title: aub[HN]/[QC] mutant small RNAseq

status: Public on Jun 25 2020

city: pasadena

first: xiawei

last: huang

state: CALIFORNIA

address: 1200 E California Blvd

institute: caltech

description:
strain: aub[HN]/aub[QC]
total small RNA in aub mutant ovaries

data_processing:
The reads were mapped, after adapter trimming, to the dm6 assembly of the Drosophila melanogaster genome to identify all piRNAs matching 100% to genomic sequences.
Annotation of small RNAs was done using the following databases: Repbase (http://www.girinst.org/), Transposable element canonical sequences (http://www.fruitfly.org/p_disrupt/TE.html), Flybase annotations for coding and noncoding genes (extracted from http://genome.ucsc.edu), and microRNA annotations from Rfam (http://microrna.sanger.ac.uk/sequences).
Density analysis of transposons along chromosome arms was by counting all nucleotides in a 50 kb window (10 kb offset) annotated as transposons.
Genome_build: dm6
Supplementary_files_format_and_content: tables show the sequences raw counts of sequencing reads, map numbers, orientation, chromosome coordinates and the annotation.

organism: Drosophila melanogaster

source_name: adult fly ovaries small RNA

growth_protocol: Fly stocks were maintained at 24C on standard diet

extract_protocol: Small RNAs (19-30nt) were isolated from total ovary RNA and then libraries were cloned using the NEBNext Small RNA Library Prep Kit for Illumina,Total RNA was isolated from ovaries using Ribozol followed by precipitation.  Libraries were prepared using the NEBNext Small RNA Library Prep Set for Illumina according to the protocol using NEBNext Multiplex Oligos for Illumina.

treatment_protocol: Flies were fed with yeast for 2-3 days prior to dissection

value: adult fly ovaries

value: 3 days after hatch


title: GFP-mdAub rescue small RNAseq

type: SRA

country: USA

description:
strain: aub[HN]/aub[QC]; (BAC)-GFP-mdAub
total small RNA in GFP tag arginine methylation mutant Aub (GFP-mdAub) rescued aub mutant ovaries.

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: age


title: Line 13 WT H3.3 rep2

status: Public on Jun 29 2020

city: Sacramento

first: Paul

last: Knoepfler

state: CA

address: 2425 Stockton Blvd, Room 633

department: Cell Biology and Human Anatomy

institute: University of California Davis

description: Line 13 WT H3.3 rep2

library_source: genomic

data_processing:
Reads were called with illumina bclfastq
Reads were aligned to the hg19 genome with BWA (version 0.7.13-r1126 )
Peaks were called with MACS2 (version 2.1.0.20151222)
Differential peak occupancy analysis was performed with DiffBind (R version 3.5.2)
Downstream analysis was performed on the Galaxy webserver
Genome_build: hg19
Supplementary_files_format_and_content: bed files of peaks

molecule: genomic DNA

organism: Homo sapiens

source_name: Line XIII DIPG

growth_protocol: All DIPG cells were cultured in Tumor Stem Medium (Nagaraja et al, 2017), which contains DMEM/F12 1:1 (Invitrogen), Neurobasal-A (Invitrogen), 10mM HEPES (Invitrogen), 1X MEM sodium pyruvate (Invitrogen), 1X MEM nonessential amino acids (Invitrogen), 1% GlutaMax (Invitrogen), human-bFGF (20 ng/ml) (Shenandoah), human-EGF (20 ng/ml) (Shenandoah), human PDGF-A and PDGF-B (20ng/ml) (Shenandoah), heparin (10 ng/ml) (StemCell Technologies) and B27 without Vitamin A (Invitrogen).

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibodies to H3K27me3 (Cell Signaling C36B11) or H3.3  (Millipore #09-838).
Libraries were prepared with the Nextera library prep kit
Libraries were sequenced on the NovaSeq machine with 150 base paired-end sequencing

treatment_protocol: Single-stranded donor oligonucleotide (ssODN) templates were designed with the desired mutations to facilitate homology directed repair (HDR) after cleavage of H3F3A by Cas9n. cells were co-transfected with a combination of pSpCas9n(BB)-2A-GFP-guideA (0.5μg/well), pSpCas9n(BB)-2A-Puro-guideB (0.5μg/well), and ssODN HDR (1μg/well) template using XtremeGene-HP (Sigma).

tag: histone h3.3 status

value: WT

tag: antibody


title: GFP-mdAub_het small RNAseq

description:
Strain: aub[HN]/Cyo; (BAC)-GFP-mdAub
total small RNA in Aub+/- heterzygous ovaries expressing GFP tag arginine methylation mutant Aub (GFP-mdAub)


title: GFP-mdAub IPseq

description:
Strain: Aub+/+; (BAC)-GFP-mdAub
total small RNA isolated from GFP tag arginine methylation deficient Aub(GFP-mdAub) IP from ovaries. Rabbit anti-GFP (Covance,affinity-purified in our laboratory) antibody was used for IP.

extract_protocol: Rabbit anti-GFP (Covance,affinity-purified in our laboratory) antibody was used for GFP tag arginine methylation deficient Aub(GFP-mdAub) immunoprecipitation from wild-type ovaries expressing GFP-mdAub under the control of endogenous promoter.  IP RNAs were isolated from IP GFP-wtAub.Small RNAs (19-30nt) were isolated from IP RNAs by size selection and then libraries were cloned using the NEBNext Small RNA Library Prep Kit for Illumina.


title: GFP-wtAub IPseq

description:
Strain: Aub+/+; (BAC)-GFP-wtAub
total small RNA isolated from GFP-wtAub IP from ovaries. Rabbit anti-GFP (Covance, affinity-purified in our laboratory) antibody was used for IP.

extract_protocol: Rabbit anti-GFP (Covance,affinity-purified in our laboratory) antibody was used for GFP-wtAub immunoprecipitation from wild-type ovaries.  IP RNAs were isolated from IP GFP-wtAub.Small RNAs (19-30nt) were isolated from IP RNAs by size selection and then libraries were cloned using the NEBNext Small RNA Library Prep Kit for Illumina.


title: GFP-wtAub rescue small RNAseq

description:
aub[HN]/aub[QC]; (BAC)-GFP-wtAub
total small RNA in GFP-wtAub rescued aub mutant ovaries


title: Line 13 WT H3K27me3 rep2

description: Line 13 WT H3K27me3 rep2


title: OT1 CD8+ T cells activated with N4 Peptide rep4-total IP

status: Public on Jun 04 2020

city: Edinburgh

first: Amy

last: Buck

address: Ashworth Labs, Charlotte Auerbach Road

department: IIIR

country: United Kingdom

institute: The University of Edinburgh

description:
Activated_IP4
Small RNA sequencing
AGO2 immunoprecipitation carried followed by small RNA sequencing.

data_processing:
QuickMIRSeq miRNA counting, 18-28 bp, trimming 3' adapter TGGAATTCTCGGGTGCCAAGG.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: GEO_HMWLMWactivated.quickmirseq.grouped_by_mirna.csv: Comma-separated text file with columns: miRNA, sample1, sample2, …, rows have miRNA counts.

organism: Mus musculus

source_name: OT1 CD8+ T cell

extract_protocol:
miRNeasy (Qiagen)
CleanTag (Trilink)

tag: strain

value: Lymph nodes

tag: cell type

value: Activated CD8+ T cells

tag: purified cellular fraction

value: Total cell lysate


title: Naïve OT1 CD8+ T cells rep3-total IP

description:
Na_ve_IP3
Small RNA sequencing
AGO2 immunoprecipitation carried followed by small RNA sequencing.

value: Naive CD8+ T cells


title: OT1 CD8+ T cells activated with N4 Peptide rep1-total IP

description:
Activated_IP1
Small RNA sequencing
AGO2 immunoprecipitation carried followed by small RNA sequencing.


title: Naïve OT1 CD8+ T cells rep2-total IP

description:
Na_ve_IP2
Small RNA sequencing
AGO2 immunoprecipitation carried followed by small RNA sequencing.


title: OT1 CD8+ T cells activated with N4 Peptide rep2-total IP

description:
Activated_IP2
Small RNA sequencing
AGO2 immunoprecipitation carried followed by small RNA sequencing.


title: OT1 CD8+ T cells activated with N4 Peptide rep3-LMW IP

description:
LMW_IP3
Small RNA sequencing
AGO2 immunoprecipitation carried followed by small RNA sequencing.

value: LMW RISC Complexes purified by Superose 6 fractionation


title: OT1 CD8+ T cells activated with N4 Peptide rep1-LMW IP

description:
LMW_IP1
Small RNA sequencing
AGO2 immunoprecipitation carried followed by small RNA sequencing.


title: OT1 CD8+ T cells activated with N4 Peptide rep3-HMW IP

description:
HMW_IP3
Small RNA sequencing
AGO2 immunoprecipitation carried followed by small RNA sequencing.

value: HMW RISC Complexes purified by Superose 6 fractionation


title: OT1 CD8+ T cells activated with N4 Peptide rep2-HMW IP

description:
HMW_IP2
Small RNA sequencing
AGO2 immunoprecipitation carried followed by small RNA sequencing.


title: OT1 CD8+ T cells activated with N4 Peptide rep1-HMW IP

description:
HMW_IP1
Small RNA sequencing
AGO2 immunoprecipitation carried followed by small RNA sequencing.


title: Adult_GUT_rep1_RNA

status: Public on May 28 2020

city: Los Angeles

first: Neil

last: Segil

address: 1425 san pablo st, BCC 503K

department: BCC

institute: University of Southern California

data_processing:
Sequenced reads were mapped to Gencode Mm10v11 genome using STAR (v2.5.4b).
Transcript quantification was performed with RSEM.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.isoforms.results.tsv: Tab-delimited text files of transcript quantification were generated with RSEM.

source_name: Intestine

growth_protocol: Intestine was dissected from P1 mice and enzymatically dissociated with 0.25% trypsin. Cells were pelleted and resuspended in DMEM/F12 and then FACS purified to collect the Atoh1-GFP positive cells.

extract_protocol:
Cells were FACS purified and collected in RNA lysis buffer. Total RNA was extracted with Quick-RNA Microprep kit (Zymo Research).
Libraries were prepared using QIAseq FX Single Cell RNA Library Kit (Qiagen).

tag: genotype

tag: developmental stage

value: Adult

value: Intestine


title: V_2: SARS-CoV-2_rep2

status: Public on May 26 2020

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: SARS-CoV-2-infected human bronchial organoids_rep2

data_processing:
Sequencing was performed on an Illumina NextSeq500 or NovaSeq6000 platform in a 152 or 101-base single-end mode, respectively.
Illumina RTA 2.4.11 and Casava1.8.2 softwares were used for basecalling for an Illumina NextSeq500 or NovaSeq6000 platform, respectively.  .
Fastq files were generated using bcl2fastq2.
Adapter sequences were trimmed from raw reads by cutadapt ver 2.7 and then trimmed reads were mapped to the human reference genome sequences (hg19) using HISAT2 v2.1.0.
The raw counts were calculated using featureCounts v 2.0.0.
Genome_build: hg19

growth_protocol: Normal human bronchial epithelial cells (hBEpC, Lonza) were suspended in 10 mg/ml cold Matrigel growth factor reduced (GFR) basement membrane matrix. 50 μL drops of cell suspension were solidify on pre-warmed Nunc cell-culture treated multidishes (24 well plate) at 37°C for 10 min, and then 500 μL of the expansion medium was added to each well. The expansion medium was changed every 2 days. HBO were passaged every 10-12 days. To passage the hBO, organoids were suspended in 1 mL 0.5 mM EDTA/PBS (Nacalai tesque) and mechanically sheared using P1000 pipette tip, and 2 mL TrypLE Select (Thermo Fisher Scientific) was added to the suspension. After incubating for 5 min at room temperature, organoids were mechanically sheared using P1000 pipette tip. 7 mL of the expansion medium was added, and the organoid suspension tubes were centrifuged at 400 rpm. Organoid fragments were re-suspended in the cold expansion medium and seeded as above. The hBO were passaged every 10 days. To maturate the hBO, the expanded hBO were cultured with the differentiation medium for 5 days.

