title: Ebbait_NlaIII_DN_cells_rep2

data_processing:
Library strategy: 4C-Seq
Reads were mapped to a reduced genome of unique 25 bp sequences adjacent to the primary restriction enzyme sequence used in each experiment.
Alignment was done with bowtie with -N 0.
Self-ligated and undigested fragments were removed after mapping.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: bedGraph: Raw 4C-Seq signal.

source_name: Double-negative T cells, Eb bait

growth_protocol: Mice from C57BL/6 background were used to isolate lymphocytes from the thymus.

extract_protocol:
Cells were fixed in 2% formaldehyde.
4C template was prepared by digestion with NlaIII and subsequent ligation, and then a second digest with DpnII and another ligation.
Adaptors were introduced in the gene-specific inverse PCR step.
Single end 100 cycles.

treatment_protocol: Thy1.2+, TCRb-/lo, CD4-CD8-, CD25+CD44-/+ (DN2/3) cells were sorted from the thymi of 5-6w old mice.

value: wild-type

value: 5-6 weeks

value: double-negative T cells

tag: bait

value: Eb

tag: restriction enzymes

value: primary NlaIII, secondary DpnII


title: Ebbait_NlaIII_immb_cells_rep2

status: Public on Feb 27 2016

type: SRA

city: New York

first: Jane

last: Skok

state: NY

address: 550 First Ave, Smillow 307

country: USA

institute: NYU

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: Immature B cells, Eb bait

growth_protocol: Mice from C57BL/6 background were used to isolate lymphocytes from bone marrow.

treatment_protocol: CD19+, IgD-, B220+, IgM+ cells were sorted from the bone marrow of 5-6w old mice.

tag: strain/background

tag: genotype/variation

tag: age

tag: cell type

value: immature B cells


title: Ebbait_NlaIII_immb_cells_rep1


title: Ebbait_NlaIII_DN_cells_rep1


title: Ighbait_HindIII_B_cells_rep2

source_name: Splenic B cells, IgH bait

growth_protocol: Mice from C57BL/6 background were used to isolate lymphocytes from the spleen.

extract_protocol:
Cells were fixed in 2% formaldehyde.
4C template was prepared by digestion with HindIII and subsequent ligation, and then a second digest with DpnII and another ligation.
Adaptors were introduced in the gene-specific inverse PCR step.
Single end 50 cycles.

treatment_protocol: Mature splenic CD43-negative cells were activated for 2 days with anti-CD40.

value: splenic B cells

value: Igh

value: primary HindIII, secondary DpnII


title: DN_WT_rep1_ATAC

data_processing:
Library strategy: ATAC-Seq
RNA-Seq: reads were mapped using Tophat2 to the mm10 genome. Counts per gene was obtained using htseq-count and normalization was done using DESeq2.
ATAC-Seq:Reads were mapped to the mm10 genome using Bowtie2. Peaks were called using PeakDeck
Genome_build: mm10

source_name: Double negative T cells

growth_protocol:
Mice from C57BL/6 were used to isolate lymphocytes from either the thymus or spleen
Thy1.2+, TCRb-/lo, CD4-CD8-, CD25+CD44-/+ (DN2/3) cells are sorted from the thymi of 5-6w old mice

extract_protocol:
ATAC-Seq libraries were amplified with KAPA HiFi polymerase.
ATAC-Seq; Paired-end 50 cycles

value: Wild-type

value: Double negative T cells


title: Ighbait_HindIII_B_cells_rep1


title: CD83bait_HindIII_B_cells_rep2

source_name: Splenic B cells, CD83 bait


title: DM-AA2

city: Beijing

first: Jun

last: Cai

address: NO.1 Beichen West Road, Chaoyang District

country: China

institute: Beijing Institute of Genomics

library_source: transcriptomic

data_processing:
Illumina Casava1.82 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence，then mapped to mm9 whole genome using bwa 0.5.9-r16
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from DEGseq
Genome_build: mm9
Supplementary_files_format_and_content: text file containing RPKM

molecule: total RNA

source_name: C2C12 myoblasts_DM-AA

extract_protocol:
Lyse cells directly in a culture dish by adding 1 ml of TRIZOL Reagent per 3.5 cmdiameter dish. Mix the cell lysate several times through a pipette. Vortex thoroughly.
Incubate the homogenized sample for 5 minutes at room temperature to permit the complete dissociation of nucleoprotein complexes.
Add 0.2 ml of chloroform per 1 ml of TRIZOL Reagent. Cap sample tubes securely. Vortex samples vigorously for 15 seconds and incubate them at room temperature for 10 minutes. Centrifuge the samples at no more than 12,000 x g for 15 minutes at 4 ℃. Following centrifugation, the mixture separates into lower red, phenolchloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. Transfer upper aqueous phase carefully without disturbing the interphase into fresh tube. Measure the volume of the aqueous phase
Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 ml of isopropyl alcohol per 1 ml of TRIZOL Reagent used for the initial homogenization. Incubate samples at 4 ℃ for 12 hours and centrifuge at not more than 12,000 x g for 10 minutes at 4 ℃.
Remove the supernatant completely. Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per 1 ml of TRIZOL Reagent used for the initial homogenization. Mix the samples gently and centrifuge at no more than 12,000 x g for 10 minutes at 4 ℃. Remove all leftover ethanol.
Air-dry or vacuum dry RNA pellet for 5-10 minutes. Do not dry the RNA pellet by centrifuge under vacuum. It is important not to let the RNA pellet dry completely as this will greatly decrease its solubility. Dissolve RNA in DEPC-treated water by passing solution a few times through a pipette tip.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: mouse myoblast cells

tag: culture medium

value: differentiation medium (DM)

tag: treated with

value: Acetoacetate (AA) for 12hr


title: DM-PBS3

source_name: C2C12 myoblasts_DM-PBS

value: PBS for 12hr (control)


title: GM-AA1

source_name: C2C12 myoblasts_GM-AA

value: growth medium (GM)


title: GM-PBS2

source_name: C2C12 myoblasts_GM-PBS


title: GM-AA3


title: GM-PBS3


title: DM-AA1


title: GM-PBS1


title: GM-AA2


title: DM-PBS1


title: CD83bait_HindIII_B_cells_rep1


title: DM-PBS2


title: P. aeruginosa_parS_AB_rep2

status: Public on Feb 26 2016

city: College station

first: Dongping

last: Wang

state: TX

address: Wellborn

institute: TAMU

description:
ParS_2
mutant strain

data_processing:
Paired-end sequencing was carried out by the University of Texas Genomic Sequencing and Analysis Facility (UTGSAF: http://www.ti3d.utexas.edu/facilities/gene-expression) on a Life Technologies SOLiD 5500xl sequencing system. Targeted sequencing depth was six-million paired-end reads per sample.
Filtering and alignment of the SOLiD 4 paired-end data was performed at the UTGSAF using the AB SOLiD BioScope Whole Transcriptome pipeline (v1.3), for whole-transcriptome RNA-seq analysis.
Based on gene annotation information, the pipeline produced genome alignment results as a compressed binary version of the Sequence Alignment Map (BAM files).
Mapped reads were visualized using BamView in Artemis 13.2.0 (Rutherford et al. 2000).
The number of reads per kb of transcript per million mapped reads (RPKM) was used to normalize the raw data (Mortazavi et al., 2008), and mean RPKM values were determined for both the wild-type and mutant samples.
Genome_build: ASM676v1 (BioProject Accession# PRJNA57945)
Supplementary_files_format_and_content: A .txt file containing the RPKM values for each gene

organism: Pseudomonas aeruginosa PAO1

source_name: parS mutant cells

growth_protocol: Three biological replicates of every strain were started from single colonies located on three separate plates containing AB + 2% CAA and then transferred to 10 ml AB + 2% CAA broth. All cultures were grown at 28˚C with shaking (150 rpm) to an approximate OD600 = 1.2.

extract_protocol:
Transfer 700 μl lysate into RNeasy Mini column place in a 2 ml collection tube and centrifuge for 30 s at highest speed. Add 350 μl Buffer RW1 to the column and centrifuge for 30 s. Discard flow-through and reuse the collection tube. Add 10 μl DNase stock solution to 70 μ l RDD Buffer. Add the DNase I solution into the column and incubate at RT for 15 min. Add 350 μl Buffer RW1 to the column and wait for 5 min, centrifuge for 30 s. Discard the flow-through and collection tubes. Place the RNeasy Mini spin column in a new 2 ml collection tube. Add 500 μl Buffer RPE to the column. Centrifuge for 30 s. Place the column in a new 1.5 ml tube, and centrifuge for 1 min to eliminate any residue ethanol. Place the column in a new collection tube. Add 50 μl RNase free water, centrifuge for 1 min. Store RNA samples at -20°C
Strand-specific cDNA libraries were constructed using the SOLiD Total RNA-Seq kit according to the manufacturer’s instructions with the following modifications: 1) For RNA fragmentation, 300 ng of rRNA-depleted RNA were incubated at 95˚C for 5 min. Bioanalyzer traces were used to confirm that the largest proportion of RNA fragments were around 200 bp. 2) Bioanalyzer traces following reverse transcription were used to confirm that hybrization and ligation of RNA adapters and subsequent reverse transcription of the RNA to cDNA was successful. 3) Amplification of cDNA was carried out following reverse transcription, but preceding the size-selection step. Samples were barcoded by replacing the SOLiD 3’ primer with the appropriate barcoding primer as directed in the SOLiD instructions. Size selection of DNA amplicons ranging from 200-300 bp was performed using an E-Gel iBase system (SYBR Safe 2% SizeSelect gel) (Life Technologies, Carlsbad, CA).  This step was repeated to ensure that adapter-adapter dimers were fully eliminated before sequencing. Paired-end sequencing was carried out by the University of Texas Genomic Sequencing and Analysis Facility (UTGSAF: http://www.ti3d.utexas.edu/facilities/gene-expression) on a Life Technologies SOLiD 5500xl sequencing system. Targeted sequencing depth was six-million paired-end reads per sample.

value: parS mutant

tag: growth protocol

value: AB minimal medium

tag: growth stage

value: logarithmic phase

tag: strain


title: P. aeruginosa_parR_AB_rep3

description:
ParR_3
mutant strain

source_name: parR mutant cells

value: parR mutant


title: P. aeruginosa_parR_AB_rep2

description:
ParR_2
mutant strain


title: P. aeruginosa_parS_AB_rep3

description:
ParS_3
mutant strain


title: P. aeruginosa_parR_AB_rep1

description:
ParR_1
mutant strain


title: P. aeruginosa_parS_AB_rep1

description:
ParS_1
mutant strain


title: DM-AA3


title: P. aeruginosa_WT_AB_rep3

description:
PAO1_3
wild type strain

source_name: wild type bacterial cells

value: wild type


title: P. aeruginosa_WT_AB_rep2

description:
PAO1_2
wild type strain


title: caRep3

city: Boulder

first: Dylan

last: Taatjes

state: Colorado

address: 3415 Colorado Ave.

department: Molecular and Cell Biology

institute: University of Colorado, Boulder

data_processing:
Fastq quality control via Fastqc ; Command = fastqc <.fastq>
Alignment to reference transcriptome via Tophat2 version 2.0.6; Command = tophat2 -p 16 --b2-very-sensitive --no-novel-juncs --microexon-search --no-convert-bam --no-mixed --library-type fr-firststrand -G hg19.gtf
Gene counts quantified via Cufflinks version 2.1.1; Command = cufflinks -p 8 -u --library-type fr-firststrand -b hg19.fasta -G hg19.gtf
Transcriptome profiles merged across samples via Cufflinks version 2.1.1; Command = cuffmerge -p 1 -g hg19.gtf -s hg19.fa
Differential expression analysis via Cufflinks version 2.1.1; Command = -p 16 -L dmso,ca -b hg19.fa -u merged.gtf
Genome_build: hg19
Supplementary_files_format_and_content: Cuffdiff formated differential expressed gene file. Tab-delimited;  test_id, gene_id, gene, locus, sample_1, sample_2, status, value_1, value_2, log2(fold_change), test_stat, p_value, q_value, significant

organism: Homo sapiens

source_name: HCT116 - colorectal carcinoma

growth_protocol: HCT116 cells were grown in 10cm dishes to approximately 80% confluency in DMEM supplemented with 10% FBS at 37 degrees C with 5% CO2.

extract_protocol:
Cells were washed in cold PBS, then scraped in TRIzol RNA purification reagent, which was added directly to each plate according to the manufacterers' instructions. Subsequently, RNA was further purified with a Qiagen Rneasy kit using an on-column DNAse I digestion.
500ng per sample total RNA was used (measured with a NanoDrop 1000 and Agilent 2100 Bioanalyzer) to construct libraries following the Illumina TruSeq Stranded RNA Sample Preparation Guide, polyA seq (mRNA)

treatment_protocol: Cortistatin A in 100% DMSO (or vehicle; 100% DMSO only)  was added at a final concentration of 100nM directly to the media for each replicate. Three biological replicates were performed for both CA and DMSO treatment.

