title: Fix_80B_L2.D705

city: RTP

first: Susan

last: Hester

address: 109 TW Alexander Dr

institute: US EPA

description: Raw files were unavailable at the time of submission due to the COVID-19 epidemic

data_processing:
After sequencing, basecall files were converted into FASTQ output files using CASAVA (1.8.2). RNA-sequencing FASTQ data were demultiplexed, and sequencing adapters and other low-quality bases were removed from the ends of reads during clipping and trimming using the fastq-mcf3 tool (available at https://github.com/ExpressionAnalysis/ea-utils/blob/wiki/FastqMcf.md). Trimming included removal of Illumina adapters, homopolymers at read ends and nucleotides with quality scores (Phred Q-scores) <7. Any read with one base >95% frequency, homopolymers ≥ 4 within a read, and an average Q-score below 25, or length < 25 bases were also filtered by fastq-mcf3 tool.
Total RNA-seq reads from Studies 1 and 2 were aligned to External RNA Controls Consortium (ERCC) spike-ins to assess the success of library construction and sequencing. A subset of the reads (~1 million) was aligned to other added control sequences (PhiX and other Illumina controls used during library preparation), residual sequences (globin and rRNA), and poly-A/T sequences that persisted after clipping. Reads were also aligned to a sampling of intergenic regions to assess the level of DNA contamination.
Subsequent data analysis was carried out using Partek Flow NGS® v 6.17.1128 (Partek Inc., St. Louis, MO). Total RNA-seq reads were aligned using STAR v2.5.3a and counts matrices were generated using the Expectation-Maximization algorithm (Xing et al. 2006) implemented in Partek Flow. For mouse samples, clipped FASTQ files were aligned to the Mus musculus reference genome (GRCm38/mm10) and quantified to the transcriptome (RefSeq transcript 81-2017-05-02).  A 0.0001 offset was added to gene features with zero counts. Gene features with geometric mean of ≤ 1 count across all samples were filtered prior to counts per million normalization (CPM). Filtered, normalized gene counts were then analyzed for differential gene expression using Partek Gene Specific Analysis™ algorithm (GSA). Significance was defined as false discovery rate (FDR)-adjusted p-value of <0.05 and absolute fold change count ≥ 2.
For TempO-sequencing data, reads from FASTQ files involving rat were directly aligned to the Rattus norvegicus reference genome (rn6) using STAR v2.5.3a and quantified to rn6 - Ensembl Transcripts release 90 transcriptome annotation model. Reads from FASTQ files involving the AML12 cells were aligned to the Mus musculus reference genome (GRCm38/mm10) and quantified to the RefSeq transcript 81-2017-05-02 annotation model. Counts matrices were generated using the Expectation-Maximization algorithm (Xing et al. 2006) implemented in Partek Flow. One FR rat lung sample (RNA-Rat-54) was removed from subsequent analyses due to low read counts. Differentially expressed genes were identified using Partek Gene Specific Analysis™ algorithm (GSA). Significance was defined as false discovery rate (FDR)-adjusted p-value of <0.05 and absolute fold change count ≥ 2.
Genome_build: Rattus norvegicus rn6
Genome_build: Mus musculus mm10
Supplementary_files_format_and_content: raw and normalized gene counts

source_name: Liver

extract_protocol:
For frozen tissue samples, total RNA was extracted and purified using homogenization in RNAzol® RT (Molecular Research Center, Cincinnati, OH) and elution with RNeasy MinElute columns (Qiagen GmbH, Hilden, Germany) (Lake et al. 2016). The RNA quality of each sample was evaluated by Agilent 2100 Bioanalyzer and quantitated via Nanodrop and/or Qubit fluorometer (ThermoFisher Scientific, Waltham, MA). For FFPE samples that underwent RNA-sequencing, blocks were first sectioned into two 10-μm thick curls per sample using a Leica RM 2155 microtome (Leica Biosystems, Buffalo Grove, IL). RNA was then extracted following deparaffinization, proteinase K digestion (56°C for 15 min), heating (80°C for 15 min), DNAse treatment, RNeasy MinElute spin column (Qiagen GmbH, Hilden, Germany) clean up, and elution in 20-30 μl nuclease free water according to Qiagen AllPrep ® DNA/RNA FFPE kit protocols. RNA quality and concentration were quantified as for frozen samples.
For RNA-sequencing, 100 ng of total RNA was converted into cDNA libraries using the Illumina TruSeq Stranded Total RNA, as previously described (Wehmas et al. 2017 ). Ribosomal RNA was removed from samples through sequence-specific rRNA depletion using biotinylated probes and strepavadin bead immobilization (Ribo-Zero Gold Library Prep Kit, #RS-122-2303, Illumina, San Diego, CA). Samples were fragmented by heating with divalent cations. FFPE samples were subjected to reduced fragmentation/heating times to enable consistent library size distributions with frozen (FR). This process was quantified by Agilent Bioanalyzer (DNA 1000 kit #5067-1504) and qPCR (KAPA Library Quant Kit #KK4824, KAPA Biosystems, Wilmington, MA) followed by library normalization and sequencing. Samples were labeled with a barcode, mixed together in a sequencing pool, and run at eight per sequencing lane. Sequencing was performed at Expression Analysis (EA) (EA Genomic Services, Q2 Solutions – a Quintiles Quest Joint Venture, Durham, NC) using the Illumina HiSeq platform with 2x50bp-paired end reads

value: Male

value: Liver

tag: cell line

tag: preservation

value: directly fixed in 10% neutral buffered formallin for 18-24h. prior to paraffin embedding

tag: chemical treatment

value: 600 ppm phenobarbital


title: Fix_90C_L1.D711

status: Public on Sep 08 2020

type: SRA

state: NC

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: Sex

tag: tissue

value: Vehicle control (water)


title: Young_Tet1-/-_201_1_TGTACCTT (whs v16)

city: Tianjin

first: wang

middle: hua

last: song

address: Tianjin city, China

country: China

institute: nankai university

description: whs v16.txt

data_processing:
we analysed the raw data of fq.gz files by Hisat2,samtools  and featurecounts to get the raw counts.
Genome_build: mm10
Supplementary_files_format_and_content: The reads counts of 133 samples, containg young WT, young Tet2-/-, old WT and old Tet2-/-, and some of Tet1 samples.

source_name: oocyte

extract_protocol:
For oocyte sequence, we obtained 133 ovulated oocytes; for PGC sequence, we purified E13.5 PGC from 4-6 embryos each group
oocyte library were prepared using standard  Illumina protocols; PGC library were prepared according to micro RNA construction

tag: age

tag: genotype

value: Tet1 knock out

tag: cell type

value: single MII oocyte


title: Fix_82B_L1.D707


title: 4M-Wt-Spleen-CD8--T-RNA

city: Bronx

first: Boris

last: Bartholdy

state: NY

address: 1300 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

data_processing:
Sequencing and base calling was performed by GeneWiz (https://www.genewiz.com/)
Raw reads were subjected to adapter and quality trimming using bbduk.sh from BBTools.
RNA-seq reads were aligned to the mm10 genome assembly using STAR  with default parameters
Aligned bam files were processed in R/Bioconductor using SummarizeOverlaps to summarize the bam for the intervals in TxDb.Mmusculus.UCSC.mm10.knownGene (exons by gene) generating a "summarized experiment".
The "summarized experiment" was analyzed using deseq2 with default parameters. Deseq2 results summary was used to generate a CSV of base mean expression, fold change and p-value comparing wildtype and h1cTKO;vav-iCre expression which was exported as a CSV.
Genome_build: mm10 (GENCODE Release M20 (GRCm38.p6))
Supplementary_files_format_and_content: Results of differential expression between WT and cTKO cells from DESeq2 in comma-separated file format

source_name: CD8+ splenic T cells

extract_protocol:
5x10E5 B, and CD4+ and CD8+ T cells were sorted to Trizol by FACS.
paired-end RNA seq libraries were prepared from polyA-enriched RNA by  GeneWiz (https://www.genewiz.com/)

value: CD8+ splenic T cells

value: WT

value: M


title: 4M-Wt-Spleen-CD4--T-RNA

source_name: CD4+ splenic T cells

value: CD4+ splenic T cells


title: X63M_post

city: Boston

first: James

middle: M.

