title: RDS_G164_SVF_2

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

institute: Queen Mary University of London

data_processing:
RNA-Seq reads were mapped to the human genome (hg19, Genome Reference Consortium GRCh37)  using BWA mem (version 0.7.15-r1140) as part of the Oxford Genomics Centre pipeline.
Number of reads aligned to the exonic region of each gene were counted using htseq-count based on the Ensembl annotation.
Genes that achieved at least one read count per million reads (CPM) in at least 25% of the samples were kept. Conditional quantile normalisation (cqn) was performed counting for gene length and GC content and the log2 RPKM expression matrix was generated
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include log2 RPKM values for each Sample

source_name: G164 plus fibroblasts co-culture

growth_protocol: DMEM/F12 (Gibco, UK)

extract_protocol:
RNA was prepared from cell cultures using the RNeasy Mini Kit and the RNase free DNase set (Qiagen)
Extracted RNA samples were sent to the Oxford Genomics Centre for processing. Library preps were made using RNA-Seq Ribozero kits (Illumina, Inc)

treatment_protocol: SB431542 and GANT61 (Sigma-Aldrich, UK)

tag: cell types

value: G164 plus fibroblasts

tag: culture type

value: co-culture

tag: growth

value: Malignant cell and fibroblast co-cultured in COL1-gels for 21 days

value: Untreated


title: YMB9245 ChIP rep1

status: Public on Feb 21 2020

type: SRA

city: Worcester

first: Richard

middle: E

last: Baker

state: MA

address: 55 Lake Avenue North

department: Microbiology & Physiological Systems

country: USA

institute: University of Massachusetts Medical School

library_source: genomic

data_processing:
Basecalls performed using Illumina RTA v2.4.11
ChIP-seq reads were aligned to the sacCer3 genome assembly using Bowtie version 1.0.0 with the following parameters: -n2 -3 40 -m3 --best --strata
Peaks were called using MACS version 2.1.1.20160226 in paired-end mode with the following settings:  -g 1.21e7 --keep-dup auto -B --SPMR
Regions in common between the replicate peak calls were identified using the merge function of bedtools v2.25.0.
Genome_build: sacCer3
Supplementary_files_format_and_content: narrowPeak files were generated during peak calling; scores are -10*log10qvalue
Supplementary_files_format_and_content: Averaged enrichment of the merged replicate peaks was calculated during the bedtools merge and reported in column 5 of the bed files.

molecule: genomic DNA

organism: Saccharomyces cerevisiae S288C

source_name: sonicated spheroplasts

growth_protocol: Cells were grown to logarithmic phase of growth in a 2% raffinose synthetic complete medium at 30 degrees C.

extract_protocol:
Spheroplasts were prepared, washed, and lysed in detergent containing  buffer with protease inhibitors. Lysate was sonicated to obtain DNA fragments of average size 100 bp.
Libraries were prepared using Illumina Nextera DNA Library Kit #FC-121-1031

treatment_protocol: Galactose was added to the media to a final concentration of 2% for 2 hrs at 30 degrees C to induce Cse4 expression from the GAL promoter.

tag: genetic background

value: psh1delta pGAL-6His-3HA-cse4 K215/216A

tag: antibody

value: anti-HA agarose beads (A2095, Sigma)


title: RDS_G164_SVF_1

country: United Kingdom

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: treatment


title: YMB8953 ChIP rep1

value: psh1delta pGAL-6His-3HA-CSE4


title: C790_+dox_day20_3

type: RNA

city: Heidelberg

first: Jochen

last: Utikal

address: Im Neuenheimer Feld 280

department: Clinical Cooperation Unit Dermato-Oncology

country: Germany

institute: German Cancer Research Center

description: Gene expression data from cells reprogrammed partially at day 20 a

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were analyzed with Chispter using Illumina default analysis settings

label: biotin

organism: Mus musculus

source_name: melanoma

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol

growth_protocol: All cells were culture under standar conditions of CO2 and temperature.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed.

treatment_protocol: Cells were treated with doxycycline to induce expression of Sox2, Oct4 and Klf4 murine genes

tag: cell type

tag: dox

value: plus


title: ASC-shGL2-rep1

city: Beijing

first: Shuai

last: Ma

address: No.15, Da Tun road

country: China

institute: Chinese Academy of Sciences

description: ASCs transduced with lentiviral vectors expressing shGL2

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to hg19 genome using hisat2 software.
Reads were counted by featureCounts.
Differentially expressed genes were calculated by DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: The fomat of processed data is tab seprated file. And, the content is featureCounts reads count.

source_name: primary GL2-knockdown-human-ASCs

growth_protocol: Primary human ASCs were cultured ASC culture medium containing α-MEM with 1× GlutaMAX supplement (Gibco), 10% FBS (Gibco), 1% penicillin/streptomycin and 1 ng/ml bFGF was added to 0.1% gelatin-coated plates.

extract_protocol:
Total RNA was extracted by TRIzol (Thermo Fisher Scientific). Genomic DNA was removed
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: Lentiviral particles were collected from the supernatant of HEK293T cells by ultracentrifugation at 64,300 × g and 4°C for 135 min and were used to transduce ASCs.

tag: tissue

value: human cell


title: C790_-dox_day20_3

description: Gene expression data from control cells (non induced with doxycycline) at day 20

value: negative


title: C790_-dox_day20_1


title: CA_uninjured_AdvSca1-SM_Exp1

status: Public on Feb 20 2020

city: Aurora

first: Mary

last: Weiser-Evans

state: CO

address: 12700 East 19th Avenue, C281

department: Renal Diseases & Hypertension

data_processing:
Basecalls were performed using bcl2fastq_v1.8.4
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 version 2.1.0 with default parameters
For the RNA-seq experiments comparing AdvSca1-SM, AdvSca1-MA, and SMCs, Cufflinks 2.2.1 was employed to assemble the transcript from the aligned sequencing data and generate fragments per kilobase of exon per million fragments mapped (FPKM) data.
For carotid artery injury experiments, raw gene counts were generated with HTSeq 0.10.0 for subsequent analysis and EdgeR 3.10 was used to filter out low expression genes (CPM>=4 in at least 2 samples), perform paired comparison and generate Normalized counts per million (CPM) data.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM or CPM values for each Sample

source_name: AdvSca1-SM cells

extract_protocol:
Harvested descending aortas and combined aortic arch plus left and right carotid arteries were digested to single cells at 37°C for 1 hour. For flow sorting, single cell suspensions were suspended in 100 μl PBS + 0.1% CS and incubated with a rat anti-mouse monoclonal anti-Sca1 antibody; live cells were sorted based on Sca1-APC and endogenous YFP expression. Total RNA was extracted from flow cytometry-sorted cells using QIAshredders and an RNeasy Plus Micro kit (Qiagen). RNA quality and quantity were analyzed using a NanoDrop and Bioanalyzer.
RNA-Seq library preparation and sequencing were conducted at the Genomics and Microarray Core at the University of Colorado Anschutz Medical Campus. Libraries were constructed using a SMARTer Stranded Total RNA-Seq kit (Clontech) customized with mouse specific oligos for rRNA removal.

tag: strain

value: AdvSca1-SM cells

value: Carotid arteries

tag: age

value: 8 weeks

tag: genotype

value: uninjured


title: Gli1_AO_AdvSca1-SM_Exp3

institute: University of Colorado Anschutz Medical Campus

value: Aortae

value: no treatment


title: CA_injured_AdvSca1-SM_Exp2

value: injured


title: Gli1_CA_AdvSca1-SM_Exp2


title: Gli1_CA_AdvSca1-SM_Exp3


title: CA_uninjured_AdvSca1-SM_Exp2


title: Gli1_AO_AdvSca1-SM_Exp2


title: CA_uninjured_AdvSca1-SM_Exp3


title: CA_injured_AdvSca1-SM_Exp4


title: CA_uninjured_AdvSca1-SM_Exp4


title: CA_injured_AdvSca1-SM_Exp1


title: C790_+dox_day20_2


title: C790_-dox_day20_2


title: C790_+dox_day20_1


title: mouse inguinal ATAC-seq cre-2

city: Ann Arbor

first: Jiandie

last: Lin

state: MI

address: 210 Washtenaw Ave

department: Cell & Developmental Biology, Life Science Institute

institute: University of Michigan

description:
beige.cre.nml.broad.peaks.bw
ATAC_beige_nml_anno_res.csv

data_processing:
FastQC was used to assess the sequencing quality on fastq files.
fastx was used for trimming reads from150bp to 38bp.
atactk (0.1.5) was used for adapator trimming.
bwa (0.7.17-r1188) was used for alignment to generate bam files.
Duplicates were marked by Picard (v.2.8.14).
Samtools was used to remove duplicates.
macs2 (2.1.1.20160309) was used for peak calling.
The treat_pileup.bedgraph files (generated by macs2) from each individual samples were normalized to its own library size and converted to bigwig file by bedGraphToBigWig (v.4).
Broad peaks were filtered against an mm10 blacklist (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz).
The master peaks list was generated from the union of all blacklist-filtered broad peaks, which were kept those overlapping with peak calls (FDR < 0.1) from at least 2 of 3 biological replicates
Bedtools (v.2.27.1) was used to count reads in each peak for each sample.
The R package DESeq2 (v.1.20.0) was used to perform the differential peak analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files contain DESeq2-normalized read counts from ATAC-seq, bigwig file of ATAC-seq coverage.

source_name: inguinal adipose tissue

extract_protocol: Nuclei from frozen mouse inguinal fat were isolated by gradient centrifugation. 50000 isolated nuclei were used in each transposase reaction (Illumina). The sequencing libraries were barcoded and amplified by 2-step PCR. DNA sequencing were performed on Illumina NextSeq-500 instrument with 38-bp paired-end reads.

value: whole inguinal adipose tissue

tag: phenotype

value: AKO


title: whole_blood_D3_IFNlambda

city: New York

first: Joseph

middle: C

last: Devlin

state: NY

address: 430 East 29th Street

department: Microbiology

institute: New York University Langone Health

data_processing:
Reads were mapped by Bowtie (v2.3.1) to the hg38 reference genome
Uniquely mapped indices (UMI) determined by HTSeq-counts
Normalized count tables were generated in R (v3.5.1) using DESeq2 (v1.18.1)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized count values for each Sample

molecule: polyA RNA

source_name: whole blood

growth_protocol: Blood was drawn from healthy human donors according to our IRB protocol (S14-02129). 1 mL of blood per tube was then added to TruCulture tubes and inverted gently to mix.

extract_protocol:
RNA for each donor was then isolated with the RNeasy Plus Mini Kit (Qiagen) following the protocol with on column DNAse Digestion (Qiagen).
RNA libraries were prepared using standard CelSeq2 protocols.

treatment_protocol: Stimulations were added to appropriate tubes at the following final concentrations: buffer control (PBS), 500 U/mL IFN-b1a (referred to as IFN-b) (Carrier Free; R&D Systems), 10 ng/mL IFN-g (Carrier Free, R&D Systems), 100 ng/mL IFN-l2 (referred to as IFN-l) (Carrier Free, R&D Systems), 78.125 ng/mL IL-4 (Carrier Free, R&D Systems), 100 IU/mL IL-10 (Carrier Free, R&D Systems), and 100 IU/mL IL-13 (Carrier Free, R&D Systems). Tubes were inverted gently to mix. Tubes were incubated for 4 hours at 37°C with gentle rotation. Tubes were spun for 10 minutes at 450 x g without break. Supernatants were removed, and the pellets were resuspended in 2 mL of PAXGENE reagent. Tubes were incubated at room temperature for 2 hours and placed at 4°C overnight. RNA was then isolated using the PAXGene protocol.

value: whole blood

tag: donor

tag: stimulation

value: IFNlambda


title: mouse inguinal ATAC-seq lox-3

description:
beige.lox.nml.broad.peaks.bw
ATAC_beige_nml_anno_res.csv

value: flox/flox


title: mouse inguinal ATAC-seq cre-1


title: CA_injured_AdvSca1-SM_Exp3


title: mouse inguinal ATAC-seq lox-2


title: mouse inguinal ATAC-seq lox-1


title: STZ estrogen

city: Neuherberg

first: Sophie

last: Tritschler

address: Ingolstädter Landstrasse 1

institute: Helmholtz Zentrum Munich

data_processing:
The 10X Genomics core computational software Cellranger v.2.0 was used for alignment and processing of next generation sequencing reads of the scRNA-seq data as recommended (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome). For read 2 150bp were considered for alignment.
For QC, filtering, normalization, and doublet exclusion the scanpy python package v.1.0.4, anndata v0.5.10 and scrublet v.0.1 were used. Scripts for preprocessing with detailed descriptions are available here: https://github.com/theislab/pancreas-targeted_pharmacology/
Genome_build: mm10
Supplementary_files_format_and_content: Raw UMI count matrix (feature x cell barcode) from 10X Genomics single cell RNAseq experiments. gzipped files contains count matrix in market matrix format, cell barcodes as tab-delimited text file and feature names as tab-delimited text file.
Supplementary_files_format_and_content: anndata (annotated data matrix) object saved in h5ad-file format. File contains raw or preprocessed and annotated count data for all experiments.

source_name: Single cells of islet of Langerhans

extract_protocol:
Islet isolation was performed by collagenase P (Roche) digestion of the adult pancreas. For single cell suspension of islets, the islets were handpicked in an 1.5 mL Eppendorf tube, pelleted (800 rpm, 1 min) washed with PBS (-Mg/Ca, Gibco) and digested with 0.25% Trypsin with EDTA (Gibco) at 37°C for 8 min. Mechanical disaggregation every 2-3 min was required.
Single cell libraries were generated using the ChromiumTM Single cell 3`library and gel bead kit v2 (PN #120237) from 10x Genomics. Libraries were sequenced on the HiSeq4000 (Illumina) with 150bp paired-end sequencing of read2.

treatment_protocol: Healthy and STZ diabetic mice were treated daily with subcutaneous injections at a volume of 5µl per g body weight for 100 days. Healthy and STZ control groups were treated with vehicle (PBS). Additionally, STZ diabetic mice were treated with either insulin (25 nmol/kg/day), GLP-1 (100 nmol/kg/day), estrogen (100 nmol/kg/day), GLP-1/estrogen (100 nmol/kg/day), or the combination of GLP-1/estrogen + insulin (100 nmol/kg/day + 10 nmol/kg/day).

