LIF (Chemicon) and 2i, i.e. 1 μM PD0325901 (Axon Medchem) and 3 μM CHIR99021 (Axon MedChem). ESCs were split between 1:4 and 1:8 every 2–3 days and dissociated with Accutase (Sigma). Cells were cultured at 37°C in 5% CO2. Three wild-type control and three Chd9 knockout derived ESC lines were used. For all the experiments early passage MEFs and ESCs were used.
1959_2_WT


title: D20 Control 2: hAECs_ Day 20_ Control 2

source_name: Untreated control hAECs on day20, biological rep 2


title: D10 Iso 2: hAECs_ Day 10_isorhamnetin 2

source_name: hAECs treated with isorhamnetin for 10 days, biological rep 2


title: HepG2_Ctrl_3


title: D10 Iso 1: hAECs_ Day 10_isorhamnetin 1

source_name: hAECs treated with isorhamnetin for 10 days, biological rep 1


title: MB60_ATGGCG Salmonella large bowel CX3CR1 int MFs

description: Salmonella large bowel CX3CR1 int MFs

source_name: Salmonella large bowel CX3CR1 int MFs

value: Salmonella

value: large bowel

value: CX3CR1 int MFs


title: HepG2_GII_TCDD_2


title: HepG2_GII_3

value: GII


title: MB59_GCTCGA Salmonella large bowel CX3CR1 int MFs

description: Salmonella large bowel CX3CR1 int MFs

value: D


title: D20 Iso 2: hAECs_ Day 20_isorhamnetin 2

description: Gene expression data from isorhamnetin treated hAECs on day 20

source_name: hAECs treated with isorhamnetin for 20 days, biological rep 2


title: CHD9#KO3_ES

description:
ESCs were cultured on 0.1% gelatin-coated plates in N2B27 medium (DMEM/F12 from Gibco, Neurobasal medium, N2 supplement and B27 supplement from Invitrogen) with LIF (Chemicon) and 2i, i.e. 1 μM PD0325901 (Axon Medchem) and 3 μM CHIR99021 (Axon MedChem). ESCs were split between 1:4 and 1:8 every 2–3 days and dissociated with Accutase (Sigma). Cells were cultured at 37°C in 5% CO2. Three wild-type control and three Chd9 knockout derived ESC lines were used. For all the experiments early passage MEFs and ESCs were used.
2418_2_KO


title: D20 Iso 1: hAECs_ Day 20_isorhamnetin 1

source_name: hAECs treated with isorhamnetin for 20 days, biological rep 1


title: Cyanidine 2: hAECs_Day 7_Cyanidine 2

description: Gene expression data from Cyanidine treated hAECs on 7th day

data_processing:
The raw data were normalized using Expression Console Software provided by the Affymetrix following robust multichip average (RMA) algorithm (http://www.affymetrix.com). Subsequent analysis of the gene expression data was carried out in the freely available Transcriptome Analysis Console (TAC) version 4 (Thermofisher inc.). Further analysis was conducted using an online data mining tool DAVID (Database for Annotation, Visualization and Integrated Discovery, ver. 6.8). We used 'Functional Annotation' tool of DAVID to identify the most relevant biological terms, including gene ontology (GO) terms, biological pathways, tissue expression, and disease associations (Huang da et al., 2009). We also performed gene set enrichment analysis (GSEA) [https://www.gsea-msigdb.org/gsea/index.jsp]
Signal intensity for all samples were derived from Expression console. For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, we used freely available Transcriptome Analysis Console software (CHP files ).

source_name: hAECs treated with Cyanidine for 7 days, biological rep2

treatment_protocol: After the initial 24 hour culture, the medium was changed with 20 μM of Cyanidine 3-glucoside (Cyanidine) every 48 hours for three times (7days) for the treatment samples. Control samples were maintained in Placental medium that was also changed every 48 hours. Finally, we collected the treatment and control samples from one-week culture.


title: Control 1: hAECs_Day 7_placental basal medium_Control 1

description: Gene expression data from untreated control hAECs on 7th day

source_name: Untreated control hAECs on day7, biological rep1


title: Control 2: hAECs_Day 7_placental basal medium_Control 2

source_name: Untreated control hAECs on day7, biological rep2


title: HepG2_GI_TCDD_2

source_name: Liver hepatocellular carcinoma cell


title: CHD9#KO2_ES

description:
ESCs were cultured on 0.1% gelatin-coated plates in N2B27 medium (DMEM/F12 from Gibco, Neurobasal medium, N2 supplement and B27 supplement from Invitrogen) with LIF (Chemicon) and 2i, i.e. 1 μM PD0325901 (Axon Medchem) and 3 μM CHIR99021 (Axon MedChem). ESCs were split between 1:4 and 1:8 every 2–3 days and dissociated with Accutase (Sigma). Cells were cultured at 37°C in 5% CO2. Three wild-type control and three Chd9 knockout derived ESC lines were used. For all the experiments early passage MEFs and ESCs were used.
2367_2_KO


title: MB58_AGACCA Salmonella large bowel CX3CR1 int MFs

description: Salmonella large bowel CX3CR1 int MFs


title: MB61_GAAGTG Salmonella large bowel CD45- stromal cells

value: A


title: CHD9#KO1_ES

description:
ESCs were cultured on 0.1% gelatin-coated plates in N2B27 medium (DMEM/F12 from Gibco, Neurobasal medium, N2 supplement and B27 supplement from Invitrogen) with LIF (Chemicon) and 2i, i.e. 1 μM PD0325901 (Axon Medchem) and 3 μM CHIR99021 (Axon MedChem). ESCs were split between 1:4 and 1:8 every 2–3 days and dissociated with Accutase (Sigma). Cells were cultured at 37°C in 5% CO2. Three wild-type control and three Chd9 knockout derived ESC lines were used. For all the experiments early passage MEFs and ESCs were used.
1959_1_KO


title: input_week4_Het-CKO

city: Chicago

first: Yong

last: Peng

state: IL

address: 929 E 57th Street

department: Department of Chemistry

institute: University of Chicago

description: input

data_processing:
Basecalls performed using CASAVA version 1.8.2
Raw reads were filtered by using Trimmomatic v0.35
ChIP-seq reads were aligned to the UCSC mm10 genome assembly using bwa v0.7.12 with default settings.
Only the reads with no more than  4% (2 bp) mismatches and uniquely mapped to reference genome were kept by using Bash Shell script.
H2BGFP ChIP signal was calculated by using DANPOS2 version2.2.2.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using DANPOS2

source_name: Heart

growth_protocol: All animal procedures were approved by the Institutional Animal Care and Use Committee of Peking University and Boston Children’s Hospital.

extract_protocol:
Fragments 150-300 bp were size-selected by 2% agarose gel electrophoresis. Recovered DNA was amplified using Phusion DNA polysome (NEB), multiplexing PCR primer 1.0, and one indexed primer. The amplified libraries were purified with Agencourt AMPure XP beads (Beckman Coulter). The libraries were quantitated using the Quant-iT DNA quantitation kit (Invitrogen). The DNA size distribution of the library was measured by an Agilent Bioanalyzer.
ChIP-seq library preparation were performed according to the instruction of NEB NEXT-generation library preparation kit. 1 or 2 independent ChIP samples were used for one single ChIP-seq library preparation.

