title: IAA-treated samples at 3 day rep3 [I6]

status: Public on Dec 31 2021

type: SRA

city: Ningbo

first: Xiaojiao

last: Chen

state: Zhejiang

address: Qixing South Road

country: China

institute: Ningbo University

description: processed data file: DEGs_3d.txt

library_source: transcriptomic

data_processing:
BGISEQ-500
Trinity (v2.0.6) was used to assemble the clean reads and Tgicl (v2.0.6) to perform clustering and eliminate redundant data in the assembled transcripts to obtain unique genes.
Clean reads were obtained from removing the low-quality reads (those exceeding 50% low-quality bases with Q15), reads that contained adaptor sequences or unidentified nucleotides more than 10% to the total read pool.
Clean reads were mapped to the assembled unique genes by Bowtie2 (v2.2.5).
Supplementary_files_format_and_content: tab-delimited text files include FPKM values
Supplementary_files_format_and_content: Differentially expressed genes between control and IAA-treated samples

molecule: total RNA

organism: Gracilariopsis lemaneiformis

source_name: branch rhizoids and 2 cm primary rhizoids

extract_protocol:
Rhizoids were collected and ground on liquid nitrogen, and RNA was extracted with RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Three replicate was IAA treated for 1 and 3 days, respectively.

tag: strain

tag: tissue

value: rhizoids

tag: treatment

value: treated with 100 μM IAA for 3d


title: IAA-treated samples at 3 day rep2 [I5]

description: processed data file: DEGs_3d.txt


title: mihou_D2EB

city: Kunming

first: Jian

last: Liu

address: Zhiyuan Road,Chenggong

institute: Institute of Primate Translational Medicine, KUST

description: cells within EBs

data_processing:
Sequencing data were first processed using the 10X Genomics Cell Ranger pipeline and sequence was aligned using STAR against the Macaca fascicularis reference genome(ensemble release-91).
Subsequently, unique molecular identifiers (UMI) matrices from each sample were merged in R and imported to Seurat.
For pseudotime analysis, the UMI matrix calculated in Seurat was passed into Monocle2,and highly variable genes identified by Seurat were used as ordering genes for trajectory calculation.
After trajectory reconstruction, we used BEAM to identify genes with branch-dependent expression and used plot_multiple_branches_heatmap to visualize the genes along branches.
Genome_build: rheMac8
Supplementary_files_format_and_content: H5, MTX, TSV files were generated using the 10X Genomics Cell Ranger pipeline.

organism: Macaca mulatta

source_name: embryoid body

growth_protocol: Male (XX) and female (XY) monkey embryonic stem cells (ESCs) were cultured on mitomycin C-inactivated mouse embryonic fibroblasts (MEF). Briefly, ESCs colonies were cultured in Nutrient Mixture F-12(DMEM/F12,Invitrogen) medium containing 20% KOSR (Invitrogen) supplemented with 4 ng/mL bFGF (Chemicon), 1% nonessential amino acids (Invitrogen), 0.1 mM β-mercaptoethanol (Invitrogen), 1% penicillin-streptomycin-L-glutamate (Invitrogen). For naive state conversion, ESC colonies were dissociated by collagenase IV and reseeded on MEF with naïve conversion medium. The naïve conversion medium comprised ESCs culture medium supplemented with 10 ng/mL human LIF (PeproTech), CHIR99021(3μM) (Tocris), PD0325901 (0.5μM) (R&D Systems), SP600125 (10μM) (Selleck) and SB203580 (10μM) (Selleck).

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen).
The scRNA-seq libraries were generated using the Chromium Single Cell 3′Reagent Kit (10X Genomics) . Briefly, a single-cell suspension (500 cells /μL in PBS) was mixed with RT-PCR master mix and loaded together with Single Cell 3′Gel Beads and Partitioning Oil into a Single Cell 3′Chip (10X Genomics) according to the manufacturer’s instructions. RNA transcripts from single cells were uniquely barcoded and reverse-transcribed within droplets. cDNA molecules were preamplified and pooled followed by library construction. All libraries were quantified on a 2100 Bioanalyzer (Agilent) and realtime quantitative PCR, and then subjected to 150 bp paired-end sequencing on an Illumina Xten platform (sequenced by Novogene).

treatment_protocol: Monkey PGCLCs differentiation; Immunofluorescence.

value: embryoid body

tag: gender

value: male

tag: cell type

value: day 2 Ebs


title: mihou_D4EB

description: cells within EBs

value: day 4 Ebs


title: IAA-treated samples at 1 day rep2 [I2]

description: processed data file: DEGs_1d.txt

value: treated with 100 μM IAA for 1d


title: IAA-treated samples at 3 day rep1 [I4]

description: processed data file: DEGs_3d.txt


title: IAA-treated samples at 1 day rep1 [I1]

description: processed data file: DEGs_1d.txt


title: control samples at 1 day rep3 [C3_1d]

description: processed data file: DEGs_1d.txt

value: untreated


title: mihou_naive

description: naïve cells

source_name: embryonic stem cell

value: embryonic stem cell

value: naive cells


title: Intol_3_brain

city: Haikou

first: JunLong

last: Sun

state: Hainan

address: No.58 Renmin Avenue, Haikou City, Hainan Province

institute: Hainan University

description: mRNA derived from brain tissue of the hypoxia intolerance group (Intol) fish

data_processing:
The de novo assembly was performed on cleaned reads using Trinity (Grabherr et al., 2011). Before assembly, raw reads were trimmed by removing adaptor sequences and ambiguous nucleotides. Reads with quality scores less than 20 and length below 30 bp were all trimmed. The resulting high-quality sequences were used in subsequent assembly. Briefly, the raw reads were assembled into the unique sequences of transcripts in Inchworm via greedy K-mer extension (k-mer 25).
After mapping of reads to Inchworm contig bundles, Chrysalis incorporated reads into de Bruijn graphs. Butterfly then processed the individual graphs in parallel, reporting full-length transcripts and paralogous genes. After assembly, the open reading frame (ORF) of each unisequence was predicted by using Trinity software. Unisequences were used for BLAST search and annotation against the NR, NT, STRING (http://string-db.org/) (Franceschini et al., 2013), COG (http://www.ncbi.nlm.nih.gov/COG/), KEGG (http://www.genome.jp/kegg/) databases using an E-value cut-off of 10-5 (Camacho et al., 2009). Functional annotation by gene ontology (GO, http://www.geneontology.org) terms was analysed by using BLAST2GO software (NCBI) (Conesa et al., 2005).
Supplementary_files_format_and_content: Identified mRNAs in each library with count reads and normalized data

organism: Trachinotus blochii

source_name: brain

growth_protocol: We constructed three parallel tanks under severe hypoxia conditions (0.9 ± 0.1 mg / L), randomly assigned 80 golden pompanos to each tank, and simultaneously subjected to acute hypoxic stress. After the experiment started, the DO level was adjusted by pumping nitrogen into these tanks to reduce the DO to the level required for the experiment within 2 hours, and it was recorded as 0 h at this time. Under this condition, 14 randomly selected fish from each tank with dying (floating head and losing balance) within 1 hour of hypoxic stress was constructed as the hypoxic intolerant group (Intol), 14 randomly selected fish from each tank with still normal after 24 hours of hypoxic stress was constructed as the hypoxic tolerant group (Tol) (Fig. 1). During the experiment, except for DO, the water environment was maintained at the same conditions as the experimental fish temporary culture conditions. The water samples from each experimental tank were collected every hour. The DO level was monitored by measuring the water quality using the classic iodine quantity method (Beadle, 1958), and adjust the DO in time. The fish fasted during the experiment.

extract_protocol:
The total RNA was harvested using Trizol-LS reagent.
Total RNA was extracted from liver and brain using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s directions. RNA samples were digested using DNase I to remove potential genomic DNA and stored at -80℃. RNA was quantified and quality was assessed by NanoDrop Spectrophotometer 2000c (NanoDrop Technologies, Wilmington, DE, USA) and 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and all samples were standardised to 500 ng/μl. Three samples from per group at each time point were used for RNA library construction which OD ratios of 260/280 and 260/230 greater than 1.8 and RNA Integrity Number (RIN) greater than 8. RNA-seq library preparation and sequencing were carried out by Annoroad Gene Technology Co., Ltd (Beijing, China), forty five sequencing libraries were constructed using a TruSeq™ RNA Sample Preparation Kit (Illumina) according to the manufacturer’s directions. The next step was KAPA quantifcation and dilution, after which the library was sequenced on an Illumina HiSeq.2500 with 125-bp paired-end reads. After removing adaptor sequences, ambiguous N nucleotides (those an N ratio <5%) and low quality sequences (reads with <50% bases of quality value), the remaining clean reads were assembled using Trinity sofware

treatment_protocol: At different time points of the stress experiment, 42 experimental fish were taken from the hypoxic intolerant group (Intol) and the hypoxic tolerant group (Tol) (14 fish per tank) to collect brain and liver samples, anesthetized with excess MS-222, quickly killed the fish and immediately dissected for sampling the brain and liver tissue, and then freeze the tissue immediately in liquid nitrogen and store at -80 °C until use.

tag: group

value: hypoxia intolerance group (Intol) fish

value: brain

tag: developmental stage


title: Intol_2_brain


title: control samples at 3 day rep3 [C6]

description: processed data file: DEGs_3d.txt


title: Intol_1_brain


title: IAA-treated samples at 1 day rep3 [I3]

description: processed data file: DEGs_1d.txt


title: control samples at 3 day rep2 [C5]

description: processed data file: DEGs_3d.txt


title: control samples at 3 day rep1 [C4]

description: processed data file: DEGs_3d.txt


title: Tol_1_brain

description: mRNA derived from brain tissue of the hypoxia tolerance group (Tol) fish

value: hypoxia tolerance group (Tol) fish


title: Intol_1_liver

description: mRNA derived from liver tissue of the hypoxia intolerance group (Intol) fish

source_name: liver

value: liver


title: Tol_3_liver

description: mRNA derived from liver tissue of the hypoxia tolerance group (Tol) fish


title: control samples at 1 day rep1 [C1_1d]

description: processed data file: DEGs_1d.txt


title: Tol_1_liver


title: LSRR2

city: Beijing

first: Weizhe

last: Wang

state: Beijing

address: No. 17 Tsing Hua East Road, HaiDian District

institute: China Agricultural University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation  System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an  Illumina Hiseq platform and paired-end reads were generated.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of reference genome and aligning clean reads to reference genome were built by Bowtie2-2.2.3.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing   reads containing adapter, reads containing ploy-N and low quality reads from  raw data. At the same time, Q20, Q30 and GC content sequence of the clean   data were calculated. All the downstream analyses were based on the clean data  with high quality.
Genome_build: Bowtie2-2.2.3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample .

organism: Ligilactobacillus salivarius

source_name: probiotics isolated from human feces

extract_protocol:
For RNA extraction, total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA) and purified using the TURBO DNA-free Kit (Ambion, Austin, TX, USA) according to the manufacturer’s instructions.
Sequencing libraries were generated using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample

tag: medium

value: raffinose MRS medium


title: Tol_3_brain


title: LSRR3


title: LSRG2

value: glucose MRS medium


title: LSRG3


title: LSRG1


title: Intol_2_liver


title: control samples at 1 day rep2 [C2_1d]

description: processed data file: DEGs_1d.txt


title: LSRR1


title: Tol_2_brain


title: 2dpi-4

city: Ames

first: Melissa

middle: Susan

last: Monson

state: Iowa

address: 2255 Kildee Hall, 806 Stange Road

department: Animal Science

country: USA

institute: Iowa State University

data_processing:
The Trim Sequences tool in CLC Genomic workbench 9.5.2 (QIAGEN) was used to quality trim sequence reads according to default parameters: limit = 0.05, and maximum number of ambiguities = 2.
The RNA-seq Analysis tool in CLC Genomic workbench 9.5.2 (QIAGEN) was used to map the trimmed reads to the reference genome (GCA_000146605.3) according to default parameters: mismatch cost =2, insertion cost = 3, deletion cost = 3, length fraction = 0.8, similarity fraction = 0.8, not strand specific, and maximum number of hits = 10.
The RNA-seq Analysis tool in CLC Genomic workbench 9.5.2 (QIAGEN) was used to obtain read counts for each gene in the NCBI genome annotation (GCF_000146605.2). Read pairs were counted as "one" and only pairs that uniquely mapped were counted.
Genome_build: GCA_000146605.3 (Turkey_5.0)
Supplementary_files_format_and_content: Tab-delimited text files contain absolute unique gene read counts (non-normalized) for each sample

organism: Meleagris gallopavo

source_name: Blood leukocytes

extract_protocol:
Blood was collected from the brachial vein into EDTA tubes and fractionated using the LeukoLOCK Fractionation & Stabilization Kit (Thermo Fisher Scientific). Total RNA from the resulting leukocytes was isolated using the LeukoLOCK Total RNA Isolation System (Thermo Fisher Scientific).
Indexed cDNA libraries were prepared from the RNA samples using the TruSeq RNA Sample Prep Kit v2 (Illumina Inc.).

treatment_protocol: 3-week-old turkeys were assayed at two time points: prior to inoculation (0 dpi) and 2 days post inoculation (2 dpi) with 10^10 CFU of S. Typhimurium UK1.

value: leukocytes

value: 2 days post inoculation

tag: breed

value: Hybrid turkeys

tag: age

value: 3 weeks

tag: Sex


title: Intol_3_liver


title: 0dpi-3

value: 0 days post inoculation

value: male


title: 2dpi-8


title: 0dpi-7


title: Tol_2_liver


title: 2dpi-6


title: 0dpi-5


title: 2dpi-2


title: T7572

type: RNA

city: paris

first: Elodie

last: chapeaublanc

address: 26 rue d'ulm

department: UMR 144

country: France

institute: Institut Curie

hyb_protocol: Affymetrix microarrays were hybridized with 10µg of biotinylated cRNA according the supplier recommendations. Microarrays were washed and stained using FS450 fluidics upon a protocol provided by Affymetrix, corresponding to the  Affymetrix Mouse Exon 1.0 ST. Array gene

scan_protocol: Microarrays were scanned using a 7G, Affymetrix GCS3000 scanner, raw data were acquired with Affymetrix Genechip Command Console.