last: Billingsley

state: MA

address: Landmark Center, 3rd Floor East, 401 Park Drive

institute: harvard T.H. Chan school of public health

data_processing:
Pooled libraries were normalized to 2nM and denatured using 0.1 N NaOH prior to sequencing. Flowcell cluster amplification and sequencing were performed according to the manufacturer’s protocols using the NovaSeq S2 to produce 101bp paired-end reads with eight-base index barcodes. Data was analyzed using the Broad Picard Pipeline, which includes de-multiplexing and data aggregation.
Transcripts were annotated using Ensembl release 94
Counts of reads aligning to known genes were generated by featureCounts
transcripts per million (TPM) measurements per isoform were generated by quasialignment using Salmon.(9) Differential expression at the gene level was called with DESeq2(10) using counts per gene estimated from the Salmon quasialignments by tximport,
Genome_build: UCSC build hg38
Supplementary_files_format_and_content: normalized readcounts

organism: Homo sapiens

source_name: liver biopsy

extract_protocol:
sample preparation: Participant baseline evaluation included an ultrasound-guided percutaneous liver biopsy yielding two cores, which was completed on all participants except for those with a contraindication (e.g., anticoagulation). The first core was fixed in formalin, and subsequently underwent histopathologic review by a single expert pathologist blinded to treatment (D.E.K., National Institutes of Health). Histological scoring, including NAFLD Activity Score (NAS) and fibrosis stage, was performed according to the Nonalcoholic Steatohepatitis Clinical Research Network scoring system.(4) The second core was placed in an RNA stabilization reagent (RNAlater, Qiagen) and stored at -80o C for gene expression analysis. Both 1H-MRS and liver biopsy were repeated at 12 months following randomization. A total of 19 participants randomized to tesamorelin and 24 participants randomized to placebo had paired liver specimens available for gene sequencing.
Liver cores were placed in an RNA stabilization reagent (RNAlater, Qiagen) and stored at -80 C for gene expression analysis
Following extraction from liver tissue using RNeasy Plus Mini Kit (Qiagen), total RNA was quantified using the Quant-iT™ RiboGreen® RNA Assay Kit and normalized to 5ng/ul. Following plating, 2 uL of ERCC controls (using a 1:1000 dilution) and a k562 control were spiked into each sample. An 200ng aliquot of each sample was taken for library preparation using the Illumina TruSeq™ Stranded mRNA Sample Preparation Kit. oligo dT beads were used to select mRNA from the total RNA sample, followed by heat fragmentation and cDNA synthesis from the RNA template. The resultant 400bp cDNA underwent dual-indexed library preparation: ‘A’ base addition, adapter ligation using P7 adapters, and PCR enrichment using P5 adapters. After enrichment the libraries were quantified using Quant-iT PicoGreen (1:200 dilution).

value: liver

tag: patient diagnosis

value: HIV with NAFLD

tag: participant

tag: timepoint

tag: treatment

value: TESAMORELIN


title: 5F-Exp-Spleen-CD8-T-RNA

value: cTKO

value: F


title: Young_WT__246_11_GGCTACAG (whs v16)

description: whs v16.txt

value: wild type


title: Fix_75C_L2.D704

value: Male


title: Young_WT__246_10_TAGCTTGT (whs v16)

description: whs v16.txt


title: X55M_pre

value: PLACEBO


title: 4M-Wt-Spleen-B-RNA

source_name: splenic B cells

value: splenic B cells


title: Young_WT__246_8_ACTTGATG (whs v16)

description: whs v16.txt


title: 1F-Wt-Spleen-CD4--T-RNA


title: Fix_21C_L1.D706

value: Liver

value: directly fixed in 10% neutral buffered formallin for 18-24h. prior to paraffin embedding


title: X63M_pre


title: X54M_post


title: Fix_20B_L1.D702

value: 600 ppm phenobarbital


title: Fix_18D_L1.D701


title: 1F-Wt-Spleen-CD8-T-RNA


title: Young_WT__246_5_ACAGTGGT (whs v16)

description: whs v16.txt

value: single MII oocyte


title: Young_WT__246_6_GCCAATGT (whs v16)

description: whs v16.txt


title: Fix_20D_L1.D703


title: Young_WT__246_7_CAGATCTG (whs v16)

description: whs v16.txt


title: Fix_18B_L1.D712


title: X54M_pre


title: Young_WT__246_4_TGACCACT (whs v16)

description: whs v16.txt


title: 1F-Wt-Spleen-B-RNA


title: X51M_post


title: Young_WT__246_2_CGATGTTT (whs v16)

description: whs v16.txt


title: X51M_pre


title: Fix_8C_L1.D709

value: Vehicle control (water)


title: 10M-Exp-Spleen-B-RNA


title: 10M-Exp-Spleen-CD8-T-RNA

value: CD8+ splenic T cells


title: Fix_8D_L1.D710


title: 12-ctko-k36me2-2

library_source: genomic

data_processing:
Sequencing and base calling was performed by GeneWiz (https://www.genewiz.com/)
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2  with default parameters
THOR from the Regulatory Genomics Toolbox ( https://www.regulatory-genomics.org/thor-2) was used to generate postprocessed ChIP-seq signal (in bigWig format) , after  normalization to housekeeping genes.
Genome_build: mm10 (GENCODE Release M20 (GRCm38.p6))
Supplementary_files_format_and_content: bigWig: postprocessed ChIP-seq signal from THOR pipeline; bed: bed files with coordinates of control regions used for normalization.

molecule: genomic DNA

extract_protocol:
CD8+ splenic T cells from wildtype and cTKO animals were isolated by flow cytometry, and ChIP-seq using anti-H3K27me3 and anti-H3K36me2 antibodies was performed
see https://doi.org/10.1038/ncomms7033

tag: chip antibody


title: Young_WT__246_3_TTAGGCAT (whs v16)

description: whs v16.txt


title: X55M_post


title: 11-wt-k36me2-2

value: WT


title: X45M_pre


title: X45M_post


title: Young_WT__246_1_ATCACGTT (whs v16)

description: whs v16.txt


title: Fix_8A_L1.D708


title: Old_Tet2-/-_S1618 (whs v17)

value: Tet2 knock out


title: Old_Tet2-/-_S1617 (whs v17)


title: X44M_post

value: liver


title: 09-wt-k27me3-2


title: 10-ctko-27me3-2


title: 08-ctko-input-2


title: X40M_post

value: HIV with NAFLD


title: Old_Tet2-/-_S1616 (whs v17)


title: X40M_pre

value: TESAMORELIN


title: EtOH_80B_L5.D705

value: frozen first and then fixed in 70% ethanol prior to paraffin embedding


title: EtOH_90C_L5.D711


title: EtOH_82B_L4.D707


title: EtOH_75C_L5.D704


title: Old_Tet2-/-_S1614 (whs v17)


title: X38M_post


title: X38M_pre


title: Old_Tet2-/-_S1613 (whs v17)


title: 06-ctko-k36me2-1

value: cTKO


title: Old_Tet2-/-_S1615 (whs v17)


title: X44M_pre


title: 05-wt-k36me2-1


title: EtOH_20D_L5.D703


title: X37M_pre


title: EtOH_20B_L5.D702


title: Old_Tet2-/-_S1612 (whs v17)


title: 04-ctko-27me3-1


title: Old_Tet1-/-_315_1_TTCCATTG (whs v17)


title: 03-wt-k27me3-1


title: EtOH_18D_L5.D701


title: 07-wt-input-2


title: Old_Tet1-/-_209_7_TACTAGTC (whs v17)


title: EtOH_18B_L5.D712


title: X35N_pre


title: 01-wt-input-1


title: X35N_post


title: CD8+ splenic T cells_MAW-Lane2-8

data_processing:
Sequencing and base calling was performed by GeneWiz (https://www.genewiz.com/)
Raw reads were subjected to adapter and quality trimming on left side using bbduk.sh from BBTools.
For the determination of fragment sizes and nucleosome repeat length profiles, ATAC-seq reads were aligned to the mm10 genome assembly using bowtie2  with the parameters -reorder --mm --no-mixed --no-discordant --very-sensitive -X 1000.
Only uniquely aligned, correctly paired reads were retained and bed files containing the identified fragments were generated using custom python scripts, and shifted by +4 bp or -5bp, respectively, for reads mapped to the + or - strand.
Genome_build: mm10 (GENCODE Release M20 (GRCm38.p6))
Supplementary_files_format_and_content: The BED files contain the ATAC-seq fragments of properly paired reads only, and shifted by +4 bp or -5bp, respectively, for reads mapped to the + or - strand , and this data can be directly used to extract fragment sizes and nucleosome repeat lengths in selected genomic regions.

