title: Coho smolt White muscle_40 [65070]

description:
Sample array position within slide:
Array3Onkism0809_WM_10491
raw data files:
Onkism0809_WM_10491.txt
Onkism0809_WM_10491_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65070

value: Hatchery

value: chilliwack


title: Coho smolt White muscle_38 [64979]

status: Public on Dec 03 2019

type: RNA

city: Nanaimo

first: Shaorong

last: Li

state: British Columbia

address: 3190 Hammond Bay Road

department: Salmon and Freshwater Ecosystems Division

country: Canada

institute: Fisheries and Oceans Canada

description:
Sample array position within slide:
Array2Onkism0809_WM_10445
raw data files:
Onkism0809_WM_10445.txt
Onkism0809_WM_10445_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64979

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_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.

label: Alexa 555

molecule: total RNA

organism: Oncorhynchus kisutch

source_name: white muscle

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: white muscle

tag: FISH #

tag: fw/sw

value: FW

tag: year

tag: season

tag: origin

tag: fork length (cm)

tag: total mass (g)

tag: Sex

value: U

tag: latitude

tag: longitude

label: Alexa 647

source_name: white muscle from all samples in the series

tag: sample type

value: Pooled cRNA reference


title: LPM1H7

type: SRA

city: Great Chesterford

first: Nicolas

last: Gambardella

state: Essex

address: Lewis House, Great Chesterford Court

country: United Kingdom

institute: aSciStance Ltd

library_source: transcriptomic

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

organism: Homo sapiens

source_name: engineered lateral mesoderm cell

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

tag: cell type

value: hPSC-derived lateral mesoderm

tag: es line


title: Coho smolt White muscle_97 [65004]

description:
Sample array position within slide:
Array2Onkism0809_WM_10471
raw data files:
Onkism0809_WM_10471.txt
Onkism0809_WM_10471_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65004

value: Wild


title: Coho smolt White muscle_95 [65113]

description:
Sample array position within slide:
Array4Onkism0809_WM_10470
raw data files:
Onkism0809_WM_10470.txt
Onkism0809_WM_10470_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65113


title: Coho smolt White muscle_36 [65088]

description:
Sample array position within slide:
Array4Onkism0809_WM_10444
raw data files:
Onkism0809_WM_10444.txt
Onkism0809_WM_10444_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65088


title: Coho smolt White muscle_98 [65059]

description:
Sample array position within slide:
Array3Onkism0809_WM_10471
raw data files:
Onkism0809_WM_10471.txt
Onkism0809_WM_10471_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65059


title: Coho smolt White muscle_37 [64922]

description:
Sample array position within slide:
Array1Onkism0809_WM_10445
raw data files:
Onkism0809_WM_10445.txt
Onkism0809_WM_10445_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64922


title: Coho smolt White muscle_35 [65034]

description:
Sample array position within slide:
Array3Onkism0809_WM_10444
raw data files:
Onkism0809_WM_10444.txt
Onkism0809_WM_10444_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65034


title: Coho smolt White muscle_34 [64978]

description:
Sample array position within slide:
Array2Onkism0809_WM_10444
raw data files:
Onkism0809_WM_10444.txt
Onkism0809_WM_10444_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64978


title: Coho smolt White muscle_33 [64921]

description:
Sample array position within slide:
Array1Onkism0809_WM_10444
raw data files:
Onkism0809_WM_10444.txt
Onkism0809_WM_10444_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64921


title: 3889_Treg_Lung_87_S87_P1

city: Cambridge

first: Rebecca

middle: H

last: Herbst

state: MA

address: 415 Main Street

department: Klarman Cell Observatory

country: USA

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)

organism: Mus musculus

source_name: mouse tissue

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

tag: mouse-id

value: Lung

tag: cell-id-assigned

value: Treg

tag: cell-id-sorted


title: Coho smolt White muscle_32 [65087]

description:
Sample array position within slide:
Array4Onkism0809_WM_10443
raw data files:
Onkism0809_WM_10443.txt
Onkism0809_WM_10443_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65087

tag: tissue


title: LPM1H5


title: LPM1H4


title: LPM1H3


title: 3889_Treg_Lung_40_S40_P1

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


title: Coho smolt Gill_4215 [73040]

description:
Sample array position within slide:
Array3OnneOnki_gill_10537
raw data files:
OnneOnki_gill_10537.txt
OnneOnki_gill_10537_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73040

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_gill_withallcontrols.txt includes Normalized log2 background-subtracted intensity ratio (each fish/reference) with 'flagged' spots or poor signals removed for all probes including controls. Sample tables do not include control probes.

source_name: gill

value: gill

tag: FISH #

value: SW

value: M

value: WCVI

source_name: gill from all samples in the series


title: 3889_Treg_Lung_84_S84_P1

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


title: LPM1H12


title: 3889_Treg_Lung_21_S21_P1

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


title: LPM1H2


title: LPM1H11


title: Coho smolt Gill_3311 [73115]

description:
Sample array position within slide:
Array4OnneOnki_gill_10547
raw data files:
OnneOnki_gill_10547.txt
OnneOnki_gill_10547_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73115

tag: fw/sw

value: Fraser


title: 3889_Treg_Lung_71_S71_P1

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


title: Coho smolt Gill_4207 [72907]

description:
Sample array position within slide:
Array1OnneOnki_gill_10532
raw data files:
OnneOnki_gill_10532.txt
OnneOnki_gill_10532_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72907

tag: year


title: LPM1H10


title: Coho smolt White muscle_31 [65033]

description:
Sample array position within slide:
Array3Onkism0809_WM_10443
raw data files:
Onkism0809_WM_10443.txt
Onkism0809_WM_10443_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65033

tag: season


title: 3889_Treg_Lung_12_S12_P1

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


title: Coho smolt Gill_3329 [72925]

description:
Sample array position within slide:
Array1OnneOnki_gill_10559
raw data files:
OnneOnki_gill_10559.txt
OnneOnki_gill_10559_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72925

tag: origin


title: Coho smolt Gill_3320 [73120]

description:
Sample array position within slide:
Array4OnneOnki_gill_10558
raw data files:
OnneOnki_gill_10558.txt
OnneOnki_gill_10558_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73120

tag: fork length (cm)

value: F


title: 3889_Treg_Lung_67_S67_P1

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


title: LPM1H1


title: Coho smolt Gill_3298 [72918]

description:
Sample array position within slide:
Array1OnneOnki_gill_10546
raw data files:
OnneOnki_gill_10546.txt
OnneOnki_gill_10546_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72918

tag: total mass (g)


title: Coho smolt Gill_3188 [73053]

description:
Sample array position within slide:
Array3OnneOnki_gill_10558
raw data files:
OnneOnki_gill_10558.txt
OnneOnki_gill_10558_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73053

tag: Sex


title: LPM1G9


title: Coho smolt Gill_3166 [72991]

description:
Sample array position within slide:
Array2OnneOnki_gill_10558
raw data files:
OnneOnki_gill_10558.txt
OnneOnki_gill_10558_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72991

tag: latitude


title: Coho smolt Gill_3233 [72924]

description:
Sample array position within slide:
Array1OnneOnki_gill_10558
raw data files:
OnneOnki_gill_10558.txt
OnneOnki_gill_10558_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72924

tag: longitude


title: Coho smolt Gill_3029 [73048]

description:
Sample array position within slide:
Array3OnneOnki_gill_10547
raw data files:
OnneOnki_gill_10547.txt
OnneOnki_gill_10547_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73048

tag: sample type


title: Coho smolt Gill_3299 [73106]

description:
Sample array position within slide:
Array4OnneOnki_gill_10536
raw data files:
OnneOnki_gill_10536.txt
OnneOnki_gill_10536_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73106


title: 3889_Treg_Lung_44_S44_P1

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


title: Coho smolt Gill_3232 [73119]

description:
Sample array position within slide:
Array4OnneOnki_gill_10557
raw data files:
OnneOnki_gill_10557.txt
OnneOnki_gill_10557_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73119


title: Coho smolt Gill_3020 [73039]

description:
Sample array position within slide:
Array3OnneOnki_gill_10536
raw data files:
OnneOnki_gill_10536.txt
OnneOnki_gill_10536_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73039


title: Coho smolt Gill_2944 [72986]

description:
Sample array position within slide:
Array2OnneOnki_gill_10547
raw data files:
OnneOnki_gill_10547.txt
OnneOnki_gill_10547_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72986


title: 3889_Treg_Lung_9_S9_P1

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


title: 3889_Treg_Lung_42_S42_P1

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


title: 3889_Treg_Lung_41_S41_P1

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


title: LPM1G7

tag: cell type


title: LPM1G6

tag: es line


title: Coho smolt Gill_2856 [73046]

description:
Sample array position within slide:
Array3OnneOnki_gill_10545
raw data files:
OnneOnki_gill_10545.txt
OnneOnki_gill_10545_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73046


title: Coho smolt Gill_2800 [73107]

description:
Sample array position within slide:
Array4OnneOnki_gill_10537
raw data files:
OnneOnki_gill_10537.txt
OnneOnki_gill_10537_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73107


title: Coho smolt White muscle_1622 [65116]

description:
Sample array position within slide:
Array4Onkism0809_WM_10473
raw data files:
Onkism0809_WM_10473.txt
Onkism0809_WM_10473_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
65116

value: chehalis


title: Coho smolt Gill_2857 [72977]

description:
Sample array position within slide:
Array2OnneOnki_gill_10536
raw data files:
OnneOnki_gill_10536.txt
OnneOnki_gill_10536_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72977


title: Coho smolt Gill_2794 [72974]

description:
Sample array position within slide:
Array2OnneOnki_gill_10532
raw data files:
OnneOnki_gill_10532.txt
OnneOnki_gill_10532_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72974

value: Hatchery


title: LPM1G4


title: 3889_Treg_Lung_46_S46_P1

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

tag: mouse-id


title: LPM1G3


title: 3889_Treg_Lung_95_S95_P1

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

tag: cell-id-assigned


title: LPM1G8


title: Coho smolt Gill_2786 [73098]

description:
Sample array position within slide:
Array4OnneOnki_gill_10527
raw data files:
OnneOnki_gill_10527.txt
OnneOnki_gill_10527_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73098


title: Coho smolt Gill_2727 [72917]

description:
Sample array position within slide:
Array1OnneOnki_gill_10545
raw data files:
OnneOnki_gill_10545.txt
OnneOnki_gill_10545_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72917


title: Coho smolt Gill_2921 [72979]

description:
Sample array position within slide:
Array2OnneOnki_gill_10540
raw data files:
OnneOnki_gill_10540.txt
OnneOnki_gill_10540_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72979