tag: source tissue

value: pancreas

tag: developmental day

value: post natal day 182

value: estrogen


title: STZ GLP-1/estrogen + insulin

value: GLP-1/estrogen + insulin


title: STZ GLP-1/estrogen


title: STZ GLP-1


title: Gli1_CA_AdvSca1-SM_Exp1


title: mouse inguinal ATAC-seq cre-3


title: Gli1_AO_AdvSca1-SM_Exp1


title: STZ insulin

value: insulin


title: STZ


title: No STZ


title: Hematopoietic stem cell (HSC) 275

city: Dresden

first: Alexander

last: Gerbaulet

state: Saxony

address: Fetscherstr. 74

department: Institute for Immunology

institute: Medical Faculty TU Dresden

description:
featureCounts.mm10.E87.csv.gz
L32239_HSC-5_02_E02

data_processing:
Alignment of the samples with GSNAP (version 2018-07-04) to the mm10 reference, and using Ensembl 87 for the support of splicesite detection
featureCounts (version1.6.2) was used to assign the reads to genes with the help of Ensembl 87 annotation
Genome_build: mm10
Supplementary_files_format_and_content: featureCounts.mm10.E87.csv.gz This is a ";" separated text file, containing the following files: GeneID, Strand, Length, Chromosome, Start, End position, followed by the 282 single cells (samples)

source_name: bone marrow hematopoieitic stem cell (LSK CD48-/loCD150+)

extract_protocol:
Whole bone marrow cells  were isolated by crushing long bones with mortar and pestle using PBS/2% FCS/2 mM EDTA and filtered through a 100 µm mesh. After erythrocyte lysis in hypotonic NH4Cl-buffer, cells were filtered through a 40 µm mesh. Cells were incubated with antibodies in PBS / 2% FCS for 30 min, washed twice with PBS / 2% FCS. Single BM LSK CD48-/loCD150+ cells were sorted on an BD ARIA II SORP flow cytometer into 96 well plates containing 2 µl of nuclease free water with 0.2% Triton-X 100 and 4 U murine RNase Inhibitor (NEB), spun down and frozen at ‑80°C. After thawing, 2 µl of a primer mix were added (5 mM dNTP (Invitrogen), 0.5 µM dT-primer (C6-aminolinker-AAGCAGTGGTATCAACGCAGAGTCGACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN), 4 U RNase Inhibitor (NEB)). RNA was denatured for 3 minutes at 72°C and the reverse transcription (RT) was performed at 42°C for 90 min after filling up to 10 µl with RT buffer mix for a final concentration of 1x superscript II buffer (Invitrogen), 1 M betaine, 5 mM DTT, 6 mM MgCl2, 1 µM TSO-primer (AAGCAGTGGTATCAACGCAGAGTACATrGrGrG), 9 U RNase Inhibitor and 90 U Superscript II (Invitrogen). After synthesis, the reverse transcriptase was inactivated at 70°C for 15 min. The cDNA was amplified using Kapa HiFi HotStart Readymix (Peqlab) at a final 1x concentration and 0.1 µM UP-primer (AAGCAGTGGTATCAACGCAGAGT) under following cycling conditions: initial denaturation at 98°C for 3 min, 22 cycles [98°C 20 sec, 67°C 15 sec, 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA was purified using 1x volume of hydrophobic Sera-Mag SpeedBeads (GE Healthcare) and DNA was eluted in 12 µl nuclease free water. The concentration of the samples was measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates (Corning) using AccuBlue Broad range chemistry (Biotium).
For library preparation 700 pg cDNA in 2 µl was mixed with 0.5 µl Tagment DNA Enzyme and 2.5 µl Tagment DNA Buffer (Nextera, Illumina) and tagmented at 55°C for 5 min. Subsequently, Illumina indices were added during PCR (72°C 3 min, 98°C 30 sec, 12 cycles [98°C 10 sec, 63°C 20 sec, 72°C 1 min], 72°C 5 min) with 1x concentrated KAPA HiFi HotStart Ready Mix and 0.7 µM dual indexing primers. After PCR, libraries were quantified with AccuBlue Broad range chemistry, equimolarly pooled and purified twice with 1x volume Sera-Mag SpeedBeads. This was followed by Illumina single-end sequencing (76bp) on a Nextseq550 aiming at an average sequencing depth of 0.5 mio reads per cell.