tag: agent

value: 100nM CA


title: caRep2


title: caRep1


title: dmsoRep2

value: DMSO


title: dmsoRep3


title: P. aeruginosa_WT_AB_rep1

description:
PAO1_1
wild type strain


title: dmsoRep1


title: KO-E2-2

city: Rochester

first: Stephen

middle: R

last: Hammes

address: 601 Elmwood Ave, Box 693

department: Medicine

institute: University of Rochester

data_processing:
DATA FORMATTING (Illumina -> FastQ) & DEMULTIPLEXING - bcltofastq-1.8.4
seqclean -c 4 -l 25 -s adaptors.fasta -v vectors.fasta
SHRiMP_2_2_3/bin/gmapper-ls -N 4 --qv-offset 33 --all-contigs
cufflinks-2.0.2.Linux_x86_64/cuffdiff --FDR 0.05 -u -b genome.fa -p 12
Genome_build: Mus musculus genome (NCBI build 37.2)
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each sample

source_name: KO, E2

growth_protocol: treated or untreated wild-type and Uterine-specific Tsc2-null mice were sacrificed at 12 weeks of age for uteri removal.

extract_protocol:
Uteri were removed, flash frozen with liquid nitrogen, and RNA was harvested using RNeasy plus mini kit (Qiagen).
Illumina compatible library construction was performed using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, California). Amplified libraries were hybridized to the Illumina single end flow cell and amplified using the cBot (Illumina) at a concentration of 8 pM per lane.

treatment_protocol: four-week old wild-type and Uterine-specific Tsc2-null mice were either oophorectomized or left intact (ovaries present). Oophorectomized mice were treated with or without a 90-day-release pellet of 17β-estradiol (0.5 mg/pellet) (Innovative Research of America) for 8 weeks.

value: mixed 129Sv X C57BL/6

value: Uterine-specific Tsc2-null

tag: treatment

tag: tissue

value: Uterus (cross section)

value: 12 weeks old


title: KO-E2-1


title: WT-E2-2

source_name: WT, E2

value: Wild-type


title: WT-E2-1


title: WT-ovx-2

source_name: WT, ovx

value: ovx


title: KO12-4 intact

source_name: KO, intact

value: intact


title: WT-ovx-3


title: KO-ovx-4

source_name: KO, ovx


title: KO-ovx-2


title: WT-ovx-1


title: KO12-3 intact


title: KO12-1 intact


title: 129-1-male

city: Nanjing

first: Quan

last: Zhou

state: Jiangsu

address: NO. 140, Hanzhong Road

institute: Nanjing Medical University

data_processing:
Sequencing reads were mapped to the mouse genome (mm9) using Bismark v0.13.1 (Babraham Bioinformatics) after adapter trimming by Trim Galore (Babraham Bioinformatics).
The methylation level of each covered cytosine in CpG context was calculated as the number of reported C divided by the total number of reported C and T.
Genome_build: mm9
Supplementary_files_format_and_content: The processed data files are the coverage files generated by Bismark (chr, start, end, methylation%, number of reported C, number of reported T).

source_name: tail tip of male offspring from the in vitro derived spermatids like cells

extract_protocol:
Genome DNAs were isolated using Promega MagaZorb® DNA Mini-Prep Kit.
13 µl of MspI digestion master mix containing 10 units of MspI (Thermo Scientific) and 1.8 µl 10x Buffer Tango (Thermo Scientific) was added followed by 3 hours of incubation at 37 ℃ and 20 minutes of inactivation at 80 ℃.The digested DNA was then filled-in and tailed with an extra A to the 3’ end by adding 2 µl of end-preparation master mix containing 5 units of Klenow Fragment (exo-; Thermo Scientific), 1.8 µl of 10x Buffer Tango, 0.4 mM dATP, and 0.04 mM each of dGTP and dCTP (Thermo Scientific), followed by 40 minutes of incubation at 37 ℃ and 15 minutes of inactivation at 75 ℃. Adaptor ligation was then performed by adding 5 µl of ligation master mix, which contains 30 Weiss Units of T4 DNA Ligase (HC, Thermo Scientific), 0.5 µl of 10x Buffer Tango, 5mM ATP (Thermo Scientific), and 150 nM of methylated custom adaptor (Forward: 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATC*T-3’, Reverse: 5’-/5Phos/GATCGGAAGAGCACACGTCTGAACTCCAGTC-3’, where * indicates phosphorothioate bond). After three incubation steps (16 ℃ for 30 min, 4 ℃ overnight, and 65 ℃ for 20 min), the reaction mix was subjected to EpiTect Fast Bisulfite Conversion Kit (QIAGEN) following manufacturer’s low-concentration protocol. The bisulfite converted DNA was immediately subjected to PCR amplification using KAPA HiFi HotStart Uracil+ ReadyMix (Kapa Biosystems) and NEBNext Primers for Illumina (New England Biolabs). Typically, 21 PCR cycles were required when starting with ~20 pronuclei. After amplification, final libraries were obtained by size selection of 150-500 bp DNA fragments using SPRIselect beads (Beckman Coulter).

value: somatic cell

tag: Sex

value: male

value: tail tip

tag: developmental stage

value: adult


title: 129-1-female

source_name: tail tip of female offspring from the in vitro derived spermatids like cells

value: female


title: WT12-2 intact

source_name: WT, intact


title: WT12-4-2 intact


title: F1-female

source_name: tail tip of normal female mouse


title: WT12-1 intact


title: F1-male

source_name: tail tip of normal male mouse


title: Skin_SCA1p_3

city: Montreal

first: Julien

last: Patenaude

state: Quebec

address: 2950 chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and cancer (IRIC)

data_processing:
Basecalls performed using CASAVA 1.8.2
Sequenced reads were trimmed for adaptor sequence and mapped to the reference genome using CASAVA 1.8.2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CASAVA 1.8.2.
Read counts where estimated using HTSeq version 0.5.4 and the htseq-count tool using the intersection-strict argument.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values where columns are: Chromosome, Start location, Stop location, Gene, RPKM, basecount.  Readcount files include Gene name and readcount.

source_name: Skin

extract_protocol:
(thymus MCs): Thymi were extracted, mechanically disrupted and enzymatically digested at 37oC for 3x15 minutes using 0.01% (w/v) Liberase TM (Roche) and 0.1% (w/v) DNase I (Sigma-Aldrich). Final digests were harvested, pooled and maintained at 4oC in FACS buffer (PBS, 0.1% (w/v) BSA, 0.02% (w/v) NaN3). Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen).
(Bone MCs) Femurs, tibias and pelvis were collected, cleaned and washed 3 times in cold PBS. Using sharp surgical scissors, each bone was first cut longitudinally and then transversely to generate tiny fragments of ~1 mm2.  Bone fragments were then washed 3 times in cold PBS and incubated with agitation (80 RPM) for 3x20 minutes at 37oC in the same enzymatic cocktail as above. Following each incubation, supernatants were added to HBSS medium (Invitrogen) supplemented with 2% (v/v) FBS, 10mM HEPES and 1% (v/v) penicillin-streptomycin. To further retrieve endosteal stromal cells, remaining bone fragments were gently crushed in supplemented HBSS medium using a pestle and mortar (5 x 50 gentle taps) and supernatants were pooled to previous ones. Red blood cell lysis was then performed on the resulting cell suspension prior to its filtration and resuspension in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen).
(Skin MCs) Mouse trunk and dorsal skin (~12 cm2 / mouse) was aseptically dissected and incubated for 45 minutes in 0.01% (w/v) liberase. Dermis was then mechanically isolated and incubated with agitation (80 RPM) at 37oC for 2x30 minutes in the same enzymatic cocktail as above. Post-incubation, supernatants were filtered and pooled to 25 mL of PBS supplemented with 1% FBS and 5mM EDTA. Final cell suspension was then centrifuged and resuspended in FACS buffer. Primary cells were then stained with monoclonal antibodies prior to being sorted by FACS directly in 300 ul of Trizol reagent. Sorted cells were sorted according to the cell surface phenotype Lin- SCA1+ (Lineage negative cocktail being CD45, CD2, CD4, CD11b, GR-1,  B220, TER119, CD41, EpCAM, CD31). A minimum of 25 000 primary sorted cells were used per sample. Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified using the RNeasy micro kit (Qiagen).
Transcriptome librairies were generated from total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol. Enrichment of RNA-seq stranded libraries with adapter molecules on both ends was done using 15 cycles of PCR amplification using the Illumina PCR mix and primers cocktail. Paired-end (2 x 100 bp) sequencing was peformed using the Illumina HiSeq 2000 running TruSeq v3 chemistry. Three RNA-seq librairies were sequenced per lane (8 lanes per flow cell).

value: Mesenchymal cells (Lin- SCA1+ cells)

value: abdominal and back dermis (truncal skin)

value: 3 to 4 wks-old


title: Thymus_SCA1p_3

source_name: Thymus

value: Thymus


title: Thymus_SCA1p_1-3


title: Skin_SCA1p_2


title: Skin_SCA1p_1


title: Thymus_SCA1p_2


title: WT-E2-5


title: in_vivo_group (conventionally bred - MeDIP)

city: Wuhan

first: Changchun

last: Li

state: Hu Bei

address: No.1, Shizishan Street · Hongshan District

institute: Huazhong Agriculture University

description: MeDIP library for the paired-end sequencing in 50 bp read length

data_processing:
Raw sequencing data were processed by Illumina base-calling pipeline. After filtering the low quality reads, the MeDIP-seq data were aligned to the ensembl pig reference genome (Sscrofa9.61) using SOAP2 (Version 2.21). The unique reads were used to scan the peaks using MACS1.4.0
Genome_build: Sscrofa9.61
Supplementary_files_format_and_content: The processed data is wig file, which contains chromosome position and tag counts.

organism: Sus scrofa

source_name: leg muscle

growth_protocol: newborn piglets

extract_protocol:
DNA of each collected tissue was extracted using using the phenol-chloroform method
DNA was sonicated to gain fragments in the range 100–500 bp after isolation from muscle samples with phenol-chloroform and DNA quality was evaluated by agarose gel electrophoresis and spectrophotometer. The detailed steps of DNA preparation for MeDIP-Seq can be referenced from the protocol of the Paired-End DNA Sample Prep kit (Illumina). We denature the double-stranded DNA and subsequently immunoprecipitated sheared genomic DNA with an antibody that specifically recognizes 5’-methylcytosine. After PCR amplification of the enriched fragments, we selected the 220–320 bp fragments using a Gel Extraction kit (28706; Qiagen) and quantified them with Agilent 2100 Analyzer.

tag: development stage

value: newborn

value: leg muscle


title: Bone_SCA1p_3

source_name: Bone

value: Femur, tibia and pelvis


title: KO-ovx-1

value: mixed 129Sv X C57BL/6

value: Uterine-specific Tsc2-null

value: Uterus (cross section)


title: Bone_SCA1p_2


title: KO-E2-3

value: 12 weeks old


title: in_vivo_group (conventionally bred - RNA)

data_processing:
Original data were transferred into sequence data by base calling.
To obtain clean reads, raw reads were filtered before data analyses. First, the adaptors were removed; second, reads in which unknown bases were > 10% were discarded; third, low-quality reads (the percentage of low-quality bases of quality value ≤ 5 in a read were > 50%) were removed. Clean reads were mapped to reference sequences using SOAPaligner/soap2. Mismatches of no more than 2 bases were allowed in the alignment. The message abundance was calculated using the RPKM method.
Genome_build: Sscrofa9.61
Supplementary_files_format_and_content: The processed data is xls file, which contains the GeneID,Uniq_reads_num,Length,Coverage,RPKM,Symbol,Description,Blast nr

extract_protocol:
Total RNA was extracted from samples of biceps femoris muscle using TRIzol Reagent (Invitrogen).
The concentration and quality of RNA was confirmed using an Agilent 2100 system and agarose gel electrophoresis (AGE). Equal amounts of RNA from the tissue samples of three abnormal cloned piglets, three normal cloned piglets were mixed into three pools. The two independent RNA pools were then used for library construction and sequencing by the Beijing Genome Institute. Briefly, after evaluation of the quality of total RNA, mRNA was enriched by using oligo(dT) magnetic beads. After adding the fragmentation buffer, mRNA was interrupted to short fragments (≈200 bp). First-strand cDNA was synthesized using a random hexamer primer using the mRNA fragments as templates. Then buffer, dNTPs, RNase H and DNA polymerase I were added to synthesize the second strand. Double-strand cDNA was purified with a QiaQuick PCR Extraction kit and washed with Ethidium Bromide buffer for end repair and addition of single nucleotide A (adenine). Finally, sequencing adaptors were ligated to the fragments. Required fragments were purified by AGE and enriched by PCR amplification.


title: Bone_SCA1p_1


title: ESC_RNASeq_Rep2

status: Public on Feb 25 2016

city: Leeds

first: MS

last: Vijayabaskar

address: Woodhouse Lane

department: School of Molecular and Cellular Biology

country: United Kingdom

institute: University of Leeds

data_processing:
Reads aligned to mm10 using Bowtie
bigWig files were created using HOMER software
Genome_build: mm10
Supplementary_files_format_and_content: csfasta (unmapped reads), qual (quality file) and txt (processed expression data)

source_name: Embryonic Stem Cells

growth_protocol: A mouse ES cell line carrying a brachyury GFP+ reporter gene (Fehling et al, 2003, Development 130, 4217-4227) was cultured on MEFs then differentiated as described previously (Sroczynska et al, 2009, Methods Mol Biol 538, 317-334.). Both GFP and cell surface markers were used to isolate each cell population. After differentiation of ESC into embryoid bodies, mesodermal cells were isolated by FACs sorting GFP/Brachyury (Bry+, Flk1- negative cells. A proportion of these cells were allowed to differentiate towards hemangioblasts (HBs, Bry+/Flk1+), hemogenic endothelium (HEs, Tie2+/cKit+/CD41-) and haematopoietic progenitors (HPs, CD41+). Macrophages were isolated by terminal differentiation of CD41+ cells to those expressing the macrophage marker CD11b.

