title: Kasumi-1_ETO2 INPUT

status: Public on May 29 2019

city: St. Louis

first: Jinsong

last: Zhang

address: 1402 South Grand Blvd.

department: Department of Pharmacology & Physiology

institute: Saint Louis University School of Medicine

data_processing:
Base-calling performed with Illumina analysis pipeline.
ChIP-Seq reads were aligned to the human hg19 genome using STAR (2.5.2).
ChIP-Seq reads were further analyzed using HOMER (4.9) with default settings.
BedGraph files were generated with the “makeUCSCfile” tool accompanying the HOMER package.
Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: BedGraph files showing ChIP-Seq binding signals.

source_name: human AML cells

growth_protocol: Kasumi-1 and U937 cells were maintained in RPMI 1640 with 10% fetal bovine serum (FBS). CD34+ HSPCs were purified from umbilical cord blood of unidentified human donors (STEMCELL Technologies) and cultured in IMDM supplemented with 20% FBS, FLT3L (100 ng/ml), SCF (100 ng/ml), TPO (100 ng/ml), IL-6 (20 ng/ml), GM-CSF (20 ng/ml), and IL-3 (50 ng/ml) (PeproTech). Kasumi-1 cells were transduced with a mouse ETO2 cDNA expression vector.

extract_protocol:
ChIP was performed using SimpleChIP® Enzymatic Chromatin IP Kits (Magnetic Beads, Cell Signaling Technology #9003) following the manufacturer’s instructions.
Libraries were constructed following instructions accompanying the library preparation kit designed for Illumina sequencing.

treatment_protocol: Kasumi-1 cells were transduced with lentiviruses expressing ETO2. Transduced cells were selected with Puromycin.

value: human t(8;21) AML cells

tag: chip antibody

value: ETO2 (Santa Cruz, SC-9741)

tag: transduced with

value: lentiviruses expressing ETO2


title: anti-ETO2 U937

type: SRA

state: MO

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: cell type

value: human AML cells


title: anti-ETO2 Kasumi-1_ETO2


title: anti-ETO2 CD34+ HSPC

source_name: human normal CD34+ HSPCs

value: human CD34+ HSPCs


title: Hu1113.NoTx

status: Public on Mar 01 2019

city: Indianapolis

first: Debbie

middle: Carolyn

last: Thurmond

state: IN

address: 635 Barnhill Drive, MS 2031

department: Pediatrics

institute: Indiana University

description:
RNA-Seq data, Islets from Donor 12 , NONE
Stranded, polyA library

library_source: transcriptomic

data_processing:
RTA v1.18.64 and bcl2fastq v2.18 was used to base calling and FASTQ generation.
Reads aligned using TopHat2 (v2.0.14), with --no-coverage-search (with --library-type fr-firststrand for stranded library samples)
Unique reads quantified using htseq-count (version 0.6.0), with database generated from TxDb.Hsapiens.UCSC.hg19.knownGene (Bioconductor annotations, downloaded 6/8/2016).  For unstranded counts, strand was to "no" for "Unstranded" counts / FPKM (and strand was set to "reverse" for "Stranded" counts / FPKM)
Genome_build: hg19
Supplementary_files_format_and_content: RPKM normalized expression (using quantified reads and TxDb annotations in R) and read counts (calculated using htseq-count)

molecule: polyA RNA

source_name: Islets from Hu1113 , NONE (untreated)

growth_protocol: human islets were cultured in CMRL, 10% FBS and 1% PSG

extract_protocol:
RNAs were isolated by qiagen RNAeasy plus mini Kit
for samples 1-2: TruSeq unstranded polyA kit, for samples 3-8: KAPA stranded polyA kit
for samples 1-2: unstranded polyA RNA-Seq, for samples 3-8: stranded polyA RNA-Seq

treatment_protocol: 100 moi of adenoviral particles conferring beta cell specific expression of STX4, compared tosimilar moi of control adenovirus (same vector backbone) were applied to human islets for 1 hr. Cells were then washed to remove excess adenovirus and growth media applied for 2 days.

tag: treatment

tag: subject

tag: disease status

value: Non-Diabetics

tag: delivery vector


title: No Injury

status: Public on Mar 30 2019

city: Minneapolis

first: Mayank

last: Verma

state: MN

address: 2001 6th st se

department: Stem Cell Institute

institute: University of Minnesota

description: Endothelial and satellie cells

data_processing:
We used Cell Ranger(10X Genomics) to process raw sequencing data. This pipeline converted Illumina basecall files to fastq format, aligned sequencing reads to the mm10 transcriptome using the STAR aligner, quantified the expression of transcripts in each cell using Chromium barcodes. We carried out analyses of the filtered data using Seurat suite version 2.0 (Butler and Satija, 2017) in R studio (RStudio Team, 2015). We obtained data from 786(Basal) and 703(Injured) cells that passed quality control steps implemented in Cell Ranger. We further filtered out cells based on UMI and percent mitochondrial gene and were left with 775(Basal) and 702(Injury) cells. The two different runs were scaled and normalized individually with the nUMI and percent mitochondrial gene regressed out. The top 2000 variable genes from each run were combined and batch effect was factored out using diagonal CCA implemented in Seurat 2.0. The CCA dimensions were selected based on the CCA heatmaps. Clustering resolution is a subjective parameter that could be varied quantitatively as a function of the number of cells being clustered, and is difficult to choose an appropriate resolution in an automated fashion. To maintain a standard procedure for clustering, we used a value of 0.9 for the resolution based on trial and error. The clustering procedure was relatively insensitive to mild variation in the values of other user-specified parameters (data not shown). Clustering was performed in Seurat 2.0 based on the CCA based alignment. Clusters were classified based on expression of prototypic gene expression. Differentiation gene expression (DGE) was performed between adjacent clusters to parse out the identity of the clusters based on known markers.
R1 read- first 16bp is the cell barcode, the next 10bp is the UMI.
The Index 1 read is 8bp in length and is the sample barcode.
R2 read- 98bp in length and contains the cDNA (biological) sequence.
Genome_build: mm10
Supplementary_files_format_and_content: Alignment:Cellranger v2, Count:Cellranger v3
Supplementary_files_format_and_content: Loupe Cell Browser
Supplementary_files_format_and_content: 10X feature count

molecule: total RNA

organism: Mus musculus

source_name: TA muscle

growth_protocol: Freshly isolated FACS sorted cells

extract_protocol:
B6.Cg-Pax7tm1(cre/ERT2)Gaka/J (Pax7CreERT2) was crossed with the B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J(Ai9) to yield the Pax7Tdt(Pax7CreERT2:R26Rtdtomato) mice, which were both obtained from Jackson Labratory. Kdrtm2.1Jrt/J(Flk1GFP) were obtained from Jannet Rossant(Ema et al. 2006). Cre recombination was induced using tamoxifen (Sigma-Aldrich, T5648) dosed as 75mg/kg body weight x 3 times over one week, followed by a 5 day chase period, in 8 week old Pax7CreERT2/ CreERT2:R26Rtdtomato/tdtomato Flk1GFP/+. To induce injury and regeneration, TA muscle were injected with 20 ul of 3 mM cardiotoxin (CTX; Sigma-Aldrich, 217503). Both TA muscles from each mice were dissected and a single cell was obtained following enzymatic digestion as previously described (Verma M. 2018. Cell Stem Cell).
We loaded ~5,000 cells into 1 channel of the Chromium system for each of these samples and prepared libraries according to the manufacturer’s protocol using version 2.0 chemistry (10x Genomics). Following capture and lysis, we synthesized cDNA and amplified for 12 cycles as per the manufacturer’s protocol (10X Genomics). The amplified cDNA was used to construct Illumina sequencing libraries that were each sequenced on one lane of an Illumina HiSeq 2500 machine

tag: protocol

value: No Injury

tag: tissue

value: hind limb muscles

tag: strain

tag: Sex

value: Male

tag: age

value: 10 weeks


title: U937 INPUT


title: AdRIP.STX4.3

description:
RNA-Seq data, Islets from Donor3 , STX4 Over-Expression
Stranded, polyA library

data_processing:
Real Time Analysis (RTA) was used for base calling and bcl2fastq v1.8.4 was used to generate FASTQ files
Reads aligned using TopHat2 (v2.0.14), with --no-coverage-search (with --library-type fr-firststrand for stranded library samples)
Unique reads quantified using htseq-count (version 0.6.0), with database generated from TxDb.Hsapiens.UCSC.hg19.knownGene (Bioconductor annotations, downloaded 6/8/2016).  For unstranded counts, strand was to "no" for "Unstranded" counts / FPKM (and strand was set to "reverse" for "Stranded" counts / FPKM)
Genome_build: hg19
Supplementary_files_format_and_content: RPKM normalized expression (using quantified reads and TxDb annotations in R) and read counts (calculated using htseq-count)

value: STX4 Over-Expression

value: AdRIP


title: AdRIP.Ctrl.3

description:
RNA-Seq data, Islets from Donor3 , GFP Vector Control
Stranded, polyA library

source_name: Islets from Donor3 , GFP Vector Control

value: GFP Vector Control


title: heart_rnaseq_wt_a

status: Public on May 31 2019

city: San Francisco

first: Deepak

last: Srivastava

state: CA

address: 1650 Owens St, 4A

institute: Gladstone Institutes

data_processing:
Illumina Casava v1.8 was used for basecalling.
Reads were trimmed and aligned with STAR (v2.5.2).
Transcritps were quantified using Cufflinks (v2.2.1) and differential expression was computed using Cuffdiff (v2.2.1).
Genome_build: mm9
Supplementary_files_format_and_content: cuffdiff output; normalized abundance estimates and differential expression

extract_protocol:
The Zymo Direct-zol kit was used to extract RNA and DNaseI was used to eliminate residual DNA.
Takara Stranded Total RNA Sample Prep (cat# 634876)

treatment_protocol: The atria were trimmed off and the Next Advance Bullet Blender was used to dissociate the remaining mouse ventricular tissue.

tag: genotype/variation

value: wild type

tag: timepoint/age

value: post natal day 7

value: heart ventricular tissue


title: AdRIP.STX4.2

description:
RNA-Seq data, Islets from Donor2 , STX4 Over-Expression
Stranded, polyA library


title: heart_rnaseq_mkmy_c

value: double mutant


title: AdRIP.STX4.1

description:
RNA-Seq data, Islets from Donor1 , STX4 Over-Expression
Unstranded, polyA library


title: AdRIP.Ctrl.2

description:
RNA-Seq data, Islets from Donor2 , GFP Vector Control
Stranded, polyA library

source_name: Islets from Donor2 , GFP Vector Control


title: AdRIP.Ctrl.1

description:
RNA-Seq data, Islets from Donor1 , GFP Vector Control
Unstranded, polyA library

source_name: Islets from Donor1 , GFP Vector Control


title: WT large intestine 4

status: Public on Dec 31 2018

first: Suzanne

middle: M

last: Noble

address: 513 Parnassus Ave., Box 0414

institute: UCSF

description: animals sacrificed, dissected and large intestine contents extracted

data_processing:
Real time base calling on Illumina HiSeq 4000
kallisto to align reads to genome with parameters: --plaintext --bias --single --rf-stranded -l $AvgLibSize -s $SD (AvgLibSize and SD pulled from BioAnalyzer traces)
extract estimated counts and tpms from abundances.tsv files
tpms and estimated counts = 0 replaced with 1, transcripts filtered to included only those with values greater than 10 in at least one sample
limma/voom with genotype.environment as factor to produce log base 2 fold changes and adj. p values from estimated counts
tpms were used for heat map generation
Genome_build: C. albicans SC5314 Assembly 21
Supplementary_files_format_and_content: excel files containing 1. fold changes and adjusted p-values and 2. tpms

organism:
Candida albicans
Mus musculus

source_name: Murine large intestine colonization

extract_protocol:
Acid phenol chloroform extraction 4 times, phenol chloroform isoamyl extraction 4 times, additional cleanup using RNA SPRI bead mix
NEB Ultra Directional mRNA-seq

tag: strain (c. albicans/mus musculus)

tag: growth condition

value: large intestine

tag: time point

value: 10 days


title: WT large intestine 2


title: WT large intestine 3


title: wild-type 30C Rpb1 ChIP-nexus 1

status: Public on Nov 01 2018

city: Boston

first: Fred

last: Winston

state: MA

address: 77 Avenue Louis Pasteur, Room 239

department: Genetics

institute: Harvard Medical School

description: ChIP-nexus of Rpb1 in a wild-type S. cerevisiae strain grown at 30ºC.

