title: 3889_CD4_Lung_92_S188_P1

description: Full-length RNAseq (SMART-Seq2) reads

tag: tissue

value: Tconv


title: Coho smolt Liver_32 [62870]

status: Public on Dec 03 2019

type: RNA

city: Nanaimo

first: Shaorong

last: Li

state: British Columbia

address: 3190 Hammond Bay Road

department: Salmon and Freshwater Ecosystems Division

country: Canada

institute: Fisheries and Oceans Canada

description:
Sample array position within slide:
Array2Onkism0809_liver_10288
raw data files:
Onkism0809_liver_10288.txt
Onkism0809_liver_10288_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62870

hyb_protocol: Gene expression was quantified using 44K cGRASP salmonid microarrays (Koop et al., 2008) for each of the four tissues. Fragmented sample and reference cRNA (dye coupled aRNA) in GEx Hybridization HI-RPM buffer (Agilent) were hybridized to microarray slides using aHS4800 Pro Hybridization Station (TecanTrading AG), which automatically washed, hybridized, denatured, and dried the slides. To reduce technical variance, hybridizations were performed by a single technician in batches of up to 48 samples during a two-week period.

scan_protocol: Slides were read using a LS Reloaded scanner (TecanTrading AG) and Array- Pro Analyzer software. Images were quantified using ImaGene software (BioDiscovery) with spots being automatically flagged if both dye wavelengths were empty, poor, or negative and manually flagged for reasons such as filaments, blobs, or smears.

data_processing:
Low quality slides (>50% missing spots or spatial problems) and spots (<2 standard deviations from the mean background at both dye wavelengths) were removed using BASE software (Lund University). Local background correction using background mean and a lowess normalization algorithm were also applied.
The file processed_data_liver_withallcontrols.txt includes the normalized log2 background-subtracted intensity ratio (each fish/reference) with 'flagged' spots or poor signals removed for all probes including the DCP* controls. Sample data tables do not include the DCP* control probes.

label: Alexa 555

molecule: total RNA

organism: Oncorhynchus kisutch

source_name: liver

label_protocol: RNA extracts were amplified for microarray hybridizations using Amino Allyl MessageAmpª II-96 kits (Ambion). Amplified RNA extracts (5?g, aRNA) were labelled with Alexa dyes using Indirect Labelling kits (Invitrogen). Dye coupling reactions were performed using all aRNA samples with Alexa 555 dye and the reference aRNA (a pool of all samples for a tissue) with Alexa 647.

extract_protocol: RNA was extracted from four tissues separately: brain, gill, muscle, and liver. Tissues (10mg) were homogenized in TRI reagent (Ambion) using stainless steel beads on a MM301 mixer mill (Retsch Inc.). Aqueous layer homogenate aliquots (100?L) were transferred to three U-bottom 96 well plates. RNA was extracted from the homogenates using the ÔNo-Spin ProcedureÕ of MagMAX-96 for Microarrays Total RNA Isolation kits (Ambion) and a Biomek NXP automation workstation (Beckman- Coulter). RNA yield and purity were measured by spectrophotometry (A?260 value or A?260/A?280 ratio). RNA extracts were stored in a ?80¡C freezer.

value: liver

tag: FISH #

tag: fw/sw

value: FW

tag: year

tag: season

tag: origin

value: Hatchery

tag: fork length (cm)

tag: total mass (g)

tag: Sex

value: U

tag: latitude

tag: longitude

value: chilliwack

label: Alexa 647

source_name: liver from all samples in the series

tag: sample type

value: Pooled cRNA reference


title: Coho smolt Liver_31 [62924]

description:
Sample array position within slide:
Array1Onkism0809_liver_10288
raw data files:
Onkism0809_liver_10288.txt
Onkism0809_liver_10288_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62924


title: S07_t0_rep2

type: SRA

city: New Haven

first: James

last: Noonan

state: CT

address: 333 Cedar St

country: USA

institute: Yale University

library_source: genomic

data_processing:
For each sample, fastq reads were trimmed to only contain the variable 20nt sgRNA sequence targeting Cas9 for genetic disruption.  #cutadapt version 1.16  cutadapt -j 20 -l 20 -g GACGAAACACCG  --trimmed-only <input>
Model-based analysis of CRISPR knock-out (MaGeCK) was utilized to generate read counts for all sgRNAs included in each sample.  #mageck v0.5.8  mageck count --norm-method none --list-seq <sgRNAs_sublibrary> --fastq <trimmed_fastq_all_reps_timepoints> --trim-5 0
Model-based analysis of CRISPR knock-out (MaGeCK) was utilized to estimate the biological effects of genetic disruption for each sgRNA in the sample at each timepoint across replicates.  #mageck v0.5.8  mageck mle --threads 10 --update-efficiency --permutation-round 10 --norm-method control --control-sgrna lib/NTC_sgRNA_ID.txt --count-table results/count/<sublibrary_count_matrix> --design-matrix designmatrix.txt
Supplementary_files_format_and_content: Normalized summary file contains estimates of the biological effects relative to non-targeting controls (NTCs) following genetic disruption.  Biological effects are jointly modeled for across two replicates for sgRNAs targeting a single conserved region or targeting a single gene.  Summary files include estimates for 4, 8, or 12 cell divisions and measures of statistical significance.

molecule: genomic DNA

organism: Homo sapiens

source_name: H9-derived neural stem cells

growth_protocol: H9-derived human neural stem cells were cultured in Knockout DMEM/F-12 (Life Technologies, c/n 12660012) supplemented with EGF (Connstem, E1000-100UG) and FGF (ConnStem, F1001-10UG), GlutaMax-I (Life Technologies, c/n 35050-061) and StemPro neural supplement (Life Technologies, A1050801) as recommended by the manufacturer.  In addition, cells were cultured on Matrigel–coated (Corning, c/n 354230) flasks seeded at ~50,000 cells per square centimeter.  The doubling time of H9-derived human neural stem cells is approximately 48 hours.

extract_protocol:
Genomic DNA was isolated from ~50 milliion cells per sub-library, per transduction replicate at each timepoint.  Frozen cell pellets were thawed and genomic DNA was isolated using the standard protocol (Qiagen Blood and Cell Culture Maxi Kit, c/n 13362).
Each sgRNA subpool library readout was performed using two steps of PCR as described in Chen et al. Cell (2015).  Second PCR round products were purified using column-based cleanup (NEB Monarch PCR and DNA Cleanup Kit, c/n T1030S).  Libraries of each time point for each sub-library were internally controlled by uniquely barcoding and combining for sequencing on the same channel(s) of a sequencing run.  Diluted libraries were spiked in with whole-exome libraries and sequenced on HiSeq4000 instruments (Illumina).

treatment_protocol: Target cells in 25 cm tissue culture flasks at 250,000 cells per cm2 were transduced in low volume media containing 8ug/mL polybrene, 24 hours after infection virus was removed and cells were passaged to normal density of 50,000 cells per cm2.  For lentiviral titer, varying amounts of concentrated virus were added to 25 cm tissue culture flasks and inoculated for 24 hours.  Cells were then passaged to normal seeding density and infection rate was determined 48 hours later by flow cytometry for GFP expression.  For high-throughput screening, each sub-library was transduced by plating 50 million cells across eight 25 cm flasks and adding the appropriate volume of lentivirus to each flask.  Initial multiplicity-of-infection was ~0.3-0.4 to achieve >1000-fold library coverage and infection was monitored after 24 hours by flow cytometry for GFP expression over the course of the experiment (at 4, 8, and 12 cell divisions).  Cells were harvested at each passage and stored as a cell pellet at -20C for genomic DNA extraction.

tag: timepoint

value: 0 cell divisions

tag: replicate


title: 3889_CD4_Lung_43_S139_P1

city: Cambridge

first: Rebecca

middle: H

last: Herbst

state: MA

address: 415 Main Street

department: Klarman Cell Observatory

institute: Broad Institute of MIT and Harvard

description: Full-length RNAseq (SMART-Seq2) reads

library_source: transcriptomic

data_processing:
Full-length RNAseq (SMART-Seq2)
Tophat
Bowtie mapping to UCSC mm10 mouse transcriptome with parameters `-n 0 -m 10`
RSEM v1.2.8
Supplementary_files_format_and_content: Transcripts per million (TPM) expression values (derived from RSEM  for each gene (rows) in each cell (columns)

organism: Mus musculus

source_name: mouse tissue

extract_protocol:
Dissociated individual cells from lung. Isolated Treg and Tconv cells by FACS based on CD4, Thy1.2, FoxP3, GFP staining.
Full length RNAseq (SMART-Seq2)

tag: mouse-id

value: Lung

tag: cell-id-assigned

tag: cell-id-sorted


title: S07_t12_rep1

value: 12 cell divisions


title: 3889_CD4_Lung_32_S320_P2

description: Full-length RNAseq (SMART-Seq2) reads

tag: tissue


title: S07_t8_rep1

value: 8 cell divisions


title: 3889_CD4_Lung_67_S163_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: S07_t4_rep1

value: 4 cell divisions


title: S07_t0_rep1


title: S06_t12_rep2


title: 3889_CD4_Lung_28_S316_P2

description: Full-length RNAseq (SMART-Seq2) reads


title: 3889_CD4_Lung_17_S305_P2

description: Full-length RNAseq (SMART-Seq2) reads


title: Coho smolt White muscle_4216 [64939]

description:
Sample array position within slide:
Array1Onkism0809_WM_10464
raw data files:
Onkism0809_WM_10464.txt
Onkism0809_WM_10464_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64939

data_processing:
Low quality slides (>50% missing spots or spatial problems) and spots (<2 standard deviations from the mean background at both dye wavelengths) were removed using BASE software (Lund University). Local background correction using background mean and a lowess normalization algorithm were also applied.
The file processed_data_muscle_withallcontrols.txt includes the Normalized log2 background-subtracted intensity ratio (each fish/reference) with 'flagged' spots or poor signals removed for all probes including the controls. Sample tables do not include the  controls.

