title: PBS2-1

city: Rochester

first: Xuewei

address: 200 1st street

institute: Mayo Clinic

data_processing:
Base calling by CASAVA
Alignment by STAR
Gene count by FeatureCount
Genome_build: mm10
Supplementary_files_format_and_content: text file for gene count

extract_protocol:
miRNeasy mini kits (Qiagen) were used to isolate total RNA.
TruSeq RNA Library Prep Kit V2  was used to prepare RNA-seq libraries. Illumina HiSeq 4000 platform for sequencing.

treatment_protocol: 7 week C57BL6 male mice were injected with 1 X 10E 6 cells or vehicle.   14 days later, cardiac function was assessed by echocardiography, and cardiac tissue was dissected for obtaining mRNA.

tag: treatment

value: PBS

value: heart

value: male


title: Coho smolt Liver_4137 [62762]

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:
Array4Onkism0809_liver_10275
raw data files:
Onkism0809_liver_10275.txt
Onkism0809_liver_10275_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62762

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.

tag: tissue

value: liver

tag: FISH #

tag: fw/sw

value: SW

tag: year

tag: season

tag: origin

value: Hatchery

tag: fork length (cm)

tag: total mass (g)

tag: Sex

value: F

tag: latitude

tag: longitude

value: Mainland

label: Alexa 647

source_name: liver from all samples in the series

tag: sample type

value: Pooled cRNA reference


title: IDD patient-1

city: Chengdu

first: Yi

last: Wang

state: Sichuan

address: 132 West First Section First Ring Road

country: China

institute: Sichuan Provincial Orthopedic Hospital

description: Gene expression in  human blood

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Homo sapiens

source_name: Peripheral Blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Not provided

value: whole blood

tag: diagnosis

value: intervertebral disc degeneration


title: PBS2-5

type: SRA

country: USA

library_source: transcriptomic

organism: Mus musculus

tag: strain


title: PBS1-3


title: 3642_Treg_Lung_95_S383_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

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)

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

value: Treg

tag: cell-id-sorted


title: Coho smolt Liver_4201 [62931]

description:
Sample array position within slide:
Array1Onkism0809_liver_10276
raw data files:
Onkism0809_liver_10276.txt
Onkism0809_liver_10276_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62931

tag: tissue

value: M

value: WCVI

value: Salish


title: PBS1-1

tag: treatment


title: 3642_CD4_Lung_32_S32_P1

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

value: Tconv


title: Coho smolt Liver_4129 [62763]

description:
Sample array position within slide:
Array4Onkism0809_liver_10274
raw data files:
Onkism0809_liver_10274.txt
Onkism0809_liver_10274_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62763

tag: FISH #

tag: fw/sw

value: Wild

value: Fraser


title: Coho smolt Liver_4215 [62818]

description:
Sample array position within slide:
Array3Onkism0809_liver_10276
raw data files:
Onkism0809_liver_10276.txt
Onkism0809_liver_10276_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62818

tag: year

tag: season


title: LLC2-2

value: injected with LLC1 lung adenocarcinoma cells

value: heart

value: male


title: 3642_Treg_Lung_12_S300_P1

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


title: LLC1-5


title: Coho smolt Liver_4126 [62878]

description:
Sample array position within slide:
Array2Onkism0809_liver_10274
raw data files:
Onkism0809_liver_10274.txt
Onkism0809_liver_10274_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62878

value: liver

value: SW

tag: origin

tag: fork length (cm)


title: Coho smolt Liver_3628 [62758]

description:
Sample array position within slide:
Array4Onkism0809_liver_10279
raw data files:
Onkism0809_liver_10279.txt
Onkism0809_liver_10279_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62758

tag: total mass (g)

tag: Sex

value: F

value: Columbia

value: Oregon


title: 3642_CD4_Lung_83_S83_P1

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


title: Coho smolt Liver_4128 [62820]

description:
Sample array position within slide:
Array3Onkism0809_liver_10274
raw data files:
Onkism0809_liver_10274.txt
Onkism0809_liver_10274_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62820

tag: latitude

tag: longitude

value: Mainland

value: Pooled cRNA reference


title: Coho smolt Liver_4125 [62933]

description:
Sample array position within slide:
Array1Onkism0809_liver_10274
raw data files:
Onkism0809_liver_10274.txt
Onkism0809_liver_10274_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62933

tag: sample type


title: Coho smolt Liver_3538 [62874]

description:
Sample array position within slide:
Array2Onkism0809_liver_10279
raw data files:
Onkism0809_liver_10279.txt
Onkism0809_liver_10279_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62874

value: North


title: Coho smolt Liver_3539 [62815]

description:
Sample array position within slide:
Array3Onkism0809_liver_10279
raw data files:
Onkism0809_liver_10279.txt
Onkism0809_liver_10279_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62815

value: M

value: ECVI


title: Coho smolt Liver_3534 [62850]

description:
Sample array position within slide:
Array2Onkism0809_liver_10311
raw data files:
Onkism0809_liver_10311.txt
Onkism0809_liver_10311_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62850

value: WCVI


title: Coho smolt Liver_3537 [62928]

description:
Sample array position within slide:
Array1Onkism0809_liver_10279
raw data files:
Onkism0809_liver_10279.txt
Onkism0809_liver_10279_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62928


title: 3642_CD4_Lung_22_S22_P1

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

value: Lung

value: Tconv


title: LLC1-3

tag: strain


title: 3642_CD4_Lung_64_S64_P1

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

tag: mouse-id


title: Coho smolt Liver_3533 [62903]

description:
Sample array position within slide:
Array1Onkism0809_liver_10311
raw data files:
Onkism0809_liver_10311.txt
Onkism0809_liver_10311_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62903

value: Wild


title: Coho smolt Liver_3531 [62792]

description:
Sample array position within slide:
Array3Onkism0809_liver_10310
raw data files:
Onkism0809_liver_10310.txt
Onkism0809_liver_10310_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62792

value: Salish


title: LLC1-2

value: injected with LLC1 lung adenocarcinoma cells

value: heart


title: 3642_CD4_Lung_36_S36_P1

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

tag: cell-id-assigned


title: 3642_CD4_Lung_87_S87_P1

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

tag: cell-id-sorted


title: FWL9

city: Los Angeles

first: Xia

last: Yang

state: CA

address: 2000A, 610 Charles E Young Dr S

institute: UCLA

description: Total RNA was extracted from liver, hypothalamus and mesenteric adipose using All-Prep DNA/RNA/miRNA Universal Kit (Qiagen, CA. USA) according to the manufacturer’s instructions, including treatment with DNase I. RNA quality was evaluated with Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA).  All RNA samples had RNA integrity number (RIN) over 8.

data_processing:
HISAT was used to align the RNA-Seq reads against the Mus musculus genome to discover the locations from which the reads originated and to determine the transcript sites.
StringTie was used to assemble the RNA-seq alignments into potential transcripts.
Ballgown determines the differential gene expression (DEG) of transcripts after filtering genes with low expression levels (FPKM < 1) using linear model test [23].
Genome_build: UCSC version mm10
Supplementary_files_format_and_content: Transcription abundances in terms of the FPKM measure of the expressed transcripts in each sample were obtained by using Ballgown R tool.

source_name: Liver tissue

growth_protocol: Male DBA, B6 and FVB mice (Jackson Laboratory) of 7 weeks old weighing 20-25 g were randomly assigned to 8% fructose treatment (n=8-12, 8% w/v fructose in the drinking water) and control group (n=8-10, drinking water) for 14 weeks. All experiments were performed in accordance with the United States National Institutes of Health Guide for the Care and Use of Laboratory Animals. The animal studies and experimental procedures were approved by the University of California at Los Angeles Chancellor's Animal Research Committee (ARC).

extract_protocol:
Total RNA was extracted from hypothalamus and liver using All-Prep DNA/RNA/miRNA Universal Kit (Qiagen, CA. USA) according to the manufacturer’s instructions, including treatment with DNase I. RNA quality was evaluated with Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA).  All RNA samples had RNA integrity number (RIN) over 8.
Sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold Library Prep kit.
Libraries were sequenced in pair-end mode on an Illumina HiSeq 4000 sequencing system.

treatment_protocol: Mice had free access to water and diets and were maintained under standard housing condition (room temperature 22-24 °C) with 12 h light/dark cycle. Daily food and drink intake were monitored on per-cage basis. The mice were examined for changes in metabolic phenotypes including body weight, body fat, lean mass, intraperitoneal glucose tolerance test (IPGTT), and serum levels of insulin, glucose, total cholesterol (TC), high density lipoprotein cholesterol (HDL), un-esterified cholesterol, free fatty acids (FFA), and triglycerides (TG), as detailed in the following sections. Mice were sacrificed at the end of the 14-week fructose treatment experiment, and hypothalamus and liver tissues were dissected out, flash frozen and stored at −70°C until use.

