title: GM12878, 800U, Cell 93

description:
800U MNase
GM-800U_093.allValidPairs.gz
GM-800U_093.hic
GM-800U_093.mcool
GM-800U_093.clean.smooth.bw
GM-800U_093_20kb_1.3dg.gz
GM-800U_093_20kb_2.3dg.gz
GM-800U_093_20kb_3.3dg.gz
GM-800U_093_20kb_4.3dg.gz
GM-800U_093_20kb_5.3dg.gz
GM-800U_093_10kb_1.3dg.gz
GM-800U_093_10kb_2.3dg.gz
GM-800U_093_10kb_3.3dg.gz
GM-800U_093_10kb_4.3dg.gz
GM-800U_093_10kb_5.3dg.gz
GM-800U_093_5kb_1.3dg.gz
GM-800U_093_5kb_2.3dg.gz
GM-800U_093_5kb_3.3dg.gz
GM-800U_093_5kb_4.3dg.gz
GM-800U_093_5kb_5.3dg.gz
GM-800U_093_20kb_1.clean.3dg.gz
GM-800U_093_20kb_2.clean.3dg.gz
GM-800U_093_20kb_3.clean.3dg.gz
GM-800U_093_20kb_4.clean.3dg.gz
GM-800U_093_20kb_5.clean.3dg.gz
GM-800U_093_10kb_1.clean.3dg.gz
GM-800U_093_10kb_2.clean.3dg.gz
GM-800U_093_10kb_3.clean.3dg.gz
GM-800U_093_10kb_4.clean.3dg.gz
GM-800U_093_10kb_5.clean.3dg.gz
GM-800U_093_5kb_1.clean.3dg.gz
GM-800U_093_5kb_2.clean.3dg.gz
GM-800U_093_5kb_3.clean.3dg.gz
GM-800U_093_5kb_4.clean.3dg.gz
GM-800U_093_5kb_5.clean.3dg.gz


title: cell_258

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

city: Hangzhou

first: Qingbo

last: Lv

state: Zhejiang

address: 3 East Qingchun Road

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

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

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 for the isolation of adult mice cardiac myocytes 4 weeks after TAC surgery.

value: Heart

tag: strain

value: Cardiomyocyte

tag: genotype

value: PRODH Overexpression

tag: treatment

value: sham


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer35 [35U]

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: Summer

tag: location

tag: building

value: University


title: GM12878, 800U, Cell 92

description:
800U MNase
GM-800U_092.allValidPairs.gz
GM-800U_092.hic
GM-800U_092.mcool
GM-800U_092.clean.smooth.bw
GM-800U_092_20kb_1.3dg.gz
GM-800U_092_20kb_2.3dg.gz
GM-800U_092_20kb_3.3dg.gz
GM-800U_092_20kb_4.3dg.gz
GM-800U_092_20kb_5.3dg.gz
GM-800U_092_10kb_1.3dg.gz
GM-800U_092_10kb_2.3dg.gz
GM-800U_092_10kb_3.3dg.gz
GM-800U_092_10kb_4.3dg.gz
GM-800U_092_10kb_5.3dg.gz
GM-800U_092_5kb_1.3dg.gz
GM-800U_092_5kb_2.3dg.gz
GM-800U_092_5kb_3.3dg.gz
GM-800U_092_5kb_4.3dg.gz
GM-800U_092_5kb_5.3dg.gz
GM-800U_092_20kb_1.clean.3dg.gz
GM-800U_092_20kb_2.clean.3dg.gz
GM-800U_092_20kb_3.clean.3dg.gz
GM-800U_092_20kb_4.clean.3dg.gz
GM-800U_092_20kb_5.clean.3dg.gz
GM-800U_092_10kb_1.clean.3dg.gz
GM-800U_092_10kb_2.clean.3dg.gz
GM-800U_092_10kb_3.clean.3dg.gz
GM-800U_092_10kb_4.clean.3dg.gz
GM-800U_092_10kb_5.clean.3dg.gz
GM-800U_092_5kb_1.clean.3dg.gz
GM-800U_092_5kb_2.clean.3dg.gz
GM-800U_092_5kb_3.clean.3dg.gz
GM-800U_092_5kb_4.clean.3dg.gz
GM-800U_092_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

value: WT


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


title: cell_257


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer34 [34U]


title: cell_256


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer33 [33U]


title: cell_255


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


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


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer31 [31U]


title: cell_254


title: GM12878, 800U, Cell 90

description:
800U MNase
GM-800U_090.allValidPairs.gz
GM-800U_090.hic
GM-800U_090.mcool
GM-800U_090.clean.smooth.bw
GM-800U_090_20kb_1.3dg.gz
GM-800U_090_20kb_2.3dg.gz
GM-800U_090_20kb_3.3dg.gz
GM-800U_090_20kb_4.3dg.gz
GM-800U_090_20kb_5.3dg.gz
GM-800U_090_10kb_1.3dg.gz
GM-800U_090_10kb_2.3dg.gz
GM-800U_090_10kb_3.3dg.gz
GM-800U_090_10kb_4.3dg.gz
GM-800U_090_10kb_5.3dg.gz
GM-800U_090_5kb_1.3dg.gz
GM-800U_090_5kb_2.3dg.gz
GM-800U_090_5kb_3.3dg.gz
GM-800U_090_5kb_4.3dg.gz
GM-800U_090_5kb_5.3dg.gz
GM-800U_090_20kb_1.clean.3dg.gz
GM-800U_090_20kb_2.clean.3dg.gz
GM-800U_090_20kb_3.clean.3dg.gz
GM-800U_090_20kb_4.clean.3dg.gz
GM-800U_090_20kb_5.clean.3dg.gz
GM-800U_090_10kb_1.clean.3dg.gz
GM-800U_090_10kb_2.clean.3dg.gz
GM-800U_090_10kb_3.clean.3dg.gz
GM-800U_090_10kb_4.clean.3dg.gz
GM-800U_090_10kb_5.clean.3dg.gz
GM-800U_090_5kb_1.clean.3dg.gz
GM-800U_090_5kb_2.clean.3dg.gz
GM-800U_090_5kb_3.clean.3dg.gz
GM-800U_090_5kb_4.clean.3dg.gz
GM-800U_090_5kb_5.clean.3dg.gz


title: GM12878, 800U, Cell 91

description:
800U MNase
GM-800U_091.allValidPairs.gz
GM-800U_091.hic
GM-800U_091.mcool
GM-800U_091.clean.smooth.bw
GM-800U_091_20kb_1.3dg.gz
GM-800U_091_20kb_2.3dg.gz
GM-800U_091_20kb_3.3dg.gz
GM-800U_091_20kb_4.3dg.gz
GM-800U_091_20kb_5.3dg.gz
GM-800U_091_10kb_1.3dg.gz
GM-800U_091_10kb_2.3dg.gz
GM-800U_091_10kb_3.3dg.gz
GM-800U_091_10kb_4.3dg.gz
GM-800U_091_10kb_5.3dg.gz
GM-800U_091_5kb_1.3dg.gz
GM-800U_091_5kb_2.3dg.gz
GM-800U_091_5kb_3.3dg.gz
GM-800U_091_5kb_4.3dg.gz
GM-800U_091_5kb_5.3dg.gz
GM-800U_091_20kb_1.clean.3dg.gz
GM-800U_091_20kb_2.clean.3dg.gz
GM-800U_091_20kb_3.clean.3dg.gz
GM-800U_091_20kb_4.clean.3dg.gz
GM-800U_091_20kb_5.clean.3dg.gz
GM-800U_091_10kb_1.clean.3dg.gz
GM-800U_091_10kb_2.clean.3dg.gz
GM-800U_091_10kb_3.clean.3dg.gz
GM-800U_091_10kb_4.clean.3dg.gz
GM-800U_091_10kb_5.clean.3dg.gz
GM-800U_091_5kb_1.clean.3dg.gz
GM-800U_091_5kb_2.clean.3dg.gz
GM-800U_091_5kb_3.clean.3dg.gz
GM-800U_091_5kb_4.clean.3dg.gz
GM-800U_091_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer32 [32U]


title: DT 5 DPA rep3

city: BErgen

first: Simona

last: Chera

address: Haukelandsbakken 15

country: Norway

institute: University of Bergen

data_processing:
CLC Genomics Workbench 24.0
Trimming
Alignment
Assembly: mm10
Supplementary files format and content: Tab separated file with Raw counts per sample

source_name: Pancreatic Islet

extract_protocol:
Qiagen RNEasy Mini kit
QIAseq  stranded mRNA kit Qiagen

value: Pancreatic Islet

tag: Sex

value: F

value: NSG RIP-DTR Htz

value: DT


title: GM12878, 800U, Cell 88

description:
800U MNase
GM-800U_088.allValidPairs.gz
GM-800U_088.hic
GM-800U_088.mcool
GM-800U_088.clean.smooth.bw
GM-800U_088_20kb_1.3dg.gz
GM-800U_088_20kb_2.3dg.gz
GM-800U_088_20kb_3.3dg.gz
GM-800U_088_20kb_4.3dg.gz
GM-800U_088_20kb_5.3dg.gz
GM-800U_088_10kb_1.3dg.gz
GM-800U_088_10kb_2.3dg.gz
GM-800U_088_10kb_3.3dg.gz
GM-800U_088_10kb_4.3dg.gz
GM-800U_088_10kb_5.3dg.gz
GM-800U_088_5kb_1.3dg.gz
GM-800U_088_5kb_2.3dg.gz
GM-800U_088_5kb_3.3dg.gz
GM-800U_088_5kb_4.3dg.gz
GM-800U_088_5kb_5.3dg.gz
GM-800U_088_20kb_1.clean.3dg.gz
GM-800U_088_20kb_2.clean.3dg.gz
GM-800U_088_20kb_3.clean.3dg.gz
GM-800U_088_20kb_4.clean.3dg.gz
GM-800U_088_20kb_5.clean.3dg.gz
GM-800U_088_10kb_1.clean.3dg.gz
GM-800U_088_10kb_2.clean.3dg.gz
GM-800U_088_10kb_3.clean.3dg.gz
GM-800U_088_10kb_4.clean.3dg.gz
GM-800U_088_10kb_5.clean.3dg.gz
GM-800U_088_5kb_1.clean.3dg.gz
GM-800U_088_5kb_2.clean.3dg.gz
GM-800U_088_5kb_3.clean.3dg.gz
GM-800U_088_5kb_4.clean.3dg.gz
GM-800U_088_5kb_5.clean.3dg.gz


title: DT 5 DPA rep2


title: GM12878, 800U, Cell 89

description:
800U MNase
GM-800U_089.allValidPairs.gz
GM-800U_089.hic
GM-800U_089.mcool
GM-800U_089.clean.smooth.bw
GM-800U_089_20kb_1.3dg.gz
GM-800U_089_20kb_2.3dg.gz
GM-800U_089_20kb_3.3dg.gz
GM-800U_089_20kb_4.3dg.gz
GM-800U_089_20kb_5.3dg.gz
GM-800U_089_10kb_1.3dg.gz
GM-800U_089_10kb_2.3dg.gz
GM-800U_089_10kb_3.3dg.gz
GM-800U_089_10kb_4.3dg.gz
GM-800U_089_10kb_5.3dg.gz
GM-800U_089_5kb_1.3dg.gz
GM-800U_089_5kb_2.3dg.gz
GM-800U_089_5kb_3.3dg.gz
GM-800U_089_5kb_4.3dg.gz
GM-800U_089_5kb_5.3dg.gz
GM-800U_089_20kb_1.clean.3dg.gz
GM-800U_089_20kb_2.clean.3dg.gz
GM-800U_089_20kb_3.clean.3dg.gz
GM-800U_089_20kb_4.clean.3dg.gz
GM-800U_089_20kb_5.clean.3dg.gz
GM-800U_089_10kb_1.clean.3dg.gz
GM-800U_089_10kb_2.clean.3dg.gz
GM-800U_089_10kb_3.clean.3dg.gz
GM-800U_089_10kb_4.clean.3dg.gz
GM-800U_089_10kb_5.clean.3dg.gz
GM-800U_089_5kb_1.clean.3dg.gz
GM-800U_089_5kb_2.clean.3dg.gz
GM-800U_089_5kb_3.clean.3dg.gz
GM-800U_089_5kb_4.clean.3dg.gz
GM-800U_089_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer30 [30U]


title: cell_251


title: DT 5 DPA rep1


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer29 [29U]


title: GM12878, 800U, Cell 87

description:
800U MNase
GM-800U_087.allValidPairs.gz
GM-800U_087.hic
GM-800U_087.mcool
GM-800U_087.clean.smooth.bw
GM-800U_087_20kb_3.3dg.gz
GM-800U_087_20kb_4.3dg.gz
GM-800U_087_20kb_5.3dg.gz
GM-800U_087_10kb_3.3dg.gz
GM-800U_087_10kb_4.3dg.gz
GM-800U_087_10kb_5.3dg.gz
GM-800U_087_5kb_3.3dg.gz
GM-800U_087_5kb_4.3dg.gz
GM-800U_087_5kb_5.3dg.gz
GM-800U_087_20kb_3.clean.3dg.gz
GM-800U_087_20kb_4.clean.3dg.gz
GM-800U_087_20kb_5.clean.3dg.gz
GM-800U_087_10kb_3.clean.3dg.gz
GM-800U_087_10kb_4.clean.3dg.gz
GM-800U_087_10kb_5.clean.3dg.gz
GM-800U_087_5kb_3.clean.3dg.gz
GM-800U_087_5kb_4.clean.3dg.gz
GM-800U_087_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer28 [28U]


title: GM12878, 800U, Cell 85

description:
800U MNase
GM-800U_085.allValidPairs.gz
GM-800U_085.hic
GM-800U_085.mcool
GM-800U_085.clean.smooth.bw
GM-800U_085_20kb_1.3dg.gz
GM-800U_085_20kb_2.3dg.gz
GM-800U_085_20kb_4.3dg.gz
GM-800U_085_10kb_1.3dg.gz
GM-800U_085_10kb_2.3dg.gz
GM-800U_085_10kb_4.3dg.gz
GM-800U_085_5kb_1.3dg.gz
GM-800U_085_5kb_2.3dg.gz
GM-800U_085_5kb_4.3dg.gz
GM-800U_085_20kb_1.clean.3dg.gz
GM-800U_085_20kb_2.clean.3dg.gz
GM-800U_085_20kb_4.clean.3dg.gz
GM-800U_085_10kb_1.clean.3dg.gz
GM-800U_085_10kb_2.clean.3dg.gz
GM-800U_085_10kb_4.clean.3dg.gz
GM-800U_085_5kb_1.clean.3dg.gz
GM-800U_085_5kb_2.clean.3dg.gz
GM-800U_085_5kb_4.clean.3dg.gz


title: cell_250


title: DT 3 DPA rep3


title: cell_252


title: DT 3 DPA rep2


title: GM12878, 800U, Cell 84

description:
800U MNase
GM-800U_084.allValidPairs.gz
GM-800U_084.hic
GM-800U_084.mcool
GM-800U_084.clean.smooth.bw
GM-800U_084_20kb_1.3dg.gz
GM-800U_084_20kb_2.3dg.gz
GM-800U_084_20kb_3.3dg.gz
GM-800U_084_20kb_4.3dg.gz
GM-800U_084_20kb_5.3dg.gz
GM-800U_084_10kb_1.3dg.gz
GM-800U_084_10kb_2.3dg.gz
GM-800U_084_10kb_3.3dg.gz
GM-800U_084_10kb_4.3dg.gz
GM-800U_084_10kb_5.3dg.gz
GM-800U_084_5kb_1.3dg.gz
GM-800U_084_5kb_2.3dg.gz
GM-800U_084_5kb_3.3dg.gz
GM-800U_084_5kb_4.3dg.gz
GM-800U_084_5kb_5.3dg.gz
GM-800U_084_20kb_1.clean.3dg.gz
GM-800U_084_20kb_2.clean.3dg.gz
GM-800U_084_20kb_3.clean.3dg.gz
GM-800U_084_20kb_4.clean.3dg.gz
GM-800U_084_20kb_5.clean.3dg.gz
GM-800U_084_10kb_1.clean.3dg.gz
GM-800U_084_10kb_2.clean.3dg.gz
GM-800U_084_10kb_3.clean.3dg.gz
GM-800U_084_10kb_4.clean.3dg.gz
GM-800U_084_10kb_5.clean.3dg.gz
GM-800U_084_5kb_1.clean.3dg.gz
GM-800U_084_5kb_2.clean.3dg.gz
GM-800U_084_5kb_3.clean.3dg.gz
GM-800U_084_5kb_4.clean.3dg.gz
GM-800U_084_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer26 [26U]


title: cell_248


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer24 [24U]


title: GM12878, 800U, Cell 83

description:
800U MNase
GM-800U_083.allValidPairs.gz
GM-800U_083.hic
GM-800U_083.mcool
GM-800U_083.clean.smooth.bw
GM-800U_083_20kb_1.3dg.gz
GM-800U_083_20kb_2.3dg.gz
GM-800U_083_20kb_4.3dg.gz
GM-800U_083_20kb_5.3dg.gz
GM-800U_083_10kb_1.3dg.gz
GM-800U_083_10kb_2.3dg.gz
GM-800U_083_10kb_4.3dg.gz
GM-800U_083_10kb_5.3dg.gz
GM-800U_083_5kb_1.3dg.gz
GM-800U_083_5kb_2.3dg.gz
GM-800U_083_5kb_4.3dg.gz
GM-800U_083_5kb_5.3dg.gz
GM-800U_083_20kb_1.clean.3dg.gz
GM-800U_083_20kb_2.clean.3dg.gz
GM-800U_083_20kb_4.clean.3dg.gz
GM-800U_083_20kb_5.clean.3dg.gz
GM-800U_083_10kb_1.clean.3dg.gz
GM-800U_083_10kb_2.clean.3dg.gz
GM-800U_083_10kb_4.clean.3dg.gz
GM-800U_083_10kb_5.clean.3dg.gz
GM-800U_083_5kb_1.clean.3dg.gz
GM-800U_083_5kb_2.clean.3dg.gz
GM-800U_083_5kb_4.clean.3dg.gz
GM-800U_083_5kb_5.clean.3dg.gz


title: cell_249


title: cell_253


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer25 [25U]


