title: hdip1-2-3_RNAseq_rep1

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to the Arabidopsis genome (TAIR10) using hisat2.
The expression of genes were obtained with the R package edgeR.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text file include normalized reads for each sample.

source_name: seedlings

growth_protocol: Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates and soil for 20 days, under a 16 h light/8 h dark photoperiod at 22°C.

extract_protocol:
Total RNA was extracted from 20-day-old Arabidopsis seedlings with TRIzol reagent (Invitrogen).
Sequencing libraries were built for RNA-seq (DNBSEQ platform, single-end 50bp).

value: seedlings


title: cell_327

status: Public on Feb 28 2025

type: SRA

city: Beijing

first: Xiaoliang

middle: Sunney

last: Xie

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

country: China

institute: Peking University

description:
gm12878_pooled.allValidPairs.gz
gm12878_pooled.hic
gm12878_pooled.mcool
gm12878_pooled.ligation_junctions.bed
scmicroc_gm12878.snaphic.10kb.postprocessed.summits.bedpe
gm12878.RELA.peaks.con.txt.gz
gm12878.RELA.top5k.peaks.con.txt.gz

library_source: genomic

data_processing:
Raw sequencing reads were mapped to the reference genome with BWA mem (0.7.17-r1188) with parameters -5SP. Single-cell contacts were generated with the dip-c and hickit (v0.1.1) packages with default parameters.
PCR duplicates were removed from raw SAM files with samblaster (0.1.26) package with parameters --ignoreUnmated -r. Subsequently, nucleosome occupancy signals were calculated with the DANPOS2 package with paramter -a 5 -count 1000000.
Chromatin loop calling was performed with SnapHiC and Chromosight package with default parameters.
Single-cell 3D genome structures were generated with the hickit v0.1.1 package with parameters  -M and -Sr1m -c1 -r10m -c2 -b4m -b1m -b200k -D5 -b50k -D5 -b20k -D5 -b10k -D5 -b5k.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include contacts for each sample. bigWig files include nucleosome occupancy and ligation junction signals for each sample. hic and mcool files included contact matrices for each sample.

molecule: genomic DNA

organism: Homo sapiens

source_name: blood

growth_protocol: GM12878 lymphoblastoid cells were grown in RPMI1640 medium (Gibco, Thermo Fisher Scientific, Cat. # 11875093) media supplemented with 15% FBS and 1% Pen/Strep. GM12878 were cultured at 37° C with 5% CO2 at recommended density.

extract_protocol:
1 million cells were permeabilized with 100 μL Micro-C buffer1 (50 mM NaCl, 10 mM Tris-HCl pH 7.5, 5 mM MgCl2, 1 mM CaCl2, 0.2% IGEPAL CA630, 1 x PIC), incubate on ice for 20 min.
Single cells were amplified with the state-of-art transposase-based WGA (Multiplexed End Tagging Amplification), barcoded in 96-well plate, then pooled for library preparation.

tag: tissue

value: blood

tag: cell line

tag: cell type

value: lymphoblastoid


title: GM12878, 200U, Cell 66

description:
200U MNase
GM-200U_066.allValidPairs.gz
GM-200U_066.hic
GM-200U_066.mcool
GM-200U_066.clean.smooth.bw
GM-200U_066_20kb_1.3dg.gz
GM-200U_066_20kb_2.3dg.gz
GM-200U_066_20kb_3.3dg.gz
GM-200U_066_20kb_4.3dg.gz
GM-200U_066_20kb_5.3dg.gz
GM-200U_066_10kb_1.3dg.gz
GM-200U_066_10kb_2.3dg.gz
GM-200U_066_10kb_3.3dg.gz
GM-200U_066_10kb_4.3dg.gz
GM-200U_066_10kb_5.3dg.gz
GM-200U_066_5kb_1.3dg.gz
GM-200U_066_5kb_2.3dg.gz
GM-200U_066_5kb_3.3dg.gz
GM-200U_066_5kb_4.3dg.gz
GM-200U_066_5kb_5.3dg.gz
GM-200U_066_20kb_1.clean.3dg.gz
GM-200U_066_20kb_2.clean.3dg.gz
GM-200U_066_20kb_3.clean.3dg.gz
GM-200U_066_20kb_4.clean.3dg.gz
GM-200U_066_20kb_5.clean.3dg.gz
GM-200U_066_10kb_1.clean.3dg.gz
GM-200U_066_10kb_2.clean.3dg.gz
GM-200U_066_10kb_3.clean.3dg.gz
GM-200U_066_10kb_4.clean.3dg.gz
GM-200U_066_10kb_5.clean.3dg.gz
GM-200U_066_5kb_1.clean.3dg.gz
GM-200U_066_5kb_2.clean.3dg.gz
GM-200U_066_5kb_3.clean.3dg.gz
GM-200U_066_5kb_4.clean.3dg.gz
GM-200U_066_5kb_5.clean.3dg.gz

data_processing:
Raw sequencing reads were mapped to the reference genome with BWA mem (0.7.17-r1188) with parameters -5SP. Single-cell contacts were generated with the dip-c and hickit (v0.1.1) packages with default parameters.
PCR duplicates were removed from raw SAM files with samblaster (0.1.26) package with parameters --ignoreUnmated -r. Subsequently, nucleosome occupancy signals were calculated with the DANPOS2 package with paramter -a 5 -count 1000000.
Single-cell 3D genome structures were generated with the hickit v0.1.1 package with parameters  -M and -Sr1m -c1 -r10m -c2 -b4m -b1m -b200k -D5 -b50k -D5 -b20k -D5 -b10k -D5 -b5k.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include contacts for each sample. bigWig files include nucleosome occupancy for each sample. hic and mcool files included contact matrices for each sample.
Supplementary files format and content: .3dg files of single-cell 3D genome structures

tag: genotype

value: WT


title: IL2 CTL, Pim1/2 dKO, bio rep 3

city: Dundee

first: Laura

last: Spinelli

address: Dow Street

department: Cell Signalling and Immunology

country: United Kingdom

institute: University of Dundee

description: Illumina TruSeq Stranded mRNA

library_source: transcriptomic

data_processing:
bcl2fastq2 conversion software (NovaSeq 6000) for base calling and automatic adapter trimming.
Trimmed sequence reads were mapper to GRCm38.p6 using STAR (version 2.7.1a) with ‘outFilterType BySJout’ option switched on to reduce spurious junctions. STAR quantMode GeneCounts option was used to map aligned reads to genes to generate a gene counts matrix, using the annotation file GRCm38.101.
Low count genes reduced using filterByExpr function in EdgeR.
Count matrix was normalised using Trimmed Mean of M-values (TMM) method in EdgeR.
CalculateTPM function from Scater was used on TMM-normalised counts to calculate TPM values, with total exon length calculated using GenomicRanges as the sum of the non-overlapping exonic regions for a gene.
Assembly: GRCm38p6
Supplementary files format and content: Comma-separated values file containing raw counts for each sample.
Supplementary files format and content: Comma-separated values file containing TPM values for each sample.

molecule: total RNA

organism: Mus musculus

source_name: lymph node

growth_protocol: Lymph node cell suspension from Pim1/Pim2 WT (WT) and Pim1/Pim2 double knockout (Pim dKO) mice were stimulated for 2 days with anti-CD3/anti-CD28 (0.5 µg/mL) + h-IL2 (20 ng/mL) or h-IL15 (20 ng/mL) in RPMI 1640 containing glutamine, 10%FBS, pen/strep, 50 µM 2-mercaptoethanol. Cells were washed out of activation media then split daily into fresh media and IL2 or IL15 at a density of 0.3 million live cells/mL or 0.5 million live cells/mL respectively. On day 3 of culture (1 day after removal form activation media) CD4 T cells were magnetically depleted.

extract_protocol:
Total RNA was extracted using RNeasy mini kit (Qiagen). 2 µg of total RNA was submitted per sample for library prep.
300 ng of total RNA was used for library preparation using the Illumina TruSeq Stranded mRNA sample preparation kit (15031047) as per manufacturer instructions.

treatment_protocol: On day 6 of culture CD8 T cell were cultured in fresh warm media + IL2 (20 ng/mL) or IL15 (20 ng/mL) for 2 hours prior to harvesting pellets for transcriptomic analysis.

value: lymph node

tag: Sex

value: male

value: CD8 T cell

value: Pim1/2 dKO

tag: treatment

value: IL2 differentiated effector T cells


title: GM12878, 200U, Cell 65

description:
200U MNase
GM-200U_065.allValidPairs.gz
GM-200U_065.hic
GM-200U_065.mcool
GM-200U_065.clean.smooth.bw
GM-200U_065_20kb_1.3dg.gz
GM-200U_065_20kb_2.3dg.gz
GM-200U_065_20kb_3.3dg.gz
GM-200U_065_20kb_4.3dg.gz
GM-200U_065_20kb_5.3dg.gz
GM-200U_065_10kb_1.3dg.gz
GM-200U_065_10kb_2.3dg.gz
GM-200U_065_10kb_3.3dg.gz
GM-200U_065_10kb_4.3dg.gz
GM-200U_065_10kb_5.3dg.gz
GM-200U_065_5kb_1.3dg.gz
GM-200U_065_5kb_2.3dg.gz
GM-200U_065_5kb_3.3dg.gz
GM-200U_065_5kb_4.3dg.gz
GM-200U_065_5kb_5.3dg.gz
GM-200U_065_20kb_1.clean.3dg.gz
GM-200U_065_20kb_2.clean.3dg.gz
GM-200U_065_20kb_3.clean.3dg.gz
GM-200U_065_20kb_4.clean.3dg.gz
GM-200U_065_20kb_5.clean.3dg.gz
GM-200U_065_10kb_1.clean.3dg.gz
GM-200U_065_10kb_2.clean.3dg.gz
GM-200U_065_10kb_3.clean.3dg.gz
GM-200U_065_10kb_4.clean.3dg.gz
GM-200U_065_10kb_5.clean.3dg.gz
GM-200U_065_5kb_1.clean.3dg.gz
GM-200U_065_5kb_2.clean.3dg.gz
GM-200U_065_5kb_3.clean.3dg.gz
GM-200U_065_5kb_4.clean.3dg.gz
GM-200U_065_5kb_5.clean.3dg.gz


title: hda19_RNAseq_rep2

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

organism: Arabidopsis thaliana

tag: time


title: GM12878, 200U, Cell 70

description:
200U MNase
GM-200U_070.allValidPairs.gz
GM-200U_070.hic
GM-200U_070.mcool
GM-200U_070.clean.smooth.bw
GM-200U_070_20kb_1.3dg.gz
GM-200U_070_20kb_2.3dg.gz
GM-200U_070_20kb_3.3dg.gz
GM-200U_070_20kb_4.3dg.gz
GM-200U_070_20kb_5.3dg.gz
GM-200U_070_10kb_1.3dg.gz
GM-200U_070_10kb_2.3dg.gz
GM-200U_070_10kb_3.3dg.gz
GM-200U_070_10kb_4.3dg.gz
GM-200U_070_10kb_5.3dg.gz
GM-200U_070_5kb_1.3dg.gz
GM-200U_070_5kb_2.3dg.gz
GM-200U_070_5kb_3.3dg.gz
GM-200U_070_5kb_4.3dg.gz
GM-200U_070_5kb_5.3dg.gz
GM-200U_070_20kb_1.clean.3dg.gz
GM-200U_070_20kb_2.clean.3dg.gz
GM-200U_070_20kb_3.clean.3dg.gz
GM-200U_070_20kb_4.clean.3dg.gz
GM-200U_070_20kb_5.clean.3dg.gz
GM-200U_070_10kb_1.clean.3dg.gz
GM-200U_070_10kb_2.clean.3dg.gz
GM-200U_070_10kb_3.clean.3dg.gz
GM-200U_070_10kb_4.clean.3dg.gz
GM-200U_070_10kb_5.clean.3dg.gz
GM-200U_070_5kb_1.clean.3dg.gz
GM-200U_070_5kb_2.clean.3dg.gz
GM-200U_070_5kb_3.clean.3dg.gz
GM-200U_070_5kb_4.clean.3dg.gz
GM-200U_070_5kb_5.clean.3dg.gz


title: cell_325


title: GM12878, 200U, Cell 64

description:
200U MNase
GM-200U_064.allValidPairs.gz
GM-200U_064.hic
GM-200U_064.mcool
GM-200U_064.clean.smooth.bw
GM-200U_064_20kb_2.3dg.gz
GM-200U_064_20kb_3.3dg.gz
GM-200U_064_20kb_4.3dg.gz
GM-200U_064_20kb_5.3dg.gz
GM-200U_064_10kb_2.3dg.gz
GM-200U_064_10kb_3.3dg.gz
GM-200U_064_10kb_4.3dg.gz
GM-200U_064_10kb_5.3dg.gz
GM-200U_064_5kb_2.3dg.gz
GM-200U_064_5kb_3.3dg.gz
GM-200U_064_5kb_4.3dg.gz
GM-200U_064_5kb_5.3dg.gz
GM-200U_064_20kb_2.clean.3dg.gz
GM-200U_064_20kb_3.clean.3dg.gz
GM-200U_064_20kb_4.clean.3dg.gz
GM-200U_064_20kb_5.clean.3dg.gz
GM-200U_064_10kb_2.clean.3dg.gz
GM-200U_064_10kb_3.clean.3dg.gz
GM-200U_064_10kb_4.clean.3dg.gz
GM-200U_064_10kb_5.clean.3dg.gz
GM-200U_064_5kb_2.clean.3dg.gz
GM-200U_064_5kb_3.clean.3dg.gz
GM-200U_064_5kb_4.clean.3dg.gz
GM-200U_064_5kb_5.clean.3dg.gz


title: hda19_RNAseq_rep1


title: E_1435

city: Indianapolis

first: Ricardo

last: Cordova

state: IN

address: 635 Barnhill Drive, MS4067

country: USA

institute: Indiana University School of Medicine

data_processing:
Barcodes and sequencing adapters were trimmed using TrimGalore
Reads were aligned to Human reference genome mm39 (ENSEMBL) using HISAT2 aligner
Mapped reads were assigned to annotated genomic features of GRCh38 using featureCounts
Differential expression analysis was carried out using DESeq2 package
Assembly: mm39
Supplementary files format and content: comma-separated values (csv) file shows the number of reads (unnormalized counts) mapped to each gene (shown as Ensembl ID) for all the samples

source_name: B6MyC-CaP tumor

growth_protocol: B6MyC CaP cell line was derived from the Hi-MYC transgenic mouse model on a C57BL/6 background (B6MYC), which we previously establisehd by backcrossing FVB Hi-MYC mice with C57BL/6N mice. B6MyC-CaP cells were implanted subcutaneously into 6-week-old male C57BL/6 mice.

extract_protocol:
Total RNA was extracted using RNeasy Plus Kit (Qiagen) according to the manufacturer’s instructions.
RNA quality control, library preparation, and NGS paired-end sequencing on the Illumina NovaSeq platform were performed by the University at Buffalo Genomics and Bioinformatics core.

treatment_protocol: Once tumors were established, mice were randomized into four treatment groups: vehicle, enzalutamide (ENZ), alternate-day fasting (ADF), or ADF + ENZ. ENZ and ADF + ENZ groups were treated with 20mg/kg Enzalutamide by oral gavage once a day. Mice in the Vehicle and ENZ groups were fed normal chow ad libitum. Mice in the ADF and ADF + ENZ groups were fasted for 24 hours and fed ad libitum for 24 hours.

value: B6MyC-CaP tumor

value: Prostate Cancer

value: ENZ


title: IL2 CTL, Pim1/2 dKO, bio rep 1

description: Illumina TruSeq Stranded mRNA


title: Input_HDIP1-WT_FLAG

description: Library name: Sample 1

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to Arabidopsis genome (TAIR10) using Bowtie2.
Assembly: TAIR10
Supplementary files format and content: bigWig files were generated using bamCoverage.

source_name: Arabidopsis thaliana

growth_protocol: The Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates or soil with a 16 h light/8 h dark photoperiod at 22°C.

extract_protocol:
Arabidopsis seedlings were corss-linked by 1% formaldehyde. Chromatin were clarified from sonicated nuclei and were isolated with antibody.
Libraries were built for ChIP-seq (Illumina Novaseq 6000; 150-bp pair-end sequencing)

value: Arabidopsis thaliana

value: Arabidopsis seedlings

tag: chip antibody

value: SIGMA, F1804

value: 1305-HDIP1-FLAG transformed plants (in Col-0)


title: GM12878, 200U, Cell 68

description:
200U MNase
GM-200U_068.allValidPairs.gz
GM-200U_068.hic
GM-200U_068.mcool
GM-200U_068.clean.smooth.bw
GM-200U_068_20kb_1.3dg.gz
GM-200U_068_20kb_2.3dg.gz
GM-200U_068_20kb_3.3dg.gz
GM-200U_068_20kb_4.3dg.gz
GM-200U_068_20kb_5.3dg.gz
GM-200U_068_10kb_1.3dg.gz
GM-200U_068_10kb_2.3dg.gz
GM-200U_068_10kb_3.3dg.gz
GM-200U_068_10kb_4.3dg.gz
GM-200U_068_10kb_5.3dg.gz
GM-200U_068_5kb_1.3dg.gz
GM-200U_068_5kb_2.3dg.gz
GM-200U_068_5kb_3.3dg.gz
GM-200U_068_5kb_4.3dg.gz
GM-200U_068_5kb_5.3dg.gz
GM-200U_068_20kb_1.clean.3dg.gz
GM-200U_068_20kb_2.clean.3dg.gz
GM-200U_068_20kb_3.clean.3dg.gz
GM-200U_068_20kb_4.clean.3dg.gz
GM-200U_068_20kb_5.clean.3dg.gz
GM-200U_068_10kb_1.clean.3dg.gz
GM-200U_068_10kb_2.clean.3dg.gz
GM-200U_068_10kb_3.clean.3dg.gz
GM-200U_068_10kb_4.clean.3dg.gz
GM-200U_068_10kb_5.clean.3dg.gz
GM-200U_068_5kb_1.clean.3dg.gz
GM-200U_068_5kb_2.clean.3dg.gz
GM-200U_068_5kb_3.clean.3dg.gz
GM-200U_068_5kb_4.clean.3dg.gz
GM-200U_068_5kb_5.clean.3dg.gz


title: Col-0_RNAseq_rep2

value: wild type


title: GM12878, 200U, Cell 63

description:
200U MNase
GM-200U_063.allValidPairs.gz
GM-200U_063.hic
GM-200U_063.mcool
GM-200U_063.clean.smooth.bw
GM-200U_063_20kb_1.3dg.gz
GM-200U_063_20kb_2.3dg.gz
GM-200U_063_20kb_3.3dg.gz
GM-200U_063_20kb_4.3dg.gz
GM-200U_063_20kb_5.3dg.gz
GM-200U_063_10kb_1.3dg.gz
GM-200U_063_10kb_2.3dg.gz
GM-200U_063_10kb_3.3dg.gz
GM-200U_063_10kb_4.3dg.gz
GM-200U_063_10kb_5.3dg.gz
GM-200U_063_5kb_1.3dg.gz
GM-200U_063_5kb_2.3dg.gz
GM-200U_063_5kb_3.3dg.gz
GM-200U_063_5kb_4.3dg.gz
GM-200U_063_5kb_5.3dg.gz
GM-200U_063_20kb_1.clean.3dg.gz
GM-200U_063_20kb_2.clean.3dg.gz
GM-200U_063_20kb_3.clean.3dg.gz
GM-200U_063_20kb_4.clean.3dg.gz
GM-200U_063_20kb_5.clean.3dg.gz
GM-200U_063_10kb_1.clean.3dg.gz
GM-200U_063_10kb_2.clean.3dg.gz
GM-200U_063_10kb_3.clean.3dg.gz
GM-200U_063_10kb_4.clean.3dg.gz
GM-200U_063_10kb_5.clean.3dg.gz
GM-200U_063_5kb_1.clean.3dg.gz
GM-200U_063_5kb_2.clean.3dg.gz
GM-200U_063_5kb_3.clean.3dg.gz
GM-200U_063_5kb_4.clean.3dg.gz
GM-200U_063_5kb_5.clean.3dg.gz


title: IL15 CTL, WT, bio rep 2

description: Illumina TruSeq Stranded mRNA

value: IL15 differentiated memory T cells


title: IL2 CTL, WT, bio rep 3

description: Illumina TruSeq Stranded mRNA


title: cell_324

value: blood


title: hdip1-2-3_RNAseq_rep2

value: seedlings


title: Embryo, Cd2.4, 2

city: Stockholm

first: Linus

last: Wiklund

address: Nobels väg 13

department: Institute of Environmental Medicine

country: Sweden

institute: Karolinska Institutet

description:
Library name: Cd2_4b
Cd2_4b

data_processing:
Raw data QC, e.g. remove reads with: adapter contamination, more than 10% uncertain nucleotides, or base quality lower than 5 for more than 50% of reads.
Alignment against reference genome with HISAT2 v2.0.5 and quantification with featureCounts v1.5.0-p3
Removal of genes with fewer than 5 reads or that were detected in fewer than 3 replicates.
Normalization of data with TPM
Assembly: Danio rerio GRCz11 GCA_000002035
Supplementary files format and content: comma-separated text file containing raw counts for all samples
Supplementary files format and content: comma-separated text file containing TPM normalized counts for all samples

organism: Danio rerio

source_name: whole-organism

growth_protocol: Zebrafish embryos were kept in petri-dishes containing E3 medium in an incubator at 28.5 °C.