treatment_protocol: mice were injected with AAV9 by intraperitoneal or intravascular injection where indicated as described previously (Lin, et al. Circ Res. 2015)

value: heart

value: isolated adult ventricular cardiomyocytes

tag: developmental stage

value: adult

tag: genotype/variation

tag: injected with

tag: chip antibody

value: No


title: HepG2_GI_2

tag: cell type

value: Liver hepatocellular carcinoma cell

value: GI


title: MB56_TGACAC Salmonella large bowel CX3CR1 int MFs

description: Salmonella large bowel CX3CR1 int MFs

tag: tissue


title: MB57_ACAGAT Salmonella large bowel CX3CR1 int MFs

description: Salmonella large bowel CX3CR1 int MFs

value: B


title: Cyanidine 1: hAECs_Day 7_Cyanidine 1

source_name: hAECs treated with Cyanidine for 7 days, biological rep1

value: amnion epithelial cells


title: MB55_TATGTC Salmonella large bowel CX3CR1 high MFs

description: Salmonella large bowel CX3CR1 high MFs

source_name: Salmonella large bowel CX3CR1 high MFs

value: CX3CR1 high MFs

value: E


title: input_week0_Het-CKO

description: input

tag: strain


title: HepG2_Ctrl_2

value: Control


title: H2BGFP_week4_CKO_rep2

description:
input sample: input_week4_Het-CKO
ChIP_DNA


title: MB54_CCGACC Salmonella large bowel CX3CR1 high MFs

description: Salmonella large bowel CX3CR1 high MFs

value: Salmonella


title: HepG2_GII_2


title: MB65_CATCTA Salmonella large bowel CD45+ CD11c- CD11b- lymphocytes

value: large bowel

value: CD45+ CD11c- CD11b- lymphocytes


title: HepG2_TCDD_2

value: TCDD


title: H2BGFP_week4_CKO_rep1


title: H2BGFP_week4_Het


title: D0 Control 1: CD34+cells_Day0_Control 1

description: Gene expression data from untreated control CD34+ cells on day 0

data_processing:
The raw data were normalized using Expression Console Software provided by the Affymetrix following robust multichip average (RMA) algorithm (http://www.affymetrix.com). Subsequent analysis of the gene expression data was carried out in the freely available Transcriptome Analysis Console (TAC) version 4 (Thermofisher inc.). Further analysis was conducted using an online data mining tool DAVID (Database for Annotation, Visualization and Integrated Discovery, ver. 6.8). We used 'Functional Annotation' tool of DAVID to identify the most relevant biological terms, including gene ontology (GO) terms, biological pathways, tissue expression, and disease associations (Huang da et al., 2009). We also performed gene set enrichment analysis (GSEA) [https://www.gsea-msigdb.org/gsea/index.jsp]. We prepared heat maps in online visualization tool Morpheus (https://software.broadinstitute.org/morpheus/).
Signal intensity of all the samples deraived from Expression Console (2nd sheet). For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, we used freely available Transcriptome Analysis Console software (CHP files ).  Data are given in the sheets named as D12 WOL vs D12 Control and D12 WOL vs D0 Control

source_name: CD34+ cells maintained in culture medium at day 0_Control 1

growth_protocol: CD34＋ cells  were purchased from Lonza (2M-101A, Basel, Switzerland) and were maintained in StemPro-34 complete medium on 60 mm dish for 7 days (day 0 - day 7)  .

treatment_protocol: On day 8, the cells were seeded at a concentraton of 2 × 103 cells/well in the complete medium to each well of a 24-well plate. From day 9 to day 21, the cells were treated with or without 40 µg/mL WOL (treatment for 12 days). The medium was changed every 3 days.


title: D0 Control 2: CD34+cells_Day0_Control 2

source_name: CD34+ cells maintained in culture medium at day 0_Control 2


title: HepG2_GII_TCDD_1

value: GII+TCDD


title: D12 Control 3: CD34+cells_Day12_Control 3

description: Gene expression data from untreated control CD34+ cells on day 12

source_name: CD34+ cells maintained in culture medium at day 12_Control 3


title: D0 Control 3: CD34+cells_Day0_Control 3

source_name: CD34+ cells maintained in culture medium at day 0_Control 3


title: MB52_GCAGCC Salmonella large bowel CX3CR1 high MFs

description: Salmonella large bowel CX3CR1 high MFs


title: D12 Control 2: CD34+cells_Day12_Control 2

source_name: CD34+ cells maintained in culture medium at day 12_Control 2


title: HepG2_GII_1

value: GII


title: D12 Control 1: CD34+cells_Day12_Control 1

source_name: CD34+ cells maintained in culture medium at day 12_Control 1


title: MB50_ACCTAC Salmonella large bowel CX3CR1- MFs

description: Salmonella large bowel CX3CR1- MFs

source_name: Salmonella large bowel CX3CR1- MFs

value: CX3CR1- MFs


title: HepG2_GI_1


title: MB51_TGGATT Salmonella large bowel CX3CR1 high MFs

description: Salmonella large bowel CX3CR1 high MFs

value: A


title: H2BGFP_week0_CKO

description:
input sample: input_week0_Het-CKO
ChIP_DNA

value: heart

value: isolated adult ventricular cardiomyocytes

value: adult


title: H2BGFP_week0_Het_rep2


title: H2BGFP_week0_Het_rep1


title: MB53_CGCCTG Salmonella large bowel CX3CR1 high MFs

description: Salmonella large bowel CX3CR1 high MFs

value: C


title: D12 WOL 3: CD34+cells_Day12_WOL 3

description: Gene expression data from CD34+cells treated with WOL at day 12

source_name: CD34+ cells treated with WOL 3 at day 12


title: HepG2_GI_TCDD_1

value: Liver hepatocellular carcinoma cell

value: GI+TCDD


title: MB49_AGGCAT Salmonella large bowel CX3CR1- MFs

description: Salmonella large bowel CX3CR1- MFs

value: D


title: MMB48_GACATC Salmonella large bowel CX3CR1- MFs

description: Salmonella large bowel CX3CR1- MFs


title: AD12m2A

city: shenzhen

first: jie

last: pan

address: Lian Hua Lu 1120, FuTian District  Guangdong

country: China

institute: Shenzhen	Peking	University	– The	Hong	Kong	University	of	Science	and	Technology	Medical	Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
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: mm8
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample ...

source_name: Brain

extract_protocol:
RNA was isolated from flow cytometry-sorted cell populations using RNeasy Micro Kit (74004, Qiagen)
A total amount of 10 ng RNA per sample was used as input material for the RNA sample preparations. Libraries were generated using SMART-Seq v4 Ultra Low Input RNA Kit (634892, Takara Bio USA, Mountain View, CA, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, first-strand cDNA synthesis from total RNA is primed by the 3’ SMART-Seq CDS Primer II A and uses the SMART-Seq v4 Oligonucleotide for template switching at the 5’ end of the transcript. PCR Primer II A amplifies cDNA from the SMART sequences introduced by 3’ SMART-Seq CDS Primer II A and the SMART-Seq v4 Oligonucleotide for 8 cycles. LD-PCR amplified cDNA is purified by immobilization on AMPure XP beads and then quantified with Agilent Bioanalyzer 2100 system. Approximately 200 pg was used for Nextera XT DNA Library Preparation Kit (Illumina, Cat. Nos. FC-131-1024 and FC-131-1096, San Diego, CA) to make cDNA libraries suitable for Illumina sequencing. Tagmented fragments were amplified for 12 cycles and dual indexes were added to each well to uniquely label each library. Concentrations were assessed with KAPA Library Quantification Kits (KK4844, KAPA, Biosystems, USA) and samples were diluted to ~2 nM and pooled. Pooled libraries were sequenced on the Illumina Novaseq platform and 150 bp paired-end reads were generated.


