title: Knockout spermatogonia replicate 2

description: Cells were isolated from KO mouse of 6-7 dpp

source_name: Isolated spermatogonia

value: 6-7 dpp


title: NG_2

status: Public on Feb 15 2020

type: SRA

city: Jiangyin

first: Longjuan

last: Qin

state: Jiangsu

address: Sha shan road no. 85

country: China

institute: puhebio

library_source: transcriptomic

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 mm10 whole genome using bowtie v2.0.6.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene.
RPKM of each gene was aclculated based on the length of the gene and reads count mapped to this gene.
Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Mortazavi et al., 2008).
Genome_build: mm10

molecule: total RNA

organism: Mus musculus

source_name: neuron

growth_protocol: Neuron-derived spinal cord neurons were routinely cultured on complete DMEM medium.

extract_protocol:
Neuron were harvested, frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Neuron in NG-group were injured, and Hydrogen incubation on the mechanical injury neurons cells which named TG-group, while IG-group neuron without any processing.

tag: strain

value: ICR

tag: age

value: post natal day 3

tag: tissue

value: spinal cord

tag: treatment

value: neurons were injured mechanically


title: Knockout spermatogonia replicate 1

city: Beijing

first: Xiwen

last: Lin

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology,CAS

data_processing:
The sequencing reads were mapped to the mouse genome (UCSC mm9) by TopHat (v2.0.6).
The expression level of mRNAs was represented by FPKM calculated by Cufflinks (v2.0.2).
Genome_build: UCSC mm9
Supplementary_files_format_and_content: FPKM

growth_protocol: Spermatogonial stem cells were cultured in medium containing GDNF and bFGF.

extract_protocol:
Total RNA from SSCs was isolated by TRIzol.
The RNA libraries were constructed by NEBNext Ultra Directional RNA Library Prep Kit for Illumina from NEB.
High-throughput sequencing was performed on HiSeq-X10.

treatment_protocol: All cell types contain both wildtype and knockout.

tag: gender

value: Male

tag: development stage

tag: genotype

value: KO


title: IG_1

value: control


title: HEK293_Phase_Inhibition_5min_KAS-IP.rep1

city: Chicago

first: Ruitu

last: Lyu

state: IL

address: 929 E 57th Street

department: Chemistry

country: USA

institute: The University of Chicago

library_source: genomic

data_processing:
Low-quality and adapter-containing reads were trimmed from KAS-seq raw data using trim-galore package under single-end mode, reads shorter than 50 bp were removed.
Trimmed reads were aligned to reference genome (hg19 for HEK293T cells or mm10 for mESC) using bowtie2 (v2.3.3.1) under default parameters. Mapped sam files were subsequently converted and sorted to bam files using samtools sort (v1.9).
Duplicates were removed using samtools rmdup (v1.9) to get the unique mapped reads. The unique and monoclonal mapped reads were extended to 150 bp to match the average length of insert DNA fragments of the KAS-seq libraries.
Bam files were converted to bed files and bedGraph files using bedtools. BedGraph files were then converted to bigWig files using bedgraphtobigwig from UCSC pre-compiled utilities. BedGraph files were used for visualization at UCSC genome browser and bigWig files were used to calculate tag density under 50-bp resolution.
We used MACS2 to call all reported KAS-seq peaks in this manuscript. Based on the KAS-seq profile on UCSC genome browser, most KAS-seq peaks on gene body are very broad. Therefore, MACS2 was run using broad peaks-call mode under default parameters, except for --broad-cutoff 0.1 and –qvalue 0.01.
hg19&mm10
KAS-seq tag density files(bigWig)&Peaks files(bed)

molecule: genomic DNA

organism: Homo sapiens

source_name: HEK293 cells

growth_protocol: HEK293T cells were cultured in DMEM (Gibco 11995) supplemented with 10% (v/v) fetal bovine serum (Gibco), 1% penicillin and streptomycin (Gibco) and grown at 37 ˚C with 5% CO2

extract_protocol:
Cells were harvested and genomic DNA (gDNA) was isolated from cells by PureLink genomic DNA mini kit. 1 µg genomic DNA was then suspended in 95 µL DNA elution buffer supplemented with 5 µL 20 mM DBCO-PEG4-biotin (DMSO solution, Sigma, 760749), and incubated at 37 ˚C for 1.5 h with gentle shake. 5 µL RNase A (Thermo, 12091039) was added into the reaction mixture followed by an incubation at 37 ˚C for 5 min. Biotinylated gDNA was then recovered by DNA Clean & Concentrator-5 kit (Zymo). gDNA was suspended into 100 µL water and subjected to sonication by using Bioruptor Pico at 30s-on/30s-off setting for 30 cycles. 5% of the fragmented DNA was saved as input, and the rest 95% was used to enrich biotin-tagged DNA by incubating with 10 µL pre-washed Dynabeads MyOne Streptavidin C1 (Thermo, 65001) at room temperature for 15 min. The beads were washed and DNA was eluted by heating the beads in 15 µL H2O at 95 ˚C for 10 min.
Eluted DNA and its corresponding input were used for library construction by using Accel-NGS Methyl-seq DNA library kit (Swift, 30024).

treatment_protocol: Cells were incubated in completed culture medium containing 1‰ N3-kethoxal and for 5-10 min at 37 ˚C, 5% CO2.

tag: ip method or chip antibody

value: N3-kethoxal biotin IP

value: Wild type

value: Treated with 1.5% (v/v) 1,6-hexanediol (Sigma, 240117) for 5min


title: RNA2

city: Lausanne

first: Frédéric

last: Schütz

address: Batiment Amphipole

country: Switzerland

institute: Swiss Institute of Bioinformatics

description:
knockdown 1 experiment
RNA2_L6_R1_001

data_processing:
Base calling was performed using the HiSeq Control Software (version 2.2.38 for the RNA1, RNA2, RNA3, RNA4, RNA5,RNA6 samples, and version HD 3.4.0.38 for the other samples)
Alignment to the GRh38 human genome was performed using the hiSat2 aligner (2.1.0)
Abundance quantification of transcripts on input libraries was performed with Salmon (0.8.2)
Genome_build: GRh38
Supplementary_files_format_and_content: Tab-separated raw counts with Ensembl gene ID

source_name: squamous cell carcinoma

growth_protocol: SCC13 cell line were kindly provided by K. Lefort (Departement of Biochemistry, UNIL-Epalinge, Lausanne, Switzerland) and cultured like it previously reported (Lefort K et al. A miR-34a-SIRT6 axis in the squamous cell differentiation network. The EMBO journal 2013;32(16):2248-63).

extract_protocol:
Total RNA (tRNA) was extracted from cultured cells using the RNeasy Mini Kit (Qiagen, Hombrechtikon, Switzerland) according to manufacturer’s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tag

tag: condition

tag: cell type

tag: shRNA

value: shRNA-502, named H1


title: HEK293_Phase_Inhibition_5min_KAS-Input.rep2


title: Wildtype spermatogonia replicate 2

description: Cells were isolated from WT mouse of 6-7 dpp

value: WT


title: KI432_mRNA_HG16

city: Cincinnati

first: Kohta

last: Ikegami

state: OH

address: 240 Albert Sabin Way, Cincinnati, OH 45229

department: Division of Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

description:
KI429-452_GencodeBasicV19_ERCC92_PerGeneSymbolTranscript_rpkm.bed
KI429-452_GencodeBasicV19_ERCC92_PerGeneSymbolTranscript_count.bed

data_processing:
RNA-seq reads were aligned to the hg19 human reference genome using Tophat2 with the default parameter. Reads with MAPQ score greater than 50 were used in downstream analyses.
To compute RPKM (Reads Per Kilobase of transcript per Million mapped reads) for each transcribed region, the sum of perbase read coverage in exons was computed, and this was divided by the read length (50), then by the sum of the exon size in kb, and then by the total number of reads in million. In directional RNA-seq datasets, only reads whose direction matches that of the gene model were used to compute RPKM.
Genome_build: hg19
Supplementary_files_format_and_content: *_rpkm.bed: text file (with a header) listing rpkm scores (containing header). *_count.bed: text file (with a header) listing the sum of exon basecounts.

molecule: polyA RNA

growth_protocol: Cells were cultured in high-glucose DMEM (Gibco, 11965-092) containing 9% fetal bovine serum (FBS) and penicillin-streptomycin.

extract_protocol:
For non-FUCCI cells, total RNAs were purified by Trizol (Invitrogen 15596026). After DNase treatment, mRNAs were isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs E7490) and fragmented by Fragmentation Buffer (Ambion AM8740). cDNAs were synthesized using SuperScript II (Invitrogen 18064014) and used to prepare non-directional high-throughput sequencing libraries using NEBNext Ultra DNA Library Prep Kit (New England Biolabs, E7370). For non-FUCCI cells, total RNAs were purified by Trizol LS (Invitrogen 10296028). After DNase treatment, mRNAs were isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs E7490). Fragmentation, cDNA synthesis, and directional library construction were performed using NEBNext Ultra II Directional RNA Library Prep kit (New England Biolabs E7760).
For non-FUCCI cells, non-directional high-throughput sequencing libraries were prepared using NEBNext Ultra DNA Library Prep Kit (New England Biolabs, E7370). For FUCCI cells, directional libraries were prepared using NEBNext Ultra II Directional RNA Library Prep kit (New England Biolabs E7760).

treatment_protocol: In the FUCCI4 system, asynchronously cultured BJ-5ta-FUCCI cells were cultured at 50-70% density to prevent G0 entry. Cells were trypsinized and used for FACS in BD FACS Aria II (sorting IDs 2834 and 2847) or BD FACS Aria IIIu (sorting ID 2858). With FACS, mKO2-positive/Clover-negative population was sorted as G1-phase cells, mKO2-negative/Clover-positive population was sorted as G2/M-phase cells, mKO2-negative/Clover-negative population was sorted as EG1-phase cells, and mKO2-positive/Clover-positive/mTurquoise2-positive population was sorted as S-phase cells. Pre-sorting and post-sorting cells were kept in the culture medium on ice. Sorted cells were pelleted and resuspended in Trizol LS (Invitrogen 10296028) for RNA-seq.

tag: lmna genotype

value: LMNA G608G

tag: transgene

value: No

tag: cell sorting

value: No sorting


title: HEK293_Phase_Inhibition_5min_KAS-Input.rep1


title: RNA1

description:
knockdown 1 experiment
RNA1_L6_R1_001

value: control shRNA SHC2


title: mRNA seq from PancB1V knock down

city: Leuven

first: Diether

last: Lambrechts

address: Herestraat 49

department: Human Genetics

country: Belgium

institute: KU Leuven

data_processing:
Optical duplicates were removed using clumpify
Adaptors were removed using fastx_clipper
reads were mapped using Star 2.6
mapped reads were sorted with SAMtools
counts (the number of reads mapped to genes) were extracted using HTSeq
Genome_build: GRCh3
Supplementary_files_format_and_content: Tab delimited text files, raw counts

source_name: cultured cells

growth_protocol: HepG2 cell lines were cultured in William’s E medium with 10% fetal bovine serum (FBS) and 1% pencillin-streptomycin (PS, Life Technology). HCC4006 and Panc03.27 cell lines and their derivatives were cultured in RPMI 1640 glutaMAX medium supplemented with 10 % FBS and 1% PS. All cells were cultured at 37˚C, in atmospheric oxygen concentration (21%) with 5% CO2. Splitting of cells was performed using trypsin-EDTA. Cell cultures were regularly confirmed to be mycoplasm-free.

extract_protocol:
Cell culture medium was removed, cells were washed with DPBS, TRIzol (Life Technologies) was added and cells were processed according to manufacturer’s guidelines.
Around 500 ng total RNA was used as an input for QuantSeq 3' mRNA-Seq Library Prep (Lexogen). The double stranded cDNA library is made by first strand synthesis with a oligo-dT primer containing the Illumina-specific Read 2 linker and second strand synthesis with random primer containing the Illumina-specific Read 1 linker sequence. Library amplification introduces a unique i7 index for each sample and sequences required for cluster generation.

treatment_protocol: Cells were reverse transfected using RNAiMAX, either with negative control non-targeting siRNAs, or pools of siRNAs targeting all three DNMTs

tag: establishment status

value: Derived in vitro cell line

tag: resistant status

value: resistant

tag: drug

tag: reference

value: Lund et al., 2015


title: HEK293_Phase_Inhibition_0min_KAS-IP.rep2

value: Treated with 1.5% (v/v) 1,6-hexanediol (Sigma, 240117) for 0min


title: Wildtype spermatogonia replicate 1

tag: strain

value: 6-7 dpp


title: HEK293_Phase_Inhibition_0min_KAS-IP.rep1

tag: treatment


title: genomic DNA from HepG2S3_hydroxymethylation

type: genomic

description: van Malenstein et al., 2012

hyb_protocol: TAB-seq processed DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K or EPIC Beadchips using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Data processing was done using Bioconductor’s minfi package in R. Briefly, raw intensity files were read into R. Samples were normalized using Subset-quantile Within Array Normalization (SWAN).