extract_protocol:
RNA was extracted with the QIAGEN RNeasy Plus Universal Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: Zebrafish embryos were treated with three doses each of cadmium or PCB126 from 1 day post fertilization (dpf) to 5 dpf.

value: whole-organism

value: WT, AB strain

value: Cd 2.4 ug/L


title: cell_323

value: lymphoblastoid


title: Col-0_RNAseq_rep1


title: GM12878, 200U, Cell 62

description:
200U MNase
GM-200U_062.allValidPairs.gz
GM-200U_062.hic
GM-200U_062.mcool
GM-200U_062.clean.smooth.bw
GM-200U_062_20kb_2.3dg.gz
GM-200U_062_20kb_3.3dg.gz
GM-200U_062_20kb_5.3dg.gz
GM-200U_062_10kb_2.3dg.gz
GM-200U_062_10kb_3.3dg.gz
GM-200U_062_10kb_5.3dg.gz
GM-200U_062_5kb_2.3dg.gz
GM-200U_062_5kb_3.3dg.gz
GM-200U_062_5kb_5.3dg.gz
GM-200U_062_20kb_2.clean.3dg.gz
GM-200U_062_20kb_3.clean.3dg.gz
GM-200U_062_20kb_5.clean.3dg.gz
GM-200U_062_10kb_2.clean.3dg.gz
GM-200U_062_10kb_3.clean.3dg.gz
GM-200U_062_10kb_5.clean.3dg.gz
GM-200U_062_5kb_2.clean.3dg.gz
GM-200U_062_5kb_3.clean.3dg.gz
GM-200U_062_5kb_5.clean.3dg.gz

value: WT


title: hdip1-2-3_H3Ac_rep2

value: Millipore, 06-599


title: cell_322


title: GM12878, 200U, Cell 61

description:
200U MNase
GM-200U_061.allValidPairs.gz
GM-200U_061.hic
GM-200U_061.mcool
GM-200U_061.clean.smooth.bw
GM-200U_061_20kb_1.3dg.gz
GM-200U_061_20kb_3.3dg.gz
GM-200U_061_20kb_5.3dg.gz
GM-200U_061_10kb_1.3dg.gz
GM-200U_061_10kb_3.3dg.gz
GM-200U_061_10kb_5.3dg.gz
GM-200U_061_5kb_1.3dg.gz
GM-200U_061_5kb_3.3dg.gz
GM-200U_061_5kb_5.3dg.gz
GM-200U_061_20kb_1.clean.3dg.gz
GM-200U_061_20kb_3.clean.3dg.gz
GM-200U_061_20kb_5.clean.3dg.gz
GM-200U_061_10kb_1.clean.3dg.gz
GM-200U_061_10kb_3.clean.3dg.gz
GM-200U_061_10kb_5.clean.3dg.gz
GM-200U_061_5kb_1.clean.3dg.gz
GM-200U_061_5kb_3.clean.3dg.gz
GM-200U_061_5kb_5.clean.3dg.gz


title: IL2 CTL, WT, bio rep 2

description: Illumina TruSeq Stranded mRNA

value: lymph node

value: male

value: CD8 T cell

value: IL2 differentiated effector T cells


title: cell_321


title: hdip1-2-3_H3Ac_rep1


title: IL2 CTL, WT, bio rep 1

description: Illumina TruSeq Stranded mRNA


title: IL2 CTL, Pim1/2 dKO, bio rep 2

description: Illumina TruSeq Stranded mRNA

value: Pim1/2 dKO


title: GM12878, 200U, Cell 60

description:
200U MNase
GM-200U_060.allValidPairs.gz
GM-200U_060.hic
GM-200U_060.mcool
GM-200U_060.clean.smooth.bw
GM-200U_060_20kb_1.3dg.gz
GM-200U_060_20kb_2.3dg.gz
GM-200U_060_20kb_3.3dg.gz
GM-200U_060_20kb_4.3dg.gz
GM-200U_060_20kb_5.3dg.gz
GM-200U_060_10kb_1.3dg.gz
GM-200U_060_10kb_2.3dg.gz
GM-200U_060_10kb_3.3dg.gz
GM-200U_060_10kb_4.3dg.gz
GM-200U_060_10kb_5.3dg.gz
GM-200U_060_5kb_1.3dg.gz
GM-200U_060_5kb_2.3dg.gz
GM-200U_060_5kb_3.3dg.gz
GM-200U_060_5kb_4.3dg.gz
GM-200U_060_5kb_5.3dg.gz
GM-200U_060_20kb_1.clean.3dg.gz
GM-200U_060_20kb_2.clean.3dg.gz
GM-200U_060_20kb_3.clean.3dg.gz
GM-200U_060_20kb_4.clean.3dg.gz
GM-200U_060_20kb_5.clean.3dg.gz
GM-200U_060_10kb_1.clean.3dg.gz
GM-200U_060_10kb_2.clean.3dg.gz
GM-200U_060_10kb_3.clean.3dg.gz
GM-200U_060_10kb_4.clean.3dg.gz
GM-200U_060_10kb_5.clean.3dg.gz
GM-200U_060_5kb_1.clean.3dg.gz
GM-200U_060_5kb_2.clean.3dg.gz
GM-200U_060_5kb_3.clean.3dg.gz
GM-200U_060_5kb_4.clean.3dg.gz
GM-200U_060_5kb_5.clean.3dg.gz


title: cell_326


title: E13.5 trachea cartilage Notum mutant 4

city: Cincinnati

first: Debora

last: Sinner

state: OH

address: 3333 Burnet Ave

department: Neonatology and Pulmonary Biology

institute: CCHMC

data_processing:
Partek Flow Genomic Analysis Software
Trimming low quality bases (Phred < 20) from 3-prime end
Aligning reads to a reference genome (mm10)
Quantifying to annotation model (mm10 Ensembl Transcripts release101)
Normalizing counts (Quantile normalization)
Differential Expression analysis using Limma-trend
Assembly: mm10
Supplementary files format and content: A Tab-deliminated file includes raw counts for each sample

source_name: E13.5 trachea

extract_protocol:
RNA was isolated using RLT lysis buffer according to manufacturer’s instructions
Libraries were generated from Ultra-Low Input mRNA (eukaryotic) Poly(A) selection with enrichment for full-length transcripts. Reverse transcription and cDNA amplification were performed with the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech). Libraries were constructed using the Illumina Nextera™ XT kit.

treatment_protocol: Each E11.5 sample, composed of 5 tracheas, was enzymatically homogenizing  with TrypLE express, total RNA was extracted using a commercial available kit (quick RNA microprep kit-Zymo Research). E13.5 tracheal tissue was cut into small pieces and enzymatically treated with TrypLE express for 15 minutes to generate a single-cell suspension. Afterward, cells were stained with Epcam APC antibody, filtered, and sorted using FACS.

value: E13.5 trachea

value: Embryonic epithelial and mesenchymal

value: Notum 150/150;gamma SMA eGFP

value: E13.5, Chondroblasts,Epithelial cells, and Myoblasts  were isolated by FACS  selection from, Bmp4 f/f; gammaSMAeGFP, Notum 300/300; gamma SMAeGFP or Notum 150/150; gamma SMAeGFP mouse trachea using APC-Epcam stain to select epithelial cells and GFP to isolate muscle cells. Double negative cells (Apc-, gfp-) were collected and represented the chondroblast population.


title: cell_320

value: blood


title: hda19_H3Ac_rep2

value: seedlings


title: GM12878, 200U, Cell 59

description:
200U MNase
GM-200U_059.allValidPairs.gz
GM-200U_059.hic
GM-200U_059.mcool
GM-200U_059.clean.smooth.bw
GM-200U_059_20kb_1.3dg.gz
GM-200U_059_20kb_2.3dg.gz
GM-200U_059_20kb_3.3dg.gz
GM-200U_059_20kb_5.3dg.gz
GM-200U_059_10kb_1.3dg.gz
GM-200U_059_10kb_2.3dg.gz
GM-200U_059_10kb_3.3dg.gz
GM-200U_059_10kb_5.3dg.gz
GM-200U_059_5kb_1.3dg.gz
GM-200U_059_5kb_2.3dg.gz
GM-200U_059_5kb_3.3dg.gz
GM-200U_059_5kb_5.3dg.gz
GM-200U_059_20kb_1.clean.3dg.gz
GM-200U_059_20kb_2.clean.3dg.gz
GM-200U_059_20kb_3.clean.3dg.gz
GM-200U_059_20kb_5.clean.3dg.gz
GM-200U_059_10kb_1.clean.3dg.gz
GM-200U_059_10kb_2.clean.3dg.gz
GM-200U_059_10kb_3.clean.3dg.gz
GM-200U_059_10kb_5.clean.3dg.gz
GM-200U_059_5kb_1.clean.3dg.gz
GM-200U_059_5kb_2.clean.3dg.gz
GM-200U_059_5kb_3.clean.3dg.gz
GM-200U_059_5kb_5.clean.3dg.gz


title: cell_319


title: hda19_H3Ac_rep1


title: E13.5 trachea cartilage Notum mutant 3


title: GM12878, 200U, Cell 58

description:
200U MNase
GM-200U_058.allValidPairs.gz
GM-200U_058.hic
GM-200U_058.mcool
GM-200U_058.clean.smooth.bw
GM-200U_058_20kb_1.3dg.gz
GM-200U_058_20kb_2.3dg.gz
GM-200U_058_20kb_3.3dg.gz
GM-200U_058_20kb_5.3dg.gz
GM-200U_058_10kb_1.3dg.gz
GM-200U_058_10kb_2.3dg.gz
GM-200U_058_10kb_3.3dg.gz
GM-200U_058_10kb_5.3dg.gz
GM-200U_058_5kb_1.3dg.gz
GM-200U_058_5kb_2.3dg.gz
GM-200U_058_5kb_3.3dg.gz
GM-200U_058_5kb_5.3dg.gz
GM-200U_058_20kb_1.clean.3dg.gz
GM-200U_058_20kb_2.clean.3dg.gz
GM-200U_058_20kb_3.clean.3dg.gz
GM-200U_058_20kb_5.clean.3dg.gz
GM-200U_058_10kb_1.clean.3dg.gz
GM-200U_058_10kb_2.clean.3dg.gz
GM-200U_058_10kb_3.clean.3dg.gz
GM-200U_058_10kb_5.clean.3dg.gz
GM-200U_058_5kb_1.clean.3dg.gz
GM-200U_058_5kb_2.clean.3dg.gz
GM-200U_058_5kb_3.clean.3dg.gz
GM-200U_058_5kb_5.clean.3dg.gz


title: E13.5 trachea cartilage Notum mutant 2


title: Col-0_H3Ac_rep2

value: wild type


title: cell_318


title: GM12878, 200U, Cell 57

description:
200U MNase
GM-200U_057.allValidPairs.gz
GM-200U_057.hic
GM-200U_057.mcool
GM-200U_057.clean.smooth.bw
GM-200U_057_20kb_1.3dg.gz
GM-200U_057_20kb_2.3dg.gz
GM-200U_057_20kb_3.3dg.gz
GM-200U_057_20kb_4.3dg.gz
GM-200U_057_20kb_5.3dg.gz
GM-200U_057_10kb_1.3dg.gz
GM-200U_057_10kb_2.3dg.gz
GM-200U_057_10kb_3.3dg.gz
GM-200U_057_10kb_4.3dg.gz
GM-200U_057_10kb_5.3dg.gz
GM-200U_057_5kb_1.3dg.gz
GM-200U_057_5kb_2.3dg.gz
GM-200U_057_5kb_3.3dg.gz
GM-200U_057_5kb_4.3dg.gz
GM-200U_057_5kb_5.3dg.gz
GM-200U_057_20kb_1.clean.3dg.gz
GM-200U_057_20kb_2.clean.3dg.gz
GM-200U_057_20kb_3.clean.3dg.gz
GM-200U_057_20kb_4.clean.3dg.gz
GM-200U_057_20kb_5.clean.3dg.gz
GM-200U_057_10kb_1.clean.3dg.gz
GM-200U_057_10kb_2.clean.3dg.gz
GM-200U_057_10kb_3.clean.3dg.gz
GM-200U_057_10kb_4.clean.3dg.gz
GM-200U_057_10kb_5.clean.3dg.gz
GM-200U_057_5kb_1.clean.3dg.gz
GM-200U_057_5kb_2.clean.3dg.gz
GM-200U_057_5kb_3.clean.3dg.gz
GM-200U_057_5kb_4.clean.3dg.gz
GM-200U_057_5kb_5.clean.3dg.gz


title: Col-0_H3Ac_rep1


title: GM12878, 200U, Cell 55

description:
200U MNase
GM-200U_055.allValidPairs.gz
GM-200U_055.hic
GM-200U_055.mcool
GM-200U_055.clean.smooth.bw
GM-200U_055_20kb_1.3dg.gz
GM-200U_055_20kb_2.3dg.gz
GM-200U_055_20kb_3.3dg.gz
GM-200U_055_20kb_4.3dg.gz
GM-200U_055_20kb_5.3dg.gz
GM-200U_055_10kb_1.3dg.gz
GM-200U_055_10kb_2.3dg.gz
GM-200U_055_10kb_3.3dg.gz
GM-200U_055_10kb_4.3dg.gz
GM-200U_055_10kb_5.3dg.gz
GM-200U_055_5kb_1.3dg.gz
GM-200U_055_5kb_2.3dg.gz
GM-200U_055_5kb_3.3dg.gz
GM-200U_055_5kb_4.3dg.gz
GM-200U_055_5kb_5.3dg.gz
GM-200U_055_20kb_1.clean.3dg.gz
GM-200U_055_20kb_2.clean.3dg.gz
GM-200U_055_20kb_3.clean.3dg.gz
GM-200U_055_20kb_4.clean.3dg.gz
GM-200U_055_20kb_5.clean.3dg.gz
GM-200U_055_10kb_1.clean.3dg.gz
GM-200U_055_10kb_2.clean.3dg.gz
GM-200U_055_10kb_3.clean.3dg.gz
GM-200U_055_10kb_4.clean.3dg.gz
GM-200U_055_10kb_5.clean.3dg.gz
GM-200U_055_5kb_1.clean.3dg.gz
GM-200U_055_5kb_2.clean.3dg.gz
GM-200U_055_5kb_3.clean.3dg.gz
GM-200U_055_5kb_4.clean.3dg.gz
GM-200U_055_5kb_5.clean.3dg.gz


title: IP_HDIP1-in-Col-0_FLAG_rep2

value: SIGMA, F1804

value: 1305-HDIP1-FLAG transformed plants (in Col-0)


title: E13.5 trachea cartilage control 3

value: Notum 300/300;gamma SMA eGFP


title: E13.5 trachea cartilage control 1

value: Bmp4 f/f; gamma SMA eGFP


title: cell_315

value: lymphoblastoid


title: E13.5 trachea cartilage Notum mutant 1


title: cell_314


title: GM12878, 200U, Cell 54

description:
200U MNase
GM-200U_054.allValidPairs.gz
GM-200U_054.hic
GM-200U_054.mcool
GM-200U_054.clean.smooth.bw
GM-200U_054_20kb_1.3dg.gz
GM-200U_054_20kb_2.3dg.gz
GM-200U_054_20kb_3.3dg.gz
GM-200U_054_20kb_4.3dg.gz
GM-200U_054_20kb_5.3dg.gz
GM-200U_054_10kb_1.3dg.gz
GM-200U_054_10kb_2.3dg.gz
GM-200U_054_10kb_3.3dg.gz
GM-200U_054_10kb_4.3dg.gz
GM-200U_054_10kb_5.3dg.gz
GM-200U_054_5kb_1.3dg.gz
GM-200U_054_5kb_2.3dg.gz
GM-200U_054_5kb_3.3dg.gz
GM-200U_054_5kb_4.3dg.gz
GM-200U_054_5kb_5.3dg.gz
GM-200U_054_20kb_1.clean.3dg.gz
GM-200U_054_20kb_2.clean.3dg.gz
GM-200U_054_20kb_3.clean.3dg.gz
GM-200U_054_20kb_4.clean.3dg.gz
GM-200U_054_20kb_5.clean.3dg.gz
GM-200U_054_10kb_1.clean.3dg.gz
GM-200U_054_10kb_2.clean.3dg.gz
GM-200U_054_10kb_3.clean.3dg.gz
GM-200U_054_10kb_4.clean.3dg.gz
GM-200U_054_10kb_5.clean.3dg.gz
GM-200U_054_5kb_1.clean.3dg.gz
GM-200U_054_5kb_2.clean.3dg.gz
GM-200U_054_5kb_3.clean.3dg.gz
GM-200U_054_5kb_4.clean.3dg.gz
GM-200U_054_5kb_5.clean.3dg.gz