tag: col1a1 genotype

tag: rosa26 genotype

value: rtTA/rtTA

tag: doxycyclin induction

value: not induced


title: Hematopoietic stem cell (HSC) 272

description:
featureCounts.mm10.E87.csv.gz
L32269_HSC-5_02_C06


title: Hematopoietic stem cell (HSC) 279

description:
featureCounts.mm10.E87.csv.gz
L32241_HSC-5_02_G02


title: Hematopoietic stem cell (HSC) 280

description:
featureCounts.mm10.E87.csv.gz
L32273_HSC-5_02_G06


title: Hematopoietic stem cell (HSC) 267

description:
featureCounts.mm10.E87.csv.gz
L32235_HSC-5_02_A02


title: Hematopoietic stem cell (HSC) 273

description:
featureCounts.mm10.E87.csv.gz
L32238_HSC-5_02_D02


title: Hematopoietic stem cell (HSC) 282

description:
featureCounts.mm10.E87.csv.gz
L32274_HSC-5_02_H06


title: Hematopoietic stem cell (HSC) 278

description:
featureCounts.mm10.E87.csv.gz
L32272_HSC-5_02_F06


title: Hematopoietic stem cell (HSC) 276

description:
featureCounts.mm10.E87.csv.gz
L32271_HSC-5_02_E06


title: Hematopoietic stem cell (HSC) 271

description:
featureCounts.mm10.E87.csv.gz
L32237_HSC-5_02_C02


title: Hematopoietic stem cell (HSC) 281

description:
featureCounts.mm10.E87.csv.gz
L32242_HSC-5_02_H02


title: Hematopoietic stem cell (HSC) 277

description:
featureCounts.mm10.E87.csv.gz
L32240_HSC-5_02_F02


title: Hematopoietic stem cell (HSC) 268

description:
featureCounts.mm10.E87.csv.gz
L32267_HSC-5_02_A06


title: Hematopoietic stem cell (HSC) 269

description:
featureCounts.mm10.E87.csv.gz
L32236_HSC-5_02_B02


title: Hematopoietic stem cell (HSC) 266

description:
featureCounts.mm10.E87.csv.gz
L32226_HSC-5_01_H12


title: Hematopoietic stem cell (HSC) 263

description:
featureCounts.mm10.E87.csv.gz
L32225_HSC-5_01_G12


title: Hematopoietic stem cell (HSC) 270

description:
featureCounts.mm10.E87.csv.gz
L32268_HSC-5_02_B06


title: Hematopoietic stem cell (HSC) 265

description:
featureCounts.mm10.E87.csv.gz
L32194_HSC-5_01_H08


title: Hematopoietic stem cell (HSC) 264

description:
featureCounts.mm10.E87.csv.gz
L32162_HSC-5_01_H04


title: Hematopoietic stem cell (HSC) 261

description:
featureCounts.mm10.E87.csv.gz
L32161_HSC-5_01_G04


title: Hematopoietic stem cell (HSC) 262

description:
featureCounts.mm10.E87.csv.gz
L32193_HSC-5_01_G08


title: Hematopoietic stem cell (HSC) 258

description:
featureCounts.mm10.E87.csv.gz
L32160_HSC-5_01_F04


title: Hematopoietic stem cell (HSC) 260

description:
featureCounts.mm10.E87.csv.gz
L32224_HSC-5_01_F12


title: Hematopoietic stem cell (HSC) 259

description:
featureCounts.mm10.E87.csv.gz
L32192_HSC-5_01_F08


title: Hematopoietic stem cell (HSC) 257

description:
featureCounts.mm10.E87.csv.gz
L32223_HSC-5_01_E12


title: Hematopoietic stem cell (HSC) 256

description:
featureCounts.mm10.E87.csv.gz
L32159_HSC-5_01_E04


title: Hematopoietic stem cell (HSC) 255

description:
featureCounts.mm10.E87.csv.gz
L32222_HSC-5_01_D12


title: Hematopoietic stem cell (HSC) 274

description:
featureCounts.mm10.E87.csv.gz
L32270_HSC-5_02_D06


title: Hematopoietic stem cell (HSC) 254

description:
featureCounts.mm10.E87.csv.gz
L32190_HSC-5_01_D08


title: Hematopoietic stem cell (HSC) 253

description:
featureCounts.mm10.E87.csv.gz
L32158_HSC-5_01_D04


title: Hematopoietic stem cell (HSC) 251

description:
featureCounts.mm10.E87.csv.gz
L32189_HSC-5_01_C08


title: Hematopoietic stem cell (HSC) 252

description:
featureCounts.mm10.E87.csv.gz
L32221_HSC-5_01_C12


title: Hematopoietic stem cell (HSC) 250

description:
featureCounts.mm10.E87.csv.gz
L32157_HSC-5_01_C04


title: Hematopoietic stem cell (HSC) 247

description:
featureCounts.mm10.E87.csv.gz
L32156_HSC-5_01_B04


title: Hematopoietic stem cell (HSC) 249

description:
featureCounts.mm10.E87.csv.gz
L32220_HSC-5_01_B12


title: Hematopoietic stem cell (HSC) 244

description:
featureCounts.mm10.E87.csv.gz
L32155_HSC-5_01_A04


title: Hematopoietic stem cell (HSC) 246

description:
featureCounts.mm10.E87.csv.gz
L32219_HSC-5_01_A12


title: Hematopoietic stem cell (HSC) 238

description:
featureCounts.mm10.E87.csv.gz
L32256_HSC-4_02_F04


title: Hematopoietic stem cell (HSC) 248

description:
featureCounts.mm10.E87.csv.gz
L32188_HSC-5_01_B08


title: Hematopoietic stem cell (HSC) 240

description:
featureCounts.mm10.E87.csv.gz
L32257_HSC-4_02_G04


title: Hematopoietic stem cell (HSC) 232

description:
featureCounts.mm10.E87.csv.gz
L32284_HSC-4_02_B08


title: Hematopoietic stem cell (HSC) 233

description:
featureCounts.mm10.E87.csv.gz
L32253_HSC-4_02_C04


title: Hematopoietic stem cell (HSC) 243

description:
featureCounts.mm10.E87.csv.gz
L32290_HSC-4_02_H08


title: Hematopoietic stem cell (HSC) 236

description:
featureCounts.mm10.E87.csv.gz
L32286_HSC-4_02_D08


title: Hematopoietic stem cell (HSC) 234

description:
featureCounts.mm10.E87.csv.gz
L32285_HSC-4_02_C08


title: Hematopoietic stem cell (HSC) 231

description:
featureCounts.mm10.E87.csv.gz
L32252_HSC-4_02_B04


title: Hematopoietic stem cell (HSC) 241

description:
featureCounts.mm10.E87.csv.gz
L32289_HSC-4_02_G08


title: Hematopoietic stem cell (HSC) 239

description:
featureCounts.mm10.E87.csv.gz
L32288_HSC-4_02_F08


title: Hematopoietic stem cell (HSC) 228

description:
featureCounts.mm10.E87.csv.gz
L32218_HSC-4_01_H11


title: Hematopoietic stem cell (HSC) 230

description:
featureCounts.mm10.E87.csv.gz
L32283_HSC-4_02_A08


title: Hematopoietic stem cell (HSC) 245

description:
featureCounts.mm10.E87.csv.gz
L32187_HSC-5_01_A08


title: Hematopoietic stem cell (HSC) 237

description:
featureCounts.mm10.E87.csv.gz
L32255_HSC-4_02_E04


title: Hematopoietic stem cell (HSC) 242

description:
featureCounts.mm10.E87.csv.gz
L32258_HSC-4_02_H04


title: Hematopoietic stem cell (HSC) 235

description:
featureCounts.mm10.E87.csv.gz
L32254_HSC-4_02_D04


title: Hematopoietic stem cell (HSC) 227

description:
featureCounts.mm10.E87.csv.gz
L32186_HSC-4_01_H07


title: Hematopoietic stem cell (HSC) 225

description:
featureCounts.mm10.E87.csv.gz
L32217_HSC-4_01_G11


title: Hematopoietic stem cell (HSC) 226

description:
featureCounts.mm10.E87.csv.gz
L32154_HSC-4_01_H03


title: Hematopoietic stem cell (HSC) 229

description:
featureCounts.mm10.E87.csv.gz
L32251_HSC-4_02_A04


title: Hematopoietic stem cell (HSC) 224

description:
featureCounts.mm10.E87.csv.gz
L32185_HSC-4_01_G07


title: Hematopoietic stem cell (HSC) 223

description:
featureCounts.mm10.E87.csv.gz
L32153_HSC-4_01_G03


title: Hematopoietic stem cell (HSC) 222

description:
featureCounts.mm10.E87.csv.gz
L32216_HSC-4_01_F11


title: Hematopoietic stem cell (HSC) 220

description:
featureCounts.mm10.E87.csv.gz
L32152_HSC-4_01_F03


title: Hematopoietic stem cell (HSC) 221

description:
featureCounts.mm10.E87.csv.gz
L32184_HSC-4_01_F07


title: Hematopoietic stem cell (HSC) 219

description:
featureCounts.mm10.E87.csv.gz
L32215_HSC-4_01_E11


title: Hematopoietic stem cell (HSC) 215

description:
featureCounts.mm10.E87.csv.gz
L32150_HSC-4_01_D03


title: Hematopoietic stem cell (HSC) 217

description:
featureCounts.mm10.E87.csv.gz
L32214_HSC-4_01_D11


title: Hematopoietic stem cell (HSC) 218

description:
featureCounts.mm10.E87.csv.gz
L32151_HSC-4_01_E03


title: Hematopoietic stem cell (HSC) 214

description:
featureCounts.mm10.E87.csv.gz
L32213_HSC-4_01_C11


title: Hematopoietic stem cell (HSC) 210

description:
featureCounts.mm10.E87.csv.gz
L32180_HSC-4_01_B07


title: Hematopoietic stem cell (HSC) 212

description:
featureCounts.mm10.E87.csv.gz
L32149_HSC-4_01_C03


title: Hematopoietic stem cell (HSC) 207

description:
featureCounts.mm10.E87.csv.gz
L32179_HSC-4_01_A07


title: Hematopoietic stem cell (HSC) 205

description:
featureCounts.mm10.E87.csv.gz
L32322_HSC-3_02_H12


title: Hematopoietic stem cell (HSC) 208

description:
featureCounts.mm10.E87.csv.gz
L32211_HSC-4_01_A11


title: Hematopoietic stem cell (HSC) 209

description:
featureCounts.mm10.E87.csv.gz
L32148_HSC-4_01_B03


title: Hematopoietic stem cell (HSC) 216

description:
featureCounts.mm10.E87.csv.gz
L32182_HSC-4_01_D07


title: Hematopoietic stem cell (HSC) 213

description:
featureCounts.mm10.E87.csv.gz
L32181_HSC-4_01_C07


title: Hematopoietic stem cell (HSC) 211

description:
featureCounts.mm10.E87.csv.gz
L32212_HSC-4_01_B11


title: Hematopoietic stem cell (HSC) 200

description:
featureCounts.mm10.E87.csv.gz
L32321_HSC-3_02_G12


title: Hematopoietic stem cell (HSC) 203

description:
featureCounts.mm10.E87.csv.gz
L32298_HSC-3_02_H09


title: Hematopoietic stem cell (HSC) 202

description:
featureCounts.mm10.E87.csv.gz
L32266_HSC-3_02_H05


title: Hematopoietic stem cell (HSC) 204

description:
featureCounts.mm10.E87.csv.gz
L32306_HSC-3_02_H10


title: Hematopoietic stem cell (HSC) 198

description:
featureCounts.mm10.E87.csv.gz
L32297_HSC-3_02_G09


title: Hematopoietic stem cell (HSC) 199

description:
featureCounts.mm10.E87.csv.gz
L32305_HSC-3_02_G10


title: Hematopoietic stem cell (HSC) 197

description:
featureCounts.mm10.E87.csv.gz
L32265_HSC-3_02_G05


title: Hematopoietic stem cell (HSC) 196

description:
featureCounts.mm10.E87.csv.gz
L32233_HSC-3_02_G01


title: Hematopoietic stem cell (HSC) 194

description:
featureCounts.mm10.E87.csv.gz
L32304_HSC-3_02_F10


title: Hematopoietic stem cell (HSC) 195

description:
featureCounts.mm10.E87.csv.gz
L32320_HSC-3_02_F12


title: Hematopoietic stem cell (HSC) 193

description:
featureCounts.mm10.E87.csv.gz
L32296_HSC-3_02_F09


title: Hematopoietic stem cell (HSC) 201

description:
featureCounts.mm10.E87.csv.gz
L32234_HSC-3_02_H01


title: Hematopoietic stem cell (HSC) 192

description:
featureCounts.mm10.E87.csv.gz
L32264_HSC-3_02_F05


title: Hematopoietic stem cell (HSC) 191

description:
featureCounts.mm10.E87.csv.gz
L32232_HSC-3_02_F01


title: Hematopoietic stem cell (HSC) 190

description:
featureCounts.mm10.E87.csv.gz
L32319_HSC-3_02_E12


title: Hematopoietic stem cell (HSC) 206

description:
featureCounts.mm10.E87.csv.gz
L32147_HSC-4_01_A03


title: Hematopoietic stem cell (HSC) 189

description:
featureCounts.mm10.E87.csv.gz
L32303_HSC-3_02_E10


title: Hematopoietic stem cell (HSC) 188

description:
featureCounts.mm10.E87.csv.gz
L32295_HSC-3_02_E09


title: Hematopoietic stem cell (HSC) 185

description:
featureCounts.mm10.E87.csv.gz
L32318_HSC-3_02_D12


title: Hematopoietic stem cell (HSC) 182

description:
featureCounts.mm10.E87.csv.gz
L32262_HSC-3_02_D05


title: Hematopoietic stem cell (HSC) 181

description:
featureCounts.mm10.E87.csv.gz
L32230_HSC-3_02_D01


title: Hematopoietic stem cell (HSC) 183

description:
featureCounts.mm10.E87.csv.gz
L32294_HSC-3_02_D09


title: Hematopoietic stem cell (HSC) 186

description:
featureCounts.mm10.E87.csv.gz
L32231_HSC-3_02_E01


title: Hematopoietic stem cell (HSC) 184

description:
featureCounts.mm10.E87.csv.gz
L32302_HSC-3_02_D10


title: Hematopoietic stem cell (HSC) 180

description:
featureCounts.mm10.E87.csv.gz
L32317_HSC-3_02_C12


title: Hematopoietic stem cell (HSC) 179

description:
featureCounts.mm10.E87.csv.gz
L32301_HSC-3_02_C10


title: Hematopoietic stem cell (HSC) 178

description:
featureCounts.mm10.E87.csv.gz
L32293_HSC-3_02_C09


title: Hematopoietic stem cell (HSC) 175

description:
featureCounts.mm10.E87.csv.gz
L32316_HSC-3_02_B12


title: Hematopoietic stem cell (HSC) 176

description:
featureCounts.mm10.E87.csv.gz
L32229_HSC-3_02_C01


title: Hematopoietic stem cell (HSC) 172

description:
featureCounts.mm10.E87.csv.gz
L32260_HSC-3_02_B05


title: Hematopoietic stem cell (HSC) 171

description:
featureCounts.mm10.E87.csv.gz
L32228_HSC-3_02_B01


title: Hematopoietic stem cell (HSC) 170

description:
featureCounts.mm10.E87.csv.gz
L32315_HSC-3_02_A12


title: Hematopoietic stem cell (HSC) 168

description:
featureCounts.mm10.E87.csv.gz
L32291_HSC-3_02_A09


title: Hematopoietic stem cell (HSC) 169

description:
featureCounts.mm10.E87.csv.gz
L32299_HSC-3_02_A10


title: Hematopoietic stem cell (HSC) 167

description:
featureCounts.mm10.E87.csv.gz
L32259_HSC-3_02_A05


title: Hematopoietic stem cell (HSC) 165

description:
featureCounts.mm10.E87.csv.gz
L32210_HSC-3_01_H10


title: Hematopoietic stem cell (HSC) 164

description:
featureCounts.mm10.E87.csv.gz
L32178_HSC-3_01_H06


title: Hematopoietic stem cell (HSC) 166

description:
featureCounts.mm10.E87.csv.gz
L32227_HSC-3_02_A01


title: Hematopoietic stem cell (HSC) 163

description:
featureCounts.mm10.E87.csv.gz
L32146_HSC-3_01_H02


title: Hematopoietic stem cell (HSC) 162

description:
featureCounts.mm10.E87.csv.gz
L32209_HSC-3_01_G10


title: Hematopoietic stem cell (HSC) 187

description:
featureCounts.mm10.E87.csv.gz
L32263_HSC-3_02_E05


title: Hematopoietic stem cell (HSC) 161

description:
featureCounts.mm10.E87.csv.gz
L32177_HSC-3_01_G06


title: Hematopoietic stem cell (HSC) 160

description:
featureCounts.mm10.E87.csv.gz
L32145_HSC-3_01_G02


title: Hematopoietic stem cell (HSC) 177

description:
featureCounts.mm10.E87.csv.gz
L32261_HSC-3_02_C05


title: Hematopoietic stem cell (HSC) 159

description:
featureCounts.mm10.E87.csv.gz
L32208_HSC-3_01_F10


title: Hematopoietic stem cell (HSC) 156

description:
featureCounts.mm10.E87.csv.gz
L32207_HSC-3_01_E10


title: Hematopoietic stem cell (HSC) 174

description:
featureCounts.mm10.E87.csv.gz
L32300_HSC-3_02_B10


title: Hematopoietic stem cell (HSC) 155

description:
featureCounts.mm10.E87.csv.gz
L32175_HSC-3_01_E06


title: Hematopoietic stem cell (HSC) 153

description:
featureCounts.mm10.E87.csv.gz
L32206_HSC-3_01_D10


title: Hematopoietic stem cell (HSC) 151

description:
featureCounts.mm10.E87.csv.gz
L32142_HSC-3_01_D02


title: Hematopoietic stem cell (HSC) 173

description:
featureCounts.mm10.E87.csv.gz
L32292_HSC-3_02_B09


title: Hematopoietic stem cell (HSC) 152

description:
featureCounts.mm10.E87.csv.gz
L32174_HSC-3_01_D06


title: Hematopoietic stem cell (HSC) 146

description:
featureCounts.mm10.E87.csv.gz
L32172_HSC-3_01_B06


title: Hematopoietic stem cell (HSC) 147

description:
featureCounts.mm10.E87.csv.gz
L32204_HSC-3_01_B10


title: Hematopoietic stem cell (HSC) 145

description:
featureCounts.mm10.E87.csv.gz
L32140_HSC-3_01_B02


title: Hematopoietic stem cell (HSC) 144

description:
featureCounts.mm10.E87.csv.gz
L32203_HSC-3_01_A10


title: Hematopoietic stem cell (HSC) 139

description:
featureCounts.mm10.E87.csv.gz
L32250_HSC-2_02_H03


title: Hematopoietic stem cell (HSC) 137

description:
featureCounts.mm10.E87.csv.gz
L32281_HSC-2_02_G07


title: Hematopoietic stem cell (HSC) 143

description:
featureCounts.mm10.E87.csv.gz
L32171_HSC-3_01_A06


title: Hematopoietic stem cell (HSC) 141

description:
featureCounts.mm10.E87.csv.gz
L32314_HSC-2_02_H11


title: Hematopoietic stem cell (HSC) 142

description:
featureCounts.mm10.E87.csv.gz
L32139_HSC-3_01_A02


title: Hematopoietic stem cell (HSC) 136

description:
featureCounts.mm10.E87.csv.gz
L32249_HSC-2_02_G03


title: Hematopoietic stem cell (HSC) 158

description:
featureCounts.mm10.E87.csv.gz
L32176_HSC-3_01_F06


title: Hematopoietic stem cell (HSC) 157

description:
featureCounts.mm10.E87.csv.gz
L32144_HSC-3_01_F02


title: Hematopoietic stem cell (HSC) 135

description:
featureCounts.mm10.E87.csv.gz
L32312_HSC-2_02_F11


title: Hematopoietic stem cell (HSC) 134

description:
featureCounts.mm10.E87.csv.gz
L32280_HSC-2_02_F07


title: Hematopoietic stem cell (HSC) 132

description:
featureCounts.mm10.E87.csv.gz
L32311_HSC-2_02_E11


title: Hematopoietic stem cell (HSC) 150

description:
featureCounts.mm10.E87.csv.gz
L32205_HSC-3_01_C10


title: Hematopoietic stem cell (HSC) 133

description:
featureCounts.mm10.E87.csv.gz
L32248_HSC-2_02_F03


title: Hematopoietic stem cell (HSC) 154

description:
featureCounts.mm10.E87.csv.gz
L32143_HSC-3_01_E02


title: Hematopoietic stem cell (HSC) 131

description:
featureCounts.mm10.E87.csv.gz
L32247_HSC-2_02_E03


title: Hematopoietic stem cell (HSC) 130

description:
featureCounts.mm10.E87.csv.gz
L32310_HSC-2_02_D11


title: Hematopoietic stem cell (HSC) 148

description:
featureCounts.mm10.E87.csv.gz