title: HepG2_Ctrl_1


title: AD12m3A


title: HepG2_TCDD_1


title: input_week2_sham-TAC

description: input

value: WT

value: No


title: D12 WOL 2: CD34+cells_Day12_WOL 2

source_name: CD34+cells treated with WOL 2 at day 12


title: MB47_GAGTCC Salmonella large bowel CX3CR1- MFs

description: Salmonella large bowel CX3CR1- MFs

value: Salmonella

value: B


title: AD12m1A


title: H2BGFP_week2_sham_rep2

description:
input sample: input_week2_sham-TAC
ChIP_DNA


title: MDA-MB-231_GI_TCDD_5

source_name: Breast adenocarcinoma cell

value: Breast adenocarcinoma cell


title: MB46_ACGTCT Salmonella large bowel CX3CR1- MFs

description: Salmonella large bowel CX3CR1- MFs

value: large bowel


title: D12 WOL 1: CD34+cells_Day12_WOL 1

source_name: CD34+cells treated with WOL 1 at day 12


title: MDA-MB-231_GII_TCDD_5

value: GII+TCDD


title: single cellf from YS [LIB019717_GEN00050537_S84_R1]

source_name: yolk sac (YS)

value: embryonic tissue


title: MDA-MB-231_GII_5

value: GII


title: H2BGFP_week2_sham_rep1


title: H2BGFP_week2_TAC_rep2


title: MDA-MB-231_GI_5

value: GI


title: H2BGFP_week2_TAC_rep1

value: heart


title: AD9m1A


title: MB44_CTCCAT Salmonella large bowel CD103+ CD11b- DC

description: Salmonella large bowel CD103+ CD11b- DC

source_name: Salmonella large bowel CD103+ CD11b- DC

value: CD103+ CD11b- DC


title: AD9m2A


title: MB45_GTCAGG Salmonella large bowel CD103+ CD11b- DC

description: Salmonella large bowel CD103+ CD11b- DC

value: E


title: input_WT2

description: input

source_name: Heart

value: isolated adult ventricular cardiomyocytes

value: adult


title: MDA-MB-231_TCDD_5

value: TCDD


title: AD6m3A


title: AD6m2A


title: input_WT1

description: input


title: MB43_CCGCAA Salmonella large bowel CD103+ CD11b- DC

description: Salmonella large bowel CD103+ CD11b- DC

value: C


title: MB42_TCTTAA Salmonella large bowel CD103+ CD11b- DC

description: Salmonella large bowel CD103+ CD11b- DC


title: H3

description:
input sample: input_WT1
ChIP_DNA

value: WT

value: H3 (Abcam, ab1791)


title: AD9m3A


title: MB41_TGCTAT Salmonella large bowel CD103+ CD11b- DC

description: Salmonella large bowel CD103+ CD11b- DC

value: Salmonella

value: A


title: MDA-MB-231_GII_TCDD_4

value: Breast adenocarcinoma cell


title: H2BGFP_week8

description:
input sample: input_WT1
ChIP_DNA

value: No


title: MB40_CAGGCT large bowel CD45+ CD11c- CD11b- lymphocytes

value: control

value: large bowel

value: CD45+ CD11c- CD11b- lymphocytes


title: AD4m3A


title: AD6m1A


title: H2BGFP_week6

description:
input sample: input_WT1
ChIP_DNA


title: MB39_CACACT large bowel CD45+ CD11c- CD11b- lymphocytes

value: D


title: AD4m2A


title: MDA-MB-231_GI_4

value: GI


title: H2BGFP_week4_rep3

description:
input sample: input_WT2
ChIP_DNA

value: heart


title: MDA-MB-231_Ctrl_5

value: Control


title: AD4m1A


title: MDA-MB-231_TCDD_4


title: MB37_AGTTGA large bowel CD45+ CD11c- CD11b- lymphocytes

value: B


title: H2BGFP_week4_rep1

description:
input sample: input_WT1
ChIP_DNA

value: isolated adult ventricular cardiomyocytes

value: adult


title: MDA-MB-231_Ctrl_4


title: H2BGFP_week4_rep2

description:
input sample: input_WT2
ChIP_DNA


title: MB36_ATGAAC large bowel CD45+ CD11c- CD11b- lymphocytes


title: MDA-MB-231_GII_TCDD_3

value: GII+TCDD


title: AD2m2A


title: MB35_ATACTG large bowel CD45- stromal cells

description: large bowel CD45- stromal cells

source_name: large bowel CD45- stromal cells

value: CD45- stromal cells

value: E


title: MDA-MB-231_GII_4

value: GII


title: AD2m1A


title: MDA-MB-231_GI_TCDD_3

value: GI+TCDD


title: MDA-MB-231_GI_TCDD_4

value: Breast adenocarcinoma cell


title: H2BGFP_week2_rep2

description:
input sample: input_WT1
ChIP_DNA

value: WT

value: No


title: H2BGFP_week2_rep1

description:
input sample: input_WT1
ChIP_DNA


title: WT12m3A


title: MDA-MB-231_GII_3


title: MDA-MB-231_GI_3


title: WT12m2A


title: H2BGFP_week1_rep1

description:
input sample: input_WT1
ChIP_DNA


title: H2BGFP_week1_rep2

description:
input sample: input_WT1
ChIP_DNA


title: MB38_GACGAT large bowel CD45+ CD11c- CD11b- lymphocytes

value: control

value: large bowel

value: C


title: MB33_TGTGCA large bowel CD45- stromal cells

description: large bowel CD45- stromal cells


title: MB32_CGTCGC large bowel CD45- stromal cells

description: large bowel CD45- stromal cells


title: AD2m3A


title: WT12m1A


title: MDA-MB-231_TCDD_3

value: TCDD


title: MB31_TTCGAG large bowel CD45- stromal cells

description: large bowel CD45- stromal cells

value: A


title: D10 Control 1: hAECs_ Day 10_ Control 1

description: Gene expression data from untreated control hAECs on day 10

source_name: Untreated control hAECs on day10, biological rep 1

value: amnion epithelial cells


title: MB30_CCAATT large bowel CX3CR1 int MFs

description: large bowel CX3CR1 int MFs

source_name: large bowel CX3CR1 int MFs

value: CX3CR1 int MFs


title: WT9m3A


title: WT9m2A


title: MB29_CTCTCG large bowel CX3CR1 int MFs

description: large bowel CX3CR1 int MFs

value: D


title: H2BGFP_week0_rep2

description:
input sample: input_WT2
ChIP_DNA

value: heart

value: isolated adult ventricular cardiomyocytes

value: adult


title: MDA-MB-231_GII_TCDD_2

value: GII+TCDD


title: MDA-MB-231_Ctrl_3

value: Control


title: MB34_ACCGTG large bowel CD45- stromal cells

description: large bowel CD45- stromal cells

value: CD45- stromal cells


title: WT9m1A


title: MDA-MB-231_GI_TCDD_2

value: Breast adenocarcinoma cell

value: GI+TCDD


title: MB28_GTTACC large bowel CX3CR1 int MFs

description: large bowel CX3CR1 int MFs


title: WT6m3A


title: MB27_CAAGCA large bowel CX3CR1 int MFs

description: large bowel CX3CR1 int MFs

value: B


title: MDA-MB-231_GII_2

value: GII


title: WT6m2A


title: MDA-MB-231_GI_2

value: GI


title: MB26_GCGCTG large bowel CX3CR1 int MFs

description: large bowel CX3CR1 int MFs

value: control

value: large bowel


title: WT6m1A


title: MDA-MB-231_TCDD_2

value: TCDD


title: WT4m3A


title: H2BGFP_week0_rep1

description:
input sample: input_WT2
ChIP_DNA

value: WT

value: No


title: MDA-MB-231_Ctrl_2


title: MB24_TCGAGG large bowel CX3CR1 high MFs

description: large bowel CX3CR1 high MFs

source_name: large bowel CX3CR1 high MFs

value: CX3CR1 high MFs

value: D


title: MDA-MB-231_GII_TCDD_1


title: WT4m2A


title: WT4m1A


title: MB23_AGATAG large bowel CX3CR1 high MFs

description: large bowel CX3CR1 high MFs

value: C


title: MB22_GTGCCA large bowel CX3CR1 high MFs

description: large bowel CX3CR1 high MFs


title: WT2m3A


title: MDA-MB-231_GII_1


title: MDA-MB-231_GI_TCDD_1


title: 291_CD8_S

city: Nantes

first: Delphine

last: Fradin

address: 8 quai Moncousu

institute: CRCI2NA, Inserm UMR1307, CNRS UMR6075

description: sample 291

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: human T cell form melanoma patients