extract_protocol:
RNA was isolated from snap frozen cells with the RNeasy Plus Mini Kit (Qiagen) and ribosome depleted with the Ribozero Gold Kit (Epicentre) according to manufacturers instructions.
RNA-seq libraries were generated with the SOLiD Total RNA-Seq Kit (Life Technologies, 4445374).

value: ES


title: ESC_RNASeq_Rep1


title: MAC_RNASeq_Rep1

data_processing:
The sequence reads were mapped to the mm10 mouse genome build using SHRiMP.
The resulting alignment files were used to obtain the transcript abundances as RPKM using Cufflinks.
Genome_build: mm10
Supplementary_files_format_and_content: csfasta and qual files (unmapped reads) and normalised expression as RPKM in a tab delimited file as calculated from Cufflinks

source_name: Macrophages

value: ES derived Macrophages (CD11b+)


title: MAC_RNASeq_Rep2


title: HP_RNASeq_Rep2

source_name: Hematopoietic Progenitors

value: ES derived Hematopoietic progenitors (CD41+)


title: HB_RNASeq_Rep1

source_name: Hemangioblast

value: ES derived Hemangioblasts (Bry.GFP+, FLK1+)


title: MES_RNASeq_Rep1

source_name: Mesoderm

value: ES derived mesoderm (Bry.GFP+, FLK1-)


title: BV2-input-control

city: Singapore

first: Vibhor

last: Kumar

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

data_processing:
The peak calling on ChIP-seq data set was done using DFilter. The UCSC tracks were made after GC bias correction at 200 base pairs
genome build: mm9
processed data files format and content: The tracks of ChIP-seq are in wiggle format

source_name: BV2 microglia cells

growth_protocol: GM12878 Cells were grown in RPMI 1640 medium (15% FBS, 2 mM L-glutamine) to approximately 1 million cells per ml and then collected for ChIP-seq or snap-frozen in liquid nitrogen and stored at －80 °C . Cell culture and Transfection Feeder-free E14 mouse ES cells were cultured at 37 °C with 5% CO2. All cells were maintained on 0.1% gelatin-coated dishes in DMEM (Gibco), supplemented with 15% heat-inactivated ES FBS (Gibco), 0.055 mM β-mercaptoethanol (Gibco), 2 mM l-glutamine, 0.1 mM MEM nonessential amino acid, 5,000 units per ml gentamycin and 1,000 units per ml LIF (Chemicon).

extract_protocol:
ChIP-seq: Cells and tissues were cross-linked with 1% formaldehyde for 15 min. Glycine (0.625 M) was added to quench excess formaldehyde. Cells were washed in cold PBS and spun down (3,000 r.p.m. (800g) for 10 min at 4 °C; Kubota 3500). The pellet was  resuspended  in FA lysis buffer and incubated for 15minutes (0.25% Triton X-100, 10 mM EDTA, 10 mM Tris HCl [pH 8.0], 100 mM NaCl, Roche 1X cOmplete protease inhibitor). Nuclei were extracted (3,000 r.p.m. for 10 min at 4 °C; Kubota 3500) and resuspended in 300 μl SDS lysis buffer (1% SDS, 1% Triton X-100, 2 mM EDTA, 50 mM HEPES-KOH [pH 7.5], 0.1% Na dodecyl sulfate, Roche 1X cOmplete protease inhibitor). After 15 min incubation, chromatin was fragmented to an average size of 200–300 bp (Bioruptor Next gen, Diagenode). Cellular debris was removed by centrifuging at 15,000 r.p.m. at 4 °C (Kubota 3500). Nuclear lysates were diluted (1:10) with a dilution buffer (1% Triton X-100, 2 mM EDTA, 50 mM HEPES-KOH [pH 7.5], 0.1% Na dodecyl sulfate, Roche 1X cOmplete protease inhibitor).   Chromatin immunoprecipitation (ChIP)  was done coupled to 50 μl protein G Dynabeads (Invitrogen) overnight. The antibodies used for ChIP were : H3K4me2 (Abcam ab32356, lot 780430)), H3K4me1(Abcam:ab8895, lot 718019), H3K27ac( Abcam ab4729, lot 509313), H3K27me3 ( Millipore 07-449, lot DAM1588246 ), PolII ( Abcam ab5131, lot 536530) , H2BK20ac ( Abcam ab52988, lot 527003). After ChIP overnight, beads were washed, and protein-DNA complexes were eluted with  elution buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl [pH 8]).  Protease treatment and de-cross-linking was done at 65 °C overnight., DNA was extracted using phenol/chloroform and purified by ethanol precipitation.
ChIP material was used for library preparation using the Biooscientific library preparation kit with the following modification. The provided adapters were diluted down 40-fold in order to prevent adapter dimer formation that would affect enrichment. Libraries were then enriched for 15 cycles with PFX polymerase (Invitrogen) followed by gel size selection (300-500bp).

treatment_protocol: Mouse microglia cells (BV2) were stimulated by lipopolysaccaheride(LPS) for 3 hours for few samples.  Approximately ten million cells from each cell line were cross-linked with 1% formaldehyde for 15 minutes.

tag: chip antibody


title: RNAseq-LPS-stimulated-BV2

data_processing:
RNA abundance was estimated as FPKM using cufflinks
genome build: mm9
processed data files format and content: processed gene expression files have FPKM value

extract_protocol:
RNA-seq: Total RNA was extracted from the cells using Trizol (Invitrogen). The amount of total RNA was measured with a NanoDrop 2000 (Thermo Fisher Scientific, MA, USA) and a Qubit® RNA Assay Kit (Invitrogen,USA), respectively. RNA integrity was measured using the Agilent RNA 6000 Nano chip on a Bioanalyzer 2100 (Agilent, USA).
RNA-seq: sequencing libraries were prepared from the extracted RNA  using NEBNext Ultra Directional RNA Library Prep (Cat. No.E7420L) according to the manufacturer's instructions. About 100–250 ng of total RNAs was used as starting materials, and library construction was done using distinct adapters for each library. From each library, equal volumes were pooled together and sequenced in a Illumina platform generating 76-bp tags


title: RNAseq-Unstimulated-BV2


title: TGFbeta-KD-LPS-stimulated-BV2-H2BK20ac


title: LPS-stimulated-BV2-H2BK20ac


title: HB_RNASeq_Rep2


title: LPS-stimulated-BV2-H3K27ac


title: MES_Pou5F1

data_processing:
Reads aligned to mm10 using Bowtie
bedGraphs created using bedtools
bigWigs created using UCSC utilities
Peaks called using MACS
Genome_build: mm10
Supplementary_files_format_and_content: fastq (unmapped reads), bigWig (density profile of mapped reads) and bed (peaks)

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature. The reaction was quenched with 0.125M glycine, incubating at room temperature for 5 minutes. Cells were immediately harvested and washed in cold 1x PBS. Cells were harvested and resuspended in 1.5 x pellet volume of cell lysis buffer (10mM Tris pH 8.0, 10mM NaCl and 0.2% NP40) containing protease inhibitors (leupeptin, NaBu and PMSF), the cells were homogenised and incubated on ice for 10 minutes. The following conditions are for 108 cells and were scaled down for lower cell numbers.  nuclei were harvested at 600 x g for 5 minutes at 4oC and resuspended in 1 ml of nuclei lysis buffer (50mM Tris pH 8.0, 10mM EDTA, 1% SDS) containing protease inhibitors (leupeptin, NaBu and PMSF), the cells were homogensised and incubated on ice for 10 minutes. An equal volume of IP dilution buffer (20mM Tris pH 8.0, 2mM EDTA, 150mM NaCl, 1% Triton X-100, 0.01% SDS) containing protease inhibitors (leupeptin, NaBu and PMSF) was added. Cells were sonicated on ice-water or chilled water (Biorupter or Biorupter-plus, Diagenode) for 5 cycles (30s on, 30s off). The chromatin solution was centrifuged for 10 minutes at 3220 x g. After transferring the chromatin solution to a clean falcon tube, a further 3 mls of IP buffer was added. The chromatin solution was pre-cleared by the addition of 50μl of IgG (2 μg/μl, raised in the same species as the experimental antibody) and incubated at 4oC for 1 hour, then 200μl of Protein G sepharose beads (1:1 slurry in IP dilution buffer) were added to the chromatin solution and further incubated at 4oC for 2 hours. The beads/IgG were collected by centrifugation at 1791 x g for 2 minutes. The chromatin was transferred to 1.5 ml tubes, an input sample was removed and antibodies/IgG were added then incubated overnight at 4oC with rotation. In the case of low cell number samples (HEs) 1 μl mouse mRNA (diluted 1:5, cat# 338114, Qiagen) and 4 μl Recombinant Histone 2B (M2505S; New England Biolabs) was added prior to the antibody. 60μl of protein G agarose beads (1:1 slurry in IP dilution buffer) were added and incubated with the samples for 2 hours. The beads were harvested at 5400 x g for 2 minutes and washed twice with low salt buffer (20mM Tris pH 8.0, 2mM EDTA, 50mM NaCl, 1% Triton X-100, 0.1% SDS), then once with LiCl buffer (10mM Tris pH 8.0, 1mM EDTA, 0.25M LiCl, 1% NP40, 1% Sodium deoxycholate monohydrate) and twice with 1x TE pH 8.0. The complexes were eluted twice from the beads by adding 150μl elution buffer (100mM NaHCO3, 1% SDS). To reverse the cross-linking 0.3M NaCl was added to all the IP samples and input, RNase was added and the samples were incubated at 65oC overnight. The samples were then treated with Proteinase K for 2 hours at 45oC. DNA was purified using Qiagen PCR clean up columns.
The libraries were prepared according to Illumina TruSeq DNA Sample Prep Kit

value: Pou5F1 Santa Cruz sc8628


title: Unstimulated-BV2-H2BK20ac


title: Unstimulated-BV2-H3K27ac


title: MES_RNASeq_Rep2


title: MES_Elk4

value: Elk4 Santa Cruz sc13030


title: SP1173_WT ChIP-seq

city: Eugene

first: Hideki

last: Tanizawa

state: OR

address: 1370 Franklin Blvd

department: Institute of Molecular Biology

institute: University of Oregon

data_processing:
Basecalls performed Illumina CASAVA version 8
ChIp-seq reads were aligned to S.pombe genome (ASM294v1.18) using BWA version 0.6.2
Fragment shift length was estimated by using HOMER version 4.4
Treatment and control read density were normalized by using the ratio of total read number.  The score of the peaks were determined by the subtraction of control read density from treatment read density and calculate 200bp window average.
Genome_build: ASM294v1.18 (download from ftp://ftp.ensemblgenomes.org/pub/fungi/release-18/fasta/schizosaccharomyces_pombe/dna/)
Supplementary_files_format_and_content: wig files. Score represent subraction of control read density from treatment read density

organism: Schizosaccharomyces pombe

source_name: fission yeast cells

growth_protocol: Cells were grown in liquid YEA media in a 32C shaker until exponential phase

extract_protocol:
Exponentially growing cells were fixed in 3% paraformaldehyde, and chromatin was sheared into 500 to 700-bp fragments using a Misonix Sonicator 3000 (Qsonica, Newtown, CT). Chromatinassociated proteins were then immunoprecipitated using mouse monoclonal anti-V5/Pk SV5-Pk1 (AbD Serotec, Kidlington, UK) antibodies in combination with Protein G-coupled Dynabeads (Life Technologies, Carlsbad, CA).
Libraries were prepared from 3.1 ng of DNA using the NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina® with the NEBNext® Multiplex Oligos for Illumina® following manufacture’s protocol. Sequencing was perofromed by an Illumina HiSeq2000

value: mat1M leu1-32 ade6-216 his2 ura4-D18

value: mouse monoclonal anti-V5/Pk1

tag: chip antibody vendor

value: AbD Serotec, Kidlington, UK

tag: chip antibody cat. #

tag: chip antibody batch


title: Rad52_WT ChIP-seq

tag: genotype/variation

value: h+ leu1-32 ura4-D18 rad52-12PK:kanMX6


title: MAC_Tal1

tag: cell type

value: Tal1 Santa Cruz sc12984


title: MAC_Runx1

value: Runx1 AbCam ab23980


title: MAC_Lmo2

value: Lmo2 R&D systems AF2726


title: MES_Cebpb

value: Cebpb Santa Cruz sc150


title: Rad52_swi1d ChIP-seq

value: h+ leu1-32 ura4-D18 rad52-12PK:kanMX6 swi1::natMX6


title: MAC_Fli1

value: Fli1 Santa Cruz sc356


title: HP_Gfi1

value: Gfi1 AbCam ab21061


title: HP_Gata1

value: Gata1 AbCam ab11963


title: TGFbeta-KD-LPS-stimulated-BV2-H3K27ac

tag: cell line


title: HP_Cebpb

value: ES derived Hematopoietic progenitors (CD41+)


title: HP_Fli1


title: HE_Lmo2

source_name: Hemogenic Endothelium

value: ES derived Hemogenic endothelium (Bry.GFP+, Tie2+/Ckit+/CD41-)


title: HE_Fli1


title: HE_Meis1

value: Meis1 Santa Cruz sc10599


title: HB_Lmo2

value: ES derived Hemangioblasts (Bry.GFP+, FLK1+)