value: FVB/NJ

value: Water


title: 3642_CD4_Lung_28_S28_P1

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

tag: tissue


title: Coho smolt Liver_3532 [62734]

description:
Sample array position within slide:
Array4Onkism0809_liver_10310
raw data files:
Onkism0809_liver_10310.txt
Onkism0809_liver_10310_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62734

value: liver

value: SW

value: Hatchery

value: F


title: 3642_CD4_Lung_79_S79_P1

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


title: FWL2

tag: treatment


title: FWL1


title: Coho smolt Liver_3511 [62834]

description:
Sample array position within slide:
Array3Onkism0809_liver_10100
raw data files:
Onkism0809_liver_10100.txt
Onkism0809_liver_10100_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62834

tag: FISH #

value: Pooled cRNA reference


title: Coho smolt Liver_3303 [62875]

description:
Sample array position within slide:
Array2Onkism0809_liver_10278
raw data files:
Onkism0809_liver_10278.txt
Onkism0809_liver_10278_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62875

tag: fw/sw

value: Mainland

value: Fraser


title: Coho smolt Liver_3329 [62723]

description:
Sample array position within slide:
Array4Onkism0809_liver_10321
raw data files:
Onkism0809_liver_10321.txt
Onkism0809_liver_10321_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62723

tag: year

value: M


title: Coho smolt Liver_3308 [62744]

description:
Sample array position within slide:
Array4Onkism0809_liver_10298
raw data files:
Onkism0809_liver_10298.txt
Onkism0809_liver_10298_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62744

tag: season


title: Coho smolt Liver_3299 [62929]

description:
Sample array position within slide:
Array1Onkism0809_liver_10278
raw data files:
Onkism0809_liver_10278.txt
Onkism0809_liver_10278_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62929

tag: origin


title: Coho smolt Liver_3530 [62783]

description:
Sample array position within slide:
Array3Onkism0809_liver_10319
raw data files:
Onkism0809_liver_10319.txt
Onkism0809_liver_10319_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62783

tag: fork length (cm)

value: WCVI


title: Coho smolt Liver_3311 [62904]

description:
Sample array position within slide:
Array1Onkism0809_liver_10310
raw data files:
Onkism0809_liver_10310.txt
Onkism0809_liver_10310_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62904

tag: total mass (g)


title: Coho smolt Liver_3356 [62772]

description:
Sample array position within slide:
Array4Onkism0809_liver_10265
raw data files:
Onkism0809_liver_10265.txt
Onkism0809_liver_10265_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62772

tag: Sex


title: Coho smolt Liver_3320 [62781]

description:
Sample array position within slide:
Array3Onkism0809_liver_10321
raw data files:
Onkism0809_liver_10321.txt
Onkism0809_liver_10321_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62781

tag: latitude


title: FWL17


title: 3642_CD4_Lung_92_S92_P1

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

value: Lung


title: 3642_CD4_Lung_86_S86_P1

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

value: Tconv


title: Coho smolt Liver_3298 [62760]

description:
Sample array position within slide:
Array4Onkism0809_liver_10277
raw data files:
Onkism0809_liver_10277.txt
Onkism0809_liver_10277_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62760

tag: longitude


title: 3642_CD4_Lung_90_S90_P1

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


title: FWL15


title: FWL8


title: FFL6

value: Fructose


title: Coho smolt Liver_3242 [62881]

description:
Sample array position within slide:
Array2Onkism0809_liver_10270
raw data files:
Onkism0809_liver_10270.txt
Onkism0809_liver_10270_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62881

tag: sample type


title: Coho smolt Liver_3237 [62751]

description:
Sample array position within slide:
Array4Onkism0809_liver_10291
raw data files:
Onkism0809_liver_10291.txt
Onkism0809_liver_10291_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62751


title: Coho smolt Liver_3250 [62817]

description:
Sample array position within slide:
Array3Onkism0809_liver_10277
raw data files:
Onkism0809_liver_10277.txt
Onkism0809_liver_10277_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62817


title: Coho smolt Liver_3190 [62808]

description:
Sample array position within slide:
Array3Onkism0809_liver_10292
raw data files:
Onkism0809_liver_10292.txt
Onkism0809_liver_10292_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62808

value: Wild


title: Coho smolt Liver_3229 [62854]

description:
Sample array position within slide:
Array2Onkism0809_liver_10306
raw data files:
Onkism0809_liver_10306.txt
Onkism0809_liver_10306_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62854

value: Salish

value: ECVI


title: Coho smolt Liver_3232 [62930]

description:
Sample array position within slide:
Array1Onkism0809_liver_10277
raw data files:
Onkism0809_liver_10277.txt
Onkism0809_liver_10277_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62930


title: FFL5

description: Total RNA was extracted from liver, hypothalamus and mesenteric adipose using All-Prep DNA/RNA/miRNA Universal Kit (Qiagen, CA. USA) according to the manufacturer’s instructions, including treatment with DNase I. RNA quality was evaluated with Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA).  All RNA samples had RNA integrity number (RIN) over 8.

tag: strain

value: FVB/NJ


title: Coho smolt Liver_3233 [62876]

description:
Sample array position within slide:
Array2Onkism0809_liver_10277
raw data files:
Onkism0809_liver_10277.txt
Onkism0809_liver_10277_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62876


title: Coho smolt Liver_3240 [62937]

description:
Sample array position within slide:
Array1Onkism0809_liver_10270
raw data files:
Onkism0809_liver_10270.txt
Onkism0809_liver_10270_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62937


title: 3642_Treg_Lung_7_S295_P1

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

tag: mouse-id

value: Treg


title: 3642_CD4_Lung_29_S29_P1

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

tag: cell-id-assigned


title: FFL19


title: 3642_Treg_Lung_9_S297_P1

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

tag: cell-id-sorted


title: 3642_CD4_Lung_15_S15_P1

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

tag: tissue


title: Coho smolt Liver_3187 [62866]

description:
Sample array position within slide:
Array2Onkism0809_liver_10292
raw data files:
Onkism0809_liver_10292.txt
Onkism0809_liver_10292_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62866

value: liver


title: FFL12

tag: treatment


title: FFL10


title: FFL18


title: 3642_CD4_Lung_51_S51_P1

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


title: 3642_CD4_Lung_27_S27_P1

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


title: DWL7

value: Water


title: 3642_CD4_Lung_71_S71_P1

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


title: DWL6


title: 3642_Treg_Lung_60_S348_P1

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


title: Coho smolt Liver_3176 [62727]

description:
Sample array position within slide:
Array4Onkism0809_liver_10317
raw data files:
Onkism0809_liver_10317.txt
Onkism0809_liver_10317_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62727

tag: FISH #

value: SW

value: Hatchery


title: Coho smolt Liver_3184 [62920]

description:
Sample array position within slide:
Array1Onkism0809_liver_10292
raw data files:
Onkism0809_liver_10292.txt
Onkism0809_liver_10292_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62920

tag: fw/sw

value: F

value: Pooled cRNA reference


title: Coho smolt Liver_3166 [62813]

description:
Sample array position within slide:
Array3Onkism0809_liver_10285
raw data files:
Onkism0809_liver_10285.txt
Onkism0809_liver_10285_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62813

tag: year

value: Mainland

value: Fraser


title: Coho smolt Liver_3159 [62846]

description:
Sample array position within slide:
Array2Onkism0809_liver_10315
raw data files:
Onkism0809_liver_10315.txt
Onkism0809_liver_10315_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62846

tag: season

value: M


title: 3642_Treg_Lung_42_S330_P1

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

value: Lung


title: Coho smolt Liver_3188 [62756]

description:
Sample array position within slide:
Array4Onkism0809_liver_10285
raw data files:
Onkism0809_liver_10285.txt
Onkism0809_liver_10285_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62756

tag: origin


title: Coho smolt Liver_3161 [62757]

description:
Sample array position within slide:
Array4Onkism0809_liver_10284
raw data files:
Onkism0809_liver_10284.txt
Onkism0809_liver_10284_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62757

tag: fork length (cm)


title: DWL4


title: DWL5


title: 3642_CD4_Lung_78_S78_P1

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

value: Tconv


title: Coho smolt Liver_3168 [62755]

description:
Sample array position within slide:
Array4Onkism0809_liver_10287
raw data files:
Onkism0809_liver_10287.txt
Onkism0809_liver_10287_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62755

tag: total mass (g)


title: 3642_CD4_Lung_46_S46_P1

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


title: DWL3


title: Coho smolt Liver_3130 [62729]

description:
Sample array position within slide:
Array4Onkism0809_liver_10315
raw data files:
Onkism0809_liver_10315.txt
Onkism0809_liver_10315_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62729

tag: Sex


title: Coho smolt Liver_3158 [62872]

description:
Sample array position within slide:
Array2Onkism0809_liver_10285
raw data files:
Onkism0809_liver_10285.txt
Onkism0809_liver_10285_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62872

tag: latitude


title: Coho smolt Liver_3107 [62770]