source_name: white muscle

value: white muscle

tag: FISH #

value: SW

value: F

value: WCVI

value: North

source_name: white muscle from all samples in the series


title: Coho smolt White muscle_4215 [65031]

description:
Sample array position within slide:
Array3Onkism0809_WM_10441
raw data files:
Onkism0809_WM_10441.txt
Onkism0809_WM_10441_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65031

tag: fw/sw

value: M


title: Coho smolt White muscle_4137 [65003]

description:
Sample array position within slide:
Array2Onkism0809_WM_10470
raw data files:
Onkism0809_WM_10470.txt
Onkism0809_WM_10470_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65003

tag: year


title: S06_t8_rep2


title: Coho smolt White muscle_4207 [64975]

description:
Sample array position within slide:
Array2Onkism0809_WM_10441
raw data files:
Onkism0809_WM_10441.txt
Onkism0809_WM_10441_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64975

tag: season


title: 3889_CD4_Lung_57_S345_P2

description: Full-length RNAseq (SMART-Seq2) reads

value: Tconv


title: S06_t4_rep2


title: 3889_CD4_Lung_35_S131_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: 3889_CD4_Lung_47_S143_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: Coho smolt White muscle_3539 [64948]

description:
Sample array position within slide:
Array1Onkism0809_WM_10473
raw data files:
Onkism0809_WM_10473.txt
Onkism0809_WM_10473_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64948

tag: origin

value: Wild

value: ECVI


title: Coho smolt White muscle_4213 [65096]

description:
Sample array position within slide:
Array4Onkism0809_WM_10452
raw data files:
Onkism0809_WM_10452.txt
Onkism0809_WM_10452_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65096

tag: fork length (cm)


title: Coho smolt Liver_503 [62848]

description:
Sample array position within slide:
Array2Onkism0809_liver_10313
raw data files:
Onkism0809_liver_10313.txt
Onkism0809_liver_10313_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62848

value: liver

tag: total mass (g)

value: Mainland

value: Fraser


title: Coho smolt White muscle_4126 [64986]

description:
Sample array position within slide:
Array2Onkism0809_WM_10452
raw data files:
Onkism0809_WM_10452.txt
Onkism0809_WM_10452_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64986

tag: Sex

value: Pooled cRNA reference


title: Coho smolt White muscle_4129 [65063]

description:
Sample array position within slide:
Array3Onkism0809_WM_10475
raw data files:
Onkism0809_WM_10475.txt
Onkism0809_WM_10475_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65063

tag: latitude


title: Coho smolt White muscle_3537 [65074]

description:
Sample array position within slide:
Array3Onkism0809_WM_10495b
raw data files:
Onkism0809_WM_10495b.txt
Onkism0809_WM_10495b_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65074

tag: longitude

value: Columbia


title: Coho smolt White muscle_3538 [65115]

description:
Sample array position within slide:
Array4Onkism0809_WM_10472
raw data files:
Onkism0809_WM_10472.txt
Onkism0809_WM_10472_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65115

tag: sample type


title: Coho smolt White muscle_3533 [64914]

description:
Sample array position within slide:
Array1Onkism0809_WM_10436
raw data files:
Onkism0809_WM_10436.txt
Onkism0809_WM_10436_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64914


title: Coho smolt White muscle_3532 [65079]

description:
Sample array position within slide:
Array4Onkism0809_WM_10435
raw data files:
Onkism0809_WM_10435.txt
Onkism0809_WM_10435_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65079

value: Hatchery


title: Coho smolt White muscle_3531 [65025]

description:
Sample array position within slide:
Array3Onkism0809_WM_10435
raw data files:
Onkism0809_WM_10435.txt
Onkism0809_WM_10435_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65025


title: S06_t0_rep2

tag: timepoint

value: 0 cell divisions


title: Coho smolt White muscle_3530 [64969]

description:
Sample array position within slide:
Array2Onkism0809_WM_10435
raw data files:
Onkism0809_WM_10435.txt
Onkism0809_WM_10435_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64969


title: Coho smolt White muscle_3534 [64970]

description:
Sample array position within slide:
Array2Onkism0809_WM_10436
raw data files:
Onkism0809_WM_10436.txt
Onkism0809_WM_10436_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64970

value: Oregon


title: Coho smolt White muscle_3511 [65119]

description:
Sample array position within slide:
Array4Onkism0809_WM_10477
raw data files:
Onkism0809_WM_10477.txt
Onkism0809_WM_10477_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65119

value: white muscle


title: Coho smolt White muscle_3356 [65017]

description:
Sample array position within slide:
Array2Onkism0809_WM_10491
raw data files:
Onkism0809_WM_10491.txt
Onkism0809_WM_10491_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65017

value: SW


title: 3889_CD4_Lung_31_S319_P2

description: Full-length RNAseq (SMART-Seq2) reads

value: Lung


title: 3889_CD4_Lung_69_S357_P2

description: Full-length RNAseq (SMART-Seq2) reads


title: S06_t12_rep1

value: 12 cell divisions

tag: replicate


title: S06_t8_rep1

value: 8 cell divisions


title: 3889_CD4_Lung_65_S353_P2

description: Full-length RNAseq (SMART-Seq2) reads

tag: mouse-id


title: S06_t4_rep1

value: 4 cell divisions


title: S06_t0_rep1


title: Coho smolt White muscle_3298 [64976]

description:
Sample array position within slide:
Array2Onkism0809_WM_10442
raw data files:
Onkism0809_WM_10442.txt
Onkism0809_WM_10442_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64976

value: M


title: Coho smolt White muscle_3311 [64913]

description:
Sample array position within slide:
Array1Onkism0809_WM_10435
raw data files:
Onkism0809_WM_10435.txt
Onkism0809_WM_10435_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64913


title: Coho smolt White muscle_3308 [65061]

description:
Sample array position within slide:
Array3Onkism0809_WM_10473
raw data files:
Onkism0809_WM_10473.txt
Onkism0809_WM_10473_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65061

value: Wild


title: Coho smolt White muscle_3329 [65041]

description:
Sample array position within slide:
Array3Onkism0809_WM_10451
raw data files:
Onkism0809_WM_10451.txt
Onkism0809_WM_10451_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65041


title: 3889_CD4_Lung_68_S356_P2

description: Full-length RNAseq (SMART-Seq2) reads

tag: cell-id-assigned

value: Tconv


title: Coho smolt White muscle_3320 [64985]

description:
Sample array position within slide:
Array2Onkism0809_WM_10451
raw data files:
Onkism0809_WM_10451.txt
Onkism0809_WM_10451_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64985

value: F


title: Coho smolt White muscle_3250 [64944]

description:
Sample array position within slide:
Array1Onkism0809_WM_10469
raw data files:
Onkism0809_WM_10469.txt
Onkism0809_WM_10469_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64944


title: 3889_CD4_Lung_33_S129_P1

description: Full-length RNAseq (SMART-Seq2) reads

tag: cell-id-sorted


title: Coho smolt White muscle_3299 [65032]

description:
Sample array position within slide:
Array3Onkism0809_WM_10442
raw data files:
Onkism0809_WM_10442.txt
Onkism0809_WM_10442_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65032

tag: tissue


title: 3889_CD4_Lung_45_S333_P2

description: Full-length RNAseq (SMART-Seq2) reads


title: S05_t8_rep2


title: S05_t4_rep2


title: Coho smolt White muscle_3240 [65027]

description:
Sample array position within slide:
Array3Onkism0809_WM_10437
raw data files:
Onkism0809_WM_10437.txt
Onkism0809_WM_10437_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65027

tag: FISH #


title: Coho smolt White muscle_3233 [65111]

description:
Sample array position within slide:
Array4Onkism0809_WM_10468
raw data files:
Onkism0809_WM_10468.txt
Onkism0809_WM_10468_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65111

tag: fw/sw


title: 3889_CD4_Lung_71_S359_P2

description: Full-length RNAseq (SMART-Seq2) reads


title: Coho smolt White muscle_3242 [65081]

description:
Sample array position within slide:
Array4Onkism0809_WM_10437
raw data files:
Onkism0809_WM_10437.txt
Onkism0809_WM_10437_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65081

tag: year


title: Coho smolt White muscle_3237 [64971]

description:
Sample array position within slide:
Array2Onkism0809_WM_10437
raw data files:
Onkism0809_WM_10437.txt
Onkism0809_WM_10437_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64971

tag: season


title: S05_t0_rep2


title: 3889_CD4_Lung_26_S314_P2

description: Full-length RNAseq (SMART-Seq2) reads


title: Coho smolt White muscle_3232 [64919]

description:
Sample array position within slide:
Array1Onkism0809_WM_10442
raw data files:
Onkism0809_WM_10442.txt
Onkism0809_WM_10442_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64919

tag: origin


title: Coho smolt White muscle_3303 [65002]

description:
Sample array position within slide:
Array2Onkism0809_WM_10469
raw data files:
Onkism0809_WM_10469.txt
Onkism0809_WM_10469_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65002

tag: fork length (cm)


title: Coho smolt White muscle_3190 [65105]

description:
Sample array position within slide:
Array4Onkism0809_WM_10462
raw data files:
Onkism0809_WM_10462.txt
Onkism0809_WM_10462_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65105

tag: total mass (g)


title: S05_t12_rep2


title: Coho smolt White muscle_3188 [65065]

description:
Sample array position within slide:
Array3Onkism0809_WM_10478
raw data files:
Onkism0809_WM_10478.txt
Onkism0809_WM_10478_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65065

tag: Sex


title: Coho smolt White muscle_3187 [65050]

description:
Sample array position within slide:
Array3Onkism0809_WM_10462
raw data files:
Onkism0809_WM_10462.txt
Onkism0809_WM_10462_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65050

tag: latitude


title: Coho smolt White muscle_3176 [64937]

description:
Sample array position within slide:
Array1Onkism0809_WM_10462
raw data files:
Onkism0809_WM_10462.txt
Onkism0809_WM_10462_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64937

tag: longitude


title: S05_t12_rep1


title: 3889_CD4_Lung_79_S175_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: 3889_CD4_Lung_15_S303_P2

description: Full-length RNAseq (SMART-Seq2) reads


title: 3889_CD4_Lung_59_S347_P2

description: Full-length RNAseq (SMART-Seq2) reads


title: Coho smolt White muscle_3184 [64995]

description:
Sample array position within slide:
Array2Onkism0809_WM_10462
raw data files:
Onkism0809_WM_10462.txt
Onkism0809_WM_10462_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64995

tag: sample type


title: Coho smolt White muscle_3229 [65015]

description:
Sample array position within slide:
Array2Onkism0809_WM_10489
raw data files:
Onkism0809_WM_10489.txt
Onkism0809_WM_10489_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65015

value: ECVI


title: S05_t8_rep1

tag: timepoint


title: S05_t4_rep1

tag: replicate


title: 3889_CD4_Lung_51_S339_P2

description: Full-length RNAseq (SMART-Seq2) reads

tag: mouse-id


title: S05_t0_rep1


title: 3889_CD4_Lung_11_S107_P1

description: Full-length RNAseq (SMART-Seq2) reads

tag: cell-id-assigned


title: 3889_CD4_Lung_14_S302_P2

description: Full-length RNAseq (SMART-Seq2) reads

tag: cell-id-sorted


title: S04_t12_rep2


title: S04_t8_rep2


title: Coho smolt White muscle_3161 [64964]