extract_protocol: ATACseq libraries were prepared for primary cells using the FAST-ATACseq protocol described previously (PMID: 27526324)

value: M


title: Old_Tet1-/-_209_6_TGTGGTTG (whs v17)


title: EtOH_21C_L4.D706

value: Male


title: EtOH_8D_L5.D710


title: X35M_pre

value: PLACEBO


title: EtOH_8C_L5.D709


title: Old_Tet1-/-_209_4_TACAGGAT (whs v17)


title: EtOH_8A_L4.D708


title: Old_Tet1-/-_209_3_TAGTGACT (whs v17)


title: X37M_post


title: CD8+ splenic T cells_MAW-Lane2-7

value: F


title: CD8+ splenic T cells_MAW-Lane2-6


title: X30N_pre


title: X35M_post


title: 18hr_90C_L3.D711

value: Liver

value: frozen first and then fixed in 10% neutral buffered formalin for 18-24h. prior to paraffin embedding


title: 18hr_82B_L3.D707


title: X30N_post


title: Old_Tet1-/-_209_2_TTCCTGCT (whs v17)


title: 02-ctko-input-1


title: X30M_pre


title: Old_WT_247_7_TGGCTCAG (whs v17)


title: CD8+ splenic T cells_MAW-Lane2-5


title: 18hr_80B_L4.D705

value: 600 ppm phenobarbital


title: Old_WT_247_6_TCATTGAG (whs v17)

value: single MII oocyte


title: CD4+ splenic T cells_MAW-Lane2-4

value: CD4+ splenic T cells


title: Old_WT_247_5_TGTATGCG (whs v17)


title: X30M_post


title: 18hr_75C_L4.D704


title: X27M_pre


title: CD4+ splenic T cells_MAW-Lane2-3


title: Old_WT_247_4_TCCAGTCG (whs v17)

value: Tet1 knock out


title: 18hr_21C_L3.D706

value: Vehicle control (water)


title: CD4+ splenic T cells_MAW-Lane2-2

value: WT


title: X27M_post

value: liver


title: 18hr_20D_L4.D703


title: CD4+ splenic T cells_MAW-Lane2-1


title: X26M_pre

value: HIV with NAFLD


title: peripheral blood B cells_MAW-Lane1-8

source_name: peripheral blood B cells

value: peripheral blood B cells


title: X26M_post


title: Old_WT_247_2_TCAGGAGG (whs v17)


title: peripheral blood B cells_MAW-Lane1-7


title: Old_WT_247_1_TCTCACGG (whs v17)


title: X25M_pre


title: peripheral blood B cells_MAW-Lane1-6


title: 18hr_18D_L4.D701


title: 18hr_20B_L4.D702


title: 18hr_18B_L4.D712


title: X25M_post


title: Old_WT_365_4_TGAACTGG (whs v17)


title: 18hr_8D_L3.D710


title: X21M_pre


title: 18hr_8C_L3.D709


title: X21M_post


title: peripheral blood B cells_MAW-Lane1-5


title: 18hr_8A_L3.D708


title: Old_WT_247_3_TAAGTTCG (whs v17)


title: X19N_pre


title: Old_WT_365_1_TCGAAGTG (whs v17)

value: wild type


title: 1-90C_L2.D711

value: frozen


title: CD4+ splenic T cells_MAW-Lane1-3

value: cTKO

value: M


title: CD4+ splenic T cells_MAW-Lane1-1


title: Old_WT_365_2_TAACGCTG (whs v17)


title: X18N_pre

value: TESAMORELIN


title: RNA-Rat-72

data_processing:
Library strategy: TempO-sequencing
After sequencing, basecall files were converted into FASTQ output files using CASAVA (1.8.2). RNA-sequencing FASTQ data were demultiplexed, and sequencing adapters and other low-quality bases were removed from the ends of reads during clipping and trimming using the fastq-mcf3 tool (available at https://github.com/ExpressionAnalysis/ea-utils/blob/wiki/FastqMcf.md). Trimming included removal of Illumina adapters, homopolymers at read ends and nucleotides with quality scores (Phred Q-scores) <7. Any read with one base >95% frequency, homopolymers ≥ 4 within a read, and an average Q-score below 25, or length < 25 bases were also filtered by fastq-mcf3 tool.
Total RNA-seq reads from Studies 1 and 2 were aligned to External RNA Controls Consortium (ERCC) spike-ins to assess the success of library construction and sequencing. A subset of the reads (~1 million) was aligned to other added control sequences (PhiX and other Illumina controls used during library preparation), residual sequences (globin and rRNA), and poly-A/T sequences that persisted after clipping. Reads were also aligned to a sampling of intergenic regions to assess the level of DNA contamination.
Subsequent data analysis was carried out using Partek Flow NGS® v 6.17.1128 (Partek Inc., St. Louis, MO). Total RNA-seq reads were aligned using STAR v2.5.3a and counts matrices were generated using the Expectation-Maximization algorithm (Xing et al. 2006) implemented in Partek Flow. For mouse samples, clipped FASTQ files were aligned to the Mus musculus reference genome (GRCm38/mm10) and quantified to the transcriptome (RefSeq transcript 81-2017-05-02).  A 0.0001 offset was added to gene features with zero counts. Gene features with geometric mean of ≤ 1 count across all samples were filtered prior to counts per million normalization (CPM). Filtered, normalized gene counts were then analyzed for differential gene expression using Partek Gene Specific Analysis™ algorithm (GSA). Significance was defined as false discovery rate (FDR)-adjusted p-value of <0.05 and absolute fold change count ≥ 2.
For TempO-sequencing data, reads from FASTQ files involving rat were directly aligned to the Rattus norvegicus reference genome (rn6) using STAR v2.5.3a and quantified to rn6 - Ensembl Transcripts release 90 transcriptome annotation model. Reads from FASTQ files involving the AML12 cells were aligned to the Mus musculus reference genome (GRCm38/mm10) and quantified to the RefSeq transcript 81-2017-05-02 annotation model. Counts matrices were generated using the Expectation-Maximization algorithm (Xing et al. 2006) implemented in Partek Flow. One FR rat lung sample (RNA-Rat-54) was removed from subsequent analyses due to low read counts. Differentially expressed genes were identified using Partek Gene Specific Analysis™ algorithm (GSA). Significance was defined as false discovery rate (FDR)-adjusted p-value of <0.05 and absolute fold change count ≥ 2.
Genome_build: Rattus norvegicus rn6
Genome_build: Mus musculus mm10
Supplementary_files_format_and_content: raw and normalized gene counts

organism: Rattus norvegicus

extract_protocol:
FFPE and cell samples that underwent TempO-sequencing were lysed using BioSpyder 2X lysis buffer
FFPE lysates were first deparaffinized by an overlay of mineral oil and heated to 95°C for 5 min. RNA, cellular lysate, and deparaffinized FFPE lysates were then treated with Protease K followed by annealing of a pair of detector oligos 25 nt adjacent to the target RNA. Excess oligos were digested with nuclease while those bound adjacent to the target were ligated (Yeakley et al. 2017) and amplified. Each sample was assigned a specific barcode pair that hybridized with the universal detector oligos allowing for sample identification following sequencing and library generation for the s1500+ rat and mouse transcriptome assays. The s1500+ rat measures 2603 genes (2636 probes) and the s1500+ mouse measures 2756 genes (3045 probes) targeting a subset of protein-coding genes considered representative of the entire transcriptome. Sample amplicons were pooled and purified using a PCR clean-up kit (Clontech, Mountain View, California). Libraries were sequenced using a NextSeq 550 sequencing platform by BioSpyder

value: Male

value: vehicle control


title: 1-82B_L2.D707

value: Liver


title: Old_WT_365_5_TACTTCGG (whs v17)


title: RNA-Rat-71


title: Young_Tet1-/-_201_6_TGATACGT (whs v17)


title: X13N_pre


title: Old_WT_365_3_TTGGTATG (whs v17)


title: X18N_post


title: Young_Tet1-/-_201_8_TTGACTCT (whs v17)


title: 1-80B_L3.D705

value: 600 ppm phenobarbital


title: RNA-Rat-70


title: 1-75C_L3.D704


title: Young_Tet1-/-_201_4_TTGGAGGT (whs v17)

value: single MII oocyte


title: CD4+ splenic T cells_MAW-Lane1-4

value: CD4+ splenic T cells


title: 1-21C_L2.D706


title: X13N_post


title: Young_Tet1-/-_201_3_TCTGCTGT (whs v17)


