title: LMM.16.99_type II pneumocyte

status: Public on Mar 26 2019

description:
miRNA
LMM-16.99-P01-CD326

data_processing:
Samples were analyzed with the NanoString (nCounter miRGE Assay, https://www.nanostring.com/products/mirna-assays/mirge-assay). Readout of the relative abundance of each miRNA expression is conducted by the nCounter Analysis System (NanoString). More information is available at: https://www.lungmap.net/breath-omics-experiment-page/?experimentTypeId=LMXT0000000021&experimentId=LMEX0000000227&analysisId=LMAN0000000035&view=allEntities#jump-protocols
Genome reference is mm10.

extract_protocol:
Samples were extracted and preped using the nCounter Mouse miRNA Sample Prep Kit using the automated nCounter Analysis System workflow (NanoString). Further information can be found at: https://www.lungmap.net/breath-omics-experiment-page/?experimentTypeId=LMXT0000000021&experimentId=LMEX0000000227&analysisId=LMAN0000000035&view=allEntities#jump-protocols
Mouse miRNA Panel CodeSet as apart of the mouse miRNA Expression Assay Kit (Nanostring). More information is available at: https://www.lungmap.net/breath-omics-experiment-page/?experimentTypeId=LMXT0000000021&experimentId=LMEX0000000227&analysisId=LMAN0000000035&view=allEntities#jump-protocols

treatment_protocol: Lungs were sugically dissected and cells were isolated. More information is available at: https://lungmap-sops.s3.amazonaws.com/LMSO0000000078/CCHMC%20-%20Adult%20Mouse%20Type%20II%20Cell%20Isolation.pdf

value: type II pneumocyte

value: post natal day 1


title: LMM.16.96_type II pneumocyte

type: RNA

city: Cincinnati

first: LungMAPP

last: DCC

state: OH

address: 3333 Burnet Ave

country: USA

institute: LungMAP DCC

description:
miRNA
LMM-16.96-P01-CD326

molecule: total RNA

organism: Mus musculus

source_name: type II pneumocyte

tag: strain

tag: cell type

tag: age

tag: genotype

value: WT


title: Endo-18.5-Rep1

status: Public on Mar 29 2019

type: SRA

library_source: transcriptomic

data_processing:
Next-generation sequencing of equimolar pools of cDNA libraries was performed using a single read 75 rapid flow cell on a HiSeq 2500 sequencing platform (Illumina), generating greater than 30 million raw reads per sample.  The raw sequenced reads were aligned from FASTQ files to the human genome build GRCm38/mm10 and the UCSC reference transcriptome (http://ccb.jhu.edu/software/tophat/index.shtml) using Tophat 2.0.9.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

growth_protocol: Embryos and mice for this study were collected from timed pregnant mice.

extract_protocol:
Total RNA was extracted from cells using the QIAamp Circulating Nucleic Acid Kit (QIAGEN). RNA was quality checked, transcribed into complementary DNA using the Verso complementary DNA synthesis kit (AB-1453; LifeTechnologies, Carlsbad, CA), sheared, amplified, adaptor ligated and sequenced for pair-end RNA-Seq reads (Illumina Inc. San Diego, CA, USA)
Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation Kit (Illumina).

treatment_protocol: Whole lungs were surgically dissected at embryonic (E) days 16.5, 18.5 and postnatal days (PND) P7 and P28 wild-type C57BL6 mice

tag: genotype/variation

tag: tissue

value: lung

value: endothelial cell


title: LMM.16.96_endothelial cell

description:
miRNA
LMM-16.96 P01CD31

source_name: endothelial cell


title: Epi-P28-Rep1

description: run1233_lane12_indexN701-S517=1_15.52A_CD326_plus_ve-mouse10_align

value: epithelial cell


title: Immune-P28-Rep2

description: run1233_lane12_indexN706-S506=6_15.57A_CD45_plus_ve-mouse10_align

value: immune cell


title: LMM.16.90_type II pneumocyte

description:
miRNA
LMM-16.90-P14-CD326

value: post natal day 14


title: LMM.16.79A_endothelial cell

description:
miRNA
LMM-16.79P28CD31

value: post natal day 28


title: LMM.16.112_type II pneumocyte

description:
miRNA
LMM-16.112E16.5-CD326

value: Embryonic day 16.5


title: LMM.16.79A_type II pneumocyte

description:
miRNA
LMM-16.79-P28-CD326


title: LMM.16.87_type II pneumocyte

description:
miRNA
LMM-16.87-P14-CD326


title: LMM.16.87_endothelial cell

description:
miRNA
LMM-16.87P14CD31


title: LMM.16.112_endothelial cell

description:
miRNA
LMM-16.112 EI6.5CD31


title: LMM.16.110_endothelial cell

description:
miRNA
LMM-16.110 EI6.5CD31


title: LMM.15.93_endothelial cell

description:
miRNA
LMM-15.93 EI8.5CD31

value: Embryonic day 18.5


title: LMM.16.110_type II pneumocyte

description:
miRNA
LMM-16.110E16.5-CD326


title: LMM.15.74A_type II pneumocyte

description:
miRNA
LMM-15.74-P28-CD326


title: LMM.15.68A_type II pneumocyte

description:
miRNA
LMM-15.68-P07-CD326

value: post natal day 7


title: LMM.15.93_type II pneumocyte

description:
miRNA
LMM-15.93E18.5-CD326


title: Lung Alveolar Septa_P28c

status: Public on Mar 19 2019

data_processing:
Basecalling was performed with RTA 1.18.64
After quality control for adapter contamination and trimming, Fastq files were mapped on mouse genome (mm10) by STAR  2.5.1 software.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks 2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each sample

source_name: Lung Alveolar Septa

growth_protocol: All of the animal procedures were approved by the Institutional Animal Care and Use Committee  (IACUC) at the University of Alabama at Birmingham. The lung tissue used in this study is obtained from  pups born to C57BL/6 timed-pregnant females purchased from Jackson Laboratories (Bar Harbor, ME).  Mice lung samples are collected over the first 28 days of lung development (every 12h for the first 14d,  then every 24h). Tissues are labeled as P0 (P zero), P0.5, P1, and so on, right at birth, at 12h or 24h  respectively. Furthermore pups are labeled alphabetically within each time point in each  group (n=5-6). For example 1 day old pups are labeled P1a, P1b, P1c, P1d, P1e, and P1f (6 per group).  The pup’s sex is determined by PCR (P0-P5) or by naked eye in older pups (P6-P28) and labeled M (male)  and F (female). At the time of sectioning the frozen tissue, the lungs are first labeled as left (L) and right  (R), and furthermore upper (U) (from upper lobe, if right lung), mid (M) (from middle lobe, if right lung)  and lower (L) zone (from lower lobe, if right lung). The accessory lobe in mouse lung is generally not  used for LCM. For example P1aFLM means - the left lung mid zone of first 1 day old female pup is  sectioned for LCM. For more details please view the SOP here: https://lungmap-sops.s3.amazonaws.com/LMSO0000000066/UAB_tissue_prep_LCM.pdf

extract_protocol:
For best visibility and imaging of the lung alveoli the OCT slides were washed and briefly dehydrated  prior to LCM using Arcturus® HistoGene® LCM Frozen Cection Ctaining Kit.  Using the ArcturusXT system, lung alveoli samples are collected in CapCure® LCM Caps (#LCM0211) and  stored in lysis buffer (Invitrogen) at - 80°C or flash frozen in liquid N2, and then shipped in bulk on dry  ice to our collaborators for further downstream analysis. More specifically we use the IR laser to select  the alveolar areas, and then cut widely around the selected areas using the UV laser to avoid large blood  vessels and bronchi. For more details please view the SOP here: https://lungmap-sops.s3.amazonaws.com/LMSO0000000066/UAB_tissue_prep_LCM.pdf
library preparation was performed  by Illumina® TruSeq® Stranded Total RNA Sample Preparation kits with Ribo-Zero according manufacturer’s protocols

treatment_protocol: Tissue sections (16 μm; can be 10-20) are cut with a MICROM-HM550 cryostat (Thermo scientific) onto  membrane-glass slides (Arcturus PEN#LCM0522) at B25 °C. CecDons are stored Erst at B80  °C and LCM performed no later than one week after sectioning. For more details please view the SOP here: https://lungmap-sops.s3.amazonaws.com/LMSO0000000066/UAB_tissue_prep_LCM.pdf

value: wild type

tag: body weight (g)

tag: gender

value: Female

value: lung alveolar septa


title: Lung Alveolar Septa_P19f

value: post natal day 19


title: Lung Alveolar Septa_P23e

value: post natal day 23

value: Male


title: LMM.15.94_type II pneumocyte

description:
miRNA
LMM-15.94E18.5-CD326

value: type II pneumocyte


title: LMM.15.68A_endothelial cell

description:
miRNA
LMM-15.68P07CD31

value: WT


title: LMM.15.57A_type II pneumocyte

description:
miRNA
LMM-15.57-P28-CD326


title: LMM.15.90_endothelial cell

description:
miRNA
LMM-15.90P14CD31


title: LMM.15.62A_endothelial cell

description:
miRNA
LMM-15.62 P07CD31


title: LMM.15.57A_endothelial cell

description:
miRNA
LMM-15.57P28CD31


title: LMM.15.62A_type II pneumocyte

description:
miRNA
LMM-15.62-P07-CD326


title: Lung Alveolar Septa_P19d


title: Lung Alveolar Septa_P15c

value: post natal day 15


title: Lung Alveolar Septa_P13.5c

value: post natal day 13.5


title: Lung Alveolar Septa_P13.5d


title: Lung Alveolar Septa_P10f

value: post natal day 10


title: Lung Alveolar Septa_P10a


title: Lung Alveolar Septa_P23f


title: Lung Alveolar Septa_P7c

value: 6 g


title: Lung Alveolar Septa_P7d


title: Lung Alveolar Septa_P5e

value: post natal day 5


title: Lung Alveolar Septa_P5b


title: Lung Alveolar Septa_P4e

value: post natal day 4


title: Lung Alveolar Septa_P4a


title: Lung Alveolar Septa_P2.5i

value: post natal day 2.5


title: Lung Alveolar Septa_P1.5e

value: post natal day 1.5


title: Lung Alveolar Septa_P1e

value: post natal day 1


title: Lung Alveolar Septa_E18.5-4

value: Embryonic day 18.5

value: wild type


title: Lung Alveolar Septa_P0.5f

value: post natal day 0.5

value: lung alveolar septa


title: Lung Alveolar Septa_P1d

value: Female


title: Lung Alveolar Septa_P15e


title: Lung Alveolar Septa_P0.5e


title: Lung Alveolar Septa_E16.5-9

value: Embryonic day 16.5


title: Lung Alveolar Septa_E18.5-3

value: Male


title: GFP+ sorted cells - bulk RNAseq 4

status: Public on Mar 16 2019

city: New York

first: Dieter

last: Egli

state: New York

address: 701 West 168th Street

institute: Columbia University

description: hESC-HNF1A-KO2 (A72)-DB002

data_processing:
Bulk RNA-seq: the reads were mapped to a reference genome (Human: NCBI/build37.2; Mouse: UCSC/mm9) using Tophat (version 2.1.0) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10). To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation.  The relative abundance (aka expression level) of genes and splice isoforms is estimated using cufflinks6 (version 2.0.2) with default settings.
Single Cell RNA-seq: the raw fastq files was processed via 10X Cell Ranger pipeline (cellranger-2.1.1). To note that GRCh38 reference genome was applied for the whole analysis. “cellranger count” with “--expect-cells=3000” was run for each library respectively and “cellranger aggr” with default parameters was run to aggregate results generated from multiple libraries. A normalized umi-count matrix for all the cells was then generated.  As for the quality control, cell and gene filtering process, cells with umi-count<5000 and umi-count>40000 and cells with <2000 detected genes were removed. Also, genes with <~1% (25) non-zero counts across all the cells were eliminated from the analysis. To get rid of the Mitochondria cells, cells with more than 10% Mitochondria genes’ count were also removed.
Genome_build: GRCh38 for single cell RNA-seq, GRCh37 for bulk RNA-seq
Supplementary_files_format_and_content: .csv files are the processed raw count files with label information.