title: Coho smolt Gill_2728 [73105]

description:
Sample array position within slide:
Array4OnneOnki_gill_10535
raw data files:
OnneOnki_gill_10535.txt
OnneOnki_gill_10535_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73105


title: Coho smolt Gill_2905 [73036]

description:
Sample array position within slide:
Array3OnneOnki_gill_10532
raw data files:
OnneOnki_gill_10532.txt
OnneOnki_gill_10532_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73036


title: LPM1G2


title: 3889_Treg_Lung_68_S68_P1

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

tag: cell-id-sorted


title: LPM1G12


title: 3889_Treg_Lung_64_S64_P1

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

tag: tissue


title: LPM1G11


title: LPM1G10


title: Coho smolt Gill_2658 [73034]

description:
Sample array position within slide:
Array3OnneOnki_gill_10530
raw data files:
OnneOnki_gill_10530.txt
OnneOnki_gill_10530_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73034

tag: FISH #


title: 3889_Treg_Lung_49_S49_P1

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


title: Coho smolt White muscle_1442 [64941]

description:
Sample array position within slide:
Array1Onkism0809_WM_10466
raw data files:
Onkism0809_WM_10466.txt
Onkism0809_WM_10466_ref.txt
*ref.txt is the raw file for the pooled reference sample.
sample name in processed data file:
64941

tag: fw/sw

value: salmon


title: LPM1F9


title: Coho smolt Gill_2623 [73113]

description:
Sample array position within slide:
Array4OnneOnki_gill_10545
raw data files:
OnneOnki_gill_10545.txt
OnneOnki_gill_10545_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73113

tag: year


title: Coho smolt Gill_2675 [73038]

description:
Sample array position within slide:
Array3OnneOnki_gill_10535
raw data files:
OnneOnki_gill_10535.txt
OnneOnki_gill_10535_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73038

tag: season


title: Coho smolt Gill_2713 [73104]

description:
Sample array position within slide:
Array4OnneOnki_gill_10533
raw data files:
OnneOnki_gill_10533.txt
OnneOnki_gill_10533_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73104

tag: origin


title: Coho smolt Gill_2133 [73103]

description:
Sample array position within slide:
Array4OnneOnki_gill_10532
raw data files:
OnneOnki_gill_10532.txt
OnneOnki_gill_10532_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73103

tag: fork length (cm)


title: 3889_Treg_Lung_56_S56_P1

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


title: 3889_Treg_Lung_8_S8_P1

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


title: Coho smolt Gill_2247 [72969]

description:
Sample array position within slide:
Array2OnneOnki_gill_10527
raw data files:
OnneOnki_gill_10527.txt
OnneOnki_gill_10527_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72969

tag: total mass (g)


title: Coho smolt Gill_2134 [72916]

description:
Sample array position within slide:
Array1OnneOnki_gill_10544
raw data files:
OnneOnki_gill_10544.txt
OnneOnki_gill_10544_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72916

tag: Sex


title: Coho smolt Gill_2656 [73111]

description:
Sample array position within slide:
Array4OnneOnki_gill_10543
raw data files:
OnneOnki_gill_10543.txt
OnneOnki_gill_10543_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73111

tag: latitude


title: Coho smolt Gill_2248 [72975]

description:
Sample array position within slide:
Array2OnneOnki_gill_10533
raw data files:
OnneOnki_gill_10533.txt
OnneOnki_gill_10533_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72975

tag: longitude


title: Coho smolt Gill_1621 [73031]

description:
Sample array position within slide:
Array3OnneOnki_gill_10527
raw data files:
OnneOnki_gill_10527.txt
OnneOnki_gill_10527_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73031

tag: sample type


title: Coho smolt Gill_2014 [73094]

description:
Sample array position within slide:
Array4OnneOnki_gill_10523
raw data files:
OnneOnki_gill_10523.txt
OnneOnki_gill_10523_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73094


title: Coho smolt Gill_1620 [73069]

description:
Sample array position within slide:
Array4OnneOnki_gill_10416
raw data files:
OnneOnki_gill_10416.txt
OnneOnki_gill_10416_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73069


title: Coho smolt Gill_1624 [72984]

description:
Sample array position within slide:
Array2OnneOnki_gill_10545
raw data files:
OnneOnki_gill_10545.txt
OnneOnki_gill_10545_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72984


title: Coho smolt Gill_1619 [73029]

description:
Sample array position within slide:
Array3OnneOnki_gill_10525
raw data files:
OnneOnki_gill_10525.txt
OnneOnki_gill_10525_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73029


title: 3889_Treg_Lung_5_S5_P1

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


title: 3889_Treg_Lung_10_S10_P1

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


title: LPM1G1

tag: cell type


title: 3889_Treg_Lung_6_S6_P1

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


title: Coho smolt Gill_1617 [73027]

description:
Sample array position within slide:
Array3OnneOnki_gill_10523
raw data files:
OnneOnki_gill_10523.txt
OnneOnki_gill_10523_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73027


title: Coho smolt Gill_1616 [72937]

description:
Sample array position within slide:
Array2OnneOnki_gill_10413
raw data files:
OnneOnki_gill_10413.txt
OnneOnki_gill_10413_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72937


title: Coho smolt Gill_1615 [73026]

description:
Sample array position within slide:
Array3OnneOnki_gill_10521
raw data files:
OnneOnki_gill_10521.txt
OnneOnki_gill_10521_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73026


title: Coho smolt Gill_1618 [72873]

description:
Sample array position within slide:
Array1OnneOnki_gill_10415
raw data files:
OnneOnki_gill_10415.txt
OnneOnki_gill_10415_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72873


title: LPM1F7

tag: es line


title: 3889_Treg_Lung_28_S28_P1

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

tag: mouse-id


title: Coho smolt Gill_1442 [72877]

description:
Sample array position within slide:
Array1OnneOnki_gill_10480
raw data files:
OnneOnki_gill_10529.txt
OnneOnki_gill_10529_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72877


title: LPM1F6


title: LPM1F5


title: LPM1F4


title: 3889_Treg_Lung_96_S96_P1

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

tag: cell-id-assigned


title: LPM1F8


title: 3889_Treg_Lung_54_S54_P1

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

tag: cell-id-sorted


title: 3889_Treg_Lung_81_S81_P1

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

tag: tissue


title: LPM1F12


title: LPM1F2


title: 3889_Treg_Lung_61_S61_P1

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


title: Coho smolt Gill_1441 [73047]

description:
Sample array position within slide:
Array3OnneOnki_gill_10546
raw data files:
OnneOnki_gill_10546.txt
OnneOnki_gill_10546_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73047

tag: FISH #


title: LPM1F11


title: Coho smolt Gill_1012 [73114]

description:
Sample array position within slide:
Array4OnneOnki_gill_10546
raw data files:
OnneOnki_gill_10546.txt
OnneOnki_gill_10546_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73114

tag: fw/sw


title: Coho smolt Gill_1439 [73045]

description:
Sample array position within slide:
Array3OnneOnki_gill_10544
raw data files:
OnneOnki_gill_10544.txt
OnneOnki_gill_10544_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73045

tag: year


title: Coho smolt Gill_826 [72976]

description:
Sample array position within slide:
Array2OnneOnki_gill_10535
raw data files:
OnneOnki_gill_10535.txt
OnneOnki_gill_10535_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72976

tag: season


title: Coho smolt Gill_836 [73037]

description:
Sample array position within slide:
Array3OnneOnki_gill_10533
raw data files:
OnneOnki_gill_10533.txt
OnneOnki_gill_10533_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73037

tag: origin


title: Coho smolt Gill_824 [72985]

description:
Sample array position within slide:
Array2OnneOnki_gill_10546
raw data files:
OnneOnki_gill_10546.txt
OnneOnki_gill_10546_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72985

tag: fork length (cm)


title: LPM1F3


title: Coho smolt Gill_922 [73112]

description:
Sample array position within slide:
Array4OnneOnki_gill_10544
raw data files:
OnneOnki_gill_10544.txt
OnneOnki_gill_10544_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73112

tag: total mass (g)


title: LPM1F10


title: 3889_Treg_Lung_89_S89_P1

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


title: 3889_Treg_Lung_57_S57_P1

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


title: Coho smolt Gill_1435 [72982]

description:
Sample array position within slide:
Array2OnneOnki_gill_10543
raw data files:
OnneOnki_gill_10543.txt
OnneOnki_gill_10543_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72982

tag: Sex


title: Coho smolt Gill_796 [72908]

description:
Sample array position within slide:
Array1OnneOnki_gill_10533
raw data files:
OnneOnki_gill_10533.txt
OnneOnki_gill_10533_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72908

tag: latitude


title: Coho smolt Gill_797 [72983]

description:
Sample array position within slide:
Array2OnneOnki_gill_10544
raw data files:
OnneOnki_gill_10544.txt
OnneOnki_gill_10544_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72983

tag: longitude


title: Coho smolt Gill_785 [72901]

description:
Sample array position within slide:
Array1OnneOnki_gill_10525
raw data files:
OnneOnki_gill_10525.txt
OnneOnki_gill_10525_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72901

tag: sample type


title: Coho smolt Gill_811 [72909]

description:
Sample array position within slide:
Array1OnneOnki_gill_10535
raw data files:
OnneOnki_gill_10535.txt
OnneOnki_gill_10535_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72909


title: Coho smolt Gill_793 [72903]

description:
Sample array position within slide:
Array1OnneOnki_gill_10527
raw data files:
OnneOnki_gill_10527.txt
OnneOnki_gill_10527_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72903


title: Coho smolt Gill_786 [72940]

description:
Sample array position within slide:
Array2OnneOnki_gill_10416
raw data files:
OnneOnki_gill_10416.txt
OnneOnki_gill_10416_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72940


title: Coho smolt Gill_766 [73067]

description:
Sample array position within slide:
Array4OnneOnki_gill_10414
raw data files:
OnneOnki_gill_10414.txt
OnneOnki_gill_10414_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73067


title: LPM1F1

tag: cell type


title: 3889_Treg_Lung_36_S36_P1

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


title: 3889_Treg_Lung_30_S30_P1

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


title: LPM1E8

tag: es line


title: LPM1E6


title: 3889_Treg_Lung_93_S93_P1

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

tag: mouse-id


title: TILs_CD44+_PD+ rep 2

city: Bethesda

first: Assaf

last: Magen

state: MD

address: 37 Convent Dr

institute: NIH

description:
TILs_CD44+_PD+
CD44high CD4+ PD-1+ T cells were sorted and captured.
R2 read is biological, R1 and I1 (Index File) reads are technical.
processed data file: Genes.tsv

data_processing:
Basecalling was performed using RTA 1.12.4.2.
Sequencing reads were demultiplexed using Bcl2fastq 2.17.
10x data for scRNA samples are run through Cell Ranger software to produce the fastq files.
The fastq files are processed through the cellranger count to get differential expression counts.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_barcodes.tsv: Barcode Files.
Supplementary_files_format_and_content: Genes.tsv: Gene File.
Supplementary_files_format_and_content: *_matrix.mtx: Gene expression matrices.