title: 1-20D_L3.D703


title: CD4+ splenic T cells_MAW-Lane1-2


title: X19N_post

value: PLACEBO


title: RNA-Rat-69


title: RNA-Rat-68


title: X11N_pre


title: X11N_post


title: RNA-Rat-67


title: 1-20B_L3.D702


title: Young_Tet1-/-_201_7_TGCATAGT (whs v17)


title: FFPE-Rat-84

value: directly fixed in 10% neutral buffered formallin for 18-24h. prior to paraffin embedding


title: 1-18D_L2.D701


title: X10M_pre


title: Young_Tet1-/-_201_1_TGTACCTT (whs v17)


title: 1-18B_L2.D712


title: Young_WT__246_15_TAAGCGTT (whs v17)


title: X10M_post


title: FFPE-Rat-83


title: X106M_pre


title: 1-8D_L2.D710

value: Vehicle control (water)


title: Young_WT__246_14_TCTCGGTT (whs v17)


title: FFPE-Rat-82


title: 1-8C_L2.D709


title: FFPE-Rat-81


title: Young_WT__246_13_TGGTTGTT (whs v17)


title: X106M_post

value: liver


title: Young_WT__246_12_CTTGTACT (whs v17)


title: X09M_pre

value: HIV with NAFLD


title: FFPE-Rat-80


title: Young_WT__246_11_GGCTACAG (whs v17)


title: Young_Tet1-/-_201_2_TTCTGTGT (whs v17)


title: 1-8A_L2.D708


title: Young_WT__246_10_TAGCTTGT (whs v17)


title: X09M_post


title: X08N_pre


title: FFPE-Rat-78

value: frozen first and then fixed in 10% neutral buffered formalin for 18-24h. prior to paraffin embedding


title: X08N_post


title: Young_WT__246_7_CAGATCTG (whs v17)

value: wild type


title: X03N_pre


title: FFPE-Rat-76


title: FFPE-Rat-77


title: FFPE-Rat-75


title: Young_WT__246_5_ACAGTGGT (whs v17)


title: X03N_post


title: X03M_post


title: FFPE-Rat-73


title: Young_WT__246_4_TGACCACT (whs v17)


title: X03M_pre


title: FFPE-Rat-74


title: X02N_pre


title: Young_WT__246_3_TTAGGCAT (whs v17)


title: RNA-Rat-54

source_name: Lung

value: WKY

value: Lung

value: frozen


title: RNA-Rat-53


title: RNA-Rat-52


title: Young_WT__246_1_ATCACGTT (whs v17)


title: Young_WT__246_2_CGATGTTT (whs v17)


title: FFPE-Rat-79


title: X02N_post


title: RNA-Rat-51


title: Young_WT__246_8_ACTTGATG (whs v17)


title: X02M_pre

value: TESAMORELIN


title: Young_Tet2-/-_T2147 (whs v17)

value: Tet2 knock out


title: X02M_post


title: Young_WT__246_6_GCCAATGT (whs v17)


title: RNA-Rat-50

value: Male

value: vehicle control


title: Young_Tet2-/-_T2148 (whs v17)


title: Young_Tet2-/-_T2146 (whs v17)


title: X01N_post


title: RNA-Rat-49


title: Young_Tet2-/-_T2145 (whs v17)


title: FFPE-Rat-66

value: directly fixed in 10% neutral buffered formallin for 1 yr. prior to paraffin embedding


title: FFPE-Rat-64


title: FFPE-Rat-63


title: FFPE-Rat-62


title: FFPE-Rat-65


title: Young_Tet2-/-_T2142 (whs v17)

value: single MII oocyte


title: X01N_pre


title: Pool 5 controls

type: RNA

city: Botucatu

first: Tainara

middle: Francini

last: Felix

state: SP

address: Av. Prof. Mário Rubens Guimarães Montenegro, s/n, s/n

department: Surgery and Orthopedics

country: Brazil

institute: UNESP

hyb_protocol: This assay was performed at the Princess Margaret Genomics Centre (https://www.pmgenomics.ca/pmgenomics/),according to the manufacturer’s protocol (available at https://www.nanostring.com/application/files/9614/8964/8051/MAN-C0009-05_nCounter_miRNA_Expression_Assay.pdf).

data_processing: The nSolver™ Analysis Software (www.nanostring.com/nsolver) was used to normalizemiRNA expression data against positive and negative controls, exogenous and endogenous controls, and to calculate fold change (FC) and associated p-values for deregulated miRNAs in patient plasma compared to reference, healthy controls.

label: Color codes

source_name: Plasma samples from non-diseased individuals

extract_protocol: Two hundred microliters (200µL) of plasma were used for RNA extraction with the miRNeasy Serum/Plasma Kit (Qiagen, Canada), following the manufacturer’s protocol.

treatment_protocol: 5µL of a 200pM solution of two exogenous synthetic spike-in controls (ath-miR-159a and cel-miR-248; Integrated DNA Technologies - IDT, Coralville, IA, USA), were added after sample lysis, according to the Nanostring protocol

tag: gender

value: Paired by sex

value: Paired by age

tag: histology

value: Not aplicable

value: Plasma

tag: smoking

value: Current

tag: Stage


title: Pool 7 controls

scan_protocol: This assay was performed at the Princess Margaret Genomics Centre (https://www.pmgenomics.ca/pmgenomics/),according to the manufacturer’s protocol (available at https://www.nanostring.com/application/files/9614/8964/8051/MAN-C0009-05_nCounter_miRNA_Expression_Assay.pdf).


title: Pool 4 controls

label_protocol: This assay was performed at the Princess Margaret Genomics Centre (https://www.pmgenomics.ca/pmgenomics/),according to the manufacturer’s protocol (available at https://www.nanostring.com/application/files/9614/8964/8051/MAN-C0009-05_nCounter_miRNA_Expression_Assay.pdf).


title: Pool 6 controls


title: Young_Tet2-/-_T2136 (whs v17)


title: FFPE-Rat-59

tag: cell line

tag: preservation


title: Young_Tet2-/-_T2137 (whs v17)

tag: strain


title: FFPE-Rat-60

tag: Sex

tag: chemical treatment


title: Pool 3 controls

tag: age

tag: tissue


title: FFPE-Rat-58


title: Young_Tet2-/-_T2134 (whs v17)

tag: genotype

tag: cell type


title: Young_Tet2-/-_T2138 (whs v17)


title: Young_Tet2-/-_T2143 (whs v17)


title: Young_Tet2-/-_T2144 (whs v17)


title: Pool 1 controls


title: Patient 1600

source_name: Plasma samples from patient with Lung cancer

value: M

value: ADC


title: Patient 2192

value: SQC


title: Young_Tet2-/-_T2135 (whs v17)


title: Pool 2 controls


title: FFPE-Rat-57

value: WKY

value: frozen first and then fixed in 10% neutral buffered formalin for 18-24h. prior to paraffin embedding


title: Young_Tet2-/-_T2141 (whs v17)


title: FFPE-Rat-61

value: Lung


title: Young_Tet2-/-_T2132 (whs v17)


title: Patient 1577


title: Young_Tet2-/-_T2131 (whs v17)


title: Young_Tet1-/-_T1468 (whs v17)

value: Tet1 knock out


title: Anp32e_Null_NTsiRNA_ATAC_seq_Rep1

city: Rochester

first: Fanju

last: Meng

address: 601 Elmwood Avenue

department: Biomedical Genetics

institute: University of Rochester Medical Center

description:
processed data file:
Anp32e_Null_NTsiRNA_ATAC.RPKM.bw
Anp32e_Null_NTsiRNA_ATAC.narrowPeak

data_processing:
Sequencing reads were aligned to Mm10 genome using Bowtie2, and then PCR duplicates were removed using Picard
Peak calling was performed using MACS2 with the following parameters: -f BAMPE --SPMR --nomodel -B, and mitochondrial peaks and peaks overlapping blacklisted regions were filtered out for downstream analysis.
Read count normalized genome browser tracks were generated using bamCoverage from merged bam files of triplicates with the following parameters: --normalizeUsing RPKM --binSize 10
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files and peak files

source_name: mouse embryonic fibroblasts

growth_protocol: MEFs were cultured in DMEM media (Thermo 11995073) containing 10% FBS and antibiotics. Approximately 200,000 cells were seeded on 10cm plates 1 day prior to RNA isolation or ATAC library preparation.

extract_protocol: ATAC-Seq libraries were prepared using the Illumina Nextera DNA Flex Library Prep Kit (cat: 20018704) according to standard methods.