title: HE_Cebpb


title: HB_Tal1


title: HB_Gata2

value: Gata2 Santa Cruz sc267


title: MAC_H3K4me3

data_processing:
The sequence reads in fastq format were mapped to the mm10 mouse genome build using Bowtie and the reads from the SOLiD sequencer were mapped using SHRiMP. The resulting alignment files were used to generate density maps using HOMER.
Genome_build: mm10
Supplementary_files_format_and_content: fastq (unmapped reads), solid_native_csfasta and solid_native_qual files (unmapped reads), and bigWig (density profile of mapped reads)

extract_protocol:
For histone modification ChIP, nuclei of approximately 2x 10^6 sorted and crosslinked cells were isolated in hypotonic buffer A (10 mM Hepes, pH 8.0, 10 mM EDTA, 0.5 mM EGTA, 0.25 % TritonX100) and washed in  buffer B (10 mM Hepes, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.25 % TritonX100). Chromatin was then sonicated in immunoprecipitation buffer I (25 mM Tris 1 M, pH 8.0, 150 mM NaCl, 2 mM EDTA, pH 8.0, 1 % TritonX100 and 0.25 % SDS) using a Bioruptor water bath (Diagenode). After centrifugation the sheared 200 – 500 bp chromatin fragments were diluted with 2x volume of immunoprecipitation buffer II (25 mM Tris, pH 8.0, 150mM NaCl, 2 mM EDTA, pH 8.0, 1 % TritonX100, 7.5 % glycerol), 5 – 10% of input chromatin was saved and the precipitation was carried out with remaining chromatin for 2 - 4 hours at 4 °C using 0.2 - 2 ?g of specific antibody (H3K9ac: Abcam ab4441 and Millipore ABE18, H3K27ac: Abcam ab4729, H3K4me3: Millipore 04-745, H3K27me3: Abcam ab6002) coupled to 15 ?l protein G Dynabeads (Dynal). Beads were washed with low salt buffer (20 mM Tris 1 M, pH 8.0, 150 mM NaCl, 2 mM EDTA, pH 8.0, 1 % TritonX100, 0.1 % SDS), high salt buffer (20 mM Tris, pH 8.0, 500 mM NaCl, 2 mM EDTA, pH 8.0, 1 % TritonX100, 0.1 % SDS), LiCl buffer (10 mM Tris, pH 8.0, 250 mM lithium chloride, 1 mM EDTA, pH 8.0, 0.5 % NP40, 0.5 % sodium-deoxycholate) and TE pH 8.0 containing 50 mM sodium chloride. The immune complexes were eluted in 100 ?l elution buffer (100 mM NaHCO3, 1 % SDS) and, after adding 5 ?l of 5M sodium chloride and proteinase K, the crosslinks were reversed at 65°C overnight. DNA was extracted by using the Ampure PCR purification kit and ChIP quality was validated by realtime PCR.
The libraries were prepared according to Illumina TruSeq DNA Sample Prep Kit

value: ES derived Macrophages (CD11b+)

value: H3K4me3 Millipore 04-745


title: MAC_Cebpb


title: HE_Input


title: MES_Input

value: ES derived mesoderm (Bry.GFP+, FLK1-)


title: HP_Input


title: MAC_H3K27me3

value: H3K27me3 Abcam ab6002


title: MAC_H3K27ac

value: H3K27ac Abcam ab4729


title: MAC_Input


title: HP_Gfi1b

value: Gfi1b Santa Cruz sc8559


title: HP_H3K9ac

value: H3K9ac Abcam ab4441 & Millipore ABE18


title: HE_H3K27ac


title: HE_H3K4me3


title: HE_H3K27me3


title: MAC_H3K9ac


title: HB_Cebpb

value: Cebpb Santa Cruz sc150


title: MES_H3K27me3


title: HB_H3K9ac


title: HB_H3K27ac


title: HB_Input


title: MES_H3K27ac


title: MES_H3K9ac


title: HP_H3K27me3


title: HP_H3K4me3


title: MES_DHS

data_processing:
The sequence reads in fastq format were mapped to the mm10 mouse genome build using Bowtie. The resulting alignment files were used to generate density maps using HOMER.
DNaseI Hypersensitive Sites are the enriched sites obtained using DFilter (default parameters)
Genome_build: mm10
Supplementary_files_format_and_content: fastq (unmapped reads), bigWig (density profile of mapped reads) and bed (peaks)

extract_protocol:
At least 1x 10^6 up tp 3x 10^6 freshly sorted and thoroughly counted cells were resuspended at 3x 10^6 cells per 100 µl DNase I buffer (60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 10 mM Tris pH 7.4, 0.3 M sucrose), mixed with an equal volume of DNase I NP-40 buffer (60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 10 mM Tris pH 7.4, 0.3 M sucrose, 0.4% NP-40, 2 mM CaCl2) with suitable 2-fold concentration of DNase I enzyme (final concentration ranging between 15 U and 260 U) and incubated at 22°C for 3 min. The reaction was stopped by addition of 2x volume of lysis buffer (300 mM NaAcetate, 10 mM EDTA pH 7.4, 1% SDS, 1 mg/ml proteinase K) and samples were incubated over night at 45°C. After phenol-phenol/chloroform-chloroform extraction DNA was precipitated with 2x volume of 100% ethanol, 10 µg of digested DNA were run on a 1.2% agarose gel in TAE buffer, 50 - 300 bp fragments were size-selected and purified using Qiagen MinElute gel extraction kit. Before library preparation the DNase I digested and size-selected material was validated by realtime PCR analysis.
For library preparation ChIP material was end-repaired, respective adaptors were ligated and fragments were PCR-amplified with 9 to 18 cycles. Size-selection and adaptor-dimer removal was done via gel purification or Ampure bead purification (for SOLiD libraries only). Libraries were validated using realtime PCR for known target/accessible sites, quality was assessed by Agilent Technologies 2100 Bioanalyser and in case of multiplexing the quantity of libraries was measured by the Kapa Library Quantification Kit.


title: HB_DHS


title: MES_H3K4me3


title: mESC_H3K27ac_ChIPSeq

source_name: Mouse embryonic stem cell


title: HP_H3K27ac


title: Forebrain_Input_control_2

data_processing:
The peak calling on ChIP-seq data set was done using DFilter. The UCSC tracks were made after GC bias correction at 200 base pairs
genome build: mm8
processed data files format and content: The tracks of ChIP-seq are in wiggle format

source_name: E11.5 Mouse forebrain

value: forebrain


title: mESC_Input_control


title: HB_H3K4me3


title: HE_H3K9ac


title: Forebrain_H2BK20ac_ChIPSeq


title: Forebrain_Input_control_1


title: Forebrain_Pol2_ChIPSeq

value: PolII ( Abcam ab5131, lot 536530)


title: H2O2-treated cells

city: Shijiazhuang

first: Rui

last: Zhang

address: No.89, Donggang Road

institute: The First Hospital of Hebei Medical University

description: cells treated with 400 umol/LH2O2 for 24h

data_processing:
All obtained reads from each sample were mapped against the human genome (hg19 build) with Bowtie/Tophat v2.0.2 which allows mapping across splice sites by reads segmentation (Trapnell et al., 2012). All programs were performed with default setting (unless otherwise specified).
The unique mapped reads (85-90% of total reads) were subsequently assembled into transcripts guided by reference annotation (Gencode v20 and Refseq gene models) with Cufflinks v2.0.2 (Trapnell et al., 2012).  Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments).
For the analyses of lncRNAs, cufflinks was used to estimate the transcript level FPKM values with the Gencode v20 lincRNA annotation (Derrien et al., 2012), and human body map lincRNA annotations (Cabili et al., 2011).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: endothelial cells_H2O2-treated

growth_protocol: HUVECs were incubated with medium in a humidified atmosphere of 95% air and 5% CO2. Medium was changed every 48 hours until the cells were grown to 80 to 90% confluency.

extract_protocol:
Total RNA from each sample was extracted using TRK1001 (LC Sciences, Cat. TRK-1001, Total RNA Purification Kit) according to the manufacturer's procedure. Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HUVECs were treated with 400μmol H2O2 diluted with medium for 24h.

value: umbilical vein

value: endothelial cells

tag: passage


title: Forebrain_H3K27ac_ChIPSeq


title: mESC_H2BK20ac_ChIPSeq


title: HE_Tal1

value: Tal1 Santa Cruz sc12984


title: HB_H3K27me3


title: Forebrain_H3K4me1_ChIPSeq


title: MAC_DHS Rep1 and Rep2


title: MAC_Spi1

value: Spi1 Santa Cruz sc352


title: Forebrain_H3K27me3_ChIPSeq


title: HP_Tal1

value: ES derived Hematopoietic progenitors (CD41+)


title: HP_Lmo2

value: Lmo2 R&D systems AF2726


title: HP_Gata2

value: Gata2 Santa Cruz sc267


title: HP_DHS


title: HP_Spi1


title: HP_Runx1

value: Runx1 AbCam ab23980


title: Input_control

data_processing:
The peak calling on ChIP-seq data set was done using DFilter. The UCSC tracks were made after GC bias correction at 200 base pairs
genome build: hg19
processed data files format and content: The tracks of ChIP-seq are in wiggle format

source_name: GM12878 cells


title: normal cells

description: Normal culture

source_name: endothelial cells_control


title: H2BK20ac_ChIPSeq


title: H3K27ac_ChIPSeq


title: Patient 2 (P2)

city: Athens

first: Lance

last: Wells

state: Georgia

address: 315 Riverbend Road

department: Biochemistry and Molecular Biology

institute: University of Georgia

data_processing:
Quality control checks on raw sequence data from each sample was performed using FastQC (Babraham Bioinformatics, London, UK). Raw reads were mapped to the reference human genome hg19/GRCh37 using TopHat v1.4 with two mismatches allowed and other default parameters.  The alignment metrics of the mapped reads was estimated using SAMtools . Aligned reads were then imported onto the commercial data analysis platform, Avadis NGS (Strand Scientifics, CA, USA). After quality inspection, the aligned reads were filtered on the basis of read quality metrics where reads with a base quality score less than 30, alignment score less than 95, and mapping quality less than 40 were removed. Remaining reads were then filtered on the basis of their read statistics, where missing mates, translocated, unaligned and flipped reads were removed. The reads list was then filtered to remove duplicates. Samples were grouped as patient and control identifiers and quantification of transcript abundance was done on this final read list using Trimmed Means of M-values (TMM) as the normalization method. Differential expression of genes was calculated on the basis of fold change (using default cut-off ≥ ±2.0) observed between defined conditions, and the p-value of the differentially expressed gene list was estimated by z-score calculations with Benjamini Hochberg False discovery rate (FDR) correction of 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: txt file contains normalized expressions for each sample

source_name: Lymphoblastoids

growth_protocol: Lymphoblastoids were cultured in RPMI 1640 medium containing 15% fetal bovine serum and 1% antibacterial/ antimycotics. Cells were passaged every week and grown in suspension to desired density for assays at 37°C in 10% CO2.

extract_protocol:
Total RNA was extracted using Qiagen Rneasy kit as per manufacturer's protocol.
RNA samples with a RNA integrity Number (RIN) value of at least 9.5 or higher was used for further processing. From each 4 samples, 1000ng RNA was used for PolyA mRNA library prep using NEBNext PolyA magnetic Isolation module New England BioLabs Inc., Ipswich, MA, USA) according to manufacturer's protocol. Samples were individually barcoded with unique in-house genomics service lab (GSL) primers and amplified through 10 cycles of PCR using KAPA HiFi HotStart Ready Mix (Kapa Biosystems, Inc., Woburn, MA, USA). The quality of the libraries were assessed by Qubit® 2.0 Fluorometer , and the concentration of the libraries was estimated by utilizing a DNA 1000 chip on an Agilent 2100 Bioanalyzer, respectively. Accurate quantification of the prepared mRNA libraries for downstream sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification kit (Kapa Biosystems, Inc., Woburn, MA, USA). Each library was then diluted to a final concentration of 12.5nM and pooled equimolar prior to clustering.  Cluster generation was carried out on a cBot v1.4.36.0 using the Truseq Paired-end (PE) Cluster Kit v3.0 (Illumina, Inc., San Diego, CA, USA).   Paired End (PE) sequencing was performed using a 200 cycle TruSeq SBS HS v3 kit on an Illumina HiSeq2000, running HiSeq Control Software (HCS) v1.5.15.1 (Illumina, Inc., San Diego, CA, USA). Image analysis and base calling was performed using the standard Illumina Pipeline consisting of Real time Analysis (RTA) version v1.13. Raw reads were demultiplexed using a bcl2fastq conversion software v1.8.3 (Illumina, Inc., San Diego, CA, USA) with default settings.

value: Lymphocytes

tag: genotype

value: L254F OGT

tag: relationship

value: Affected brother


title: Rb49 leaves with 4 hours post mock treatment, technical replicate 2

city: WUHAN

first: hanming

last: hong

address: SHIZHISHAN

institute: NCPGR

description: Leaf fragments approximately 2 cm in length that were immediately next to the clipping site were collected.

data_processing:
Illumina  instrument software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rice (MSU, version7.0, http://rice.plantbiology.msu.edu) whole genome using bowtie.
A software mireap was used to identify novel miRNA.
Genome_build: MSU, version 7.0
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample.

organism: Oryza sativa Japonica Group

growth_protocol: Rice plants were grown in the field under nonstressed conditions during the rice-growing season in Wuhan, Hubei provice, China.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Plants were inoculated with the Xoo strain PXO61 at the four-leaf to five-leaf stage by the leaf-clipping method. Control rice plants were inoculated with water (mock inoculation).

