title: HepG2_Ins10nM_4h_9

data_processing:
RNA samples were processed using an RNA-seq pipeline implemented in the bcbio-nextgen project (v0.9.1a; https://bcbio-nextgen.readthedocs.org/en/latest/).
Adapter sequences were trimmed from reads using Cutadapt (v1.4.2) (Martin, 2011).
Trimmed reads were aligned to the hg19 genome using STAR (v2.4.1d) (Dobin et al., 2013).
Read quantitation was performed with featureCounts (v1.4.4) (Liao et al., 2014).
Differential expression of genes was performed using DESeq2 (v1.16.1) (Love et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: CSV matrix file of normalized counts generated using DESeq2.

growth_protocol: For RNA-seq, nine biological replicates were used for each condition. HepG2 cells were maintained in EMEM supplemented with 10% final concentration of fetal bovine serum (FBS) and 1% penicillin-streptomycin in a humidified incubator with 5% CO2 at 37˚C.

extract_protocol:
Total RNA from cells was extracted using the RNeasy Plus Mini kit (Qiagen).
RNA-seq libraries were constructed using TruSeq Stranded mRNA (Illumina) according to manufacturer’s instruction.

treatment_protocol: For serum starvation, medium was removed, cells were washed three times with PBS, and medium supplemented with 0.1% BSA was added to cells for 16h. Cells were stimulated with 10 nM insulin for 4h.

value: insulin, 10 nM


title: HepG2_IRb_rep1

status: Public on Apr 04 2019

type: SRA

city: Boston

first: John

middle: G

last: Flanagan

state: MA

address: 200 Longwood Ave, Building C2, Room 523

department: Cell Biology

country: USA

institute: Harvard Medical School

library_source: genomic

data_processing:
ChIP-seq data quality was evaluated by using FASTQC (Andrews, 2010), and if required, reads were trimmed with Cutadapt (v1.4.2) (Martin, 2011).
High quality sequencing reads were mapped to the human genome UCSC build hg19 using Bowtie2 2.2.8 (Langmead and Salzberg, 2012). Alignments (BAM files) were filtered to retain only reads with a unique mapping to the genome.
Peaks were called with MACS2 2.1.1 (Zhang et al., 2008) using default parameters, and a narrow peak cutoff of P<0.001.
To assess the reproducibility of peaks across replicates, samples were run through the IDR pipeline (Babu et al., 2011), in which peak consistency was validated by use of pooled pseudo-replicates.
Genome_build: hg19
Supplementary_files_format_and_content: BED files contain genomic coordinates for peaks that were identified as reproducible, per the IDR analysis. BigWig files were generated from BAM files using Deeptools within the Galaxy platform (v1.0.4).

molecule: genomic DNA

organism: Homo sapiens

source_name: HepG2 cells

growth_protocol: For ChIP-seq, two biological replicates from independent experiments were used for each condition. HepG2 and SH-SY5Y cells were maintained in EMEM or a 1:1 mixture of EMEM and F-12 medium, respectively. Medium was supplemented with 10% final concentration of fetal bovine serum (FBS) and 1% penicillin-streptomycin in a humidified incubator with 5% CO2 at 37˚C.

extract_protocol:
Lysates were clarified from sonicated nuclei and IR-DNA or Pol2-DNA complexes were isolated with antibody.
ChIP-seq libraries were constructed using Thruplex DNAseq kit (Rubicon) according to manufacturer’s instruction.

treatment_protocol: For serum starvation, medium was removed, cells were washed three times with PBS, and medium supplemented with 0.1% BSA was added to cells for 16h. Cells were stimulated with 10 nM insulin for 20min.

tag: chip antibody

value: rabbit, anti-IR_beta, sc-711


title: HepG2_Ins10nM_4h_4

library_source: transcriptomic

molecule: total RNA

tag: treatment


title: HepG2_Ins10nM_4h_5


title: HepG2_Ins0nM_4h_4

value: control


title: HepG2_Ins10nM_4h_2


title: HepG2_Ins10nM_4h_8


title: HepG2_Ins0nM_4h_2


title: HepG2_Ins0nM_4h_6


title: HepG2_Ins10nM_4h_7


title: HepG2_Ins0nM_4h_5


title: SH-SY5Y_input_rep1

source_name: SH-SY5Y cells


title: HepG2_Ins0nM_4h_9


title: HepG2_Ins10nM_4h_1


title: HepG2_Ins0nM_4h_8


title: HepG2_Ins0nM_4h_7


title: SH-SY5Y_IRb_rep2


title: HepG2_Ins0nM_4h_1


title: HepG2_IRb_rep2


title: RNA-seq in K562 cell line with shRNA for MTHFD1 knockdown, replicate 2

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

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

data_processing:
Base calls provided by the Illumina Realtime Analysis software were converted into BAM format using Illumina2bam and demultiplexed using BamIndexDecoder (https://github.com/wtsi-npg/illumina2bam)
Sequenced reads were trimmed for adaptor sequences
Reads were mapped to hg19 whole genome using bowtie2 v2.2.4 with the –very-sensitive parameter
Duplicate reads were marked and removed with picard tools version 1.118
Library quality was assessed with the phantomPeakQualtools scripts (Landt SG, Genome Research 2012).
Transcriptome analysis was performed using the Tuxedo suite. TopHat2 was supplied with reads passing vendor quality filtering (PF reads) and the Ensembl transcript set (Homo sapiens, e75, February 2014) as reference. TopHat2 analyses were run independently for each replicate.
Cufflinks (v2.2.1) was used to assemble transcripts from spliced read alignments, using the Ensembl e73 transcriptome as the reference as well as de novo assembly of transcript models.
Differential expression was assessed with Cuffdiff v2.2.1. Transcriptome sets of all replicates for each sample group were combined with Cuffmerge. Finally, cummeRbund and biomaRt were used to perform quality assessment and refine analysis results.
Genome_build: hg19
Supplementary_files_format_and_content: tsv file contains FPKM values for each sample at gene level

source_name: K562 cell line

growth_protocol: HAP1 cell lines were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM, Gibco), supplemented with 10% Fetal Bovine Serum (FBS; Gibco) and incubated in 5% CO2 atmosphere at 37°C.

extract_protocol:
RNA extraction was performed with Qiagen RNeasy Mini Kit (Cat No. 74106) according to the manufacturer's instructions.
Total RNA was quantified using Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the RNA integrity number (RIN) was determined using Experion Automated Electrophoresis System (Bio-Rad). RNA-seq libraries were prepared with TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library amount was quantified using Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using Experion Automated Electrophoresis System (Bio-Rad). For sequencing libraries were pooled, diluted and sequenced on Illumina HiSeq 3000 using 50 bp single-read chemistry.

tag: cell line

value: cell line


title: RNA-seq in K562 cell line with shRNA for MTHBRD knockdown, replicate 2

value: shMTHBRD


title: RNA-seq in K562 cell line with shRNA for PLKO knockdown, replicate 2

value: shPLKO


title: RNA-seq in K562 cell line with shRNA for MTHFD1 knockdown, replicate 1


title: RNA-seq in K562 cell line with shRNA for PLKO knockdown, replicate 1


title: RNA-seq in K562 cell line with shRNA for MTHBRD knockdown, replicate 1


title: RNA-seq in K562 cell line treated with Methotrexate for 6h, replicate 2

value: MTX

tag: timepoint


title: RNA-seq in K562 cell line with shRNA for BRD4 knockdown, replicate 2


title: RNA-seq in K562 cell line with shRNA for BRD4 knockdown, replicate 1


title: HepG2_Ins10nM_4h_6


title: HepG2_Ins10nM_4h_3


title: HepG2_Ins0nM_4h_3


title: RNA-seq in K562 cell line treated with Methotrexate for 6h, replicate 1


title: RNA-seq in K562 cell line treated with Methotrexate for 1h, replicate 1


title: RNA-seq in K562 cell line treated with JQ1 and Methotrexate for 1h, replicate 2

value: JQMT


title: RNA-seq in K562 cell line treated with Methotrexate for 1h, replicate 2


title: RNA-seq in K562 cell line treated with JQ1 and Methotrexate for 6h, replicate 2


title: RNA-seq in K562 cell line treated with JQ1 and Methotrexate for 6h, replicate 1


title: RNA-seq in K562 cell line treated with JQ1 and Methotrexate for 1h, replicate 1


title: RNA-seq in K562 cell line treated with JQ1 for 6h, replicate 2


title: RNA-seq in K562 cell line treated with JQ1 for 6h, replicate 1


title: RNA-seq in K562 cell line treated with JQ1 for 1h, replicate 1


title: ChIP-seq for H3K27ac in HAP1 cell line, replicate 1

data_processing:
Illumina Casava1.7 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequences
Reads were mapped to hg19 whole genome using bowtie2 v2.2.4 with the –very-sensitive parameter
Duplicate reads were marked and removed with picard tools version 1.118
Library quality was assessed with the phantomPeakQualtools scripts (Landt SG, Genome Research 2012).
Peaks for ChIP-seq samples were called with MACS2 version 2.1.1.20160309 using the “–nomodel” and “–extsize 147” parameters
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files contain counts of reads per basepair

source_name: ChIP-seq for H3K27ac in HAP1 cell line

extract_protocol:
For each immunoprecipitation 30 million nuclei were isolated. Cells were fixed with 1% paraformaldehyde for 10 min at room temperature. The fixation was stopped by addition of glycine. The collected pellet was sonicated using a Covaris S220 sonicator for 43 minutes to fragment the DNA to 200-700 bp. For immunoprecipitation, the sonicated chromatin was added to antibody-conjugated Protein A or G beads (Life Technologies) and incubated rotating at 4°C overnight. Used antibodies were: anti-MTHFD1 (C3, Santa Cruz), anti-BRD4 (A301‐985A, Bethyl Labs), anti-H3K27Ac (ab4729, Abcam) and mouse IgG (sc-2025, Santa Cruz).
Tagmentation was performed by resuspending the magnetic beads in 100 μl tagmentation reaction mix (10 mM Tris pH 8.0, 5 mM MgCl2, 10 % v/v dimethylformamide) containing 2 μl Tagment DNA Enzyme from the Nextera DNA Sample Prep Kit (Illumina) followed by an incubation for 3 min at 37°C. Subsequently, formaldehyde crosslinks were reverted by incubation in elution buffer (0.5% SDS, 300 mM NaCl, 5 mM EDTA and 10 mM Tris-HCl pH 8.0) containing 2 µl of Proteinase K for 1 h at 55°C, and then at 65°C overnight. The DNA was purified using the QIAquick PCR Purification kit (Qiagen). The enrichment of the libraries was performed in a 50 µl-reaction using Kapa HiFi HotStart ReadyMix (Kapa Biosystems) and 0.75 μM primers. Each DNA library was purified and size selected for a fragment length of 200-400 bp using SPRI AMPure XP beads (Beckman Coulter).

value: A


title: ChIP-seq for MTHFD1 in HAP1 cell line treated with DMSO, replicate 1

value: B

value: DMSO


title: ChIP-seq for MTHFD1 in HAP1 cell line treated with dBET6, replicate 2


title: ChIP-seq for H3K27ac in HAP1 cell line, replicate 2


title: ChIP-seq for MTHFD1 in HAP1 cell line treated with DMSO, replicate 2


title: RNA-seq in K562 cell line treated with DMSO for 6h, replicate 2


title: RNA-seq in K562 cell line treated with DMSO for 1h, replicate 2


title: ChIP-seq with mock IgG antibody in HAP1 cell line


title: RNA-seq in K562 cell line treated with DMSO for 6h, replicate 1


title: ChIP-seq for MTHFD1 in HAP1 cell line treated with dBET6, replicate 1


title: RNA-seq in K562 cell line treated with DMSO for 1h, replicate 1


title: ChIP-seq for Input in HAP1 cell line treated with DMSO, replicate 2


title: RNA-seq in K562 cell line treated with dBet6 for 6h, replicate 2


title: RNA-seq in K562 cell line treated with dBet6 for 6h, replicate 1


title: RNA-seq in K562 cell line treated with dBet6 for 1h, replicate 1

source_name: HAP1 cell line


title: RNA-seq in K562 cell line treated with dBet6 for 1h, replicate 2


title: RNA-seq in HAP1 cell line with shRNA for PLKO knockdown, replicate 2


title: ChIP-seq for Input in HAP1 cell line treated with dBET6, replicate 2


title: RNA-seq in K562 cell line treated with JQ1 for 1h, replicate 2


title: RNA-seq in HAP1 cell line with shRNA for PLKO knockdown, replicate 1


title: ChIP-seq with mock IgG antibody in HAP1 cell line treated with DMSO, replicate 2


title: ChIP-seq with mock IgG antibody in HAP1 cell line treated with DMSO, replicate 1