description:
Sample array position within slide:
Array1Onkism0809_WM_10494
raw data files:
Onkism0809_WM_10494.txt
Onkism0809_WM_10494_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64964

tag: tissue


title: Coho smolt White muscle_3137 [64920]

description:
Sample array position within slide:
Array1Onkism0809_WM_10443
raw data files:
Onkism0809_WM_10443.txt
Onkism0809_WM_10443_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64920

tag: FISH #


title: Coho smolt White muscle_3166 [65077]

description:
Sample array position within slide:
Array3Onkism0809_WM_10498
raw data files:
Onkism0809_WM_10498.txt
Onkism0809_WM_10498_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65077

tag: fw/sw

value: Fraser


title: Coho smolt White muscle_3159 [65101]

description:
Sample array position within slide:
Array4Onkism0809_WM_10458
raw data files:
Onkism0809_WM_10458.txt
Onkism0809_WM_10458_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65101

tag: year

value: Pooled cRNA reference


title: 3889_CD4_Lung_24_S312_P2

description: Full-length RNAseq (SMART-Seq2) reads


title: S04_t4_rep2


title: 3889_CD4_Lung_20_S116_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: 3889_CD4_Lung_30_S126_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: 3889_CD4_Lung_25_S313_P2

description: Full-length RNAseq (SMART-Seq2) reads


title: Coho smolt White muscle_3168 [64977]

description:
Sample array position within slide:
Array2Onkism0809_WM_10443
raw data files:
Onkism0809_WM_10443.txt
Onkism0809_WM_10443_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64977

tag: season


title: Coho smolt White muscle_3155 [64951]

description:
Sample array position within slide:
Array1Onkism0809_WM_10476
raw data files:
Onkism0809_WM_10476.txt
Onkism0809_WM_10476_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64951

tag: origin


title: Coho smolt White muscle_3118 [65099]

description:
Sample array position within slide:
Array4Onkism0809_WM_10456
raw data files:
Onkism0809_WM_10456.txt
Onkism0809_WM_10456_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65099

tag: fork length (cm)


title: 3889_CD4_Lung_49_S145_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: Coho smolt White muscle_3105 [65011]

description:
Sample array position within slide:
Array2Onkism0809_WM_10478
raw data files:
Onkism0809_WM_10478.txt
Onkism0809_WM_10478_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65011

tag: total mass (g)


title: Coho smolt White muscle_3107 [64953]

description:
Sample array position within slide:
Array1Onkism0809_WM_10478
raw data files:
Onkism0809_WM_10478.txt
Onkism0809_WM_10478_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64953

tag: Sex


title: Coho smolt White muscle_3020 [64918]

description:
Sample array position within slide:
Array1Onkism0809_WM_10440
raw data files:
Onkism0809_WM_10440.txt
Onkism0809_WM_10440_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64918

tag: latitude


title: Coho smolt White muscle_3064 [64926]

description:
Sample array position within slide:
Array1Onkism0809_WM_10449
raw data files:
Onkism0809_WM_10449.txt
Onkism0809_WM_10449_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64926

tag: longitude


title: S04_t4_rep1


title: Coho smolt White muscle_3128 [64968]

description:
Sample array position within slide:
Array1Onkism0809_WM_10498
raw data files:
Onkism0809_WM_10498.txt
Onkism0809_WM_10498_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64968

tag: sample type


title: Coho smolt White muscle_3158 [65024]

description:
Sample array position within slide:
Array2Onkism0809_WM_10498
raw data files:
Onkism0809_WM_10498.txt
Onkism0809_WM_10498_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65024


title: Coho smolt White muscle_3124 [64934]

description:
Sample array position within slide:
Array1Onkism0809_WM_10459
raw data files:
Onkism0809_WM_10459.txt
Onkism0809_WM_10459_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64934


title: Coho smolt White muscle_3082 [65092]

description:
Sample array position within slide:
Array4Onkism0809_WM_10448
raw data files:
Onkism0809_WM_10448.txt
Onkism0809_WM_10448_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65092


title: S04_t0_rep2

tag: timepoint


title: Coho smolt White muscle_3130 [65118]

description:
Sample array position within slide:
Array4Onkism0809_WM_10475
raw data files:
Onkism0809_WM_10475.txt
Onkism0809_WM_10475_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65118


title: Coho smolt White muscle_3029 [64974]

description:
Sample array position within slide:
Array2Onkism0809_WM_10440
raw data files:
Onkism0809_WM_10440.txt
Onkism0809_WM_10440_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64974


title: S04_t12_rep1

tag: replicate


title: 3889_CD4_Lung_9_S297_P2

description: Full-length RNAseq (SMART-Seq2) reads

tag: mouse-id


title: S04_t0_rep1


title: 3889_CD4_Lung_4_S292_P2

description: Full-length RNAseq (SMART-Seq2) reads

tag: cell-id-assigned


title: Coho smolt White muscle_3004 [64983]

description:
Sample array position within slide:
Array2Onkism0809_WM_10449b
raw data files:
Onkism0809_WM_10449b.txt
Onkism0809_WM_10449b_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64983


title: S04_t8_rep1


title: Coho smolt White muscle_2979 [65093]

description:
Sample array position within slide:
Array4Onkism0809_WM_10449
raw data files:
Onkism0809_WM_10449.txt
Onkism0809_WM_10449_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65093


title: S03_t12_rep2


title: 3889_CD4_Lung_7_S103_P1

description: Full-length RNAseq (SMART-Seq2) reads

tag: cell-id-sorted


title: S03_t8_rep2


title: S03_t0_rep2


title: 3889_CD4_Lung_55_S151_P1

description: Full-length RNAseq (SMART-Seq2) reads

tag: tissue


title: 3889_CD4_Lung_21_S309_P2

description: Full-length RNAseq (SMART-Seq2) reads


title: S03_t4_rep2


title: 3889_CD4_Lung_10_S106_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: Coho smolt White muscle_2924 [65016]

description:
Sample array position within slide:
Array2Onkism0809_WM_10490
raw data files:
Onkism0809_WM_10490.txt
Onkism0809_WM_10490_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65016

tag: FISH #


title: Coho smolt White muscle_3005 [65038]

description:
Sample array position within slide:
Array3Onkism0809_WM_10448
raw data files:
Onkism0809_WM_10448.txt
Onkism0809_WM_10448_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65038

tag: fw/sw


title: Coho smolt White muscle_2984 [65039]

description:
Sample array position within slide:
Array3Onkism0809_WM_10449
raw data files:
Onkism0809_WM_10449.txt
Onkism0809_WM_10449_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65039

tag: year


title: Coho smolt White muscle_2977 [65083]

description:
Sample array position within slide:
Array4Onkism0809_WM_10439
raw data files:
Onkism0809_WM_10439.txt
Onkism0809_WM_10439_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65083

tag: season


title: S03_t12_rep1


title: 3889_CD4_Lung_53_S341_P2

description: Full-length RNAseq (SMART-Seq2) reads


title: S03_t8_rep1


title: Coho smolt White muscle_2918 [65125]

description:
Sample array position within slide:
Array4Onkism0809_WM_10489
raw data files:
Onkism0809_WM_10489.txt
Onkism0809_WM_10489_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65125

tag: origin


title: 3889_CD4_Lung_3_S291_P2

description: Full-length RNAseq (SMART-Seq2) reads


title: S03_t4_rep1


title: 3889_CD4_Lung_80_S368_P2

description: Full-length RNAseq (SMART-Seq2) reads


title: S03_t0_rep1


title: S02_t12_rep2


title: 3889_CD4_Lung_52_S340_P2

description: Full-length RNAseq (SMART-Seq2) reads


title: Coho smolt White muscle_2811 [64966]

description:
Sample array position within slide:
Array1Onkism0809_WM_10496
raw data files:
Onkism0809_WM_10496.txt
Onkism0809_WM_10496_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64966

tag: fork length (cm)


title: Coho smolt White muscle_2881 [65056]

description:
Sample array position within slide:
Array3Onkism0809_WM_10468
raw data files:
Onkism0809_WM_10468.txt
Onkism0809_WM_10468_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65056

tag: total mass (g)


title: Coho smolt White muscle_2809 [64923]

description:
Sample array position within slide:
Array1Onkism0809_WM_10446
raw data files:
Onkism0809_WM_10446.txt
Onkism0809_WM_10446_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64923

tag: Sex


title: 3889_CD4_Lung_46_S334_P2

description: Full-length RNAseq (SMART-Seq2) reads


title: S02_t8_rep2


title: Coho smolt White muscle_2858 [65010]

description:
Sample array position within slide:
Array2Onkism0809_WM_10477
raw data files:
Onkism0809_WM_10477.txt
Onkism0809_WM_10477_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65010

tag: latitude


title: Coho smolt White muscle_2794 [65035]

description:
Sample array position within slide:
Array3Onkism0809_WM_10445
raw data files:
Onkism0809_WM_10445.txt
Onkism0809_WM_10445_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65035

tag: longitude


title: Coho smolt White muscle_2890 [64960]

description:
Sample array position within slide:
Array1Onkism0809_WM_10490
raw data files:
Onkism0809_WM_10490.txt
Onkism0809_WM_10490_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64960

tag: sample type


title: Coho smolt White muscle_2791 [65012]

description:
Sample array position within slide:
Array2Onkism0809_WM_10479
raw data files:
Onkism0809_WM_10479.txt
Onkism0809_WM_10479_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65012


title: Coho smolt White muscle_2800 [65089]

description:
Sample array position within slide:
Array4Onkism0809_WM_10445
raw data files:
Onkism0809_WM_10445.txt
Onkism0809_WM_10445_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65089


title: 3889_CD4_Lung_54_S150_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: Coho smolt White muscle_2856 [64980]

description:
Sample array position within slide:
Array2Onkism0809_WM_10446
raw data files:
Onkism0809_WM_10446.txt
Onkism0809_WM_10446_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64980


title: Coho smolt White muscle_2905 [64956]

description:
Sample array position within slide:
Array1Onkism0809_WM_10486
raw data files:
Onkism0809_WM_10486.txt
Onkism0809_WM_10486_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64956


title: Coho smolt White muscle_2790 [65131]

description:
Sample array position within slide:
Array4Onkism0809_WM_10495b
raw data files:
Onkism0809_WM_10495b.txt
Onkism0809_WM_10495b_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65131


title: Coho smolt White muscle_2807 [65064]

description:
Sample array position within slide:
Array3Onkism0809_WM_10477
raw data files:
Onkism0809_WM_10477.txt
Onkism0809_WM_10477_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65064


title: Coho smolt White muscle_2857 [65036]

description:
Sample array position within slide:
Array3Onkism0809_WM_10446
raw data files:
Onkism0809_WM_10446.txt
Onkism0809_WM_10446_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65036