L32141_HSC-3_01_C02


title: Hematopoietic stem cell (HSC) 149

description:
featureCounts.mm10.E87.csv.gz
L32173_HSC-3_01_C06


title: Hematopoietic stem cell (HSC) 129

description:
featureCounts.mm10.E87.csv.gz
L32278_HSC-2_02_D07


title: Hematopoietic stem cell (HSC) 128

description:
featureCounts.mm10.E87.csv.gz
L32246_HSC-2_02_D03


title: Hematopoietic stem cell (HSC) 125

description:
featureCounts.mm10.E87.csv.gz
L32245_HSC-2_02_C03


title: Hematopoietic stem cell (HSC) 126

description:
featureCounts.mm10.E87.csv.gz
L32277_HSC-2_02_C07


title: Hematopoietic stem cell (HSC) 140

description:
featureCounts.mm10.E87.csv.gz
L32282_HSC-2_02_H07


title: Hematopoietic stem cell (HSC) 138

description:
featureCounts.mm10.E87.csv.gz
L32313_HSC-2_02_G11


title: Hematopoietic stem cell (HSC) 121

description:
featureCounts.mm10.E87.csv.gz
L32307_HSC-2_02_A11


title: Hematopoietic stem cell (HSC) 123

description:
featureCounts.mm10.E87.csv.gz
L32276_HSC-2_02_B07


title: Hematopoietic stem cell (HSC) 120

description:
featureCounts.mm10.E87.csv.gz
L32275_HSC-2_02_A07


title: Hematopoietic stem cell (HSC) 116

description:
featureCounts.mm10.E87.csv.gz
L32138_HSC-2_01_H01


title: Hematopoietic stem cell (HSC) 115

description:
featureCounts.mm10.E87.csv.gz
L32201_HSC-2_01_G09


title: Hematopoietic stem cell (HSC) 112

description:
featureCounts.mm10.E87.csv.gz
L32200_HSC-2_01_F09


title: Hematopoietic stem cell (HSC) 113

description:
featureCounts.mm10.E87.csv.gz
L32137_HSC-2_01_G01


title: Hematopoietic stem cell (HSC) 111

description:
featureCounts.mm10.E87.csv.gz
L32168_HSC-2_01_F05


title: Hematopoietic stem cell (HSC) 127

description:
featureCounts.mm10.E87.csv.gz
L32309_HSC-2_02_C11


title: Hematopoietic stem cell (HSC) 109

description:
featureCounts.mm10.E87.csv.gz
L32199_HSC-2_01_E09


title: Hematopoietic stem cell (HSC) 110

description:
featureCounts.mm10.E87.csv.gz
L32136_HSC-2_01_F01


title: Hematopoietic stem cell (HSC) 122

description:
featureCounts.mm10.E87.csv.gz
L32244_HSC-2_02_B03


title: Hematopoietic stem cell (HSC) 124

description:
featureCounts.mm10.E87.csv.gz
L32308_HSC-2_02_B11


title: Hematopoietic stem cell (HSC) 117

description:
featureCounts.mm10.E87.csv.gz
L32170_HSC-2_01_H05


title: Hematopoietic stem cell (HSC) 118

description:
featureCounts.mm10.E87.csv.gz
L32202_HSC-2_01_H09


title: Hematopoietic stem cell (HSC) 114

description:
featureCounts.mm10.E87.csv.gz
L32169_HSC-2_01_G05


title: Hematopoietic stem cell (HSC) 106

description:
featureCounts.mm10.E87.csv.gz
L32198_HSC-2_01_D09


title: Hematopoietic stem cell (HSC) 107

description:
featureCounts.mm10.E87.csv.gz
L32135_HSC-2_01_E01


title: Hematopoietic stem cell (HSC) 95

description:
featureCounts.mm10.E87.csv.gz
L32131_HSC-2_01_A01


title: Hematopoietic stem cell (HSC) 108

description:
featureCounts.mm10.E87.csv.gz
L32167_HSC-2_01_E05


title: Hematopoietic stem cell (HSC) 98

description:
featureCounts.mm10.E87.csv.gz
L32132_HSC-2_01_B01


title: Hematopoietic stem cell (HSC) 102

description:
featureCounts.mm10.E87.csv.gz
L32165_HSC-2_01_C05


title: Hematopoietic stem cell (HSC) 96

description:
featureCounts.mm10.E87.csv.gz
L32163_HSC-2_01_A05


title: Hematopoietic stem cell (HSC) 94

description:
featureCounts.mm10.E87.csv.gz
L29589_HSC-4_01_H12


title: Hematopoietic stem cell (HSC) 101

description:
featureCounts.mm10.E87.csv.gz
L32133_HSC-2_01_C01


title: Hematopoietic stem cell (HSC) 93

description:
featureCounts.mm10.E87.csv.gz
L29581_HSC-4_01_H11


title: Hematopoietic stem cell (HSC) 103

description:
featureCounts.mm10.E87.csv.gz
L32197_HSC-2_01_C09


title: Hematopoietic stem cell (HSC) 99

description:
featureCounts.mm10.E87.csv.gz
L32164_HSC-2_01_B05


title: Hematopoietic stem cell (HSC) 91

description:
featureCounts.mm10.E87.csv.gz
L29565_HSC-4_01_H09


title: Hematopoietic stem cell (HSC) 105

description:
featureCounts.mm10.E87.csv.gz
L32166_HSC-2_01_D05


title: Hematopoietic stem cell (HSC) 97

description:
featureCounts.mm10.E87.csv.gz
L32195_HSC-2_01_A09


title: Hematopoietic stem cell (HSC) 104

description:
featureCounts.mm10.E87.csv.gz
L32134_HSC-2_01_D01


title: Hematopoietic stem cell (HSC) 89

description:
featureCounts.mm10.E87.csv.gz
L29549_HSC-4_01_H07


title: Hematopoietic stem cell (HSC) 90

description:
featureCounts.mm10.E87.csv.gz
L29557_HSC-4_01_H08


title: Hematopoietic stem cell (HSC) 87

description:
featureCounts.mm10.E87.csv.gz
L29580_HSC-4_01_G11


title: Hematopoietic stem cell (HSC) 88

description:
featureCounts.mm10.E87.csv.gz
L29588_HSC-4_01_G12


title: Hematopoietic stem cell (HSC) 86

description:
featureCounts.mm10.E87.csv.gz
L29572_HSC-4_01_G10


title: Hematopoietic stem cell (HSC) 119

description:
featureCounts.mm10.E87.csv.gz
L32243_HSC-2_02_A03


title: Hematopoietic stem cell (HSC) 85

description:
featureCounts.mm10.E87.csv.gz
L29564_HSC-4_01_G09


title: Hematopoietic stem cell (HSC) 100

description:
featureCounts.mm10.E87.csv.gz
L32196_HSC-2_01_B09


title: Hematopoietic stem cell (HSC) 84

description:
featureCounts.mm10.E87.csv.gz
L29556_HSC-4_01_G08


title: Hematopoietic stem cell (HSC) 83

description:
featureCounts.mm10.E87.csv.gz
L29548_HSC-4_01_G07


title: Hematopoietic stem cell (HSC) 92

description:
featureCounts.mm10.E87.csv.gz
L29573_HSC-4_01_H10


title: Hematopoietic stem cell (HSC) 82

description:
featureCounts.mm10.E87.csv.gz
L29587_HSC-4_01_F12


title: Hematopoietic stem cell (HSC) 80

description:
featureCounts.mm10.E87.csv.gz
L29571_HSC-4_01_F10


title: Hematopoietic stem cell (HSC) 81

description:
featureCounts.mm10.E87.csv.gz
L29579_HSC-4_01_F11


title: Hematopoietic stem cell (HSC) 79

description:
featureCounts.mm10.E87.csv.gz
L29563_HSC-4_01_F09


title: Hematopoietic stem cell (HSC) 73

description:
featureCounts.mm10.E87.csv.gz
L29562_HSC-4_01_E09


title: Hematopoietic stem cell (HSC) 77

description:
featureCounts.mm10.E87.csv.gz
L29547_HSC-4_01_F07


title: Hematopoietic stem cell (HSC) 74

description:
featureCounts.mm10.E87.csv.gz
L29570_HSC-4_01_E10


title: Hematopoietic stem cell (HSC) 72

description:
featureCounts.mm10.E87.csv.gz
L29554_HSC-4_01_E08


title: Hematopoietic stem cell (HSC) 65

description:
featureCounts.mm10.E87.csv.gz
L29584_HSC-4_01_C12


title: Hematopoietic stem cell (HSC) 78

description:
featureCounts.mm10.E87.csv.gz
L29555_HSC-4_01_F08


title: Hematopoietic stem cell (HSC) 67

description:
featureCounts.mm10.E87.csv.gz
L29553_HSC-4_01_D08


title: Hematopoietic stem cell (HSC) 56

description:
featureCounts.mm10.E87.csv.gz
L29559_HSC-4_01_B09


title: Hematopoietic stem cell (HSC) 64

description:
featureCounts.mm10.E87.csv.gz
L29576_HSC-4_01_C11


title: Hematopoietic stem cell (HSC) 69

description:
featureCounts.mm10.E87.csv.gz
L29569_HSC-4_01_D10


title: Hematopoietic stem cell (HSC) 68

description:
featureCounts.mm10.E87.csv.gz
L29561_HSC-4_01_D09


title: Hematopoietic stem cell (HSC) 75

description:
featureCounts.mm10.E87.csv.gz
L29578_HSC-4_01_E11


title: Hematopoietic stem cell (HSC) 59

description:
featureCounts.mm10.E87.csv.gz
L29583_HSC-4_01_B12


title: Hematopoietic stem cell (HSC) 76

description:
featureCounts.mm10.E87.csv.gz
L29586_HSC-4_01_E12


title: Hematopoietic stem cell (HSC) 57

description:
featureCounts.mm10.E87.csv.gz
L29567_HSC-4_01_B10


title: Hematopoietic stem cell (HSC) 71

description:
featureCounts.mm10.E87.csv.gz
L29585_HSC-4_01_D12


title: Hematopoietic stem cell (HSC) 61

description:
featureCounts.mm10.E87.csv.gz
L29552_HSC-4_01_C08


title: Hematopoietic stem cell (HSC) 58

description:
featureCounts.mm10.E87.csv.gz
L29575_HSC-4_01_B11


title: Hematopoietic stem cell (HSC) 70

description:
featureCounts.mm10.E87.csv.gz
L29577_HSC-4_01_D11


title: Hematopoietic stem cell (HSC) 60

description:
featureCounts.mm10.E87.csv.gz
L29544_HSC-4_01_C07


title: Hematopoietic stem cell (HSC) 63

description:
featureCounts.mm10.E87.csv.gz
L29568_HSC-4_01_C10


title: Hematopoietic stem cell (HSC) 55

description:
featureCounts.mm10.E87.csv.gz
L29551_HSC-4_01_B08


title: Hematopoietic stem cell (HSC) 62

description:
featureCounts.mm10.E87.csv.gz
L29560_HSC-4_01_C09


title: Hematopoietic stem cell (HSC) 54

description:
featureCounts.mm10.E87.csv.gz
L29543_HSC-4_01_B07


title: Hematopoietic stem cell (HSC) 53

description:
featureCounts.mm10.E87.csv.gz
L29582_HSC-4_01_A12


title: Hematopoietic stem cell (HSC) 66

description:
featureCounts.mm10.E87.csv.gz
L29545_HSC-4_01_D07


title: Hematopoietic stem cell (HSC) 52

description:
featureCounts.mm10.E87.csv.gz
L29574_HSC-4_01_A11


title: Hematopoietic stem cell (HSC) 49

description:
featureCounts.mm10.E87.csv.gz
L29550_HSC-4_01_A08


title: Hematopoietic stem cell (HSC) 51

description:
featureCounts.mm10.E87.csv.gz
L29566_HSC-4_01_A10


title: Hematopoietic stem cell (HSC) 50

description:
featureCounts.mm10.E87.csv.gz
L29558_HSC-4_01_A09


title: Hematopoietic stem cell (HSC) 48

description:
featureCounts.mm10.E87.csv.gz
L29542_HSC-4_01_A07


title: Hematopoietic stem cell (HSC) 47

description:
featureCounts.mm10.E87.csv.gz
L29541_HSC-3_01_H06


title: Hematopoietic stem cell (HSC) 44

description:
featureCounts.mm10.E87.csv.gz
L29517_HSC-3_01_H03


title: Hematopoietic stem cell (HSC) 45

description:
featureCounts.mm10.E87.csv.gz
L29525_HSC-3_01_H04


title: Hematopoietic stem cell (HSC) 43

description:
featureCounts.mm10.E87.csv.gz
L29509_HSC-3_01_H02


title: Hematopoietic stem cell (HSC) 40

description:
featureCounts.mm10.E87.csv.gz
L29532_HSC-3_01_G05


title: Hematopoietic stem cell (HSC) 41

description:
featureCounts.mm10.E87.csv.gz
L29540_HSC-3_01_G06


title: Hematopoietic stem cell (HSC) 42

description:
featureCounts.mm10.E87.csv.gz
L29501_HSC-3_01_H01


title: Hematopoietic stem cell (HSC) 46

description:
featureCounts.mm10.E87.csv.gz
L29533_HSC-3_01_H05


title: Hematopoietic stem cell (HSC) 39

description:
featureCounts.mm10.E87.csv.gz
L29524_HSC-3_01_G04


title: Hematopoietic stem cell (HSC) 36

description:
featureCounts.mm10.E87.csv.gz
L29500_HSC-3_01_G01


title: Hematopoietic stem cell (HSC) 35

description:
featureCounts.mm10.E87.csv.gz
L29539_HSC-3_01_F06


title: Hematopoietic stem cell (HSC) 33

description:
featureCounts.mm10.E87.csv.gz
L29523_HSC-3_01_F04


title: Hematopoietic stem cell (HSC) 30

description:
featureCounts.mm10.E87.csv.gz
L29499_HSC-3_01_F01


title: Hematopoietic stem cell (HSC) 29

description:
featureCounts.mm10.E87.csv.gz
L29530_HSC-3_01_E05


title: Hematopoietic stem cell (HSC) 27

description:
featureCounts.mm10.E87.csv.gz
L29514_HSC-3_01_E03


title: Hematopoietic stem cell (HSC) 32

description:
featureCounts.mm10.E87.csv.gz
L29515_HSC-3_01_F03


title: Hematopoietic stem cell (HSC) 38

description:
featureCounts.mm10.E87.csv.gz
L29516_HSC-3_01_G03


title: Hematopoietic stem cell (HSC) 31

description:
featureCounts.mm10.E87.csv.gz
L29507_HSC-3_01_F02


title: Hematopoietic stem cell (HSC) 26

description:
featureCounts.mm10.E87.csv.gz
L29506_HSC-3_01_E02


title: Hematopoietic stem cell (HSC) 28

description:
featureCounts.mm10.E87.csv.gz
L29522_HSC-3_01_E04


title: Hematopoietic stem cell (HSC) 25

description:
featureCounts.mm10.E87.csv.gz
L29498_HSC-3_01_E01


title: Hematopoietic stem cell (HSC) 24

description:
featureCounts.mm10.E87.csv.gz
L29537_HSC-3_01_D06


title: Hematopoietic stem cell (HSC) 23

description:
featureCounts.mm10.E87.csv.gz
L29529_HSC-3_01_D05


title: Hematopoietic stem cell (HSC) 21

description:
featureCounts.mm10.E87.csv.gz
L29513_HSC-3_01_D03


title: Hematopoietic stem cell (HSC) 22

description:
featureCounts.mm10.E87.csv.gz
L29521_HSC-3_01_D04


title: Hematopoietic stem cell (HSC) 34

description:
featureCounts.mm10.E87.csv.gz
L29531_HSC-3_01_F05


title: Hematopoietic stem cell (HSC) 37

description:
featureCounts.mm10.E87.csv.gz
L29508_HSC-3_01_G02


title: Hematopoietic stem cell (HSC) 18

description:
featureCounts.mm10.E87.csv.gz
L29536_HSC-3_01_C06


title: Hematopoietic stem cell (HSC) 20

description:
featureCounts.mm10.E87.csv.gz
L29505_HSC-3_01_D02


title: Hematopoietic stem cell (HSC) 17

description:
featureCounts.mm10.E87.csv.gz
L29528_HSC-3_01_C05


title: Hematopoietic stem cell (HSC) 19

description:
featureCounts.mm10.E87.csv.gz
L29497_HSC-3_01_D01


title: Hematopoietic stem cell (HSC) 16

description:
featureCounts.mm10.E87.csv.gz
L29520_HSC-3_01_C04


title: Hematopoietic stem cell (HSC) 15

description:
featureCounts.mm10.E87.csv.gz
L29512_HSC-3_01_C03


title: Hematopoietic stem cell (HSC) 12

description:
featureCounts.mm10.E87.csv.gz
L29535_HSC-3_01_B06


title: Hematopoietic stem cell (HSC) 14

description:
featureCounts.mm10.E87.csv.gz
L29504_HSC-3_01_C02


title: Hematopoietic stem cell (HSC) 11

description:
featureCounts.mm10.E87.csv.gz
L29527_HSC-3_01_B05


title: Hematopoietic stem cell (HSC) 13

description:
featureCounts.mm10.E87.csv.gz
L29496_HSC-3_01_C01


title: Hematopoietic stem cell (HSC) 10

description:
featureCounts.mm10.E87.csv.gz
L29519_HSC-3_01_B04


title: Hematopoietic stem cell (HSC) 9

description:
featureCounts.mm10.E87.csv.gz
L29511_HSC-3_01_B03


title: Hematopoietic stem cell (HSC) 6

description:
featureCounts.mm10.E87.csv.gz
L29534_HSC-3_01_A06


title: Hematopoietic stem cell (HSC) 5

description:
featureCounts.mm10.E87.csv.gz
L29526_HSC-3_01_A05


title: Hematopoietic stem cell (HSC) 4

description:
featureCounts.mm10.E87.csv.gz
L29518_HSC-3_01_A04


title: Hop2-/- END-seq

city: Shanghai

first: Wei

last: Wu

state: Shanghai

address: 320 yueyang road

department: Center for Excellence in Molecular Cell Science

data_processing:
Library strategy: END-seq
mouse reads were aligned to the GRCm38p2/mm10 .Alignment is done using bowtie version 1.1.2, with the parameters: -l 50 -n 3 -k 1. Hybrid mice reads were aligned N-masked mm10. Alignment was done by Bowtie2 version 2.3.5.1 with options -N 1 -k 1. Then split the alignments into parental genomes by SNPsplit version 0.3.2.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were made for plus (*.plus.bw) and minus (*.neg.bw) strand separately using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig

source_name: Testis

extract_protocol:
Testes were removed, and spermatocytes isolated and embedded into agarose plugs (Bio-Rad cat#1703591). Cells were lysed in agarose using proteinase K, follwed by Rnase treatment. DNA was later precipitated after plug melting and shearing
Libraries were quantified using with the KAPA Library Quantification Kit (Kapa Biosciences) and sequenced in a NextSeq 550 system (Illumina, 75 bp single end reads).  libraries were prepared and sequenced following standard Illumina protocols

value: Testis

value: juvenile


title: Hematopoietic stem cell (HSC) 8

description:
featureCounts.mm10.E87.csv.gz
L29503_HSC-3_01_B02


title: Hematopoietic stem cell (HSC) 7

description:
featureCounts.mm10.E87.csv.gz
L29495_HSC-3_01_B01


title: WT END-seq with MRN+Mn

institute: Center for Excellence in Molecular Cell Science

value: WT

value: MRN and manganese


title: ATM-/- END-seq with ExoT+TDP2 rep2

value: 4 weeks

value: ExoT blunting only with purified TDP2


title: Hematopoietic stem cell (HSC) 2

description:
featureCounts.mm10.E87.csv.gz
L29502_HSC-3_01_A02


title: WT END-seq with MRN+CtIP-Mn

value: MRN, CtIP and no manganese


title: Hematopoietic stem cell (HSC) 1

description:
featureCounts.mm10.E87.csv.gz
L29494_HSC-3_01_A01


title: Hematopoietic stem cell (HSC) 3

description:
featureCounts.mm10.E87.csv.gz
L29510_HSC-3_01_A03


title: PRDM9-/- END-seq rep2


title: ETO+BTZ WO rep2

data_processing:
Library strategy: END-seq
mouse reads were aligned to the GRCm38p2/mm10 .Alignment is done using bowtie version 1.1.2, with the parameters: -l 50 -n 3 -k 1.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were made by Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig and the value is normalized by spike-in intensity.