title: ChIP-seq for Input in HAP1 cell line treated with dBET6, replicate 1


title: RNA-seq in HAP1 cell line with shRNA for MTHFD1 knockdown, replicate 2


title: ChIP-seq with mock IgG antibody in HAP1 cell line treated with dBET6, replicate 2


title: RNA-seq in HAP1 cell line with shRNA for MTHFD1 knockdown, replicate 1


title: RNA-seq in HAP1 cell line with shRNA for MTHBRD knockdown, replicate 2


title: RNA-seq in HAP1 cell line with shRNA for MTHBRD knockdown, replicate 1


title: ChIP-seq with mock IgG antibody in HAP1 cell line treated with dBET6, replicate 1


title: RNA-seq in HAP1 cell line with shRNA for BRD4 knockdown, replicate 2


title: ChIP-seq for BRD4 in HAP1 cell line treated with DMSO, replicate 2


title: ChIP-seq for BRD4 in HAP1 cell line treated with DMSO, replicate 1


title: RNA-seq in HAP1 cell line with shRNA for BRD4 knockdown, replicate 1


title: ChIP-seq for BRD4 in HAP1 cell line treated with dBET6, replicate 1


title: ChIP-seq for BRD4 in HAP1 cell line treated with dBET6, replicate 2


title: RNA-seq in HAP1 cell line treated with Methotrexate for 6h, replicate 1


title: RNA-seq in HAP1 cell line treated with JQ1 and Methotrexate for 6h, replicate 2


title: ChIP-seq for Input in HAP1 cell line treated with DMSO, replicate 1


title: RNA-seq in HAP1 cell line treated with Methotrexate for 6h, replicate 2


title: RNA-seq in HAP1 cell line treated with Methotrexate for 1h, replicate 2


title: RNA-seq in HAP1 cell line treated with JQ1 and Methotrexate for 1h, replicate 2


title: RNA-seq in HAP1 cell line treated with JQ1 and Methotrexate for 1h, replicate 1


title: RNA-seq in HAP1 cell line treated with JQ1 for 6h, replicate 2


title: RNA-seq in HAP1 cell line treated with Methotrexate for 1h, replicate 1


title: RNA-seq in HAP1 cell line treated with JQ1 and Methotrexate for 6h, replicate 1


title: RNA-seq in HAP1 cell line treated with JQ1 for 1h, replicate 2


title: RNA-seq in HAP1 cell line treated with JQ1 for 6h, replicate 1


title: RNA-seq in HAP1 cell line treated with JQ1 for 1h, replicate 1


title: RNA-seq in HAP1 cell line treated with DMSO for 6h, replicate 2


title: RNA-seq in HAP1 cell line treated with DMSO for 1h, replicate 1


title: RNA-seq in HAP1 cell line treated with DMSO for 6h, replicate 1


title: RNA-seq in HAP1 cell line treated with DMSO for 1h, replicate 2


title: RNA-seq in HAP1 cell line treated with dBet6 for 6h, replicate 2


title: RNA-seq in HAP1 cell line treated with dBet6 for 6h, replicate 1


title: RNA-seq in HAP1 cell line treated with dBet6 for 1h, replicate 1


title: RNA-seq in HAP1 cell line treated with dBet6 for 1h, replicate 2


title: RNA-seq in A549 cell line with shRNA for PLKO knockdown, replicate 1

source_name: A549 cell line


title: RNA-seq in A549 cell line with shRNA for PLKO knockdown, replicate 2


title: RNA-seq in A549 cell line with shRNA for MTHBRD knockdown, replicate 2


title: RNA-seq in A549 cell line with shRNA for BRD4 knockdown, replicate 2


title: RNA-seq in A549 cell line with shRNA for BRD4 knockdown, replicate 1


title: RNA-seq in A549 cell line with shRNA for MTHFD1 knockdown, replicate 1


title: RNA-seq in A549 cell line treated with Methotrexate for 6h, replicate 1


title: RNA-seq in A549 cell line treated with Methotrexate for 6h, replicate 2


title: RNA-seq in A549 cell line treated with JQ1 and Methotrexate for 6h, replicate 2


title: RNA-seq in A549 cell line treated with JQ1 and Methotrexate for 1h, replicate 1


title: RNA-seq in A549 cell line with shRNA for MTHBRD knockdown, replicate 1


title: RNA-seq in A549 cell line treated with JQ1 and Methotrexate for 1h, replicate 2


title: RNA-seq in A549 cell line treated with Methotrexate for 1h, replicate 1


title: RNA-seq in A549 cell line treated with JQ1 and Methotrexate for 6h, replicate 1


title: RNA-seq in A549 cell line treated with JQ1 for 6h, replicate 2


title: RNA-seq in A549 cell line treated with Methotrexate for 1h, replicate 2


title: RNA-seq in A549 cell line treated with JQ1 for 6h, replicate 1


title: RNA-seq in A549 cell line treated with JQ1 for 1h, replicate 2


title: RNA-seq in A549 cell line treated with JQ1 for 1h, replicate 1


title: RNA-seq in A549 cell line treated with DMSO for 1h, replicate 2


title: RNA-seq in A549 cell line treated with DMSO for 6h, replicate 2


title: RNA-seq in A549 cell line treated with DMSO for 6h, replicate 1


title: RNA-seq in A549 cell line treated with dBet6 for 6h, replicate 1


title: RNA-seq in A549 cell line with shRNA for MTHFD1 knockdown, replicate 2


title: RNA-seq in A549 cell line treated with dBet6 for 1h, replicate 2


title: RNA-seq in A549 cell line treated with dBet6 for 1h, replicate 1


title: eGFP-Bsn-N2A-scRNA-seq

status: Public on Apr 03 2019

city: Hamburg

first: Manuel

middle: A

last: Friese

address: Falkenried 94

department: Institut für Neuroimmunologie und Multiple Sklerose

country: Germany

institute: Universitätsklinikum Hamburg-Eppendorf

description:
This sample represents ~500 single cells.
Read 1 contains the cell barcode, Read 2 contains the sequence.

data_processing:
Base calls performed with bcl2fastq v2.17.1.14
Drop-seq pipeline was run with standard parameters.
Genome_build: A custom reference genome was created from the Ensembl mouse reference genome (mm10) by replacing the murine with the rat Bsn gene.
Supplementary_files_format_and_content: Digital expression matrix; columns are cells, rows are genes.

molecule: polyA RNA

organism: Mus musculus

source_name: N2A cells, rat Bsn

extract_protocol:
Single cell suspensions were processed through Drop-Seq to generate a single-cell cDNA library.
Modified Nextera XT protocol

tag: genotype/variation

value: transfected with eGFP-Bsn (rat)


title: BMMSC-PolyIC-10ug-3

city: Ansan

first: Young Gyu

last: Chai

state: Gyeonggi-do

address: 55 Hanyangdaehak-ro

department: Molecualr & Life Science

country: South Korea

institute: Hanyang Univ.

data_processing:
Illumina CASAVA v1.8.2 software was used for basecalling.
To avoid low-quality data, we clipped and trimmed the reads using Trimmomatic (v0.33)
For the analysis of differentially expressed genes, the data of quality-checked reads for each condition were processed with the STAR (version 2.5.1) software based on reference genome sequence (Homo sapiens UCSC hg19) and the differential gene expressed values of each sample were calculated by the DESeq2 Bioconductor package.
The number of reads mapped to gene ID features were counted using STAR.
Genome_build: Homo sapiens UCSC hg19
Supplementary_files_format_and_content: tab-delimited text files including normalized read counts for each sample

source_name: Bone marrow Mesenchymal Stem Cells

growth_protocol: BM-MSC cells were cultured in low-glucose Dulbecco’s modified Eagle’s medium (DMEM) (Gibco, Carlsbad, CA) supplemented with 10% fetal bovine serum (FBS) (Hyclone, Logan, UT) and penicillin (100 U/ml)/streptomycin (100 mg/ml) (Gibco, Carlsbad, CA, USA). The cells were maintained in a humidified incubator with a 95% air/5% CO2 atmosphere at 37°C.The cells were maintained in a humidified incubator with 95% air and a 5% CO2 atmosphere at 37°C. The medium was replaced every 3–4 days. In this study, MSCs were used at passages 5 or 6.

extract_protocol:
Total RNA was extracted using RNAiso Plus (Takara, Shiga, Japan) and QIAGEN RNeasy® Mini kit (QIAGEN, Hilden, Germany). hMSCs or LPS-treated hMSCs were completely lysed with RNAiso Plus, then 200 μl of chloroform was added, and the tubes inverted for 5 min. The mixture was centrifuged at 12,000 x g for 15 min at 4°C, and the upper phase was placed into a new tube and 600 μl of 70% ethanol was added. The mixture was applied to an RNeasy mini column. The column was washed with wash buffer. To elute, RNase-free water (30 μl) was added directly onto the RNase mini column, followed by centrifugation at 12,000 x g for 3 min at 4°C. For ribosomal RNA (rRNA) depletion in total RNA, the RiboMinus Eukaryote kit (Life Technologies, Carlsbad, CA) was employed according to the manufacturer’s instructions. RNA libraries were created using the NEBNext® Ultra™ directional RNA library preparation kit for Illumina® (New England Biolabs, Ipswich, MA). rRNA-depleted total RNA was fragmented into small pieces using divalent cations at elevated temperatures. The first-strand cDNA was synthesized using reverse transcriptase and random primers, and then second-strand cDNA synthesis was performed using DNA polymerase I and RNase H. The cDNA fragments were processed using an end-repair reaction after the addition of a single ‘A’ base, followed by adapter ligation. These products were purified and amplified through PCR to generate the final cDNA library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells were incubated with Poly(I:C)(10 ug/ml, Sigma-Aldrich) for the specified time intervals (for 4 hours) under normal culture conditions.

tag: cell type

value: Lonza (donor 7F3915; Walkersville, MD)

value: treated with poly(I:C) (10ug/ml) for 4 hrs

tag: passages

value: passages 5 or 6


title: BMMSC-PolyIC-10ug-1


title: BMMSC-PolyIC-10ug-2


title: RNA-seq in A549 cell line treated with DMSO for 1h, replicate 1


title: RNA-seq in A549 cell line treated with dBet6 for 6h, replicate 2


title: CML2_HSC11

city: Worcester

first: Michael

middle: R.

last: Green

address: 364 Plantation Street

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

data_processing:
Illumina Casava software used for basecalling.
The reads qualities were assessed using fastqc (version 0.10.1) ;
Aligned the reads to hg19 using tophat (version 2.0.14), with default setting except set parameter read-mismatches to 2
HTseq-count (version 0.6.1p1) was used to generate gene count table.
Genome_build: hg19
Supplementary_files_format_and_content: htseq.counts.txt: tab-delimited text file includes the raw counts for each sample generated by htseq-count.
Supplementary_files_format_and_content: TPMs.txt: tab-delimited text file includes the TPM (Transcript Per Million) values generated by RSEM (version 1.3.0). The annotation of the genes are also provided in the file.

growth_protocol: Primary CML cells were subjected directly to flow sorting

extract_protocol:
Single cells were directly collected into lysis buffer and converted to cDNA.
Library was prepared using Nextera XT DNA sample preparation following Smart-seq2 protocol.