data_processing:
The Snakemake pipeline used to process ChIP-nexus libraries is available at github.com/winston-lab. Filtering for reads containing the constant region of the adapter on the 5’ end of the read, 3’ adapter removal, and 3’ quality trimming were performed using cutadapt. The random pentamer molecular barcode on the 5’ end of the read was then removed and processed using a custom Python script. Reads were aligned to the combined S. cerevisiae and S. pombe genomes using Bowtie2, and uniquely mapping reads were selected using SAMtools. Reads mapping to the same location as another read with the same molecular barcode were identified as PCR duplciates and removed using a custom Python script. Coverage of the 5’-most base, corresponding to the point of crosslinking, was extracted using bedtools genomecov. The median fragment size estimated by MACS2 over all ChIP-nexus samples for the same factor was used to generate coverage of factor protection and fragment midpoints, by extending reads to the fragment size, or by shifting reads by half the fragment size, respectively. Coverage was normalized to the total number of reads uniquely mapping to S. cerevisiae.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: TSS-seq “plus” and “minus” files are bigWig files of spike-in normalized S. cerevisiae transcription start sites on the positive and negative strands, respectively. ChIP-nexus “plus” and “minus” files are bigWig files of library-size normalized S. cerevisiae coverage of the points of crosslinking on the positive and negative strand, respectively. ChIP-nexus “midpoint” and “protection” files are library-size normalized S. cerevisiae coverage of either the midpoint of the fragment predicted to be protected by the ChIP’ed factor by MACS2, or the entire fragment. NET-seq “plus” and “minus” files are bigWig files of library-size normalized S. cerevisiae coverage of the positions of transcribing RNA polymerase II on the positive and negative strands, respectively. MNase-seq “midpoint” files are bigWig files of spike-in normalized S. cerevisiae dyad coverage determined by taking the midpoint of each sequenced fragment. MNase-seq “midpoint_smoothed” files are bigWig files of the same spike-in normalized dyad coverage, smoothed with a Gaussian kernel of 20bp bandwidth. MNase-seq “wholefrag” files are bigWig files of spike-in normalized S. cerevisiae  coverage of the entire fragment protected from MNase digestion.

organism: Saccharomyces cerevisiae

source_name: log phase S. cerevisiae

growth_protocol: Cells were grown in YPD at 30ºC to approximately 1x107 cells/ml (OD600=0.6).

extract_protocol:
Cultures were cooled to 25ºC with medium pre-chilled to 4ºC before cross-linking in 1% formaldehyde while shaking at 25ºC for 30 minutes. Chromatin was extracted using standard methods (DeGennaro, 2013) and sheared in a QSONICA sonicating water bath. 2.5-3 mg of S. cerevisiae chromatin containing 5% S. pombe spike-in chromatin by mass was immunoprecipiated using 40μL 8WG16 antibody that was pre-bound to 100μL ProteinG Dynabeads (Invitrogen).
Library construction for Illumina sequencing was performed essentially as previously described (He, 2017), except buffers were optimized for yeast: Buffer A (10 mM TE, 0.1% Triton X), Buffer B (50mM HEPES.KOH pH 7.4, 140mM NaCl, 1mM EDTA, 1% Triton-X, 0.1% sodium deoxycholate), Buffer C (Buffer B with 250mM NaCl), Buffer D (10mM Tris pH 7.5, 250mM LiCl, 10mM EDTA, 0.5% IGEPAL CA-360, 0.1% sodium deoxycholate).

tag: temperature

value: log phase S. cerevisiae

tag: experiment type

value: ChIP-nexus of Rpb1

tag: target molecule

value: genomic DNA


title: 3d CTX injury

description: Endothelial and satellie cells

molecule: other

value: 3d CTX injury


title: wild-type 30C Rpb1 ChIP-nexus 2


title: MDA_RR_8h_2g_S30

status: Public on Oct 04 2018

city: Edinburgh

first: Carlos

last: Martinez-Perez

address: Western General Hospital, Crewe Road South

department: Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: The University of Edinburgh

description: MDA RR 8h 2g

data_processing:
Total RNA samples underwent quality control using Agilent Bioanalyser and RNA 600 Nanochips and quantified using the Qubit 2.0 fluorometer and the RNA BR assay.
Libraries generated from 500ng of each total RNA sample using the Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit for Illumina (FWD).
After amplification and purification, libraries were quantified using the Qubit dsDNA HS assay kit and assessed for size/quality using Agilent DNA HS kit.
Sequencing performed using the NextSeq 500/550 High-Output v2 kit (#FC-404-2005) on the NextSeq 550 platform (Illumina, #SY-415-1002).
Demultiplexed FASTQ files were generated using Bcl2fastq2 v2.17.1.14 software provided by Illumina.
Individual FASTQ files processed using the BlueBee software provided by Lexogen: trimming of low quality tails and adapter contamination, alighment with ENCODE settings and generate read counts using HTSeq-count.
Working on MS Excel: transfer gene read counts from each sample on to a single file, filter genes with low read counts for the majority of samples, relabel genes to Ensemble IDs obtained from Biomart and do log2 transformation.
Perform quantile normalisation using R the preprocessorCore package by Bioconductor.
Where data that to be integrated with data from publically-available datasets, integration batch effects were corrected using ComBat (Bioconductor).
Genome_build: GRCh38
Supplementary_files_format_and_content: .txt file containing read counts per gene for every samples after filtering, log2 transformation and quantile normalisation as decribed.

source_name: Breast cancer cell line model

growth_protocol: All cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% foetal calf serum (FCS), 50 U ml-1 penicillin and 50 mg ml-1 streptomycin and incubated at 37oC in a humidified atmosphere with 5% CO2.

extract_protocol:
Pellets of up to 1x10^7 cells were collected by trypsinization at 0, 2 and 8 h post-radiation, snap-frozen on dry ice and stored at – 70oC for subsequent RNA extraction. Total RNA was extracted from cells with the RNeasy Mini Kit using QIAshredder technology (UK Qiagen, Ltd). The manufacturer’s protocol for purification of total RNA from animal cells using spin technology was followed.
Lexogen QuantSeq 3' mRNA-Seq Prep Kit for Illumina (FWD)

treatment_protocol:
Cells were irradiated using a Faxitron cabinet X-ray system 43855D.
Radioresistant cell lines (MCF-7 RR, ZR-751 RR and MDA-MB-231 RR) were developed from their respective parental cell lines (MCF-7, ZR-751 and MDA-MB-231) by weekly exposure to single fractions of radiation. Radiation doses were increased from 0.5 Gy to 10 Gy over a period of 12 weeks and then maintained by weekly doses.

tag: parental cell line

tag: cell type

value: Radioresistant breast cancer cell line

value: 8h post-radiation


title: wild-type 30C Spt6 ChIP-nexus 2

description: ChIP-nexus of Spt6 in a wild-type S. cerevisiae strain grown at 30ºC.

extract_protocol:
Cultures were cooled to 25ºC with medium pre-chilled to 4ºC before cross-linking in 1% formaldehyde while shaking at 25ºC for 30 minutes. Chromatin was extracted using standard methods (DeGennaro, 2013) and sheared in a QSONICA sonicating water bath. 2.5-3 mg of S. cerevisiae chromatin containing 5% S. pombe spike-in chromatin by mass was affinity purified using 100μL Pan Mouse IgG Dynabeads (Invitrogen).
Library construction for Illumina sequencing was performed essentially as previously described (He, 2017), except buffers were optimized for yeast: Buffer A (10 mM TE, 0.1% Triton X), Buffer B (50mM HEPES.KOH pH 7.4, 140mM NaCl, 1mM EDTA, 1% Triton-X, 0.1% sodium deoxycholate), Buffer C (Buffer B with 250mM NaCl), Buffer D (10mM Tris pH 7.5, 250mM LiCl, 10mM EDTA, 0.5% IGEPAL CA-360, 0.1% sodium deoxycholate).

value: ChIP-nexus of Spt6


title: WT large intestine 5


title: WT large intestine 1


title: MDA_RR_8h_0g_S29

description: MDA RR 8h 0g


title: MDA_RR_2h_0g_S27

description: MDA RR 2h 0g

value: 2h post-radiation


title: MDA_RR_2h_2g_S28

description: MDA RR 2h 2g


title: MDA_2h_2g_S23

description: MDA 2h 2g

value: breast cancer cell line


title: MDA_8h_2g_S25

description: MDA 8h 2g


title: MDA_8h_0g_S24

description: MDA 8h 0g


title: MDA_RR_0h_0g_S26

description: MDA RR 0h 0g

value: 0h post-radiation


title: ZR_RR_8h_2g_S49

description: ZR RR 8h 2g


title: ZR_RR_8h_0g_S48

description: ZR RR 8h 0g


title: MDA_2h_0g_S22

description: MDA 2h 0g


title: ZR_RR_2h_2g_S47

description: ZR RR 2h 2g


title: ZR_8h_2g_S44

description: ZR 8h 2g


title: MDA_0h_0g_S21

description: MDA 0h 0g


title: ZR_RR_2h_0g_S46

description: ZR RR 2h 0g


title: ZR_2h_0g_S42

description: ZR 2h 0g


title: ZR_RR_0h_0g_S45

description: ZR RR 0h 0g


title: ZR_8h_0g_S43

description: ZR 8h 0g


title: ZR_0h_0g_S41

description: ZR 0h 0g


title: wild-type 30C Spt6 ChIP-nexus 1


title: MCF7_RR_8h_0g_S19

description: MCF7 RR 8h 0g


title: MCF7_RR_2h_0g_S17

description: MCF7 RR 2h 0g


title: MCF7_0h_0g_S11

description: MCF7 0h 0g


title: MCF7_8h_2g_S15

description: MCF7 8h 2g


title: MCF7_RR_2h_2g_S18

description: MCF7 RR 2h 2g


title: MCF7_RR_0h_0g_S16

description: MCF7 RR 0h 0g


title: Endothelium WT rep 2

status: Public on Aug 30 2018

city: Oxford

first: Marella

last: de Bruijn

address: MRC MHU, WIMM, John Radcliffe Hospital

department: Radcliffe Department of Medicine

institute: University of Oxford

data_processing:
Paired end reads mapped to mm9 mouse reference genome using STAR v2.4.2a, with lane replicates pooled into a single BAM file for each sample
Read counts for genes determined using the featureCounts program from the Subread package v1.4.5.
Counts were normalised and analysed for differential expression using R and the package DESEQ2 v1.12.4. P values were corrected for multiple testing using the Benjamini & Hochberg method, and differentially expressed genes were identified as those with p<0.05 and adjusted p value (FDR) < 0.1.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file containing raw counts for each sample

source_name: Endothelium of embryonic dorsal aorta

extract_protocol:
E11.5 AGM was manually dissected and prepared as single cell suspensions using a Collagenase I-based digestion, then hematopoietic clusters (Ter119- VE-Cadherin+ c-Kit+) were FACS-sorted into lysis buffer (1:20 Rnase inhibitor, 0.2% Triton X-100).
RNA-Seq libraries prepared using Smart-seq2 protocol (Picelli et al., Nature Protocols 2014)

value: embryonic dorsal aorta

tag: genotype

value: WT

tag: developmental stage

value: Endothelium (Ter119- VE-Cadherin+ c-Kit- CD41- CD45-)


title: MCF7_8h_0g_S14

description: MCF7 8h 0g


title: Endothelium WT rep 1


title: MCF7_2h_0g_S12

description: MCF7 2h 0g


title: MCF7_2h_2g_S13

description: MCF7 2h 2g


title: Endothelium Kitl null 1

value: Sl/Sl


title: Clusters WT rep 2

source_name: Haematopoietic clusters of embryonic dorsal aorta

value: Hematopoietic clusters (Ter119- VE-Cadherin+ c-Kit+)


title: Clusters Kitl null 1


title: Clusters Kitl null 2


title: Clusters WT rep 1


title: MCF7_RR_8h_2g_S20

description: MCF7 RR 8h 2g


title: PEL2958A70

status: Public on Jun 22 2018

first: Eshita

last: Sharma

state: Oxfordshire

address: Roosevelt Drive, Headington

department: Bioinformatics

institute: Wellcome Trust Centre for Human Genetics

description:
MDS168ERY
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.

data_processing:
Real time Analysis (RTA):  HiSeq 4000 - RTA v2.73, HCS v3.3.52
Base-calling: bcl2fastq v2.17.1.14
Adapter trimming: RNA-seq reads were trimmed for SMARTer and Illumina  adapter sequences using skewer-v0.1.125
Alignment: Reads in gzipped fastq format were aligned using Hisat2 version-2.0.0-beta with default parameters to a modified reference genome comprising the human genome, Homo sapiens GRCh37 - human_g1k_v37, and fasta sequences for ERCC spike-ins
Read counts (abundance measurement): Reads mapping uniquely to genes annotated in ENSEMBL release 76 were counted using featureCounts implemented in subread-v1.5.0
Normalized Counts: Read counts were normalized to counts per million (CPM) and Transcripts per Million (TPM) by dividing each gene-count by total reads mapped (uniquely mapped to exonic regions) per million and using ENSEMBL annotated read-lengths
Genome_build: GRCh37
Supplementary_files_format_and_content: Count_table_fractions.txt: raw read counts for all 63677 ENSEMBL annotated genes
Supplementary_files_format_and_content: CPM_table_fractions.txt:  Counts per million normalized counts all 63677 ENSEMBL annotated genes
Supplementary_files_format_and_content: TPM_table_fractions.txt:  Transcripts per million (gene-length and sequencing depth normalized counts) all 63677 ENSEMBL annotated genes
Supplementary_files_format_and_content: Text

source_name: Bone marrow erythroid precursor

extract_protocol:
Total RNA was extracted using Trizol with a linear acrylamide carrier, Dnase treated (Invitrogen) and purified using Agencourt RNA Clean XP beads (Beckman Coulter)
Libraries were produced using a SMARTer library preparation protocol (Clontech)

value: bone marrow

value: Erythroid precursor

tag: disease status

value: Myelodysplastic Syndrome

tag: sf3b1 mutational status

tag: srsf2 mutational status

value: MUT

tag: patient id


title: PEL2958A78

description:
HBM187MON
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.