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer23 [23U]


title: DT 1 DPA rep3


title: DT 3 DPA rep1


title: GM12878, 800U, Cell 82

description:
800U MNase
GM-800U_082.allValidPairs.gz
GM-800U_082.hic
GM-800U_082.mcool
GM-800U_082.clean.smooth.bw
GM-800U_082_20kb_1.3dg.gz
GM-800U_082_20kb_2.3dg.gz
GM-800U_082_20kb_3.3dg.gz
GM-800U_082_20kb_4.3dg.gz
GM-800U_082_20kb_5.3dg.gz
GM-800U_082_10kb_1.3dg.gz
GM-800U_082_10kb_2.3dg.gz
GM-800U_082_10kb_3.3dg.gz
GM-800U_082_10kb_4.3dg.gz
GM-800U_082_10kb_5.3dg.gz
GM-800U_082_5kb_1.3dg.gz
GM-800U_082_5kb_2.3dg.gz
GM-800U_082_5kb_3.3dg.gz
GM-800U_082_5kb_4.3dg.gz
GM-800U_082_5kb_5.3dg.gz
GM-800U_082_20kb_1.clean.3dg.gz
GM-800U_082_20kb_2.clean.3dg.gz
GM-800U_082_20kb_3.clean.3dg.gz
GM-800U_082_20kb_4.clean.3dg.gz
GM-800U_082_20kb_5.clean.3dg.gz
GM-800U_082_10kb_1.clean.3dg.gz
GM-800U_082_10kb_2.clean.3dg.gz
GM-800U_082_10kb_3.clean.3dg.gz
GM-800U_082_10kb_4.clean.3dg.gz
GM-800U_082_10kb_5.clean.3dg.gz
GM-800U_082_5kb_1.clean.3dg.gz
GM-800U_082_5kb_2.clean.3dg.gz
GM-800U_082_5kb_3.clean.3dg.gz
GM-800U_082_5kb_4.clean.3dg.gz
GM-800U_082_5kb_5.clean.3dg.gz


title: cell_246


title: GM12878, 800U, Cell 81

description:
800U MNase
GM-800U_081.allValidPairs.gz
GM-800U_081.hic
GM-800U_081.mcool
GM-800U_081.clean.smooth.bw
GM-800U_081_20kb_1.3dg.gz
GM-800U_081_20kb_2.3dg.gz
GM-800U_081_20kb_3.3dg.gz
GM-800U_081_20kb_4.3dg.gz
GM-800U_081_20kb_5.3dg.gz
GM-800U_081_10kb_1.3dg.gz
GM-800U_081_10kb_2.3dg.gz
GM-800U_081_10kb_3.3dg.gz
GM-800U_081_10kb_4.3dg.gz
GM-800U_081_10kb_5.3dg.gz
GM-800U_081_5kb_1.3dg.gz
GM-800U_081_5kb_2.3dg.gz
GM-800U_081_5kb_3.3dg.gz
GM-800U_081_5kb_4.3dg.gz
GM-800U_081_5kb_5.3dg.gz
GM-800U_081_20kb_1.clean.3dg.gz
GM-800U_081_20kb_2.clean.3dg.gz
GM-800U_081_20kb_3.clean.3dg.gz
GM-800U_081_20kb_4.clean.3dg.gz
GM-800U_081_20kb_5.clean.3dg.gz
GM-800U_081_10kb_1.clean.3dg.gz
GM-800U_081_10kb_2.clean.3dg.gz
GM-800U_081_10kb_3.clean.3dg.gz
GM-800U_081_10kb_4.clean.3dg.gz
GM-800U_081_10kb_5.clean.3dg.gz
GM-800U_081_5kb_1.clean.3dg.gz
GM-800U_081_5kb_2.clean.3dg.gz
GM-800U_081_5kb_3.clean.3dg.gz
GM-800U_081_5kb_4.clean.3dg.gz
GM-800U_081_5kb_5.clean.3dg.gz


title: cell_245


title: cell_247


title: DT 1 DPA rep2


title: DT 1 DPA rep1


title: GM12878, 800U, Cell 86

description:
800U MNase
GM-800U_086.allValidPairs.gz
GM-800U_086.hic
GM-800U_086.mcool
GM-800U_086.clean.smooth.bw
GM-800U_086_20kb_1.3dg.gz
GM-800U_086_20kb_2.3dg.gz
GM-800U_086_20kb_3.3dg.gz
GM-800U_086_20kb_4.3dg.gz
GM-800U_086_20kb_5.3dg.gz
GM-800U_086_10kb_1.3dg.gz
GM-800U_086_10kb_2.3dg.gz
GM-800U_086_10kb_3.3dg.gz
GM-800U_086_10kb_4.3dg.gz
GM-800U_086_10kb_5.3dg.gz
GM-800U_086_5kb_1.3dg.gz
GM-800U_086_5kb_2.3dg.gz
GM-800U_086_5kb_3.3dg.gz
GM-800U_086_5kb_4.3dg.gz
GM-800U_086_5kb_5.3dg.gz
GM-800U_086_20kb_1.clean.3dg.gz
GM-800U_086_20kb_2.clean.3dg.gz
GM-800U_086_20kb_3.clean.3dg.gz
GM-800U_086_20kb_4.clean.3dg.gz
GM-800U_086_20kb_5.clean.3dg.gz
GM-800U_086_10kb_1.clean.3dg.gz
GM-800U_086_10kb_2.clean.3dg.gz
GM-800U_086_10kb_3.clean.3dg.gz
GM-800U_086_10kb_4.clean.3dg.gz
GM-800U_086_10kb_5.clean.3dg.gz
GM-800U_086_5kb_1.clean.3dg.gz
GM-800U_086_5kb_2.clean.3dg.gz
GM-800U_086_5kb_3.clean.3dg.gz
GM-800U_086_5kb_4.clean.3dg.gz
GM-800U_086_5kb_5.clean.3dg.gz


title: GM12878, 800U, Cell 80

description:
800U MNase
GM-800U_080.allValidPairs.gz
GM-800U_080.hic
GM-800U_080.mcool
GM-800U_080.clean.smooth.bw
GM-800U_080_20kb_1.3dg.gz
GM-800U_080_20kb_2.3dg.gz
GM-800U_080_20kb_3.3dg.gz
GM-800U_080_20kb_4.3dg.gz
GM-800U_080_20kb_5.3dg.gz
GM-800U_080_10kb_1.3dg.gz
GM-800U_080_10kb_2.3dg.gz
GM-800U_080_10kb_3.3dg.gz
GM-800U_080_10kb_4.3dg.gz
GM-800U_080_10kb_5.3dg.gz
GM-800U_080_5kb_1.3dg.gz
GM-800U_080_5kb_2.3dg.gz
GM-800U_080_5kb_3.3dg.gz
GM-800U_080_5kb_4.3dg.gz
GM-800U_080_5kb_5.3dg.gz
GM-800U_080_20kb_1.clean.3dg.gz
GM-800U_080_20kb_2.clean.3dg.gz
GM-800U_080_20kb_3.clean.3dg.gz
GM-800U_080_20kb_4.clean.3dg.gz
GM-800U_080_20kb_5.clean.3dg.gz
GM-800U_080_10kb_1.clean.3dg.gz
GM-800U_080_10kb_2.clean.3dg.gz
GM-800U_080_10kb_3.clean.3dg.gz
GM-800U_080_10kb_4.clean.3dg.gz
GM-800U_080_10kb_5.clean.3dg.gz
GM-800U_080_5kb_1.clean.3dg.gz
GM-800U_080_5kb_2.clean.3dg.gz
GM-800U_080_5kb_3.clean.3dg.gz
GM-800U_080_5kb_4.clean.3dg.gz
GM-800U_080_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer27 [27U]


title: cell_244


title: CTRL rep3


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer21 [21U]


title: GM12878, 800U, Cell 79

description:
800U MNase
GM-800U_079.allValidPairs.gz
GM-800U_079.hic
GM-800U_079.mcool
GM-800U_079.clean.smooth.bw
GM-800U_079_20kb_1.3dg.gz
GM-800U_079_20kb_2.3dg.gz
GM-800U_079_20kb_3.3dg.gz
GM-800U_079_20kb_4.3dg.gz
GM-800U_079_20kb_5.3dg.gz
GM-800U_079_10kb_1.3dg.gz
GM-800U_079_10kb_2.3dg.gz
GM-800U_079_10kb_3.3dg.gz
GM-800U_079_10kb_4.3dg.gz
GM-800U_079_10kb_5.3dg.gz
GM-800U_079_5kb_1.3dg.gz
GM-800U_079_5kb_2.3dg.gz
GM-800U_079_5kb_3.3dg.gz
GM-800U_079_5kb_4.3dg.gz
GM-800U_079_5kb_5.3dg.gz
GM-800U_079_20kb_1.clean.3dg.gz
GM-800U_079_20kb_2.clean.3dg.gz
GM-800U_079_20kb_3.clean.3dg.gz
GM-800U_079_20kb_4.clean.3dg.gz
GM-800U_079_20kb_5.clean.3dg.gz
GM-800U_079_10kb_1.clean.3dg.gz
GM-800U_079_10kb_2.clean.3dg.gz
GM-800U_079_10kb_3.clean.3dg.gz
GM-800U_079_10kb_4.clean.3dg.gz
GM-800U_079_10kb_5.clean.3dg.gz
GM-800U_079_5kb_1.clean.3dg.gz
GM-800U_079_5kb_2.clean.3dg.gz
GM-800U_079_5kb_3.clean.3dg.gz
GM-800U_079_5kb_4.clean.3dg.gz
GM-800U_079_5kb_5.clean.3dg.gz


title: cell_243


title: CTRL rep2


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer20 [20H]

value: Hospital


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer22 [22U]


title: cell_242


title: CTRL rep1


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer18 [18H]


title: GM12878, 800U, Cell 78

description:
800U MNase
GM-800U_078.allValidPairs.gz
GM-800U_078.hic
GM-800U_078.mcool
GM-800U_078.clean.smooth.bw
GM-800U_078_20kb_1.3dg.gz
GM-800U_078_20kb_2.3dg.gz
GM-800U_078_20kb_3.3dg.gz
GM-800U_078_20kb_4.3dg.gz
GM-800U_078_20kb_5.3dg.gz
GM-800U_078_10kb_1.3dg.gz
GM-800U_078_10kb_2.3dg.gz
GM-800U_078_10kb_3.3dg.gz
GM-800U_078_10kb_4.3dg.gz
GM-800U_078_10kb_5.3dg.gz
GM-800U_078_5kb_1.3dg.gz
GM-800U_078_5kb_2.3dg.gz
GM-800U_078_5kb_3.3dg.gz
GM-800U_078_5kb_4.3dg.gz
GM-800U_078_5kb_5.3dg.gz
GM-800U_078_20kb_1.clean.3dg.gz
GM-800U_078_20kb_2.clean.3dg.gz
GM-800U_078_20kb_3.clean.3dg.gz
GM-800U_078_20kb_4.clean.3dg.gz
GM-800U_078_20kb_5.clean.3dg.gz
GM-800U_078_10kb_1.clean.3dg.gz
GM-800U_078_10kb_2.clean.3dg.gz
GM-800U_078_10kb_3.clean.3dg.gz
GM-800U_078_10kb_4.clean.3dg.gz
GM-800U_078_10kb_5.clean.3dg.gz
GM-800U_078_5kb_1.clean.3dg.gz
GM-800U_078_5kb_2.clean.3dg.gz
GM-800U_078_5kb_3.clean.3dg.gz
GM-800U_078_5kb_4.clean.3dg.gz
GM-800U_078_5kb_5.clean.3dg.gz


title: GM12878, 800U, Cell 77

description:
800U MNase
GM-800U_077.allValidPairs.gz
GM-800U_077.hic
GM-800U_077.mcool
GM-800U_077.clean.smooth.bw
GM-800U_077_20kb_1.3dg.gz
GM-800U_077_20kb_2.3dg.gz
GM-800U_077_20kb_3.3dg.gz
GM-800U_077_20kb_4.3dg.gz
GM-800U_077_20kb_5.3dg.gz
GM-800U_077_10kb_1.3dg.gz
GM-800U_077_10kb_2.3dg.gz
GM-800U_077_10kb_3.3dg.gz
GM-800U_077_10kb_4.3dg.gz
GM-800U_077_10kb_5.3dg.gz
GM-800U_077_5kb_1.3dg.gz
GM-800U_077_5kb_2.3dg.gz
GM-800U_077_5kb_3.3dg.gz
GM-800U_077_5kb_4.3dg.gz
GM-800U_077_5kb_5.3dg.gz
GM-800U_077_20kb_1.clean.3dg.gz
GM-800U_077_20kb_2.clean.3dg.gz
GM-800U_077_20kb_3.clean.3dg.gz
GM-800U_077_20kb_4.clean.3dg.gz
GM-800U_077_20kb_5.clean.3dg.gz
GM-800U_077_10kb_1.clean.3dg.gz
GM-800U_077_10kb_2.clean.3dg.gz
GM-800U_077_10kb_3.clean.3dg.gz
GM-800U_077_10kb_4.clean.3dg.gz
GM-800U_077_10kb_5.clean.3dg.gz
GM-800U_077_5kb_1.clean.3dg.gz
GM-800U_077_5kb_2.clean.3dg.gz
GM-800U_077_5kb_3.clean.3dg.gz
GM-800U_077_5kb_4.clean.3dg.gz
GM-800U_077_5kb_5.clean.3dg.gz


title: cell_240

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: Nox2 Infected Neutrophil Replicate 3

city: Columbus

first: Xin

last: Wang

state: OH

address: 700 Children's Dr,

department: The Kidney and Urinary Tract Center

country: USA

institute: Nationwide Children's hosptial

data_processing:
FASTQ files were employed in a comprehensive analysis pipeline, encompassing data normalization, differential gene expression detection, and functional enrichment. The mm10 mouse genome and its corresponding reference gene set were obtained from UCSC. After removing adapter sequences, high-quality filtered reads were generated using Trim Galore v0.6.6.
Tophat v2.1.2 was utilized for mapping these high-quality reads to the mm10 genome. Successfully mapped reads were sorted, and unique mapped reads were retained using SAMtools v1.15. Htseq-count v0.12.4 with a union gene region parameter was employed for quantifying reads per gene. EdgeR_3.42.4 was then applied to identify differentially expressed genes (DEGs). Genes sparsely quantified in samples with loose criteria (i.e., a total count less than five across all samples and more than two samples with cpm greater than 0.5) were filtered out. Subsequently, quantile normalization was employed to eliminate or minimize technical variability. Principal component analysis (PCA) served as an unsupervised dimensionality reduction method for gene abundance levels across samples.
DEGs were defined as those with a fold change greater than 1.5 and an adjusted P value smaller than 0.05. Gene ontology (GO) analysis for the functional enrichments of up-regulated and down-regulated genes was conducted using clusterProfiler_4.8.2. The significance threshold for detecting enriched molecular functions, biological processes, and cellular components was set at an FDR of ≤ 0.05, determined by a Chi-square test for statistically enriched pathways.
Assembly: mm10
Supplementary files format and content: Ensembl gene ID, Count

source_name: Bone marrow

growth_protocol: Neutrophils were isolated from bone marrow of femurs and tibiae of wilde-type (WT) and NOX2 KO (Cybb-/-) mice using the Mojosort Kit 480058 (BioLegend).

extract_protocol:
RNA was isolated from WT and NOX2 KO neutrophils (n = 3 replicates/group) using the MirVanaTM ParisTM kit (AM1556, ThermoFisher Scientific). 0.5ug were used for the construction of sequencing libraries.
Total RNA was ribo-depleted using NEBNext Mouse ribodepletion kit from 100-1000ng input material, and NEBNext UltraII Directional RNA library prep kit to generate the library.