treatment_protocol: No treatment

tag: subject status

value: Chronic Myelogenous Leukemia (CML) patient

tag: subject id

tag: leukemia stage

value: Chronic Phase (Newly diagnosed)

tag: bcr-abl status

value: ABSENCE

tag: tissue

value: bone marrow

value: normal hematopoietic stem cells (HSCs)


title: CML2_HSC23


title: CML2_HSC17


title: CML2_HSC9


title: CML2_CMLSC21

value: PRESENCE

value: CML stem cells (CMLSCs)


title: CML2_HSC14


title: CML2_CMLSC19


title: CML2_HSC10


title: CML2_CMLSC23


title: CML2_CMLSC20


title: CML2_HSC21


title: CML2_CMLSC17


title: CML2_HSC15


title: CML2_CMLSC24


title: CML2_HSC16


title: CML2_HSC19


title: CML2_HSC12


title: CML2_HSC20


title: CML2_HSC24


title: CML2_HSC22


title: CML2_HSC13


title: CML2_CMLSC22


title: CML2_HSC18


title: CML2_HSC8


title: CML2_HSC7


title: CML2_HSC6


title: CML2_HSC5


title: CML2_HSC4


title: CML2_CMLSC18


title: CML2_HSC3


title: CML2_CMLSC15


title: CML2_HSC1


title: CML2_HSC2


title: CML2_CMLSC16


title: CML2_CMLSC6


title: CML2_CMLSC11


title: CML2_CMLSC2


title: CML2_CMLSC4


title: CML2_CMLSC14


title: CML2_CMLSC3


title: CML2_CMLSC1


title: CML3_HSC40


title: CML2_CMLSC5


title: CML2_CMLSC12


title: CML2_CMLSC9


title: CML3_HSC41


title: CML2_CMLSC13


title: CML3_HSC45


title: CML3_HSC42


title: CML2_CMLSC10


title: CML3_CMLSC51


title: CML3_CMLSC50


title: CML3_CMLSC49


title: CML3_CMLSC48


title: CML3_CMLSC47


title: CML3_CMLSC46


title: CML2_CMLSC7


title: CML2_CMLSC8


title: CML3_HSC43


title: CML3_HSC44


title: CML3_HSC36


title: CML3_HSC34


title: CML3_CMLSC45


title: CML3_HSC37


title: CML3_CMLSC44


title: CML3_CMLSC41


title: CML3_HSC32


title: CML3_CMLSC42


title: CML3_HSC35


title: CML3_HSC28


title: CML3_HSC29


title: CML3_HSC33


title: CML3_CMLSC38


title: CML3_HSC31


title: CML3_HSC30


title: CML3_CMLSC39


title: CML3_CMLSC37


title: CML3_CMLSC35


title: CML3_CMLSC34


title: CML3_HSC27


title: CML3_HSC24


title: CML3_HSC25


title: CML3_HSC23


title: CML3_HSC26


title: CML3_HSC22


title: CML3_CMLSC43


title: CML3_CMLSC40


title: CML3_HSC39


title: CML3_HSC38


title: CML3_CMLSC30


title: CML3_CMLSC32


title: CML3_CMLSC29


title: CML3_CMLSC31


title: CML3_HSC17


title: CML3_HSC21


title: CML3_HSC16


title: CML3_CMLSC28


title: CML3_CMLSC36


title: CML3_HSC18


title: CML3_CMLSC26


title: CML3_CMLSC27


title: CML3_CMLSC23


title: CML3_CMLSC24


title: CML3_CMLSC22


title: CML3_CMLSC25


title: CML3_HSC14


title: CML3_HSC15


title: CML3_HSC12


title: CML3_HSC13


title: CML3_CMLSC21


title: CML3_CMLSC20


title: CML3_HSC20


title: CML3_CMLSC19


title: CML3_HSC11


title: CML3_CMLSC17


title: CML3_HSC10


title: CML3_CMLSC16


title: CML3_CMLSC18


title: CML3_HSC8


title: CML3_HSC9


title: CML3_HSC7


title: CML3_CMLSC33


title: CML3_CMLSC14


title: CML3_CMLSC9


title: CML3_CMLSC13


title: CML3_HSC6


title: CML3_CMLSC12


title: CML3_HSC4


title: CML3_HSC3


title: CML3_HSC19


title: CML3_HSC2


title: CML3_CMLSC6


title: CML3_CMLSC5


title: CML3_HSC1


title: CML3_CMLSC4


title: CML3_CMLSC3


title: CML3_CMLSC15


title: CML3_CMLSC7


title: CML3_CMLSC11


title: CML2_HSC47


title: CML3_CMLSC1


title: CML2_HSC43


title: CML2_HSC45


title: CML2_HSC44


title: CML3_CMLSC10


title: CML2_HSC40


title: CML2_HSC41


title: CML3_CMLSC2


title: CML2_HSC37


title: CML2_HSC35


title: CML2_HSC39


title: CML2_HSC42


title: CML3_CMLSC8


title: CML3_HSC5


title: CML2_HSC36


title: CML2_HSC33


title: CML2_HSC32


title: CML2_HSC38


title: CML2_HSC31


title: CML2_HSC46


title: CML2_HSC28


title: CML2_HSC27


title: CML2_HSC26


title: CML2_HSC25


title: CML2_HSC29


title: CML2_HSC30


title: CML2_CMLSC49


title: CML2_CMLSC48


title: CML2_CMLSC45


title: CML2_CMLSC46


title: CML2_CMLSC44


title: CML2_CMLSC43


title: CML2_CMLSC41


title: CML2_CMLSC47


title: CML2_CMLSC40


title: CML2_CMLSC42


title: CML2_CMLSC37


title: CML2_CMLSC38


title: CML2_CMLSC31


title: CML2_CMLSC33


title: CML2_CMLSC39


title: CML2_CMLSC36


title: CML2_CMLSC30


title: CML2_CMLSC29


title: CML2_HSC34


title: CML2_CMLSC35


title: CML2_CMLSC32


title: CML2_CMLSC28


title: CML1_HSC46


title: CML2_CMLSC27


title: CML2_CMLSC25


title: CML1_HSC43


title: CML1_HSC44


title: CML1_HSC42


title: CML2_CMLSC26


title: CML1_HSC45


title: CML1_HSC41


title: CML1_CMLSC49


title: CML2_CMLSC34


title: CML1_CMLSC48


title: CML1_CMLSC45


title: CML1_HSC39


title: CML1_HSC38


title: CML1_HSC40


title: CML1_CMLSC47


title: CML1_HSC37


title: CML1_HSC36


title: CML1_CMLSC43


title: CML1_CMLSC40


title: CML1_CMLSC39


title: CML1_HSC35


title: CML1_HSC34


title: CML1_CMLSC37


title: CML1_HSC33


title: CML1_HSC30


title: CML1_HSC31


title: CML1_CMLSC50


title: CML1_CMLSC36


title: CML1_HSC32


title: CML1_CMLSC34


title: CML1_CMLSC32


title: CML1_HSC29


title: CML1_CMLSC33


title: CML1_CMLSC46


title: CML1_CMLSC35


title: CML1_HSC27


title: CML1_CMLSC42


title: CML1_CMLSC31


title: CML1_HSC24


title: CML1_HSC25


title: CML1_HSC28


title: CML1_CMLSC38


title: CML1_CMLSC44


title: CML1_CMLSC26


title: CML1_HSC26


title: CML1_CMLSC28


title: CML1_CMLSC41


title: CML1_HSC23


title: CML1_HSC22


title: CML1_HSC21


title: CML1_HSC18


title: CML1_CMLSC25


title: CML1_CMLSC24


title: CML1_CMLSC29


title: CML1_HSC19


title: CML1_HSC20


title: CML1_CMLSC21


title: CML1_CMLSC22


title: CML1_CMLSC23


title: CML1_CMLSC20


title: CML1_HSC17


title: CML1_HSC16


title: CML1_HSC15


title: CML1_HSC14


title: CML1_CMLSC27


title: CML1_CMLSC30


title: CML1_CMLSC17


title: CML1_CMLSC18


title: CML1_CMLSC16


title: CML1_HSC13


title: CML1_CMLSC14


title: CML1_HSC12


title: CML1_CMLSC15


title: CML1_HSC11


title: CML1_HSC10


title: CML1_HSC7


title: CML1_CMLSC13


title: CML1_CMLSC11


title: CML1_HSC9


title: CML1_HSC8


title: CML1_CMLSC10


title: CML1_CMLSC7


title: CML1_CMLSC9


title: CML1_HSC6


title: CML1_HSC3


title: CML1_CMLSC8


title: CML1_HSC5


title: CML1_CMLSC12


title: CML1_HSC4


title: CML1_CMLSC19


title: CML1_HSC2


title: CML1_HSC1


title: CML1_CMLSC6


title: CML1_CMLSC5


title: CML1_CMLSC4


title: CML1_CMLSC2


title: BMMSC-LPS-1ug-3

treatment_protocol: The cells were incubated with LPS (1ug/ml, Sigma-Aldrich) for the specified time intervals (for 4 hours) under normal culture conditions.

value: Lonza (donor 7F3674; Walkersville, MD)

value: treated with LPS (1ug/ml) for 4 hrs


title: BMMSC-LPS-1ug-2


title: CML1_CMLSC3


title: CML1_CMLSC1


title: BMMSC-LPS-1ug-1


title: MN-EAE-rep5

data_processing:
Library strategy: TRAP-seq
STAR aligment
Counting by featureCounts
DESeq2 analysis
Genome_build: mm10
Supplementary_files_format_and_content:Files include either raw or normalized counts. Rows represent genes

source_name: Cervical spinal cord

extract_protocol:
Translating ribosome affinity purification (TRAP)
NEBNext UltraTM RNA Library Prep Kit for Illumina (New England Biolabs)

tag: strain

value: Chat bacTRAP line DW167

tag: background strain

tag: disease state

value: EAE day 15

value: Cervical spinal cord

value: Motor neurons


title: MN-EAE-rep3


title: MN-EAE-rep2


title: MN-EAE-rep4


title: MN-Healthy-rep4

value: Healthy, not immunized


title: MN-Healthy-rep1


title: MN-Healthy-rep3


title: MN-Healthy-rep2


title: SC-EAE-rep3

value: All spinal cord cells


title: SC-EAE-rep5


title: SC-Healthy-rep4


title: SC-Healthy-rep5


title: SC-EAE-rep1


title: SC-EAE-rep4


title: SC-Healthy-rep3


title: SC-EAE-rep2


title: SC-Healthy-rep2


title: LRH1+APAP, liver 1

status: Public on Apr 02 2019

city: Seoul

first: Sang Geon

last: Kim

state: Seoul

address: San56-1, Sillim-dong, Kwanak-gu

department: College of Pharmacy

institute: Seoul National University

description:
Expression_Profile.FPKM.mm10.transcript.xlsx
23

data_processing:
Built-in software (HCS 2.2.70) was used for basecalling.
Quality check of basecalling was done using FastQC v0.10.0 by calculating phred quality score.
Sequenced reads were trimmed for adaptor sequence using Trimmomatic0.32, then mapped to mm10 whole genome using HISTAT2 v2.0.5 and Bowtie2 v2.2.6
Transcript assembly and calculation of normalized Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were done using StringTie v1.3.3b.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file include FPKM values for each Sample

source_name: LRH1+APAP, liver

extract_protocol:
Liver tissues were excised from mice and stored in RNAlater solution. Total RNA was extracted using Trizol.
A library was prepared with 1ug of total RNA for each sample by Illumina TruSeq mRNA Sample Prep kit.

value: Balb/c

value: Liver

tag: age

value: 9 weeks


title: LRH1+APAP, liver 3

description:
Expression_Profile.FPKM.mm10.transcript.xlsx
32


title: APAP, liver 3

description:
Expression_Profile.FPKM.mm10.transcript.xlsx
19

source_name: APAP, liver

value: APAP


title: APAP, liver 2

description:
Expression_Profile.FPKM.mm10.transcript.xlsx
18


title: APAP, liver 1

description:
Expression_Profile.FPKM.mm10.transcript.xlsx
16


title: Vehicle, liver 3

description:
Expression_Profile.FPKM.mm10.transcript.xlsx
11

source_name: Vehicle, liver

value: Vehicle


title: SC-Healthy-rep1


title: Vehicle, liver 1

description:
Expression_Profile.FPKM.mm10.transcript.xlsx
7


title: Vehicle, liver 2

description:
Expression_Profile.FPKM.mm10.transcript.xlsx
10


title: MN-Healthy-rep5


title: MN-EAE-rep1


title: L/L, cre rep4 (total RNA)

status: Public on Apr 01 2019

city: Perth

first: Stefan

middle: J

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

country: Australia

institute: The Kids Research Institute Australia

description: L/L, cre-S8

data_processing:
Basecalling performed with MSR: Generate FASTQ v1.0.0
Sequenced reads were aligned to the mouse genome reference sequence (mm10), masked for NUMTs regions, with bowtie2, and the subsequent alignments filtered with SAMtools v.1.3.1 (-q 2 -f 2 -F 256) to retain mapped proper pairs and exclude secondary alignments and multireads (read alignments with equal primary and secondary alignment scores).
Mitochondrial alignments were extracted, split by template strand and converted to full-length RNA fragment BED files, before coverage was calculated with BEDtools genomecov (-d -scale [1e+06/total mapped reads]), normalized to the total number of fragments mapped to the mouse whole genome (reads per million; RPM), and converted to wig format for visualisation.
Gene-level counts for the nuclear genome were calculated with featureCounts (-s 2) using the GENCODE vM12 annotation (excluding mitochondrial annotations), while counts for mitochondrial genes were calculated with BEDtools coverage (-counts -s -F 0.80) using a GENCODE-based annotation with contiguous mt-Atp8/6 and mt-Nd4l/4 intervals, and an approximate 7S RNA annotation (chrM:16035-16188). BEDtools coverage was used for mitochondrial genes due to their compact genomic organization and the subsequent overlapping of multiple genes by read alignments with post-transcriptional 5′ or 3′ extensions, which is addressed by specifying an minimum 80% overlap between the read and the annotation.
Count tables were collated in R v3.3.2 and differential expression between conditions was analyzed with DESeq2 v1.14.1.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files containing raw counts, normalised counts, WIG files of normalized coverage across chrM, and differential expression results

source_name: L/L, cre, Heart mitochondria

growth_protocol: To generate conditional TEFM knockout mice, an exon of this gene was loxP-flanked (Taconic Artemis GmbH, Cologne, Germany) and excised by breeding to mice expressing cre from the muscle creatinine kinase promoter.