source_name: Bone marrow monocytic precursor

tag: tissue

value: Monocytic precursor

value: Healthy


title: PEL2958A72

description:
MDS166ERY
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2958A80

description:
MDS163ERY
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2958A56

description:
MDS155ERY
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2958A65

description:
MDS191GRA
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.

source_name: Bone marrow granulocytic precursor

value: Granulocytic precursor


title: PEL2958A67

description:
MDS166MON
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2958A61

description:
HBM141ERY
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2958A62

description:
MDS191MON
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2958A53

description:
MDS168MON
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2958A63

description:
HBM141MON
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: Endothelium Kitl null 2


title: PEL2958A49

description:
MDS152ERY
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2958A50

description:
MDS155GRA
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2958A45

description:
HBM190ERY
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2958A40

description:
HBM141GRA
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2958A43

description:
MDS177ERY
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2958A44

description:
HBM187ERY
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2958A34

description:
MDS152MON
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2958A38

description:
HBM190MON
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2958A32

description:
MDS218ERY
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2958A36

description:
MDS178MON
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2958A30

description:
MDS178ERY
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2958A27

description:
MDS166GRA
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2958A3

description:
MDS142MON
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2958A29

description:
HBM190GRA
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2958A22

description:
MDS218MON
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2958A2

description:
MDS189GRA
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2958A24

description:
HBM160ERY
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2958A18

description:
HBM160GRA
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2958A21

description:
MDS163MON
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2958A54

description:
MDS189ERY
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2958A23

description:
MDS218GRA
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2958A10

description:
MDS163GRA
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2958A14

description:
MDS189MON
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2958A17

description:
HBM165MON
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2958A15

description:
HBM187GRA
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2958A19

description:
HBM160MON
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2958A13

description:
HBM165GRA
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2958A47

description:
MDS177MON
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2031A207

data_processing:
Real time Analysis (RTA):  HiSeq 4000 - RTA v2.73, HCS v3.3.52
Base-calling: bcl2fastq v2.17.1.14
Adapter trimming: RNA-seq reads were trimmed for SMARTer and Illumina  adapter sequences using skewer-v0.1.125
Alignment: Reads in gzipped fastq format were aligned using Hisat2 version-2.0.0-beta with default parameters to a modified reference genome comprising the human genome, Homo sapiens GRCh37 - human_g1k_v37, and fasta sequences for ERCC spike-ins
Mark Duplicates: Duplicate reads were marked using MarkDuplicates.jar implemented in Picard tools v1.92
Read counts (abundance measurement): Reads mapping uniquely to genes annotated in ENSEMBL release 76 were counted using featureCounts implemented in subread-v1.5.0
Normalized Counts: Read counts were normalized to counts per million (CPM) and Transcripts per Million (TPM) by dividing each gene-count by total reads mapped (uniquely mapped to exonic regions) per million and using ENSEMBL annotated read-lengths
Genome_build: GRCh37
Supplementary_files_format_and_content: Count_table.txt: raw read counts for all 63677 ENSEMBL annotated genes
Supplementary_files_format_and_content: CPM_table.txt:  Counts per million normalized counts all 63677 ENSEMBL annotated genes
Supplementary_files_format_and_content: TPM_table.txt:  Transcripts per million (gene-length and sequencing depth normalized counts) all 63677 ENSEMBL annotated genes
Supplementary_files_format_and_content: Text

source_name: Bone marrow CD34+ hematopoietic stem/progenitor cells

tag: u2af1 mutational status

tag: zrsr2 mutational status


title: PEL2031A208

value: CD34+ hematopoietic stem/progenitor cells


title: PEL2031A205


title: PEL2031A198


title: PEL2031A209


title: PEL2031A194


title: PEL2031A195


title: PEL2031A203


title: PEL2031A206


title: PEL2031A188


title: PEL2031A204


title: PEL2958A25

description:
MDS178GRA
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2031A192


title: PEL2031A200


title: PEL2031A196


title: PEL2031A186


title: PEL2031A197


title: PEL2031A191


title: PEL2031A184


title: PEL2031A182


title: PEL2031A193


title: PEL2031A199


title: PEL2031A179


title: PEL2031A190


title: PEL2031A180


title: PEL2958A11

description:
MDS155MON
Sequenced on 6 lanes, paired-end, 12 FASTQ
Processed data are in the *_table_fractions.txt files.


title: PEL2031A189


title: PEL2031A178


title: PEL2031A177


title: PEL2031A176


title: PEL2031A187


title: PEL2031A183


title: PEL2031A173


title: PEL2031A185


title: PEL2031A181


title: PEL2031A169

tag: gender

value: Female


title: PEL2031A175


title: PEL2031A172


title: PEL2031A167


title: PEL2031A168


title: PEL2031A171


title: PEL2031A170


title: PEL2031A166


title: PEL2031A163


title: PEL2031A161


title: PEL2031A162

value: Male


title: PEL2031A159


title: PEL2031A165


title: PEL2031A155


title: PEL2031A156


title: PEL2031A164


title: PEL2031A149


title: PEL2031A158


title: PEL2031A153


title: PEL2031A151


title: PEL2031A150


title: PEL2031A147


title: PEL2031A154


title: PEL2031A146


title: PEL2031A145


title: PEL2031A143


title: PEL2031A139


title: PEL2031A140


title: PEL2031A141


title: PEL2031A136


title: PEL2031A137


title: PEL2031A138


title: PEL2031A133


title: PEL2031A135


title: PEL2031A130


title: PEL2031A131


title: PEL2031A128


title: PEL2031A148


title: PEL2031A129


title: PEL2031A132


title: PEL2031A126


title: PEL2031A125


title: PEL2031A122


title: PEL2031A124


title: PEL2031A120


title: PEL2031A121


title: PEL2031A115


title: PEL2031A117


title: PEL2031A116


title: PEL2031A114


title: PEL2031A119


title: PEL2031A118


title: PEL2031A142


title: CRISPR-Targeted Embryo tyrosinase C

status: Public on Apr 26 2018

first: Daniel

middle: E

last: Wagner

address: 200 Longwood Ave, Harvard Medical School, Systems Biology, Warren Alpert 536

department: Systems Biology

description:
Sample_18

LibraryName(s):
DEW203
DEW204
DEW205

data_processing:
inDrops FASTQ files were demultiplexed using a custom python pipeline as previously described (see Zilionis et al., Nature Protocols 2017 and https://github.com/indrops/).  Each sequencing spot is associated with a single biological read and 1-3 technical reads, depending on the specific inDrops library preparation chemistry used.  FASTQs DEW001-DEW003 used V1 chemistry in which read2 is the biological read and read1 is the metadata read.  DEW010-DEW057 used V2 chemistry in which read1 is the biological read and read2 is the metadata read.  DEW101-208 used V3 chemistry in which read1 is the biological read, read2 carries the first half of the cell barcode, read3 carries the library index, and read4 carries the second half of the cell barcode and the UMI.
Sequencing reads were first sorted according to sample of origin; Individual samples were then formatted as a single demultiplexed FASTQ in which single-cell and UMI barcodes for each read are listed in the header. These FASTQ files are deposited in NCBI SRA and can be used to resume the inDrops.py read processing pipeline at step 2 ("Identify abundant barcodes", see https://github.com/indrops/).
Each cDNA read was trimmed using Trimomatic (version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20 MINLEN:16).
Cell-specific barcodes for each cDNA read were then matched against a set of pre-determined barcodes. Up to two nucleotide mismatch errors were corrected; other reads were discarded.
cDNA reads were then aligned to a zebrafish transcriptome using Bowtie (version 1.1.1, parameters: -n 1 -l 15 -e 200 -m 200 -best -strata -a). The reference transcriptome was built from the zebrafish GRCz10 genome assembly (Accesion: GCF_000002035.5).Mapped reads were then processed into counts of UMI-filtered transcripts per gene.
UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads.  This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode, and thresholding only the top ~95% of the largest (and often the only) mode of the distribution.
UMI counts matrices originating from the same biological sample were combined into a single table.  UMI counts were adjusted by a total counts normalization.
For TracerSeq embryos, inDrops FASTQ files generated from GFP-targeted sequencing libraries were demultiplexed as described above.  These FASTQ files were then parsed to generate TracerVSCellBarcodes tables using custom Matlab scripts (see: https://github.com/wagnerde/TracerSeq).
Genome_build: GRCz10
Supplementary_files_format_and_content:
Raw UMI-filtered counts (csv). Matrix rows are transcripts, columns are single cells.  Column headers are in the following format: LibraryName_CellBarcodePart1_CellBarcodePart2
Normalized UMI-filtered counts (csv). Matrix rows are transcripts, columns are single cells.  Column headers are in the following format: LibraryName_CellBarcodePart1_CellBarcodePart2
ClusterIDs (txt).  An array of clusterID assignments for each cell column in the associated CSV tables
ClusterNames (csv).  A table of annotations for each ClusterID.
Convert_DEW_to_SRR (csv).  A table for converting between DEW and NCBI library names.
CellTracerCounts (csv).  A table where each row is a unique TracerSeq transcript barcode; column1: inDrops cell barcode; column2: TracerSeq clone # assignment; column3: corrected TracerSeq barcode sequence; column4: UMI counts.

organism: Danio rerio

source_name: Zebrafish Embryo Dissociated Cells

extract_protocol:
Zebrafish embryos were incubated to the indicated times post-fertilization and chorions were removed by incubating in 1mg/mL Pronase (Sigma P5147-1G) for 3-4 min followed by washing in 0.3X Danieau Buffer. [10X Danieau Buffer = 174 mM NaCl, 2.1 mM KCl,1.2 mM MgSO4, 1.8 mM Ca(NO3)2, 15 mM HEPES,  pH 7.6].  Dissociation of embryonic tissues was performed similarly as previously described (Manoli & Driever, Cold Spring Harbor Protocols 2012) with the following specifications. Wild-type and CRISPR-targeted samples were each prepared from 20-100 embryos. Embryo tissues were triturated to homogeneity in 1-5mL FACSmax cell dissociation solution (Genlantis T200100) and incubated for 4-5 minutes at room temperature.  Cells were then filtered through a 40μm cell strainer mesh (Fisher 352340), and centrifuged in a swinging bucket rotor at 310g for 5 minutes.  Cell pellets were resuspended in 1X DPBS (no Ca/Mg, Life Technologies 14190-144) containing 1% BSA (Sigma A3311-100G), and subjected to 2-3 additional rounds of centrifugation and resuspension.  After washing, cells were resuspended in 0.5% BSA / DPBS containing 18% optiprep density medium (Sigma D1556-250ML).  Cell density was quantified manually using INCYTO™ C-Chip™ Disposable Hemacytometers (Fisher 22-600-100), and adjusted to ~100,000 cells per mL.  For single-embryo dissociations, all FACSmax and wash volumes were reduced to a volume 0.5 mL and were carried out in 0.5mL LoBind microcentrifuge tubes (Eppendorf 022431005) that had been pre-coated with 10% BSA/DPBS for 15 minutes at room temperature.  Single-cell transcriptomes were then barcoded using the inDrops platform as previously described (Zilionis et al., Nature Protocols 2017). Following the within-droplet reverse transcription step, emulsions were split into batches of approximately 1,000-2,000 cells, frozen at -80C, and subsequently processed as individual RNA-seq libraries.
Single-cell RNA-Seq libraries were prepared using a protocol customized for the inDrops platform (see Zilionis et al., Nature Protocols 2017)

tag: strain

value: AB

tag: treatment

value: embryos injected with sgRNA and Cas9 protein at 1-cell stage

value: tyrosinase-targeted (Cas9)


title: PEL2031A112

value: WT


title: CRISPR-Targeted Embryo tyrosinase A

description:
Sample_16

LibraryName(s):
DEW191
DEW192


title: CRISPR-Targeted Embryo chordin C

description:
Sample_15

LibraryName(s):
DEW206
DEW207
DEW208

value: chordin-targeted (Cas9)