data_processing: Signal reconstruction was performed with the RMA algorithm as implemented in Bioconductor affy package on R statistical software using the Dai custom CDF package: moex10stmmentrezg_21,  Brainarray Custom CDF EntrezG version 21.

label: biotin

organism: Mus musculus

source_name: tumor lesion

label_protocol: 100ng of total RNA were amplified to produced biotinylated complementary RNAs, as recommended by Affymetrix.

extract_protocol: Total RNA (200ng) from 20-month-old UII-hFGFR3-S249C mouse normal urothelium, hyperplastic lesions and urothelial carcinomas  was obtained using the RNeasy mini kit (Qiagen, Courtaboeuf, France) according to the manufacturer’s instructions. Gene expression was evaluated using the Affymetrix Mouse Exon 1.0 ST array.

tag: genotype

value: FGFR3 +/-

value: tumor lesion


title: T7283

value: FGFR3 +/+


title: H7282

source_name: hyperplastic lesion

value: hyperplastic lesion


title: H7431


title: T7019

source_name: tumor lession

value: tumor lession


title: H7496


title: T7439


title: N7578

source_name: normal urothelum

value: FGFR3 -/-

value: normal urothelum


title: ATAC-Seq DBA mEpiSCs

city: New York

first: Daniel

last: Medina Cano

email: medinacd@mskcc.org, dmcdmc156@gmail.com

state: New York

address: 411E 67th St

department: Developmental Biology

institute: MSKCC

description:
DBA mEpiSCs
ATAC-seq on mEpiSCs and derivates

library_source: genomic

data_processing:
The raw reads were trimmed using fastp to remove low-quality bases from reads (quality < 20) and adapter sequences.
The trimmed reads were aligned using Bowtie2 (PMID: 22388286) to UCSC genome assembly mm10.
Duplicate reads were removed using Sambamba.
Peaks were identified with MACS2 (doi: https://doi.org/10.1101/496521) and those overlapping with satellite repeat regions were discarded.
The peaks were merged to create a union peak atlas - featureCounts was used to generate a matrix of reads per peak per sample
The resulting matrix was analyzed with Deseq2 package and PCAexplorer (PMID: 25516281 and 31195976)
Genome_build: mm10
Supplementary_files_format_and_content: txt - normalized counts per sample
Supplementary_files_format_and_content: AllPeaks_EpiSC_VS_DE: Count matrix for ATAC-seq EpiSC VS DE, after FeatureCounts ATAC-seq analyses of EpiSC samples VS Definitive endoderm, only 4 EpiSC samples and 4 DE samples are uncluded (all from the B6 bakcground), used for figure 3
Supplementary_files_format_and_content: AllPeaks_EpiSC_VS_Biblio: Count matrix for ATAC-seq EpiSC VS FX, AFX and in vivo samples, after FeatureCounts ATAC-seq analyses of EpiSC samples developed in the present study , EpiSC cells (AF and AFX) from PMID: 33271069 and in vivo samples obtained from PMID 31844322, used for figure 1
Supplementary_files_format_and_content: RNA_Epi_VS_De.txt: Deseq2 matrix for RNA-seq EpiSC VS DE RNA-seq analyses of EpiSC samples VS Definitive endoderm, only 5 EpiSC samples and 4 DE samples are uncluded (all from the B6 bakcground), used for figure 3
Supplementary_files_format_and_content: RNA_EpiS.txt: Deseq2 matrix for RNA-seq EpiSC from different genetic backgrounds RNA-seq analyses of EpiSC samples from different backgrounds, used for figure 1

molecule: genomic DNA

source_name: Mouse epiblast stem cells in vitro

growth_protocol: mEpiSCs were grown on feeders and in a N2B27-based media with Fgf2, ActivinA and NVP-TNKS656 as Wnt inhibitor

extract_protocol:
mEpiSCs were lifted with collagenase (to avoid feeder contamination) and resuspended to single cells with accutase. Next, we performed nuclei isolation and 20 or 40 thousand cells (duplicate 1 and 2, respectively) were transposed.
Libraries were generated as previously described in https://www.med.upenn.edu/kaestnerlab/assets/user-content/documents/ATAC-seq%20Protocol%20(Omni)%20-%20Kaestner%20Lab.pdf

tag: passage


title: N7403


title: H7543


title: T7538


title: H7547


title: H7520


title: N7548


title: ATAC-Seq B6 Definitive Endoderm BioRep 51

description:
B6 Definitive Endoderm BioRep 51
ATAC-seq on mEpiSCs and derivates

source_name: Mouse definitive endoderm cells in vitro

growth_protocol: Definitive endoderm cells were generated from mEpiSCs in 46h. mEpiSCs were induced with chemically defined media with CHIR99201 and ActivinA for 16h. Afterwards, the media was changed to chemically defined media with ActivinA and LDN193189 for 24h more, when the cells were collected. To avoid background noise, we MACS-sorted CXCR4+ cells and used those for further analyses.

extract_protocol:
DE cells  were lifted with accutase. Next, we performed nuclei isolation and 20 or 40 thousand cells (duplicate 1 and 2, respectively) were transposed.
Libraries were generated as previously described in https://www.med.upenn.edu/kaestnerlab/assets/user-content/documents/ATAC-seq%20Protocol%20(Omni)%20-%20Kaestner%20Lab.pdf


title: ATAC-Seq PWK mEpiSCs BioRep698

description:
PWK mEpiSCs BioRep698
ATAC-seq on mEpiSCs and derivates

value: PWK/PhJ


title: ATAC-Seq B6 Definitive Endoderm BioRep 4

description:
B6 Definitive Endoderm BioRep 4
ATAC-seq on mEpiSCs and derivates


title: TM_GL_C2

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

data_processing:
BaseCalls performed using Illumina
Demultiplexing performed using Cell Ranger v3.1.0 with default settings
Reads were aligned to mm10 reference genome using Cell Ranger v3.1.0 with --expect-cells=2500
Genome_build: mm10
Supplementary_files_format_and_content: matrix table with raw gene counts for all genes and samples

source_name: whole lung cells

extract_protocol:
Single cells, reagents, and a single Gel Bead containing barcoded oligonucleotides are encapsulated into nanoliter-sized GEMs (Gel Bead-in-Emulsion) using the GemCode platform. Lysis and barcoded reverse transcription of RNAs from single cells is performed.
Enzyme fragmentation, A tailing, adaptor ligation and PCR are performed to obtain final libraries containing P5 and P7 primers used in Illumina bridge amplification. Size distribution and molarity of resulting cDNA libraries were assessed via Bioanalyzer High Sensitivity DNA Assay (Agilent Technologies, USA)

value: lung

value: ERG fl/fl


title: ATAC-Seq B6 mEpiSCs BioRep 4

description:
B6 mEpiSCs BioRep 4
ATAC-seq on mEpiSCs and derivates


title: ATAC-Seq B6 mEpiSCs BioRep 51

description:
B6 mEpiSCs BioRep 51
ATAC-seq on mEpiSCs and derivates


title: ATAC-Seq B6 Definitive Endoderm BioRep 44

description:
B6 Definitive Endoderm BioRep 44
ATAC-seq on mEpiSCs and derivates


title: ATAC-Seq PWK mEpiSCs BioRepALT

description:
PWK mEpiSCs BioRepALT
ATAC-seq on mEpiSCs and derivates


title: TM_GL_C1


title: ATAC-Seq B6 mEpiSCs BioRep 44

description:
B6 mEpiSCs BioRep 44
ATAC-seq on mEpiSCs and derivates


title: Joint KO9  (KO3 arthritis -RA-)

city: Vigo

first: Samuel

last: Garcia

address: Estrada Clara Campoamor 341

department: Rheumatology & Immune-mediated Diseases (IRIDIS) group

country: Spain

institute: Galicia Sur Health Research Institute (IIS Galicia Sur)

description: IIS-SP #22

data_processing:
Read 1 was used to identify the Illumina library index and CEL-Seq sample barcode. Read 2 was aligned to the mm10 mouse reference transcriptome using BWA. Reads that mapped equally well to multiple locations were discarded.
Mapping and generation of count tables was done using the MapAndGo script (https://github.com/anna-alemany/transcriptomics/tree/master/mapandgo).
Samples were normalized using Reads per million mapped reads (RPM) normalization.
The differential expression analysis based on the Negative Binomial was performed using R/Bioconductor package DESeq2 v.1.32.  Negative Binomial GLM fitting and Paired Wald-test was used to assess the differentially expressed genes (DEG) and p-values were adjusted (p-adj) for multiple testing errors with 5% false discovery rate (FDR) according to Benjamini-Hochberg (BH). DEG were defined as fold change ≥ 2 and p-adj < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: csv file includes RPM values for each Sample
Supplementary_files_format_and_content: csv file include Differentially Expressed Genes between experimental groups

source_name: Forepaw

extract_protocol:
Total RNA from mouse forepaws was extracted using the RNeasy Kit and RNase-Free DNase Set (Qiagen) and used for library preparation and sequencing.
Samples were barcoded with CEL-seq primers during a reverse transcription and pooled after second strand synthesis. The resulting cDNA was amplified with an overnight in vitro transcription reaction. From this amplified RNA, sequencing libraries were prepared with Illumina Truseq small RNA primers.
Single-cell mRNA seq protocol of CEL-Seq. Paired-end sequencing was performed on the Illumina Nextseq500 platform

value: Arthritis

value: Forepaw


title: Joint WT9  (WT4 arthritis -RA-)

description: IIS-SP #16

value: WT


title: TM_GL_E2

value: CDH5-CreER(T):ERG fl/fl


title: Joint KO11 (KO5 arthritis -RA-)

description: IIS-SP #24


title: ATAC-Seq B6 mEpiSCs BioRep 1

description:
B6 mEpiSCs BioRep 1
ATAC-seq on mEpiSCs and derivates


title: TM_GL_E1


title: KO2 RA (KO2 arthritis -RA-)

description: IIS-SP #26


title: WT10 RA  (WT5 arthritis -RA-)

description: IS-SP #25


title: T7521


title: Joint WT8  (WT3  arthritis -RA-)

description: IIS-SP #15


title: MI KO15 (KO3 Control)

description: IIS-SP #8

value: Control


title: Joint W7  (WT2 arthritis -RA-)

description: IIS-SP #14


title: Joint W2  (WT1 arthritis -RA-)

description: IIS-SP #9


title: KO1 RA (KO1 arthritis -RA-)

description: IIS-SP #27


title: MI KO12 (KO1 Control)

description: IIS-SP #5


title: MI WT13 (WT3 Control)

description: IIS-SP #3


title: MI WT12 (WT2 Control)

description: IIS-SP #2


title: MI WT14 (WT4 Control)

description: IIS-SP #4


title: MI KO13 (KO2 Control)

description: IIS-SP #6


title: MI KO14 (KO3 Control)

description: IIS-SP #7


title: MI WT11 (WT1 Control)

description: IIS-SP #1


title: 300mg48Std

city: Frankfurt

first: Malte

last: Bachmann

address: Theodor Stern Kai 7

department: General Pharmacology

country: Germany

institute: University Hospital Frankfurt

data_processing:
Performed using MACE-kit v.2 (GenXPro, Frankfurt, Germany)
Poly(A) mRNA underwent poly-A specific reverse transcription and template-switched based second strand synthesis followed by competitive PCR
Duplicate reads verified by implemented unique molecular identifiers (TrueQuant IDs) were eliminated from raw dataset
Low quality sequence-bases were eliminated (https://github.com/marcelm/cutadept/)
Poly(A)-tails were clipped by an in-house Phyton-Script
transcripts were quantified by HTSeq. Differentially expressed gens were identified by DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: all_comparisons_merged_300mg.txt file include log2normalized values for each sample

extract_protocol:
Hepatic RNA was isolated by trizol and DNase I digested
Library preparation was done with MACE-kit v.2 (GenXPro, Frankfurt, Germany)

treatment_protocol: 0.9%  NaCl-solution or 300mg/kg APAP i.p. for 24h or 48h

tag: agent

value: 300mg/kg APAP

tag: time point


title: Kontr48Std

value: NaCl


title: siC_2

city: Torino

first: Aurora

last: Savino

state: Piemonte

address: via Nizza, 52

country: Italy

institute: Università di Torino

data_processing:
Reads were mapped to the Mus musculus mm9 reference assembly using TopHat v2.0.10
Gene counts were computed using the htseq-count tool from the HTSeq package
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: primary CAFs_control siRNA

growth_protocol: CAFs were derived from mammary tumors NeuT transgenic mice, cultured at 37°C in a 5% CO2 atmosphere in high glucose complete DMEM supplemented with: 10% heat inactivated FBS, 50 u/ml penicillin, 50ug/ml streptomycin.

extract_protocol:
Total TRIzol-extracted RNA from primary CAFs was subjected to quality assessment on an Agilent 2100 Bioanalyzer (RIN ≥ 9). 2 μg of total RNA were subjected to poly(A) selection.
Libraries were prepared with the TruSeq RNA Sample Prep Kit (Illumina).

treatment_protocol: Cells were treated with the siSTAT3 or control nanoparticles, 1ug/mL, for 72 hours.