organism: Homo sapiens

source_name: Endocrine cells

growth_protocol: The initial stages of differentiation were conducted in planar culture (d0-d11). For definitive endoderm stage (d1-d3) cells were cultured using STEMdiffTM Definitive Endoderm Differentiation Kit (Stemcell Technologies, 05110). For primitive gut stage (d4-d6), cells were cultured in RPMI containing GlutaMAX (Life Technology, 61870-127), 1% (v/v) Penicillin-Streptomycin (PS) (Thermo Fisher Scientific, 15070-063), 1% (v/v) B27 Serum-Free Supplement (50x) (Life Technology, 17504044) and 50 ng/ml FGF7 (R&D System, 251-KG). For posterior foregut stage (d7-d8), cells were cultured in DMEM containing GlutaMax, 1% (v/v) PS, 1% (v/v) B27, 0.25 μM KAAD-Cyclopamine (Stemgent, 04-0028), 2 μM Retinoic acid (Stemgent, 04-0021) and 0.25 μM LDN193189 (Stemgent, 04-0074). For pancreatic progenitor stage (d9-d11), cells were cultured in DMEM containing GlutaMax, 1% (v/v) PS, 1% (v/v) B27 and 50 ng/ml EGF (R&D System, 236-EG). Cells were then dissociated using TrypLE™ Express (Life Technology, 12605036) and seeded into low-attachment 96 well-plates (Corning, 7007) (1 well of 6 well-plate to 60 wells of 96-well-plate) for clustering step to form aggregates or clusters of endocrine cells in DMEM containing GlutaMax, 1% (v/v) PS, 1% (v/v) B27, 0.25 μM Cyclopamine, 1 μM thyroid hormone (T3) (Sigma, T6397), 10 μM Alk5i, 10 μM Zinc sulfate (Sigma-Aldrich, Z4750) and 10 μg/ml Heparin (Sigma-Aldrich, H3149) for 2 days (d12-d13). For pancreatic endocrine stage (d14-20) cells were cultured using DMEM containing GlutaMax, 1% (v/v) PS, 1% (v/v) B27, 100 nM LDN, 1 μM T3, 10 μM Alk5i, 10 μM Zinc sulfate, 10 μg/ml Heparin and 100 nM gamma-secretase inhibitor (DBZ) (EMD Millipore, 565789). For mature pancreatic endocrine stage (d21-d27) cells were cultured using DMEM containing GlutaMax, 1% (v/v) PS, 1% (v/v) B27, 1 μM T3, 10 μM Alk5i, 10 μM Zinc sulfate, 10 μg/ml Heparin, 1 mM N-acetyl cysteine (N-Cys) (Sigma-Aldrich, A9165-5G), 10 μM Trolox (EMD Millipore, 648471-500MG) and 2 μM R428 (Tyrosine kinase receptor AXL inhibitor) (ApexBio, A8329). From d1 to d11 media was changed every day and from d12 to d27 media was changed every other day. All differentiations were done for 27 to 30 days.

extract_protocol:
Single Cell RNA-seq: around 100 clusters of cells per genotype at day 27 of differentiation are dissociated. Single cells were suspended in PBS+0.04% BSA. Cellular suspensions (~6,000 cells) were loaded on a Chromium Single Cell Instrument (10X Genomics) to generate single cell GEMs. Single-cell RNAseq libraries were prepared using Chromium Single cell 3¢ Library, Gel beads & Mutiplex kit (10X Genomics). Sequencing was performed on Illumina NextSeq500 using the following read length: 59-bp Read1 for transcript read, 14-bp I7 Index for Cell Barcode read, 8-bp I5 Index for sample index read, and 10-bp Read2 for UMI read. The samples were sequenced in ten different libraries (batches). Among all these samples, Batch 980379 and Batch 993091 (2 libraries) are HNF1A mutants (R200Q), Batch 980380 and Batch 993090 (2 libraries) are HNF1A knockouts (KO) while Batch 989516 and Batch 993089 (2 libraries) are HNF1A wildtype cells (WT).
Bulk RNA-seq: around 200 clusters of cells are dissociated and sorted for GFP using BD FACS Aria II cell sorter. Sorted cells are pelleted by centrifugation and RNA extracted using total the RNA purification micro (Norgen Biotek, 35300) kit according to the manufactures protocol. RNA quality and concentration is determined by an Agilent bioanalyzer and RNAseq performed by the Columbia University Genome Center. A poly-A pull-down was used to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq RNA prep kit. Libraries are then sequenced using an Illumina HiSeq2000.  RTA (Illumina) was used for base calling and bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming.

treatment_protocol: Cells are untreated

value: ES-derived endocrine cells

tag: passages

tag: chip antibody

tag: differentiation day

value: HNF1A KO

tag: experiment number


title: Lung Alveolar Septa_P1.5d

value: 2 g


title: GFP+ sorted cells - bulk RNAseq 2

description: hESC-HNF1A-WT (A79)-DB003

value: HNF1A WT


title: GFP+ sorted cells - bulk RNAseq 3


title: GFP+ sorted cells - bulk RNAseq 1

description: hESC-HNF1A-WT (A72)-DB001


title: GFP+ sorted cells - bulk RNAseq 5


title: Unsorted endocrine cells - single cell RNAseq 6

description: hESC-HNF1A-R200Q-C18 (980379_1_1_1)

value: HNF1A R200Q homozygous


title: Unsorted endocrine cells - single cell RNAseq 1

description: hESC-HNF1A-WT (989516_1_1_1, 989516_2_1_1)


title: Unsorted endocrine cells - single cell RNAseq 5

description: hESC-HNF1A-R200Q-C15 (993091_1_1_1, 993091_2_1_1)


title: Lung Alveolar Septa_P2.5h


title: Unsorted endocrine cells - single cell RNAseq 3

description: hESC-HNF1A-KO1 (980380_1_1_1)


title: Unsorted endocrine cells - single cell RNAseq 2

description: hESC-HNF1A-WT (993089_1_1_1, 993089_2_1_1)


title: Lung Alveolar Septa_E16.5-2


title: gamma toxin CHX profiling

status: Public on Jan 27 2019

city: Frederick

first: Colin

last: Wu

state: MD

department: RNA Biology Laboratory

institute: NCI

description:
processed data file:
CHX_21ntRPF_occupancy3.csv
gamma_CHX

data_processing:
Base calling was performed at Johns Hopkins core facilities with CASAVA 1.8
Adapter sequence (NNNNNNCACTCGGGCACCAAGGA) removed with Skewer
4 random nucleotides included in RT primer (RNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC/iSP18/TTCAGACGTGTGCTCTTCCGATCTGTCCTTGGTGCCCGAGTG) were removed from the 5’ end of reads. Trimmed reads longer than 15 nt were aligned to yeast ribosomal and non-coding RNA sequences using STAR with ‘--outFilterMismatchNoverLmax 0.3’.
Unmapped reads were then mapped to genome using the following options ‘--outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.1’.
Genome_build: SacCer3 R64-1-1, Ce10, hg19
Supplementary_files_format_and_content: Count tables for relative codon occupancies or fixed-step WIG density files for mapped reads

organism: Saccharomyces cerevisiae

source_name: gamma toxin CHX profiling

growth_protocol: Yeast cells were grown to OD ~0.5; mammalian cells were grown to ~75% confluence; Synchronized L1 worms were plated on HT115 bacteria transformed with pL4440 vector and cultured at 25˚C for ~48 hours.

extract_protocol:
Lysates were clarified and monosomes were isolated by sucrose gradient centrifugation after RNaseI treatment. RNA was extracted using SDS/hot phenol/chloroform.
Fragments ranging from 15-34 nt were gel purified and rRNA was depleted from this pool through Ribo-Zero Gold treatment. Upon dephosphorylation of sample RNA, linker was ligated and this product was once again gel purified. This was followed by reverse transcription as well as circularization of cDNAs. PCR amplification of this library was then sent for sequencing.

treatment_protocol: Yeast cells were harvested by vacuum filtration and flash frozen. Samples were homogenized and lysed with lysis buffer using a freezer mill.

tag: plasmid

tag: molecule subtype

value: Ribosome Protected mRNA (15-34 nt)


title: C91-1-4

status: Public on Dec 23 2018

city: Los Angeles

first: Kathrin

last: Plath

state: CA

address: 615 Charles E. Young Drive South

department: Biological Chemistry

institute: UCLA

description: P1 αMHC+ single cell

data_processing:
RNA-seq data was mapped with OLego (v.1.1.5) and normalized by using TPM (transcripts per millions) analysis
Total number of reads mapped to a known transcript annotation was estimated using featureCounts version v1.5.0-p2
Expression levels for each transcript were determined by normalizing the counts returned by featureCounts using a custom Perl script
Genome_build: UCSC Dec. 2011 (GRCm38/mm10)
Supplementary_files_format_and_content: Raw feature counts for each sample
Supplementary_files_format_and_content: TPM for each sample

source_name: P1 αMHC+ single cell

extract_protocol:
Lysis, reverse transcription, and PCR performed withFluidigm 'mRNA Seq: RT + Amp (1772x/1773x)' script and commercially available kits from Life Technologies (Life Technologies Superscript II reverse transcriptase) and Clonetech (dSMART-Seq V4 Kit) according to manufacturer’s instructions.
Illumina Nextera XT DNA library preparation protocol for single-cell mRNA sequencing library preparation for sequencing from cDNA acquired from the C1 system

value: aMHC-GFP

value: Heart


title: C82-1-5

description: P1 αMHC+ single cell


title: C95-1-4

description: P1 αMHC+ single cell


title: C94-1-2

description: P1 αMHC+ single cell


title: C78-1-8

description: P1 αMHC+ single cell


title: C90-1-2

description: P1 αMHC+ single cell


title: C81-1-3

description: P1 αMHC+ single cell


title: C80-1-2

description: P1 αMHC+ single cell


title: C86-1-2

description: P1 αMHC+ single cell


title: C89-1-5

description: P1 αMHC+ single cell


title: C73-1-5

description: P1 αMHC+ single cell


title: C85-1-4

description: P1 αMHC+ single cell


title: C96-no

description: P1 αMHC+ single cell


title: Unsorted endocrine cells - single cell RNAseq 4

description: hESC-HNF1A-KO2 (993090_1_1_1,993090_2_1_1)