extract_protocol:
Total RNA was isolated from hBO and A549 cells using ISOGENE II (NIPPON GENE).
Library preparation was performed using a NEBNext Ultra II Directional RNA Library Prep Kit for an Illumina NextSeq500 and a TruSeq stranded mRNA sample prep kit for NovaSeq6000 platform according to the manufacturer’s instructions.

treatment_protocol: Approximately 100 organoids were infected with 7.0×10^4 TCID50 of SARS-CoV-2 in 24 well plate containing 500 uL differentiation medium. The one-half of differentiation medium containing SARS-CoV-2 was replaced with fresh differentiation medium every day. After 5 days from the infection, the hBO and their supernatant were collected. In the drug treatment experiment, the infected hBO were cultured with the differentiation medium containing 10 μM camostat (Sigma-Aldrich) for 5 days.

value: Bronchi


title: Naïve OT1 CD8+ T cells rep1-total IP

description:
Na_ve_IP1
Small RNA sequencing
AGO2 immunoprecipitation carried followed by small RNA sequencing.


title: dot1∆ SIR3-EBD G1_estradiol_3_hr input rep. 1

status: Public on May 19 2020

city: Berkeley

first: Davis

last: Goodnight

address: 440 Barker Hall

department: Molecular & Cell Biology

institute: UC Berkeley

data_processing:
For samples sequenced on the Illumina NovaSeq 6000, FASTQ generation was performed using Illumina Casava v2.2. For samples sequenced on the Illumina Miniseq, FASTQ generation was performed using the Generate FASTQ module of Illumina Local Run Manager
Raw reads were mapped to SacCer3 genome modified to include hml∆::HML* and mat∆ using Bowtie2 with following options: --local --soft-clipped-unmapped-tlen --no-unal --no-mixed --no-discordant
bedgraph files were generated from aligned reads and normalized to the genome-wide median (median excluded subtelomeres, chromosome III, and rDNA). For MNase samples, only reads between 130-180 bp (mononucleosome) were included in bedgraphs.
Genome_build: SacCer3 (modified)
Supplementary_files_format_and_content: bedgraph (normalized to genome-wide median)

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: Yeast were cultured at 37° in YPD.

extract_protocol:
Cells were lysed by mechanical disruption in a bead beater. Chromatin was fragmented using either sonication (all H3K79me3 samples) or MNase (all Sir4-myc and Sir3-EBD samples except for a subset fragmented by sonication, noted in the sample title). DNA was purified using Qiagen spin column kit
NEB Ultra II library prep kit

treatment_protocol: For SIR3-EBD cultures, estradiol was used at 50 µM. "No estradiol" samples were grown with 0.5% ethanol (solvent control). For G1 arrests, 10 nM alpha factor was added. For G2/M arrests, 15 µg/mL nocodazole was added.

tag: chip antibody

tag: condition

value: G1 (alpha factor) arrest followed by addition of estradiol for 3 hours

value: mat{delta} hml{delta}::HML* bar1{delta} SIR4-13xMyc; SIR3-EBD78; dot1{delta}


title: dot1∆ SIR3-EBD G1_estradiol_1.5_hr input rep. 1

value: G1 (alpha factor) arrest followed by addition of estradiol for 1.5 hours


title: dot1∆ SIR3-EBD pre-estradiol input rep. 2

value: G1 (alpha factor) arrest without estradiol


title: dot1∆ SIR3-EBD G1_no_estradiol_3_hr input rep. 1

value: G1 (alpha factor) arrest followed by addition of ethanol (solvent control) for 3 hours


title: dot1∆ SIR3-EBD G1_estradiol_3_hr input rep. 2


title: dot1∆ SIR3-EBD G1_no_estradiol_3_hr input rep. 2


title: OT1 CD8+ T cells activated with N4 Peptide rep3-total IP

description:
Activated_IP3
Small RNA sequencing
AGO2 immunoprecipitation carried followed by small RNA sequencing.


title: dot1∆ SIR3-EBD G1_estradiol_1.5_hr input rep. 2


title: SIR3-EBD G2_estradiol input rep. 2

value: G1 (alpha factor) arrest followed by release to G2/M (nocodazole) and addition of estradiol for 3 hours

value: mat{delta} hml{delta}::HML* bar1{delta} SIR4-13xMyc; SIR3-EBD78


title: OT1 CD8+ T cells activated with N4 Peptide rep2-LMW IP

description:
LMW_IP2
Small RNA sequencing
AGO2 immunoprecipitation carried followed by small RNA sequencing.


title: SIR3-EBD G2_no_estradiol input rep. 2

value: G1 (alpha factor) arrest followed by release to G2/M (nocodazole) and addition of ethanol (solvent control) for 3 hours


title: STG_subject01067_NPC_rep1 [X1067.C]

status: Public on Jun 30 2020

type: genomic

city: Pittsburgh

first: Brandon

middle: Chad

last: McKinney

state: PA

address: 3811 O'Hara Street

department: Psychiatry

institute: University of Pittsburgh

hyb_protocol: Following manufacturer's protocol

scan_protocol: Following manufacturer's protocol

data_processing:
Data analyses of raw image array files were performed using the R software environment (www.r-project.org). Color adjustment and background correction were performed using the bgAdjust2C method. Before filtering, normalization was performed using the preprocessQuantile method. In data quality control analysis, probe data for each sample demonstrated mean detection p-values<0.05, so no data was exluded due to failed detection for any sample. At the filtering stage, data from any probes that failed detection in any sample at p>=0.01 (N=12,350) were removed from the dataset. Data from probes on sex chromosomes (N=18,628) and from probes with known SNPs (N=27,395) in any sample were removed from the dataset. Probes that cross-react with multiple genomic regions (N=39,269) were also removed. The remaining data presented here reflects signals at 768,268 probes.
The 'processed_data.txt' contains the normalized (preprocessQuantile method) and Averaged Beta (for 8 subject samples replicated) values.

source_name: postmortem STG of NPC subject 1067

label_protocol: Following manufacturer's protocol

extract_protocol: DNA (~10 micrograms) was isolated from STG grey matter (~20 micrograms) using AllPrep DNA/RNA/Protein Mini Kit (Qiagen, Valencia, CA, USA).

treatment_protocol: Bisulfite conversion of 10 micrograms genomic DNA was performed with the EZ DNA methylation kit (Zymo Research).

value: Control

tag: Sex

value: Male

tag: race

value: White

tag: age (years)

tag: postmortem interval (hours)

tag: mechanism of death

value: Natural

tag: illness duration (years)

value: postmortem superior temporal gyrus (STG)

tag: molecule subtype

value: bisulfite-treated genomic DNA


title: SIR3-EBD pre-estradiol input rep. 2


title: SIR3-EBD G1_no_estradiol input rep. 2


title: SIR3-EBD G1_estradiol input rep. 2


title: SIR3-EBD G2_estradiol input rep. 1


title: SIR3-EBD G2_no_estradiol input rep. 1


title: SIR3-EBD G1_no_estradiol input rep. 1


title: SIR3-EBD G1_estradiol input rep. 1


title: Adult_GUT_rep2_RNA

growth_protocol: Intestine was dissected from adult mice and enzymatically dissociated with 0.25% trypsin. Cells were pelleted and resuspended in DMEM/F12 and then FACS purified to collect the Atoh1-GFP positive cells.

value: Adult

tag: tissue


title: no_tag 15min_crosslink input

value: Cycling

value: mat{delta} hml{delta}::HML* bar1{delta}


title: WT 15min_crosslink input

value: mat{delta} hml{delta}::HML* bar1{delta} SIR4-13xMyc


title: SIR3-EBD pre-estradiol input rep. 1


title: dot1∆ SIR3-EBD pre-estradiol input rep. 1

value: mat{delta} hml{delta}::HML* bar1{delta} SIR4-13xMyc; SIR3-EBD78; dot1{delta}


title: sir3∆ 60min_crosslink input

value: mat{delta} hml{delta}::HML* bar1{delta} SIR4-13xMyc; sir3{delta}


title: dot1∆ SIR3-EBD G1_no_estradiol_3_hr Sir4-myc ChIP rep. 2

value: Pierce Anti-c-myc magnetic beads (Thermo Fisher Scientific 88843, lot # UF283471)


title: SIR3-EBD +estradiol 60min_crosslink input


title: VC_2: SARS-CoV-2+camostat_rep2

description: SARS-CoV-2-infected human bronchial organoids treated with camostat_rep2

value: Bronchi


title: SIR3-EBD no_estradiol 60min_crosslink input


title: sir3∆ 15min_crosslink input


title: dot1∆ SIR3-EBD G1_estradiol_3_hr Sir4-myc ChIP rep. 2

value: G1 (alpha factor) arrest followed by addition of estradiol for 3 hours


title: dot1∆ SIR3-EBD pre-estradiol Sir4-myc ChIP rep. 2

value: G1 (alpha factor) arrest without estradiol


title: SIR3-EBD G1_no_estradiol Sir4-myc ChIP rep. 2

value: G1 (alpha factor) arrest followed by addition of ethanol (solvent control) for 3 hours

value: mat{delta} hml{delta}::HML* bar1{delta} SIR4-13xMyc; SIR3-EBD78


title: SIR3-EBD G2_estradiol Sir4-myc ChIP rep. 2

value: G1 (alpha factor) arrest followed by release to G2/M (nocodazole) and addition of estradiol for 3 hours


title: SIR3-EBD G1_estradiol Sir4-myc ChIP rep. 2


title: SIR3-EBD pre-estradiol Sir4-myc ChIP rep. 2


title: SIR3-EBD G2_no_estradiol Sir4-myc ChIP rep. 2

value: G1 (alpha factor) arrest followed by release to G2/M (nocodazole) and addition of ethanol (solvent control) for 3 hours


title: SIR3-EBD pre-estradiol Sir4-myc ChIP rep. 1


title: SIR3-EBD G2_estradiol Sir4-myc ChIP rep. 1


title: SIR3-EBD G2_no_estradiol Sir4-myc ChIP rep. 1


title: SIR3-EBD G1_no_estradiol Sir4-myc ChIP rep. 1


title: no_tag 15min_crosslink Sir4-myc ChIP


title: sir3∆ 60min_crosslink Sir4-myc ChIP

value: Pierce Anti-c-myc magnetic beads (Thermo Fisher Scientific 88843, lot # TD260777)


title: WT 15min_crosslink Sir4-myc ChIP


title: SIR3-EBD G1_estradiol Sir4-myc ChIP rep. 1


title: dot1∆ SIR3-EBD G1_no_estradiol_3_hr Sir4-myc ChIP rep. 1


title: SIR3-EBD no_estradiol 60min_crosslink Sir4-myc ChIP


title: WT 60min_crosslink Sir4-myc ChIP


title: SIR3-EBD +estradiol 60min_crosslink Sir4-myc ChIP


title: dot1∆ SIR3-EBD G1_estradiol_3_hr Sir4-myc ChIP rep. 1


title: High Quality eggs from domesticated female 3

type: RNA

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

country: France

institute: INRA

hyb_protocol: 600 ng of Cy3-cRNA was fragmented and hybridized on a sub-array. Hybridization was carried out for 17 hours at 65°C in a rotating hybridization oven prior to washing

scan_protocol: Microarrays were scanned with an Agilent Scanner (Agilent DNA Microarray Scanner, Agilent Technologies, Massy, France) using the standard parameters for a gene expression 8x60K oligoarray (3µm and 20bits)

data_processing: Data were then obtained with the Agilent Feature Extraction software (10.7.1.1) according to the appropriate GE protocol (GE1_107_Sep09). Normalization and statistical analysis were performed using GeneSpring software (Agilent).