source_name: WT-BCell-BTZ-ETO-WO

growth_protocol: Mature resting B-cells were isolated from mouse spleen with anti-CD43 MicroBeads (Miltenyi Biotech). B-cells were activated with LPS (25 μg/ml; Sigma), IL-4 (5 ng/ml; Sigma-Aldrich) and RP105 (0.5 μg/ml; BD Biosciences) for 12 hr as described (Callen et al., 2013; Callen et al., 2007).

extract_protocol:
Single cell suspensions of B cells (20 million per agarose plug) were washed in PBS, embedded in agarose and transferred into plug molds (Bio-Rad CHEF Mammalian Genomic DNA plug kit) and processed as previously described (Canela et al., 2016).END-seq was performed as described in Canela et al., 2017. Agarose plugs were made using the Bio-Rad CHEF Mammalian Genomic DNA plug kit. Embedded cells were lysed and digested using Proteinase K (50º C, 1 hour then 37ºC for 7 hours). Plugs were rinsed in TE buffer and treated with RNase A at 37ºC, 1 hour. The next enzymatic reactions were performed with the DNA in agarose plugs to prevent shearing. DNA ends were blunted for 1 hour at 37C with Exonuclease VII followed by Exonuclease T (NEB) for 1 hour at 25ºC to detect all TOP2 lesions, or only with Exonuclease T (NEB) 1 hour at 25C to detect only DSBs, "ExoT END-seq". After blunting, A-tailing was performed, followed by ligation of “END-seq hairpin adaptor 1”, 5′-Phos-GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGUU[Biotin-dT]U[Biotin-dT]UUACACTCTTTCCCTACACGACGCTCTTCCGATC*T-3′ [*phosphorothioate bond], using NEB Quick Ligase. Agarose plugs were then melted and dialyzed and DNA was sonicated to a median shear length of 170bp using Covaris S220 sonicator. DNA was ethanol-precipitated and dissolved in 70 ul TE buffer. Biotinylated DNA was isolated using MyOne Streptavidin C1 Beads (ThermoFisher #650-01), followed by end repair and dA-tailing. The second end was ligated to “END-seq hairpin adaptor 2”, 5′-Phos-GATCGGAAGAGCACACGTCUUUUUUUUAGACGTGTGCTCTTCCGATC*T-3′ [*phosphorothioate bond], using NEB Quick Ligase. Hairpins were digested using USER (NEB), and the resulting DNA fragments were PCR amplified using TruSeq barcoded primer p5, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATC*T and TruSeq barcoded primer p7, CAAGCAGAAGACGGCATACGAGANNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T, (NNNNNNNN represents barcode and * a phosphothiorate bond). PCR fragments were isolated by size selection from agarose gel, selecting 200-500 bp fragments followed by DNA purification using QIAquick Gel Extraction Kit.
Libraries were quantified using KAPA Library Quantification Kit and sequenced using Illumina NextSeq 550.

treatment_protocol: B-cells were pre-treated with proteasome inhibitor, either 10 μM MG132 (Sigma-Aldrich) or 5 μM Bortezomib (Millipore) for 1 hr then co-treated for an additional 2 hr with 50 μM Etoposide (E1383, Sigma-Aldrich). Following the ETO pulse, the cells were either harvested in the presence of the drugs, or washed three times in drug free media, and returned to 37°C to recover in fresh drug free media, until they were harvested at various timepoints post-washout for END-seq

tag: strain background

tag: genotype/variation

value: primary B cells

value: ETO+BTZ washout 0 hour


title: ETO+BTZ WO 2h rep2

tag: treatment

value: ETO+BTZ washout 2 hours


title: ETO+BTZ rep2

source_name: WT-BCell-BTZ-ETO

tag: cell type

value: ETO+BTZ


title: ETO WO 2h rep2

value: ETO washout 2 hours


title: ETO WO rep2

source_name: WT-BCell-ETO-WO

value: ETO washout 0 hour


title: RNF4 ETO ExoT only

value: ETO ExoT only


title: WT ETO ExoT only

source_name: WT-BCell-ETO-ExoT

value: ETO


title: co-BTZ+ETO

value: co-BTZ+ETO


title: co-BTZ+ETO WO 2h

value: co-BTZ+ETO washout 2 hours


title: no BTZ+ETO WO 2h

value: no BTZ+ETO washout 2 hours


title: ETO rep2

source_name: WT-BCell-ETO


title: no BTZ+ETO

value: no BTZ+ETO


title: WT ETO Exo7+ExoT

value: WT


title: BTZ rep2

source_name: WT-BCell-BTZ

value: BTZ


title: pre-BTZ+ETO WO 2h

value: pre-BTZ+ETO washout 2 hours


title: ETO+BTZ WO Exo7+ExoT


title: ETO WO ExoT

value: ETO washout 0 hour ExoT only


title: ETO+BTZ Exo7+ExoT


title: ETO Exo7+ExoT


title: ETO ExoT


title: ETO+BTZ ExoT

source_name: WT-BCell-BTZ-ETO-ExoT

value: ETO+BTZ ExoT only


title: ETO WO Exo7+ExoT

value: primary B cells


title: ETO+BTZ WO ExoT

value: ETO+BTZ washout 0 hour ExoT only


title: ETO+BTZ WO

value: ETO+BTZ washout 0 hour


title: ETO+BTZ WO 2h

value: ETO+BTZ washout 2 hours


title: NT rep2

source_name: WT-BCell-NT

value: nontreated


title: RNF4 ETO Exo7+ExoT


title: BTZ


title: ETO WO 2h

value: ETO washout 2 hours


title: ETO WO

value: ETO washout 0 hour


title: ETO

value: ETO


title: post-BTZ+ETO WO 2h

value: post-BTZ+ETO washout 2 hours


title: NT


title: pre-BTZ+ETO

value: pre-BTZ+ETO


title: WT MRE11 ChIP-seq

data_processing:
mouse reads were aligned to the GRCm38p2/mm10.Alignment was done using bowtie version 1.1.2, with the parameters: -l 50 -n 2 -m 1.
processed data files format and content: bigwig files were made for plus (*.plus.bw) and minus (*.neg.bw) strand separately using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig
Genome_build: mm10

extract_protocol:
Testes were removed, and spermatocytes isolated and fixed in 1% formaldehyde. Cells were sonicated, lysates clarified, and protein-DNA complexes immunoprecipitated.
Libraries were quantified using with the KAPA Library Quantification Kit (Kapa Biosciences) and sequenced in a NextSeq 550 system (Illumina, 75 bp single end reads).  libraries were prepared and sequenced following standard Illumina protocols

value: Testis

value: juvenile


title: ATM-/- H3K4me3 ChIP-seq

value: ATM-/-


title: ATM-/- MRE11 ChIP-seq


title: ETO+BTZ

value: WT

value: ETO+BTZ


title: B6xCAST hybrid END-seq rep2

data_processing:
Library strategy: END-seq
mouse reads were aligned to the GRCm38p2/mm10 .Alignment is done using bowtie version 1.1.2, with the parameters: -l 50 -n 3 -k 1. Hybrid mice reads were aligned N-masked mm10. Alignment was done by Bowtie2 version 2.3.5.1 with options -N 1 -k 1. Then split the alignments into parental genomes by SNPsplit version 0.3.2.
processed data files format and content: bigwig files were made for plus (*.plus.bw) and minus (*.neg.bw) strand separately using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig
Genome_build: mm10

tag: treament


title: WT for PRDM9-/- END-seq

tag: tissue


title: B6xCAST hybrid END-seq rep1

tag: strain


title: DMC1-/- END-seq

tag: age


title: CAST END-seq

value: CAST/EiJ

value: adult

tag: genotype


title: p53+/- END-seq


title: WT H3K4me3 ChIP-seq


title: BRCA1del11 53BP1-/- END-seq

value: BRCA1del11 53BP1-/-


title: WT for EXO1-/- END-seq


title: WT for BRCA1del11 53BP1 S25A END-seq


title: 53BP1-/- END-seq


title: BRCA1del11 p53+/- END-seq

value: BRCA1del11 p53+/-


title: EXO1-/- END-seq


title: BRCA1del11 53BP1 S25A END-seq

value: BRCA1del11 53BP1 S25A


title: ATM-/- END-seq with ExoT+TDP2

value: ExoT blunting only with purified TDP2


title: ATM-/- END-seq


title: ATM-/- END-seq with ExoT only

value: ExoT blunting only


title: WT END-seq with MRN+CtIP+Mn

value: MRN, CtIP and mangase


title: WT END-seq with ExoT+TDP2


title: WT END-seq with 20 mice rep1


title: WT END-seq with ExoT only


title: WT END-seq with 20 mice rep2


title: WT END-seq with 1 mouse


title: PRDM9-/- END-seq


title: CPTH6_Vehicle_3

city: Rochester

first: Shubham

last: Basu

state: Minnesota

address: 200 First St. SW

department: Division of Biomedical Statistics and Informatics

institute: Mayo Clinic

data_processing:
OMNI ATAC-seq data were analyzed using the HiChIP pipeline developed by the Mayo Bioinformatics Core
Paired-end reads were mapped to the HG38 genome reference using Burrows-Wheeler Alignment tool (BWA) (27). Pairs of reads with one or both reads uniquely mapped were retained and duplicates removed using Picard MarkDuplicates command (http://broadinstitute.github.io/picard/).
Peaks were identified using the Model-based Analysis of ChIP-Seq (MACS2) software package at FDR <=1%
For data visualization, BEDTools in combination with in-house scripts were used to generate normalized tag density profiles at a window size of 200 bp and step size of 20 bp.
Differential analysis of chromatin accessibility was performed using the DiffBind package
Raw read counts were normalized using the trimmed mean of M values (TMM) method, and sites with fold changes >=2 and FDR <=0.05 in the DiffBind test were extracted to represent differential chromatin accessibility sites.
Genome_build: hg38
Supplementary_files_format_and_content: peaks.bed

source_name: Biliary Epithelial Cells

growth_protocol: Cells grown in H69 media used for cholangiocyte cell lines

extract_protocol:
cell pellet snap frozen
50,000 cells were subjected to OMNI ATAC-seq following the published protocol. The enrichment of accessible region was determined by the fold difference between positive and negative genomic loci using real-time PCR. The libraries were sequenced to 51 base pairs from both ends on an Illumina HiSeq 4000 instrument.

treatment_protocol: Recombinat human TGF beta at 10ng/ml for 16 hours in presence or absence of CPTH6 50 uM

tag: cell line

value: H69 cholangiocyte cell line

tag: agent

tag: passage


title: DMSO_Vehicle_3

description: 50,000 cells were subjected to OMNI ATAC-seq


title: DMSO_TGF_beta_3


title: CPTH6_TGF_beta_2


title: CPTH6_TGF_beta_3


title: CPTH6_TGF_beta_1


title: CPTH6_Vehicle_2


title: DMSO_Vehicle_2


title: CPTH6_Vehicle_1


title: DMSO_TGF_beta_2


title: DMSO_TGF_beta_1


title: H69_5Vehicle_3_SMAD3

description: ChIP-seq library using the ThruPLEX® DNA-seq Kit V2 sequenced to on an Illumina HiSeq 4000

data_processing:
ChIP-Seq data were analyzed using the HiChIP pipeline developed by the Mayo Bioinformatics Core
Paired-end reads were mapped to the HG38 genome reference using Burrows-Wheeler Alignment tool (BWA) (27). Pairs of reads with one or both reads uniquely mapped were retained and duplicates removed using Picard MarkDuplicates command (http://broadinstitute.github.io/picard/).
Peaks were identified using the Model-based Analysis of ChIP-Seq (MACS2) software package at FDR <=1%
For data visualization, BEDTools in combination with in-house scripts were used to generate normalized tag density profiles at a window size of 200 bp and step size of 20 bp.
Genome_build: hg38
Supplementary_files_format_and_content: peaks.bed

extract_protocol:
Cross linked with 1% formaldehyde for 10 mins followed by quinching with glycine and washed with TBS. ChIP-seq was performed as described by Zhong et al., 2017.
ChIP-seq libraries were prepared from about 1 - 10 ng ChIP and input DNA using the ThruPLEX® DNA-seq Kit V2 (Rubicon Genomics, Ann Arbor, MI). The libraries were sequenced to 51 base pairs from both ends on an Illumina HiSeq 4000 instrument in the Mayo Clinic Center for Individualized Medicine Medical Genomics Facility.

treatment_protocol: Recombinat human TGF beta at 10ng/ml for 16 hours

value: Vehicle

tag: antibody


title: DMSO_Vehicle_1


title: H69_5Vehicle_input


title: H69_5TGF_beta_3_SMAD3

value: TGF beta


title: H69_4TGF_beta_input


title: H69_4TGF_beta_3_SMAD3


title: Vehicle_2_K9_ac


title: H69_2Vehicle_input


title: Vehicle_1_K9ac


title: H69_4Vehicle_3_SMAD3


title: Vehicle_1_K27ac


title: H69_1TGF_beta_input


title: Vehicle_2_K27ac


title: TGF_beta_2_K9ac


title: TGF_beta_1_K9ac


title: TGF_beta_2_K27ac


title: TGF_beta_1_K27ac


title: HCC1569 HDACi 10h DOX biological replicate 2

first: Paola

last: Scaffidi

address: 1 Midland Road

institute: Francis Crick Institute

data_processing:
Adapter trimming was performed with cutadapt (version 1.9.1) (Martin M, 2011) with parameters “--minimum-length=25 --quality-cutoff=20 -a AGATCGGAAGAGC”.
The RSEM package (version 1.2.31) (Li and Dewey, 2011) in conjunction with the STAR alignment algorithm (version 2.5.2a) (Dobin et al., 2013) was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to hg19 RefSeq genes downloaded from the UCSC Table Browser (Karolchik et al., 2004) on 7th June 2017. The parameters used were “--star-output-genome-bam --forward-prob 0”.
Differential expression analysis was performed with the DESeq2 package (version 1.14.1) (Love et al., 2014) within the R programming environment (version 3.3.2) (http://www.R-project.org/). An adjusted p-value of <= 0.01 was used as the significance threshold for the identification of differentially expressed genes.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file containing TPM values generated by RSEM where gene names are rows and columns represent all RNA-Seq samples generated in the study

source_name: HCC1569 HDACi 10h DOX

growth_protocol: Cells were grown in RPMI medium containing Tet-free 10% fetal bovine serum (FBS), 2 mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin, at 37 °C in 5% CO2.