title: C70-no

description: P1 αMHC+ single cell


title: C71-1-6

description: P1 αMHC+ single cell


title: C69-1-4

description: P1 αMHC+ single cell


title: C60-1-4

description: P1 αMHC+ single cell


title: C6-1-3

description: P1 αMHC+ single cell


title: C67-1-4

description: P1 αMHC+ single cell


title: C63-1-2

description: P1 αMHC+ single cell


title: C56-1-4

description: P1 αMHC+ single cell


title: C57-1-4

description: P1 αMHC+ single cell


title: C53-no

description: P1 αMHC+ single cell


title: C72-1-5

description: P1 αMHC+ single cell


title: C62-1-3

description: P1 αMHC+ single cell


title: C36-1-8

description: P1 αMHC+ single cell


title: C50-1-2

description: P1 αMHC+ single cell


title: C59-1-8

description: P1 αMHC+ single cell


title: C66-1-3

description: P1 αMHC+ single cell


title: C33-1-8

description: P1 αMHC+ single cell


title: C35-1-8

description: P1 αMHC+ single cell


title: C42-1-8

description: P1 αMHC+ single cell


title: C77-1-3

description: P1 αMHC+ single cell


title: C25-1-4

description: P1 αMHC+ single cell


title: C26-1-4

description: P1 αMHC+ single cell


title: C34-1-5

description: P1 αMHC+ single cell


title: C4-1-4

description: P1 αMHC+ single cell


title: C54-no

description: P1 αMHC+ single cell


title: C3-1-2

description: P1 αMHC+ single cell


title: C24-1-4

description: P1 αMHC+ single cell


title: C28-1-5

description: P1 αMHC+ single cell


title: C21-1-2

description: P1 αMHC+ single cell


title: C20-1-2

description: P1 αMHC+ single cell


title: C23-1-4

description: P1 αMHC+ single cell


title: C2-1-4

description: P1 αMHC+ single cell


title: C51-no

description: P1 αMHC+ single cell


title: C15-1-2

description: P1 αMHC+ single cell


title: C13-1-3

description: P1 αMHC+ single cell


title: C10-1-4

description: P1 αMHC+ single cell


title: C1-1-2

description: P1 αMHC+ single cell


title: C18-1-4

description: P1 αMHC+ single cell


title: C14-1-5

description: P1 αMHC+ single cell


title: N523-7-B3-1-C07

description: E12.5 αMHC+ single cell

source_name: E12.5 αMHC+ single cell


title: N523-6-A3-1-C01

description: E12.5 αMHC+ single cell


title: N523-1-F1-1-C31

description: E12.5 αMHC+ single cell


title: N523-19-G9-1-C42

description: E12.5 αMHC+ single cell


title: N523-17-A9-1-C04

description: E12.5 αMHC+ single cell


title: N523-14-G7-1-C40

description: E12.5 αMHC+ single cell


title: C95-no

description: E12.5 αMHC+ single cell


title: C77-1-2

description: E12.5 αMHC+ single cell


title: C67-1-2

description: E12.5 αMHC+ single cell


title: N523-10-H3-1-C45

description: E12.5 αMHC+ single cell


title: C58-1-4

description: E12.5 αMHC+ single cell


title: C50-1-3

description: E12.5 αMHC+ single cell


title: E12-5b-1-2

description: E12.5 αMHC+ single cell


title: C73-no

description: E12.5 αMHC+ single cell


title: C88-no

description: E12.5 αMHC+ single cell


title: C41-1-3

description: E12.5 αMHC+ single cell


title: C60-no

description: E12.5 αMHC+ single cell


title: C32-1-2

description: E12.5 αMHC+ single cell


title: C49-1-3

description: E12.5 αMHC+ single cell


title: C36-no

description: E12.5 αMHC+ single cell


title: C31-no

description: E12.5 αMHC+ single cell


title: C40-no

description: E12.5 αMHC+ single cell


title: C22-1-3

description: E12.5 αMHC+ single cell


title: C16-no

description: E12.5 αMHC+ single cell


title: C11-1-2

description: E12.5 αMHC+ single cell


title: C09-no

description: E12.5 αMHC+ single cell


title: C05-1-3

description: E12.5 αMHC+ single cell


title: C01-1-2

description: E12.5 αMHC+ single cell


title: N530-9-D2-1-C20

description: E9.5 αMHC+ single cell

source_name: E9.5 αMHC+ single cell


title: N530-7-A2-1-C02

description: E9.5 αMHC+ single cell


title: N523-18-E9-1-C30

description: E12.5 αMHC+ single cell


title: N530-8-C2-1-C14

description: E9.5 αMHC+ single cell


title: N530-6-G1-1-C37

description: E9.5 αMHC+ single cell


title: N530-4-E1-1-C25

description: E9.5 αMHC+ single cell


title: N530-3-D1-1-C21

description: E9.5 αMHC+ single cell


title: N530-5-F1-1-C31

description: E9.5 αMHC+ single cell


title: N530-31-D12-1-C72

description: E9.5 αMHC+ single cell


title: N530-28-E9-1-C30

description: E9.5 αMHC+ single cell


title: N530-29-F9-1-C36

description: E9.5 αMHC+ single cell


title: N530-2-B1-1-C09

description: E9.5 αMHC+ single cell


title: N530-27-B9-1-C10

description: E9.5 αMHC+ single cell


title: N530-23-D8-1-C23

description: E9.5 αMHC+ single cell


title: N530-21-B8-1-C11

description: E9.5 αMHC+ single cell


title: N530-26-G8-1-C41

description: E9.5 αMHC+ single cell


title: N530-25-F8-1-C35

description: E9.5 αMHC+ single cell


title: N530-17-D7-1-C24

description: E9.5 αMHC+ single cell


title: N530-18-F7-1-C34

description: E9.5 αMHC+ single cell


title: N530-20-H7-1-C46

description: E9.5 αMHC+ single cell


title: N530-16-D6-1-C69

description: E9.5 αMHC+ single cell


title: N530-13-E3-1-C27

description: E9.5 αMHC+ single cell


title: N530-14-F3-1-C33

description: E9.5 αMHC+ single cell


title: N530-12-B3-1-C07

description: E9.5 αMHC+ single cell


title: N530-11-G2-1-C38

description: E9.5 αMHC+ single cell


title: C81-1-5

description: E9.5 αMHC+ single cell


title: C42-1-6

description: E9.5 αMHC+ single cell


title: C39-1-6

description: E9.5 αMHC+ single cell


title: C40-1-6

description: E9.5 αMHC+ single cell


title: C38-1-2

description: E9.5 αMHC+ single cell


title: C29-1-5

description: E9.5 αMHC+ single cell


title: N530-30-G9-1-C42

description: E9.5 αMHC+ single cell


title: C26-1-5

description: E9.5 αMHC+ single cell


title: C23-1-5

description: E9.5 αMHC+ single cell


title: N530-22-C8-1-C17

description: E9.5 αMHC+ single cell


title: C19-1-8

description: E9.5 αMHC+ single cell


title: N530-1-A1-1-C03

description: E9.5 αMHC+ single cell


title: C18-1-6

description: E9.5 αMHC+ single cell


title: C02-no

description: E9.5 αMHC+ single cell


title: C12-1-5

description: E9.5 αMHC+ single cell


title: C25-1-6

description: E9.5 αMHC+ single cell


title: N530-10-E2-1-C26

description: E9.5 αMHC+ single cell


title: LSK.sf3b1_k700e-srsf2_wt.C

status: Public on Aug 13 2018

city: Seattle

first: Khrystyna

middle: Dilai

last: North

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences Division

institute: Fred Hutchinson Cancer Research Center

description: Sf3b1 K700E mutant (Vav-Cre Sf3b1K700E/+)

data_processing:
Illumina CASAVA software was used for basecalling and sample de-multiplexing.
Reads were mapped to the mm10 mouse genome assembly using Bowtie v1.0.0 and RSEM v1.2.4. RSEM was modified to call Bowtie  with the -v 2 mapping strategy. RSEM was then invoked with the arguments --bowtie-m 100 --bowtie-chunkmbs 500 --calc-ci --output-genome- bam on the gene annotation file.
Genome_build: mm10
Supplementary_files_format_and_content: Text files with RSEM-based expression estimates for coding and non-coding RNA transcripts.

molecule: polyA RNA

source_name: fetal liver

extract_protocol:
RNA was extracted from sorted mouse cell populations using Qiagen RNeasy columns
Poly(A)-selected, unstranded (bone marrow)  and stranded (fetal liver) Illumina libraries were prepared with a modified TruSeq protocol. 0.5X AMPure XP beads were added to the sample library to select for fragments <400 bp, followed by 1X beads to select for fragments >100 bp. These fragments were then amplified with PCR (15 cycles) and separated by gel electrophoresis (2% agarose).

tag: strain/background

value: liver

value: LSK

tag: developmental stage

value: fetal

tag: mouse replicate

value: C

tag: srsf2 genotype

value: Wildtype

tag: sf3b1 genotype


title: LSK.sf3b1_k700e-srsf2_wt.B

tag: cell type

value: B


title: LSK.sf3b1_k700e-srsf2_p95h.C

description: Sf3b1 K700E Srsf2 P95H double mutant (Vav-Cre Srsf2P95H/+/ Sf3b1K700E/+)


title: LSK.sf3b1_k700e-srsf2_p95h.B


title: LSK.sf3b1_wt-srsf2_wt.A

description: Sf3b1 wildtype Srsf2 wildtype (Vav-Cre +)

value: A


title: LSKsf3b1_wt-srsf2_wt.C


title: LSK.sf3b1_wt-srsf2_p95h.C

description: Srsf2 P95H mutant (Vav-Cre Srsf2P95H/+)


title: LSK.sf3b1_k700e-srsf2_p95h.A


title: HH20_HL_WT_CHi-C

status: Public on Nov 27 2018

city: Yokohama

first: Nayuta

last: Yakushiji-Kaminatsui

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

description: chick HH20 WT whole hindlimb bud CHi-C

library_source: genomic

data_processing:
Library strategy: Capture Hi-C
Briefly, the reads were truncated at "GATCGATC" occurrence, then aligned independently in the end-to-end --very-sensitive mode. Then, for each pair, if the two reads maped uniquely [(1) only one alignment reported or (2) the difference of quality score between the first match and the second match is greater than 10 and the mapping quality is over 30] and they are assigned to fragments which are neither the same nor neighbors, the pair is consider as a valid pair.  Then, duplicates were removed (HiCUP v6.1.0). Finally, the output bam was converted to the juiceboxFormat using the position of the middle of the DpnII fragment as position.
The position of each read was asigned to a bin and the balanced matrix were used thanks to ICE correction with cooler.
For the matrices around the capture region (chr7:14,000,000-18,000,000), the pairs with at least one read outside the capture region (chr7:14,946,000-17,870,000) were excluded to avoid biais in normalization.
Genome_build: galGal5
Supplementary_files_format_and_content: validPair_juiceboxFormat.txt.gz contains every valid pair for each dataset. Each line is a pair: <readname> <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2> <frag2> <mapq1> <mapq2> str = strand (0 for forward, anything else for reverse)  *.txt.gz are raw or ICEd (balanced) cis matrices of interactions. At 5kb and 10kb resolution, only the matrices for chr7: 14,000,000-18,000,000 (galGal5) are provided. At 40kb resolution, cis interactions for chr2 are provided.

molecule: genomic DNA

organism: Gallus gallus

source_name: Hindlimb

extract_protocol:
Dissected tissues were dissociated in 10% FCS/PBS with collagenase (C7657, Sigma) to a final concentration of about 1.3 ug/uL, and sample were incubated in Thermomixer at 37°C at 800 rpm for 20 min. After discarding the supernatant, cells were crosslinked with 1% formaldehyde/PBS at RT for 10 min, quenched with glycine and centrifuged to discard the supernatant. Cells were resuspended with PBS containing proteinase inhibitor and then centrifuged again. After removing supernatant, cells were kept at -80°C before use.
Hi-C library preparation was performed as described in Belaghzal et al. (Belaghzal et al. 2017) with following changes: (i) Resuspended crosslinked cells in ice-cold Lysis buffer were placed on rotation wheel at 4°C at 30 rpm for 30 min for cell lysis. (ii) For chromatin digestion, 400U DpnII (R0543M, New England Biolabs) was added to the sample and incubated at 37°C at 700 rpm for 4 hrs. Another 400U DpnII was added and sample was incubated overnight. (iii) Blunt-end ligation of biotin filled-in DNA was performed at RT at 30 rpm on rotating wheel for 4 hrs. (iv) No removal of biotin from un-ligated end was performed. (v) DNA was sheared to a size of 200 - 800 bp by using COVARIS E220 with following condition, 175W, 10% Duty factor, 200 Cycles per Burst, 60 sec. (vi) DNA pulldown was done with Dynabeads MyOne Streptavidin T1 (65601, Thermo Fisher). (vii) DNA was measured by Qubit and 200 ng was used for further treatment followed by manufacturer’s protocol (SureSelectXT Target Enrichment System for Illumina Paired-End Multiplexed Sequencing Library).

tag: breed

value: White Leghorn

tag: age

value: Whole hindlimb bud

tag: genotype

value: wild type


title: LSK.sf3b1_wt-srsf2_p95h.B

description: Srsf2 P95H mutant (Vav-Cre Srsf2P95H/+)

tag: tissue


title: MP.sf3b1_wt-srsf2_wt.B

description:
Sample 14
Sf3b1 wildtype Srsf2 wildtype (Mx1-Cre +)
PolyA RNA

data_processing:
Illumina CASAVA software was used for basecalling and sample de-multiplexing.
Reads were mapped to the mm10 mouse genome assembly using Bowtie v1.0.0 and RSEM v1.2.4. RSEM was modified to call Bowtie with the -v 2 mapping strategy. RSEM was then invoked with the arguments --bowtie-m 100 --bowtie-chunkmbs 500 --calc-ci --output-genome- bam on the gene annotation file.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *txt: Tab-delimited text files with RSEM-based expression estimates for coding and non-coding RNA transcripts.

source_name: Bone marrow

extract_protocol:
RNA was extracted from sorted mouse cell populations using Qiagen RNeasy columns.
Poly(A)-selected, unstranded Illumina libraries were prepared with a modified TruSeq protocol. 0.5X AMPure XP beads were added to the sample library to select for fragments <400 bp, followed by 1X beads to select for fragments >100 bp. These fragments were then amplified with PCR (15 cycles) and separated by gel electrophoresis (2% agarose).

value: Myeloid progenitor


title: MP.sf3b1_wt-srsf2_wt.C

description:
Sample 15
Sf3b1 wildtype Srsf2 wildtype (Mx1-Cre +)
PolyA RNA


title: MP.sf3b1_wt-srsf2_p95h.C

description:
Sample 12
Srsf2 P95H mutant (Mx1-Cre Srsf2P95H/+)
PolyA RNA


title: LSK.sf3b1_wt-srsf2_wt.B


title: MP.sf3b1_wt-srsf2_p95h.A

description:
Sample 10
Srsf2 P95H mutant (Mx1-Cre Srsf2P95H/+)
PolyA RNA


title: LSK.sf3b1_wt-srsf2_p95h.A

description: Srsf2 P95H mutant (Vav-Cre Srsf2P95H/+)


title: MP.sf3b1_wt-srsf2_p95h.B

description:
Sample 11
Srsf2 P95H mutant (Mx1-Cre Srsf2P95H/+)
PolyA RNA


title: MP.sf3b1_k700e-srsf2_wt.A

description:
Sample 7
Sf3b1 K700E mutant (Mx1-Cre Sf3b1K700E/+)
PolyA RNA


title: MP.sf3b1_k700e-srsf2_p95h.B

description:
Sample 2
Sf3b1 K700E Srsf2 P95H double mutant (Mx1-Cre Srsf2P95H/+/ Sf3b1K700E/+)
PolyA RNA


title: MP.sf3b1_k700e-srsf2_p95h.C

description:
Sample 3
Sf3b1 K700E Srsf2 P95H double mutant (Mx1-Cre Srsf2P95H/+/ Sf3b1K700E/+)
PolyA RNA


title: MP.sf3b1_k700e-srsf2_wt.B

description:
Sample 8
Sf3b1 K700E mutant (Mx1-Cre Sf3b1K700E/+)
PolyA RNA


title: MP.sf3b1_k700e-srsf2_wt.C

description:
Sample 9
Sf3b1 K700E mutant (Mx1-Cre Sf3b1K700E/+)
PolyA RNA


title: MP.sf3b1_hetko.C

description:
Sample 6
Sf3b1 heterozygous knockout (Mx1-Cre negative Sf3b1K700E/KO)
PolyA RNA


title: HH20_FL_WT_CHi-C

description: chick HH20 WT whole forelimb bud CHi-C

source_name: Forelimb

value: Whole forelimb bud


title: LSK.sf3b1_k700e-srsf2_wt.A


title: C22-1-6

description: E9.5 αMHC+ single cell

tag: strain


title: empty-4h-3

status: Public on Aug 10 2018

city: London

first: Philip

last: East

state: London

address: 1 Midland Road, London

department: Bioinformatics

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Basecalls were performed using bcl2fastq v1.8.4
Reads were aligned to the mouse genome mm10 using Bowtie2
Gene-level quantifications were generated using RSEM against the knownGene annotation from UCSC
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text output files from RSEM. The gene_id column is an Entrez gene id.