treatment_protocol: Anp32e-/- MEFs were transfected using Lipofectamine RNAiMax (Thermo) with siRNAs, either non-targeting pool (Dharmacon D-001810-10-05) or a pool of 4 H2A.Z siRNAs (Dharmacon J-063612-10-0002, J-042994-10-0002, J-063612-09-0002, J-042994-09-0002).

value: mouse embryonic fibroblasts

tag: passage

value: below 8

tag: genotype/variation

value: Anp32e null

tag: sirna

value: Non-targeting


title: Young_Tet1-/-_T1466 (whs v17)

value: single MII oocyte


title: Anp32e_Null_H2AZsiRNA_ATAC_seq_Rep2

description:
processed data file:
Anp32e_Null_H2AZsiRNA_ATAC.RPKM.bw
Anp32e_Null_H2AZsiRNA_ATAC.narrowPeak


title: FFPE-Rat-55

value: Male

value: vehicle control


title: Lysate-Mouse-96

value: Liver

value: cells treated with 0.1% neutral buffered formalin for 10 minutes


title: Patient 1605

value: Plasma

value: Ex-Smoker


title: Anp32e_Null_H2AZsiRNA_ATAC_seq_Rep1


title: Young_Tet1-/-_T1465 (whs v17)


title: Lysate-Mouse-94

value: cells treated with vehicle (1x phosphate buffered saline) for 10 minutes


title: Young_Tet1-/-_T1467 (whs v17)


title: Lysate-Mouse-95


title: Young_Tet1-/-_T1463 (whs v17)


title: Young_Tet2-/-_T2133 (whs v17)

value: Tet2 knock out


title: Young_Tet1-/-_T1464 (whs v17)


title: Patient 1557

value: M

value: ADC


title: Lysate-Mouse-93


title: Patient 3753

value: F

value: Current


title: FFPE-Rat-56

value: WKY

value: Lung

value: frozen first and then fixed in 10% neutral buffered formalin for 18-24h. prior to paraffin embedding


title: Patient 2740


title: Patient 3612


title: Patient 3244

value: SQC


title: Patient 1173


title: Patient 1574


title: Young_Tet1-/-_T1461 (whs v17)

value: Tet1 knock out

value: single MII oocyte


title: Young_Tet1-/-_T1462 (whs v17)


title: Patient 1424


title: Lysate-Mouse-91

value: Male

value: cells treated with 0.006% neutral buffered formalin for 10 minutes


title: Young_WT_T2318 (whs v17)

value: wild type


title: Patient 2330

value: Plasma

value: Never


title: Lysate-Mouse-90

value: Liver

value: cells treated with vehicle (1x phosphate buffered saline) for 10 minutes


title: Kit_tdTomato_aortic_graft_4wk

city: London

first: Jiacheng

last: Deng

state: Not Applicable

address: James Black Centre, 125 Coldharbour Lane

country: United Kingdom

institute: King's College London

data_processing:
Data were processed following standard protocols using Cell Ranger version 3.0.2.
Cellranger mkfastq was used to demultiplex raw base call files into fastq files.
Cellranger count was used to perform alignment, filtering, barcode counting,  UMI counting, and to generate  feature-barcode matices.
Genome_build: mm10
Supplementary_files_format_and_content: H5 files includes tdTomato-labeled c-Kit lineage cells from 2-week and 4-week aortic grafts.

source_name: Aortic graft

extract_protocol:
Aoritc segments from donor BALB/c mice were transplanted into recipient Kit-CreERT2; ROSA26-tdTomato mice. Aortic grafts were harvested from Kit-CreERT2; ROSA26-tdTomato mice two or four weeks after surgury. Adventitial layer of the grafts was first dissected from the medial and neointimal layers. After three times washes of PBS, grafts were cut into fine pieces and digested in digestion solutions (which consist of 1 mg/ml papain, 0.5 mg/ml 1,4-Dithioerythritol, 0.156 mg/ml Taurine; 0.25 mg/ml bovine serum albumin in PBS) at 37 °C with reciprocal shaking for a total 40 min. Detached cells were then collected through a 40 μm cell strainer and suspended in DMEM with 10% FBS. Cells were further stained with DRAQ5 for 20 mins, followed by DAPI staining before loading to a Flow Cytometer. Single nucleated live tdTomato+ cells (DRAQ5+DAPI-tdTomato+) were sorted into PBS with 0.04% BSA and were then analyzed on a 10x Chromium instrument using Chromium Single Cell 3' Reagent Kit v3 chemistry (10X Genomics), following a standard protocol.
Library was generated and sequenced on a Hiseq 2500 System (Illumina)

value: Aortic graft

value: Kit-CreERT2; ROSA26-tdTomato


title: Young_WT_T2317 (whs v17)


title: Kit_tdTomato_aortic_graft_2wk


title: Patient 2296

value: M

value: Ex-Smoker


title: Young_WT_T2316 (whs v17)


title: Patient 2270

value: Current


title: Lysate-Mouse-89

value: cells treated with 0.03% neutral buffered formalin for 10 minutes


title: Patient 2284


title: KO_DE_2: RSK2(-/-) WT Diestrous

city: Nashville

first: Deborah

last: Lannigan

state: TN

address: 2220 Pierce Ave

department: Pathology, Microbiology and Immunology

institute: Vanderbilt University

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to the mm10 mouse genome with STAR
The transcripts were assembled using Gencode version 15 as gene models
Genes and transcripts were quantified with HTSeq
Batch correction was done with SVA, and differential gene expression analysis was performed with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: CSV file containing normalized raw reads for each sample anotated as ENSMUSG ID.

source_name: Mammary epithelial cells EpCam+Cd49f-lowSca+CD49b-

extract_protocol:
4th mammary glands were isolated from donor mice, minced, and digested in DMEM/F12 supplemented with 2mg/ml Collagenase A and 100U/ml Pen/Strep for 2.5h in 37oC 5% CO2 incubator.  Digested material was pelleted at 180g for 5 min and the pellet was resusupended in DNAse I (1000U/ml) for 3-5 min in 37oC 5% CO2 incubator.  Fetal bovine serum (FBS) was added and the digested tissue was pelleted at 180g for 10 min.  The pellet was washed with phosphate-buffer saline, pelleted, resuspended in Accumax and placed in Thermomixer at 37oC for 10 min.  Digested material was pelleted at 180g for 3 min, resuspended in 5x trypsin for 5 min at 37oC.  Trypsin was quenched with FBS and cells were pelleted and resuspended in PBS or DMEM/F12.  The cell preparation was filterd through 70-mm mesh to obtain single cell suspension. Cells were stained with primary Ab: EpCam, CD49f, Sca1, and CD49b and sorted using FACSAriaII. For RNA isolation, 5x10^4 EpCAMhiCD49f+Sca1+Cd49b- cells were FACS sorted and total RNA extraction (RNeasy Micro Kit) was performed. The RNA quality was tested using Agilent 100 Bioanalyzer (RIN 8)
Library constructions were performed using TruSeq RNA Library Prep Kit (Illumina)

treatment_protocol: RSK2(+/+) or RSK2(-/-) mice were aged to 12 wk and estrous cycle monitored. Mammary glands were harvested from mice in estrus (E) or diestrus (DE) stages.

value: 12 wk

value: mamamry gland

tag: cell population


title: Young_WT_T2315 (whs v17)


title: Lysate-Mouse-87


title: Young_WT_T2314 (whs v17)


title: Lysate-Mouse-86


title: Patient 2149

tag: gender

value: F

value: ADC


title: KO_E_3: RSK2(-/-) WT Estrous


title: KO_E_2: RSK2(-/-) WT Estrous


title: Lysate-Mouse-92

value: Male


title: Patient 2039

tag: histology

value: SQC


title: Young_WT_T2312 (whs v17)

value: wild type

value: single MII oocyte


title: Patient 1902

value: Plasma

tag: smoking


title: KO_DE_1: RSK2(-/-) WT Diestrous


title: Anp32e_Null_RNA-seq_Rep3

description:
processed data file:
Anp32e_Null_RNA-seq_RPKM.bw

data_processing:
Sequencing reads were aligned to Mm10 genome build using RNA-STAR with default setting.
Differential gene expression analysis was performed using Subread featureCounts, and DESeq2 with default setting.
Read count normalized genome browser tracks were generated using bamCoverage from merged Sam files of triplicates with the following parameters: --normalizeUsing RPKM
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files and DESeq2 differential gene expression table