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: Cultured cells were washed with DPBS and detached with trypsin-EDTA (0.25%) (Thermofisher). Cell pellets were obtained by centrifugation and were washed once in DPBS. Subsequently, nucleic acids were extracted using the Wizard Genomic DNA Purification kit (Promega) according to manufacturer’s instructions. All buffers were supplemented with deferoxamine (DFO, 200µM). DNA was dissolved in 80 µL PBS-DFO with RNaseA (200 U, NEB) and incubated for 10 min at 37 ˚C. Next, proteinase K (200 U) was added and the mixture was incubated for 30 min at 56˚C. DNA was purified using the QIAQuick blood and tissue kit (all buffers supplemented with DFO). Elution was performed in 100 µL of a 10 mM Tris, 1mM EDTA solution (pH 8) and stored at -20˚C until further processing

tag: cell line

value: sorafenib

tag: illumina platform_id

value: genomic DNA


title: mRNA seq from PancB1V negative conrol


title: KI430_mRNA_GM07

source_name: GM07492 normal fibroblast


title: KI531_K4me3_BJ5ta

description: K4me3_BJ5ta_macs2hg19_t529t531c307c481_fe.bw

data_processing:
ChIP-seq reads were mapped to the hg19 human reference genome using Bowtie2 with the default “--sensitive” parameter. Reads with MAPQ score greater than 20 were used in downstream analyses.
Reads from biological replicates of ChIP and corresponding input samples were used as input files for MACS2. In MACS2, duplicate reads were removed first, and then significantly enriched peak regions were called, and input-normalized perbase coverage of 200 nt-extended reads was computed (“fold enrichment bedgraph”).
Genome_build: hg19
Supplementary_files_format_and_content: Input-normalized replicate-combined fold enrichment scores computed by MACS2 in bigWig format. For input samples, depth-normalized perbase count in bigWig format.

growth_protocol: Cells were cultured in high-glucose DMEM (Gibco, 11965-092) containing 9% fetal bovine serum (FBS) and penicillin-streptomycin. Progeria-patient primary skin fibroblasts AG11498 (Coriell Cell Repository) and primary skin fibroblasts from a healthy donor GM08398 (Coriell Cell Repository) were grown in MEM Alpha (Life Technologies, 12561-056) with 9% FBS and penicillin-streptomycin.

extract_protocol:
Cells in culture dishes were crosslinked in 1% formaldehyde for 15 min and the reaction was quenched by 125 mM glycine. Cross-linked cells were washed with LB1 (50 mM HEPES-KOH pH7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100) and then with LB2 (200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, and 10 mM Tris-HCl pH 8.0). For cell-cycle-stage specific ChIP, cross-linked cells were stained by DAPI (5 µg/mL) in LB1 for 5 min at RT, sorted based on the cellular DNA content using BD FACS Aria II or BD FACS Aria IIIu, and then washed with LB2. Chromatin was extracted by sonication in LB3-Triton (1 mM EDTA, 0.5 mM EGTA, 10 mM Tris-HCl pH 8, 100 mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroyl sarcosine, 1% Triton). LB1, LB2, and LB3-Triton used during extraction were supplmented with 1x protease inhibitor cocktail (Calbiochem 539131) and 100 nM phosphatase inhibitor Nodularin (Enzo ALX-350-061).  One million cells were used in a single 200-µL ChIP reaction. Antibodies used in ChIP are: rabbit monoclonal anti-phospho-Ser22-LMNA antibody D2B2E (Cell Signaling 13448S, Lot # 1; 5 µL per IP); mouse monoclonal anti-unphospho-Ser22-LMNA antibody E1 (Santa Cruz Biotechnology sc-376248, Lot # H2812; 10 µL per IP); mouse monoclonal anti-acetyl-Lys27 histone H3 antibody (Wako MABI0309, Lot # 14007; 2 µL per IP); mouse monoclonal anti-trimethyl-Lys4 histone H3 antibody (Wako MABI14004, Lot # 14004; 2 µL per IP); mouse monoclonal anti-Ty1 antibody (Diagenode C15200054, Lot # 005; 1 µL per IP).
Immunoprecipitated DNA was reverse-crosslinked and used to construct high-throughput sequencing libraries using NEBNext Ultra DNA Library Prep Kit (New England Biolabs, E7370).

tag: antibody


title: KI530_K27ac_BJ5ta

description: K27ac_BJ5ta_macs2hg19_t530t532c307c481_fe.bw


title: mRNA seq from PancVB knock down

value: Established in vitro cell line

value: sensitive


title: KI532_K27ac_BJ5ta

value: Wild type


title: HEK293_Phase_Inhibition_0min_KAS-Input.rep2

tag: genotype


title: genomic DNA from HepG2_hydroxymethylation

description: van Malenstein et al., 2012


title: KI529_K4me3_BJ5ta


title: genomic DNA from HepG2S1_hydroxymethylation

description: van Malenstein et al., 2012


title: mRNA seq from PancVB negative conrol


title: HEK293_Phase_Inhibition_0min_KAS-Input.rep1


title: mRNA seq from HCC406ER knock down

value: erlotinib

value: Jia et al., 2013


title: genomic DNA from IGROV-1 / CDDP

description: Ma et al., 1998

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K or EPIC Beadchips using standard Illumina protocol

data_processing:
Data processing was done using Bioconductor’s minfi package in R. Briefly, raw intensity files were read into R. Samples were normalized using Subset-quantile Within Array Normalization (SWAN).
normalized data matrix includes Average SWAN normalized Beta of CpGs included on both EPIC and 450K arrays and detection P-values

extract_protocol: genomic DNA was extracted and purified from cultured cells using Qiagen DNeasy Kit according to standard instructions

value: IGROV-1 / CDDP

value: cisplatin


title: KI503_E1_LAKO

source_name: LMNA knockout cc1170-1AD2

value: LMNA null

value: No

value: anti-unphospho-Ser22-LMNA (Santa Cruz E-1 sc-376248)


title: KI429_mRNA_GM08

source_name: GM08398 normal fibroblast

value: No sorting


title: HEK293_1kcells_KAS-IP.rep2

tag: ip method or chip antibody

value: N3-kethoxal biotin IP


title: genomic DNA from IGROV-1

description: Ma et al., 1998


title: mRNA seq from HCC4006ER negative conrol

value: Derived in vitro cell line

value: resistant


title: HEK293_Phase_Inhibition_30min_Pol2_ChIP-seq.rep1

data_processing:
Trimmed reads were aligned to reference genome using bowtie2 (v2.3.3.1) under default parameters. Mapped sam files were subsequently converted and sorted to bam files using samtools sort (v1.9).
Duplicates were removed using samtools rmdup (v1.9) to get the unique mapped reads. The unique and monoclonal mapped reads were extended to 150 bp to match the average length of insert DNA fragments of the ChIP-seq libraries.
Bam files were converted to bed files and bedGraph files using bedtools. BedGraph files were then converted to bigWig files using bedgraphtobigwig from UCSC pre-compiled utilities. BedGraph files were used for visualization at UCSC genome browser and bigWig files were used to calculate tag density under 50-bp resolution.
hg19
ChIP-seq tag density files(bigWig)

extract_protocol: 5 million cells were used for all ChIP reactions. Crosslinked cells were resuspend in ice-cold lysis buffer (50 mM HEPES, pH=7.9, 5 mM MgCl2, 0.2% Triton X-100, 20% glycerol, 300 mM NaCl) and incubated on ice for 10 min before centrifuged at 500 g for 5 m

treatment_protocol: Cells were crosslinked in 1% formaldehyde diluted in culture medium for 10 min and then quenched with 125 mM glycine for 5 min.

value: Pol II(8WG16):BioLegend No. 664911

value: Treated with 1.5% (v/v) 1,6-hexanediol (Sigma, 240117) for 30min


title: genomic DNA from HCC4006ER, 2nd replicate

description: Jia et al., 2013


title: HEK293_1kcells_KAS-IP.rep1


title: KI499_E1_BJ5ta

description: E1_BJ5ta_macs2hg19_t464t499c307c481_fe.bw


title: mRNA seq from HCC4006 knock down


title: KI497_D2B2E_BJ5ta

description: D2B2E_BJ5ta_macs2hg19_t411t453t497c307c481_fe.bw

value: anti-phospho-Ser22-LMNA (Cell Signaling D2B2E 13448)


title: genomic DNA from HCC4006P1, 2nd replicate

description: Jia et al., 2013

value: Established in vitro cell line


title: HEK293_1kcells_KAS-Input.rep2


title: HEK293_1kcells_KAS-Input.rep1


title: HEK293_5kcells_KAS-IP.rep1


title: genomic DNA from HCC4006ER, 1st replicate

description: Jia et al., 2013


title: HEK293_5kcells_KAS-IP.rep2


title: KI481_Input_BJ5ta

description: KI481_Input_BJ5ta_267015_hg19_BT2q20x200n.bw


title: KI489_Input_LAKO

description: KI489_Input_LAKO_269312_hg19_BT2q20x200n.bw


title: genomic DNA from PancB1V

description: Lund et al., 2015


title: KI465_E1_LAKO


title: mRNA seq from HepG2S3 knock down

value: sorafenib

value: van Malenstein et al., 2012


title: KI501_D2B2E_LAKO


title: genomic DNA from PancB1Q

description: Lund et al., 2015


title: mRNA seq from HepG2S3 negative conrol


title: KI464_E1_BJ5ta

value: Wild type


title: mRNA seq from HepG2 knock down

value: sensitive


title: HEK293_5kcells_KAS-Input.rep2


title: genomic DNA from HCC4006P1, 1st replicate

description: Jia et al., 2013


title: mRNA seq from HepG2 negative conrol


title: HEK293_5kcells_KAS-Input.rep1


title: genomic DNA from PancVB

description: Lund et al., 2015

value: PancVB


title: HEK293_10kcells_KAS-IP.rep2


title: genomic DNA from HepG2S3

description: van Malenstein et al., 2012


title: HEK293_SP1.rep1

data_processing:
Bam files were converted to bed files and bedGraph files using bedtools. BedGraph files were then converted to bigWig files using bedgraphtobigwig from UCSC pre-compiled utilities. BedGraph files were used for visualization at UCSC genome browser and bigWig files were used to calculate tag density under 50-bp resolution.
hg19
ChIP-seq tag density files(bigWig)


title: KI454_D2B2E_LAKO


title: HEK293_10kcells_KAS-IP.rep1


title: mRNA seq from HC4006 negative conrol

value: Jia et al., 2013


title: genomic DNA from HepG2S1

description: van Malenstein et al., 2012


title: HEK293_SP1_Input.rep2

data_processing:
Low-quality and adapter-containing reads were trimmed from ChIP-seq raw data using trim-galore package under single-end mode, reads shorter than 50 bp were removed.
Trimmed reads were aligned to reference genome using bowtie2 (v2.3.3.1) under default parameters. Mapped sam files were subsequently converted and sorted to bam files using samtools sort (v1.9).
Duplicates were removed using samtools rmdup (v1.9) to get the unique mapped reads. The unique and monoclonal mapped reads were extended to 150 bp to match the average length of insert DNA fragments of the ChIP-seq libraries.
Bam files were converted to bed files and bedGraph files using bedtools. BedGraph files were then converted to bigWig files using bedgraphtobigwig from UCSC pre-compiled utilities. BedGraph files were used for visualization at UCSC genome browser and bigWig files were used to calculate tag density under 50-bp resolution.
hg19
ChIP-seq tag density files(bigWig)

extract_protocol:
5 million cells were used for all ChIP reactions. Crosslinked cells were resuspend in ice-cold lysis buffer (50 mM HEPES, pH=7.9, 5 mM MgCl2, 0.2% Triton X-100, 20% glycerol, 300 mM NaCl) and incubated on ice for 10 min before centrifuged at 500 g for 5 min. The pellets were resuspended in 0.1% SDS lysis buffer (50 mM HEPES, pH=7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, 150 mM NaCl) and incubate on ice for 10 min and then sheared by using Bioruptor Pico at 30s-on/30s-off setting for 20 cycles. 5% of sheared chromatin was saved as input and the rest was subjected to pre-clear and then mixed with 30 µL protein A/G bead coated with 5-10 µg antibodies. Immunoprecipitation was performed overnight and the beads were washed twice with 0.1% SDS lysis buffer, high salt buffer (50 mM HEPES, pH=7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 0.1% SDS, 350 mM NaCl), LiCl wash buffer (10 mM Tris-HCl, pH=8.0, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate, 250 mM LiCl) and once with TE buffer (10 mM Tris-HCl, pH=8.0, 1 mM EDTA, 0.2% Triton X-100). Enriched chromatin was eluted from the beads by incubating with elution buffer (50 mM NaHCO3, 10 mM EDTA, 1% SDS) at room temperature for 1 h. The eluent and the input were subjected to reverse crosslink and proteinase K digestion, before DNA were purified from the mixture by using DNA Clean & Concentrator-5 kit (Zymo).
Recovered DNA was used for library construction by Kapa HyperPlus kit (Kapa, KK8515).


title: HEK293_10kcells_KAS-Input.rep2


title: KI411_D2B2E_BJ5ta


title: genomic DNA from HepG2

description: van Malenstein et al., 2012


title: HEK293_SP1_Input.rep1


title: HEK293_10kcells_KAS-Input.rep1


title: KI307_Input_BJ5ta

description: KI307_Input_BJ5ta_25747_hg19_BT2q20x200n.bw


title: 35SP_Astrain_rep2

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

country: Netherlands

institute: Natl. Inst. Public Health & Environment

data_processing:
Library strategy: DNA-seq
FASTQ sequence files were generated using the Illumina Casava pipeline version 1.8.3. Initial quality assessment was based on data passing the Illumina Chastity filtering.
Reads containing PhiX control signal were removed. Reads containing (partial) adapters were clipped up to minimum read length of 50bp.
The second quality assessment was based on the remaining reads using the FASTQC quality control tool version 0.10.0.
FASTQ sequence reads were trimmed to their first 50 nucleotides, in order to limit the chance of reads mapping to more than one gene.
Trimmed read sequences were mapped to the E88 chromosome and plasmid reference sequence using bowtie2 (version 2.2.4) with default settings, after which a table with the number of counts per gene was obtained using samtools (version 1.1).
Gene count data output was further analyzed in R software (version 3.5.1).
Genome_build: NC_004557.1 (chromosome) and NC_004565.1 (plasmid)
Supplementary_files_format_and_content: Countdata.xlsx: count data per sample plus gene annotation

organism: Clostridium tetani

source_name: bacterial cells

growth_protocol: C. tetani inoculums were propagated for 48 hrs in thioglycollate media containing resazurine (Biomerieux, Craponne, France) at 35 °C.

extract_protocol:
Genomic DNA purification was performed with GenElute bacterial genomic DNA Kit (Sigma, St Louis, Missouri, USA) using standard protocol. After harvesting, cell pellets were normalized at ~10^10 cells by centrifuging enough cell suspension at 12,000 g for 5 min. Cell pellet was re-suspended in 4 x 106 UI/mL lysozyme solution (Sigma) for 30 min at 37 °C. RNase solution (Sigma) was added and incubation was done at room temperature for 2 min. Then protein digestion was done by addition of a lysis solution containing proteinase K (Sigma) C for 10 min at 55 °C. Then samples were processed for DNA isolation. Quality control of each purified DNA was performed by determining the purity by a spectrophotometer (ratio A260/A280, ratio A260/A230) and double-stranded DNA quantification by Qubit fluorimeter (Fisher Scientific, Waltham, Massachusetts, USA).
For sequencing at BaseClear, samples were used for Illumina genomic Nextera XT library preparation (including quality control and quantification), followed by Illumina HiSeq 2500 125 bp paired end sequencing. At Sanofi Pasteur, samples were processed using Illumina MiSeq equipment and reagent kits, for paired-end 250 bp paired-end sequencing.