source_name: tumor microenvironment

extract_protocol:
Single Cell 3 Reagent Kits v2 per the manufacturer instructions (10X Genomics).
Libraries were pooled and sequenced with paired-end reads of 26x57bp on a NextSeq500 sequencer (Illumina).

tag: strain/background

value: tumor microenvironment

value: CD44high CD4+ T cells

tag: time point

value: Day 14 after MC38-GP tumor injection


title: Coho smolt Gill_663 [73065]

description:
Sample array position within slide:
Array4OnneOnki_gill_10412
raw data files:
OnneOnki_gill_10412.txt
OnneOnki_gill_10412_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73065

tag: tissue

value: Pooled cRNA reference


title: Coho smolt Gill_579 [73044]

description:
Sample array position within slide:
Array3OnneOnki_gill_10543
raw data files:
OnneOnki_gill_10543.txt
OnneOnki_gill_10543_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73044

tag: FISH #


title: Coho smolt Gill_666 [72899]

description:
Sample array position within slide:
Array1OnneOnki_gill_10523
raw data files:
OnneOnki_gill_10523.txt
OnneOnki_gill_10523_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72899

tag: fw/sw

value: U


title: Coho smolt Gill_576 [73092]

description:
Sample array position within slide:
Array4OnneOnki_gill_10521
raw data files:
OnneOnki_gill_10521.txt
OnneOnki_gill_10521_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73092

tag: year

value: Wild


title: Coho smolt Gill_661 [72897]

description:
Sample array position within slide:
Array1OnneOnki_gill_10521
raw data files:
OnneOnki_gill_10521.txt
OnneOnki_gill_10521_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72897

tag: season


title: 3889_Treg_Lung_83_S83_P1

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

value: Lung

tag: cell-id-assigned

tag: cell-id-sorted


title: LPM1E9

value: hPSC-derived lateral mesoderm


title: LPM1E5


title: LCMV_GP66+ rep 2

description:
LCMV_GP66+
CD44high CD4+ GP66:I-Ab+ T cells were sorted and captured.
R2 read is biological, R1 and I1 (Index File) reads are technical.
processed data file: Genes.tsv

source_name: spleen

value: spleen

value: Day 7 after LCMV (Armstrong) infection


title: LPM1E7


title: Coho smolt Gill_99 [72943]

description:
Sample array position within slide:
Array2OnneOnki_gill_10480
raw data files:
OnneOnki_gill_10480.txt
OnneOnki_gill_10480_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72943

value: gill

value: FW

tag: origin

tag: fork length (cm)

tag: total mass (g)

value: chilliwack


title: Coho smolt Gill_552 [72902]

description:
Sample array position within slide:
Array1OnneOnki_gill_10526
raw data files:
OnneOnki_gill_10526.txt
OnneOnki_gill_10526_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72902

value: SW

tag: Sex

tag: latitude

tag: longitude

value: Fraser


title: Coho smolt Gill_532 [72939]

description:
Sample array position within slide:
Array2OnneOnki_gill_10415
raw data files:
OnneOnki_gill_10415.txt
OnneOnki_gill_10415_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72939

value: M

tag: sample type


title: Coho smolt Gill_572 [72941]

description:
Sample array position within slide:
Array2OnneOnki_gill_10417
raw data files:
OnneOnki_gill_10417.txt
OnneOnki_gill_10417_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72941

value: Hatchery


title: dLN_GP66+ rep 2

description:
dLN_GP66+
CD44high CD4+ GP66:I-Ab+ T cells were sorted and captured.
R2 read is biological, R1 and I1 (Index File) reads are technical.
processed data file: Genes.tsv

source_name: draining lymph nodes

value: draining lymph nodes

tag: cell type


title: TILs_CD44+_PD+ rep 1

description:
5_TILs-CD44+PD+
CD44high CD4+ PD-1+ T cells were sorted and captured.
R2 read is biological, R1 and I1 (Index File) reads are technical.
processed data file: Genes.tsv

tag: strain/background

value: tumor microenvironment

value: CD44high CD4+ T cells


title: LCMV_CD44+IL7R-

description:
3_Arm-CD44+IL7R-
CD44high CD4+ CD127low T cells were sorted and captured.
R2 read is biological, R1 and I1 (Index File) reads are technical.
processed data file: Genes.tsv

tag: time point


title: Coho smolt Gill_502 [72910]

description:
Sample array position within slide:
Array1OnneOnki_gill_10536
raw data files:
OnneOnki_gill_10536.txt
OnneOnki_gill_10536_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72910

tag: tissue

value: Pooled cRNA reference


title: LPM1E4

tag: es line


title: LPM1E12


title: LCMV_GP66+ rep 1

description:
2_Arm-GP66+
CD44high CD4+ GP66:I-Ab+ T cells were sorted and captured.
R2 read is biological, R1 and I1 (Index File) reads are technical.
processed data file: Genes.tsv


title: LPM1E3


title: Coho smolt Gill_97 [73006]

description:
Sample array position within slide:
Array3OnneOnki_gill_10416
raw data files:
OnneOnki_gill_10416.txt
OnneOnki_gill_10416_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73006

tag: FISH #

tag: fw/sw

value: U


title: LPM1E10


title: Coho smolt Gill_100 [72963]

description:
Sample array position within slide:
Array2OnneOnki_gill_10521
raw data files:
OnneOnki_gill_10521.txt
OnneOnki_gill_10521_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72963

tag: year

tag: season

value: Wild


title: Coho smolt Gill_94 [72965]

description:
Sample array position within slide:
Array2OnneOnki_gill_10523
raw data files:
OnneOnki_gill_10523.txt
OnneOnki_gill_10523_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72965


title: Coho smolt Gill_96 [72967]

description:
Sample array position within slide:
Array2OnneOnki_gill_10525
raw data files:
OnneOnki_gill_10525.txt
OnneOnki_gill_10525_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72967


title: Coho smolt Gill_7 [73097]

description:
Sample array position within slide:
Array4OnneOnki_gill_10526
raw data files:
OnneOnki_gill_10526.txt
OnneOnki_gill_10526_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73097


title: HCT116_5p-UTR_Lib B_Unsorted_Replicate 2 (HM34)

city: Dallas

first: Joshua

last: Mendell

state: TX

address: 6000 Harry Hines Blvd., NA6.200A

department: Molecular Biology

institute: UT Southwestern Medical Center

description: sgRNA sequence amplified out of genomic DNA

library_source: genomic

data_processing:
Library strategy: CRISPR/Cas9-mediated loss of function screening
Reads were mapped to GeCKO v2 library sgRNA reference files.
Normalized read counts were calculated as described in Shalem et al., Science, 2014.
MAGeCK (Li et al., Genome Biology, 2014) was used to assign significance to each gene targeted by the sgRNAs in the GeCKO library.
The gene NFE2L2 was removed from our analysis due to contaminant reads arising from cloning sgRNAs targeting NFE2L2 into the LCv2 vector.
Genome_build: GeCKO v2 library sgRNA reference files obtained from Addgene
Supplementary_files_format_and_content: A table of normalized read counts for each sgRNA in each sample is provided.

molecule: genomic DNA

source_name: HCT116 colon cancer cell line

growth_protocol: Fluorescent-reporter coupled CRISPR/Cas9-mediated loss of function screening was carried out as described in Golden et al., Nature, 2017, in both MYC 5' UTR and control EGFP reporter cell lines. Reporter cell line generation is described in the manuscript.

extract_protocol:
Genomic DNA was extracted from cell pellets using either a gDNA isolation method that has been previously described Golden et al., Nature, 2017 for the sorted cells or the DNeasy Blood and Tissue Kit (Qiagen) for the unsorted cells.
PCR amplicon libraries were generated as described in Golden et al., Nature, 2017.

tag: reporter cell line

value: MYC 5' UTR reporter

tag: lentiviral library received

value: GeCKO v2_Library B

value: HCT116 colon cancer cell line


title: Coho smolt Gill_503 [72919]

description:
Sample array position within slide:
Array1OnneOnki_gill_10547
raw data files:
OnneOnki_gill_10547.txt
OnneOnki_gill_10547_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72919

tag: origin

tag: fork length (cm)

value: F


title: LPM1E2

value: hPSC-derived lateral mesoderm


title: Coho smolt Gill_93 [72871]

description:
Sample array position within slide:
Array1OnneOnki_gill_10413
raw data files:
OnneOnki_gill_10413.txt
OnneOnki_gill_10413_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72871

value: gill

value: FW

tag: total mass (g)

tag: Sex


title: Coho smolt Gill_5 [73095]

description:
Sample array position within slide:
Array4OnneOnki_gill_10524
raw data files:
OnneOnki_gill_10524.txt
OnneOnki_gill_10524_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73095

tag: latitude

tag: longitude

value: chilliwack


title: Coho smolt Gill_36 [72875]

description:
Sample array position within slide:
Array1OnneOnki_gill_10417
raw data files:
OnneOnki_gill_10417.txt
OnneOnki_gill_10417_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72875

tag: sample type


title: LPM1E1

tag: cell type


title: Coho smolt Gill_6 [72874]

description:
Sample array position within slide:
Array1OnneOnki_gill_10416
raw data files:
OnneOnki_gill_10416.txt
OnneOnki_gill_10416_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72874


title: HCT116_5p-UTR_Lib A_Unsorted_Replicate 2 (HM33)

value: GeCKO v2_Library A


title: Coho smolt Brain_4218 [56058]

description:
Sample array position within slide:
Array4Onkism0809_B_10114
raw data files:
Onkism0809_B_10114.txt
Onkism0809_B_10114_ref.txt
sample name in processed data file:
56058
*ref.txt file is the raw data for channel 2 (pooled reference.