tag: strain background

value: BalbC

value: control siRNA

tag: tissue source

value: NeuT trasgenic mammary tumors

value: primary Cancer Associated Fibroblasts (CAFs)


title: siS3_2

source_name: primary CAFs_anti-Stat3 siRNA

value: anti-Stat3 siRNA


title: siC_1


title: siS3_3


title: siS3_1


title: siC_3


title: Kontr24Std

tag: strain


title: RNA-seq asynchronous rep2

first: Kristian

last: Helin

address: 430 East 67 street

description:
fresh cells
HTseqCount_synchronized.txt.gz
normCount_DEseq2_synchronized.txt.gz

data_processing:
Basecalls performed using CASAVA version 1.8
Omni-ATAC-seq and CUT&Tag: The reads were trimmed with cutadapt (Martin et al. 2011) in the pair-end mode and default parameters. After alignment with bowtie2 (Langmead et lal. 2012) to mm10; reads were filtered (-q 10) and duplicates were removed with Picard tools. We called ATAC-seq peaks with MACS2 (Zhang et al. 2008) on individual samples and combined all peaks to count reads over the union of all peaks with bamCoverage (deepTools (Ramirez et al. 2016)) or over CAGE-defined p1 and p2 TSSs (Lizio et al. 2019). The read counts were normalized and further processed with DESeq2 (Love et al. 2014). The regions were classified based on DESeq2 fold-changes and padj.
SLAM-seq data combined with 3’UTR mRNA-seq were aligned with SLAMDUNK (slamdunk all -5 12 -n 100 -t 3 -m -rl 75) (Neumann et al. 2019). Mutational rates were obtained with alleyoop utrrates (-l 75). ReadCounts and TcCounts outputs were used for the analysis and normalized with DESeq2 (Love et al. 2014).
RNA-seq: The reads were trimmed with cutadapt 1.15 (Martin et al. 2011) in the single end mode (--quality 15) and aligned with STAR (default parameters) to mm10 followed by filtering with samtools (-q 10). Aligned reads were counted with HT-seq over Genecode vM17 annotation, normalized and further processed with DESeq2 (Love et al. 2014).
Activity-by-contact model: we predicted enhancer-gene pairs by using the activity-by-contact model (Fulco et al. 2019) with the following input data for mESCs: ATAC-seq, RNA-seq, H3K27ac (SRR5110896 and SRR5110902) (Atlasi et al. 2019) and in situ Hi-C (4DNESU4BQU4G) (Yan et al. 2018). We used default threshold (0.02) to obtain significant ABC scores and contacts (excluding promoter elements).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files with scores for each genomic position. The scores were normalized using DEseq2 normalization factors or normalized to sequencing depth.
Supplementary_files_format_and_content: Matrix table with all MACS2 regions for sorted phases and raw counts for omni-ATAC-seq samples (G1, S, G2M)
Supplementary_files_format_and_content: Matrix table with all MACS2 regions for synchronized samples and raw counts for omni-ATAC-seq samples (nocodazole, thymidine, CDK1i, WT)
Supplementary_files_format_and_content: txt files with outputs from Slamdunk for SLAM-seq samples for 3'UTRs
Supplementary_files_format_and_content: matrix table with raw (HTseq) and normalized (DEseq2) counts for genes in treated samples (nocodazole, thymidine, CDK1, WT)
Supplementary_files_format_and_content: matrix table with enhancer-promoter predictions for mESCs (based on Fulco et al. 2019)

molecule: polyA RNA

source_name: mouse embryonic stem cells

growth_protocol: E14 mouse ES cells (male, RRID: CVCL_C320) were cultured in the serum/LIF medium containing Glasgow Minimum Essential Media (Sigma), 10% heat-inactivated FBS (HyClone), 1x Penicillin-Streptomycin (Thermo Fisher Scientific), 2 mM GlutaMAX (Thermo Fisher Scientific), 100 µM β-Mercaptoethanol (Thermo Fisher Scientific), 1 mM sodium pyruvate (Thermo Fisher Scientific), 0.1 mM MEM Non-Essential Amino Acids Solution (Thermo Fisher Scientific) and Leukemia Inhibitory Factor (homemade).

extract_protocol:
RNA-seq: with Illumina TruSeq v2 kit (Illumina, RS-122-2001).
After sorting, we performed omni-ATAC-seq, CUT&Tag with different abtibodies, SLAM-seq or RNA-seq.

treatment_protocol:
mESCs were seeded at 30-50% confluency 8 hours before the start of treatment. Cells were treated with 2 mM thymidine (Sigma, T1895) for 14 hr, washed with PBS and grown for 11 hrs before additional thymidine treatment for 14 hrs; 100 ng/ml nocodazole (Sigma, M1404) for 14 hr; 10 µM CDK1 inhibitor (Ro-3306, Selleckchem, S7747) for 14 hrs.
After three washes with PBS, treated or non-treated cells were incubated in media supplemented with 20 nM EdU (Lumiprobe, 10540) for 10 min in the incubator, washed with PBS three times and trypsinized (Sigma).  For SLAM-seq mESCs were incubated with 100 uM 4-thiouridine (Sigma, T4509) for 2 hrs before EdU labeling. Cell pellets were additionally washed 3 times with PBS before fixation. Ethanol fixation (for flow cytometer analysis or sorting followed by RNA-seq or SLAM-seq) was done by drop-wise addition of 100% cold ethanol to cells resuspended in PBS, so that the resulting concentration was 70% of ethanol. Cell were fixed and stored at -20°C for minimum 12 hours. mESC for omni-ATAC-seq and CUT&Tag were fixed in 1% formaldehyde (Thermo Fisher SCIENTIFIC) and quenched by adding glycine (final concentration 0.125M) (Sigma). Up to 5 million cells per reaction were extensively washed in PBS with 1% FBS. The cells were resuspended in 200 ml of 1x BD Perm/wash buffer (BD Biosciences, 554723) and incubated at room temperature for 15 min. Before Click reaction, the cells were washed in PBS with 1% FBS. Cell pellets were resuspended in 400 ml Click reaction [1x PBS, 2 mM CuSO4 (Sigma, 12849), 20 mg/ml L-ascorbic acid sodium salt (Acros Organics, AC352685000), 10 mM Sulfo-Cyanine5 azide (Lumiprobe, A3330)] and incubated in the dark at room temperature for 30 min. After two washes with 1% FBS in PBS, the cells were resuspended in 1x BD Perm/wash buffer (BD Biosciences, 554723) with 2.5 ng/ml DAPI (Sigma) and incubated for 1 hr at +4°C before the flow cytometry analysis (Beckman Coulter CytoFlex) or sorting (SONY MA900).


title: ATAC-Seq B6 Definitive Endoderm BioRep 2

description:
B6 Definitive Endoderm BioRep 2
ATAC-seq on mEpiSCs and derivates


title: RNA-seq asynchronous rep1


title: RNA-seq CDK1i rep2

description:
fixed, stained cells
HTseqCount_synchronized.txt.gz
normCount_DEseq2_synchronized.txt.gz

value: EdU-labeled, CDK1i-treated


title: RNA-seq CDK1i rep1


title: RNA-seq thymidine rep2

value: EdU-labeled, thymidine-treated


title: RNA-seq nocodazole rep2

value: EdU-labeled, nocodazole-treated


title: RNA-seq thymidine rep1


title: RNA-seq nocodazole rep1


title: ATAC-seq CDK1i rep2

description:
fresh cells
ATACseq_CDK1i_fresh_merged.NormPeaks.bw
ATAC-seq_rawCounts_synchronized_over_macs2Peaks.txt.gz

extract_protocol:
omni-ATAC-seq was perfromed as described in Corses et al. 2017
After sorting, we performed omni-ATAC-seq, CUT&Tag with different abtibodies, SLAM-seq or RNA-seq.


title: ATAC-seq CDK1i rep1


title: 300mg24Std


title: ATAC-seq thymidine rep1

description:
fresh cells
ATACseq_thymidine_fresh_merged.NormPeaks.bw
ATAC-seq_rawCounts_synchronized_over_macs2Peaks.txt.gz


title: ATAC-seq thymidine rep2


title: ATAC-seq EtOH-fixed cells rep2

description: EtOH fixed, stained cells

value: EdU-labeled


title: ATAC-seq nocodazole rep2

description:
fresh cells
ATACseq_noc_fresh_merged.NormPeaks.bw
ATAC-seq_rawCounts_synchronized_over_macs2Peaks.txt.gz


title: ATAC-seq nocodazole rep1


title: ATAC-seq EtOH-fixed cells rep1

description: EtOH fixed, stained cells


title: ATAC-seq FA-fixed cells rep1

description: FA fixed, stained cells


title: ATAC-seq fresh cells rep2

description:
fresh cells
ATACseq_WT_fresh_merged.NormPeaks.bw
ATAC-seq_rawCounts_synchronized_over_macs2Peaks.txt.gz


title: ATAC-seq FA-fixed cells rep2

description: FA fixed, stained cells


title: SLAM-seq S rep3

description:
fixed, stained and sorted cells, S phase
ABC_model_mESC_EnhancerPredictionsAllPutative.txt.gz

extract_protocol:
SLAM-seq: with QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, 015.24) and as described in Herzog et al. 2020.
After sorting, we performed omni-ATAC-seq, CUT&Tag with different abtibodies, SLAM-seq or RNA-seq.

value: EdU-labeled, 4sU-labeled


title: SLAM-seq S rep2


title: SLAM-seq G2M rep1

description:
fixed, stained and sorted cells, G2M phase
ABC_model_mESC_EnhancerPredictionsAllPutative.txt.gz


title: CUT&Tag H3K27ac G2M rep1

description:
fixed, stained and sorted cells, G2M phase
CT_H3K27ac_G2M_merged.rmdup.depthNorm.bw

data_processing:
Library strategy: CUT&Tag
Basecalls performed using CASAVA version 1.8
Omni-ATAC-seq and CUT&Tag: The reads were trimmed with cutadapt (Martin et al. 2011) in the pair-end mode and default parameters. After alignment with bowtie2 (Langmead et lal. 2012) to mm10; reads were filtered (-q 10) and duplicates were removed with Picard tools. We called ATAC-seq peaks with MACS2 (Zhang et al. 2008) on individual samples and combined all peaks to count reads over the union of all peaks with bamCoverage (deepTools (Ramirez et al. 2016)) or over CAGE-defined p1 and p2 TSSs (Lizio et al. 2019). The read counts were normalized and further processed with DESeq2 (Love et al. 2014). The regions were classified based on DESeq2 fold-changes and padj.
SLAM-seq data combined with 3’UTR mRNA-seq were aligned with SLAMDUNK (slamdunk all -5 12 -n 100 -t 3 -m -rl 75) (Neumann et al. 2019). Mutational rates were obtained with alleyoop utrrates (-l 75). ReadCounts and TcCounts outputs were used for the analysis and normalized with DESeq2 (Love et al. 2014).
RNA-seq: The reads were trimmed with cutadapt 1.15 (Martin et al. 2011) in the single end mode (--quality 15) and aligned with STAR (default parameters) to mm10 followed by filtering with samtools (-q 10). Aligned reads were counted with HT-seq over Genecode vM17 annotation, normalized and further processed with DESeq2 (Love et al. 2014).
Activity-by-contact model: we predicted enhancer-gene pairs by using the activity-by-contact model (Fulco et al. 2019) with the following input data for mESCs: ATAC-seq, RNA-seq, H3K27ac (SRR5110896 and SRR5110902) (Atlasi et al. 2019) and in situ Hi-C (4DNESU4BQU4G) (Yan et al. 2018). We used default threshold (0.02) to obtain significant ABC scores and contacts (excluding promoter elements).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files with scores for each genomic position. The scores were normalized using DEseq2 normalization factors or normalized to sequencing depth.
Supplementary_files_format_and_content: Matrix table with all MACS2 regions for sorted phases and raw counts for omni-ATAC-seq samples (G1, S, G2M)
Supplementary_files_format_and_content: Matrix table with all MACS2 regions for synchronized samples and raw counts for omni-ATAC-seq samples (nocodazole, thymidine, CDK1i, WT)
Supplementary_files_format_and_content: txt files with outputs from Slamdunk for SLAM-seq samples for 3'UTRs
Supplementary_files_format_and_content: matrix table with raw (HTseq) and normalized (DEseq2) counts for genes in treated samples (nocodazole, thymidine, CDK1, WT)
Supplementary_files_format_and_content: matrix table with enhancer-promoter predictions for mESCs (based on Fulco et al. 2019)

extract_protocol:
CUT&Tag: as descried in Kaya-Okur et al. 2019
After sorting, we performed omni-ATAC-seq, CUT&Tag with different abtibodies, SLAM-seq or RNA-seq.