value: Astrain

tag: lab

value: Sanofi Pasteur

tag: replicate

value: repeat 2


title: Nor-3 (mRNA)

city: Deyang

first: hong

middle: Yue

last: Liu

state: Sichuan

address: No. 173, Taishan North Road, Jingyang District

department: People’s Hospital of Deyang City

institute: Department of Orthopedics

description:
Nor-3B
mRNA_raw_count.txt

data_processing:
The clean reads were aligned with the human reference genome, Ensemble GRCh38.p7 (ftp://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens) by using TopHat release 2.2.1 (http://tophat.cbcb.umd.edu/). With Cuffquant version 2.2.1 (http://cufflinks.cbcb.umd.edu/), expression of mRNAs was normalized and outputted.
To determine the transcription abundance of mRNAs, fragments per Kilobase of exon per million fragments mapped (FPKM) was used. With Cuffdiff version 2.2.1 (http://cufflinks.cbcb.umd.edu/), FPKMs of mRNAs were calculated.
With Bowtie (bowtie-bio.sourceforge.net), the alignment between the cleaned miRNA sequencing reads was aligned to the human genome (GRCh38.p7 assembly) based on Genome human UCSC reference annotation. With miRDeep2 (https://www.mdc-berlin.de/8551903/en/), the transcription abundance of miRNAs was determined.
Based on the read count of each sample, the DEmiRNAs in OA compared to normal controls were calculated with an R-bioconductor package, DESeq2 (http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html).
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: raw counts

source_name: synovial tissues of normal controls

extract_protocol:
Following the manufacturer’s protocol, we used TRIzol reagent (Invitrogen, Carlsbad, CA, USA) to isolate total RNA from samples.
With QiaQuick PCR Purification Kit, the mRNA library was constructed.

tag: disease state

value: control

tag: tissue

value: synovial tissues


title: 32BC_Astrain_rep2

value: BaseClear


title: Nor-3 (miRNA)

description:
Nor-3B
miRNA_raw_count.txt


title: Nor-1 (miRNA)

description:
Nor-1B
miRNA_raw_count.txt


title: 36SP_Astrain_rep3

value: repeat 3


title: Nor-4 (mRNA)

description:
Nor-4A
mRNA_raw_count.txt


title: 31BC_Astrain_rep1

value: repeat 1


title: HEK293_SP1.rep2


title: KI453_D2B2E_BJ5ta

tag: lmna genotype

tag: transgene

value: No

value: No sorting


title: Nor-1 (mRNA)

description:
Nor-1B
mRNA_raw_count.txt


title: OA-8 (mRNA)

description:
OA-8A
mRNA_raw_count.txt

source_name: synovial tissues of patients with OA

value: OA


title: 14BC_ATCC454


title: OA-8 (miRNA)

description:
OA-8A
miRNA_raw_count.txt


title: OA-5 (mRNA)

description:
OA-5B
mRNA_raw_count.txt


title: OA-5 (miRNA)

description:
OA-5B
miRNA_raw_count.txt


title: 13BC_ATCC700157


title: OA-3 (mRNA)

description:
OA-3B
mRNA_raw_count.txt


title: Nor-4 (miRNA)

description:
Nor-4A
miRNA_raw_count.txt


title: OA-2 (mRNA)

description:
OA-2B
mRNA_raw_count.txt


title: 33BC_Astrain_rep3


title: 12BC_ATCC19406


title: OA-2 (miRNA)

description:
OA-2B
miRNA_raw_count.txt


title: 21SP_Astrain


title: 34SP_Astrain_rep1


title: 24SP_ATCC454


title: OA-1 (mRNA)

description:
OA-1B
mRNA_raw_count.txt


title: 11BC_Astrain


title: OA-1 (miRNA)

description:
OA-1B
miRNA_raw_count.txt


title: OA-3 (miRNA)

description:
OA-3B
miRNA_raw_count.txt


title: 22SP_ATCC19406


title: Responder4

status: Public on Feb 14 2020

city: SOUTH SAN FRANCISCO

first: Kobe

last: Yuen

state: California

address: 1 DNA WAY

department: Oncology Biomarker Development

institute: Genentech

data_processing:
Illumina base call (BCL) files converted to FASTQ using "cellranger mkfastq". Expression data processed with "cellranger count" using a custom reference package of 30,727 genes from RefSeq gene models
Genome_build: hg38
Supplementary_files_format_and_content: Cellranger version 2.2.0

source_name: Peripheral blood mononuclear cells

growth_protocol: Baseline PBMC samples were used. No further cell culture was performed.

extract_protocol:
Frozen PBMC samples containing at least 1 million cells were thawed for 1 minute at 37°C and washed twice with RPMI complete media (RPMI containing 10% fetal bovine serum with 2 mM L-glutamine and Pen/Strep). Samples with >50% red blood cells were treated with RBC Lysis buffer for 3 minutes at RT to remove red blood cells and then washed one more time with RPMI complete media. The cell density and viability of the single-cell suspension were then determined by Vi-CELL XR cell counter (Beckman Coulter, Pasadena, CA). All of the samples had >80% viable cells. Sample processing for single-cell RNA-seq was done using Chromium Single Cell 3’ Library and Gel bead kit v2 following the manufacturer’s user guide (10x Genomics)
The total cell density was used to impute the volume of single cell suspension needed in the reverse transcription (RT) master mix, aiming to achieve ~ 6,000 cells per sample. cDNAs and libraries were prepared following the manufacturer’s user guide (10x Genomics). cDNA amplification and indexed libraries were prepared using 12 and 14 cycles of PCR, respectively.

treatment_protocol: No treatment was performed.

tag: patient

tag: Sex

value: Female

tag: response

value: Responder


title: Responder1


title: Responder2

value: Male


title: NonResponder4

value: Nonresponder


title: Responder3


title: NonResponder3


title: NonResponder5


title: NonResponder1


title: Responder5


title: NonResponder2


title: MCF-7 rep3_RNA-seq

city: indianapolis

first: siwen

last: xu

state: IN

address: 410 W 10th St

department: School of Medicine

institute: Indiana University

description: RNA 1

data_processing:
For ATAC-seq footprinting analysis, all of the read start sites were adjusted to represent the center of the transposon binding event; reads aligning to the forward strand were offset by +4 bp and reads aligning to the reverse strand were offset by -5 bp (Buenrostro et al., 2013). MACS2 (Feng et al., 2011) was used with default parameters to identify all ATAC-seq peaks. Since ATAC-seq also detects nucleosome positions in the genome, we exempted such regions (total number of cutting sites in each peak < 200) from downstream analysis.
Heterozygous SNPs were identified using SAMtools-1.6 and bcftools-1.6 with the parameters mpileup -uf and view -Nvcg, respectively (Li et al., 2009). SNPs were further filtered by vcffilter with the parameter DP > 10 & MQ > 20 (Erik, 2016). In each open chromatin region, we used FIMO (Grant et al., 2011) to recognize potential TF binding sites from both reference and alternative alleles. Lastly, we used BEDTools IntersectBed (Quinlan and Hall, 2010) to merge the loci of heterozygous variants and potential TF binding sites. The set of TF binding sites intersecting SNPs were regarded as potential allele-specific TF binding sites.
Genome_build: hg19
Supplementary_files_format_and_content: ATAC-seq peaks, RNA-seq counts

source_name: MCF-7 breast cancer cells

extract_protocol: Standard methods were used for RNA-seq library construction, EZBead preparation, and sequencing, based on the Life Technologies SOLiD 5500xl system. Briefly, 2 μg of total RNA per sample was used for library preparation. The rRNA was first depleted using the standard protocol of RiboMinus Eukaryote Kit for RNA-Seq (Ambion), and rRNA-depleted RNA was concentrated using a PureLink RNA Micro Kit (Invitrogen). Whole transcriptome libraries were prepared and individually barcoded using the the SOLiD Total RNA-seq kit (Life Technologies). Each barcoded library was quantified by quantitative polymerase chain reaction (qPCR) using SOLiD Library Taqman qPCR Module (Life Technologies) and pooled in equal molarity. EZBead preparation, bead library amplification, and bead enrichment were then conducted using the EZ Bead E80 System (Life Technologies). Finally, sequencing by ligation was performed using a standard single-read, 5’-3’ strand-specific sequencing procedure (75 nt-read) on a SOLiD 5500xl instrument.

tag: cell type

value: MCF-7 breast cancer cells


title: MCF-7 rep2_RNA-seq

description: RNA 1


title: MCF-7 rep4_RNA-seq

description: RNA 2


title: MCF-7 rep1_RNA-seq

description: RNA 1


title: MCF-7 rep6_RNA-seq

description: RNA 2


title: HUVEC_controlKD_RNAseq2

city: Worcester

first: Nathan

middle: D.

last: Lawson

state: MA

address: 364 Plantation Street

department: Molecular, Cell, and Cancer Biology

institute: University of Massachusetts Medical School

description:
NR2F2kd_RNAseqForGEO.txt
TRC-NS-2

data_processing:
basecalls were made with standard Illumina pipeline for indicated instrument
for ChIPSeq and Cut&Run, reads were aligned to hg19 using Bowtie2
peak-calling was performed using MACS or MACS2
for RNA-seq, reads were mapped to ENSEMBL annotated transcripts using Tophat2 and differentially expressed genes were identified using EdgeR
Genome_build: hg19
Supplementary_files_format_and_content: big wig and bed files

source_name: venous endothelial cells

growth_protocol: Umbilical cords were collected from UMass Memorial Medical Center and washed with phosphate-buffered saline (PBS) to remove excessive blood. For HUVEC isolation, the vein was cannulated at one end and perfused with 0.1% type 2 collagenase in PBS (Worthington Biochemical), then clamped at both ends, wrapped in aluminum foil and placed in a humidified incubator for 20 minutes at 37°C. Endothelial cells were collected by flushing collagenase solution through the vein with ECCM (EGM Endothelial Cell Growth Medium with SingleQuots Supplement, Lonza).  Cells were centrifuged and re-suspended in ECCM, seeded in 0.2% gelatin-coated flasks and allowed to attach overnight at in a humidified incubator (37°C, 5% CO2).  Medium was replaced the following day to remove erythrocytes and cells were grown to confluence (2-3 days).  The same cords were used for HUAEC isolation by dissecting out arteries, which were washed twice with PBS and perfused with 0.05% Collagenase using a 20-gauge needle (Fisher) attached to a 20 ml syringe. Arteries were clamped on both ends, placed in a beaker containing PBS and incubated for 20 minutes in a 37°C water bath.  Detached endothelial cells were collected by flushing the collagenase with EC complete medium followed by centrifugation. For passaging, cells were re-suspended in ECCM and grown for 3-4 days, or until ~80% confluence.

extract_protocol:
mRNA was isolated using the NEB PolyA mRNA magnetic bead isolation module
RNA-seq libraries were constructed as described in the NEB Poly(A) mRNA magnetic isolation module (#E7490S) and NEB RNA-Seq Library Prep Reagent Set for Illumina (#E6100 L), using mRNA isolated from 5 μg of total RNA with NEB magnetic Oligo d(T)25 beads. In all cases, library quality and concentration were determined using an Agilent bioanalyzer (UMass Medical School Deep Sequencing Core)

treatment_protocol: HUAEC and HUVEC were used prior to passage 3; for knockdown experiments, HUVEC were transduced with lentiviral vectors expressing a control shRNA or an shRNA targeting NR2F2

value: HUVEC

tag: passage

value: control KD

tag: chip antibody


title: HUVEC_NR2F2KD_RNAseq3

description:
NR2F2kd_RNAseqForGEO.txt
shNR2F2-3

value: NR2F2 KD


title: HUVEC_controlKD_RNAseq1

description:
NR2F2kd_RNAseqForGEO.txt
TRC-NS-1


title: HUVEC_controlKD_RNAseq3

description:
NR2F2kd_RNAseqForGEO.txt
TRC-NS-3


title: HUVEC_NR2F2KD_RNAseq2

description:
NR2F2kd_RNAseqForGEO.txt
shNR2F2-2


title: HUVEC_NR2F2KD_RNAseq1

description:
NR2F2kd_RNAseqForGEO.txt
shNR2F2-1


title: HUVEC_K27acTRC-NS_rep2

extract_protocol:
For ChIP-seq, DNA was extracted using phenol-chloroform followed by ethanol precipitation and quantified using Qubit Fluorometric Quantitation assay
ChIP-Seq libraries were constructed using NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (New England Biolabs) with 50-100 ng of ChIP DNA according to manufacturer's protocol. In all cases, library quality and concentration were determined using an Agilent bioanalyzer (UMass Medical School Deep Sequencing Core)

value: TRC-NS (control shRNA)

value: H3K27ac (Abcam, catalog number ab4729)


title: HUVEC_K27acTRC-NS_rep1


title: HUVEC_input_K27acTRC-NS_rep3

value: none (input)


title: HUVEC_input_K27acTRC-NS_rep2


title: HUVEC_K27acTRC-NS_rep3


title: MCF-7 rep5_RNA-seq

description: RNA 2


title: HUVEC_input_K27acTRC-NS_rep1


title: HUVEC_K27acNR2F2kd_rep3


title: HUVEC_K27acNR2F2kd_rep2


title: HUVEC_K27acNR2F2kd_rep1


title: HUVEC_input_K27acNR2F2kd_rep1


title: HUVEC_input_K27acNR2F2kd_rep3


title: HUVEC_input_K27acNR2F2kd_rep2


title: Bmal1-/- CT12 37C

city: Philadelphia

first: Utham Kashyap

last: Valekunja

state: PA

address: 3400 Civic Center Boulevard,

department: Department of Systems Pharmacology & Therapeutics, Perelman School of Medicine,

institute: University of Pennsylvania

data_processing:
A TopHat-Cuffdiff pipeline was used to analyse the sequencing reads [Trapnell et al. Nat. Biotechnol. 2013].
Sequence reads were aligned to the Ensembl built mouse reference genome (GRCm38) using TopHat version 2.1.0 [Kim et al. Genome Biol.  2013].
FPKM values were computed with Cuffdiff, normalized via the median of the geometric means of fragment counts across all libraries as available in Cuffdiff package [Anders and Huber, Genome Biol. 2010].
Genome_build: GRCm38
Supplementary_files_format_and_content: FPKM

source_name: mouse skin fibroblast

growth_protocol: Wild-type and Bmal1-/- MSF cells were grown in Dulbecco’s Modified Eagle Medium (DMEM) containing 10% (v/v) HyClone III Serum (Analab; Cat # SH30109.03), 1/100  Glutamax-I (Invitrogen; Cat # 35050-038), 1/100 Penicillin-Streptomycin (SIGMA; Cat # P4333) and 1/500 MycoZap™ (Lonza; Cat # VZA-2022) in multiple six-well plates until complete confluency (n=3, per time-point, per genotype).

extract_protocol:
Wild-type and Bmal1-/- MSF cells time-course samples were lysed in TRI-Reagent® and Direct-zol™ RNA MiniPrep kit was used for RNA extraction following the manufacturer's instructions (Zymo Research; Cat # R2052).
mRNA contents in those samples were enriched using a NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB; Cat # E7490). The enriched mRNA samples were subjected to an Illumina TrueSeq platform compatible multiplex library preparation protocol using KAPA Stranded RNA-Seq Library Preparation Kit (Kapa Biosystems; Cat # KK8401) and libraries were prepared with TruSeq LT index adapter.