value: WT


title: cell_317


title: cell_312


title: cell_316


title: IP_HDIP1-in-Col-0_FLAG_rep1


title: Input_HDIP1-in-Col-0_FLAG


title: GM12878, 200U, Cell 56

description:
200U MNase
GM-200U_056.allValidPairs.gz
GM-200U_056.hic
GM-200U_056.mcool
GM-200U_056.clean.smooth.bw
GM-200U_056_20kb_1.3dg.gz
GM-200U_056_20kb_2.3dg.gz
GM-200U_056_20kb_3.3dg.gz
GM-200U_056_10kb_1.3dg.gz
GM-200U_056_10kb_2.3dg.gz
GM-200U_056_10kb_3.3dg.gz
GM-200U_056_5kb_1.3dg.gz
GM-200U_056_5kb_2.3dg.gz
GM-200U_056_5kb_3.3dg.gz
GM-200U_056_20kb_1.clean.3dg.gz
GM-200U_056_20kb_2.clean.3dg.gz
GM-200U_056_20kb_3.clean.3dg.gz
GM-200U_056_10kb_1.clean.3dg.gz
GM-200U_056_10kb_2.clean.3dg.gz
GM-200U_056_10kb_3.clean.3dg.gz
GM-200U_056_5kb_1.clean.3dg.gz
GM-200U_056_5kb_2.clean.3dg.gz
GM-200U_056_5kb_3.clean.3dg.gz


title: GM12878, 200U, Cell 52

description:
200U MNase
GM-200U_052.allValidPairs.gz
GM-200U_052.hic
GM-200U_052.mcool
GM-200U_052.clean.smooth.bw
GM-200U_052_20kb_1.3dg.gz
GM-200U_052_20kb_2.3dg.gz
GM-200U_052_20kb_3.3dg.gz
GM-200U_052_20kb_4.3dg.gz
GM-200U_052_20kb_5.3dg.gz
GM-200U_052_10kb_1.3dg.gz
GM-200U_052_10kb_2.3dg.gz
GM-200U_052_10kb_3.3dg.gz
GM-200U_052_10kb_4.3dg.gz
GM-200U_052_10kb_5.3dg.gz
GM-200U_052_5kb_1.3dg.gz
GM-200U_052_5kb_2.3dg.gz
GM-200U_052_5kb_3.3dg.gz
GM-200U_052_5kb_4.3dg.gz
GM-200U_052_5kb_5.3dg.gz
GM-200U_052_20kb_1.clean.3dg.gz
GM-200U_052_20kb_2.clean.3dg.gz
GM-200U_052_20kb_3.clean.3dg.gz
GM-200U_052_20kb_4.clean.3dg.gz
GM-200U_052_20kb_5.clean.3dg.gz
GM-200U_052_10kb_1.clean.3dg.gz
GM-200U_052_10kb_2.clean.3dg.gz
GM-200U_052_10kb_3.clean.3dg.gz
GM-200U_052_10kb_4.clean.3dg.gz
GM-200U_052_10kb_5.clean.3dg.gz
GM-200U_052_5kb_1.clean.3dg.gz
GM-200U_052_5kb_2.clean.3dg.gz
GM-200U_052_5kb_3.clean.3dg.gz
GM-200U_052_5kb_4.clean.3dg.gz
GM-200U_052_5kb_5.clean.3dg.gz


title: E13.5 trachea muscle control 3


title: GM12878, 200U, Cell 53

description:
200U MNase
GM-200U_053.allValidPairs.gz
GM-200U_053.hic
GM-200U_053.mcool
GM-200U_053.clean.smooth.bw
GM-200U_053_20kb_1.3dg.gz
GM-200U_053_20kb_2.3dg.gz
GM-200U_053_20kb_3.3dg.gz
GM-200U_053_20kb_4.3dg.gz
GM-200U_053_20kb_5.3dg.gz
GM-200U_053_10kb_1.3dg.gz
GM-200U_053_10kb_2.3dg.gz
GM-200U_053_10kb_3.3dg.gz
GM-200U_053_10kb_4.3dg.gz
GM-200U_053_10kb_5.3dg.gz
GM-200U_053_5kb_1.3dg.gz
GM-200U_053_5kb_2.3dg.gz
GM-200U_053_5kb_3.3dg.gz
GM-200U_053_5kb_4.3dg.gz
GM-200U_053_5kb_5.3dg.gz
GM-200U_053_20kb_1.clean.3dg.gz
GM-200U_053_20kb_2.clean.3dg.gz
GM-200U_053_20kb_3.clean.3dg.gz
GM-200U_053_20kb_4.clean.3dg.gz
GM-200U_053_20kb_5.clean.3dg.gz
GM-200U_053_10kb_1.clean.3dg.gz
GM-200U_053_10kb_2.clean.3dg.gz
GM-200U_053_10kb_3.clean.3dg.gz
GM-200U_053_10kb_4.clean.3dg.gz
GM-200U_053_10kb_5.clean.3dg.gz
GM-200U_053_5kb_1.clean.3dg.gz
GM-200U_053_5kb_2.clean.3dg.gz
GM-200U_053_5kb_3.clean.3dg.gz
GM-200U_053_5kb_4.clean.3dg.gz
GM-200U_053_5kb_5.clean.3dg.gz


title: E13.5 trachea cartilage control 2


title: IP_HDA19-in-hda19-hdip1-2-3_FLAG_rep2

value: 1305-HDA19-FLAG transformed plants (in hda19/hdip1/2/3)


title: cell_311

description:
gm12878_pooled.allValidPairs.gz
gm12878_pooled.hic
gm12878_pooled.mcool
gm12878_pooled.ligation_junctions.bed
scmicroc_gm12878.snaphic.10kb.postprocessed.summits.bedpe
gm12878.RELA.peaks.con.txt.gz
gm12878.RELA.top5k.peaks.con.txt.gz


title: E13.5 trachea muscle control 1


title: E13.5 trachea muscle control 2


title: E13.5 trachea epithelium control 3


title: IP_HDA19-in-hda19-hdip1-2-3_FLAG_rep1


title: cell_310


title: Input_HDA19-in-hda19-hdip1-2-3_FLAG


title: cell_313


title: IP_HDA19-in-hda19_FLAG_rep3

value: 1305-HDA19-FLAG transformed plants (in hda19)


title: GM12878, 200U, Cell 48

description:
200U MNase
GM-200U_048.allValidPairs.gz
GM-200U_048.hic
GM-200U_048.mcool
GM-200U_048.clean.smooth.bw
GM-200U_048_20kb_1.3dg.gz
GM-200U_048_20kb_2.3dg.gz
GM-200U_048_20kb_3.3dg.gz
GM-200U_048_20kb_4.3dg.gz
GM-200U_048_20kb_5.3dg.gz
GM-200U_048_10kb_1.3dg.gz
GM-200U_048_10kb_2.3dg.gz
GM-200U_048_10kb_3.3dg.gz
GM-200U_048_10kb_4.3dg.gz
GM-200U_048_10kb_5.3dg.gz
GM-200U_048_5kb_1.3dg.gz
GM-200U_048_5kb_2.3dg.gz
GM-200U_048_5kb_3.3dg.gz
GM-200U_048_5kb_4.3dg.gz
GM-200U_048_5kb_5.3dg.gz
GM-200U_048_20kb_1.clean.3dg.gz
GM-200U_048_20kb_2.clean.3dg.gz
GM-200U_048_20kb_3.clean.3dg.gz
GM-200U_048_20kb_4.clean.3dg.gz
GM-200U_048_20kb_5.clean.3dg.gz
GM-200U_048_10kb_1.clean.3dg.gz
GM-200U_048_10kb_2.clean.3dg.gz
GM-200U_048_10kb_3.clean.3dg.gz
GM-200U_048_10kb_4.clean.3dg.gz
GM-200U_048_10kb_5.clean.3dg.gz
GM-200U_048_5kb_1.clean.3dg.gz
GM-200U_048_5kb_2.clean.3dg.gz
GM-200U_048_5kb_3.clean.3dg.gz
GM-200U_048_5kb_4.clean.3dg.gz
GM-200U_048_5kb_5.clean.3dg.gz


title: cell_309


title: E13.5 trachea epithelium control 1


title: E11.5 trachea, Mutant Dermo1Cre; Wnt5af/f, rep.9

source_name: E11.5 trachea

value: E11.5 trachea

value: Dermo1Cre; Wnt5af/f

value: E11.5 tracheas were isolated from Wnt5af/f or Dermo1Cre;Wnt5a f/f.


title: GM12878, 200U, Cell 50

description:
200U MNase
GM-200U_050.allValidPairs.gz
GM-200U_050.hic
GM-200U_050.mcool
GM-200U_050.clean.smooth.bw
GM-200U_050_20kb_1.3dg.gz
GM-200U_050_20kb_2.3dg.gz
GM-200U_050_20kb_3.3dg.gz
GM-200U_050_20kb_4.3dg.gz
GM-200U_050_20kb_5.3dg.gz
GM-200U_050_10kb_1.3dg.gz
GM-200U_050_10kb_2.3dg.gz
GM-200U_050_10kb_3.3dg.gz
GM-200U_050_10kb_4.3dg.gz
GM-200U_050_10kb_5.3dg.gz
GM-200U_050_5kb_1.3dg.gz
GM-200U_050_5kb_2.3dg.gz
GM-200U_050_5kb_3.3dg.gz
GM-200U_050_5kb_4.3dg.gz
GM-200U_050_5kb_5.3dg.gz
GM-200U_050_20kb_1.clean.3dg.gz
GM-200U_050_20kb_2.clean.3dg.gz
GM-200U_050_20kb_3.clean.3dg.gz
GM-200U_050_20kb_4.clean.3dg.gz
GM-200U_050_20kb_5.clean.3dg.gz
GM-200U_050_10kb_1.clean.3dg.gz
GM-200U_050_10kb_2.clean.3dg.gz
GM-200U_050_10kb_3.clean.3dg.gz
GM-200U_050_10kb_4.clean.3dg.gz
GM-200U_050_10kb_5.clean.3dg.gz
GM-200U_050_5kb_1.clean.3dg.gz
GM-200U_050_5kb_2.clean.3dg.gz
GM-200U_050_5kb_3.clean.3dg.gz
GM-200U_050_5kb_4.clean.3dg.gz
GM-200U_050_5kb_5.clean.3dg.gz


title: E11.5 trachea, Mutant Dermo1Cre; Wnt5af/f, rep.7

value: Embryonic epithelial and mesenchymal


title: E11.5 trachea, Mutant Dermo1Cre; Wnt5af/f, rep.8


title: GM12878, 200U, Cell 45

description:
200U MNase
GM-200U_045.allValidPairs.gz
GM-200U_045.hic
GM-200U_045.mcool
GM-200U_045.clean.smooth.bw
GM-200U_045_20kb_1.3dg.gz
GM-200U_045_20kb_3.3dg.gz
GM-200U_045_20kb_4.3dg.gz
GM-200U_045_10kb_1.3dg.gz
GM-200U_045_10kb_3.3dg.gz
GM-200U_045_10kb_4.3dg.gz
GM-200U_045_5kb_1.3dg.gz
GM-200U_045_5kb_3.3dg.gz
GM-200U_045_5kb_4.3dg.gz
GM-200U_045_20kb_1.clean.3dg.gz
GM-200U_045_20kb_3.clean.3dg.gz
GM-200U_045_20kb_4.clean.3dg.gz
GM-200U_045_10kb_1.clean.3dg.gz
GM-200U_045_10kb_3.clean.3dg.gz
GM-200U_045_10kb_4.clean.3dg.gz
GM-200U_045_5kb_1.clean.3dg.gz
GM-200U_045_5kb_3.clean.3dg.gz
GM-200U_045_5kb_4.clean.3dg.gz


title: GM12878, 200U, Cell 46

description:
200U MNase
GM-200U_046.allValidPairs.gz
GM-200U_046.hic
GM-200U_046.mcool
GM-200U_046.clean.smooth.bw
GM-200U_046_20kb_1.3dg.gz
GM-200U_046_20kb_2.3dg.gz
GM-200U_046_20kb_3.3dg.gz
GM-200U_046_20kb_4.3dg.gz
GM-200U_046_20kb_5.3dg.gz
GM-200U_046_10kb_1.3dg.gz
GM-200U_046_10kb_2.3dg.gz
GM-200U_046_10kb_3.3dg.gz
GM-200U_046_10kb_4.3dg.gz
GM-200U_046_10kb_5.3dg.gz
GM-200U_046_5kb_1.3dg.gz
GM-200U_046_5kb_2.3dg.gz
GM-200U_046_5kb_3.3dg.gz
GM-200U_046_5kb_4.3dg.gz
GM-200U_046_5kb_5.3dg.gz
GM-200U_046_20kb_1.clean.3dg.gz
GM-200U_046_20kb_2.clean.3dg.gz
GM-200U_046_20kb_3.clean.3dg.gz
GM-200U_046_20kb_4.clean.3dg.gz
GM-200U_046_20kb_5.clean.3dg.gz
GM-200U_046_10kb_1.clean.3dg.gz
GM-200U_046_10kb_2.clean.3dg.gz
GM-200U_046_10kb_3.clean.3dg.gz
GM-200U_046_10kb_4.clean.3dg.gz
GM-200U_046_10kb_5.clean.3dg.gz
GM-200U_046_5kb_1.clean.3dg.gz
GM-200U_046_5kb_2.clean.3dg.gz
GM-200U_046_5kb_3.clean.3dg.gz
GM-200U_046_5kb_4.clean.3dg.gz
GM-200U_046_5kb_5.clean.3dg.gz


title: cell_307


title: Input_HDA19-in-hda19_FLAG


title: GM12878, 200U, Cell 51

description:
200U MNase
GM-200U_051.allValidPairs.gz
GM-200U_051.hic
GM-200U_051.mcool
GM-200U_051.clean.smooth.bw
GM-200U_051_20kb_1.3dg.gz
GM-200U_051_20kb_2.3dg.gz
GM-200U_051_20kb_3.3dg.gz
GM-200U_051_20kb_4.3dg.gz
GM-200U_051_20kb_5.3dg.gz
GM-200U_051_10kb_1.3dg.gz
GM-200U_051_10kb_2.3dg.gz
GM-200U_051_10kb_3.3dg.gz
GM-200U_051_10kb_4.3dg.gz
GM-200U_051_10kb_5.3dg.gz
GM-200U_051_5kb_1.3dg.gz
GM-200U_051_5kb_2.3dg.gz
GM-200U_051_5kb_3.3dg.gz
GM-200U_051_5kb_4.3dg.gz
GM-200U_051_5kb_5.3dg.gz
GM-200U_051_20kb_1.clean.3dg.gz
GM-200U_051_20kb_2.clean.3dg.gz
GM-200U_051_20kb_3.clean.3dg.gz
GM-200U_051_20kb_4.clean.3dg.gz
GM-200U_051_20kb_5.clean.3dg.gz
GM-200U_051_10kb_1.clean.3dg.gz
GM-200U_051_10kb_2.clean.3dg.gz
GM-200U_051_10kb_3.clean.3dg.gz
GM-200U_051_10kb_4.clean.3dg.gz
GM-200U_051_10kb_5.clean.3dg.gz
GM-200U_051_5kb_1.clean.3dg.gz
GM-200U_051_5kb_2.clean.3dg.gz
GM-200U_051_5kb_3.clean.3dg.gz
GM-200U_051_5kb_4.clean.3dg.gz
GM-200U_051_5kb_5.clean.3dg.gz


title: cell_306


title: cell_308


title: GM12878, 200U, Cell 43

description:
200U MNase
GM-200U_043.allValidPairs.gz
GM-200U_043.hic
GM-200U_043.mcool
GM-200U_043.clean.smooth.bw
GM-200U_043_20kb_1.3dg.gz
GM-200U_043_20kb_2.3dg.gz
GM-200U_043_20kb_3.3dg.gz
GM-200U_043_10kb_1.3dg.gz
GM-200U_043_10kb_2.3dg.gz
GM-200U_043_10kb_3.3dg.gz
GM-200U_043_5kb_1.3dg.gz
GM-200U_043_5kb_2.3dg.gz
GM-200U_043_5kb_3.3dg.gz
GM-200U_043_20kb_1.clean.3dg.gz
GM-200U_043_20kb_2.clean.3dg.gz
GM-200U_043_20kb_3.clean.3dg.gz
GM-200U_043_10kb_1.clean.3dg.gz
GM-200U_043_10kb_2.clean.3dg.gz
GM-200U_043_10kb_3.clean.3dg.gz
GM-200U_043_5kb_1.clean.3dg.gz
GM-200U_043_5kb_2.clean.3dg.gz
GM-200U_043_5kb_3.clean.3dg.gz


title: cell_305


title: GM12878, 200U, Cell 44

description:
200U MNase
GM-200U_044.allValidPairs.gz
GM-200U_044.hic
GM-200U_044.mcool
GM-200U_044.clean.smooth.bw
GM-200U_044_20kb_1.3dg.gz
GM-200U_044_20kb_2.3dg.gz
GM-200U_044_20kb_3.3dg.gz
GM-200U_044_20kb_4.3dg.gz
GM-200U_044_20kb_5.3dg.gz
GM-200U_044_10kb_1.3dg.gz
GM-200U_044_10kb_2.3dg.gz
GM-200U_044_10kb_3.3dg.gz
GM-200U_044_10kb_4.3dg.gz
GM-200U_044_10kb_5.3dg.gz
GM-200U_044_5kb_1.3dg.gz
GM-200U_044_5kb_2.3dg.gz
GM-200U_044_5kb_3.3dg.gz
GM-200U_044_5kb_4.3dg.gz
GM-200U_044_5kb_5.3dg.gz
GM-200U_044_20kb_1.clean.3dg.gz
GM-200U_044_20kb_2.clean.3dg.gz
GM-200U_044_20kb_3.clean.3dg.gz
GM-200U_044_20kb_4.clean.3dg.gz
GM-200U_044_20kb_5.clean.3dg.gz
GM-200U_044_10kb_1.clean.3dg.gz
GM-200U_044_10kb_2.clean.3dg.gz
GM-200U_044_10kb_3.clean.3dg.gz
GM-200U_044_10kb_4.clean.3dg.gz
GM-200U_044_10kb_5.clean.3dg.gz
GM-200U_044_5kb_1.clean.3dg.gz
GM-200U_044_5kb_2.clean.3dg.gz
GM-200U_044_5kb_3.clean.3dg.gz
GM-200U_044_5kb_4.clean.3dg.gz
GM-200U_044_5kb_5.clean.3dg.gz