value: leaf (four-leaf to five-leaf stage)

value: Rb49 transgenic line carrying Xa3/Xa26

value: 4 hours post mock treatment


title: Rb49 leaves with 24 hours post PXO61 treatment

value: 24 hours post PXO61 treatment


title: Patient 1 (P1)

value: Affected nephew


title: NA18507 WGBS

city: London

first: Emanuele

last: Libertini

address: 1 Midland Road

institute: Francis Crick Institute

description:
bisulfte converted DNA
genome-wide methylated and non-methylated read counts

data_processing:
GEM mapper for alignment to the bisulfite converted human genome
Genotype and methylation calling were performed simultaneously, and heterozygous positions, positions with a genotype error, greater than 250 were filtered out. probability greater than 0.01, and positions with a read depth less than 6 (WGBS Blueprint pipeline, custom software).
Only cytosines with six or more reads informative for methylation status were considered.
Methylated non-CpGs were defined as those cytosines with at least two unconverted reads and a methylation probability greater than two standard deviations above zero, where the probability of the following base being a guanine was at least two orders of magnitude smaller than the most  probable base (WGBS Blueprint pipeline, custom software).
Genome_build: hg19
Supplementary_files_format_and_content: text file including coordinates of CpG positions and counts of methylated reads and coverage at each position. Data is superimposed on + strand.

source_name: lymphoblastoid

extract_protocol: bisulfite-treated single-stranded DNA undergoes subsequent DNA synthesis, terminal tagging, amplification, library purification, quantification and cluster generation. The EpiGnome library concentration was measured to be 17ng/ul using the Qubit HS kit (Life Technologies, USA) with a median library size of 361bp on a Bioanalyzer High Sensitivity DNA chip (Agilent Technologies Inc., USA).  Whole genome bisulfite sequencing using an Illumina HiSeq 2500 instrument in high output run mode

treatment_protocol: EZ DNA Methylation-Lightning bisulfite conversion kit (Zymo Research, USA)

value: modified B cell (lymphoblastoid)

tag: assay

value: DNA methylation assay (genome-wide)

value: HapMap GM18507; Coriell NA18507


title: Rb49 leaves with 2 hours post PXO61 treatment

value: 2 hours post PXO61 treatment


title: Control 2 (C2)

value: WT OGT

value: Unaffected brother


title: Rb49 leaves with 24 hours post mock treatment

value: 24 hours post mock treatment


title: Control 1 (C1)


title: Rb49 leaves with 2 hours post mock treatment

value: 2 hours post mock treatment


title: Rb49 leaves with 4 hours post mock treatment, technical replicate 1


title: Rb49 leaves with 4 hours post PXO61 treatment

value: 4 hours post PXO61 treatment


title: Forebrain_H3K4me2_ChIPSeq

tag: strain

value: forebrain


title: MDJ8 leaves with 24 hours post PXO61 treatment

value: MDJ8 wild type

tag: treatment


title: MDJ8 leaves before treatment, biological replicate 2

source_name: MDJ8 leaves before treatment as control, biological replicate 2

tag: tissue

value: control


title: Rb49 leaves before treatment

source_name: Rb49 leaves before treatment as control

value: leaf (four-leaf to five-leaf stage)


title: 12_SL

data_processing:
Aligned using TopHat
Expression analysis using Cufflinks
Genome_build: mm10
Supplementary_files_format_and_content: fastq (unmapped reads), txt (gene expression)

source_name: Mouse Embryonic Fibroblasts

growth_protocol: Embryonic day 14.5 murine wild type fibroblasts (MEFs) or from iTal1-2A-GFP transgenic mouse carrying rtTA and TRE-TAL1 cassettes allowing inducible transgenic mouse carrying rtTA and TRE-TAL1 cassettes allowing inducible expression of TAL1 upon addition of doxycyclin were prepared as described before (Sroczynska et al., 2009). Reprogramming experiments were carried out with either wild type (n=5) or iTal1-2A-GFP (n=2) MEFs as described in (Batta et al., 2014)

extract_protocol:
RNA preparation and sequencing were performed as described previously (Lie-A-Ling et al 2014).
RNA-seq libraries were generated with the Total RNA-Seq Kit.

value: MEF

value: MEFs (Scl/Lmo2) (12 days)


title: FlkPlus_Tead4

growth_protocol: A single cell suspension of ES cells was transferred into IVD media on 15 cm low adherence bacteriological plates (Sterilin) at a concentration of 2.5 X 104/ml. IVD media - IMDM supplemented with 15 % FCS, 100 units/ml Penicillin and 100 g/ml Streptomycin, 1 mM glutamine, 0.15 mM MTG, 0.18  mg/ml Human transferrin (Roche 652202) and 50 g/ml ascorbic acid. After 3.25 days the embryoid bodies were collected, briefly digested in Tryple-Express protease mix (Life  Technologies) and gently dissociated. A single cell suspension was obtained by passing the cells through a cell strainer and resuspending in IMDM + 20 % FCS. Flk1+ (CD309)  cells were isolated using a biotinylated Flk1 antibody (eBioscience 13-5821) at 5 l per 107 cells for 15 minutes on ice, followed by 2 washes with MACS buffer (PBS + 5 % BSA  and 0.5 mM EDTA). Cells bound by the antibody were then isolated using MACS antibiotin beads and MACS LS columns (Miltenyi Biotec) according to the manufacturers  instructions. Isolated Flk1+ve cells were subsequently used for chromatin immunoprecipitation.

extract_protocol:
As described in Wilson et al., Cell Stem Cell. 2010 Oct 8;7(4):532-44
According to Illumina TruSeq DNA Sample Prep Kit

value: ES derived Hemangioblasts (FLK1+)

value: Abcam ab58310


title: 12_SFGL

value: MEFs (Scl/Fli1/Gata2/Lmo2) (12 days)


title: HE_DHS

value: ES derived Hemogenic endothelium (Bry.GFP+, Tie2+/Ckit+/CD41-)


title: 12_FGL

value: MEFs (Fli1/Gata2/Lmo2) (12 days)


title: MDJ8 leaves with 24 hours post mock treatment


title: MDJ8 leaves with 4 hours post PXO61 treatment


title: 21_FGL

value: MEFs (Fli1/Gata2/Lmo2) (21 days)


title: MDJ8 leaves with 2 hours post PXO61 treatment

value: 2 hours post PXO61 treatment


title: 12_uFIB

value: untreated Fibroblasts (12 days)


title: MDJ8 leaves with 4 hours post mock treatment

value: 4 hours post mock treatment


title: MDJ8 leaves before treatment, biological replicate 1

source_name: MDJ8 leaves before treatment as control, biological replicate 1


title: 21_SFGL

value: MEFs (Scl/Fli1/Gata2/Lmo2) (21 days)


title: 21_uFIB

value: untreated Fibroblasts (21 days)


title: mRNAs from Fusarium graminearum Z-3639 wild type after 9 h after induction of conidiogenesis

city: Seoul

first: Hokyoung

last: Son

address: Daehak-dong, Gwanak-gu

department: Center for Food and Bioconvergence

country: South Korea

institute: Seoul National University

data_processing:
BWA software was used for basecalling and genome alignment.
Sequenced reads were mapped to MIPS FGDB_v32 genome (obtained from ftp://ftpmips.gsf.de/fungi/FGDB/v32/) using bwa with parameters aln -q 20 and paired-end results were generated by sampe option.
Reads within exon were counted by the HTSEQ package of Python.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript was counted and normalized by the size of the meta-transcript and by the size of the library.
RPK100M = 100 x RPKM
Genome_build: FGDB_v32
Supplementary_files_format_and_content: tab-delimited text files include gene information and raw counts, RPK100M, RPKM values for each Sample …
Genome Build:
WT_9h_processed.txt: FGDB_v32

organism: Fusarium graminearum

source_name: Fungi culture

growth_protocol: Each fungal strain was grown on YMA medium for induction of condiogensis for 3 h and 9 h

extract_protocol: Illumina TruSeqTM RNA sample prep kit with standard low throughput (LT) protocol

value: wild type

tag: time point

value: 9 h after induction of conidiogenesis


title: pns1

city: Seattle

first: Jay

last: Parrish

state: Washington

department: Department of Biology

institute: University of Washington

data_processing:
Bases were called and reads were demultiplexed with Illumina CASAVA 1.8.2
Reads were aligned to the transcriptome using TopHat2 version 2.0.14 and Bowtie2 version 2.2.3 with default parameters except -p 2
Gene expression per sample, in fragments per kilobase of transcript per million mapped reads (FPKM), was calculated with Cufflinks version 2.2.1 with default parameters except -p 2 and providing a known transcriptome with -G genes_all.gff
Genome_build: FlyBase genome release 6.04
Supplementary_files_format_and_content: Tab delimited text files showing fpkm for all genes (*Genes.txt) and isoforms (*Isoforms.txt) for each sample

organism: Drosophila melanogaster

source_name: md sensory neurons

extract_protocol:
100 neurons per sample were isolated by FACS on an AriaII.  Total RNA was isolated, converted to cDNA, and pre-amplified as described in the SMARTer Ultra-low input kit (Clontech PN 634833) but with modified procedures for low cell number analysis (Fluidigm)
RNA libraries were prepared for sequencing following Illumina protocols.  cDNA libraries were diluted to 0.25ng/ul, fragmented with the Nextera XT DNA kit (Illumina PN FC-131-1024), multiplexed, and sequenced on a Hi-Seq2500

tag: Stage

value: third instar

value: Gal4(21-7), UAS:RedStinger

value: multi-dendritic sensory neurons


title: mRNAs from Fusarium graminearum Z-3639 wild type after 3 h after induction of conidiogenesis

data_processing:
BWA software was used for basecalling and genome alignment.
Sequenced reads were mapped to MIPS FGDB_v32 genome (obtained from ftp://ftpmips.gsf.de/fungi/FGDB/v32/) using bwa with parameters aln -q 20 and paired-end results were generated by sampe option.
Reads within exon were counted by the HTSEQ package of Python.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript was counted and normalized by the size of the meta-transcript and by the size of the library.
RPK100M = 100 x RPKM
Genome_build: FGDB_v32
Supplementary_files_format_and_content: tab-delimited text files include gene information and raw counts, RPK100M, RPKM values for each Sample …
Genome Build:
WT_3h_processed.txt: FGDB_v32

value: 3 h after induction of conidiogenesis


title: Punica granatum_small RNA sequencing

city: Institute

first: Umesh

middle: K

last: Reddy

state: West Virginia

address: 141, Hamblin Hall, WVSU

institute: West Virginia State University

data_processing:
Base calling Illumina GA pipeline v1.5
SOAP2 was used to map clean reads to Poplar genome since pomegranate genome is not available.
miRBase (release 20.0) was used to identify known miRNA and expression
sRNA tags were aligned to Genbank and Rfam to identify different types of small RNAs
Novel miRNA prediction was performed with Mireap
Genome_build: Populus trichocarpa v3.0; https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa
Supplementary_files_format_and_content: tab-delimited text files

organism: Punica granatum

source_name: pool of all tissues from young seedling to matured fruits

extract_protocol:
total RNA was extracted from leaf, male and female flowers, different stages of fruits using trizol method, and purified using zymoresearch clean up colum after DNAse I treatment.
Libraries were prepared by BGI tech, Hong Kong according to Illumina's instructions


title: pns3


title: PEO1-GRHL2_ChIP

status: Public on Feb 24 2016

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

institute: National University of Singapore

description: GRHL2 ChIP-seq data of PEO1

data_processing:
Basecalls performed using CASAVA version 1.8.2.
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2.0 with parameters: -N 1 --sensitive -p 2 --no-unal
Only unique alignments are kept for downstream analysis.
Peaks were called using MACS version 2.0.9 using a maximum of 2 reads per unique position and otherwise default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: peaks

source_name: Ovarian cancer cell line PEO1

growth_protocol: OVCAR3 cells were grown in RPMI 1640 with 20% FBS and 10µg/ml insulin; PEO1 cells were grown in RPMI 1640 with 10% FBS; OVCA429 cells were grown in DMEM with 10% FBS. All cells were incubated at 37°C in 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
a ChIP-seq library was constructed using NEBNext® ChIP-seq sample preparation kit (E6200, New England Biolabs) according to the manufacturer’s protocol. Size-selection was performed by gel extraction after agarose gel electrophoresis or by magnetic separation using AMPure XP beads. Multiplexing sample preparation oligonucleotide kit (#PE-400-1001, Illumina) was used for index labelling. Sample quality was analyzed using an Agilent 2100 Bioanalyzer prior to sequencing.