source_name: melan-a melanocytes

growth_protocol: Cells were cultured in in RPMI with 10% FCS and the mitogen 12-O-tetradecanoylphorbol-13-acetate (TPA) at 200 nM in 5% CO2. Twenty-four hours before lysis, monolayers were washed once with PBS and medium was changed to medium lacking TPA.

extract_protocol:
Cells were lysed and total RNA was isolated using the RNeasy Mini Kit (Qiagen). The experiment was performed three times on a different day to obtain three independent replicates. RNA integrity was verified using the RNA 6000 Nano Kit in combination with the 2100 Bioanalyzer (both from Agilent).
mRNA libraries were prepared with the KAPA mRNA Hyper Prep kit (Roche Applied Science) and sequenced as 9-plex pools on the HiSeq 4000 (Roche Applied Science) and sequenced as 9-plex pools on the HiSeq 4000 (Illumina).

treatment_protocol: Cells were treated with 4OHT (Sigma-Aldrich, H6278) as described under "overall design".

tag: vector

value: empty

value: 4 hours

tag: batch


title: empty-40h-3

value: 40 hours


title: MP.sf3b1_k700e-srsf2_p95h.A

description:
Sample 1
Sf3b1 K700E Srsf2 P95H double mutant (Mx1-Cre Srsf2P95H/+/ Sf3b1K700E/+)
PolyA RNA


title: empty-0h-3

value: 0 hours


title: ER-RAC1-40h-3


title: ER-RAC1-4h-3


title: empty-40h-2


title: MP.sf3b1_wt-srsf2_wt.A

description:
Sample 13
Sf3b1 wildtype Srsf2 wildtype (Mx1-Cre +)
PolyA RNA


title: empty-0h-2


title: MP.sf3b1_hetko.B

description:
Sample 5
Sf3b1 heterozygous knockout (Mx1-Cre negative Sf3b1K700E/KO)
PolyA RNA


title: ER-RAC1-40h-2


title: empty-0h-1


title: empty-4h-1


title: ER-RAC1-0h-2


title: ER-RAC1-4h-2


title: empty-40h-1


title: ER-RAC1-40h-1


title: ER-RAC1-4h-1


title: ER-RAC1-0h-3


title: mESC_WT_control

status: Public on Jan 11 2018

city: Chicago

first: David

last: Pincus

state: IL

institute: University of Chicago

description:
processed data file:
mESC_RNA.txt

data_processing:
bases called by Illumina software
aligned to sacCer3 or mm10 by bowtie
quantified by cufflinks and cuffdiff
Genome_build: saccer3 and mm10
Supplementary_files_format_and_content: .txt files with RPKM values

extract_protocol:
Total  RNA was extracted using RNeasy kits (Qiagen) according to the manufacturer’s directions.
Illumina tru-seq

tag: strain/cell line

tag: genotype/variation

value: mESC

tag: perturbation

value: control

value: mRNA


title: mESC_hsf1_control

description:
processed data file:
mESC_RNA.txt

value: mESC hsf1-/-

tag: molecule subtype


title: mESC_hsf1_HS

description:
processed data file:
mESC_RNA.txt

value: heat shock


title: mESC_WT_HS

description:
processed data file:
mESC_RNA.txt


title: MEF_hsf1_control

description:
processed data file:
MEF_RNA.txt

value: MEF hsf1-/-


title: MP.sf3b1_hetko.A

description:
Sample 4
Sf3b1 heterozygous knockout (Mx1-Cre negative Sf3b1K700E/KO)
PolyA RNA

tag: strain/background

value: Wildtype


title: msn2/4_control

description:
processed data file:
msn24_RNA_C_HS_1NM.txt

value: TPK1/2/3-as msn2/4{delta}


title: MEF_hsf1_HS

description:
processed data file:
MEF_RNA.txt


title: MEF_WT_HS

description:
processed data file:
MEF_RNA.txt

value: MEF


title: Hsf1-3xFLAG-V5_HS

description:
processed data file:
ChIP-seq.txt

value: ChIP DNA


title: ER-RAC1-0h-1


title: MEF_WT_control

description:
processed data file:
MEF_RNA.txt


title: msn2/4_HS

value: TPK1/2/3-as msn2/4-delta


title: TPK1/2/3-AS_control

description:
processed data file:
tpk123_RNA_C_HS_1NM.txt


title: msn2/4_1NM


title: Hsf1-3xFLAG-V5_control

description:
processed data file:
ChIP-seq.txt


title: thymus_untreated_rep2

status: Public on May 04 2018

first: Kirsten

last: Cooper

address: 1100 Fairview Ave. N, Rm S3-208

description: Gene expression from CD45- thymic stromal cells

hyb_protocol: 10 ug of cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

scan_protocol: Affymetrix GeneArray scanner 7G

data_processing: Feature intensity was extracted by Affymetrix GeneChip Command Console as CEL files. Used Bioconductor Affy for normalization (GC-RMA) and gene annotation

label: Biotin

source_name: Mouse thymus harvested, no damage

label_protocol: 500 ng total RNA converted to cRNA using Affymetrix GeneChip®3' IVT Kit and in vitro transcription resulting into biotin-labeled cRNA, fragmented prior to hybridization (Affymetrix Expression Analysis Technical Manual, as described).

growth_protocol: To propigate exECs, cell culture medium containing murine recombinant VEGF (50ng/ml) and FGF-2 (100ng/ml), endothelial growth supplement (bovine hypothalamus) (Alfa Aesar), sb431542 (Tocris Biosciences), heparin (50g/ml) (Sigma-Aldrich), 1% Glutamax (Life Technologies), 1% non-essential amino acids (Life Technologies), 1% HEPES Buffer (Life Technologies), 1% antibiotic-antimycotic (Life Technologies) was replaced every 48h.

extract_protocol: RNA extraction plus kit was used to isolate RNA, and cDNA was made with Invitrogen Superscriptase.

treatment_protocol: Cells were first isolated using CD45 MACS cell depletion, then endothelial cells were FACS purified (CD45- EpCAM- VE-Cad+). To generate exECs, CD45-VE-Cadherin+ cells were FACS purified and incubated with lentivirus containing the E4ORF1 construct for 48 hours. To obtain sufficient RNA for every timepoint, thymic ECs of several mice were pooled.

tag: gender

value: female

value: thymus

value: thymic endothelial cells


title: thymus_untreated_rep1


title: thymus_untreated_rep3


title: Hsf1-AA_RNA_HS

description:
processed data file:
Hsf1-AA_RNA_C_R_H_RH.txt


title: Hsf1-AA_RNA_60_rapa

description:
processed data file:
Hsf1-AA_RNA_R_tc.txt

value: 60 min rapamycin


title: Hsf1-AA_RNA_0_rapa


title: TPK1/2/3-AS_HS


title: TPK1/2/3-AS_1NM


title: Hsf1-AA_RNA_240_rapa

value: 240 min rapamycin


title: Hsf1-AA_NET_60_3

description:
processed data file:
NET-seq_data.txt

data_processing:
library strategy: NET-seq
bases called by Illumina software
aligned to sacCer3 or mm10 by bowtie
quantified by cufflinks and cuffdiff
Genome_build: saccer3 and mm10
Supplementary_files_format_and_content: .txt files with RPKM values

value: nascent RNA


title: Hsf1-AA_RNA_control


title: Hsf1-AA_NET_60_4

description:
processed data file:
NET-seq_data.txt


title: Hsf1-AA_RNA_15_rapa

value: 15 min rapamycin


title: Hsf1-AA_NET_15_4

description:
processed data file:
NET-seq_data.txt


title: Hsf1-AA_RNA_rapa

value: rapamycin


title: Hsf1-AA_NET_15_2

description:
processed data file:
NET-seq_data.txt


title: Hsf1-AA_NET_60_2

description:
processed data file:
NET-seq_data.txt


title: Hsf1-AA_NET_0_4

description:
processed data file:
NET-seq_data.txt

value: control


title: Hsf1-AA_NET_60_1

description:
processed data file:
NET-seq_data.txt


title: Hsf1-AA_NET_30_2

description:
processed data file:
NET-seq_data.txt

value: 30 min rapamycin


title: Hsf1-AA_NET_30_1

description:
processed data file:
NET-seq_data.txt


title: Hsf1-AA_NET_30_3

description:
processed data file:
NET-seq_data.txt


title: Hsf1-AA_NET_0_3

description:
processed data file:
NET-seq_data.txt


title: Hsf1-AA_NET_0_1

description:
processed data file:
NET-seq_data.txt


title: Hsf1-AA_NET_15_1

description:
processed data file:
NET-seq_data.txt


title: Hsf1-AA_NET_0_2

description:
processed data file:
NET-seq_data.txt


title: DL_HiC_E12_Wt

status: Public on Dec 22 2017

city: Geneva

first: Eddie

last: Rodríguez-Carballo

address: 4, Boulevard d'Yvoy

department: Department of Genetics and Evolution

country: Switzerland

institute: Université de Genève

description: Distal limb mouse E12.5_Wt_HiC

data_processing:
Reads were mapped, filtered and bias corrected as described before (Lajoie et al. Methods 2015, Giorgetti Nature 2016).
Briefly, read pairs were mapped independently, starting at 25bp and iterated every 5bp using bowtie2 (version 2.2.4 (Langmead et al. 2009)) (as described in Imakaev Nature methods 2012) with parameter: --very-sensitive, either on mouse genome (mm10), or on the mutant genomes generated in silico. Each read was assigned to a fragment using the 5’ mapped-position shifted 3 bp toward the 3’ position to assign correctly the reads overlapping the cutting sites. The fragment assignment and mapping strand from R1 and R2 was combined and used to filter out the single-side mapped pairs, dangling-end pairs, error pairs and self-circle pairs. For each condition (same tissue and same genotype), two replicates were merged (fifteen replicates for CH12) and the interactions were filtered to discard duplicates. Each fragment was assigned to a bin (40 or 20kb) based on the position of the middle of the fragment and each valid interaction was assigned to a couple pair of bins (one bin for the R1 and one bin for the R2) and reported in the raw matrix. Prior to the ICE normalization (Imakaev et al. 2012), the rows and columns were masked if the sum of reads in this region was 10 fold less the expectation with uniform coverage, or if the number of fragments covered by at least two reads in this region was less than half the number of the fragments of this region.
Genome_build: mm10 (for DL_Wt, PL_Wt, DL_delattP-Rel5d9lac, PL_delattP-Rel5d9lac, CH12 and mESC) and mutant genomes (for DL_delattP-Rel5d9lac, PL_delattP-Rel5d9lac, DL_del1-13d9lac and PL_del1-13d9lac which are available at DOI: 10.6084/m9.figshare.5220637)
Supplementary_files_format_and_content: validPair.txt.gz contains every valid pair (not asigned to the same fragments) for each dataset. Each line is a read, column 2 is the chromosome name of the first read, column 3 is the coordinate of this read, column 4 is the strand, column 5 is the read name, column 6 is the fragment number to which this read has been asigned, columns 8-12 are the same for the other read. This file is not filtered for duplicates.  __txt.tar contains all cis matrices of interactions in one folder for each resolution (20kb or 40kb bin size) and then one subfolder for the raw and one subfolder for the iced (normalised) matrices. At the 40kb resolution, cis interactions for all chromosomes are provided. At 20kb resolution, only the matrices for chr2 are provided.

source_name: Distal forelimbs and distal hindlimbs

extract_protocol: Hi-C libraries were generated using the HindIII enzyme as described in the protocol outlined in (Belton et al. 2012).

value: Distal forelimbs and distal hindlimbs

value: wild type

tag: embryonic day


title: Asx subject at Day 0 [3266_246797_HG-U133A_2_39861_DU11-04S00752]

status: Public on Feb 22 2017

city: Durham

first: Sunil

last: Suchindran

state: NC

address: 101 Science Drive

department: Center for Applied Genomics and Precision Medicine

institute: Duke University

description: Gene expression at Day 0 for Asx subject

hyb_protocol: A hybridization cocktail is prepared, including the fragmented target, and probe array controls. It is then hybridized to the probe array during a 16-hour incubation

scan_protocol: Following hybridization, arrays are washed and stained using standard Affymetrix procedures before scanning on the Affymetrix GeneChip Scanner and data extraction using Affymetrix GCOS software.

data_processing: The data were RMA normalized with the Bioconductor Affy package.

label: biotin

source_name: Whole peripheral blood at Day 0

label_protocol: Total RNA specimens were converted into double-stranded cDNA using an olgio dT-T7 primer. Double stranded cDNA was then used as a template for an invitro transcription reaction to produce a biotinylated cRNA target.  The biotinylated cRNA was fragmented and hybridized to the appropriate GeneChip microarray

extract_protocol: RNA isolation was completed using the PAXgene Blood miRNA Kit.  PAXgene Blood RNA Tubes were first centrifuged to pellet the samples, then washed with water and resuspended.  After digestion with Proteinase K, the samples were homogenized by centrifugation through PAXgene Shredder spin columns.  Isopropanol was added to the samples to optimize binding conditions, and the samples were then centrifuged through PAXgene RNA spin columns, where total RNA >18 nucleotides (including miRNA) was bound to the silica-membrane.  The bound RNA was treated with DNase to remove genomic DNA contamination and washed.  Pure RNA was then eluted.

treatment_protocol: Subjects were orally administered ETEC strain H10407  in a bicarbonate solution, with random assignment to a dose of either 1 × 10^5 or 1 × 10^6 colony-forming units.