title: E11.5 trachea, Mutant Dermo1Cre; Wnt5af/f, rep.6


title: cell_303


title: cell_304


title: E13.5 trachea epithelium control 2

value: E13.5 trachea


title: E11.5 trachea, Control Wnt5af/f, rep.5

value: Wnt5a f/f


title: IP_HDA19-in-hda19_FLAG_rep2


title: GM12878, 200U, Cell 49

description:
200U MNase
GM-200U_049.allValidPairs.gz
GM-200U_049.hic
GM-200U_049.mcool
GM-200U_049.clean.smooth.bw
GM-200U_049_20kb_1.3dg.gz
GM-200U_049_20kb_2.3dg.gz
GM-200U_049_20kb_3.3dg.gz
GM-200U_049_20kb_4.3dg.gz
GM-200U_049_10kb_1.3dg.gz
GM-200U_049_10kb_2.3dg.gz
GM-200U_049_10kb_3.3dg.gz
GM-200U_049_10kb_4.3dg.gz
GM-200U_049_5kb_1.3dg.gz
GM-200U_049_5kb_2.3dg.gz
GM-200U_049_5kb_3.3dg.gz
GM-200U_049_5kb_4.3dg.gz
GM-200U_049_20kb_1.clean.3dg.gz
GM-200U_049_20kb_2.clean.3dg.gz
GM-200U_049_20kb_3.clean.3dg.gz
GM-200U_049_20kb_4.clean.3dg.gz
GM-200U_049_10kb_1.clean.3dg.gz
GM-200U_049_10kb_2.clean.3dg.gz
GM-200U_049_10kb_3.clean.3dg.gz
GM-200U_049_10kb_4.clean.3dg.gz
GM-200U_049_5kb_1.clean.3dg.gz
GM-200U_049_5kb_2.clean.3dg.gz
GM-200U_049_5kb_3.clean.3dg.gz
GM-200U_049_5kb_4.clean.3dg.gz

value: blood


title: IP_HDA19-in-hda19_FLAG_rep1

value: seedlings


title: GM12878, 200U, Cell 42

description:
200U MNase
GM-200U_042.allValidPairs.gz
GM-200U_042.hic
GM-200U_042.mcool
GM-200U_042.clean.smooth.bw
GM-200U_042_20kb_1.3dg.gz
GM-200U_042_20kb_2.3dg.gz
GM-200U_042_20kb_3.3dg.gz
GM-200U_042_20kb_4.3dg.gz
GM-200U_042_20kb_5.3dg.gz
GM-200U_042_10kb_1.3dg.gz
GM-200U_042_10kb_2.3dg.gz
GM-200U_042_10kb_3.3dg.gz
GM-200U_042_10kb_4.3dg.gz
GM-200U_042_10kb_5.3dg.gz
GM-200U_042_5kb_1.3dg.gz
GM-200U_042_5kb_2.3dg.gz
GM-200U_042_5kb_3.3dg.gz
GM-200U_042_5kb_4.3dg.gz
GM-200U_042_5kb_5.3dg.gz
GM-200U_042_20kb_1.clean.3dg.gz
GM-200U_042_20kb_2.clean.3dg.gz
GM-200U_042_20kb_3.clean.3dg.gz
GM-200U_042_20kb_4.clean.3dg.gz
GM-200U_042_20kb_5.clean.3dg.gz
GM-200U_042_10kb_1.clean.3dg.gz
GM-200U_042_10kb_2.clean.3dg.gz
GM-200U_042_10kb_3.clean.3dg.gz
GM-200U_042_10kb_4.clean.3dg.gz
GM-200U_042_10kb_5.clean.3dg.gz
GM-200U_042_5kb_1.clean.3dg.gz
GM-200U_042_5kb_2.clean.3dg.gz
GM-200U_042_5kb_3.clean.3dg.gz
GM-200U_042_5kb_4.clean.3dg.gz
GM-200U_042_5kb_5.clean.3dg.gz


title: E11.5 trachea, Control Wnt5af/f, rep.4


title: cell_302


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter39 [39U]

city: Bundoora

first: Anya

last: Shindler

state: VIC

address: 1 Kingsbury Drive

country: Australia

institute: La Trobe University

data_processing:
Library strategy: 16S Metagenomic
Fastq files obtained from the Miseq machine were processed using QIIME2 2021.11
Excel files were the end product from the QIIME2 processing
Assembly: N/A
Supplementary files format and content: Processed files are in excel .csv format.  The MOTU contains the OTUs obtained, the Mtax.csv files contains the Taxonomy identified during the QIIME2 processing, and MSamples.csv contains the metadata for the other two .csv files.

organism: Bacteria

source_name: soil sample

extract_protocol:
Qiagen DNeasy® PowerSoil® Kits
Illumina 16S Metagenomic Sequencing Library Preparation

value: soil sample

tag: season

value: Winter

tag: location

tag: building

value: University


title: high-level blocking containing medium

type: RNA

city: Fukuoka

first: Takayuki

last: Fujii

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Neurology

country: Japan

institute: Kyushu University

description: Gene expression after incubation with  DMEM+B27+recombinant SEMA3E 1 μg/ml+SEMA3E-blocking IgG 1 μg/ml

hyb_protocol: cRNA was hybridized to Themo Fisher  Clariom D Assay Mouse array, washed and stained according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Affymetrix scanner.

data_processing: The data were analyzed with median polish summarization and quantile normalization by Affymetrix® Expression Console™ 1.1 software, and obtained normalized intensity values.

label: biotin

source_name: mouse primary DRG neurons, incubated with DMEM+B27+recombinant SEMA3E 1 μg/ml+SEMA3E-blocking IgG 1 μg/ml, 72hr

label_protocol: The cRNA was amplified, labeled using GeneChip WT Pico Reagent Kit according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

tag: cells

value: mouse primary DRG neurons

tag: strain

value: ICR

tag: gender

value: male

tag: age


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter38 [38U]


title: SEMA3E medium

description: Gene expression after incubation with  DMEM+B27+recombinant SEMA3E 1 μg/ml

source_name: mouse primary DRG neurons, incubated with DMEM+B27+recombinant SEMA3E 1 μg/ml, 72hr


title: E11.5 trachea, Control Wnt5af/f, rep.3


title: GM12878, 200U, Cell 41

description:
200U MNase
GM-200U_041.allValidPairs.gz
GM-200U_041.hic
GM-200U_041.mcool
GM-200U_041.clean.smooth.bw
GM-200U_041_20kb_1.3dg.gz
GM-200U_041_20kb_2.3dg.gz
GM-200U_041_20kb_3.3dg.gz
GM-200U_041_20kb_4.3dg.gz
GM-200U_041_20kb_5.3dg.gz
GM-200U_041_10kb_1.3dg.gz
GM-200U_041_10kb_2.3dg.gz
GM-200U_041_10kb_3.3dg.gz
GM-200U_041_10kb_4.3dg.gz
GM-200U_041_10kb_5.3dg.gz
GM-200U_041_5kb_1.3dg.gz
GM-200U_041_5kb_2.3dg.gz
GM-200U_041_5kb_3.3dg.gz
GM-200U_041_5kb_4.3dg.gz
GM-200U_041_5kb_5.3dg.gz
GM-200U_041_20kb_1.clean.3dg.gz
GM-200U_041_20kb_2.clean.3dg.gz
GM-200U_041_20kb_3.clean.3dg.gz
GM-200U_041_20kb_4.clean.3dg.gz
GM-200U_041_20kb_5.clean.3dg.gz
GM-200U_041_10kb_1.clean.3dg.gz
GM-200U_041_10kb_2.clean.3dg.gz
GM-200U_041_10kb_3.clean.3dg.gz
GM-200U_041_10kb_4.clean.3dg.gz
GM-200U_041_10kb_5.clean.3dg.gz
GM-200U_041_5kb_1.clean.3dg.gz
GM-200U_041_5kb_2.clean.3dg.gz
GM-200U_041_5kb_3.clean.3dg.gz
GM-200U_041_5kb_4.clean.3dg.gz
GM-200U_041_5kb_5.clean.3dg.gz

value: lymphoblastoid

value: WT


title: GM12878, 200U, Cell 40

description:
200U MNase
GM-200U_040.allValidPairs.gz
GM-200U_040.hic
GM-200U_040.mcool
GM-200U_040.clean.smooth.bw
GM-200U_040_20kb_1.3dg.gz
GM-200U_040_20kb_2.3dg.gz
GM-200U_040_20kb_3.3dg.gz
GM-200U_040_20kb_4.3dg.gz
GM-200U_040_20kb_5.3dg.gz
GM-200U_040_10kb_1.3dg.gz
GM-200U_040_10kb_2.3dg.gz
GM-200U_040_10kb_3.3dg.gz
GM-200U_040_10kb_4.3dg.gz
GM-200U_040_10kb_5.3dg.gz
GM-200U_040_5kb_1.3dg.gz
GM-200U_040_5kb_2.3dg.gz
GM-200U_040_5kb_3.3dg.gz
GM-200U_040_5kb_4.3dg.gz
GM-200U_040_5kb_5.3dg.gz
GM-200U_040_20kb_1.clean.3dg.gz
GM-200U_040_20kb_2.clean.3dg.gz
GM-200U_040_20kb_3.clean.3dg.gz
GM-200U_040_20kb_4.clean.3dg.gz
GM-200U_040_20kb_5.clean.3dg.gz
GM-200U_040_10kb_1.clean.3dg.gz
GM-200U_040_10kb_2.clean.3dg.gz
GM-200U_040_10kb_3.clean.3dg.gz
GM-200U_040_10kb_4.clean.3dg.gz
GM-200U_040_10kb_5.clean.3dg.gz
GM-200U_040_5kb_1.clean.3dg.gz
GM-200U_040_5kb_2.clean.3dg.gz
GM-200U_040_5kb_3.clean.3dg.gz
GM-200U_040_5kb_4.clean.3dg.gz
GM-200U_040_5kb_5.clean.3dg.gz


title: Control medium

description: Gene expression after incubation with DMEM+B27

source_name: mouse primary DRG neurons, incubated with DMEM+B27, 72hr


title: cell_300


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter37 [37U]


title: GM12878, 200U, Cell 39

description:
200U MNase
GM-200U_039.allValidPairs.gz
GM-200U_039.hic
GM-200U_039.mcool
GM-200U_039.clean.smooth.bw
GM-200U_039_20kb_1.3dg.gz
GM-200U_039_20kb_2.3dg.gz
GM-200U_039_20kb_3.3dg.gz
GM-200U_039_20kb_4.3dg.gz
GM-200U_039_20kb_5.3dg.gz
GM-200U_039_10kb_1.3dg.gz
GM-200U_039_10kb_2.3dg.gz
GM-200U_039_10kb_3.3dg.gz
GM-200U_039_10kb_4.3dg.gz
GM-200U_039_10kb_5.3dg.gz
GM-200U_039_5kb_1.3dg.gz
GM-200U_039_5kb_2.3dg.gz
GM-200U_039_5kb_3.3dg.gz
GM-200U_039_5kb_4.3dg.gz
GM-200U_039_5kb_5.3dg.gz
GM-200U_039_20kb_1.clean.3dg.gz
GM-200U_039_20kb_2.clean.3dg.gz
GM-200U_039_20kb_3.clean.3dg.gz
GM-200U_039_20kb_4.clean.3dg.gz
GM-200U_039_20kb_5.clean.3dg.gz
GM-200U_039_10kb_1.clean.3dg.gz
GM-200U_039_10kb_2.clean.3dg.gz
GM-200U_039_10kb_3.clean.3dg.gz
GM-200U_039_10kb_4.clean.3dg.gz
GM-200U_039_10kb_5.clean.3dg.gz
GM-200U_039_5kb_1.clean.3dg.gz
GM-200U_039_5kb_2.clean.3dg.gz
GM-200U_039_5kb_3.clean.3dg.gz
GM-200U_039_5kb_4.clean.3dg.gz
GM-200U_039_5kb_5.clean.3dg.gz


title: E11.5 trachea, Control Wnt5af/f, rep.1


title: cell_298


title: GM12878, 200U, Cell 38

description:
200U MNase
GM-200U_038.allValidPairs.gz
GM-200U_038.hic
GM-200U_038.mcool
GM-200U_038.clean.smooth.bw
GM-200U_038_20kb_1.3dg.gz
GM-200U_038_20kb_2.3dg.gz
GM-200U_038_20kb_3.3dg.gz
GM-200U_038_20kb_4.3dg.gz
GM-200U_038_20kb_5.3dg.gz
GM-200U_038_10kb_1.3dg.gz
GM-200U_038_10kb_2.3dg.gz
GM-200U_038_10kb_3.3dg.gz
GM-200U_038_10kb_4.3dg.gz
GM-200U_038_10kb_5.3dg.gz
GM-200U_038_5kb_1.3dg.gz
GM-200U_038_5kb_2.3dg.gz
GM-200U_038_5kb_3.3dg.gz
GM-200U_038_5kb_4.3dg.gz
GM-200U_038_5kb_5.3dg.gz
GM-200U_038_20kb_1.clean.3dg.gz
GM-200U_038_20kb_2.clean.3dg.gz
GM-200U_038_20kb_3.clean.3dg.gz
GM-200U_038_20kb_4.clean.3dg.gz
GM-200U_038_20kb_5.clean.3dg.gz
GM-200U_038_10kb_1.clean.3dg.gz
GM-200U_038_10kb_2.clean.3dg.gz
GM-200U_038_10kb_3.clean.3dg.gz
GM-200U_038_10kb_4.clean.3dg.gz
GM-200U_038_10kb_5.clean.3dg.gz
GM-200U_038_5kb_1.clean.3dg.gz
GM-200U_038_5kb_2.clean.3dg.gz
GM-200U_038_5kb_3.clean.3dg.gz
GM-200U_038_5kb_4.clean.3dg.gz
GM-200U_038_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter36 [36U]


title: E9.5 FCPG experimental 3

city: New York

first: James

middle: F

last: Clark

state: New York

address: 1468 Madison Ave, Annenberg 25-70, Box 1020

department: Cell Developmental Regenerative Biology

institute: Icahn School of Medicine at Mount Sinai

description:
counts.csv
deseq_results.csv

data_processing:
Illumina NovaSeq 6000 SP was used for sequencing.
RStudio was used to process and analyze data.
Bowtie package was used to align sequences from BAM
Reference genome Mus musculus mm39 was used for alignments.
featureCounts package was used to produce raw counts data.
DESeq2 package was used for differential expression profiling
Assembly: mm39
Supplementary files format and content: counts.csv contains raw gene counts for all samples
Supplementary files format and content: deseq_results.csv contains DESeq2 analysis from comparing wild-type to Fgfr1 FCPG/FCPG tissue

molecule: polyA RNA

source_name: tailbud, mesoderm

extract_protocol:
Microdissection was used to excise tailbud tissue from E9.5 mouse embryos. RNA was extracted using Qiagin RNeasy kits. 1ug of RNA was used for library contsruction.
Libraries were constructed using Illumina stranded mRNA prep kits.

value: tailbud, mesoderm

value: NMPs, somitic mesoderm, intermediate mesoderm

value: Fgfr1 FCPG/FCPG


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter35 [35U]


title: cell_299

description:
gm12878_pooled.allValidPairs.gz
gm12878_pooled.hic
gm12878_pooled.mcool
gm12878_pooled.ligation_junctions.bed
scmicroc_gm12878.snaphic.10kb.postprocessed.summits.bedpe
gm12878.RELA.peaks.con.txt.gz
gm12878.RELA.top5k.peaks.con.txt.gz


title: E9.5 FCPG experimental 2

description:
counts.csv
deseq_results.csv


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter40 [40U]


title: GM12878, 200U, Cell 36

description:
200U MNase
GM-200U_036.allValidPairs.gz
GM-200U_036.hic
GM-200U_036.mcool
GM-200U_036.clean.smooth.bw
GM-200U_036_20kb_2.3dg.gz
GM-200U_036_20kb_3.3dg.gz
GM-200U_036_20kb_4.3dg.gz
GM-200U_036_20kb_5.3dg.gz
GM-200U_036_10kb_2.3dg.gz
GM-200U_036_10kb_3.3dg.gz
GM-200U_036_10kb_4.3dg.gz
GM-200U_036_10kb_5.3dg.gz
GM-200U_036_5kb_2.3dg.gz
GM-200U_036_5kb_3.3dg.gz
GM-200U_036_5kb_4.3dg.gz
GM-200U_036_5kb_5.3dg.gz
GM-200U_036_20kb_2.clean.3dg.gz
GM-200U_036_20kb_3.clean.3dg.gz
GM-200U_036_20kb_4.clean.3dg.gz
GM-200U_036_20kb_5.clean.3dg.gz
GM-200U_036_10kb_2.clean.3dg.gz
GM-200U_036_10kb_3.clean.3dg.gz
GM-200U_036_10kb_4.clean.3dg.gz
GM-200U_036_10kb_5.clean.3dg.gz
GM-200U_036_5kb_2.clean.3dg.gz
GM-200U_036_5kb_3.clean.3dg.gz
GM-200U_036_5kb_4.clean.3dg.gz
GM-200U_036_5kb_5.clean.3dg.gz


title: cell_297


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter34 [34U]


title: GM12878, 200U, Cell 37

description:
200U MNase
GM-200U_037.allValidPairs.gz
GM-200U_037.hic
GM-200U_037.mcool
GM-200U_037.clean.smooth.bw
GM-200U_037_20kb_1.3dg.gz
GM-200U_037_20kb_2.3dg.gz
GM-200U_037_20kb_3.3dg.gz
GM-200U_037_20kb_4.3dg.gz
GM-200U_037_20kb_5.3dg.gz
GM-200U_037_10kb_1.3dg.gz
GM-200U_037_10kb_2.3dg.gz
GM-200U_037_10kb_3.3dg.gz
GM-200U_037_10kb_4.3dg.gz
GM-200U_037_10kb_5.3dg.gz
GM-200U_037_5kb_1.3dg.gz
GM-200U_037_5kb_2.3dg.gz
GM-200U_037_5kb_3.3dg.gz
GM-200U_037_5kb_4.3dg.gz
GM-200U_037_5kb_5.3dg.gz
GM-200U_037_20kb_1.clean.3dg.gz
GM-200U_037_20kb_2.clean.3dg.gz
GM-200U_037_20kb_3.clean.3dg.gz
GM-200U_037_20kb_4.clean.3dg.gz
GM-200U_037_20kb_5.clean.3dg.gz
GM-200U_037_10kb_1.clean.3dg.gz
GM-200U_037_10kb_2.clean.3dg.gz
GM-200U_037_10kb_3.clean.3dg.gz
GM-200U_037_10kb_4.clean.3dg.gz
GM-200U_037_10kb_5.clean.3dg.gz
GM-200U_037_5kb_1.clean.3dg.gz
GM-200U_037_5kb_2.clean.3dg.gz
GM-200U_037_5kb_3.clean.3dg.gz
GM-200U_037_5kb_4.clean.3dg.gz
GM-200U_037_5kb_5.clean.3dg.gz


title: cell_301


title: E11.5 trachea, Control Wnt5af/f, rep.2

value: E11.5 trachea

value: E11.5 tracheas were isolated from Wnt5af/f or Dermo1Cre;Wnt5a f/f.