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: human CD8+ T cell stimulated


title: 265_CD8_S

description: sample 265


title: 125_CD8_S

description: sample 125


title: MB21_ACCAGT large bowel CX3CR1 high MFs

description: large bowel CX3CR1 high MFs

value: A


title: 329_CD8_S

description: sample 329


title: WT2m2A


title: MB20_GGCTGC large bowel CX3CR1- MFs

description: large bowel CX3CR1- MFs

source_name: large bowel CX3CR1- MFs

value: CX3CR1- MFs

value: E


title: MB25_ACAACG large bowel CX3CR1 high MFs

description: large bowel CX3CR1 high MFs


title: 288_CD8_S

description: sample 288


title: 314_CD8_S

description: sample 314


title: MDA-MB-231_TCDD_1

value: Breast adenocarcinoma cell


title: 305_CD8_S

description: sample 305


title: MDA-MB-231_GI_1


title: WT2m1A


title: MB19_CCTAAG large bowel CX3CR1- MFs

description: large bowel CX3CR1- MFs


title: 291_CD8_NS

description: sample 291

value: human CD8+ T cell unstimulated


title: AD12m3M


title: MDA-MB-231_Ctrl_1

value: Control


title: MB18_CGCGGA large bowel CX3CR1- MFs

description: large bowel CX3CR1- MFs


title: 298_CD8_S

description: sample 298


title: MB17_GATCAC large bowel CX3CR1- MFs

description: large bowel CX3CR1- MFs

value: B


title: AD12m1M


title: HCC03 tumor region #9

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

data_processing:
Trimming adaptor sequences and removing reads of low quality were performed by cutadapt (v2.3).
Quantified reads were aligned to the human genome (GRCh38.p12) by STAR (v2.6.1a) and then gene-level read counts were generated based on the annotations of Gencode (v28).
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene-level read counts

source_name: Hepatocellular carcinoma

extract_protocol:
Total RNA was extracted from frozen snaps using an AllPrep DNA/RNA mini kit (Qiagen,  Hilden, Germany).
Poly-A enriched strand-specific libraries were generated with the TruSeq stranded mRNA library prep kit (Illumina, San Diego, United States) following the manufacturer’s instructions.

value: Hepatocellular carcinoma

tag: sample


title: HCC01 tumor region #5


title: MB16_CAGATG large bowel CX3CR1- MFs

description: large bowel CX3CR1- MFs

value: control


title: HCC14 tumor region #5


title: AD9m3M

tag: age


title: HCC14 tumor region #3


title: MB15_AACGCC large bowel CD103+ CD11b- DC

description: large bowel CD103+ CD11b- DC

source_name: large bowel CD103+ CD11b- DC

value: large bowel

value: CD103+ CD11b- DC


title: AD9m2M


title: AD9m1M


title: HCC14 tumor region #1


title: AD6m3M


title: MB14_CGGTTA large bowel CD103+ CD11b- DC

description: large bowel CD103+ CD11b- DC


title: HCC13 tumor region #2


title: MB13_GAACCT large bowel CD103+ CD11b- DC

description: large bowel CD103+ CD11b- DC


title: AD12m2M


title: AD6m2M


title: HCC13 tumor region #1


title: MB11_ATAAGA large bowel CD103+ CD11b- DC

description: large bowel CD103+ CD11b- DC


title: MB12_GCCACA large bowel CD103+ CD11b- DC

description: large bowel CD103+ CD11b- DC


title: AD6m1M


title: HCC12 tumor region #6


title: 125_CD8_NS

description: sample 125


title: 265_CD8_NS

description: sample 265


title: MB10_GATTGT peritoneal CD115+ F4/80+ MHCII- MFs

description: peritoneal CD115+ F4/80+ MHCII- MFs

source_name: peritoneal CD115+ F4/80+ MHCII- MFs

value: peritoneal

value: CD115+ F4/80+ MHCII- MFs


title: 288_CD8_NS

description: sample 288


title: 329_CD8_NS

description: sample 329


title: 305_CD8_NS

description: sample 305


title: 314_CD8_NS

description: sample 314


title: 298_CD8_NS

description: sample 298


title: 291_DP_S

description: sample 291

value: human CD4+/CD8+ DP T cell stimulated


title: AD4m2M


title: MB09_AATGAA peritoneal CD115+ F4/80+ MHCII- MFs

description: peritoneal CD115+ F4/80+ MHCII- MFs

value: D


title: HCC12 tumor region #1


title: HCC11 tumor region #5


title: HCC12 tumor region #2


title: HCC11 tumor region #4


title: AD4m3M


title: MB08_TTAACT peritoneal CD115+ F4/80+ MHCII- MFs

description: peritoneal CD115+ F4/80+ MHCII- MFs

value: C


title: AD4m1M


title: AD2m3M


title: HCC09 tumor region #4


title: MB04_AAGACA small bowel CD103+ CD11b+ DC

description: small bowel CD103+ CD11b+ DC

source_name: small bowel CD103+ CD11b+ DC

value: small bowel

value: CD103+ CD11b+ DC


title: HCC11 tumor region #1


title: MB07_AATAGC peritoneal CD115+ F4/80+ MHCII-  MFs

description: peritoneal CD115+ F4/80+ MHCII-  MFs

source_name: peritoneal CD115+ F4/80+ MHCII-  MFs


title: WT12m3M

source_name: Brain


title: AD2m2M


title: AD2m1M


title: HCC09 tumor region #3


title: WT12m2M


title: HCC09 tumor region #1


title: WT12m1M


title: MB02_GGTGAG small bowel CD103+ CD11b+ DC

description: small bowel CD103+ CD11b+ DC


title: HCC08 tumor region #5


title: MB05_TAATCG small bowel CD103+ CD11b+ DC

description: small bowel CD103+ CD11b+ DC


title: WT9m3M


title: HCC08 tumor region #4


title: MB03_CGAAGG small bowel CD103+ CD11b+ DC

description: small bowel CD103+ CD11b+ DC


title: 305_DP_S

description: sample 305


title: 329_DP_S

description: sample 329


title: 265_DP_S

description: sample 265


title: 288_DP_S

description: sample 288


title: WT9m2M


title: 291_DP_NS

description: sample 291

value: human CD4+/CD8+ DP T cell unstimulated


title: 125_DP_S

description: sample 125


title: Genomic_Input_control

first: Eddie

last: Loh

address: 1425 Madison Avenue

department: Department of Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The ChIP-seq data was first checked for quality using the various metrics generated by FastQC (v0.11.2). Raw sequencing reads were then aligned to the mouse mm10 genome using default settings of Bowtie (v2.2.0). Only uniquely-mapped reads were retained and duplicates were removed.
Peak-calling was performed using MACS (v2.1.1) with qvalue (minimum FDR) cutoff of 0.05. Motif enrichment analysis was performed using the Homer package (v4.8.3). The peak annotation and gene ontology analysis was performed using the GREAT program and Panther classification system.
Genome_build: MM10
Supplementary_files_format_and_content: bigwig files

source_name: Mouse cochlea

extract_protocol:
The tissues were fixed with 1%PFA in PBS for 30 min at RT. After washing, the tissues were homogenized to a fine powder using BeadBugTM high-energy benchtop homogenizer in the lysis buffer. Chromatin shearing was performed using the Covaris E220 focused-ultrasonicator system. After preclearing with Protein A beads, the chromatin was immunoprecipitated with antibodies. After IP, the beads were washed in sequential low salt buffer, high salt buffer, LiCl washing buffer and TE buffer.
The libraries were prepared using the ThruPlex DNA-seq Kit (Rubicon Genomics) and according to the manufacturer's instructions.