tag: phenotype

value: asymptomatic

tag: time

value: Day 0


title: Hsf1-AA_RNA_rapa_HS

value: rapamycin + heat shock

value: mRNA


title: Sx subject at Day 0 [3266_246803_HG-U133A_2_39867_DU11-04S00796]

description: Gene expression at Day 0 for Sx subject

value: symptomatic


title: Asx subject at Day 1 [3266_246798_HG-U133A_2_39862_DU11-04S01166]

description: Gene expression at Day 1 for Asx subject

source_name: Whole peripheral blood at Day 1

value: Day 1


title: Asx subject at Day 1 [3266_246792_HG-U133A_2_39856_DU11-04S01136]


title: Sx subject at Day 1 [3266_246804_HG-U133A_2_39868_DU11-04S01128]

description: Gene expression at Day 1 for Sx subject


title: Sx subject at Day 7 [3266_246805_HG-U133A_2_39869_DU11-04S01621]

description: Gene expression at Day 7 for Sx subject

source_name: Whole peripheral blood at Day 7

value: Day 7


title: Asx subject at Day 7 [3266_246799_HG-U133A_2_39863_DU11-04S01583]

description: Gene expression at Day 7 for Asx subject


title: Asx subject at Day 7 [3266_246793_HG-U133A_2_39857_DU11-04S01587]


title: Asx subject at Day 4 [3266_246796_HG-U133A_2_39860_DU11-04S03693]

description: Gene expression at Day 4 for Asx subject

source_name: Whole peripheral blood at Day 4

value: Day 4


title: Asx subject at Day 4 [3266_246802_HG-U133A_2_39866_DU11-04S03705]


title: Asx subject at Day 2 [3266_246800_HG-U133A_2_39864_DU11-04S02993]

description: Gene expression at Day 2 for Asx subject

source_name: Whole peripheral blood at Day 2

value: Day 2


title: Sx subject at Day 4 [3266_246808_HG-U133A_2_39872_DU11-04S03679]

description: Gene expression at Day 4 for Sx subject


title: Sx subject at Day 2 [3266_246806_HG-U133A_2_39870_DU11-04S02969]

description: Gene expression at Day 2 for Sx subject


title: Sx subject at Day 4 [3266_246790_HG-U133A_2_39854_DU11-04S03681]

description: Gene expression at Day 4 for Sx subject


title: Sx subject at Day 0 [3266_246785_HG-U133A_2_39849_DU11-04S00748]

description: Gene expression at Day 0 for Sx subject


title: empty-4h-2

value: empty

value: 4 hours


title: Asx subject at Day 3 [3266_246795_HG-U133A_2_39859_DU11-04S03359]

description: Gene expression at Day 3 for Asx subject

source_name: Whole peripheral blood at Day 3

value: Day 3


title: Asx subject at Day 3 [3266_246801_HG-U133A_2_39865_DU11-04S03345]


title: Sx subject at Day 3 [3266_246807_HG-U133A_2_39871_DU11-04S03347]

description: Gene expression at Day 3 for Sx subject


title: Sx subject at Day 7 [3266_246781_HG-U133A_2_39845_DU11-04S01625]

description: Gene expression at Day 7 for Sx subject


title: Sx subject at Day 3 [3266_246789_HG-U133A_2_39853_DU11-04S03349]

description: Gene expression at Day 3 for Sx subject


title: Sx subject at Day 3 [3266_246783_HG-U133A_2_39847_DU11-04S03315]

description: Gene expression at Day 3 for Sx subject


title: Asx subject at Day 0 [3266_246791_HG-U133A_2_39855_DU11-04S00766]


title: Sx subject at Day 7 [3266_246787_HG-U133A_2_39851_DU11-04S01609]

description: Gene expression at Day 7 for Sx subject


title: Sx subject at Day 2 [3266_246788_HG-U133A_2_39852_DU11-04S02979]

description: Gene expression at Day 2 for Sx subject


title: Sx subject at Day 2 [3266_246782_HG-U133A_2_39846_DU11-04S02965]

description: Gene expression at Day 2 for Sx subject


title: Asx subject at Day 2 [3266_246794_HG-U133A_2_39858_DU11-04S02943]


title: Sx subject at Day 1 [3266_246780_HG-U133A_2_39844_DU11-04S01120]

description: Gene expression at Day 1 for Sx subject


title: Sx subject at Day 7 [3266_246775_HG-U133A_2_39839_DU11-04S01627__T2]

description: Gene expression at Day 7 for Sx subject


title: Sx subject at Day 4 [3266_246778_HG-U133A_2_39842_DU11-04S03697__T2]

description: Gene expression at Day 4 for Sx subject


title: Sx subject at Day 4 [3266_246784_HG-U133A_2_39848_DU11-04S03671]

description: Gene expression at Day 4 for Sx subject


title: Asx subject at Day 3 [3266_246771_HG-U133A_2_39835_DU11-04S03337]


title: Asx subject at Day 4 [3266_246772_HG-U133A_2_39836_DU11-04S03675]


title: Sx subject at Day 3 [3266_246777_HG-U133A_2_39841_DU11-04S03355__T2]

description: Gene expression at Day 3 for Sx subject


title: Sx subject at Day 3 [3266_246765_HG-U133A_2_39829_DU11-04S03321]

description: Gene expression at Day 3 for Sx subject


title: Asx subject at Day 1 [3266_246768_HG-U133A_2_39832_DU11-04S01150]


title: Sx subject at Day 0 [3266_246779_HG-U133A_2_39843_DU11-04S00774__T2]

description: Gene expression at Day 0 for Sx subject


title: Asx subject at Day 3 [3266_246759_HG-U133A_2_39823_DU11-04S03331]


title: Asx subject at Day 7 [3266_246757_HG-U133A_2_39821_DU11-04S01597]


title: Sx subject at Day 7 [3266_246763_HG-U133A_2_39827_DU11-04S01623]

description: Gene expression at Day 7 for Sx subject


title: Asx subject at Day 0 [3266_246767_HG-U133A_2_39831_DU11-04S00794]


title: Sx subject at Day 1 [3266_246762_HG-U133A_2_39826_DU11-04S01140]

description: Gene expression at Day 1 for Sx subject


title: Sx subject at Day 0 [3266_246773_HG-U133A_2_39837_DU11-04S00802]

description: Gene expression at Day 0 for Sx subject


title: Asx subject at Day 4 [3266_246760_HG-U133A_2_39824_DU11-04S03685]


title: Sx subject at Day 4 [3266_246766_HG-U133A_2_39830_DU11-04S03707]

description: Gene expression at Day 4 for Sx subject


title: Sx subject at Day 0 [3266_246761_HG-U133A_2_39825_DU11-04S00788]

description: Gene expression at Day 0 for Sx subject


title: Asx subject at Day 0 [3266_246755_HG-U133A_2_39819_DU11-04S00744]


title: Sx subject at Day 7 [3266_246751_HG-U133A_2_39815_DU11-04S01575]

description: Gene expression at Day 7 for Sx subject


title: Asx subject at Day 2 [3266_246758_HG-U133A_2_39822_DU11-04S02991]


title: Asx subject at Day 2 [3266_246770_HG-U133A_2_39834_DU11-04S02961]


title: Sx subject at Day 1 [3266_246774_HG-U133A_2_39838_DU11-04S01170]

description: Gene expression at Day 1 for Sx subject


title: Sx subject at Day 4 [3266_248402_HG-U133A_2_39932_DU11-04S03674]

description: Gene expression at Day 4 for Sx subject


title: Asx subject at Day 1 [3266_246756_HG-U133A_2_39820_DU11-04S01116]


title: Asx subject at Day 4 [3266_246748_HG-U133A_2_39812_DU11-04S03669]


title: Sx subject at Day 1 [3266_246750_HG-U133A_2_39814_DU11-04S01126]

description: Gene expression at Day 1 for Sx subject


title: RRBS_UCLA1_Clone9_XIST_Pos_Rep2

status: Public on Oct 21 2016

description:
RRBS UCLA1 5iLAF Clone9 XIST Positive Replicate2
RRBS_UCLA1_Clone9_XIST_Pos.CGmap.gz

data_processing:
RRBS library reads were mapped to the hg19 reference genome using BS-Seeker v2.0.32 (Guo et al., 2013), which called bowtie v0.12.9  (Langmead et al., 2009). Reads with adapter contamination were trimmed. The adapter sequence used for the contamination check was as follows: CGAGATCGGAAGAGCACACGTC, i.e. meCG end repair + A tail + 10.bp of Illumina adapter sequence.
Genome_build: Homo sapiens UCSC hg19
Supplementary_files_format_and_content: CGmap files are produced by BS-Seeker2 and contain C and T counts per cytosine for both strands.
Supplementary_files_format_and_content: The format is fully described here: https://github.com/BSSeeker/BSseeker2#output-files
Supplementary_files_format_and_content: Briefly, each column of the represents the following:
Supplementary_files_format_and_content: (1) chromosome
Supplementary_files_format_and_content: (2) nucleotide on Watson (+) strand
Supplementary_files_format_and_content: (3) position
Supplementary_files_format_and_content: (4) context (CG/CHG/CHH)
Supplementary_files_format_and_content: (5) dinucleotide-context (CA/CC/CG/CT)
Supplementary_files_format_and_content: (6) methylation-level = #_of_C / (#_of_C + #_of_T)
Supplementary_files_format_and_content: (7) #_of_C (methylated C, the count of reads showing C here)
Supplementary_files_format_and_content: (8) = #_of_C + #_of_T (all Cytosines, the count of reads showing C or T here)

source_name: Human embryonic stem cells

extract_protocol:
none provided by the submitter
none provided by the submitter
RRBS

tag: cell type

value: embryonic stem cells


title: RRBS_UCLA1_Primed_Rep1

description:
RRBS UCLA1 Primed Replicate1
RRBS_UCLA1_Primed.CGmap.gz


title: RRBS_UCLA1_Primed_Rep2

description:
RRBS UCLA1 Primed Replicate2
RRBS_UCLA1_Primed.CGmap.gz


title: Sx subject at Day 3 [3266_246753_HG-U133A_2_39817_DU11-04S03303]

description: Gene expression at Day 3 for Sx subject


title: RRBS_UCLA1_Clone4_XIST_Neg_Rep2

description:
RRBS UCLA1 5iLAF Clone4 XIST Negative Replicate2
RRBS_UCLA1_Clone4_XIST_Neg.CGmap.gz


title: Asx subject at Day 3 [3266_246747_HG-U133A_2_39811_DU11-04S03307]


title: RRBS_UCLA1_Clone12_XIST_Pos_Rep2

description:
RRBS UCLA1 5iLAF Clone12 XIST Positive Replicate2
RRBS_UCLA1_Clone12_XIST_Pos.CGmap.gz


title: Sx subject at Day 2 [3266_246752_HG-U133A_2_39816_DU11-04S02955]

description: Gene expression at Day 2 for Sx subject


title: RRBS_UCLA1_Clone9_XIST_Pos_Rep1

description:
RRBS UCLA1 5iLAF Clone9 XIST Positive Replicate1
RRBS_UCLA1_Clone9_XIST_Pos.CGmap.gz


title: Asx subject at Day 7 [3266_246745_HG-U133A_2_39809_DU11-04S01581]


title: RRBS_UCLA1_Clone12_XIST_Pos_Rep1

description:
RRBS UCLA1 5iLAF Clone12 XIST Positive Replicate1
RRBS_UCLA1_Clone12_XIST_Pos.CGmap.gz


title: UCLA1_Primed_Rep2

description: UCLA1 Primed Replicate2

data_processing:
RNA-seq library reads were mapped to the hg19 reference genome using TopHat v2.1.0 (Trapnell et al., 2009) with parameters set to '--b2-sensitive --no-novel-juncs --library-type fr-unstranded --no-mixed --no-discordant --prefilter-multihits --transcriptome-max-hits 1 --max-multihits 15'
The annotation of aligned reads with genomic features was prefomed using HTSeq 0.6.1p1 (Anders et al., 2014) with parameters set to '--type=exon --mode=union --minaqual=0 --stranded=no'
Genome_build: Homo sapiens UCSC hg19
Supplementary_files_format_and_content: Raw read counts for each samples

extract_protocol:
none provided by the submitter
none provided by the submitter
stranded RNA-seq


title: Sx subject at Day 0 [3266_246749_HG-U133A_2_39813_DU11-04S00798]

description: Gene expression at Day 0 for Sx subject


title: Asx subject at Day 3 [3266_246741_HG-U133A_2_39805_DU11-04S03341]


title: Asx subject at Day 1 [3266_246744_HG-U133A_2_39808_DU11-04S01164]


title: Asx subject at Day 4 [3266_246742_HG-U133A_2_39806_DU11-04S03689]


title: Asx subject at Day 0 [3266_246743_HG-U133A_2_39807_DU11-04S00792]


title: Asx subject at Day 7 [3266_246739_HG-U133A_2_39803_DU11-04S01613]


title: Asx subject at Day 1 [3266_246738_HG-U133A_2_39802_DU11-04S01158]


title: Asx subject at Day 0 [3266_246737_HG-U133A_2_39801_DU11-04S00760]


title: Asx subject at Day 2 [3266_246746_HG-U133A_2_39810_DU11-04S02987]


title: Asx subject at Day 2 [3266_246740_HG-U133A_2_39804_DU11-04S02959]