organism: Sander lucioperca

label_protocol: Labeling and hybridization steps were performed following the “One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling)”Agilent protocol. Briefly, for each sample, 150 ng of total RNA was amplified and labeled using Cy3-CTP. Yield (>0.825µg cRNA) and specific activity (> 6pmol of Cy3 per µg of cRNA) of Cy3-cRNA produced were checked with the Nanodrop.

growth_protocol: Domesticated pikeperch broodstock was reared for 6 years in recirculating aquaculture system (RAS) under fully controlled environmental conditions (oxygen level always >80% of saturation, ammonia in the range 0.2–1.1 mg l−1 and nitrite from 0.05–0.70 mg l−1). Water temperature was maintained automatically within the range 8-23°C (±0.5°C). Before the collection of the samples the fish were already successfully reproduced 3 times. The fish were exposed to annual fluctuations of photo-thermal conditions described in our previous studies (Żarski et al. 2019, Aquaculture 503; 527–536). The fish throughout the year were fed with compound feed (50% protein, 11% fat, 10% moisture, 1.55% crude fibre, 1.35% phosphorus, 9.5% ash and 17.9% nitrogen-free extract; Le Gouessant, France) at a rate between 0.2 and 1% of biomass daily, depending on the temperature and appearance of satiation. Wild pikeperch were collected during the spawning season from Vistula Lagoon (North of Poland) with fyke nets, when the average daily water temperature in the lagoon reached for the first time (after wintering) about 10°C.

extract_protocol: The total RNA from eggs was extracted using Total RNA Mini kit (Cat. No. 031-25, A&A Biotechnology, Gdynia, Poland) according to the producer’s protocol. For extraction approximately 50 mg of samples were taken. A NanoDrop® 2000 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA) was used to determine the concentration of the RNA samples. The quality of the RNA samples was checked using a 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, USA) and only samples exhibiting RIN value higher than 8.0 were taken for analysis. Genomic DNA was removed from the samples using DNA-free™ DNA Removal Kit (AM1906, Life Technologies, Carlsbad, CA, USA).

treatment_protocol: Controlled reproduction of the fish was performed with the methods described by Żarski et al. (2019, Aquaculture 503; 527–536), where hormonal stimulation of ovulation and spermiation with human chorionic gonadotropin (hCG; Chorulon, Intervet, France) at a dose of 500 and 250 IU kg-1 for males and females, respectively, was applied. At the time of injection the water temperature was 12°C and was kept constant until ovulation. Photoperiod following the induction of ovulation was 14 h of photo-phase. Eggs, for RNA extraction, from each female separately were snap frozen in liquid nitrogen right after collection.

tag: environment

value: Domesticated

value: female

value: eggs


title: dek53-mu1-3

status: Public on May 16 2020

city: Gainesville

first: Dawei

last: Dai

state: Florida

address: 2550 Hull Rd

department: Horticultural Sciences

institute: University of Florida

data_processing:
fastq reads were aligned using bowtie2 (v2.3.5) with default setting (customized genome build mtcds.fa)
SAM file were converted and sorted by samtools (v1.9) to BAM format
allele frequencies were count by bam-readcount (v0.8.0) with -q 30 -b 30 -d 10000000
Genome_build: mtcds.fa (supplemental data)
Supplementary_files_format_and_content: Tab-delimited text files include allele frequencies for each nucleotide (supplemental data)

organism: Zea mays

source_name: kernel

extract_protocol:
RNA was extracted with Trizol reagent (Tiangen), followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.
Maize 35 mitochondrial genes were PCR-amplified from dek53-ref and WT-ref, dek53-mu1 and WT-mu1 kernel cDNA.RT-PCR amplicons obtained from each template were mixed in an equimolar ratio and  sheared by sonication. Sequencing libraries were generated using a NEB Next Ultra DNA.

value: kernel

tag: age

value: 15 DAP


title: WT-mu1-2

value: WT


title: dek53-mu1-2


title: WT-mu1-3


title: Taipei milkripe seeds (10 DAF) rep4

city: Madison

first: Sarah

middle: J

last: Whitcomb

state: WI

address: 502 Walnut St

department: Cereal Crops Research Unit

institute: USDA-ARS

data_processing:
Raw data were mapped against the rice genome using STAR  version 2.7.1a with the parameters --quantMode TranscriptomeSAM GeneCounts, --outSAMtype BAM Unsorted, and --outReadsUnmapped Fastx.
Genome_build: Ensembl version 43 (IRGSP 1.0) genome reference in FASTA format (ftp://ftp.ensemblgenomes.org/pub/release-43/plants/fasta/oryza_sativa/dna/Oryza_sativa.IRGSP-1.0.dna.toplevel.fa.gz) and Ensembl version 43 cDNA Annotation in GTF format (ftp://ftp.ensemblgenomes.org/pub/release-43/plants/gtf/oryza_sativa/Oryza_sativa.IRGSP-1.0.43.gtf.gz) were used for genome indexing (--sjdbOverhang 149 --genomeSAindexNbases 13)
Supplementary_files_format_and_content: Default STAR output files (ASCII format, tab delimited): Gene identifier, Read count (unstranded RNA-seq), Read count (counts for the 1st read strand aligned with RNA), Read count (counts for the 2nd read strand aligned with RNA)

organism: Oryza sativa Japonica Group

source_name: milkripe seeds (10 DAF)

growth_protocol: Seeds were allowed to germinate at 28°C in the dark on tap water-soaked paper towels. After 10 days, seedlings were transferred to a growth chamber with the following conditions: 12 h day length with a photon flux density of 600 μE m-2 s-1 (Lamps: Iwasaki Eye MT 400 DL/BH E40, DHL Licht, Wülfrath, Germany); 26 °C in the light and 22 °C in the dark; relative humidity of 75 % in the light and 70% in the dark. Single seedlings were transplanted into individual pots (18 cm deep, 10 cm diameter) of waterlogged soil after 7 days of acclimation to the growth chamber. Soil was a mixture of 2 parts potting soil (70 % white moss peat, 30 % clay) and one-part sand. 1 g of slow-release fertilizer (Plantacote Depot 4 M; Lanxess, Langenfeld, Germany) and 0.1 g Fetrilon Combi (Compo, Münster, Germany) was mixed into the soil in each pot. Pots were kept partially submerged in water. Milkripe seed samples were harvested 10 days after flowering on an individual panicle basis.

extract_protocol:
Total RNA was prepared from approximately 100 mg of frozen, finely ground tissue with RibospinTM Seed/Fruit kit (GeneAll Biotechnology, Korea) followed by two rounds of DNase treatment (first round with RiboclearTM plus! from GeneAll, second round with TURBO DNA-free Kit from Invitrogen) and PCR was performed to assess possible remaining genomic DNA contamination. Only those total RNA samples with RIN quality scores greater than 7.3 by Bioanalyzer were submitted for RNA sequencing
Library preparation and sequencing were performed at the Max Planck Genome Center, Cologne, Germany (https://mpgc.mpipz.mpg.de/home). rRNA depletion was performed on 1000 ng total RNA samples with the Ribo-Zero™ rRNA Removal Kit (seed/root) from Illumina. Subsequent library preparation was performed with NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biolabs) according to the manufacturer's instructions. Quality and quantity were assessed at all steps via capillary electrophoresis (TapeStation, Agilent Technologies) and fluorometry (Qubit, Thermo Fisher Scientific).

tag: line

value: Taipei

tag: replicate


title: dot1∆ SIR3-EBD G1_estradiol_1.5_hr Sir4-myc ChIP rep. 2

tag: strain

value: G1 (alpha factor) arrest followed by addition of estradiol for 1.5 hours

value: mat{delta} hml{delta}::HML* bar1{delta} SIR4-13xMyc; SIR3-EBD78; dot1{delta}


title: dek53-ref-3

tag: genotype


title: WT-ref-3


title: dek53-ref-2


title: WT-mu1-1


title: sir3∆ 15min_crosslink Sir4-myc ChIP

value: Pierce Anti-c-myc magnetic beads (Thermo Fisher Scientific 88843, lot # UF283471)

value: Cycling

value: mat{delta} hml{delta}::HML* bar1{delta} SIR4-13xMyc; sir3{delta}


title: dek53-ref-1


title: WT-ref-1


title: OppZ rep 2

status: Public on May 07 2020

city: Jena

first: Mona

last: Hoyos

address: Winzerlaer Straße 2

department: Institute for General Microbiology

country: Germany

institute: FSU Jena

data_processing:
Sequencing of the cDNA libraries was performed by the LAFUGA service unit (Gene Center, Munich, Blum group).
cDNA reads were imported into CLC Genomics Workbench v11.0.
adaptor- and quality trimming was performed using the trim reads command with the following settings: sequence=NEB P7:AGATCGGAAGAGCACACGTCTGAACTCCAGTCA, NEB P5:AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; reads: all; when an adapter is found: trim 3'end; for reads without adapters: keep the read; scores=mismatch:2, gapcost:3, cutoff:10; cutoff at end: 4
The trimmed reads were checked for quality and mapped with CLC Genomics Workbench v12.0.3 to the V. cholerae reference genome (NCBI Acc.number: NC_002505, NC_002506) using the following settings: Mismatch cost=2, Insertion cost=3, Deletion cost=3, Length fraction=0.8, Similarity fraction=0.8, Global alignment=yes, Strand specific=reverse, Maximum number of hits for a read=10
Reads mapping in CDS were counted, and genes with a total count cutoff of >15 in all samples were considered for analysis. Read counts were normalized (CPM), and transformed (log2). Differential expression was tested using the built in tool corresponding to edgeR in exact mode with tagwise dispersions. Genes with a fold-change of > 3.0 and a FDR adjusted p-value < 0.05 were considered to be differentially expressed.
Genome_build: NC_002505, NC_002506
Supplementary_files_format_and_content: Read count table and edgeR (exact mode) analysis

organism: Vibrio cholerae

source_name: whole bacterial cells

growth_protocol: V. cholerae C6706 wild-type strains carrying pBAD1K-ctrl or pBAD1K-oppZ were cultivated to exponential phase (OD600=0.5) in 50 ml LB media containing 50 µg/ml kanamycin.

extract_protocol:
RNA was isolated using AGPC with EXTRAzol according to standard protocols. Prepared RNA was DNase digested and cleaned up using standard nucleic acid precipitation procedures. Depletion of ribosomal RNA was performed using the Ribo-Zero rRNA Removal kit (Epicentre) for gram-negative bacteria. Integrity of the prepared RNA was tested using a Bioanalyzer.
cDNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB E7760), according to the manufacturer's instructions. Quality of the prepared libraries was tested using a Bioanalyzer.

treatment_protocol: L-arabinose (0.2% final conc.) was added when cells reached exponential phase (OD600=0.5). After 15 minutes of treatment, 4 OD600 units of cells were harvested in tubes containing 20% "stop-mix" (95% ethanol, 5% phenol) and snap-frozen in liquid nitrogen until further processing.