title: GM12878, 200U, Cell 35

description:
200U MNase
GM-200U_035.allValidPairs.gz
GM-200U_035.hic
GM-200U_035.mcool
GM-200U_035.clean.smooth.bw
GM-200U_035_20kb_1.3dg.gz
GM-200U_035_20kb_2.3dg.gz
GM-200U_035_20kb_3.3dg.gz
GM-200U_035_20kb_4.3dg.gz
GM-200U_035_20kb_5.3dg.gz
GM-200U_035_10kb_1.3dg.gz
GM-200U_035_10kb_2.3dg.gz
GM-200U_035_10kb_3.3dg.gz
GM-200U_035_10kb_4.3dg.gz
GM-200U_035_10kb_5.3dg.gz
GM-200U_035_5kb_1.3dg.gz
GM-200U_035_5kb_2.3dg.gz
GM-200U_035_5kb_3.3dg.gz
GM-200U_035_5kb_4.3dg.gz
GM-200U_035_5kb_5.3dg.gz
GM-200U_035_20kb_1.clean.3dg.gz
GM-200U_035_20kb_2.clean.3dg.gz
GM-200U_035_20kb_3.clean.3dg.gz
GM-200U_035_20kb_4.clean.3dg.gz
GM-200U_035_20kb_5.clean.3dg.gz
GM-200U_035_10kb_1.clean.3dg.gz
GM-200U_035_10kb_2.clean.3dg.gz
GM-200U_035_10kb_3.clean.3dg.gz
GM-200U_035_10kb_4.clean.3dg.gz
GM-200U_035_10kb_5.clean.3dg.gz
GM-200U_035_5kb_1.clean.3dg.gz
GM-200U_035_5kb_2.clean.3dg.gz
GM-200U_035_5kb_3.clean.3dg.gz
GM-200U_035_5kb_4.clean.3dg.gz
GM-200U_035_5kb_5.clean.3dg.gz


title: GM12878, 200U, Cell 47

description:
200U MNase
GM-200U_047.allValidPairs.gz
GM-200U_047.hic
GM-200U_047.mcool
GM-200U_047.clean.smooth.bw
GM-200U_047_20kb_1.3dg.gz
GM-200U_047_20kb_2.3dg.gz
GM-200U_047_20kb_3.3dg.gz
GM-200U_047_20kb_4.3dg.gz
GM-200U_047_20kb_5.3dg.gz
GM-200U_047_10kb_1.3dg.gz
GM-200U_047_10kb_2.3dg.gz
GM-200U_047_10kb_3.3dg.gz
GM-200U_047_10kb_4.3dg.gz
GM-200U_047_10kb_5.3dg.gz
GM-200U_047_5kb_1.3dg.gz
GM-200U_047_5kb_2.3dg.gz
GM-200U_047_5kb_3.3dg.gz
GM-200U_047_5kb_4.3dg.gz
GM-200U_047_5kb_5.3dg.gz
GM-200U_047_20kb_1.clean.3dg.gz
GM-200U_047_20kb_2.clean.3dg.gz
GM-200U_047_20kb_3.clean.3dg.gz
GM-200U_047_20kb_4.clean.3dg.gz
GM-200U_047_20kb_5.clean.3dg.gz
GM-200U_047_10kb_1.clean.3dg.gz
GM-200U_047_10kb_2.clean.3dg.gz
GM-200U_047_10kb_3.clean.3dg.gz
GM-200U_047_10kb_4.clean.3dg.gz
GM-200U_047_10kb_5.clean.3dg.gz
GM-200U_047_5kb_1.clean.3dg.gz
GM-200U_047_5kb_2.clean.3dg.gz
GM-200U_047_5kb_3.clean.3dg.gz
GM-200U_047_5kb_4.clean.3dg.gz
GM-200U_047_5kb_5.clean.3dg.gz


title: cell_296


title: E9.5 Wild-type control 3

description:
counts.csv
deseq_results.csv

value: Wild-type


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter32 [32U]


title: cell_295


title: GM12878, 200U, Cell 34

description:
200U MNase
GM-200U_034.allValidPairs.gz
GM-200U_034.hic
GM-200U_034.mcool
GM-200U_034.clean.smooth.bw
GM-200U_034_20kb_2.3dg.gz
GM-200U_034_20kb_3.3dg.gz
GM-200U_034_20kb_4.3dg.gz
GM-200U_034_20kb_5.3dg.gz
GM-200U_034_10kb_2.3dg.gz
GM-200U_034_10kb_3.3dg.gz
GM-200U_034_10kb_4.3dg.gz
GM-200U_034_10kb_5.3dg.gz
GM-200U_034_5kb_2.3dg.gz
GM-200U_034_5kb_3.3dg.gz
GM-200U_034_5kb_4.3dg.gz
GM-200U_034_5kb_5.3dg.gz
GM-200U_034_20kb_2.clean.3dg.gz
GM-200U_034_20kb_3.clean.3dg.gz
GM-200U_034_20kb_4.clean.3dg.gz
GM-200U_034_20kb_5.clean.3dg.gz
GM-200U_034_10kb_2.clean.3dg.gz
GM-200U_034_10kb_3.clean.3dg.gz
GM-200U_034_10kb_4.clean.3dg.gz
GM-200U_034_10kb_5.clean.3dg.gz
GM-200U_034_5kb_2.clean.3dg.gz
GM-200U_034_5kb_3.clean.3dg.gz
GM-200U_034_5kb_4.clean.3dg.gz
GM-200U_034_5kb_5.clean.3dg.gz


title: cell_294


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter31 [31U]


title: GM12878, 200U, Cell 33

description:
200U MNase
GM-200U_033.allValidPairs.gz
GM-200U_033.hic
GM-200U_033.mcool
GM-200U_033.clean.smooth.bw
GM-200U_033_20kb_1.3dg.gz
GM-200U_033_20kb_2.3dg.gz
GM-200U_033_20kb_3.3dg.gz
GM-200U_033_20kb_4.3dg.gz
GM-200U_033_20kb_5.3dg.gz
GM-200U_033_10kb_1.3dg.gz
GM-200U_033_10kb_2.3dg.gz
GM-200U_033_10kb_3.3dg.gz
GM-200U_033_10kb_4.3dg.gz
GM-200U_033_10kb_5.3dg.gz
GM-200U_033_5kb_1.3dg.gz
GM-200U_033_5kb_2.3dg.gz
GM-200U_033_5kb_3.3dg.gz
GM-200U_033_5kb_4.3dg.gz
GM-200U_033_5kb_5.3dg.gz
GM-200U_033_20kb_1.clean.3dg.gz
GM-200U_033_20kb_2.clean.3dg.gz
GM-200U_033_20kb_3.clean.3dg.gz
GM-200U_033_20kb_4.clean.3dg.gz
GM-200U_033_20kb_5.clean.3dg.gz
GM-200U_033_10kb_1.clean.3dg.gz
GM-200U_033_10kb_2.clean.3dg.gz
GM-200U_033_10kb_3.clean.3dg.gz
GM-200U_033_10kb_4.clean.3dg.gz
GM-200U_033_10kb_5.clean.3dg.gz
GM-200U_033_5kb_1.clean.3dg.gz
GM-200U_033_5kb_2.clean.3dg.gz
GM-200U_033_5kb_3.clean.3dg.gz
GM-200U_033_5kb_4.clean.3dg.gz
GM-200U_033_5kb_5.clean.3dg.gz


title: cell_293


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter30 [30U]


title: E9.5 Wild-type control 1

description:
counts.csv
deseq_results.csv


title: E8.5 FCSPG experimental 4

description:
gene_counts.xls
gene_fpkm.xls
WTvsFCSPG_deg_all.xls
FCPGvsFCSPG_deg_all.xls

data_processing:
Illumina NovaSeq 6000 SP was used for sequencing.
RStudio was used to process and analyze data.
HISAT2 package was used to align sequences.
Reference genome Mus musculus mm39 was used for alignments.
featureCounts package was used to produce raw counts data.
DESeq2 package was used for differential expression profiling
Assembly: mm39
Supplementary files format and content: gene_counts.xls contains RAW gene counts for all samples
Supplementary files format and content: gene_fpkm.xls contains normalized gene counts as FPKM for all samples
Supplementary files format and content: WTvFCPG_deg_all.xls contains DESeq2 analysis from comparing wild-type to Fgfr1 FCPG/FCPG tissue
Supplementary files format and content: WTvFCSPG_deg_all.xls contains DESeq2 analysis from comparing wild-type to Fgfr1 FCSPG/FCSPG tissue
Supplementary files format and content: FCPGvFCSPG_deg_all.xls contains DESeq2 analysis from comparing Fgfr1 FCPG/FCPG to Fgfr1 FCSPG/FCSPG tissue

extract_protocol:
Microdissection was used to excise tailbud tissue from E8.5 mouse embryos. RNA was extracted using Qiagin RNeasy kits. 1ug of RNA was used for library contsruction.
Libraries were constructed using Illumina stranded mRNA prep kits.

value: Fgfr1 FCSPG/FCSPG


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter29 [29U]


title: E8.5 FCSPG experimental 3


title: cell_291

value: blood


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter28 [28U]


title: GM12878, 200U, Cell 30

description:
200U MNase
GM-200U_030.allValidPairs.gz
GM-200U_030.hic
GM-200U_030.mcool
GM-200U_030.clean.smooth.bw
GM-200U_030_20kb_1.3dg.gz
GM-200U_030_20kb_2.3dg.gz
GM-200U_030_20kb_3.3dg.gz
GM-200U_030_20kb_4.3dg.gz
GM-200U_030_20kb_5.3dg.gz
GM-200U_030_10kb_1.3dg.gz
GM-200U_030_10kb_2.3dg.gz
GM-200U_030_10kb_3.3dg.gz
GM-200U_030_10kb_4.3dg.gz
GM-200U_030_10kb_5.3dg.gz
GM-200U_030_5kb_1.3dg.gz
GM-200U_030_5kb_2.3dg.gz
GM-200U_030_5kb_3.3dg.gz
GM-200U_030_5kb_4.3dg.gz
GM-200U_030_5kb_5.3dg.gz
GM-200U_030_20kb_1.clean.3dg.gz
GM-200U_030_20kb_2.clean.3dg.gz
GM-200U_030_20kb_3.clean.3dg.gz
GM-200U_030_20kb_4.clean.3dg.gz
GM-200U_030_20kb_5.clean.3dg.gz
GM-200U_030_10kb_1.clean.3dg.gz
GM-200U_030_10kb_2.clean.3dg.gz
GM-200U_030_10kb_3.clean.3dg.gz
GM-200U_030_10kb_4.clean.3dg.gz
GM-200U_030_10kb_5.clean.3dg.gz
GM-200U_030_5kb_1.clean.3dg.gz
GM-200U_030_5kb_2.clean.3dg.gz
GM-200U_030_5kb_3.clean.3dg.gz
GM-200U_030_5kb_4.clean.3dg.gz
GM-200U_030_5kb_5.clean.3dg.gz


title: cell_290


title: E8.5 FCSPG experimental 2


title: E9.5 FCPG experimental 1

description:
counts.csv
deseq_results.csv


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter33 [33U]


title: GM12878, 200U, Cell 29

description:
200U MNase
GM-200U_029.allValidPairs.gz
GM-200U_029.hic
GM-200U_029.mcool
GM-200U_029.clean.smooth.bw
GM-200U_029_20kb_1.3dg.gz
GM-200U_029_20kb_2.3dg.gz
GM-200U_029_20kb_3.3dg.gz
GM-200U_029_20kb_4.3dg.gz
GM-200U_029_20kb_5.3dg.gz
GM-200U_029_10kb_1.3dg.gz
GM-200U_029_10kb_2.3dg.gz
GM-200U_029_10kb_3.3dg.gz
GM-200U_029_10kb_4.3dg.gz
GM-200U_029_10kb_5.3dg.gz
GM-200U_029_5kb_1.3dg.gz
GM-200U_029_5kb_2.3dg.gz
GM-200U_029_5kb_3.3dg.gz
GM-200U_029_5kb_4.3dg.gz
GM-200U_029_5kb_5.3dg.gz
GM-200U_029_20kb_1.clean.3dg.gz
GM-200U_029_20kb_2.clean.3dg.gz
GM-200U_029_20kb_3.clean.3dg.gz
GM-200U_029_20kb_4.clean.3dg.gz
GM-200U_029_20kb_5.clean.3dg.gz
GM-200U_029_10kb_1.clean.3dg.gz
GM-200U_029_10kb_2.clean.3dg.gz
GM-200U_029_10kb_3.clean.3dg.gz
GM-200U_029_10kb_4.clean.3dg.gz
GM-200U_029_10kb_5.clean.3dg.gz
GM-200U_029_5kb_1.clean.3dg.gz
GM-200U_029_5kb_2.clean.3dg.gz
GM-200U_029_5kb_3.clean.3dg.gz
GM-200U_029_5kb_4.clean.3dg.gz
GM-200U_029_5kb_5.clean.3dg.gz


title: GM12878, 200U, Cell 31

description:
200U MNase
GM-200U_031.allValidPairs.gz
GM-200U_031.hic
GM-200U_031.mcool
GM-200U_031.clean.smooth.bw
GM-200U_031_20kb_1.3dg.gz
GM-200U_031_20kb_2.3dg.gz
GM-200U_031_20kb_4.3dg.gz
GM-200U_031_20kb_5.3dg.gz
GM-200U_031_10kb_1.3dg.gz
GM-200U_031_10kb_2.3dg.gz
GM-200U_031_10kb_4.3dg.gz
GM-200U_031_10kb_5.3dg.gz
GM-200U_031_5kb_1.3dg.gz
GM-200U_031_5kb_2.3dg.gz
GM-200U_031_5kb_4.3dg.gz
GM-200U_031_5kb_5.3dg.gz
GM-200U_031_20kb_1.clean.3dg.gz
GM-200U_031_20kb_2.clean.3dg.gz
GM-200U_031_20kb_4.clean.3dg.gz
GM-200U_031_20kb_5.clean.3dg.gz
GM-200U_031_10kb_1.clean.3dg.gz
GM-200U_031_10kb_2.clean.3dg.gz
GM-200U_031_10kb_4.clean.3dg.gz
GM-200U_031_10kb_5.clean.3dg.gz
GM-200U_031_5kb_1.clean.3dg.gz
GM-200U_031_5kb_2.clean.3dg.gz
GM-200U_031_5kb_4.clean.3dg.gz
GM-200U_031_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter27 [27U]


title: cell_289


title: E9.5 Wild-type control 2

description:
counts.csv
deseq_results.csv


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter25 [25U]


title: E8.5 FCPG experimental 3

description:
gene_counts.xls
gene_fpkm.xls
WTvsFCPG_deg_all.xls
FCPGvsFCSPG_deg_all.xls


title: GM12878, 200U, Cell 27

description:
200U MNase
GM-200U_027.allValidPairs.gz
GM-200U_027.hic
GM-200U_027.mcool
GM-200U_027.clean.smooth.bw
GM-200U_027_20kb_1.3dg.gz
GM-200U_027_20kb_2.3dg.gz
GM-200U_027_20kb_3.3dg.gz
GM-200U_027_20kb_4.3dg.gz
GM-200U_027_20kb_5.3dg.gz
GM-200U_027_10kb_1.3dg.gz
GM-200U_027_10kb_2.3dg.gz
GM-200U_027_10kb_3.3dg.gz
GM-200U_027_10kb_4.3dg.gz
GM-200U_027_10kb_5.3dg.gz
GM-200U_027_5kb_1.3dg.gz
GM-200U_027_5kb_2.3dg.gz
GM-200U_027_5kb_3.3dg.gz
GM-200U_027_5kb_4.3dg.gz
GM-200U_027_5kb_5.3dg.gz
GM-200U_027_20kb_1.clean.3dg.gz
GM-200U_027_20kb_2.clean.3dg.gz
GM-200U_027_20kb_3.clean.3dg.gz
GM-200U_027_20kb_4.clean.3dg.gz
GM-200U_027_20kb_5.clean.3dg.gz
GM-200U_027_10kb_1.clean.3dg.gz
GM-200U_027_10kb_2.clean.3dg.gz
GM-200U_027_10kb_3.clean.3dg.gz
GM-200U_027_10kb_4.clean.3dg.gz
GM-200U_027_10kb_5.clean.3dg.gz
GM-200U_027_5kb_1.clean.3dg.gz
GM-200U_027_5kb_2.clean.3dg.gz
GM-200U_027_5kb_3.clean.3dg.gz
GM-200U_027_5kb_4.clean.3dg.gz
GM-200U_027_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter26 [26U]