treatment_protocol: Isolated neutrophils were trated with PBS (uninfected) or uropathogenic E. coli (infected, CFT073 strain) for 3 hours at a multiplicity of infection (MOI) 100

value: Bone marrow

value: Primary cells

value: Neutrophils

value: NOX2 KO (Cybb-/-)

value: Uropathogenic E coli (UPEC, CFT073 strain)


title: GM12878, 800U, Cell 74

description:
800U MNase
GM-800U_074.allValidPairs.gz
GM-800U_074.hic
GM-800U_074.mcool
GM-800U_074.clean.smooth.bw
GM-800U_074_20kb_1.3dg.gz
GM-800U_074_20kb_2.3dg.gz
GM-800U_074_20kb_4.3dg.gz
GM-800U_074_20kb_5.3dg.gz
GM-800U_074_10kb_1.3dg.gz
GM-800U_074_10kb_2.3dg.gz
GM-800U_074_10kb_4.3dg.gz
GM-800U_074_10kb_5.3dg.gz
GM-800U_074_5kb_1.3dg.gz
GM-800U_074_5kb_2.3dg.gz
GM-800U_074_5kb_4.3dg.gz
GM-800U_074_5kb_5.3dg.gz
GM-800U_074_20kb_1.clean.3dg.gz
GM-800U_074_20kb_2.clean.3dg.gz
GM-800U_074_20kb_4.clean.3dg.gz
GM-800U_074_20kb_5.clean.3dg.gz
GM-800U_074_10kb_1.clean.3dg.gz
GM-800U_074_10kb_2.clean.3dg.gz
GM-800U_074_10kb_4.clean.3dg.gz
GM-800U_074_10kb_5.clean.3dg.gz
GM-800U_074_5kb_1.clean.3dg.gz
GM-800U_074_5kb_2.clean.3dg.gz
GM-800U_074_5kb_4.clean.3dg.gz
GM-800U_074_5kb_5.clean.3dg.gz

value: blood

value: lymphoblastoid


title: Nox2 Infected Neutrophil Replicate 2


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer17 [17H]


title: cell_241


title: Nox2 Uninfected Neutrophil Replicate 3

value: PBS


title: cell_238


title: Nox2 Infected Neutrophil Replicate 1


title: cell_239


title: GM12878, 800U, Cell 76

description:
800U MNase
GM-800U_076.allValidPairs.gz
GM-800U_076.hic
GM-800U_076.mcool
GM-800U_076.clean.smooth.bw
GM-800U_076_20kb_1.3dg.gz
GM-800U_076_20kb_2.3dg.gz
GM-800U_076_20kb_3.3dg.gz
GM-800U_076_20kb_5.3dg.gz
GM-800U_076_10kb_1.3dg.gz
GM-800U_076_10kb_2.3dg.gz
GM-800U_076_10kb_3.3dg.gz
GM-800U_076_10kb_5.3dg.gz
GM-800U_076_5kb_1.3dg.gz
GM-800U_076_5kb_2.3dg.gz
GM-800U_076_5kb_3.3dg.gz
GM-800U_076_5kb_5.3dg.gz
GM-800U_076_20kb_1.clean.3dg.gz
GM-800U_076_20kb_2.clean.3dg.gz
GM-800U_076_20kb_3.clean.3dg.gz
GM-800U_076_20kb_5.clean.3dg.gz
GM-800U_076_10kb_1.clean.3dg.gz
GM-800U_076_10kb_2.clean.3dg.gz
GM-800U_076_10kb_3.clean.3dg.gz
GM-800U_076_10kb_5.clean.3dg.gz
GM-800U_076_5kb_1.clean.3dg.gz
GM-800U_076_5kb_2.clean.3dg.gz
GM-800U_076_5kb_3.clean.3dg.gz
GM-800U_076_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer16 [26H]

value: soil sample


title: GM12878, 800U, Cell 75

description:
800U MNase
GM-800U_075.allValidPairs.gz
GM-800U_075.hic
GM-800U_075.mcool
GM-800U_075.clean.smooth.bw
GM-800U_075_20kb_1.3dg.gz
GM-800U_075_20kb_2.3dg.gz
GM-800U_075_20kb_3.3dg.gz
GM-800U_075_20kb_5.3dg.gz
GM-800U_075_10kb_1.3dg.gz
GM-800U_075_10kb_2.3dg.gz
GM-800U_075_10kb_3.3dg.gz
GM-800U_075_10kb_5.3dg.gz
GM-800U_075_5kb_1.3dg.gz
GM-800U_075_5kb_2.3dg.gz
GM-800U_075_5kb_3.3dg.gz
GM-800U_075_5kb_5.3dg.gz
GM-800U_075_20kb_1.clean.3dg.gz
GM-800U_075_20kb_2.clean.3dg.gz
GM-800U_075_20kb_3.clean.3dg.gz
GM-800U_075_20kb_5.clean.3dg.gz
GM-800U_075_10kb_1.clean.3dg.gz
GM-800U_075_10kb_2.clean.3dg.gz
GM-800U_075_10kb_3.clean.3dg.gz
GM-800U_075_10kb_5.clean.3dg.gz
GM-800U_075_5kb_1.clean.3dg.gz
GM-800U_075_5kb_2.clean.3dg.gz
GM-800U_075_5kb_3.clean.3dg.gz
GM-800U_075_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer15 [15H]

value: Summer


title: Nox2 Uninfected Neutrophil Replicate 2


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer14 [14H]


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer19 [19H]


title: cell_237


title: GM12878, 800U, Cell 72

description:
800U MNase
GM-800U_072.allValidPairs.gz
GM-800U_072.hic
GM-800U_072.mcool
GM-800U_072.clean.smooth.bw
GM-800U_072_20kb_1.3dg.gz
GM-800U_072_20kb_2.3dg.gz
GM-800U_072_20kb_3.3dg.gz
GM-800U_072_20kb_4.3dg.gz
GM-800U_072_20kb_5.3dg.gz
GM-800U_072_10kb_1.3dg.gz
GM-800U_072_10kb_2.3dg.gz
GM-800U_072_10kb_3.3dg.gz
GM-800U_072_10kb_4.3dg.gz
GM-800U_072_10kb_5.3dg.gz
GM-800U_072_5kb_1.3dg.gz
GM-800U_072_5kb_2.3dg.gz
GM-800U_072_5kb_3.3dg.gz
GM-800U_072_5kb_4.3dg.gz
GM-800U_072_5kb_5.3dg.gz
GM-800U_072_20kb_1.clean.3dg.gz
GM-800U_072_20kb_2.clean.3dg.gz
GM-800U_072_20kb_3.clean.3dg.gz
GM-800U_072_20kb_4.clean.3dg.gz
GM-800U_072_20kb_5.clean.3dg.gz
GM-800U_072_10kb_1.clean.3dg.gz
GM-800U_072_10kb_2.clean.3dg.gz
GM-800U_072_10kb_3.clean.3dg.gz
GM-800U_072_10kb_4.clean.3dg.gz
GM-800U_072_10kb_5.clean.3dg.gz
GM-800U_072_5kb_1.clean.3dg.gz
GM-800U_072_5kb_2.clean.3dg.gz
GM-800U_072_5kb_3.clean.3dg.gz
GM-800U_072_5kb_4.clean.3dg.gz
GM-800U_072_5kb_5.clean.3dg.gz


title: cell_236


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer13 [13H]


title: Nox2 Uninfected Neutrophil Replicate 1


title: GM12878, 800U, Cell 71

description:
800U MNase
GM-800U_071.allValidPairs.gz
GM-800U_071.hic
GM-800U_071.mcool
GM-800U_071.clean.smooth.bw
GM-800U_071_20kb_1.3dg.gz
GM-800U_071_20kb_2.3dg.gz
GM-800U_071_20kb_3.3dg.gz
GM-800U_071_20kb_4.3dg.gz
GM-800U_071_20kb_5.3dg.gz
GM-800U_071_10kb_1.3dg.gz
GM-800U_071_10kb_2.3dg.gz
GM-800U_071_10kb_3.3dg.gz
GM-800U_071_10kb_4.3dg.gz
GM-800U_071_10kb_5.3dg.gz
GM-800U_071_5kb_1.3dg.gz
GM-800U_071_5kb_2.3dg.gz
GM-800U_071_5kb_3.3dg.gz
GM-800U_071_5kb_4.3dg.gz
GM-800U_071_5kb_5.3dg.gz
GM-800U_071_20kb_1.clean.3dg.gz
GM-800U_071_20kb_2.clean.3dg.gz
GM-800U_071_20kb_3.clean.3dg.gz
GM-800U_071_20kb_4.clean.3dg.gz
GM-800U_071_20kb_5.clean.3dg.gz
GM-800U_071_10kb_1.clean.3dg.gz
GM-800U_071_10kb_2.clean.3dg.gz
GM-800U_071_10kb_3.clean.3dg.gz
GM-800U_071_10kb_4.clean.3dg.gz
GM-800U_071_10kb_5.clean.3dg.gz
GM-800U_071_5kb_1.clean.3dg.gz
GM-800U_071_5kb_2.clean.3dg.gz
GM-800U_071_5kb_3.clean.3dg.gz
GM-800U_071_5kb_4.clean.3dg.gz
GM-800U_071_5kb_5.clean.3dg.gz


title: WT Infected Neutrophil Replicate 3

value: Wild-type (WT)


title: cell_235


title: GM12878, 800U, Cell 70

description:
800U MNase
GM-800U_070.allValidPairs.gz
GM-800U_070.hic
GM-800U_070.mcool
GM-800U_070.clean.smooth.bw
GM-800U_070_20kb_1.3dg.gz
GM-800U_070_20kb_2.3dg.gz
GM-800U_070_20kb_3.3dg.gz
GM-800U_070_20kb_4.3dg.gz
GM-800U_070_20kb_5.3dg.gz
GM-800U_070_10kb_1.3dg.gz
GM-800U_070_10kb_2.3dg.gz
GM-800U_070_10kb_3.3dg.gz
GM-800U_070_10kb_4.3dg.gz
GM-800U_070_10kb_5.3dg.gz
GM-800U_070_5kb_1.3dg.gz
GM-800U_070_5kb_2.3dg.gz
GM-800U_070_5kb_3.3dg.gz
GM-800U_070_5kb_4.3dg.gz
GM-800U_070_5kb_5.3dg.gz
GM-800U_070_20kb_1.clean.3dg.gz
GM-800U_070_20kb_2.clean.3dg.gz
GM-800U_070_20kb_3.clean.3dg.gz
GM-800U_070_20kb_4.clean.3dg.gz
GM-800U_070_20kb_5.clean.3dg.gz
GM-800U_070_10kb_1.clean.3dg.gz
GM-800U_070_10kb_2.clean.3dg.gz
GM-800U_070_10kb_3.clean.3dg.gz
GM-800U_070_10kb_4.clean.3dg.gz
GM-800U_070_10kb_5.clean.3dg.gz
GM-800U_070_5kb_1.clean.3dg.gz
GM-800U_070_5kb_2.clean.3dg.gz
GM-800U_070_5kb_3.clean.3dg.gz
GM-800U_070_5kb_4.clean.3dg.gz
GM-800U_070_5kb_5.clean.3dg.gz

value: WT


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer12 [12H]


title: WT Infected Neutrophil Replicate 2


title: GM12878, 800U, Cell 73

description:
800U MNase
GM-800U_073.allValidPairs.gz
GM-800U_073.hic
GM-800U_073.mcool
GM-800U_073.clean.smooth.bw
GM-800U_073_20kb_1.3dg.gz
GM-800U_073_20kb_2.3dg.gz
GM-800U_073_20kb_3.3dg.gz
GM-800U_073_20kb_4.3dg.gz
GM-800U_073_20kb_5.3dg.gz
GM-800U_073_10kb_1.3dg.gz
GM-800U_073_10kb_2.3dg.gz
GM-800U_073_10kb_3.3dg.gz
GM-800U_073_10kb_4.3dg.gz
GM-800U_073_10kb_5.3dg.gz
GM-800U_073_5kb_1.3dg.gz
GM-800U_073_5kb_2.3dg.gz
GM-800U_073_5kb_3.3dg.gz
GM-800U_073_5kb_4.3dg.gz
GM-800U_073_5kb_5.3dg.gz
GM-800U_073_20kb_1.clean.3dg.gz
GM-800U_073_20kb_2.clean.3dg.gz
GM-800U_073_20kb_3.clean.3dg.gz
GM-800U_073_20kb_4.clean.3dg.gz
GM-800U_073_20kb_5.clean.3dg.gz
GM-800U_073_10kb_1.clean.3dg.gz
GM-800U_073_10kb_2.clean.3dg.gz
GM-800U_073_10kb_3.clean.3dg.gz
GM-800U_073_10kb_4.clean.3dg.gz
GM-800U_073_10kb_5.clean.3dg.gz
GM-800U_073_5kb_1.clean.3dg.gz
GM-800U_073_5kb_2.clean.3dg.gz
GM-800U_073_5kb_3.clean.3dg.gz
GM-800U_073_5kb_4.clean.3dg.gz
GM-800U_073_5kb_5.clean.3dg.gz


title: cell_234


title: WT Infected Neutrophil Replicate 1


title: GM12878, 800U, Cell 68

description:
800U MNase
GM-800U_068.allValidPairs.gz
GM-800U_068.hic
GM-800U_068.mcool
GM-800U_068.clean.smooth.bw
GM-800U_068_20kb_1.3dg.gz
GM-800U_068_20kb_2.3dg.gz
GM-800U_068_20kb_3.3dg.gz
GM-800U_068_20kb_4.3dg.gz
GM-800U_068_20kb_5.3dg.gz
GM-800U_068_10kb_1.3dg.gz
GM-800U_068_10kb_2.3dg.gz
GM-800U_068_10kb_3.3dg.gz
GM-800U_068_10kb_4.3dg.gz
GM-800U_068_10kb_5.3dg.gz
GM-800U_068_5kb_1.3dg.gz
GM-800U_068_5kb_2.3dg.gz
GM-800U_068_5kb_3.3dg.gz
GM-800U_068_5kb_4.3dg.gz
GM-800U_068_5kb_5.3dg.gz
GM-800U_068_20kb_1.clean.3dg.gz
GM-800U_068_20kb_2.clean.3dg.gz
GM-800U_068_20kb_3.clean.3dg.gz
GM-800U_068_20kb_4.clean.3dg.gz
GM-800U_068_20kb_5.clean.3dg.gz
GM-800U_068_10kb_1.clean.3dg.gz
GM-800U_068_10kb_2.clean.3dg.gz
GM-800U_068_10kb_3.clean.3dg.gz
GM-800U_068_10kb_4.clean.3dg.gz
GM-800U_068_10kb_5.clean.3dg.gz
GM-800U_068_5kb_1.clean.3dg.gz
GM-800U_068_5kb_2.clean.3dg.gz
GM-800U_068_5kb_3.clean.3dg.gz
GM-800U_068_5kb_4.clean.3dg.gz
GM-800U_068_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer10 [10H]


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer9 [9H]


title: cell_232


title: cell_231


title: WT Uninfected Neutrophil Replicate 3


title: WT Uninfected Neutrophil Replicate 2


title: GM12878, 800U, Cell 66

description:
800U MNase
GM-800U_066.allValidPairs.gz
GM-800U_066.hic
GM-800U_066.mcool
GM-800U_066.clean.smooth.bw
GM-800U_066_20kb_1.3dg.gz
GM-800U_066_20kb_2.3dg.gz
GM-800U_066_20kb_3.3dg.gz
GM-800U_066_20kb_4.3dg.gz
GM-800U_066_20kb_5.3dg.gz
GM-800U_066_10kb_1.3dg.gz
GM-800U_066_10kb_2.3dg.gz
GM-800U_066_10kb_3.3dg.gz
GM-800U_066_10kb_4.3dg.gz
GM-800U_066_10kb_5.3dg.gz
GM-800U_066_5kb_1.3dg.gz
GM-800U_066_5kb_2.3dg.gz
GM-800U_066_5kb_3.3dg.gz
GM-800U_066_5kb_4.3dg.gz
GM-800U_066_5kb_5.3dg.gz
GM-800U_066_20kb_1.clean.3dg.gz
GM-800U_066_20kb_2.clean.3dg.gz
GM-800U_066_20kb_3.clean.3dg.gz
GM-800U_066_20kb_4.clean.3dg.gz
GM-800U_066_20kb_5.clean.3dg.gz
GM-800U_066_10kb_1.clean.3dg.gz
GM-800U_066_10kb_2.clean.3dg.gz
GM-800U_066_10kb_3.clean.3dg.gz
GM-800U_066_10kb_4.clean.3dg.gz
GM-800U_066_10kb_5.clean.3dg.gz
GM-800U_066_5kb_1.clean.3dg.gz
GM-800U_066_5kb_2.clean.3dg.gz
GM-800U_066_5kb_3.clean.3dg.gz
GM-800U_066_5kb_4.clean.3dg.gz
GM-800U_066_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer8 [8H]


title: WT Uninfected Neutrophil Replicate 1


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer7 [7H]


title: GM12878, 800U, Cell 65

description:
800U MNase
GM-800U_065.allValidPairs.gz
GM-800U_065.hic
GM-800U_065.mcool
GM-800U_065.clean.smooth.bw
GM-800U_065_20kb_1.3dg.gz
GM-800U_065_20kb_2.3dg.gz
GM-800U_065_20kb_3.3dg.gz
GM-800U_065_20kb_4.3dg.gz
GM-800U_065_20kb_5.3dg.gz
GM-800U_065_10kb_1.3dg.gz
GM-800U_065_10kb_2.3dg.gz
GM-800U_065_10kb_3.3dg.gz
GM-800U_065_10kb_4.3dg.gz
GM-800U_065_10kb_5.3dg.gz
GM-800U_065_5kb_1.3dg.gz
GM-800U_065_5kb_2.3dg.gz
GM-800U_065_5kb_3.3dg.gz
GM-800U_065_5kb_4.3dg.gz
GM-800U_065_5kb_5.3dg.gz
GM-800U_065_20kb_1.clean.3dg.gz
GM-800U_065_20kb_2.clean.3dg.gz
GM-800U_065_20kb_3.clean.3dg.gz
GM-800U_065_20kb_4.clean.3dg.gz
GM-800U_065_20kb_5.clean.3dg.gz
GM-800U_065_10kb_1.clean.3dg.gz
GM-800U_065_10kb_2.clean.3dg.gz
GM-800U_065_10kb_3.clean.3dg.gz
GM-800U_065_10kb_4.clean.3dg.gz
GM-800U_065_10kb_5.clean.3dg.gz
GM-800U_065_5kb_1.clean.3dg.gz
GM-800U_065_5kb_2.clean.3dg.gz
GM-800U_065_5kb_3.clean.3dg.gz
GM-800U_065_5kb_4.clean.3dg.gz
GM-800U_065_5kb_5.clean.3dg.gz