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_brain_withallcontrols.txt includes normalized log2 background-subtracted intensity ratio (each fish/reference) with 'flagged' spots or poor signals removed for all probes including controls. Sample data tables do not include control probes.

source_name: brain

value: SW

value: WCVI

source_name: brain from all samples in the series


title: Coho smolt Gill_101 [72915]

description:
Sample array position within slide:
Array1OnneOnki_gill_10543
raw data files:
OnneOnki_gill_10543.txt
OnneOnki_gill_10543_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72915


title: HCT116_5p-UTR_Lib A_Bright_Replicate 2 (HM27)


title: Coho smolt Brain_4217 [56251]

description:
Sample array position within slide:
Array1Onkism0809_B_10092
raw data files:
Onkism0809_B_10092.txt
Onkism0809_B_10092_ref.txt
sample name in processed data file:
56251
*ref.txt file is the raw data for channel 2 (pooled reference.

value: Hatchery


title: LPM1E11


title: HCT116_EGFP_Lib B_Bright_Replicate 2 (HM7)

value: control EGFP reporter


title: Coho smolt Gill_8 [72876]

description:
Sample array position within slide:
Array1OnneOnki_gill_10418
raw data files:
OnneOnki_gill_10418.txt
OnneOnki_gill_10418_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
72876


title: Coho smolt Brain_4216 [56177]

description:
Sample array position within slide:
Array2Onkism0809_B_10113
raw data files:
Onkism0809_B_10113.txt
Onkism0809_B_10113_ref.txt
sample name in processed data file:
56177
*ref.txt file is the raw data for channel 2 (pooled reference.

value: North


title: Coho smolt Gill_4 [73004]

description:
Sample array position within slide:
Array3OnneOnki_gill_10414
raw data files:
OnneOnki_gill_10414.txt
OnneOnki_gill_10414_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73004

value: Pooled cRNA reference


title: dLN_GP66+ rep 1

description:
1_dLN-GP66+
CD44high CD4+ GP66:I-Ab+ T cells were sorted and captured.
R2 read is biological, R1 and I1 (Index File) reads are technical.
processed data file: Genes.tsv

tag: strain/background

value: draining lymph nodes

value: CD44high CD4+ T cells

tag: time point

value: Day 14 after MC38-GP tumor injection


title: Coho smolt Gill_3 [73093]

description:
Sample array position within slide:
Array4OnneOnki_gill_10522
raw data files:
OnneOnki_gill_10522.txt
OnneOnki_gill_10522_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73093

tag: tissue

value: U


title: LPM1D7

tag: es line


title: Coho smolt Gill_1 [73091]

description:
Sample array position within slide:
Array4OnneOnki_gill_10520
raw data files:
OnneOnki_gill_10520.txt
OnneOnki_gill_10520_ref.txt
*ref.txt files are the raw files for the pooled reference samples.
sample name in processed data file:
73091

tag: FISH #

tag: fw/sw


title: LPM1D9


title: LPM1D6


title: LPM1D8


title: HCT116_EGFP_Lib B_Unsorted_Replicate 2 (HM12)

value: GeCKO v2_Library B

value: HCT116 colon cancer cell line


title: HCT116_5p-UTR_Lib A_Bright_Replicate 1 (HM23)

value: MYC 5' UTR reporter


title: HCT116_EGFP_Lib A_Unsorted_Replicate 2 (HM11)


title: HCT116_5p-UTR_Lib B_Unsorted_Replicate 1 (HM32)


title: HCT116_EGFP_Lib A_Bright_Replicate 2 (HM5)


title: Coho smolt Brain_4215 [56070]

description:
Sample array position within slide:
Array4Onkism0809_B_10094
raw data files:
Onkism0809_B_10094.txt
Onkism0809_B_10094_ref.txt
sample name in processed data file:
56070
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: year

tag: season

value: M


title: HCT116_5p-UTR_Lib B_Bright_Replicate 1 (HM25)

tag: reporter cell line

tag: lentiviral library received


title: Coho smolt Brain_4125 [56236]

description:
Sample array position within slide:
Array1Onkism0809_B_10115
raw data files:
Onkism0809_B_10115.txt
Onkism0809_B_10115_ref.txt
sample name in processed data file:
56236
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: origin

value: Wild

tag: fork length (cm)

value: Fraser


title: Coho smolt Brain_4207 [56130]

description:
Sample array position within slide:
Array3Onkism0809_B_10089
raw data files:
Onkism0809_B_10089.txt
Onkism0809_B_10089_ref.txt
sample name in processed data file:
56130
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: total mass (g)

tag: Sex


title: Coho smolt Brain_4213 [56252]

description:
Sample array position within slide:
Array1Onkism0809_B_10091
raw data files:
Onkism0809_B_10091.txt
Onkism0809_B_10091_ref.txt
sample name in processed data file:
56252
*ref.txt file is the raw data for channel 2 (pooled reference.

value: F

tag: latitude

tag: longitude


title: HCT116_5p-UTR_Lib A_Unsorted_Replicate 1 (HM31)

description: sgRNA sequence amplified out of genomic DNA

value: GeCKO v2_Library A


title: Coho smolt Brain_3712 [56105]

description:
Sample array position within slide:
Array3Onkism0809_B_10128
raw data files:
Onkism0809_B_10128.txt
Onkism0809_B_10128_ref.txt
sample name in processed data file:
56105
*ref.txt file is the raw data for channel 2 (pooled reference.

value: SW

value: WCVI

value: ECVI

tag: sample type


title: Coho smolt Brain_3538 [56051]

description:
Sample array position within slide:
Array4Onkism0809_B_10124
raw data files:
Onkism0809_B_10124.txt
Onkism0809_B_10124_ref.txt
sample name in processed data file:
56051
*ref.txt file is the raw data for channel 2 (pooled reference.

value: North


title: Coho smolt Brain_3628 [56226]

description:
Sample array position within slide:
Array1Onkism0809_B_10128
raw data files:
Onkism0809_B_10128.txt
Onkism0809_B_10128_ref.txt
sample name in processed data file:
56226
*ref.txt file is the raw data for channel 2 (pooled reference.

value: Oregon

value: Pooled cRNA reference


title: LPM1D5

tag: cell type

value: hPSC-derived lateral mesoderm


title: Coho smolt Brain_4128 [56250]

description:
Sample array position within slide:
Array1Onkism0809_B_10093
raw data files:
Onkism0809_B_10093.txt
Onkism0809_B_10093_ref.txt
sample name in processed data file:
56250
*ref.txt file is the raw data for channel 2 (pooled reference.


title: HCT116_EGFP_Lib B_Bright_Replicate 1 (HM3)

value: control EGFP reporter


title: Coho smolt Brain_3537 [56038]

description:
Sample array position within slide:
Array4Onkism0809_B_10167
raw data files:
Onkism0809_B_10167.txt
Onkism0809_B_10167_ref.txt
sample name in processed data file:
56038
*ref.txt file is the raw data for channel 2 (pooled reference.

value: Columbia


title: Coho smolt Brain_3329 [56159]

description:
Sample array position within slide:
Array2Onkism0809_B_10136
raw data files:
Onkism0809_B_10136.txt
Onkism0809_B_10136_ref.txt
sample name in processed data file:
56159
*ref.txt file is the raw data for channel 2 (pooled reference.


title: LPM1D3


title: Coho smolt Brain_3356 [56110]

description:
Sample array position within slide:
Array3Onkism0809_B_10123
raw data files:
Onkism0809_B_10123.txt
Onkism0809_B_10123_ref.txt
sample name in processed data file:
56110
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_4129 [56238]

description:
Sample array position within slide:
Array1Onkism0809_B_10113
raw data files:
Onkism0809_B_10113.txt
Onkism0809_B_10113_ref.txt
sample name in processed data file:
56238
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_3534 [56204]

description:
Sample array position within slide:
Array1Onkism0809_B_10184
raw data files:
Onkism0809_B_10184.txt
Onkism0809_B_10184_ref.txt
sample name in processed data file:
56204
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_3530 [56173]

description:
Sample array position within slide:
Array2Onkism0809_B_10120
raw data files:
Onkism0809_B_10120.txt
Onkism0809_B_10120_ref.txt
sample name in processed data file:
56173
*ref.txt file is the raw data for channel 2 (pooled reference.


title: LPM1D11


title: Coho smolt Brain_3511 [56084]

description:
Sample array position within slide:
Array3Onkism0809_B_10198
raw data files:
Onkism0809_B_10198.txt
Onkism0809_B_10198_ref.txt
sample name in processed data file:
56084
*ref.txt file is the raw data for channel 2 (pooled reference.


title: LPM1D1


title: LPM1D4


title: LPM1D2


title: LPM1C9


title: RNA-seq_NT_g2

description: mRNA

data_processing:
Reads were mapped to reference genome using HISAT2.1.0
Number of reads mapped to each transcript were estimated using featurecounts v1.6.0
Genome_build: GRCh38

growth_protocol: HCT116 cells were infected with lentivirus to deliver Cas9 and sgRNAs targeting either EIF5A or DOHH, or non-target sgRNAs. Successfully transduced cells were selected in puromycin for 6 days, before harvesting for both ribosome profiling and RNA-sequencing as described in McGlincy and Ingolia, Methods, 2017.

extract_protocol:
Cells were harvested in lysis buffer and RNA was extracted using the Direct-zol RNA miniprep kit (Zymoresearch) as described in McGlincy and Ingolia, Methods, 2017.
RNA-seq libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit (Illumina) and sequenced using the 75 bp single-read protocol on a NextSeq 500 platform (Illumina).

treatment_protocol: N/A.

tag: genotype

tag: sgrna received

value: NT sgRNA #2


title: Coho smolt Brain_3250 [56044]

description:
Sample array position within slide:
Array4Onkism0809_B_10131
raw data files:
Onkism0809_B_10131.txt
Onkism0809_B_10131_ref.txt
sample name in processed data file:
56044
*ref.txt file is the raw data for channel 2 (pooled reference.

value: Hatchery


title: Coho smolt Brain_3308 [56232]

description:
Sample array position within slide:
Array1Onkism0809_B_10122
raw data files:
Onkism0809_B_10122.txt
Onkism0809_B_10122_ref.txt
sample name in processed data file:
56232
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_3299 [56247]

description:
Sample array position within slide:
Array1Onkism0809_B_10104
raw data files:
Onkism0809_B_10104.txt
Onkism0809_B_10104_ref.txt
sample name in processed data file:
56247
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_3237 [56125]

description:
Sample array position within slide:
Array3Onkism0809_B_10095
raw data files:
Onkism0809_B_10095.txt
Onkism0809_B_10095_ref.txt
sample name in processed data file:
56125
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_3188 [56169]

description:
Sample array position within slide:
Array2Onkism0809_B_10124
raw data files:
Onkism0809_B_10124.txt
Onkism0809_B_10124_ref.txt
sample name in processed data file:
56169
*ref.txt file is the raw data for channel 2 (pooled reference.