value: cochlea

tag: antibody


title: Cochlea_IgG_control


title: WT9m1M


title: 314_DP_S

description: sample 314


title: HCC08 tumor region #1


title: 265_DP_NS

description: sample 265


title: WT6m3M


title: HCC07 tumor region #5


title: 288_DP_NS

description: sample 288


title: 329_DP_NS

description: sample 329


title: 125_DP_NS

description: sample 125


title: HCC07 tumor region #4


title: MB01_ACATTA small bowel CD103+ CD11b+ DC

description: small bowel CD103+ CD11b+ DC

value: A


title: WT6m2M


title: HCC07 tumor region #2


title: E10.5_Embryo_Six1_ChIP-seq

source_name: Mouse whole embryo

value: embryo

value: Six1 (HPA001893, Sigma)


title: 298_DP_S

description: sample 298


title: E13.5_Cochlea_Six1_ChIP-seq


title: HCC05 tumor region #6


title: 305_DP_NS

description: sample 305


title: WT6m1M


title: HCC05 tumor region #4


title: y1_460_2

city: Planegg

first: Tatjana

last: Kleine

address: Großhaderner Straße 2

department: Biologie I, Botanik

country: Germany

institute: Ludwig-Maximilians-Universität München

data_processing:
Galaxy platform
adaptors were removed with Trimmomatic (Bolger et al., 2014)
sequencing quality was accessed with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were mapped to the Arabidopsis genome (TAIR10) with the gapped-read mapper TopHat 2.1.1 (Kim et al., 2013) set for Forward Read (FR) unstranded libraries and adjusting the maximum intron length to 5000 bp.
Reads were counted with featureCounts (Liao et al., 2014) with the help of the gene annotation in Araport11 (www.araport.org/data/araport11).
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited files include read count values for each sample

organism: Arabidopsis thaliana

source_name: 6-d-old flu/ex1/ydl1, 4h in dark, 60 min in light

growth_protocol: The Arabidopsis flu/ex1 and flu/ex1/ydl1 were grown in soil for 6 days under continous light

extract_protocol:
Total RNA from plants was isolated using Trizol (Invitrogen, Carlsbad, USA) and purified using Direct-zol™ RNA MiniPrep Plus columns (Zymo Research, Irvine, USA) according to the manufacturer’s instructions. RNA integrity and quality was assessed by an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, USA).
Illumina Tru-Seq

treatment_protocol: Put in darkness for up to 4 hours

value: 4h in dark, 60 min in light


title: WT4m2M


title: HCC05 tumor region #2

value: Hepatocellular carcinoma


title: HCC05 tumor region #1


title: WT4m1M


title: WT2m3M


title: HCC04 tumor region #5


title: y1_430_3

source_name: 6-d-old flu/ex1/ydl1, 4h in dark, 30 min in light

value: 4h in dark, 30 min in light


title: y1_430_1


title: 314_DP_NS

description: sample 314


title: 288_CD4_S

description: sample 288

value: human CD4+ T cell stimulated


title: 291_CD4_S

description: sample 291


title: y1_400_1

source_name: 6-d-old flu/ex1/ydl1, 4h in dark

value: 4h in dark


title: WT2m2M


title: 265_CD4_S

description: sample 265


title: 329_CD4_S

description: sample 329


title: y1_400_3


title: WT2m1M


title: WT4m3M


title: 125_CD4_S

description: sample 125


title: HCC04 tumor region #3


title: y1_460_1


title: HCC04 tumor region #2


title: 305_CD4_S

description: sample 305


title: ex_460_3

source_name: 6-d-old flu/ex1, 4h in dark, 60 min in light


title: ex_430_3

source_name: 6-d-old flu/ex1, 4h in dark, 30 min in light


title: HCC03 tumor region #8


title: ex_460_1


title: HCC03 tumor region #4


title: HCC03 tumor region #5


title: ex_430_2


title: ex_400_3

source_name: 6-d-old flu/ex1, 4h in dark


title: HCC04 tumor region #4


title: ex_400_2


title: HCC02 tumor region #12


title: HCC02 tumor region #6


title: 265_CD4_NS

description: sample 265

value: human CD4+ T cell unstimulated


title: 291_CD4_NS

description: sample 291


title: 298_CD4_S

description: sample 298


title: 288_CD4_NS

description: sample 288


title: 314_CD4_S

description: sample 314


title: 125_CD4_NS

description: sample 125


title: 314_CD4_NS

description: sample 314


title: MB06_CGCAAC peritoneal CD115+ F4/80+ MHCII- MFs

description: peritoneal CD115+ F4/80+ MHCII- MFs

value: control

value: peritoneal

value: CD115+ F4/80+ MHCII- MFs


title: 329_CD4_NS

description: sample 329


title: HCC02 tumor region #1


title: HCC01 tumor region #3


title: mub1D mtl1-1 (YP992)-R2

city: Oxford

first: Adrien

last: Birot

address: South Parks Rd

department: Departement of Biochemistry

institute: University of Oxford

data_processing:
Quality trimming was performed using Trimmomatic (Galaxy Version 0.32.3, RRID:SCR_011848).
Reads were aligned to the S. pombe genomic reference sequence (ASM294v2.19) using Bowtie 2 (TopHat).
Genome_build: S. pombe genome (ASM294v2.19)
Supplementary_files_format_and_content: bedGraph

organism: Schizosaccharomyces pombe

source_name: mub1D mtl1-1 (YP992)

growth_protocol: Cultures on YES to mid-log phase, at 30°C.

extract_protocol:
Total RNA was extracted by phenol/chloroform precipitation and DNase-treated. Ribodepletion was performed using ribominus transcriptome isolation kit (Invitrogen, K155003).
Library preparation was performed with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (E7760S) by using 50ng of RNA as starting material.
Paired-end sequencing was made using the Illumina NextSeq 500 platform.

value: mub1D mtl1-1


title: HCC02 tumor region #9


title: HCC01 tumor region #4


title: mub1D mtl1-1 (YP992)-R1


title: mub1D(YP1081)-R2


title: hr3042

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

institute: German Diabetes Center

hyb_protocol: Amplified cDNA was hybridized on Affymetrix human HTA 2.0 arrays (Affymetrix)

scan_protocol: Detection of probe intensities was performed using a GeneChip scanner 3000 7G (GDAS 1.4 package, Affymetrix).

data_processing:
The data were analyzed with Affymetrix Expression  Console  using default analysis settings for RMA analyses  for  gene default and exon default .CHP files.
affymetrix-algorithm-name = gc-correction,scale-intensities,rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish
affymetrix-algorithm-version = 1.0
affymetrix-array-type = HTA-2_0
program_name = q_probeset_summarize.exe

source_name: Primary HCF-v_0.5%_Rhein 35mM

label_protocol: 150 ng total RNAwas amplified using the Ambion WT Expression Kit and the WT Terminal Labeling Kit (Affymetrix, Freiburg, Germany).

growth_protocol: Primary HCF-v of 5 different donors were purchased (Lonza, Basel, Switzerland; Promocell, Heidelberg, Germany) and cultured in FGMTM-3 medium (Lonza, Basel, Switzerland) (37°C, 5% CO2).

extract_protocol: Total RNA extraction was made with RNeasy mini kit (Qiagen, Hilden, Germany) including DNAse digestion according to the manufacturer's instructions. RNA quality was evaluated using an Agilent 2100 Bioanalyzer and only high quality RNA (RIN > 8) was used for microarray analysis.

treatment_protocol: Prior treatment HCF-v were seeded in 145mm dishes. After 16h, cells were subjected to the hypoxic workstation (Xvivo System (Biospherix, Parish, NY, USA) set to 0.5% O2, 5% CO2, 94.5% N2 and 37°C) with N2-pre-gassed DMEM (10% FCS, 1% glutamine, 1% antibiotic/antimycotic). After 60h, sub-confluent cells were washed (1x PBS) and serum-starved nitrogenated serum-free media (DMEM, 1% glutamine, 1% antibiotic/antimycotic) for 36h. Normoxic control cells were treated in parallel in a second incubator of the hypoxic workstation (21% O2, 74% N2, 5% CO2 and 37°C). For Rhein treatment, 35µM Rhein was added during normoxic or hypoxic treatment for a total incubation time of 96h.

value: Primary human ventricular cardiac fibroblasts

tag: cell type batch

value: C12375, lot 3042901.1 Promocell, Heidelberg, Germany

tag: gender

value: male

tag: oxigen concentration

tag: rhein


title: HCC01 tumor region #2


title: HCC02 tumor region #3


title: mub1D(YP1081)-R1


title: mtl1-1(YP-729)-R2


title: nr3042

source_name: Primary HCF-v_21%_Rhein 35mM


title: BS_Seq_NRPD1-3xMYC#1

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

description: treated with bisulfite

data_processing:
For BS-seq, adapter,and low-quality sequences (q < 20) were trimmed and clean reads were mapped to Arabidopsis thaliana TAIR 10 genome using BSMAP allowing two mismatches. Only cytosines with a depth of at least four in all libraries were retained for further analysis.
For SRNA-seq, after trimming off adapter sequences, clean reads with size ranging from 18-30 nt were mapped to the TAIR 10 genome using Bowtie (Langmead et al., 2009). Only reads that had at least one perfect match to the genome and cannot be mapped to annotated structural RNAs (rRNAs, tRNAs, snRNAs and snoRNAs) were retained for downstream analysis. 24-nt reads counts of regions were normalized to reads per 10 million (RPTM) based on total mapped clean reads (excluding structural sRNAs) in the library.
Genome_build: TAIR10
Supplementary_files_format_and_content: BS-seq WIG files give methylation level for Cs with depth >= 4; SRNA-seq TDF files represent normalized RPTM (reads per ten million) counts of 24-nt RNAs that are uniquely mapped to the TAIR10 genome.