description:
Sample array position within slide:
Array4Onkism0809_liver_10267
raw data files:
Onkism0809_liver_10267.txt
Onkism0809_liver_10267_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62770

tag: longitude


title: Coho smolt Liver_3124 [62787]

description:
Sample array position within slide:
Array3Onkism0809_liver_10315
raw data files:
Onkism0809_liver_10315.txt
Onkism0809_liver_10315_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62787

tag: sample type


title: Coho smolt Liver_3118 [62888]

description:
Sample array position within slide:
Array2Onkism0809_liver_10100
raw data files:
Onkism0809_liver_10100.txt
Onkism0809_liver_10100_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62888


title: Coho smolt Liver_3082 [62911]

description:
Sample array position within slide:
Array1Onkism0809_liver_10301
raw data files:
Onkism0809_liver_10301.txt
Onkism0809_liver_10301_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62911


title: Coho smolt Liver_3105 [62946]

description:
Sample array position within slide:
Array1Onkism0809_liver_10101
raw data files:
Onkism0809_liver_10101.txt
Onkism0809_liver_10101_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62946


title: Coho smolt Liver_3128 [62926]

description:
Sample array position within slide:
Array1Onkism0809_liver_10285
raw data files:
Onkism0809_liver_10285.txt
Onkism0809_liver_10285_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62926


title: Coho smolt Liver_3064 [62857]

description:
Sample array position within slide:
Array2Onkism0809_liver_10301
raw data files:
Onkism0809_liver_10301.txt
Onkism0809_liver_10301_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62857


title: Coho smolt Liver_3029 [62814]

description:
Sample array position within slide:
Array3Onkism0809_liver_10284
raw data files:
Onkism0809_liver_10284.txt
Onkism0809_liver_10284_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62814


title: 3642_CD4_Lung_38_S38_P1

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


title: Coho smolt Liver_3005 [62742]

description:
Sample array position within slide:
Array4Onkism0809_liver_10300
raw data files:
Onkism0809_liver_10300.txt
Onkism0809_liver_10300_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62742


title: DFL9

description: Total RNA was extracted from liver, hypothalamus and mesenteric adipose using All-Prep DNA/RNA/miRNA Universal Kit (Qiagen, CA. USA) according to the manufacturer’s instructions, including treatment with DNase I. RNA quality was evaluated with Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA).  All RNA samples had RNA integrity number (RIN) over 8.

tag: strain

value: Fructose


title: DWL2


title: 3642_CD4_Lung_31_S31_P1

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

tag: mouse-id


title: DFL14


title: 3642_Treg_Lung_63_S351_P1

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

tag: cell-id-assigned


title: Coho smolt Liver_2977 [62927]

description:
Sample array position within slide:
Array1Onkism0809_liver_10284
raw data files:
Onkism0809_liver_10284.txt
Onkism0809_liver_10284_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62927


title: Coho smolt Liver_2979 [62741]

description:
Sample array position within slide:
Array4Onkism0809_liver_10301
raw data files:
Onkism0809_liver_10301.txt
Onkism0809_liver_10301_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62741

value: Wild


title: Coho smolt Liver_2984 [62799]

description:
Sample array position within slide:
Array3Onkism0809_liver_10301
raw data files:
Onkism0809_liver_10301.txt
Onkism0809_liver_10301_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62799

value: Salish


title: 3642_CD4_Lung_65_S65_P1

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

tag: cell-id-sorted


title: 3642_CD4_Lung_52_S52_P1

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

tag: tissue


title: DFL12

tag: treatment


title: 3642_Treg_Lung_5_S293_P1

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


title: DFL11


title: 3642_Treg_Lung_89_S377_P1

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


title: DFL10


title: 3642_CD4_Lung_39_S39_P1

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


title: CWL6


title: Coho smolt Liver_2921 [62749]

description:
Sample array position within slide:
Array4Onkism0809_liver_10293
raw data files:
Onkism0809_liver_10293.txt
Onkism0809_liver_10293_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62749

tag: FISH #


title: Coho smolt Liver_3020 [62873]

description:
Sample array position within slide:
Array2Onkism0809_liver_10284
raw data files:
Onkism0809_liver_10284.txt
Onkism0809_liver_10284_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62873

tag: fw/sw


title: Coho smolt Liver_2890 [62896]

description:
Sample array position within slide:
Array1Onkism0809_liver_10318
raw data files:
Onkism0809_liver_10318.txt
Onkism0809_liver_10318_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62896

tag: year


title: Coho smolt Liver_2905 [62807]

description:
Sample array position within slide:
Array3Onkism0809_liver_10293
raw data files:
Onkism0809_liver_10293.txt
Onkism0809_liver_10293_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62807

tag: season


title: Coho smolt Liver_2922 [62884]

description:
Sample array position within slide:
Array2Onkism0809_liver_10265
raw data files:
Onkism0809_liver_10265.txt
Onkism0809_liver_10265_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62884

tag: origin


title: 3642_CD4_Lung_66_S66_P1

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


title: Coho smolt Liver_2918 [62738]

description:
Sample array position within slide:
Array4Onkism0809_liver_10306
raw data files:
Onkism0809_liver_10306.txt
Onkism0809_liver_10306_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62738

tag: fork length (cm)


title: 3642_CD4_Lung_47_S47_P1

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


title: Coho smolt Liver_2924 [62843]

description:
Sample array position within slide:
Array2Onkism0809_liver_10318
raw data files:
Onkism0809_liver_10318.txt
Onkism0809_liver_10318_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62843

tag: total mass (g)


title: Coho smolt Liver_2857 [62802]

description:
Sample array position within slide:
Array3Onkism0809_liver_10298
raw data files:
Onkism0809_liver_10298.txt
Onkism0809_liver_10298_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62802

tag: Sex


title: DFL13


title: Coho smolt Liver_2856 [62860]

description:
Sample array position within slide:
Array2Onkism0809_liver_10298
raw data files:
Onkism0809_liver_10298.txt
Onkism0809_liver_10298_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62860

tag: latitude


title: Coho smolt Liver_2811 [62720]

description:
Sample array position within slide:
Array4Onkism0809_liver_10327
raw data files:
Onkism0809_liver_10327.txt
Onkism0809_liver_10327_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62720

tag: longitude


title: CWL3


title: CWL5


title: Coho smolt Liver_2881 [62793]

description:
Sample array position within slide:
Array3Onkism0809_liver_10309
raw data files:
Onkism0809_liver_10309.txt
Onkism0809_liver_10309_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62793

value: ECVI

tag: sample type


title: CWL2

tag: strain


title: Coho smolt Liver_2858 [62889]

description:
Sample array position within slide:
Array1Onkism0809_liver_10328
raw data files:
Onkism0809_liver_10328.txt
Onkism0809_liver_10328_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62889


title: 3642_CD4_Lung_96_S96_P1

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

tag: mouse-id


title: CWL4


title: 3642_CD4_Lung_77_S77_P1

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

tag: cell-id-assigned


title: Coho smolt Liver_2800 [62745]

description:
Sample array position within slide:
Array4Onkism0809_liver_10297
raw data files:
Onkism0809_liver_10297.txt
Onkism0809_liver_10297_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62745


title: CWL1

description: Total RNA was extracted from liver, hypothalamus and mesenteric adipose using All-Prep DNA/RNA/miRNA Universal Kit (Qiagen, CA. USA) according to the manufacturer’s instructions, including treatment with DNase I. RNA quality was evaluated with Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA).  All RNA samples had RNA integrity number (RIN) over 8.


title: Coho smolt Liver_2809 [62914]

description:
Sample array position within slide:
Array1Onkism0809_liver_10298
raw data files:
Onkism0809_liver_10298.txt
Onkism0809_liver_10298_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62914


title: CFL15


title: 3642_CD4_Lung_50_S50_P1

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

tag: cell-id-sorted


title: Coho smolt Liver_2790 [62861]

description:
Sample array position within slide:
Array2Onkism0809_liver_10297
raw data files:
Onkism0809_liver_10297.txt
Onkism0809_liver_10297_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62861

tag: tissue


title: Coho smolt Liver_2794 [62803]

description:
Sample array position within slide:
Array3Onkism0809_liver_10297
raw data files:
Onkism0809_liver_10297.txt
Onkism0809_liver_10297_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62803


title: CFL14

tag: treatment


title: Coho smolt Liver_2786 [62915]

description:
Sample array position within slide:
Array1Onkism0809_liver_10297
raw data files:
Onkism0809_liver_10297.txt
Onkism0809_liver_10297_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62915

tag: FISH #


title: Coho smolt Liver_2762 [62778]

description:
Sample array position within slide:
Array3Onkism0809_liver_10327
raw data files:
Onkism0809_liver_10327.txt
Onkism0809_liver_10327_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62778

tag: fw/sw


title: Coho smolt Liver_2791 [62837]

description:
Sample array position within slide:
Array2Onkism0809_liver_10327
raw data files:
Onkism0809_liver_10327.txt
Onkism0809_liver_10327_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62837