title: LPM1D12

tag: es line


title: HCT116_EGFP_Lib A_Bright_Replicate 1 (HM1)

description: sgRNA sequence amplified out of genomic DNA

tag: tissue

value: HCT116 colon cancer cell line


title: Coho smolt Brain_3311 [56200]

description:
Sample array position within slide:
Array1Onkism0809_B_10200
raw data files:
Onkism0809_B_10200.txt
Onkism0809_B_10200_ref.txt
sample name in processed data file:
56200
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: FISH #

tag: fw/sw

value: M


title: HCT116_EGFP_Lib B_Unsorted_Replicate 1 (HM10)

value: GeCKO v2_Library B


title: LPM1D10


title: RNA-seq_DOHH_g2

description: mRNA

value: DOHH-/-

value: DOHH sgRNA #2


title: HCT116_EGFP_Lib A_Unsorted_Replicate 1 (HM9)

value: GeCKO v2_Library A


title: Coho smolt Brain_3240 [56161]

description:
Sample array position within slide:
Array2Onkism0809_B_10133
raw data files:
Onkism0809_B_10133.txt
Onkism0809_B_10133_ref.txt
sample name in processed data file:
56161
*ref.txt file is the raw data for channel 2 (pooled reference.

value: SW

tag: year

tag: season

value: F


title: LPM1C7


title: Coho smolt Brain_3232 [56101]

description:
Sample array position within slide:
Array3Onkism0809_B_10134
raw data files:
Onkism0809_B_10134.txt
Onkism0809_B_10134_ref.txt
sample name in processed data file:
56101
*ref.txt file is the raw data for channel 2 (pooled reference.

value: Wild


title: RNA-seq_NT_g1

description: mRNA

value: NT sgRNA #1


title: RNA-seq_DOHH_g1

description: mRNA

value: DOHH sgRNA #1


title: LPM1C6


title: LPM1C8


title: LPM1C5


title: RNA-seq_EIF5A_g2

description: mRNA

value: EIF5A sgRNA #2


title: LPM1C4

value: hPSC-derived lateral mesoderm


title: HCT116_5p-UTR_Lib B_Bright_Replicate 2 (HM29)

tag: reporter cell line

value: MYC 5' UTR reporter

tag: lentiviral library received


title: RNA-seq_EIF5A_g1

description: mRNA

value: EIF5A sgRNA #1


title: Ribo.prof._NT_g2

description: ribosome protected mRNA fragments

data_processing:
Library strategy: Ribosome profiling
For each sample, fastq files from two runs were combined
Adapter was trimmed using custom scripts
Reads that mapped to noncoding RNA were discarded
Reads were mapped to human reference genome using HISAT2.1.0
Uniquely mapped reads between 24 and 31nt were kept
Genome_build: GRCh38

extract_protocol:
Ribosome protected fragments were isolated as described in McGlincy and Ingolia, Methods, 2017.
Ribosome profiling libraries were prepared as described in Ingolia et al., Nature Protocols, 2012, and McGlincy and Ingolia, Methods, 2017, and sequenced on a NextSeq500 platform.

value: NT sgRNA #2


title: Ribo.prof._NT_g1

description: ribosome protected mRNA fragments


title: LPM1C3


title: LPM1C2


title: Ribo.prof._DOHH_g2

description: ribosome protected mRNA fragments


title: LPM1C12


title: Ribo.prof._DOHH_g1

description: ribosome protected mRNA fragments


title: LPM1C11


title: Ribo.prof._EIF5A_g2

description: ribosome protected mRNA fragments


title: LPM1C10


title: Ribo.prof._EIF5A_g1

description: ribosome protected mRNA fragments


title: Coho smolt Brain_3233 [56042]

description:
Sample array position within slide:
Array4Onkism0809_B_10136
raw data files:
Onkism0809_B_10136.txt
Onkism0809_B_10136_ref.txt
sample name in processed data file:
56042
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: origin

value: Hatchery

tag: fork length (cm)

value: Fraser

value: Pooled cRNA reference


title: Coho smolt Brain_3166 [56158]

description:
Sample array position within slide:
Array2Onkism0809_B_10137
raw data files:
Onkism0809_B_10137.txt
Onkism0809_B_10137_ref.txt
sample name in processed data file:
56158
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: total mass (g)

tag: Sex


title: Coho smolt Brain_3320 [56025]

description:
Sample array position within slide:
Array4Onkism0809_B_10201
raw data files:
Onkism0809_B_10201.txt
Onkism0809_B_10201_ref.txt
sample name in processed data file:
56025
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: latitude

tag: longitude


title: Coho smolt Brain_3159 [56083]

description:
Sample array position within slide:
Array3Onkism0809_B_10200
raw data files:
Onkism0809_B_10200.txt
Onkism0809_B_10200_ref.txt
sample name in processed data file:
56083
*ref.txt file is the raw data for channel 2 (pooled reference.

value: M

value: ECVI

tag: sample type


title: Coho smolt Brain_3184 [56082]

description:
Sample array position within slide:
Array3Onkism0809_B_10201
raw data files:
Onkism0809_B_10201.txt
Onkism0809_B_10201_ref.txt
sample name in processed data file:
56082
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_3124 [56165]

description:
Sample array position within slide:
Array2Onkism0809_B_10128
raw data files:
Onkism0809_B_10128.txt
Onkism0809_B_10128_ref.txt
sample name in processed data file:
56165
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_3155 [56171]

description:
Sample array position within slide:
Array2Onkism0809_B_10122
raw data files:
Onkism0809_B_10122.txt
Onkism0809_B_10122_ref.txt
sample name in processed data file:
56171
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_3005 [56128]

description:
Sample array position within slide:
Array3Onkism0809_B_10092
raw data files:
Onkism0809_B_10092.txt
Onkism0809_B_10092_ref.txt
sample name in processed data file:
56128
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_3187 [56026]

description:
Sample array position within slide:
Array4Onkism0809_B_10200
raw data files:
Onkism0809_B_10200.txt
Onkism0809_B_10200_ref.txt
sample name in processed data file:
56026
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_3064 [56227]

description:
Sample array position within slide:
Array1Onkism0809_B_10127
raw data files:
Onkism0809_B_10127.txt
Onkism0809_B_10127_ref.txt
sample name in processed data file:
56227
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_3105 [56224]

description:
Sample array position within slide:
Array1Onkism0809_B_10130
raw data files:
Onkism0809_B_10130.txt
Onkism0809_B_10130_ref.txt
sample name in processed data file:
56224
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_3020 [56249]

description:
Sample array position within slide:
Array1Onkism0809_B_10094
raw data files:
Onkism0809_B_10094.txt
Onkism0809_B_10094_ref.txt
sample name in processed data file:
56249
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_3118 [56047]

description:
Sample array position within slide:
Array4Onkism0809_B_10128
raw data files:
Onkism0809_B_10128.txt
Onkism0809_B_10128_ref.txt
sample name in processed data file:
56047
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_3130 [56186]

description:
Sample array position within slide:
Array2Onkism0809_B_10104
raw data files:
Onkism0809_B_10104.txt
Onkism0809_B_10104_ref.txt
sample name in processed data file:
56186
*ref.txt file is the raw data for channel 2 (pooled reference.


title: LPM1B9

tag: cell type


title: Coho smolt Brain_2979 [56191]

description:
Sample array position within slide:
Array2Onkism0809_B_10089
raw data files:
Onkism0809_B_10089.txt
Onkism0809_B_10089_ref.txt
sample name in processed data file:
56191
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_3082 [56102]

description:
Sample array position within slide:
Array3Onkism0809_B_10131
raw data files:
Onkism0809_B_10131.txt
Onkism0809_B_10131_ref.txt
sample name in processed data file:
56102
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_3004 [56114]

description:
Sample array position within slide:
Array3Onkism0809_B_10114
raw data files:
Onkism0809_B_10114.txt
Onkism0809_B_10114_ref.txt
sample name in processed data file:
56114
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_2977 [56174]

description:
Sample array position within slide:
Array2Onkism0809_B_10116
raw data files:
Onkism0809_B_10116.txt
Onkism0809_B_10116_ref.txt
sample name in processed data file:
56174
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_3029 [56060]

description:
Sample array position within slide:
Array4Onkism0809_B_10112
raw data files:
Onkism0809_B_10112.txt
Onkism0809_B_10112_ref.txt
sample name in processed data file:
56060
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_3107 [56091]

description:
Sample array position within slide:
Array3Onkism0809_B_10175
raw data files:
Onkism0809_B_10175.txt
Onkism0809_B_10175_ref.txt
sample name in processed data file:
56091
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_2924 [56151]

description:
Sample array position within slide:
Array2Onkism0809_B_10170
raw data files:
Onkism0809_B_10170.txt
Onkism0809_B_10170_ref.txt
sample name in processed data file:
56151
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_2984 [56072]

description:
Sample array position within slide:
Array4Onkism0809_B_10092
raw data files:
Onkism0809_B_10092.txt
Onkism0809_B_10092_ref.txt
sample name in processed data file:
56072
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_2921 [56166]

description:
Sample array position within slide:
Array2Onkism0809_B_10127
raw data files:
Onkism0809_B_10127.txt
Onkism0809_B_10127_ref.txt
sample name in processed data file:
56166
*ref.txt file is the raw data for channel 2 (pooled reference.