tag: antibody


title: SLAM-seq G1 rep2

description:
fixed, stained and sorted cells, G1 phase
ABC_model_mESC_EnhancerPredictionsAllPutative.txt.gz

tag: treatment


title: CUT&Tag H3K27ac S rep2

description:
fixed, stained and sorted cells, S phase
CT_H3K27ac_S_merged.rmdup.depthNorm.bw


title: ATAC-seq fresh cells rep1


title: SLAM-seq G1 rep1


title: SLAM-seq G1 rep3


title: CUT&Tag H3K27ac S rep1


title: CUT&Tag H3K27ac G1 rep1

description:
fixed, stained and sorted cells, G1 phase
CT_H3K27ac_G1_merged.rmdup.depthNorm.bw


title: CUT&Tag H3K27ac G1 rep2


title: CUT&Tag H3K27me3 G2M rep2

description:
fixed, stained and sorted cells, G2M phase
CT_H3K27me3_G2M_merged.depthNorm.bw

value: anti-H3K27me3 (Cell signaling, 9733)


title: CUT&Tag H3K27me3 G1 rep1

description:
fixed, stained and sorted cells, G1 phase
CT_H3K27me3_G1_merged.depthNorm.bw


title: CUT&Tag H3K27me3 G2M rep1


title: CUT&Tag H3K4me3 G2M rep1

description:
fixed, stained and sorted cells, G2M phase
CT_H3K4me3_G2M_merged.rmdup.depthNorm.bw

value: anti-H3K4me3 (Cell Signaling, 9751)


title: CUT&Tag H3K27me3 G1 rep2


title: SLAM-seq G2M rep2


title: CUT&Tag H3K4me3 S rep2

description:
fixed, stained and sorted cells, S phase
CT_H3K4me3_S_merged.rmdup.depthNorm.bw


title: CUT&Tag H3K4me3 G2M rep2


title: CUT&Tag H3K27me3 S rep1

description:
fixed, stained and sorted cells, S phase
CT_H3K27me3_S_merged.depthNorm.bw


title: CUT&Tag H3K27me3 S rep2


title: CUT&Tag H3K4me3 S rep1


title: CUT&Tag H3K27ac G2M rep2


title: CUT&Tag H3K4me3 G1 rep2

description:
fixed, stained and sorted cells, G1 phase
CT_H3K4me3_G1_merged.rmdup.depthNorm.bw


title: CUT&Tag H3K4me3 G1 rep1


title: ATAC-seq G2M rep2

description:
fixed, stained and sorted cells, G2M phase
ATACseq_G2M_FA_merged.NormPeaks.bw
ATAC-seq_rawCounts_G1_S_G2M_over_macs2Peaks.txt.gz


title: ATAC-seq S rep2

description:
fixed, stained and sorted cells, S phase
ATACseq_S_FA_merged.NormPeaks.bw
ATAC-seq_rawCounts_G1_S_G2M_over_macs2Peaks.txt.gz


title: M4_Fibroblast_HC

city: Chicago

first: Ziyou

last: Ren

state: IL

address: 303 E Chicago Ave

institute: Northwestern University

data_processing:
Reads were demultiplexed using bcl2fastq (version 2.17.1.14).
Quality was assessed with FastQC. Reads were then trimmed and aligned to the Mus musculus reference genome (with mm10 assembly) using TopHat2 (version 2.1.0)
Read counts were associated with genes using HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including raw htseq count

growth_protocol: 9-11 weeks old male mice were obtained from Jackson Laboratories

extract_protocol:
Total RNA from fibroblasts cells was extracted using Qiagen RNeasy Plus Mini kit (Qiagen) and quality and quantity were assessed 4200 TapeStation  Agilent
RNA-Seq libraries were prepared using a full-length transcript coverage NEBNext Ultra RNA (New England Biolabs)
DNA libraries sequencing was performed using an Illumina NextSeq 500 instrument (Illumina) of the average dept of 5–7.5 million aligned reads per sample

treatment_protocol: 3 mice were kept at room air, 3 mice were exposed to 10%CO2 for 10 days. Mice were ansthetized and both lungs were harvested for flow-sorting of fibroblast cells

value: flow-sorted PDGFR+ lung fibroblast cells

tag: organ

value: Lung


title: M6_Fibroblast_HC

tag: cell type

value: flow-sorted PDGFR+ lung  fibroblast cells


title: ATAC-seq G1 rep1

description:
fixed, stained and sorted cells, G1 phase
ATACseq_G1_FA_merged.NormPeaks.bw
ATAC-seq_rawCounts_G1_S_G2M_over_macs2Peaks.txt.gz


title: M1_Fibroblast_RA

value: Naïve (Room Air exposure)

value: flow-sorted PDGFRa+ lung fibroblast cells


title: ATAC-seq G2M rep1


title: M2_Fibroblast_RA

value: flow-sorted PDGFRA+ lung fibroblast cells


title: scr-Day4-rep2

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
RNA-seq reads were check for sequencing quality with FastQC (v0.11.2). After sequencing, reads were aligned to the mouse reference genome (mm9) using STAR (v.2.3.0e) with default parameters.
SAMtools (v0.1.19) was used to filter out alignments with mapping quality score less than 10 and alignments on mitochondria or non-chromosome contigs. Finally, FeatureCounts (v.1.6.2) was used to generate a matrix of mapped fragments per RefSeq annotated gene.
Differential gene expression analysis was performed using the DESeq2 R package (v.1.16.1) with an FDR cutoff of 0.05 and log2 fold change cutoff of 1.5X. Bedtools (v2.27.1) was used to generate bedgraph files for visualization on genome browser, in which each sample was normalized to 10 million reads per library.
Genome_build: mm9
Supplementary_files_format_and_content: read count table for each RefSeq gene in each library.

source_name: CCE-Nanog-GFP mESCs

extract_protocol:
RNA was extracted utilizing RNAeasy Kit (Qiagen) following manufacturer’s instructions. Treatment with DNAse for 15 minutes was included to degrade all genomic DNA.
Libraries were prepared using NEBNext Poly(A) mRNA magnetic isolation module and NEB Ultra Directional RNA Library kit for Illumina (New England Biolabs).

value: WT


title: ATAC-seq G1 rep2


title: scr-Day4-rep1


title: M5_Fibroblast_HC


title: ATAC-seq S rep1


title: M3_Fibroblast_RA

value: flow-sorted PDGFRa+ lung  fibroblast cells


title: scr-Day2-rep2


title: KD-Day4-rep1

value: CTSL KD


title: KD-Day2-rep2


title: KD-Day2-rep1


title: scr-Day0-rep1


title: scr-Day2-rep1


title: KD-Day4-rep2


title: scr-Day0-rep2


title: scr-4-K9ac.rep2

data_processing:
Reads were check for sequencing quality with FastQC (v0.11.2). After that, reads were aligned to the mouse reference genome (mm9) using Bowtie2 (v2.2.9) with soft-clipping allowed. SAMtools (v0.1.19) was used to filter out non-primary alignments, alignments with mapping quality score less than 10, PCA duplicates, alignments on non-chromosome contigs and on ENCODE blacklist regions.
Peaks were detected for each sample against the corresponding input control using SICER (v1.1) with default parameters. Bedtools (v2.27.1) was used to generate bedgraph files for visualization on genome browser, in which each sample was normalized to 10 million reads per library and corresponding input subtracted.
Genome_build: mm9
Supplementary_files_format_and_content: peaks called for each IP library over corresponding input control.

extract_protocol:
ChIP-seq was done as previously reported (Lin-Shiao et al., 2018) . Briefly, 1X107 mESCs were fixed in 1% formaldehyde in PBS for 10 minutes, the fixation was quenched with 125mm glycine for 5 minutes.  Chromatin was sonicated with a S220 Focused-ultrasonicator (Covaris) for 15 min and immunoprecipitated with H2AK9ac (Abcam). Antibodies were conjugated to protein G Dynabeads (Thermo). Eluted samples were reverse cross-linked overnight at 65°C, and DNA as purified after treatment with RNAse (Thermo) and Proteinase K (Thermo).
Purified DNA was quantified using Qubit dsDNA kit (Thermo) and 50ng was used to prepare sequencing libraries. Input samples were also included and prepared using the same protocol. NEBNext Ultra DNA library kit from Illumina (New England Biolabs) was used to prepare the libraries and the quality was assessed by Agilent BioAnalyzer 2100 (Agilent). Quantification was done using KAPA library quantification kits (KAPA Biosystems) or NEBNext library Quant kit (New England Biolabs).

tag: chip antibody

value: H2AK9ac (Abcam)


title: KD-Day0-rep2

tag: developmental stage


title: KD-Day0-rep1


title: scr-4-K9ac.rep1


title: scr-4-input.rep2


title: scr-4-input.rep1


title: scr-2-K9ac.rep2


title: SLAM-seq S rep1


title: scr-2-K9ac.rep1


title: KD-2-K9ac.rep1


title: KD-2-input.rep2


title: KD-2-K9ac.rep2


title: KD-4-K9ac.rep1


title: KD-4-K9ac.rep2


title: scr-0-K9ac.rep1


title: KD-4-input.rep2


title: KD-4-input.rep1


title: scr-2-input.rep2


title: KD-2-input.rep1


title: 20% oxygen rep2 [Hif1a_WT_20_O2_ex2]

city: Kyoto

first: Takashi

last: Shinohara

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Graduate School of Medicine

country: Japan

institute: Kyoto University

data_processing:
The sequenced reads were mapped to the mm10 mouse reference genome using STAR (version 2.6.0c), with the GENCODE M21 annotation gtf file after trimming adaptor sequences and low-quality bases by cutadapt-1.16.
The gene expression levels were caluculated using HTSeq (version 0.11.2) and DESeq2 (v1.22.2) with GENCODE M21 annotation gtf file (protein-coding genes).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include RPM values for each Sample

source_name: 20% oxygen_GS cells

growth_protocol: GS cells were cultured in the presence of glial cell line-derived neurotrophic factor and fibroblast growth factor 2 on mouse embryonic fibroblasts.

extract_protocol:
Total RNA was extracted from GS cells using the RNeasy Plus Micro Kit (Qiagen, Valencia, CA).
Sequencing libraries were generated from 200 ng total RNA using a TruSeq stranded mRNA library preparation kit (Illumina, San Diego, CA).

treatment_protocol: For hypoxic culture,  GS cells were placed into plastic bags and gassed with 1% O2/5% CO2/94% N2. For Hif1a KO GS cells, cells were treated with AxCANCre to delete the target gene on the day of hypoxia treatment.

value: 129 x C57BL/6 mixed

tag: genotype/variation

value: Hif1a wild-type

value: 20% oxygen

tag: tissue

value: testis

value: Germline stem (GS) cells


title: KD-0-input.rep1


title: 20% oxygen rep1 [Hif1a_WT_20_O2_ex1]


title: 20% oxygen rep1 [Hif1a_KO_20_O2_ex1]

value: Hif1a KO


title: 1% oxygen rep2 [Hif1a_WT_1_O2_ex2]

source_name: 1% oxygen_GS cells

value: 1% oxygen


title: 20% oxygen rep2 [Hif1a_KO_20_O2_ex2]


title: 1% oxygen rep2 [Hif1a_KO_1_O2_ex2]


title: 1% oxygen rep1 [Hif1a_KO_1_O2_ex1]


title: scr-0-input.rep1


title: scr-2-input.rep1


title: 1% oxygen rep1 [Top1mt_WT_1_O2_ex1]

value: Top1mt wild type


title: 1% oxygen rep2 [Top1mt_WT_1_O2_ex2]


title: 1% oxygen rep2 [Top1mt_KO_1_O2_ex2]

value: Top1mt KO


title: 1% oxygen rep1 [Hif1a_WT_1_O2_ex1]


title: 1% oxygen rep1 [Top1mt_KO_1_O2_ex1]


title: 1% oxygen rep2 [WT_1_O2_ex2]

value: wild type


title: 1% oxygen rep1 [WT_1_O2_ex1]


title: Joint KO10 (KO4 arthritis -RA-)

description: IIS-SP #23

value: Arthritis

value: Forepaw


title: 20% oxygen rep2 [WT_20_O2_ex2]


title: KD-0-K9ac.rep1


title: 20% oxygen rep1 [WT_20_O2_ex1]


title: M58_Lung_12M_F150_6

first: Alexander

last: Misharin

address: SQBRC 303 E Superior St 5-404

department: Medicine (Pulmonary Division)

description: mRNA-seq

data_processing:
Basecalls performed using Illumina RTA2 software.
Indexed samples were demultiplexed to fastq files with bcl2fastq v2.17.1.14.
Reads were  trimmed using trimmomatic (version 0.36) to remove primer and adapter sequences.
Reads were then aligned to the Mus musculus reference genome (GRCm38.p3y) using the TopHat2 aligner (version 2.1.0). Counts tables were generated using HTSeq.
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: comma-separated values file including raw htseq count

growth_protocol: Male C57BL/6J mice were provided by NIA NIH

extract_protocol:
RNA was isolated using an RNeasy DNA/RNA kit after homogenization and lysis in guanidine thiocyanate buffer supplemented with β-mercaptoethanol. RNA concentration and quality were assessed using an Agilent TapeStation. RNAseq libraries were prepared using an NEB Next RNA Ultra kit with polyA enrichment module using an Agilent Bravo NGS Automated fluidics handling platform as described elsewhere (Misharin et al., 2017, J Exp Med 214). Libraries were multiplexed and sequenced on an Illumina NextSeq 500 platform using 75 cycles of high-output flow cells and a dual indexing strategy.
RNA-Seq libraries were prepared using a full-length transcript coverage NEBNext Ultra RNA (New England Biolabs)
DNA libraries sequencing was performed using an Illumina NextSeq 500 instrument (Illumina) using 75 cycles of high-output flow cells and a dual indexing strategy.

treatment_protocol: Mice were housed at Northwestern University Feinberg School of Medicine Center for Comparative Medicine for 4 weeks prior to sacrifice.