title: PEL2031A134


title: CRISPR-Targeted Embryo chordin B

description:
Sample_14

LibraryName(s):
DEW200
DEW201
DEW202


title: PEL2031A127


title: PEL2031A123


title: TracerSeq Embryo 5

description:
Sample_12

LibraryName(s):
DEW167
DEW168
DEW169

value: embryos injected with TracerSeq library and Tol2 transposase mRNA at 1-cell stage

value: wild type


title: TracerSeq Embryo 4

description:
Sample_11

LibraryName(s):
DEW162
DEW163
DEW164
DEW165
DEW166


title: TracerSeq Embryo 3

description:
Sample_10

LibraryName(s):
DEW158
DEW159
DEW160
DEW161


title: TracerSeq Embryo 2

description:
Sample_09

LibraryName(s):
DEW105
DEW106
DEW107
DEW108
DEW109
DEW110


title: TracerSeq Embryo 1

description:
Sample_08

LibraryName(s):
DEW101
DEW102
DEW103
DEW104


title: Zebrafish Embryos, 24hpf

description:
Sample_07

LibraryName(s):
DEW021
DEW052
DEW053
DEW054
DEW055
DEW056
DEW057

value: TU

value: untreated embryos


title: Zebrafish Embryos, 6hpf

description:
Sample_02

LibraryName(s):
DEW042
DEW043
DEW044
DEW045


title: Zebrafish Embryos, 14hpf

description:
Sample_05

LibraryName(s):
DEW011
DEW035
DEW036
DEW037


title: CRISPR-Targeted Embryo tyrosinase B

description:
Sample_17

LibraryName(s):
DEW198
DEW199


title: Zebrafish Embryos, 18hpf

description:
Sample_06

LibraryName(s):
DEW001
DEW003
DEW012
DEW038
DEW039
DEW040
DEW041


title: Zebrafish Embryos, 8hpf

description:
Sample_03

LibraryName(s):
DEW046
DEW047
DEW048
DEW049


title: Zebrafish Embryos, 4hpf

description:
Sample_01

LibraryName(s):
DEW050
DEW051


title: Postia placenta 0-5 mm_rep2

status: Public on Jan 05 2018

city: saint paul

first: Jonathan

last: Schilling

state: minnesota

address: 2004 folwell ave

description:
Temporal seperation of brown rot was sptially acomplished by wafer design
UMN_augustus_PplATCC44394.aa
UMN_augustus_PplATCC44394.gtf
Dataset_1_All_genes_expression_profiles_during_wood_decay_in_brown_and_white_rot_fungi.xlsx

data_processing:
Raw RNA-seq reads were trimmed for Truseq2 adapters and for low-quality sequence with Trimmomatic (v0.33) and quality control was integrated using FastQC (v0.11.5). Remaining reads were mapped to the respective reference genome using Genomic Short-read Nucleotide Alignment Program (GSNAP) (Wu and Nacu, 2010). Beaker (v1.8) was used to annotate the genome by incorporating the above RNA-seq mapping data. These newly annotated genomes (AA files and GTF files) were compared with JGI’s (Joint Genome Institute, http://jgi.doe.gov/) genome annotation by testing the location of RNA-seq reads relative to exons, and this generated significantly improved annotations for all four fungi. The aligned read counts were computed using the “featureCounts” function of the Rsubread package (v1.22.2), and normalized as Reads Per Kilobase of transcript per Million mapped reads (RPKM) as gene expression level. The test of differential expression was made using edgeR's (v3.14) “glmQLFit” routine on the design matrix. The profiling data for whole-genome transcripts and DEGs are available in Dataset 1 (Excel file).
Genome_build: Postia placenta MAD-698-R-SB12 v1.0, Gloeophyllum trabeum v1.0, Trametes versicolor v1.0 and Pleurotus ostreatus PC15 v2.0 from JGI (https://genome.jgi.doe.gov/programs/fungi/index.jsf)
Supplementary_files_format_and_content: AA files include amino acid sequences; GTF files include genome annotations; Excel file (.xlsx) includes pairwise comparison and RPKM levels.

organism: Rhodonia placenta

source_name: brown rot decayed wood

growth_protocol: Directional growth of fungi on wood wafers was used to segregate fungal wood decay stages (space-for-time) in modified ASTM soil-block microcosms, described in detail, previously (Zhang et al., 2016). Sterilized wood wafers (length × width × thickness = 60 × 25 × 2.5 mm) cut from aspen (Populus sp.) lumber were propped in microcosms with the 25-mm edge resting on the soil surface, colonized from the base by one of four test fungi. Soil medium was a 1:1:1 mixture of soil, peat, and vermiculite hydrated to 40–45% (wt/vol) moisture content. Two brown rot fungi Postia placenta ATCC 44394 and Gloeophyllum trabeum ATCC 11539 and two white rot fungi Trametes versicolor A1-ATF (Minnesota Forest Pathology culture collection, University of Minnesota, USA) and Pleurotus ostreatus ATCC 32237 were maintained on 1.5% (wt/vol) malt extract agar prior to inoculating microcosms. Wafers were harvested when fungi had progressed 50 mm up the length of a wafer. By defining the visible hyphal front as a benchmark (0 mm), four 5-mm sections (5 x 25 x 2.5 mm) were extracted, one from 5 mm above the hyphal front (no fungus), one that included the hyphal front (0-5 mm), and two from further behind the hyphal front (15-20, 30-35 mm).

extract_protocol:
Total fungal RNA was extracted from fresh wood sections with TRIzol (Life Technologies) and cleaned up with a Qiagen RNeasy Mini Kit (Qiagen, Inc.) prior to RNA sequencing or quantitative RT-PCR (qRT-PCR), a method validated in Zhang et al. (2016).
For RNA sequencing, TruSeq RNA v2 libraries were prepared and sequenced on a HiSeq 2500 System (Illumina Inc., San Diego, CA) by using the standard protocols from Illumina.

tag: wafer locus

tag: decay stage

value: early decay


title: Zebrafish Embryos, 10hpf

description:
Sample_04

LibraryName(s):
DEW010
DEW032
DEW033
DEW034


title: Gloeophyllum trabeum 0-5 mm_rep2

description:
Temporal seperation of brown rot was sptially acomplished by wafer design
UMN_augustus_GtrATCC11539.aa
UMN_augustus_GtrATCC11539.gtf
Dataset_1_All_genes_expression_profiles_during_wood_decay_in_brown_and_white_rot_fungi.xlsx

organism: Gloeophyllum trabeum


title: Postia placenta 0-5 mm_rep1


title: Gloeophyllum trabeum 0-5 mm_rep3


title: STAT6 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF

status: Public on Jan 01 2018

city: Debrecen

first: Gergely

last: Nagy

address: Egyetem ter 1.

department: Department of Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

data_processing:
alignment with bwa v0.7.10 using default parameters
bam generation with samtools v0.1.19 using default parameters
tag directory generation with homer v4.2 makeTagDirectory using -checkGC parameter
bedgraph generation with homer v4.2 makeUCSCfile using -fsize 1e50 -norm parameters
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph

source_name: bone marrow-derived macrophage

extract_protocol:
Bone marrow-derived macrophages were differentiated in the presence of M-CSF for 6 days. Cells were treated with IL-4 20ng/ul) for the indicated period of time and were double crosslinked and lysed. Immunoprecipitation was carried out with antibodies against PU.1 (sc-352), STAT6 (sc-981), RXR (sc-774), PPARγ (Perseus #PP-A3409A), P300 (sc-585), RNAPII-pS2 (ab5095) and RAD21 (ab992). Protein antibody complexes were washed six times and eluted from Protein A coated paramagnetic beads. DNA was purified with the Qiagen Minelute kit.
Libraries were prepared with the Ovation Ultralow Library Systems (Nugen) according to the manufacturer protocol.

tag: breed

tag: age

value: 3 months

tag: Sex

value: male

tag: chip antibody


title: Gloeophyllum trabeum 0-5 mm_rep1


title: RXR ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4)


title: PU.1 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4)


title: Postia placenta 0-5 mm_rep3


title: PU.1 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (6hIL4)


title: CRISPR-Targeted Embryo chordin A

description:
Sample_13

LibraryName(s):
DEW193
DEW194
DEW195
DEW196
DEW197

tag: developmental stage

tag: genotype


title: FAE.Mcell.GFI1B+

status: Public on Nov 06 2017

first: Adam

last: Haber

state: Massachusetts

address: 665 Huntington Ave, HSPH Building 1, Room 305

institute: Harvard T. H. Chan School of Public Health

data_processing:
3' polyA RNA-seq
CellRanger 1.0
PCA (prcomp in R)
kNN-based graph clustering (R code)
Genome_build: mm10
Supplementary_files_format_and_content: 3' polyA RNA-seq. The expression levels for each gene (rows) in each single cell (column) in UMI counts as calculated using the CellRanger pipeline. Each column header provides the sequencing batch id, the cell barcode, and the cell type as identified by cluster analysis. Each ID is seperated by '_'

source_name: WT Mouse intestinal epithelial cells extracted from follicle-associated epithelia (FAE)

extract_protocol:
3' polyA RNA seq
10X Genomics Chromium Prep

tag: time point


title: FAE.epi2.GFI1B-

value: Wild-type


title: FAE.epi1.GFI1B-


title: Sample 9_IL-14-12_9

status: Public on Aug 04 2017

city: Innsbruck

first: Gabriel

last: Schneebauer

address: Technikerstrasse 25

country: Austria

institute: University of Innsbruck

description: processed data: DESeq_silver_uninfected_vs_silver_infected.xlsx

data_processing:
Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61
Reads were aligned to the draft genome sequence of the European eel (Henkel et al., 2012) using TopHat (version 2.0.5) (Trapnell et al., 2009)
The resulting files were filtered using SAMtools (version 0.1.18) (Li et al., 2009) to exclude secondary alignment of reads
Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq (Anders et al., 2015)
Differentially expressed genes were identified using DESeq (Anders and Huber, 2010) and data were further processed using Microsoft Excel
Genome_build: Anguilla_anguilla_genome_v1_09_nov_10
Supplementary_files_format_and_content: Microsoft Office Excel file (.xlsx) with the following columns: id; Name; Best hit; Description; Alternate descriptions; Min e-value; Similarity; GO molecular function; GO biological process; GO cellular component; Transcripts; Longest transcript length; Total length; sample x; BaseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj

organism: Anguilla anguilla

source_name: silver eel_uninfected

growth_protocol: European eels were caught by local fishermen and kept in freshwater for a few days.

extract_protocol:
Total RNA was isolated from gas gland tissue using the Qiagen miRNeasy kit. Quality and integrity of the RNA waere checked on an Agilent Bioanalyzer 2100 total RNA Nano series II chip.
Illumina RNASeq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2.

treatment_protocol: Prior to dissection, animals were either killed with an overdose of tricaine methanosulfonate or anesthetized with tricaine methanosulfonate and subsequently decerebrated. The swimbladder was dissected, freed from connective tissue to reveal the actual gas gland tissue, immediately shock frozen in liquid nitrogen and stored at -80°C until futher use.

value: silver eel

tag: infection status

value: uninfected

value: swimbladder; gas gland tissue


title: Sample 12_IL-14-12_12


title: Sample 6_IL-14-12_6


title: Sample 3_IL-14-12_3


title: Sample 2_IL-14-12_2


title: CS17-12341 [H3K36me3]

status: Public on May 04 2017

city: Philadelphia

first: Justin

last: Cotney

state: PA

address: 3501 Civic Center Blvd

department: Surgery

institute: Children's Hospital of Philadelphia

data_processing:
The raw FASTQ sequence files are being deposited in dbGAP

Data processing details are included in supplementary file (GSE97752_DATA_PROCESSING_INFO.xls) linked at the foot of GSE97752.

source_name: Embryonic Craniofacial Tissue

growth_protocol: Samples flash frozen immediately after collection by HDBR

extract_protocol:
Cotney and Noonan, CSHL Protocols 2015.
Rubicon Genomics Thruplex 48S

treatment_protocol: Cotney and Noonan, CSHL Protocols 2015.