title: cell_229


title: Transplanted_mouse_lung, hashtagged, TCR sequencing2

city: Saint Louis

first: Daniel

last: Kreisel

state: Missouri

address: 660 S Euclid Ave

department: Surgery

institute: Washington University

description: 10x Genomics TCR VDJ sequencing

library_source: other

data_processing:
Analysis was performed using the R Seurat v4.0.0 package. The following quality control steps were performed to filter the count matrices: 1) Cells expressing fewer than 500 genes were removed; 2) cells expressing over 10,000 genes were discarded as these could be potential multiplet events where more than a single cell was encapsulated within the same barcoded GEM; 3) cells with >5% mitochondrial content were filtered out as these were deemed to be of low-quality (PMID: 32840568). Following quality control, Normalization and variance-stabilization of raw counts was performed using SCTransform, and cell cycle scores were computed and regressed out in combination with percentage mitochondrial reads (PMID: 31870423). The normalized R object was then used for subsequent clustering and differential expression testing and integration with harmony was performed (PMID: 31740819). Differential gene expression was performed with the FindAllMarkers function and the Wilcoxon rank sum test with a min.pct = 0.25 and logfc.threshold = 0.25. Highly differentially expressed genes between groups were visualized through the magick and dittoheatmap packages. For downstream TCR analysis, TCRs with only one pair of productive rearrangements for TCRα and TCRβ chains were selected. Clonotypes in each sample were defined based on identical CDR3 nucleotide sequences together with identical V and J genes in both TCRα and TCRβ chains. Gini coefficients in each sample were calculated using Gini function from the DescTools package v0.99.50. Shared clonotypes were defined as clonotypes coming from different tissues within same mouse and containing identical CDR3 nucleotide sequences together with identical V and J genes. Visualization was performed with ggalluvial package v0.12.5
Assembly: mm10-2020-A
Supplementary files format and content: This is a processed data file containing both merged datasets, including 2 samples of Treg_Rejecting_Lung, 2 samples of CD4_Tolerant_Lung, 2 samples of Treg_Tolerant_Lung, and 2 samples of Treg_Tolerant_Spleen. Each sample has been labeled with Hastagging as described abover and pooled.
Library strategy: RNA Total SeqC with VDJ enrichment

molecule: protein

source_name: Mouse lung and spleen

extract_protocol: Transplanted left lungs and recipient spleens from four mice were collected 7 days following transplantation. Two samples were collected at a time and pooled for further processing. Lung tissue was digested, and single-cell suspensions were prepared as previously described (PMID: 28615357). Cells were stained using DAPI (BD Biosciences, #564907) and were sorted by flow cytometry for CD45+CD4+Foxp3+ Tregs into 250 μL cell resuspension buffer (0.04% BSA in PBS). Collected cells were centrifuged (300 rcf for 5 min at 4 °C) and resuspended in collection buffer to a target concentration of 1,000 cells/μL. Cells were counted on a hemocytometer before proceeding. Single-cell suspensions of sorted lung and spleen Tregs were submitted to the Genome Technology Access Center core facility (Washington University in St. Louis) for single-cell GEM construction and cDNA synthesis and library construction. Two sets of hashtagged samples were submitted as follows: tolerant lung CD4+, tolerant lung Treg, tolerant spleen Treg, rejecting lung Treg. Sorted cell types were labeled using a TotalSeq anti-mouse hashtag antibody (Biolegend, #155861, #155863, #155865, #155807) prior to pooling for sample submission. Samples were processed using the Chromium Single Cell 3′ Library & Gel Bead Kit (10X Genomics, v3) and Chromium Single Cell V(D)J Reagent Kits (10x Genomics) following manufacturer’s protocols. The libraries were sequenced on NovaSeq S4 (Illumina) targeting 50,000 reads per cell and 500 million read pairs per library. Cells were aligned to the mouse mm10-2020-A transcriptome using CellRanger (10× Genomics, v6.1.1) to generate feature-barcoded count matrices.

treatment_protocol: Lungs from tolerant mice were treated with co-stimulatory blockade and sacrificed after 30 days. Lungs from rejecting mice received no immunosuppression and were sacrificed at 7 days.

value: Mouse lung and spleen

value: Hashtagged:A- Treg_Rejecting_Lung, B- CD4_Tolerant_Lung, C- Treg_Tolerant_Lung, D- Treg_Tolerant_Spleen


title: cell_228


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer11 [11H]


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer5 [5H]


title: GM12878, 800U, Cell 69

description:
800U MNase
GM-800U_069.allValidPairs.gz
GM-800U_069.hic
GM-800U_069.mcool
GM-800U_069.clean.smooth.bw
GM-800U_069_20kb_1.3dg.gz
GM-800U_069_20kb_2.3dg.gz
GM-800U_069_20kb_3.3dg.gz
GM-800U_069_20kb_4.3dg.gz
GM-800U_069_20kb_5.3dg.gz
GM-800U_069_10kb_1.3dg.gz
GM-800U_069_10kb_2.3dg.gz
GM-800U_069_10kb_3.3dg.gz
GM-800U_069_10kb_4.3dg.gz
GM-800U_069_10kb_5.3dg.gz
GM-800U_069_5kb_1.3dg.gz
GM-800U_069_5kb_2.3dg.gz
GM-800U_069_5kb_3.3dg.gz
GM-800U_069_5kb_4.3dg.gz
GM-800U_069_5kb_5.3dg.gz
GM-800U_069_20kb_1.clean.3dg.gz
GM-800U_069_20kb_2.clean.3dg.gz
GM-800U_069_20kb_3.clean.3dg.gz
GM-800U_069_20kb_4.clean.3dg.gz
GM-800U_069_20kb_5.clean.3dg.gz
GM-800U_069_10kb_1.clean.3dg.gz
GM-800U_069_10kb_2.clean.3dg.gz
GM-800U_069_10kb_3.clean.3dg.gz
GM-800U_069_10kb_4.clean.3dg.gz
GM-800U_069_10kb_5.clean.3dg.gz
GM-800U_069_5kb_1.clean.3dg.gz
GM-800U_069_5kb_2.clean.3dg.gz
GM-800U_069_5kb_3.clean.3dg.gz
GM-800U_069_5kb_4.clean.3dg.gz
GM-800U_069_5kb_5.clean.3dg.gz


title: GM12878, 800U, Cell 63

description:
800U MNase
GM-800U_063.allValidPairs.gz
GM-800U_063.hic
GM-800U_063.mcool
GM-800U_063.clean.smooth.bw
GM-800U_063_20kb_1.3dg.gz
GM-800U_063_20kb_2.3dg.gz
GM-800U_063_20kb_3.3dg.gz
GM-800U_063_20kb_4.3dg.gz
GM-800U_063_20kb_5.3dg.gz
GM-800U_063_10kb_1.3dg.gz
GM-800U_063_10kb_2.3dg.gz
GM-800U_063_10kb_3.3dg.gz
GM-800U_063_10kb_4.3dg.gz
GM-800U_063_10kb_5.3dg.gz
GM-800U_063_5kb_1.3dg.gz
GM-800U_063_5kb_2.3dg.gz
GM-800U_063_5kb_3.3dg.gz
GM-800U_063_5kb_4.3dg.gz
GM-800U_063_5kb_5.3dg.gz
GM-800U_063_20kb_1.clean.3dg.gz
GM-800U_063_20kb_2.clean.3dg.gz
GM-800U_063_20kb_3.clean.3dg.gz
GM-800U_063_20kb_4.clean.3dg.gz
GM-800U_063_20kb_5.clean.3dg.gz
GM-800U_063_10kb_1.clean.3dg.gz
GM-800U_063_10kb_2.clean.3dg.gz
GM-800U_063_10kb_3.clean.3dg.gz
GM-800U_063_10kb_4.clean.3dg.gz
GM-800U_063_10kb_5.clean.3dg.gz
GM-800U_063_5kb_1.clean.3dg.gz
GM-800U_063_5kb_2.clean.3dg.gz
GM-800U_063_5kb_3.clean.3dg.gz
GM-800U_063_5kb_4.clean.3dg.gz
GM-800U_063_5kb_5.clean.3dg.gz


title: Transplanted_mouse_lung, hashtagged, genome sequencing2

description: 10x Genomics


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer4 [4H]


title: cell_233


title: Transplanted_mouse_lung, hashtagged, genome sequencing1

description: 10x Genomics


title: GM12878, 800U, Cell 62

description:
800U MNase
GM-800U_062.allValidPairs.gz
GM-800U_062.hic
GM-800U_062.mcool
GM-800U_062.clean.smooth.bw
GM-800U_062_20kb_1.3dg.gz
GM-800U_062_20kb_2.3dg.gz
GM-800U_062_20kb_3.3dg.gz
GM-800U_062_20kb_4.3dg.gz
GM-800U_062_20kb_5.3dg.gz
GM-800U_062_10kb_1.3dg.gz
GM-800U_062_10kb_2.3dg.gz
GM-800U_062_10kb_3.3dg.gz
GM-800U_062_10kb_4.3dg.gz
GM-800U_062_10kb_5.3dg.gz
GM-800U_062_5kb_1.3dg.gz
GM-800U_062_5kb_2.3dg.gz
GM-800U_062_5kb_3.3dg.gz
GM-800U_062_5kb_4.3dg.gz
GM-800U_062_5kb_5.3dg.gz
GM-800U_062_20kb_1.clean.3dg.gz
GM-800U_062_20kb_2.clean.3dg.gz
GM-800U_062_20kb_3.clean.3dg.gz
GM-800U_062_20kb_4.clean.3dg.gz
GM-800U_062_20kb_5.clean.3dg.gz
GM-800U_062_10kb_1.clean.3dg.gz
GM-800U_062_10kb_2.clean.3dg.gz
GM-800U_062_10kb_3.clean.3dg.gz
GM-800U_062_10kb_4.clean.3dg.gz
GM-800U_062_10kb_5.clean.3dg.gz
GM-800U_062_5kb_1.clean.3dg.gz
GM-800U_062_5kb_2.clean.3dg.gz
GM-800U_062_5kb_3.clean.3dg.gz
GM-800U_062_5kb_4.clean.3dg.gz
GM-800U_062_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer3 [3H]


title: cell_230


title: cell_226


title: GM12878, 800U, Cell 60

description:
800U MNase
GM-800U_060.allValidPairs.gz
GM-800U_060.hic
GM-800U_060.mcool
GM-800U_060.clean.smooth.bw
GM-800U_060_20kb_1.3dg.gz
GM-800U_060_20kb_2.3dg.gz
GM-800U_060_20kb_3.3dg.gz
GM-800U_060_20kb_4.3dg.gz
GM-800U_060_20kb_5.3dg.gz
GM-800U_060_10kb_1.3dg.gz
GM-800U_060_10kb_2.3dg.gz
GM-800U_060_10kb_3.3dg.gz
GM-800U_060_10kb_4.3dg.gz
GM-800U_060_10kb_5.3dg.gz
GM-800U_060_5kb_1.3dg.gz
GM-800U_060_5kb_2.3dg.gz
GM-800U_060_5kb_3.3dg.gz
GM-800U_060_5kb_4.3dg.gz
GM-800U_060_5kb_5.3dg.gz
GM-800U_060_20kb_1.clean.3dg.gz
GM-800U_060_20kb_2.clean.3dg.gz
GM-800U_060_20kb_3.clean.3dg.gz
GM-800U_060_20kb_4.clean.3dg.gz
GM-800U_060_20kb_5.clean.3dg.gz
GM-800U_060_10kb_1.clean.3dg.gz
GM-800U_060_10kb_2.clean.3dg.gz
GM-800U_060_10kb_3.clean.3dg.gz
GM-800U_060_10kb_4.clean.3dg.gz
GM-800U_060_10kb_5.clean.3dg.gz
GM-800U_060_5kb_1.clean.3dg.gz
GM-800U_060_5kb_2.clean.3dg.gz
GM-800U_060_5kb_3.clean.3dg.gz
GM-800U_060_5kb_4.clean.3dg.gz
GM-800U_060_5kb_5.clean.3dg.gz


title: cell_224


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer2 [2H]


title: GM12878, 800U, Cell 59

description:
800U MNase
GM-800U_059.allValidPairs.gz
GM-800U_059.hic
GM-800U_059.mcool
GM-800U_059.clean.smooth.bw
GM-800U_059_20kb_1.3dg.gz
GM-800U_059_20kb_2.3dg.gz
GM-800U_059_20kb_3.3dg.gz
GM-800U_059_20kb_4.3dg.gz
GM-800U_059_20kb_5.3dg.gz
GM-800U_059_10kb_1.3dg.gz
GM-800U_059_10kb_2.3dg.gz
GM-800U_059_10kb_3.3dg.gz
GM-800U_059_10kb_4.3dg.gz
GM-800U_059_10kb_5.3dg.gz
GM-800U_059_5kb_1.3dg.gz
GM-800U_059_5kb_2.3dg.gz
GM-800U_059_5kb_3.3dg.gz
GM-800U_059_5kb_4.3dg.gz
GM-800U_059_5kb_5.3dg.gz
GM-800U_059_20kb_1.clean.3dg.gz
GM-800U_059_20kb_2.clean.3dg.gz
GM-800U_059_20kb_3.clean.3dg.gz
GM-800U_059_20kb_4.clean.3dg.gz
GM-800U_059_20kb_5.clean.3dg.gz
GM-800U_059_10kb_1.clean.3dg.gz
GM-800U_059_10kb_2.clean.3dg.gz
GM-800U_059_10kb_3.clean.3dg.gz
GM-800U_059_10kb_4.clean.3dg.gz
GM-800U_059_10kb_5.clean.3dg.gz
GM-800U_059_5kb_1.clean.3dg.gz
GM-800U_059_5kb_2.clean.3dg.gz
GM-800U_059_5kb_3.clean.3dg.gz
GM-800U_059_5kb_4.clean.3dg.gz
GM-800U_059_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer1 [1H]


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Summer6 [6H]


title: Transplanted_mouse_lung, hashtagged, TCR sequencing1

description: 10x Genomics TCR VDJ sequencing


title: cell_223


title: GM12878, 800U, Cell 61

description:
800U MNase
GM-800U_061.allValidPairs.gz
GM-800U_061.hic
GM-800U_061.mcool
GM-800U_061.clean.smooth.bw
GM-800U_061_20kb_1.3dg.gz
GM-800U_061_20kb_2.3dg.gz
GM-800U_061_20kb_3.3dg.gz
GM-800U_061_20kb_4.3dg.gz
GM-800U_061_20kb_5.3dg.gz
GM-800U_061_10kb_1.3dg.gz
GM-800U_061_10kb_2.3dg.gz
GM-800U_061_10kb_3.3dg.gz
GM-800U_061_10kb_4.3dg.gz
GM-800U_061_10kb_5.3dg.gz
GM-800U_061_5kb_1.3dg.gz
GM-800U_061_5kb_2.3dg.gz
GM-800U_061_5kb_3.3dg.gz
GM-800U_061_5kb_4.3dg.gz
GM-800U_061_5kb_5.3dg.gz
GM-800U_061_20kb_1.clean.3dg.gz
GM-800U_061_20kb_2.clean.3dg.gz
GM-800U_061_20kb_3.clean.3dg.gz
GM-800U_061_20kb_4.clean.3dg.gz
GM-800U_061_20kb_5.clean.3dg.gz
GM-800U_061_10kb_1.clean.3dg.gz
GM-800U_061_10kb_2.clean.3dg.gz
GM-800U_061_10kb_3.clean.3dg.gz
GM-800U_061_10kb_4.clean.3dg.gz
GM-800U_061_10kb_5.clean.3dg.gz
GM-800U_061_5kb_1.clean.3dg.gz
GM-800U_061_5kb_2.clean.3dg.gz
GM-800U_061_5kb_3.clean.3dg.gz
GM-800U_061_5kb_4.clean.3dg.gz
GM-800U_061_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon40 [40U]

value: Monsoon

value: University


title: Sham, wildtype, lung, scRNAseq

city: St. Louis

first: Andreas

last: Herrlich

address: 660 South Euclid Avenue

department: Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v3.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files (tsv) and matrix files (mtx)

source_name: lung

extract_protocol:
All mice were perfused with 20 ml of  ice-cold PBS to remove remaining blood in the vasculature. Freshly collected organs (kidney or lung) were diced by scapels and razor blade and incubated with 40 U/ml of DNase (Sigma) and 50 microg/ml of Liberase (Roche) in RPMI media (gibco) for 60 minutes at 37°C in a shaking incubator. Digested organs were strained through 70 micron filters and then red blood cells were lysed with ACK lysis buffer. The cell mixtures were again strained through 40 micron filters. Aquired single cell suspensions were washed and re-suspended in PBS, stained with propidium iodide, washed and resuspended in FACS buffer (PBS, 0.5% BSA, 2mM EDTA, 0.01% NaN3), and live cells were sorted using FACS Aria III (BD Biosciences).
Libraries were prepared using the Chromium Single Cell 5′ Library Kit v2 and Chromium instrument (10× Genomics, Pleasanton, CA, USA) according to manufacturer’s instruction. Briefly, for the gel bead-in-emulsion (GEM) generation, single-cell samples were resuspended in the master mix and applied together with partitioning oil and barcoded gel beads onto the Chromium Chip. Incubation of the individual GEMs including cell lysate and reverse transcription (RT) reagents generated full-length cDNA with barcodes from polyadenylated mRNA in every single GEM. The RT products contained Illumina R1 primer sequence, Unique Molecular Identifier (UMI), template switch oligo (TSO), and the 10x Barcode. Then GEMS were broken, pooled, and purified with Silane magnetic beads. The full-length cDNA was amplified by PCR, followed by enzymatic fragmentation and size selection for library construction. During the library construction, P5, P7, i5 and i7 sample indexes, and Illumina R2 primer sequence were added.