title: S02_t4_rep2

tag: timepoint


title: Coho smolt White muscle_3628 [65006]

description:
Sample array position within slide:
Array2Onkism0809_WM_10473
raw data files:
Onkism0809_WM_10473.txt
Onkism0809_WM_10473_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65006

value: WCVI


title: 3889_CD4_Lung_47_S335_P2

description: Full-length RNAseq (SMART-Seq2) reads


title: Coho smolt White muscle_2730 [65106]

description:
Sample array position within slide:
Array4Onkism0809_WM_10463
raw data files:
Onkism0809_WM_10463.txt
Onkism0809_WM_10463_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65106


title: Coho smolt White muscle_2727 [64996]

description:
Sample array position within slide:
Array2Onkism0809_WM_10463
raw data files:
Onkism0809_WM_10463.txt
Onkism0809_WM_10463_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64996


title: Coho smolt White muscle_2742 [64955]

description:
Sample array position within slide:
Array1Onkism0809_WM_10485
raw data files:
Onkism0809_WM_10485.txt
Onkism0809_WM_10485_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64955


title: Coho smolt White muscle_2713 [64952]

description:
Sample array position within slide:
Array1Onkism0809_WM_10477
raw data files:
Onkism0809_WM_10477.txt
Onkism0809_WM_10477_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64952


title: Coho smolt White muscle_2763 [64943]

description:
Sample array position within slide:
Array1Onkism0809_WM_10468
raw data files:
Onkism0809_WM_10468.txt
Onkism0809_WM_10468_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64943

value: Hatchery


title: Coho smolt White muscle_2728 [65051]

description:
Sample array position within slide:
Array3Onkism0809_WM_10463
raw data files:
Onkism0809_WM_10463.txt
Onkism0809_WM_10463_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65051


title: Coho smolt White muscle_2785 [65001]

description:
Sample array position within slide:
Array2Onkism0809_WM_10468
raw data files:
Onkism0809_WM_10468.txt
Onkism0809_WM_10468_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65001


title: Coho smolt White muscle_2705 [64915]

description:
Sample array position within slide:
Array1Onkism0809_WM_10437
raw data files:
Onkism0809_WM_10437.txt
Onkism0809_WM_10437_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64915


title: S02_t0_rep2

value: 0 cell divisions

tag: replicate


title: 3889_CD4_Lung_4_S100_P1

description: Full-length RNAseq (SMART-Seq2) reads

tag: mouse-id


title: S02_t12_rep1


title: 3889_CD4_Lung_76_S364_P2

description: Full-length RNAseq (SMART-Seq2) reads

tag: cell-id-assigned


title: 3889_CD4_Lung_78_S174_P1

description: Full-length RNAseq (SMART-Seq2) reads

tag: cell-id-sorted


title: S02_t8_rep1


title: Coho smolt White muscle_2701 [65110]

description:
Sample array position within slide:
Array4Onkism0809_WM_10467
raw data files:
Onkism0809_WM_10467.txt
Onkism0809_WM_10467_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65110

tag: tissue


title: Coho smolt White muscle_2712 [64938]

description:
Sample array position within slide:
Array1Onkism0809_WM_10463
raw data files:
Onkism0809_WM_10463.txt
Onkism0809_WM_10463_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64938

tag: FISH #


title: Coho smolt White muscle_2690 [65053]

description:
Sample array position within slide:
Array3Onkism0809_WM_10465
raw data files:
Onkism0809_WM_10465.txt
Onkism0809_WM_10465_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65053

tag: fw/sw


title: S02_t4_rep1


title: 3889_CD4_Lung_56_S152_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: S02_t0_rep1


title: S01_t12_rep2


title: S01_t4_rep2


title: 3889_CD4_Lung_91_S379_P2

description: Full-length RNAseq (SMART-Seq2) reads


title: S01_t8_rep2


title: 3889_CD4_Lung_89_S377_P2

description: Full-length RNAseq (SMART-Seq2) reads


title: 3889_CD4_Lung_77_S173_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: Coho smolt White muscle_2665 [64912]

description:
Sample array position within slide:
Array1Onkism0809_WM_10434
raw data files:
Onkism0809_WM_10434.txt
Onkism0809_WM_10434_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64912

tag: year


title: Coho smolt White muscle_2698 [65066]

description:
Sample array position within slide:
Array3Onkism0809_WM_10479
raw data files:
Onkism0809_WM_10479.txt
Onkism0809_WM_10479_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65066

tag: season


title: Coho smolt White muscle_2675 [65060]

description:
Sample array position within slide:
Array3Onkism0809_WM_10472
raw data files:
Onkism0809_WM_10472.txt
Onkism0809_WM_10472_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65060

tag: origin


title: Coho smolt White muscle_2656 [65130]

description:
Sample array position within slide:
Array4Onkism0809_WM_10494
raw data files:
Onkism0809_WM_10494.txt
Onkism0809_WM_10494_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65130

tag: fork length (cm)


title: Coho smolt White muscle_2650 [65097]

description:
Sample array position within slide:
Array4Onkism0809_WM_10453
raw data files:
Onkism0809_WM_10453.txt
Onkism0809_WM_10453_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65097

tag: total mass (g)


title: Coho smolt White muscle_2670 [65021]

description:
Sample array position within slide:
Array2Onkism0809_WM_10495b
raw data files:
Onkism0809_WM_10495b.txt
Onkism0809_WM_10495b_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65021

tag: Sex


title: Coho smolt White muscle_2658 [64965]

description:
Sample array position within slide:
Array1Onkism0809_WM_10495b
raw data files:
Onkism0809_WM_10495b.txt
Onkism0809_WM_10495b_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64965

tag: latitude


title: Coho smolt White muscle_2640 [65042]

description:
Sample array position within slide:
Array3Onkism0809_WM_10453
raw data files:
Onkism0809_WM_10453.txt
Onkism0809_WM_10453_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65042

tag: longitude


title: 3889_CD4_Lung_58_S154_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: S01_t0_rep2


title: Coho smolt White muscle_2653 [65046]

description:
Sample array position within slide:
Array3Onkism0809_WM_10458
raw data files:
Onkism0809_WM_10458.txt
Onkism0809_WM_10458_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65046

tag: sample type


title: S01_t12_rep1

tag: timepoint


title: 3889_CD4_Lung_19_S307_P2

description: Full-length RNAseq (SMART-Seq2) reads


title: Coho smolt White muscle_2626 [64991]

description:
Sample array position within slide:
Array2Onkism0809_WM_10458
raw data files:
Onkism0809_WM_10458.txt
Onkism0809_WM_10458_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64991


title: Coho smolt White muscle_2618 [65076]

description:
Sample array position within slide:
Array3Onkism0809_WM_10497
raw data files:
Onkism0809_WM_10497.txt
Onkism0809_WM_10497_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65076


title: Coho smolt White muscle_2617 [65120]

description:
Sample array position within slide:
Array4Onkism0809_WM_10478
raw data files:
Onkism0809_WM_10478.txt
Onkism0809_WM_10478_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65120


title: 3889_CD4_Lung_94_S190_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: S01_t8_rep1

tag: replicate


title: Coho smolt White muscle_2621 [65086]

description:
Sample array position within slide:
Array4Onkism0809_WM_10442
raw data files:
Onkism0809_WM_10442.txt
Onkism0809_WM_10442_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65086


title: 3889_CD4_Lung_11_S299_P2

description: Full-length RNAseq (SMART-Seq2) reads

tag: mouse-id


title: S01_t4_rep1


title: S01_t0_rep1


title: Coho smolt White muscle_2601 [65023]

description:
Sample array position within slide:
Array2Onkism0809_WM_10497
raw data files:
Onkism0809_WM_10497.txt
Onkism0809_WM_10497_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65023


title: Coho smolt White muscle_2593 [65126]

description:
Sample array position within slide:
Array4Onkism0809_WM_10490
raw data files:
Onkism0809_WM_10490.txt
Onkism0809_WM_10490_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65126


title: Coho smolt White muscle_2623 [65133]

description:
Sample array position within slide:
Array4Onkism0809_WM_10497
raw data files:
Onkism0809_WM_10497.txt
Onkism0809_WM_10497_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65133


title: Coho smolt White muscle_2637 [64987]

description:
Sample array position within slide:
Array2Onkism0809_WM_10453
raw data files:
Onkism0809_WM_10453.txt
Onkism0809_WM_10453_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64987


title: Coho smolt White muscle_2622 [64928]

description:
Sample array position within slide:
Array1Onkism0809_WM_10453
raw data files:
Onkism0809_WM_10453.txt
Onkism0809_WM_10453_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64928


title: Coho smolt White muscle_2582 [65122]

description:
Sample array position within slide:
Array4Onkism0809_WM_10486
raw data files:
Onkism0809_WM_10486.txt
Onkism0809_WM_10486_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65122


title: Coho smolt White muscle_2614 [64961]

description:
Sample array position within slide:
Array1Onkism0809_WM_10491
raw data files:
Onkism0809_WM_10491.txt
Onkism0809_WM_10491_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64961


title: 3889_CD4_Lung_21_S117_P1

description: Full-length RNAseq (SMART-Seq2) reads

tag: cell-id-assigned


title: Coho smolt White muscle_2577 [64933]

description:
Sample array position within slide:
Array1Onkism0809_WM_10458
raw data files:
Onkism0809_WM_10458.txt
Onkism0809_WM_10458_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64933


title: 3889_CD4_Lung_90_S186_P1

description: Full-length RNAseq (SMART-Seq2) reads

tag: cell-id-sorted


title: 3889_CD4_Lung_66_S354_P2

description: Full-length RNAseq (SMART-Seq2) reads

tag: tissue


title: HyIL6_ChIPSeq

city: WEST LAFAYETTE

first: Majid

last: Kazemian

state: IN

address: 201 S. University Street

department: Biochemistry and Computer Science

institute: Purdue University

data_processing:
The expression values obtained by RSEM v1.3.1 using the following parameters (rsem-calculate-expression --no-bam-output --bowtie-n 1 --bowtie-m 100 --seed-length 28 --paired-end). Rsem index was created based on hg19.
Differentially expressed genes between any two conditions were obtained using edgeR. The raw read counts were obtained from the "expected counts" column in rsem results. The criteria for selecting differentially expressed genes are Fold Change >1.5 FDR<=0.05, and RPKM>4 in at least one of the two compared conditions.
Alignment for ChIP-seq data were generated by Bowtie1 with following parameters (bowtie --chunkmbs 1000 -S -m 1).
Peak calling for ChIP-seq data was done using macs2 2.1.2 using parameters (macs2 callpeak -f BAMPE --nomodel)
Bigwig files were generated using bamCoverage 3.2.0 with parameters (bamCoverage --normalizeUsing BPM --minMappingQuality 30 --ignoreDuplicates --extendReads 250 --blackListFileName hg19.blacklist.bed)
Genome_build: hg19
Supplementary_files_format_and_content: normalized abundance measurements (text file) include RPKM values for each sample
Supplementary_files_format_and_content: bigwig files (.bw)

source_name: primary human TH1 cells

growth_protocol: resting primary human CD4 T cells differentiated into Th1 cells were expanded in the presence of IL2 for 10 days.