value: Ovarian cancer cell line PEO1


title: OVCAR3-GRHL2_ChIP

description: GRHL2 ChIP-seq data of OVCAR3

source_name: Ovarian cancer cell line OVCAR3

value: Ovarian cancer cell line OVCAR3


title: pns2


title: OVCA429-GRHL2_ChIP

description: GRHL2 ChIP-seq data of OVCA429

source_name: Ovarian cancer cell line OVCA429

value: Ovarian cancer cell line OVCA429


title: pns4


title: OVCAR3-inputDNA

description: input DNA for GRHL2 ChIP-seq of OVCAR3


title: PEO1-inputDNA

description: input DNA for GRHL2 ChIP-seq of PEO1


title: MDJ8 leaves with 2 hours post mock treatment

value: leaf (four-leaf to five-leaf stage)

value: MDJ8 wild type

value: 2 hours post mock treatment


title: Het (Q50) 6 months Male Liver mRNA rep3 398914_68873_1_L5.D704

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

data_processing:
Illumina CASAVA 1.8.2 software used for basecalling
Genome mapped via Omicsoft OSA 4.0
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using fastq-mcf sequence quality filter, clipping and processor with following settings for Omicsoft: Trimming  /Mode=TrimByQuality /ReadTrimQuality=2;  Options  /ParallelJobNumber=4 /PairedEnd=True /FileFormat=FASTQ /AutoPenalty=True /FixedPenalty=2 /Greedy=false /IndelPenalty=2 /DetectIndels=False /MaxMiddleInsertionSize=10 /MaxMiddleDeletionSize=10 /MaxEndInsertionSize=10 /MaxEndDeletionSize=10 /MinDistalEndSize=3 /ExcludeNonUniqueMapping=False /ReportCutoff=10 /WriteReadsInSeparateFiles=True /GenerateSamFiles=False /ThreadNumber=6 /InsertSizeStandardDeviation=40 /ExpectedInsertSize=300 /MatePair=False /InsertOnSameStrand=False /InsertOnDifferentStrand=True /QualityEncoding=Automatic /CompressionMethod=Gzip /Gzip=True /SearchNovelExonJunction=False /ExcludeUnmappedInBam=False /KeepFullRead=False /Replace=False /Platform=ILLUMINA /CompressBam=False;
Genome_build: Genome version Mouse B.38, gene models version Ensembl R.75
Supplementary_files_format_and_content: Excel files include FPKM and Count values for each Sample

source_name: Liver

extract_protocol:
Tissue specimens were removed, flash frozen on dry ice, and total RNA was harvested using the Qiagen miRNeasy kit. RNA quality and integrity were monitored via Agilent Bioanalyzer. A minimum of 3.75 ug of total RNA were used to collect enriched RNA subfractions for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Liver

value: Het (Q50) Knock-In

tag: age

value: 6 months

tag: Sex

value: Male

tag: housing condition

value: housed with Wild Type and Het (Q50) mice


title: Het (Q50) 10 months Male Liver mRNA rep3 399103_92274_1_L4.D703

value: 10 months


title: Het (Q50) 6 months Male Liver mRNA rep1 398903_68721_1_L3.D705


title: Het (Q50) 6 months Male Liver mRNA rep4 398933_68645_1_L8.D711


title: Het (Q50) 10 months Female Liver mRNA rep3 399114_92806_1_L9

value: Female


title: Het (Q50) 10 months Male Liver mRNA rep4 399107_92426_1_L5.D707


title: Het (Q50) 6 months Male Liver mRNA rep2 398912_68797_1_L5.D702


title: Het (Q50) 10 months Male Liver mRNA rep1 399084_92502_1_L1.D708


title: Het (Q50) 10 months Female Liver mRNA rep2 399109_92654_1_L5.D709


title: Het (Q50) 10 months Female Liver mRNA rep1 399095_92730_1_L3.D707


title: Het (Q50) 6 months Female Liver mRNA rep4 398935_68949_1_L5


title: Het (Q50) 6 months Female Liver mRNA rep3 398906_69101_1_L4.D708


title: 21_SL

value: MEF

value: MEFs (Scl/Lmo2) (21 days)


title: Het (Q50) 6 months Female Liver mRNA rep1 398898_69025_1_L2.D712


title: Het (Q20) 6 months Male Liver mRNA rep4 398930_65643_1_L8.D708

value: Het (Q20) Knock-In

value: housed with Wild Type and Het (Q20) mice


title: Het (Q20) 10 months Female Liver mRNA rep4 399120_85358_1_L7.D708


title: Het (Q20) 6 months Male Liver mRNA rep3 398910_65719_1_L4.D712


title: OVCA429-inputDNA

description: input DNA for GRHL2 ChIP-seq of OVCA429

tag: chip antibody


title: Het (Q20) 10 months Male Liver mRNA rep2 399106_85054_1_L5.D706


title: Het (Q20) 6 months Male Liver mRNA rep1 398908_65871_1_L4.D710


title: Het (Q20) 10 months Male Liver mRNA rep1 399093_85206_1_L3.D705


title: Het (Q50) 10 months Male Liver mRNA rep2 399088_92350_1_L2.D712


title: Het (Q20) 6 months Male Liver mRNA rep2 398909_65795_1_L4.D711


title: Het (Q20) 10 months Female Liver mRNA rep3 399112_85282_1_L6.D712


title: Het (Q20) 10 months Female Liver mRNA rep2 399111_85434_1_L6.D711


title: Het (Q50) 10 months Female Liver mRNA rep4 399115_92578_1_L6.D703


title: Het (Q20) 6 months Female Liver mRNA rep1 398905_66099_1_L3.D707


title: Het (Q20) 6 months Female Liver mRNA rep4 398928_65947_1_L7.D706


title: Het (Q140) 10 months Male Liver mRNA rep2 399101_90640_1_L4.D701

value: Het (Q140) Knock-In

value: housed with Het (Q140) mice


title: Het (Q20) 6 months Female Liver mRNA rep2 398907_66175_1_L4.D709


title: Het (Q140) 10 months Male Liver mRNA rep3 399118_90488_1_L7.D706


title: Het (Q20) 10 months Female Liver mRNA rep1 399098_85510_1_L3


title: Het (Q50) 6 months Female Liver mRNA rep2 398899_69177_1_L34


title: Het (Q140) 10 months Male Liver mRNA rep1 399097_90564_1_L3.D709


title: Het (Q20) 6 months Female Liver mRNA rep3 398926_66023_1_L7.D704


title: Het (Q140) 6 months Male Liver mRNA rep2 398893_63209_1_L1.D707


title: Het (Q140) 6 months Male Liver mRNA rep4 398902_63361_1_L3.D704


title: Het (Q140) 10 months Female Liver mRNA rep4 399126_90716_1_L8


title: Het (Q140) 6 months Male Liver mRNA rep3 398894_63437_1_L2.D708


title: Het (Q140) 10 months Female Liver mRNA rep3 399123_90792_1_L7.D711


title: Het (Q140) 6 months Male Liver mRNA rep1 398890_63285_1_L1.D704


title: Het (Q20) 10 months Male Liver mRNA rep3 399121_84978_1_L10


title: Het (Q140) 10 months Female Liver mRNA rep2 399086_90944_1_L26


title: WT 10 months Male Cortex mRNA rep3 399022_92447_1_L7.D705

source_name: Cortex

value: Cortex

value: Wild Type


title: WT 10 months Male Cortex mRNA rep4 399027_92295_1_L8.D710


title: Het (Q140) 6 months Female Liver mRNA rep3 398922_63665_1_L6.D712


title: Het (Q140) 6 months Female Liver mRNA rep1 398900_63589_1_L3.D702


title: Het (Q140) 6 months Female Liver mRNA rep2 398916_63741_1_L5.D706


title: Het (Q140) 6 months Female Liver mRNA rep4 398932_63513_1_L8.D710


title: WT 10 months Male Cortex mRNA rep2 399015_92371_1_L6.D710


title: WT 6 months Male Cortex mRNA rep3 398774_68666_1_L6.D707


title: WT 6 months Male Cortex mRNA rep4 398780_68894_1_L7.D701


title: WT 6 months Male Cortex mRNA rep2 398753_68742_1_L2.D710


title: HP_RNASeq_Rep1

data_processing:
The sequence reads were mapped to the mm10 mouse genome build using SHRiMP.
The resulting alignment files were used to obtain the transcript abundances as RPKM using Cufflinks.
Genome_build: mm10
Supplementary_files_format_and_content: csfasta and qual files (unmapped reads) and normalised expression as RPKM in a tab delimited file as calculated from Cufflinks

source_name: Hematopoietic Progenitors

extract_protocol:
RNA was isolated from snap frozen cells with the RNeasy Plus Mini Kit (Qiagen) and ribosome depleted with the Ribozero Gold Kit (Epicentre) according to manufacturers instructions.
RNA-seq libraries were generated with the SOLiD Total RNA-Seq Kit (Life Technologies, 4445374).

value: ES derived Hematopoietic progenitors (CD41+)