value: craniofacial prominences

tag: antibody

tag: cat no./lot


title: CS17-12331 [H3K36me3]

tag: tissue


title: CS17-12611 [H3K36me3]


title: CS15-13000 [H3K36me3]


title: CS15-13019 [H3K36me3]


title: CS14-12913 [H3K36me3]


title: CS15-13128 [H3K36me3]


title: CS14-12408 [H3K36me3]


title: CS13-12877 [H3K36me3]


title: CS13-12383 [H3K36me3]


title: CS17-12341 [H3K27ac]


title: CS13-12829 [H3K36me3]


title: CS13-12690 [H3K36me3]


title: CS17-12331 [H3K27ac]


title: CS15-13019 [H3K27ac]


title: CS17-12611 [H3K27ac]


title: CS15-13128 [H3K27ac]


title: CS15-13000 [H3K27ac]


title: CS14-12408 [H3K27ac]


title: CS14-12709 [H3K27ac]


title: CS14-12913 [H3K27ac]


title: CS13-12877 [H3K27ac]


title: CS13-12830 [H3K27ac]


title: F2-N2108 [H3K27ac]

value: 10 pcw


title: CS20-12104 [H3K27ac]


title: CS13-12690 [H3K27ac]


title: CS13-12829 [H3K27ac]


title: CS13-12383 [H3K27ac]


title: CS14-12709 [H3K36me3]


title: CS15-13128 [H3K27me3]


title: CS17-12331 [H3K27me3]


title: CS17-12341 [H3K27me3]


title: CS17-12191 [H3K27ac]


title: CS14-12709 [H3K27me3]


title: CS14-12913 [H3K27me3]


title: CS13-12829 [H3K27me3]


title: CS13-12830 [H3K27me3]


title: CS15-13019 [H3K27me3]


title: CS15-13000 [H3K27me3]


title: CS13-12830 [H3K36me3]


title: CS15-13000 [H3K4me3]


title: CS14-12709 [H3K4me3]


title: CS13-12690 [H3K27me3]


title: CS13-12383 [H3K27me3]


title: CS14-12408 [H3K27me3]


title: CS13-12877 [H3K27me3]


title: CS17-12611 [H3K27me3]


title: CS13-12877 [H3K4me3]


title: CS13-12383 [H3K4me3]


title: CS13-12690 [H3K4me3]


title: CS17-12341 [H3K4me3]


title: CS15-13128 [H3K4me3]


title: CS15-13019 [H3K4me3]


title: CS13-12829 [H3K4me3]


title: CS14-12913 [H3K4me3]


title: CS17-12611 [H3K4me2]


title: CS17-12341 [H3K4me2]


title: CS14-12913 [H3K4me2]


title: CS14-12408 [H3K4me3]


title: CS13-12830 [H3K4me3]


title: CS17-12331 [H3K4me3]


title: CS17-12611 [H3K4me3]


title: CS17-12331 [H3K4me2]


title: CS17-12341 [H3K4me1]


title: CS13-12690 [H3K4me2]


title: CS17-12191 [H3K4me2]


title: CS15-13019 [H3K4me2]


title: CS15-13128 [H3K4me2]


title: CS14-12408 [H3K4me2]


title: CS13-12830 [H3K4me2]


title: CS13-12877 [H3K4me2]


title: CS15-13000 [H3K4me1]


title: CS14-12913 [H3K4me1]


title: CS13-12829 [H3K4me2]


title: CS14-12709 [H3K4me1]


title: CS14-12709 [H3K4me2]


title: CS13-12877 [H3K4me1]


title: CS20-12104 [H3K4me2]


title: CS13-12830 [H3K4me1]


title: CS13-12829 [H3K4me1]


title: CS15-13019 [H3K4me1]


title: CS15-13128 [H3K4me1]


title: CS13-12383 [H3K4me2]


title: CS17-12331 [H3K4me1]


title: CS13-12690 [H3K4me1]


title: CS17-12611 [H3K4me1]


title: CS13-12383 [H3K4me1]


title: HSF1 ZT14

status: Public on Dec 31 2016

city: Lausanne

middle: Aryeh

last: Sobel

state: Vaud

address: EPFL SV IBI-SV UPNAE AAB 0 36 (Batiment AAB) Station 15

department: School of Life Sciences

country: Switzerland

institute: EPFL

description: ZT 14

data_processing:
All alignments were performed using the BBCF HTSstation (available at http://htsstation.epfl.ch, David et al., 2014)
Genome_build: mm9

source_name: Liver

extract_protocol:
For the HSF1 ChIP-Seq, chromatin preparation and chromatin immunoprecipitation were performed as in Rey et al., PLoS Biol 2011. The HSF1 polyclonal antibody is from Stressgen (Enzo Life Sciences). For each IP, 5ul of HSF1 antibody was used with 250ul of pre-cleared chromatin.
Libraries for ultra-high throughput sequencing were prepared with the ChIP-Seq DNA sample kit (Illumina) as recommended by the manufacturer.

value: C57/BL6 WT

tag: feeding

value: ad libitum

tag: technique

value: ChIP-seq

value: liver

value: ZT 14


title: CS15-13000 [H3K4me2]


title: CS14-12408 [H3K4me1]


title: Input NRC ZT 26 Bmal1 KO

description: Chromatin

data_processing:
All alignments were performed using the BBCF HTSstation (available at http://htsstation.epfl.ch , David et al., 2014).
Peak calling was done using ChIP-peak (Schmid CD, Bucher P. 2010, Ambrosini G., Dreos R. and Bucher P. IWBBIO 2014, Available: http://ccg.vital-it.ch/chipseq/chip_peak.php) on DNase signal using all ZT concatenated with the following parameters: cutoff=100,vicinity=400,window size=600, threshold=1000. A peak calling was done as well specifically for ZT6 in the WT and in the Bmal1KO context with the following parameters: cutoff=100,vicinity=1000,window size=600, threshold=200. Detected peaks were quantified using the DNase and PolII signal with a window of +/-300 bp around peak center and using the H3K27ac with a window of +/-1kb peak center for each time point and in each context.
Wig files were generated using bam2wig (see David et al., 2014) and were normalized according to the number mapped reads divided by 10e7. DNase I signal is represented using the first position of the reads considered as the cutting position and without strand shifting. Pol II and H3K27ac are represented using the whole read length and a shift of respectively 80bp and 90bp for PolII and H3K27ac.
DNase hypersensitive sites footprints were detected using Wellington algorithm (Piper et al. 2013) with the following parameters: -sh 20,36,5 -fdr 0.05
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: Processed data files contain the normalized signal for each mark at each time point in BigWig format. In addition, the DNaseI hypersensitive peaks detected by the peak calling tool are provided in BigBed format. The footprints detected by Wellington algorithm are provided in BigWig format where the footprint score is reproted in negative scale (see Piper 2013). A table of quantile-normalized quantification of each mark at each time point and in WT and Bmal1KO context is provided in text format.

source_name: Liver, Bmal1 KO, ZT 26, input

growth_protocol: C57/BL6 male, 12- to 14-wk-old (at time of sacrifice) mice were housed in a 12 h light/12 h dark (LD) regimen for 2 wk with water and food available ad libitum. They were then phase-entrained to a 12 h/12 h LD regimen with water ad libitum but food access between ZT12 and ZT24 for 7 d (ZT, Zeitgeber time; ZT0 is defined as the time when the lights are turned on and ZT12 as the time when lights are turned off). At each ZT2, ZT06, ZT10, ZT14, ZT18, ZT22, and ZT26, five mice were anesthetized with isoflurane and decapitated. The livers were perfused with 2 ml of PBS through the spleen and immediately collected. A small piece of liver tissue (approx. 100 mg) was snap-frozen in liquid nitrogen and kept at -80°C for RNA extraction. The remaining liver tissue was immediately homogenized in PBS containing 1% formaldehyde for chromatin preparation. All animal care and handling was performed according to the State of Geneva's law for animal protection.

extract_protocol:
DNase1-seq protocol: Mouse liver nuclei were prepared as described in (Tian and Schibler 1991). Freshly prepared nuclei were suspended in ice-cold Ψ-buffer (11 mM KPO4 pH 7.4, 108 mM KCl, 22 mM NaCl, 5mM MgCl, 1 mM CaCl2, 1 mM DTT) and pelleted. 5x10^6 nuclei were suspended in 200 μl of Ψ-buffer supplemented with 0.2% of NP40 and 1 u/ml of DNaseI (DPFF Worthington Biochemical Corporation). DNase1 digestion was performed for 6 minutes in room temperature and the reaction was stopped by adding 200 μl of lysis buffer (50mM Tris-HCl pH 8, 20 mM EDTA, 1% SDS, 200 μg/ml proteinaseK). Protease digestion was performed overnight at 55 oC. RNaseA (100 μg/ml) was then added and samples were incubated at 37 oC for an hour. DNA was then extracted twice with phenol-chloroform and precipitated with isopropanol in the presence of 0.5 M NaCl. DNAs were dissolved in 5 mM Tris-HCl pH 8. DNAs from 4 animals were pooled and 75 μg of DNA was loaded on 11 ml 10%-50% sucrose gradient in STE buffer (1M NaCl, 20 mM Tris-HCl pH 8, 5 mM EDTA) and centrifuged at 30000 rpm for 16 hours at 20 oC (SW 40 Ti rotor, Beckman Coulter Inc). The sucrose gradients were then fractionated and DNA was precipitated by two volumes of ethanol in the presence of 5 μg of glycogen. Fractions containing DNA sized around 300bp were pooled and used for Illumina library preparation.
ChIP-seq PolII protocol: Perfused livers were processed for chromatin preparation as described in Ripperger JA, Schibler U (2006). The chromatin samples from the five mice were then pooled, frozen in liquid nitrogen, and stored at -80°C. For the ChIP experiments, the following antibody was used: anti-RPB2 (Santa Cruz Biotechnology, sc-673-18). To determine the optimal amounts of antibody, we performed pilot ChIP assays and determined the enrichment for a set of promoters by real-time qPCR according to Ripperger JA, Schibler U (2006). A total of 1 ml of each chromatin suspension (containing about 60 µg of DNA) was incubated with 10 µg of anti-RPB2 in buffer A (20 mM Tris/HCl (pH 7.5), 150 mM NaCl, 2 mM EDTA) overnight at 4°C on a rotating wheel. Ten µl of protein A bead suspension (25% slurry in buffer A), pre-blocked with 10 µg/ml of salmon sperm DNA and BSA at 4°C overnight, was then added and the incubation was continued for 1 h at room temperature on a rotating wheel. The beads were then washed with dialysis buffer and ChIP wash buffer as described in O'Geen H, Nicolet CM, Blahnik K, Green R, Farnham PJ (2006). Protein-DNA complexes were eluted from the beads, de-cross-linked, and treated with RNase A and, subsequently, with proteinase K, as described in O'Geen H, Nicolet CM, Blahnik K, Green R, Farnham PJ (2006). The DNA concentration was determined by fluorometry on the Qubit system (Invitrogen). A total of 10-12 ng DNA were used for the preparation of the library.
ChIP-seq H3K27ac protocol: ChIPs were performed according to the method described by Reddy et al. (2009) with a few modifications. The 100 ul chromatin aliquots were used for each IP and diluted with 900 ul of RIPA buffer (1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS in PBS at pH 7.4) and added to dynal magnetic beads conjugated with (sheep anti-mouse IgG Dynabeads, Invitrogen, Cat no: 110-31) pre-treated with 3 ul of polyclonal antibody for H3K27ac (Active Motif, Cat no: 39135) for immunoprecipitation of specific complexes. The samples were incubated overnight at 4°C on rotator, then magnetic beads washed 7 times with lithiumchloride wash buffer (100mM Tris at pH 7.5, 500mM LiCl, 1% NP-40 and 1% sodiumdeoxycholate) and finally once with 1X TE buffer (10mM Tris-HCl at pH 7.5, 0.1mM Na2EDTA). The chromatin complex was eluted using elution buffer (1% SDS, 0.1M NaHCO3) for 1 h at 65°C using eppendorf thermo-mixer. The chromatin was then de-crosslinked overnight at 65°C and ChIP DNA purified using Qiagen PCR purification kit and eluted in 50 ul of elution buffer. For qPCR reaction, 1.5 ul of 1/10 diluted ChIP DNA is used.
Libraries for ultra-high-throughput sequencing were prepared with the ChIP-Seq DNA sample kit (Illumina) as recommended by the manufacturer.

tag: strain/background

tag: genotype/variation

value: Bmal1 KO

tag: gender

value: night-restricted feeding

value: ZT 26


title: Input NRC ZT 22 Bmal1 KO

description: Chromatin

source_name: Liver, Bmal1 KO, ZT 22, input

value: ZT 22


title: Input NRC ZT 18 Bmal1 KO

description: Chromatin

source_name: Liver, Bmal1 KO, ZT 18, input

value: ZT 18


title: Input NRC ZT 14 Bmal1 KO

description: Chromatin

source_name: Liver, Bmal1 KO, ZT 14, input

value: male


title: Input NRC ZT 10 Bmal1 KO

description: Chromatin

source_name: Liver, Bmal1 KO, ZT 10, input

value: ZT 10


title: Input NRC ZT 06 Bmal1 KO

description: Chromatin

source_name: Liver, Bmal1 KO, ZT 6, input

value: ZT 6


title: Input NRC ZT 02 Bmal1 KO

description: Chromatin

source_name: Liver, Bmal1 KO, ZT 2, input

value: ZT 2


title: Patient 342

status: Public on Jul 06 2016

type: RNA

city: South San Francisco

first: Richard

last: Bourgon

address: 1 DNA Way, MS 93

department: Bioinformatics & Computational Biology

institute: Genentech, Inc.