extract_protocol:
For STAT3 ChIP-seq, formaldehyde-fixed human Th1 cells were sonicated using sonicator (Vibra Cell, SONICS) and resulting chromatin fragments equivalent to 10 million cells were isolated by centrifugation and STAT3 bound chromatin complexes were isolated with the anti-STAT3 antibody. For RNA-seq experiments, Total RNA isolated from human Th1 cells that were either not stimulated or stimulated with different IL-6 variants for 6 hours.
ChIP-Seq libraries were prepared using the KAPA LTP library preparation kit (Roche Sequencing) and the NextFlex DNA barcode adoptors (Bioo Scientific, PerkinElmer) for multiplexing and libraries were then sequenced on Illumina Hi-Seq 4000 platform (GeneWiz).

treatment_protocol: after 24 hours starvation in the absence of IL2, cells were stimulated with the different IL6 mutants for 1 hour (ChIP-seq experiments) or 6 hours (RNA-seq experiments)

tag: chip antibody

tag: cell type

value: Human TH1 cells

tag: stimulated with


title: 3889_CD4_Lung_48_S144_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: Mut3_ChIPSeq


title: Coho smolt White muscle_2315 [65007]

description:
Sample array position within slide:
Array2Onkism0809_WM_10474b
raw data files:
Onkism0809_WM_10474b.txt
Onkism0809_WM_10474b_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65007

value: white muscle

tag: FISH #

tag: fw/sw

tag: year

tag: season

value: U

value: Columbia


title: C7_ChIPSeq


title: Coho smolt White muscle_2361 [64950]

description:
Sample array position within slide:
Array1Onkism0809_WM_10475
raw data files:
Onkism0809_WM_10475.txt
Onkism0809_WM_10475_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64950

value: SW

tag: origin

tag: fork length (cm)

tag: total mass (g)

tag: Sex


title: Coho smolt White muscle_2578 [65100]

description:
Sample array position within slide:
Array4Onkism0809_WM_10457
raw data files:
Onkism0809_WM_10457.txt
Onkism0809_WM_10457_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65100

tag: latitude

tag: longitude

tag: sample type


title: Coho smolt White muscle_2311 [65078]

description:
Sample array position within slide:
Array4Onkism0809_WM_10434
raw data files:
Onkism0809_WM_10434.txt
Onkism0809_WM_10434_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65078

value: Oregon


title: Coho smolt White muscle_2288 [65049]

description:
Sample array position within slide:
Array3Onkism0809_WM_10461
raw data files:
Onkism0809_WM_10461.txt
Onkism0809_WM_10461_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65049


title: Coho smolt White muscle_2314 [64949]

description:
Sample array position within slide:
Array1Onkism0809_WM_10474b
raw data files:
Onkism0809_WM_10474b.txt
Onkism0809_WM_10474b_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64949


title: Coho smolt White muscle_2289 [65104]

description:
Sample array position within slide:
Array4Onkism0809_WM_10461
raw data files:
Onkism0809_WM_10461.txt
Onkism0809_WM_10461_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65104


title: 3889_CD4_Lung_63_S351_P2

description: Full-length RNAseq (SMART-Seq2) reads

tag: mouse-id

value: Lung

tag: cell-id-assigned


title: input_ChIPSeq

value: Input


title: A1_ChIPSeq


title: 3889_CD4_Lung_87_S183_P1

description: Full-length RNAseq (SMART-Seq2) reads

tag: tissue

tag: cell-id-sorted


title: Donor_3_Mut3_RNAseq

molecule: polyA RNA

tag: donor

tag: chip antibody

tag: cell type


title: 3889_CD4_Lung_62_S350_P2

description: Full-length RNAseq (SMART-Seq2) reads


title: Donor_3_Unstimulated_RNAseq

tag: stimulated with

value: Unstimulated


title: 3889_CD4_Lung_71_S167_P1

description: Full-length RNAseq (SMART-Seq2) reads

value: Tconv


title: 3889_CD4_Lung_93_S381_P2

description: Full-length RNAseq (SMART-Seq2) reads


title: Donor_3_HyIl6_RNAseq


title: Coho smolt White muscle_2287 [64994]

description:
Sample array position within slide:
Array2Onkism0809_WM_10461
raw data files:
Onkism0809_WM_10461.txt
Onkism0809_WM_10461_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64994

tag: FISH #

tag: fw/sw

tag: year

value: Wild


title: Coho smolt White muscle_2239 [64927]

description:
Sample array position within slide:
Array1Onkism0809_WM_10451
raw data files:
Onkism0809_WM_10451.txt
Onkism0809_WM_10451_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64927

tag: season

tag: origin

tag: fork length (cm)


title: Coho smolt White muscle_2313 [65129]

description:
Sample array position within slide:
Array4Onkism0809_WM_10493
raw data files:
Onkism0809_WM_10493.txt
Onkism0809_WM_10493_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65129

tag: total mass (g)

tag: Sex

tag: latitude

value: North


title: Coho smolt White muscle_2247 [65030]

description:
Sample array position within slide:
Array3Onkism0809_WM_10440
raw data files:
Onkism0809_WM_10440.txt
Onkism0809_WM_10440_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65030

tag: longitude

value: Fraser

tag: sample type


title: Coho smolt White muscle_2130 [65103]

description:
Sample array position within slide:
Array4Onkism0809_WM_10460
raw data files:
Onkism0809_WM_10460.txt
Onkism0809_WM_10460_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65103

tag: tissue

value: ECVI

value: Pooled cRNA reference


title: Coho smolt White muscle_2132 [64984]

description:
Sample array position within slide:
Array2Onkism0809_WM_10450
raw data files:
Onkism0809_WM_10450.txt
Onkism0809_WM_10450_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64984


title: Coho smolt White muscle_2153 [65094]

description:
Sample array position within slide:
Array4Onkism0809_WM_10450
raw data files:
Onkism0809_WM_10450.txt
Onkism0809_WM_10450_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65094


title: Coho smolt White muscle_2131 [65008]

description:
Sample array position within slide:
Array2Onkism0809_WM_10475
raw data files:
Onkism0809_WM_10475.txt
Onkism0809_WM_10475_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65008


title: Donor_3_C7_RNAseq


title: Coho smolt White muscle_2248 [65084]

description:
Sample array position within slide:
Array4Onkism0809_WM_10440
raw data files:
Onkism0809_WM_10440.txt
Onkism0809_WM_10440_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65084


title: Coho smolt White muscle_2134 [65040]

description:
Sample array position within slide:
Array3Onkism0809_WM_10450
raw data files:
Onkism0809_WM_10450.txt
Onkism0809_WM_10450_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65040


title: 3889_CD4_Lung_84_S180_P1

description: Full-length RNAseq (SMART-Seq2) reads

tag: mouse-id

tag: cell-id-assigned

tag: cell-id-sorted


title: Donor_3_A1_RNAseq

tag: donor

tag: chip antibody

tag: cell type


title: Coho smolt White muscle_2129 [65048]

description:
Sample array position within slide:
Array3Onkism0809_WM_10460
raw data files:
Onkism0809_WM_10460.txt
Onkism0809_WM_10460_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65048

tag: FISH #

tag: fw/sw


title: 3889_Treg_Lung_52_S52_P1

description: Full-length RNAseq (SMART-Seq2) reads

value: Treg


title: Donor_2_Unstimulated_RNAseq

tag: stimulated with


title: Donor_2_Mut3_RNAseq


title: 3889_Treg_Lung_11_S11_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: Coho smolt White muscle_2125 [65047]

description:
Sample array position within slide:
Array3Onkism0809_WM_10459
raw data files:
Onkism0809_WM_10459.txt
Onkism0809_WM_10459_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65047

tag: year

tag: season

tag: origin


title: 3889_Treg_Lung_59_S59_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: Coho smolt White muscle_2115 [64992]

description:
Sample array position within slide:
Array2Onkism0809_WM_10459
raw data files:
Onkism0809_WM_10459.txt
Onkism0809_WM_10459_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64992

tag: fork length (cm)

tag: total mass (g)

tag: Sex


title: Coho smolt White muscle_2126 [65102]

description:
Sample array position within slide:
Array4Onkism0809_WM_10459
raw data files:
Onkism0809_WM_10459.txt
Onkism0809_WM_10459_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65102

tag: latitude

tag: longitude

tag: sample type


title: Coho smolt White muscle_2128 [64993]

description:
Sample array position within slide:
Array2Onkism0809_WM_10460
raw data files:
Onkism0809_WM_10460.txt
Onkism0809_WM_10460_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64993

tag: tissue


title: Coho smolt White muscle_2098 [65073]

description:
Sample array position within slide:
Array3Onkism0809_WM_10494
raw data files:
Onkism0809_WM_10494.txt
Onkism0809_WM_10494_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65073

value: Hatchery

value: M


title: Coho smolt White muscle_2099 [65080]

description:
Sample array position within slide:
Array4Onkism0809_WM_10436
raw data files:
Onkism0809_WM_10436.txt
Onkism0809_WM_10436_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65080

value: white muscle


title: Coho smolt White muscle_2114 [64936]

description:
Sample array position within slide:
Array1Onkism0809_WM_10461
raw data files:
Onkism0809_WM_10461.txt
Onkism0809_WM_10461_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64936

value: U


title: Donor_2_C7_RNAseq

value: Human TH1 cells


title: Coho smolt White muscle_2127 [64935]

description:
Sample array position within slide:
Array1Onkism0809_WM_10460
raw data files:
Onkism0809_WM_10460.txt
Onkism0809_WM_10460_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64935

value: SW


title: Donor_2_A1_RNAseq


title: 3889_Treg_Lung_86_S86_P1

description: Full-length RNAseq (SMART-Seq2) reads

tag: mouse-id

tag: cell-id-assigned

tag: cell-id-sorted


title: 3889_Treg_Lung_23_S23_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: 3889_Treg_Lung_58_S58_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: Donor_1_Unstimulated_RNAseq

tag: donor

tag: chip antibody

tag: cell type


title: 3889_Treg_Lung_77_S77_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: Donor_1_Mut3_RNAseq