extract_protocol:
Total cell RNA was prepared from the cells using RNAeasy reagents (Qiagen).
The total RNA samples were quality controlled (QC) using the 6000 Nano RNA Chip on the BioAnalyser 2100 (Agilent, Santa Clara, CA, USA) to insure RNA integrity and concentration before starting the procedure.  mRNA libraries were generated using the KAPA mRNA Hyper Prep Kit (Roche) following manufacturer’s instructions. Library QC was reperformed on the BioAnalyser 2100 followed by sequencing on the Illumina HiSeq 4000 to generate 76bp strand-specific single-end reads.

treatment_protocol: Cells were treated with 1µg/ml Doxycicline (dox) starting 4 days before HDACi treatment and throughout the treatment. HDACi (JNJ-26481585) was added at 25nM concentration.

value: breast cancer cells

value: HDACi treated at 10h minutes, induced shRNA


title: HCC1569 HDACi 10h DOX biological replicate 3


title: HCC1569 HDACi 10h DOX biological replicate 1


title: HCC1569 HDACi 3h DOX biological replicate 3

source_name: HCC1569 HDACi 3h DOX

value: HDACi treated at 3h, induced shRNA


title: HCC1569 HDACi 10h NT biological replicate 2

source_name: HCC1569 HDACi 10h NT

value: HDACi treated at 10h, uninduced shRNA


title: HCC1569 HDACi 10h NT biological replicate 3


title: HCC1569 HDACi 10h NT biological replicate 1


title: HCC1569 HDACi 3h DOX biological replicate 2


title: HCC1569 HDACi 3h DOX biological replicate 1


title: HCC1569 HDACi 3h NT biological replicate 3

source_name: HCC1569 HDACi 3h NT

value: HDACi treated at 3h, uninduced shRNA


title: HCC1569 HDACi 1h DOX biological replicate 3

source_name: HCC1569 HDACi 1h DOX

value: HDACi treated at 1h, induced shRNA


title: HCC1569 HDACi 1h DOX biological replicate 1


title: HCC1569 HDACi 3h NT biological replicate 2


title: HCC1569 HDACi 1h NT biological replicate 3

source_name: HCC1569 HDACi 1h NT

value: HDACi treated at 1h, uninduced shRNA


title: HCC1569 HDACi 1h DOX biological replicate 2


title: HCC1569 HDACi 30min DOX biological replicate 3

source_name: HCC1569 HDACi 30min DOX

value: HDACi treated at 30 minutes, induced shRNA


title: HCC1569 HDACi 1h NT biological replicate 2


title: HCC1569 HDACi 1h NT biological replicate 1


title: HCC1569 HDACi 30min DOX biological replicate 2


title: HCC1569 HDACi 3h NT biological replicate 1


title: HCC1569 HDACi 30min DOX biological replicate 1


title: HCC1569 DMSO DOX biological replicate 2

source_name: HCC1569 DMSO DOX

value: DMSO treated, induced shRNA


title: HCC1569 HDACi 30min NT biological replicate 3

source_name: HCC1569 HDACi 30min NT

value: HDACi treated at 30 minutes, uninduced shRNA


title: HCC1569 HDACi 30min NT biological replicate 2


title: HCC1569 DMSO DOX biological replicate 3


title: HCC1569 DMSO DOX biological replicate 1


title: HCC1569 DMSO NT biological replicate 3

source_name: HCC1569 DMSO NT

value: DMSO treated, uninduced shRNA


title: HCC1569 DMSO NT biological replicate 2


title: HCC1569 DMSO NT biological replicate 1


title: HCC1569 HDACi 30min NT biological replicate 1


title: TGFb3

description: Qiagen Kit was utilized to isolate mRNA

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by STAR-2.6.1 aligner
Gene counts were generated using Subread featureCounts (http://subread.sourceforge.net/)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each gene per sample

extract_protocol:
Qiagen Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: TGF beta at 10ng/ml for 16 hours


title: TGFb2

description: Qiagen Kit was utilized to isolate mRNA


title: Veh2

description: Qiagen Kit was utilized to isolate mRNA

value: vehicle


title: 0h human control rep1 (trophozoites)

city: Uppsala

first: Feifei

last: Xu

address: Husargatan 3

country: Sweden

institute: Uppsala University

data_processing:
Illumina HiSeq 2500, Demultiplexing and conversion to FASTQ performed using the bclfastq2
FASTQ files were mapped to combined Giardia WB genome and human GRCh38 using STAR v2.5.2b. ReadsPerGene.out.tab output from STAR with specifying --quantMode GeneCounts were used as the raw counts input for downstream analysis
Gene differential expression analysis was carried out in R using edgeR v3.26.8 workflow. Quasi-likelihood F test was used to determine significant differential gene expression.
Genome_build: Giardia WB, AACB03000000
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts from STAR mapping for each sample, separated by host and parasite

growth_protocol: Trophozoites were grown in TYI-S33 until 80% confluency after cells were detached and spun down. Giardia cells were resuspended in DMEM (HI-FBS) for 10 minutes and incubated with previously grown and differenatiated Caco2 cells for 1.5, 3 and 4.5 h. Prior interaction Giardia cells and Caco-2 cells were collected.

extract_protocol:
Performed according to the instructions provided with the Trizol reagent. RNA was then treated with DNaseI and extracted again by phenol chloroform extraction
Sequencing libraries were prepared from 250 ng total RNA using the TruSeq stranded mRNA library preparation kit (Cat# 20020594/5, Illumina Inc.) including polyA selection.The library preparation was performed according to the manufacturers’ protocol (#1000000040498).

treatment_protocol: Upon reaching 80% confluence, trophozoites were detached on ice (10m), pelleted and lysed in 1ml of Trizol and collected in Eppendorf tubes. Samples were frozen immediatedly in liquid nitrogen and kept at -80 until RNA extraction

tag: growth medium

value: DMEM

tag: time

value: 0h human control


title: 0h human control rep2 (trophozoites)


title: HCI002_262_T_PT_96

city: Irvine

first: Devon

middle: A

last: Lawson

state: CA

address: 839 Health Science Road, Sprague Hall 114

department: Physiology and Biophysics

institute: UC Irvine

data_processing:
Files from the HiSeq2500 were demultiplexed and converted to FASTQ files. Paired-end 100bp reads were aligned to the hg21 human transcriptome using Bowtie2 and quantified using RSEM with the following parameters: rsem-calculate-expression -p $CORES --bowtie2 --paired-end READ1 READ2 gencodehg21. Expression values were log-transformed into log(TPM+1) matrices and loaded into the Seurat analysis package with the following parameters: p10 <- CreateSeuratObject(raw.data = p10.mat, min.cells = 8, min.genes = 1000,  project = "HCI010").
Genome_build: hg21
Supplementary_files_format_and_content: genes.results.FPKM.txt

source_name: Patient Derived Xenograft Single Cells

extract_protocol:
Animals at endpoint were euthanized by asphyxiation with CO2 followed by cervical dislocation and perfusion with 10mM EDTA in D-PBS.  Prior to perfusion, Evan’s Blue (Sigma-Aldrich, Cat. No. E2129-10G) was injected into the footpads and ears of anesthetized mice to aid in lymph node visualization. Solid tissues from the mice, which includes the primary tumour, lung, and lymph nodes were processed for flow cytometry by mechanically chopping with blades, followed by Collagenase IV digest (Sigma-Aldrich Cat. No. C5138-1G) in media (DMEM/F12 with 5% FBS, 5µg/mL insulin, and 1% Penstrep/Ampho B) for 45 min at 37°C. Cell suspensions were washed with 2 µg/mL DNAseI for 5 min and further dissociated with 0.05% Trypsin for 10 min. Following a wash with HBBS/2% FBS, cells were passed through a 70µm filter. Lung and primary tumour cells were treated with 1X RBC lysis buffer, followed by resuspension in DMEM/F12 with 10% FBS for FACS. We used the human-specific antibody CD298 (PE, BioLegend, Cat. No. 341704) and the mouse-specific antibody MHCI (APC, ThermoFisher, Scientific Cat. No. 17-5957-80). Flow cytometry was performed using the BD FACSAria Fusion cell sorter. Cell viability was determined by negative staining for SYTOX Blue (ThermoFisher Scientific Cat. No. S34857). Forward scatter area by forward scatter width (FSC W x FSC A) and side scatter area by side scatter width (SSC W x SSC A) was used to discriminate single cells from doublet and multiplet cells. Mouse cells were excluded by gating out CD298-MHCI+. Human primary tumour cells and metastatic cells were selected by gating on Sytox-CD298+MHC-I-.
Single cells were sorted directly into each well of a skirted 96-well PCR plate (Fisher Scientific, Eppendorf, Cat. No. E951020443) containing lysis buffer (0.2% Triton X-100, 2 U/µL RNAseOUT, 10µM oligo-dT30VN, and 10µM dNTPs). The plates were snap frozen on dry ice and stored at -80°C until further processing. Total RNA was converted into cDNA using the SmartSeq2 protocol and prepared for Illumina sequencing with the Nextera XT DNA Library Preparation Kit (Illumina, Cat No. FC-131-1096). Cells were sequenced at a depth of 1 million reads/cell on the HiSeq2500.

tag: patient id

tag: status

value: Tumor

tag: tissue source

value: Primary Tumor

tag: mouse


title: HCI002_262_T_PT_94


title: Veh1

description: Qiagen Kit was utilized to isolate mRNA

tag: treatment


title: Veh3

description: Qiagen Kit was utilized to isolate mRNA


title: HCI002_262_T_PT_95


title: HCI002_262_T_PT_92


title: HCI002_262_T_PT_86


title: HCI002_262_T_PT_88


title: HCI002_262_T_PT_89


title: HCI002_262_T_PT_91


title: HCI002_262_T_PT_87


title: HCI002_262_T_PT_90


title: Spontaneously immortalized murine keratinocytes_A20 cDNA-containing vector,TNF treatment_replicate 1

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human and Mouse Gene 2.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.46.0).

source_name: Spontaneously immortalized murine keratinocytes, isolated from the skin of newborn C57BL/6 mice, transduced with A20 cDNA-containing vector (pCF G5 A20), treatment with 500 µg/ml TNF for 1h

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: The generation and characterization of the HaCaT immortalized human keratinocytes has been previously described [PMID: 2450098]. Cells were transduced with lentiviral vector PF 5x UAS MCS W SV40 Prom either empty or containing human A20 cDNA. Murine keratinocytes were isolated from the skin of newborn C57BL/6 mice and spontaneously immortalized in CnT-07 medium (CELLnTEC). Murine keratinocytes were transduced with pCF G5 either empty or containing murine A20 cDNA.

extract_protocol: Total RNA was isolated from samples using the RNeasy kit (Qiagen) with a DNase digestion step according to the manufacturer’s protocol.

treatment_protocol: Cells were pre-stimulated with 100nM 4-Hydroxy-Tamoxifen 24h before experiment for A20 overexpression. Cells were starved 6h in medium without FSC medium 6h before experiment. Cells were treated with 500ng/ml HF-TNF for 1h.

tag: strain background

tag: cell type

tag: cell culture medium

value: CnT Prime

tag: passage number of cells

value: TNF in CnT-Prime 500ng/ml for 1h

tag: experiment


title: Spontaneously immortalized murine keratinocytes_empty vector_control treatment_replicate 2

source_name: Spontaneously immortalized murine keratinocytes, isolated from the skin of newborn C57BL/6 mice, transduced with empty vector (pCF G5), control treatment (vehicle; PBS:CnT-Prime ratio 1:1000)

value: vehicle (PBS:CnT-Prime 1:1000)


title: HCI002_262_T_PT_85


title: Spontaneously immortalized murine keratinocytes_A20 cDNA-containing vector_control treatment_replicate 2

source_name: Spontaneously immortalized murine keratinocytes, isolated from the skin of newborn C57BL/6 mice, transduced with A20 cDNA-containing vector (pCF G5 A20), control treatment (vehicle; PBS:CnT-Prime ratio 1:1000)


title: Spontaneously immortalized murine keratinocytes_A20 cDNA-containing vector_control treatment_replicate 1

value: Spontaneously immortalized murine keratinocytes, isolated from the skin of newborn C57BL/6 mice


title: Spontaneously immortalized murine keratinocytes_empty vector,TNF treatment_replicate 1

source_name: Spontaneously immortalized murine keratinocytes, isolated from the skin of newborn C57BL/6 mice, transduced with empty vector (pCF G5), treatment with 500 µg/ml TNF for 1h


title: Spontaneously immortalized murine keratinocytes_A20 cDNA-containing vector,TNF treatment_replicate 2


title: Spontaneously immortalized murine keratinocytes_empty vector,TNF treatment_replicate 2


title: TGFb1

description: Qiagen Kit was utilized to isolate mRNA


title: Spontaneously immortalized murine keratinocytes_empty vector_control treatment_replicate 1


title: 0h human control rep3 (trophozoites)