title: Sx subject at Day 2 [3266_246776_HG-U133A_2_39840_DU11-04S02945__T2]

description: Gene expression at Day 2 for Sx subject


title: RRBS_UCLA1_Clone4_XIST_Neg_Rep1

description:
RRBS UCLA1 5iLAF Clone4 XIST Negative Replicate1
RRBS_UCLA1_Clone4_XIST_Neg.CGmap.gz


title: UCLA1_Clone9_XIST_Pos_Rep1

description: UCLA1 5iLAF Clone9 XIST Positive Replicate1


title: UCLA1_Clone9_XIST_Pos_Rep2

description: UCLA1 5iLAF Clone9 XIST Positive Replicate2


title: UCLA1_Clone4_XIST_Neg_Rep2

description: UCLA1 5iLAF Clone4 XIST Negative Replicate2


title: Exp2_H8

description: Exp2 H8 Paired End1

data_processing:
RNA-seq library reads were mapped to the hg19 reference genome using TopHat v2.1.0 (Trapnell et al., 2009) with parameters set to '--b2-sensitive --no-novel-juncs --library-type fr-firststrand'
The annotation of aligned reads with genomic features was prefomed using HTSeq 0.6.1p1 (Anders et al., 2014) with parameters set to '--type=exon --mode=union --minaqual=0 --stranded=reverse'
Genome_build: Homo sapiens UCSC hg19
Supplementary_files_format_and_content: Raw read counts for each samples

source_name: Human embryonic stem cell

extract_protocol:
none provided by the submitter
none provided by the submitter
single cell RNA-seq

value: Human embryonic stem cell


title: UCLA1_Clone4_XIST_Neg_Rep1

description: UCLA1 5iLAF Clone4 XIST Negative Replicate1


title: Exp2_H9

description: Exp2 H9 Paired End1


title: UCLA1_Clone12_XIST_Pos_Rep1

description: UCLA1 5iLAF Clone12 XIST Positive Replicate1


title: UCLA1_Clone12_XIST_Pos_Rep2

description: UCLA1 5iLAF Clone12 XIST Positive Replicate2


title: Exp2_H7

description: Exp2 H7 Paired End1


title: Exp2_H6

description: Exp2 H6 Paired End1


title: Exp2_H5

description: Exp2 H5 Paired End1


title: Exp2_H3

description: Exp2 H3 Paired End1


title: Exp2_H4

description: Exp2 H4 Paired End1


title: Exp2_H2

description: Exp2 H2 Paired End1


title: Exp2_H1

description: Exp2 H1 Paired End1


title: Exp2_G9

description: Exp2 G9 Paired End1


title: Exp2_H12

description: Exp2 H12 Paired End1


title: Exp2_H11

description: Exp2 H11 Paired End1


title: Exp2_G8

description: Exp2 G8 Paired End1


title: Exp2_G7

description: Exp2 G7 Paired End1


title: Exp2_G6

description: Exp2 G6 Paired End1


title: Exp2_G5

description: Exp2 G5 Paired End1


title: Exp2_G4

description: Exp2 G4 Paired End1


title: Exp2_G3

description: Exp2 G3 Paired End1


title: Exp2_G2

description: Exp2 G2 Paired End1


title: Exp2_G12

description: Exp2 G12 Paired End1


title: Exp2_G1

description: Exp2 G1 Paired End1


title: Exp2_G11

description: Exp2 G11 Paired End1


title: Exp2_G10

description: Exp2 G10 Paired End1


title: Exp2_F9

description: Exp2 F9 Paired End1


title: Exp2_F5

description: Exp2 F5 Paired End1


title: Exp2_F4

description: Exp2 F4 Paired End1


title: Exp2_F6

description: Exp2 F6 Paired End1


title: Exp2_F8

description: Exp2 F8 Paired End1


title: Exp2_F3

description: Exp2 F3 Paired End1


title: Exp2_F2

description: Exp2 F2 Paired End1


title: Exp2_F1

description: Exp2 F1 Paired End1


title: Exp2_F11

description: Exp2 F11 Paired End1


title: Exp2_H10

description: Exp2 H10 Paired End1


title: Exp2_E9

description: Exp2 E9 Paired End1


title: Exp2_E6

description: Exp2 E6 Paired End1


title: Exp2_E8

description: Exp2 E8 Paired End1


title: Exp2_E5

description: Exp2 E5 Paired End1


title: Exp2_E7

description: Exp2 E7 Paired End1


title: Exp2_E4

description: Exp2 E4 Paired End1


title: Exp2_F12

description: Exp2 F12 Paired End1


title: Exp2_E3

description: Exp2 E3 Paired End1


title: Exp2_F7

description: Exp2 F7 Paired End1


title: Exp2_E2

description: Exp2 E2 Paired End1


title: Exp2_E12

description: Exp2 E12 Paired End1


title: Exp2_E11

description: Exp2 E11 Paired End1


title: Exp2_E1

description: Exp2 E1 Paired End1


title: Exp2_D9

description: Exp2 D9 Paired End1


title: Exp2_E10

description: Exp2 E10 Paired End1


title: Exp2_D8

description: Exp2 D8 Paired End1


title: Exp2_D4

description: Exp2 D4 Paired End1


title: Exp2_D7

description: Exp2 D7 Paired End1


title: Exp2_D6

description: Exp2 D6 Paired End1


title: Exp2_D5

description: Exp2 D5 Paired End1


title: Exp2_F10

description: Exp2 F10 Paired End1


title: Sx subject at Day 1 [3266_246786_HG-U133A_2_39850_DU11-04S01114]

description: Gene expression at Day 1 for Sx subject


title: Exp2_D2

description: Exp2 D2 Paired End1


title: Exp2_D12

description: Exp2 D12 Paired End1


title: Exp2_D3

description: Exp2 D3 Paired End1


title: Exp2_D10

description: Exp2 D10 Paired End1


title: Exp2_D11

description: Exp2 D11 Paired End1


title: Exp2_C8

description: Exp2 C8 Paired End1


title: Exp2_C6

description: Exp2 C6 Paired End1


title: Exp2_C7

description: Exp2 C7 Paired End1


title: Exp2_C5

description: Exp2 C5 Paired End1


title: Exp2_C9

description: Exp2 C9 Paired End1


title: Exp2_C4

description: Exp2 C4 Paired End1


title: Exp2_C2

description: Exp2 C2 Paired End1


title: Exp2_C1

description: Exp2 C1 Paired End1


title: Exp2_C11

description: Exp2 C11 Paired End1


title: Exp2_C12

description: Exp2 C12 Paired End1


title: Exp2_B9

description: Exp2 B9 Paired End1


title: Exp2_C10

description: Exp2 C10 Paired End1


title: Exp2_B8

description: Exp2 B8 Paired End1


title: Exp2_B7

description: Exp2 B7 Paired End1


title: Exp2_B5

description: Exp2 B5 Paired End1


title: Exp2_B3

description: Exp2 B3 Paired End1


title: Exp2_B6

description: Exp2 B6 Paired End1


title: Exp2_B4

description: Exp2 B4 Paired End1


title: UCLA1_Primed_Rep1

description: UCLA1 Primed Replicate1


title: Exp2_B1

description: Exp2 B1 Paired End1


title: Exp2_B2

description: Exp2 B2 Paired End1


title: Exp2_B11

description: Exp2 B11 Paired End1


title: Exp2_B12

description: Exp2 B12 Paired End1


title: Exp2_C3

description: Exp2 C3 Paired End1


title: Exp2_B10

description: Exp2 B10 Paired End1


title: Exp2_A7

description: Exp2 A7 Paired End1


title: Exp2_A9

description: Exp2 A9 Paired End1


title: Exp2_A4

description: Exp2 A4 Paired End1


title: Exp2_A6

description: Exp2 A6 Paired End1


title: Exp2_A8

description: Exp2 A8 Paired End1


title: Exp2_A5

description: Exp2 A5 Paired End1


title: Exp2_A3

description: Exp2 A3 Paired End1


title: Exp2_A12

description: Exp2 A12 Paired End1


title: Exp2_A1

description: Exp2 A1 Paired End1


title: Sx subject at Day 2 [3266_246764_HG-U133A_2_39828_DU11-04S02967]

description: Gene expression at Day 2 for Sx subject


title: Exp1_H8

description: Experiment1 H8 Paired End1


title: Asx subject at Day 7 [3266_246769_HG-U133A_2_39833_DU11-04S01573]