extract_protocol:
RNA was isolated from crude heart mitochondria using the miRNeasy mini kit (QIAGEN) and the concentration, purity, and integrity was confirmed using a BioAnalyzer.
RNA sequencing libraries were constructed using the Illumina TruSeq Sample Prep Kit. Paired end deep sequencing of the mitochondrial RNAs was performed on an Illumina MiSeq according to the manufacturer’s instructions.

value: Heart mitochondria

tag: genotype

value: Tefm -/-


title: L/L, rep3 (total RNA)

source_name: L/L, Heart mitochondria

value: Tefm +/+


title: L/L, cre rep1 (total RNA)

description: L/L, cre-S5


title: L/L, rep4 (total RNA)


title: L/L, rep2 (total RNA)


title: L/L, cre rep2 (total RNA)

description: L/L, cre-S6


title: L/L, cre rep3 (total RNA)

description: L/L, cre-S7


title: LRH1+APAP, liver 2

description:
Expression_Profile.FPKM.mm10.transcript.xlsx
27


title: L/L, cre rep1 (small RNA)

description: L/L, cre-S2

data_processing:
Basecalling performed with MSR: Generate FASTQ v1.0.0
Reads were trimmed of 3′ adapter sequences with cutadapt v1.10 (-m 15 -a  TGGAATTCTCGGGTGCCAAGG).
Trimmed reads were aligned to the mouse genome reference sequence (mm10), masked for NUMTs regions, with bowtie2 and the subsequent alignments filtered with SAMtools v1.3.1 (-q 2 -F 260) to exclude unmapped reads, secondary alignments and multireads.
Mitochondrial alignments were extracted and split by strand, and coverage was calculated with BEDtools genomecov (-d -scale [1e+06/total mapped reads]), normalized to the total number of mapped reads to the mouse whole genome (reads per million; RPM) and converted to wig format for visualisation.
Gene-level counts for the nuclear genome were calculated with featureCounts (-s 1), while counts for mitochondrial genes were calculated with BEDtools coverage (-counts -s -F 0.80).
Count tables were collated in R v3.3.2 and differential expression between conditions was analyzed with DESeq2 v1.14.1.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files containing raw counts, normalized counts, WIG files of normalized coverage across chrM, and differential expression results

extract_protocol:
RNA was isolated from crude heart mitochondria using the miRNeasy mini kit (QIAGEN) and the concentration, purity, and integrity was confirmed using a BioAnalyzer.
RNA sequencing libraries were constructed using the Illumina Small RNA Sample Prep Kit. Single end deep sequencing of the mitochondrial RNAs was performed on an Illumina MiSeq according to the manufacturer’s instructions.


title: L/L, rep3 (small RNA)


title: L/L, cre rep3 (small RNA)

description: L/L, cre-S5


title: L/L, rep1 (total RNA)


title: L/L, cre rep2 (small RNA)

description: L/L, cre-S3


title: NS-3

city: Nanchang

first: Xiaoning

last: Zhang

address: 999 Xuefu R.D., Nanchang

country: China

institute: Nanchang University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using HISAT. Ana then the transcripts were assembled using Cufflinks.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Assembly transcripts were compared with annotated lncRNA in NONCODE database (http://www.noncode.org/) using Cuffcompare. The novel transcripts were predicted with CPC, txCdsPredict, CNCI and pfam algorithm. The chromosome coordinates of novel lncRNAs have been provided in the 'Novel_lncRNA.txt'.
Genome_build: hg19
Supplementary_files_format_and_content: txt files include gene_id, transcript_id(s), length expected_count, FPKM values for each Sample

source_name: Sperm

extract_protocol:
Ejaculated sperm were purified in two steps to ensure complete absence of somatic cell contamination. Firstly, seven groups sperm samples were subjected to 40 and 80% discontinuous percoll (Sigma Aldrich, USA) centrifugation gradient, as described elsewhere. Secondly, the purified spermatozoa were treated with somatic cell lysis buffer (SCL buffer: 0.2% SDS, 1.0% Triton X in diethylpyrocarbonate (DEPC) treated water) to eliminate the residual somatic cells. The incubation was extended until microscopic inspection confirmed the absence of somatic cells in the sperm suspension (non sperm cells < 0.2%). Finally, the sperm suspension was centrifuged at 5000 g for 5 minutes at 4°C and saved in -80°C. Moreover, the purity of spermatogenic cells was confirmed by the failure of amplification of somatic cell markers (E-cadherin, CD4 and c-kit). Total RNA were extracted from the purified sperm samples (n = 7) using RNeasy® Plus Micro (Qiagen, Duesseldorf, Germany) according to the manufacturer’s instructions with some modifications. Briefly, 1 ml of buffer RLT (a guanidine-thiocyanate lysis buffer supplemented with 10 mM DL-Dithiothreitol) was added to the sperm pellets, and then homogenized by passing through a 20-G needle attached to a 1-ml syringe 10 to 15 times. After total RNA was bound to the membrane and other contaminants are efficiently washed away, on-column DNase digestion was performed to eliminate trace amounts DNA contamination. Testis total RNA was purchased from cell applications,inc (San Diego, CA, USA). The concentration and integrity of the total RNA samples were evaluated using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific Inc., Wilmington, DE, USA) and a 2100-Bioanalyzer with the RNA 6000 Nano Chip (AppliedBiosystems, Carlsbad, CA, USA), respectively.
Strand-specific LncRNA library was generated with The SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian (Cat. Nos. 635005, Clontech Laboratories, Mountain View, CA, USA). The sequencing was conducted using Illumina HiSeqTM 4000 with PE100 according to the manufacturer’s instructions developed by BGI (Wuhan, China). About 10 G clean data were used to bioinformatic analysis.

treatment_protocol: Semen samples were collected after five to seven days of sexual abstinence in a clean, labeled, and widemouthed plastic container followed by incubation at 37°C till liquefaction. Semen samples parameters were assessed according to the WHO criteria (Fifth Edition). The sperm of asthenozoospermic patients (n = 36) obtained from The Maternal and Child Health Hospital in Jiangxi Province were divided into three biological replicates, each replicate has 12 samples. The normal sperm samples (n = 48) were provided by the Reproductive Hospital of Nanchang. Mixed pool of 12 random donors prepared four control sperm samples.

value: normal/control subject

value: 20-40 years old

value: Sperm


title: ATNZ-3

value: asthenozoospermic patient


title: NS-2


title: NS-1


title: testis

description: Testis total RNA was purchased from cell application Inc (San Diego, CA, USA).

source_name: Testes

value: 45 years old

value: Testis


title: L/L, rep2 (small RNA)


title: NS-4


title: control_spermatid_H3K27ac_ChIPseq

city: New Haven

first: Bluma

last: Lesch

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

description:
processed data files:
control_spermatid_H3K27ac_peaks.bed

data_processing:
ChIP-seq reads were filtered using fastq_quality_filter from FASTX Toolkit version 0.0.14 with parameters –q 20 –p80, and aligned to the mm10 mouse genome using bowtie version 1.2 with parameters –m 1 –k 1 –n 1  -l 40. Peaks were called using MACS version 1.4.2 with parameters –p 1e-5 –keep-dup 1 --nomodel.
Genome_build: mm10
Supplementary_files_format_and_content: .bed file with peak coordinates (on series record)

source_name: round spermatid

extract_protocol:
Adult testes were dissociated and round spermatids were collected by flow cytometry. Cells were fixed in 1% formaldehyde and sonicated.  Histone-DNA complexes were isolated with antibody.
Libraries were prepared using the TruSeq ChIP Sample Prep Kit (Illumina #IP-202-1012) according to the manufacturer’s instructions, except that size selection was performed after (instead of before) PCR amplification. Sequencing was done on an Illumina HiSeq2500 with 40 bp single-end reads, with multiplexing (3 samples per lane). Barcode: AGTTCC.

value: round spermatid

tag: chip antibody

value: H3K27ac (Abcam, ab4729)

tag: condition

value: control


title: ATNZ-2


title: UtxF1_BM_RNAseq_rep2

description: processed data file: Utx_F1_RNAseq_GEO.txt

data_processing:
RNA-seq data was quantified using kallisto version 0.43.0 with default parameters and with Ensembl build 85 transcripts as the set of target sequences.  Transcripts per million for individual transcripts from a single gene were summed to get one value per gene.
genome build: mm10
processed data files format and content: single tab-delimited .txt file with TPM values for each sample for each Ensembl (build 85) gene model.

source_name: bone marrow

extract_protocol:
Spine, pelvice bones, and long bones of the leg were collected and macerated.  Cells were washed, filtered, viably frozen, and stored in liquid nitrogen.  Cells were thawed in a water bath, and RNA was extracted from 2-6 million cells using an RNEasy Plus Mini kit (Qiagen).
Libraries were prepared using the Illumina TruSeq RNA library prep kit (Illumina #RS-122-2001) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 40 bp paired-end reads, with mulitplexing (4 samples per lane). Barcode: CTTGTA

value: bone marrow

value: healthy Utx F1


title: UtxF1_BM_RNAseq_rep5

extract_protocol:
Spine, pelvice bones, and long bones of the leg were collected and macerated.  Cells were washed, filtered, viably frozen, and stored in liquid nitrogen.  Cells were thawed in a water bath, and RNA was extracted from 2-6 million cells using an RNEasy Plus Mini kit (Qiagen).
Libraries were prepared using the Illumina TruSeq RNA library prep kit (Illumina #RS-122-2001) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 40 bp paired-end reads, with mulitplexing (4 samples per lane). Barcode: TTAGGC

value: sarcoma Utx F1


title: L/L, rep1 (small RNA)


title: UtxF1_BM_RNAseq_rep3

extract_protocol:
Spine, pelvice bones, and long bones of the leg were collected and macerated.  Cells were washed, filtered, viably frozen, and stored in liquid nitrogen.  Cells were thawed in a water bath, and RNA was extracted from 2-6 million cells using an RNEasy Plus Mini kit (Qiagen).
Libraries were prepared using the Illumina TruSeq RNA library prep kit (Illumina #RS-122-2001) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 40 bp paired-end reads, with mulitplexing (4 samples per lane). Barcode: CAGATC


title: L/L, cre rep4 (small RNA)

description: L/L, cre-S7


title: controlF1_BM_RNAseq_rep4

extract_protocol:
Spine, pelvice bones, and long bones of the leg were collected and macerated.  Cells were washed, filtered, viably frozen, and stored in liquid nitrogen.  Cells were thawed in a water bath, and RNA was extracted from 2-6 million cells using an RNEasy Plus Mini kit (Qiagen).
Libraries were prepared using the Illumina TruSeq RNA library prep kit (Illumina #RS-122-2001) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 40 bp paired-end reads, with mulitplexing (4 samples per lane). Barcode: CGATGT

value: control F1


title: controlF1_BM_RNAseq_rep5

extract_protocol:
Spine, pelvice bones, and long bones of the leg were collected and macerated.  Cells were washed, filtered, viably frozen, and stored in liquid nitrogen.  Cells were thawed in a water bath, and RNA was extracted from 2-6 million cells using an RNEasy Plus Mini kit (Qiagen).
Libraries were prepared using the Illumina TruSeq RNA library prep kit (Illumina #RS-122-2001) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 40 bp paired-end reads, with mulitplexing (4 samples per lane). Barcode: TAGCTT


title: controlF1_BM_RNAseq_rep3

extract_protocol:
Spine, pelvice bones, and long bones of the leg were collected and macerated.  Cells were washed, filtered, viably frozen, and stored in liquid nitrogen.  Cells were thawed in a water bath, and RNA was extracted from 2-6 million cells using an RNEasy Plus Mini kit (Qiagen).
Libraries were prepared using the Illumina TruSeq RNA library prep kit (Illumina #RS-122-2001) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 40 bp paired-end reads, with mulitplexing (4 samples per lane). Barcode: TGACCA


title: UtxF1_BM_RNAseq_rep1

extract_protocol:
Spine, pelvice bones, and long bones of the leg were collected and macerated.  Cells were washed, filtered, viably frozen, and stored in liquid nitrogen.  Cells were thawed in a water bath, and RNA was extracted from 2-6 million cells using an RNEasy Plus Mini kit (Qiagen).
Libraries were prepared using the Illumina TruSeq RNA library prep kit (Illumina #RS-122-2001) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 40 bp paired-end reads, with mulitplexing (4 samples per lane). Barcode: ACAGTG


title: controlF1_BM_RNAseq_rep2

extract_protocol:
Spine, pelvice bones, and long bones of the leg were collected and macerated.  Cells were washed, filtered, viably frozen, and stored in liquid nitrogen.  Cells were thawed in a water bath, and RNA was extracted from 2-6 million cells using an RNEasy Plus Mini kit (Qiagen).
Libraries were prepared using the Illumina TruSeq RNA library prep kit (Illumina #RS-122-2001) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 40 bp paired-end reads, with mulitplexing (4 samples per lane). Barcode: ACTTGA


title: UtxF1_BM_RRBS_rep3

description: bisulfite-converted genomic DNA

data_processing:
trim_galore version 0.4.2 was used to remove adapter sequences from RRBS reads, and a script provided with the NuGen Ovation RRBS kit was used to trim diversity sequences.  Reads were aligned to the genome using Bismark version 0.16.3 and bowtie2.  PCR duplicates were removed using the unique molecular identifiers (UMIs) added during library prep.  Percent methylation in 100 bp tiles across the genome was called using the methylKit package in R, and only tiles covered by at least 10 reads were considered in further analyses.
genome build: mm10
processed data files format and content: tab-delimited .txt files with percent methylation (percentage of reads with C vs T after bisulfite conversion) at each CpG covered by at least 10 reads.