title: LPM1B8


title: LPM1C1


title: HOTTIP-KO-2-CHIRP-seq

city: Hangzhou

first: Huacheng

last: Luo

state: Zhejiang

address: No. 150, Fucheng Road, Qiantang District

country: China

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

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

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

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

treatment_protocol: Immediately extract RNA from LSK and MOLM13 cells without any treatment

tag: cell line

tag: cell types

value: Human-derived acute myeloid leukemia cells

tag: tissue origin

value: peripheral blood

tag: genotype/variation

value: HOTTIP-KO


title: LPM1B5

tag: es line


title: HOTTIP-KO-1-ATAC-seq-2


title: WT-CHIRP-seq.fastq.gz

value: WT


title: LPM1B7


title: LPM1B4


title: HOTTIP-KO-1-ATAC-seq-1


title: LPM1B6


title: HOTTIP-KO-2-ATAC-seq-2


title: HOTTIP-KO-2-ATAC-seq-1


title: Coho smolt Brain_2918 [56033]

description:
Sample array position within slide:
Array4Onkism0809_B_10176
raw data files:
Onkism0809_B_10176.txt
Onkism0809_B_10176_ref.txt
sample name in processed data file:
56033
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: FISH #

tag: fw/sw

value: SW

tag: year

value: Wild


title: Coho smolt Brain_2856 [56155]

description:
Sample array position within slide:
Array2Onkism0809_B_10162
raw data files:
Onkism0809_B_10162.txt
Onkism0809_B_10162_ref.txt
sample name in processed data file:
56155
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: season

value: F


title: HOTTIP-KO-1-CHIRP-seq


title: Coho smolt Brain_2857 [56120]

description:
Sample array position within slide:
Array3Onkism0809_B_10108
raw data files:
Onkism0809_B_10108.txt
Onkism0809_B_10108_ref.txt
sample name in processed data file:
56120
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: origin


title: Coho smolt Brain_2809 [56027]

description:
Sample array position within slide:
Array4Onkism0809_B_10198
raw data files:
Onkism0809_B_10198.txt
Onkism0809_B_10198_ref.txt
sample name in processed data file:
56027
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: fork length (cm)


title: Coho smolt Brain_2890 [56090]

description:
Sample array position within slide:
Array3Onkism0809_B_10176
raw data files:
Onkism0809_B_10176.txt
Onkism0809_B_10176_ref.txt
sample name in processed data file:
56090
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: total mass (g)


title: Coho smolt Brain_2905 [56223]

description:
Sample array position within slide:
Array1Onkism0809_B_10131
raw data files:
Onkism0809_B_10131.txt
Onkism0809_B_10131_ref.txt
sample name in processed data file:
56223
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: Sex


title: Coho smolt Brain_2791 [56215]

description:
Sample array position within slide:
Array1Onkism0809_B_10167
raw data files:
Onkism0809_B_10167.txt
Onkism0809_B_10167_ref.txt
sample name in processed data file:
56215
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: latitude


title: Coho smolt Brain_2811 [56031]

description:
Sample array position within slide:
Array4Onkism0809_B_10180
raw data files:
Onkism0809_B_10180.txt
Onkism0809_B_10180_ref.txt
sample name in processed data file:
56031
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: longitude


title: Coho smolt Brain_2790 [56205]

description:
Sample array position within slide:
Array1Onkism0809_B_10183
raw data files:
Onkism0809_B_10183.txt
Onkism0809_B_10183_ref.txt
sample name in processed data file:
56205
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: sample type


title: Coho smolt Brain_2800 [56132]

description:
Sample array position within slide:
Array2Onkism0809_B_10211
raw data files:
Onkism0809_B_10211.txt
Onkism0809_B_10211_ref.txt
sample name in processed data file:
56132
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_2794 [56094]

description:
Sample array position within slide:
Array3Onkism0809_B_10168
raw data files:
Onkism0809_B_10168.txt
Onkism0809_B_10168_ref.txt
sample name in processed data file:
56094
*ref.txt file is the raw data for channel 2 (pooled reference.


title: WT-ATAC-seq-1.fastq.gz

source_name: WT-ATAC-seq


title: Coho smolt Brain_2727 [56154]

description:
Sample array position within slide:
Array2Onkism0809_B_10167
raw data files:
Onkism0809_B_10167.txt
Onkism0809_B_10167_ref.txt
sample name in processed data file:
56154
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_2786 [56152]

description:
Sample array position within slide:
Array2Onkism0809_B_10169
raw data files:
Onkism0809_B_10169.txt
Onkism0809_B_10169_ref.txt
sample name in processed data file:
56152
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_2762 [56055]

description:
Sample array position within slide:
Array4Onkism0809_B_10120
raw data files:
Onkism0809_B_10120.txt
Onkism0809_B_10120_ref.txt
sample name in processed data file:
56055
*ref.txt file is the raw data for channel 2 (pooled reference.


title: LPM1B12

tag: cell type


title: LPM1B3


title: LPM1B11


title: stch4_24hr_rep-3

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

description: 14-day-old stch4-1 seedlings grown on 1/2 MS medium with  4 ℃ treatment for 24 hours

data_processing:
Reads were mapped to TAIR10 using Tophat2
Differetial gene expresssion was analysed by cufflinks
Genome_build: TAIR10

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: 14-day-old wild-type and stch4-1 seedlings grown on 1/2 MS medium(1/2 × MS salts, 2% sucrose, 0.6% agar, pH 5.7)

extract_protocol:
Total RNA was isolated with the Trizol reagent (Invitrogen, USA) and treated with TURBO DNA-free Kit (Ambion) to remove genomic DNA contaminants.
RNA-seq libraries were constructed following the standard Illumina protocols.
Illumina sequencing was performed in the Shanghai Center for Plant Stress Biology with an Illumina HiSeq 2500 System.

treatment_protocol: plants were treated without or with 4 ℃ for 4 or 24 hours for total RNA extraction.

tag: tissue

value: seedling

tag: cultivar

tag: treatment

value: 24 ℃ treatment for 4 hours


title: stch4_24hr_rep-2

tag: genotype/variation


title: WT-ATAC-seq-2.fastq.gz

tag: cell line

tag: cell types

tag: tissue origin


title: LPM1B2

value: hPSC-derived lateral mesoderm

tag: es line


title: Coho smolt Brain_2713 [56066]

description:
Sample array position within slide:
Array4Onkism0809_B_10106
raw data files:
Onkism0809_B_10106.txt
Onkism0809_B_10106_ref.txt
sample name in processed data file:
56066
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: FISH #

tag: fw/sw

tag: year

tag: season


title: Coho smolt Brain_2698 [56208]

description:
Sample array position within slide:
Array1Onkism0809_B_10179
raw data files:
Onkism0809_B_10179.txt
Onkism0809_B_10179_ref.txt
sample name in processed data file:
56208
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: origin

tag: fork length (cm)

tag: total mass (g)

tag: Sex


title: Coho smolt Brain_2785 [56037]

description:
Sample array position within slide:
Array4Onkism0809_B_10168
raw data files:
Onkism0809_B_10168.txt
Onkism0809_B_10168_ref.txt
sample name in processed data file:
56037
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: latitude

tag: longitude

tag: sample type


title: Coho smolt Brain_2728 [56029]

description:
Sample array position within slide:
Array4Onkism0809_B_10184
raw data files:
Onkism0809_B_10184.txt
Onkism0809_B_10184_ref.txt
sample name in processed data file:
56029
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_2705 [56089]

description:
Sample array position within slide:
Array3Onkism0809_B_10179
raw data files:
Onkism0809_B_10179.txt
Onkism0809_B_10179_ref.txt
sample name in processed data file:
56089
*ref.txt file is the raw data for channel 2 (pooled reference.


title: stch4_24hr_rep-1

tag: tissue

tag: cultivar

tag: treatment


title: Coho smolt Brain_2701 [56207]

description:
Sample array position within slide:
Array1Onkism0809_B_10180
raw data files:
Onkism0809_B_10180.txt
Onkism0809_B_10180_ref.txt
sample name in processed data file:
56207
*ref.txt file is the raw data for channel 2 (pooled reference.


title: LPM1A8

tag: cell type


title: LPM1A7


title: LPM1B10


title: stch4_0hr_rep-3

description: 14-day-old stch4-1 seedlings grown on 1/2 MS medium without  4 ℃ treatment

tag: genotype/variation

value: without  4 ℃ treatment


title: stch4_4hr_rep-3

description: 14-day-old stch4-1 seedlings grown on 1/2 MS medium with  4 ℃ treatment for 4 hours

value: 4 ℃ treatment for 4 hours


title: LPM1A9

tag: es line


title: LPM1B1


title: stch4_4hr_rep-2


title: LPM1A6


title: LPM1A5


title: Coho smolt Brain_2674 [56147]

description:
Sample array position within slide:
Array2Onkism0809_B_10179
raw data files:
Onkism0809_B_10179.txt
Onkism0809_B_10179_ref.txt
sample name in processed data file:
56147
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: FISH #

value: Hatchery


title: Coho smolt Brain_2712 [56032]

description:
Sample array position within slide:
Array4Onkism0809_B_10179
raw data files:
Onkism0809_B_10179.txt
Onkism0809_B_10179_ref.txt
sample name in processed data file:
56032
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: fw/sw

value: Fraser


title: Coho smolt Brain_2656 [56092]

description:
Sample array position within slide:
Array3Onkism0809_B_10170
raw data files:
Onkism0809_B_10170.txt
Onkism0809_B_10170_ref.txt
sample name in processed data file:
56092
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: year

value: Pooled cRNA reference


title: Coho smolt Brain_2690 [56123]

description:
Sample array position within slide:
Array3Onkism0809_B_10105
raw data files:
Onkism0809_B_10105.txt
Onkism0809_B_10105_ref.txt
sample name in processed data file:
56123
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: season

value: M


title: Coho smolt Brain_2665 [56234]

description:
Sample array position within slide:
Array1Onkism0809_B_10120
raw data files:
Onkism0809_B_10120.txt
Onkism0809_B_10120_ref.txt
sample name in processed data file:
56234
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: origin

value: ECVI


title: Coho smolt Brain_2640 [56045]

description:
Sample array position within slide:
Array4Onkism0809_B_10130
raw data files:
Onkism0809_B_10130.txt
Onkism0809_B_10130_ref.txt
sample name in processed data file:
56045
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: fork length (cm)


title: Coho smolt Brain_2650 [56137]

description:
Sample array position within slide:
Array2Onkism0809_B_10202
raw data files:
Onkism0809_B_10202.txt
Onkism0809_B_10202_ref.txt
sample name in processed data file:
56137
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: total mass (g)


title: Coho smolt Brain_2623 [56160]

description:
Sample array position within slide:
Array2Onkism0809_B_10134
raw data files:
Onkism0809_B_10134.txt
Onkism0809_B_10134_ref.txt
sample name in processed data file:
56160
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: Sex


title: LPM1A4


title: LPM1A3


title: Coho smolt Brain_2675 [56030]

description:
Sample array position within slide:
Array4Onkism0809_B_10183
raw data files:
Onkism0809_B_10183.txt
Onkism0809_B_10183_ref.txt
sample name in processed data file:
56030
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: latitude


title: Coho smolt Brain_2626 [56085]

description:
Sample array position within slide:
Array3Onkism0809_B_10185
raw data files:
Onkism0809_B_10185.txt
Onkism0809_B_10185_ref.txt
sample name in processed data file:
56085
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: longitude


title: col-0_24hr_rep-2

description: 14-day-old col-0 seedlings grown on 1/2 MS medium with  4 ℃ treatment for 24 hours

value: wild type


title: Coho smolt Brain_2578 [56124]

description:
Sample array position within slide:
Array3Onkism0809_B_10104
raw data files:
Onkism0809_B_10104.txt
Onkism0809_B_10104_ref.txt
sample name in processed data file:
56124
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: sample type


title: Coho smolt Brain_2653 [56198]

description:
Sample array position within slide:
Array1Onkism0809_B_10202
raw data files:
Onkism0809_B_10202.txt
Onkism0809_B_10202_ref.txt
sample name in processed data file:
56198
*ref.txt file is the raw data for channel 2 (pooled reference.