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter24 [24U]


title: cell_287


title: cell_292


title: cell_288


title: E8.5 FCPG experimental 1


title: GM12878, 200U, Cell 26

description:
200U MNase
GM-200U_026.allValidPairs.gz
GM-200U_026.hic
GM-200U_026.mcool
GM-200U_026.clean.smooth.bw
GM-200U_026_20kb_1.3dg.gz
GM-200U_026_20kb_2.3dg.gz
GM-200U_026_20kb_3.3dg.gz
GM-200U_026_20kb_5.3dg.gz
GM-200U_026_10kb_1.3dg.gz
GM-200U_026_10kb_2.3dg.gz
GM-200U_026_10kb_3.3dg.gz
GM-200U_026_10kb_5.3dg.gz
GM-200U_026_5kb_1.3dg.gz
GM-200U_026_5kb_2.3dg.gz
GM-200U_026_5kb_3.3dg.gz
GM-200U_026_5kb_5.3dg.gz
GM-200U_026_20kb_1.clean.3dg.gz
GM-200U_026_20kb_2.clean.3dg.gz
GM-200U_026_20kb_3.clean.3dg.gz
GM-200U_026_20kb_5.clean.3dg.gz
GM-200U_026_10kb_1.clean.3dg.gz
GM-200U_026_10kb_2.clean.3dg.gz
GM-200U_026_10kb_3.clean.3dg.gz
GM-200U_026_10kb_5.clean.3dg.gz
GM-200U_026_5kb_1.clean.3dg.gz
GM-200U_026_5kb_2.clean.3dg.gz
GM-200U_026_5kb_3.clean.3dg.gz
GM-200U_026_5kb_5.clean.3dg.gz


title: cell_286


title: GM12878, 200U, Cell 32

description:
200U MNase
GM-200U_032.allValidPairs.gz
GM-200U_032.hic
GM-200U_032.mcool
GM-200U_032.clean.smooth.bw
GM-200U_032_20kb_1.3dg.gz
GM-200U_032_20kb_2.3dg.gz
GM-200U_032_20kb_3.3dg.gz
GM-200U_032_20kb_4.3dg.gz
GM-200U_032_20kb_5.3dg.gz
GM-200U_032_10kb_1.3dg.gz
GM-200U_032_10kb_2.3dg.gz
GM-200U_032_10kb_3.3dg.gz
GM-200U_032_10kb_4.3dg.gz
GM-200U_032_10kb_5.3dg.gz
GM-200U_032_5kb_1.3dg.gz
GM-200U_032_5kb_2.3dg.gz
GM-200U_032_5kb_3.3dg.gz
GM-200U_032_5kb_4.3dg.gz
GM-200U_032_5kb_5.3dg.gz
GM-200U_032_20kb_1.clean.3dg.gz
GM-200U_032_20kb_2.clean.3dg.gz
GM-200U_032_20kb_3.clean.3dg.gz
GM-200U_032_20kb_4.clean.3dg.gz
GM-200U_032_20kb_5.clean.3dg.gz
GM-200U_032_10kb_1.clean.3dg.gz
GM-200U_032_10kb_2.clean.3dg.gz
GM-200U_032_10kb_3.clean.3dg.gz
GM-200U_032_10kb_4.clean.3dg.gz
GM-200U_032_10kb_5.clean.3dg.gz
GM-200U_032_5kb_1.clean.3dg.gz
GM-200U_032_5kb_2.clean.3dg.gz
GM-200U_032_5kb_3.clean.3dg.gz
GM-200U_032_5kb_4.clean.3dg.gz
GM-200U_032_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter23 [23U]


title: GM12878, 200U, Cell 25

description:
200U MNase
GM-200U_025.allValidPairs.gz
GM-200U_025.hic
GM-200U_025.mcool
GM-200U_025.clean.smooth.bw
GM-200U_025_20kb_1.3dg.gz
GM-200U_025_20kb_2.3dg.gz
GM-200U_025_20kb_3.3dg.gz
GM-200U_025_20kb_5.3dg.gz
GM-200U_025_10kb_1.3dg.gz
GM-200U_025_10kb_2.3dg.gz
GM-200U_025_10kb_3.3dg.gz
GM-200U_025_10kb_5.3dg.gz
GM-200U_025_5kb_1.3dg.gz
GM-200U_025_5kb_2.3dg.gz
GM-200U_025_5kb_3.3dg.gz
GM-200U_025_5kb_5.3dg.gz
GM-200U_025_20kb_1.clean.3dg.gz
GM-200U_025_20kb_2.clean.3dg.gz
GM-200U_025_20kb_3.clean.3dg.gz
GM-200U_025_20kb_5.clean.3dg.gz
GM-200U_025_10kb_1.clean.3dg.gz
GM-200U_025_10kb_2.clean.3dg.gz
GM-200U_025_10kb_3.clean.3dg.gz
GM-200U_025_10kb_5.clean.3dg.gz
GM-200U_025_5kb_1.clean.3dg.gz
GM-200U_025_5kb_2.clean.3dg.gz
GM-200U_025_5kb_3.clean.3dg.gz
GM-200U_025_5kb_5.clean.3dg.gz


title: E8.5 Wild-type control 4

description:
gene_counts.xls
gene_fpkm.xls
WTvsFCPG_deg_all.xls
WTvsFCSPG_deg_all.xls


title: cell_285

description:
gm12878_pooled.allValidPairs.gz
gm12878_pooled.hic
gm12878_pooled.mcool
gm12878_pooled.ligation_junctions.bed
scmicroc_gm12878.snaphic.10kb.postprocessed.summits.bedpe
gm12878.RELA.peaks.con.txt.gz
gm12878.RELA.top5k.peaks.con.txt.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter22 [22U]


title: GM12878, 200U, Cell 24

description:
200U MNase
GM-200U_024.allValidPairs.gz
GM-200U_024.hic
GM-200U_024.mcool
GM-200U_024.clean.smooth.bw
GM-200U_024_20kb_1.3dg.gz
GM-200U_024_20kb_2.3dg.gz
GM-200U_024_20kb_3.3dg.gz
GM-200U_024_20kb_4.3dg.gz
GM-200U_024_20kb_5.3dg.gz
GM-200U_024_10kb_1.3dg.gz
GM-200U_024_10kb_2.3dg.gz
GM-200U_024_10kb_3.3dg.gz
GM-200U_024_10kb_4.3dg.gz
GM-200U_024_10kb_5.3dg.gz
GM-200U_024_5kb_1.3dg.gz
GM-200U_024_5kb_2.3dg.gz
GM-200U_024_5kb_3.3dg.gz
GM-200U_024_5kb_4.3dg.gz
GM-200U_024_5kb_5.3dg.gz
GM-200U_024_20kb_1.clean.3dg.gz
GM-200U_024_20kb_2.clean.3dg.gz
GM-200U_024_20kb_3.clean.3dg.gz
GM-200U_024_20kb_4.clean.3dg.gz
GM-200U_024_20kb_5.clean.3dg.gz
GM-200U_024_10kb_1.clean.3dg.gz
GM-200U_024_10kb_2.clean.3dg.gz
GM-200U_024_10kb_3.clean.3dg.gz
GM-200U_024_10kb_4.clean.3dg.gz
GM-200U_024_10kb_5.clean.3dg.gz
GM-200U_024_5kb_1.clean.3dg.gz
GM-200U_024_5kb_2.clean.3dg.gz
GM-200U_024_5kb_3.clean.3dg.gz
GM-200U_024_5kb_4.clean.3dg.gz
GM-200U_024_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter21 [21U]


title: E8.5 Wild-type control 3


title: GM12878, 200U, Cell 23

description:
200U MNase
GM-200U_023.allValidPairs.gz
GM-200U_023.hic
GM-200U_023.mcool
GM-200U_023.clean.smooth.bw
GM-200U_023_20kb_3.3dg.gz
GM-200U_023_20kb_4.3dg.gz
GM-200U_023_20kb_5.3dg.gz
GM-200U_023_10kb_3.3dg.gz
GM-200U_023_10kb_4.3dg.gz
GM-200U_023_10kb_5.3dg.gz
GM-200U_023_5kb_3.3dg.gz
GM-200U_023_5kb_4.3dg.gz
GM-200U_023_5kb_5.3dg.gz
GM-200U_023_20kb_3.clean.3dg.gz
GM-200U_023_20kb_4.clean.3dg.gz
GM-200U_023_20kb_5.clean.3dg.gz
GM-200U_023_10kb_3.clean.3dg.gz
GM-200U_023_10kb_4.clean.3dg.gz
GM-200U_023_10kb_5.clean.3dg.gz
GM-200U_023_5kb_3.clean.3dg.gz
GM-200U_023_5kb_4.clean.3dg.gz
GM-200U_023_5kb_5.clean.3dg.gz


title: E8.5 FCSPG experimental 1


title: cell_284


title: E8.5 Wild-type control 2


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter20 [20H]

value: Hospital


title: cell_283


title: GM12878, 200U, Cell 22

description:
200U MNase
GM-200U_022.allValidPairs.gz
GM-200U_022.hic
GM-200U_022.mcool
GM-200U_022.clean.smooth.bw
GM-200U_022_20kb_1.3dg.gz
GM-200U_022_20kb_2.3dg.gz
GM-200U_022_20kb_3.3dg.gz
GM-200U_022_20kb_4.3dg.gz
GM-200U_022_10kb_1.3dg.gz
GM-200U_022_10kb_2.3dg.gz
GM-200U_022_10kb_3.3dg.gz
GM-200U_022_10kb_4.3dg.gz
GM-200U_022_5kb_1.3dg.gz
GM-200U_022_5kb_2.3dg.gz
GM-200U_022_5kb_3.3dg.gz
GM-200U_022_5kb_4.3dg.gz
GM-200U_022_20kb_1.clean.3dg.gz
GM-200U_022_20kb_2.clean.3dg.gz
GM-200U_022_20kb_3.clean.3dg.gz
GM-200U_022_20kb_4.clean.3dg.gz
GM-200U_022_10kb_1.clean.3dg.gz
GM-200U_022_10kb_2.clean.3dg.gz
GM-200U_022_10kb_3.clean.3dg.gz
GM-200U_022_10kb_4.clean.3dg.gz
GM-200U_022_5kb_1.clean.3dg.gz
GM-200U_022_5kb_2.clean.3dg.gz
GM-200U_022_5kb_3.clean.3dg.gz
GM-200U_022_5kb_4.clean.3dg.gz


title: GM12878, 200U, Cell 28

description:
200U MNase
GM-200U_028.allValidPairs.gz
GM-200U_028.hic
GM-200U_028.mcool
GM-200U_028.clean.smooth.bw
GM-200U_028_20kb_1.3dg.gz
GM-200U_028_20kb_2.3dg.gz
GM-200U_028_20kb_3.3dg.gz
GM-200U_028_20kb_4.3dg.gz
GM-200U_028_20kb_5.3dg.gz
GM-200U_028_10kb_1.3dg.gz
GM-200U_028_10kb_2.3dg.gz
GM-200U_028_10kb_3.3dg.gz
GM-200U_028_10kb_4.3dg.gz
GM-200U_028_10kb_5.3dg.gz
GM-200U_028_5kb_1.3dg.gz
GM-200U_028_5kb_2.3dg.gz
GM-200U_028_5kb_3.3dg.gz
GM-200U_028_5kb_4.3dg.gz
GM-200U_028_5kb_5.3dg.gz
GM-200U_028_20kb_1.clean.3dg.gz
GM-200U_028_20kb_2.clean.3dg.gz
GM-200U_028_20kb_3.clean.3dg.gz
GM-200U_028_20kb_4.clean.3dg.gz
GM-200U_028_20kb_5.clean.3dg.gz
GM-200U_028_10kb_1.clean.3dg.gz
GM-200U_028_10kb_2.clean.3dg.gz
GM-200U_028_10kb_3.clean.3dg.gz
GM-200U_028_10kb_4.clean.3dg.gz
GM-200U_028_10kb_5.clean.3dg.gz
GM-200U_028_5kb_1.clean.3dg.gz
GM-200U_028_5kb_2.clean.3dg.gz
GM-200U_028_5kb_3.clean.3dg.gz
GM-200U_028_5kb_4.clean.3dg.gz
GM-200U_028_5kb_5.clean.3dg.gz


title: E8.5 FCPG experimental 2


title: cell_282


title: E8.5 Wild-type control 1


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter19 [19H]

value: soil sample


title: C57BL/6  mice, AAV9-PRODH, TAC 3 [BT 3]

city: Hangzhou

first: Qingbo

last: Lv

state: Zhejiang

address: 3 East Qingchun Road

institute: Sir Run Run Hospital, School of Medicine, Zhejiang University

data_processing:
The raw paired-end reads were trimmed and quality controlled by SeqPrep (https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters.
Then clean data from K. obovata samples was used to do denovo assembly with Trinity (http://trinityrnaseq.sourceforge.net/)
All the assembled transcripts were searched against the (National Center for Biotechnology Information) NCBI protein non-redundant (NR), Clusters of Orthologous Genes (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases using BLASTX to identify the proteins that had the highest sequence similarity with the given transcripts to retrieve their function annotations and a typical cut-off E-values less than 1.0×10−5 was set. Blast2GO software
Assembly: genome assembly
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Heart

extract_protocol:
Total RNA from each sample was extracted using TRIzol® Reagent according to the manufacturer’s instructions (Invitrogen, Carlsbard, CA, USA) and genomic DNA was removed using DNase I (TaKara, Shiga, Japan)
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Mice were randomly injected with AAV9-Vector or AAV9-PRODH viruses, followed by undergoing either Sham or TAC surgery 3 weeks post-injection. The cardiac tissues were collected 4 weeks after TAC surgery.

value: Heart

value: PRODH Overexpression

value: Transverse aortic constriction (TAC) surgery


title: GM12878, 200U, Cell 20

description:
200U MNase
GM-200U_020.allValidPairs.gz
GM-200U_020.hic
GM-200U_020.mcool
GM-200U_020.clean.smooth.bw
GM-200U_020_20kb_1.3dg.gz
GM-200U_020_20kb_2.3dg.gz
GM-200U_020_20kb_3.3dg.gz
GM-200U_020_20kb_4.3dg.gz
GM-200U_020_20kb_5.3dg.gz
GM-200U_020_10kb_1.3dg.gz
GM-200U_020_10kb_2.3dg.gz
GM-200U_020_10kb_3.3dg.gz
GM-200U_020_10kb_4.3dg.gz
GM-200U_020_10kb_5.3dg.gz
GM-200U_020_5kb_1.3dg.gz
GM-200U_020_5kb_2.3dg.gz
GM-200U_020_5kb_3.3dg.gz
GM-200U_020_5kb_4.3dg.gz
GM-200U_020_5kb_5.3dg.gz
GM-200U_020_20kb_1.clean.3dg.gz
GM-200U_020_20kb_2.clean.3dg.gz
GM-200U_020_20kb_3.clean.3dg.gz
GM-200U_020_20kb_4.clean.3dg.gz
GM-200U_020_20kb_5.clean.3dg.gz
GM-200U_020_10kb_1.clean.3dg.gz
GM-200U_020_10kb_2.clean.3dg.gz
GM-200U_020_10kb_3.clean.3dg.gz
GM-200U_020_10kb_4.clean.3dg.gz
GM-200U_020_10kb_5.clean.3dg.gz
GM-200U_020_5kb_1.clean.3dg.gz
GM-200U_020_5kb_2.clean.3dg.gz
GM-200U_020_5kb_3.clean.3dg.gz
GM-200U_020_5kb_4.clean.3dg.gz
GM-200U_020_5kb_5.clean.3dg.gz


title: C57BL/6  mice, AAV9-PRODH, TAC 2 [BT 2]


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter18 [18H]

value: Winter


title: cell_281


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter17 [17H]


title: C57BL/6  mice, AAV9-PRODH, TAC 1 [BT 1]


title: cell_280


title: GM12878, 200U, Cell 19

description:
200U MNase
GM-200U_019.allValidPairs.gz
GM-200U_019.hic
GM-200U_019.mcool
GM-200U_019.clean.smooth.bw
GM-200U_019_20kb_1.3dg.gz
GM-200U_019_20kb_2.3dg.gz
GM-200U_019_20kb_3.3dg.gz
GM-200U_019_20kb_4.3dg.gz
GM-200U_019_20kb_5.3dg.gz
GM-200U_019_10kb_1.3dg.gz
GM-200U_019_10kb_2.3dg.gz
GM-200U_019_10kb_3.3dg.gz
GM-200U_019_10kb_4.3dg.gz
GM-200U_019_10kb_5.3dg.gz
GM-200U_019_5kb_1.3dg.gz
GM-200U_019_5kb_2.3dg.gz
GM-200U_019_5kb_3.3dg.gz
GM-200U_019_5kb_4.3dg.gz
GM-200U_019_5kb_5.3dg.gz
GM-200U_019_20kb_1.clean.3dg.gz
GM-200U_019_20kb_2.clean.3dg.gz
GM-200U_019_20kb_3.clean.3dg.gz
GM-200U_019_20kb_4.clean.3dg.gz
GM-200U_019_20kb_5.clean.3dg.gz
GM-200U_019_10kb_1.clean.3dg.gz
GM-200U_019_10kb_2.clean.3dg.gz
GM-200U_019_10kb_3.clean.3dg.gz
GM-200U_019_10kb_4.clean.3dg.gz
GM-200U_019_10kb_5.clean.3dg.gz
GM-200U_019_5kb_1.clean.3dg.gz
GM-200U_019_5kb_2.clean.3dg.gz
GM-200U_019_5kb_3.clean.3dg.gz
GM-200U_019_5kb_4.clean.3dg.gz
GM-200U_019_5kb_5.clean.3dg.gz


title: cell_279


title: GM12878, 200U, Cell 18

description:
200U MNase
GM-200U_018.allValidPairs.gz
GM-200U_018.hic
GM-200U_018.mcool
GM-200U_018.clean.smooth.bw
GM-200U_018_20kb_1.3dg.gz
GM-200U_018_20kb_2.3dg.gz
GM-200U_018_20kb_3.3dg.gz
GM-200U_018_20kb_4.3dg.gz
GM-200U_018_20kb_5.3dg.gz
GM-200U_018_10kb_1.3dg.gz
GM-200U_018_10kb_2.3dg.gz
GM-200U_018_10kb_3.3dg.gz
GM-200U_018_10kb_4.3dg.gz
GM-200U_018_10kb_5.3dg.gz
GM-200U_018_5kb_1.3dg.gz
GM-200U_018_5kb_2.3dg.gz
GM-200U_018_5kb_3.3dg.gz
GM-200U_018_5kb_4.3dg.gz
GM-200U_018_5kb_5.3dg.gz
GM-200U_018_20kb_1.clean.3dg.gz
GM-200U_018_20kb_2.clean.3dg.gz
GM-200U_018_20kb_3.clean.3dg.gz
GM-200U_018_20kb_4.clean.3dg.gz
GM-200U_018_20kb_5.clean.3dg.gz
GM-200U_018_10kb_1.clean.3dg.gz
GM-200U_018_10kb_2.clean.3dg.gz
GM-200U_018_10kb_3.clean.3dg.gz
GM-200U_018_10kb_4.clean.3dg.gz
GM-200U_018_10kb_5.clean.3dg.gz
GM-200U_018_5kb_1.clean.3dg.gz
GM-200U_018_5kb_2.clean.3dg.gz
GM-200U_018_5kb_3.clean.3dg.gz
GM-200U_018_5kb_4.clean.3dg.gz
GM-200U_018_5kb_5.clean.3dg.gz


title: cell_278


title: C57BL/6  mice, AAV9-Vector, TAC 3 [AT 3]


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter15 [15H]


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter16 [26H]


title: C57BL/6  mice, AAV9-Vector, TAC 2 [AT 2]