tag: year


title: Coho smolt Liver_2785 [62851]

description:
Sample array position within slide:
Array2Onkism0809_liver_10309
raw data files:
Onkism0809_liver_10309.txt
Onkism0809_liver_10309_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62851

tag: season


title: Coho smolt Liver_2742 [62890]

description:
Sample array position within slide:
Array1Onkism0809_liver_10327
raw data files:
Onkism0809_liver_10327.txt
Onkism0809_liver_10327_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62890

tag: origin


title: 3642_CD4_Lung_82_S82_P1

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


title: Coho smolt Liver_2730 [62865]

description:
Sample array position within slide:
Array2Onkism0809_liver_10293
raw data files:
Onkism0809_liver_10293.txt
Onkism0809_liver_10293_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62865

tag: fork length (cm)


title: Coho smolt Liver_3155 [62791]

description:
Sample array position within slide:
Array3Onkism0809_liver_10311
raw data files:
Onkism0809_liver_10311.txt
Onkism0809_liver_10311_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62791

tag: total mass (g)


title: CFL13


title: Coho smolt Liver_2727 [62919]

description:
Sample array position within slide:
Array1Onkism0809_liver_10293
raw data files:
Onkism0809_liver_10293.txt
Onkism0809_liver_10293_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62919

tag: Sex


title: Coho smolt Liver_2728 [62835]

description:
Sample array position within slide:
Array3Onkism0809_liver_10087
raw data files:
Onkism0809_liver_10087.txt
Onkism0809_liver_10087_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62835

tag: latitude


title: Coho smolt Liver_2713 [62721]

description:
Sample array position within slide:
Array4Onkism0809_liver_10326
raw data files:
Onkism0809_liver_10326.txt
Onkism0809_liver_10326_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62721

tag: longitude


title: Coho smolt Liver_2763 [62905]

description:
Sample array position within slide:
Array1Onkism0809_liver_10309
raw data files:
Onkism0809_liver_10309.txt
Onkism0809_liver_10309_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62905

tag: sample type


title: 3642_Treg_Lung_96_S384_P1

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


title: 3642_CD4_Lung_91_S91_P1

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


title: CFL12

tag: strain


title: Coho smolt Liver_2698 [62794]

description:
Sample array position within slide:
Array3Onkism0809_liver_10308
raw data files:
Onkism0809_liver_10308.txt
Onkism0809_liver_10308_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62794


title: CFL11


title: CFL10


title: 3889_CD4_Lung_35_S323_P2

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

tag: mouse-id


title: 3889_CD4_Lung_54_S342_P2

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

tag: cell-id-assigned


title: 3889_CD4_Lung_48_S336_P2

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

tag: cell-id-sorted


title: FWHyp8

source_name: Hypothalamus tissue

value: FVB/NJ


title: 3889_CD4_Lung_74_S362_P2

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

tag: tissue


title: 3889_CD4_Lung_12_S300_P2

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


title: Coho smolt Liver_2705 [62795]

description:
Sample array position within slide:
Array3Onkism0809_liver_10307
raw data files:
Onkism0809_liver_10307.txt
Onkism0809_liver_10307_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62795


title: FWHyp2

description: Total RNA was extracted from liver, hypothalamus and mesenteric adipose using All-Prep DNA/RNA/miRNA Universal Kit (Qiagen, CA. USA) according to the manufacturer’s instructions, including treatment with DNase I. RNA quality was evaluated with Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA).  All RNA samples had RNA integrity number (RIN) over 8.

tag: treatment


title: FWHyp1


title: Coho smolt Liver_2701 [62906]

description:
Sample array position within slide:
Array1Onkism0809_liver_10308
raw data files:
Onkism0809_liver_10308.txt
Onkism0809_liver_10308_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62906

tag: FISH #


title: Coho smolt Liver_2712 [62724]

description:
Sample array position within slide:
Array4Onkism0809_liver_10320
raw data files:
Onkism0809_liver_10320.txt
Onkism0809_liver_10320_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62724

tag: fw/sw


title: 3889_CD4_Lung_60_S156_P1

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


title: FFHyp6


title: FWHyp9


title: Coho smolt Liver_2690 [62809]

description:
Sample array position within slide:
Array3Onkism0809_liver_10291
raw data files:
Onkism0809_liver_10291.txt
Onkism0809_liver_10291_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62809

tag: year


title: Coho smolt Liver_2665 [62852]

description:
Sample array position within slide:
Array2Onkism0809_liver_10308
raw data files:
Onkism0809_liver_10308.txt
Onkism0809_liver_10308_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62852

tag: season


title: Coho smolt Liver_2670 [62816]

description:
Sample array position within slide:
Array3Onkism0809_liver_10278
raw data files:
Onkism0809_liver_10278.txt
Onkism0809_liver_10278_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62816

tag: origin


title: Coho smolt Liver_2653 [62899]

description:
Sample array position within slide:
Array1Onkism0809_liver_10315
raw data files:
Onkism0809_liver_10315.txt
Onkism0809_liver_10315_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62899

tag: fork length (cm)


title: Coho smolt Liver_2650 [62871]

description:
Sample array position within slide:
Array2Onkism0809_liver_10287
raw data files:
Onkism0809_liver_10287.txt
Onkism0809_liver_10287_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62871

tag: total mass (g)


title: Coho smolt Liver_2674 [62736]

description:
Sample array position within slide:
Array4Onkism0809_liver_10308
raw data files:
Onkism0809_liver_10308.txt
Onkism0809_liver_10308_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62736

tag: Sex


title: Coho smolt Liver_2675 [62759]

description:
Sample array position within slide:
Array4Onkism0809_liver_10278
raw data files:
Onkism0809_liver_10278.txt
Onkism0809_liver_10278_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62759

tag: latitude


title: FFHyp5


title: 3889_CD4_Lung_6_S294_P2

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


title: Coho smolt Liver_2626 [62841]

description:
Sample array position within slide:
Array2Onkism0809_liver_10320
raw data files:
Onkism0809_liver_10320.txt
Onkism0809_liver_10320_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62841

tag: longitude


title: Coho smolt Liver_2658 [62746]

description:
Sample array position within slide:
Array4Onkism0809_liver_10296
raw data files:
Onkism0809_liver_10296.txt
Onkism0809_liver_10296_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62746

tag: sample type


title: Coho smolt Liver_2640 [62925]

description:
Sample array position within slide:
Array1Onkism0809_liver_10287
raw data files:
Onkism0809_liver_10287.txt
Onkism0809_liver_10287_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62925


title: Coho smolt Liver_2637 [62725]

description:
Sample array position within slide:
Array4Onkism0809_liver_10319
raw data files:
Onkism0809_liver_10319.txt
Onkism0809_liver_10319_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62725


title: Coho smolt Liver_2656 [62804]

description:
Sample array position within slide:
Array3Onkism0809_liver_10296
raw data files:
Onkism0809_liver_10296.txt
Onkism0809_liver_10296_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62804


title: Coho smolt Liver_2618 [62777]

description:
Sample array position within slide:
Array3Onkism0809_liver_10328
raw data files:
Onkism0809_liver_10328.txt
Onkism0809_liver_10328_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62777


title: Coho smolt Liver_2601 [62722]

description:
Sample array position within slide:
Array4Onkism0809_liver_10322
raw data files:
Onkism0809_liver_10322.txt
Onkism0809_liver_10322_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62722


title: 3889_CD4_Lung_39_S327_P2

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


title: FFHyp12

description: Total RNA was extracted from liver, hypothalamus and mesenteric adipose using All-Prep DNA/RNA/miRNA Universal Kit (Qiagen, CA. USA) according to the manufacturer’s instructions, including treatment with DNase I. RNA quality was evaluated with Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA).  All RNA samples had RNA integrity number (RIN) over 8.