value: lung

value: all cells

value: male

value: wildtype

tag: age

value: 8-12 weeks old

value: Sham

tag: time

value: 24 hours


title: AKI, wildtype, kidney, scRNAseq

description: 10x Genomics

source_name: kidney

value: kidney

value: renal IRI


title: cell_225

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

value: blood

value: lymphoblastoid


title: GM12878, 800U, Cell 64

description:
800U MNase
GM-800U_064.allValidPairs.gz
GM-800U_064.hic
GM-800U_064.mcool
GM-800U_064.clean.smooth.bw
GM-800U_064_20kb_1.3dg.gz
GM-800U_064_20kb_2.3dg.gz
GM-800U_064_20kb_3.3dg.gz
GM-800U_064_20kb_4.3dg.gz
GM-800U_064_20kb_5.3dg.gz
GM-800U_064_10kb_1.3dg.gz
GM-800U_064_10kb_2.3dg.gz
GM-800U_064_10kb_3.3dg.gz
GM-800U_064_10kb_4.3dg.gz
GM-800U_064_10kb_5.3dg.gz
GM-800U_064_5kb_1.3dg.gz
GM-800U_064_5kb_2.3dg.gz
GM-800U_064_5kb_3.3dg.gz
GM-800U_064_5kb_4.3dg.gz
GM-800U_064_5kb_5.3dg.gz
GM-800U_064_20kb_1.clean.3dg.gz
GM-800U_064_20kb_2.clean.3dg.gz
GM-800U_064_20kb_3.clean.3dg.gz
GM-800U_064_20kb_4.clean.3dg.gz
GM-800U_064_20kb_5.clean.3dg.gz
GM-800U_064_10kb_1.clean.3dg.gz
GM-800U_064_10kb_2.clean.3dg.gz
GM-800U_064_10kb_3.clean.3dg.gz
GM-800U_064_10kb_4.clean.3dg.gz
GM-800U_064_10kb_5.clean.3dg.gz
GM-800U_064_5kb_1.clean.3dg.gz
GM-800U_064_5kb_2.clean.3dg.gz
GM-800U_064_5kb_3.clean.3dg.gz
GM-800U_064_5kb_4.clean.3dg.gz
GM-800U_064_5kb_5.clean.3dg.gz


title: cell_227


title: Sham, wildtype, kidney, scRNAseq

description: 10x Genomics


title: cell_222


title: GM12878, 800U, Cell 58

description:
800U MNase
GM-800U_058.allValidPairs.gz
GM-800U_058.hic
GM-800U_058.mcool
GM-800U_058.clean.smooth.bw
GM-800U_058_20kb_1.3dg.gz
GM-800U_058_20kb_2.3dg.gz
GM-800U_058_20kb_3.3dg.gz
GM-800U_058_20kb_4.3dg.gz
GM-800U_058_10kb_1.3dg.gz
GM-800U_058_10kb_2.3dg.gz
GM-800U_058_10kb_3.3dg.gz
GM-800U_058_10kb_4.3dg.gz
GM-800U_058_5kb_1.3dg.gz
GM-800U_058_5kb_2.3dg.gz
GM-800U_058_5kb_3.3dg.gz
GM-800U_058_5kb_4.3dg.gz
GM-800U_058_20kb_1.clean.3dg.gz
GM-800U_058_20kb_2.clean.3dg.gz
GM-800U_058_20kb_3.clean.3dg.gz
GM-800U_058_20kb_4.clean.3dg.gz
GM-800U_058_10kb_1.clean.3dg.gz
GM-800U_058_10kb_2.clean.3dg.gz
GM-800U_058_10kb_3.clean.3dg.gz
GM-800U_058_10kb_4.clean.3dg.gz
GM-800U_058_5kb_1.clean.3dg.gz
GM-800U_058_5kb_2.clean.3dg.gz
GM-800U_058_5kb_3.clean.3dg.gz
GM-800U_058_5kb_4.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon39 [39U]

value: soil sample


title: AKI, wildtype, lung, scRNAseq

description: 10x Genomics


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon38 [38U]


title: cell_221


title: young control 4

city: Novato

first: Pankaj

last: Kapahi

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute

data_processing:
Data quality was assessed and adaptor reads and low quality reads were removed.
Reads that passed the quality filtering process were mapped paired-end to the reference genome (GRCm38) using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count reads that mapped to each gene.
Differential expression analysis was performed using DESEq2 (1.20.0).
Assembly: GRCm38
Supplementary files format and content: GEO_rawCounts.txt is a tab-delimited text file containing raw transcript counts

molecule: polyA RNA

source_name: hypothalamus

extract_protocol:
RNA was isolated from flash-frozen hypothalamus using Zymo research quick RNA miniprep kit (cat # 11-328) according to the manufacturer's recommendations. Isolated RNA was sent for library construction and sequencing by Novogene Corporation Inc.
RNA was poly-A selected using poly-T oligo-attached magnetic beads, fragmented, reverse transcribed using random hexamer primers followed by second strand cDNA synthesis using dTTP for non-directional library preparation. Samples underwent end repair, A-tailing, adapter ligated, size selected, amplified, and purified. Illumina libraries were quantified using Qubit and qPCR and analyzed for size distribution using a bioanalyzer.

value: hypothalamus

value: 3 months

tag: treatment duration

value: 1 week

value: control diet


title: GM12878, 800U, Cell 56

description:
800U MNase
GM-800U_056.allValidPairs.gz
GM-800U_056.hic
GM-800U_056.mcool
GM-800U_056.clean.smooth.bw
GM-800U_056_20kb_1.3dg.gz
GM-800U_056_20kb_2.3dg.gz
GM-800U_056_20kb_3.3dg.gz
GM-800U_056_20kb_4.3dg.gz
GM-800U_056_20kb_5.3dg.gz
GM-800U_056_10kb_1.3dg.gz
GM-800U_056_10kb_2.3dg.gz
GM-800U_056_10kb_3.3dg.gz
GM-800U_056_10kb_4.3dg.gz
GM-800U_056_10kb_5.3dg.gz
GM-800U_056_5kb_1.3dg.gz
GM-800U_056_5kb_2.3dg.gz
GM-800U_056_5kb_3.3dg.gz
GM-800U_056_5kb_4.3dg.gz
GM-800U_056_5kb_5.3dg.gz
GM-800U_056_20kb_1.clean.3dg.gz
GM-800U_056_20kb_2.clean.3dg.gz
GM-800U_056_20kb_3.clean.3dg.gz
GM-800U_056_20kb_4.clean.3dg.gz
GM-800U_056_20kb_5.clean.3dg.gz
GM-800U_056_10kb_1.clean.3dg.gz
GM-800U_056_10kb_2.clean.3dg.gz
GM-800U_056_10kb_3.clean.3dg.gz
GM-800U_056_10kb_4.clean.3dg.gz
GM-800U_056_10kb_5.clean.3dg.gz
GM-800U_056_5kb_1.clean.3dg.gz
GM-800U_056_5kb_2.clean.3dg.gz
GM-800U_056_5kb_3.clean.3dg.gz
GM-800U_056_5kb_4.clean.3dg.gz
GM-800U_056_5kb_5.clean.3dg.gz

value: WT


title: GM12878, 800U, Cell 57

description:
800U MNase
GM-800U_057.allValidPairs.gz
GM-800U_057.hic
GM-800U_057.mcool
GM-800U_057.clean.smooth.bw
GM-800U_057_20kb_1.3dg.gz
GM-800U_057_20kb_2.3dg.gz
GM-800U_057_20kb_3.3dg.gz
GM-800U_057_20kb_4.3dg.gz
GM-800U_057_20kb_5.3dg.gz
GM-800U_057_10kb_1.3dg.gz
GM-800U_057_10kb_2.3dg.gz
GM-800U_057_10kb_3.3dg.gz
GM-800U_057_10kb_4.3dg.gz
GM-800U_057_10kb_5.3dg.gz
GM-800U_057_5kb_1.3dg.gz
GM-800U_057_5kb_2.3dg.gz
GM-800U_057_5kb_3.3dg.gz
GM-800U_057_5kb_4.3dg.gz
GM-800U_057_5kb_5.3dg.gz
GM-800U_057_20kb_1.clean.3dg.gz
GM-800U_057_20kb_2.clean.3dg.gz
GM-800U_057_20kb_3.clean.3dg.gz
GM-800U_057_20kb_4.clean.3dg.gz
GM-800U_057_20kb_5.clean.3dg.gz
GM-800U_057_10kb_1.clean.3dg.gz
GM-800U_057_10kb_2.clean.3dg.gz
GM-800U_057_10kb_3.clean.3dg.gz
GM-800U_057_10kb_4.clean.3dg.gz
GM-800U_057_10kb_5.clean.3dg.gz
GM-800U_057_5kb_1.clean.3dg.gz
GM-800U_057_5kb_2.clean.3dg.gz
GM-800U_057_5kb_3.clean.3dg.gz
GM-800U_057_5kb_4.clean.3dg.gz
GM-800U_057_5kb_5.clean.3dg.gz


title: cell_220


title: GM12878, 800U, Cell 55

description:
800U MNase
GM-800U_055.allValidPairs.gz
GM-800U_055.hic
GM-800U_055.mcool
GM-800U_055.clean.smooth.bw
GM-800U_055_20kb_1.3dg.gz
GM-800U_055_20kb_2.3dg.gz
GM-800U_055_20kb_3.3dg.gz
GM-800U_055_20kb_4.3dg.gz
GM-800U_055_20kb_5.3dg.gz
GM-800U_055_10kb_1.3dg.gz
GM-800U_055_10kb_2.3dg.gz
GM-800U_055_10kb_3.3dg.gz
GM-800U_055_10kb_4.3dg.gz
GM-800U_055_10kb_5.3dg.gz
GM-800U_055_5kb_1.3dg.gz
GM-800U_055_5kb_2.3dg.gz
GM-800U_055_5kb_3.3dg.gz
GM-800U_055_5kb_4.3dg.gz
GM-800U_055_5kb_5.3dg.gz
GM-800U_055_20kb_1.clean.3dg.gz
GM-800U_055_20kb_2.clean.3dg.gz
GM-800U_055_20kb_3.clean.3dg.gz
GM-800U_055_20kb_4.clean.3dg.gz
GM-800U_055_20kb_5.clean.3dg.gz
GM-800U_055_10kb_1.clean.3dg.gz
GM-800U_055_10kb_2.clean.3dg.gz
GM-800U_055_10kb_3.clean.3dg.gz
GM-800U_055_10kb_4.clean.3dg.gz
GM-800U_055_10kb_5.clean.3dg.gz
GM-800U_055_5kb_1.clean.3dg.gz
GM-800U_055_5kb_2.clean.3dg.gz
GM-800U_055_5kb_3.clean.3dg.gz
GM-800U_055_5kb_4.clean.3dg.gz
GM-800U_055_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon37 [37U]

value: Monsoon

value: University


title: young control 2


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon35 [35U]


title: young control 1


title: GM12878, 800U, Cell 54

description:
800U MNase
GM-800U_054.allValidPairs.gz
GM-800U_054.hic
GM-800U_054.mcool
GM-800U_054.clean.smooth.bw
GM-800U_054_20kb_1.3dg.gz
GM-800U_054_20kb_2.3dg.gz
GM-800U_054_20kb_3.3dg.gz
GM-800U_054_20kb_4.3dg.gz
GM-800U_054_20kb_5.3dg.gz
GM-800U_054_10kb_1.3dg.gz
GM-800U_054_10kb_2.3dg.gz
GM-800U_054_10kb_3.3dg.gz
GM-800U_054_10kb_4.3dg.gz
GM-800U_054_10kb_5.3dg.gz
GM-800U_054_5kb_1.3dg.gz
GM-800U_054_5kb_2.3dg.gz
GM-800U_054_5kb_3.3dg.gz
GM-800U_054_5kb_4.3dg.gz
GM-800U_054_5kb_5.3dg.gz
GM-800U_054_20kb_1.clean.3dg.gz
GM-800U_054_20kb_2.clean.3dg.gz
GM-800U_054_20kb_3.clean.3dg.gz
GM-800U_054_20kb_4.clean.3dg.gz
GM-800U_054_20kb_5.clean.3dg.gz
GM-800U_054_10kb_1.clean.3dg.gz
GM-800U_054_10kb_2.clean.3dg.gz
GM-800U_054_10kb_3.clean.3dg.gz
GM-800U_054_10kb_4.clean.3dg.gz
GM-800U_054_10kb_5.clean.3dg.gz
GM-800U_054_5kb_1.clean.3dg.gz
GM-800U_054_5kb_2.clean.3dg.gz
GM-800U_054_5kb_3.clean.3dg.gz
GM-800U_054_5kb_4.clean.3dg.gz
GM-800U_054_5kb_5.clean.3dg.gz


title: GM12878, 800U, Cell 53

description:
800U MNase
GM-800U_053.allValidPairs.gz
GM-800U_053.hic
GM-800U_053.mcool
GM-800U_053.clean.smooth.bw
GM-800U_053_20kb_1.3dg.gz
GM-800U_053_20kb_2.3dg.gz
GM-800U_053_20kb_3.3dg.gz
GM-800U_053_20kb_4.3dg.gz
GM-800U_053_20kb_5.3dg.gz
GM-800U_053_10kb_1.3dg.gz
GM-800U_053_10kb_2.3dg.gz
GM-800U_053_10kb_3.3dg.gz
GM-800U_053_10kb_4.3dg.gz
GM-800U_053_10kb_5.3dg.gz
GM-800U_053_5kb_1.3dg.gz
GM-800U_053_5kb_2.3dg.gz
GM-800U_053_5kb_3.3dg.gz
GM-800U_053_5kb_4.3dg.gz
GM-800U_053_5kb_5.3dg.gz
GM-800U_053_20kb_1.clean.3dg.gz
GM-800U_053_20kb_2.clean.3dg.gz
GM-800U_053_20kb_3.clean.3dg.gz
GM-800U_053_20kb_4.clean.3dg.gz
GM-800U_053_20kb_5.clean.3dg.gz
GM-800U_053_10kb_1.clean.3dg.gz
GM-800U_053_10kb_2.clean.3dg.gz
GM-800U_053_10kb_3.clean.3dg.gz
GM-800U_053_10kb_4.clean.3dg.gz
GM-800U_053_10kb_5.clean.3dg.gz
GM-800U_053_5kb_1.clean.3dg.gz
GM-800U_053_5kb_2.clean.3dg.gz
GM-800U_053_5kb_3.clean.3dg.gz
GM-800U_053_5kb_4.clean.3dg.gz
GM-800U_053_5kb_5.clean.3dg.gz


title: GM12878, 800U, Cell 52

description:
800U MNase
GM-800U_052.allValidPairs.gz
GM-800U_052.hic
GM-800U_052.mcool
GM-800U_052.clean.smooth.bw
GM-800U_052_20kb_1.3dg.gz
GM-800U_052_20kb_2.3dg.gz
GM-800U_052_20kb_3.3dg.gz
GM-800U_052_20kb_4.3dg.gz
GM-800U_052_20kb_5.3dg.gz
GM-800U_052_10kb_1.3dg.gz
GM-800U_052_10kb_2.3dg.gz
GM-800U_052_10kb_3.3dg.gz
GM-800U_052_10kb_4.3dg.gz
GM-800U_052_10kb_5.3dg.gz
GM-800U_052_5kb_1.3dg.gz
GM-800U_052_5kb_2.3dg.gz
GM-800U_052_5kb_3.3dg.gz
GM-800U_052_5kb_4.3dg.gz
GM-800U_052_5kb_5.3dg.gz
GM-800U_052_20kb_1.clean.3dg.gz
GM-800U_052_20kb_2.clean.3dg.gz
GM-800U_052_20kb_3.clean.3dg.gz
GM-800U_052_20kb_4.clean.3dg.gz
GM-800U_052_20kb_5.clean.3dg.gz
GM-800U_052_10kb_1.clean.3dg.gz
GM-800U_052_10kb_2.clean.3dg.gz
GM-800U_052_10kb_3.clean.3dg.gz
GM-800U_052_10kb_4.clean.3dg.gz
GM-800U_052_10kb_5.clean.3dg.gz
GM-800U_052_5kb_1.clean.3dg.gz
GM-800U_052_5kb_2.clean.3dg.gz
GM-800U_052_5kb_3.clean.3dg.gz
GM-800U_052_5kb_4.clean.3dg.gz
GM-800U_052_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon36 [36U]