value: wt pBAD1K-oppZ

tag: growth phase

value: exponential phase

tag: treatment

value: 0.2% L-arabinose


title: OppZ rep 1


title: WT-ref-2


title: OppZ rep 3


title: W257_young_leaf_DNAmeth

status: Public on Apr 25 2020

city: Wuhan

first: Liang

last: Xie

state: Hubei

address: No.1,Shizishan Street

country: China

institute: Huazhong Agricultural University

data_processing:
The sequence quality of the whole-genome bisulfite sequencing (WGBS) libraries was evaluated using FastQC, and the adapter sequences and low-quality reads were filtered using Trimmomatic
The cleaned reads were then mapped to the MH63/ZS97 reference genome using BatMeth
The uniquely mapped reads were used for further analysis. Individual cytosines with coverage of at least 3 were considered for methylation-level calling.
The DNA methylation level of each cytosine was obtained by dividing the depth of methylated reads by the total coverage of individual cytosines
Genome_build: MH63,MSU7.0

organism: Oryza sativa

growth_protocol: Germinating seeds were obtained by soaking dry seeds in water for 72 h at 37 °C. For roots and young leaves, the germinated seeds were grown in a phytotron with the day/night cycle set at 14 h/10 h and a temperature of 32 °C/28 °C. Roots were obtained 7 d after planting on moist filter paper, and young leaves were obtained from 2-week-old plants cultured hydroponically as described34. Approximately 20-d-old seedlings were transplanted to the field and managed under normal agricultural conditions on the experimental farm of Huazhong Agricultural University, Wuhan, China. Mature leaves at the floral induction phase and young panicles were harvested.

extract_protocol:
Genomic DNA was extracted using a DNeasy plant mini kit according to the manufacturer’s instructions (QIAGEN, 69104).
Bisulfite conversion of DNA was conducted using the EZ DNA Methylation-GoldTM kit (ZYMO, D5005), and the bisulfite-treated DNA libraries were constructed using the Illumina TruSeq DNA sample prep kit, following the manufacturers’ instructions.

treatment_protocol: Fresh samples are frozen using liquid nitrogen.

tag: tissues

value: young leaf

value: young leaves from two-week old seedlings

tag: cultivar


title: W294_young_leaf_DNAmeth

value: LABELLE


title: W306_young_leaf_DNAmeth

value: BASMATI 385


title: W128_young_leaf_DNAmeth

value: TAINO 38


title: W261_young_leaf_DNAmeth

value: Ginga


title: dek53-mu1-1

value: kernel

value: 15 DAP


title: dot1∆ SIR3-EBD G1_estradiol_1.5_hr Sir4-myc ChIP rep. 1

tag: chip antibody

tag: condition


title: W161_young_leaf_DNAmeth


title: dot1∆ SIR3-EBD pre-estradiol Sir4-myc ChIP rep. 1

value: G1 (alpha factor) arrest without estradiol


title: C148_young_leaf_DNAmeth


title: C139_young_leaf_DNAmeth


title: W286_young_leaf_DNAmeth

value: Garia


title: W081_young_leaf_DNAmeth

value: Gasym Hany


title: C051_young_leaf_H3K4me1_rep1

data_processing:
Trimmomatic fitered the raw reads
ChIP-seq reads were aligned to the MSU.7.0/MH63 genome assembly using bwa mem
Data were filtered using the SAMTOOLS MAPQ30 and filter the  duplication reads
peaks were called using MACS.2.2.1 with narrow(H3K4me3,H3K27ac,PII)/broad(H3K27me3,H3K4me1,H3K9me2) parameters
Genome_build: MSU.7.0,MH63
Supplementary_files_format_and_content: bigWig by deepTools bamCoverage

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-DNA was extracted with phenol:chloroform:isoamyl alcohol (Sigma–Aldrich, P3803), precipitated with ethanol, and resuspended in TE buffer. ChIP DNA libraries were prepared using an NEBNext® Ultra™ II DNA library prep kit for Illumina® (New England BioLabs, E7645). Briefly, ChIP DNA was end-repaired, ligated with an adaptor, and followed by 6–10 cycles of PCR amplification, per the manufacturer’s guidelines. Next, library fragments of 250–650 bp were selected using AMPure XP beads (Beckman, A63881). Finally, the DNA fragments were sequenced using an Illumina HiSeq X Ten system (paired-end 150-bp reads)

treatment_protocol: Tissues were cross-linked with 1% formaldehyde for 10–15 min and quenched with 0.2 M glycine at room temperature.

tag: development stage


title: W105_young_leaf_DNAmeth

value: HKG 98


title: C019_young_leaf_FAIRE_rep1

data_processing:
Library strategy: FAIRE-seq
Trimmomatic fitered the raw reads
ChIP-seq reads were aligned to the MSU.7.0/MH63 genome assembly using bwa mem
Data were filtered using the SAMTOOLS MAPQ30 and filter the  duplication reads
Peak was calling using MACS2 with callpeak -t <input file> --nomodel --shift -100 --extsize 200 -f BAM –n <output peak file> -B -q 0.05 -g 3.6e+8
Genome_build: MH63,MSU7.0
Supplementary_files_format_and_content: bigWig by deepTools bamCoverage

extract_protocol:
The isolated nuclei pellet was resuspended in 400 ml of Sonic-FAIRE buffer (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5% SDS, and protease inhibitor cocktail) and fragmented into 200–400-bp pieces by sonication in a Bioruptor (Diagenode). Lysates were centrifuged at 20,000 × g for 10 min at 4 °C, and the supernatant was transferred to a new tube. To prepare FAIRE DNA, 1 volume of phenol:chloroform:isoamyl alcohol was added to the supernatant; the mixture was vortex-mixed and centrifuged at 20,000 × g for 10 min; and the supernatant was transferred to a new tube. These steps were repeated at least twice to remove nucleosome-coated DNA. After ethanol precipitation, FAIRE DNA was resuspended in TE buffer.
DNA libraries were prepared using an NEBNext® Ultra™ II DNA library prep kit for Illumina® (New England BioLabs, E7645).

value: Aijiaonante


title: C019_young_leaf_FAIRE_rep2


title: C051_young_leaf_FAIRE_rep1


title: W257_young_leaf_H3K4me3_rep2


title: C051_young_leaf_FAIRE_rep2


title: YH10_3_BT20_BCL2L14-E4_ETV6_E2_rep3

status: Public on Mar 28 2020

first: Xiaosong

last: Wang

state: Pennsylvania

address: 5150 Centre Ave

department: Pathology

description:
BCL2L14_Exon4-ETV6_Exon2_s3
BT20_BCL2L14-E4_ETV6-E2_rep3

data_processing:
Quality control test on the sequencing data was done with error rate calculation and a Phred Q20 and Q30 score. All samples passed with error rate (%) < 0.03, Q20 > 97%, and Q30 > 92%.
The preprocessed reads (fastq.gz) were mapped into reference genome (GCF_000001405.39_GRCh38.p13_genomic.fna) using Rsubread R package (ver. 1.30.5, Liao et al. 2013).
The transcripts of each sample were assembled based on Transcripts Per Million (TPM) method. The sequence read alignment was annotated with gene IDs by using NCBI gene annotation data, "GCF_000001405.39_GRCh38.p13_genomic.gtf."
The selection of differentially expressed genes (DEGs) among samples was performed based on the TPM log2 values of transcripts. We used Limma R pacakge (ver. 3.36.2, Ritchie et al. 2015).
Genome_build: As reference genome, we downloaded "GCF_000001405.39_GRCh38.p13_genomic.fna" file from NCBI. For gene ID annotation, we downloaded "GCF_000001405.39_GRCh38.p13_genomic.gtf" from NCBI FTP.
Supplementary_files_format_and_content: Tab-delimited text files include TPM log2 values for each Sample.

growth_protocol: BT20 cells were cultured in EMEM (ATCC) with 10 % fetal bovine serum (Hyclone).

extract_protocol:
Total RNA was extracted from cells in individual confluent 10 cm dish, using the standard procedure of Qiagen RNeasy kit. The primary quantitation of the extracted RNA were checked by nanodrop. The integrity and purity of RNA were examined by Agilent 2100.
The NovaSeq 6000 library for DNA sequencing was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) following the protocol provided by the manufacturer.
The final libraries were normalized by quantification with LightCycler 480 II (Roche Applied Science, Indianapolis, IN, USA) and qualification with Bioanalyzer (Agilent, Palo Alto, CA, USA).

treatment_protocol: transduction protocol: The BCL2L14-ETV6 fusion or wt ETV6 cDNA containing the full-length ORFs were subcloned into the lentiviral pLenti7.3 vector, and the lentivirus was further transduced to BT20 cell line.

tag: cell line

tag: cell type

value: human breast cancer cell line

tag: transfection vector

value: BCL2L14 Exon4 - ETV6 Exon2 fusion variant


title: W169_young_leaf_DNAmeth


title: YH10_2_BT20_BCL2L14-E4_ETV6_E2_rep2

description:
BCL2L14_Exon4-ETV6_Exon2_s2
BT20_BCL2L14-E4_ETV6-E2_rep2


title: C151_young_leaf_DNAmeth


title: YH10_1_BT20_BCL2L14-E4_ETV6_E2_rep1

description:
BCL2L14_Exon4-ETV6_Exon2_s1
BT20_BCL2L14-E4_ETV6-E2_rep1


title: YH8_1_BT20_BCL2L14-E2_ETV6_E3_rep1

description:
BCL2L14_Exon2-ETV6_Exon3_s1
BT20_BCL2L14-E2_ETV6-E3_rep1

value: BCL2L14 Exon2 - ETV6 Exon3 fusion variant


title: YH8_2_BT20_BCL2L14-E2_ETV6_E3_rep2

description:
BCL2L14_Exon2-ETV6_Exon3_s2
BT20_BCL2L14-E2_ETV6-E3_rep2


title: YH9_2_BT20_BCL2L14-E4_ETV6_E3_rep2

description:
BCL2L14_Exon4-ETV6_Exon3_s2
BT20_BCL2L14-E4_ETV6-E3_rep2

value: BCL2L14 Exon4 - ETV6 Exon3 fusion variant


title: YH8_3_BT20_BCL2L14-E2_ETV6_E3_rep3

description:
BCL2L14_Exon2-ETV6_Exon3_s3
BT20_BCL2L14-E2_ETV6-E3_rep3


title: YH9_1_BT20_BCL2L14-E4_ETV6_E3_rep1

description:
BCL2L14_Exon4-ETV6_Exon3_s1
BT20_BCL2L14-E4_ETV6-E3_rep1


title: YH7_3_BT20_wtETV6_rep3

description:
WildtypeETV6_s3
BT20_wtETV6_rep3

value: Wild type ETV6 cDNA


title: YH7_2_BT20_wtETV6_rep2

description:
WildtypeETV6_s2
BT20_wtETV6_rep2


title: W125_young_leaf_DNAmeth

value: young leaf

value: young leaves from two-week old seedlings

value: Yong Chal Byo


title: YH7_1_BT20_wtETV6_rep1

description:
WildtypeETV6_s1
BT20_wtETV6_rep1


title: YH6_3_BT20_Control_rep3

description:
Control_EmptyVector_s3
BT20_Control_rep3

value: Negative control:only lentiviral pLenti7.3 vector


title: YH6_2_BT20_Control_rep2

description:
Control_EmptyVector_s2
BT20_Control_rep2


title: MH63_root_H3K9me2_rep1

source_name: MH63 root

tag: tissue

value: root

value: one-week old root after planting

value: Minghui 63


title: Sperm_cells_rep3

status: Public on Mar 17 2020

city: Tübingen

first: Michael

last: Borg

address: Max Planck Ring 5

department: Algal Development & Evolution

institute: Max Planck Insititue for Biology

description: Smart-Seq2 library from sperm cells rep3

data_processing:
Raw, unaligned BAM files were first sorted with samtools sort -n and then converted to fastq files with bedtools bamtofastq.
Adapter trimming was performed using TrimGalore version 0.4.1.
Reads were aligned to the Arabidopsis genome (TAIR10) using the STAR aligner version 2.5.2a.
Transcripts per million (TPM) values were generated using Kallisto version 0.43.1 (21) with an index built on TAIR10 cDNA sequences.
Genome_build: TAIR10 cDNA sequences (Arabidopsis_thaliana.TAIR10.cdna.all.fa.gz)
Supplementary_files_format_and_content: *.txt: Table of TPM values for sperm and pollen RNA-seq. Publicly-available RNA-seq datasets (see Table S2 in manuscript)  were processed in the same pipeline and are included for reference.