treatment_protocol: The confluent MSF cells were treated with 100nM (final concentration) of dexamethasone (DEX) for 15 min to synchronize the cells [Balsalobre et al. Science 2000]. MSF cells were then washed three times with PBS (37°C) and were incubated in HEPES-buffered Medium at 37°C or 32°C or 27°C.

tag: genotype/variation

tag: circadian clock

tag: temperature

tag: strain

value: mouse skin fibroblast

tag: age

value: not applicable


title: Bmal1-/- CT22 37C


title: Bmal1-/- CT14 37C


title: Bmal1-/- CT30 37C


title: Bmal1-/- CT18 37C


title: Bmal1-/- CT38 37C


title: Bmal1-/- CT28 37C


title: Bmal1-/- CT32 37C


title: Bmal1-/- CT24 37C


title: Bmal1-/- CT20 37C


title: Bmal1-/- CT26 37C


title: Bmal1-/- CT16 37C


title: Bmal1-/- CT36 37C


title: Bmal1-/- CT34 37C


title: Bmal1-/- CT46 37C


title: Bmal1-/- CT44 37C


title: Bmal1-/- CT40 37C


title: Bmal1-/- CT42 37C


title: Bmal1-/- CT10 37C


title: Bmal1-/- CT06 37C


title: Bmal1-/- CT08 37C


title: Bmal1-/- CT04 37C


title: Bmal1-/- CT00 37C


title: Bmal1-/- CT02 37C


title: WT CT46 37C

value: WT


title: WT CT44 37C


title: WT CT42 37C


title: WT CT38 37C


title: WT CT40 37C


title: 23SP_ATCC7000157

tag: lab

value: Sanofi Pasteur


title: WT CT12 37C


title: WT CT22 37C


title: WT CT30 37C


title: WT CT18 37C


title: WT CT32 37C


title: WT CT20 37C


title: WT CT26 37C


title: WT CT36 37C


title: WT CT28 37C


title: WT CT14 37C


title: Bmal1-/- CT46 32C


title: WT CT24 37C


title: WT CT08 37C


title: WT CT06 37C


title: WT CT16 37C


title: WT CT10 37C


title: Bmal1-/- CT44 32C


title: WT CT02 37C


title: Bmal1-/- CT40 32C


title: Bmal1-/- CT42 32C


title: Bmal1-/- CT38 32C


title: Bmal1-/- CT36 32C


title: Bmal1-/- CT34 32C


title: Bmal1-/- CT32 32C


title: Bmal1-/- CT28 32C


title: Bmal1-/- CT30 32C


title: Bmal1-/- CT26 32C


title: WT CT34 37C


title: WT CT04 37C


title: WT CT00 37C


title: Bmal1-/- CT20 32C


title: Bmal1-/- CT16 32C


title: Bmal1-/- CT12 32C


title: Bmal1-/- CT14 32C


title: Bmal1-/- CT06 32C


title: WT CT46 32C


title: WT CT44 32C


title: Bmal1-/- CT02 32C


title: Bmal1-/- CT18 32C


title: Bmal1-/- CT22 32C


title: WT CT36 32C


title: WT CT38 32C


title: WT CT42 32C


title: Bmal1-/- CT04 32C


title: Bmal1-/- CT10 32C


title: Bmal1-/- CT00 32C


title: WT CT26 32C


title: WT CT30 32C


title: WT CT28 32C


title: WT CT34 32C


title: WT CT32 32C


title: WT CT22 32C


title: WT CT20 32C


title: WT CT18 32C


title: WT CT16 32C


title: WT CT14 32C


title: WT CT08 32C


title: WT CT10 32C


title: WT CT06 32C


title: WT CT04 32C


title: Bmal1-/- CT40 27C


title: Bmal1-/- CT42 27C


title: Bmal1-/- CT44 27C


title: Bmal1-/- CT32 27C


title: Bmal1-/- CT34 27C


title: Bmal1-/- CT30 27C


title: Bmal1-/- CT24 27C


title: Bmal1-/- CT26 27C


title: Bmal1-/- CT28 27C


title: Bmal1-/- CT20 27C


title: Bmal1-/- CT22 27C


title: Bmal1-/- CT14 27C


title: Bmal1-/- CT12 27C


title: Bmal1-/- CT10 27C


title: WT CT00 32C


title: Bmal1-/- CT46 27C


title: WT CT02 32C


title: Bmal1-/- CT02 27C


title: Bmal1-/- CT04 27C


title: Bmal1-/- CT00 27C


title: WT CT46 27C


title: Bmal1-/- CT06 27C


title: WT CT42 27C


title: Bmal1-/- CT24 32C


title: Bmal1-/- CT16 27C


title: WT CT38 27C


title: WT CT36 27C


title: WT CT34 27C


title: WT CT32 27C


title: WT CT30 27C


title: Bmal1-/- CT36 27C


title: WT CT12 32C


title: Bmal1-/- CT18 27C


title: WT CT28 27C


title: WT CT24 27C


title: WT CT22 27C


title: WT CT20 27C


title: WT CT40 32C


title: WT CT18 27C


title: WT CT16 27C


title: Bmal1-/- CT08 27C


title: WT CT40 27C


title: WT CT44 27C


title: WT CT26 27C


title: WT CT14 27C


title: WT CT10 27C


title: WT CT12 27C


title: WT CT06 27C


title: WT CT02 27C


title: WT CT00 27C


title: WT CT08 27C


title: Bmal1-/- CT45 PM

value: CT45 PM


title: Bmal1-/- CT48 PM

value: CT48 PM


title: Bmal1-/- CT33 PM

value: CT33 PM


title: Bmal1-/- CT24 PM

value: CT24 PM


title: Bmal1-/- CT27 PM

value: CT27 PM


title: Bmal1-/- CT39 PM

value: CT39 PM


title: Bmal1-/- CT36 PM

value: CT36 PM


title: Bmal1-/- CT42 PM

value: CT42 PM


title: Bmal1-/- CT21 PM

value: CT21 PM


title: Bmal1-/- CT18 PM

value: CT18 PM


title: Bmal1-/- CT09 PM

value: CT09 PM


title: Bmal1-/- CT15 PM

value: CT15 PM


title: Bmal1-/- CT12 PM

value: CT12 PM


title: Bmal1-/- CT06 PM

value: CT06 PM

value: mouse skin fibroblast


title: WT CT48 PM

value: WT

value: not applicable


title: Bmal1-/- CT03 PM

value: CT03 PM


title: Bmal1-/- CT00 PM

value: CT00 PM


title: WT CT45 PM

value: CT45 PM


title: WT CT42 PM


title: WT CT04 27C


title: WT CT39 PM


title: WT CT33 PM

value: CT33 PM


title: WT CT30 PM

value: CT30 PM


title: WT CT36 PM


title: WT CT27 PM

value: CT27 PM


title: Bmal1-/- CT30 PM


title: WT CT12 PM


title: WT CT15 PM


title: WT CT00 PM


title: WT CT03 PM


title: WT CT06 PM


title: Bmal1-/- CT48 AM

value: CT48 AM


title: Bmal1-/- CT45 AM

value: CT45 AM


title: Bmal1-/- CT38 27C


title: Bmal1-/- CT42 AM

value: CT42 AM


title: Bmal1-/- CT36 AM

value: CT36 AM


title: Bmal1-/- CT39 AM

value: CT39 AM


title: Bmal1-/- CT33 AM

value: CT33 AM


title: Bmal1-/- CT24 AM

value: CT24 AM


title: Bmal1-/- CT27 AM

value: CT27 AM


title: Bmal1-/- CT30 AM

value: CT30 AM

value: mouse skin fibroblast


title: Bmal1-/- CT21 AM

value: CT21 AM

value: not applicable


title: Bmal1-/- CT18 AM

value: CT18 AM


title: Bmal1-/- CT08 32C


title: WT CT24 PM

value: WT

value: CT24 PM


title: Bmal1-/- CT15 AM

value: CT15 AM


title: Bmal1-/- CT12 AM

value: CT12 AM


title: Bmal1-/- CT09 AM

value: CT09 AM


title: WT CT21 PM

value: CT21 PM


title: Bmal1-/- CT06 AM

value: CT06 AM


title: Bmal1-/- CT03 AM

value: CT03 AM


title: WT CT18 PM

value: CT18 PM


title: WT CT09 PM

value: CT09 PM


title: WT CT48 AM

value: CT48 AM


title: Bmal1-/- CT00 AM

value: CT00 AM


title: WT CT24 32C


title: WT CT45 AM

value: CT45 AM


title: WT CT39 AM

value: CT39 AM

value: mouse skin fibroblast


title: WT CT42 AM

value: CT42 AM

value: not applicable


title: WT CT27 AM

value: WT

value: CT27 AM


title: WT CT30 AM

value: CT30 AM


title: WT CT18 AM

value: CT18 AM


title: WT CT15 AM

value: CT15 AM


title: WT CT24 AM

value: CT24 AM


title: WT CT21 AM

value: CT21 AM


title: WT CT36 AM

value: CT36 AM


title: WT CT33 AM

value: CT33 AM


title: WT CT12 AM

value: CT12 AM


title: WT CT06 AM

value: CT06 AM


title: WT CT03 AM

value: CT03 AM


title: WT CT00 AM

value: CT00 AM


title: WT CT09 AM

value: CT09 AM


title: WT MSF CT69 run2

description:
mRNA_Seq,50bpSE
SLX-11124.A027.HFCCCBBXX.s_3.r

source_name: WT MSF CT69

growth_protocol: Wild-type and Bmal1-/- MSF cells were grown in Dulbecco’s Modified Eagle Medium (DMEM) containing 10% (v/v) HyClone III Serum (Analab; Cat # SH30109.03), 1/100  Glutamax-I (Invitrogen; Cat # 35050-038), 1/100 Penicillin-Streptomycin (SIGMA; Cat # P4333) and 1/500 MycoZap™ (Lonza; Cat # VZA-2022) in multiple six-well plates until complete confluency (n=3, per time-point, per genotype). Wild-type and Bmal1-/-  mice liver tissues were sliced in small pieces (~500 micron) and were placed on membrane discs in multiple 24 well plates (n=3, per time-point, per genotype).

extract_protocol:
Wild-type and Bmal1-/- MSF cells and mice liver tissue time-course samples were lysed in TRI-Reagent® and Direct-zol™ RNA MiniPrep kit was used for RNA extraction following the manufacturer's instructions (Zymo Research; Cat # R2052).
mRNA contents in those samples were enriched using a NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB; Cat # E7490). The enriched mRNA samples were subjected to an Illumina TrueSeq platform compatible multiplex library preparation protocol using KAPA Stranded RNA-Seq Library Preparation Kit (Kapa Biosystems; Cat # KK8401) and libraries were prepared with TruSeq LT index adapter.

treatment_protocol: The confluent MSF cells and mice liver tissue slices were treated with 100nM (final concentration) of dexamethasone (DEX) for 15 min to synchronize the cells/tissues [Balsalobre et al. Science 2000]. MSF cells/liver tissue slices were then washed three times with PBS (37°C) and were incubated in HEPES-buffered Medium