tag: stimulated with


title: Coho smolt White muscle_2033 [64998]

description:
Sample array position within slide:
Array2Onkism0809_WM_10465
raw data files:
Onkism0809_WM_10465.txt
Onkism0809_WM_10465_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64998

tag: FISH #

tag: fw/sw

tag: year


title: Donor_2_HyIl6_RNAseq


title: Coho smolt White muscle_1894 [65082]

description:
Sample array position within slide:
Array4Onkism0809_WM_10438
raw data files:
Onkism0809_WM_10438.txt
Onkism0809_WM_10438_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65082

tag: season

tag: origin

tag: fork length (cm)


title: Donor_1_HyIl6_RNAseq


title: Coho smolt White muscle_1915 [64940]

description:
Sample array position within slide:
Array1Onkism0809_WM_10465
raw data files:
Onkism0809_WM_10465.txt
Onkism0809_WM_10465_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64940

tag: total mass (g)

tag: Sex

tag: latitude


title: Coho smolt White muscle_1897 [64973]

description:
Sample array position within slide:
Array2Onkism0809_WM_10439
raw data files:
Onkism0809_WM_10439.txt
Onkism0809_WM_10439_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64973

tag: tissue

tag: longitude

tag: sample type


title: Coho smolt White muscle_2058 [65026]

description:
Sample array position within slide:
Array3Onkism0809_WM_10436
raw data files:
Onkism0809_WM_10436.txt
Onkism0809_WM_10436_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65026


title: Coho smolt White muscle_2014 [65020]

description:
Sample array position within slide:
Array2Onkism0809_WM_10494
raw data files:
Onkism0809_WM_10494.txt
Onkism0809_WM_10494_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65020


title: Coho smolt White muscle_2002 [65055]

description:
Sample array position within slide:
Array3Onkism0809_WM_10467
raw data files:
Onkism0809_WM_10467.txt
Onkism0809_WM_10467_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65055


title: Coho smolt White muscle_1896 [64917]

description:
Sample array position within slide:
Array1Onkism0809_WM_10439
raw data files:
Onkism0809_WM_10439.txt
Onkism0809_WM_10439_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64917

value: F


title: Coho smolt White muscle_1884 [64959]

description:
Sample array position within slide:
Array1Onkism0809_WM_10489
raw data files:
Onkism0809_WM_10489.txt
Onkism0809_WM_10489_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64959


title: 3889_Treg_Lung_20_S20_P1

description: Full-length RNAseq (SMART-Seq2) reads

tag: mouse-id

value: Lung

tag: cell-id-assigned

tag: cell-id-sorted


title: 3889_Treg_Lung_69_S69_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: Coho smolt White muscle_1877 [65107]

description:
Sample array position within slide:
Array4Onkism0809_WM_10464
raw data files:
Onkism0809_WM_10464.txt
Onkism0809_WM_10464_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65107


title: 3889_CD4_Lung_95_S383_P2

description: Full-length RNAseq (SMART-Seq2) reads


title: Coho smolt White muscle_1946 [65029]

description:
Sample array position within slide:
Array3Onkism0809_WM_10439
raw data files:
Onkism0809_WM_10439.txt
Onkism0809_WM_10439_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65029


title: Donor_1_A1_RNAseq

tag: donor

tag: chip antibody

tag: cell type


title: Donor_1_C7_RNAseq

tag: stimulated with


title: 3889_Treg_Lung_88_S88_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: 3889_Treg_Lung_15_S15_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: Coho smolt White muscle_1876 [65124]

description:
Sample array position within slide:
Array4Onkism0809_WM_10488
raw data files:
Onkism0809_WM_10488.txt
Onkism0809_WM_10488_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65124

tag: FISH #

tag: fw/sw

tag: year


title: 3889_Treg_Lung_90_S90_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: Coho smolt White muscle_1873 [65068]

description:
Sample array position within slide:
Array3Onkism0809_WM_10488
raw data files:
Onkism0809_WM_10488.txt
Onkism0809_WM_10488_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65068

tag: season

tag: origin

tag: fork length (cm)


title: 3889_Treg_Lung_27_S27_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: 3889_Treg_Lung_94_S94_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: Coho smolt White muscle_1871 [65014]

description:
Sample array position within slide:
Array2Onkism0809_WM_10488
raw data files:
Onkism0809_WM_10488.txt
Onkism0809_WM_10488_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65014

tag: total mass (g)

tag: Sex

tag: latitude


title: Coho smolt White muscle_1692 [64945]

description:
Sample array position within slide:
Array1Onkism0809_WM_10470
raw data files:
Onkism0809_WM_10470.txt
Onkism0809_WM_10470_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64945

tag: tissue

value: FW

tag: longitude

value: puntledge

tag: sample type


title: 3889_Treg_Lung_79_S79_P1

description: Full-length RNAseq (SMART-Seq2) reads

tag: mouse-id

tag: cell-id-assigned

tag: cell-id-sorted


title: 3889_Treg_Lung_45_S45_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: Coho smolt White muscle_1691 [65109]

description:
Sample array position within slide:
Array4Onkism0809_WM_10466
raw data files:
Onkism0809_WM_10466.txt
Onkism0809_WM_10466_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65109


title: Coho smolt White muscle_1688 [65019]

description:
Sample array position within slide:
Array2Onkism0809_WM_10493
raw data files:
Onkism0809_WM_10493.txt
Onkism0809_WM_10493_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65019


title: IL-8 4

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from skeletal muscle injected intraperitoneally with recombinant IL-8.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray mogene20stmmentrezgcdf R package (version 17.0.0).

label: biotin

source_name: skeletal muscle

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: Mice were maintained in a temperature and humidity-controlled facility with a 12-h light/dark cycle and water and standard diet were provided ad libitum.

extract_protocol: Biopsies from the rectus abdominis muscle were harvested from patients at the beginning of surgery, and a portion to be used for RNA isolation was immediately snap-frozen in liquid nitrogen followed by storage at -80⁰C.  Muscles were minced and homogenized in TRIzol for RNA extraction.

treatment_protocol: Mice were injected, intraperitoneally, with 50µg/kg of recombinant IL-8 or KC, or 0.1% BSA as control, every other day for 6 days

tag: treatment

value: recombinant IL-8


title: 3889_Treg_Lung_53_S53_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: Coho smolt White muscle_1689 [65072]

description:
Sample array position within slide:
Array3Onkism0809_WM_10493
raw data files:
Onkism0809_WM_10493.txt
Onkism0809_WM_10493_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65072


title: 3889_Treg_Lung_48_S48_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: Coho smolt White muscle_1686 [65128]

description:
Sample array position within slide:
Array4Onkism0809_WM_10492
raw data files:
Onkism0809_WM_10492.txt
Onkism0809_WM_10492_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65128


title: IL-8 5


title: IL-8 3


title: Coho smolt White muscle_1620 [64925]

description:
Sample array position within slide:
Array1Onkism0809_WM_10448
raw data files:
Onkism0809_WM_10448.txt
Onkism0809_WM_10448_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64925

value: chehalis


title: 3889_Treg_Lung_92_S92_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: Coho smolt White muscle_1684 [65018]

description:
Sample array position within slide:
Array2Onkism0809_WM_10492
raw data files:
Onkism0809_WM_10492.txt
Onkism0809_WM_10492_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65018


title: Coho smolt White muscle_1687 [64963]

description:
Sample array position within slide:
Array1Onkism0809_WM_10493
raw data files:
Onkism0809_WM_10493.txt
Onkism0809_WM_10493_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64963


title: IL-8 2


title: Coho smolt White muscle_1621 [64982]

description:
Sample array position within slide:
Array2Onkism0809_WM_10448
raw data files:
Onkism0809_WM_10448.txt
Onkism0809_WM_10448_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64982


title: Coho smolt White muscle_1624 [64962]

description:
Sample array position within slide:
Array1Onkism0809_WM_10492
raw data files:
Onkism0809_WM_10492.txt
Onkism0809_WM_10492_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64962


title: KC 4

description: Gene expression data from skeletal muscle injected intraperitoneally with recombinant KC.

value: recombinant KC


title: Coho smolt White muscle_1685 [65071]

description:
Sample array position within slide:
Array3Onkism0809_WM_10492
raw data files:
Onkism0809_WM_10492.txt
Onkism0809_WM_10492_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65071


title: IL-8 1


title: Coho smolt White muscle_1618 [65037]

description:
Sample array position within slide:
Array3Onkism0809_WM_10447
raw data files:
Onkism0809_WM_10447.txt
Onkism0809_WM_10447_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65037

value: Fraser


title: Coho smolt White muscle_1619 [65091]

description:
Sample array position within slide:
Array4Onkism0809_WM_10447
raw data files:
Onkism0809_WM_10447.txt
Onkism0809_WM_10447_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65091


title: Coho smolt White muscle_1623 [65127]

description:
Sample array position within slide:
Array4Onkism0809_WM_10491
raw data files:
Onkism0809_WM_10491.txt
Onkism0809_WM_10491_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65127


title: Coho smolt White muscle_1690 [65054]

description:
Sample array position within slide:
Array3Onkism0809_WM_10466
raw data files:
Onkism0809_WM_10466.txt
Onkism0809_WM_10466_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65054

value: ECVI


title: 3889_Treg_Lung_3_S3_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: KC 3


title: KC 2


title: Coho smolt White muscle_1617 [64981]

description:
Sample array position within slide:
Array2Onkism0809_WM_10447
raw data files:
Onkism0809_WM_10447.txt
Onkism0809_WM_10447_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64981

value: Pooled cRNA reference


title: Coho smolt White muscle_1615 [65090]

description:
Sample array position within slide:
Array4Onkism0809_WM_10446
raw data files:
Onkism0809_WM_10446.txt
Onkism0809_WM_10446_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65090


title: Coho smolt White muscle_1551 [65112]

description:
Sample array position within slide:
Array4Onkism0809_WM_10469
raw data files:
Onkism0809_WM_10469.txt
Onkism0809_WM_10469_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65112

value: Wild

value: capilano


title: Coho smolt White muscle_1616 [64924]

description:
Sample array position within slide:
Array1Onkism0809_WM_10447
raw data files:
Onkism0809_WM_10447.txt
Onkism0809_WM_10447_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64924

value: Hatchery

value: M


title: 3889_Treg_Lung_34_S34_P1

description: Full-length RNAseq (SMART-Seq2) reads

value: Treg


title: KC 1


title: Coho smolt White muscle_1550 [64972]

description:
Sample array position within slide:
Array2Onkism0809_WM_10438
raw data files:
Onkism0809_WM_10438.txt
Onkism0809_WM_10438_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64972

value: white muscle

value: U


title: Coho smolt White muscle_1552 [65117]