organism: Arabidopsis thaliana

source_name: Sperm cells

extract_protocol:
RNA-seq libraries were generated from total RNA of mature pollen and FACS-isolated sperm cells using Smart-seq2.
Smart-seq2

tag: ecotype

value: wild type


title: Sperm_cells_rep2

description: Smart-Seq2 library from sperm cells rep2


title: Sperm_cells_rep1

description: Smart-Seq2 library from sperm cells rep1


title: Day9_ME-Parental_2

status: Public on Feb 07 2020

city: Shanghai

first: Xiaonan

address: 227 Chongqing South Road

department: School of Public Health

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Reads were aligned to Mus musculus genome (GRCm38.81) using Bowtie2, obtaining 55% of unique mappable reads. Peak calling was run using F-Seq 65 with the following parameters: -t14, -f1.
Genome_build: mm10
Supplementary_files_format_and_content: HT-Seq counts / peak counts (.txt)
Supplementary_files_format_and_content: Merged peak file (.bed)
Supplementary_files_format_and_content: Peak annotation (.txt)
Supplementary_files_format_and_content: Day0 Parental peak file (.bed)
Supplementary_files_format_and_content: Day6 Parental peak file (.bed)
Supplementary_files_format_and_content: Day6 ME-Parental peak file (.bed)
Supplementary_files_format_and_content: Day9 Parental peak file (.bed)
Supplementary_files_format_and_content: Day9 ME-Parental peak file (.bed)
Supplementary_files_format_and_content: Day0 Parental wig file (.wig)
Supplementary_files_format_and_content: Day6 Parental wig file (.wig)
Supplementary_files_format_and_content: Day6 ME-Parental wig file (.wig)
Supplementary_files_format_and_content: Day9 Parental wig file (.wig)
Supplementary_files_format_and_content: Day9 ME-Parental wig file (.wig)

source_name: Hoxb8 Cell line

growth_protocol: Three pools of 50,000 ME-Parental and Parental cells each, cultured in the presence of Flt3L  and β-estradiol, were bulk sorted into 1.5ml tubes and processed as previously described in Buenrostro et al. Nature methods 2013

extract_protocol:
Immediately following the nuclei prep, the pellet was resuspended in the transposase reaction mix (25 μL 2× TD buffer, 2.5 μL transposase (Illumina) and 22.5 μL nuclease-free water). The transposition reaction was carried out for 30 min at 37 °C. Directly following transposition the sample was purified using a Qiagen MinElute kit.
Following purification, we amplified library fragments using 1× NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers 1 and 2 (Supplementary Table 1), using the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min. To reduce GC and size bias in our PCR, we monitored the PCR reaction using qPCR in order to stop amplification before saturation. To do this, we amplified the full libraries for five cycles, after which we took an aliquot of the PCR reaction and added 10 μl of the PCR cocktail with Sybr Green at a final concentration of 0.6×. We ran this reaction for 20 cycles to determine the additional number of cycles needed for the remaining 45-μL reaction. The libraries were purified using a Qiagen PCR cleanup kit yielding a final library concentration of ∼30 nM in 20 μL. Libraries were amplified for a total of 10–12 cycles.

treatment_protocol: To prepare nuclei, we spun 50,000 cells at 500g for 5 min, which was followed by a wash using 50 μL of cold 1× PBS and centrifugation at 500g for 5 min. Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500g for 10 min using a refrigerated centrifuge. To avoid losing cells during the nuclei prep, we used a fixed-angle centrifuge and carefully pipetted away from the pellet after centrifugations.

value: Untreated

tag: day


title: Day9_ME-Parental_3


title: YH9_3_BT20_BCL2L14-E4_ETV6_E3_rep3

description:
BCL2L14_Exon4-ETV6_Exon3_s3
BT20_BCL2L14-E4_ETV6-E3_rep3


title: Day9_Parental_2


title: Day9_ME-Parental_1


title: Day9_Parental_3


title: ONT_GM12878_R2

status: Public on Mar 18 2020

city: Irvine

first: Ali

last: Mortazavi

state: California

address: 2218 Biological Sciences III

department: Developmental and cell biology

country: Canada

institute: University of California at Irvine

description: Library selection: Direct RNA

data_processing:
Fast5 basecalled with Guppy
Mapping was done using Minimap2 settings for direct-RNA seq
TranscriptClean was used for error correction using the default settings. The splice junction file was obtained using GENCODE v29 using one of the accesory scripts
TALON was used for annotation and quantification. The database was initialized with GENCODE v29
Genome_build: hg38
Supplementary_files_format_and_content: TXT table format;transcript counts not filtered: no spike-in or SIRV quantification

growth_protocol: ENCODE protocols cell line specific

extract_protocol:
The RNeasy Plus Mini Kit was used for RNA extraction following the manufacturer instructions
Starting from 3 μg of depleted RNA, we proceeded to the direct-RNA library prep following the RNA-002 kit instructions. Reverse transcription was used to get rid of secondary RNA structures


title: ONT_GM12878_R1

description: Library selection: Direct RNA


title: HD_10_S78

status: Public on Feb 03 2020

city: Bethesda

first: Laura

last: Dillon

state: Maryland

address: Room 10CRC 6-5142, 10 Center Drive

department: Hematology Branch

institute: National Heart Lung and Blood Institute, NIH

data_processing:
Reads were aligned to human genome assembly GRCh37/hg19 by HISAT2 (version 2.1.0) with default setting for paired-end reads. The aligned reads were converted to BAM files and sorted by SAMtools 1.9 with index files created. The sorted BAM files were processed in R (version 3.5; R Foundation for Statistical Computing, Vienna, Austria) with Bioconductor packages. The count matrix on gene level was generated by featureCounts in Rsubread function.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Gene raw count matrix in csv

source_name: Bone marrow

extract_protocol:
RNA was isolated from PAXgeneTM BM RNA tubes using the PAXgene BM RNA kit (PreAnalytiX). RNA quantity was measured using a Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA) and RNA quality was assessed using the TapeStation system (Agilent Technologies, Santa Clara, CA). All samples had RNA Integrity Numbers (RIN) of seven or higher.
Libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina Inc., San Diego, CA) using 1 μg of total RNA input and paired-end 75-bp sequencing on a HiSeq 3000 (Illumina, San Diego, CA).

treatment_protocol: No treatment

tag: age

tag: gender

value: F

tag: disease status

value: Healthy


title: Day6_Parental_2

tag: replicate


title: Day6_ME-Parental_1


title: HD_9_S75


title: Day6_ME-Parental_2


title: Day6_ME-Parental_3


title: Day6_Parental_1


title: YH6_1_BT20_Control_rep1

description:
Control_EmptyVector_s1
BT20_Control_rep1


title: HD_8_S74


title: Day9_Parental_1


title: HD_3_S65

value: M


title: HD_1_S60


title: HD_6_S71


title: Day6_Parental_3


title: HD_5_S69


title: AML_9_S33

value: AML


title: AML_8_S29


title: HD_4_S67


title: AML_7_S25


title: AML_3_S7


title: AML_6_S22


title: HD_7_S73


title: AML_2_S5


title: AML_1_S1


title: HD_2_S64


title: Sample_9_C1B

status: Public on Jan 07 2020

city: Cardiff

first: Caleb

last: Webber

address: Hadyn Ellis Building, Maindy road

department: School of Medicine

institute: Cardiff University

data_processing:
Paired end Fastq files for the human samples each had read 1( R1) of length 26 bp and Read 2 (R2) 98 bp
Sequencing reads were aligned against the GRCh38_premrna build for SN and cortex samples using 10x Cell Ranger v2.1
Digital gene expression matrices (with gene expression counts) for detected cell associated barcodes and unique molecular identifiers (UMIs) were generated by Cell Ranger software (v2.1 for SN  and cortex samples)
Digital gene expression matrices were analyzed for cell type clustering and identification for all SN and cortex samples using Seurat (v2.3.4)
Genome_build: GRCh38_premrna
Supplementary_files_format_and_content: digital gene expression matrix (sparse format): matrix market format, rows = genes/transcripts, columns = barcodes/cells ; barcodes list: names of barcodes/cells for corresponding DGE matrix file;genes list: names of transcripts/genes for corresponding DGE matrix file for each cortex and SN sample

molecule: polyA RNA

source_name: Brain

extract_protocol:
Briefly, 3mm2 pieces of fresh-frozen brain tissue were placed in homogenization buffer (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris Buffer pH 8.0, 1 mM DTT, 1X protease inhibitor, 0.4 U ul-1 RNaseIN, 0.2 U ul-1 Superasin, 0.1% v/v Triton X-100) for 10 minutes prior to mechanical disruption with a dounce homogenizer.  Homogenate was filtered through a 35 mM cell strainer before concentrating nuclei by centrifugation 400 g 5 minutes.  Nuclei were resuspended in FACS buffer (1 XPBS, 1 RNase-Free BSA, 0.2 U μl−1 of RNasin Plus RNase inhibitor, 10 ng ml-1 Hoechst 33342) prior to FACS to obtain a population of nuclei free cellular debris.Nuclei were washed once in PBS and resuspended in 0.04% BSA in PBS for loading on the 10x Chromium 3’ chip.
Cell capturing  and library preparation was carried as per kit instructions (Chromium Single Cell Kit [v2 chemistry])

value: Brain

tag: tissue region

value: Cortex

value: Male

tag: batch

value: Day 2

tag: post-mortem-interval(hours)


title: Sample_13_C4B


title: AML_5_S15


title: Sample_12_N2B

value: Substantia nigra


title: Sample_14_N4B


title: Sample_11_C2B


title: HCT116_water

status: Public on Apr 05 2020

city: Grand Rapids

first: Scott

last: Rothbart

state: MI

address: 333 Bostwick Ave NE

department: Center for Epigenetics

institute: Van Andel Research Institute

description: water

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to the Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting.

data_processing: openSesame from SeSAMe R package.

label: Cy3, Cy5

label_protocol: Standard Illumina Protocol.

growth_protocol: 37ºC, 5% CO2, McCoy's 5A media with 10% FBS and no antibiotics.

extract_protocol: 3x extraction: phenol, phenol/chloroform/isoamyl alcohol (25:24:1), chloroform/isoamyl alcohol (24:1); precipitation; RNase treatment; precipitation.


title: Sample_15_C5B

value: Female


title: Sample_10_N1B


title: Sample_8_N5

value: Day 1


title: Sample_6_N3


title: Sample_5_C3


title: AML_10_S36


title: Mutant scRNAseq Vegfa;Shh

status: Public on Jan 01 2020

city: Chicago

first: Lisandra

last: Vila Ellis

state: IL

address: 303 E Superior

department: Cell and Developmental Biology

institute: Northwestern University

data_processing:
Chromium single-cell RNA-seq output was processed with Cell Ranger using “cellranger count” and “cellranger aggr”.
Further analysis was carried out using Loupe Cell Browser (10x Genomics) or an R package Seurat
Genome_build: mm10
Supplementary_files_format_and_content: Cloupe file can be opened with Loupe cell browser to visualize the data.

source_name: mut scRNAseq Vegfa;Shh

extract_protocol:
FACS-purified lung ECs were processed through the Chromium Single Cell Gene Expression Solution Platform (10X Genomics) using the Chromium Single Cell 3' Library and Gel Bead Kit in accordance with the manufacturer’s user guide (v2, rev D).
The libraries were sequenced on an Illumina NextSeq500 using a 26X124 sequencing run format with 8 bp index (Read1).