title: col-0_24hr_rep-3

tag: tissue


title: stch4_0hr_rep-1

tag: cultivar


title: Coho smolt Brain_2618 [56220]

description:
Sample array position within slide:
Array1Onkism0809_B_10136
raw data files:
Onkism0809_B_10136.txt
Onkism0809_B_10136_ref.txt
sample name in processed data file:
56220
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_2621 [56221]

description:
Sample array position within slide:
Array1Onkism0809_B_10134
raw data files:
Onkism0809_B_10134.txt
Onkism0809_B_10134_ref.txt
sample name in processed data file:
56221
*ref.txt file is the raw data for channel 2 (pooled reference.


title: stch4_4hr_rep-1

tag: treatment


title: Coho smolt Brain_2614 [56100]

description:
Sample array position within slide:
Array3Onkism0809_B_10136
raw data files:
Onkism0809_B_10136.txt
Onkism0809_B_10136_ref.txt
sample name in processed data file:
56100
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_2622 [56041]

description:
Sample array position within slide:
Array4Onkism0809_B_10137
raw data files:
Onkism0809_B_10137.txt
Onkism0809_B_10137_ref.txt
sample name in processed data file:
56041
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_2593 [56074]

description:
Sample array position within slide:
Array4Onkism0809_B_10089
raw data files:
Onkism0809_B_10089.txt
Onkism0809_B_10089_ref.txt
sample name in processed data file:
56074
*ref.txt file is the raw data for channel 2 (pooled reference.


title: stch4_0hr_rep-2

description: 14-day-old stch4-1 seedlings grown on 1/2 MS medium without  4 ℃ treatment


title: col-0_24hr_rep-1


title: LPM1A2

tag: cell type


title: col-0_4hr_rep-3

description: 14-day-old col-0 seedlings grown on 1/2 MS medium with  4 ℃ treatment for 4 hours

tag: genotype/variation


title: col-0_4hr_rep-2


title: LPM1A12

tag: es line


title: LPM1A11


title: Coho smolt Brain_2289 [56048]

description:
Sample array position within slide:
Array4Onkism0809_B_10127
raw data files:
Onkism0809_B_10127.txt
Onkism0809_B_10127_ref.txt
sample name in processed data file:
56048
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: FISH #

value: U

value: WCVI

value: Columbia


title: Coho smolt Brain_2314 [56210]

description:
Sample array position within slide:
Array1Onkism0809_B_10176
raw data files:
Onkism0809_B_10176.txt
Onkism0809_B_10176_ref.txt
sample name in processed data file:
56210
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: fw/sw

value: SW


title: Coho smolt Brain_2577 [56099]

description:
Sample array position within slide:
Array3Onkism0809_B_10137
raw data files:
Onkism0809_B_10137.txt
Onkism0809_B_10137_ref.txt
sample name in processed data file:
56099
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: year


title: LPM1A10


title: col-0_0hr_rep-3

description: 14-day-old col-0 seedlings grown on 1/2 MS medium without  4 ℃ treatment


title: col-0_0hr_rep-2


title: LPM1A1


title: Coho smolt Brain_2313 [56229]

description:
Sample array position within slide:
Array1Onkism0809_B_10125
raw data files:
Onkism0809_B_10125.txt
Onkism0809_B_10125_ref.txt
sample name in processed data file:
56229
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: season

value: Wild

value: North


title: EPI3H9

source_name: engineered epicardial cell

value: hPSC-derived epicardium


title: Coho smolt Brain_2311 [56202]

description:
Sample array position within slide:
Array1Onkism0809_B_10186
raw data files:
Onkism0809_B_10186.txt
Onkism0809_B_10186_ref.txt
sample name in processed data file:
56202
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: origin

value: Oregon


title: Coho smolt Brain_2360 [56185]

description:
Sample array position within slide:
Array2Onkism0809_B_10105
raw data files:
Onkism0809_B_10105.txt
Onkism0809_B_10105_ref.txt
sample name in processed data file:
56185
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: fork length (cm)


title: Coho smolt Brain_2361 [56206]

description:
Sample array position within slide:
Array1Onkism0809_B_10182
raw data files:
Onkism0809_B_10182.txt
Onkism0809_B_10182_ref.txt
sample name in processed data file:
56206
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: total mass (g)


title: Coho smolt Brain_2248 [56153]

description:
Sample array position within slide:
Array2Onkism0809_B_10168
raw data files:
Onkism0809_B_10168.txt
Onkism0809_B_10168_ref.txt
sample name in processed data file:
56153
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: Sex


title: Coho smolt Brain_2247 [56201]

description:
Sample array position within slide:
Array1Onkism0809_B_10198
raw data files:
Onkism0809_B_10198.txt
Onkism0809_B_10198_ref.txt
sample name in processed data file:
56201
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: latitude


title: Coho smolt Brain_2153 [56103]

description:
Sample array position within slide:
Array3Onkism0809_B_10130
raw data files:
Onkism0809_B_10130.txt
Onkism0809_B_10130_ref.txt
sample name in processed data file:
56103
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: longitude


title: Coho smolt Brain_2132 [56106]

description:
Sample array position within slide:
Array3Onkism0809_B_10127
raw data files:
Onkism0809_B_10127.txt
Onkism0809_B_10127_ref.txt
sample name in processed data file:
56106
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: sample type


title: Coho smolt Brain_2134 [56034]

description:
Sample array position within slide:
Array4Onkism0809_B_10175
raw data files:
Onkism0809_B_10175.txt
Onkism0809_B_10175_ref.txt
sample name in processed data file:
56034
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_2286 [56211]

description:
Sample array position within slide:
Array1Onkism0809_B_10175
raw data files:
Onkism0809_B_10175.txt
Onkism0809_B_10175_ref.txt
sample name in processed data file:
56211
*ref.txt file is the raw data for channel 2 (pooled reference.


title: EPI3H6


title: EPI3H8


title: Coho smolt Brain_2131 [56149]

description:
Sample array position within slide:
Array2Onkism0809_B_10176
raw data files:
Onkism0809_B_10176.txt
Onkism0809_B_10176_ref.txt
sample name in processed data file:
56149
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_2658 [56148]

description:
Sample array position within slide:
Array2Onkism0809_B_10177
raw data files:
Onkism0809_B_10177.txt
Onkism0809_B_10177_ref.txt
sample name in processed data file:
56148
*ref.txt file is the raw data for channel 2 (pooled reference.


title: col-0_0hr_rep-1

tag: tissue

value: seedling


title: EPI3H4


title: at-seed-replicate_2_ler_x_col

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

country: Sweden

institute: SLU

description: Arabidopsis thaliana F1-seed of Ler pi x Col-wt

data_processing:
For each replicate, 150bp-long reads were mapped to the Arabidopsis (TAIR10) genome, masked for rRNA genes, using TopHat v2.1.0 (parameters adjusted as -g 1 -a 10 -i 40 -I 5000 -F 0 -r 130). Gene expression was normalized to reads per kilobase per million mapped reads (RPKM) using GFOLD.
Genome_build: TAIR10
Supplementary_files_format_and_content: RNA-seq: expression levels (RPKM) are shown for genes  in TAIR10 for each condition and replicate.

molecule: polyA RNA

source_name: AT F1-Seed Columbia

growth_protocol: All seeds were surface sterilized (5% sodium hypochlorite and 0.01% Triton X-100), stratified for 2 days at 4°C and germinated on half-strength Murashige and Skoog medium (1% sucrose) in long-day conditions (16 h light/8 h darkness; 21°C). Plants were transferred to soil after 10 to 12 days and grown under long day conditions.

extract_protocol:
For RNA sequencing, seeds derived from indicated crosses were manually disected out of the 6DAP siliques. RNA was extracted following a mirVana kit (Ambion). mRNA extraction was performed using NEBNext Poly(A) mRNA Magnetic Isolation kit.
Libraries were produced using the NEBNext UltraTM II RNA Library Prep Kit for Illumina. The library was sequenced on a Illumina HiSep 2500 platform with 150bp paired-end reads.

value: Ler pistillata x Col-wt

value: seed


title: Coho smolt Brain_2288 [56111]

description:
Sample array position within slide:
Array3Onkism0809_B_10121
raw data files:
Onkism0809_B_10121.txt
Onkism0809_B_10121_ref.txt
sample name in processed data file:
56111
*ref.txt file is the raw data for channel 2 (pooled reference.


title: EPI3H7


title: EPI3H2


title: col-0_4hr_rep-1

description: 14-day-old col-0 seedlings grown on 1/2 MS medium with  4 ℃ treatment for 4 hours

tag: cultivar

value: 4 ℃ treatment for 4 hours


title: EPI3H3


title: at-seed-replicate_1_ler_x_col_osd1

description: Arabidopsis thaliana F1-seed of Ler pi x Col-osd1

value: Ler pistillata x Col-osd1


title: at-seed-replicate_1_ler_x_col


title: at-seed-replicate_2_ler_x_col_osd1


title: Coho smolt Brain_2127 [56141]

description:
Sample array position within slide:
Array2Onkism0809_B_10186
raw data files:
Onkism0809_B_10186.txt
Onkism0809_B_10186_ref.txt
sample name in processed data file:
56141
*ref.txt file is the raw data for channel 2 (pooled reference.

value: Pooled cRNA reference


title: Coho smolt Brain_2002 [56043]

description:
Sample array position within slide:
Array4Onkism0809_B_10134
raw data files:
Onkism0809_B_10134.txt
Onkism0809_B_10134_ref.txt
sample name in processed data file:
56043
*ref.txt file is the raw data for channel 2 (pooled reference.

value: Hatchery

value: M


title: Coho smolt Brain_2130 [56142]

description:
Sample array position within slide:
Array2Onkism0809_B_10185
raw data files:
Onkism0809_B_10185.txt
Onkism0809_B_10185_ref.txt
sample name in processed data file:
56142
*ref.txt file is the raw data for channel 2 (pooled reference.