extract_protocol:
Spine, pelvice bones, and long bones of the leg were collected and macerated.  Cells were washed and filtered.  DNA was extracted using a DNEasy Blood & Tissue kit (Qiagen).
Libraries were prepared using the NuGen Ovation RRBS Methyl-Seq System (NuGen #0353) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 75 bp single-end reads, with multiplexing (4 samples per lane).  UMI is included in sequence name. Barcode: GGAGAA.


title: UtxF1_BM_RRBS_rep2

description: bisulfite-converted genomic DNA

extract_protocol:
Spine, pelvice bones, and long bones of the leg were collected and macerated.  Cells were washed and filtered.  DNA was extracted using a DNEasy Blood & Tissue kit (Qiagen).
Libraries were prepared using the NuGen Ovation RRBS Methyl-Seq System (NuGen #0353) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 75 bp single-end reads, with multiplexing (4 samples per lane).  UMI is included in sequence name. Barcode: TCAGAG.


title: controlF1_BM_RRBS_rep4

description: bisulfite-converted genomic DNA

extract_protocol:
Spine, pelvice bones, and long bones of the leg were collected and macerated.  Cells were washed and filtered.  DNA was extracted using a DNEasy Blood & Tissue kit (Qiagen).
Libraries were prepared using the NuGen Ovation RRBS Methyl-Seq System (NuGen #0353) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 75 bp single-end reads, with multiplexing (4 samples per lane).  UMI is included in sequence name. Barcode: ACCTCA.


title: UtxF1_BM_RRBS_rep1

description:
bisulfite-converted genomic DNA
one raw file/SRA run (SRR) contains reads, one contains the 6bp UMI

extract_protocol:
Spine, pelvice bones, and long bones of the leg were collected and macerated.  Cells were washed and filtered.  DNA was extracted using a DNEasy Blood & Tissue kit (Qiagen).
Libraries were prepared using the NuGen Ovation RRBS Methyl-Seq System (NuGen #0353) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 75 bp single-end reads, with multiplexing (4 samples per lane).  "Index" fastq file contains 6bp UMI.  Barcode: GAGTCA.


title: controlF1_BM_RRBS_rep2

description: bisulfite-converted genomic DNA

extract_protocol:
Spine, pelvice bones, and long bones of the leg were collected and macerated.  Cells were washed and filtered.  DNA was extracted using a DNEasy Blood & Tissue kit (Qiagen).
Libraries were prepared using the NuGen Ovation RRBS Methyl-Seq System (NuGen #0353) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 75 bp single-end reads, with multiplexing (4 samples per lane).  UMI is included in sequence name. Barcode: AACCAG.


title: control_spermatid_H3K4me1_ChIPseq

description:
processed data files:
Utx_H3K27me3_ChIP_2kbtiles.txt
control_spermatid_H3K4me1_peaks.bed

data_processing:
ChIP-seq reads were filtered using fastq_quality_filter from FASTX Toolkit version 0.0.14 with parameters –q 20 –p80, and aligned to the mm10 mouse genome using bowtie version 1.2 with parameters –m 1 –k 1 –n 1  -l 40. Peaks were called using MACS version 1.4.2 with parameters –p 1e-5 –keep-dup 1 --nomodel.
genome build: mm10
processed data files format and content: .bed files with peak coordinates (on series record); single tab-delimited .txt file containing K27me3 ChIP signal scaled to reads per million, with input signal subtracted, in 2 kilobase tiles across the genome for all samples (on series record).

extract_protocol:
Adult testes were dissociated and round spermatids were collected by flow cytometry. Cells were fixed in 1% formaldehyde and sonicated.  Histone-DNA complexes were isolated with antibody.
Libraries were prepared using the TruSeq ChIP Sample Prep Kit (Illumina #IP-202-1012) according to the manufacturer’s instructions, except that size selection was performed after (instead of before) PCR amplification. Sequencing was done on an Illumina HiSeq2500 with 40 bp single-end reads, with multiplexing (3 samples per lane). Barcode: AGTCAA.

value: H3K4me1 (Abcam, ab8895)


title: controlF1_BM_RRBS_rep1

description: bisulfite-converted genomic DNA

extract_protocol:
Spine, pelvice bones, and long bones of the leg were collected and macerated.  Cells were washed and filtered.  DNA was extracted using a DNEasy Blood & Tissue kit (Qiagen).
Libraries were prepared using the NuGen Ovation RRBS Methyl-Seq System (NuGen #0353) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 75 bp single-end reads, with multiplexing (4 samples per lane). UMI is included in sequence name.  Barcode: AAGAGG.


title: Utx_sperm_RRBS_rep2

description: bisulfite-converted genomic DNA

source_name: sperm

extract_protocol:
Sperm were collected by swim-up and lysed.  DNA was extracted using a DNEasy Blood & Tissue kit (Qiagen).
Libraries were prepared using the NuGen Ovation RRBS Methyl-Seq System (NuGen #0353) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 75 bp single-end reads. Seven samples were multiplexed and run on three lanes each.  UMI is included in sequence name. Barcode: AGTGAG.

value: sperm

value: Utx cKO


title: Utx_sperm_RRBS_rep1

description: bisulfite-converted genomic DNA

extract_protocol:
Sperm were collected by swim-up and lysed.  DNA was extracted using a DNEasy Blood & Tissue kit (Qiagen).
Libraries were prepared using the NuGen Ovation RRBS Methyl-Seq System (NuGen #0353) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 75 bp single-end reads. Seven samples were multiplexed and run on three lanes each.  UMI is included in sequence name. Barcode: AACCAG.


title: control_spermatid_input_for_K4me1_K27ac

extract_protocol:
Adult testes were dissociated and round spermatids were collected by flow cytometry. Cells were fixed in 1% formaldehyde and sonicated.
Libraries were prepared using the  TruSeq ChIP Sample Prep Kit (Illumina #IP-202-1012) according to the manufacturer’s instructions, except that size selection was performed after (instead of before) PCR amplification. Sequencing was done on an Illumina HiSeq2500 with 40 bp single-end reads, with multiplexing (3 samples per lane). Barcode: CCGTCC.


title: Utx_sperm_RRBS_rep3

description: bisulfite-converted genomic DNA

extract_protocol:
Sperm were collected by swim-up and lysed.  DNA was extracted using a DNEasy Blood & Tissue kit (Qiagen).
Libraries were prepared using the NuGen Ovation RRBS Methyl-Seq System (NuGen #0353) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 75 bp single-end reads. Seven samples were multiplexed and run on three lanes each.  UMI is included in sequence name. Barcode: GTCGTA.


title: control_sperm_RRBS_rep2

description: bisulfite-converted genomic DNA

extract_protocol:
Sperm were collected by swim-up and lysed.  DNA was extracted using a DNEasy Blood & Tissue kit (Qiagen).
Libraries were prepared using the NuGen Ovation RRBS Methyl-Seq System (NuGen #0353) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 75 bp single-end reads. Seven samples were multiplexed and run on three lanes each.  UMI is included in sequence name. Barcode: GCACTA.


title: Utx_spermatid_input

description:
processed data files:
Utx_H3K27me3_ChIP_2kbtiles.txt
Utx_spermatid_H3K27me3_peaks.bed

data_processing:
ChIP-seq reads were filtered using fastq_quality_filter from FASTX Toolkit version 0.0.14 with parameters –q 20 –p80, and aligned to the mm10 mouse genome using bowtie version 1.2 with parameters –m 1 –k 1 –n 1  -l 40. Peaks were called using MACS version 2.1.0 with parameters –broad –broad-cutoff 0.01 –keep-dup 1 –nomodel. ChIP-seq signal was quantitated in 2 kilobase tiles across the genome using methods from Hisano et al., 2013. ChIP and input (MNase-only) data were scaled to get reads per million, input was substracted from ChIP signal for each tile and any negative values set to zero.  Each dataset was then re-scaled using the inverse of the reads-per-million scaling parameter originally used for the ChIP sample.
genome build: mm10
processed data files format and content: .bed files with peak coordinates (on series record); single tab-delimited .txt file containing K27me3 ChIP signal scaled to reads per million, with input signal subtracted, in 2 kilobase tiles across the genome for all samples (on series record).

extract_protocol:
Adult testes were dissociated and round spermatids were collected by flow cytometry. Cells were fixed in 1% formaldehyde and sonicated.
Libraries were prepared using the Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences #21024) according to the manufacturer’s instructions, except that size selection was performed after (instead of before) PCR amplification. Sequencing was done on an Illumina HiSeq2500 with 40 bp single-end reads, with multiplexing (3 samples per lane). Barcode: TTAGGC.


title: Utx_spermatid_H3K27me3_ChIPseq

extract_protocol:
Adult testes were dissociated and round spermatids were collected by flow cytometry. Cells were fixed in 1% formaldehyde and sonicated.  Histone-DNA complexes were isolated with antibody.
Libraries were prepared using the Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences #21024) according to the manufacturer’s instructions, except that size selection was performed after (instead of before) PCR amplification. Sequencing was done on an Illumina HiSeq2500 with 40 bp single-end reads, with multiplexing (3 samples per lane). Barcode: CGATGT.

value: H3K27me3 (Abcam, ab6002)


title: Utx_sperm_Mnase_seq_rep1

description:
processed data files:
Utx_H3K27me3_ChIP_2kbtiles.txt
Utx_sperm_H3K27me3_peaks.bed

extract_protocol:
Sperm were collected by swim-up and lysed.  Chromatin was digested with Mnase.
Libraries were prepared using the Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences #21024) according to the manufacturer’s instructions, except that size selection was performed after (instead of before) PCR amplification. Sequencing was done on an Illumina HiSeq2500 with 40 bp single-end reads, with multiplexing (3 samples per lane). Barcode: ATTCCT.


title: control_spermatid_H3K27me3_ChIPseq

description:
processed data files:
Utx_H3K27me3_ChIP_2kbtiles.txt
control_spermatid_H3K27me3_peaks.bed

extract_protocol:
Adult testes were dissociated and round spermatids were collected by flow cytometry. Cells were fixed in 1% formaldehyde and sonicated.  Histone-DNA complexes were isolated with antibody.
Libraries were prepared using the Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences #21024) according to the manufacturer’s instructions, except that size selection was performed after (instead of before) PCR amplification. Sequencing was done on an Illumina HiSeq2500 with 40 bp single-end reads, with multiplexing (3 samples per lane). Barcode: ACAGTG.


title: control_spermatid_input_for_K27me3

extract_protocol:
Adult testes were dissociated and round spermatids were collected by flow cytometry. Cells were fixed in 1% formaldehyde and sonicated.
Libraries were prepared using the Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences #21024) according to the manufacturer’s instructions, except that size selection was performed after (instead of before) PCR amplification. Sequencing was done on an Illumina HiSeq2500 with 40 bp single-end reads, with multiplexing (3 samples per lane). Barcode: TGACCA.


title: controlF1_BM_RNAseq_rep1

extract_protocol:
Spine, pelvice bones, and long bones of the leg were collected and macerated.  Cells were washed, filtered, viably frozen, and stored in liquid nitrogen.  Cells were thawed in a water bath, and RNA was extracted from 2-6 million cells using an RNEasy Plus Mini kit (Qiagen).
Libraries were prepared using the Illumina TruSeq RNA library prep kit (Illumina #RS-122-2001) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 40 bp paired-end reads, with mulitplexing (4 samples per lane). Barcode: GCCAAT


title: Utx_sperm_H3K27me3_ChIPseq_rep1

extract_protocol:
Sperm were collected by swim-up and lysed.  Chromatin was digested with Mnase and histone-DNA complexes were isolated with antibody.
Libraries were prepared using the Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences #21024) according to the manufacturer’s instructions, except that size selection was performed after (instead of before) PCR amplification. Sequencing was done on an Illumina HiSeq2500 with 40 bp single-end reads, with multiplexing (3 samples per lane). Barcode: AGTTCC.