tag: strain background

value: mixed

value: Postnatal day 7

tag: genotype/variation

value: mutant

value: Lung endothelial cells


title: mutant scRNAseq P6 all cells

description:
single cell RNA
Pan-epithelial deletion of Vegfa

source_name: mut scRNAseq P6 all cells

value: Postnatal day 6

value: VegfaCKO/CKO; ShhCre/+

value: endothelial, epithelial, immune, mesenchymal cells


title: Control scRNAseq Vegfa;Shh

source_name: ctrl scRNAseq Vegfa;Shh

value: control


title: control scRNAseq P6 all cells

description: single cell RNA

source_name: ctrl scRNAseq P6 all cells


title: Mutant scRNAseq Apln

source_name: mut scRNAseq Apln

value: Postnatal day 17


title: E17 wildtype scRNAseq

description: single cell RNA

source_name: E17 wildtype scRNAseq

value: Prenatal day 17

value: wildtype

value: endothelial cells


title: HCT116_FAM-LIG1-CPP


title: WT 60min_crosslink input

data_processing:
For samples sequenced on the Illumina NovaSeq 6000, FASTQ generation was performed using Illumina Casava v2.2. For samples sequenced on the Illumina Miniseq, FASTQ generation was performed using the Generate FASTQ module of Illumina Local Run Manager
Raw reads were mapped to SacCer3 genome modified to include hml∆::HML* and mat∆ using Bowtie2 with following options: --local --soft-clipped-unmapped-tlen --no-unal --no-mixed --no-discordant
bedgraph files were generated from aligned reads and normalized to the genome-wide median (median excluded subtelomeres, chromosome III, and rDNA). For MNase samples, only reads between 130-180 bp (mononucleosome) were included in bedgraphs.
Genome_build: SacCer3 (modified)
Supplementary_files_format_and_content: bedgraph (normalized to genome-wide median)

extract_protocol:
Cells were lysed by mechanical disruption in a bead beater. Chromatin was fragmented using either sonication (all H3K79me3 samples) or MNase (all Sir4-myc and Sir3-EBD samples except for a subset fragmented by sonication, noted in the sample title). DNA was purified using Qiagen spin column kit
NEB Ultra II library prep kit

tag: strain

tag: chip antibody

tag: condition

value: Cycling

tag: genotype

value: mat{delta} hml{delta}::HML* bar1{delta} SIR4-13xMyc


title: GCRC2089X

status: Public on Dec 31 2019

city: Montreal

first: Alain

last: Pacis

state: QC

address: 740 Dr Penfield Ave

institute: Canadian Centre for Computational Genomics (C3G)

description: GCRC2089X PDX

data_processing:
Illumina bcl2fastq software used for basecalling.
Adaptor sequences and low-quality score bases (Phred score < 30) were first trimmed using Trimmomatic.
The resulting reads were aligned to the human genome reference sequence (GRCh38), using STAR.
Reads originating from mouse in xenograft samples were removed using the Disambiguate algorithm.
Read counts for each sample are obtained using HTSeq.
Genome_build: GRCh38
Supplementary_files_format_and_content: *.readcounts.txt: Tab-delimited text files include count values for each sample.

growth_protocol: In vivo

extract_protocol:
AllPrep DNA/RNA Mini.
Illumina ssRNA-seq construction.

tag: sa id

tag: patient

tag: diagnosis

value: Breast cancer

value: Breast

tag: sample type

value: PDX

tag: passage


title: Wildtype scRNAseq

source_name: Wildtype scRNAseq

value: mixed

tag: age

value: Postnatal day 14

tag: cell type


title: GCRC2080T

description: GCRC2080T patient tumor

tag: tissue

value: Primary tumor


title: Sample_7_N4

value: Brain

tag: tissue region

value: Substantia nigra

tag: gender

value: Male

value: Day 1


title: GCRC2080X

description: GCRC2080X PDX


title: GCRC2076X

description: GCRC2076X PDX


title: E19 wildtype scRNAseq

description: single cell RNA

source_name: E19 wildtype scRNAseq

value: Prenatal day 19


title: GCRC2061X

description: GCRC2061X PDX


title: Control scRNAseq Apln

source_name: ctrl scRNAseq Apln

value: Postnatal day 17

value: control

value: Lung endothelial cells


title: GCRC2029X

description: GCRC2029X PDX


title: GCRC2061T

description: GCRC2061T patient tumor


title: GCRC2047X

description: GCRC2047X PDX


title: GCRC2029T

description: GCRC2029T patient tumor


title: GCRC2054X

description: GCRC2054X PDX


title: GCRC2047T

description: GCRC2047T patient tumor


title: GCRC2007X

description: GCRC2007X PDX


title: GCRC2007T

description: GCRC2007T patient tumor


title: GCRC2006X

description: GCRC2006X PDX


title: GCRC2006T

description: GCRC2006T patient tumor


title: GCRC1986X

description: GCRC1986X PDX


title: GCRC1979X

description: GCRC1979X PDX


title: GCRC1945T

description: GCRC1945T patient tumor


title: GCRC1944X

description: GCRC1944X PDX


title: GCRC1945X

description: GCRC1945X PDX


title: GCRC1738X

description: GCRC1738X PDX


title: GCRC1715T

description: GCRC1715T patient tumor


title: GCRC1738T

description: GCRC1738T patient tumor


title: GCRC1834T

description: GCRC1834T patient tumor


title: GCRC1828X

description: GCRC1828X PDX


title: GCRC1828T

description: GCRC1828T patient tumor


title: GCRC1715X

description: GCRC1715X PDX


title: GCRC1834X

description: GCRC1834X PDX


title: GCRC2001T

description: GCRC2001T patient tumor


title: GCRC2001X

description: GCRC2001X PDX


title: GCRC1863T

description: GCRC1863T patient tumor


title: GCRC1863X

description: GCRC1863X PDX


title: GCRC1939X

description: GCRC1939X PDX


title: GCRC1915X

description: GCRC1915X PDX


title: GCRC1939T

description: GCRC1939T patient tumor


title: GCRC1886X

description: GCRC1886X PDX


title: GCRC1886T

description: GCRC1886T patient tumor


title: GCRC1915T

description: GCRC1915T patient tumor


title: GCRC1882X

description: GCRC1882X PDX


title: GCRC1991T

description: GCRC1991T patient tumor


title: GCRC1991X

description: GCRC1991X PDX


title: GCRC1882T

description: GCRC1882T patient tumor


title: GCRC1856T

description: GCRC1856T patient tumor


title: GCRC1840X

description: GCRC1840X PDX


title: GCRC1971X

description: GCRC1971X PDX


title: GCRC1868X

description: GCRC1868X PDX


title: GCRC1876T

description: GCRC1876T patient tumor


title: GCRC1868T

description: GCRC1868T patient tumor


title: GCRC1856X

description: GCRC1856X PDX


title: GCRC1840T

description: GCRC1840T patient tumor


title: GCRC1876X

description: GCRC1876X PDX


title: GCRC1971T

description: GCRC1971T patient tumor


title: GCRC1851X

description: GCRC1851X PDX


title: GCRC1851T

description: GCRC1851T patient tumor


title: GCRC1905X

description: GCRC1905X PDX


title: GCRC1887X

description: GCRC1887X PDX


title: GCRC1924X

description: GCRC1924X PDX


title: GCRC1963X

description: GCRC1963X PDX


title: GCRC1735X

description: GCRC1735X PDX


title: GCRC1735T

description: GCRC1735T patient tumor


title: GCRC1887T

description: GCRC1887T patient tumor


title: GCRC1963T

description: GCRC1963T patient tumor


title: GCRC1784X_ductal

description: GCRC1784X_ductal PDX

value: Ductal PDX


title: GCRC1784X_chondroid

description: GCRC1784X_chondroid PDX

value: Chondroid PDX


title: GCRC1784T

description: GCRC1784T patient tumor


title: GCRC1905T

description: GCRC1905T patient tumor


title: 16149X12 11-V

status: Public on Dec 30 2019

city: Salt Lake City

first: Micah

last: Drummond

state: Utah

address: 520 Wakara Way

department: Physical Therapy and Athletic Training

institute: The University of Utah

data_processing:
To analyze RNA sequencing data, mouse GRCm38 FASTA and GTF files were downloaded from Ensembl release 96 and the reference database was created using STAR version 2.7.0f with splice junctions optimized for 50 base pair reads
Mapped reads were assigned to annotated genes in the GTF file using featureCounts v1.6.3
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2
Genome_build: GRCm38
Supplementary_files_format_and_content: FeatureCount output files combined into a single matrix

source_name: Visceral Fat

extract_protocol:
10-15 mg of tissue was placed in Tri reagent LS (Molecular Research Center, Cincinnati, OH, USA) and disrupted via hand-held homogenizer (Bio-Gen PRO200; Pro Scientific, Oxford, CT, USA).  Chloroform was added to separate the RNA into an aqueous phase that was then precipitated using isopropanol.   Extracted RNA was then washed with ethanol and suspended in nuclease-free water with EDTA.  RNA was purified using TURBO DNase (AM2238) with Zymo RNA Clean and Concentrator-5 clean up.  RNA integrity and quantity was determined using the EPOCH (Take3; BioTek) spectrophotometer.
Total RNA samples (100-500 ng) were hybridized with Ribo-Zero Gold to substantially deplete cytoplasmic and mitochondrial rRNA from the samples.  Stranded RNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded Total RNA Library Prep Gold kit (20020598) with TruSeq RNA UD Indexes (20022371).  Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583), and average RIN was 8.3.  The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized to 1.30 nM in preparation for Illumina sequence analysis.  Sequencing libraries (1.3 nM) were chemically denatured and applied to an Illumina NovaSeq flow cell using the NovaSeq XP chemistry workflow (20021664).

treatment_protocol: The samples used for this study are from the red portion of the gastrocnemius muscle and visceral fat.  Mice (Cre-control vs MyD88 Muscle KO) were subject to 5 weeks of wheel running followed by 8 days of restricted movement (small mouse cage; SMC).

tag: subject

value: Cre-Control

tag: Sex

value: Female

value: Visceral Fat


title: 16149X16 29-V

value: Conditional MusMyD88-/-


title: 16149X14 958-V


title: 16149X13 139-V


title: 16149X15 960-V


title: 16149X11 138-V


title: 16149X10 137-V


title: 16149X9 131-V


title: 16149X8 29-M

source_name: Red gastrocnemius Muscle

value: Red gastrocnemius Muscle


title: RNAseq OCM1 sgRNA-2_rep1

status: Public on Aug 27 2019

first: Peiwei

last: Chai

state: Shanghai

address: No.833 Zhizaoju Road

department: Opthalmology

institute: Shanghai Ninth people's hospital

data_processing:
Illumina HiSeq 4000 software used for basecalling.
WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
Genome_build: Hg19
Supplementary_files_format_and_content: wig files

source_name: melanoma cells

extract_protocol:
Retinoblastoma and peri-tumor samples were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ocular melanoma cells


title: 16149X3 138-M


title: 16149X5 139-M


title: RNAseq OCM1 sgRNA-NC_rep1


title: 16149X1 131-M


title: 16149X6 958-M


title: 16149X2 137-M


title: 16149X4 11-M


title: ADSCD10P3

status: Public on Jun 19 2019

city: Beijing

first: Zhou

last: Zhou

address: Beilishi Street 167, Xi Cheng District

institute: Fuwai Hospital, the Chinese Academy of Medical Sciences

description:
Normal upper abdomen of lymphedema patient.
PolyA RNA
mRNA-seq

data_processing:
The expression of the transcripts was quantified with kallisto v0.43.1 under default settings.
Genome_build: GRCh37
Supplementary_files_format_and_content: *tsv: Tab-delimited text files include TPM values for each sample.

source_name: adipose-derived mesenchymal stem cells

extract_protocol:
Total cellular RNA was extracted using a miRNeasy Mini Kit (217004, Qiagen) according to the manufacturer’s instructions.
Library construction was performed by using a NEBNext Ultra RNA library Prep Kit for Illumina (#E7530L, NEB).

