title: Sample_UJ-3100-z4; Conditioned medium (DOX-treated IHH)

city: Stockholm

first: Xiangyu

address: Tomtebodavägen 23, Solna

department: Science for life laboratory

institute: KTH-Royal Institute of Technology

data_processing:
Total million reads (or pairs) for a sample
Aggregated percentage of bases that have quality score more the Q30
Kallisto algorithm was used for quantification.
Assembly: Ensembl V102
Supplementary files format and content: tab-delimited text files include TPM  values for each Sample
Supplementary files format and content: tab-delimited text files include count values for each Sample

growth_protocol: IHH (immortalized human hepatocytes) cells were cultured in Williams E medium (Life Technologies) and high glucose Dulbecco’s Modified Eagle Medium (DMEM) (Life Technologies), respectively, supplemented with 10% Fetal Bovine Serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
RNA was isolated from the cells using EZNA total RNA kit (Omega Bio-tek) according to the manufacturer's instructions and treated with TURBO DNA-free kit (Invitrogen).
The RNA-seq libraries were prepared using the Illumina TruSeq RNA sample preparation kit following the manufacturer's instructions.

treatment_protocol: Cells were treated with DOX (2 μM) for 2 h in Williams’ E medium supplemented as described before.  Cells were washed once and replenished with fresh media, followed by incubation for 72 h. We also collected the media after 72h from both control cells (used as conditioned medium (Ctrl)) and DOX-treated cells (used as Conditioned medium (DOX-treated IHH)). IHH cells were cultured with different conditioned media (mixed in 50% (v/v) concentration) for 72h. After 72h treatment, cells were harvested for gene expression analysis.

value: liver

value: immortalized human hepatocytes (IHH)

value: hepatocytes

value: Conditioned medium (DOX-treated IHH)


title: Endometrial stromal cells from ESC_20

status: Public on Sep 01 2024

type: SRA

city: Herston

first: Sally

last: Mortlock

state: QLD

address: School of Public Health

department: School of Public Health

country: Australia

institute: University of Queensland

library_source: transcriptomic

data_processing:
Low quality sequencing reads and contaminating HiSeq Illumina adaptor sequences were trimmed using Trimmomatic v0.36
Trimmed reads were aligned to the human reference genome (Ensembl Homosapiens GRCh38 relesse 84) using with HISAT2 v2.05
Assembled into transcripts and counted using StringTie v1.3.1 and the EnsemblHomo sapiensGRCh38 release 91 reference assembly
Lowly expressed genes with counts per million (CPM) <0.22 (~10 counts) and expressed in <90% of the samples, were removed
Counts were normalized using the Trimmed Mean of M (TMM) method, converted to CPM and log2 transformed (log2-CPM) using the edgeR R package v3.22.3
Assembly: hg38
Supplementary files format and content: csv file containing raw counts for each sample
Supplementary files format and content: csv file containing counts normalized using the Trimmed Mean of M (TMM) method, converted to CPM and log2 transformed (log2-CPM)

molecule: total RNA

organism: Homo sapiens

source_name: endometrial stromal cells

growth_protocol: Endometrial stromal cells were maintained in IMEM with 10% fetal calf serum and 1% antibiotics in a humidified atmosphere and 5% C02

extract_protocol:
Total RNA was isolated via the AllprepDNA/RNA Mini kit. RNA was treated with Turbo DNA-free kit.
Stranded RNA-seq libraries were prepared using the Illumina Tru-seq Strandard Total RNA Gold protocol, including ribosomal depletion (Illumina, USA)

treatment_protocol: No treatment was performed

tag: cell type

value: endometrial stromal cells

tag: menstrual cycle_phase

value: Proliferative

tag: passage

tag: flowcell

tag: lane


title: EV71_S3

city: Beijing

first: wanjun

last: Peng

address: No.5, Panjiayuan Nanli,Chaoyang District, Beijing

country: China

institute: Institute of Laboratory Animal Science

data_processing:
lllumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Reasearch, 2009.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each sample
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Mus musculus

source_name: spleen

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

tag: tissue

value: spleen

tag: genotype

value: WT

tag: treatment

value: EV71 infection


title: shATF2, 1

city: Hefei

first: xiang

middle: yong

last: Li

state: Anhui

address: JiXi Avenue

department: Department of General Surgery

institute: The First Affiliated Hospital of Anhui Medical University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (version 0.36), ILLUMINACLIP:{adaptor.fa}:2:30:10  -phred33 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 HEADCROP:0 MINLEN:36 PE
Trimmed sequence reads were mapped to GRCh38 using STAR version 2.5.3a,-outSAMtype BAM SortedByCoordinate
Read count extraction and normalization were performed using featureCounts Version 1.5.1,  -T 10 -d 30 -D 1000 -C -s 1 -t {exon} -g {geneid} --primary -O -a {gff_annotation_file}
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following manufacturer's protocols.