title: control_sperm_RRBS_rep3

description: bisulfite-converted genomic DNA

extract_protocol:
Sperm were collected by swim-up and lysed.  DNA was extracted using a DNEasy Blood & Tissue kit (Qiagen).
Libraries were prepared using the NuGen Ovation RRBS Methyl-Seq System (NuGen #0353) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 75 bp single-end reads. Seven samples were multiplexed and run on three lanes each.  UMI is included in sequence name. Barcode: ACCTCA.


title: control_sperm_H3K27me3_ChIPseq_rep1

description:
processed data files:
Utx_H3K27me3_ChIP_2kbtiles.txt
control_sperm_H3K27me3_peaks.bed

extract_protocol:
Sperm were collected by swim-up and lysed.  Chromatin was digested with Mnase and histone-DNA complexes were isolated with antibody.
Libraries were prepared using the Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences #21024) according to the manufacturer’s instructions, except that size selection was performed after (instead of before) PCR amplification. Sequencing was done on an Illumina HiSeq2500 with 40 bp single-end reads, with multiplexing (3 samples per lane). Barcode: TGACCA.


title: control_sperm_Mnase_seq_rep1

extract_protocol:
Sperm were collected by swim-up and lysed.  Chromatin was digested with Mnase.
Libraries were prepared using the Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences #21024) according to the manufacturer’s instructions, except that size selection was performed after (instead of before) PCR amplification. Sequencing was done on an Illumina HiSeq2500 with 40 bp single-end reads, with multiplexing (3 samples per lane). Barcode: TTAGGC.


title: controlF1_BM_RRBS_rep3

description:
bisulfite-converted genomic DNA
one raw file/SRA run (SRR)contains reads, one contains the 6bp UMI

extract_protocol:
Spine, pelvice bones, and long bones of the leg were collected and macerated.  Cells were washed and filtered.  DNA was extracted using a DNEasy Blood & Tissue kit (Qiagen).
Libraries were prepared using the NuGen Ovation RRBS Methyl-Seq System (NuGen #0353) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 75 bp single-end reads, with multiplexing (4 samples per lane). "Index" fastq file contains 6bp UMI. Barcode: AGCATG.


title: Hdc_gfplo HSPC sample_3

city: New York

first: Timothy

middle: Cragin

last: Wang

state: NY

address: 1130 St. Nicholas Ave

department: Medicine- Liver and Digestive Diseases

institute: Columbia University Medical Center

data_processing:
Bases were called with RTA (Illumina).
Adaptors were trimmed and reads were converted from BCL to Fasta format with bcl2fastq (version 1.8.4).
Reads were mapped to the genome with Bowtie 2, Tophat 2.04 and HTSeq 0.6.1 .
Reads in each gene were counted with HTSeq-0.6.1 .
Genome_build: mm9
Supplementary_files_format_and_content: hdcpVShdcm.count.txt reports raw counts for each gene

source_name: Hdc-GFP mice (C57BL/6 background) bone marrow sorted for Hdc-GFPlo LSK(Lin-Sca-1+cKit+) cells

extract_protocol:
Total RNA was isolated from sorted 2,000 Hematopoetic Stem Progenitor Cells s using the ARCTURUS PicoPure RNA isolation kit (Life Technologies).
cDNA was amplified using the SMARTer Ultra Low Input RNA kit (Clontech Laboratories),
Libraries were constructed using the Nextera XT DNA Library Preparation kit (Illumina) according to manufacturer’s instructions.

value: Hdc-GFPlo LSK cells


title: Hdc_gfphi HSPC sample_4

source_name: Hdc-GFP mice (C57BL/6 background) bone marrow sorted for Hdc-GFPhi LSK(Lin-Sca-1+cKit+) cells

value: Hdc-GFP+ LSK cells


title: Hdc_gfplo HSPC sample_1


title: Hdc_gfphi HSPC sample_3

value: Hdc-GFPhi LSK cells


title: Hdc_gfplo HSPC sample_2


title: controlF1_BM_RRBS_rep5

description: bisulfite-converted genomic DNA

extract_protocol:
Spine, pelvice bones, and long bones of the leg were collected and macerated.  Cells were washed and filtered.  DNA was extracted using a DNEasy Blood & Tissue kit (Qiagen).
Libraries were prepared using the NuGen Ovation RRBS Methyl-Seq System (NuGen #0353) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 75 bp single-end reads, with multiplexing (4 samples per lane).  UMI is included in sequence name. Barcode: CGTAGA.


title: Hdc_gfplo HSPC sample_4


title: Hdc_gfphi HSPC sample_1

data_processing:
Bases were called with RTA (Illumina).
Adaptors were trimmed and reads were converted from BCL to Fasta format with bcl2fastq (version 1.8.4).
Reads were mapped to the genome with Bowtie 2, Tophat 2.04 and HTSeq 0.6.1
Reads in each gene were counted with HTSeq-0.6.1 .
Genome_build: mm9
Supplementary_files_format_and_content: hdcpVShdcm.count.txt reports raw counts for each gene

source_name: Hdc-GFP mice (C57BL/6 background) bone marrow sorted for Hdc-GFPhi LSK cells

extract_protocol:
Total RNA was isolated from sorted 2,000 Hematopoetic Stem Progenitor Cells using the ARCTURUS PicoPure RNA isolation kit (Life Technologies).
cDNA was amplified using the SMARTer Ultra Low Input RNA kit (Clontech Laboratories),
Libraries were constructed using the Nextera XT DNA Library Preparation kit (Illumina) according to manufacturer’s instructions.


title: control_sperm_RRBS_rep1

description: bisulfite-converted genomic DNA

extract_protocol:
Sperm were collected by swim-up and lysed.  DNA was extracted using a DNEasy Blood & Tissue kit (Qiagen).
Libraries were prepared using the NuGen Ovation RRBS Methyl-Seq System (NuGen #0353) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 75 bp single-end reads. Seven samples were multiplexed and run on three lanes each.  UMI is included in sequence name. Barcode: TGGTGA.


title: Hdc_gfphi HSPC sample_2

data_processing:
Bases were called with RTA (Illumina).
Adaptors were trimmed and reads were converted from BCL to Fasta format with bcl2fastq (version 1.8.4).
Reads were mapped to the genome with Bowtie 2, Tophat 2.04 and HTSeq 0.6.1.
Reads in each gene were counted with HTSeq-0.6.1 .
Genome_build: mm9
Supplementary_files_format_and_content: hdcpVShdcm.count.txt reports raw counts for each gene

source_name: Hdc-GFPhi mice (C57BL/6 background) bone marrow sorted for Hdc-GFPhi LSK cells

value: Hdc-GFPhi LSK(Lin-Sca-1+cKit+) cells


title: RNA from a mixture of anagen and telogen phase hair follicles, rep 3

city: Utrecht

first: Onur

last: BASAK

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Paired end reads were aligned to the transcriptome using bwa. Paired end reads obtained by CEL-seq2 were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the total number of reads for every transcript.
Genome_build: mm10
Supplementary_files_format_and_content: *Epi_org*.csv: Comma separated data file listing all genes (rows) and the number of sequenced transcripts for all samples. Column names indicate the GeneID and primer number of the sample. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.

source_name: skin

extract_protocol:
Cells were sorted into Trizol (Life Technologies) and total RNA was isolated according to the manufacturer’s instructions, with the following alterations. RNA was precipitated overnight at -20 °C, with 2.5ug GlycoBlue (Life Technologies).
RNA was processed using the previously described CEL-seq2 technique, with the indicated modifications. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

tag: source

value: tissue


title: RNA from a mixture of anagen and telogen phase hair follicles, rep 1


title: RNA from a mixture of anagen and telogen phase hair follicles, rep 2


title: Gadd45a-KO_rep6

city: Mainz

first: Emil

last: Karaulanov

address: Ackermannweg 4

institute: Institute of Molecular Biology

description: Gadd45a-/- hippocampus , replicate 6

data_processing:
NGS reads were mapped to the mouse reference genome (Illumina iGenomes reference, Ensembl NCBIM37/mm9 build) using the splice-aware mapper TopHat v.1.4.1 (https://ccb.jhu.edu/software/tophat/index.shtml) with parameters “-g 5 –G” (up to 5 best alignments allowed per read and usage of a GTF gene annotation file from iGenomes, Ensembl release 66).
The mapped reads were quality assessed with RSeQC (http://rseqc.sourceforge.net/) and ngs.plot (https://github.com/shenlab-sinai/ngsplot), sorted with SamTools (http://samtools.sourceforge.net/) and summarised on the gene level using the tool htseq-count from the package HTSeq v.0.5.4p3 (http://www-huber.embl.de/HTSeq/doc/count.html) and stranded option “-s reverse”.
Differential gene expression analysis was performed with the BioConductor package DESeq v.1.16.0 (http://bioconductor.org/packages/release/bioc/html/DESeq.html) following the standard routines recommended by the software authors.
Genome_build: NCBIM37 (mm9)
Supplementary_files_format_and_content: tab-delimited text file with summarised read counts per gene from htseq-count

source_name: hippocampus

growth_protocol: Heterozygote Gadd45a deficient mice (Hollander et al. 1999; doi:10.1038/13802) were interbred to obtain Gadd45a-/- and  wildtype embryos.

extract_protocol:
The mice were anesthetized 1 hour after the PA test with isoflurane and euthanized by decapitation. Their hippocampi were disected on ice, homogenized in a TissueLyser (Qiagen)  and total RNA was extracted using the RNeasy kit (Qiagen).
Next-generation sequencing (NGS) libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s instructions.

treatment_protocol: Six Gadd45a-/- mice and six wiltype siblings at age 6-7 months were subjected to the passive avoidance (PA) test.

value: hippocampus


title: Gadd45a-KO_rep5

description: Gadd45a-/- hippocampus , replicate 5


title: Gadd45a-KO_rep4

description: Gadd45a-/- hippocampus , replicate 4


title: P14 aIFNAR 1

city: San Diego

middle: R

last: Teijaro

state: CA

address: 10550 North Torrey Pines Rd

department: Immunology and Microbial Science

institute: The Scripps Research Institute

data_processing:
Quality of raw RNA-sequencing reads was checked using FastQC version 0.11.3 (Barbaham Institute, Cambridge, UK; http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Illumina’s bcl2fastq Conversion Software (version 2.17.1.14) was used to de-multiplex reads and convert BCL files generated by the Illumina NextSeq 500 to FASTQ.
Reads were mapped to the mouse genome (GRCm38 assembly with Ensembl v87 transcriptome annotations) and gene counts calculated using STAR version 2.5.2a (Dobin et al., 2013) using the following parameters: --quantMode GeneCounts –outSAMtype None –sjdbGTfile /Ensembl/Mus_musculus.GRCm38.87.gtf –sjdbOverhang 74
Genome_build: GRCm38
Supplementary_files_format_and_content: raw gene counts

source_name: CD8+ T cells

extract_protocol:
Cells were isolated by flow cytometry, gating on Thy1.1+ CD8+ cells and collecting live cells. RNA isolation from sorted cells was performed using the PicoPure RNA Isolation Kit (Thermo Fisher Scientific, Waltham, MA). RNA integrity was analyzed using Agilent RNA Nano Kit (Agilent, Santa Clara, CA).
Amplified cDNA was prepared using SMART-Seq v4 Ultra Low Input RNA Kit (Clontech, Mountain View, CA), sheared using Covaris tubes (Covaris, Woburn, MA) and Illumina libraries constructed using the NEBNext Ultra DNA Library Prep Kit (NEB, Ipswich, MA) and sequenced using the NextSeq 500 system (Illumina, San Diego, CA) at a depth of 20-25 million single-end 75 bp reads per sample.

treatment_protocol: P14 cells were adoptively transferred from a P14 Thy1.1 donor mouse to a Thy1.2 C57BL/6 recipient by intravenous injection. Anti-IFNAR1 antibody or IgG isotype control were administered on the same day. The following day LCMV clone 13 (2x10^6 ffu) was administered intravenously.