title: HCI002_262_T_PT_84


title: HCI002_262_T_PT_93


title: HCI002_262_T_PT_83


title: HCI002_262_T_PT_82


title: HCI002_262_T_PT_78


title: HCI002_262_T_PT_80


title: HCI002_262_T_PT_76


title: HCI002_262_T_PT_77


title: HCI002_262_T_PT_74


title: HCI002_262_T_PT_73


title: HCI002_262_T_PT_72


title: HCI002_262_T_PT_71


title: HCI002_262_T_PT_69


title: HCI002_262_T_PT_67


title: HCI002_262_T_PT_68


title: HCI002_262_T_PT_64


title: HCI002_262_T_PT_66


title: HCI002_262_T_PT_65


title: HCI002_262_T_PT_61


title: HCI002_262_T_PT_63


title: HCI002_262_T_PT_60


title: HCI002_262_T_PT_58


title: HCI002_262_T_PT_59


title: HCI002_262_T_PT_62


title: HCI002_262_T_PT_57


title: HCI002_262_T_PT_56


title: HCI002_262_T_PT_81


title: HCI002_262_T_PT_79


title: HCI002_262_T_PT_75


title: HCI002_262_T_PT_54


title: HCI002_262_T_PT_53


title: HCI002_262_T_PT_52


title: HCI002_262_T_PT_70


title: HCI002_262_T_PT_45


title: HCI002_262_T_PT_48


title: HCI002_262_T_PT_44


title: HCI002_262_T_PT_47


title: HCI002_262_T_PT_41


title: HCI002_262_T_PT_43


title: HCI002_262_T_PT_40


title: HCI002_262_T_PT_55


title: HCI002_262_T_PT_51


title: HCI002_262_T_PT_50


title: HCI002_262_T_PT_49


title: HCI001_257_I_LU_18

value: Metastasis

value: Lung


title: HCI001_257_I_LU_26


title: HCI001_257_I_LU_25


title: HCI001_257_I_LU_24


title: HCI001_257_I_LU_20


title: HCI001_257_I_LU_23


title: HCI001_257_I_LU_17


title: HCI001_257_I_LU_19


title: HCI001_257_I_LU_16


title: HCI001_257_I_LU_21


title: HCI001_257_I_LU_27


title: HCI002_262_T_PT_46


title: HCI002_262_T_PT_42


title: HCI001_257_I_LU_15


title: HCI001_257_I_LU_13


title: HCI002_262_T_PT_39


title: HCI002_262_T_PT_38


title: HCI001_257_I_LU_22


title: HCI001_257_I_LU_12


title: HCI001_257_I_LU_7


title: HCI001_257_I_LU_8


title: HCI001_257_I_LU_10


title: HCI001_257_I_LU_5


title: HCI001_257_I_LU_6


title: HCI001_257_I_LU_14


title: HCI001_257_I_LU_2


title: HCI001_257_I_LU_4


title: HCI001_257_I_LU_3


title: HCI001_259_T_PT_89


title: HCI001_259_T_PT_95


title: HCI001_257_I_LU_1


title: HCI001_257_I_LU_9


title: HCI001_259_T_PT_94


title: HCI001_259_T_PT_93


title: HCI001_259_T_PT_86


title: HCI001_259_T_PT_83


title: HCI001_259_T_PT_91


title: HCI001_257_I_LU_11


title: HCI001_259_T_PT_82


title: HCI001_259_T_PT_85


title: HCI001_259_T_PT_84


title: HCI001_259_T_PT_90


title: HCI001_259_T_PT_88


title: HCI001_259_T_PT_81


title: HCI001_259_T_PT_80


title: HCI001_259_T_PT_92


title: HCI001_259_T_PT_79


title: HCI001_259_T_PT_78


title: HCI001_259_T_PT_76


title: HCI001_259_T_PT_75


title: HCI001_259_T_PT_74


title: HCI001_259_T_PT_73


title: HCI001_259_T_PT_96


title: HCI001_259_T_PT_72


title: HCI001_259_T_PT_71


title: HCI001_259_T_PT_87


title: HCI001_259_T_PT_70


title: HCI001_259_T_PT_68


title: HCI001_259_T_PT_67


title: HCI001_259_T_PT_69


title: HCI001_259_T_PT_66


title: HCI001_259_T_PT_65


title: HCI001_259_T_PT_63


title: HCI001_259_T_PT_64


title: HCI001_259_T_PT_62


title: HCI001_259_T_PT_77


title: HCI001_259_T_PT_61


title: HCI001_259_T_PT_60


title: HCI001_259_T_PT_59


title: HCI001_259_T_PT_53


title: HCI001_259_T_PT_56


title: HCI001_259_T_PT_54


title: HCI001_259_T_PT_57


title: HCI001_259_T_PT_58


title: HCI001_259_T_PT_52


title: HCI001_259_T_PT_55


title: HCI001_259_T_PT_46


title: HCI001_259_T_PT_51


title: HCI001_259_T_PT_50


title: HCI001_259_T_PT_49


title: HCI001_259_T_PT_48


title: HCI001_259_T_PT_43


title: HCI001_259_T_PT_44


title: HCI001_259_T_PT_45


title: HCI001_259_T_PT_42


title: HCI001_259_T_PT_41


title: HCI001_259_T_PT_40


title: HCI001_259_T_PT_39


title: HCI001_259_T_PT_38


title: HCI001_259_T_PT_36


title: HCI001_259_T_PT_37


title: HCI001_259_T_PT_35


title: HCI001_259_T_PT_47


title: HCI001_259_T_PT_34


title: HCI001_259_T_PT_29


title: HCI001_259_T_PT_31


title: HCI001_259_T_PT_33


title: HCI001_259_T_PT_30


title: HCI001_259_T_PT_32


title: HCI001_259_T_PT_28


title: HCI001_259_T_PT_22


title: HCI001_259_T_PT_26


title: HCI001_259_T_PT_24


title: HCI001_259_T_PT_23


title: HCI001_259_T_PT_21


title: HCI001_259_T_PT_25


title: HCI001_259_T_PT_20


title: HCI001_259_T_PT_27


title: HCI001_259_T_PT_18


title: HCI001_259_T_PT_19


title: HCI001_259_T_PT_17


title: HCI001_259_T_PT_16


title: HCI001_259_T_PT_14


title: HCI001_259_T_PT_15


title: HCI001_259_T_PT_13


title: HCI001_259_T_PT_12


title: HCI001_259_T_PT_6


title: HCI001_259_T_PT_8


title: HCI001_259_T_PT_7


title: HCI001_259_T_PT_9


title: HCI001_259_T_PT_10


title: HCI001_259_T_PT_11


title: HCI001_259_T_PT_5


title: HCI001_259_T_PT_4


title: HCI001_259_I_LU_86


title: HCI001_259_T_PT_3


title: HCI001_259_T_PT_2


title: HCI001_259_I_LU_87


title: HCI001_259_T_PT_1


title: HCI001_259_I_LU_85


title: HCI001_259_I_LU_82


title: HCI001_259_I_LU_83


title: HCI001_259_I_LU_81


title: HCI001_259_I_LU_79


title: HCI001_259_I_LU_80


title: HCI001_259_I_LU_73


title: HCI001_259_I_LU_74


title: HCI001_259_I_LU_77


title: HCI001_259_I_LU_72


title: HCI001_259_I_LU_69


title: HCI001_259_I_LU_71


title: HCI001_259_I_LU_70


title: HCI001_259_I_LU_63


title: HCI001_259_I_LU_67


title: HCI001_259_I_LU_62


title: HCI001_259_I_LU_64


title: HCI001_259_I_LU_66


title: HCI001_259_I_LU_65


title: HCI001_259_I_LU_61


title: HCI001_259_I_LU_84


title: HCI001_259_I_LU_60


title: HCI001_259_I_LU_59


title: HCI001_259_I_LU_68


title: HCI001_259_I_LU_57


title: HCI001_259_I_LU_75


title: HCI001_259_I_LU_76


title: HCI001_259_I_LU_56


title: HCI001_259_I_LU_55


title: HCI001_259_I_LU_53


title: HCI001_259_I_LU_52


title: HCI001_259_I_LU_78


title: HCI001_259_I_LU_58


title: HCI001_259_I_LU_50


title: HCI001_259_I_LU_49


title: HCI001_259_I_LU_54


title: HCI001_259_I_LU_48


title: HCI001_259_I_LU_47


title: HCI001_259_I_LU_46


title: HCI001_259_I_LU_43


title: HCI001_259_I_LU_42


title: HCI001_259_I_LU_41


title: HCI001_259_I_LU_45


title: HCI001_259_I_LU_44


title: HCI001_259_I_LU_40


title: HCI001_259_I_LU_37


title: HCI001_259_I_LU_39


title: HCI001_259_I_LU_36


title: HCI001_259_I_LU_34


title: HCI001_259_I_LU_33


title: HCI001_259_I_LU_31


title: HCI001_259_I_LU_38


title: HCI001_259_I_LU_35


title: HCI001_259_I_LU_32


title: HCI001_259_I_LU_28


title: HCI001_259_I_LU_29


title: HCI001_259_I_LU_30


title: HCI001_259_I_LU_27


title: HCI001_259_I_LU_26


title: HCI001_259_I_LU_51


title: HCI001_259_I_LU_22


title: HCI001_259_I_LU_23


title: HCI001_259_I_LU_24


title: HCI001_259_I_LU_20


title: HCI001_259_I_LU_21


title: HCI001_259_I_LU_19


title: HCI001_259_I_LU_18


title: HCI001_259_I_LU_17


title: HCI001_259_I_LU_14


title: HCI001_259_I_LU_13


title: HCI001_259_I_LU_12


title: HCI001_259_I_LU_16


title: HCI001_259_I_LU_11


title: HCI001_259_I_LU_7


title: HCI001_259_I_LU_8


title: HCI001_259_I_LU_10


title: HCI001_259_I_LU_9


title: HCI001_259_I_LU_6


title: HCI001_259_I_LU_5


title: HCI001_259_I_LU_4


title: HCI001_259_I_LU_25


title: HCI001_259_I_LU_1


title: HCI001_259_I_LU_2


title: HCI001_259_I_LU_3


title: HCI010_468_T_PT_83


title: HCI010_468_T_PT_82


title: HCI010_468_T_PT_84


title: HCI010_468_T_PT_81


title: HCI010_468_T_PT_80


title: HCI010_468_T_PT_79


title: HCI001_259_I_LU_15


title: HCI010_468_T_PT_76


title: HCI010_468_T_PT_74


title: HCI010_468_T_PT_75


title: HCI010_468_T_PT_73


title: HCI010_468_T_PT_77


title: HCI010_468_T_PT_78


title: HCI010_468_T_PT_70


title: HCI010_468_T_PT_72


title: HCI010_468_T_PT_68


title: HCI010_468_T_PT_69


title: HCI010_468_T_PT_71


title: HCI010_468_T_PT_65


title: HCI010_468_T_PT_64


title: HCI010_468_T_PT_66


title: HCI010_468_T_PT_61


title: HCI010_468_T_PT_67


title: HCI010_468_T_PT_62


title: HCI010_468_T_PT_60


title: HCI010_468_T_PT_63


title: HCI010_468_T_PT_59


title: HCI010_468_T_PT_58


title: HCI010_468_T_PT_56


title: HCI010_468_T_PT_55


title: HCI010_468_T_PT_57


title: HCI010_468_T_PT_53


title: HCI010_468_T_PT_52


title: HCI010_468_T_PT_54


title: HCI010_468_T_PT_51


title: HCI010_468_T_PT_49


title: HCI010_468_T_PT_50


title: HCI010_468_T_PT_48


title: HCI010_468_T_PT_47


title: HCI010_468_T_PT_46


title: HCI010_468_T_PT_45


title: HCI010_468_T_PT_44


title: HCI010_468_T_PT_43


title: HCI010_468_T_PT_42


title: HCI010_468_T_PT_41


title: HCI010_468_T_PT_40


title: HCI010_468_T_PT_39


title: HCI010_468_T_PT_34


title: HCI010_468_T_PT_33


title: HCI010_468_T_PT_32


title: HCI010_468_T_PT_30


title: HCI010_468_T_PT_29


title: HCI010_468_T_PT_31


title: HCI010_468_T_PT_35


title: HCI010_468_T_PT_28


title: HCI010_468_T_PT_26


title: HCI010_468_T_PT_27


title: HCI010_468_T_PT_25


title: HCI010_468_T_PT_23


title: HCI010_468_T_PT_24


title: HCI010_468_T_PT_21


title: HCI010_468_T_PT_22


title: HCI010_468_T_PT_19


title: HCI010_468_T_PT_20


title: HCI010_468_T_PT_38


title: HCI010_468_T_PT_16


title: HCI010_468_T_PT_18


title: HCI010_468_T_PT_17


title: HCI010_468_T_PT_36


title: HCI010_468_T_PT_13


title: HCI010_468_T_PT_14


title: HCI010_468_T_PT_15


title: HCI010_468_T_PT_37


title: HCI010_468_T_PT_10


title: HCI010_468_T_PT_11


title: HCI010_468_T_PT_12


title: HCI010_468_T_PT_8


title: HCI010_468_T_PT_9


title: HCI010_468_T_PT_7


title: HCI010_468_T_PT_6


title: HCI010_468_T_PT_3


title: HCI010_468_T_PT_2


title: HCI010_468_T_PT_4


title: HCI010_468_I_LN_47

value: Lymph Node


title: HCI010_468_I_LN_48


title: HCI010_468_I_LN_43


title: HCI010_468_I_LN_44


title: HCI010_468_I_LN_41


title: HCI010_468_I_LN_42


title: HCI010_468_I_LN_40


title: HCI010_468_I_LN_45


title: HCI010_468_I_LN_46


title: HCI010_468_I_LN_35


title: HCI010_468_I_LN_39


title: HCI010_468_T_PT_5


title: HCI010_468_I_LN_31


title: HCI010_468_I_LN_33


title: HCI010_468_I_LN_37


title: HCI010_468_I_LN_29


title: HCI010_468_I_LN_30


title: HCI010_468_T_PT_1


title: HCI010_468_I_LN_27


title: HCI010_468_I_LN_25


title: HCI010_468_I_LN_20


title: HCI010_468_I_LN_21


title: HCI010_468_I_LN_38


title: HCI010_468_I_LN_19


title: HCI010_468_I_LN_36


title: HCI010_468_I_LN_22


title: HCI010_468_I_LN_32


title: HCI010_468_I_LN_34


title: HCI010_468_I_LN_28


title: HCI010_468_I_LN_24


title: HCI010_468_I_LN_26


title: HCI010_468_I_LN_23


title: HCI010_468_I_LN_4


title: HCI010_468_I_LN_10


title: HCI010_468_L_LU_46


title: HCI010_468_I_LN_3


title: HCI010_468_I_LN_1


title: HCI010_468_I_LN_11


title: HCI010_468_I_LN_16


title: HCI010_468_I_LN_14


title: HCI010_468_I_LN_7


title: HCI010_468_I_LN_18


title: HCI010_468_I_LN_9


title: HCI010_468_I_LN_5


title: HCI010_468_I_LN_15


title: HCI010_468_L_LU_47


title: HCI010_468_I_LN_12


title: HCI010_468_I_LN_8


title: HCI010_468_I_LN_17


title: HCI010_468_L_LU_43


title: HCI010_468_L_LU_44


title: HCI010_468_L_LU_45


title: HCI010_468_L_LU_48


title: HCI010_468_I_LN_13


title: HCI010_468_L_LU_42


title: HCI010_468_I_LN_6


title: HCI010_468_L_LU_41