source_name: 14-day old seedling

growth_protocol: 14-day-old seedlings were grown on 1/2 MS plates supplemented with 0.6% agarose and 1% sucrose under long-day conditions(22°C, 16-h light, 8-h dark)

extract_protocol:
Genomic DNA was extracted from 14-day-old seedlings and sent to BGI (Wuhan, China) for bisulfite treatment, library construction, and sequencing.
Libraries were prepared for sequencing according to the manufacturer's (Illumina, Inc) instructions.

tag: genotype

value: seedling


title: h3042

source_name: Primary HCF-v_0.5%_Rhein 0mM


title: mtl1-1(YP-729)-R1


title: 298_CD4_NS

description: sample 298

source_name: human T cell form melanoma patients

tag: treatment


title: BS_Seq_NRPE1-3xFLAG#2

description: treated with bisulfite


title: 305_CD4_NS

description: sample 305


title: n3042

source_name: Primary HCF-v_21%_Rhein 0mM


title: WT-(YP71)-R1

source_name: WT (YP71)

value: WT


title: TTA15_D4_scRNAseq

city: Ghent

first: Tom

last: Taghon

address: Corneel Heymanslaan 10

country: Belgium

institute: Ghent University

data_processing:
Data was demultiplexed using CellRanger
Fastq files were mapped using CellRanger
Count matrices were generated using CellRanger
Genome_build: GRCh38
Supplementary_files_format_and_content: 10X Genomics CellRanger output for scRNAseq 3’ V2 kit

source_name: Human postnatal thymus

extract_protocol:
Pediatric thymus from children undergoing cardiac surgery were obtained and used according to and with the approval of the Medical Ethical Commission of Ghent University Hospital (Belgium). The thymus tissue was mechanically disrupted to obtain a single cell suspension. CD34+ thymocytes were enriched using MACS with CD34 microbeads (Miltenyi Biotec) according to the instructions of the manufacturer.
10X Genomics Chromium V2 kit – Manufacturers recommendations were followed

value: CD44+ Thymocytes

tag: donor


title: h2836

value: CC-2094, lot 0000402836 Lonza, Basel, Switzerland

value: female


title: nr2836


title: S3_D3_scRNAseq

value: Lin-CD34+CD1a- Thymocytes


title: S2_D2_scRNAseq


title: S1_D1_scRNAseq


title: CISE11_D2_scRNAseq

value: Lin-CD34+ Thymocytes


title: n2836


title: CISE10_D1_scRNAseq


title: WT-(YP71)-R2


title: D2_CITEseq


title: D1_CITEseq


title: hr2836


title: hr1486

value: CC-2094, lot 000401462 Lonza, Basel, Switzerland


title: Heat_treated_37°_24hr_Replicate1 [37_24_rep1]

city: Aubière

first: Said

last: Mouzeyar

address: 1 Impasse Amélie Murat

department: Biology

institute: Université Clermont Auvergne

data_processing:
basecalling Illumina RTA 1.18.64
demultiplexing software bcl2fastq-1.8.4.  Sequences are demultiplexed according to the 2x8 bp index code with 1 mismatch allowed.
Mapping of reads to the reference genome using BWA-MEM (toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1)
Raw read counts created using featureCounts on a Galaxy web server (Galaxy Tool Version: 1.4.6.p5) with default parameters and feature type filter = gene. The annotation version 3.3 of P. patens genome (file Ppatens_318_v3.3.gene.gff3 was downloaded from http://plants.ensembl.org).
Genome_build: Ppatens_318_v3 (https://genome.jgi.doe.gov/)
Supplementary_files_format_and_content: featureCounts.  gene level expression estimates; tab-delimited text

organism: Physcomitrium patens

growth_protocol: protonemata were  cultivated axenically in petri dishes  containing PpNH4 medium  supplemented with 7g.L-1 agar in a growth chamber maintained at 37 °C under a photoperiod of 16/8 h and an irradiance of 100 µmol.m-2.s-1. Harvest at 24H.

extract_protocol:
Total moss RNA was extracted from 100 mg of P. patens 7-day protonemal tissues from control or heat-treated samples using Nucleospin® RNA plant (Macherey-Nagel-Germany).
Sequencing was carried out by Eurofin (Germany) using one channel and Illumina Illumina HiSeq 2500 2x 100 bp paired-end. RNA libraries were prepared for sequencing using standard Illumina protocols
strand-specific cDNA libraries; RNA selection using polyA selection. RNAseq

value: Gransden

value: protonema


title: Heat_treated_37°_24hr_Replicate2 [37_24_rep2]


title: Endo-AGO-IP-293T-DIS3L2-KO replicate 2

city: Frederick

first: Shuo

last: Gu

address: 1050 Boyles Str. Building 560 Room 11-6B

institute: National Cancer Institute

data_processing:
3ʹ adaptor sequences were removed by customized scripts. Reads without the 3′ adaptor sequences or shorter than 18 nt were discarded
For miRNA isoform analyses based on small-RNA-seq, QuagmiR (on Seven Bridges Cancer Genomics Cloud) was used with default or custermized motif files
Genome_build: miRBase21
Supplementary_files_format_and_content: isomiR profile (tsv files) (small-RNA-seq)

growth_protocol: HEK293T cells were maintained in DMEM (high glucose) (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Hyclone), 1X MEM Non-Essential Amino Acids (Gibco), 100 U/ml penicillin and 100 μg/ml streptomycin (Gibco). HEK293T-TUT4/TUT7 DKO and DIS3L2-KO cells were generated by using CRISPR/Cas9.

extract_protocol:
RNAs were extracted by using Trizol.
Sequencing libraries were constructed by either Illumina® TruSeq® RNA sample preparation kit or NEBNext® Multiplex Small RNA Library Prep Set according to the manufacturer's’ protocol with minor modifications.

treatment_protocol: HEK293T, DIS3L2-KO and TUT4/7-DKO cells were transfected with Lipofectamine 3000 (Life Technologies) according to the manufacturer's’ instructions

value: human embryonic kidney cells

tag: cell line

value: DIS3L2 Knockout

tag: ip antibody

value: Detection of endogenous miRNA bound to endogenous AGO2


title: Endo-AGO-IP-293T-DKO replicate 3

value: TUT4 and TUT7 Double Knockout


title: Endo-AGO-IP-293T-DIS3L2-KO replicate 1


title: Endo-AGO-IP-293T-DIS3L2-KO replicate 3


title: Heat_treated_37°_12hr_Replicate2 [37_12_rep2]

growth_protocol: protonemata were  cultivated axenically in petri dishes  containing PpNH4 medium  supplemented with 7g.L-1 agar in a growth chamber maintained at 37 °C under a photoperiod of 16/8 h and an irradiance of 100 µmol.m-2.s-1. Harvest at 12H.


title: Endo-AGO-IP-293T-WT replicate 3


title: Endo-AGO-IP-293T-DKO replicate 1


title: M010817_TGFb_48hC

city: Zwijnaarde

first: Jordy

last: De Coninck

address: Technologiepark 71

department: Department of Biomedical Molecular Biology

institute: University Gent

description: M010817 +TGFß 48h - Replicate 3

data_processing:
Reads were aligned to hg38 reference genome using STAR2.4.2a.
Genes were quantified on Gencode v25 GTF.
DESeq2 was used to assess differential expression with a multifactorial design to control for batch effects.
Genome_build: hg38
Supplementary_files_format_and_content: Counts table with in rows the gene names (Ensembl ID) and in columns the different samples.