hyb_protocol: Per NanoString Total RNA Standard Protocol for formalin-fixed, paraffin-embedded (FFPE) samples.

data_processing: Raw count data were logged (base 2). A synthetic target distribution was computed by averaging expression across all samples for each gene. Raw log-scale expression values for each sample were centered and scaled so as to have the same mean and standard deviation as endogenous (i.e., non-control and non-housekeeping) probes in the synthetic target distribution. Finally, normalized log-expression values were converted to z-score so that each gene had mean 0 and standard deviation 1 across the panel. Note that this conversion took place before 27 outlier samples were dropped; data presented here no longer have row-wise means and SDs of exactly 0 and 1, respectively. See NanoStringQCPro package on Bioconductor for processing of supporting raw count RCC and platform definition RLF files.

label: Nucleotide/fluorophore barcode

source_name: Microdissected FFPE tumor sample, newly diagnosed supratentorial glioblastoma

tag: idh1 status

value: Wild type

tag: phillips subtype

value: Mesenchymal

tag: tcga subtype

value: Classical

tag: treatment

value: Placebo

tag: surgical status

value: Complete resection

value: Female

tag: corticosteroids

value: On

tag: kps

tag: mgmt status

value: Non-methylated

tag: mmse

tag: rpa class

value: Grade III

tag: who

tag: os time to event (months)

tag: os event type (0 = censored)

tag: pfs time to event (months)

tag: pfs event type (0 = censored)


title: Patient 337

scan_protocol: Per NanoString Total RNA Standard Protocol for formalin-fixed, paraffin-embedded (FFPE) samples.

value: Proneural

value: Bevacizumab

value: Partial resection

tag: Sex

tag: age

value: Missing

value: Grade IV


title: Patient 341

label_protocol: Per NanoString Total RNA Standard Protocol for formalin-fixed, paraffin-embedded (FFPE) samples.

tag: idh1 status

value: Male

value: Off


title: Patient 339

extract_protocol: Per NanoString Total RNA Standard Protocol for formalin-fixed, paraffin-embedded (FFPE) samples.

tag: phillips subtype

value: Unclassified

value: Methylated

value: Grade V


title: Patient 343

value: Wild type

tag: tcga subtype


title: Patient 346

value: Neural

tag: treatment


title: Patient 338

value: Classical

value: Placebo

tag: surgical status


title: Patient 344

value: Proliferative

value: Mesenchymal

value: Female

tag: corticosteroids


title: Patient 335

value: Complete resection

tag: kps

value: Non-methylated


title: Patient 336

value: Partial resection

value: On

tag: mgmt status

value: Grade III


title: Patient 331

value: Proneural

value: Bevacizumab

tag: mmse


title: Patient 348

value: Off

value: Missing

tag: rpa class

value: Grade IV


title: Patient 349

value: Wild type

value: Grade V

tag: who


title: Patient 347

value: Male

tag: os time to event (months)


title: Patient 334

tag: os event type (0 = censored)


title: Patient 322

value: Unclassified

tag: pfs time to event (months)


title: Patient 340

value: Methylated

tag: pfs event type (0 = censored)


title: Patient 330

value: Proliferative

value: Placebo

tag: Sex


title: Patient 326

value: Mesenchymal

value: Complete resection

value: Female

tag: age


title: Patient 327

tag: idh1 status

value: Partial resection


title: Patient 328

tag: phillips subtype


title: Patient 329

tag: tcga subtype

value: Neural


title: Patient 332

tag: treatment

value: Non-methylated


title: Patient 325

value: Proneural

tag: surgical status


title: Patient 323

tag: corticosteroids

value: On


title: Patient 324

value: Classical

tag: kps


title: Patient 321

value: Bevacizumab

tag: mgmt status

value: Grade IV


title: Patient 319

value: Wild type

tag: mmse


title: Patient 318

value: Male

tag: rpa class

value: Grade III


title: Patient 317

value: Off

tag: who


title: Patient 320

value: Grade V

tag: os time to event (months)


title: Patient 314

value: Missing

tag: os event type (0 = censored)


title: Patient 312

value: Unclassified

value: Methylated

tag: pfs time to event (months)


title: Patient 313

value: Mesenchymal

value: Female

tag: pfs event type (0 = censored)


title: Patient 311

value: Placebo

value: Partial resection

tag: Sex


title: Patient 315

value: Proneural

tag: age

value: Non-methylated


title: Patient 309

tag: idh1 status

value: Complete resection


title: Patient 310

tag: phillips subtype


title: Patient 303

value: Proliferative

tag: tcga subtype

value: Classical

value: On


title: Patient 304

value: Wild type

tag: treatment

value: Bevacizumab

value: Male


title: Patient 305

tag: surgical status

value: Off

value: Grade V


title: Patient 306

tag: corticosteroids

value: Grade IV


title: Patient 308

value: Biopsy

tag: kps


title: Patient 302

tag: mgmt status


title: Patient 299

tag: mmse


title: Patient 300

value: Missing

tag: rpa class

value: Grade III


title: Patient 301

value: Mesenchymal

value: Female

value: Methylated

tag: who


title: Patient 297

value: Non-methylated

tag: os time to event (months)


title: Patient 298

value: Proneural

value: Placebo

value: Partial resection

tag: os event type (0 = censored)


title: Patient 296

tag: pfs time to event (months)


title: Patient 316

tag: pfs event type (0 = censored)


title: Patient 295

value: Classical

tag: Sex

value: On


title: Patient 293

value: Wild type

tag: age


title: Patient 294

tag: idh1 status

value: Unclassified

value: Bevacizumab

value: Complete resection

value: Male


title: Patient 292

tag: phillips subtype

value: Off


title: Patient 307

tag: tcga subtype

value: Missing

value: Grade V


title: Patient 291

value: Mesenchymal

tag: treatment

value: Grade III


title: Patient 290

tag: surgical status

value: Female

value: Grade IV


title: Patient 289

tag: corticosteroids

value: Methylated


title: Patient 287

value: Proliferative

tag: kps

value: Non-methylated


title: Patient 288

value: Classical

value: Placebo

tag: mgmt status


title: Patient 283

value: Wild type

value: Partial resection

value: On

tag: mmse


title: Patient 281

value: Proneural

value: Bevacizumab

value: Complete resection

tag: rpa class


title: Patient 282

value: Male

tag: who


title: Patient 286

value: Off

tag: os time to event (months)


title: Patient 279

value: Mesenchymal

tag: os event type (0 = censored)


title: Patient 280

value: Unclassified

value: Grade V

tag: pfs time to event (months)


title: Patient 275

value: Grade IV

tag: pfs event type (0 = censored)


title: Patient 277

tag: Sex


title: Patient 278

value: Biopsy

value: Female

tag: age

value: Missing


title: Patient 276

tag: idh1 status

value: Classical

value: Methylated


title: Patient 272

value: Wild type

tag: phillips subtype

value: Proliferative

value: Non-methylated


title: Patient 274

tag: tcga subtype

value: Placebo


title: Patient 273

value: Neural

tag: treatment

value: On


title: Patient 270

value: Bevacizumab

tag: surgical status

value: Complete resection


title: Patient 271

value: Mesenchymal

tag: corticosteroids


title: Patient 266

value: Partial resection

value: Male

value: Off

tag: kps


title: Patient 268

value: Unclassified

tag: mgmt status

value: Grade IV


title: Patient 267

value: Proneural

tag: mmse


title: Patient 265

value: Female

tag: rpa class


title: Patient 264

tag: who


title: Patient 284

value: Missing

value: Grade III

tag: os time to event (months)


title: Patient 259

value: Wild type

value: Proliferative

tag: os event type (0 = censored)


title: Patient 261

value: Placebo

value: Non-methylated

tag: pfs time to event (months)


title: Patient 263

tag: pfs event type (0 = censored)


title: Patient 262

tag: Sex


title: Patient 260

tag: age

value: Grade V


title: Patient 255

tag: idh1 status

value: Bevacizumab


title: Patient 256

tag: phillips subtype

value: Complete resection


title: Patient 251

tag: tcga subtype

value: On


title: Patient 253

value: Mesenchymal

tag: treatment


title: Patient 249

tag: surgical status


title: Patient 250

value: Partial resection

tag: corticosteroids


title: Patient 257

value: Off

tag: kps


title: Patient 252

value: Unclassified

value: Male

tag: mgmt status

value: Methylated


title: Patient 248

value: Classical

tag: mmse

value: Grade IV


title: Patient 247

tag: rpa class


title: Patient 245

value: Missing

tag: who


title: Patient 243

value: Wild type

value: Female

tag: os time to event (months)


title: Patient 244

value: Proneural

value: Placebo

tag: os event type (0 = censored)


title: Patient 246

value: Non-methylated

tag: pfs time to event (months)


title: Patient 258

value: Grade III

tag: pfs event type (0 = censored)


title: Patient 241

tag: Sex


title: Patient 254

value: Bevacizumab

tag: age

value: Grade V


title: Patient 236

tag: idh1 status

value: Proliferative

value: On


title: Patient 235

tag: phillips subtype

value: Partial resection


title: Patient 238

tag: tcga subtype

value: Complete resection

value: Off


title: Patient 237

value: Mesenchymal

tag: treatment

value: Male

value: Methylated


title: Patient 240

value: Unclassified

tag: surgical status

value: Grade IV


title: Patient 239

value: Wild type

value: Classical

value: Biopsy

tag: corticosteroids

value: Missing


title: Patient 234

value: Placebo

tag: kps

value: Non-methylated


title: Patient 233

value: Bevacizumab

tag: mgmt status


title: Patient 232

tag: mmse

value: Grade III


title: Patient 231

value: Female

tag: rpa class


title: Patient 229

value: Proliferative

tag: who


title: Patient 230

value: Complete resection

tag: os time to event (months)


title: Patient 225

value: Off

tag: os event type (0 = censored)


title: Patient 226

value: Proneural

value: Partial resection

value: On

tag: pfs time to event (months)


title: Patient 224

tag: pfs event type (0 = censored)


title: Patient 223

tag: Sex

value: Methylated


title: Patient 242

value: Mesenchymal

tag: age

value: Grade IV


title: Patient 220

tag: idh1 status

value: Wild type

value: Classical

value: Male


title: Patient 222

tag: phillips subtype

value: Unclassified

value: Placebo

value: Grade V


title: Patient 221

tag: tcga subtype

value: Bevacizumab


title: Patient 219

value: Neural

tag: treatment

value: Female


title: Patient 218

value: Proliferative

tag: surgical status

value: Complete resection

value: Non-methylated


title: Patient 215

value: Partial resection

tag: corticosteroids

value: Off


title: Patient 214

tag: kps

value: Grade III


title: Patient 213

value: Mesenchymal

tag: mgmt status

value: Missing


title: Patient 212

value: Wild type

value: On

value: Methylated

tag: mmse

value: Grade IV


title: Patient 216

value: Classical

value: Placebo

value: Biopsy

tag: rpa class


title: Patient 217

value: Bevacizumab

value: Male

value: Grade V

tag: who


title: Patient 208

tag: os time to event (months)


title: Patient 207

value: Female

tag: os event type (0 = censored)


title: Patient 206

value: Proliferative

value: Complete resection

value: Non-methylated

tag: pfs time to event (months)


title: Patient 228

value: Unclassified

value: Partial resection

value: Off

tag: pfs event type (0 = censored)


title: Patient 211

value: Wild type

value: Proneural

tag: Sex


title: Patient 205

value: Mesenchymal

tag: age

value: On

value: Missing


title: Patient 210

tag: idh1 status

value: Placebo

value: Grade III


title: Patient 209

tag: phillips subtype

value: Bevacizumab

value: Grade IV


title: Patient 204

tag: tcga subtype

value: Methylated


title: Patient 203

tag: treatment

value: Female

value: Grade V


title: Patient 202

tag: surgical status

value: Complete resection


title: Patient 201

value: Proliferative

value: Classical

tag: corticosteroids


title: Patient 200

value: Partial resection

tag: kps

value: Non-methylated


title: Patient 199

value: Wild type

value: Male

tag: mgmt status


title: Patient 198

value: Mesenchymal

value: Off

tag: mmse


title: Patient 196

value: On

tag: rpa class


title: Patient 195

value: Placebo

tag: who


title: Patient 194

value: Proneural

tag: os time to event (months)


title: Patient 193

value: Bevacizumab

tag: os event type (0 = censored)


title: Patient 197

value: Neural

tag: pfs time to event (months)


title: Patient 191

value: Grade IV

tag: pfs event type (0 = censored)