description: Gene expression at Day 7 for Asx subject


title: Exp1_H9

description: Experiment1 H9 Paired End1


title: Exp1_H7

description: Experiment1 H7 Paired End1


title: Exp1_H4

description: Experiment1 H4 Paired End1


title: Exp1_H3

description: Experiment1 H3 Paired End1


title: Exp1_H5

description: Experiment1 H5 Paired End1


title: Exp1_H2

description: Experiment1 H2 Paired End1


title: Exp1_H12

description: Experiment1 H12 Paired End1


title: Exp1_H11

description: Experiment1 H11 Paired End1


title: Exp1_G9

description: Experiment1 G9 Paired End1


title: Exp1_H10

description: Experiment1 H10 Paired End1


title: Exp1_G8

description: Experiment1 G8 Paired End1


title: Exp1_G5

description: Experiment1 G5 Paired End1


title: Exp2_A2

description: Exp2 A2 Paired End1


title: Exp1_G4

description: Experiment1 G4 Paired End1


title: Exp2_A10

description: Exp2 A10 Paired End1


title: Exp1_G2

description: Experiment1 G2 Paired End1


title: Exp1_G6

description: Experiment1 G6 Paired End1


title: Exp2_A11

description: Exp2 A11 Paired End1


title: Exp1_G10

description: Experiment1 G10 Paired End1


title: Exp1_G7

description: Experiment1 G7 Paired End1


title: Exp1_G3

description: Experiment1 G3 Paired End1


title: Exp1_G1

description: Experiment1 G1 Paired End1


title: Exp1_G11

description: Experiment1 G11 Paired End1


title: Exp1_H1

description: Experiment1 H1 Paired End1


title: Exp1_F8

description: Experiment1 F8 Paired End1


title: Exp1_F9

description: Experiment1 F9 Paired End1


title: Exp1_G12

description: Experiment1 G12 Paired End1


title: Exp1_F6

description: Experiment1 F6 Paired End1


title: Exp1_H6

description: Experiment1 H6 Paired End1


title: Exp1_F4

description: Experiment1 F4 Paired End1


title: Exp1_F7

description: Experiment1 F7 Paired End1


title: Exp1_F11

description: Experiment1 F11 Paired End1


title: Exp1_F2

description: Experiment1 F2 Paired End1


title: Exp1_E9

description: Experiment1 E9 Paired End1


title: Exp1_E8

description: Experiment1 E8 Paired End1


title: Exp1_F3

description: Experiment1 F3 Paired End1


title: Exp1_F10

description: Experiment1 F10 Paired End1


title: Exp1_F12

description: Experiment1 F12 Paired End1


title: Exp1_E2

description: Experiment1 E2 Paired End1


title: Exp1_E5

description: Experiment1 E5 Paired End1


title: Exp1_E4

description: Experiment1 E4 Paired End1


title: Exp1_E6

description: Experiment1 E6 Paired End1


title: Exp1_F5

description: Experiment1 F5 Paired End1


title: Exp1_E12

description: Experiment1 E12 Paired End1


title: Exp1_E1

description: Experiment1 E1 Paired End1


title: Exp1_E3

description: Experiment1 E3 Paired End1


title: Exp1_D8

description: Experiment1 D8 Paired End1


title: Exp1_D5

description: Experiment1 D5 Paired End1


title: Exp1_D6

description: Experiment1 D6 Paired End1


title: Exp1_F1

description: Experiment1 F1 Paired End1


title: Exp1_D9

description: Experiment1 D9 Paired End1


title: Exp1_D7

description: Experiment1 D7 Paired End1


title: Exp1_D4

description: Experiment1 D4 Paired End1


title: Exp1_E10

description: Experiment1 E10 Paired End1


title: Exp1_D3

description: Experiment1 D3 Paired End1


title: Exp1_D12

description: Experiment1 D12 Paired End1


title: Exp1_D2

description: Experiment1 D2 Paired End1


title: Exp1_C8

description: Experiment1 C8 Paired End1


title: Exp1_E7

description: Experiment1 E7 Paired End1


title: Exp1_D10

description: Experiment1 D10 Paired End1


title: Exp1_C9

description: Experiment1 C9 Paired End1


title: Exp1_D11

description: Experiment1 D11 Paired End1


title: Exp1_C4

description: Experiment1 C4 Paired End1


title: Exp1_C3

description: Experiment1 C3 Paired End1


title: Exp1_C1

description: Experiment1 C1 Paired End1


title: Exp1_B9

description: Experiment1 B9 Paired End1


title: Exp1_C12

description: Experiment1 C12 Paired End1


title: Exp1_B7

description: Experiment1 B7 Paired End1


title: Exp1_B5

description: Experiment1 B5 Paired End1


title: Exp1_E11

description: Experiment1 E11 Paired End1


title: Exp1_C5

description: Experiment1 C5 Paired End1


title: Exp1_C11

description: Experiment1 C11 Paired End1


title: Exp1_C10

description: Experiment1 C10 Paired End1


title: Exp1_D1

description: Experiment1 D1 Paired End1


title: Exp1_C6

description: Experiment1 C6 Paired End1


title: Exp1_B6

description: Experiment1 B6 Paired End1


title: Exp1_B12

description: Experiment1 B12 Paired End1


title: Exp1_C2

description: Experiment1 C2 Paired End1


title: Exp1_C7

description: Experiment1 C7 Paired End1


title: Exp1_B10

description: Experiment1 B10 Paired End1


title: Exp1_B3

description: Experiment1 B3 Paired End1


title: Exp1_A8

description: Experiment1 A8 Paired End1


title: Exp1_A9

description: Experiment1 A9 Paired End1


title: Exp1_A7

description: Experiment1 A7 Paired End1


title: Exp1_B11

description: Experiment1 B11 Paired End1


title: Exp1_A6

description: Experiment1 A6 Paired End1


title: Exp1_B8

description: Experiment1 B8 Paired End1


title: Exp1_A4

description: Experiment1 A4 Paired End1


title: Exp1_A3

description: Experiment1 A3 Paired End1


title: Exp1_B2

description: Experiment1 B2 Paired End1


title: Exp1_A11

description: Experiment1 A11 Paired End1


title: Exp1_A5

description: Experiment1 A5 Paired End1


title: Exp1_A1

description: Experiment1 A1 Paired End1


title: Exp1_A2

description: Experiment1 A2 Paired End1


title: Exp1_A10

description: Experiment1 A10 Paired End1

source_name: Differentiated human embryonic stem cell

value: Differentiated embryonic stem cell


title: Exp1_A12

description: Experiment1 A12 Paired End1


title: Diff_H9

description: Differentiated single cell H9 Paired End1


title: Exp1_B4

description: Experiment1 B4 Paired End1


title: Diff_H3

description: Differentiated single cell H3 Paired End1


title: Exp1_B1

description: Experiment1 B1 Paired End1


title: Diff_H2

description: Differentiated single cell H2 Paired End1


title: Diff_H8

description: Differentiated single cell H8 Paired End1


title: Diff_H6

description: Differentiated single cell H6 Paired End1


title: Diff_H7

description: Differentiated single cell H7 Paired End1


title: Diff_H12

description: Differentiated single cell H12 Paired End1


title: Diff_H5

description: Differentiated single cell H5 Paired End1


title: Diff_H4

description: Differentiated single cell H4 Paired End1


title: Diff_G8

description: Differentiated single cell G8 Paired End1


title: Diff_G5

description: Differentiated single cell G5 Paired End1


title: Diff_G4

description: Differentiated single cell G4 Paired End1


title: Diff_H1

description: Differentiated single cell H1 Paired End1


title: Diff_G11

description: Differentiated single cell G11 Paired End1


title: Diff_F9

description: Differentiated single cell F9 Paired End1


title: Diff_G1

description: Differentiated single cell G1 Paired End1


title: Diff_F8

description: Differentiated single cell F8 Paired End1


title: Diff_F6

description: Differentiated single cell F6 Paired End1


title: Diff_H10

description: Differentiated single cell H10 Paired End1


title: Diff_H11

description: Differentiated single cell H11 Paired End1


title: Diff_G9

description: Differentiated single cell G9 Paired End1


title: Diff_G7

description: Differentiated single cell G7 Paired End1


title: Diff_G6

description: Differentiated single cell G6 Paired End1


title: Diff_G12

description: Differentiated single cell G12 Paired End1


title: Diff_F7

description: Differentiated single cell F7 Paired End1


title: Diff_G10

description: Differentiated single cell G10 Paired End1


title: Diff_F1

description: Differentiated single cell F1 Paired End1


title: Diff_F11

description: Differentiated single cell F11 Paired End1


title: Diff_G3

description: Differentiated single cell G3 Paired End1


title: Diff_F5

description: Differentiated single cell F5 Paired End1


title: Diff_F10

description: Differentiated single cell F10 Paired End1


title: Diff_F4

description: Differentiated single cell F4 Paired End1


title: Diff_E5

description: Differentiated single cell E5 Paired End1


title: Diff_E8

description: Differentiated single cell E8 Paired End1


title: Diff_E9

description: Differentiated single cell E9 Paired End1


title: Diff_F12

description: Differentiated single cell F12 Paired End1


title: Diff_E7

description: Differentiated single cell E7 Paired End1


title: Diff_E12

description: Differentiated single cell E12 Paired End1


title: Diff_E11

description: Differentiated single cell E11 Paired End1


title: Diff_E3

description: Differentiated single cell E3 Paired End1


title: Diff_G2

description: Differentiated single cell G2 Paired End1


title: Diff_E2

description: Differentiated single cell E2 Paired End1


title: Diff_E1

description: Differentiated single cell E1 Paired End1


title: Diff_D9

description: Differentiated single cell D9 Paired End1


title: Diff_D8

description: Differentiated single cell D8 Paired End1


title: Diff_F2

description: Differentiated single cell F2 Paired End1


title: Diff_E4

description: Differentiated single cell E4 Paired End1


title: Diff_D6

description: Differentiated single cell D6 Paired End1


title: Diff_D5

description: Differentiated single cell D5 Paired End1


title: Diff_E10

description: Differentiated single cell E10 Paired End1


title: Diff_D4

description: Differentiated single cell D4 Paired End1


title: Diff_D2

description: Differentiated single cell D2 Paired End1


title: Diff_E6

description: Differentiated single cell E6 Paired End1


title: Diff_D11

description: Differentiated single cell D11 Paired End1


title: Diff_D12

description: Differentiated single cell D12 Paired End1


title: Diff_D3

description: Differentiated single cell D3 Paired End1


title: Diff_D10

description: Differentiated single cell D10 Paired End1


title: Diff_C9

description: Differentiated single cell C9 Paired End1


title: Diff_C6

description: Differentiated single cell C6 Paired End1


title: Diff_D1

description: Differentiated single cell D1 Paired End1


title: Diff_C5

description: Differentiated single cell C5 Paired End1


title: Diff_C2

description: Differentiated single cell C2 Paired End1


title: Diff_C3

description: Differentiated single cell C3 Paired End1


title: Diff_C4

description: Differentiated single cell C4 Paired End1


title: Diff_F3

description: Differentiated single cell F3 Paired End1


title: Diff_C12

description: Differentiated single cell C12 Paired End1


title: Diff_C1

description: Differentiated single cell C1 Paired End1


title: Diff_D7

description: Differentiated single cell D7 Paired End1


title: Diff_C10

description: Differentiated single cell C10 Paired End1


title: Diff_C11

description: Differentiated single cell C11 Paired End1


title: Diff_B9

description: Differentiated single cell B9 Paired End1


title: Diff_B8

description: Differentiated single cell B8 Paired End1


title: Diff_B7

description: Differentiated single cell B7 Paired End1


title: Diff_B6

description: Differentiated single cell B6 Paired End1


title: Diff_B3

description: Differentiated single cell B3 Paired End1


title: Diff_B4

description: Differentiated single cell B4 Paired End1


title: Diff_B1

description: Differentiated single cell B1 Paired End1


title: Diff_C7

description: Differentiated single cell C7 Paired End1


title: Diff_B2

description: Differentiated single cell B2 Paired End1


title: Diff_B5

description: Differentiated single cell B5 Paired End1


title: Diff_B11

description: Differentiated single cell B11 Paired End1


title: Diff_B12

description: Differentiated single cell B12 Paired End1


title: Diff_A9

description: Differentiated single cell A9 Paired End1


title: Diff_A8

description: Differentiated single cell A8 Paired End1


title: Diff_B10

description: Differentiated single cell B10 Paired End1


title: Diff_A5

description: Differentiated single cell A5 Paired End1


title: Diff_A6

description: Differentiated single cell A6 Paired End1


title: Diff_A4

description: Differentiated single cell A4 Paired End1


title: Diff_A3

description: Differentiated single cell A3 Paired End1


title: Diff_A12

description: Differentiated single cell A12 Paired End1


title: Diff_A11

description: Differentiated single cell A11 Paired End1


title: Diff_A10

description: Differentiated single cell A10 Paired End1


title: Diff_A2

description: Differentiated single cell A2 Paired End1


title: UCLA4_XIST_Neg_Rep2

description: UCLA4 5iLAF XIST Negative Replicate2


title: Diff_A1

description: Differentiated single cell A1 Paired End1


title: UCLA4_XIST_Neg_Rep1

description: UCLA4 5iLAF XIST Negative Replicate1


title: UCLA1_Clone4_LatePassage_XIST_Pos

description: UCLA1 5iLAF Clone4 LatePassage XIST Positive


title: UCLA4_XIST_Pos_Rep1

description: UCLA4 5iLAF XIST Positive Replicate1


title: UCLA1_Reprimed

description: UCLA1 Reprimed


title: UCLA4_XIST_Pos_Rep2

description: UCLA4 5iLAF XIST Positive Replicate2


title: DFL_E12_WT_Input_rep1

status: Public on May 19 2016

description: Distal forelimb mouse E12.5 WT_Input

data_processing:
Illumina Casava1.8.2 software used for basecalling.Replicate data set was concatenated together.
Demultiplexed ChIP-seq reads were mapped onto the GRCm38 (mm10) using Bowtie (Galaxy Tool Version 1.1.2) (Langmead et al., 2009), with parameters “-m1 –strata –best” according to the conditions described previously (Riising et al., 2014). Both unmapped regions containing adaptors and contamination, and PCR duplicates were removed from mapped reads.
These analyses were performed on the public server of the Galaxy Project (https://usegalaxy.org/) (Hillman-Jackson et al., 2012).
By using bamCompare (Galaxy Tool Version 1.5.9.1.0) from the Galaxy deepTools webserver (http://deeptools.ie-freiburg.mpg.de/), ChIP and input data were normalized and compared to compute the log2 of the number of reads ratio (Ramirez et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph of log2 of the normalized number of reads ratio histone marks ChIP versus Input.

extract_protocol:
Micro-dissected proximal and distal segments of E12.5 forelimbs from wild type mice were used for ChIP-seq. Samples were fixed in 1% formaldehyde/PBS for 18 minutes at room temperature, washed at least three times with cold PBS containing protease inhibitor and stored at -80°C. Pools of ten pairs of wild type proximal or distal forelimbs were used for each experiment. The samples were treated with lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl and protease inhibitor) for 10 min on ice, followed by RIPA buffer (TE with 140 mM NaCl, 0.1% deoxycholate, 0.1% SDS, 1% TritonX-100 and protease inhibitor) and fragmented to a range of 200-500 bp by a Biorupter sonication device (Diagenode). PierceTM Protein A/G magnetic beads (88803, Thermo Scientific) were conjugated with each antibody in blocking buffer (PBS, 0.5% Tween20, 0.5% BSA and protease inhibitor) for 4 hrs at 4°C and washed with blocking buffer. Chromatin was incubated with the prepared protein A/G beads overnight at 4°C with rotation. 3 µg of H3K27ac (ab4729, Abcam) and 3 µg of H3K27me3 (07-449, Millipore) were used for each immunoprecipitation. Samples were washed 6 times with RIPA buffer, twice with RIPA/500 mM NaCl buffer, twice with LiCl wash buffer (TE, 250 mM LiCl, 0.5% NP-40 and 0.5% deoxycholate) and twice with TE, followed by eluted in direct elution buffer (10 mM Tris-HCl, 5 mM EDTA, 300 mM NaCl and 0.1% SDS). Cross-links were reversed overnight at 65°C and ChIPed DNA was treated with RNase A and proteinase K, and purified by phenol chloroform extraction.
For ChIP-seq, at least 5 ng of purified DNA were used to make libraries according to the manufacturer’s protocol (Illumina). The material was sequenced with 100 bp single-end reads on the Illumine HiSeq according to the manufacturer’s specifications.

tag: tissues

value: Distal forelimb

tag: antibody


title: Diff_A7

description: Differentiated single cell A7 Paired End1


title: PFL_E12_WT_Input_rep1

description: Proximal forelimb mouse E12.5 WT_Input

tag: age

value: Proximal forelimb

tag: genotype

value: wild type


title: DFL_E12_WT_H3K27ac_rep1

description: Distal forelimb mouse E12.5 WT_H3K27ac ChIPseq

tag: strain


title: Exp2_D1

description: Exp2 D1 Paired End1


title: PFL_E12_WT_H3K27ac_rep1

description: Proximal forelimb mouse E12.5 WT_H3K27ac ChIPseq


title: DFL_E12_WT_H3K27ac_rep2

description:
Distal forelimb mouse E12.5 WT_H3K27ac ChIPseq
Processed for replicates have been combined into one file. Processed data for this sample can be found on GSM2061121

value: H3K27ac (Abcam ab4729)


title: recovery-severe-2

status: Public on Jun 06 2015

city: Wageningen

first: Dick

middle: de

last: de Ridder

address: Droevendaalsesteeg 1

department: Plant Sciences

country: Netherlands

institute: Wageningen University

hyb_protocol: Affymetrix standard 16 hours at 45 centigrades Hybridization Oven 640

scan_protocol: GeneChip® Scanner 3000 ; GCOSv1

data_processing: Data were quantile normalised and RMA was used for probeset summarisation. Overexposed PM probes (>63000) were removed; when less than 8 PM probes were left in a probeset, it was removed as well. when subsets were analysed, these were individually normalised and summarised.