tag: infection

value: LCMV clone 13

value: CD8+ T cells

tag: tcr specificity

value: transgenic P14 TCR

tag: donor mice

tag: flow cytometry population


title: P14 naive 2

value: uninfected

tag: cell type


title: P14 naive 1


title: P14 Iso 1


title: Wildtype_rep6

description: Wildtype hippocampus , replicate 6

value: wild type


title: Gadd45a-KO_rep1

description: Gadd45a-/- hippocampus , replicate 1


title: P14 Iso 3


title: P14 aIFNAR 2


title: Gadd45a-KO_rep2

description: Gadd45a-/- hippocampus , replicate 2


title: Wildtype_rep5

description: Wildtype hippocampus , replicate 5


title: Wildtype_rep3

description: Wildtype hippocampus , replicate 3


title: Wildtype_rep2

description: Wildtype hippocampus , replicate 2


title: Wildtype_rep1

description: Wildtype hippocampus , replicate 1


title: P14 aIFNAR 3


title: P125

city: Leicester

first: Nicolas

last: Sylvius

address: University Road

department: CBS-Genetics

country: United Kingdom

institute: University of Leicester

data_processing:
Demultiplexing was performed by the Illumina Miseq Reporter
Sequencing reads were aligned to the genome and MiBase database using the Illumina Miseq workflow
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw (not normalized) read counts

source_name: Peripheral Blood Mononuclear Cells

growth_protocol: Periphearl Blood mononuclear cells were isolated from whole blood by density gradient centrifugation using Histopaque (Sigma-Aldrich, UK)

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion)
Libraries were prepared using the Illumina TrueSeq Smqll RNQ kit according to Illumina's protocol. 12 barcoded samples per run was used.

tag: diagnosis

value: Asthma

tag: Sex

value: F

value: Peripheral Blood Mononuclear Cells

value: blood


title: P137

value: M


title: P152


title: P14 Iso 2


title: P124


title: P121

value: Healthy control


title: P116b


title: Wildtype_rep4

description: Wildtype hippocampus , replicate 4


title: P072


title: P042


title: P116a


title: P117


title: P158


title: P149


title: P131


title: P146


title: P094


title: ATNZ-1

extract_protocol:
Ejaculated sperm were purified in two steps to ensure complete absence of somatic cell contamination. Firstly, seven groups sperm samples were subjected to 40 and 80% discontinuous percoll (Sigma Aldrich, USA) centrifugation gradient, as described elsewhere. Secondly, the purified spermatozoa were treated with somatic cell lysis buffer (SCL buffer: 0.2% SDS, 1.0% Triton X in diethylpyrocarbonate (DEPC) treated water) to eliminate the residual somatic cells. The incubation was extended until microscopic inspection confirmed the absence of somatic cells in the sperm suspension (non sperm cells < 0.2%). Finally, the sperm suspension was centrifuged at 5000 g for 5 minutes at 4°C and saved in -80°C. Moreover, the purity of spermatogenic cells was confirmed by the failure of amplification of somatic cell markers (E-cadherin, CD4 and c-kit). Total RNA were extracted from the purified sperm samples (n = 7) using RNeasy® Plus Micro (Qiagen, Duesseldorf, Germany) according to the manufacturer’s instructions with some modifications. Briefly, 1 ml of buffer RLT (a guanidine-thiocyanate lysis buffer supplemented with 10 mM DL-Dithiothreitol) was added to the sperm pellets, and then homogenized by passing through a 20-G needle attached to a 1-ml syringe 10 to 15 times. After total RNA was bound to the membrane and other contaminants are efficiently washed away, on-column DNase digestion was performed to eliminate trace amounts DNA contamination. Testis total RNA was purchased from cell applications,inc (San Diego, CA, USA). The concentration and integrity of the total RNA samples were evaluated using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific Inc., Wilmington, DE, USA) and a 2100-Bioanalyzer with the RNA 6000 Nano Chip (AppliedBiosystems, Carlsbad, CA, USA), respectively.
Strand-specific LncRNA library was generated with The SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian (Cat. Nos. 635005, Clontech Laboratories, Mountain View, CA, USA). The sequencing was conducted using Illumina HiSeqTM 4000 with PE100 according to the manufacturer’s instructions developed by BGI (Wuhan, China). About 10 G clean data were used to bioinformatic analysis.

tag: subject status

value: asthenozoospermic patient

value: 20-40 years old

value: Sperm


title: P032

tag: tissue


title: P144


title: P044


title: P143


title: P079


title: P122


title: taz1delta-WCE

status: Public on Mar 31 2019

city: Suita

first: Junko

last: Kanoh

state: Osaka

address: 3-1 Yamadaoka

department: Institute for Protein Research

country: Japan

institute: Osaka University

data_processing:
library strategy: BrdU-DNA-Seq
Basecalls performed using MiSeq Reporter 2.5.1.3
Reads were aligned to the pombe genome assembly using bowtie-1.1.1
Peaks were called using MACS-1.4.2 with the following setting: band width (300), model fold (10,30), pvalue cutoff (1.00e-05).
Genome_build: ASM294v2
Supplementary_files_format_and_content: wig files were generated using MACS-1.4.2

organism: Schizosaccharomyces pombe

growth_protocol: Cells were cultured in 320 ml of EMM medium more than 14 hours at 25℃, shifted to 35.5℃ at the cell concentration of 0.25×107 cells/ml, and cultured for 4 hours. And then, cells were treated with 0.5M HU 3.2ml and 10mM BrdU 3.2ml at 25℃ for 90 min.

extract_protocol:
Lysates were clarified from sonicated genomic DNA and BrdU-incorpolated DNA were purified using antibody against BrdU.
Libraries were prepared according to NEB's instructions accompanying the NEBNext ChIP-Seq Library Kit for Illumina (#E6240S).

tag: strain

tag: genotype/variation

value: h- ade6:ade6+-padh1-hENT ura4:ura4+-pnmt1-TK cdc25-22 taz1::hygr


title: P113


title: rif1delta-WCE

value: h- ade6:ade6+-padh1-hENT ura4:ura4+-pnmt1-TK cdc25-22 rif1::natr


title: rap1delta-IP

value: h- ade6:ade6+-padh1-hENT ura4:ura4+-pnmt1-TK cdc25-22 rap1::kanr

value: Anti-BrdU (BD Pharmingen, 555627, lot 3263611)


title: taz1delta-IP


title: P049


title: rap1delta-WCE


title: rif1delta-IP


title: wt-IP

source_name: widl type

value: h- ade6:ade6+-padh1-hENT ura4:ura4+-pnmt1-TK cdc25-22


title: Gadd45a-KO_rep3

description: Gadd45a-/- hippocampus , replicate 3

value: hippocampus


title: P145


title: SLE PBMC 5 (P7856_CD8_1)

city: Cambridge

first: Paul

last: Blainey

state: Massachusetts

address: 415 Main St

institute: Broad Institute

description: Processed data file: SLE.matrix

data_processing:
Bcls were demultiplexed using Illumina bcl2fastq (v2.20.0.422)
Fastqs were aligned to hg19 using STAR
Gene expression matrices were generated using Bowtie2
Genome_build: hg19
Supplementary_files_format_and_content: Matrices are provided as samples (columns) vs. genes (rows)

source_name: SLE PBMC

extract_protocol:
Cells were resuspended in TCL buffer, supplemented with 1 mg/mL proteinase K, and processed through the Smart-seq2 protocol (on a microfluidic device)
Libraries were constructed using the Nextera XT (Illumina) library preparation kit

tag: disease state

value: SLE

value: PBMC

tag: cell subset

value: CD8 T cells


title: SLE PBMC 5 (P7856_CD4_2)

description: Processed data file: SLE.matrix

value: CD4 T cells


title: wt-WCE


title: SLE PBMC 5 (P7856_CD4_1)

description: Processed data file: SLE.matrix


title: SLE PBMC 5 (P7856_CD19_2)

description: Processed data file: SLE.matrix

value: B cells


title: SLE PBMC 5 (P7856_CD14_1)

description: Processed data file: SLE.matrix

value: CD14 monocytes


title: SLE PBMC 5 (P7856_CD14_2)

description: Processed data file: SLE.matrix


title: SLE PBMC 5 (P7856_CD19_1)

description: Processed data file: SLE.matrix


title: SLE PBMC 5 (P7856_CD8_2)

description: Processed data file: SLE.matrix


title: SLE PBMC 4 (P7852_CD4_2)

description: Processed data file: SLE.matrix


title: SLE PBMC 4 (P7852_CD4_1)

description: Processed data file: SLE.matrix


title: SLE PBMC 4 (P7852_CD19_1)

description: Processed data file: SLE.matrix


title: SLE PBMC 4 (P7852_CD14_2)

description: Processed data file: SLE.matrix


title: SLE PBMC 4 (P7852_CD8_2)

description: Processed data file: SLE.matrix


title: SLE PBMC 3 (P7851_CD8_1)

description: Processed data file: SLE.matrix


title: SLE PBMC 3 (P7851_CD8_2)

description: Processed data file: SLE.matrix


title: SLE PBMC 3 (P7851_CD4_2)

description: Processed data file: SLE.matrix


title: SLE PBMC 3 (P7851_CD19_2)

description: Processed data file: SLE.matrix


title: SLE PBMC 2 (P6376_CD8_2)

description: Processed data file: SLE.matrix


title: SLE PBMC 4 (P7852_CD19_2)

description: Processed data file: SLE.matrix


title: SLE PBMC 2 (P6376_CD8_1)

description: Processed data file: SLE.matrix


title: SLE PBMC 3 (P7851_CD14_2)

description: Processed data file: SLE.matrix


title: SLE PBMC 3 (P7851_CD4_1)

description: Processed data file: SLE.matrix


title: SLE PBMC 3 (P7851_CD14_1)

description: Processed data file: SLE.matrix


title: SLE PBMC 4 (P7852_CD8_1)

description: Processed data file: SLE.matrix


title: SLE PBMC 2 (P6376_CD4_2)

description: Processed data file: SLE.matrix


title: SLE PBMC 2 (P6376_CD14_2)

description: Processed data file: SLE.matrix


title: SLE PBMC 3 (P7851_CD19_1)

description: Processed data file: SLE.matrix


title: SLE PBMC 2 (P6376_CD19_2)

description: Processed data file: SLE.matrix


title: SLE PBMC 2 (P6376_CD14_1)

description: Processed data file: SLE.matrix


title: SLE PBMC 2 (P6376_CD4_1)

description: Processed data file: SLE.matrix


title: SLE PBMC 2 (P6376_CD19_1)

description: Processed data file: SLE.matrix


title: SLE PBMC 4 (P7852_CD14_1)

description: Processed data file: SLE.matrix


title: SLE PBMC 1 (P6375_CD4_1)

description: Processed data file: SLE.matrix


title: SLE PBMC 1 (P6375_CD19_2)

description: Processed data file: SLE.matrix


title: SLE PBMC 1 (P6375_CD19_1)

description: Processed data file: SLE.matrix


title: Healthy PBMC 5 (P4415_CD8_2)

description: Processed data file: SLE.matrix

source_name: Healthy PBMC

value: Healthy


title: SLE PBMC 1 (P6375_CD14_1)

description: Processed data file: SLE.matrix


title: Healthy PBMC 5 (P4415_CD4_2)

description: Processed data file: SLE.matrix


title: SLE PBMC 1 (P6375_CD14_2)

description: Processed data file: SLE.matrix


title: Healthy PBMC 5 (P4415_CD8_1)

description: Processed data file: SLE.matrix


title: Healthy PBMC 5 (P4415_CD19_2)

description: Processed data file: SLE.matrix


title: Healthy PBMC 5 (P4415_CD14_2)

description: Processed data file: SLE.matrix


title: Healthy PBMC 4 (P3449_CD8_2)

description: Processed data file: SLE.matrix


title: Healthy PBMC 5 (P4415_CD14_1)

description: Processed data file: SLE.matrix


title: Healthy PBMC 4 (P3449_CD8_1)

description: Processed data file: SLE.matrix


title: Healthy PBMC 4 (P3449_CD19_2)

description: Processed data file: SLE.matrix


title: SLE PBMC 1 (P6375_CD8_2)

description: Processed data file: SLE.matrix


title: SLE PBMC 1 (P6375_CD8_1)

description: Processed data file: SLE.matrix


title: Healthy PBMC 4 (P3449_CD4_1)

description: Processed data file: SLE.matrix


title: Healthy PBMC 5 (P4415_CD19_1)

description: Processed data file: SLE.matrix


title: Healthy PBMC 4 (P3449_CD14_2)

description: Processed data file: SLE.matrix


title: Healthy PBMC 4 (P3449_CD19_1)

description: Processed data file: SLE.matrix


title: SLE PBMC 1 (P6375_CD4_2)

description: Processed data file: SLE.matrix


title: Healthy PBMC 3 (P1353_CD8_2)

description: Processed data file: SLE.matrix


title: Healthy PBMC 3 (P1353_CD4_2)

description: Processed data file: SLE.matrix


title: Healthy PBMC 3 (P1353_CD4_1)

description: Processed data file: SLE.matrix


title: Healthy PBMC 3 (P1353_CD19_2)

description: Processed data file: SLE.matrix


title: Healthy PBMC 3 (P1353_CD14_1)

description: Processed data file: SLE.matrix


title: Healthy PBMC 5 (P4415_CD4_1)

description: Processed data file: SLE.matrix


title: Healthy PBMC 4 (P3449_CD4_2)