title: Patient 190

tag: Sex

value: Female


title: Patient 192

tag: age

value: Methylated


title: Patient 189

tag: idh1 status

value: Complete resection


title: Patient 186

tag: phillips subtype

value: Unclassified

value: Missing

value: Grade III


title: Patient 188

tag: tcga subtype

value: Classical


title: Patient 183

value: Wild type

tag: treatment


title: Patient 187

tag: surgical status

value: Partial resection

value: Male


title: Patient 185

tag: corticosteroids

value: Off

value: Non-methylated


title: Patient 175

value: Mesenchymal

value: Placebo

tag: kps


title: Patient 176

value: Proneural

value: Bevacizumab

value: Biopsy

value: On

tag: mgmt status

value: Grade V


title: Patient 181

value: Female

tag: mmse


title: Patient 180

value: Complete resection

tag: rpa class

value: Grade IV


title: Patient 182

tag: who


title: Patient 177

value: Missing

tag: os time to event (months)


title: Patient 179

tag: os event type (0 = censored)


title: Patient 178

value: Classical

tag: pfs time to event (months)


title: Patient 172

value: Wild type

value: Methylated

tag: pfs event type (0 = censored)


title: Patient 174

value: Partial resection

tag: Sex

value: Male


title: Patient 173

value: Unclassified

tag: age

value: Off


title: Patient 169

tag: idh1 status


title: Patient 170

tag: phillips subtype

value: Mesenchymal

value: Non-methylated


title: Patient 168

value: Proneural

tag: tcga subtype

value: Bevacizumab


title: Patient 167

tag: treatment

value: On


title: Patient 163

value: Placebo

tag: surgical status


title: Patient 162

tag: corticosteroids

value: Grade V


title: Patient 166

value: Complete resection

tag: kps


title: Patient 164

tag: mgmt status


title: Patient 184

tag: mmse

value: Grade IV


title: Patient 161

value: Female

tag: rpa class


title: Patient 160

value: Classical

value: Grade III

tag: who


title: Patient 157

value: Wild type

value: Methylated

tag: os time to event (months)


title: Patient 154

value: Partial resection

value: Male

tag: os event type (0 = censored)


title: Patient 155

tag: pfs time to event (months)


title: Patient 165

value: Proliferative

value: Off

tag: pfs event type (0 = censored)


title: Patient 156

value: Biopsy

tag: Sex

value: Missing


title: Patient 153

value: Unclassified

value: Mesenchymal

value: Bevacizumab

tag: age


title: Patient 150

tag: idh1 status

value: Proneural

value: Placebo

value: On

value: Non-methylated


title: Patient 148

tag: phillips subtype

value: Female


title: Patient 151

tag: tcga subtype

value: Grade IV


title: Patient 152

value: Wild type

tag: treatment


title: Patient 147

value: Classical

tag: surgical status

value: Methylated


title: Patient 145

value: Partial resection

value: Male

tag: corticosteroids


title: Patient 146

value: Neural

tag: kps

value: Grade V


title: Patient 143

value: Proliferative

value: Complete resection

tag: mgmt status


title: Patient 159

value: Off

tag: mmse


title: Patient 158

value: Mesenchymal

tag: rpa class


title: Patient 141

value: Proneural

tag: who


title: Patient 142

value: Placebo

tag: os time to event (months)


title: Patient 140

tag: os event type (0 = censored)


title: Patient 144

value: Bevacizumab

value: On

tag: pfs time to event (months)


title: Patient 133

value: Female

value: Non-methylated

tag: pfs event type (0 = censored)


title: Patient 138

value: Wild type

tag: Sex

value: Grade IV


title: Patient 136

value: Classical

tag: age

value: Methylated


title: Patient 137

tag: idh1 status

value: Partial resection

value: Missing


title: Patient 134

tag: phillips subtype

value: Male


title: Patient 132

tag: tcga subtype


title: Patient 131

value: Unclassified

tag: treatment


title: Patient 149

value: Proliferative

tag: surgical status

value: Biopsy

value: Grade V


title: Patient 129

value: Mesenchymal

value: Complete resection

tag: corticosteroids

value: Off


title: Patient 130

value: Proneural

value: Bevacizumab

tag: kps


title: Patient 139

tag: mgmt status


title: Patient 127

value: Placebo

value: Female

value: On

tag: mmse


title: Patient 126

value: Wild type

value: Non-methylated

tag: rpa class


title: Patient 125

value: Neural

value: Partial resection

value: Grade IV

tag: who


title: Patient 128

value: Classical

value: Missing

tag: os time to event (months)


title: Patient 120

tag: os event type (0 = censored)


title: Patient 122

value: Unclassified

value: Male

tag: pfs time to event (months)


title: Patient 121

tag: pfs event type (0 = censored)


title: Patient 124

value: Proliferative

value: Biopsy

tag: Sex

value: Grade V


title: Patient 123

value: Mesenchymal

value: Complete resection

tag: age

value: Off


title: Patient 118

tag: idh1 status

value: Placebo


title: Patient 135

tag: phillips subtype

value: Proneural

value: Bevacizumab

value: On


title: Patient 113

value: Wild type

tag: tcga subtype

value: Non-methylated


title: Patient 111

tag: treatment

value: Methylated

value: Grade IV


title: Patient 112

tag: surgical status

value: Partial resection


title: Patient 110

value: Female

tag: corticosteroids


title: Patient 108

value: Male

tag: kps


title: Patient 116

value: Neural

tag: mgmt status


title: Patient 115

tag: mmse


title: Patient 114

tag: rpa class


title: Patient 117

tag: who


title: Patient 106

value: Biopsy

value: Missing

tag: os time to event (months)


title: Patient 119

value: Mesenchymal

tag: os event type (0 = censored)


title: Patient 107

value: Complete resection

tag: pfs time to event (months)


title: Patient 109

tag: pfs event type (0 = censored)


title: Patient 105

value: Unclassified

value: Classical

tag: Sex

value: Grade V


title: Patient 103

value: Placebo

tag: age

value: Off


title: Patient 104

tag: idh1 status

value: Wild type

value: Proneural

value: Bevacizumab


title: Patient 101

tag: phillips subtype

value: Grade IV


title: Patient 100

tag: tcga subtype

value: Methylated


title: Patient 99

value: Proliferative

tag: treatment


title: Patient 97

tag: surgical status

value: Partial resection

value: Male

value: Non-methylated


title: Patient 98

tag: corticosteroids


title: Patient 96

tag: kps

value: Grade III


title: Patient 94

value: Mesenchymal

value: Female

value: On

tag: mgmt status


title: Patient 87

tag: mmse


title: Patient 90

value: Classical

value: Complete resection

tag: rpa class


title: Patient 85

value: Missing

tag: who


title: Patient 91

value: Placebo

value: Off

tag: os time to event (months)


title: Patient 89

value: Wild type

tag: os event type (0 = censored)


title: Patient 88

value: Proneural

value: Bevacizumab

tag: pfs time to event (months)


title: Patient 84

value: Grade IV

tag: pfs event type (0 = censored)


title: Patient 79

tag: Sex


title: Patient 76

tag: age


title: Patient 80

tag: idh1 status

value: Biopsy


title: Patient 82

tag: phillips subtype

value: Proliferative

value: Methylated

value: Grade V


title: Patient 78

tag: tcga subtype

value: Partial resection

value: Male

value: Non-methylated


title: Patient 77

value: Unclassified

value: Mesenchymal

tag: treatment

value: Female


title: Patient 75

tag: surgical status

value: Complete resection


title: Patient 83

value: Classical

value: Placebo

tag: corticosteroids


title: Patient 93

value: Wild type

value: On

tag: kps

value: Missing


title: Patient 102

value: Proneural

tag: mgmt status

value: Grade IV


title: Patient 81

value: Bevacizumab

value: Off

tag: mmse


title: Patient 73

tag: rpa class

value: Grade V


title: Patient 72

value: Proliferative

tag: who


title: Patient 86

value: Male

tag: os time to event (months)


title: Patient 70

value: Partial resection

value: Methylated

tag: os event type (0 = censored)


title: Patient 74

value: Unclassified

value: Mesenchymal

value: Non-methylated

tag: pfs time to event (months)


title: Patient 69

value: Female

value: Grade III

tag: pfs event type (0 = censored)


title: Patient 68

value: Wild type

tag: Sex


title: Patient 67

value: Placebo

tag: age


title: Patient 65

tag: idh1 status

value: On

value: Missing


title: Patient 66

tag: phillips subtype

value: Proneural

value: Grade IV


title: Patient 64

tag: tcga subtype

value: Classical

value: Complete resection


title: Patient 71

tag: treatment

value: Bevacizumab


title: Patient 51

tag: surgical status

value: Male

value: Off


title: Patient 54

tag: corticosteroids

value: Methylated


title: Patient 60

tag: kps


title: Patient 63

value: Unclassified

value: Partial resection

tag: mgmt status


title: Patient 52

value: Mesenchymal

value: Non-methylated

tag: mmse


title: Patient 56

tag: rpa class


title: Patient 46

value: Grade V

tag: who


title: Patient 58

value: Wild type

value: Neural

value: Female

tag: os time to event (months)


title: Patient 53

value: On

tag: os event type (0 = censored)


title: Patient 45

value: Proneural

value: Placebo

value: Missing

tag: pfs time to event (months)


title: Patient 49

value: Biopsy

tag: pfs event type (0 = censored)


title: Patient 44

value: Bevacizumab

value: Complete resection

tag: Sex

value: Grade IV


title: Patient 48

tag: age

value: Off


title: Patient 43

tag: idh1 status

value: Classical

value: Male


title: Patient 55

tag: phillips subtype

value: Mesenchymal

value: Partial resection


title: Patient 42

tag: tcga subtype

value: Non-methylated


title: Patient 41

value: Wild type

tag: treatment


title: Patient 47

tag: surgical status


title: Patient 38

value: Proliferative

tag: corticosteroids

value: Grade V


title: Patient 40

tag: kps

value: Methylated


title: Patient 39

tag: mgmt status


title: Patient 61

value: Proneural

value: Female

tag: mmse


title: Patient 62

tag: rpa class


title: Patient 57

tag: who


title: Patient 59

value: Unclassified

tag: os time to event (months)


title: Patient 50

value: On

tag: os event type (0 = censored)


title: Patient 34

value: Placebo

tag: pfs time to event (months)


title: Patient 37

value: Bevacizumab

tag: pfs event type (0 = censored)


title: Patient 32

tag: Sex

value: Grade IV


title: Patient 29

tag: age

value: Off


title: Patient 25

tag: idh1 status


title: Patient 33

tag: phillips subtype

value: Classical


title: Patient 26

tag: tcga subtype

value: Male

value: Missing


title: Patient 28

value: Mesenchymal

tag: treatment

value: Partial resection

value: Grade III


title: Patient 27

value: Wild type

tag: surgical status

value: Complete resection

value: Non-methylated


title: Patient 31

tag: corticosteroids

value: Grade V


title: Patient 22

value: Proliferative

tag: kps


title: Patient 30

tag: mgmt status


title: Patient 21

tag: mmse


title: Patient 19

value: Female

value: Methylated

tag: rpa class


title: Patient 23

value: Unclassified

value: Placebo

tag: who


title: Patient 20

value: Proneural

value: On

value: Grade IV

tag: os time to event (months)


title: Patient 35

value: Classical

value: Bevacizumab

value: Male

value: Off

tag: os event type (0 = censored)


title: Patient 17

value: Mesenchymal

value: Partial resection

tag: pfs time to event (months)


title: Patient 18

value: Wild type

tag: pfs event type (0 = censored)


title: Patient 36

value: Complete resection

tag: Sex

value: Non-methylated


title: Patient 13

tag: age

value: Missing

value: Grade V


title: Patient 11

tag: idh1 status

value: Grade III


title: Patient 10

tag: phillips subtype

value: Biopsy


title: Patient 15

tag: tcga subtype


title: Patient 8

tag: treatment

value: Placebo


title: Patient 24

value: Proneural

tag: surgical status

value: Female

value: Methylated


title: Patient 9

value: Unclassified

tag: corticosteroids

value: On


title: Patient 7

value: Proliferative

value: Classical

value: Bevacizumab

value: Male

tag: kps

value: Grade IV


title: Patient 5

value: Wild type

value: Partial resection

tag: mgmt status


title: Patient 6

value: Mesenchymal

value: Off

value: Non-methylated

tag: mmse


title: Patient 3

tag: rpa class


title: Patient 2

value: Grade III

tag: who


title: icSHAPE - 293T - NAI-N3 In Vitro rep1

status: Public on Apr 04 2016

city: Stanford

first: Zhipeng

last: Lu

address: 269 Campus Drive

department: Department of Dermatology

institute: Stanford University

description:
RNA secondary Structure
processed data file: HS_293T_icSHAPE_InVitro_BaseReactivities.txt