tag: strain


title: Coho smolt Liver_2614 [62829]

description:
Sample array position within slide:
Array3Onkism0809_liver_10265
raw data files:
Onkism0809_liver_10265.txt
Onkism0809_liver_10265_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62829


title: Coho smolt Liver_2623 [62719]

description:
Sample array position within slide:
Array4Onkism0809_liver_10328
raw data files:
Onkism0809_liver_10328.txt
Onkism0809_liver_10328_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62719


title: FFHyp10


title: 3889_CD4_Lung_73_S361_P2

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

tag: mouse-id


title: 3889_CD4_Lung_70_S166_P1

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

tag: cell-id-assigned


title: DWHyp5


title: DWHyp4


title: 3889_CD4_Lung_95_S191_P1

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

tag: cell-id-sorted


title: Coho smolt Liver_2582 [62864]

description:
Sample array position within slide:
Array2Onkism0809_liver_10294
raw data files:
Onkism0809_liver_10294.txt
Onkism0809_liver_10294_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62864

tag: tissue


title: Coho smolt Liver_2577 [62847]

description:
Sample array position within slide:
Array2Onkism0809_liver_10314
raw data files:
Onkism0809_liver_10314.txt
Onkism0809_liver_10314_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62847


title: 3889_CD4_Lung_56_S344_P2

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


title: Coho smolt Liver_2360 [62887]

description:
Sample array position within slide:
Array2Onkism0809_liver_10101
raw data files:
Onkism0809_liver_10101.txt
Onkism0809_liver_10101_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62887

value: U

value: WCVI

value: Columbia


title: Coho smolt Liver_2315 [62849]

description:
Sample array position within slide:
Array2Onkism0809_liver_10312
raw data files:
Onkism0809_liver_10312.txt
Onkism0809_liver_10312_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62849

value: liver

value: SW


title: Coho smolt Liver_2593 [62784]

description:
Sample array position within slide:
Array3Onkism0809_liver_10318
raw data files:
Onkism0809_liver_10318.txt
Onkism0809_liver_10318_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62784

value: F


title: Coho smolt Liver_2314 [62902]

description:
Sample array position within slide:
Array1Onkism0809_liver_10312
raw data files:
Onkism0809_liver_10312.txt
Onkism0809_liver_10312_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62902

value: Pooled cRNA reference


title: DWHyp2

tag: treatment

value: Water


title: 3889_CD4_Lung_34_S322_P2

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


title: DWHyp3


title: Coho smolt Liver_2578 [62900]

description:
Sample array position within slide:
Array1Onkism0809_liver_10314
raw data files:
Onkism0809_liver_10314.txt
Onkism0809_liver_10314_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62900

tag: FISH #

value: Hatchery


title: DFHyp9


title: Coho smolt Liver_2289 [62785]

description:
Sample array position within slide:
Array3Onkism0809_liver_10317
raw data files:
Onkism0809_liver_10317.txt
Onkism0809_liver_10317_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62785

tag: fw/sw


title: 3889_CD4_Lung_33_S321_P2

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


title: Coho smolt Liver_2311 [62735]

description:
Sample array position within slide:
Array4Onkism0809_liver_10309
raw data files:
Onkism0809_liver_10309.txt
Onkism0809_liver_10309_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62735

tag: year

value: Oregon


title: DFHyp12


title: Coho smolt Liver_2944 [62918]

description:
Sample array position within slide:
Array1Onkism0809_liver_10294
raw data files:
Onkism0809_liver_10294.txt
Onkism0809_liver_10294_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62918

tag: season

value: Mainland

value: Fraser


title: Coho smolt Liver_2313 [62733]

description:
Sample array position within slide:
Array4Onkism0809_liver_10311
raw data files:
Onkism0809_liver_10311.txt
Onkism0809_liver_10311_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62733

tag: origin

value: North


title: 3889_CD4_Lung_18_S306_P2

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

value: Lung

value: Tconv


title: 3889_CD4_Lung_7_S295_P2

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


title: Coho smolt Liver_2287 [62897]

description:
Sample array position within slide:
Array1Onkism0809_liver_10317
raw data files:
Onkism0809_liver_10317.txt
Onkism0809_liver_10317_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62897

value: Wild

tag: fork length (cm)


title: Coho smolt Liver_2288 [62844]

description:
Sample array position within slide:
Array2Onkism0809_liver_10317
raw data files:
Onkism0809_liver_10317.txt
Onkism0809_liver_10317_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62844

tag: total mass (g)


title: Coho smolt Liver_2248 [62819]

description:
Sample array position within slide:
Array3Onkism0809_liver_10275
raw data files:
Onkism0809_liver_10275.txt
Onkism0809_liver_10275_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62819

tag: Sex


title: Coho smolt Liver_2361 [62910]

description:
Sample array position within slide:
Array1Onkism0809_liver_10302
raw data files:
Onkism0809_liver_10302.txt
Onkism0809_liver_10302_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62910

tag: latitude


title: 3889_CD4_Lung_10_S298_P2

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


title: Coho smolt Liver_2247 [62776]

description:
Sample array position within slide:
Array4Onkism0809_liver_10100
raw data files:
Onkism0809_liver_10100.txt
Onkism0809_liver_10100_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62776

tag: longitude


title: Coho smolt Liver_2239 [62840]

description:
Sample array position within slide:
Array2Onkism0809_liver_10321
raw data files:
Onkism0809_liver_10321.txt
Onkism0809_liver_10321_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62840

tag: sample type


title: 3889_CD4_Lung_24_S120_P1

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


title: DFHyp10

description: Total RNA was extracted from liver, hypothalamus and mesenteric adipose using All-Prep DNA/RNA/miRNA Universal Kit (Qiagen, CA. USA) according to the manufacturer’s instructions, including treatment with DNase I. RNA quality was evaluated with Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA).  All RNA samples had RNA integrity number (RIN) over 8.

tag: strain

value: Fructose


title: CWHyp4


title: 3889_CD4_Lung_92_S380_P2

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

tag: mouse-id


title: Coho smolt Liver_2153 [62893]

description:
Sample array position within slide:
Array1Onkism0809_liver_10321
raw data files:
Onkism0809_liver_10321.txt
Onkism0809_liver_10321_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62893

value: U

value: Salish


title: 3889_CD4_Lung_12_S108_P1

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

tag: cell-id-assigned


title: CWHyp3


title: CWHyp2


title: Coho smolt Liver_2286 [62839]

description:
Sample array position within slide:
Array2Onkism0809_liver_10322
raw data files:
Onkism0809_liver_10322.txt
Onkism0809_liver_10322_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62839

value: WCVI

value: Columbia


title: Coho smolt Liver_2134 [62740]

description:
Sample array position within slide:
Array4Onkism0809_liver_10302
raw data files:
Onkism0809_liver_10302.txt
Onkism0809_liver_10302_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62740

value: liver

value: SW


title: CWHyp1


title: 3889_CD4_Lung_32_S128_P1

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

tag: cell-id-sorted


title: DFHyp11


title: Coho smolt Liver_2130 [62728]

description:
Sample array position within slide:
Array4Onkism0809_liver_10316
raw data files:
Onkism0809_liver_10316.txt
Onkism0809_liver_10316_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62728

tag: tissue

value: ECVI

value: Pooled cRNA reference


title: Coho smolt Liver_2128 [62730]

description:
Sample array position within slide:
Array4Onkism0809_liver_10314
raw data files:
Onkism0809_liver_10314.txt
Onkism0809_liver_10314_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62730


title: Coho smolt Liver_2129 [62948]

description:
Sample array position within slide:
Array1Onkism0809_liver_10087
raw data files:
Onkism0809_liver_10087.txt
Onkism0809_liver_10087_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62948


title: Coho smolt Liver_2114 [62898]

description:
Sample array position within slide:
Array1Onkism0809_liver_10316
raw data files:
Onkism0809_liver_10316.txt
Onkism0809_liver_10316_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62898


title: Coho smolt Liver_2125 [62845]

description:
Sample array position within slide:
Array2Onkism0809_liver_10316
raw data files:
Onkism0809_liver_10316.txt
Onkism0809_liver_10316_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62845


title: 3889_CD4_Lung_59_S155_P1

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


title: Coho smolt Liver_2132 [62798]

description:
Sample array position within slide:
Array3Onkism0809_liver_10302
raw data files:
Onkism0809_liver_10302.txt
Onkism0809_liver_10302_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62798


title: CFHyp13

tag: treatment


title: CFHyp12


title: 3889_CD4_Lung_42_S330_P2

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


title: CFHyp11


title: 3889_CD4_Lung_80_S176_P1

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


title: 3889_CD4_Lung_64_S352_P2

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


title: 3889_CD4_Lung_79_S367_P2

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


title: Coho smolt Liver_2058 [62895]

description:
Sample array position within slide:
Array1Onkism0809_liver_10319
raw data files:
Onkism0809_liver_10319.txt
Onkism0809_liver_10319_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62895

tag: FISH #

value: Hatchery

value: M


title: Coho smolt Liver_2127 [62786]

description:
Sample array position within slide:
Array3Onkism0809_liver_10316
raw data files:
Onkism0809_liver_10316.txt
Onkism0809_liver_10316_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62786

tag: fw/sw


title: 3889_CD4_Lung_57_S153_P1

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


title: 3889_CD4_Lung_96_S192_P1

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


title: Coho smolt Liver_2126 [62775]

description:
Sample array position within slide:
Array4Onkism0809_liver_10101
raw data files:
Onkism0809_liver_10101.txt
Onkism0809_liver_10101_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62775

tag: year


title: FWM1

source_name: Mesenteric adipose tissue

extract_protocol:
Total RNA was extracted from hypothalamus and liver using All-Prep DNA/RNA/miRNA Universal Kit (Qiagen, CA. USA) according to the manufacturer’s instructions, including treatment with DNase I. RNA quality was evaluated with Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA).  All RNA samples had RNA integrity number (RIN) over 8.
Sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold Library Prep kit.