extract_protocol: RNA-Seq libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit (cat: 20020598), according to standard methods, and total RNA was purified using the Zymo Research Direct-zol RNA Miniprep kit (cat: R2051)

value: mouse embryonic fibroblasts

value: below 8

value: Anp32e null


title: Young_WT_T2311 (whs v17)


title: Young_WT_T2118 (whs v17)


title: Lysate-Mouse-88

value: Liver

value: cells treated with 0.006% neutral buffered formalin for 10 minutes


title: WT_DE_2: RSK2(+/+) WT Diestrous


title: WT_DE_1: RSK2(+/+) WT Diestrous


title: Patient 2098

value: M

tag: Stage


title: WT_RNA-seq_Rep3

description:
processed data file:
WT_RNA-seq_RPKM.bw


title: Young_WT_T2313 (whs v17)


title: Anp32e_Null_RNA-seq_Rep1


title: WT_E_3: RSK2(+/+) WT Estrous


title: Patient 1854

value: Current


title: WT_E_2: RSK2(+/+) WT Estrous


title: Young_WT_T2117 (whs v17)


title: Lysate-Mouse-85

tag: cell line


title: Young_WT_T2115 (whs v17)


title: WT_E_1: RSK2(+/+) WT Estrous


title: Young_WT_T2116 (whs v17)


title: WT_RNA-seq_Rep2

description:
processed data file:
WT_RNA-seq_RPKM.bw


title: WT_RNA-seq_Rep1

description:
processed data file:
WT_RNA-seq_RPKM.bw


title: Anp32e_Null_RNA-seq_Rep2


title: Patient 1776

value: Ex-Smoker


title: Patient 1784


title: Young_WT_T2114 (whs v17)


title: Patient 1886

value: Never


title: Anp32e_Null_ATAC-seq_Rep3

description:
processed data file:
Anp32e_Null_ATAC-seq_RPKM.bw
Anp32e_Null_ATAC-seq.narrowPeak

data_processing:
Sequencing reads were aligned to Mm10 genome using Bowtie2, and then PCR duplicates were removed using Picard
Peak calling was performed using MACS2 with the following parameters: -f BAMPE --SPMR --nomodel -B, and mitochondrial peaks and peaks overlapping blacklisted regions were filtered out for downstream analysis.
Read count normalized genome browser tracks were generated using bamCoverage from merged Sam files of triplicates with the following parameters: --normalizeUsing RPKM
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files  and peak files


title: Young_WT_T2113 (whs v17)


title: Patient 1758


title: Patient 1807


title: Ana plus E2_a

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

data_processing:
Fastq files of pair-end RNA-Seq reads were aligned with Tophat 2.0.14  to the reference genome UCSC hg19 using Bowtie2 2.2.6 with default parameters.
Gene level counts were obtained using htseq-count with gene models from corresponding UCSC annotation packages.
Genome_build: hg19
Supplementary_files_format_and_content: raw counts in tab-delimited text file

molecule: polyA RNA

source_name: breast cancer cell line T47D

growth_protocol: T47D cells were grown in RPMI 1640 medium containing 5% (v/v) charcoal stripped FBS for 48 hours, followed with RPMI 1640 medium without FBS for additional 24 h.

extract_protocol:
RNA was prepared from cells using the TRIzol (Life Technologies) extraction kit. Genomic DNA was removed using the Ambion DNA-free kit.
NuGEN Encore reagents were used for library preparation of total RNA samples.

treatment_protocol: Cells were then treated with anastrozole (10 nM) alone, E2 (0.1 nM) alone or anastrozole (10 nM) +E2 (0.1 nM) for 12 hours.

value: breast

tag: treatment

value: anastrozole and estradiol


title: Anp32e_Null_ATAC-seq_Rep2


title: Patient 1601

value: F


title: Anp32e_Null_ATAC-seq_Rep1


title: Young_WT_T2112 (whs v17)

tag: strain


title: Young_WT_T2111 (whs v17)


title: E2_c

value: estradiol


title: Young_WT_T1488 (whs v17)


title: E2_a


title: E2_b


title: Patient 1524

value: ADC


title: Patient 1467


title: WT_ATAC-seq_Rep2

description:
processed data file:
WT_ATAC-seq_RPKM.bw
WT_ATAC-seq.narrowPeak

value: wild type


title: Young_WT_T1487 (whs v17)

value: single MII oocyte


title: Patient 1361

value: Plasma


title: Ana_c

value: anastrozole


title: WT_ATAC-seq_Rep1

value: mouse embryonic fibroblasts

value: below 8


title: Young_WT_T1485 (whs v17)


title: E193

city: Nanchang

first: Biao

last: Chen

address: Zhimin street, Jingkai district

institute: Jiangxi Agricultural University

data_processing:
Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats. Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment.
The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi).
Differential expression of miRNAs based on normalized deep-sequencing counts was analyzed by selectively using Fisher exact test, Chi-squared 2X2 test, Chi-squared nXn test, Student t test, or ANOVA based on the experiments design. The significance threshold was set to be 0.01 and 0.05 in each test.
To predict the genes targeted by most aboundant miRNAs, two computational target prediction algorithms (TargetScan 50 and Miranda 3.3a) were used to identify miRNA binding sites. Finally, the data predicted by both algorithms were combined and the overlaps were calculated. The GO terms and KEGG Pathway of these most aboundant miRNAs, miRNA targets were also annotated.
Genome_build: ftp://ftp.ensembl.org/pub/release-96/fasta/anas_platyrhynchos_platyrhynchos/dna/
Supplementary_files_format_and_content: abundance measurements

organism: Anas platyrhynchos

source_name: Breast muscle

growth_protocol: A total of 120 hatching eggs of Shanma ducks with same genetical background were obtained from Jiangxi Tianyun duck breeding farm (Nanchang, Jiangxi), and incubated in the incubator (Keyu, Shandong, China) at 37.2 °C, with 60 ± 10% humidity.

extract_protocol:
Total RNAs of six samples were extracted and purified using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Agilent 2100 with RIN number >7.0.  All samples were kept at -80 °C.
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Breast muscle samples of 15 ducks were collected every 3 days during E10 to 1-day post hatch (E10, E13, E16, E19, E22 and 1-day post hatch), quick-frozen by liquid nitrogen and stored at -80 °C until RNA extraction.

value: Shanma duck

tag: phenotype

value: most myoblasts have differentiated

value: embryo 19 days

tag: group


title: Patient 1245

tag: age


title: Ana_b

tag: tissue


title: Ana plus E2_b


title: Ana_a


title: E192


title: Patient 1204

value: SQC


title: Patient 1203

value: Current


title: Young_WT_T1484 (whs v17)

tag: genotype


title: KO_E_1: RSK2(-/-) WT Estrous

value: 12 wk

value: mamamry gland


title: WT_ATAC-seq_Rep3

tag: cell type


title: Young_WT_T1483 (whs v17)


title: Patient 1200

value: M

value: Ex-Smoker


title: Patient 1131


title: E191


title: Vehicle_c

value: breast

value: vehicle


title: Patient 1129

value: F

value: ADC


title: Young_WT_T1486 (whs v17)

value: wild type

value: single MII oocyte


title: Young_WT_T1482 (whs v17)


title: Vehicle_b


title: Vehicle_a


title: E132

value: myoblasts didn't differentiate

value: embryo 13 days


title: Young_WT_T1481 (whs v17)


title: Patient 1079

value: Plasma


title: E131

value: Shanma duck


title: Ana plus E2_c

value: anastrozole and estradiol


title: Patient 1058

value: SQC


title: E133


title: atac_PVneg_gpe_DD_rep1

status: Public on Sep 07 2020

city: Pittsburgh

first: Alyssa

middle: J

last: Lawler

state: PA

address: 4400 Fifth Ave

department: Computational Biology

institute: Carnegie Mellon University

description: transposase-accessible DNA

data_processing:
RNA-Seq alignment:  Fastq files were mapped to the mm10 genome (downloaded from UCSC in November 2015) using Hisat2 with default parameters.
RNA-Seq filtering:  Duplicate UMIs were removed using NuDup (https://github.com/tecangenomics/nudup).
Generation of RNA-Seq count matrix:  A counts per gene per sample matrix was constructed using Subread featureCounts version 1.6.4 with GRCm38 gene annotations (Ensembl version 79).
ATAC-seq alignment:  Reads were mapped to the mm10 genome with Bowtie2 using the ENCODE ATAC-seq pipeline (https://github.com/kundajelab/atac_dnase_pipelines) with default parameters.
ATAC-seq filtering:  Duplicate reads, mitochondrial reads, and blacklist region reads were filtered out as a part of the ENCODE ATAC-seq pipeline.
ATAC-seq peak calling:  Peaks were called on each sample individually using MACS2 within the ENCODE ATAC-seq pipeline workflow and reproducible peaks were determined on biological replicates with an IDR threshold of 0.1.
Generation of ATAC-seq count matrix:  The IDR peaks across all biological replicates were merged to create the genomic ranges of interest. Read counts per sample in these regions were computed with Rsubread featureCounts version 1.28.1 on the filtered bam alignments.
More information on all data processing and conclusions can be found in the publication.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw read counts for every gene and every sample
Supplementary_files_format_and_content: Genomic coordinates of merged ATAC-seq peak regions
Supplementary_files_format_and_content: Matrix table with raw read counts for every peak region and every sample
Supplementary_files_format_and_content: ATAC-seq peaks called in each sample
Supplementary_files_format_and_content: MACS2 pval signal tracks for each sample in bigwig format