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon33 [33U]


title: GM12878, 800U, Cell 51

description:
800U MNase
GM-800U_051.allValidPairs.gz
GM-800U_051.hic
GM-800U_051.mcool
GM-800U_051.clean.smooth.bw
GM-800U_051_20kb_1.3dg.gz
GM-800U_051_20kb_2.3dg.gz
GM-800U_051_20kb_3.3dg.gz
GM-800U_051_20kb_4.3dg.gz
GM-800U_051_20kb_5.3dg.gz
GM-800U_051_10kb_1.3dg.gz
GM-800U_051_10kb_2.3dg.gz
GM-800U_051_10kb_3.3dg.gz
GM-800U_051_10kb_4.3dg.gz
GM-800U_051_10kb_5.3dg.gz
GM-800U_051_5kb_1.3dg.gz
GM-800U_051_5kb_2.3dg.gz
GM-800U_051_5kb_3.3dg.gz
GM-800U_051_5kb_4.3dg.gz
GM-800U_051_5kb_5.3dg.gz
GM-800U_051_20kb_1.clean.3dg.gz
GM-800U_051_20kb_2.clean.3dg.gz
GM-800U_051_20kb_3.clean.3dg.gz
GM-800U_051_20kb_4.clean.3dg.gz
GM-800U_051_20kb_5.clean.3dg.gz
GM-800U_051_10kb_1.clean.3dg.gz
GM-800U_051_10kb_2.clean.3dg.gz
GM-800U_051_10kb_3.clean.3dg.gz
GM-800U_051_10kb_4.clean.3dg.gz
GM-800U_051_10kb_5.clean.3dg.gz
GM-800U_051_5kb_1.clean.3dg.gz
GM-800U_051_5kb_2.clean.3dg.gz
GM-800U_051_5kb_3.clean.3dg.gz
GM-800U_051_5kb_4.clean.3dg.gz
GM-800U_051_5kb_5.clean.3dg.gz


title: old Gly-Low 2

value: 25 months

value: 5 months

value: Gly-Low diet


title: cell_218


title: cell_217


title: old Gly-Low 3


title: cell_216


title: cell_215


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon32 [32U]


title: old Gly-Low 1


title: GM12878, 800U, Cell 50

description:
800U MNase
GM-800U_050.allValidPairs.gz
GM-800U_050.hic
GM-800U_050.mcool
GM-800U_050.clean.smooth.bw
GM-800U_050_20kb_1.3dg.gz
GM-800U_050_20kb_2.3dg.gz
GM-800U_050_20kb_3.3dg.gz
GM-800U_050_20kb_4.3dg.gz
GM-800U_050_20kb_5.3dg.gz
GM-800U_050_10kb_1.3dg.gz
GM-800U_050_10kb_2.3dg.gz
GM-800U_050_10kb_3.3dg.gz
GM-800U_050_10kb_4.3dg.gz
GM-800U_050_10kb_5.3dg.gz
GM-800U_050_5kb_1.3dg.gz
GM-800U_050_5kb_2.3dg.gz
GM-800U_050_5kb_3.3dg.gz
GM-800U_050_5kb_4.3dg.gz
GM-800U_050_5kb_5.3dg.gz
GM-800U_050_20kb_1.clean.3dg.gz
GM-800U_050_20kb_2.clean.3dg.gz
GM-800U_050_20kb_3.clean.3dg.gz
GM-800U_050_20kb_4.clean.3dg.gz
GM-800U_050_20kb_5.clean.3dg.gz
GM-800U_050_10kb_1.clean.3dg.gz
GM-800U_050_10kb_2.clean.3dg.gz
GM-800U_050_10kb_3.clean.3dg.gz
GM-800U_050_10kb_4.clean.3dg.gz
GM-800U_050_10kb_5.clean.3dg.gz
GM-800U_050_5kb_1.clean.3dg.gz
GM-800U_050_5kb_2.clean.3dg.gz
GM-800U_050_5kb_3.clean.3dg.gz
GM-800U_050_5kb_4.clean.3dg.gz
GM-800U_050_5kb_5.clean.3dg.gz


title: GM12878, 800U, Cell 67

description:
800U MNase
GM-800U_067.allValidPairs.gz
GM-800U_067.hic
GM-800U_067.mcool
GM-800U_067.clean.smooth.bw
GM-800U_067_20kb_3.3dg.gz
GM-800U_067_20kb_4.3dg.gz
GM-800U_067_20kb_5.3dg.gz
GM-800U_067_10kb_3.3dg.gz
GM-800U_067_10kb_4.3dg.gz
GM-800U_067_10kb_5.3dg.gz
GM-800U_067_5kb_3.3dg.gz
GM-800U_067_5kb_4.3dg.gz
GM-800U_067_5kb_5.3dg.gz
GM-800U_067_20kb_3.clean.3dg.gz
GM-800U_067_20kb_4.clean.3dg.gz
GM-800U_067_20kb_5.clean.3dg.gz
GM-800U_067_10kb_3.clean.3dg.gz
GM-800U_067_10kb_4.clean.3dg.gz
GM-800U_067_10kb_5.clean.3dg.gz
GM-800U_067_5kb_3.clean.3dg.gz
GM-800U_067_5kb_4.clean.3dg.gz
GM-800U_067_5kb_5.clean.3dg.gz


title: old control 4


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon31 [31U]


title: young control 3


title: cell_214


title: old control 3


title: cell_219


title: cell_213


title: GM12878, 800U, Cell 48

description:
800U MNase
GM-800U_048.allValidPairs.gz
GM-800U_048.hic
GM-800U_048.mcool
GM-800U_048.clean.smooth.bw
GM-800U_048_20kb_1.3dg.gz
GM-800U_048_20kb_2.3dg.gz
GM-800U_048_20kb_3.3dg.gz
GM-800U_048_20kb_4.3dg.gz
GM-800U_048_20kb_5.3dg.gz
GM-800U_048_10kb_1.3dg.gz
GM-800U_048_10kb_2.3dg.gz
GM-800U_048_10kb_3.3dg.gz
GM-800U_048_10kb_4.3dg.gz
GM-800U_048_10kb_5.3dg.gz
GM-800U_048_5kb_1.3dg.gz
GM-800U_048_5kb_2.3dg.gz
GM-800U_048_5kb_3.3dg.gz
GM-800U_048_5kb_4.3dg.gz
GM-800U_048_5kb_5.3dg.gz
GM-800U_048_20kb_1.clean.3dg.gz
GM-800U_048_20kb_2.clean.3dg.gz
GM-800U_048_20kb_3.clean.3dg.gz
GM-800U_048_20kb_4.clean.3dg.gz
GM-800U_048_20kb_5.clean.3dg.gz
GM-800U_048_10kb_1.clean.3dg.gz
GM-800U_048_10kb_2.clean.3dg.gz
GM-800U_048_10kb_3.clean.3dg.gz
GM-800U_048_10kb_4.clean.3dg.gz
GM-800U_048_10kb_5.clean.3dg.gz
GM-800U_048_5kb_1.clean.3dg.gz
GM-800U_048_5kb_2.clean.3dg.gz
GM-800U_048_5kb_3.clean.3dg.gz
GM-800U_048_5kb_4.clean.3dg.gz
GM-800U_048_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon34 [34U]


title: cell_212


title: old control 2


title: GM12878, 800U, Cell 47

description:
800U MNase
GM-800U_047.allValidPairs.gz
GM-800U_047.hic
GM-800U_047.mcool
GM-800U_047.clean.smooth.bw
GM-800U_047_20kb_1.3dg.gz
GM-800U_047_20kb_2.3dg.gz
GM-800U_047_20kb_3.3dg.gz
GM-800U_047_20kb_4.3dg.gz
GM-800U_047_20kb_5.3dg.gz
GM-800U_047_10kb_1.3dg.gz
GM-800U_047_10kb_2.3dg.gz
GM-800U_047_10kb_3.3dg.gz
GM-800U_047_10kb_4.3dg.gz
GM-800U_047_10kb_5.3dg.gz
GM-800U_047_5kb_1.3dg.gz
GM-800U_047_5kb_2.3dg.gz
GM-800U_047_5kb_3.3dg.gz
GM-800U_047_5kb_4.3dg.gz
GM-800U_047_5kb_5.3dg.gz
GM-800U_047_20kb_1.clean.3dg.gz
GM-800U_047_20kb_2.clean.3dg.gz
GM-800U_047_20kb_3.clean.3dg.gz
GM-800U_047_20kb_4.clean.3dg.gz
GM-800U_047_20kb_5.clean.3dg.gz
GM-800U_047_10kb_1.clean.3dg.gz
GM-800U_047_10kb_2.clean.3dg.gz
GM-800U_047_10kb_3.clean.3dg.gz
GM-800U_047_10kb_4.clean.3dg.gz
GM-800U_047_10kb_5.clean.3dg.gz
GM-800U_047_5kb_1.clean.3dg.gz
GM-800U_047_5kb_2.clean.3dg.gz
GM-800U_047_5kb_3.clean.3dg.gz
GM-800U_047_5kb_4.clean.3dg.gz
GM-800U_047_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon29 [29U]


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon28 [28U]


title: cell_211


title: acute-treated Gly-Low 4

value: 4 months


title: cell_210


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon27 [27U]


title: GM12878, 800U, Cell 45

description:
800U MNase
GM-800U_045.allValidPairs.gz
GM-800U_045.hic
GM-800U_045.mcool
GM-800U_045.clean.smooth.bw
GM-800U_045_20kb_1.3dg.gz
GM-800U_045_20kb_2.3dg.gz
GM-800U_045_20kb_3.3dg.gz
GM-800U_045_20kb_4.3dg.gz
GM-800U_045_20kb_5.3dg.gz
GM-800U_045_10kb_1.3dg.gz
GM-800U_045_10kb_2.3dg.gz
GM-800U_045_10kb_3.3dg.gz
GM-800U_045_10kb_4.3dg.gz
GM-800U_045_10kb_5.3dg.gz
GM-800U_045_5kb_1.3dg.gz
GM-800U_045_5kb_2.3dg.gz
GM-800U_045_5kb_3.3dg.gz
GM-800U_045_5kb_4.3dg.gz
GM-800U_045_5kb_5.3dg.gz
GM-800U_045_20kb_1.clean.3dg.gz
GM-800U_045_20kb_2.clean.3dg.gz
GM-800U_045_20kb_3.clean.3dg.gz
GM-800U_045_20kb_4.clean.3dg.gz
GM-800U_045_20kb_5.clean.3dg.gz
GM-800U_045_10kb_1.clean.3dg.gz
GM-800U_045_10kb_2.clean.3dg.gz
GM-800U_045_10kb_3.clean.3dg.gz
GM-800U_045_10kb_4.clean.3dg.gz
GM-800U_045_10kb_5.clean.3dg.gz
GM-800U_045_5kb_1.clean.3dg.gz
GM-800U_045_5kb_2.clean.3dg.gz
GM-800U_045_5kb_3.clean.3dg.gz
GM-800U_045_5kb_4.clean.3dg.gz
GM-800U_045_5kb_5.clean.3dg.gz


title: GM12878, 800U, Cell 46

description:
800U MNase
GM-800U_046.allValidPairs.gz
GM-800U_046.hic
GM-800U_046.mcool
GM-800U_046.clean.smooth.bw
GM-800U_046_20kb_1.3dg.gz
GM-800U_046_20kb_2.3dg.gz
GM-800U_046_20kb_3.3dg.gz
GM-800U_046_20kb_4.3dg.gz
GM-800U_046_20kb_5.3dg.gz
GM-800U_046_10kb_1.3dg.gz
GM-800U_046_10kb_2.3dg.gz
GM-800U_046_10kb_3.3dg.gz
GM-800U_046_10kb_4.3dg.gz
GM-800U_046_10kb_5.3dg.gz
GM-800U_046_5kb_1.3dg.gz
GM-800U_046_5kb_2.3dg.gz
GM-800U_046_5kb_3.3dg.gz
GM-800U_046_5kb_4.3dg.gz
GM-800U_046_5kb_5.3dg.gz
GM-800U_046_20kb_1.clean.3dg.gz
GM-800U_046_20kb_2.clean.3dg.gz
GM-800U_046_20kb_3.clean.3dg.gz
GM-800U_046_20kb_4.clean.3dg.gz
GM-800U_046_20kb_5.clean.3dg.gz
GM-800U_046_10kb_1.clean.3dg.gz
GM-800U_046_10kb_2.clean.3dg.gz
GM-800U_046_10kb_3.clean.3dg.gz
GM-800U_046_10kb_4.clean.3dg.gz
GM-800U_046_10kb_5.clean.3dg.gz
GM-800U_046_5kb_1.clean.3dg.gz
GM-800U_046_5kb_2.clean.3dg.gz
GM-800U_046_5kb_3.clean.3dg.gz
GM-800U_046_5kb_4.clean.3dg.gz
GM-800U_046_5kb_5.clean.3dg.gz


title: acute-treated Gly-Low 3


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon26 [26U]


title: cell_209


title: GM12878, 800U, Cell 44

description:
800U MNase
GM-800U_044.allValidPairs.gz
GM-800U_044.hic
GM-800U_044.mcool
GM-800U_044.clean.smooth.bw
GM-800U_044_20kb_1.3dg.gz
GM-800U_044_20kb_2.3dg.gz
GM-800U_044_20kb_3.3dg.gz
GM-800U_044_20kb_4.3dg.gz
GM-800U_044_20kb_5.3dg.gz
GM-800U_044_10kb_1.3dg.gz
GM-800U_044_10kb_2.3dg.gz
GM-800U_044_10kb_3.3dg.gz
GM-800U_044_10kb_4.3dg.gz
GM-800U_044_10kb_5.3dg.gz
GM-800U_044_5kb_1.3dg.gz
GM-800U_044_5kb_2.3dg.gz
GM-800U_044_5kb_3.3dg.gz
GM-800U_044_5kb_4.3dg.gz
GM-800U_044_5kb_5.3dg.gz
GM-800U_044_20kb_1.clean.3dg.gz
GM-800U_044_20kb_2.clean.3dg.gz
GM-800U_044_20kb_3.clean.3dg.gz
GM-800U_044_20kb_4.clean.3dg.gz
GM-800U_044_20kb_5.clean.3dg.gz
GM-800U_044_10kb_1.clean.3dg.gz
GM-800U_044_10kb_2.clean.3dg.gz
GM-800U_044_10kb_3.clean.3dg.gz
GM-800U_044_10kb_4.clean.3dg.gz
GM-800U_044_10kb_5.clean.3dg.gz
GM-800U_044_5kb_1.clean.3dg.gz
GM-800U_044_5kb_2.clean.3dg.gz
GM-800U_044_5kb_3.clean.3dg.gz
GM-800U_044_5kb_4.clean.3dg.gz
GM-800U_044_5kb_5.clean.3dg.gz


title: acute-treated Gly-Low 2


title: GM12878, 800U, Cell 49

description:
800U MNase
GM-800U_049.allValidPairs.gz
GM-800U_049.hic
GM-800U_049.mcool
GM-800U_049.clean.smooth.bw
GM-800U_049_20kb_1.3dg.gz
GM-800U_049_20kb_2.3dg.gz
GM-800U_049_20kb_3.3dg.gz
GM-800U_049_20kb_4.3dg.gz
GM-800U_049_20kb_5.3dg.gz
GM-800U_049_10kb_1.3dg.gz
GM-800U_049_10kb_2.3dg.gz
GM-800U_049_10kb_3.3dg.gz
GM-800U_049_10kb_4.3dg.gz
GM-800U_049_10kb_5.3dg.gz
GM-800U_049_5kb_1.3dg.gz
GM-800U_049_5kb_2.3dg.gz
GM-800U_049_5kb_3.3dg.gz
GM-800U_049_5kb_4.3dg.gz
GM-800U_049_5kb_5.3dg.gz
GM-800U_049_20kb_1.clean.3dg.gz
GM-800U_049_20kb_2.clean.3dg.gz
GM-800U_049_20kb_3.clean.3dg.gz
GM-800U_049_20kb_4.clean.3dg.gz
GM-800U_049_20kb_5.clean.3dg.gz
GM-800U_049_10kb_1.clean.3dg.gz
GM-800U_049_10kb_2.clean.3dg.gz
GM-800U_049_10kb_3.clean.3dg.gz
GM-800U_049_10kb_4.clean.3dg.gz
GM-800U_049_10kb_5.clean.3dg.gz
GM-800U_049_5kb_1.clean.3dg.gz
GM-800U_049_5kb_2.clean.3dg.gz
GM-800U_049_5kb_3.clean.3dg.gz
GM-800U_049_5kb_4.clean.3dg.gz
GM-800U_049_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon25 [25U]


title: cell_208

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: acute-treated Gly-Low 1


title: cell_207


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon30 [30U]


title: acute-treated control 5


title: cell_206


title: old control 1


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon23 [23U]


title: GM12878, 800U, Cell 41

description:
800U MNase
GM-800U_041.allValidPairs.gz
GM-800U_041.hic
GM-800U_041.mcool
GM-800U_041.clean.smooth.bw
GM-800U_041_20kb_1.3dg.gz
GM-800U_041_20kb_2.3dg.gz
GM-800U_041_20kb_4.3dg.gz
GM-800U_041_20kb_5.3dg.gz
GM-800U_041_10kb_1.3dg.gz
GM-800U_041_10kb_2.3dg.gz
GM-800U_041_10kb_4.3dg.gz
GM-800U_041_10kb_5.3dg.gz
GM-800U_041_5kb_1.3dg.gz
GM-800U_041_5kb_2.3dg.gz
GM-800U_041_5kb_4.3dg.gz
GM-800U_041_5kb_5.3dg.gz
GM-800U_041_20kb_1.clean.3dg.gz
GM-800U_041_20kb_2.clean.3dg.gz
GM-800U_041_20kb_4.clean.3dg.gz
GM-800U_041_20kb_5.clean.3dg.gz
GM-800U_041_10kb_1.clean.3dg.gz
GM-800U_041_10kb_2.clean.3dg.gz
GM-800U_041_10kb_4.clean.3dg.gz
GM-800U_041_10kb_5.clean.3dg.gz
GM-800U_041_5kb_1.clean.3dg.gz
GM-800U_041_5kb_2.clean.3dg.gz
GM-800U_041_5kb_4.clean.3dg.gz
GM-800U_041_5kb_5.clean.3dg.gz


title: acute-treated control 4


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon22 [22U]