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter14 [14H]


title: C57BL/6  mice, AAV9-Vector, TAC 1 [AT 1]


title: GM12878, 200U, Cell 16

description:
200U MNase
GM-200U_016.allValidPairs.gz
GM-200U_016.hic
GM-200U_016.mcool
GM-200U_016.clean.smooth.bw
GM-200U_016_20kb_1.3dg.gz
GM-200U_016_20kb_2.3dg.gz
GM-200U_016_20kb_3.3dg.gz
GM-200U_016_20kb_4.3dg.gz
GM-200U_016_20kb_5.3dg.gz
GM-200U_016_10kb_1.3dg.gz
GM-200U_016_10kb_2.3dg.gz
GM-200U_016_10kb_3.3dg.gz
GM-200U_016_10kb_4.3dg.gz
GM-200U_016_10kb_5.3dg.gz
GM-200U_016_5kb_1.3dg.gz
GM-200U_016_5kb_2.3dg.gz
GM-200U_016_5kb_3.3dg.gz
GM-200U_016_5kb_4.3dg.gz
GM-200U_016_5kb_5.3dg.gz
GM-200U_016_20kb_1.clean.3dg.gz
GM-200U_016_20kb_2.clean.3dg.gz
GM-200U_016_20kb_3.clean.3dg.gz
GM-200U_016_20kb_4.clean.3dg.gz
GM-200U_016_20kb_5.clean.3dg.gz
GM-200U_016_10kb_1.clean.3dg.gz
GM-200U_016_10kb_2.clean.3dg.gz
GM-200U_016_10kb_3.clean.3dg.gz
GM-200U_016_10kb_4.clean.3dg.gz
GM-200U_016_10kb_5.clean.3dg.gz
GM-200U_016_5kb_1.clean.3dg.gz
GM-200U_016_5kb_2.clean.3dg.gz
GM-200U_016_5kb_3.clean.3dg.gz
GM-200U_016_5kb_4.clean.3dg.gz
GM-200U_016_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter13 [13H]


title: cell_277


title: GM12878, 200U, Cell 17

description:
200U MNase
GM-200U_017.allValidPairs.gz
GM-200U_017.hic
GM-200U_017.mcool
GM-200U_017.clean.smooth.bw
GM-200U_017_20kb_1.3dg.gz
GM-200U_017_20kb_2.3dg.gz
GM-200U_017_20kb_3.3dg.gz
GM-200U_017_20kb_4.3dg.gz
GM-200U_017_20kb_5.3dg.gz
GM-200U_017_10kb_1.3dg.gz
GM-200U_017_10kb_2.3dg.gz
GM-200U_017_10kb_3.3dg.gz
GM-200U_017_10kb_4.3dg.gz
GM-200U_017_10kb_5.3dg.gz
GM-200U_017_5kb_1.3dg.gz
GM-200U_017_5kb_2.3dg.gz
GM-200U_017_5kb_3.3dg.gz
GM-200U_017_5kb_4.3dg.gz
GM-200U_017_5kb_5.3dg.gz
GM-200U_017_20kb_1.clean.3dg.gz
GM-200U_017_20kb_2.clean.3dg.gz
GM-200U_017_20kb_3.clean.3dg.gz
GM-200U_017_20kb_4.clean.3dg.gz
GM-200U_017_20kb_5.clean.3dg.gz
GM-200U_017_10kb_1.clean.3dg.gz
GM-200U_017_10kb_2.clean.3dg.gz
GM-200U_017_10kb_3.clean.3dg.gz
GM-200U_017_10kb_4.clean.3dg.gz
GM-200U_017_10kb_5.clean.3dg.gz
GM-200U_017_5kb_1.clean.3dg.gz
GM-200U_017_5kb_2.clean.3dg.gz
GM-200U_017_5kb_3.clean.3dg.gz
GM-200U_017_5kb_4.clean.3dg.gz
GM-200U_017_5kb_5.clean.3dg.gz


title: GM12878, 200U, Cell 15

description:
200U MNase
GM-200U_015.allValidPairs.gz
GM-200U_015.hic
GM-200U_015.mcool
GM-200U_015.clean.smooth.bw
GM-200U_015_20kb_1.3dg.gz
GM-200U_015_20kb_2.3dg.gz
GM-200U_015_20kb_3.3dg.gz
GM-200U_015_10kb_1.3dg.gz
GM-200U_015_10kb_2.3dg.gz
GM-200U_015_10kb_3.3dg.gz
GM-200U_015_5kb_1.3dg.gz
GM-200U_015_5kb_2.3dg.gz
GM-200U_015_5kb_3.3dg.gz
GM-200U_015_20kb_1.clean.3dg.gz
GM-200U_015_20kb_2.clean.3dg.gz
GM-200U_015_20kb_3.clean.3dg.gz
GM-200U_015_10kb_1.clean.3dg.gz
GM-200U_015_10kb_2.clean.3dg.gz
GM-200U_015_10kb_3.clean.3dg.gz
GM-200U_015_5kb_1.clean.3dg.gz
GM-200U_015_5kb_2.clean.3dg.gz
GM-200U_015_5kb_3.clean.3dg.gz


title: GM12878, 200U, Cell 21

description:
200U MNase
GM-200U_021.allValidPairs.gz
GM-200U_021.hic
GM-200U_021.mcool
GM-200U_021.clean.smooth.bw
GM-200U_021_20kb_1.3dg.gz
GM-200U_021_20kb_2.3dg.gz
GM-200U_021_20kb_4.3dg.gz
GM-200U_021_20kb_5.3dg.gz
GM-200U_021_10kb_1.3dg.gz
GM-200U_021_10kb_2.3dg.gz
GM-200U_021_10kb_4.3dg.gz
GM-200U_021_10kb_5.3dg.gz
GM-200U_021_5kb_1.3dg.gz
GM-200U_021_5kb_2.3dg.gz
GM-200U_021_5kb_4.3dg.gz
GM-200U_021_5kb_5.3dg.gz
GM-200U_021_20kb_1.clean.3dg.gz
GM-200U_021_20kb_2.clean.3dg.gz
GM-200U_021_20kb_4.clean.3dg.gz
GM-200U_021_20kb_5.clean.3dg.gz
GM-200U_021_10kb_1.clean.3dg.gz
GM-200U_021_10kb_2.clean.3dg.gz
GM-200U_021_10kb_4.clean.3dg.gz
GM-200U_021_10kb_5.clean.3dg.gz
GM-200U_021_5kb_1.clean.3dg.gz
GM-200U_021_5kb_2.clean.3dg.gz
GM-200U_021_5kb_4.clean.3dg.gz
GM-200U_021_5kb_5.clean.3dg.gz


title: C57BL/6  mice, AAV9-PRODH, Sham 3 [BS 3]

value: sham


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter12 [12H]


title: cell_275

value: lymphoblastoid


title: GM12878, 200U, Cell 14

description:
200U MNase
GM-200U_014.allValidPairs.gz
GM-200U_014.hic
GM-200U_014.mcool
GM-200U_014.clean.smooth.bw
GM-200U_014_20kb_1.3dg.gz
GM-200U_014_20kb_2.3dg.gz
GM-200U_014_20kb_3.3dg.gz
GM-200U_014_20kb_5.3dg.gz
GM-200U_014_10kb_1.3dg.gz
GM-200U_014_10kb_2.3dg.gz
GM-200U_014_10kb_3.3dg.gz
GM-200U_014_10kb_5.3dg.gz
GM-200U_014_5kb_1.3dg.gz
GM-200U_014_5kb_2.3dg.gz
GM-200U_014_5kb_3.3dg.gz
GM-200U_014_5kb_5.3dg.gz
GM-200U_014_20kb_1.clean.3dg.gz
GM-200U_014_20kb_2.clean.3dg.gz
GM-200U_014_20kb_3.clean.3dg.gz
GM-200U_014_20kb_5.clean.3dg.gz
GM-200U_014_10kb_1.clean.3dg.gz
GM-200U_014_10kb_2.clean.3dg.gz
GM-200U_014_10kb_3.clean.3dg.gz
GM-200U_014_10kb_5.clean.3dg.gz
GM-200U_014_5kb_1.clean.3dg.gz
GM-200U_014_5kb_2.clean.3dg.gz
GM-200U_014_5kb_3.clean.3dg.gz
GM-200U_014_5kb_5.clean.3dg.gz

value: WT


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter11 [11H]


title: C57BL/6  mice, AAV9-PRODH, Sham 2 [BS 2]


title: cell_273


title: GM12878, 200U, Cell 13

description:
200U MNase
GM-200U_013.allValidPairs.gz
GM-200U_013.hic
GM-200U_013.mcool
GM-200U_013.clean.smooth.bw
GM-200U_013_20kb_1.3dg.gz
GM-200U_013_20kb_2.3dg.gz
GM-200U_013_20kb_3.3dg.gz
GM-200U_013_20kb_4.3dg.gz
GM-200U_013_10kb_1.3dg.gz
GM-200U_013_10kb_2.3dg.gz
GM-200U_013_10kb_3.3dg.gz
GM-200U_013_10kb_4.3dg.gz
GM-200U_013_5kb_1.3dg.gz
GM-200U_013_5kb_2.3dg.gz
GM-200U_013_5kb_3.3dg.gz
GM-200U_013_5kb_4.3dg.gz
GM-200U_013_20kb_1.clean.3dg.gz
GM-200U_013_20kb_2.clean.3dg.gz
GM-200U_013_20kb_3.clean.3dg.gz
GM-200U_013_20kb_4.clean.3dg.gz
GM-200U_013_10kb_1.clean.3dg.gz
GM-200U_013_10kb_2.clean.3dg.gz
GM-200U_013_10kb_3.clean.3dg.gz
GM-200U_013_10kb_4.clean.3dg.gz
GM-200U_013_5kb_1.clean.3dg.gz
GM-200U_013_5kb_2.clean.3dg.gz
GM-200U_013_5kb_3.clean.3dg.gz
GM-200U_013_5kb_4.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter10 [10H]


title: GM12878, 200U, Cell 11

description:
200U MNase
GM-200U_011.allValidPairs.gz
GM-200U_011.hic
GM-200U_011.mcool
GM-200U_011.clean.smooth.bw
GM-200U_011_20kb_1.3dg.gz
GM-200U_011_20kb_2.3dg.gz
GM-200U_011_20kb_3.3dg.gz
GM-200U_011_20kb_4.3dg.gz
GM-200U_011_20kb_5.3dg.gz
GM-200U_011_10kb_1.3dg.gz
GM-200U_011_10kb_2.3dg.gz
GM-200U_011_10kb_3.3dg.gz
GM-200U_011_10kb_4.3dg.gz
GM-200U_011_10kb_5.3dg.gz
GM-200U_011_5kb_1.3dg.gz
GM-200U_011_5kb_2.3dg.gz
GM-200U_011_5kb_3.3dg.gz
GM-200U_011_5kb_4.3dg.gz
GM-200U_011_5kb_5.3dg.gz
GM-200U_011_20kb_1.clean.3dg.gz
GM-200U_011_20kb_2.clean.3dg.gz
GM-200U_011_20kb_3.clean.3dg.gz
GM-200U_011_20kb_4.clean.3dg.gz
GM-200U_011_20kb_5.clean.3dg.gz
GM-200U_011_10kb_1.clean.3dg.gz
GM-200U_011_10kb_2.clean.3dg.gz
GM-200U_011_10kb_3.clean.3dg.gz
GM-200U_011_10kb_4.clean.3dg.gz
GM-200U_011_10kb_5.clean.3dg.gz
GM-200U_011_5kb_1.clean.3dg.gz
GM-200U_011_5kb_2.clean.3dg.gz
GM-200U_011_5kb_3.clean.3dg.gz
GM-200U_011_5kb_4.clean.3dg.gz
GM-200U_011_5kb_5.clean.3dg.gz


title: GM12878, 200U, Cell 10

description:
200U MNase
GM-200U_010.allValidPairs.gz
GM-200U_010.hic
GM-200U_010.mcool
GM-200U_010.clean.smooth.bw
GM-200U_010_20kb_1.3dg.gz
GM-200U_010_20kb_2.3dg.gz
GM-200U_010_20kb_4.3dg.gz
GM-200U_010_20kb_5.3dg.gz
GM-200U_010_10kb_1.3dg.gz
GM-200U_010_10kb_2.3dg.gz
GM-200U_010_10kb_4.3dg.gz
GM-200U_010_10kb_5.3dg.gz
GM-200U_010_5kb_1.3dg.gz
GM-200U_010_5kb_2.3dg.gz
GM-200U_010_5kb_4.3dg.gz
GM-200U_010_5kb_5.3dg.gz
GM-200U_010_20kb_1.clean.3dg.gz
GM-200U_010_20kb_2.clean.3dg.gz
GM-200U_010_20kb_4.clean.3dg.gz
GM-200U_010_20kb_5.clean.3dg.gz
GM-200U_010_10kb_1.clean.3dg.gz
GM-200U_010_10kb_2.clean.3dg.gz
GM-200U_010_10kb_4.clean.3dg.gz
GM-200U_010_10kb_5.clean.3dg.gz
GM-200U_010_5kb_1.clean.3dg.gz
GM-200U_010_5kb_2.clean.3dg.gz
GM-200U_010_5kb_4.clean.3dg.gz
GM-200U_010_5kb_5.clean.3dg.gz


title: C57BL/6  mice, AAV9-Vector, Sham 1 [AS 1]


title: cell_276


title: C57BL/6  mice, AAV9-PRODH, Sham 1 [BS 1]


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter7 [7H]


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter9 [9H]


title: C57BL/6  mice, AAV9-Vector, Sham 3 [AS 3]


title: C57BL/6  mice, AAV9-PRODH, TAC 4 [PBT 4]

treatment_protocol: Mice were randomly injected with AAV9-Vector or AAV9-PRODH viruses, followed by undergoing either Sham or TAC surgery 3 weeks post-injection. The cardiac tissues were collected for the isolation of adult mice cardiac myocytes 4 weeks after TAC surgery.

value: Cardiomyocyte


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter8 [8H]


title: C57BL/6  mice, AAV9-Vector, Sham 2 [AS 2]


title: GM12878, 200U, Cell 9

description:
200U MNase
GM-200U_009.allValidPairs.gz
GM-200U_009.hic
GM-200U_009.mcool
GM-200U_009.clean.smooth.bw
GM-200U_009_20kb_1.3dg.gz
GM-200U_009_20kb_2.3dg.gz
GM-200U_009_20kb_3.3dg.gz
GM-200U_009_20kb_4.3dg.gz
GM-200U_009_20kb_5.3dg.gz
GM-200U_009_10kb_1.3dg.gz
GM-200U_009_10kb_2.3dg.gz
GM-200U_009_10kb_3.3dg.gz
GM-200U_009_10kb_4.3dg.gz
GM-200U_009_10kb_5.3dg.gz
GM-200U_009_5kb_1.3dg.gz
GM-200U_009_5kb_2.3dg.gz
GM-200U_009_5kb_3.3dg.gz
GM-200U_009_5kb_4.3dg.gz
GM-200U_009_5kb_5.3dg.gz
GM-200U_009_20kb_1.clean.3dg.gz
GM-200U_009_20kb_2.clean.3dg.gz
GM-200U_009_20kb_3.clean.3dg.gz
GM-200U_009_20kb_4.clean.3dg.gz
GM-200U_009_20kb_5.clean.3dg.gz
GM-200U_009_10kb_1.clean.3dg.gz
GM-200U_009_10kb_2.clean.3dg.gz
GM-200U_009_10kb_3.clean.3dg.gz
GM-200U_009_10kb_4.clean.3dg.gz
GM-200U_009_10kb_5.clean.3dg.gz
GM-200U_009_5kb_1.clean.3dg.gz
GM-200U_009_5kb_2.clean.3dg.gz
GM-200U_009_5kb_3.clean.3dg.gz
GM-200U_009_5kb_4.clean.3dg.gz
GM-200U_009_5kb_5.clean.3dg.gz


title: cell_272

description:
gm12878_pooled.allValidPairs.gz
gm12878_pooled.hic
gm12878_pooled.mcool
gm12878_pooled.ligation_junctions.bed
scmicroc_gm12878.snaphic.10kb.postprocessed.summits.bedpe
gm12878.RELA.peaks.con.txt.gz
gm12878.RELA.top5k.peaks.con.txt.gz


title: cell_269


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter6 [6H]


title: cell_271


title: GM12878, 200U, Cell 12

description:
200U MNase
GM-200U_012.allValidPairs.gz
GM-200U_012.hic
GM-200U_012.mcool
GM-200U_012.clean.smooth.bw
GM-200U_012_20kb_1.3dg.gz
GM-200U_012_20kb_2.3dg.gz
GM-200U_012_20kb_3.3dg.gz
GM-200U_012_20kb_4.3dg.gz
GM-200U_012_20kb_5.3dg.gz
GM-200U_012_10kb_1.3dg.gz
GM-200U_012_10kb_2.3dg.gz
GM-200U_012_10kb_3.3dg.gz
GM-200U_012_10kb_4.3dg.gz
GM-200U_012_10kb_5.3dg.gz
GM-200U_012_5kb_1.3dg.gz
GM-200U_012_5kb_2.3dg.gz
GM-200U_012_5kb_3.3dg.gz
GM-200U_012_5kb_4.3dg.gz
GM-200U_012_5kb_5.3dg.gz
GM-200U_012_20kb_1.clean.3dg.gz
GM-200U_012_20kb_2.clean.3dg.gz
GM-200U_012_20kb_3.clean.3dg.gz
GM-200U_012_20kb_4.clean.3dg.gz
GM-200U_012_20kb_5.clean.3dg.gz
GM-200U_012_10kb_1.clean.3dg.gz
GM-200U_012_10kb_2.clean.3dg.gz
GM-200U_012_10kb_3.clean.3dg.gz
GM-200U_012_10kb_4.clean.3dg.gz
GM-200U_012_10kb_5.clean.3dg.gz
GM-200U_012_5kb_1.clean.3dg.gz
GM-200U_012_5kb_2.clean.3dg.gz
GM-200U_012_5kb_3.clean.3dg.gz
GM-200U_012_5kb_4.clean.3dg.gz
GM-200U_012_5kb_5.clean.3dg.gz


title: cell_270


title: GM12878, 200U, Cell 8

description:
200U MNase
GM-200U_008.allValidPairs.gz
GM-200U_008.hic
GM-200U_008.mcool
GM-200U_008.clean.smooth.bw
GM-200U_008_20kb_1.3dg.gz
GM-200U_008_20kb_2.3dg.gz
GM-200U_008_20kb_3.3dg.gz
GM-200U_008_20kb_4.3dg.gz
GM-200U_008_20kb_5.3dg.gz
GM-200U_008_10kb_1.3dg.gz
GM-200U_008_10kb_2.3dg.gz
GM-200U_008_10kb_3.3dg.gz
GM-200U_008_10kb_4.3dg.gz
GM-200U_008_10kb_5.3dg.gz
GM-200U_008_5kb_1.3dg.gz
GM-200U_008_5kb_2.3dg.gz
GM-200U_008_5kb_3.3dg.gz
GM-200U_008_5kb_4.3dg.gz
GM-200U_008_5kb_5.3dg.gz
GM-200U_008_20kb_1.clean.3dg.gz
GM-200U_008_20kb_2.clean.3dg.gz
GM-200U_008_20kb_3.clean.3dg.gz
GM-200U_008_20kb_4.clean.3dg.gz
GM-200U_008_20kb_5.clean.3dg.gz
GM-200U_008_10kb_1.clean.3dg.gz
GM-200U_008_10kb_2.clean.3dg.gz
GM-200U_008_10kb_3.clean.3dg.gz
GM-200U_008_10kb_4.clean.3dg.gz
GM-200U_008_10kb_5.clean.3dg.gz
GM-200U_008_5kb_1.clean.3dg.gz
GM-200U_008_5kb_2.clean.3dg.gz
GM-200U_008_5kb_3.clean.3dg.gz
GM-200U_008_5kb_4.clean.3dg.gz
GM-200U_008_5kb_5.clean.3dg.gz


title: C57BL/6  mice, AAV9-PRODH, TAC 3 [PBT 3]