source_name: Human melanoma cell lines

growth_protocol: RPMI1640 + 10% FBS + L-Gln  + Na-pyruvate

extract_protocol:
TRIsure lysis buffer (BioLine, BIO-38032)
Illumina TruSeq RNA library construction protocol

treatment_protocol: Recombinant hTGF-ß, 5 ng/mL; PeproTech

tag: tissue type

value: melanoma cell line

value: TGF-ß

tag: treatment duration


title: M010817_TGFb_96hA

description: M010817 +TGFß 96h - Replicate 1


title: M010817_TGFb_96hB

description: M010817 +TGFß 96h - Replicate 2


title: M010817_TGFb_96hC

description: M010817 +TGFß 96h - Replicate 3


title: Heat_treated_37°_12hr_Replicate1 [37_12_rep1]

tag: cell type


title: M010817_TGFb_48hB

description: M010817 +TGFß 48h - Replicate 2


title: nr1486

value: Primary human ventricular cardiac fibroblasts


title: h1486


title: nr1712

value: CC-2094, lot:0000421712  Lonza, Basel, Switzerland

value: male


title: n1486


title: hr1712


title: M010817_TGFb_48hA

description: M010817 +TGFß 48h - Replicate 1


title: h1712


title: Endo-AGO-IP-293T-WT replicate 2

value: WT


title: Heat_treated_37°_6hr_Replicate2 [37_6_rep2]

growth_protocol: protonemata were  cultivated axenically in petri dishes  containing PpNH4 medium  supplemented with 7g.L-1 agar in a growth chamber maintained at 37 °C under a photoperiod of 16/8 h and an irradiance of 100 µmol.m-2.s-1. Harvest at 6H.


title: Endo-AGO-IP-293T-WT replicate 1


title: Endo-AGO-IP-293T-DKO replicate 2


title: M010817_controlC

description: M010817 control - Replicate 2

value: control


title: Heat_treated_37°_6hr_Replicate1 [37_6_rep1]


title: M921_TGFb_96hC

description: M000921 +TGFß 96h - Replicate 2


title: Heat_treated_37°_1hr_Replicate1 [37_1_rep1]

growth_protocol: protonemata were  cultivated axenically in petri dishes  containing PpNH4 medium  supplemented with 7g.L-1 agar in a growth chamber maintained at 37 °C under a photoperiod of 16/8 h and an irradiance of 100 µmol.m-2.s-1. Harvest at 1H.


title: Heat_treated_37°_1hr_Replicate2 [37_1_rep2]

growth_protocol: protonemata were  cultivated axenically in petri dishes  containing PpNH4 medium  supplemented with 7g.L-1 agar in a growth chamber maintained at 37°C under a photoperiod of 16/8 h and an irradiance of 100 µmol.m-2.s-1. Harvest at 1H.


title: AGO2-WT-IP-endogenous-DIS3L2KO

value: Sigma M8823-1ML anti-FLAG M2 Magnetic Beads

value: Over-expression of AGO2 construct, detection of endogenously expressed miRNA


title: M010817_controlA

description: M010817 control - Replicate 1


title: M921_TGFb_96hB

description: M000921 +TGFß 96h - Replicate 1


title: n1712


title: M921_TGFb_48hC

description: M000921 +TGFß 48h - Replicate 3


title: Heat_treated_30°_24hr_Replicate2 [30_24_rep2]

growth_protocol: protonemata were  cultivated axenically in petri dishes  containing PpNH4 medium  supplemented with 7g.L-1 agar in a growth chamber maintained at 30 °C under a photoperiod of 16/8 h and an irradiance of 100 µmol.m-2.s-1. Harvest at 24H.


title: AGO2-PAZ-IP-endogenous-HEK293T


title: AGO2-F2L3-IP-endogenous-HEK293T


title: Heat_treated_30°_24hr_Replicate1 [30_24_rep1]


title: AGO2-PAZ-IP-endogenous-DIS3L2KO


title: AGO2-F2L3-IP-endogenous-DIS3L2KO


title: M921_TGFb_48hB

description: M000921 +TGFß 48h - Replicate 2


title: AGO2-PAZ-IP-OE-miR-TUT47DKO-DIS3L2CD

value: Over-expression of AGO2, DIS3L2-mutant and miRNA cluster constructs


title: AGO2-WT-IP-endogenous-HEK293T


title: Heat_treated_30°_12hr_Replicate2 [30_12_rep2]

growth_protocol: protonemata were  cultivated axenically in petri dishes  containing PpNH4 medium  supplemented with 7g.L-1 agar in a growth chamber maintained at 30 °C under a photoperiod of 16/8 h and an irradiance of 100 µmol.m-2.s-1. Harvest at 12H.


title: Heat_treated_30°_12hr_Replicate1 [30_12_rep1]


title: M921_TGFb_48hA

description: M000921 +TGFß 48h - Replicate 1


title: M921_controlC

description: M000921 control - Replicate 3


title: AGO2-PAZ-IP-OE-miR-TUT47DKO

value: Over-expression of AGO2, empty vector and miRNA cluster constructs


title: AGO2-PAZ-IP-OE-miR-TUT7KO

value: TUT7 Knockout


title: M921_controlA

description: M000921 control - Replicate 1


title: HUDEP2_BCL11A+58KO_r2

city: Guangzhou

first: Peng

last: Huang

state: Guangdong

address: Xinzao, Panyu District

department: GMU-GIBH Joint School of Life Sciences

institute: Guangzhou Medical University

description: processed data file: 2340_2345_nor.bigwig

data_processing:
library strategy: Capture-C
Basecalls using bcl2fastq2 v2.15.0.4, and parameters --no-eamss --mismatches 1
Reads were processed using the published pipeline (https://github.com/telenius/captureC/releases).
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files with the normalized Capture-C interaction signals

growth_protocol: HUDEP2 cells were cultured with StemSpan SFEM (Stem Cell Technologies) supplemented with 1 μg/ml doxycycline, 1 μM dexamethasone, 100 ng/ml human SCF, 3 units/ml erythropoietin and 1% penicillin/streptomycin.

extract_protocol: Capture-C libraries were generated as described (Davies et al. 2016 Nature Methods).

treatment_protocol:
The GATA binding motif at the BCL11A +58 enhancer was disrupted using a CRISPR-Cas9-mediated approach in pooled HUDEP2 cells.
HUDEP2 cells were differentiated for 5 days in Iscove’s Modified Dulbecco’s Medium (IMDM) supplemented with 330 μg/ml holo-transferrin, 10 μg/ml insulin, 2 units/ml heparin, 5% FBS, 3 units/ml erythropoietin, 1 μg/ml doxycycline and 1% penicillin/streptomycin.

tag: tissue

value: Immortalized Human Erythroid Progenitor

value: Erythroid cells

tag: differentiation

value: Differentiated for 5 days


title: Heat_treated_30°_6hr_Replicate2 [30_6_rep2]

growth_protocol: protonemata were  cultivated axenically in petri dishes  containing PpNH4 medium  supplemented with 7g.L-1 agar in a growth chamber maintained at 30 °C under a photoperiod of 16/8 h and an irradiance of 100 µmol.m-2.s-1. Harvest at 6H.

tag: strain

value: Gransden

value: protonema


title: Control_24hr_Replicate2 [24_24_rep2]

growth_protocol: protonemata were  cultivated axenically in petri dishes  containing PpNH4 medium  supplemented with 7g.L-1 agar in a growth chamber maintained at 24 °C under a photoperiod of 16/8 h and an irradiance of 100 µmol.m-2.s-1. Harvest at 24H.


title: AGO2-PAZ-IP-OE-miR-TUT7KO-DIS3L2CD

value: human embryonic kidney cells


title: Heat_treated_30°_6hr_Replicate1 [30_6_rep1]


title: HUDEP2_r2

description: processed data file: 2338_2343_nor.bigwig

treatment_protocol: HUDEP2 cells were differentiated for 5 days in Iscove’s Modified Dulbecco’s Medium (IMDM) supplemented with 330 μg/ml holo-transferrin, 10 μg/ml insulin, 2 units/ml heparin, 5% FBS, 3 units/ml erythropoietin, 1 μg/ml doxycycline and 1% penicillin/streptomycin.