value: FVB/NJ

value: Water


title: CFHyp10


title: Coho smolt Liver_2131 [62856]

description:
Sample array position within slide:
Array2Onkism0809_liver_10302
raw data files:
Onkism0809_liver_10302.txt
Onkism0809_liver_10302_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62856

tag: season


title: FWM7


title: 3889_CD4_Lung_81_S369_P2

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


title: 3642_CD4_Lung_89_S89_P1

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


title: FFM6


title: Coho smolt Liver_2002 [62737]

description:
Sample array position within slide:
Array4Onkism0809_liver_10307
raw data files:
Onkism0809_liver_10307.txt
Onkism0809_liver_10307_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62737

tag: origin


title: Coho smolt Liver_1896 [62821]

description:
Sample array position within slide:
Array3Onkism0809_liver_10273
raw data files:
Onkism0809_liver_10273.txt
Onkism0809_liver_10273_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62821

tag: fork length (cm)

value: F


title: 3889_CD4_Lung_82_S178_P1

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

value: Lung


title: Coho smolt Liver_2033 [62939]

description:
Sample array position within slide:
Array1Onkism0809_liver_10268
raw data files:
Onkism0809_liver_10268.txt
Onkism0809_liver_10268_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62939

tag: total mass (g)

value: Mainland


title: Coho smolt Liver_1871 [62855]

description:
Sample array position within slide:
Array2Onkism0809_liver_10305
raw data files:
Onkism0809_liver_10305.txt
Onkism0809_liver_10305_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62855

value: Wild

tag: Sex


title: Coho smolt Liver_1946 [62764]

description:
Sample array position within slide:
Array4Onkism0809_liver_10273
raw data files:
Onkism0809_liver_10273.txt
Onkism0809_liver_10273_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62764

tag: latitude


title: Coho smolt Liver_1873 [62942]

description:
Sample array position within slide:
Array1Onkism0809_liver_10265
raw data files:
Onkism0809_liver_10265.txt
Onkism0809_liver_10265_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62942

tag: longitude


title: FFM21

value: Fructose


title: Coho smolt Liver_1885 [62894]

description:
Sample array position within slide:
Array1Onkism0809_liver_10320
raw data files:
Onkism0809_liver_10320.txt
Onkism0809_liver_10320_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62894

tag: sample type


title: Coho smolt Liver_1884 [62908]

description:
Sample array position within slide:
Array1Onkism0809_liver_10306
raw data files:
Onkism0809_liver_10306.txt
Onkism0809_liver_10306_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62908


title: Coho smolt Liver_2099 [62853]

description:
Sample array position within slide:
Array2Onkism0809_liver_10307
raw data files:
Onkism0809_liver_10307.txt
Onkism0809_liver_10307_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62853


title: Coho smolt Liver_2014 [62916]

description:
Sample array position within slide:
Array1Onkism0809_liver_10296
raw data files:
Onkism0809_liver_10296.txt
Onkism0809_liver_10296_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62916

value: Fraser


title: Coho smolt Liver_1693 [62765]

description:
Sample array position within slide:
Array4Onkism0809_liver_10272
raw data files:
Onkism0809_liver_10272.txt
Onkism0809_liver_10272_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62765

value: FW

value: U

value: puntledge

value: Salish


title: 3889_CD4_Lung_77_S365_P2

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

value: Tconv


title: Coho smolt Liver_1876 [62797]

description:
Sample array position within slide:
Array3Onkism0809_liver_10305
raw data files:
Onkism0809_liver_10305.txt
Onkism0809_liver_10305_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62797

value: liver

value: SW

value: ECVI


title: 3889_CD4_Lung_34_S130_P1

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


title: Coho smolt Liver_1915 [62796]

description:
Sample array position within slide:
Array3Onkism0809_liver_10306
raw data files:
Onkism0809_liver_10306.txt
Onkism0809_liver_10306_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62796

value: Hatchery

value: Pooled cRNA reference


title: FFM18

tag: strain

value: FVB/NJ


title: Coho smolt Liver_1690 [62842]

description:
Sample array position within slide:
Array2Onkism0809_liver_10319
raw data files:
Onkism0809_liver_10319.txt
Onkism0809_liver_10319_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62842


title: Coho smolt Liver_1877 [62739]

description:
Sample array position within slide:
Array4Onkism0809_liver_10305
raw data files:
Onkism0809_liver_10305.txt
Onkism0809_liver_10305_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62739

value: M


title: Coho smolt Liver_1691 [62825]

description:
Sample array position within slide:
Array3Onkism0809_liver_10269
raw data files:
Onkism0809_liver_10269.txt
Onkism0809_liver_10269_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62825


title: 3889_CD4_Lung_62_S158_P1

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

tag: mouse-id

value: Lung


title: FFM12


title: FFM11


title: 3889_CD4_Lung_50_S338_P2

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

tag: cell-id-assigned


title: 3889_CD4_Lung_58_S346_P2

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

tag: cell-id-sorted


title: DWM8

value: Water


title: Coho smolt Liver_1689 [62827]

description:
Sample array position within slide:
Array3Onkism0809_liver_10267
raw data files:
Onkism0809_liver_10267.txt
Onkism0809_liver_10267_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62827

tag: tissue


title: 3889_CD4_Lung_72_S168_P1

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


title: Coho smolt Liver_1687 [62882]

description:
Sample array position within slide:
Array2Onkism0809_liver_10267
raw data files:
Onkism0809_liver_10267.txt
Onkism0809_liver_10267_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62882


title: Coho smolt Liver_1688 [62726]

description:
Sample array position within slide:
Array4Onkism0809_liver_10318
raw data files:
Onkism0809_liver_10318.txt
Onkism0809_liver_10318_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62726


title: Coho smolt Liver_1686 [62940]

description:
Sample array position within slide:
Array1Onkism0809_liver_10267
raw data files:
Onkism0809_liver_10267.txt
Onkism0809_liver_10267_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62940


title: Coho smolt Liver_1692 [62822]

description:
Sample array position within slide:
Array3Onkism0809_liver_10272
raw data files:
Onkism0809_liver_10272.txt
Onkism0809_liver_10272_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62822


title: DWM4

tag: treatment


title: Coho smolt Liver_1685 [62771]

description:
Sample array position within slide:
Array4Onkism0809_liver_10266
raw data files:
Onkism0809_liver_10266.txt
Onkism0809_liver_10266_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62771

tag: FISH #


title: Coho smolt Liver_1684 [62828]

description:
Sample array position within slide:
Array3Onkism0809_liver_10266
raw data files:
Onkism0809_liver_10266.txt
Onkism0809_liver_10266_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62828

tag: fw/sw


title: 3889_CD4_Lung_30_S318_P2

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


title: FWM9


title: Coho smolt Liver_1624 [62883]

description:
Sample array position within slide:
Array2Onkism0809_liver_10266
raw data files:
Onkism0809_liver_10266.txt
Onkism0809_liver_10266_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62883

tag: year

value: F

value: chehalis

value: Mainland


title: 3889_CD4_Lung_65_S161_P1

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


title: Coho smolt Liver_1623 [62941]

description:
Sample array position within slide:
Array1Onkism0809_liver_10266
raw data files:
Onkism0809_liver_10266.txt
Onkism0809_liver_10266_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62941

value: FW

tag: season

value: Fraser


title: Coho smolt Liver_1617 [62801]

description:
Sample array position within slide:
Array3Onkism0809_liver_10299
raw data files:
Onkism0809_liver_10299.txt
Onkism0809_liver_10299_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62801

tag: origin


title: Coho smolt Liver_1621 [62858]

description:
Sample array position within slide:
Array2Onkism0809_liver_10300
raw data files:
Onkism0809_liver_10300.txt
Onkism0809_liver_10300_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62858

tag: fork length (cm)


title: 3889_CD4_Lung_23_S311_P2

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


title: Coho smolt Liver_1620 [62912]

description:
Sample array position within slide:
Array1Onkism0809_liver_10300
raw data files:
Onkism0809_liver_10300.txt
Onkism0809_liver_10300_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62912

tag: total mass (g)


title: DWM6


title: DWM2


title: Coho smolt Liver_1616 [62859]

description:
Sample array position within slide:
Array2Onkism0809_liver_10299
raw data files:
Onkism0809_liver_10299.txt
Onkism0809_liver_10299_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62859

tag: Sex


title: DWM1


title: Coho smolt Liver_1615 [62913]

description:
Sample array position within slide:
Array1Onkism0809_liver_10299
raw data files:
Onkism0809_liver_10299.txt
Onkism0809_liver_10299_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62913

tag: latitude


title: 3889_CD4_Lung_75_S363_P2

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


title: DWM3


title: 3889_CD4_Lung_55_S343_P2

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


title: 3889_CD4_Lung_41_S329_P2

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


title: DFM9

value: Fructose


title: DFM13


title: DFM12


title: 3889_CD4_Lung_81_S177_P1

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


title: Coho smolt Liver_1622 [62800]

description:
Sample array position within slide:
Array3Onkism0809_liver_10300
raw data files:
Onkism0809_liver_10300.txt
Onkism0809_liver_10300_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62800