title: HCI010_468_L_LU_40


title: HCI010_468_I_LN_2


title: HCI010_468_L_LU_39


title: HCI010_468_L_LU_37


title: HCI010_468_L_LU_38


title: HCI010_468_L_LU_35


title: HCI010_468_L_LU_34


title: HCI010_468_L_LU_27


title: HCI010_468_L_LU_22


title: HCI010_468_L_LU_32


title: HCI010_468_L_LU_20


title: HCI010_468_L_LU_28


title: HCI010_468_L_LU_21


title: HCI010_468_L_LU_23


title: HCI010_468_L_LU_12


title: HCI010_468_L_LU_18


title: HCI010_468_L_LU_31


title: HCI010_468_L_LU_26


title: HCI010_468_L_LU_16


title: HCI010_468_L_LU_10


title: HCI010_468_L_LU_17


title: HCI010_468_L_LU_30


title: HCI010_468_L_LU_8


title: HCI010_468_L_LU_9


title: HCI010_468_L_LU_15


title: HCI010_468_L_LU_13


title: HCI010_468_L_LU_29


title: HCI010_468_L_LU_11


title: HCI010_468_L_LU_7


title: HCI010_468_L_LU_33


title: HCI010_468_L_LU_36


title: HCI010_468_L_LU_14


title: HCI010_468_L_LU_19


title: HCI010_468_L_LU_25


title: HCI010_468_L_LU_3


title: HCI010_468_L_LU_4


title: HCI010_468_L_LU_5


title: HCI010_468_L_LU_6


title: HCI010_472_T_PT_96


title: HCI010_468_L_LU_1


title: HCI010_472_T_PT_95


title: HCI010_472_T_PT_93


title: HCI010_472_T_PT_94


title: HCI010_468_L_LU_24


title: HCI010_472_T_PT_91


title: HCI010_472_T_PT_84


title: HCI010_472_T_PT_90


title: HCI010_472_T_PT_86


title: HCI010_472_T_PT_88


title: HCI010_472_T_PT_82


title: HCI010_472_T_PT_83


title: HCI010_472_T_PT_92


title: HCI010_472_T_PT_89


title: HCI010_472_T_PT_87


title: HCI010_472_T_PT_77


title: HCI010_472_T_PT_78


title: HCI010_472_T_PT_85


title: HCI010_472_T_PT_76


title: HCI010_472_T_PT_75


title: HCI010_472_T_PT_81


title: HCI010_472_T_PT_80


title: HCI010_472_T_PT_73


title: HCI010_472_T_PT_74


title: HCI010_468_L_LU_2


title: HCI010_472_T_PT_67


title: HCI010_472_T_PT_72


title: HCI010_472_T_PT_68


title: HCI010_472_T_PT_70


title: HCI010_472_T_PT_69


title: HCI010_472_T_PT_71


title: HCI010_472_T_PT_66


title: HCI010_472_T_PT_64


title: HCI010_472_T_PT_65


title: HCI010_472_T_PT_63


title: HCI010_472_T_PT_58


title: HCI010_472_T_PT_54


title: HCI010_472_T_PT_59


title: HCI010_472_T_PT_56


title: HCI010_472_T_PT_57


title: HCI010_472_T_PT_50


title: HCI010_472_T_PT_51


title: HCI010_472_T_PT_60


title: HCI010_472_T_PT_46


title: HCI010_472_T_PT_55


title: HCI010_472_T_PT_61


title: HCI010_472_T_PT_53


title: HCI010_472_T_PT_47


title: HCI010_472_T_PT_48


title: HCI010_472_T_PT_52


title: HCI010_472_T_PT_62


title: HCI010_472_T_PT_49


title: HCI010_472_T_PT_79


title: HCI010_472_T_PT_40


title: HCI010_472_T_PT_42


title: HCI010_472_T_PT_44


title: HCI010_472_T_PT_39


title: HCI010_472_T_PT_43


title: HCI010_472_T_PT_37


title: HCI010_472_T_PT_41


title: HCI010_472_T_PT_35


title: HCI010_472_T_PT_45


title: HCI010_472_T_PT_36


title: HCI010_472_T_PT_38


title: HCI010_472_T_PT_34


title: HCI010_472_T_PT_22


title: HCI010_472_T_PT_26


title: HCI010_472_T_PT_27


title: HCI010_472_T_PT_31


title: HCI010_472_T_PT_33


title: HCI010_472_T_PT_28


title: HCI010_472_T_PT_20


title: HCI010_472_T_PT_30


title: HCI010_472_T_PT_29


title: HCI010_472_T_PT_21


title: HCI010_472_T_PT_19


title: HCI010_472_T_PT_18


title: HCI010_472_T_PT_15


title: HCI010_472_T_PT_16


title: HCI010_472_T_PT_13


title: HCI010_472_T_PT_25


title: HCI010_472_T_PT_23


title: HCI010_472_T_PT_8


title: HCI010_472_T_PT_10


title: HCI010_472_T_PT_11


title: HCI010_472_T_PT_17


title: HCI010_472_T_PT_14


title: HCI010_472_T_PT_7


title: HCI010_472_T_PT_5


title: HCI010_472_T_PT_6


title: HCI010_472_T_PT_4


title: HCI010_472_T_PT_32


title: HCI010_472_T_PT_24


title: HCI010_472_T_PT_1


title: HCI010_472_T_PT_3


title: HCI010_472_T_PT_9


title: HCI010_472_L_LN_32


title: HCI010_472_T_PT_2


title: HCI010_472_L_LN_36


title: HCI010_472_L_LN_33


title: HCI010_472_L_LN_35


title: HCI010_472_L_LN_34


title: HCI010_472_L_LN_30


title: HCI010_472_L_LN_26


title: HCI010_472_L_LN_27


title: HCI010_472_L_LN_29


title: HCI010_472_T_PT_12


title: HCI010_472_L_LN_25


title: HCI010_472_L_LN_28


title: HCI010_472_L_LN_31


title: HCI010_472_L_LN_20


title: HCI010_472_L_LN_17


title: HCI010_472_L_LN_23


title: HCI010_472_L_LN_21


title: HCI010_472_L_LN_24


title: HCI010_472_L_LN_14


title: HCI010_472_L_LN_15


title: HCI010_472_L_LN_16


title: HCI010_472_L_LN_13


title: HCI010_472_L_LN_19


title: HCI010_472_L_LN_12


title: HCI010_472_L_LN_11


title: HCI010_472_L_LN_22


title: HCI010_472_L_LN_10


title: HCI010_472_L_LN_9


title: HCI010_472_L_LN_6


title: HCI010_472_L_LN_7


title: HCI010_472_L_LN_4


title: HCI010_472_L_LN_8


title: HCI010_472_L_LN_18


title: HCI010_472_L_LN_1


title: HCI010_472_L_LU_56


title: HCI010_472_L_LU_58


title: HCI010_472_L_LU_53


title: HCI010_472_L_LU_55


title: HCI010_472_L_LU_60


title: HCI010_472_L_LU_57


title: HCI010_472_L_LU_59


title: HCI010_472_L_LU_49


title: HCI010_472_L_LU_51


title: HCI010_472_L_LU_50


title: HCI010_472_L_LU_54


title: HCI010_472_L_LN_2


title: HCI010_472_L_LU_52


title: HCI010_472_L_LN_3


title: HCI010_472_L_LU_47


title: HCI010_472_L_LU_46


title: HCI010_472_L_LU_48


title: HCI010_472_L_LU_45


title: HCI010_472_L_LU_44


title: HCI010_472_L_LU_43


title: HCI010_472_L_LU_42


title: HCI010_472_L_LU_41


title: HCI010_472_L_LU_40


title: HCI010_472_L_LU_38


title: HCI010_472_L_LU_39


title: HCI010_472_L_LU_37


title: HCI010_472_L_LU_36


title: HCI010_472_L_LU_15


title: HCI010_472_L_LU_28


title: HCI010_472_L_LU_29


title: HCI010_472_L_LU_25


title: HCI010_472_L_LU_35


title: HCI010_472_L_LU_34


title: HCI010_472_L_LU_30


title: HCI010_472_L_LU_20


title: HCI010_472_L_LU_27


title: HCI010_472_L_LN_5


title: HCI010_472_L_LU_16


title: HCI010_472_L_LU_32


title: HCI010_472_L_LU_31


title: HCI010_472_L_LU_26


title: HCI010_472_L_LU_22


title: HCI010_472_L_LU_21


title: HCI010_472_L_LU_33


title: HCI010_472_L_LU_23


title: HCI010_472_L_LU_24


title: HCI010_472_L_LU_19


title: HCI010_472_L_LU_17


title: HCI010_472_L_LU_14


title: HCI010_472_L_LU_18


title: HCI010_472_L_LU_12


title: HCI010_472_L_LU_13


title: HCI010_472_L_LU_10


title: HCI010_472_L_LU_8


title: HCI010_472_L_LU_7


title: HCI010_472_L_LU_9


title: HCI010_472_L_LU_6


title: HCI010_472_L_LU_11


title: HCI010_472_L_LU_5


title: HCI010_472_L_LU_1


title: HCI010_469_T_PT_95


title: HCI010_472_L_LU_2


title: HCI010_469_T_PT_94


title: HCI010_469_T_PT_96


title: HCI010_472_L_LU_3


title: HCI010_469_T_PT_92


title: HCI010_469_T_PT_91


title: HCI010_469_T_PT_86


title: HCI010_469_T_PT_90


title: HCI010_469_T_PT_87


title: HCI010_469_T_PT_88


title: HCI010_469_T_PT_84


title: HCI010_469_T_PT_83


title: HCI010_469_T_PT_82


title: HCI010_469_T_PT_80


title: HCI010_472_L_LU_4


title: HCI010_469_T_PT_81


title: HCI010_469_T_PT_79


title: HCI010_469_T_PT_89


title: HCI010_469_T_PT_85


title: HCI010_469_T_PT_76


title: HCI010_469_T_PT_75


title: HCI010_469_T_PT_77


title: HCI010_469_T_PT_78


title: HCI010_469_T_PT_93


title: HCI010_469_T_PT_70


title: HCI010_469_T_PT_74


title: HCI010_469_T_PT_72


title: HCI010_469_T_PT_71


title: HCI010_469_T_PT_73


title: HCI010_469_T_PT_69


title: HCI010_469_T_PT_67


title: HCI010_469_T_PT_68


title: HCI010_469_T_PT_66


title: HCI010_469_T_PT_64


title: HCI010_469_T_PT_63


title: HCI010_469_T_PT_62


title: HCI010_469_T_PT_60


title: HCI010_469_T_PT_55


title: HCI010_469_T_PT_56


title: HCI010_469_T_PT_54


title: HCI010_469_T_PT_61


title: HCI010_469_T_PT_52


title: HCI010_469_T_PT_59


title: HCI010_469_T_PT_58


title: HCI010_469_T_PT_50


title: HCI010_469_T_PT_47


title: HCI010_469_T_PT_42


title: HCI010_469_T_PT_43


title: HCI010_469_T_PT_46


title: HCI010_469_T_PT_45


title: HCI010_469_T_PT_44


title: HCI010_469_T_PT_65


title: HCI010_469_T_PT_51


title: HCI010_469_T_PT_36


title: HCI010_469_T_PT_57


title: HCI010_469_T_PT_49


title: HCI010_469_T_PT_41


title: HCI010_469_T_PT_31


title: HCI010_469_T_PT_30


title: HCI010_469_T_PT_27


title: HCI010_469_T_PT_24


title: HCI010_469_T_PT_40


title: HCI010_469_T_PT_20


title: HCI010_469_T_PT_37


title: HCI010_469_T_PT_19


title: HCI010_469_T_PT_16


title: HCI010_469_T_PT_32


title: HCI010_469_T_PT_53


title: HCI010_469_T_PT_34


title: HCI010_469_T_PT_35


title: HCI010_469_T_PT_26


title: HCI010_469_T_PT_23


title: HCI010_469_T_PT_48


title: HCI010_469_T_PT_29


title: HCI010_469_T_PT_28


title: HCI010_469_T_PT_39


title: HCI010_469_T_PT_13


title: HCI010_469_T_PT_38


title: HCI010_469_T_PT_6


title: HCI010_469_T_PT_3


title: HCI010_469_T_PT_4


title: HCI010_469_T_PT_10


title: HCI010_469_T_PT_22


title: HCI010_469_L_LU_95


title: HCI010_469_T_PT_17


title: HCI010_469_T_PT_33


title: HCI010_469_T_PT_14


title: HCI002_262_T_PT_37


title: HCI010_469_T_PT_12


title: HCI010_469_T_PT_25


title: HCI010_469_L_LU_93


title: HCI010_469_T_PT_11


title: HCI010_469_T_PT_21


title: HCI010_469_T_PT_18


title: HCI010_469_T_PT_8


title: HCI002_262_T_PT_33


title: HCI010_469_T_PT_7


title: HCI002_262_T_PT_31


title: HCI002_262_T_PT_28


title: HCI002_262_T_PT_30


title: HCI010_469_T_PT_15


title: HCI002_262_T_PT_25


title: HCI002_262_T_PT_23


title: HCI002_262_T_PT_24


title: HCI010_469_T_PT_5


title: HCI010_469_T_PT_2


title: HCI002_262_T_PT_18


title: HCI010_469_T_PT_1


title: HCI010_469_L_LU_96


title: HCI010_469_T_PT_9


title: HCI010_469_L_LU_94


title: HCI002_262_T_PT_26


title: HCI002_262_T_PT_36


title: HCI002_262_T_PT_15


title: HCI002_262_T_PT_14


title: HCI002_262_T_PT_35


title: HCI002_262_T_PT_10


title: HCI002_262_T_PT_32


title: HCI002_262_T_PT_11


title: HCI002_262_T_PT_8


title: HCI002_262_T_PT_12


title: HCI002_262_T_PT_9


title: HCI002_262_T_PT_27


title: HCI002_262_T_PT_29


title: HCI002_262_T_PT_22


title: HCI002_262_T_PT_34


title: HCI002_262_T_PT_4


title: HCI002_262_T_PT_21


title: HCI002_262_T_PT_3


title: HCI002_262_T_PT_1


title: HCI002_262_T_PT_19


title: HCI002_262_H_LU_96


title: HCI002_262_T_PT_17


title: HCI002_262_T_PT_16


title: HCI002_262_T_PT_13


title: HCI002_262_T_PT_7


title: HCI002_262_T_PT_5


title: HCI002_262_T_PT_2


title: HCI002_262_T_PT_6


title: HCI002_262_H_LU_87


title: HCI002_262_H_LU_89


title: HCI002_262_H_LU_95


title: HCI002_262_H_LU_94


title: HCI002_262_H_LU_93


title: HCI002_262_H_LU_85


title: HCI002_262_H_LU_83


title: HCI002_262_H_LU_92


title: HCI002_262_H_LU_91


title: HCI002_262_H_LU_88


title: HCI002_262_H_LU_82


title: HCI002_262_H_LU_79


title: HCI002_262_H_LU_81


title: HCI002_262_H_LU_80


title: HCI002_262_H_LU_86


title: HCI002_262_H_LU_76


title: HCI002_262_H_LU_84


title: HCI002_262_H_LU_77


title: HCI002_262_H_LU_74


title: HCI002_262_H_LU_75


title: HCI002_262_H_LU_73


title: HCI002_262_H_LU_90


title: HCI002_262_H_LU_72


title: HCI002_262_T_PT_20


title: HCI002_262_H_LU_70


title: HCI002_262_H_LU_71


title: HCI002_262_H_LU_68


title: HCI002_262_H_LU_67


title: HCI002_262_H_LU_69