data_processing:
Library strategy: icSHAPE
After demultiplexing, reads were stripped adaptors (PMID: 25411354) and mapped to the Homo Sapiens transcriptome - GRCh37.74 (hg19) using Bowtie2.
All samples have a 13nt barcode on the 5'end which needs to be trimmed before mapping to the transcriptome
icSHAPE reverse transcriptase (RT)  stops were isolated as the first nucleotide after the 5'end barcode. RT stops were used to calculated icSHAPE reactivity scores
Genome_build: Homo sapiens - GRCh37.74 (hg19)
Supplementary_files_format_and_content: 2 Tables (one each for In Vitro and In Vivo modified samples) of icSHAPE reactivities across human transcripts measured. Format: Transcript ID, Transcript Length (in nucleotides), RPKM value, icSHAPE reactivity scores per base for the length of each transcript (NULL values denote bases not measured by the icSHAPE experiment)

source_name: Embryonic Kidney cells

extract_protocol:
HEK293T cells were grown, treated with DMSO or NAI-N3, and RNA collected with TRIzol as previously described (PMID: 25799993).  Protocol: icSHAPE
Deep sequencing libraries were prepared using 3'end RNA ligation, cDNA synthesis with SuperScript III, cDNA circularization, and subsequent PCR amplification

tag: cell line


title: icSHAPE - 293T - NAI-N3 In Vitro rep2


title: icSHAPE - 293T - NAI-N3 In Vivo rep1


title: icSHAPE - 293T - NAI-N3 In Vivo rep2


title: Patient 14

value: Placebo

value: Complete resection

value: Missing

tag: os time to event (months)

tag: os event type (0 = censored)


title: T86_P4_H2_ILC3

status: Public on Jan 27 2016

city: Uppsala

first: Asa

middle: Kristina

last: Bjorklund

address: Box 596

department: Cell and Molecular Biology

country: Sweden

institute: Uppsala University

data_processing:
All reads were aligned to the human (hg19) genomes using STAR (Dobin et al. 2013)
Non-uniquely mapped reads were removed
Rpkmforgenes (available at http://sandberg.cmb.ki.se/rnaseq/), options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -u, was used to generate RPKM values and read counts. We used a file with unique positions from Storvall et al. 2013 PLOS ONE. Gene annotations used were transcripts in RefSeq and Ensembl  (Feb 2013) and ERCC-spike in annotations.
Genome_build: hg19
Supplementary_files_format_and_content: gene expression values (tab-delimited text)

source_name: cDNA

extract_protocol:
cDNA was generated from FACS sorted cells using to Smart-seq2 (Picelli et al. Nature Methods 2013)
Nextera XT DNA Sample Preparation Index Kit (24 index primers, Illumina)

tag: tonsil donor

value: Donor T86

tag: facs gating

tag: cell type

value: tonsil Innate lymphoid cells


title: T86_P4_H4_ILC3


title: T86_P4_H10_ILC3


title: T86_P4_H11_ILC3


title: T86_P4_H3_ILC3


title: T86_P4_G9_NK

value: NK


title: T86_P4_G6_ILC3


title: T86_P4_G8_ILC3


title: T86_P4_H5_ILC3


title: T86_P4_H12_ILC3


title: T86_P4_G5_ILC3


title: T86_P4_G1_ILC3


title: T86_P4_G3_ILC1


title: T86_P4_G12_ILC3


title: Patient 4

tag: idh1 status

tag: Sex

tag: age

tag: pfs time to event (months)

tag: pfs event type (0 = censored)


title: T86_P4_F8_ILC3


title: T86_P4_F5_ILC3


title: T86_P4_G10_ILC3


title: T86_P4_F9_ILC3


title: Patient 1

tag: phillips subtype

value: Proliferative

tag: tcga subtype

tag: treatment

tag: surgical status

value: Female

tag: corticosteroids

value: Grade V


title: T86_P4_H8_ILC3


title: T86_P4_F7_ILC3


title: T86_P4_F6_ILC3


title: T86_P4_F3_ILC3


title: T86_P4_F4_ILC3


title: T86_P4_F2_ILC3


title: T86_P4_F11_ILC3


title: T86_P4_F12_ILC3


title: T86_P4_E9_ILC3


title: T86_P4_E8_ILC3


title: T86_P4_F10_ILC3


title: T86_P4_E4_ILC3


title: T86_P4_E3_ILC3


title: T86_P4_E6_NK


title: T86_P4_E12_ILC3


title: T86_P4_E11_ILC3


title: T86_P4_E1_ILC3


title: T86_P4_E10_ILC3


title: T86_P4_D6_ILC3


title: T86_P4_D7_ILC3


title: T86_P4_E7_NK


title: T86_P4_E2_ILC3


title: T86_P4_D8_ILC3


title: T86_P4_D5_ILC2


title: T86_P4_D3_ILC3


title: T86_P4_D1_ILC3


title: T86_P4_D2_NK


title: T86_P4_D10_ILC3


title: T86_P4_D12_ILC3


title: T86_P4_F1_ILC3


title: T86_P4_D11_NK


title: T86_P4_C9_ILC3


title: T86_P4_C7_ILC3


title: T86_P4_C6_ILC3


title: T86_P4_C4_ILC3


title: T86_P4_C3_ILC3


title: T86_P4_E5_ILC3


title: T86_P4_C2_ILC3


title: T86_P4_C1_ILC3


title: T86_P4_C12_ILC3


title: T86_P4_C11_ILC3


title: T86_P4_B6_ILC3


title: T86_P4_B8_ILC3


title: T86_P4_B9_NK


title: T86_P4_B4_NK


title: T86_P4_B5_ILC3


title: T86_P4_B3_ILC3


title: T86_P4_C10_ILC3


title: T86_P4_A8_ILC3


title: T86_P4_B7_ILC3


title: T86_P4_A9_ILC3


title: T86_P4_A5_ILC3


title: T86_P4_B1_ILC3


title: T86_P4_A3_ILC3


title: T86_P4_B10_ILC3


title: T86_P4_A12_ILC3


title: T86_P4_C8_ILC3


title: T86_P4_A10_ILC3


title: T86_P4_A11_ILC3


title: T86_P4_A1_ILC3


title: T86_P3_H5_ILC1


title: T86_P3_H8_ILC1


title: T86_P3_H9_ILC1


title: T86_P3_H12_ILC1


title: T86_P3_H3_ILC1


title: T86_P4_B12_ILC3


title: T86_P3_H10_ILC1


title: T86_P3_G9_NK


title: T86_P3_G8_ILC1


title: T86_P3_G7_ILC1


title: T86_P3_G3_ILC1


title: T86_P3_G5_ILC1


title: T86_P3_G6_ILC1


title: T86_P3_F8_ILC1


title: T86_P3_G12_ILC1


title: T86_P3_G1_ILC1


title: T86_P3_G10_ILC1


title: T86_P3_F7_ILC1


title: T86_P3_F3_ILC1


title: T86_P3_F11_ILC1


title: T86_P3_F5_ILC1


title: T86_P3_F6_ILC1


title: T86_P3_F12_ILC1


title: T86_P3_F4_ILC1


title: T86_P3_H4_ILC1


title: T86_P3_F1_ILC1


title: T86_P3_E8_ILC1


title: T86_P3_E9_ILC1


title: T86_P3_E7_NK


title: T86_P3_E6_NK


title: T86_P3_E3_ILC1


title: T86_P3_E2_ILC1


title: T86_P3_E5_ILC1


title: T86_P3_H11_ILC1


title: T86_P3_E10_ILC1


title: T86_P3_D8_ILC1


title: T86_P3_E11_ILC1


title: T86_P3_D5_ILC1


title: T86_P3_D3_ILC1


title: T86_P3_D6_ILC1


title: T86_P3_D2_NK


title: T86_P3_D7_ILC1


title: T86_P3_D11_NK


title: T86_P3_D12_ILC1


title: T86_P3_D1_ILC1


title: T86_P3_C6_ILC1


title: T86_P3_C9_ILC1


title: T86_P3_C4_ILC1


title: T86_P3_C7_ILC1


title: T86_P3_C5_ILC1


title: T86_P3_D10_ILC1


title: T86_P3_C8_ILC1


title: T86_P3_C2_ILC1


title: T86_P3_C1_ILC1


title: T86_P3_E12_ILC1


title: T86_P3_C11_ILC1


title: T86_P3_B8_ILC1


title: T86_P3_C12_ILC1


title: T86_P3_B4_NK


title: T86_P3_C10_ILC1


title: T86_P3_B6_ILC1


title: T86_P3_B7_ILC1


title: T86_P3_B9_NK


title: T86_P3_B3_ILC1


title: T86_P3_B1_ILC1


title: T86_P3_B12_ILC1


title: T86_P3_A9_ILC1


title: T86_P3_A8_ILC1


title: T86_P3_A3_ILC1


title: T86_P3_A12_ILC1


title: T86_P3_A5_ILC1


title: T86_P3_A11_ILC1


title: T86_P2_H9_ILC2


title: T86_P2_H11_ILC2


title: T86_P2_H5_ILC2


title: T86_P2_H8_ILC2


title: T86_P2_H2_ILC2


title: T86_P2_H10_ILC2


title: T86_P2_G8_ILC2


title: T86_P2_G9_NK


title: T86_P2_H12_ILC2


title: T86_P2_G7_ILC2


title: T86_P2_G5_ILC2


title: T86_P2_F8_ILC2


title: T86_P2_G6_ILC2


title: T86_P2_F7_ILC2


title: T86_P2_F5_ILC2


title: T86_P2_F6_ILC2


title: T86_P2_F3_ILC2


title: T86_P2_G3_ILC2


title: T86_P2_F2_ILC2


title: T86_P2_F1_ILC2


title: T86_P2_F9_ILC2


title: T86_P3_A1_ILC1


title: T86_P2_F12_ILC2


title: T86_P2_F10_ILC2


title: T86_P2_E8_ILC2


title: T86_P2_E7_NK


title: T86_P2_E2_ILC2


title: T86_P2_G1_ILC2


title: T86_P2_E5_ILC2


title: T86_P2_E12_ILC2


title: T86_P2_E6_NK


title: T86_P2_E11_ILC2


title: T86_P2_G12_ILC2


title: T86_P2_G10_ILC2


title: T86_P2_E3_ILC2


title: T86_P2_D5_ILC2


title: T86_P2_D6_ILC2


title: T86_P2_D7_ILC2


title: T86_P2_E10_ILC2


title: T86_P2_D3_ILC2


title: T86_P2_D8_ILC2


title: T86_P2_D2_NK


title: T86_P2_D1_ILC2


title: T86_P2_F11_ILC2


title: T86_P2_D12_ILC2


title: T86_P2_C8_ILC2


title: T86_P2_C9_ILC2


title: T86_P2_C7_ILC2


title: T86_P2_C6_ILC2


title: T86_P2_C5_ILC2


title: T86_P2_C2_ILC2


title: T86_P2_C3_ILC2


title: T86_P2_E1_ILC2


title: T86_P2_C1_ILC2


title: T86_P2_C11_ILC2


title: T86_P2_C10_ILC2


title: T86_P2_C12_ILC2


title: T86_P2_B7_ILC2


title: T86_P2_B3_ILC2


title: T86_P2_B5_ILC2


title: T86_P2_B12_ILC2


title: T86_P2_B1_ILC2


title: T86_P2_B9_NK


title: T86_P2_B6_ILC2


title: T86_P2_D11_NK


title: T86_P2_A9_ILC2


title: T86_P2_A12_ILC2


title: T86_P2_A3_ILC2


title: T86_P2_A7_ILC2


title: T86_P2_A8_ILC2


title: T86_P1_H9_ILC3


title: T86_P2_A5_ILC2


title: T86_P1_H4_ILC3


title: T86_P1_H3_ILC3


title: T86_P1_H8_ILC3


title: T86_P1_H2_ILC3


title: T86_P2_A10_ILC2


title: T86_P1_H12_ILC3


title: T86_P1_H5_ILC3


title: T86_P1_G9_NK


title: T86_P1_H11_ILC3


title: T86_P1_G8_ILC3


title: T86_P1_G6_ILC3


title: T86_P1_G5_ILC3


title: T86_P1_G1_ILC3


title: T86_P1_G3_ILC3


title: T86_P1_G10_ILC3


title: T86_P1_F9_ILC3


title: T86_P1_F7_ILC3


title: T86_P1_F8_ILC3


title: T86_P1_G12_ILC3


title: T86_P1_F3_ILC3


title: T86_P1_F1_ILC3


title: T86_P1_F5_ILC3


title: T86_P1_F2_ILC3


title: T86_P1_H10_ILC3


title: T86_P1_F4_ILC3


title: T86_P1_E6_NK


title: T86_P1_F11_ILC3


title: T86_P1_E2_ILC3


title: T86_P1_E4_ILC3


title: T86_P1_F10_ILC3


title: T86_P1_E8_ILC3


title: T86_P1_F12_ILC3


title: T86_P1_G7_ILC3


title: T86_P1_E7_NK


title: T86_P1_E3_ILC3


title: T86_P1_E12_ILC3