value: male

value: Lung

tag: age (months)

tag: pfu (influenza)


title: M59_Lung_09M_F150_4

description: mRNA-seq

tag: Sex


title: M45_Lung_09M_F150_1

description: mRNA-seq


title: M39_Lung_18M_F150_2

description: mRNA-seq


title: M43_Lung_12M_F150_3

description: mRNA-seq


title: M56_Lung_12M_F150_4

description: mRNA-seq


title: M41_Lung_12M_F150_1

description: mRNA-seq


title: M55_Lung_18M_F150_6

description: mRNA-seq


title: M40_Lung_18M_F150_3

description: mRNA-seq


title: M62_Lung_04M_F150_4

description: mRNA-seq


title: M63_Lung_04M_F150_5

description: mRNA-seq


title: M60_Lung_09M_F150_5

description: mRNA-seq


title: M51_Lung_24M_F150_5

description: mRNA-seq


title: M64_Lung_04M_F150_6

description: mRNA-seq


title: M46_Lung_09M_F150_2

description: mRNA-seq


title: M38_Lung_18M_F150_1

description: mRNA-seq


title: M35_Lung_24M_F150_1

description: mRNA-seq


title: M52_Lung_24M_F150_6

description: mRNA-seq


title: M50_Lung_24M_F150_4

description: mRNA-seq


title: M36_Lung_24M_F150_2

description: mRNA-seq


title: M49_Lung_04M_F150_3

description: mRNA-seq


title: M54_Lung_18M_F150_5

description: mRNA-seq


title: M53_Lung_18M_F150_4

description: mRNA-seq


title: M57_Lung_12M_F150_5

description: mRNA-seq


title: M47_Lung_04M_F150_1

description: mRNA-seq


title: M48_Lung_04M_F150_2

description: mRNA-seq


title: M42_Lung_12M_F150_2

description: mRNA-seq


title: M37_Lung_24M_F150_3

description: mRNA-seq


title: M30_WAT_04M_F0_6

description: mRNA-seq

value: White adipose tissue


title: M30_Stomach_04M_F0_6

description: mRNA-seq

value: Stomach


title: M30_Skin_04M_F0_6

description: mRNA-seq

value: Skin


title: M30_MuscSat_04M_F0_6

description: mRNA-seq

value: Muscle


title: M30_SI_04M_F0_6

description: mRNA-seq

value: Small intestine


title: M30_LI_04M_F0_6

description: mRNA-seq

value: Large intestine


title: M30_Heart_04M_F0_6

description: mRNA-seq

value: Heart


title: M30_Lung_04M_F0_6

description: mRNA-seq


title: M30_GutEP_04M_F0_6

description: mRNA-seq

value: Gut epithelium


title: M30_Esophagus_04M_F0_6

description: mRNA-seq

value: Esophagus


title: M30_Blood_04M_F0_6

description: mRNA-seq

value: Blood


title: M29_Kidney_04M_F0_5

description: mRNA-seq

value: Kidney


title: M29_Heart_04M_F0_5

description: mRNA-seq


title: M29_Esophagus_04M_F0_5

description: mRNA-seq


title: M29_GutEP_04M_F0_5

description: mRNA-seq


title: M29_LI_04M_F0_5

description: mRNA-seq


title: M29_WAT_04M_F0_5

description: mRNA-seq


title: M29_SI_04M_F0_5

description: mRNA-seq


title: M29_Lung_04M_F0_5

description: mRNA-seq


title: M29_Stomach_04M_F0_5

description: mRNA-seq


title: M29_Skin_04M_F0_5

description: mRNA-seq


title: M30_Cerebellum_04M_F0_6

description: mRNA-seq

value: Cerebellum


title: M29_MuscSat_04M_F0_5

description: mRNA-seq


title: M29_Liver_04M_F0_5

description: mRNA-seq

value: Liver


title: M30_Adrenal_04M_F0_6

description: mRNA-seq

value: Adrenal Gland


title: M30_Brain_04M_F0_3

description: mRNA-seq

value: Frontal cortex


title: M29_Cerebellum_04M_F0_5

description: mRNA-seq

value: male


title: M30_Liver_04M_F0_6

description: mRNA-seq


title: M29_Brain_04M_F0_2

description: mRNA-seq


title: M29_Blood_04M_F0_5

description: mRNA-seq


title: M29_BAT_04M_F0_5

description: mRNA-seq

value: Brown adipose tissue


title: M30_Kidney_04M_F0_6

description: mRNA-seq


title: M30_BAT_04M_F0_6

description: mRNA-seq


title: M29_Adrenal_04M_F0_5

description: mRNA-seq


title: M28_WAT_04M_F0_4

description: mRNA-seq

value: White adipose tissue


title: M28_Stomach_04M_F0_4

description: mRNA-seq

value: Stomach


title: M28_Skin_04M_F0_4

description: mRNA-seq

value: Skin


title: M28_SI_04M_F0_4

description: mRNA-seq


title: M28_LI_04M_F0_4

description: mRNA-seq


title: M28_Lung_04M_F0_4

description: mRNA-seq

value: Lung


title: M28_Kidney_04M_F0_4

description: mRNA-seq


title: M28_GutEP_04M_F0_4

description: mRNA-seq


title: M28_Heart_04M_F0_4

description: mRNA-seq


title: M28_BAT_04M_F0_4

description: mRNA-seq


title: M28_Brain_04M_F0_1

description: mRNA-seq


title: M27_Skin_09M_F0_6

description: mRNA-seq


title: M28_Adrenal_04M_F0_4

description: mRNA-seq


title: M28_Cerebellum_04M_F0_4

description: mRNA-seq


title: M27_Lung_09M_F0_6

description: mRNA-seq


title: M27_SI_09M_F0_6

description: mRNA-seq

value: Small intestine


title: M27_MuscSat_09M_F0_6

description: mRNA-seq

value: Muscle


title: M27_LI_09M_F0_6

description: mRNA-seq

value: Large intestine


title: M27_Kidney_09M_F0_6

description: mRNA-seq


title: M28_Esophagus_04M_F0_4

description: mRNA-seq


title: M27_Heart_09M_F0_6

description: mRNA-seq

value: Heart


title: M27_GutEP_09M_F0_6

description: mRNA-seq

value: Gut epithelium


title: M27_Esophagus_09M_F0_6

description: mRNA-seq

value: Esophagus


title: M27_Stomach_09M_F0_6

description: mRNA-seq


title: M27_Cerebellum_09M_F0_6

description: mRNA-seq


title: M27_Blood_09M_F0_6

description: mRNA-seq

value: Blood


title: M28_Liver_04M_F0_4

description: mRNA-seq


title: M27_BAT_09M_F0_6

description: mRNA-seq


title: M27_Adrenal_09M_F0_6

description: mRNA-seq


title: M26_Stomach_09M_F0_5

description: mRNA-seq


title: M26_Lung_09M_F0_5

description: mRNA-seq


title: M26_SI_09M_F0_5

description: mRNA-seq


title: M26_Liver_09M_F0_5

description: mRNA-seq


title: M27_Liver_09M_F0_6

description: mRNA-seq


title: M27_WAT_09M_F0_6

description: mRNA-seq


title: M26_Skin_09M_F0_5

description: mRNA-seq


title: M27_Brain_09M_F0_3

description: mRNA-seq


title: M28_Blood_04M_F0_4

description: mRNA-seq


title: M26_Kidney_09M_F0_5

description: mRNA-seq

value: Kidney


title: M26_LI_09M_F0_5

description: mRNA-seq


title: M26_Adrenal_09M_F0_5

description: mRNA-seq


title: M26_BAT_09M_F0_5

description: mRNA-seq


title: M25_SI_09M_F0_4

description: mRNA-seq


title: M25_MuscSat_09M_F0_4

description: mRNA-seq


title: M25_WAT_09M_F0_4

description: mRNA-seq


title: M25_Skin_09M_F0_4

description: mRNA-seq


title: M26_Brain_09M_F0_2

description: mRNA-seq


title: M26_WAT_09M_F0_5

description: mRNA-seq


title: M26_MuscSat_09M_F0_5

description: mRNA-seq


title: M26_Esophagus_09M_F0_5

description: mRNA-seq


title: M25_LI_09M_F0_4

description: mRNA-seq


title: M26_GutEP_09M_F0_5

description: mRNA-seq


title: M26_Blood_09M_F0_5

description: mRNA-seq


title: M25_GutEP_09M_F0_4

description: mRNA-seq


title: M25_Heart_09M_F0_4

description: mRNA-seq


title: M25_Stomach_09M_F0_4

description: mRNA-seq


title: M26_Cerebellum_09M_F0_5

description: mRNA-seq

value: Cerebellum


title: M25_BAT_09M_F0_4

description: mRNA-seq


title: M25_Cerebellum_09M_F0_4

description: mRNA-seq


title: M25_Blood_09M_F0_4

description: mRNA-seq


title: M24_Stomach_12M_F0_6

description: mRNA-seq


title: M24_WAT_12M_F0_6

description: mRNA-seq


title: M24_Lung_12M_F0_6

description: mRNA-seq


title: M24_Skin_12M_F0_6

description: mRNA-seq


title: M25_Adrenal_09M_F0_4

description: mRNA-seq

value: Adrenal Gland


title: M24_MuscSat_12M_F0_6

description: mRNA-seq


title: M24_SI_12M_F0_6

description: mRNA-seq


title: M24_Liver_12M_F0_6

description: mRNA-seq

value: Liver


title: M25_Lung_09M_F0_4

description: mRNA-seq

value: male


title: M24_Kidney_12M_F0_6

description: mRNA-seq


title: M24_LI_12M_F0_6

description: mRNA-seq


title: M24_Heart_12M_F0_6

description: mRNA-seq


title: M25_Liver_09M_F0_4

description: mRNA-seq


title: M25_Kidney_09M_F0_4

description: mRNA-seq


title: M24_Esophagus_12M_F0_6

description: mRNA-seq


title: M24_Cerebellum_12M_F0_6

description: mRNA-seq


title: M25_Brain_09M_F0_1

description: mRNA-seq

value: Frontal cortex


title: M25_Esophagus_09M_F0_4

description: mRNA-seq


title: M24_Brain_12M_F0_3

description: mRNA-seq


title: M24_Blood_12M_F0_6

description: mRNA-seq


title: M24_BAT_12M_F0_6

description: mRNA-seq

value: Brown adipose tissue


title: M23_Stomach_12M_F0_5

description: mRNA-seq

value: Stomach


title: M24_Adrenal_12M_F0_6

description: mRNA-seq


title: M23_Skin_12M_F0_5

description: mRNA-seq

value: Skin


title: M23_SI_12M_F0_5

description: mRNA-seq


title: M23_LI_12M_F0_5

description: mRNA-seq


title: M23_Liver_12M_F0_5

description: mRNA-seq


title: M23_GutEP_12M_F0_5

description: mRNA-seq


title: M23_Cerebellum_12M_F0_5

description: mRNA-seq


title: M24_GutEP_12M_F0_6

description: mRNA-seq


title: M23_Blood_12M_F0_5

description: mRNA-seq


title: M23_MuscSat_12M_F0_5

description: mRNA-seq


title: M22_SI_12M_F0_4

description: mRNA-seq


title: M23_WAT_12M_F0_5

description: mRNA-seq

value: White adipose tissue


title: M23_Kidney_12M_F0_5

description: mRNA-seq


title: M23_BAT_12M_F0_5

description: mRNA-seq


title: M23_Esophagus_12M_F0_5

description: mRNA-seq


title: M22_WAT_12M_F0_4

description: mRNA-seq


title: M22_Lung_12M_F0_4

description: mRNA-seq

value: Lung


title: M22_Stomach_12M_F0_4

description: mRNA-seq


title: M22_LI_12M_F0_4

description: mRNA-seq


title: M22_Heart_12M_F0_4

description: mRNA-seq


title: M23_Lung_12M_F0_5

description: mRNA-seq


title: M22_MuscSat_12M_F0_4

description: mRNA-seq

value: Muscle


title: M22_Kidney_12M_F0_4

description: mRNA-seq


title: M22_Liver_12M_F0_4

description: mRNA-seq


title: M22_Brain_12M_F0_1

description: mRNA-seq


title: M23_Brain_12M_F0_2

description: mRNA-seq


title: M22_Blood_12M_F0_4

description: mRNA-seq


title: M22_GutEP_12M_F0_4

description: mRNA-seq


title: M22_Esophagus_12M_F0_4

description: mRNA-seq


title: M21_WAT_18M_F0_6

description: mRNA-seq


title: M22_Skin_12M_F0_4

description: mRNA-seq


title: M21_SI_18M_F0_6

description: mRNA-seq

value: Small intestine


title: M23_Heart_12M_F0_5

description: mRNA-seq

value: Heart


title: M21_Stomach_18M_F0_6

description: mRNA-seq


title: M21_Skin_18M_F0_6

description: mRNA-seq


title: M22_BAT_12M_F0_4

description: mRNA-seq


title: M21_MuscSat_18M_F0_6

description: mRNA-seq


title: M21_Lung_18M_F0_6

description: mRNA-seq


title: M21_LI_18M_F0_6

description: mRNA-seq

value: Large intestine


title: M21_Esophagus_18M_F0_6

description: mRNA-seq

value: Esophagus


title: M21_Cerebellum_18M_F0_6

description: mRNA-seq


title: M21_Kidney_18M_F0_6

description: mRNA-seq


title: M21_Liver_18M_F0_6

description: mRNA-seq


title: M21_Blood_18M_F0_6

description: mRNA-seq

value: Blood


title: M21_Adrenal_18M_F0_6

description: mRNA-seq


title: M21_Brain_18M_F0_3

description: mRNA-seq


title: M22_Cerebellum_12M_F0_4

description: mRNA-seq


title: M20_WAT_18M_F0_5

description: mRNA-seq


title: M20_Skin_18M_F0_5

description: mRNA-seq


title: M20_SI_18M_F0_5

description: mRNA-seq


title: M20_MuscSat_18M_F0_5

description: mRNA-seq


title: M20_Liver_18M_F0_5