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter5 [5H]


title: cell_274


title: cell_268


title: GM12878, 200U, Cell 7

description:
200U MNase
GM-200U_007.allValidPairs.gz
GM-200U_007.hic
GM-200U_007.mcool
GM-200U_007.clean.smooth.bw
GM-200U_007_20kb_1.3dg.gz
GM-200U_007_20kb_2.3dg.gz
GM-200U_007_20kb_3.3dg.gz
GM-200U_007_20kb_4.3dg.gz
GM-200U_007_20kb_5.3dg.gz
GM-200U_007_10kb_1.3dg.gz
GM-200U_007_10kb_2.3dg.gz
GM-200U_007_10kb_3.3dg.gz
GM-200U_007_10kb_4.3dg.gz
GM-200U_007_10kb_5.3dg.gz
GM-200U_007_5kb_1.3dg.gz
GM-200U_007_5kb_2.3dg.gz
GM-200U_007_5kb_3.3dg.gz
GM-200U_007_5kb_4.3dg.gz
GM-200U_007_5kb_5.3dg.gz
GM-200U_007_20kb_1.clean.3dg.gz
GM-200U_007_20kb_2.clean.3dg.gz
GM-200U_007_20kb_3.clean.3dg.gz
GM-200U_007_20kb_4.clean.3dg.gz
GM-200U_007_20kb_5.clean.3dg.gz
GM-200U_007_10kb_1.clean.3dg.gz
GM-200U_007_10kb_2.clean.3dg.gz
GM-200U_007_10kb_3.clean.3dg.gz
GM-200U_007_10kb_4.clean.3dg.gz
GM-200U_007_10kb_5.clean.3dg.gz
GM-200U_007_5kb_1.clean.3dg.gz
GM-200U_007_5kb_2.clean.3dg.gz
GM-200U_007_5kb_3.clean.3dg.gz
GM-200U_007_5kb_4.clean.3dg.gz
GM-200U_007_5kb_5.clean.3dg.gz


title: C57BL/6  mice, AAV9-PRODH, TAC 2 [PBT 2]


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter4 [4H]


title: cell_267


title: GM12878, 200U, Cell 6

description:
200U MNase
GM-200U_006.allValidPairs.gz
GM-200U_006.hic
GM-200U_006.mcool
GM-200U_006.clean.smooth.bw
GM-200U_006_20kb_1.3dg.gz
GM-200U_006_20kb_2.3dg.gz
GM-200U_006_20kb_3.3dg.gz
GM-200U_006_20kb_4.3dg.gz
GM-200U_006_20kb_5.3dg.gz
GM-200U_006_10kb_1.3dg.gz
GM-200U_006_10kb_2.3dg.gz
GM-200U_006_10kb_3.3dg.gz
GM-200U_006_10kb_4.3dg.gz
GM-200U_006_10kb_5.3dg.gz
GM-200U_006_5kb_1.3dg.gz
GM-200U_006_5kb_2.3dg.gz
GM-200U_006_5kb_3.3dg.gz
GM-200U_006_5kb_4.3dg.gz
GM-200U_006_5kb_5.3dg.gz
GM-200U_006_20kb_1.clean.3dg.gz
GM-200U_006_20kb_2.clean.3dg.gz
GM-200U_006_20kb_3.clean.3dg.gz
GM-200U_006_20kb_4.clean.3dg.gz
GM-200U_006_20kb_5.clean.3dg.gz
GM-200U_006_10kb_1.clean.3dg.gz
GM-200U_006_10kb_2.clean.3dg.gz
GM-200U_006_10kb_3.clean.3dg.gz
GM-200U_006_10kb_4.clean.3dg.gz
GM-200U_006_10kb_5.clean.3dg.gz
GM-200U_006_5kb_1.clean.3dg.gz
GM-200U_006_5kb_2.clean.3dg.gz
GM-200U_006_5kb_3.clean.3dg.gz
GM-200U_006_5kb_4.clean.3dg.gz
GM-200U_006_5kb_5.clean.3dg.gz


title: cell_266


title: C57BL/6  mice, AAV9-PRODH, TAC 1 [PBT 1]


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter2 [2H]


title: GM12878, 200U, Cell 4

description:
200U MNase
GM-200U_004.allValidPairs.gz
GM-200U_004.hic
GM-200U_004.mcool
GM-200U_004.clean.smooth.bw
GM-200U_004_20kb_1.3dg.gz
GM-200U_004_20kb_2.3dg.gz
GM-200U_004_20kb_4.3dg.gz
GM-200U_004_20kb_5.3dg.gz
GM-200U_004_10kb_1.3dg.gz
GM-200U_004_10kb_2.3dg.gz
GM-200U_004_10kb_4.3dg.gz
GM-200U_004_10kb_5.3dg.gz
GM-200U_004_5kb_1.3dg.gz
GM-200U_004_5kb_2.3dg.gz
GM-200U_004_5kb_4.3dg.gz
GM-200U_004_5kb_5.3dg.gz
GM-200U_004_20kb_1.clean.3dg.gz
GM-200U_004_20kb_2.clean.3dg.gz
GM-200U_004_20kb_4.clean.3dg.gz
GM-200U_004_20kb_5.clean.3dg.gz
GM-200U_004_10kb_1.clean.3dg.gz
GM-200U_004_10kb_2.clean.3dg.gz
GM-200U_004_10kb_4.clean.3dg.gz
GM-200U_004_10kb_5.clean.3dg.gz
GM-200U_004_5kb_1.clean.3dg.gz
GM-200U_004_5kb_2.clean.3dg.gz
GM-200U_004_5kb_4.clean.3dg.gz
GM-200U_004_5kb_5.clean.3dg.gz


title: GM12878, 200U, Cell 5

description:
200U MNase
GM-200U_005.allValidPairs.gz
GM-200U_005.hic
GM-200U_005.mcool
GM-200U_005.clean.smooth.bw
GM-200U_005_20kb_1.3dg.gz
GM-200U_005_20kb_2.3dg.gz
GM-200U_005_20kb_3.3dg.gz
GM-200U_005_20kb_4.3dg.gz
GM-200U_005_20kb_5.3dg.gz
GM-200U_005_10kb_1.3dg.gz
GM-200U_005_10kb_2.3dg.gz
GM-200U_005_10kb_3.3dg.gz
GM-200U_005_10kb_4.3dg.gz
GM-200U_005_10kb_5.3dg.gz
GM-200U_005_5kb_1.3dg.gz
GM-200U_005_5kb_2.3dg.gz
GM-200U_005_5kb_3.3dg.gz
GM-200U_005_5kb_4.3dg.gz
GM-200U_005_5kb_5.3dg.gz
GM-200U_005_20kb_1.clean.3dg.gz
GM-200U_005_20kb_2.clean.3dg.gz
GM-200U_005_20kb_3.clean.3dg.gz
GM-200U_005_20kb_4.clean.3dg.gz
GM-200U_005_20kb_5.clean.3dg.gz
GM-200U_005_10kb_1.clean.3dg.gz
GM-200U_005_10kb_2.clean.3dg.gz
GM-200U_005_10kb_3.clean.3dg.gz
GM-200U_005_10kb_4.clean.3dg.gz
GM-200U_005_10kb_5.clean.3dg.gz
GM-200U_005_5kb_1.clean.3dg.gz
GM-200U_005_5kb_2.clean.3dg.gz
GM-200U_005_5kb_3.clean.3dg.gz
GM-200U_005_5kb_4.clean.3dg.gz
GM-200U_005_5kb_5.clean.3dg.gz


title: C57BL/6  mice, AAV9-Vector, TAC 3 [PAT 3]


title: cell_264


title: cell_265


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter1 [1H]


title: C57BL/6  mice, AAV9-Vector, TAC 4 [PAT 4]


title: GM12878, 200U, Cell 3

description:
200U MNase
GM-200U_003.allValidPairs.gz
GM-200U_003.hic
GM-200U_003.mcool
GM-200U_003.clean.smooth.bw
GM-200U_003_20kb_1.3dg.gz
GM-200U_003_20kb_2.3dg.gz
GM-200U_003_20kb_3.3dg.gz
GM-200U_003_20kb_4.3dg.gz
GM-200U_003_20kb_5.3dg.gz
GM-200U_003_10kb_1.3dg.gz
GM-200U_003_10kb_2.3dg.gz
GM-200U_003_10kb_3.3dg.gz
GM-200U_003_10kb_4.3dg.gz
GM-200U_003_10kb_5.3dg.gz
GM-200U_003_5kb_1.3dg.gz
GM-200U_003_5kb_2.3dg.gz
GM-200U_003_5kb_3.3dg.gz
GM-200U_003_5kb_4.3dg.gz
GM-200U_003_5kb_5.3dg.gz
GM-200U_003_20kb_1.clean.3dg.gz
GM-200U_003_20kb_2.clean.3dg.gz
GM-200U_003_20kb_3.clean.3dg.gz
GM-200U_003_20kb_4.clean.3dg.gz
GM-200U_003_20kb_5.clean.3dg.gz
GM-200U_003_10kb_1.clean.3dg.gz
GM-200U_003_10kb_2.clean.3dg.gz
GM-200U_003_10kb_3.clean.3dg.gz
GM-200U_003_10kb_4.clean.3dg.gz
GM-200U_003_10kb_5.clean.3dg.gz
GM-200U_003_5kb_1.clean.3dg.gz
GM-200U_003_5kb_2.clean.3dg.gz
GM-200U_003_5kb_3.clean.3dg.gz
GM-200U_003_5kb_4.clean.3dg.gz
GM-200U_003_5kb_5.clean.3dg.gz


title: C57BL/6  mice, AAV9-Vector, TAC 2 [PAT 2]


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer40 [40U]

value: Summer

value: University


title: GM12878, 200U, Cell 2

description:
200U MNase
GM-200U_002.allValidPairs.gz
GM-200U_002.hic
GM-200U_002.mcool
GM-200U_002.clean.smooth.bw
GM-200U_002_20kb_1.3dg.gz
GM-200U_002_20kb_2.3dg.gz
GM-200U_002_20kb_3.3dg.gz
GM-200U_002_20kb_4.3dg.gz
GM-200U_002_20kb_5.3dg.gz
GM-200U_002_10kb_1.3dg.gz
GM-200U_002_10kb_2.3dg.gz
GM-200U_002_10kb_3.3dg.gz
GM-200U_002_10kb_4.3dg.gz
GM-200U_002_10kb_5.3dg.gz
GM-200U_002_5kb_1.3dg.gz
GM-200U_002_5kb_2.3dg.gz
GM-200U_002_5kb_3.3dg.gz
GM-200U_002_5kb_4.3dg.gz
GM-200U_002_5kb_5.3dg.gz
GM-200U_002_20kb_1.clean.3dg.gz
GM-200U_002_20kb_2.clean.3dg.gz
GM-200U_002_20kb_3.clean.3dg.gz
GM-200U_002_20kb_4.clean.3dg.gz
GM-200U_002_20kb_5.clean.3dg.gz
GM-200U_002_10kb_1.clean.3dg.gz
GM-200U_002_10kb_2.clean.3dg.gz
GM-200U_002_10kb_3.clean.3dg.gz
GM-200U_002_10kb_4.clean.3dg.gz
GM-200U_002_10kb_5.clean.3dg.gz
GM-200U_002_5kb_1.clean.3dg.gz
GM-200U_002_5kb_2.clean.3dg.gz
GM-200U_002_5kb_3.clean.3dg.gz
GM-200U_002_5kb_4.clean.3dg.gz
GM-200U_002_5kb_5.clean.3dg.gz


title: cell_263


title: C57BL/6  mice, AAV9-Vector, TAC 1 [PAT 1]


title: cell_262


title: C57BL/6  mice, AAV9-PRODH, Sham 4 [PBS 4]


title: GM12878, 200U, Cell 1

description:
200U MNase
GM-200U_001.allValidPairs.gz
GM-200U_001.hic
GM-200U_001.mcool
GM-200U_001.clean.smooth.bw
GM-200U_001_20kb_1.3dg.gz
GM-200U_001_20kb_2.3dg.gz
GM-200U_001_20kb_3.3dg.gz
GM-200U_001_20kb_4.3dg.gz
GM-200U_001_20kb_5.3dg.gz
GM-200U_001_10kb_1.3dg.gz
GM-200U_001_10kb_2.3dg.gz
GM-200U_001_10kb_3.3dg.gz
GM-200U_001_10kb_4.3dg.gz
GM-200U_001_10kb_5.3dg.gz
GM-200U_001_5kb_1.3dg.gz
GM-200U_001_5kb_2.3dg.gz
GM-200U_001_5kb_3.3dg.gz
GM-200U_001_5kb_4.3dg.gz
GM-200U_001_5kb_5.3dg.gz
GM-200U_001_20kb_1.clean.3dg.gz
GM-200U_001_20kb_2.clean.3dg.gz
GM-200U_001_20kb_3.clean.3dg.gz
GM-200U_001_20kb_4.clean.3dg.gz
GM-200U_001_20kb_5.clean.3dg.gz
GM-200U_001_10kb_1.clean.3dg.gz
GM-200U_001_10kb_2.clean.3dg.gz
GM-200U_001_10kb_3.clean.3dg.gz
GM-200U_001_10kb_4.clean.3dg.gz
GM-200U_001_10kb_5.clean.3dg.gz
GM-200U_001_5kb_1.clean.3dg.gz
GM-200U_001_5kb_2.clean.3dg.gz
GM-200U_001_5kb_3.clean.3dg.gz
GM-200U_001_5kb_4.clean.3dg.gz
GM-200U_001_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer37 [37U]


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer38 [38U]


title: cell_261


title: cell_260


title: GM12878, 800U, Cell 96

description:
800U MNase
GM-800U_096.allValidPairs.gz
GM-800U_096.hic
GM-800U_096.mcool
GM-800U_096.clean.smooth.bw
GM-800U_096_20kb_1.3dg.gz
GM-800U_096_20kb_2.3dg.gz
GM-800U_096_20kb_3.3dg.gz
GM-800U_096_20kb_4.3dg.gz
GM-800U_096_20kb_5.3dg.gz
GM-800U_096_10kb_1.3dg.gz
GM-800U_096_10kb_2.3dg.gz
GM-800U_096_10kb_3.3dg.gz
GM-800U_096_10kb_4.3dg.gz
GM-800U_096_10kb_5.3dg.gz
GM-800U_096_5kb_1.3dg.gz
GM-800U_096_5kb_2.3dg.gz
GM-800U_096_5kb_3.3dg.gz
GM-800U_096_5kb_4.3dg.gz
GM-800U_096_5kb_5.3dg.gz
GM-800U_096_20kb_1.clean.3dg.gz
GM-800U_096_20kb_2.clean.3dg.gz
GM-800U_096_20kb_3.clean.3dg.gz
GM-800U_096_20kb_4.clean.3dg.gz
GM-800U_096_20kb_5.clean.3dg.gz
GM-800U_096_10kb_1.clean.3dg.gz
GM-800U_096_10kb_2.clean.3dg.gz
GM-800U_096_10kb_3.clean.3dg.gz
GM-800U_096_10kb_4.clean.3dg.gz
GM-800U_096_10kb_5.clean.3dg.gz
GM-800U_096_5kb_1.clean.3dg.gz
GM-800U_096_5kb_2.clean.3dg.gz
GM-800U_096_5kb_3.clean.3dg.gz
GM-800U_096_5kb_4.clean.3dg.gz
GM-800U_096_5kb_5.clean.3dg.gz


title: C57BL/6  mice, AAV9-PRODH, Sham 3 [PBS 3]


title: C57BL/6  mice, AAV9-PRODH, Sham 2 [PBS 2]


title: GM12878, 800U, Cell 95

description:
800U MNase
GM-800U_095.allValidPairs.gz
GM-800U_095.hic
GM-800U_095.mcool
GM-800U_095.clean.smooth.bw
GM-800U_095_20kb_1.3dg.gz
GM-800U_095_20kb_2.3dg.gz
GM-800U_095_20kb_3.3dg.gz
GM-800U_095_20kb_4.3dg.gz
GM-800U_095_20kb_5.3dg.gz
GM-800U_095_10kb_1.3dg.gz
GM-800U_095_10kb_2.3dg.gz
GM-800U_095_10kb_3.3dg.gz
GM-800U_095_10kb_4.3dg.gz
GM-800U_095_10kb_5.3dg.gz
GM-800U_095_5kb_1.3dg.gz
GM-800U_095_5kb_2.3dg.gz
GM-800U_095_5kb_3.3dg.gz
GM-800U_095_5kb_4.3dg.gz
GM-800U_095_5kb_5.3dg.gz
GM-800U_095_20kb_1.clean.3dg.gz
GM-800U_095_20kb_2.clean.3dg.gz
GM-800U_095_20kb_3.clean.3dg.gz
GM-800U_095_20kb_4.clean.3dg.gz
GM-800U_095_20kb_5.clean.3dg.gz
GM-800U_095_10kb_1.clean.3dg.gz
GM-800U_095_10kb_2.clean.3dg.gz
GM-800U_095_10kb_3.clean.3dg.gz
GM-800U_095_10kb_4.clean.3dg.gz
GM-800U_095_10kb_5.clean.3dg.gz
GM-800U_095_5kb_1.clean.3dg.gz
GM-800U_095_5kb_2.clean.3dg.gz
GM-800U_095_5kb_3.clean.3dg.gz
GM-800U_095_5kb_4.clean.3dg.gz
GM-800U_095_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Winter3 [3H]


title: GM12878, 800U, Cell 94

description:
800U MNase
GM-800U_094.allValidPairs.gz
GM-800U_094.hic
GM-800U_094.mcool
GM-800U_094.clean.smooth.bw
GM-800U_094_20kb_1.3dg.gz
GM-800U_094_20kb_2.3dg.gz
GM-800U_094_20kb_3.3dg.gz
GM-800U_094_20kb_5.3dg.gz
GM-800U_094_10kb_1.3dg.gz
GM-800U_094_10kb_2.3dg.gz
GM-800U_094_10kb_3.3dg.gz
GM-800U_094_10kb_5.3dg.gz
GM-800U_094_5kb_1.3dg.gz
GM-800U_094_5kb_2.3dg.gz
GM-800U_094_5kb_3.3dg.gz
GM-800U_094_5kb_5.3dg.gz
GM-800U_094_20kb_1.clean.3dg.gz
GM-800U_094_20kb_2.clean.3dg.gz
GM-800U_094_20kb_3.clean.3dg.gz
GM-800U_094_20kb_5.clean.3dg.gz
GM-800U_094_10kb_1.clean.3dg.gz
GM-800U_094_10kb_2.clean.3dg.gz
GM-800U_094_10kb_3.clean.3dg.gz
GM-800U_094_10kb_5.clean.3dg.gz
GM-800U_094_5kb_1.clean.3dg.gz
GM-800U_094_5kb_2.clean.3dg.gz
GM-800U_094_5kb_3.clean.3dg.gz
GM-800U_094_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer39 [39U]


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer36 [36U]


title: cell_259


title: C57BL/6  mice, AAV9-Vector, Sham 4 [PAS 4]