source_name: Peripheral Blood Mononuclear Cells

label_protocol: Afymetrix one cycle labeling kit

extract_protocol: Qiagen RNAesy plus shredder

tag: tissue

value: PBMC

tag: acute or recovery

value: recovery

tag: disease

value: severe


title: acute-severe-8

value: acute


title: recovery-moderate-7

value: moderate


title: acute-severe-5


title: recovery-severe-7


title: recovery-moderate-11


title: recovery-moderate-2


title: acute-severe-3


title: recovery-severe-1


title: recovery-moderate-3


title: acute-severe-4


title: recovery-severe-5


title: recovery-severe-8


title: recovery-moderate-9


title: acute-severe-7


title: acute-severe-2


title: recovery-severe-6


title: recovery-moderate-4


title: acute-severe-1


title: recovery-severe-3


title: acute-moderate-10


title: recovery-moderate-8


title: recovery-moderate-6


title: acute-severe-6


title: recovery-severe-4


title: acute-moderate-8


title: acute-moderate-9


title: acute-moderate-11


title: acute-moderate-6


title: acute-moderate-7


title: acute-moderate-5


title: acute-moderate-1


title: acute-mild-5

value: mild


title: acute-moderate-2


title: acute-mild-2


title: acute-mild-8


title: acute-mild-7


title: acute-mild-4


title: 21-0001

status: Public on May 12 2015

city: Stanford

first: Timothy

middle: E

last: Sweeney

state: California

address: 1265 Welch Road, MSOB

department: Biomedical Informatics

institute: Stanford University

description: gcRMA normalized

hyb_protocol: See original GSEs for clinical and technical information.

data_processing: All samples here were downloaded as .CEL files and re-normalized together using gcRMA using R package 'affy'.

source_name: Whole Blood

value: whole blood

value: SepticShock


title: acute-mild-3


title: acute-mild-1


title: 19-0001

description: gcRMA normalized

scan_protocol: See original GSEs for clinical and technical information.


title: 21-0003

description: gcRMA normalized

label_protocol: See original GSEs for clinical and technical information.


title: 18-0002

description: gcRMA normalized

extract_protocol: See original GSEs for clinical and technical information.


title: 20-0003

description: gcRMA normalized

treatment_protocol: See original GSEs for clinical and technical information.


title: 15-0017

description: gcRMA normalized


title: Diff_C8

description: Differentiated single cell C8 Paired End1


title: 19-0005

description: gcRMA normalized


title: 11-0082

description: gcRMA normalized

value: Control


title: 11-0078

description: gcRMA normalized


title: 11-0083

description: gcRMA normalized


title: 11-0081

description: gcRMA normalized


title: 11-0080

description: gcRMA normalized


title: acute-mild-6


title: acute-mild-9


title: recovery-moderate-5


title: 10-0019

description: gcRMA normalized


title: 11-0002

description: gcRMA normalized


title: 11-0007

description: gcRMA normalized


title: 11-0035

description: gcRMA normalized


title: 10-0003

description: gcRMA normalized


title: 07-0004

description: gcRMA normalized


title: 10-0009

description: gcRMA normalized


title: 10-0018

description: gcRMA normalized


title: 01-0086

description: gcRMA normalized


title: 01-0104

description: gcRMA normalized


title: 01-0106

description: gcRMA normalized


title: 11-0077

description: gcRMA normalized


title: 01-0088

description: gcRMA normalized


title: 01-0080

description: gcRMA normalized


title: 01-0077

description: gcRMA normalized


title: 01-0078

description: gcRMA normalized


title: 01-0105

description: gcRMA normalized


title: 01-0070

description: gcRMA normalized


title: 01-0047

description: gcRMA normalized


title: 04-0015

description: gcRMA normalized


title: 01-0079

description: gcRMA normalized


title: 01-0072

description: gcRMA normalized


title: 01-0071

description: gcRMA normalized


title: 01-0074

description: gcRMA normalized


title: 01-0069

description: gcRMA normalized


title: 01-0073

description: gcRMA normalized


title: 01-0068

description: gcRMA normalized


title: 01-0103

description: gcRMA normalized


title: 01-0064

description: gcRMA normalized


title: 11-0065

description: gcRMA normalized


title: 11-0042

description: gcRMA normalized


title: 01-0101

description: gcRMA normalized


title: 04-0012

description: gcRMA normalized


title: 01-0126

description: gcRMA normalized


title: 11-0038

description: gcRMA normalized


title: 01-0125

description: gcRMA normalized


title: 01-0119

description: gcRMA normalized


title: 09-0003

description: gcRMA normalized


title: 01-0111

description: gcRMA normalized


title: 22-0023

description: gcRMA normalized


title: 01-0120

description: gcRMA normalized


title: 01-0108

description: gcRMA normalized


title: 01-0157

description: gcRMA normalized


title: 01-0123

description: gcRMA normalized


title: 01-0121

description: gcRMA normalized


title: 01-0118

description: gcRMA normalized


title: 11-0111

description: gcRMA normalized


title: 01-0102

description: gcRMA normalized


title: 01-0122

description: gcRMA normalized


title: 22-0009

description: gcRMA normalized


title: 15-0027

description: gcRMA normalized


title: 01-0130

description: gcRMA normalized


title: 22-0020

description: gcRMA normalized


title: 01-0110

description: gcRMA normalized


title: 14-0005

description: gcRMA normalized


title: 05-0030

description: gcRMA normalized


title: 22-0018

description: gcRMA normalized


title: 01-0156

description: gcRMA normalized


title: 01-0155

description: gcRMA normalized


title: 01-0151

description: gcRMA normalized


title: 01-0150

description: gcRMA normalized


title: 01-0154

description: gcRMA normalized


title: 01-0148

description: gcRMA normalized


title: 22-0010

description: gcRMA normalized


title: 18-0004

description: gcRMA normalized


title: 22-0013

description: gcRMA normalized


title: 20-0006

description: gcRMA normalized


title: 20-0007

description: gcRMA normalized


title: 19-0007

description: gcRMA normalized


title: 14-0006

description: gcRMA normalized


title: 15-0023

description: gcRMA normalized


title: 20-002

description: gcRMA normalized


title: 15-0025

description: gcRMA normalized


title: 13-0004

description: gcRMA normalized


title: 19-0008

description: gcRMA normalized


title: 13-0005

description: gcRMA normalized


title: 20-0002

description: gcRMA normalized


title: 01-0135

description: gcRMA normalized


title: 01-0149

description: gcRMA normalized


title: 01-0152

description: gcRMA normalized


title: 17-0003

description: gcRMA normalized


title: 19-0009

description: gcRMA normalized


title: 11-0109

description: gcRMA normalized


title: 19-0006

description: gcRMA normalized


title: 13-0006

description: gcRMA normalized


title: 15-0021

description: gcRMA normalized


title: 11-0090

description: gcRMA normalized


title: 11-0087

description: gcRMA normalized


title: 11-0086

description: gcRMA normalized


title: 06-0008

description: gcRMA normalized


title: 11-0084

description: gcRMA normalized


title: 06-0013

description: gcRMA normalized


title: 11-0070

description: gcRMA normalized


title: 10-0026

description: gcRMA normalized


title: 07-0007

description: gcRMA normalized


title: 05-0020

description: gcRMA normalized


title: 01-0138

description: gcRMA normalized


title: 01-0134

description: gcRMA normalized


title: 04-0006

description: gcRMA normalized


title: 01-0142

description: gcRMA normalized


title: 10-0038

description: gcRMA normalized


title: 05-0019

description: gcRMA normalized


title: 05-0028

description: gcRMA normalized


title: 11-0075

description: gcRMA normalized


title: 05-0023

description: gcRMA normalized


title: 01-0146

description: gcRMA normalized


title: 06-0012

description: gcRMA normalized


title: 01-0114

description: gcRMA normalized


title: 03-0003

description: gcRMA normalized


title: 06-0011

description: gcRMA normalized


title: 01-0112

description: gcRMA normalized


title: 05-0025

description: gcRMA normalized


title: 11-0037

description: gcRMA normalized


title: 01-0117

description: gcRMA normalized


title: 01-0129

description: gcRMA normalized


title: 01-0115

description: gcRMA normalized


title: 01-0116

description: gcRMA normalized


title: 01-0133

description: gcRMA normalized


title: 01-0095

description: gcRMA normalized


title: 15-0009

description: gcRMA normalized

value: Sepsis


title: 01-0189

description: gcRMA normalized


title: 11-0050

description: gcRMA normalized


title: 03-0001

description: gcRMA normalized


title: 01-0038

description: gcRMA normalized


title: 01-0109

description: gcRMA normalized


title: 01-0034

description: gcRMA normalized


title: 11-0053

description: gcRMA normalized


title: 15-0013

description: gcRMA normalized


title: 01-0093

description: gcRMA normalized


title: 01-0087

description: gcRMA normalized


title: 01-0055

description: gcRMA normalized


title: 01-0099

description: gcRMA normalized


title: 11-0055

description: gcRMA normalized


title: 01-0092

description: gcRMA normalized


title: 11-0044

description: gcRMA normalized


title: 14-0004

description: gcRMA normalized


title: 13-0002

description: gcRMA normalized


title: 04-0010

description: gcRMA normalized


title: 15-0011

description: gcRMA normalized


title: 04-0011

description: gcRMA normalized


title: 11-0021

description: gcRMA normalized


title: 15-0012

description: gcRMA normalized


title: 11-0052

description: gcRMA normalized


title: 17-0001

description: gcRMA normalized


title: 01-0039

description: gcRMA normalized


title: 12-0002

description: gcRMA normalized


title: 14-0002

description: gcRMA normalized


title: 11-0054

description: gcRMA normalized


title: 10-0029

description: gcRMA normalized


title: 01-0062

description: gcRMA normalized


title: 02-0002

description: gcRMA normalized


title: 06-0009

description: gcRMA normalized


title: 01-0051

description: gcRMA normalized


title: 01-0059

description: gcRMA normalized


title: 01-0060

description: gcRMA normalized


title: 01-0033

description: gcRMA normalized


title: 01-0049

description: gcRMA normalized


title: 10-0021

description: gcRMA normalized


title: 11-0096

description: gcRMA normalized


title: 01-0053

description: gcRMA normalized


title: 01-0066

description: gcRMA normalized


title: 01-0061

description: gcRMA normalized


title: 11-0057

description: gcRMA normalized


title: 01-0045

description: gcRMA normalized


title: 01-0044

description: gcRMA normalized


title: 01-0036

description: gcRMA normalized


title: 05-0008

description: gcRMA normalized


title: 01-0043

description: gcRMA normalized


title: 06-0001

description: gcRMA normalized


title: 01-0052

description: gcRMA normalized


title: 01-0058

description: gcRMA normalized


title: 05-0006

description: gcRMA normalized


title: 07-0002

description: gcRMA normalized


title: 11-0001

description: gcRMA normalized


title: 09-0001

description: gcRMA normalized


title: 01-0007

description: gcRMA normalized


title: 25-070603

description: gcRMA normalized


title: 01-0026

description: gcRMA normalized


title: 10-0005

description: gcRMA normalized


title: 07-0006

description: gcRMA normalized


title: 10-0004

description: gcRMA normalized


title: 11-0022

description: gcRMA normalized


title: 11-0003

description: gcRMA normalized


title: 11-0023

description: gcRMA normalized


title: 11-0015

description: gcRMA normalized


title: 11-0006

description: gcRMA normalized


title: 11-0024

description: gcRMA normalized


title: 01-0019

description: gcRMA normalized


title: 11-0004

description: gcRMA normalized


title: 04-0004

description: gcRMA normalized


title: 15-0007

description: gcRMA normalized


title: 01-0027

description: gcRMA normalized


title: 10-0012

description: gcRMA normalized


title: 11-0010

description: gcRMA normalized


title: 01-0021

description: gcRMA normalized


title: 01-0024

description: gcRMA normalized


title: 05-0007

description: gcRMA normalized


title: 09-0002

description: gcRMA normalized


title: 05-0003

description: gcRMA normalized


title: 06-0004

description: gcRMA normalized


title: 01-0025

description: gcRMA normalized


title: 06-0003

description: gcRMA normalized


title: 05-0010

description: gcRMA normalized


title: 11-0029

description: gcRMA normalized


title: 15-0004

description: gcRMA normalized


title: 06-0006

description: gcRMA normalized


title: 02-0001

description: gcRMA normalized


title: 01-0014

description: gcRMA normalized


title: 12-0001

description: gcRMA normalized


title: 10-0001

description: gcRMA normalized


title: 10-0020

description: gcRMA normalized


title: 04-0005

description: gcRMA normalized


title: 04-0003

description: gcRMA normalized


title: 15-0008

description: gcRMA normalized


title: 10-0017

description: gcRMA normalized


title: 26-260611

description: gcRMA normalized


title: 01-0030

description: gcRMA normalized


title: 11-0011

description: gcRMA normalized


title: 11-0013

description: gcRMA normalized


title: 05-0011

description: gcRMA normalized


title: 11-0009

description: gcRMA normalized


title: 15-0001

description: gcRMA normalized


title: 11-0017

description: gcRMA normalized


title: 11-0012

description: gcRMA normalized


title: 01-0013

description: gcRMA normalized


title: 11-0020

description: gcRMA normalized


title: 11-0019

description: gcRMA normalized


title: 11-0008

description: gcRMA normalized


title: 15-0002

description: gcRMA normalized