extract_protocol:
PV neuron nuclei were tagged and isolated using cSNAIL, a virus-based adaptation of the INTACT method. Nuclei populations were then partitioned for total RNA extraction with the Qiagen RNeasy Micro Kit or ATAC-seq tagmentation with tn5 transposase.
RNA libraries were constructed using the Ovation SoLo RNA-seq System with Mouse AnyDeplete to remove ribosomal RNA. To retain immature nuclear transcripts, no polyA selection was performed. ATAC-seq libraries were constructed with standard amplification and size selection methods. See publication for more details.

treatment_protocol: Mice underwent dopamine depletion with bilateral, acute 6-OHDA lesion to the medial forebrain bundle or received a sham surgery injecting saline instead of the toxin.

value: gpe

value: PVneg

value: DD

tag: dopamine remaining

tag: Sex

value: 9 to 12 weeks


title: atac_PVpos_gpe_DD_rep2

description: transposase-accessible DNA

value: PVpos

value: M


title: atac_PVneg_gpe_DD_rep3

description: transposase-accessible DNA


title: atac_PVpos_gpe_DD_rep1

description: transposase-accessible DNA


title: atac_PVpos_gpe_Sham_rep2

description: transposase-accessible DNA

value: Sham


title: atac_PVneg_gpe_DD_rep2

description: transposase-accessible DNA


title: atac_PVneg_striatum_DD_rep4

description: transposase-accessible DNA

value: striatum

value: F


title: atac_PVneg_gpe_Sham_rep1

description: transposase-accessible DNA


title: atac_PVneg_gpe_DD_rep4

description: transposase-accessible DNA


title: atac_PVneg_striatum_DD_rep1

description: transposase-accessible DNA


title: atac_PVneg_striatum_Sham_rep2

description: transposase-accessible DNA


title: atac_PVneg_striatum_DD_rep2

description: transposase-accessible DNA


title: atac_PVpos_gpe_DD_rep3

description: transposase-accessible DNA


title: atac_PVpos_gpe_DD_rep4

description: transposase-accessible DNA


title: atac_PVneg_striatum_Sham_rep1

description: transposase-accessible DNA


title: atac_PVpos_striatum_Sham_rep2

description: transposase-accessible DNA


title: atac_PVneg_striatum_DD_rep3

description: transposase-accessible DNA


title: atac_PVpos_striatum_DD_rep4

description: transposase-accessible DNA


title: atac_PVneg_gpe_Sham_rep2

description: transposase-accessible DNA


title: atac_PVpos_striatum_DD_rep2

description: transposase-accessible DNA


title: atac_PVpos_striatum_DD_rep3

description: transposase-accessible DNA


title: atac_PVpos_striatum_DD_rep1

description: transposase-accessible DNA


title: atac_PVpos_striatum_Sham_rep1

description: transposase-accessible DNA


title: atac_PVneg_cortex_Sham_rep2

description: transposase-accessible DNA

value: cortex


title: atac_PVpos_gpe_Sham_rep1

description: transposase-accessible DNA


title: atac_PVneg_cortex_Sham_rep1

description: transposase-accessible DNA


title: atac_PVneg_cortex_DD_rep4

description: transposase-accessible DNA


title: atac_PVneg_cortex_DD_rep3

description: transposase-accessible DNA


title: atac_PVneg_cortex_DD_rep2

description: transposase-accessible DNA


title: atac_PVneg_cortex_DD_rep1

description: transposase-accessible DNA


title: atac_PVpos_cortex_DD_rep3

description: transposase-accessible DNA


title: atac_PVpos_cortex_Sham_rep2

description: transposase-accessible DNA


title: Day0 Kdm5c 4 (RNA-Seq)

city: Los Angeles

first: Karen

last: Reue

state: CA

address: 695 Charles E. Young Drive South

institute: University of California, Los Angeles

data_processing:
RNA-seq alignment was performed with STAR v2.7.2a to the mouse genome GRCm38.97.
The read-count per gene was quantified with STAR and Ensembl Mus_musculus.GRCm38.97 GTF file.
Differential gene analysis was performed with EdgeR (v3.26.8) with trimmed mean of M values (TMM) normalization. Significance was denoted as adjusted p value<0.05 and fold change>1.25.
Genome_build: GRCm38.97
Supplementary_files_format_and_content: RNA-seq_3T3-L1_Kdm5c siRNA_CPM.csv, this processed data file contains counts per million (CPM) for all 30 samples for all mapped genes.
Supplementary_files_format_and_content: RNA-seq_3T3-L1_Kdm5c siRNA_normCounts.csv, this processed data file contains the EdgeR processed counts for all 30 samples, which are TMM normalized and filtered to remoced low expression genes.

source_name: 3T3-L1 cells

growth_protocol: 3T3-L1 cells were maintained in 3T3-L1 preadipocyte complete media (Zen-bio) at 37ºC with 5% CO2.

extract_protocol:
3T3-L1 cells were lyzed with qiazol and RNA was isolated with Qiagen miRNeasy micro kit based on manufacturer's instructions.
Strand-specific RNA-seq libraries were constructed with the Universal plus mRNA-Seq Kit (NuGEN Technologies).

treatment_protocol: 3T3-L1 preadipocytes were reverse-transfected with 50 nM non-targeting (scramble control) or Kdm5c siRNA (Dharmacon) with Lipofectamine RNAiMAX at differentiation day –3 (sub-confluent).

value: 3T3-L1 cells

tag: sirna

value: mouse Kdm5c ON-TARGET siRNA pool (Dharmacon)


title: Day0 Kdm5c 3 (RNA-Seq)


title: Day-1 Scramble 5 (RNA-Seq)

value: non-targeting control ON-TARGET siRNA (Dharmacon)


title: Day0 Scramble 5 (RNA-Seq)


title: Day-1 Scramble 4 (RNA-Seq)


title: Day0 Scramble 4 (RNA-Seq)


title: atac_PVpos_cortex_Sham_rep1

description: transposase-accessible DNA


title: Day0 Scramble 2 (RNA-Seq)


title: Day-1 Kdm5c 1 (RNA-Seq)


title: Day0 Scramble 1 (RNA-Seq)


title: Day0 Scramble 3 (RNA-Seq)


title: Day-1 Kdm5c 2 (RNA-Seq)


title: Day-1 Kdm5c 5 (RNA-Seq)


title: Day-1 Kdm5c 3 (RNA-Seq)


title: Day-1 Scramble 2 (RNA-Seq)


title: Day0 Kdm5c 5 (RNA-Seq)


title: Day-1 Kdm5c 4 (RNA-Seq)


title: Day-1 Scramble 3 (RNA-Seq)


title: Day-2 Kdm5c 5 (RNA-Seq)


title: atac_PVpos_cortex_DD_rep1

description: transposase-accessible DNA


title: atac_PVpos_cortex_DD_rep2

description: transposase-accessible DNA


title: Day-2 Kdm5c 4 (RNA-Seq)


title: Day-2 Kdm5c 3 (RNA-Seq)


title: Day-2 Kdm5c 2 (RNA-Seq)


title: Day0 Kdm5c 2 (RNA-Seq)


title: Day0 Kdm5c 1 (RNA-Seq)


title: Day-1 Scramble 1 (RNA-Seq)


title: Day-2 Kdm5c 1 (RNA-Seq)


title: Day-2 Scramble 5 (RNA-Seq)


title: Day-2 Scramble 4 (RNA-Seq)


title: Day-2 Scramble 3 (RNA-Seq)


title: Day-2 Scramble 1 (RNA-Seq)