description: mRNA-seq


title: M20_LI_18M_F0_5

description: mRNA-seq


title: M20_Lung_18M_F0_5

description: mRNA-seq


title: M20_GutEP_18M_F0_5

description: mRNA-seq

value: Gut epithelium


title: M20_Heart_18M_F0_1

description: mRNA-seq


title: M20_Esophagus_18M_F0_5

description: mRNA-seq


title: M20_Cerebellum_18M_F0_5

description: mRNA-seq

value: Cerebellum


title: M20_Blood_18M_F0_5

description: mRNA-seq


title: M20_Brain_18M_F0_2

description: mRNA-seq


title: M20_BAT_18M_F0_5

description: mRNA-seq


title: M20_Adrenal_18M_F0_5

description: mRNA-seq

value: Adrenal Gland


title: M21_GutEP_18M_F0_6

description: mRNA-seq


title: M19_WAT_18M_F0_4

description: mRNA-seq


title: M19_Stomach_18M_F0_4

description: mRNA-seq


title: M19_SI_18M_F0_4

description: mRNA-seq


title: M19_Skin_18M_F0_4

description: mRNA-seq


title: M19_Lung_18M_F0_4

description: mRNA-seq


title: M19_Liver_18M_F0_4

description: mRNA-seq

value: Liver


title: M21_BAT_18M_F0_6

description: mRNA-seq

value: male


title: M19_MuscSat_18M_F0_4

description: mRNA-seq


title: M19_Kidney_18M_F0_4

description: mRNA-seq

value: Kidney


title: M19_LI_18M_F0_4

description: mRNA-seq


title: M19_Brain_18M_F0_1

description: mRNA-seq

value: Frontal cortex


title: M19_Esophagus_18M_F0_4

description: mRNA-seq


title: M20_Stomach_18M_F0_5

description: mRNA-seq

value: Stomach


title: M19_Blood_18M_F0_4

description: mRNA-seq


title: M19_BAT_18M_F0_4

description: mRNA-seq

value: Brown adipose tissue


title: M19_Adrenal_18M_F0_4

description: mRNA-seq


title: M20_Kidney_18M_F0_5

description: mRNA-seq


title: M18_Skin_24M_F0_6

description: mRNA-seq

value: Skin


title: M18_MuscSat_24M_F0_6

description: mRNA-seq


title: M18_Stomach_24M_F0_6

description: mRNA-seq


title: M18_SI_24M_F0_6

description: mRNA-seq


title: M18_Lung_24M_F0_6

description: mRNA-seq

value: Lung


title: M18_Liver_24M_F0_6

description: mRNA-seq


title: M18_LI_24M_F0_6

description: mRNA-seq


title: M18_Kidney_24M_F0_6

description: mRNA-seq


title: M18_Esophagus_24M_F0_6

description: mRNA-seq


title: M18_Brain_24M_F0_3

description: mRNA-seq


title: M18_Cerebellum_24M_F0_6

description: mRNA-seq


title: M18_BAT_24M_F0_6

description: mRNA-seq


title: M17_WAT_24M_F0_5

description: mRNA-seq

value: White adipose tissue


title: M18_Blood_24M_F0_6

description: mRNA-seq


title: M17_Stomach_24M_F0_5

description: mRNA-seq


title: M17_MuscSat_24M_F0_5

description: mRNA-seq

value: Muscle


title: M17_Lung_24M_F0_5

description: mRNA-seq


title: M17_LI_24M_F0_5

description: mRNA-seq


title: M17_Kidney_24M_F0_5

description: mRNA-seq


title: M17_Heart_24M_F0_5

description: mRNA-seq

value: Heart


title: M17_GutEP_24M_F0_5

description: mRNA-seq


title: M17_Liver_24M_F0_5

description: mRNA-seq


title: M18_WAT_24M_F0_6

description: mRNA-seq


title: M18_GutEP_24M_F0_6

description: mRNA-seq


title: M17_Cerebellum_24M_F0_5

description: mRNA-seq


title: M17_Esophagus_24M_F0_5

description: mRNA-seq


title: M17_Brain_24M_F0_2

description: mRNA-seq


title: M16_WAT_24M_F0_4

description: mRNA-seq


title: M18_Heart_24M_F0_6

description: mRNA-seq


title: M17_Adrenal_24M_F0_5

description: mRNA-seq


title: M16_Stomach_24M_F0_4

description: mRNA-seq


title: M17_BAT_24M_F0_5

description: mRNA-seq


title: M16_Skin_24M_F0_4

description: mRNA-seq


title: M17_Skin_24M_F0_5

description: mRNA-seq


title: M18_Adrenal_24M_F0_6

description: mRNA-seq


title: M16_SI_24M_F0_4

description: mRNA-seq

value: Small intestine


title: M16_Liver_24M_F0_4

description: mRNA-seq


title: M17_Blood_24M_F0_5

description: mRNA-seq


title: M16_GutEP_24M_F0_4

description: mRNA-seq


title: M16_Esophagus_24M_F0_4

description: mRNA-seq

value: Esophagus


title: M16_Kidney_24M_F0_4

description: mRNA-seq


title: M16_LI_24M_F0_4

description: mRNA-seq

value: Large intestine


title: M16_Heart_24M_F0_4

description: mRNA-seq


title: M16_Brain_24M_F0_1

description: mRNA-seq


title: M16_Lung_24M_F0_4

description: mRNA-seq


title: M16_MuscSat_24M_F0_4

description: mRNA-seq


title: M16_Cerebellum_24M_F0_4

description: mRNA-seq


title: M16_BAT_24M_F0_4

description: mRNA-seq


title: M15_Skin_04M_F0_3

description: mRNA-seq


title: M15_SI_04M_F0_3

description: mRNA-seq


title: M15_Stomach_04M_F0_3

description: mRNA-seq


title: M15_WAT_04M_F0_3

description: mRNA-seq


title: M15_MuscSat_04M_F0_3

description: mRNA-seq


title: M16_Adrenal_24M_F0_4

description: mRNA-seq


title: M15_Lung_04M_F0_3

description: mRNA-seq


title: M15_Liver_04M_F0_3

description: mRNA-seq


title: M15_LI_04M_F0_3

description: mRNA-seq


title: M16_Blood_24M_F0_4

description: mRNA-seq

value: Blood


title: M15_GutEP_04M_F0_3

description: mRNA-seq

value: Gut epithelium


title: M15_BAT_04M_F0_3

description: mRNA-seq


title: M15_Kidney_04M_F0_3

description: mRNA-seq


title: M15_Blood_04M_F0_3

description: mRNA-seq


title: M15_Cerebellum_04M_F0_3

description: mRNA-seq

value: Cerebellum


title: M15_Brain_04M_F0_3

description: mRNA-seq


title: M15_Adrenal_04M_F0_3

description: mRNA-seq

value: Adrenal Gland


title: M14_Stomach_04M_F0_2

description: mRNA-seq

value: male


title: M15_Esophagus_04M_F0_3

description: mRNA-seq


title: M14_WAT_04M_F0_2

description: mRNA-seq


title: M14_Skin_04M_F0_2

description: mRNA-seq


title: M14_Liver_04M_F0_2

description: mRNA-seq

value: Liver


title: M14_LI_04M_F0_2

description: mRNA-seq


title: M14_SI_04M_F0_2

description: mRNA-seq


title: M14_Lung_04M_F0_2

description: mRNA-seq


title: M14_MuscSat_04M_F0_2

description: mRNA-seq


title: M14_Heart_04M_F0_2

description: mRNA-seq


title: M14_GutEP_04M_F0_2

description: mRNA-seq


title: M14_Cerebellum_04M_F0_2

description: mRNA-seq


title: M14_Esophagus_04M_F0_2

description: mRNA-seq


title: M14_Kidney_04M_F0_2

description: mRNA-seq

value: Kidney


title: M15_Heart_04M_F0_3

description: mRNA-seq


title: M14_Brain_04M_F0_2

description: mRNA-seq

value: Frontal cortex


title: M14_Blood_04M_F0_2

description: mRNA-seq


title: M13_WAT_04M_F0_1

description: mRNA-seq


title: M14_BAT_04M_F0_2

description: mRNA-seq

value: Brown adipose tissue


title: M14_Adrenal_04M_F0_2

description: mRNA-seq


title: M13_Stomach_04M_F0_1

description: mRNA-seq

value: Stomach


title: M13_Skin_04M_F0_1

description: mRNA-seq

value: Skin


title: M13_SI_04M_F0_1

description: mRNA-seq


title: M13_Lung_04M_F0_1

description: mRNA-seq

value: Lung


title: M13_MuscSat_04M_F0_1

description: mRNA-seq

value: Muscle


title: M13_LI_04M_F0_1

description: mRNA-seq


title: M13_Heart_04M_F0_1

description: mRNA-seq

value: Heart


title: M13_GutEP_04M_F0_1

description: mRNA-seq


title: M13_Kidney_04M_F0_1

description: mRNA-seq


title: M13_Liver_04M_F0_1

description: mRNA-seq


title: M13_Cerebellum_04M_F0_1

description: mRNA-seq


title: M13_Esophagus_04M_F0_1

description: mRNA-seq


title: M13_Adrenal_04M_F0_1

description: mRNA-seq


title: M13_Brain_04M_F0_1

description: mRNA-seq


title: M12_WAT_09M_F0_3

description: mRNA-seq

value: White adipose tissue


title: M13_BAT_04M_F0_1

description: mRNA-seq


title: M12_Skin_09M_F0_3

description: mRNA-seq


title: M12_Stomach_09M_F0_3

description: mRNA-seq


title: M12_SI_09M_F0_3

description: mRNA-seq

value: Small intestine


title: M19_GutEP_18M_F0_4

description: mRNA-seq


title: M12_Lung_09M_F0_3

description: mRNA-seq


title: M12_LI_09M_F0_3

description: mRNA-seq

value: Large intestine


title: M12_Kidney_09M_F0_3

description: mRNA-seq


title: M12_Esophagus_09M_F0_3

description: mRNA-seq

value: Esophagus


title: M12_GutEP_09M_F0_3

description: mRNA-seq

value: Gut epithelium


title: M12_Brain_09M_F0_3

description: mRNA-seq


title: M12_Heart_09M_F0_3

description: mRNA-seq


title: M12_Cerebellum_09M_F0_3

description: mRNA-seq

value: Cerebellum


title: M12_Liver_09M_F0_3

description: mRNA-seq


title: M12_Blood_09M_F0_3

description: mRNA-seq

value: Blood


title: M13_Blood_04M_F0_1

description: mRNA-seq

value: male


title: M12_MuscSat_09M_F0_3

description: mRNA-seq


title: M12_BAT_09M_F0_3

description: mRNA-seq


title: M11_WAT_09M_F0_2

description: mRNA-seq


title: M12_Adrenal_09M_F0_3

description: mRNA-seq

value: Adrenal Gland


title: M11_Skin_09M_F0_2

description: mRNA-seq


title: M11_MuscSat_09M_F0_2

description: mRNA-seq


title: M11_SI_09M_F0_2

description: mRNA-seq


title: M11_Liver_09M_F0_2

description: mRNA-seq

value: Liver


title: M11_Lung_09M_F0_2

description: mRNA-seq


title: M11_LI_09M_F0_2

description: mRNA-seq


title: M11_Kidney_09M_F0_2

description: mRNA-seq

value: Kidney


title: M11_GutEP_09M_F0_2

description: mRNA-seq


title: M11_Heart_09M_F0_2

description: mRNA-seq


title: M11_Esophagus_09M_F0_2

description: mRNA-seq


title: M11_Cerebellum_09M_F0_2

description: mRNA-seq


title: M11_Blood_09M_F0_2

description: mRNA-seq


title: M11_Adrenal_09M_F0_2

description: mRNA-seq


title: M11_Brain_09M_F0_2

description: mRNA-seq

value: Frontal cortex


title: M10_WAT_09M_F0_1

description: mRNA-seq


title: M10_Skin_09M_F0_1

description: mRNA-seq


title: M11_BAT_09M_F0_2

description: mRNA-seq

value: Brown adipose tissue


title: M10_Lung_09M_F0_1

description: mRNA-seq


title: M10_Liver_09M_F0_1

description: mRNA-seq


title: M10_GutEP_09M_F0_1

description: mRNA-seq


title: M10_Stomach_09M_F0_1

description: mRNA-seq

value: Stomach


title: M10_LI_09M_F0_1

description: mRNA-seq


title: M10_Cerebellum_09M_F0_1

description: mRNA-seq


title: M10_SI_09M_F0_1

description: mRNA-seq


title: M10_Heart_09M_F0_1

description: mRNA-seq


title: M10_BAT_09M_F0_1

description: mRNA-seq


title: M10_Brain_09M_F0_1

description: mRNA-seq


title: M10_Adrenal_09M_F0_1

description: mRNA-seq


title: M11_Stomach_09M_F0_2

description: mRNA-seq


title: 15LS30_Islets_S36

city: Minneapolis

first: Christopher

last: Burlak

state: Minnesota

address: 420 Delaware Street SE

institute: University of Minnesota

data_processing:
Raw sequence that passed CASAV 1.8P/F filter were assessed by fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Read mapping was performed via hisat2 (2.0.2) using the Pig genome (Sus scrofa (susSCr3)) as a reference.
Counts were quantified via Feature counts (Subread Package).
Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen, Redwood city, CA) using raw read counts.
Genome_build: susScr3

organism: Sus scrofa

source_name: Pancreatic islets

extract_protocol: Pancreas sample: A 50-mg sample of the pancreas parenchyma was collected from the duodenal lobe at the time of pancreas retrieval. Islet sampole: Islets liberated from the pancreatic tissue were purified and cultured free-floating in ME 199 media at 37◦C in humidified air without CO2 for 7 days.