description:
Sample array position within slide:
Array4Onkism0809_WM_10474b
raw data files:
Onkism0809_WM_10474b.txt
Onkism0809_WM_10474b_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65117


title: 3889_Treg_Lung_70_S70_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: 3889_Treg_Lung_25_S25_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: 3889_Treg_Lung_80_S80_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: 3889_Treg_Lung_37_S37_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: 7_AK125p1_SPH6d.count

city: Ramat Gan

first: Tomer

last: Kalisky

address: Max and Anna Webb

department: Electrical Engineering

country: Israel

institute: Bar Ilan University

data_processing:
Mapping to hg19 using TopHat v2.1.0 python 2.7.5 using the '-p 8' parameter
Indexing bam file created by tophat:  'samtools index'
Sorting bam file for later use by htseq-count:  'samtools sort -n'
Counting genes using htseq-count  version HTSeq-0.6.1p1-py2.7-linux-x86_64  on python 2.7.5  '  htseq-count -f bam -s no -a 10 '
Genome_build: hg19
Supplementary_files_format_and_content: Excel spreadsheet with gene counts per sample,  4 samples in each file, each file corresponds to different "sphere" numbered 82, 85, 104, 105

source_name: Human Adult kidney

growth_protocol: Human kidney samples were retrieved from the borders of renal cell carcinoma (RCC) tumors resected from partial and total nephrectomy patients. Collected tissues were washed with PBS,weighed and minced into ~1 mm slices using sterile surgical scalpels. The dissected tissue was then incubated for two hours at 37°C with Iscoves' Modified Dulbecco's Medium (IMDM) .(Invitrogen) supplemented with 0.1% collagenase IV (Invitrogen). The digested tissue was sieved through 100 µm cell strainers to achieve a single cell suspension. The medium was removed by centrifugation and the cells were resuspended in growth medium and plated on gelatin-coated T175 flasks. Serum containing medium (SCM) was comprised of IMDM (Biological Industries) supplemented with 10% fetal bovine serum (Invitrogen), 1% Pen-strep 100M, 1% L-glutamine (both purchased from Biological industries), 100 ng/ml EGF, 100 ng/ml bFGF and 10 ng/ml SCF (all growth factors were purchased from Peprotech Asia).

extract_protocol:
hKEpC were thawed and grown as 2D monolayers for 5-7 days. Upon reaching confluency of 80-100%, the cells were harvested and seeded on poly (2-hydroxyethylmethacrylate) (poly-HEMA; Sigma-Aldrich)-precoated plates, in serum free medium (SFM), at a concentration of 5.5–13x104 cells/mL. SFM was comprised of N2 medium (Biological Industries) supplemented with 1% Pen-strep 100M, 1% L-glutamine, 0.4% B27 supplement (Gibco), 4µg/ml heparin sodium (Intramed), 1% non-essential amino acids, 1% sodium pyruvate, 0.2% CD Lipid concentrate (all purchased from Invitrogen), 2.4mg/ml glucose, 0.4mg/ml transferrin, 10mg/ml insulin, 38.66µg/ml putrescine, 0.04% sodium selenite, 12.6µg/ml progesterone (all from Sigma-Aldrich), 10ng/ml FGF and 20ng/ml EGF.
TruSeq mRNA-Seq library kit (Illumina)

treatment_protocol: nSPH formation: hKEpC were thawed and grown as 2D monolayers for 5-7 days. Upon reaching confluency of 80-100%, the cells were harvested and seeded on poly (2-hydroxyethylmethacrylate) (poly-HEMA; Sigma-Aldrich)-precoated plates, in serum free medium (SFM), at a concentration of 5.5–13x104 cells/mL. SFM was comprised of N2 medium (Biological Industries) supplemented with 1% Pen-strep 100M, 1% L-glutamine, 0.4% B27 supplement (Gibco), 4µg/ml heparin sodium (Intramed), 1% non-essential amino acids, 1% sodium pyruvate, 0.2% CD Lipid concentrate (all purchased from Invitrogen), 2.4mg/ml glucose, 0.4mg/ml transferrin, 10mg/ml insulin, 38.66µg/ml putrescine, 0.04% sodium selenite, 12.6µg/ml progesterone (all from Sigma-Aldrich), 10ng/ml FGF and 20ng/ml EGF.

value: Kidney

tag: patients status

value: Healthy

tag: culture conditions

value: 3D (spheres)-day 6


title: Control 4

description: Gene expression data from skeletal muscle injected intraperitoneally with vehicle control.

value: vehicle control


title: 8_AK125p1_SPH9d.count

value: 3D (spheres)-day 9


title: Coho smolt White muscle_1549 [64916]

description:
Sample array position within slide:
Array1Onkism0809_WM_10438
raw data files:
Onkism0809_WM_10438.txt
Onkism0809_WM_10438_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64916

tag: FISH #

tag: fw/sw

value: FW


title: 5_AK125p1_Adh.count

value: Adherent


title: Coho smolt White muscle_1537 [65062]

description:
Sample array position within slide:
Array3Onkism0809_WM_10474b
raw data files:
Onkism0809_WM_10474b.txt
Onkism0809_WM_10474b_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65062

tag: year

tag: season


title: Coho smolt White muscle_1536 [65009]

description:
Sample array position within slide:
Array2Onkism0809_WM_10476
raw data files:
Onkism0809_WM_10476.txt
Onkism0809_WM_10476_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65009

tag: origin

tag: fork length (cm)


title: Veh Control 2


title: 6_AK125p1_SPH3d.count

value: 3D (spheres)-day 3


title: Coho smolt White muscle_1544 [65121]

description:
Sample array position within slide:
Array4Onkism0809_WM_10479
raw data files:
Onkism0809_WM_10479.txt
Onkism0809_WM_10479_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65121

tag: total mass (g)

tag: Sex


title: Coho smolt White muscle_1547 [65057]

description:
Sample array position within slide:
Array3Onkism0809_WM_10469
raw data files:
Onkism0809_WM_10469.txt
Onkism0809_WM_10469_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65057

tag: tissue

tag: latitude


title: Coho smolt White muscle_1533 [65123]

description:
Sample array position within slide:
Array4Onkism0809_WM_10487
raw data files:
Onkism0809_WM_10487.txt
Onkism0809_WM_10487_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65123

tag: longitude

tag: sample type


title: 3889_Treg_Lung_78_S78_P1

description: Full-length RNAseq (SMART-Seq2) reads

tag: mouse-id

value: Lung

tag: cell-id-assigned


title: Coho smolt White muscle_1532 [65067]

description:
Sample array position within slide:
Array3Onkism0809_WM_10487
raw data files:
Onkism0809_WM_10487.txt
Onkism0809_WM_10487_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65067

value: Pooled cRNA reference


title: Coho smolt White muscle_1535 [65052]

description:
Sample array position within slide:
Array3Onkism0809_WM_10464
raw data files:
Onkism0809_WM_10464.txt
Onkism0809_WM_10464_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65052


title: Coho smolt White muscle_1534 [64958]

description:
Sample array position within slide:
Array1Onkism0809_WM_10488
raw data files:
Onkism0809_WM_10488.txt
Onkism0809_WM_10488_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64958


title: Veh Control 1

tag: treatment


title: Coho smolt White muscle_1443 [64999]

description:
Sample array position within slide:
Array2Onkism0809_WM_10466
raw data files:
Onkism0809_WM_10466.txt
Onkism0809_WM_10466_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64999

value: Wild

value: salmon

value: Fraser


title: 3889_Treg_Lung_66_S66_P1

description: Full-length RNAseq (SMART-Seq2) reads

tag: cell-id-sorted


title: Coho smolt White muscle_1529 [65013]

description:
Sample array position within slide:
Array2Onkism0809_WM_10487
raw data files:
Onkism0809_WM_10487.txt
Onkism0809_WM_10487_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65013

value: Hatchery

value: capilano


title: Coho smolt White muscle_1530 [64997]

description:
Sample array position within slide:
Array2Onkism0809_WM_10464
raw data files:
Onkism0809_WM_10464.txt
Onkism0809_WM_10464_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64997

value: white muscle


title: 4_AK124p1_SPH9d.count

tag: patients status

value: renal disease

tag: culture conditions


title: 3889_Treg_Lung_17_S17_P1

description: Full-length RNAseq (SMART-Seq2) reads

value: Treg


title: 3889_Treg_Lung_39_S39_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: 3889_Treg_Lung_82_S82_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: 3_AK124p1_SPH6d.count

value: Kidney


title: 3889_Treg_Lung_7_S7_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: Coho smolt White muscle_1440 [65043]

description:
Sample array position within slide:
Array3Onkism0809_WM_10455
raw data files:
Onkism0809_WM_10455.txt
Onkism0809_WM_10455_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65043

tag: FISH #

tag: fw/sw

value: F


title: AK86p2-SPH10d

value: Healthy


title: 1_AK124p1_Adh.count


title: 2_AK124p1_SPH3d.count


title: Coho smolt White muscle_922 [65005]

description:
Sample array position within slide:
Array2Onkism0809_WM_10472
raw data files:
Onkism0809_WM_10472.txt
Onkism0809_WM_10472_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65005

value: SW

tag: year

tag: season

value: M


title: Coho smolt White muscle_1528 [64957]

description:
Sample array position within slide:
Array1Onkism0809_WM_10487
raw data files:
Onkism0809_WM_10487.txt
Onkism0809_WM_10487_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64957

value: FW

tag: origin

tag: fork length (cm)

value: U


title: 3889_Treg_Lung_19_S19_P1

description: Full-length RNAseq (SMART-Seq2) reads

value: Lung


title: Coho smolt White muscle_1438 [64930]

description:
Sample array position within slide:
Array1Onkism0809_WM_10455
raw data files:
Onkism0809_WM_10455.txt
Onkism0809_WM_10455_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64930

tag: total mass (g)

tag: Sex

value: Pooled cRNA reference


title: Coho smolt White muscle_1439 [64988]

description:
Sample array position within slide:
Array2Onkism0809_WM_10455
raw data files:
Onkism0809_WM_10455.txt
Onkism0809_WM_10455_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64988

tag: tissue

value: Wild

tag: latitude


title: 3889_Treg_Lung_35_S35_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: 3889_Treg_Lung_51_S51_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: AK86p2-SPH6d

value: 3D (spheres)-day 6


title: AK86p1Adh

value: Adherent


title: 3889_Treg_Lung_50_S50_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: Coho smolt White muscle_1434 [64929]

description:
Sample array position within slide:
Array1Onkism0809_WM_10454
raw data files:
Onkism0809_WM_10454.txt
Onkism0809_WM_10454_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64929