title: Het (Q140) 10 months Female Liver mRNA rep1 399085_90868_1_L1.D709


title: WT 6 months Male Cortex mRNA rep1 398746_68818_1_L17


title: WT 10 months Male Cortex mRNA rep4 399031_84999_1_L8.D703


title: WT 10 months Male Cortex mRNA rep1 399012_92219_1_L5.D707


title: WT 6 months Male Cortex mRNA rep2 398768_65662_1_L5.D701


title: WT 10 months Male Cortex mRNA rep3 399007_85075_1_L4.D702


title: WT 6 months Male Cortex mRNA rep3 398786_65738_1_L8.D707


title: WT 10 months Male Cortex mRNA rep2 398993_85151_1_L2.D712


title: WT 10 months Male Cortex mRNA rep1 398987_84923_1_L1.D706


title: WT 6 months Male Cortex mRNA rep1 398750_65586_1_L2.D707


title: WT 10 months Female Cortex mRNA rep2 398997_92751_1_L3.D704


title: WT 6 months Male Cortex mRNA rep4 398788_65814_1_L8.D709


title: WT 10 months Female Cortex mRNA rep1 398988_92523_1_L1.D707


title: WT 10 months Female Cortex mRNA rep4 399029_92675_1_L8.D701


title: WT 10 months Female Cortex mRNA rep3 398999_92599_1_L3.D706


title: WT 6 months Female Cortex mRNA rep3 398769_68970_1_L5.D702


title: WT 6 months Female Cortex mRNA rep1 398744_69046_1_L1.D701


title: WT 6 months Female Cortex mRNA rep2 398752_69198_1_L2.D709


title: WT 6 months Female Cortex mRNA rep2 398773_65890_1_L5.D706


title: WT 10 months Female Cortex mRNA rep3 399023_85455_1_L7.D706


title: WT 6 months Female Cortex mRNA rep4 398789_66042_1_L8.D710


title: WT 10 months Female Cortex mRNA rep4 399030_85379_1_L8.D702


title: WT 6 months Female Cortex mRNA rep3 398779_66118_1_L6.D712


title: WT 10 months Female Cortex mRNA rep2 399013_85303_1_L5.D708


title: WT 10 months Female Cortex mRNA rep1 399008_85227_1_L5.D703


title: WT 6 months Female Cortex mRNA rep1 398751_65966_1_L2.D708


title: Het (Q92) 10 months Male Cortex mRNA rep3 399024_87545_1_L7.D707

value: Het (Q92) Knock-In

value: housed with Het (Q92) mice


title: Het (Q92) 10 months Male Cortex mRNA rep1 398989_87393_1_L1.D708


title: Het (Q92) 10 months Male Cortex mRNA rep4 399028_87469_1_L8.D711


title: Het (Q92) 10 months Male Cortex mRNA rep2 399002_87621_1_L4.D709


title: Het (Q92) 6 months Male Cortex mRNA rep3 398775_71060_1_L6.D708


title: Het (Q92) 6 months Male Cortex mRNA rep2 398756_71212_1_L3.D701


title: WT 6 months Female Cortex mRNA rep4 398784_69122_1_L7.D705


title: Het (Q92) 10 months Female Cortex mRNA rep3 399018_87697_1_L6.D701


title: Het (Q92) 10 months Female Cortex mRNA rep4 399020_87849_1_L7.D703


title: Het (Q92) 6 months Female Cortex mRNA rep4 398791_71440_1_L8.D712


title: Het (Q92) 6 months Female Cortex mRNA rep2 398761_71364_1_L3.D706


title: Het (Q50) 10 months Male Cortex mRNA rep4 399019_92409_1_L6.D702

value: Het (Q50) Knock-In


title: Het (Q92) 6 months Male Cortex mRNA rep1 398754_71136_1_L2.D711

value: 6 months


title: Het (Q92) 10 months Female Cortex mRNA rep2 399005_87773_1_L4.D712


title: Het (Q50) 6 months Male Cortex mRNA rep4 398785_68856_1_L7.D706

value: Male


title: Het (Q50) 10 months Male Cortex mRNA rep3 399017_92257_1_L6.D712

value: housed with Wild Type and Het (Q50) mice


title: Het (Q50) 10 months Male Cortex mRNA rep1 398984_92485_1_L6

value: 10 months


title: Het (Q50) 10 months Male Cortex mRNA rep2 398985_92333_1_L11


title: Het (Q50) 10 months Female Cortex mRNA rep4 399026_92637_1_L8.D709

value: Female


title: Het (Q50) 10 months Female Cortex mRNA rep1 398998_92789_1_L3.D705


title: Het (Q50) 10 months Female Cortex mRNA rep2 399000_92561_1_L3.D707


title: Het (Q50) 6 months Male Cortex mRNA rep1 398745_68704_1_L1.D702


title: Het (Q50) 6 months Male Cortex mRNA rep3 398770_68780_1_L5.D703


title: Het (Q50) 10 months Female Cortex mRNA rep3 399014_92713_1_L6.D709


title: Het (Q50) 6 months Female Cortex mRNA rep3 398766_69084_1_L4.D711


title: Het (Q50) 6 months Female Cortex mRNA rep2 398764_69160_1_L4.D709


title: Het (Q92) 10 months Female Cortex mRNA rep1 399001_87925_1_L3.D708


title: Het (Q92) 6 months Female Cortex mRNA rep3 398771_71326_1_L5.D704


title: Het (Q50) 6 months Female Cortex mRNA rep1 398748_69008_1_L18


title: Het (Q92) 6 months Male Cortex mRNA rep4 398777_71022_1_L6.D710


title: Het (Q20) 10 months Male Cortex mRNA rep4 399025_85113_1_L7.D708


title: Het (Q20) 10 months Male Cortex mRNA rep3 399009_85189_1_L5.D704


title: Het (Q20) 10 months Male Cortex mRNA rep1 398994_85037_1_L21


title: Het (Q92) 6 months Female Cortex mRNA rep1 398755_71516_1_L2.D712


title: Het (Q20) 6 months Male Cortex mRNA rep4 398782_65852_1_L7.D703


title: Het (Q20) 10 months Male Cortex mRNA rep2 399004_84961_1_L4.D711


title: Het (Q20) 6 months Male Cortex mRNA rep2 398763_65700_1_L4.D708


title: Het (Q20) 10 months Female Cortex mRNA rep3 399003_85265_1_L4.D710


title: Het (Q20) 10 months Female Cortex mRNA rep2 398996_85417_1_L3.D703


title: Het (Q20) 10 months Female Cortex mRNA rep4 399006_85493_1_L4.D701


title: Het (Q20) 6 months Male Cortex mRNA rep1 398758_65776_1_L3.D703


title: Het (Q20) 10 months Female Cortex mRNA rep1 398992_85341_1_L29


title: Het (Q20) 6 months Female Cortex mRNA rep4 398790_66156_1_L8.D711


title: Het (Q20) 6 months Female Cortex mRNA rep3 398767_66080_1_L4.D712


title: Het (Q20) 6 months Female Cortex mRNA rep2 398765_65928_1_L4.D710


title: Het (Q50) 6 months Female Cortex mRNA rep4 398783_68932_1_L7.D704


title: Het (Q50) 6 months Male Cortex mRNA rep2 398757_68628_1_L3.D702


title: Het (Q140) 6 months Male Cortex mRNA rep4 398787_63192_1_L8.D708


title: Het (Q140) 6 months Male Cortex mRNA rep3 398762_63268_1_L4.D707


title: Het (Q140) 10 months Male Cortex mRNA rep3 399021_90471_1_L7.D704


title: Het (Q140) 10 months Male Cortex mRNA rep1 398990_90547_1_L2.D709


title: Het (Q140) 10 months Male Cortex mRNA rep2 398995_90623_1_L22


title: Het (Q140) 10 months Female Cortex mRNA rep4 399016_90775_1_L6.D711


title: Het (Q140) 10 months Female Cortex mRNA rep1 398991_90927_1_L20


title: Het (Q140) 10 months Female Cortex mRNA rep3 399011_90851_1_L5.D706


title: Het (Q140) 10 months Female Cortex mRNA rep2 399010_90699_1_L5.D705


title: Het (Q20) 6 months Female Cortex mRNA rep1 398749_66004_1_L1.D706


title: Het (Q140) 6 months Male Cortex mRNA rep2 398759_63420_1_L3.D704


title: Het (Q20) 6 months Male Cortex mRNA rep3 398781_65624_1_L7.D702


title: Het (Q140) 6 months Female Cortex mRNA rep3 398776_63496_1_L6.D709


title: Het (Q140) 6 months Female Cortex mRNA rep1 398760_63648_1_L3.D705


title: Het (Q140) 6 months Female Cortex mRNA rep4 398778_63572_1_L6.D711


title: WT 10 months Male Cerebellum mRNA rep4 398981_92217_1_L8.D712

source_name: Cerebellum

value: Cerebellum


title: WT 10 months Male Cerebellum mRNA rep3 398980_92293_1_L8.D711


title: Het (Q140) 6 months Female Cortex mRNA rep2 398772_63724_1_L30


title: Het (Q140) 6 months Male Cortex mRNA rep1 398747_63344_1_L1.D704


title: WT 10 months Male Cerebellum mRNA rep1 398956_92445_1_L4.D711


title: WT 6 months Male Cerebellum mRNA rep3 398826_68892_1_L6.D711


title: WT 10 months Male Cerebellum mRNA rep2 398961_92369_1_L5.D704


title: WT 6 months Male Cerebellum mRNA rep4 398839_68816_1_L8.D701


title: WT 6 months Male Cerebellum mRNA rep2 398824_68664_1_L6.D709


title: WT 6 months Male Cerebellum mRNA rep1 398799_68740_1_L1.D711_507


title: WT 10 months Male Cerebellum mRNA rep2 398941_84921_1_L1.D708


title: WT 10 months Male Cerebellum mRNA rep4 398973_85149_1_L7.D704


title: WT 10 months Male Cerebellum mRNA rep1 398938_85073_1_L1.D705


title: WT 6 months Male Cerebellum mRNA rep4 398837_65664_1_L8.D710


title: WT 6 months Male Cerebellum mRNA rep2 398807_65740_1_L3.D704


title: WT 6 months Male Cerebellum mRNA rep1 398793_65816_1_L1.D702


title: WT 10 months Female Cerebellum mRNA rep4 398979_92521_1_L8.D710


title: WT 6 months Male Cerebellum mRNA rep3 398833_65588_1_L7.D706


title: WT 10 months Female Cerebellum mRNA rep3 398963_92673_1_L5.D706


title: WT 6 months Female Cerebellum mRNA rep4 398822_69120_1_L6.D707


title: WT 10 months Female Cerebellum mRNA rep1 398951_92749_1_L3.D706


title: WT 10 months Female Cerebellum mRNA rep2 398962_92597_1_L5.D705


title: WT 6 months Female Cerebellum mRNA rep3 398803_69044_1_L2.D712


title: WT 6 months Female Cerebellum mRNA rep4 398834_66120_1_L8.D707


title: WT 10 months Female Cerebellum mRNA rep1 398940_85453_1_L1.D707


title: WT 10 months Female Cerebellum mRNA rep4 398968_85377_1_L6.D711


title: WT 10 months Female Cerebellum mRNA rep3 398960_85301_1_L5.D703


title: WT 10 months Female Cerebellum mRNA rep2 398946_85225_1_L2.D701


title: WT 6 months Female Cerebellum mRNA rep3 398816_65968_1_L5.D701


title: WT 6 months Female Cerebellum mRNA rep1 398806_66044_1_L3.D703


title: WT 6 months Female Cerebellum mRNA rep2 398808_65892_1_L3.D705


title: Het (Q92) 10 months Male Cerebellum mRNA rep1 398945_87467_1_L2.D712


title: Het (Q92) 6 months Male Cerebellum mRNA rep4 398832_71210_1_L7.D705


title: Het (Q92) 10 months Male Cerebellum mRNA rep4 398966_87391_1_L6.D709


title: WT 10 months Male Cerebellum mRNA rep3 398965_84997_1_L5.D708


title: Het (Q92) 6 months Male Cerebellum mRNA rep2 398818_71020_1_L5.D703


title: Het (Q92) 10 months Male Cerebellum mRNA rep2 398948_87619_1_L3.D703


title: Het (Q92) 6 months Male Cerebellum mRNA rep3 398828_71058_1_L7.D701


title: Het (Q92) 10 months Female Cerebellum mRNA rep3 398964_87695_1_L5.D707


title: Het (Q92) 10 months Female Cerebellum mRNA rep4 398969_87771_1_L6.D712


title: Het (Q92) 6 months Male Cerebellum mRNA rep1 398804_71134_1_L3.D701


title: Het (Q92) 10 months Female Cerebellum mRNA rep2 398953_87847_1_L3.D708


title: Het (Q92) 6 months Female Cerebellum mRNA rep3 398820_71438_1_L5.D705


title: Het (Q92) 6 months Female Cerebellum mRNA rep2 398814_71362_1_L4.D711


title: Het (Q92) 10 months Female Cerebellum mRNA rep1 398949_87923_1_L3.D704


title: WT 6 months Female Cerebellum mRNA rep2 398798_68968_1_L2.D707


title: Het (Q92) 6 months Female Cerebellum mRNA rep4 398821_71514_1_L5.D706


title: Het (Q92) 6 months Female Cerebellum mRNA rep1 398800_71324_1_L2.D709


title: Het (Q50) 10 months Male Cerebellum mRNA rep3 398974_92331_1_L7.D705


title: WT 6 months Female Cerebellum mRNA rep1 398797_69196_1_L1.D706


title: Het (Q50) 10 months Male Cerebellum mRNA rep4 398977_92483_1_L7.D708


title: Het (Q92) 10 months Male Cerebellum mRNA rep3 398950_87543_1_L3.D705


title: Het (Q50) 10 months Male Cerebellum mRNA rep1 398944_92255_1_L2.D711


title: Het (Q50) 6 months Male Cerebellum mRNA rep1 398823_68702_1_L6.D708


title: Het (Q50) 6 months Male Cerebellum mRNA rep2 398827_68778_1_L6.D712


title: Het (Q50) 6 months Male Cerebellum mRNA rep3 398831_68854_1_L7.D704


title: Het (Q50) 10 months Female Cerebellum mRNA rep4 398982_92787_1_L8.D701


title: Het (Q50) 10 months Female Cerebellum mRNA rep1 398937_92635_1_L1.D704


title: Het (Q20) 10 months Male Cerebellum mRNA rep4 398975_85187_1_L7.D706


title: Het (Q50) 6 months Female Cerebellum mRNA rep2 398811_68930_1_L4.D708


title: Het (Q50) 6 months Female Cerebellum mRNA rep4 398838_69006_1_L8.D711


title: Het (Q20) 10 months Male Cerebellum mRNA rep3 398971_85111_1_L6.D702


title: Het (Q50) 10 months Female Cerebellum mRNA rep2 398943_92711_1_L2.D710


title: Het (Q20) 10 months Male Cerebellum mRNA rep2 398967_85035_1_L6.D710


title: Het (Q20) 10 months Male Cerebellum mRNA rep1 398952_84959_1_L3.D707


title: Het (Q20) 6 months Male Cerebellum mRNA rep4 398825_65778_1_L6.D710


title: Het (Q20) 6 months Male Cerebellum mRNA rep1 398795_65626_1_L1.D704


title: Het (Q20) 6 months Male Cerebellum mRNA rep2 398801_65854_1_L2.D710


title: Het (Q20) 10 months Female Cerebellum mRNA rep2 398947_85263_1_L2.D702


title: Het (Q20) 10 months Female Cerebellum mRNA rep3 398957_85339_1_L4.D712


title: Het (Q20) 10 months Female Cerebellum mRNA rep4 398983_85491_1_L8.D702


title: Het (Q20) 6 months Female Cerebellum mRNA rep3 398819_65930_1_L5.D704


title: Het (Q20) 6 months Female Cerebellum mRNA rep2 398817_66158_1_L5.D702


title: Het (Q50) 6 months Male Cerebellum mRNA rep4 398836_68626_1_L8.D709


title: Het (Q20) 6 months Female Cerebellum mRNA rep4 398830_66082_1_L7.D703