tag: longitude


title: Coho smolt Liver_1555 [62833]

description:
Sample array position within slide:
Array3Onkism0809_liver_10101
raw data files:
Onkism0809_liver_10101.txt
Onkism0809_liver_10101_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62833

value: Wild

value: capilano

tag: sample type


title: Coho smolt Liver_1554 [62779]

description:
Sample array position within slide:
Array3Onkism0809_liver_10326
raw data files:
Onkism0809_liver_10326.txt
Onkism0809_liver_10326_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62779

value: liver


title: Coho smolt Liver_1552 [62838]

description:
Sample array position within slide:
Array2Onkism0809_liver_10326
raw data files:
Onkism0809_liver_10326.txt
Onkism0809_liver_10326_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62838


title: Coho smolt Liver_1551 [62867]

description:
Sample array position within slide:
Array2Onkism0809_liver_10291
raw data files:
Onkism0809_liver_10291.txt
Onkism0809_liver_10291_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62867


title: Coho smolt Liver_1550 [62921]

description:
Sample array position within slide:
Array1Onkism0809_liver_10291
raw data files:
Onkism0809_liver_10291.txt
Onkism0809_liver_10291_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62921

value: U


title: Coho smolt Liver_1549 [62752]

description:
Sample array position within slide:
Array4Onkism0809_liver_10290
raw data files:
Onkism0809_liver_10290.txt
Onkism0809_liver_10290_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62752


title: 3889_CD4_Lung_86_S374_P2

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

value: Tconv


title: Coho smolt Liver_1548 [62810]

description:
Sample array position within slide:
Array3Onkism0809_liver_10290
raw data files:
Onkism0809_liver_10290.txt
Onkism0809_liver_10290_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62810


title: DFM11

tag: strain


title: Coho smolt Liver_1547 [62868]

description:
Sample array position within slide:
Array2Onkism0809_liver_10290
raw data files:
Onkism0809_liver_10290.txt
Onkism0809_liver_10290_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62868


title: 3889_CD4_Lung_28_S124_P1

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

tag: mouse-id


title: CWM8


title: DFM10


title: 3889_CD4_Lung_36_S324_P2

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

tag: cell-id-assigned


title: Coho smolt Liver_1537 [62732]

description:
Sample array position within slide:
Array4Onkism0809_liver_10312
raw data files:
Onkism0809_liver_10312.txt
Onkism0809_liver_10312_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62732

value: Hatchery


title: CWM7


title: Coho smolt Liver_1543 [62891]

description:
Sample array position within slide:
Array1Onkism0809_liver_10326
raw data files:
Onkism0809_liver_10326.txt
Onkism0809_liver_10326_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62891

value: Pooled cRNA reference


title: Coho smolt Liver_1531 [62748]

description:
Sample array position within slide:
Array4Onkism0809_liver_10294
raw data files:
Onkism0809_liver_10294.txt
Onkism0809_liver_10294_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62748


title: Coho smolt Liver_1534 [62830]

description:
Sample array position within slide:
Array3Onkism0809_liver_10264
raw data files:
Onkism0809_liver_10264.txt
Onkism0809_liver_10264_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62830


title: Coho smolt Liver_1544 [62922]

description:
Sample array position within slide:
Array1Onkism0809_liver_10290
raw data files:
Onkism0809_liver_10290.txt
Onkism0809_liver_10290_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62922


title: Coho smolt Liver_1533 [62885]

description:
Sample array position within slide:
Array2Onkism0809_liver_10264
raw data files:
Onkism0809_liver_10264.txt
Onkism0809_liver_10264_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62885


title: Coho smolt Liver_1530 [62806]

description:
Sample array position within slide:
Array3Onkism0809_liver_10294
raw data files:
Onkism0809_liver_10294.txt
Onkism0809_liver_10294_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62806


title: 3889_CD4_Lung_44_S332_P2

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

tag: cell-id-sorted


title: 3889_CD4_Lung_9_S105_P1

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

tag: tissue


title: CWM5

tag: treatment


title: CFM15


title: 3889_CD4_Lung_93_S189_P1

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


title: 3889_CD4_Lung_78_S366_P2

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


title: 3889_CD4_Lung_83_S179_P1

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


title: CFM9


title: 72_4R

city: New York

first: Bin

last: Zhang

state: NY

address: 1470 Madison Ave

institute: Icahn School of Medicine At Mount Sinai

data_processing:
Fastqc for reads quality control
Qced reads were aligned to mm10 by STAR2.5.3a
ReadsPerGene file output by STAR2.5.3a was merged into a count matrix as the input for EdgeR package in R 3.3.2
differentially expressed genes were identified by EdgeR using a fold change >1.2, fdr<0.05
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include counts per gene for each sample

source_name: control

extract_protocol:
total RNA was extracted from infected midbrain tissue by Qiagen Rneasy mini kit. About 2ug RNA was sent for sequencing
1 ug of RNA was used for cDNA library construction at Novogene using an NEBNext® Ultra RNA Library Prep Kit for Illumina®(cat# E7420S, New England Biolabs, Ipswich, MA, USA) according to the manufacturer’s protocol. rRNA is removed using the Ribo-Zero kit that leaves the mRNA; mRNA from eukaryotic organisms is enriched using oligo(dT) beads

treatment_protocol: 2 month old male C57 mice were injected with 1ul 10^13gc/ml AAV that carries either Stmn2 shRNA or scrambled sequence unilaterally in the substantia nigra

value: midbrain

tag: age

value: 3 mo

value: male

tag: aav injected

value: scrambled


title: 3889_CD4_Lung_27_S315_P2

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

value: Lung


title: Coho smolt Liver_1536 [62790]

description:
Sample array position within slide:
Array3Onkism0809_liver_10312
raw data files:
Onkism0809_liver_10312.txt
Onkism0809_liver_10312_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62790

tag: FISH #

tag: fw/sw

tag: year


title: 72_3R

source_name: Stmn2 knockdown

value: Stmn2 knockdown


title: Coho smolt Liver_1535 [62773]

description:
Sample array position within slide:
Array4Onkism0809_liver_10264
raw data files:
Onkism0809_liver_10264.txt
Onkism0809_liver_10264_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62773

tag: season

tag: origin

tag: fork length (cm)

value: Mainland


title: 3889_CD4_Lung_68_S164_P1

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


title: CWM6

value: Water


title: 71_5R

tag: Sex


title: Coho smolt Liver_1434 [62945]

description:
Sample array position within slide:
Array1Onkism0809_liver_10102
raw data files:
Onkism0809_liver_10102.txt
Onkism0809_liver_10102_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62945

value: FW

tag: total mass (g)

tag: latitude

tag: longitude

value: salmon

value: Fraser


title: 71_2R

tag: strain


title: Coho smolt Liver_1529 [62909]

description:
Sample array position within slide:
Array1Onkism0809_liver_10305
raw data files:
Onkism0809_liver_10305.txt
Onkism0809_liver_10305_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62909

value: capilano

tag: sample type


title: 3889_CD4_Lung_63_S159_P1

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

tag: mouse-id

tag: cell-id-assigned

tag: cell-id-sorted


title: 3889_CD4_Lung_6_S102_P1

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

tag: tissue


title: Coho smolt Liver_1440 [62831]

description:
Sample array position within slide:
Array3Onkism0809_liver_10103
raw data files:
Onkism0809_liver_10103.txt
Onkism0809_liver_10103_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62831

value: liver

value: Wild

value: F


title: Coho smolt Liver_1528 [62780]

description:
Sample array position within slide:
Array3Onkism0809_liver_10322
raw data files:
Onkism0809_liver_10322.txt
Onkism0809_liver_10322_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62780

value: Hatchery

value: U


title: 70_3R

value: midbrain

tag: age

tag: aav injected


title: 3889_CD4_Lung_5_S101_P1

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

value: Tconv


title: Coho smolt Liver_796 [62879]

description:
Sample array position within slide:
Array2Onkism0809_liver_10272
raw data files:
Onkism0809_liver_10272.txt
Onkism0809_liver_10272_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62879

tag: FISH #

tag: fw/sw

value: SW

value: Pooled cRNA reference


title: Coho smolt Liver_1443 [62938]

description:
Sample array position within slide:
Array1Onkism0809_liver_10269
raw data files:
Onkism0809_liver_10269.txt
Onkism0809_liver_10269_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62938

tag: year

tag: season

value: M


title: Coho smolt Liver_1532 [62943]

description:
Sample array position within slide:
Array1Onkism0809_liver_10264
raw data files:
Onkism0809_liver_10264.txt
Onkism0809_liver_10264_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62943

tag: origin

tag: fork length (cm)


title: Coho smolt Liver_1438 [62944]

description:
Sample array position within slide:
Array1Onkism0809_liver_10103
raw data files:
Onkism0809_liver_10103.txt
Onkism0809_liver_10103_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62944

tag: total mass (g)

tag: Sex


title: Coho smolt Liver_1441 [62774]