tag: strain background

value: mouse skin fibroblast

tag: time point


title: WT MSF CT60 run2

description:
mRNA_Seq,50bpSE
SLX-11124.A022.HFCCCBBXX.s_3.r

source_name: WT MSF CT60

tag: tissue


title: WT MSF CT63 run1

description:
mRNA_Seq,50bpSE
SLX-11124.A023.HFCCCBBXX.s_2.r

source_name: WT MSF CT63


title: WT MSF CT60 run3

description:
mRNA_Seq,50bpSE
SLX-11124.A022.HFCCCBBXX.s_4.r


title: WT MSF CT66 run2

description:
mRNA_Seq,50bpSE
SLX-11124.A025.HFCCCBBXX.s_3.r

source_name: WT MSF CT66


title: WT MSF CT66 run1

description:
mRNA_Seq,50bpSE
SLX-11124.A025.HFCCCBBXX.s_2.r


title: WT MSF CT63 run3

description:
mRNA_Seq,50bpSE
SLX-11124.A023.HFCCCBBXX.s_4.r


title: WT MSF CT69 run3

description:
mRNA_Seq,50bpSE
SLX-11124.A027.HFCCCBBXX.s_4.r


title: WT MSF CT57 run1

description:
mRNA_Seq,50bpSE
SLX-11124.A021.HFCCCBBXX.s_2.r

source_name: WT MSF CT57


title: WT MSF CT57 run2

description:
mRNA_Seq,50bpSE
SLX-11124.A021.HFCCCBBXX.s_3.r


title: WT MSF CT69 run1

description:
mRNA_Seq,50bpSE
SLX-11124.A027.HFCCCBBXX.s_2.r


title: WT MSF CT57 run3

description:
mRNA_Seq,50bpSE
SLX-11124.A021.HFCCCBBXX.s_4.r


title: WT MSF CT60 run1

description:
mRNA_Seq,50bpSE
SLX-11124.A022.HFCCCBBXX.s_2.r


title: WT MSF CT66 run3

description:
mRNA_Seq,50bpSE
SLX-11124.A025.HFCCCBBXX.s_4.r


title: WT MSF CT51 run3

description:
mRNA_Seq,50bpSE
SLX-11124.A011.HFCCCBBXX.s_4.r

source_name: WT MSF CT51


title: WT MSF CT51 run2

description:
mRNA_Seq,50bpSE
SLX-11124.A011.HFCCCBBXX.s_3.r


title: WT MSF CT54 run2

description:
mRNA_Seq,50bpSE
SLX-11124.A020.HFCCCBBXX.s_3.r

source_name: WT MSF CT54


title: WT MSF CT48 run3

description:
mRNA_Seq,50bpSE
SLX-11124.A010.HFCCCBBXX.s_4.r

source_name: WT MSF CT48


title: WT MSF CT51 run1

description:
mRNA_Seq,50bpSE
SLX-11124.A011.HFCCCBBXX.s_2.r


title: WT MSF CT54 run1

description:
mRNA_Seq,50bpSE
SLX-11124.A020.HFCCCBBXX.s_2.r


title: WT MSF CT48 run2

description:
mRNA_Seq,50bpSE
SLX-11124.A010.HFCCCBBXX.s_3.r


title: WT MSF CT48 run1

description:
mRNA_Seq,50bpSE
SLX-11124.A010.HFCCCBBXX.s_2.r


title: WT MSF CT45 run2

description:
mRNA_Seq,50bpSE
SLX-11124.A009.HFCCCBBXX.s_3.r

source_name: WT MSF CT45


title: WT MSF CT45 run1

description:
mRNA_Seq,50bpSE
SLX-11124.A009.HFCCCBBXX.s_2.r


title: WT MSF CT42 run2

description:
mRNA_Seq,50bpSE
SLX-11124.A008.HFCCCBBXX.s_3.r

source_name: WT MSF CT42


title: WT MSF CT63 run2

description:
mRNA_Seq,50bpSE
SLX-11124.A023.HFCCCBBXX.s_3.r


title: WT MSF CT42 run3

description:
mRNA_Seq,50bpSE
SLX-11124.A008.HFCCCBBXX.s_4.r


title: WT MSF CT42 run1

description:
mRNA_Seq,50bpSE
SLX-11124.A008.HFCCCBBXX.s_2.r


title: WT MSF CT54 run3

description:
mRNA_Seq,50bpSE
SLX-11124.A020.HFCCCBBXX.s_4.r


title: WT MSF CT39 run2

description:
mRNA_Seq,50bpSE
SLX-11124.A003.HFCCCBBXX.s_3.r

source_name: WT MSF CT39


title: WT MSF CT33 run1

description:
mRNA_Seq,50bpSE
SLX-11124.A019.HFCCCBBXX.s_2.r

source_name: WT MSF CT33


title: WT MSF CT36 run3

description:
mRNA_Seq,50bpSE
SLX-11124.A001.HFCCCBBXX.s_4.r

source_name: WT MSF CT36


title: WT MSF CT33 run3

description:
mRNA_Seq,50bpSE
SLX-11124.A019.HFCCCBBXX.s_4.r


title: WT MSF CT45 run3

description:
mRNA_Seq,50bpSE
SLX-11124.A009.HFCCCBBXX.s_4.r


title: WT MSF CT39 run3

description:
mRNA_Seq,50bpSE
SLX-11124.A003.HFCCCBBXX.s_4.r


title: WT MSF CT30 run2

description:
mRNA_Seq,50bpSE
SLX-11124.A018.HFCCCBBXX.s_3.r

source_name: WT MSF CT30


title: WT MSF CT27 run1

description:
mRNA_Seq,50bpSE
SLX-11124.A016.HFCCCBBXX.s_2.r

source_name: WT MSF CT27


title: WT MSF CT27 run2

description:
mRNA_Seq,50bpSE
SLX-11124.A016.HFCCCBBXX.s_3.r


title: WT MSF CT21 run1

description:
mRNA_Seq,50bpSE
SLX-11124.A014.HFCCCBBXX.s_2.r

source_name: WT MSF CT21


title: WT MSF CT30 run1

description:
mRNA_Seq,50bpSE
SLX-11124.A018.HFCCCBBXX.s_2.r


title: WT MSF CT18 run2

description:
mRNA_Seq,50bpSE
SLX-11124.A013.HFCCCBBXX.s_3.r

source_name: WT MSF CT18


title: WT MSF CT21 run2

description:
mRNA_Seq,50bpSE
SLX-11124.A014.HFCCCBBXX.s_3.r


title: WT MSF CT21 run3

description:
mRNA_Seq,50bpSE
SLX-11124.A014.HFCCCBBXX.s_4.r


title: WT MSF CT27 run3

description:
mRNA_Seq,50bpSE
SLX-11124.A016.HFCCCBBXX.s_4.r


title: WT MSF CT18 run1

description:
mRNA_Seq,50bpSE
SLX-11124.A013.HFCCCBBXX.s_2.r


title: WT MSF CT24 run1

description:
mRNA_Seq,50bpSE
SLX-11124.A015.HFCCCBBXX.s_2.r

source_name: WT MSF CT24


title: WT MSF CT15 run2

description:
mRNA_Seq,50bpSE
SLX-11124.A012.HFCCCBBXX.s_3.r

source_name: WT MSF CT15


title: WT MSF CT15 run3

description:
mRNA_Seq,50bpSE
SLX-11124.A012.HFCCCBBXX.s_4.r


title: WT MSF CT15 run1

description:
mRNA_Seq,50bpSE
SLX-11124.A012.HFCCCBBXX.s_2.r


title: WT MSF CT39 run1

description:
mRNA_Seq,50bpSE
SLX-11124.A003.HFCCCBBXX.s_2.r


title: WT MSF CT36 run2

description:
mRNA_Seq,50bpSE
SLX-11124.A001.HFCCCBBXX.s_3.r


title: WT MSF CT33 run2

description:
mRNA_Seq,50bpSE
SLX-11124.A019.HFCCCBBXX.s_3.r


title: WT MSF CT30 run3

description:
mRNA_Seq,50bpSE
SLX-11124.A018.HFCCCBBXX.s_4.r


title: WT MSF CT36 run1

description:
mRNA_Seq,50bpSE
SLX-11124.A001.HFCCCBBXX.s_2.r


title: WT MSF CT12 run2

description:
mRNA_Seq,50bpSE
SLX-11124.A007.HFCCCBBXX.s_3.r

source_name: WT MSF CT12


title: WT MSF CT24 run2

description:
mRNA_Seq,50bpSE
SLX-11124.A015.HFCCCBBXX.s_3.r


title: WT MSF CT12 run1

description:
mRNA_Seq,50bpSE
SLX-11124.A007.HFCCCBBXX.s_2.r


title: WT MSF CT24 run3

description:
mRNA_Seq,50bpSE
SLX-11124.A015.HFCCCBBXX.s_4.r


title: WT MSF CT09 run2

description:
mRNA_Seq,50bpSE
SLX-11124.A006.HFCCCBBXX.s_3.r

source_name: WT MSF CT09


title: WT MSF CT18 run3

description:
mRNA_Seq,50bpSE
SLX-11124.A013.HFCCCBBXX.s_4.r


title: WT MSF CT09 run1

description:
mRNA_Seq,50bpSE
SLX-11124.A006.HFCCCBBXX.s_2.r


title: WT MSF CT06 run3

description:
mRNA_Seq,50bpSE
SLX-11124.A005.HFCCCBBXX.s_4.r

source_name: WT MSF CT06


title: WT MSF CT06 run1

description:
mRNA_Seq,50bpSE
SLX-11124.A005.HFCCCBBXX.s_2.r


title: WT MSF CT06 run2

description:
mRNA_Seq,50bpSE
SLX-11124.A005.HFCCCBBXX.s_3.r


title: WT MSF CT03 run2

description:
mRNA_Seq,50bpSE
SLX-11124.A004.HFCCCBBXX.s_3.r

source_name: WT MSF CT03


title: WT MSF CT03 run3

description:
mRNA_Seq,50bpSE
SLX-11124.A004.HFCCCBBXX.s_4.r


title: WT MSF CT00 run3

description:
mRNA_Seq,50bpSE
SLX-11124.A002.HFCCCBBXX.s_4.r

source_name: WT MSF CT00


title: WT MSF CT00 run2

description:
mRNA_Seq,50bpSE
SLX-11124.A002.HFCCCBBXX.s_3.r


title: WT MSF CT03 run1

description:
mRNA_Seq,50bpSE
SLX-11124.A004.HFCCCBBXX.s_2.r


title: WT MSF CT00 run1

description:
mRNA_Seq,50bpSE
SLX-11124.A002.HFCCCBBXX.s_2.r


title: Bmal1-/- MSF CT69 run3

description:
mRNA_Seq,50bpSE
SLX-11126.A027.HFCCCBBXX.s_7.r

source_name: Bmal1-/- MSF CT69


title: Bmal1-/- MSF CT69 run2

description:
mRNA_Seq,50bpSE
SLX-11126.A027.HFCCCBBXX.s_6.r


title: Bmal1-/- MSF CT66 run3

description:
mRNA_Seq,50bpSE
SLX-11126.A025.HFCCCBBXX.s_7.r

source_name: Bmal1-/- MSF CT66


title: Bmal1-/- MSF CT69 run1

description:
mRNA_Seq,50bpSE
SLX-11126.A027.HFCCCBBXX.s_5.r


title: WT MSF CT12 run3

description:
mRNA_Seq,50bpSE
SLX-11124.A007.HFCCCBBXX.s_4.r


title: Bmal1-/- MSF CT66 run1

description:
mRNA_Seq,50bpSE
SLX-11126.A025.HFCCCBBXX.s_5.r


title: Bmal1-/- MSF CT66 run2

description:
mRNA_Seq,50bpSE
SLX-11126.A025.HFCCCBBXX.s_6.r


title: Bmal1-/- MSF CT63 run3

description:
mRNA_Seq,50bpSE
SLX-11126.A023.HFCCCBBXX.s_7.r

source_name: Bmal1-/- MSF CT63


title: Bmal1-/- MSF CT63 run1

description:
mRNA_Seq,50bpSE
SLX-11126.A023.HFCCCBBXX.s_5.r


title: Bmal1-/- MSF CT60 run3

description:
mRNA_Seq,50bpSE
SLX-11126.A022.HFCCCBBXX.s_7.r

source_name: Bmal1-/- MSF CT60


title: Bmal1-/- MSF CT60 run1

description:
mRNA_Seq,50bpSE
SLX-11126.A022.HFCCCBBXX.s_5.r


title: WT MSF CT09 run3

description:
mRNA_Seq,50bpSE
SLX-11124.A006.HFCCCBBXX.s_4.r


title: Bmal1-/- MSF CT60 run2

description:
mRNA_Seq,50bpSE
SLX-11126.A022.HFCCCBBXX.s_6.r


title: Bmal1-/- MSF CT63 run2

description:
mRNA_Seq,50bpSE
SLX-11126.A023.HFCCCBBXX.s_6.r


title: Bmal1-/- MSF CT57 run1

description:
mRNA_Seq,50bpSE
SLX-11126.A021.HFCCCBBXX.s_5.r

source_name: Bmal1-/- MSF CT57


title: Bmal1-/- MSF CT54 run2

description:
mRNA_Seq,50bpSE
SLX-11126.A020.HFCCCBBXX.s_6.r

source_name: Bmal1-/- MSF CT54


title: Bmal1-/- MSF CT57 run3

description:
mRNA_Seq,50bpSE
SLX-11126.A021.HFCCCBBXX.s_7.r


title: Bmal1-/- MSF CT51 run3

description:
mRNA_Seq,50bpSE
SLX-11126.A011.HFCCCBBXX.s_7.r

source_name: Bmal1-/- MSF CT51


title: Bmal1-/- MSF CT57 run2

description:
mRNA_Seq,50bpSE
SLX-11126.A021.HFCCCBBXX.s_6.r


title: Bmal1-/- MSF CT54 run3

description:
mRNA_Seq,50bpSE
SLX-11126.A020.HFCCCBBXX.s_7.r


title: Bmal1-/- MSF CT54 run1

description:
mRNA_Seq,50bpSE
SLX-11126.A020.HFCCCBBXX.s_5.r


title: Bmal1-/- MSF CT48 run1

description:
mRNA_Seq,50bpSE
SLX-11126.A010.HFCCCBBXX.s_5.r

source_name: Bmal1-/- MSF CT48


title: Bmal1-/- MSF CT45 run3

description:
mRNA_Seq,50bpSE
SLX-11126.A009.HFCCCBBXX.s_7.r

source_name: Bmal1-/- MSF CT45


title: Bmal1-/- MSF CT45 run2

description:
mRNA_Seq,50bpSE
SLX-11126.A009.HFCCCBBXX.s_6.r


title: Bmal1-/- MSF CT42 run3

description:
mRNA_Seq,50bpSE
SLX-11126.A008.HFCCCBBXX.s_7.r

source_name: Bmal1-/- MSF CT42


title: Bmal1-/- MSF CT42 run2

description:
mRNA_Seq,50bpSE
SLX-11126.A008.HFCCCBBXX.s_6.r


title: Bmal1-/- MSF CT45 run1

description:
mRNA_Seq,50bpSE
SLX-11126.A009.HFCCCBBXX.s_5.r


title: Bmal1-/- MSF CT42 run1

description:
mRNA_Seq,50bpSE
SLX-11126.A008.HFCCCBBXX.s_5.r


title: Bmal1-/- MSF CT51 run1

description:
mRNA_Seq,50bpSE
SLX-11126.A011.HFCCCBBXX.s_5.r


title: Bmal1-/- MSF CT51 run2

description:
mRNA_Seq,50bpSE
SLX-11126.A011.HFCCCBBXX.s_6.r


title: Bmal1-/- MSF CT48 run2

description:
mRNA_Seq,50bpSE
SLX-11126.A010.HFCCCBBXX.s_6.r


title: Bmal1-/- MSF CT39 run3

description:
mRNA_Seq,50bpSE
SLX-11126.A003.HFCCCBBXX.s_7.r

source_name: Bmal1-/- MSF CT39


title: Bmal1-/- MSF CT39 run2

description:
mRNA_Seq,50bpSE
SLX-11126.A003.HFCCCBBXX.s_6.r


title: Bmal1-/- MSF CT39 run1

description:
mRNA_Seq,50bpSE
SLX-11126.A003.HFCCCBBXX.s_5.r


title: Bmal1-/- MSF CT36 run2

description:
mRNA_Seq,50bpSE
SLX-11126.A001.HFCCCBBXX.s_6.r

source_name: Bmal1-/- MSF CT36


title: Bmal1-/- MSF CT36 run1

description:
mRNA_Seq,50bpSE
SLX-11126.A001.HFCCCBBXX.s_5.r


title: Bmal1-/- MSF CT36 run3

description:
mRNA_Seq,50bpSE
SLX-11126.A001.HFCCCBBXX.s_7.r


title: Bmal1-/- MSF CT33 run1

description:
mRNA_Seq,50bpSE
SLX-11126.A019.HFCCCBBXX.s_5.r

source_name: Bmal1-/- MSF CT33


title: Bmal1-/- MSF CT33 run3