tag: islet density

value: High


title: M09_WAT_12M_F0_3

description: mRNA-seq


title: 16CS60_Islets_S27


title: 15LS29_Islets_S16


title: 16IS5_Islets_S17

value: Low


title: M09_Stomach_12M_F0_3

description: mRNA-seq


title: 15LS26_Islets_S7


title: 14HS27_Islets_S8


title: 15AS28_Islets_S6


title: 15LS27_Islets_S26


title: 14ES73_Islets_S38


title: 14BS54_Islets_S28


title: 14HS7_Islets_S37


title: 14ES72_Islets_S19


title: 14HS26_Islets_S18


title: M10_Esophagus_09M_F0_1

description: mRNA-seq


title: 12FS131_Islets_S39


title: 12AS51_Islets_S40

source_name: Pancreas


title: 12FS133_Islets_S29


title: 16CS60_Pancreas_S22


title: 12FS162_Islets_S10


title: 12FS161_Islets_S20


title: 11KS28_Islets_S30


title: 16IS5_Pancreas_S12


title: 14HS27_Pancreas_S3


title: 15LS26_Pancreas_S2


title: 12FS135_Islets_S9


title: 15LS29_Pancreas_S11


title: 15LS30_Pancreas_S31


title: 14HS26_Pancreas_S13


title: 14BS54_Pancreas_S23


title: 12FS135_Pancreas_S4


title: 12FS161_Pancreas_S15


title: 14ES73_Pancreas_S33


title: 12FS133_Pancreas_S24


title: 12FS131_Pancreas_S34


title: 11KS28_Pancreas_S25


title: E. crypticus_Gesaprim EC10 7days_replicate3

city: Aveiro

first: Susana

middle: Isabel Lopes

last: Gomes

address: Campus Universitário de Santiago, Departement of Biology, University of Aveiro

department: Biology

country: Portugal

institute: CESAM & University of Aveiro

hyb_protocol: The cRNA samples were hybridized on the Custom Gene Expression Agilent Microarrays (4 x 44k format) developed for Enchytraeus crypticus. Hybridizations were performed using the Agilent Gene Expression Hybridization Kit (Agilent Technologies, Palo Alto, CA, USA) and each biological replicate was individually hybridized on one array. The arrays were hybridized at 65ºC with a rotation of 10 rpm, during 17h. After that the microarrays were washed using Agilent Gene Expression Wash Buffer Kit (Agilent Technologies, Palo Alto, CA, USA)

scan_protocol: Scanning was performed using the Agilent DNA microarray scanner G2505B (Agilent Technologies). Fluorescence intensity data was obtained with Feature Extraction (10.5.1.1) Software (Agilent Technologies).

data_processing: Background correction was provided by Agilent Feature Extraction software and only gene probes with good signal quality (flag IsPosAndSignif = True) in all samples were employed in the analyses.

organism: Enchytraeus crypticus

source_name: Whole body extracts

label_protocol: Labelling and hybridizations followed the protocol “One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling” from Agilent Technologies (Agilent Technologies, Palo Alto, CA, USA)). Briefly, 500 ng of total RNA was amplified and labelled with Agilent Low Input Quick Amp Labelling Kit (Agilent Technologies, Palo Alto, CA, USA). Positive controls were added with the Agilent one-colour RNA Spike-In Kit (Agilent Technologies, Palo Alto, CA, USA). Purification of the amplified and labelled cRNA was performed with the RNeasy columns (Qiagen, Valencia, CA, USA).

extract_protocol: Total RNA was extracted using SV Total RNA Isolation System (Promega Corporation, USA).The quantity and purity of the RNA samples was checked using the ND-1000 spectrophotometer (Nanodrop®, USA) through measurement of the 260nm/280nm and 260nm/230nm absorbance. For all used samples these ratios were approximately 2. To verify the integrity of the RNA samples, a denaturating formaldehyde agarose gel electrophoresis was performed.

tag: exposure

value: Gesaprim EC10 (effect concentration on reproduction) in soil for 7 days

tag: stage of development

value: Adult organisms with well developed clitellum


title: E. crypticus_ATZ EC10 7days_replicate3

value: ATZ EC10 (effect concentration on reproduction) in soil for 7 days


title: 14HS7_Pancreas_S32


title: 14ES72_Pancreas_S14


title: 12AS51_Pancreas_S35


title: E. crypticus_ATZ EC10 7days_replicate2


title: E. crypticus_ATZ EC10 7days_replicate1


title: E. crypticus_ATZ EC50 7days_replicate3

value: ATZ EC50 (effect concentration on reproduction) in soil for 7 days


title: E. crypticus_Gesaprim EC10 7days_replicate2


title: E. crypticus_Gesaprim EC50 7days_replicate2

value: Gesaprim EC50 (effect concentration on reproduction) in soil for 7 days


title: E. crypticus_Gesaprim EC50 7days_replicate1


title: E. crypticus_Gesaprim EC10 7days_replicate1


title: E. crypticus_nano_ATZ EC50 7days_replicate2

value: nano_ATZ EC50 (effect concentration on reproduction) in soil for 7 days


title: E. crypticus_nano_ATZ EC50 7days_replicate1


title: E. crypticus_nano_ATZ EC10 7days_replicate2

value: nano_ATZ EC10 (effect concentration on reproduction) in soil for 7 days


title: E. crypticus_Gesaprim EC50 7days_replicate3


title: E. crypticus_Control-acetone 7days_replicate2

value: soil + acetone for 7 days


title: E. crypticus_ATZ EC50 7days_replicate2


title: E. crypticus_Control 7days_replicate2

value: un-spiked soil for 7 days


title: E. crypticus_Control-acetone 7days_replicate3


title: E. crypticus_Control 7days_replicate3


title: E. crypticus_nano_ATZ EC10 7days_replicate3


title: E. crypticus_Gesaprim EC50 3days_replicate1

value: Gesaprim EC50 (effect concentration on reproduction) in soil for 3 days


title: E. crypticus_Gesaprim EC50 3days_replicate3


title: E. crypticus_Control 7days_replicate1


title: E. crypticus_nano_ATZ EC10 7days_replicate1


title: E. crypticus_Control-acetone 7days_replicate1


title: E. crypticus_ATZ EC50 7days_replicate1


title: E. crypticus_nano_ATZ EC50 7days_replicate3


title: E. crypticus_Gesaprim EC50 3days_replicate2


title: E. crypticus_ATZ EC50 3days_replicate2

value: ATZ EC50 (effect concentration on reproduction) in soil for 3 days


title: E. crypticus_ATZ EC50 3days_replicate3


title: E. crypticus_Gesaprim EC10 3days_replicate1

value: Gesaprim EC10 (effect concentration on reproduction) in soil for 3 days


title: E. crypticus_Gesaprim EC10 3days_replicate2


title: E. crypticus_Gesaprim EC10 3days_replicate3


title: E. crypticus_nano_ATZ EC50 3days_replicate2

value: nano_ATZ EC50 (effect concentration on reproduction) in soil for 3 days


title: sst1_1_ins_30dpf_3

city: Greater Noida

first: Sumeet

middle: Pal

last: Singh

state: Uttar Pradesh

address: NH91, Tehsil Dadri

department: Life Sciences

country: India

institute: Shiv Nadar Institution of Eminence

data_processing:
Trimming using trim_galore using default parameters
Mapping using HISAT2 against GRCz11with default parameters
Counts per gene generated using FeatureCounts with default parameters
Genome_build: Zebrafish GRCz11
Supplementary_files_format_and_content: read counts as csv file

organism: Danio rerio

extract_protocol:
Enzymatic Dissociation
Smart-Seq2, followed by llumina NextSeq

value: Tg(ins:BB1.0L), TgBAC(sst1.1:memEGFP)