title: cell_205


title: cell_204


title: acute-treated control 3


title: GM12878, 800U, Cell 40

description:
800U MNase
GM-800U_040.allValidPairs.gz
GM-800U_040.hic
GM-800U_040.mcool
GM-800U_040.clean.smooth.bw
GM-800U_040_20kb_1.3dg.gz
GM-800U_040_20kb_2.3dg.gz
GM-800U_040_20kb_4.3dg.gz
GM-800U_040_20kb_5.3dg.gz
GM-800U_040_10kb_1.3dg.gz
GM-800U_040_10kb_2.3dg.gz
GM-800U_040_10kb_4.3dg.gz
GM-800U_040_10kb_5.3dg.gz
GM-800U_040_5kb_1.3dg.gz
GM-800U_040_5kb_2.3dg.gz
GM-800U_040_5kb_4.3dg.gz
GM-800U_040_5kb_5.3dg.gz
GM-800U_040_20kb_1.clean.3dg.gz
GM-800U_040_20kb_2.clean.3dg.gz
GM-800U_040_20kb_4.clean.3dg.gz
GM-800U_040_20kb_5.clean.3dg.gz
GM-800U_040_10kb_1.clean.3dg.gz
GM-800U_040_10kb_2.clean.3dg.gz
GM-800U_040_10kb_4.clean.3dg.gz
GM-800U_040_10kb_5.clean.3dg.gz
GM-800U_040_5kb_1.clean.3dg.gz
GM-800U_040_5kb_2.clean.3dg.gz
GM-800U_040_5kb_4.clean.3dg.gz
GM-800U_040_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon21 [21U]


title: GM12878, 800U, Cell 39

description:
800U MNase
GM-800U_039.allValidPairs.gz
GM-800U_039.hic
GM-800U_039.mcool
GM-800U_039.clean.smooth.bw
GM-800U_039_20kb_1.3dg.gz
GM-800U_039_20kb_2.3dg.gz
GM-800U_039_20kb_3.3dg.gz
GM-800U_039_20kb_5.3dg.gz
GM-800U_039_10kb_1.3dg.gz
GM-800U_039_10kb_2.3dg.gz
GM-800U_039_10kb_3.3dg.gz
GM-800U_039_10kb_5.3dg.gz
GM-800U_039_5kb_1.3dg.gz
GM-800U_039_5kb_2.3dg.gz
GM-800U_039_5kb_3.3dg.gz
GM-800U_039_5kb_5.3dg.gz
GM-800U_039_20kb_1.clean.3dg.gz
GM-800U_039_20kb_2.clean.3dg.gz
GM-800U_039_20kb_3.clean.3dg.gz
GM-800U_039_20kb_5.clean.3dg.gz
GM-800U_039_10kb_1.clean.3dg.gz
GM-800U_039_10kb_2.clean.3dg.gz
GM-800U_039_10kb_3.clean.3dg.gz
GM-800U_039_10kb_5.clean.3dg.gz
GM-800U_039_5kb_1.clean.3dg.gz
GM-800U_039_5kb_2.clean.3dg.gz
GM-800U_039_5kb_3.clean.3dg.gz
GM-800U_039_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon20 [20H]

value: Hospital


title: acute-treated control 2


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon19 [19H]


title: GM12878, 800U, Cell 43

description:
800U MNase
GM-800U_043.allValidPairs.gz
GM-800U_043.hic
GM-800U_043.mcool
GM-800U_043.clean.smooth.bw
GM-800U_043_20kb_1.3dg.gz
GM-800U_043_20kb_2.3dg.gz
GM-800U_043_20kb_3.3dg.gz
GM-800U_043_20kb_4.3dg.gz
GM-800U_043_20kb_5.3dg.gz
GM-800U_043_10kb_1.3dg.gz
GM-800U_043_10kb_2.3dg.gz
GM-800U_043_10kb_3.3dg.gz
GM-800U_043_10kb_4.3dg.gz
GM-800U_043_10kb_5.3dg.gz
GM-800U_043_5kb_1.3dg.gz
GM-800U_043_5kb_2.3dg.gz
GM-800U_043_5kb_3.3dg.gz
GM-800U_043_5kb_4.3dg.gz
GM-800U_043_5kb_5.3dg.gz
GM-800U_043_20kb_1.clean.3dg.gz
GM-800U_043_20kb_2.clean.3dg.gz
GM-800U_043_20kb_3.clean.3dg.gz
GM-800U_043_20kb_4.clean.3dg.gz
GM-800U_043_20kb_5.clean.3dg.gz
GM-800U_043_10kb_1.clean.3dg.gz
GM-800U_043_10kb_2.clean.3dg.gz
GM-800U_043_10kb_3.clean.3dg.gz
GM-800U_043_10kb_4.clean.3dg.gz
GM-800U_043_10kb_5.clean.3dg.gz
GM-800U_043_5kb_1.clean.3dg.gz
GM-800U_043_5kb_2.clean.3dg.gz
GM-800U_043_5kb_3.clean.3dg.gz
GM-800U_043_5kb_4.clean.3dg.gz
GM-800U_043_5kb_5.clean.3dg.gz


title: acute-treated control 1


title: cell_203


title: WT,Ly49HposNK,D1,Spleen,4,12637

city: New York

first: Endi

middle: K

last: Santosa

state: New York

address: 417 E 68th St

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
BCL files were converted to fastq using bcl2fastq (v2.20.0.422).
paired-end reads were trimmed for adaptors and subjected to removal of low-quality reads using Trimmomatic (v0.36)
Transcript quantification was based on the mm10 UCSC Known Gene models and performed using the quasi-mapping-based mode of Salmon (v0.13.1) correcting for potential GC bias
Transcripts were summarized to gene level using tximport (v1.10.1) and differential analyses were executed with DESeq2 (v1.34.0) using the UCSC Known Gene models as reference annotations.
Assembly: mm10
Supplementary files format and content: Raw counts in txt format

source_name: Spleen

extract_protocol:
Ly49H+ NK cells (Ly49H+ CD49b+ TCRb- CD3- CD19- F480-) were sorted from the spleen and livers of wildtype mice that were uninfected or 24 hours p.i with MCMV. In each independent experiment, RNA was isolated from sorted cells using the Arcturus PicoPure RNA Isolation Kit (ThermoFisher) in accordance with the manufacturer instructions.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 0.7-2 ng total RNA with RNA integrity numbers ranging from 9.2 to 10 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech catalog # 63488), with 12 cycles of amplification. Subsequently, 9-10 ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) using 8 cycles of PCR. Samples were barcoded and run on a NovaSeq 6000 in a PE100 run, using the NovaSeq 6000 S1 or S4 Reagent Kit (100 or 200 cycles) (Illumina).

treatment_protocol: In vivo MCMV infection

value: Spleen

tag: replicate

tag: time point

value: D1 post MCMV infection

tag: projectnumber


title: cell_201

value: blood


title: cell_202

value: lymphoblastoid


title: GM12878, 800U, Cell 37

description:
800U MNase
GM-800U_037.allValidPairs.gz
GM-800U_037.hic
GM-800U_037.mcool
GM-800U_037.clean.smooth.bw
GM-800U_037_20kb_1.3dg.gz
GM-800U_037_20kb_2.3dg.gz
GM-800U_037_20kb_3.3dg.gz
GM-800U_037_20kb_4.3dg.gz
GM-800U_037_20kb_5.3dg.gz
GM-800U_037_10kb_1.3dg.gz
GM-800U_037_10kb_2.3dg.gz
GM-800U_037_10kb_3.3dg.gz
GM-800U_037_10kb_4.3dg.gz
GM-800U_037_10kb_5.3dg.gz
GM-800U_037_5kb_1.3dg.gz
GM-800U_037_5kb_2.3dg.gz
GM-800U_037_5kb_3.3dg.gz
GM-800U_037_5kb_4.3dg.gz
GM-800U_037_5kb_5.3dg.gz
GM-800U_037_20kb_1.clean.3dg.gz
GM-800U_037_20kb_2.clean.3dg.gz
GM-800U_037_20kb_3.clean.3dg.gz
GM-800U_037_20kb_4.clean.3dg.gz
GM-800U_037_20kb_5.clean.3dg.gz
GM-800U_037_10kb_1.clean.3dg.gz
GM-800U_037_10kb_2.clean.3dg.gz
GM-800U_037_10kb_3.clean.3dg.gz
GM-800U_037_10kb_4.clean.3dg.gz
GM-800U_037_10kb_5.clean.3dg.gz
GM-800U_037_5kb_1.clean.3dg.gz
GM-800U_037_5kb_2.clean.3dg.gz
GM-800U_037_5kb_3.clean.3dg.gz
GM-800U_037_5kb_4.clean.3dg.gz
GM-800U_037_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon24 [24U]

value: soil sample


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon18 [18H]


title: cell_200


title: GM12878, 800U, Cell 36

description:
800U MNase
GM-800U_036.allValidPairs.gz
GM-800U_036.hic
GM-800U_036.mcool
GM-800U_036.clean.smooth.bw
GM-800U_036_20kb_1.3dg.gz
GM-800U_036_20kb_2.3dg.gz
GM-800U_036_20kb_3.3dg.gz
GM-800U_036_20kb_4.3dg.gz
GM-800U_036_20kb_5.3dg.gz
GM-800U_036_10kb_1.3dg.gz
GM-800U_036_10kb_2.3dg.gz
GM-800U_036_10kb_3.3dg.gz
GM-800U_036_10kb_4.3dg.gz
GM-800U_036_10kb_5.3dg.gz
GM-800U_036_5kb_1.3dg.gz
GM-800U_036_5kb_2.3dg.gz
GM-800U_036_5kb_3.3dg.gz
GM-800U_036_5kb_4.3dg.gz
GM-800U_036_5kb_5.3dg.gz
GM-800U_036_20kb_1.clean.3dg.gz
GM-800U_036_20kb_2.clean.3dg.gz
GM-800U_036_20kb_3.clean.3dg.gz
GM-800U_036_20kb_4.clean.3dg.gz
GM-800U_036_20kb_5.clean.3dg.gz
GM-800U_036_10kb_1.clean.3dg.gz
GM-800U_036_10kb_2.clean.3dg.gz
GM-800U_036_10kb_3.clean.3dg.gz
GM-800U_036_10kb_4.clean.3dg.gz
GM-800U_036_10kb_5.clean.3dg.gz
GM-800U_036_5kb_1.clean.3dg.gz
GM-800U_036_5kb_2.clean.3dg.gz
GM-800U_036_5kb_3.clean.3dg.gz
GM-800U_036_5kb_4.clean.3dg.gz
GM-800U_036_5kb_5.clean.3dg.gz


title: GM12878, 800U, Cell 42

description:
800U MNase
GM-800U_042.allValidPairs.gz
GM-800U_042.hic
GM-800U_042.mcool
GM-800U_042.clean.smooth.bw
GM-800U_042_20kb_1.3dg.gz
GM-800U_042_20kb_2.3dg.gz
GM-800U_042_20kb_3.3dg.gz
GM-800U_042_20kb_4.3dg.gz
GM-800U_042_20kb_5.3dg.gz
GM-800U_042_10kb_1.3dg.gz
GM-800U_042_10kb_2.3dg.gz
GM-800U_042_10kb_3.3dg.gz
GM-800U_042_10kb_4.3dg.gz
GM-800U_042_10kb_5.3dg.gz
GM-800U_042_5kb_1.3dg.gz
GM-800U_042_5kb_2.3dg.gz
GM-800U_042_5kb_3.3dg.gz
GM-800U_042_5kb_4.3dg.gz
GM-800U_042_5kb_5.3dg.gz
GM-800U_042_20kb_1.clean.3dg.gz
GM-800U_042_20kb_2.clean.3dg.gz
GM-800U_042_20kb_3.clean.3dg.gz
GM-800U_042_20kb_4.clean.3dg.gz
GM-800U_042_20kb_5.clean.3dg.gz
GM-800U_042_10kb_1.clean.3dg.gz
GM-800U_042_10kb_2.clean.3dg.gz
GM-800U_042_10kb_3.clean.3dg.gz
GM-800U_042_10kb_4.clean.3dg.gz
GM-800U_042_10kb_5.clean.3dg.gz
GM-800U_042_5kb_1.clean.3dg.gz
GM-800U_042_5kb_2.clean.3dg.gz
GM-800U_042_5kb_3.clean.3dg.gz
GM-800U_042_5kb_4.clean.3dg.gz
GM-800U_042_5kb_5.clean.3dg.gz


title: WT,Ly49HposNK,D1,Spleen,3,12637


title: GM12878, 800U, Cell 35

description:
800U MNase
GM-800U_035.allValidPairs.gz
GM-800U_035.hic
GM-800U_035.mcool
GM-800U_035.clean.smooth.bw
GM-800U_035_20kb_1.3dg.gz
GM-800U_035_20kb_2.3dg.gz
GM-800U_035_20kb_3.3dg.gz
GM-800U_035_20kb_4.3dg.gz
GM-800U_035_20kb_5.3dg.gz
GM-800U_035_10kb_1.3dg.gz
GM-800U_035_10kb_2.3dg.gz
GM-800U_035_10kb_3.3dg.gz
GM-800U_035_10kb_4.3dg.gz
GM-800U_035_10kb_5.3dg.gz
GM-800U_035_5kb_1.3dg.gz
GM-800U_035_5kb_2.3dg.gz
GM-800U_035_5kb_3.3dg.gz
GM-800U_035_5kb_4.3dg.gz
GM-800U_035_5kb_5.3dg.gz
GM-800U_035_20kb_1.clean.3dg.gz
GM-800U_035_20kb_2.clean.3dg.gz
GM-800U_035_20kb_3.clean.3dg.gz
GM-800U_035_20kb_4.clean.3dg.gz
GM-800U_035_20kb_5.clean.3dg.gz
GM-800U_035_10kb_1.clean.3dg.gz
GM-800U_035_10kb_2.clean.3dg.gz
GM-800U_035_10kb_3.clean.3dg.gz
GM-800U_035_10kb_4.clean.3dg.gz
GM-800U_035_10kb_5.clean.3dg.gz
GM-800U_035_5kb_1.clean.3dg.gz
GM-800U_035_5kb_2.clean.3dg.gz
GM-800U_035_5kb_3.clean.3dg.gz
GM-800U_035_5kb_4.clean.3dg.gz
GM-800U_035_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon17 [17H]


title: WT,Ly49HposNK,D1,Spleen,2,12637


title: GM12878, 800U, Cell 34

description:
800U MNase
GM-800U_034.allValidPairs.gz
GM-800U_034.hic
GM-800U_034.mcool
GM-800U_034.clean.smooth.bw
GM-800U_034_20kb_2.3dg.gz
GM-800U_034_20kb_3.3dg.gz
GM-800U_034_20kb_4.3dg.gz
GM-800U_034_20kb_5.3dg.gz
GM-800U_034_10kb_2.3dg.gz
GM-800U_034_10kb_3.3dg.gz
GM-800U_034_10kb_4.3dg.gz
GM-800U_034_10kb_5.3dg.gz
GM-800U_034_5kb_2.3dg.gz
GM-800U_034_5kb_3.3dg.gz
GM-800U_034_5kb_4.3dg.gz
GM-800U_034_5kb_5.3dg.gz
GM-800U_034_20kb_2.clean.3dg.gz
GM-800U_034_20kb_3.clean.3dg.gz
GM-800U_034_20kb_4.clean.3dg.gz
GM-800U_034_20kb_5.clean.3dg.gz
GM-800U_034_10kb_2.clean.3dg.gz
GM-800U_034_10kb_3.clean.3dg.gz
GM-800U_034_10kb_4.clean.3dg.gz
GM-800U_034_10kb_5.clean.3dg.gz
GM-800U_034_5kb_2.clean.3dg.gz
GM-800U_034_5kb_3.clean.3dg.gz
GM-800U_034_5kb_4.clean.3dg.gz
GM-800U_034_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon16 [26H]


title: cell_199


title: cell_198


title: WT,Ly49HposNK,D0,Spleen,3,12637

value: D0 post MCMV infection


title: GM12878, 800U, Cell 38

description:
800U MNase
GM-800U_038.allValidPairs.gz
GM-800U_038.hic
GM-800U_038.mcool
GM-800U_038.clean.smooth.bw
GM-800U_038_20kb_1.3dg.gz
GM-800U_038_20kb_4.3dg.gz
GM-800U_038_20kb_5.3dg.gz
GM-800U_038_10kb_1.3dg.gz
GM-800U_038_10kb_4.3dg.gz
GM-800U_038_10kb_5.3dg.gz
GM-800U_038_5kb_1.3dg.gz
GM-800U_038_5kb_4.3dg.gz
GM-800U_038_5kb_5.3dg.gz
GM-800U_038_20kb_1.clean.3dg.gz
GM-800U_038_20kb_4.clean.3dg.gz
GM-800U_038_20kb_5.clean.3dg.gz
GM-800U_038_10kb_1.clean.3dg.gz
GM-800U_038_10kb_4.clean.3dg.gz
GM-800U_038_10kb_5.clean.3dg.gz
GM-800U_038_5kb_1.clean.3dg.gz
GM-800U_038_5kb_4.clean.3dg.gz
GM-800U_038_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon15 [15H]