tag: disease diagnosis

value: Lymphedema

value: Adipose-derived mesenchymal stem cells

tag: sampling position

value: Normal upper abdomen


title: 16149X7 960-M


title: globular-seed-WOX9-like ChIP replicate 1

status: Public on Aug 02 2019

city: Los Angeles

first: Bob

last: Goldberg

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: Whole seeds 1.0 - 1.5 mm in length were collected

data_processing:
Basecalls performed using RTA version 1.12.4.2
Sequenced reads passing Illumina quality filter were aligned to the Glycine max genome (Wm82.a2.v1) using Bowtie v0.12.7 with parameters -v 2 -5 0 -3 0 -m 1 --best --strata
Reads were filtered to remove PCR duplicates using samtools (v.0.1.18).
Peaks were identified using MACS2 with default parameters and a q-value threshold of 0.01.
Genome_build: Wm82.a2.v1
Supplementary_files_format_and_content: NarrowPeak files generated by MACS2

organism: Glycine max

source_name: Soybean seeds containing globular stage embryos

growth_protocol: Soybean plants (Williams 82) were grown under standard greenhouse conditions (Le et al., PNAS 2010).

extract_protocol:
Chromatin isolation and immunoprecipitation were performed as described in Gendrel AV, Lippman Z, Martienssen R, Colot V. Nat Methods. 2005;2:213–218, except that the isolated nuclei were resuspended in lysis buffer described in by Johnson et al. (2002) and sonicated to achieve chromatin fragments ranging from 100 to 500 bp. Nuclear extracts were either set aside for whole genome extracts (input control) or incubated overnight with 10ug of polyclonal antibody raised against GmWOX9-like peptide NHHTPTSLPQTATTA in rabbit. Crosslinks were reversed and protein digested as described in Dahl and Collas, Nat Protoc. 2008;3(6):1032-45, extracted with phenol:chloroform and precipitated using standard procedures.
ChIP and Input libraries were generated using Nugen Ovation Ultralow DR Multiplex System, following the manufaturer's instructions and enriched by PCR using 15 cycles.

treatment_protocol: Whole seeds were collected and crosslinked under vaccuum for 10 minutes in Buffer A (0.4M sucrose, 10 mM Tris pH 8.0, 1mM EDTA pH 8.0) containing 1% formaldehyde, at room temperature, then quenched in 100 mM Glycine for 5 minutes. Tissues were rinsed twice with deionized water and stored at -80C until use.

tag: cultivar

value: Williams 82

tag: developmental stage

value: globular stage

value: whole seeds

tag: chip antibody

value: anti-peptide GmWOX9-like


title: ani_E. verrucosus, gradual temperature increase, 24 degrees C, sample 2

status: Public on May 23 2019

city: Irkutsk

first: Polina

last: Drozdova

state: Irkutsk region

address: Lenin str. 3

department: Institute of Biology

country: Russia

institute: Irkutsk State University

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 23 days at 24.4 degrees C.
EveT24_2
differential expression file:
EveT24annot.csv

data_processing:
Raw reads were mapped onto transcriptome assemblies with salmon v0.9.1.
DESeq2 abundance estimation was performed with an in-house R script, which can be found at https://github.com/drozdovapb/EveEcyGlaDE.
Transcript abundances were merged with transcript annotation.
Genome_build: de novo transcriptome assembly of the corresponding species (FASTA files on series record)
Supplementary_files_format_and_content: Salmon output files as TPM (transcript per million counts, text files) and DESeq2 output files with custom annotation (*annot.csv)
Supplementary_files_format_and_content: GSE129069_update_Ecy_Eve_Gla_differential_expression_T12_T18_and_T24_to_B6.tar.gz: Differential expression for the samples fixed at 12.4, 18, and 24.4 degrees C (T12, T18, and T24, respectively) was analyzed relative to the initial control at 6 degrees C (B6) separately for each species; the species-specific assemblies EveBCdTP1_ani, EcyBCdTP1_ani, and GlaBCdTP1_ani were used. The abundance of each transcript was estimated with salmon (Patro et al., 2017, https://doi.org/10.1038/nmeth.4197), and differential expression was calculated with the DESeq2 (Love et al., 2014; https://doi.org/10.1186/s13059-014-0550-8) package for the R statistical environment (R Core Team, 2017) using scripts provided by Trinity (Haas et al., 2013, https://doi.org/10.1038/nprot.2013.084).

organism: Eulimnogammarus verrucosus

source_name: whole body

extract_protocol:
Total RNA for RNA sequencing was extracted from either a single individual or from a pool of up to 5 individuals (see individual BioSample description). Amphipods were homogenized in 1 ml of Qiazol Reagent (Qiagen) with MM400 homogenizer (Retsch). RNA isolation from the aqueous phases was performed with a Qiacube (Qiagen) and miRNeasy kit (Qiagen).
mRNA was isolated from the total RNA sample using Oligotex mRNA Mini Kit (Qiagen). The quality of RNA was checked with RNA 6000 Nano Kit on the Agilent Bioanalyzer 2100. mRNA libraries were prepared with ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre, # SSV21124).

treatment_protocol: Animals were acclimated at 6 degrees C for 3-5 days before the experiment. Please refer to description of individual samples for species- and sample-specific details

value: whole body

value: rocky littoral zone

value: Russia:Irkutsk region, Lake Baikal, Bolshie Koty village

value: Till Luckenbach, Daria Bedulina

tag: depth

value: adult

value: littoral zone

value: Maxim Timofeyev, Daria Bedulina

tag: condition


title: ani_E. verrucosus, gradual temperature increase, 18 degrees C, sample 3

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 15 days at 18 degrees C.
EveT18_3
differential expression file:
EveT18annot.csv


title: ani_E. verrucosus, gradual temperature increase, 24 degrees C, sample 3

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 23 days at 24.4 degrees C.
EveT24_3
differential expression file:
EveT24annot.csv


title: ani_E. verrucosus, gradual temperature increase, 18 degrees C, sample 4

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 15 days at 18 degrees C.
EveT18_4
differential expression file:
EveT18annot.csv


title: ani_E. verrucosus, gradual temperature increase, 24 degrees C, sample 4

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 23 days at 24.4 degrees C.
EveT24_4
differential expression file:
EveT24annot.csv


title: ani_E. verrucosus, gradual temperature increase, 12 degrees C, sample 3

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 8 days at 12.4 degrees C.
EveT12_3
differential expression file:
EveT12annot.csv


title: ani_E. verrucosus, gradual temperature increase, 12 degrees C, sample 2

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 8 days at 12.4 degrees C.
EveT12_2
differential expression file:
EveT12annot.csv


title: ani_E. verrucosus, gradual temperature increase, 12 degrees C, sample 1

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 8 days at 12.4 degrees C.
EveT12_1
differential expression file:
EveT12annot.csv


title: RNAseq OCM1 sgRNA-1_rep1


title: ani_E. verrucosus, parallel control for EveT24, sample 3

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 23 days (parallel control for gradual temperature rise).
EveB247
differential expression file:
EveT24annot.csv


title: ani_E. verrucosus, parallel control for EveT18, sample 4

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 15 days (parallel control for gradual temperature rise).
EveB18_4
differential expression file:
EveT18annot.csv


title: ani_E. verrucosus, parallel control for EveT24, sample 1

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 23 days (parallel control for gradual temperature rise).
EveB24_1_6
differential expression file:
EveT24annot.csv


title: ani_E. verrucosus, parallel control for EveT24, sample 4

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 23 days (parallel control for gradual temperature rise).
EveB24_4
differential expression file:
EveT24annot.csv


title: ani_E. verrucosus, gradual temperature increase, 24 degrees C, sample 1

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 23 days at 24.4 degrees C.
EveT24_1
differential expression file:
EveT24annot.csv


title: ani_E. verrucosus, parallel control for EveT18, sample 3

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 15 days (parallel control for gradual temperature rise).
EveB18_3
differential expression file:
EveT18annot.csv


title: ani_E. cyaneus, gradual temperature increase, 24 degrees C, sample 4

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 23 days at 24.4 degrees C.
EcyT24_4
differential expression file:
EcyT24annot.csv

organism: Eulimnogammarus cyaneus


title: ani_E. cyaneus, gradual temperature increase, 24 degrees C, sample 3

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 23 days at 24.4 degrees C.
EcyT24_3
differential expression file:
EcyT24annot.csv


title: ani_E. verrucosus, parallel control for EveT18, sample 2

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 15 days (parallel control for gradual temperature rise).
EveB18_2
differential expression file:
EveT18annot.csv


title: ani_E. verrucosus, parallel control for EveT18, sample 1

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 15 days (parallel control for gradual temperature rise).
EveB18_1
differential expression file:
EveT18annot.csv


title: ani_E. verrucosus, parallel control for EveT12, sample 2

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 8 days (parallel control for gradual temperature rise).
EveB12_2
differential expression file:
EveT12annot.csv


title: ani_E. verrucosus, parallel control for EveT12, sample 3

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 8 days (parallel control for gradual temperature rise).
EveB12_3
differential expression file:
EveT12annot.csv


title: ani_E. cyaneus, gradual temperature increase, 24 degrees C, sample 1

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 23 days at 24.4 degrees C.
EcyT24_1
differential expression file:
EcyT24annot.csv


title: ani_E. cyaneus, gradual temperature increase, 24 degrees C, sample 2

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 23 days at 24.4 degrees C.
EcyT24_2
differential expression file:
EcyT24annot.csv


title: ani_E. cyaneus, gradual temperature increase, 18 degrees C, sample 1

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 15 days at 18 degrees C.
EcyT18_1
differential expression file:
EcyT18annot.csv


title: ani_E. cyaneus, gradual temperature increase, 18 degrees C, sample 4

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 15 days at 18 degrees C.
EcyT18_4
differential expression file:
EcyT18annot.csv


title: ani_E. cyaneus, gradual temperature increase, 12 degrees C, sample 1

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 8 days at 12.4 degrees C.
EcyT12_1
differential expression file:
EcyT12annot.csv


title: ani_E. cyaneus, gradual temperature increase, 12 degrees C, sample 2

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 8 days at 12.4 degrees C.
EcyT12_2
differential expression file:
EcyT12annot.csv


title: ani_E. cyaneus, parallel control for EcyT24, sample 4

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 23 days (parallel control for gradual temperature rise).
EcyB24_4_7
differential expression file:
EcyT24annot.csv


title: ani_E. cyaneus, gradual temperature increase, 18 degrees C, sample 2

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 15 days at 18 degrees C.
EcyT18_2
differential expression file:
EcyT18annot.csv


title: ani_E. cyaneus, gradual temperature increase, 18 degrees C, sample 3

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 15 days at 18 degrees C.
EcyT18_3
differential expression file:
EcyT18annot.csv


title: ani_E. verrucosus, gradual temperature increase, 18 degrees C, sample 1

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 15 days at 18 degrees C.
EveT18_1
differential expression file:
EveT18annot.csv


title: ani_E. cyaneus, parallel control for EcyT24, sample 2

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 23 days (parallel control for gradual temperature rise).
EcyB24_2_6
differential expression file:
EcyT24annot.csv


title: ani_E. verrucosus, gradual temperature increase, 18 degrees C, sample 2

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 15 days at 18 degrees C.
EveT18_2
differential expression file:
EveT18annot.csv


title: ani_E. cyaneus, parallel control for EcyT18, sample 4

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 15 days (parallel control for gradual temperature rise).
EcyB18_4
differential expression file:
EcyT18annot.csv


title: ani_E. cyaneus, parallel control for EcyT18, sample 2

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 15 days (parallel control for gradual temperature rise).
EcyB18_2
differential expression file:
EcyT18annot.csv