title: Day-1 Kdm5c 3

data_processing:
ATAC-seq fastq files were trimmed to remove low quality reads and adapters using Cutadapt v2.3.
The reads were aligned to the reference mouse GRCm38/mm10 genome with bowtie2 v2.2.9.
Peak calling was performed with model-based analysis of ChIP-Seq (MACS2, v.2.1.1) with q value of 0.05. The peaks for each experimental group were merged into a single bed file and HTseq v0.9.1 was used to count the number of reads that overlap each peak per sample.
The peak counts were analyzed with DESeq2 v1.24.0 to identify differentially accessible genomic regions with significance as p value<0.05.
Genome_build: GRCm38.97
Supplementary_files_format_and_content: ATAC-seq_d-2_K_S_raw_counts.txt, this processed data file contains raw counts for all peaks called for the 8 samples for Day -2 timepoint.
Supplementary_files_format_and_content: ATAC-seq_d-1_K_S_raw_counts.txt, this processed data file contains raw counts for all peaks called for the 8 samples for Day -1 timepoint.
Supplementary_files_format_and_content: ATAC-seq_d0_K_S_raw_counts.txt, this processed data file contains raw counts for all peaks called for the 7 samples for Day 0 timepoint.
Supplementary_files_format_and_content: ATAC-seq_d-2_K_S_DESeq2_normcounts.txt, this processed data file contains DESeq2 normalized and filtered counts for all promoter defined peaks called for the 8 samples for Day -2 timepoint.
Supplementary_files_format_and_content: ATAC-seq_d-1_K_S_DESeq2_normcounts.txt, this processed data file contains DESeq2 normalized and filtered counts for all promoter defined peaks called for the 8 samples for Day -1 timepoint.
Supplementary_files_format_and_content: ATAC-seq_d0_K_S_DESeq2_normcounts.txt, this processed data file contains DESeq2 normalized and filtered counts for all promoter defined peaks called for the 7 samples for Day 0 timepoint.

extract_protocol:
Prepared the samples for ATAC-seq following Buenrostro, J.D., et. Al. 2015. ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Curr. Protoc. Mol. Biol. 109:21.29.1-21.29.9.
Libraries were constructed with Illumina Nextera unique dual indexes and library amplification was confirmed with qPCR and ultimately quantified with Kapa library quantification kit.


title: Day0 Scramble 3


title: Day-1 Scramble 1


title: Day-2 Scramble 4


title: Day-2 Kdm5c 4


title: Day0 Scramble 1


title: Day-2 Scramble 3


title: Day0 Kdm5c 2


title: Day-1 Scramble 3


title: Day0 Scramble 4


title: Day-1 Scramble 2


title: Day0 Kdm5c 4


title: Day-1 Kdm5c 1


title: Day-2 Kdm5c 2


title: Day-2 Scramble 1


title: Day-2 Scramble 2


title: Day-2 Scramble 2 (RNA-Seq)


title: Day0 Scramble 2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H9_AD007_indexed

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: PAL

value: male


title: Day0 Kdm5c 1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H9_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H9_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_A2_AD008_indexed


title: Day-1 Scramble 4


title: Day-1 Kdm5c 2


title: Day-1 Kdm5c 4


title: Day-2 Kdm5c 1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H9_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H9_AD001_indexed


title: Day-2 Kdm5c 3


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H8_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H8_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H7_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H8_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H7_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H8_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H8_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H6_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H6_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H6_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H5_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H7_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H6_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H7_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H5_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H5_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H4_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H4_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H4_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H4_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H4_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H3_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H3_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H3_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H3_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H2_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H2_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H7_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H3_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H2_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H2_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H2_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H1_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H1_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H1_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H12_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H12_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H12_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H1_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H11_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H12_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H11_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H1_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H11_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H11_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H10_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H10_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H10_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H10_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H10_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_H10_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G9_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G9_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G9_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G9_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G8_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G8_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G9_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G8_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G7_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G7_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G7_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G7_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G7_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G6_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G5_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G5_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G6_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G5_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G4_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G7_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G4_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G4_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G3_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G4_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G3_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G2_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G3_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G3_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G4_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G8_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G4_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G2_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G3_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G6_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G6_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G5_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G2_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G1_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G2_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G2_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G1_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G1_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G1_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G1_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G5_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G12_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G12_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G11_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G11_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G10_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_F9_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_F9_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G10_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_F9_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_G10_AD002_indexed


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title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H7_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H7_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H6_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H6_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H6_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H6_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H6_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H4_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H8_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H4_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H1_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H8_AD012_indexed


title: DNMT3A/DNMT3B/USP7-TKO

city: Shanghai

first: Jialun

address: N0.500, Dongchuan road

department: School of life science

institute: ECNU

data_processing:
The Illumina sequencing results were converted to fastq format and quality control and optimization was performed on the raw data using FastQC software.
The sequencing reads were mapped to the reference genome (UCSC hg19) using the Bismark software (www.bioinformatics.babraham.ac.uk/projects/bismark/) with default parameters.
MethylKIT R package software (http://www.bioconductor.org/packages/release/bioc/html/methylKit.html) was then used to obtain site-specific methylation information.
The methylation of each CpG site was defined as the fraction of methylated reads to that of methylated and unmethylated reads combined.
Other simulations and calculations in this study were accomplished by R script (R Core Team, 2013, Austria).
Genome_build: UCSC hg19
Supplementary_files_format_and_content: tab-delimited text files include methylation of each CpG sites for each Sample

source_name: HeLa cells

growth_protocol: HeLa cell lines (wild-type, USP7-KO-1, DNMT3A/3B-DKO and DNMT3A/DNMT3B/USP7-TKO) were maintained in DMEM medium (Gibco) containing 10% fetal calf serum (Gemini), 100 U/mL penicillin and 100 μg/mL streptomycin (Gibco).

extract_protocol:
To prepare genomic DNA, cells were resuspended with cell lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM EDTA, 10 mM NaCl, 0.5% sarcosyl, 0.1 mg/mL RNase (CWBIO)) and incubated at 37 °C overnight. Then, protease K (Merck) was added to a final concentration of 0.2 mg/mL and incubated at 65 °C for 24 hr. Genomic DNA was extracted by phenol/chloroform and ethanol precipitated. The DNA was dissolve in ddH2O.
The purified genomic DNA was digested overnight with MspI (NEB). The sticky ends produced by MspI digestion were filled with CG nucleotides, and 3′A overhangs were added. Methylated Illumina sequencing adapters with 3′T overhangs were ligated to the digested DNA. 40–220 bp insert sizes were converted by bisulfite using an EZ DNA Methylation Gold kit (Zymo Research, USA). The libraries were PCR amplified and each library was sequenced by an Illumina HiSeq platform PE150 (150 bp paired-end reads).

value: HeLa

value: DNMT3A/DNMT3B/USP7 double knockout

tag: passages


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H4_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H3_AD006_indexed


title: DNMT3A/DNMT3B-DKO

value: DNMT3A/DNMT3B double knockout


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H3_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H3_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H1_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H1_AD007_indexed


title: USP7-KO-1

value: USP7 knockout


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H1_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H1_AD006_indexed


title: wild-type

value: wildtype


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H12_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H1_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H11_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H11_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H11_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H1_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H12_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H11_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H11_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H10_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H10_AD007_indexed


title: V208_Plus08

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

institute: Centre for Immunity, Infection and Evolution

hyb_protocol: GeneChip Hybridization, Wash and Stain Kit (Affymetrix)

scan_protocol: GeneChip Human Transcriptome Array 2.0 (Affymetrix)

data_processing: Scan data were processed in the R environment using oligo and affy packages, with raw data summarised at transcript level with pd.hta.2.0

source_name: whole blood

label_protocol: GeneChip WT Plus Reagent Kit (Affymetrix)

extract_protocol: Tempus Spin RNA Isolation Kit (Applied Biosystems) with DNase-treatment

value: whole blood

tag: day

value: day 8

tag: individual

tag: gender

tag: country

value: Pakistan


title: V208_Plus02

value: day 2

value: M


title: V208_Plus06

value: day 6


title: V208_Plus04

value: day 4


title: V208_PlusDOD

value: diagnosis


title: V206_Minus01

value: day -1

value: Kenya


title: V206_Plus08


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H10_AD004_indexed

value: PAL


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H10_AD002_indexed

value: male


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H11_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H10_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H10_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_H10_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G9_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G9_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G9_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G9_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_2_A12_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_1_G8_AD012_indexed