description:
mRNA_Seq,50bpSE
SLX-11126.A019.HFCCCBBXX.s_7.r


title: Bmal1-/- MSF CT33 run2

description:
mRNA_Seq,50bpSE
SLX-11126.A019.HFCCCBBXX.s_6.r


title: Bmal1-/- MSF CT30 run1

description:
mRNA_Seq,50bpSE
SLX-11126.A018.HFCCCBBXX.s_5.r

source_name: Bmal1-/- MSF CT30


title: Bmal1-/- MSF CT30 run2

description:
mRNA_Seq,50bpSE
SLX-11126.A018.HFCCCBBXX.s_6.r


title: Bmal1-/- MSF CT30 run3

description:
mRNA_Seq,50bpSE
SLX-11126.A018.HFCCCBBXX.s_7.r


title: Bmal1-/- MSF CT48 run3

description:
mRNA_Seq,50bpSE
SLX-11126.A010.HFCCCBBXX.s_7.r


title: Bmal1-/- MSF CT24 run1

description:
mRNA_Seq,50bpSE
SLX-11126.A015.HFCCCBBXX.s_5.r

source_name: Bmal1-/- MSF CT24


title: Bmal1-/- MSF CT24 run2

description:
mRNA_Seq,50bpSE
SLX-11126.A015.HFCCCBBXX.s_6.r


title: Bmal1-/- MSF CT24 run3

description:
mRNA_Seq,50bpSE
SLX-11126.A015.HFCCCBBXX.s_7.r


title: Bmal1-/- MSF CT27 run1

description:
mRNA_Seq,50bpSE
SLX-11126.A016.HFCCCBBXX.s_5.r

source_name: Bmal1-/- MSF CT27


title: Bmal1-/- MSF CT27 run2

description:
mRNA_Seq,50bpSE
SLX-11126.A016.HFCCCBBXX.s_6.r


title: Bmal1-/- MSF CT21 run3

description:
mRNA_Seq,50bpSE
SLX-11126.A014.HFCCCBBXX.s_7.r

source_name: Bmal1-/- MSF CT21


title: Bmal1-/- MSF CT15 run3

description:
mRNA_Seq,50bpSE
SLX-11126.A012.HFCCCBBXX.s_7.r

source_name: Bmal1-/- MSF CT15


title: Bmal1-/- MSF CT18 run1

description:
mRNA_Seq,50bpSE
SLX-11126.A013.HFCCCBBXX.s_5.r

source_name: Bmal1-/- MSF CT18


title: Bmal1-/- MSF CT15 run2

description:
mRNA_Seq,50bpSE
SLX-11126.A012.HFCCCBBXX.s_6.r


title: Bmal1-/- MSF CT21 run1

description:
mRNA_Seq,50bpSE
SLX-11126.A014.HFCCCBBXX.s_5.r


title: Bmal1-/- MSF CT18 run3

description:
mRNA_Seq,50bpSE
SLX-11126.A013.HFCCCBBXX.s_7.r


title: Bmal1-/- MSF CT09 run1

description:
mRNA_Seq,50bpSE
SLX-11126.A006.HFCCCBBXX.s_5.r

source_name: Bmal1-/- MSF CT09


title: Bmal1-/- MSF CT15 run1

description:
mRNA_Seq,50bpSE
SLX-11126.A012.HFCCCBBXX.s_5.r


title: Bmal1-/- MSF CT06 run3

description:
mRNA_Seq,50bpSE
SLX-11126.A005.HFCCCBBXX.s_7.r

source_name: Bmal1-/- MSF CT06


title: Bmal1-/- MSF CT12 run3

description:
mRNA_Seq,50bpSE
SLX-11126.A007.HFCCCBBXX.s_7.r

source_name: Bmal1-/- MSF CT12


title: Bmal1-/- MSF CT12 run1

description:
mRNA_Seq,50bpSE
SLX-11126.A007.HFCCCBBXX.s_5.r


title: Bmal1-/- MSF CT09 run2

description:
mRNA_Seq,50bpSE
SLX-11126.A006.HFCCCBBXX.s_6.r


title: Bmal1-/- MSF CT09 run3

description:
mRNA_Seq,50bpSE
SLX-11126.A006.HFCCCBBXX.s_7.r


title: Bmal1-/- MSF CT12 run2

description:
mRNA_Seq,50bpSE
SLX-11126.A007.HFCCCBBXX.s_6.r


title: Bmal1-/- MSF CT06 run1

description:
mRNA_Seq,50bpSE
SLX-11126.A005.HFCCCBBXX.s_5.r


title: Bmal1-/- MSF CT03 run2

description:
mRNA_Seq,50bpSE
SLX-11126.A004.HFCCCBBXX.s_6.r

source_name: Bmal1-/- MSF CT03


title: Bmal1-/- MSF CT03 run3

description:
mRNA_Seq,50bpSE
SLX-11126.A004.HFCCCBBXX.s_7.r


title: Bmal1-/- MSF CT00 run3

description:
mRNA_Seq,50bpSE
SLX-11126.A002.HFCCCBBXX.s_7.r

source_name: Bmal1-/- MSF CT00


title: Bmal1-/- MSF CT03 run1

description:
mRNA_Seq,50bpSE
SLX-11126.A004.HFCCCBBXX.s_5.r


title: Bmal1-/- MSF CT00 run1

description:
mRNA_Seq,50bpSE
SLX-11126.A002.HFCCCBBXX.s_5.r


title: Bmal1-/- MSF CT21 run2

description:
mRNA_Seq,50bpSE
SLX-11126.A014.HFCCCBBXX.s_6.r


title: Bmal1-/- MSF CT00 run2

description:
mRNA_Seq,50bpSE
SLX-11126.A002.HFCCCBBXX.s_6.r


title: Bmal1-/- MSF CT18 run2

description:
mRNA_Seq,50bpSE
SLX-11126.A013.HFCCCBBXX.s_6.r


title: CLB-BERLUD: A399U64

city: Paris

first: Olivier

last: Delattre

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description: CLB-BERLUD Neuroblastoma cell line

data_processing:
Reads obtained from sequencing of cells were aligned on the human genome (v. hg19) using TopHat (version 2.0.6). Reads mapping more than once (parameter -x 1) or having edit distances of more than 3 (-N 3) were discarded.
Counting of reads on annotated genes from the GRCh37 gene build was done using htseq-count (v. HTSeq-0.5.3p9) with the following parameters: reads with a quality score less than 10 (-a 10) were discarded and reads partially overlapping with the annotated gene transcript were included in the counts unless they overlapped with another read. In all experiments analysed the STRANDED=no option was used.
Sample-to-sample normalization was performed by rescaling using DESeq-type size factors. For all data analyses the number of reads was log10(x+1) transformed.
Genome_build: hg19
Supplementary_files_format_and_content: GeneXCell tab-delimited text file with read counts

source_name: CLB-BERLUD

growth_protocol: CLB-berlud are cultured in RPMI (Gibco) 10% FBS (Eurobio), 100U/mL

extract_protocol:
Dissociated cells were captured and processed with the C1 Single-Cell Auto Prep System (FluidigmTM) following the manufacturer’s protocol
After harvest from the C1 device, each cDNA library was tagmented using the Nextera XT DNA Sample Preparation Kit (Illumina).
Libraries were quantified by Qubit fluorometric assay (Invitrogen) with dsDNA HS (High Sensitivity) Assay Kit and qualified using LabChip (LabChip® GX Touch™ PerkinElmer)

treatment_protocol: No treatment

value: Neuroblastoma

value: Neuroblastoma cell line

tag: cell line

value: CLB-BERLUD


title: CLB-BERLUD: A399U63

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U62

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U60

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U61

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U59

description: CLB-BERLUD Neuroblastoma cell line


title: Bmal1-/- MSF CT06 run2

description:
mRNA_Seq,50bpSE
SLX-11126.A005.HFCCCBBXX.s_6.r

value: not applicable


title: CLB-BERLUD: A399U58

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U55

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U54

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U56

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U51

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U50

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U57

description: CLB-BERLUD Neuroblastoma cell line


title: rhabdoid.7: A159R95

description: Dox-/Smarcb1+/non-proliferative rhabdoid cells. Rhabdoid cells from the I2A cell line in which a doxycycline inducible system has been engineered to control the expression of tumor suppressor gene SmarcB1. In the presence of Dox, cells are proliferative and can be cultured

growth_protocol: I2A cells were grown in RPMI (Gibco), 10% FBS (Eurobio) with 50 μg/mL hygromycin B (Life Technology), 300 μg/mL G418 (geneticin) and 50 ng/mL DOX (doxycyclin, Invitrogen) added ex-tempo when indicated

treatment_protocol: DOX was removed and cells were washed three times to induce SMARCB1 expression

value: Rhabdoid

value: Dox-/Smarcb1+/non-proliferative rhabdoid cells (I2A cell line)


title: CLB-BERLUD: A399U53

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U52

description: CLB-BERLUD Neuroblastoma cell line


title: rhabdoid.7: A159R96


title: CLB-BERLUD: A399U49

description: CLB-BERLUD Neuroblastoma cell line


title: rhabdoid.7: A159R94


title: rhabdoid.7: A159R92


title: rhabdoid.7: A159R91


title: rhabdoid.7: A159R93


title: rhabdoid.7: A159R88


title: rhabdoid.7: A159R86


title: rhabdoid.7: A159R90


title: rhabdoid.7: A159R87


title: rhabdoid.7: A159R89


title: rhabdoid.7: A159R85


title: rhabdoid.7: A159R83


title: rhabdoid.7: A159R84


title: rhabdoid.7: A159R82


title: rhabdoid.7: A159R81


title: rhabdoid.7: A159R78


title: rhabdoid.7: A159R80


title: rhabdoid.7: A159R79


title: rhabdoid.7: A159R76


title: rhabdoid.7: A159R69


title: rhabdoid.7: A159R74


title: rhabdoid.7: A159R70


title: rhabdoid.7: A159R67


title: rhabdoid.7: A159R72


title: rhabdoid.7: A159R68


title: rhabdoid.7: A159R73


title: rhabdoid.7: A159R66


title: rhabdoid.7: A159R65


title: rhabdoid.7: A159R64


title: rhabdoid.7: A159R61


title: rhabdoid.7: A159R62


title: rhabdoid.7: A159R60


title: rhabdoid.7: A159R57


title: rhabdoid.7: A159R63


title: rhabdoid.7: A159R59


title: rhabdoid.7: A159R58


title: rhabdoid.7: A159R56


title: rhabdoid.7: A159R54


title: rhabdoid.7: A159R75


title: rhabdoid.7: A159R52


title: rhabdoid.7: A159R55


title: rhabdoid.7: A159R77


title: rhabdoid.0: A159R42

description: Dox+/Smarcb1-/proliferative rhabdoid cells. Rhabdoid cells from the I2A cell line in which a doxycycline inducible system has been engineered to control the expression of tumor suppressor gene SmarcB1. In the presence of Dox, cells are proliferative and can be cultured

value: Dox+/Smarcb1-/proliferative rhabdoid cells (I2A cell line)


title: rhabdoid.7: A159R50


title: rhabdoid.0: A159R43


title: rhabdoid.0: A159R44


title: rhabdoid.0: A159R46


title: rhabdoid.7: A159R49


title: rhabdoid.7: A159R53


title: rhabdoid.0: A159R47


title: rhabdoid.0: A159R39


title: rhabdoid.0: A159R38


title: rhabdoid.0: A159R40


title: rhabdoid.0: A159R37


title: rhabdoid.0: A159R35


title: rhabdoid.0: A159R33


title: rhabdoid.0: A159R34


title: rhabdoid.0: A159R32


title: rhabdoid.0: A159R36


title: rhabdoid.0: A159R31


title: rhabdoid.0: A159R30


title: rhabdoid.0: A159R27


title: rhabdoid.0: A159R28


title: rhabdoid.0: A159R29


title: rhabdoid.0: A159R48


title: rhabdoid.0: A159R45


title: rhabdoid.0: A159R26


title: rhabdoid.0: A159R41


title: rhabdoid.0: A159R23


title: rhabdoid.0: A159R24


title: rhabdoid.0: A159R18


title: rhabdoid.0: A159R20


title: rhabdoid.0: A159R25


title: rhabdoid.0: A159R22


title: rhabdoid.0: A159R19


title: rhabdoid.0: A159R21


title: rhabdoid.0: A159R17


title: rhabdoid.0: A159R16


title: rhabdoid.0: A159R15


title: rhabdoid.0: A159R14


title: rhabdoid.0: A159R11


title: rhabdoid.0: A159R13


title: rhabdoid.0: A159R12


title: rhabdoid.0: A159R10


title: rhabdoid.0: A159R9


title: rhabdoid.0: A159R6


title: rhabdoid.0: A159R8


title: rhabdoid.0: A159R7


title: rhabdoid.0: A159R5


title: rhabdoid.0: A159R3


title: rhabdoid.0: A159R2


title: rhabdoid.0: A159R4


title: rhabdoid.0: A159R1


title: rhabdoid.0: A120T21


title: rhabdoid.0: A120T22


title: Bmal1-/- MSF CT27 run3

description:
mRNA_Seq,50bpSE
SLX-11126.A016.HFCCCBBXX.s_7.r


title: MSC-15FL: A263T96

description: Mesenchymal stem cells

source_name: bone marrow

growth_protocol: MSCs from bone marrow Ewing patients were isolated by density-gradient centrifugation using Ficoll technique and were cultured in alpha MEM (Gibco), MSC-qualified serum (Gibco), 1% L-glutamine (Gibco) and 1 ng/mL bFGF (Sigma), added ex-tempo. CLB-berlud are cultured in RPMI (Gibco) 10% FBS (Eurobio), 100U/mL.