tag: longitude

value: salmon

value: Fraser

tag: sample type


title: Coho smolt White muscle_796 [64947]

description:
Sample array position within slide:
Array1Onkism0809_WM_10472
raw data files:
Onkism0809_WM_10472.txt
Onkism0809_WM_10472_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64947

value: white muscle


title: Coho smolt White muscle_661 [65022]

description:
Sample array position within slide:
Array2Onkism0809_WM_10496
raw data files:
Onkism0809_WM_10496.txt
Onkism0809_WM_10496_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65022


title: Coho smolt White muscle_576 [64989]

description:
Sample array position within slide:
Array2Onkism0809_WM_10456
raw data files:
Onkism0809_WM_10456.txt
Onkism0809_WM_10456_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64989


title: AK86p2-SPH3d

value: 3D (spheres)-day 3


title: 3889_Treg_Lung_72_S72_P1

description: Full-length RNAseq (SMART-Seq2) reads

tag: mouse-id

tag: cell-id-assigned

value: Treg


title: AK82p3SPH10d

value: Kidney

value: 3D (spheres)-day 9


title: 3889_Treg_Lung_29_S29_P1

description: Full-length RNAseq (SMART-Seq2) reads

tag: cell-id-sorted


title: Coho smolt White muscle_785 [64967]

description:
Sample array position within slide:
Array1Onkism0809_WM_10497
raw data files:
Onkism0809_WM_10497.txt
Onkism0809_WM_10497_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64967

value: F

value: North


title: Coho smolt White muscle_766 [65132]

description:
Sample array position within slide:
Array4Onkism0809_WM_10496
raw data files:
Onkism0809_WM_10496.txt
Onkism0809_WM_10496_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65132

value: SW


title: Coho smolt White muscle_579 [65044]

description:
Sample array position within slide:
Array3Onkism0809_WM_10456
raw data files:
Onkism0809_WM_10456.txt
Onkism0809_WM_10456_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65044


title: Coho smolt White muscle_572 [65045]

description:
Sample array position within slide:
Array3Onkism0809_WM_10457
raw data files:
Onkism0809_WM_10457.txt
Onkism0809_WM_10457_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65045

value: Hatchery

value: M


title: AK82p3SPH3d

tag: patients status

value: Healthy


title: AK82p3SPH6d

tag: culture conditions


title: 3889_Treg_Lung_91_S91_P1

description: Full-length RNAseq (SMART-Seq2) reads

value: Lung


title: Coho smolt White muscle_786 [65000]

description:
Sample array position within slide:
Array2Onkism0809_WM_10467
raw data files:
Onkism0809_WM_10467.txt
Onkism0809_WM_10467_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65000

tag: FISH #

value: Wild

value: Pooled cRNA reference


title: Coho smolt White muscle_666 [65075]

description:
Sample array position within slide:
Array3Onkism0809_WM_10496
raw data files:
Onkism0809_WM_10496.txt
Onkism0809_WM_10496_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65075

tag: fw/sw

value: U


title: Coho smolt White muscle_1885 [65028]

description:
Sample array position within slide:
Array3Onkism0809_WM_10438
raw data files:
Onkism0809_WM_10438.txt
Onkism0809_WM_10438_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65028

tag: year

value: ECVI


title: Coho smolt White muscle_663 [64942]

description:
Sample array position within slide:
Array1Onkism0809_WM_10467
raw data files:
Onkism0809_WM_10467.txt
Onkism0809_WM_10467_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64942

tag: season

value: Fraser


title: AK82p2Adh

value: Adherent


title: 3889_Treg_Lung_33_S33_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: Coho smolt White muscle_552 [64990]

description:
Sample array position within slide:
Array2Onkism0809_WM_10457
raw data files:
Onkism0809_WM_10457.txt
Onkism0809_WM_10457_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64990

value: white muscle

tag: origin

value: LWFR


title: Coho smolt White muscle_101 [64954]

description:
Sample array position within slide:
Array1Onkism0809_WM_10479
raw data files:
Onkism0809_WM_10479.txt
Onkism0809_WM_10479_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64954

value: FW

tag: fork length (cm)

value: chilliwack


title: Coho smolt White muscle_100 [65108]

description:
Sample array position within slide:
Array4Onkism0809_WM_10465
raw data files:
Onkism0809_WM_10465.txt
Onkism0809_WM_10465_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65108

tag: total mass (g)


title: Coho smolt White muscle_502 [65098]

description:
Sample array position within slide:
Array4Onkism0809_WM_10455
raw data files:
Onkism0809_WM_10455.txt
Onkism0809_WM_10455_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65098

tag: Sex


title: Coho smolt White muscle_99 [65114]

description:
Sample array position within slide:
Array4Onkism0809_WM_10471
raw data files:
Onkism0809_WM_10471.txt
Onkism0809_WM_10471_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65114

tag: tissue


title: 3889_Treg_Lung_62_S62_P1

description: Full-length RNAseq (SMART-Seq2) reads

value: Treg


title: Coho smolt White muscle_503 [64931]

description:
Sample array position within slide:
Array1Onkism0809_WM_10456
raw data files:
Onkism0809_WM_10456.txt
Onkism0809_WM_10456_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64931

value: F

tag: latitude


title: CBS79KO-VP-HOTTIP-MLL-ChIP-seq

city: Hangzhou

first: Huacheng

last: Luo

state: Zhejiang

address: No. 150, Fucheng Road, Qiantang District

country: China

institute: Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences

data_processing:
Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end).
Paired end RNA-seq reads from mice were aligned to the mm9 genome assembly using Tophat, and ATAC-seq, ChIP-seq, HiC-seq and CHIRP-seq reads from human cells were aligned to the hg19 genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1).
Genome coverage tracks were created using deepTools version 3.0.
Chromatin structure HiC-seq was calculated and displayed with HOMER, Juicer and Juicebox software.
Genome_build: mm9, hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for RNA-seq Samples, and peaks annotation for ATAC-seq, ChIP-seq and CHIRP-seq.

source_name: MOLM13 leukemia cells

growth_protocol: Total bone marrow cells were isolated from WT and Hottip-Tg mice, and sorted with Lin-, Sca1+ and Kit+ markers. Human MOLM13 leukemia cells were cultured at RMPI1640 and 10% FBS media.

extract_protocol:
RNA samples extracted with Trizol and treated with DNase I. ChIP Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K4me3, H3K27me3, H3K79me2 and MLL antibody (antibody: Anti-H3K4me3, Millipore, Cat No. 04-745; Anti-H3K27me3, Millipore, Cat No. 07-449; Anti-H3K79me2, Abcam, Cat No. ab3594.; Anti-MLL, Millipore, #05-765). ATAC-seq samples derived according to Nextera Tn5 Transposase kits. CHIRP-seq library constructs with the Illumina TruSeq CHIP DNA library kit. HiC-DNA was prepared with Arima-HiC kit (Arima, #A410030).
RNA-seq libraries were prepared according to TruSeq Stranded mRNA Library Prep (#20020594). ChIP-seq and CHIRP-seq libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Preparation Kit (#IP-202-1012). ATAC-seq libraries were prepared according to Nextera DNA Library Prep Kit (#FC-121-1030). 4C-seq libraries were prepared according to TruSeq ChIP Library Preparation Kit (#IP-202-1012). HiC library was prepared according to Arima-HiC Kit (Catlog: A410030). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Immediately extract RNA from LSK, HSC cells from transgenic mice and MOLM13 AML cells without any treatment.

tag: cell line

tag: cell types

value: Human-derived acute myeloid leukemia cells

tag: tissue origin

value: peripheral blood

tag: genotype/variation

tag: chip antibody

value: Anti-MLL, Millipore, #05-765


title: HOTTIP-KO-MLL-ChIP-seq

value: HOTTIP-KO


title: CBS79-KO-MLL-ChIP-seq


title: 3889_Treg_Lung_55_S55_P1

description: Full-length RNAseq (SMART-Seq2) reads

tag: mouse-id

value: Lung

tag: cell-id-assigned

tag: cell-id-sorted


title: 3889_Treg_Lung_65_S65_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: LPM1H9

city: Great Chesterford

first: Nicolas

last: Gambardella

state: Essex

address: Lewis House, Great Chesterford Court

country: United Kingdom

institute: aSciStance Ltd

data_processing:
Sequenced reads were trimmed for adaptor sequence with Trim Galore version: 0.4.1 (a wrapper for Cutadapt 1.8.1 with parameters  -f fastq -e 0.1 -q 20 -O 1 and FastQC)
Reads were mapped to GRCh38 whole genome using HiSAT2 v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Counts were produced using SeqMonk 0.34. All reads overlapping an exon were counted, all reads from all exons of all isoforms added, counting each one once.
Counts Per Million reads (CPM) were calculated dividing reads from all exons of all isoforms by the size of the library in reads, multiplied by 1 million.
Genome_build: GRCh38
Supplementary_files_format_and_content: Comma Separated Value file containing Counts Per Million reads. Rows are genes (rownames are Gene Symbols) and columns are cells.

source_name: engineered lateral mesoderm cell

extract_protocol:
Total RNA was extracted from cultures using RNeasy mini from Qiagen. DNA contamination was removed from the samples using DNA-free™ DNA Removal Kit from Ambion (Thermofisher).
cDNA synthesis and Illumina libraries were performed using SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit from TAKARA.

tag: cell type

value: hPSC-derived lateral mesoderm

tag: es line


title: Coho smolt White muscle_532 [64932]

description:
Sample array position within slide:
Array1Onkism0809_WM_10457
raw data files:
Onkism0809_WM_10457.txt
Onkism0809_WM_10457_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64932

tag: FISH #

tag: fw/sw

value: SW

tag: year

tag: season

value: Wild

value: M

tag: longitude

tag: sample type

value: Pooled cRNA reference


title: 3889_Treg_Lung_38_S38_P1

description: Full-length RNAseq (SMART-Seq2) reads

tag: tissue


title: 3889_Treg_Lung_18_S18_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: WT-MLL-ChIP-seq

tag: cell line

value: WT


title: LPM1H8


title: 3889_Treg_Lung_63_S63_P1

description: Full-length RNAseq (SMART-Seq2) reads


title: Coho smolt White muscle_96 [64946]

description:
Sample array position within slide:
Array1Onkism0809_WM_10471
raw data files:
Onkism0809_WM_10471.txt
Onkism0809_WM_10471_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64946

value: white muscle

tag: origin

tag: fork length (cm)

tag: total mass (g)

tag: Sex

value: U

tag: latitude


title: Coho smolt White muscle_92 [65058]

description:
Sample array position within slide:
Array3Onkism0809_WM_10470
raw data files:
Onkism0809_WM_10470.txt
Onkism0809_WM_10470_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65058

value: FW