title: WT,Ly49HposNK,D0,Spleen,2,12637


title: GM12878, 800U, Cell 33

description:
800U MNase
GM-800U_033.allValidPairs.gz
GM-800U_033.hic
GM-800U_033.mcool
GM-800U_033.clean.smooth.bw
GM-800U_033_20kb_1.3dg.gz
GM-800U_033_20kb_2.3dg.gz
GM-800U_033_20kb_3.3dg.gz
GM-800U_033_20kb_4.3dg.gz
GM-800U_033_20kb_5.3dg.gz
GM-800U_033_10kb_1.3dg.gz
GM-800U_033_10kb_2.3dg.gz
GM-800U_033_10kb_3.3dg.gz
GM-800U_033_10kb_4.3dg.gz
GM-800U_033_10kb_5.3dg.gz
GM-800U_033_5kb_1.3dg.gz
GM-800U_033_5kb_2.3dg.gz
GM-800U_033_5kb_3.3dg.gz
GM-800U_033_5kb_4.3dg.gz
GM-800U_033_5kb_5.3dg.gz
GM-800U_033_20kb_1.clean.3dg.gz
GM-800U_033_20kb_2.clean.3dg.gz
GM-800U_033_20kb_3.clean.3dg.gz
GM-800U_033_20kb_4.clean.3dg.gz
GM-800U_033_20kb_5.clean.3dg.gz
GM-800U_033_10kb_1.clean.3dg.gz
GM-800U_033_10kb_2.clean.3dg.gz
GM-800U_033_10kb_3.clean.3dg.gz
GM-800U_033_10kb_4.clean.3dg.gz
GM-800U_033_10kb_5.clean.3dg.gz
GM-800U_033_5kb_1.clean.3dg.gz
GM-800U_033_5kb_2.clean.3dg.gz
GM-800U_033_5kb_3.clean.3dg.gz
GM-800U_033_5kb_4.clean.3dg.gz
GM-800U_033_5kb_5.clean.3dg.gz


title: cell_197


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon14 [14H]


title: WT,Ly49HposNK,D0,Spleen,1,12637


title: cell_196


title: GM12878, 800U, Cell 32

description:
800U MNase
GM-800U_032.allValidPairs.gz
GM-800U_032.hic
GM-800U_032.mcool
GM-800U_032.clean.smooth.bw
GM-800U_032_20kb_1.3dg.gz
GM-800U_032_20kb_2.3dg.gz
GM-800U_032_20kb_3.3dg.gz
GM-800U_032_20kb_4.3dg.gz
GM-800U_032_20kb_5.3dg.gz
GM-800U_032_10kb_1.3dg.gz
GM-800U_032_10kb_2.3dg.gz
GM-800U_032_10kb_3.3dg.gz
GM-800U_032_10kb_4.3dg.gz
GM-800U_032_10kb_5.3dg.gz
GM-800U_032_5kb_1.3dg.gz
GM-800U_032_5kb_2.3dg.gz
GM-800U_032_5kb_3.3dg.gz
GM-800U_032_5kb_4.3dg.gz
GM-800U_032_5kb_5.3dg.gz
GM-800U_032_20kb_1.clean.3dg.gz
GM-800U_032_20kb_2.clean.3dg.gz
GM-800U_032_20kb_3.clean.3dg.gz
GM-800U_032_20kb_4.clean.3dg.gz
GM-800U_032_20kb_5.clean.3dg.gz
GM-800U_032_10kb_1.clean.3dg.gz
GM-800U_032_10kb_2.clean.3dg.gz
GM-800U_032_10kb_3.clean.3dg.gz
GM-800U_032_10kb_4.clean.3dg.gz
GM-800U_032_10kb_5.clean.3dg.gz
GM-800U_032_5kb_1.clean.3dg.gz
GM-800U_032_5kb_2.clean.3dg.gz
GM-800U_032_5kb_3.clean.3dg.gz
GM-800U_032_5kb_4.clean.3dg.gz
GM-800U_032_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon12 [12H]


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon13 [13H]


title: cell_194


title: cell_195


title: WT,Ly49HposNK,D1,Liver,3,12637

source_name: Liver

value: Liver


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon11 [11H]


title: GM12878, 800U, Cell 30

description:
800U MNase
GM-800U_030.allValidPairs.gz
GM-800U_030.hic
GM-800U_030.mcool
GM-800U_030.clean.smooth.bw
GM-800U_030_20kb_1.3dg.gz
GM-800U_030_20kb_2.3dg.gz
GM-800U_030_20kb_3.3dg.gz
GM-800U_030_20kb_4.3dg.gz
GM-800U_030_20kb_5.3dg.gz
GM-800U_030_10kb_1.3dg.gz
GM-800U_030_10kb_2.3dg.gz
GM-800U_030_10kb_3.3dg.gz
GM-800U_030_10kb_4.3dg.gz
GM-800U_030_10kb_5.3dg.gz
GM-800U_030_5kb_1.3dg.gz
GM-800U_030_5kb_2.3dg.gz
GM-800U_030_5kb_3.3dg.gz
GM-800U_030_5kb_4.3dg.gz
GM-800U_030_5kb_5.3dg.gz
GM-800U_030_20kb_1.clean.3dg.gz
GM-800U_030_20kb_2.clean.3dg.gz
GM-800U_030_20kb_3.clean.3dg.gz
GM-800U_030_20kb_4.clean.3dg.gz
GM-800U_030_20kb_5.clean.3dg.gz
GM-800U_030_10kb_1.clean.3dg.gz
GM-800U_030_10kb_2.clean.3dg.gz
GM-800U_030_10kb_3.clean.3dg.gz
GM-800U_030_10kb_4.clean.3dg.gz
GM-800U_030_10kb_5.clean.3dg.gz
GM-800U_030_5kb_1.clean.3dg.gz
GM-800U_030_5kb_2.clean.3dg.gz
GM-800U_030_5kb_3.clean.3dg.gz
GM-800U_030_5kb_4.clean.3dg.gz
GM-800U_030_5kb_5.clean.3dg.gz


title: WT,Ly49HposNK,D1,Liver,2,12637


title: GM12878, 800U, Cell 29

description:
800U MNase
GM-800U_029.allValidPairs.gz
GM-800U_029.hic
GM-800U_029.mcool
GM-800U_029.clean.smooth.bw
GM-800U_029_20kb_1.3dg.gz
GM-800U_029_20kb_2.3dg.gz
GM-800U_029_20kb_3.3dg.gz
GM-800U_029_20kb_4.3dg.gz
GM-800U_029_20kb_5.3dg.gz
GM-800U_029_10kb_1.3dg.gz
GM-800U_029_10kb_2.3dg.gz
GM-800U_029_10kb_3.3dg.gz
GM-800U_029_10kb_4.3dg.gz
GM-800U_029_10kb_5.3dg.gz
GM-800U_029_5kb_1.3dg.gz
GM-800U_029_5kb_2.3dg.gz
GM-800U_029_5kb_3.3dg.gz
GM-800U_029_5kb_4.3dg.gz
GM-800U_029_5kb_5.3dg.gz
GM-800U_029_20kb_1.clean.3dg.gz
GM-800U_029_20kb_2.clean.3dg.gz
GM-800U_029_20kb_3.clean.3dg.gz
GM-800U_029_20kb_4.clean.3dg.gz
GM-800U_029_20kb_5.clean.3dg.gz
GM-800U_029_10kb_1.clean.3dg.gz
GM-800U_029_10kb_2.clean.3dg.gz
GM-800U_029_10kb_3.clean.3dg.gz
GM-800U_029_10kb_4.clean.3dg.gz
GM-800U_029_10kb_5.clean.3dg.gz
GM-800U_029_5kb_1.clean.3dg.gz
GM-800U_029_5kb_2.clean.3dg.gz
GM-800U_029_5kb_3.clean.3dg.gz
GM-800U_029_5kb_4.clean.3dg.gz
GM-800U_029_5kb_5.clean.3dg.gz


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon10 [10H]


title: cell_193


title: GM12878, 800U, Cell 28

description:
800U MNase
GM-800U_028.allValidPairs.gz
GM-800U_028.hic
GM-800U_028.mcool
GM-800U_028.clean.smooth.bw
GM-800U_028_20kb_1.3dg.gz
GM-800U_028_20kb_2.3dg.gz
GM-800U_028_20kb_3.3dg.gz
GM-800U_028_20kb_4.3dg.gz
GM-800U_028_20kb_5.3dg.gz
GM-800U_028_10kb_1.3dg.gz
GM-800U_028_10kb_2.3dg.gz
GM-800U_028_10kb_3.3dg.gz
GM-800U_028_10kb_4.3dg.gz
GM-800U_028_10kb_5.3dg.gz
GM-800U_028_5kb_1.3dg.gz
GM-800U_028_5kb_2.3dg.gz
GM-800U_028_5kb_3.3dg.gz
GM-800U_028_5kb_4.3dg.gz
GM-800U_028_5kb_5.3dg.gz
GM-800U_028_20kb_1.clean.3dg.gz
GM-800U_028_20kb_2.clean.3dg.gz
GM-800U_028_20kb_3.clean.3dg.gz
GM-800U_028_20kb_4.clean.3dg.gz
GM-800U_028_20kb_5.clean.3dg.gz
GM-800U_028_10kb_1.clean.3dg.gz
GM-800U_028_10kb_2.clean.3dg.gz
GM-800U_028_10kb_3.clean.3dg.gz
GM-800U_028_10kb_4.clean.3dg.gz
GM-800U_028_10kb_5.clean.3dg.gz
GM-800U_028_5kb_1.clean.3dg.gz
GM-800U_028_5kb_2.clean.3dg.gz
GM-800U_028_5kb_3.clean.3dg.gz
GM-800U_028_5kb_4.clean.3dg.gz
GM-800U_028_5kb_5.clean.3dg.gz


title: GM12878, 800U, Cell 27

description:
800U MNase
GM-800U_027.allValidPairs.gz
GM-800U_027.hic
GM-800U_027.mcool
GM-800U_027.clean.smooth.bw
GM-800U_027_20kb_1.3dg.gz
GM-800U_027_20kb_2.3dg.gz
GM-800U_027_20kb_3.3dg.gz
GM-800U_027_20kb_4.3dg.gz
GM-800U_027_20kb_5.3dg.gz
GM-800U_027_10kb_1.3dg.gz
GM-800U_027_10kb_2.3dg.gz
GM-800U_027_10kb_3.3dg.gz
GM-800U_027_10kb_4.3dg.gz
GM-800U_027_10kb_5.3dg.gz
GM-800U_027_5kb_1.3dg.gz
GM-800U_027_5kb_2.3dg.gz
GM-800U_027_5kb_3.3dg.gz
GM-800U_027_5kb_4.3dg.gz
GM-800U_027_5kb_5.3dg.gz
GM-800U_027_20kb_1.clean.3dg.gz
GM-800U_027_20kb_2.clean.3dg.gz
GM-800U_027_20kb_3.clean.3dg.gz
GM-800U_027_20kb_4.clean.3dg.gz
GM-800U_027_20kb_5.clean.3dg.gz
GM-800U_027_10kb_1.clean.3dg.gz
GM-800U_027_10kb_2.clean.3dg.gz
GM-800U_027_10kb_3.clean.3dg.gz
GM-800U_027_10kb_4.clean.3dg.gz
GM-800U_027_10kb_5.clean.3dg.gz
GM-800U_027_5kb_1.clean.3dg.gz
GM-800U_027_5kb_2.clean.3dg.gz
GM-800U_027_5kb_3.clean.3dg.gz
GM-800U_027_5kb_4.clean.3dg.gz
GM-800U_027_5kb_5.clean.3dg.gz


title: WT,Ly49HposNK,D0,Liver,3,12637


title: WT,Ly49HposNK,D0,Liver,2,12637


title: cell_191

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_Monsoon8 [8H]


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon9 [9H]


title: GM12878, 800U, Cell 26

description:
800U MNase
GM-800U_026.allValidPairs.gz
GM-800U_026.hic
GM-800U_026.mcool
GM-800U_026.clean.smooth.bw
GM-800U_026_20kb_1.3dg.gz
GM-800U_026_20kb_2.3dg.gz
GM-800U_026_20kb_3.3dg.gz
GM-800U_026_20kb_4.3dg.gz
GM-800U_026_20kb_5.3dg.gz
GM-800U_026_10kb_1.3dg.gz
GM-800U_026_10kb_2.3dg.gz
GM-800U_026_10kb_3.3dg.gz
GM-800U_026_10kb_4.3dg.gz
GM-800U_026_10kb_5.3dg.gz
GM-800U_026_5kb_1.3dg.gz
GM-800U_026_5kb_2.3dg.gz
GM-800U_026_5kb_3.3dg.gz
GM-800U_026_5kb_4.3dg.gz
GM-800U_026_5kb_5.3dg.gz
GM-800U_026_20kb_1.clean.3dg.gz
GM-800U_026_20kb_2.clean.3dg.gz
GM-800U_026_20kb_3.clean.3dg.gz
GM-800U_026_20kb_4.clean.3dg.gz
GM-800U_026_20kb_5.clean.3dg.gz
GM-800U_026_10kb_1.clean.3dg.gz
GM-800U_026_10kb_2.clean.3dg.gz
GM-800U_026_10kb_3.clean.3dg.gz
GM-800U_026_10kb_4.clean.3dg.gz
GM-800U_026_10kb_5.clean.3dg.gz
GM-800U_026_5kb_1.clean.3dg.gz
GM-800U_026_5kb_2.clean.3dg.gz
GM-800U_026_5kb_3.clean.3dg.gz
GM-800U_026_5kb_4.clean.3dg.gz
GM-800U_026_5kb_5.clean.3dg.gz


title: WT,Ly49HposNK,D0,Liver,1,12637


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon7 [7H]


title: WT,Ly49HposNK,D1,Liver,4,12637


title: GM12878, 800U, Cell 31

description:
800U MNase
GM-800U_031.allValidPairs.gz
GM-800U_031.hic
GM-800U_031.mcool
GM-800U_031.clean.smooth.bw
GM-800U_031_20kb_1.3dg.gz
GM-800U_031_20kb_3.3dg.gz
GM-800U_031_20kb_4.3dg.gz
GM-800U_031_10kb_1.3dg.gz
GM-800U_031_10kb_3.3dg.gz
GM-800U_031_10kb_4.3dg.gz
GM-800U_031_5kb_1.3dg.gz
GM-800U_031_5kb_3.3dg.gz
GM-800U_031_5kb_4.3dg.gz
GM-800U_031_20kb_1.clean.3dg.gz
GM-800U_031_20kb_3.clean.3dg.gz
GM-800U_031_20kb_4.clean.3dg.gz
GM-800U_031_10kb_1.clean.3dg.gz
GM-800U_031_10kb_3.clean.3dg.gz
GM-800U_031_10kb_4.clean.3dg.gz
GM-800U_031_5kb_1.clean.3dg.gz
GM-800U_031_5kb_3.clean.3dg.gz
GM-800U_031_5kb_4.clean.3dg.gz


title: GM12878, 800U, Cell 25

description:
800U MNase
GM-800U_025.allValidPairs.gz
GM-800U_025.hic
GM-800U_025.mcool
GM-800U_025.clean.smooth.bw
GM-800U_025_20kb_1.3dg.gz
GM-800U_025_20kb_2.3dg.gz
GM-800U_025_20kb_3.3dg.gz
GM-800U_025_20kb_4.3dg.gz
GM-800U_025_20kb_5.3dg.gz
GM-800U_025_10kb_1.3dg.gz
GM-800U_025_10kb_2.3dg.gz
GM-800U_025_10kb_3.3dg.gz
GM-800U_025_10kb_4.3dg.gz
GM-800U_025_10kb_5.3dg.gz
GM-800U_025_5kb_1.3dg.gz
GM-800U_025_5kb_2.3dg.gz
GM-800U_025_5kb_3.3dg.gz
GM-800U_025_5kb_4.3dg.gz
GM-800U_025_5kb_5.3dg.gz
GM-800U_025_20kb_1.clean.3dg.gz
GM-800U_025_20kb_2.clean.3dg.gz
GM-800U_025_20kb_3.clean.3dg.gz
GM-800U_025_20kb_4.clean.3dg.gz
GM-800U_025_20kb_5.clean.3dg.gz
GM-800U_025_10kb_1.clean.3dg.gz
GM-800U_025_10kb_2.clean.3dg.gz
GM-800U_025_10kb_3.clean.3dg.gz
GM-800U_025_10kb_4.clean.3dg.gz
GM-800U_025_10kb_5.clean.3dg.gz
GM-800U_025_5kb_1.clean.3dg.gz
GM-800U_025_5kb_2.clean.3dg.gz
GM-800U_025_5kb_3.clean.3dg.gz
GM-800U_025_5kb_4.clean.3dg.gz
GM-800U_025_5kb_5.clean.3dg.gz


title: cell_189


title: WT,pDC,d2,Spleen,7,12080

extract_protocol:
cDC1s (Lineage- XCR1+ CD11c+), red-pulp macrophages (Lineage- F4/80+ CD64+), and pDCs (Lineage- F4/80- B220+ BST2+ Ly6C+) were sorted from the spleens of uninfected wildtype mice, or those that were d1 or d2 p.i with MCMV. where Lineage refers to CD3, TCRb, CD19, NK1.1, Ly6G. In each independent experiment, RNA was isolated from sorted cells using the Arcturus PicoPure RNA Isolation Kit (ThermoFisher) in accordance with the manufacturer instructions.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 0.7-2 ng total RNA with RNA integrity numbers ranging from 9.2 to 10 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech catalog # 63488), with 12 cycles of amplification. Subsequently, 9-10 ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) using 8 cycles of PCR. Samples were barcoded and run on a PE100 run, using the NovaSeq 6000 S1 or S4 Reagent Kit (100 or 200 cycles) (Illumina).

value: pDC

value: d2 post MCMV infection


title: Soil Community DNA Seqeunces from Southern Indian Hospital and University_Monsoon6 [6H]