description: Processed data file: SLE.matrix


title: Healthy PBMC 2 (P1002_CD8_2)

description: Processed data file: SLE.matrix


title: Healthy PBMC 2 (P1002_CD8_1)

description: Processed data file: SLE.matrix


title: Healthy PBMC 2 (P1002_CD4_1)

description: Processed data file: SLE.matrix


title: Healthy PBMC 2 (P1002_CD4_2)

description: Processed data file: SLE.matrix


title: Healthy PBMC 2 (P1002_CD19_2)

description: Processed data file: SLE.matrix


title: Healthy PBMC 4 (P3449_CD14_1)

description: Processed data file: SLE.matrix


title: Healthy PBMC 3 (P1353_CD8_1)

description: Processed data file: SLE.matrix


title: Healthy PBMC 2 (P1002_CD14_2)

description: Processed data file: SLE.matrix


title: Healthy PBMC 2 (P1002_CD19_1)

description: Processed data file: SLE.matrix


title: Healthy PBMC 2 (P1002_CD14_1)

description: Processed data file: SLE.matrix


title: Healthy PBMC 1 (P0772_CD8_2)

description: Processed data file: SLE.matrix


title: Healthy PBMC 3 (P1353_CD14_2)

description: Processed data file: SLE.matrix


title: Healthy PBMC 1 (P0772_CD4_2)

description: Processed data file: SLE.matrix


title: Healthy PBMC 1 (P0772_CD4_1)

description: Processed data file: SLE.matrix


title: Healthy PBMC 1 (P0772_CD19_2)

description: Processed data file: SLE.matrix


title: Leukemic stem cells (LSC) from NPM1c+ AML humanized mouse 2

city: CAMBRIDGE

first: Mandeep

last: Kaur

address: 500 MAIN STREET

institute: MIT

data_processing:
Sequences were trimmed (8 first base pairs) based on published protocols when using NuGen method
RSEM with BOWTIE2 default was used to align sequences to hg19.
EdgeR was then used to calculate differential expression and normalized to library size
Data was log2 transformed
Genome_build: hg19
Supplementary_files_format_and_content: [AML_norm_edgeR.txt] Tab-delimited txt file with pairwise comparison, average expression, fold change (FC) and normalized CPM values for all genes, along with p-value and FDR.

source_name: AML, LSC

extract_protocol:
Bone marrow cells were extracted from humanized NSG mice with AML. Cells were labeled with anti-CD123 and anti-CD33 antibodies followed by cell sorting with an ARIA cell sorter. Populations expressing GFP and CD33 (AML bulk leukemic cells) and populations expressing GFP, CD33 and CD123 (AML LSCs) were sorted. RNA was extracted with the RNeasy micro kit from Qiagen. cDNA was generated and amplified with the NUGEN OVATION kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: NSG

value: NPM1c driven de novo AML

value: Bone marrow

value: Leukemic stem cells


title: Bulk leukemic cells from NPM1c+ AML humanized mouse 2

source_name: AML, bulk leukemic

value: Bulk leukemic cells


title: Bulk leukemic cells from NPM1c+ AML humanized mouse 3


title: Healthy PBMC 1 (P0772_CD8_1)

description: Processed data file: SLE.matrix


title: Healthy PBMC 1 (P0772_CD14_2)

description: Processed data file: SLE.matrix


title: Healthy PBMC 3 (P1353_CD19_1)

description: Processed data file: SLE.matrix


title: Leukemic stem cells (LSC) from NPM1c+ AML humanized mouse 3


title: Healthy PBMC 1 (P0772_CD19_1)

description: Processed data file: SLE.matrix


title: Healthy PBMC 1 (P0772_CD14_1)

description: Processed data file: SLE.matrix


title: Leukemic stem cells (LSC) from NPM1c+ AML humanized mouse 1


title: AICAR2_3

status: Public on Mar 30 2019

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

institute: CyberomiX Inc

description: Bulk RNA-Seq data

data_processing:
All sequence reads were extracted in FASTQ format using BCL2FASTQ Conversion Software 1.8.4 in the CASAVA 1.8.2 pipeline.
The sequenced short reads were trimmed by Trimmomatic 0.3.3 and mapped to the human reference genome hg19 using TopHat 2.0.14 and Bowtie 2.2.5.
RPKM counts for each gene were obtained using the RPKMforgenes software.
Genome_build: The sequence reads were mapped to hg19 reference genes, downloaded on 25th April 2014
Supplementary_files_format_and_content: Calculation of gene expression value and normalization were performed by RPKMforgenes (10th, Dec, 2012). The processed data file contains Genename, Refseq, RPKM, and Rawcount columns (from left to right), and the expression level was represented by RPKM.

growth_protocol: Human ESCs (H9) which carried a PB-EOS-GFP/puroR reporter were cultured on MEF feeder cells in primate ES cell medium supplemented with 4 ng/mL bFGF. Cells were passaged every 5-7 days and medium was changed every day.

extract_protocol:
Total RNA was isolated using the RNeasy Mini kit (QIAGEN).
The sequencing libraries were constructed using KAPA stranded mRNA-seq Kit (KAPA Biosystems) from 20 ng or higher amount of total RNA and were sequenced in 100 cycle Single-Read mode of HiSeq2500.

treatment_protocol: Human ES cells (H9-EOS) were dissociated by TrypLE (Invitrogen) or Trypsin (Invitrogen) and re-plated (on MEF feeder) in primate medium  supplemented with bFGF and Y-27632 10 μM for the first 1 day, then medium was changed for Ndiff 227 with t2iL (PD0325901: 1 μM; CHIR99021: 1 μM; Lif: 1000 U/mL)+Gö6983 (5 μM)+Y-27632 and AICAR (1mM) for 2 weeks, t2iLGö+Y27632+AICAR (0.5 mM) for next 1 week. Then medium was changed for t2iLGö+puromycin (1 μg/mL) for 1 week selection. Reset cells were passaged every 3-5 days in t2iLGö. Medium was changed every day.

value: ESC

tag: treatment protocol

value: AICAR for 21 days

tag: Stage

value: reversion


title: AICAR2_1

description: Bulk RNA-Seq data


title: AICAR1_2

description: Bulk RNA-Seq data


title: AICAR2_2

description: Bulk RNA-Seq data


title: AICAR1_3

description: Bulk RNA-Seq data


title: Primed 2_2

description: Bulk RNA-Seq data

source_name: Primed 2_ESCs

value: no treatment

value: undifferentiated


title: Primed 2_1

description: Bulk RNA-Seq data


title: Bulk leukemic cells from NPM1c+ AML humanized mouse 1


title: Primed 2_3

description: Bulk RNA-Seq data


title: AICAR1_1

description: Bulk RNA-Seq data


title: NK2 Naive3

description: Bulk RNA-Seq data

source_name: NK2 Naive_ESCs

value: induction of NANOG and KLF2 for 14 days


title: NK2 Naive1

description: Bulk RNA-Seq data


title: Primed1_3

description: Bulk RNA-Seq data


title: 5iL/A3

description: Bulk RNA-Seq data

value: 5iL/A (MEKi, GSK3i, ROCKi, BRAFi, SRCi, Activin, LIF) for 12 days


title: SSEA1-GFP-_A15day_GFP+1

description: Bulk RNA-Seq data

data_processing:
All sequence reads were extracted in FASTQ format using BCL2FASTQ Conversion Software 1.8.4 in the CASAVA 1.8.2 pipeline.
The sequenced short reads were trimmed by Trimmomatic 0.3.3 and mapped to the human reference genome mm9 using TopHat 2.0.14 and Bowtie 2.2.5.
RPKM counts for each gene were obtained using the RPKMforgenes software.
Genome_build: The sequence reads were mapped to mm9 reference genes, downloaded on 30th Sept 2015
Supplementary_files_format_and_content: Calculation of gene expression value and normalization were performed by RPKMforgenes (10th, Dec, 2012). The processed data file contains Genename, Refseq, RPKM, and Rawcount columns (from left to right), and the expression level was represented by RPKM.

source_name: Rex1 GFPd2 ESC

growth_protocol: mESCs Rex1 GFPd2 were cultured on 0.1% gelatin-coated dishes in basal medium (GMEM supplemented with 10% Knockout™ Serum Replacement, 1% fetal bovine serum , 0.1 mM MEM non-essential amino acids, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, penicillin/streptomycin) and were differentiated on 0.1% gelatin-coated dishes in differentiation medium (DM) (alpha minimal essential medium MEM; supplemented with 10% fetal bovine serum and 50 nM 2-mercaptoethanol).

extract_protocol:
Total RNA was isolated using the RNeasy Mini kit (QIAGEN).
The sequencing libraries were constructed using KAPA stranded mRNA-seq Kit (KAPA Biosystems) from 20 ng or higher amount of total RNA

treatment_protocol: After 2 days differentiation in DM, SSEA1/GFP double negative cells were sorted and differentiated in DM without or with AICAR  until 15days. We also picked up naïve-like GFP+ colonies or sorted GFP+ cells. Those GFP+ cells were expanded on gelatin-coated plates in basal maintenance medium with Lif+2i and passaged every 3-4 days.

value: Lif+2i (Meki Gsk3i, Lif)

tag: gfp expression

value: positive

tag: sorting

value: maintenance after reversion


title: Primed1_2

description: Bulk RNA-Seq data


title: SSEA1-GFP-_A15day_colony10

description: Bulk RNA-Seq data


title: NK2 Naive2

description: Bulk RNA-Seq data


title: SSEA1-GFP-_A15day_GFP+_1

description: Bulk RNA-Seq data

value: AICAR for 15 days

value: reversion 15days

value: no sorting


title: SSEA1-GFP-_A15day_GFP+_2

description: Bulk RNA-Seq data


title: SSEA1-GFP-_A15day_colony7

description: Bulk RNA-Seq data


title: 5iL/A1

description: Bulk RNA-Seq data


title: SSEA1-GFP-_A15day_colony9

description: Bulk RNA-Seq data


title: SSEA1-GFP-_A15day_colony4

description: Bulk RNA-Seq data


title: SSEA1-GFP-_A15day_colony6

description: Bulk RNA-Seq data


title: SSEA1-GFP-_A15day_colony3

description: Bulk RNA-Seq data


title: SSEA1-GFP-_A15day

description: Bulk RNA-Seq data

value: negative


title: SSEA1-GFP-_A15day_GFP+

description: Bulk RNA-Seq data


title: SSEA1-GFP-_A15day_colony5

description: Bulk RNA-Seq data


title: SSEA1-GFP-_A15day_GFP-

description: Bulk RNA-Seq data


title: 5iL/A2

description: Bulk RNA-Seq data


title: differ_2day_SSEA1-GFP-

description: Bulk RNA-Seq data

value: differentiated 2days

value: sorting for SSEA1-GFP-


title: rex-1_differ_2day

description: Bulk RNA-Seq data


title: rex-1_undiffer

description: Bulk RNA-Seq data


title: SSEA1-GFP-_A15day_GFP+2

description: Bulk RNA-Seq data


title: SSEA1-GFP-_differ_15day

description: Bulk RNA-Seq data

value: differentiated 15days


title: Tet2 homo ko bio1 rep1

status: Public on Mar 28 2019

city: Shanghai

first: Shaorong

last: Gao

address: Siping Road NO.1239

institute: Tongji University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to mm9 reference genome using tophat(v1.3.3) default commands.
Differential gene expression was detemined using R package edgeR,genes with absolute value of log2 fold change less than 1 or p-value more than 0.05 were excluded.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM files and Counts files of gene were generated using cufflinks(v1.2.0) and htseq-count(v0.6.0) default commands

source_name: Tet2-/- TSC cell line 1

growth_protocol: TSCs were cultured on 70% FCM+25 ng/ml F4H (25 ng/ml fibroblast growth factor 4 (FGF4); Peprotech and 1.0 μg/ml heparin; Sigma).

extract_protocol:
Total RNA was isolated from cell pellets by Trizol reagent
RNA-Seq library were generated using KAPA Strandard mRNA-Seq Kits according to the manufacturer’s recommendations (Cat No. KK8440 box1 and KK8420 box2). Briefly, the mRNA was enriched using oligo(dT) magnetic beads and sheared to create short fragments of approximately 300 bp. cDNA was synthesized using random hexamer primers and purified using 1.8X Agencourt AMPure XP beads (Beckman). Finally, the sequencing primers linked to the cDNA fragments (approximately 300 bp) were isolated by gel electrophoresis and enriched by PCR amplification to construct the library. The sequencing was performed at the Sequencing Center in National Institute of Biology, Beijing using the HiSeq 2500 system developed by Illumina. Paired-end 100-bp sequencing was applied.


title: Tet2 homo ko bio1 rep2


title: Tet2 hetero ko bio1 rep1

source_name: Tet2+/- TSC cell line 1