title: Heat_treated_30°_1hr_Replicate2 [30_1_rep2]

growth_protocol: protonemata were  cultivated axenically in petri dishes  containing PpNH4 medium  supplemented with 7g.L-1 agar in a growth chamber maintained at 30°C under a photoperiod of 16/8 h and an irradiance of 100 µmol.m-2.s-1. Harvest at 1H.


title: AGO2-PAZ-IP-OE-miR-DIS3L2KO

value: DIS3L2 Knockout

value: Over-expression of AGO2 and miRNA cluster constructs


title: Control_24hr_Replicate1 [24_24_rep1]


title: Heat_treated_30°_1hr_Replicate1 [30_1_rep1]

growth_protocol: protonemata were  cultivated axenically in petri dishes  containing PpNH4 medium  supplemented with 7g.L-1 agar in a growth chamber maintained at 30 °C under a photoperiod of 16/8 h and an irradiance of 100 µmol.m-2.s-1. Harvest at 1H.


title: HUDEP2_BCL11A+55KO_r2

description: processed data file: 2341_2346_nor.bigwig

treatment_protocol:
The ATF4 binding motif at the BCL11A +55 enhancer was disrupted using a CRISPR-Cas9-mediated approach in pooled HUDEP2 cells.
HUDEP2 cells were differentiated for 5 days in Iscove’s Modified Dulbecco’s Medium (IMDM) supplemented with 330 μg/ml holo-transferrin, 10 μg/ml insulin, 2 units/ml heparin, 5% FBS, 3 units/ml erythropoietin, 1 μg/ml doxycycline and 1% penicillin/streptomycin.


title: 298_DP_NS

description: sample 298

value: human CD4+/CD8+ DP T cell unstimulated


title: AGO2-WT-IP-OE-miR-DIS3L2KO


title: Control_12hr_Replicate2 [24_12_rep2]

growth_protocol: protonemata were  cultivated axenically in petri dishes  containing PpNH4 medium  supplemented with 7g.L-1 agar in a growth chamber maintained at 24 °C under a photoperiod of 16/8 h and an irradiance of 100 µmol.m-2.s-1. Harvest at 12H.


title: AGO2-F2L3-IP-OE-miR-HEK293T


title: HUDEP2_BCL11A+55KO_r1


title: Control_12hr_Replicate1 [24_12_rep1]


title: M921_controlB

description: M000921 control - Replicate 2

value: melanoma cell line


title: Control_6hr_Replicate2 [24_6_rep2]

growth_protocol: protonemata were  cultivated axenically in petri dishes  containing PpNH4 medium  supplemented with 7g.L-1 agar in a growth chamber maintained at 24 °C under a photoperiod of 16/8 h and an irradiance of 100 µmol.m-2.s-1. Harvest at 6H.


title: AGO2-PAZ-IP-OE-miR-HEK293T

value: WT


title: AGO2-WT-IP-OE-miR-HEK293T


title: HUDEP2_ATF4KO_r1

description: processed data file: 2339_2344_nor.bigwig

treatment_protocol:
ATF4 was depleted using a CRISPR-Cas9-mediated approach in pooled HUDEP2 cells.
HUDEP2 cells were differentiated for 5 days in Iscove’s Modified Dulbecco’s Medium (IMDM) supplemented with 330 μg/ml holo-transferrin, 10 μg/ml insulin, 2 units/ml heparin, 5% FBS, 3 units/ml erythropoietin, 1 μg/ml doxycycline and 1% penicillin/streptomycin.


title: UbiqTdT_ATACseq

city: New York

first: Sruti

last: Patoori

address: 85 Saint Nicholas Terrace

institute: CUNY The City College of New York

description: electroporated at E5 and cultured for one day before dissociation, cell sorting, and ATAC-seq

data_processing:
Tags from ATAC-seq primers were trimmed using FASTQ Groomer through usegalaxy.org under default parameters
Trimmed FASTQ files were aligned to chick genome using Bowtie for Illumina in usegalaxy.org under default paramters except for -X 1000 -m 1
SAM files were converted to BAM files using SAM-to-BAM in usegalaxy.org under default parameters
BAM files were converted to .bigwig files in usegalaxy.org
Peaks were called manually
Genome_build: galGal5
Supplementary_files_format_and_content: .bigwig files show chromatin accessibility along the genome

organism: Gallus gallus

source_name: Developing retinal cells

extract_protocol:
Chromatin was extracted from dissociated retinal cells using Lysis Buffer outlined by the ATAC-seq protocol from Buenrostro et al., 2013
Libraries were generated via treatment of lysate with Tn5 transposase, followed by purification and amplification with primers outlined in ATAC-seq protocol from Buenrostro et al., 2013

value: retina

tag: developmental stage

tag: fluorescent cell sorting

value: GFP-negative and TdT-positive


title: HUDEP2_ATF4KO_r2


title: Control_1hr_Replicate2 [24_1_rep2]

growth_protocol: protonemata were  cultivated axenically in petri dishes  containing PpNH4 medium  supplemented with 7g.L-1 agar in a growth chamber maintained at 24 °C under a photoperiod of 16/8 h and an irradiance of 100 µmol.m-2.s-1. Harvest at 1H.


title: ThrbCRM1GFP_ATACseq

value: GFP-positive and TdT-positive


title: AGO2-F2L3-IP-OE-miR-DIS3L2KO

value: Sigma M8823-1ML anti-FLAG M2 Magnetic Beads


title: Primary_erythroblast_ATF4-r2

data_processing:
Basecalls using bcl2fastq2 v2.15.0.4, and parameters --no-eamss --mismatches 1
Mapping to reference genome hg38 with Bowtie 1.0.0 using parameters --chunkmbs 1024 -y -n 2 --best -k 1 --maxbts 800 -l 28 -e 80 --sam-nohead --sam
Genome_build: hg38;
Supplementary_files_format_and_content: bigWig files with read coverage; bed files of peaks

growth_protocol: Human CD34+ HSPCs were cultured using a three-phase protocol. For Phase I medium, IMDM was supplemented with 100 ng/mL human SCF, 50 ng/mL IL3, 3 units/ml erythropoietin, 1% penicillin/streptomycin, 330 μg/ml holo-transferrin, 10 μg/ml insulin, 5% human A/B plasma and 2 units/ml heparin. For Phase II medium, the IL3 was withdrawn after 9 days of culture. For Phase III medium, the cells were cultured with IMDM supplemented with 3 units/ml erythropoietin, 1% penicillin/streptomycin, 330 μg/ml holo-transferrin, 10 μg/ml insulin, 5% human A/B plasma and 2 units/ml heparin.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature. Fixed cells were lysised in 1mL Cell Lysis Buffer (10mM Tris-HCl pH 8, 10mM NaCl, 0.2% NP-40/Igepal). Nuclei were collected and lysised in 1mL Nuclear Lysis Buffer (50mM Tris-HCl pH 8, 10mM EDTA pH 8, 1% SDS). Chromatin was sonicated at 4 degrees C (Epishear, Active Motif). Chromatin was incubated with antibody and then decrosslink at 65C overnight.
Libraries were prepared using TruSeq ChIP-seq Sample Preparation Kit (Part# IP-202-1012) according to Illumina's instructions.

value: Adult peripheral blood

value: CD34+ derived erythroblasts

value: Day 11

tag: chip antibody

value: ATF4 (Cell Signaling Technology, 11815S, lot 4)


title: Primary_erythroblast_ATF4-r1


title: HUDEP2_BCL11A+55KO_ATF4-r2

treatment_protocol: The ATF4 binding motif at the BCL11A +55 enhancer was disrupted using a CRISPR-Cas9-mediated approach in pooled HUDEP2 cells.

value: Immortalized Human Erythroid Progenitor

value: Erythroid cells

value: Undifferentiated