value: ECVI


title: at-seed-replicate_2_ler_x_col_osd1_phe1

description: Arabidopsis thaliana F1-seed of Ler pi x Col-osd1-phe1-phe2

value: Ler pistillata x Col-osd1-phe1-phe2


title: EPI3H12


title: Coho smolt Brain_2115 [56150]

description:
Sample array position within slide:
Array2Onkism0809_B_10175
raw data files:
Onkism0809_B_10175.txt
Onkism0809_B_10175_ref.txt
sample name in processed data file:
56150
*ref.txt file is the raw data for channel 2 (pooled reference.

value: U


title: Coho smolt Brain_1946 [56162]

description:
Sample array position within slide:
Array2Onkism0809_B_10131
raw data files:
Onkism0809_B_10131.txt
Onkism0809_B_10131_ref.txt
sample name in processed data file:
56162
*ref.txt file is the raw data for channel 2 (pooled reference.


title: Coho smolt Brain_2239 [56246]

description:
Sample array position within slide:
Array1Onkism0809_B_10105
raw data files:
Onkism0809_B_10105.txt
Onkism0809_B_10105_ref.txt
sample name in processed data file:
56246
*ref.txt file is the raw data for channel 2 (pooled reference.

value: Fraser


title: Coho smolt Brain_2129 [56163]

description:
Sample array position within slide:
Array2Onkism0809_B_10130
raw data files:
Onkism0809_B_10130.txt
Onkism0809_B_10130_ref.txt
sample name in processed data file:
56163
*ref.txt file is the raw data for channel 2 (pooled reference.

value: SW


title: Coho smolt Brain_2014 [56146]

description:
Sample array position within slide:
Array2Onkism0809_B_10180
raw data files:
Onkism0809_B_10180.txt
Onkism0809_B_10180_ref.txt
sample name in processed data file:
56146
*ref.txt file is the raw data for channel 2 (pooled reference.


title: at-seed-replicate_1_ler_x_col_osd1_phe1


title: EPI3H11


title: EPI3H10


title: Coho smolt Brain_2125 [56209]

description:
Sample array position within slide:
Array1Onkism0809_B_10177
raw data files:
Onkism0809_B_10177.txt
Onkism0809_B_10177_ref.txt
sample name in processed data file:
56209
*ref.txt file is the raw data for channel 2 (pooled reference.

value: Wild


title: HMZ014_Dione_2DAT_rep1

city: Shanghai

first: Huiming

last: Zhang

address: No. 3888 Chenhua Road

institute: Shanghai Center for Plant Stress Biology, and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences

description:
200µM Diacetyl
HMZ014_Dione_featureCounts_output.txt

data_processing:
Reads were aligned to the Arabidopsis genome (TAIR10) using TopHat2 with "-G tair10_ensembl.gtf".
Genome_build: TAIR10
Supplementary_files_format_and_content: The processed file was generated using featureCounts with parameter "-p -t exon -g gene_id -a tair10_ensembl.gtf".

source_name: 7 DAG seedlings treated for 48 h

growth_protocol: Wild type Arabidopsis thaliana Col-0  surface sterilized seeds were planted on 1/2-strength Murashige & Skoog medium (0.5MS) with 0.7% (w/v) agar and 1.5% (w/v) sucrose, and were vernalized at 4oC in dark for 2 days. Seedlings were grown under sterile conditions with 200 µmol photons m-2sec-1 light, 21 ± 2 oC, at a 16hr light/8hr dark cycle. Five days after germination, Arabidopsis seedlings were transferred to fresh 0.5 MS medium.

extract_protocol: For experiments with GMVs, plants grown on 0.5 MS and 0.05 MS were harvested at 5 DAT. For experiments with DA, plants were harvested at 48 hours after the seedlings were transferred. RNA was extracted by  Plant RNeasy Kit (Qiagen) and the integrity was monitored using the RNA Nano 6000 Assay of the Agilent BioAnalyzer 2100 system (Agilent). RNA purity and concentration was checked using a Nanodrop ND-1000 spectrophotometer.

treatment_protocol: The GMV treatment: One day before transferring seedlings, Bacillus amyloliquefaciens GB03 was cultured in liquid LB medium at 28 oC overnight. Shortly after 5 DAG seedlings were transferred to new growth medium, 20µL of GB03 suspension culture or double distilled water (DDW) was applied to the non-plant side of tri-partite Petri dish plates, containing 0.5 MS or 0.05 MS medium, with 0.7% (w/v) agar and 1.5% (w/v) sucrose. For Diacetyl treatment:  7 DAG seedlings were transferred to Petri dish plates, containing 0.5 MS medium, with 0.7% (w/v) agar and 1.5% with and without 200µM Diacetyl for mock and treatment, respectively.

value: seedlings

tag: time point

value: 2 day

tag: agent

value: Diacetyl


title: HMZ014_Dione_2DAT_rep2


title: HMZ014_CK_2DAT_rep2

source_name: 7 DAG seedlings treated for 48 h mock

value: mock


title: EPI3G9

tag: cell type

value: hPSC-derived epicardium


title: EPI3G8

tag: es line


title: 200687170029_R06C02

type: genomic

city: Los Angeles

first: Daniel

last: Nachun

state: CA

address: 695 Charles E Young Dr S

institute: UCLA

description: colon crypt

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k or MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Data from 450k and EPIC IDAT files were read in separately with RnBeads and combined, only keeping the probes shared by the two platforms.  Probes were filtered to remove those outside CpG contexts, in SNP, on the sex chromosomes, if they missing values, or if their standard deviation was below 0.005, indicating low variability.  The greedy cut algorithm was used to remove probes with poor detection score p-values.  After filtering of probes, data were normalized using BMIQ with the ENMix oob background correction method.
BMIQ and ENMix oob normalized beta values

label: Cy5 and Cy3

source_name: colon

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified using standard phenol-chloroform extraction with ethanol precipitation

value: crypt

tag: age

value: female

tag: batch


title: EPI3H1


title: HMZ008_0.5T_5DAT_rep2

description:
Volatile emitted from GB04
HMZ008_featureCounts_output.txt

source_name: 5 DAG seedlings treated for 5 days

value: 5 day

value: GMV


title: EPI3G7


title: Coho smolt Brain_1896 [56219]

description:
Sample array position within slide:
Array1Onkism0809_B_10137
raw data files:
Onkism0809_B_10137.txt
Onkism0809_B_10137_ref.txt
sample name in processed data file:
56219
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: FISH #

tag: fw/sw

tag: year

value: F

value: Pooled cRNA reference


title: HMZ008_0.5T_5DAT_rep1

description:
Volatile emitted from GB03
HMZ008_featureCounts_output.txt


title: 200687170029_R05C02

description: duodenum crypt

source_name: duodenum

value: male


title: HMZ014_CK_2DAT_rep1


title: Coho smolt Brain_1884 [56222]

description:
Sample array position within slide:
Array1Onkism0809_B_10133
raw data files:
Onkism0809_B_10133.txt
Onkism0809_B_10133_ref.txt
sample name in processed data file:
56222
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: season

tag: origin

tag: fork length (cm)

value: ECVI


title: Coho smolt Brain_1876 [56069]

description:
Sample array position within slide:
Array4Onkism0809_B_10095
raw data files:
Onkism0809_B_10095.txt
Onkism0809_B_10095_ref.txt
sample name in processed data file:
56069
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: total mass (g)

tag: Sex

value: M

tag: latitude


title: Coho smolt Brain_1692 [56107]

description:
Sample array position within slide:
Array3Onkism0809_B_10126
raw data files:
Onkism0809_B_10126.txt
Onkism0809_B_10126_ref.txt
sample name in processed data file:
56107
*ref.txt file is the raw data for channel 2 (pooled reference.

value: FW

value: Hatchery

value: U

tag: longitude

value: puntledge

tag: sample type


title: EPI3G6


title: HMZ008_0.5C_5DAT_rep2

source_name: 5 DAG seedlings treated for 5 days mock

tag: tissue

value: seedlings

tag: time point

tag: cultivar


title: EPI3G5

tag: cell type

tag: es line


title: 200687170029_R04C02

description: colon crypt

tag: age

tag: batch


title: Coho smolt Brain_1691 [56167]

description:
Sample array position within slide:
Array2Onkism0809_B_10126
raw data files:
Onkism0809_B_10126.txt
Onkism0809_B_10126_ref.txt
sample name in processed data file:
56167
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: FISH #

tag: fw/sw


title: EPI3G3


title: Coho smolt Brain_1690 [56054]

description:
Sample array position within slide:
Array4Onkism0809_B_10121
raw data files:
Onkism0809_B_10121.txt
Onkism0809_B_10121_ref.txt
sample name in processed data file:
56054
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: year

tag: season


title: 200687170029_R01C02

description: duodenum mucosa

value: mucosa


title: 200687170029_R03C02

description: colon crypt


title: EPI3G2


title: 200687170029_R02C02

description: colon mucosa


title: Coho smolt Brain_1687 [56050]

description:
Sample array position within slide:
Array4Onkism0809_B_10125
raw data files:
Onkism0809_B_10125.txt
Onkism0809_B_10125_ref.txt
sample name in processed data file:
56050
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: origin

tag: fork length (cm)


title: Coho smolt Brain_1688 [56122]

description:
Sample array position within slide:
Array3Onkism0809_B_10106
raw data files:
Onkism0809_B_10106.txt
Onkism0809_B_10106_ref.txt
sample name in processed data file:
56122
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: total mass (g)

tag: Sex


title: EPI3G12


title: Coho smolt Brain_1686 [56172]

description:
Sample array position within slide:
Array2Onkism0809_B_10121
raw data files:
Onkism0809_B_10121.txt
Onkism0809_B_10121_ref.txt
sample name in processed data file:
56172
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: latitude

tag: longitude


title: EPI3G11


title: HMZ008_0.5C_5DAT_rep1

tag: tissue

tag: agent

value: mock


title: Coho smolt Brain_1685 [56145]

description:
Sample array position within slide:
Array2Onkism0809_B_10182
raw data files:
Onkism0809_B_10182.txt
Onkism0809_B_10182_ref.txt
sample name in processed data file:
56145
*ref.txt file is the raw data for channel 2 (pooled reference.

tag: sample type


title: 200687170029_R06C01

description: colon mucosa

tag: cell type


title: EPI3G10

value: hPSC-derived epicardium

tag: es line


title: 200687170029_R05C01

description: duodenum mucosa

tag: age


title: HMZ008_0.05T_5DAT_rep2

tag: time point

tag: cultivar


title: HMZ008_0.05C_5DAT_rep2


title: 200687170029_R04C01

description: colon mucosa

tag: batch


title: HMZ008_0.05T_5DAT_rep1