description:
Sample array position within slide:
Array4Onkism0809_liver_10103
raw data files:
Onkism0809_liver_10103.txt
Onkism0809_liver_10103_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62774

tag: latitude

tag: longitude


title: Coho smolt Liver_1442 [62782]

description:
Sample array position within slide:
Array3Onkism0809_liver_10320
raw data files:
Onkism0809_liver_10320.txt
Onkism0809_liver_10320_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62782

tag: sample type


title: Coho smolt Liver_922 [62934]

description:
Sample array position within slide:
Array1Onkism0809_liver_10273
raw data files:
Onkism0809_liver_10273.txt
Onkism0809_liver_10273_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62934


title: 69_5R

value: 3 mo

value: male

tag: strain

value: Stmn2 knockdown


title: Coho smolt Liver_1436 [62832]

description:
Sample array position within slide:
Array3Onkism0809_liver_10102
raw data files:
Onkism0809_liver_10102.txt
Onkism0809_liver_10102_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62832

value: FW

value: Mainland


title: 3889_CD4_Lung_61_S349_P2

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

tag: mouse-id

value: Lung

tag: cell-id-assigned


title: Coho smolt Liver_766 [62805]

description:
Sample array position within slide:
Array3Onkism0809_liver_10295
raw data files:
Onkism0809_liver_10295.txt
Onkism0809_liver_10295_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62805

tag: tissue

value: Fraser


title: Coho smolt Liver_666 [62863]

description:
Sample array position within slide:
Array2Onkism0809_liver_10295
raw data files:
Onkism0809_liver_10295.txt
Onkism0809_liver_10295_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62863

value: liver


title: Coho smolt Liver_786 [62907]

description:
Sample array position within slide:
Array1Onkism0809_liver_10307
raw data files:
Onkism0809_liver_10307.txt
Onkism0809_liver_10307_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62907

value: Wild


title: Coho smolt Liver_785 [62747]

description:
Sample array position within slide:
Array4Onkism0809_liver_10295
raw data files:
Onkism0809_liver_10295.txt
Onkism0809_liver_10295_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62747

value: F

value: Columbia

value: North


title: Coho smolt Liver_663 [62917]

description:
Sample array position within slide:
Array1Onkism0809_liver_10295
raw data files:
Onkism0809_liver_10295.txt
Onkism0809_liver_10295_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62917


title: Coho smolt Liver_661 [62768]

description:
Sample array position within slide:
Array4Onkism0809_liver_10269
raw data files:
Onkism0809_liver_10269.txt
Onkism0809_liver_10269_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62768


title: Coho smolt Liver_576 [62789]

description:
Sample array position within slide:
Array3Onkism0809_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:
62789


title: 3889_CD4_Lung_20_S308_P2

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

tag: cell-id-sorted


title: 69_2R

value: midbrain

tag: age

tag: aav injected

value: scrambled


title: Coho smolt Liver_2098 [62862]

description:
Sample array position within slide:
Array2Onkism0809_liver_10296
raw data files:
Onkism0809_liver_10296.txt
Onkism0809_liver_10296_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62862

tag: FISH #

tag: fw/sw

value: SW

value: Hatchery


title: Coho smolt Liver_579 [62947]

description:
Sample array position within slide:
Array1Onkism0809_liver_10100
raw data files:
Onkism0809_liver_10100.txt
Onkism0809_liver_10100_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62947

tag: year

tag: season

value: Pooled cRNA reference


title: 3889_CD4_Lung_69_S165_P1

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

value: Tconv


title: 3889_CD4_Lung_84_S372_P2

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


title: S08_t12_rep2

city: New Haven

first: James

last: Noonan

state: CT

address: 333 Cedar St

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

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: 12 cell divisions

tag: replicate


title: S08_t8_rep2

value: 8 cell divisions


title: Coho smolt Liver_572 [62731]

description:
Sample array position within slide:
Array4Onkism0809_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:
62731

tag: origin

tag: fork length (cm)

tag: total mass (g)

tag: Sex

value: M


title: 3889_CD4_Lung_82_S370_P2

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


title: S08_t0_rep2

value: 0 cell divisions


title: Coho smolt Liver_99 [62935]

description:
Sample array position within slide:
Array1Onkism0809_liver_10272
raw data files:
Onkism0809_liver_10272.txt
Onkism0809_liver_10272_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62935

value: FW

value: U

tag: latitude

tag: longitude

value: chilliwack

tag: sample type


title: Coho smolt Liver_502 [62901]

description:
Sample array position within slide:
Array1Onkism0809_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:
62901

tag: tissue

value: liver

value: Wild

value: Mainland

value: Fraser


title: 3889_CD4_Lung_49_S337_P2

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

tag: mouse-id

value: Lung

tag: cell-id-assigned

tag: cell-id-sorted


title: Coho smolt Liver_101 [62826]

description:
Sample array position within slide:
Array3Onkism0809_liver_10268
raw data files:
Onkism0809_liver_10268.txt
Onkism0809_liver_10268_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62826

tag: FISH #


title: Coho smolt Liver_98 [62766]

description:
Sample array position within slide:
Array4Onkism0809_liver_10271
raw data files:
Onkism0809_liver_10271.txt
Onkism0809_liver_10271_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62766

tag: fw/sw


title: Coho smolt Liver_92 [62824]

description:
Sample array position within slide:
Array3Onkism0809_liver_10270
raw data files:
Onkism0809_liver_10270.txt
Onkism0809_liver_10270_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62824

tag: year


title: S08_t12_rep1


title: Coho smolt Liver_96 [62823]

description:
Sample array position within slide:
Array3Onkism0809_liver_10271
raw data files:
Onkism0809_liver_10271.txt
Onkism0809_liver_10271_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62823

tag: season


title: Coho smolt Liver_95 [62880]

description:
Sample array position within slide:
Array2Onkism0809_liver_10271
raw data files:
Onkism0809_liver_10271.txt
Onkism0809_liver_10271_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62880


title: Coho smolt Liver_94 [62936]

description:
Sample array position within slide:
Array1Onkism0809_liver_10271
raw data files:
Onkism0809_liver_10271.txt
Onkism0809_liver_10271_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62936


title: 3889_CD4_Lung_5_S293_P2

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


title: Coho smolt Liver_93 [62767]

description:
Sample array position within slide:
Array4Onkism0809_liver_10270
raw data files:
Onkism0809_liver_10270.txt
Onkism0809_liver_10270_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62767


title: Coho smolt Liver_40 [62753]

description:
Sample array position within slide:
Array4Onkism0809_liver_10289
raw data files:
Onkism0809_liver_10289.txt
Onkism0809_liver_10289_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62753


title: 3889_CD4_Lung_31_S127_P1

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


title: Coho smolt Liver_1618 [62743]

description:
Sample array position within slide:
Array4Onkism0809_liver_10299
raw data files:
Onkism0809_liver_10299.txt
Onkism0809_liver_10299_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62743

value: chehalis


title: S08_t8_rep1

tag: timepoint


title: S07_t12_rep2

tag: replicate


title: 3889_CD4_Lung_87_S375_P2

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


title: Coho smolt Liver_39 [62811]

description:
Sample array position within slide:
Array3Onkism0809_liver_10289
raw data files:
Onkism0809_liver_10289.txt
Onkism0809_liver_10289_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62811

tag: origin


title: Coho smolt Liver_35 [62754]

description:
Sample array position within slide:
Array4Onkism0809_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:
62754

tag: fork length (cm)


title: S08_t4_rep2

value: 4 cell divisions


title: S08_t4_rep1


title: S08_t0_rep1


title: 3889_CD4_Lung_85_S373_P2

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


title: S07_t8_rep2


title: Coho smolt Liver_38 [62869]

description:
Sample array position within slide:
Array2Onkism0809_liver_10289
raw data files:
Onkism0809_liver_10289.txt
Onkism0809_liver_10289_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62869

value: Hatchery

tag: total mass (g)


title: S07_t4_rep2


title: 3889_CD4_Lung_43_S331_P2

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


title: 3889_CD4_Lung_67_S355_P2

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


title: Coho smolt White muscle_4218 [65095]

description:
Sample array position within slide:
Array4Onkism0809_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:
65095

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

value: SW

tag: Sex

value: F

value: WCVI

source_name: white muscle from all samples in the series

value: Pooled cRNA reference


title: Coho smolt Liver_36 [62923]

description:
Sample array position within slide:
Array1Onkism0809_liver_10289
raw data files:
Onkism0809_liver_10289.txt
Onkism0809_liver_10289_ref.txt
*ref.txt is the raw file for the pooled reference sample
sample name in processed data file:
62923

tag: latitude


title: Coho smolt White muscle_4217 [65085]

description:
Sample array position within slide:
Array4Onkism0809_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:
65085

tag: longitude


title: Coho smolt Liver_34 [62812]

description:
Sample array position within slide:
Array3Onkism0809_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:
62812

tag: sample type