extract_protocol:
Dissociated cells were captured and processed with the C1 Single-Cell Auto Prep System (FluidigmTM) following the manufacturer’s protocol
After harvest from the C1 device, each cDNA library was tagmented using the Nextera XT DNA Sample Preparation Kit (Illumina).   Libraries were quantified by Qubit fluorometric assay (Invitrogen) with dsDNA HS (High Sensitivity) Assay Kit and qualified using LabChip (LabChip® GX Touch™ PerkinElmer)

value: Mesenchymal Stem Cell

value: MSC primary cell line


title: MSC-15FL: A263T94

description: Mesenchymal stem cells


title: MSC-15FL: A263T91

description: Mesenchymal stem cells


title: MSC-15FL: A263T90

description: Mesenchymal stem cells


title: MSC-15FL: A263T92

description: Mesenchymal stem cells


title: MSC-15FL: A263T95

description: Mesenchymal stem cells


title: MSC-15FL: A263T88

description: Mesenchymal stem cells


title: MSC-15FL: A263T89

description: Mesenchymal stem cells


title: MSC-15FL: A263T86

description: Mesenchymal stem cells


title: MSC-15FL: A263T84

description: Mesenchymal stem cells


title: MSC-15FL: A263T83

description: Mesenchymal stem cells


title: MSC-15FL: A263T82

description: Mesenchymal stem cells


title: MSC-15FL: A263T81

description: Mesenchymal stem cells


title: MSC-15FL: A263T77

description: Mesenchymal stem cells


title: MSC-15FL: A263T80

description: Mesenchymal stem cells


title: MSC-15FL: A263T79

description: Mesenchymal stem cells


title: MSC-15FL: A263T74

description: Mesenchymal stem cells


title: MSC-15FL: A263T73

description: Mesenchymal stem cells


title: MSC-15FL: A263T78

description: Mesenchymal stem cells


title: MSC-15FL: A263T72

description: Mesenchymal stem cells


title: MSC-15FL: A263T75

description: Mesenchymal stem cells


title: MSC-15FL: A263T70

description: Mesenchymal stem cells


title: MSC-15FL: A263T69

description: Mesenchymal stem cells


title: MSC-15FL: A263T68

description: Mesenchymal stem cells


title: MSC-15FL: A263T85

description: Mesenchymal stem cells


title: MSC-15FL: A263T65

description: Mesenchymal stem cells


title: MSC-15FL: A263T64

description: Mesenchymal stem cells


title: MSC-15FL: A263T93

description: Mesenchymal stem cells


title: MSC-15FL: A263T61

description: Mesenchymal stem cells


title: MSC-15FL: A263T62

description: Mesenchymal stem cells


title: MSC-15FL: A263T87

description: Mesenchymal stem cells


title: MSC-15FL: A263T71

description: Mesenchymal stem cells


title: MSC-15FL: A263T66

description: Mesenchymal stem cells


title: MSC-15FL: A263T60

description: Mesenchymal stem cells


title: MSC-15FL: A263T58

description: Mesenchymal stem cells


title: MSC-15FL: A263T76

description: Mesenchymal stem cells


title: MSC-15FL: A263T57

description: Mesenchymal stem cells


title: MSC-15FL: A263T59

description: Mesenchymal stem cells


title: MSC-15FL: A263T56

description: Mesenchymal stem cells


title: MSC-15FL: A263T54

description: Mesenchymal stem cells


title: MSC-15FL: A263T55

description: Mesenchymal stem cells


title: MSC-15FL: A263T53

description: Mesenchymal stem cells


title: MSC-15FL: A263T51

description: Mesenchymal stem cells


title: MSC-15FL: A263T50

description: Mesenchymal stem cells


title: MSC-15FL: A263T49

description: Mesenchymal stem cells


title: MSC-15FL: A263T52

description: Mesenchymal stem cells


title: MSC-15FL: A263T63

description: Mesenchymal stem cells


title: MSC-7BJ: A263T46

description: Mesenchymal stem cells


title: MSC-15FL: A263T67

description: Mesenchymal stem cells


title: MSC-7BJ: A263T47

description: Mesenchymal stem cells


title: MSC-7BJ: A263T48

description: Mesenchymal stem cells


title: MSC-7BJ: A263T43

description: Mesenchymal stem cells


title: MSC-7BJ: A263T41

description: Mesenchymal stem cells


title: MSC-7BJ: A263T45

description: Mesenchymal stem cells


title: MSC-7BJ: A263T44

description: Mesenchymal stem cells


title: MSC-7BJ: A263T37

description: Mesenchymal stem cells


title: rhabdoid.7: A159R51


title: MSC-7BJ: A263T40

description: Mesenchymal stem cells


title: MSC-7BJ: A263T42

description: Mesenchymal stem cells


title: MSC-7BJ: A263T38

description: Mesenchymal stem cells


title: MSC-7BJ: A263T36

description: Mesenchymal stem cells


title: MSC-7BJ: A263T35

description: Mesenchymal stem cells


title: MSC-7BJ: A263T30

description: Mesenchymal stem cells


title: MSC-7BJ: A263T31

description: Mesenchymal stem cells


title: MSC-7BJ: A263T34

description: Mesenchymal stem cells


title: MSC-7BJ: A263T32

description: Mesenchymal stem cells


title: MSC-7BJ: A263T33

description: Mesenchymal stem cells


title: MSC-7BJ: A263T29

description: Mesenchymal stem cells


title: MSC-7BJ: A263T25

description: Mesenchymal stem cells


title: MSC-7BJ: A263T27

description: Mesenchymal stem cells


title: MSC-7BJ: A263T28

description: Mesenchymal stem cells


title: MSC-7BJ: A263T23

description: Mesenchymal stem cells


title: MSC-7BJ: A263T24

description: Mesenchymal stem cells


title: MSC-7BJ: A263T26

description: Mesenchymal stem cells


title: MSC-7BJ: A263T18

description: Mesenchymal stem cells


title: MSC-7BJ: A263T22

description: Mesenchymal stem cells


title: MSC-7BJ: A263T21

description: Mesenchymal stem cells


title: MSC-7BJ: A263T20

description: Mesenchymal stem cells


title: MSC-7BJ: A263T39

description: Mesenchymal stem cells


title: MSC-7BJ: A263T19

description: Mesenchymal stem cells


title: MSC-7BJ: A263T13

description: Mesenchymal stem cells


title: MSC-7BJ: A263T14

description: Mesenchymal stem cells


title: MSC-7BJ: A263T16

description: Mesenchymal stem cells


title: MSC-7BJ: A263T12

description: Mesenchymal stem cells


title: MSC-7BJ: A263T17

description: Mesenchymal stem cells


title: MSC-7BJ: A263T11

description: Mesenchymal stem cells


title: MSC-7BJ: A263T9

description: Mesenchymal stem cells


title: MSC-7BJ: A263T10

description: Mesenchymal stem cells


title: MSC-7BJ: A263T3

description: Mesenchymal stem cells


title: MSC-7BJ: A263T2

description: Mesenchymal stem cells


title: MSC-7BJ: A263T4

description: Mesenchymal stem cells


title: A673/TR_xenograft_d0: A540U485

description: A673TRshEF cells xenografted on SCID mice, without any doxycycline treatment (EF1-low)

growth_protocol: A673/TR/shEF are cultured in DMEM (Gibco) 10% FBS (Eurobio), with 50 μg/mL Zeocin (Invitrogen), 2 μg/mL Blasticidin (Invitrogen) added ex-tempo.

treatment_protocol: EWSR1-FLI1 specific small hairpin RNA was induced in A673/TR/shEF cells by adding DOX at 1 ug/mL. After 7 days, DOX was removed and cells were washed three times to allow silencing of the shRNA and induction of EWSR1-FLI1. For ASP14 xenograft, 20 millions cells were resuspended in 200 µL of PBS and subcutaneously injected into severe combined immunodeficiency (SCID) mice. When tumor volume reached 1,000 mm3, DOX was added in the drinking water of a subset of mice (+ DOX group) for 7 days.

tag: passages

value: Ewing sarcoma


title: A673/TR_xenograft_d0: A540U483


title: A673/TR_xenograft_d0: A540U484


title: A673/TR_xenograft_d0: A540U481


title: A673/TR_xenograft_d0: A540U482


title: A673/TR_xenograft_d0: A540U478


title: A673/TR_xenograft_d0: A540U479


title: A673/TR_xenograft_d0: A540U477


title: MSC-7BJ: A263T15

description: Mesenchymal stem cells


title: A673/TR_xenograft_d0: A540U476


title: MSC-7BJ: A263T8

description: Mesenchymal stem cells


title: rhabdoid.7: A159R71


title: MSC-7BJ: A263T7

description: Mesenchymal stem cells


title: MSC-7BJ: A263T6

description: Mesenchymal stem cells


title: A673/TR_xenograft_d7: A413U239


title: A673/TR_xenograft_d7: A413U244


title: A673/TR_xenograft_d7: A413U243


title: A673/TR_xenograft_d7: A413U242


title: A673/TR_xenograft_d7: A413U245


title: MSC-7BJ: A263T5

description: Mesenchymal stem cells


title: A673/TR_xenograft_d7: A413U238


title: A673/TR_xenograft_d0: A540U486


title: MSC-7BJ: A263T1

description: Mesenchymal stem cells


title: A673/TR_xenograft_d7: A413U236


title: A673/TR_xenograft_d7: A413U234


title: A673/TR_xenograft_d0: A540U480


title: A673/TR_xenograft_d7: A413U233


title: A673/TR_xenograft_d7: A413U232


title: A673/TR_xenograft_d7: A413U231


title: A673/TR_xenograft_d7: A413U235


title: A673/TR_xenograft_d7: A413U230


title: A673/TR_xenograft_d7: A413U228


title: A673/TR_xenograft_d7: A413U226


title: A673/TR_xenograft_d7: A413U246


title: A673/TR_xenograft_d7: A413U225


title: A673/TR_xenograft_d7: A413U224


title: A673/TR_xenograft_d7: A413U241


title: A673/TR_xenograft_d7: A413U240


title: A673/TR_xenograft_d7: A413U219


title: A673/TR_xenograft_d7: A413U215


title: A673/TR_xenograft_d7: A413U216


title: A673/TR_xenograft_d7: A413U212


title: A673/TR_xenograft_d7: A413U211


title: A673/TR_xenograft_d7: A413U209


title: A673/TR_xenograft_d7: A413U204


title: A673/TR_xenograft_d7: A413U237


title: A673/TR_xenograft_d7: A412U294


title: A673/TR_xenograft_d7: A413U227


title: A673/TR_xenograft_d7: A413U200


title: A673/TR_xenograft_d7: A413U199


title: A673/TR_xenograft_d7: A412U293


title: A673/TR_xenograft_d7: A412U292


title: A673/TR_xenograft_d7: A412U291


title: A673/TR_xenograft_d7: A413U222


title: A673/TR_xenograft_d7: A412U290


title: A673/TR_xenograft_d7: A412U289


title: A673/TR_xenograft_d7: A412U287


title: A673/TR_xenograft_d7: A412U286


title: A673/TR_xenograft_d7: A412U288


title: A673/TR_xenograft_d7: A412U281


title: A673/TR_xenograft_d7: A412U280


title: A673/TR_xenograft_d7: A412U283


title: A673/TR_xenograft_d7: A412U279


title: A673/TR_xenograft_d7: A412U277


title: A673/TR_xenograft_d7: A412U275


title: A673/TR_xenograft_d7: A412U274


title: A673/TR_xenograft_d7: A412U276


title: A673/TR_xenograft_d7: A412U271


title: A673/TR_xenograft_d7: A412U270


title: A673/TR_xenograft_d7: A412U267


title: A673/TR_xenograft_d7: A412U272


title: A673/TR_xenograft_d7: A412U268


title: A673/TR_xenograft_d7: A412U265


title: A673/TR_xenograft_d7: A412U266


title: A673/TR_xenograft_d7: A412U264


title: A673/TR_xenograft_d7: A412U263


title: A673/TR_xenograft_d7: A412U285


title: A673/TR_xenograft_d7: A412U258


title: A673/TR_xenograft_d7: A412U257


title: A673/TR_xenograft_d7: A412U261


title: A673/TR_xenograft_d7: A412U262


title: A673/TR_xenograft_d7: A412U259


title: A673/TR_xenograft_d7: A412U260


title: A673/TR_xenograft_d7: A412U282


title: A673/TR_xenograft_d7: A412U255


title: A673/TR_xenograft_d7: A412U253


title: A673/TR_xenograft_d7: A412U251


title: A673/TR_xenograft_d7: A412U249


title: A673/TR_xenograft_d7: A412U250


title: A673/TR_xenograft_d7: A412U247


title: A673/TR_xenograft_d7: A412U248


title: A673/TR_xenograft_d7: A540U475

description: A673TRshEF cells xenografted on SCID mice, after 7 days of doxycycline treatment