tag: growth

value: Normal

value: pancreas


title: ins_30dpf_2


title: E. crypticus_ATZ EC50 3days_replicate1


title: E. crypticus_nano_ATZ EC10 3days_replicate3

value: nano_ATZ EC10 (effect concentration on reproduction) in soil for 3 days


title: ins_30dpf_1


title: sst1_1_30dpf_3


title: E. crypticus_ATZ EC10 3days_replicate3

value: ATZ EC10 (effect concentration on reproduction) in soil for 3 days


title: sst1_1_30dpf_2


title: sst1_1_ins_30dpf_1


title: E. crypticus_nano_ATZ EC10 3days_replicate1

value: Adult organisms with well developed clitellum


title: E. crypticus_Control-acetone 3days_replicate3

value: soil + acetone for 3 days


title: sst1_1_ins_30dpf_2


title: E. crypticus_nano_ATZ EC50 3days_replicate3


title: E. crypticus_ATZ EC10 3days_replicate2


title: sst1_1_30dpf_04_H12


title: E. crypticus_nano_ATZ EC10 3days_replicate2


title: sst1_1_30dpf_04_G12


title: sst1_1_30dpf_04_F12


title: E. crypticus_nano_ATZ EC50 3days_replicate1


title: E. crypticus_ATZ EC10 3days_replicate1


title: sst1_1_30dpf_04_E12


title: E. crypticus_Control-acetone 3days_replicate1


title: E. crypticus_Control-acetone 3days_replicate2


title: E. crypticus_Control 3days_replicate2

value: un-spiked soil for 3 days


title: sst1_1_30dpf_04_C12


title: E. crypticus_Control 3days_ replicate1


title: E. crypticus_Control 3days_replicate3


title: sst1_1_30dpf_1


title: ins_30dpf_04_B12


title: sst1_1_30dpf_04_D12


title: sst1_1_30dpf_04_F11


title: sst1_1_30dpf_04_H11


title: sst1_1_30dpf_04_G11


title: sst1_1_30dpf_04_C11


title: sst1_1_30dpf_04_F10


title: sst1_1_30dpf_04_G10


title: ins_30dpf_04_A12


title: ins_30dpf_04_A11


title: sst1_1_30dpf_04_H10


title: sst1_1_30dpf_04_E10


title: sst1_1_30dpf_04_D10


title: ins_30dpf_04_B11


title: sst1_1_30dpf_04_E11


title: ins_30dpf_04_A10


title: sst1_1_30dpf_04_C09


title: ins_30dpf_04_B10


title: sst1_1_30dpf_04_H09


title: sst1_1_30dpf_04_F09


title: sst1_1_30dpf_04_D09


title: sst1_1_30dpf_04_H08


title: ins_30dpf_04_A09


title: sst1_1_30dpf_04_E09


title: sst1_1_30dpf_04_G09


title: sst1_1_30dpf_04_C10


title: sst1_1_30dpf_04_F08


title: ins_30dpf_04_B09


title: sst1_1_30dpf_04_D11


title: sst1_1_30dpf_04_D08


title: sst1_1_30dpf_04_C08


title: sst1_1_30dpf_04_G07


title: sst1_1_30dpf_04_E08


title: ins_30dpf_04_A08


title: sst1_1_30dpf_04_H07


title: sst1_1_30dpf_04_F07


title: ins_30dpf_04_B08


title: sst1_1_30dpf_04_C07


title: ins_30dpf_04_B07


title: ins_30dpf_04_A07


title: sst1_1_30dpf_04_G06


title: sst1_1_30dpf_04_D07


title: ins_30dpf_04_A06


title: ins_30dpf_04_B06


title: sst1_1_30dpf_04_H06


title: sst1_1_30dpf_04_G08


title: sst1_1_30dpf_04_F06


title: ins_30dpf_04_A05


title: sst1_1_30dpf_04_H05


title: sst1_1_30dpf_04_D05


title: ins_30dpf_04_B05


title: sst1_1_30dpf_04_D06


title: sst1_1_30dpf_04_C05


title: sst1_1_30dpf_04_F05


title: sst1_1_30dpf_04_G05


title: sst1_1_30dpf_04_E04


title: sst1_1_30dpf_04_D04


title: sst1_1_30dpf_04_G04


title: sst1_1_30dpf_04_H04


title: sst1_1_30dpf_04_F04


title: sst1_1_30dpf_04_C04


title: ins_30dpf_04_A04


title: sst1_1_30dpf_04_H03


title: sst1_1_30dpf_04_G03


title: sst1_1_30dpf_04_F03


title: sst1_1_30dpf_04_C06


title: sst1_1_30dpf_04_E03


title: sst1_1_30dpf_04_D03


title: ins_30dpf_04_C03


title: ins_30dpf_04_A03


title: sst1_1_30dpf_04_G02


title: sst1_1_30dpf_04_H02


title: ins_30dpf_04_B03


title: sst1_1_30dpf_04_D02


title: sst1_1_30dpf_04_E02


title: ins_30dpf_04_B02


title: sst1_1_30dpf_04_H01


title: ins_30dpf_04_A02


title: sst1_1_30dpf_04_G01


title: sst1_1_30dpf_04_F01


title: ins_30dpf_04_C02


title: ins_30dpf_04_B04


title: sst1_1_30dpf_04_E01


title: sst1_1_30dpf_04_D01


title: ins_30dpf_04_C01


title: ins_30dpf_03_F12


title: ins_30dpf_03_H12


title: sst1_1_ins_30dpf_03_E12


title: sst1_1_ins_30dpf_03_D12


title: sst1_1_ins_30dpf_03_C12


title: ins_30dpf_03_G12


title: sst1_1_ins_30dpf_03_B12


title: ins_30dpf_03_H11


title: sst1_1_ins_30dpf_03_A12


title: ins_30dpf_04_A01


title: sst1_1_30dpf_04_F02


title: ins_30dpf_03_F11


title: sst1_1_ins_30dpf_03_C11


title: sst1_1_ins_30dpf_03_E11


title: sst1_1_ins_30dpf_03_D11


title: sst1_1_ins_30dpf_03_B11


title: sst1_1_ins_30dpf_03_A11


title: ins_30dpf_03_H10


title: ins_30dpf_03_F10


title: sst1_1_ins_30dpf_03_D10


title: sst1_1_ins_30dpf_03_E10


title: sst1_1_ins_30dpf_03_C10


title: ins_30dpf_03_G10


title: sst1_1_ins_30dpf_03_B10


title: sst1_1_ins_30dpf_03_A10


title: ins_30dpf_04_B01


title: ins_30dpf_03_G09


title: ins_30dpf_03_F09


title: sst1_1_ins_30dpf_03_C09


title: ins_30dpf_03_G11


title: sst1_1_ins_30dpf_03_D09


title: sst1_1_ins_30dpf_03_B09


title: sst1_1_ins_30dpf_03_D08


title: sst1_1_ins_30dpf_03_A09


title: ins_30dpf_03_G08


title: ins_30dpf_03_H08


title: sst1_1_ins_30dpf_03_E09


title: sst1_1_ins_30dpf_03_C08


title: sst1_1_ins_30dpf_03_A08


title: sst1_1_ins_30dpf_03_B08


title: ins_30dpf_03_H07


title: ins_30dpf_03_F08


title: ins_30dpf_03_F07


title: sst1_1_ins_30dpf_03_E08


title: sst1_1_ins_30dpf_03_D07


title: sst1_1_ins_30dpf_03_B07


title: sst1_1_ins_30dpf_03_A07


title: ins_30dpf_03_H06


title: ins_30dpf_03_H09


title: sst1_1_ins_30dpf_03_C07


title: ins_30dpf_03_F06


title: ins_30dpf_03_G06


title: sst1_1_ins_30dpf_03_C06


title: sst1_1_ins_30dpf_03_B06


title: sst1_1_ins_30dpf_03_A06


title: sst1_1_ins_30dpf_03_D05


title: sst1_1_ins_30dpf_03_C05


title: ins_30dpf_03_G05


title: ins_30dpf_03_F05


title: ins_30dpf_03_H05


title: sst1_1_ins_30dpf_03_B05


title: sst1_1_ins_30dpf_03_A05


title: sst1_1_ins_30dpf_03_E04


title: ins_30dpf_03_G07


title: sst1_1_ins_30dpf_03_D04


title: ins_30dpf_03_H04


title: sst1_1_ins_30dpf_03_B04


title: sst1_1_ins_30dpf_03_A04


title: sst1_1_ins_30dpf_03_F03


title: sst1_1_ins_30dpf_03_C03


title: sst1_1_ins_30dpf_03_D03


title: sst1_1_ins_30dpf_03_E03


title: ins_30dpf_03_G04


title: sst1_1_ins_30dpf_03_A03


title: ins_30dpf_03_H03


title: ins_30dpf_03_H02


title: sst1_1_ins_30dpf_03_F02


title: sst1_1_ins_30dpf_03_E02


title: ins_30dpf_03_G03


title: sst1_1_ins_30dpf_03_B03


title: ins_30dpf_03_F04


title: sst1_1_ins_30dpf_03_D02


title: ins_30dpf_03_G02


title: sst1_1_ins_30dpf_03_C02


title: sst1_1_ins_30dpf_03_C04


title: ins_30dpf_03_G01


title: sst1_1_ins_30dpf_03_A02


title: sst1_1_ins_30dpf_03_E01


title: ins_30dpf_03_H01


title: sst1_1_ins_30dpf_03_D01


title: sst1_1_ins_30dpf_03_B01


title: sst1_1_ins_30dpf_03_A01


title: sst1_1_ins_30dpf_03_C01


title: sst1_1_ins_30dpf_03_F01


title: Olive flounder with shy personality (SP), replicate 3

city: Hong Kong

first: Runsheng

last: Li

address: To Yuen Building, 31 To Yuen Street, City University of Hong Kong

country: Hong Kong

institute: City University of Hong Kong

data_processing:
Raw data were trimmed using Trimmomatic(V 0.30).
The clean reads were mapped to olive flounder genome (GCF_001970005.1) using TopHat2 (V2.0.11) with default parameters.
The mapped bam files were counted using HTSeq-count (V0.11.1).
Genome_build: GCF_001970005.1
Supplementary_files_format_and_content: Two column table file containing the read count for each gene

organism: Paralichthys olivaceus

growth_protocol: Olive flounder (101.06 ± 6.39 g, mean ± SD) were obtained in central experimental station of Chinese academy of fisheries sciences (Hebei, China), and preserved in aquarium facilities in aerated 500 L tanks under a 12:12 light: dark cycle at 18 °C at Shanghai Ocean University. Fish were fed to satiation twice daily (8:00 and 18:00) with commercial fish pellets.

extract_protocol:
Total RNA was extracted from each sample using Trizol Reagent according to the manufacturer’s protocol, and was treated with DNaseI to eliminate potential genomic DNA contamination. The concentration and integrity were were determined by spectrophotometry (NanoDrop ND-1000 system, Thermo Fisher Scientific, DE, USA)) and gel electrophoresis. Equal amounts of RNA from the hindbrain were obtained from six individuals.
The Illumina TruSeq mRNA Stranded Sample Preparation kit was used in constructing the Illumina sequencing libraries according to previous methods (Zhang et al., 2017). The libraries were then sequenced on Illumina HiSeq 2000 using a 100-bp paired-end sequencing module.

treatment_protocol: Bold personality (BP) and shy personality (SP) flounder were selected according to methods previous reported (Rupia et al, 2016b).

tag: personality

value: bold personality (BP)

value: hindbrain


title: Olive flounder with shy personality (SP), replicate 1


title: Olive flounder with shy personality (SP), replicate 2


title: Olive flounder with bold personality (BP), replicate 3

value: shy personality (SP)


title: Olive flounder with bold personality (BP), replicate 1


title: Olive flounder with bold personality (BP), replicate 2


title: six month old small RNA2

city: Xinyang

first: Yun

last: Ma

address: Shihe

institute: Xinyang Normal University

data_processing:
The primer and adaptor sequence as well as the junk reads and fragments < 18 nt and > 26 nt were removed. For the buffalo genome was not available, the remaining 18~26 nt reads were screened against and mapped to the cattle genome (UMD3.1) by Bowtie software.
To discard rRNA, tRNA, snRNA, ncRNA and other snoRNA sequences, the reads mapped to the reference genome were further filtered by blasting against the Rfam database, RepBase database, mRNA database, miRBase database, respectively.
The clean miRNA reads were further used for novel miRNAs prediction by miRDeep.
Transcripts per kilobase million (TPM) was used as the index to calculate the expression level of each miRNA in every library. The expression level was indicated as log2TPM.

organism: Bubalus bubalis

source_name: Six month old adipose tissue

growth_protocol: Tthree adipose samples from Chinese swamp buffalo were collected from Benniu abattoir, a local slaughterhouse of Xinayang, P.R. China. Tissue samples were snap-frozen in liquid nitrogen and stored at –80°C freezer until use.

extract_protocol:
Total RNA was extracted using TRIzol reagent. Total RNA was assessed by electrophoresis on a denaturing agarose gel and quantified by NanoDrop spectrophotometer (NanoDrop, USA) and Agilent 2100 Bioanalyzer. The total RNA samples (3 mg) were treated with the epicentre Ribo-ZeroTM Kit to remove rRNA before constructing the RNA-seq libraries.
Approximately 1 μg total RNA per sample was used for small RNA library construction according to protocol of the TruSeq® miRNA Sample Prep Kit v2 (Illumina, USA). Briefly, the 5’ and 3’ adaptors were ligated using T4 RNA ligase. Then the modified small RNA was subjected to RT-PCR for amplification. The 145-160 bp cDNA fragment was extracted and purified from the polyacrylamide gel electrophoresis.
The enriched cDNA was sequenced in a HiSeq 2500 sequencing system (Illumina, San Diego, USA) at the Genergy Biotechnology Co., Ltd. (Shanghai, China).

value: adipose

tag: age

value: six month old


title: six month old small RNA3


title: input1_Met-

city: Hangzhou

first: Xiao

last: Shu

state: Zhejiang Province

address: Zheda Road 38

department: Department of Polymer Science and Engineering

institute: Zhejiang university

data_processing:
Raw reads data was first subject to fastqc (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) for quality control, and adapters were trimmed using fastp (https://github.com/OpenGene/fastp). The minimum quality threshold was set to 20, and the maximum amplicon end distance was 146 nt.
For alignment, reads data was mapped to hg38 as the reference genome using hisat2 (http://daehwankimlab.github.io/hisat2/). The sam files aligned uniquely (flag: 83/163, 99/147) were sorted and reordered into bam files with samtools (http://www.htslib.org/)
To quantify the number of mutation reads with A-to-C and A-to-T, we used sam2tsv (http://lindenb.github.io/jvarkit/Sam2Tsv.html) to analyze each aligned read with mutation sites and counted the reads for RNA-seq.
Genome_build: hg38

organism: Homo sapiens

source_name: HeLa cells

growth_protocol: HeLa cells were cultured in DMEM/high-glucose medium supplemented with 10% FBS  and 1% 100× pen-strep at 37 °C with 5% CO2.

extract_protocol:
Total RNAs of HeLa cells were isolated using Trizol Reagent, and the mRNA was purified from the total RNA by GenEluteTM mRNA Miniprep Kit.
Library preparations were conducted following the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina E7760 manual. For reverse transcription, HIV (Reverse transcriptase recombinant HIV, Worthington Biochemical Corporation, LS05003) was used.

treatment_protocol: Methionine-deficient medium supplemented with 10% FBS, 1% 100× pen-strep and 1 mM l-cysteine for samples Met-, while 1 mM methionine was added for samples Met+.

tag: cell line

value: HeLa

value: Methionine-deficient


title: cyc2_Met+

tag: treatment

value: methionine-sufficient


title: cyc2_Met-


title: input2_Met-


title: cyc1_Met+


title: input2_Met+


title: input1_Met+


title: cyc1_Met-


title: six month old small RNA1


title: A549-ACE2 cells infected with Alpha SARS-CoV-2 strain at 24hpi, Replicate3

city: Oxford

first: Jeffrey

middle: Y

last: Lee

address: Dorothy Hodgkin Road

country: United Kingdom

institute: University of Oxford

data_processing:
Basecalling was done on the Illumina NextSeq sequencer with the Illumina Real Time Analysis software version 2.11.3
Sequenced reads were demultiplexed and adapter trimmed.
Reads were aligned to GRCh38 and SARS-CoV-2 reference sequence using STAR.
Gene counts were calculated using HTSeq-count.
Gene count normalisation and differential expression analysis were performed using the R package DESeq2.
Genome_build: GRCh38, NC_045512.2
Supplementary_files_format_and_content: Tab delimited file of DESeq2 normalised count and differential gene expression

source_name: A549 cells expressing ACE2

growth_protocol: A549-ACE2 (Klein et al., 2020) cells were maintained in standard DMEM supplemented with 10% fetal bovine serum, 2mM L-glutamine, 100 U/mL penicillin and 10μg/mL streptomycin and non-essential amino acids. The cells were maintained at 37°C and 5% CO2 in a standard culture incubator.

extract_protocol:
Infected cells were harvested in RLT buffer and RNA extracted using the Qiagen RNAeasy kit, following manufacturer instructions.
Sequencing libraries were prepared using the Illumina Total RNA Prep with Ribo-Zero Plus library kit (Cat# 20040525) according to manufacturer’s guidelines.

treatment_protocol: SARS-CoV-2 strains: Victoria 01/20 (BVIC01) (Caly et al., 2020) (Provided by PHE Porton Down after supply from the Doherty Centre Melbourne, Australia) and B.1.1.7 (Tegally et al., 2020) (20I/501Y.V1.HMPP1) (provided by PHE Porton Down). Cells were infected at an MOI of 1 for 2h followed by extensive washing in PBS. Residual cell surface associated virus was removed by trypsin treatment of the cell monolayer for 2mins followed by neutralisation of the trypsin using serum containing media. Infected cells were then maintained for defined periods up to 24h.

tag: infection

value: Infected with SARS-CoV-2

tag: sars-cov-2 strain

value: Alpha

tag: hours post infection


title: A549-ACE2 cells infected with Alpha SARS-CoV-2 strain at 24hpi, Replicate2


title: A549-ACE2 cells infected with Alpha SARS-CoV-2 strain at 24hpi, Replicate1


title: A549-ACE2 cells infected with Alpha SARS-CoV-2 strain at 8hpi, Replicate3


title: A549-ACE2 cells infected with Alpha SARS-CoV-2 strain at 8hpi, Replicate2


title: A549-ACE2 cells infected with Alpha SARS-CoV-2 strain at 8hpi, Replicate1


title: A549-ACE2 cells infected with Alpha SARS-CoV-2 strain at 2hpi, Replicate1


title: A549-ACE2 cells infected with VIC SARS-CoV-2 strain at 24hpi, Replicate2

value: VIC


title: A549-ACE2 cells infected with Alpha SARS-CoV-2 strain at 2hpi, Replicate2


title: A549-ACE2 cells infected with VIC SARS-CoV-2 strain at 24hpi, Replicate3


title: A549-ACE2 cells infected with Alpha SARS-CoV-2 strain at 2hpi, Replicate3


title: sst1_1_ins_30dpf_03_B02

value: Tg(ins:BB1.0L), TgBAC(sst1.1:memEGFP)

tag: developmental stage

value: Normal

value: pancreas


title: A549-ACE2 cells infected with VIC SARS-CoV-2 strain at 24hpi, Replicate1


title: A549-ACE2 cells infected with VIC SARS-CoV-2 strain at 8hpi, Replicate3


title: Ctrl3_S3_L003

city: Houston

first: Qiang

last: Wang

state: Texas

address: 6550 FANNIN STREET

institute: HOUSTON METHODIST RESEARCH INSTITUTE

description: DMSO 11

data_processing:
data filtering: fastp 0.20.0
read alignment: kallisto 0.46.2
gene abundance: DESeq2
Genome_build: human genome genecode release 34
Supplementary_files_format_and_content: FPM

source_name: Human MM cell line MM.1S

growth_protocol: MM.1S MM cells were cultured in RPMI1640 medium containing 10% fetal bovine serum and 100 U penicillin / 0.1 mg/ml streptomycin.

extract_protocol:
RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 2 x 106 MM.1S MM cells were pulsed with DMSO or Cfz for 1 hours and then cultured with fresh growth medium containing DMSO or 10 µM ATRA for 12 h.

value: Human Multiple Myeloma cell line

value: DMSO


title: A549-ACE2 cells infected with VIC SARS-CoV-2 strain at 2hpi, Replicate3


title: Ctrl3_S3_L004

description: DMSO 12


title: Ctrl2_S2_L004

description: DMSO 8


title: Ctrl3_S3_L002

description: DMSO 10


title: Ctrl2_S2_L003

description: DMSO 7


title: A549-ACE2 cells infected with VIC SARS-CoV-2 strain at 8hpi, Replicate2


title: A549-ACE2 cells infected with VIC SARS-CoV-2 strain at 2hpi, Replicate1


title: A549-ACE2 cells Mock infection control, Replicate3

value: Uninfected


title: Ctrl2_S2_L002

description: DMSO 6


title: A549-ACE2 cells Mock infection control, Replicate1