title: ani_E. cyaneus, gradual temperature increase, 12 degrees C, sample 3

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 8 days at 12.4 degrees C.
EcyT12_3
differential expression file:
EcyT12annot.csv


title: ani_E. cyaneus, parallel control for EcyT24, sample 1

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 23 days (parallel control for gradual temperature rise).
EcyB24_1_6
differential expression file:
EcyT24annot.csv


title: ani_E. cyaneus, parallel control for EcyT24, sample 3

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 23 days (parallel control for gradual temperature rise).
EcyB247
differential expression file:
EcyT24annot.csv


title: ani_E. cyaneus, parallel control for EcyT18, sample 1b

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 15 days (parallel control for gradual temperature rise).
EcyB18_1b
differential expression file:
EcyT18annot.csv


title: ani_E. cyaneus, parallel control for EcyT18, sample 1

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 15 days (parallel control for gradual temperature rise).
EcyB18_1a
differential expression file:
EcyT18annot.csv


title: ani_E. verrucosus, parallel control for EveT12, sample 4

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 8 days (parallel control for gradual temperature rise).
EveB12_4
differential expression file:
EveT12annot.csv


title: ani_E. cyaneus, parallel control for EcyT12, sample 4

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 8 days (parallel control for gradual temperature rise).
EcyB12_4
differential expression file:
EcyT12annot.csv


title: ani_E. cyaneus, parallel control for EcyT12, sample 3

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 8 days (parallel control for gradual temperature rise).
EcyB12_3
differential expression file:
EcyT12annot.csv


title: ani_E. cyaneus, parallel control for EcyT12, sample 1

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 8 days (parallel control for gradual temperature rise).
EcyB12_1
differential expression file:
EcyT12annot.csv


title: ani_E. cyaneus, initial control for EcyT, sample 3

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and acclimated to 6 degrees C (initial control).
EcyB6_3
differential expression file:


title: ani_E. cyaneus, initial control for EcyT, sample 4

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and acclimated to 6 degrees C (initial control).
EcyB6_4
differential expression file:


title: ani_E. cyaneus, initial control for EcyT, sample 2

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and acclimated to 6 degrees C (initial control).
EcyB6_2
differential expression file:


title: ani_E. cyaneus, 1 mg/L phenanthrene, 24 hours, sample 4

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene (dissolved in acetone) for 24 hours.
EcyP24_4
differential expression file:
EcyPh24_annot.csv
EcyPhB24_annot.csv


title: ani_E. cyaneus, parallel control for EcyT12, sample 2

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 8 days (parallel control for gradual temperature rise).
EcyB12_2
differential expression file:
EcyT12annot.csv


title: ani_E. cyaneus, initial control for EcyT, sample 1

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and acclimated to 6 degrees C (initial control).
EcyB6_1
differential expression file:


title: ani_E. cyaneus, 1 mg/L phenanthrene, 24 hours, sample 3

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene (dissolved in acetone) for 24 hours.
EcyP24_3
differential expression file:
EcyPh24_annot.csv
EcyPhB24_annot.csv


title: ani_E. cyaneus, 1 mg/L phenanthrene, 24 hours, sample 1

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene (dissolved in acetone) for 24 hours.
EcyP24_1
differential expression file:
EcyPh24_annot.csv
EcyPhB24_annot.csv


title: ani_E. cyaneus, 0.1% acetone, 24 hours, sample 3

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to 0.1% acetone (phenanthrene solvent) for 24 hours.
EcyPB24_3
differential expression file:
EcyPB24_annot.csv


title: ani_E. cyaneus, 1 mg/L phenanthrene, 3 hours, sample 2

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene (dissolved in acetone) for 3 hours.
EcyP3_2
differential expression file:
EcyPh3_annot.csv
EcyPhB3_annot.csv


title: ani_E. cyaneus, 1 mg/L phenanthrene, 3 hours, sample 1

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene (dissolved in acetone) for 3 hours.
EcyP3_1
differential expression file:
EcyPh3_annot.csv
EcyPhB3_annot.csv


title: ani_E. cyaneus, 1 mg/L phenanthrene, 3 hours, sample 4

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene (dissolved in acetone) for 3 hours.
EcyP3_4
differential expression file:
EcyPh3_annot.csv
EcyPhB3_annot.csv


title: ani_E. cyaneus, 1 mg/L phenanthrene, 3 hours, sample 3

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene (dissolved in acetone) for 3 hours.
EcyP3_3
differential expression file:
EcyPh3_annot.csv
EcyPhB3_annot.csv


title: ani_E. cyaneus, 0.1% acetone, 3 hours, sample 3

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to 0.1% acetone (phenanthrene solvent) for 3 hours.
EcyPB3_3
differential expression file:
EcyPB3_annot.csv


title: ani_E. cyaneus, 0.1% acetone, 24 hours, sample 1

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to 0.1% acetone (phenanthrene solvent) for 24 hours.
EcyPB24_1
differential expression file:
EcyPB24_annot.csv


title: ani_E. cyaneus, 0.1% acetone, 3 hours, sample 2

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to 0.1% acetone (phenanthrene solvent) for 3 hours.
EcyPB3_2
differential expression file:
EcyPB3_annot.csv


title: ani_E. cyaneus, LT10, 24 hours, sample 2

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and subjected to LT10 (24.6 degrees C) for 24 hours.
Ecy10LT24_2
differential expression file:
Ecy10LT24_annot.csv


title: ani_E. cyaneus, LT10, 3 hours, sample 2

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and subjected to LT10 (24.6 degrees C) for 3 hours.
Ecy10LT3_2
differential expression file:
Ecy10LT3_annot.csv


title: ani_E. cyaneus, LT10, 24 hours, sample 3

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and subjected to LT10 (24.6 degrees C) for 24 hours.
Ecy10LT24_3
differential expression file:
Ecy10LT24_annot.csv


title: ani_E. cyaneus, LT10, 3 hours, sample 4

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and subjected to LT10 (24.6 degrees C) for 3 hours.
Ecy10LT3_4
differential expression file:
Ecy10LT3_annot.csv


title: ani_E. cyaneus, LT10, 24 hours, sample 4

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and subjected to LT10 (24.6 degrees C) for 24 hours.
Ecy10LT24_4
differential expression file:
Ecy10LT24_annot.csv


title: ani_E. cyaneus, LT10, 3 hours, sample 1

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and subjected to LT10 (24.6 degrees C) for 3 hours.
Ecy10LT3_1
differential expression file:
Ecy10LT3_annot.csv


title: ani_E. cyaneus, 0.1% acetone, 3 hours, sample 1

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to 0.1% acetone (phenanthrene solvent) for 3 hours.
EcyPB3_1
differential expression file:
EcyPB3_annot.csv


title: ani_E. cyaneus, LT10, 24 hours, sample 1

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and subjected to LT10 (24.6 degrees C) for 24 hours.
Ecy10LT24_1
differential expression file:
Ecy10LT24_annot.csv


title: ani_E. cyaneus, 0.1% acetone, 24 hours, sample 2

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to 0.1% acetone (phenanthrene solvent) for 24 hours.
EcyPB24_2
differential expression file:
EcyPB24_annot.csv


title: ani_E. cyaneus, 1 mg/L phenanthrene, 24 hours, sample 2

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene (dissolved in acetone) for 24 hours.
EcyP24_2
differential expression file:
EcyPh24_annot.csv
EcyPhB24_annot.csv


title: ani_E. cyaneus, LC10 cadmium, 3 hours, sample 2

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to LC10 (3.7 uM) cadmium chloride for 3 hours.
EcyCd3_2
differential expression file:
EcyCd3_annot.csv


title: ani_E. cyaneus, LC10 cadmium, 3 hours, sample 4

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to LC10 (3.7 uM) cadmium chloride for 3 hours.
EcyCd3_4
differential expression file:
EcyCd3_annot.csv


title: ani_E. cyaneus, LC10 cadmium, 24 hours, sample 1

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to LC10 (3.7 uM) cadmium chloride for 24 hours.
EcyCd24_1
differential expression file:
EcyCd24_annot.csv


title: ani_E. cyaneus, LC10 cadmium, 24 hours, sample 2

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to LC10 (3.7 uM) cadmium chloride for 24 hours.
EcyCd24_2
differential expression file:
EcyCd24_annot.csv


title: ani_E. cyaneus, LC10 cadmium, 3 hours, sample 3

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to LC10 (3.7 uM) cadmium chloride for 3 hours.
EcyCd3_3
differential expression file:
EcyCd3_annot.csv


title: ani_E. cyaneus, LC10 cadmium, 3 hours, sample 1

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to LC10 (3.7 uM) cadmium chloride for 3 hours.
EcyCd3_1
differential expression file:
EcyCd3_annot.csv


title: ani_E. cyaneus, control, 3 hours, sample 2

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 3 hours (parallel control).
EcyB3_2
differential expression file:
EcyCd3_annot.csv
Ecy10LT3_annot.csv
EcyPB3_annot.csv
EcyPhB3_annot.csv


title: ani_E. cyaneus, control, 3 hours, sample 4

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 3 hours (parallel control).
EcyB3_4
differential expression file:
EcyCd3_annot.csv
Ecy10LT3_annot.csv
EcyPB3_annot.csv
EcyPhB3_annot.csv


title: ani_G. lacustris, gradual temperature increase, 24 degrees C, sample 3

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 23 days at 24.4 degrees C.
GlaT24_4
differential expression file:
GlaT24annot.csv

organism: Gammarus lacustris

value: Russia:Irkutsk region, Bolshie Koty village, Lake No14


title: ani_E. cyaneus, control, 3 hours, sample 3

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 3 hours (parallel control).
EcyB3_3
differential expression file:
EcyCd3_annot.csv
Ecy10LT3_annot.csv
EcyPB3_annot.csv
EcyPhB3_annot.csv


title: ani_E. cyaneus, control, 3 hours, sample 1

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 3 hours (parallel control).
EcyB3_1
differential expression file:
EcyCd3_annot.csv
Ecy10LT3_annot.csv
EcyPB3_annot.csv
EcyPhB3_annot.csv


title: ani_G. lacustris, gradual temperature increase, 24 degrees C, sample 2

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 23 days at 24.4 degrees C.
GlaT24_3
differential expression file:
GlaT24annot.csv


title: ani_E. cyaneus, LT10, 3 hours, sample 3

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 5 days and subjected to LT10 (24.6 degrees C) for 3 hours.
Ecy10LT3_3
differential expression file:
Ecy10LT3_annot.csv


title: ani_G. lacustris, gradual temperature increase, 24 degrees C, sample 1

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 23 days at 24.4 degrees C.
GlaT24_2
differential expression file:
GlaT24annot.csv


title: ani_E. cyaneus, LC10 cadmium, 24 hours, sample 3

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to LC10 (3.7 uM) cadmium chloride for 24 hours.
EcyCd24_3
differential expression file:
EcyCd24_annot.csv


title: ani_E. cyaneus, LC10 cadmium, 24 hours, sample 4

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and subjected to LC10 (3.7 uM) cadmium chloride for 24 hours.
EcyCd24_4
differential expression file:
EcyCd24_annot.csv


title: ani_E. cyaneus, control, 24 hours, sample 1

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 24 hours (parallel control).
EcyB24_1
differential expression file:
EcyCd24_annot.csv
Ecy10LT24_annot.csv
EcyPB24_annot.csv
EcyPhB24_annot.csv


title: ani_G. lacustris, gradual temperature increase, 18 degrees C, sample 1

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 15 days at 18 degrees C.
GlaT18_1
differential expression file:
GlaT18annot.csv


title: ani_G. lacustris, gradual temperature increase, 18 degrees C, sample 2

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 15 days at 18 degrees C.
GlaT18_2
differential expression file:
GlaT18annot.csv