title: A673/TR_xenograft_d7: A540U472


title: A673/TR_xenograft_d7: A540U473


title: A673/TR_xenograft_d7: A540U471


title: A673/TR_xenograft_d7: A540U474


title: A673/TR_xenograft_d7: A540U469


title: A673/TR_xenograft_d7: A540U466


title: A673/TR_xenograft_d7: A540U467


title: A673/TR_xenograft_d7: A540U470


title: A673/TR_xenograft_d7: A540U465


title: A673/TR_xenograft_d7: A540U464


title: A673/TR_xenograft_d7: A412U256


title: A673/TR_xenograft_d7: A540U463


title: A673/TR_xenograft_d7: A540U462


title: A673/TR_xenograft_d7: A540U458


title: A673/TR_xenograft_d7: A540U459


title: A673/TR_xenograft_d7: A540U460


title: A673/TR_xenograft_d7: A540U453


title: A673/TR_xenograft_d7: A540U456


title: A673/TR_xenograft_d7: A540U455


title: A673/TR_xenograft_d7: A540U461


title: A673/TR_xenograft_d7: A412U254


title: A673/TR_xenograft_d7: A540U448


title: A673/TR_xenograft_d7: A540U451


title: A673/TR_xenograft_d7: A540U447


title: A673/TR_xenograft_d7: A540U449


title: A673/TR_xenograft_d7: A540U457


title: A673/TR_xenograft_d7: A540U446


title: A673/TR_xenograft_d7: A540U444


title: A673/TR_xenograft_d7: A540U442


title: A673/TR_xenograft_d7: A540U441


title: A673/TR_xenograft_d7: A540U443


title: A673/TR_xenograft_d7: A540U445


title: A673/TR_xenograft_d7: A540U440


title: A673/TR_xenograft_d7: A540U452


title: A673/TR_xenograft_d7: A540U439


title: A673/TR_xenograft_d0: A413U198


title: A673/TR_xenograft_d0: A413U196


title: A673/TR_xenograft_d0: A413U197


title: A673/TR_xenograft_d0: A413U195


title: A673/TR_xenograft_d0: A413U193


title: A673/TR_xenograft_d0: A413U194


title: A673/TR_xenograft_d0: A413U192


title: A673/TR_xenograft_d0: A413U191


title: A673/TR_xenograft_d0: A413U189


title: A673/TR_xenograft_d0: A413U187


title: A673/TR_xenograft_d0: A413U190


title: A673/TR_xenograft_d0: A413U186


title: A673/TR_xenograft_d0: A413U185


title: A673/TR_xenograft_d0: A413U188


title: A673/TR_xenograft_d0: A413U183


title: A673/TR_xenograft_d0: A413U184


title: A673/TR_xenograft_d0: A413U179


title: A673/TR_xenograft_d0: A413U178


title: A673/TR_xenograft_d0: A413U177


title: A673/TR_xenograft_d0: A413U182


title: A673/TR_xenograft_d0: A413U180


title: A673/TR_xenograft_d0: A413U176


title: A673/TR_xenograft_d0: A413U175


title: A673/TR_xenograft_d0: A413U174


title: A673/TR_xenograft_d0: A413U172


title: A673/TR_xenograft_d0: A413U171


title: A673/TR_xenograft_d0: A413U170


title: A673/TR_xenograft_d0: A413U173


title: A673/TR_xenograft_d0: A413U167


title: A673/TR_xenograft_d0: A413U166


title: A673/TR_xenograft_d0: A413U169


title: A673/TR_xenograft_d0: A413U164


title: A673/TR_xenograft_d0: A413U165


title: A673/TR_xenograft_d0: A413U163


title: A673/TR_xenograft_d0: A413U168


title: A673/TR_xenograft_d0: A413U160


title: A673/TR_xenograft_d0: A413U158


title: A673/TR_xenograft_d0: A413U161


title: A673/TR_xenograft_d0: A413U157


title: A673/TR_xenograft_d0: A413U181


title: A673/TR_xenograft_d0: A413U155


title: A673/TR_xenograft_d0: A413U154


title: A673/TR_xenograft_d0: A413U159


title: A673/TR_xenograft_d0: A413U156


title: A673/TR_xenograft_d0: A413U153


title: A673/TR_xenograft_d0: A413U151


title: A673/TR_xenograft_d0: A412U150


title: A673/TR_xenograft_d0: A412U148


title: A673/TR_xenograft_d0: A412U149


title: A673/TR_xenograft_d0: A412U146


title: A673/TR_xenograft_d0: A412U147


title: A673/TR_xenograft_d0: A412U145


title: A673/TR_xenograft_d0: A412U143


title: A673/TR_xenograft_d0: A412U142


title: A673/TR_xenograft_d0: A413U162


title: A673/TR_xenograft_d0: A412U140


title: A673/TR_xenograft_d0: A412U141


title: A673/TR_xenograft_d0: A412U139


title: A673/TR_xenograft_d0: A412U137


title: A673/TR_xenograft_d0: A412U138


title: A673/TR_xenograft_d0: A412U136


title: A673/TR_xenograft_d0: A412U135


title: A673/TR_xenograft_d0: A412U134


title: A673/TR_xenograft_d0: A412U132


title: A673/TR_xenograft_d0: A412U133


title: A673/TR_xenograft_d0: A412U129


title: A673/TR_xenograft_d0: A412U130


title: A673/TR_xenograft_d0: A413U152


title: A673/TR_xenograft_d0: A412U131


title: A673/TR_xenograft_d0: A412U128


title: A673/TR_xenograft_d0: A412U127


title: A673/TR_xenograft_d0: A412U126


title: A673/TR_xenograft_d0: A412U122


title: A673/TR_xenograft_d0: A412U125


title: A673/TR_xenograft_d0: A412U124


title: A673/TR_xenograft_d0: A412U121


title: A673/TR_xenograft_d0: A412U144


title: A673/TR_xenograft_d0: A412U115


title: A673/TR_xenograft_d0: A412U113


title: A673/TR_xenograft_d0: A412U120


title: A673/TR_xenograft_d0: A412U111


title: A673/TR_xenograft_d0: A412U119


title: A673/TR_xenograft_d0: A412U118


title: A673/TR_xenograft_d0: A412U109


title: A673/TR_xenograft_d0: A412U117


title: A673/TR_xenograft_d0: A412U116


title: A673/TR_xenograft_d0: A412U103


title: ASP14_day22: A296U192

description: A673TRshEF cells, after 15 days of doxycycline removal in media of cells that were previously subjected to 7 days of doxycycline inducing downregulation of EWS-FLI1 (“d7+15”)


title: A673/TR_xenograft_d0: A412U110


title: A673/TR_xenograft_d0: A412U112


title: A673/TR_xenograft_d0: A412U123


title: ASP14_day22: A296U189


title: ASP14_day22: A296U190


title: ASP14_day22: A296U191


title: ASP14_day22: A296U188


title: A673/TR_xenograft_d0: A412U108


title: A673/TR_xenograft_d0: A412U107


title: A673/TR_xenograft_d0: A412U105


title: A673/TR_xenograft_d0: A412U104


title: ASP14_day22: A296U187


title: ASP14_day22: A296U182


title: A673/TR_xenograft_d0: A412U106


title: ASP14_day22: A296U186


title: ASP14_day22: A296U180


title: ASP14_day22: A296U185


title: ASP14_day22: A296U179


title: ASP14_day22: A296U174


title: ASP14_day22: A296U177


title: ASP14_day22: A296U184


title: ASP14_day22: A296U173


title: ASP14_day22: A296U171


title: ASP14_day22: A296U183


title: ASP14_day22: A296U169


title: ASP14_day22: A296U181


title: ASP14_day22: A296U178


title: ASP14_day22: A295U93


title: ASP14_day22: A296U175


title: ASP14_day22: A295U94


title: ASP14_day22: A295U95


title: ASP14_day22: A295U92


title: ASP14_day22: A296U172


title: ASP14_day22: A295U84


title: ASP14_day22: A295U89


title: ASP14_day22: A295U82


title: ASP14_day22: A295U96


title: ASP14_day22: A295U86


title: ASP14_day22: A295U87


title: ASP14_day22: A295U79


title: ASP14_day22: A295U80


title: ASP14_day22: A295U76


title: ASP14_day22: A295U77


title: ASP14_day22: A295U90


title: ASP14_day22: A295U83


title: ASP14_day22: A295U81


title: ASP14_day22: A295U78


title: ASP14_day22: A296U176


title: ASP14_day17: A296U163

description: A673TRshEF cells, after 10 days of doxycycline removal in media of cells that were previously subjected to 7 days of doxycycline inducing downregulation of EWS-FLI1 (“d7+10”)


title: ASP14_day17: A296U162


title: ASP14_day22: A295U75


title: ASP14_day17: A296U158


title: ASP14_day22: A295U74


title: ASP14_day17: A296U167


title: ASP14_day22: A295U91


title: ASP14_day17: A296U157


title: ASP14_day22: A295U73


title: ASP14_day17: A296U168


title: ASP14_day17: A296U166


title: ASP14_day22: A295U88


title: ASP14_day17: A296U153


title: ASP14_day17: A296U151


title: ASP14_day17: A296U150


title: ASP14_day17: A296U164


title: ASP14_day17: A296U147


title: ASP14_day17: A296U165


title: ASP14_day22: A295U85


title: ASP14_day17: A296U156


title: ASP14_day17: A296U159


title: ASP14_day17: A296U160


title: ASP14_day17: A296U161


title: ASP14_day17: A295U72


title: ASP14_day17: A296U145


title: ASP14_day17: A296U155


title: ASP14_day17: A296U154


title: ASP14_day17: A295U68


title: ASP14_day17: A296U152


title: ASP14_day17: A296U149


title: ASP14_day17: A296U146


title: ASP14_day17: A296U148


title: ASP14_day17: A295U71


title: ASP14_day17: A295U60


title: ASP14_day17: A295U57


title: ASP14_day17: A295U70


title: ASP14_day17: A295U69


title: ASP14_day17: A295U67


title: ASP14_day17: A295U54


title: ASP14_day17: A295U66


title: ASP14_day17: A295U53


title: ASP14_day17: A295U65


title: ASP14_day17: A295U63


title: ASP14_day17: A295U62


title: ASP14_day17: A295U50


title: ASP14_day17: A295U61


title: ASP14_day14: A296U142

description: A673TRshEF cells, after 7 days of doxycycline removal in media of cells that were previously subjected to 7 days of doxycycline inducing downregulation of EWS-FLI1 (“d7+7”)


title: ASP14_day17: A295U58


title: ASP14_day17: A295U59


title: ASP14_day14: A296U141


title: ASP14_day14: A296U139


title: ASP14_day17: A295U56


title: ASP14_day17: A295U51


title: ASP14_day17: A295U55


title: ASP14_day17: A295U52


title: ASP14_day14: A296U144


title: ASP14_day14: A296U135


title: ASP14_day14: A296U131


title: ASP14_day14: A296U143


title: ASP14_day17: A295U49


title: ASP14_day14: A296U138


title: ASP14_day14: A296U134


title: ASP14_day14: A296U130


title: ASP14_day14: A296U129


title: ASP14_day14: A296U132


title: ASP14_day14: A296U128


title: ASP14_day14: A296U125


title: ASP14_day14: A296U123


title: ASP14_day14: A296U124


title: ASP14_day14: A296U121


title: ASP14_day14: A296U126


title: ASP14_day14: A296U140


title: ASP14_day14: A295U44


title: ASP14_day14: A296U122


title: ASP14_day14: A296U137


title: ASP14_day14: A295U46


title: ASP14_day14: A296U136


title: ASP14_day14: A295U41


title: ASP14_day14: A295U40


title: ASP14_day22: A296U170


title: ASP14_day14: A296U133


title: ASP14_day14: A295U42


title: ASP14_day14: A295U35


title: ASP14_day14: A295U39


title: ASP14_day14: A295U43


title: ASP14_day14: A295U33


title: ASP14_day14: A295U37


title: ASP14_day14: A296U127


title: ASP14_day14: A295U48


title: ASP14_day14: A295U47


title: ASP14_day14: A295U34


title: ASP14_day14: A295U29


title: ASP14_day14: A295U32


title: ASP14_day14: A295U31


title: ASP14_day14: A295U30


title: ASP14_day14: A295U45


title: ASP14_day14: A295U25


title: ASP14_day14: A295U26


title: ASP14_day14: A295U27


title: ASP14_day11: A296U120

description: A673TRshEF cells, after 4 days of doxycycline removal in media of cells that were previously subjected to 7 days of doxycycline inducing downregulation of EWS-FLI1 (“d7+4”)


title: ASP14_day11: A296U118


title: ASP14_day11: A296U117


title: ASP14_day14: A295U38


title: ASP14_day11: A296U119


title: ASP14_day11: A296U115


title: ASP14_day11: A296U116


title: ASP14_day11: A296U114


title: ASP14_day14: A295U36


title: ASP14_day11: A296U113


title: ASP14_day11: A296U109


title: ASP14_day11: A296U110


title: ASP14_day11: A296U112


title: ASP14_day11: A296U108


title: ASP14_day11: A296U107


title: ASP14_day11: A296U106


title: ASP14_day11: A296U104


title: ASP14_day11: A296U105


title: ASP14_day14: A295U28


title: ASP14_day11: A296U102


title: ASP14_day11: A296U103


title: ASP14_day11: A296U99


title: ASP14_day11: A296U101


title: ASP14_day11: A296U100


title: ASP14_day11: A296U98


title: ASP14_day11: A295U23


title: ASP14_day11: A295U24


title: ASP14_day11: A295U22


title: ASP14_day11: A295U21


title: ASP14_day11: A295U20


title: ASP14_day11: A296U97


title: ASP14_day11: A295U14


title: ASP14_day11: A296U111


title: ASP14_day11: A295U18


title: ASP14_day11: A295U16


title: ASP14_day11: A295U15


title: ASP14_day11: A295U12


title: ASP14_day11: A295U11


title: ASP14_day11: A295U8


title: ASP14_day11: A295U13


title: ASP14_day11: A295U9


title: ASP14_day11: A295U7


title: ASP14_day11: A295U10


title: ASP14_day11: A295U2


title: ASP14_day11: A295U4


title: ASP14_day11: A281U191


title: ASP14_day11: A295U6


title: ASP14_day11: A295U5


title: ASP14_day11: A295U1


title: ASP14_day11: A295U3


title: ASP14_day11: A295U19


title: ASP14_day11: A281U189


title: ASP14_day11: A281U188


title: ASP14_day11: A281U187


title: ASP14_day11: A281U185


title: ASP14_day11: A295U17


title: ASP14_day11: A281U186


title: ASP14_day11: A281U184


title: ASP14_day11: A281U182


title: ASP14_day11: A281U183


title: ASP14_day11: A281U180


title: ASP14_day11: A281U181


title: ASP14_day11: A281U179


title: ASP14_day11: A281U178


title: ASP14_day11: A281U175


title: ASP14_day11: A281U174


title: ASP14_day11: A281U173


title: ASP14_day11: A281U177


title: ASP14_day11: A281U176


title: ASP14_day11: A281U192


title: ASP14_day11: A267T95


title: ASP14_day11: A267T92


title: ASP14_day11: A281U172


title: ASP14_day11: A267T93


title: ASP14_day11: A281U190


title: ASP14_day11: A281U171


title: ASP14_day11: A267T96


title: ASP14_day11: A281U169


title: ASP14_day11: A267T94


title: ASP14_day11: A281U170


title: ASP14_day11: A267T91


title: ASP14_day11: A267T90


title: ASP14_day11: A267T86


title: ASP14_day11: A267T87


title: ASP14_day11: A267T88


title: ASP14_day11: A267T89


title: ASP14_day11: A267T80


title: ASP14_day11: A267T85


title: ASP14_day11: A267T81


title: ASP14_day11: A267T84


title: ASP14_day11: A267T82


title: ASP14_day11: A267T79


title: ASP14_day11: A267T77


title: ASP14_day11: A267T76


title: ASP14_day11: A267T74


title: ASP14_day11: A267T78


title: ASP14_day10: A281U168

description: A673TRshEF cells, after 3 days of doxycycline removal in media of cells that were previously subjected to 7 days of doxycycline inducing downregulation of EWS-FLI1 (“d7+3”)


title: ASP14_day11: A267T75


title: ASP14_day11: A267T73


title: ASP14_day10: A281U167


title: ASP14_day10: A281U165


title: ASP14_day10: A281U166


title: ASP14_day10: A281U164


title: ASP14_day10: A281U161


title: ASP14_day10: A281U163


title: ASP14_day10: A281U155


title: ASP14_day10: A281U159


title: ASP14_day10: A281U157


title: ASP14_day10: A281U156


title: ASP14_day10: A281U158


title: ASP14_day10: A281U162


title: ASP14_day10: A281U152


title: ASP14_day10: A281U160


title: ASP14_day11: A267T83


title: ASP14_day10: A281U153


title: ASP14_day10: A281U154


title: ASP14_day10: A281U151


title: ACH3K18_shaml1-eto_DMSO_ChIP-Seq

city: St. Louis

first: Jinsong

last: Zhang

state: MO

address: 1402 South Grand Blvd.

department: Department of Pharmacology & Physiology

institute: Saint Louis University School of Medicine

data_processing:
Base-calling performed with Illumina analysis pipeline.
ChIP-Seq reads were aligned to the human hg19 genome using STAR (2.5.2).
ChIP-Seq reads were further analyzed using HOMER (4.9) with default settings.
BedGraph files were generated with the “makeUCSCfile” tool accompanying the HOMER package.
Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: BedGraph files showing ChIP-Seq binding signals.

source_name: human AML cells

growth_protocol: Kasumi-1 cells were maintained in RPMI 1640 with 10% fetal bovine serum (FBS).

extract_protocol:
ChIP was performed using SimpleChIP® Enzymatic Chromatin IP Kits (Magnetic Beads, Cell Signaling Technology #9003) following the manufacturer’s instructions.
Libraries were constructed following instructions accompanying the library preparation kit designed for Illumina sequencing.

treatment_protocol: Kasumi-1 cells were transduced with control or AML1-ETO-specific shRNAs. Transduced cells were selected with Puromycin. If appropriate, the cells were also treated with DMSO or TSA (HDAC-specific inhibitor Trichostatin A).

value: human t(8;21) AML cells

tag: transduction

value: AML1-ETO-specific shRNA

value: ACH3K18 (Abcam, ab1191)

tag: treatment

value: DMSO


title: ACH3K18_shaml1-eto_TSA_ChIP-Seq

value: TSA (Trichosanthin)


title: ACH3K18_shcontrol_TSA_ChIP-Seq

value: shcontrol