title: Het (Q20) 10 months Female Cerebellum mRNA rep1 398939_85415_1_L1.D706


title: Het (Q50) 10 months Female Cerebellum mRNA rep3 398955_92559_1_L4.D710


title: Het (Q20) 6 months Female Cerebellum mRNA rep1 398813_66006_1_L4.D710


title: Het (Q140) 10 months Male Cerebellum mRNA rep1 398936_90545_1_L1.D703


title: Het (Q50) 6 months Female Cerebellum mRNA rep1 398810_69158_1_L4.D707


title: Het (Q140) 10 months Male Cerebellum mRNA rep3 398958_90469_1_L4.D701


title: Het (Q140) 6 months Male Cerebellum mRNA rep4 398805_63217_1_L3.D702


title: Het (Q140) 10 months Male Cerebellum mRNA rep4 398959_90393_1_L4.D702


title: Het (Q50) 6 months Female Cerebellum mRNA rep3 398829_69082_1_L7.D702


title: Het (Q140) 6 months Male Cerebellum mRNA rep1 398794_63293_1_L1.D703


title: Het (Q140) 10 months Female Cerebellum mRNA rep3 398976_90697_1_L7.D707


title: Het (Q140) 6 months Male Cerebellum mRNA rep2 398796_63369_1_L1.D705


title: Het (Q140) 10 months Female Cerebellum mRNA rep2 398970_90925_1_L32


title: Het (Q140) 10 months Female Cerebellum mRNA rep4 398978_90773_1_L8.D709


title: Het (Q140) 10 months Female Cerebellum mRNA rep1 398954_90849_1_L4.D709


title: Het (Q20) 6 months Male Cerebellum mRNA rep3 398815_65702_1_L4.D712


title: Het (Q140) 6 months Female Cerebellum mRNA rep3 398812_63521_1_L4.D709


title: Het (Q140) 6 months Female Cerebellum mRNA rep2 398809_63749_1_L3.D706


title: Het (Q140) 6 months Female Cerebellum mRNA rep4 398835_63597_1_L8.D708


title: Het (Q140) 6 months Female Cerebellum mRNA rep1 398792_63673_1_L1.D701


title: WT 10 months Male Striatum mRNA rep4 399064_92453_1_L6.D712

source_name: Striatum

value: Striatum


title: WT 10 months Male Striatum mRNA rep3 399062_92377_1_L6.D710


title: WT 6 months Male Striatum mRNA rep1 398847_68900_1_L2.D709


title: Het (Q140) 10 months Male Cerebellum mRNA rep2 398942_90621_1_L2.D709


title: WT 10 months Male Striatum mRNA rep1 399032_92301_1_L1.D704


title: WT 6 months Male Striatum mRNA rep3 398858_68824_1_L4.D708


title: WT 10 months Male Striatum mRNA rep3 399075_84929_1_L8.D711


title: WT 10 months Male Striatum mRNA rep4 399078_85157_1_L8.D702


title: WT 6 months Male Striatum mRNA rep4 398868_68672_1_L5.D706


title: Het (Q140) 6 months Male Cerebellum mRNA rep3 398802_63445_1_L2.D711


title: WT 6 months Male Striatum mRNA rep4 398880_65670_1_L7.D706


title: Het (Q50) 10 months Male Cerebellum mRNA rep2 398972_92407_1_L7.D703


title: WT 6 months Male Striatum mRNA rep2 398849_68748_1_L2.D711


title: WT 6 months Male Striatum mRNA rep2 398860_65746_1_L4.D710


title: WT 10 months Male Striatum mRNA rep2 399045_85081_1_L3.D705


title: WT 6 months Male Striatum mRNA rep1 398850_65594_1_L2.D712


title: WT 10 months Female Striatum mRNA rep4 399076_92681_1_L8.D712


title: WT 10 months Male Striatum mRNA rep1 399039_85005_1_L2.D711


title: WT 10 months Female Striatum mRNA rep3 399056_92605_1_L5.D704


title: WT 10 months Female Striatum mRNA rep1 399040_92529_1_L2.D712


title: WT 6 months Female Striatum mRNA rep3 398862_69052_1_L4.D712


title: WT 6 months Female Striatum mRNA rep2 398854_69204_1_L3.D704


title: WT 10 months Male Striatum mRNA rep2 399038_92225_1_L2.D710


title: WT 6 months Female Striatum mRNA rep1 398843_68976_1_L1.D705


title: WT 10 months Female Striatum mRNA rep3 399067_85233_1_L6.D703


title: WT 6 months Female Striatum mRNA rep3 398875_66126_1_L6.D701


title: WT 6 months Female Striatum mRNA rep4 398881_65974_1_L7.D707


title: WT 6 months Female Striatum mRNA rep1 398863_66050_1_L4.D701


title: WT 6 months Female Striatum mRNA rep2 398873_65898_1_L6.D711


title: WT 10 months Female Striatum mRNA rep2 399048_85385_1_L3.D708


title: Het (Q92) 10 months Male Striatum mRNA rep4 399070_87551_1_L7.D706


title: Het (Q92) 10 months Male Striatum mRNA rep3 399042_87627_1_L2.D702


title: WT 10 months Female Striatum mRNA rep1 399033_85461_1_L1.D705


title: Het (Q92) 10 months Male Striatum mRNA rep1 399034_87475_1_L1.D706


title: Het (Q92) 10 months Male Striatum mRNA rep2 399037_87399_1_L1.D709


title: Het (Q92) 6 months Male Striatum mRNA rep4 398885_71028_1_L8.D711


title: WT 6 months Male Striatum mRNA rep3 398870_65822_1_L6.D708


title: Het (Q92) 6 months Male Striatum mRNA rep3 398866_71142_1_L5.D704


title: Het (Q92) 6 months Male Striatum mRNA rep2 398855_71066_1_L3.D705


title: Het (Q92) 6 months Male Striatum mRNA rep1 398845_71218_1_L1.D707


title: WT 10 months Female Striatum mRNA rep2 399049_92757_1_L3.D709


title: Het (Q92) 10 months Female Striatum mRNA rep4 399063_87855_1_L6.D711


title: Het (Q92) 10 months Female Striatum mRNA rep2 399058_87779_1_L5.D706


title: Het (Q92) 10 months Female Striatum mRNA rep1 399035_87703_1_L1.D707


title: Het (Q92) 10 months Female Striatum mRNA rep3 399060_87931_1_L5.D708


title: Het (Q92) 6 months Female Striatum mRNA rep3 398859_71332_1_L4.D709


title: WT 10 months Female Striatum mRNA rep4 399068_85309_1_L7.D704


title: Het (Q92) 6 months Female Striatum mRNA rep4 398869_71522_1_L5.D707


title: Het (Q50) 10 months Male Striatum mRNA rep4 399079_92415_1_L8.D703


title: Het (Q92) 6 months Female Striatum mRNA rep1 398841_71370_1_L1.D703


title: Het (Q92) 6 months Female Striatum mRNA rep2 398848_71446_1_L2.D710


title: Het (Q50) 10 months Male Striatum mRNA rep3 399077_92339_1_L8.D701


title: Het (Q50) 10 months Male Striatum mRNA rep1 399069_92263_1_L7.D705


title: Het (Q50) 6 months Male Striatum mRNA rep2 398846_68786_1_L2.D708


title: Het (Q50) 6 months Male Striatum mRNA rep4 398879_68710_1_L7.D705


title: Het (Q50) 6 months Male Striatum mRNA rep1 398840_68862_1_L1.D702


title: Het (Q50) 10 months Female Striatum mRNA rep2 399059_92719_1_L5.D707


title: Het (Q50) 10 months Female Striatum mRNA rep3 399066_92567_1_L6.D702


title: Het (Q50) 6 months Male Striatum mRNA rep3 398852_68634_1_L3.D702


title: Het (Q50) 6 months Female Striatum mRNA rep3 398877_69014_1_L7.D703


title: Het (Q50) 10 months Female Striatum mRNA rep4 399071_92795_1_L7.D707


title: Het (Q50) 6 months Female Striatum mRNA rep2 398865_69166_1_L5.D703


title: Het (Q50) 6 months Female Striatum mRNA rep4 398886_69090_1_L8.D712


title: WT 6 months Female Striatum mRNA rep4 398872_69128_1_L6.D710


title: Het (Q50) 6 months Female Striatum mRNA rep1 398853_68938_1_L3.D703


title: Het (Q20) 10 months Male Striatum mRNA rep1 399050_85043_1_L4.D710

value: Het (Q20) Knock-In


title: Het (Q20) 10 months Male Striatum mRNA rep4 399061_85119_1_L5.D709

value: housed with Wild Type and Het (Q20) mice


title: Het (Q20) 10 months Male Striatum mRNA rep2 399053_84967_1_L4.D701


title: Het (Q50) 10 months Female Striatum mRNA rep1 399043_92643_1_L2.D703


title: Het (Q20) 6 months Male Striatum mRNA rep3 398874_65860_1_L6.D712


title: Het (Q20) 6 months Male Striatum mRNA rep1 398844_65784_1_L1.D706


title: Het (Q20) 6 months Male Striatum mRNA rep2 398864_65632_1_L5.D702


title: Het (Q20) 10 months Female Striatum mRNA rep1 399036_85423_1_L1.D708


title: Het (Q20) 10 months Female Striatum mRNA rep4 399074_85271_1_L8.D710


title: Het (Q20) 6 months Male Striatum mRNA rep4 398878_65708_1_L7.D704


title: Het (Q50) 10 months Male Striatum mRNA rep2 399072_92491_1_L7.D708


title: Het (Q20) 10 months Female Striatum mRNA rep3 399052_85347_1_L4.D712


title: Het (Q20) 6 months Female Striatum mRNA rep4 398884_66164_1_L8.D710


title: Het (Q20) 6 months Female Striatum mRNA rep3 398871_65936_1_L6.D709


title: Het (Q20) 10 months Female Striatum mRNA rep2 399046_85499_1_L3.D706


title: Het (Q20) 6 months Female Striatum mRNA rep2 398867_66088_1_L5.D705


title: Het (Q20) 6 months Female Striatum mRNA rep1 398856_66012_1_L3.D706


title: Het (Q140) 10 months Male Striatum mRNA rep4 399073_90401_1_L7.D709

value: Het (Q140) Knock-In


title: Het (Q140) 10 months Male Striatum mRNA rep3 399065_90477_1_L6.D701

value: housed with Het (Q140) mice


title: Het (Q140) 10 months Male Striatum mRNA rep2 399054_90553_1_L19


title: Het (Q20) 10 months Male Striatum mRNA rep3 399055_85195_1_L36


title: Het (Q140) 6 months Male Striatum mRNA rep4 398887_63350_1_L8.D701


title: Het (Q140) 6 months Male Striatum mRNA rep3 398883_63426_1_L8.D709


title: Het (Q140) 10 months Male Striatum mRNA rep1 399047_90629_1_L3.D707


title: Het (Q140) 10 months Female Striatum mRNA rep3 399051_90857_1_L4.D711


title: Het (Q140) 10 months Female Striatum mRNA rep4 399057_90781_1_L5.D705


title: Het (Q140) 10 months Female Striatum mRNA rep2 399044_90705_1_L3.D704


title: Het (Q140) 6 months Male Striatum mRNA rep2 398857_63198_1_L3.D707


title: Het (Q140) 6 months Female Striatum mRNA rep4 398882_63730_1_L8.D708


title: Het (Q140) 10 months Female Striatum mRNA rep1 399041_90933_1_L2.D701


title: Het (Q140) 6 months Female Striatum mRNA rep3 398876_63654_1_L7.D702


title: Het (Q140) 6 months Female Striatum mRNA rep2 398861_63578_1_L4.D711


title: WT 10 months Male Liver mRNA rep4 399122_92236_1_L8.D710

value: Liver


title: WT 10 months Male Liver mRNA rep3 399102_92464_1_L4.D702

value: Wild Type


title: WT 10 months Male Liver mRNA rep2 399094_92312_1_L3.D706


title: WT 10 months Male Liver mRNA rep1 399091_92388_1_L2.D703


title: WT 6 months Male Liver mRNA rep1 398915_68911_1_L5.D705


title: WT 6 months Male Liver mRNA rep2 398920_68759_1_L6.D710


title: WT 10 months Male Liver mRNA rep4 399119_85016_1_L7.D707


title: WT 10 months Male Liver mRNA rep3 399104_84940_1_L5.D704


title: WT 10 months Male Liver mRNA rep2 399096_85168_1_L3.D708


title: WT 10 months Male Liver mRNA rep1 399082_85092_1_L1.D706


title: WT 6 months Male Liver mRNA rep4 398929_65757_1_L7.D707


title: Het (Q140) 6 months Male Striatum mRNA rep1 398851_63274_1_L2.D701


title: WT 6 months Male Liver mRNA rep1 398888_65833_1_L1.D702


title: WT 6 months Male Liver mRNA rep2 398892_65605_1_L12


title: WT 10 months Female Liver mRNA rep1 399081_92616_1_L28


title: WT 10 months Female Liver mRNA rep2 399089_92692_1_L25


title: WT 6 months Female Liver mRNA rep3 398897_69063_1_L2.D711


title: WT 6 months Female Liver mRNA rep4 398923_69139_1_L6.D701


title: WT 10 months Female Liver mRNA rep3 399117_92540_1_L7.D705


title: WT 10 months Female Liver mRNA rep4 399124_92768_1_L13


title: Het (Q140) 6 months Female Striatum mRNA rep1 398842_63502_1_L1.D704


title: WT 10 months Female Liver mRNA rep1 399083_85244_1_L1.D707


title: WT 10 months Female Liver mRNA rep2 399087_85472_1_L7


title: WT 10 months Female Liver mRNA rep4 399108_85396_1_L5.D708


title: WT 10 months Female Liver mRNA rep3 399092_85320_1_L3.D704


title: WT 6 months Female Liver mRNA rep3 398919_65985_1_L6.D709


title: WT 6 months Female Liver mRNA rep2 398913_66137_1_L5.D703


title: WT 6 months Female Liver mRNA rep1 398889_68987_1_L1.D703


title: WT 6 months Female Liver mRNA rep4 398925_66061_1_L7.D703


title: WT 6 months Male Liver mRNA rep4 398927_68683_1_L7.D705


title: WT 6 months Female Liver mRNA rep1 398911_65909_1_L4.D701


title: Het (Q92) 6 months Male Liver mRNA rep4 398934_71077_1_L1


title: WT 6 months Male Liver mRNA rep3 398921_68835_1_L6.D711


title: Het (Q92) 6 months Male Liver mRNA rep3 398931_71039_1_L8.D709


title: Het (Q92) 10 months Male Liver mRNA rep2 399125_87638_1_L8.D712


title: Het (Q92) 10 months Male Liver mRNA rep1 399105_87410_1_L5.D705


title: Het (Q92) 6 months Male Liver mRNA rep2 398924_71229_1_L7.D702


title: Het (Q92) 10 months Male Liver mRNA rep3 399127_87562_1_L4


title: Het (Q92) 6 months Male Liver mRNA rep1 398918_71153_1_L6.D708


title: WT 6 months Male Liver mRNA rep3 398896_65681_1_L27


title: Het (Q92) 10 months Female Liver mRNA rep4 399116_87866_1_L7.D704


title: Het (Q92) 10 months Female Liver mRNA rep2 399100_87714_1_L4.D712


title: Het (Q92) 10 months Female Liver mRNA rep1 399099_87942_1_L14


title: Het (Q92) 6 months Female Liver mRNA rep1 398895_71533_1_L2.D709


title: WT 6 months Female Liver mRNA rep2 398891_69215_1_L1.D705


title: Het (Q92) 6 months Female Liver mRNA rep4 398917_71343_1_L5.D707


title: Het (Q92) 10 months Female Liver mRNA rep3 399110_87790_1_L6.D710