tag: cell line

value: gastric cancer cell

value: ATF2 knockdown


title: Endometrial stromal cells from ESC_19


title: Sample_UJ-3100-z5; Conditioned medium (DOX-treated IHH)

country: Sweden

source_name: liver


title: y1-mouse-blood-KOH

city: Göteborg

first: Anders R.

last: Clausen

address: Box 440

institute: University of Gothenburg

library_source: genomic

data_processing:
Library strategy: HydEn-seq
All reads were trimmed for quality and adaptor sequence with cutadapt 1.2.1 (-m 15 -q 10–match-read-wildcards). Pairs with one or both reads shorter than 15 nt were discarded. Mate 1 of the remaining pairs was aligned to an index containing the sequence of all oligonucleotides used in the preparation of these libraries using Bowtie 0.12.8 (DOI: 10.1186/gb-2009-10-3-r25) and the flags -m1 -v2. All pairs with successful alignments were discarded. Pairs passing this filter were subsequently aligned to the mm10 Mus musculus UCSC reference genome (-m1 -v2 -X10000–best). Single-end alignments were then performed with mate 1 of all unaligned pairs with the flags -m1 -v2.
Genome_build: mm10
Supplementary_files_format_and_content: bed: tab-separated bedgraph file format. Column one holds the chromosome name, column two and three hold the nucleotide position, column four holds the read count.

molecule: genomic DNA

source_name: blood

growth_protocol: All procedures were performed in accordance with the institutional guidelines of the University of Gothenburg and experiments were approved by the Institutional Review Board of the Swedish Board of Agriculture (Ethical approval number 62/14 and 1469/2019). Samples from three 7.5-week-old and three 30-week-old male mice (C57BL6) were used for our experiments. Mice were euthanized by placing them into an induction chamber (Abbott Scandinavia AB) for 10 min with 4% isoflurane (Forene isoflurane, Abbott Scandinavia AB) followed by cervical dislocation. Whole blood was immediately harvested and the heart surgically excised thereafter. 300-600 µL of whole blood were thoroughly mixed with 30 µl 0.1 M EDTA to prevent coagulation, 200 µL aliquots were transferred to 1.5 mL tubes and frozen at -80 °C. Tibia and femur bones (for extraction of bone marrow), brain, heart, kidney, liver, lung, thigh muscle and spleen were removed and small sections were flash frozen with liquid nitrogen, then stored at -80 °C until further processing.

extract_protocol:
DNA was extracted using the MasterPure Complete DNA and RNA purification kit (MC85201, lucigen) preceded by adjusted approaches for homogenization and lysis of tissues. DNA from whole blood was extracted using the kit following manufacturer’s instruction for the extraction from whole blood with RBC lysis. DNA from bone marrow originated from tibia and fibula. Bones were freed from any remaining tissue and broken at the knee joints. Placing this opening downward in a perforated 0.5 mL tube set in a 1.5 mL tube allowed to centrifuge out the bone marrow at 10,000 g for 20 s. 100 µL of RCB lysis buffer were added and mixed and then incubated at RT for 10 min while vortexing every 5 min. Samples were centrifuged at 10,000 g for 25 s and supernatant discarded. 300 µL of tissue and cell lysis buffer including proteinase K were added and incubated at 65 °C for 15 min while shaking at 1,500 rpm. Further extraction steps were performed following the kit’s instructions. 2-70 mg of brain, heart, kidney, liver, lung, muscle or spleen tissue were added to a 1.5 mL tube containing 5-15 stainless steel homogenizing beads (0.9-2 mm, SSB14B, next advanced Inc.) and 100 µL tissue and cell lysis buffer including proteinase K. Samples were vortexed for about 20-30 min until tissue pieces were no longer visible. Beads were pelleted using a magnetic rack (DynaMag-2, Invitrogen) and the supernatant was transferred to a new tube containing 200 µL of tissue and cell lysis buffer including proteinase K. Samples were incubated at 65 °C for 15 min while shaking briefly every 5 min. After cooling the samples on ice for 5 min, further extraction steps were performed as instructed. Final DNA concentrations were determined using the Qubit dsDNA BR Assay Kit (molecular probes life technologies).
1 µg extracted DNA was mixed with 0.3 M KOH and incubated at 55°C for 2 hours. After ethanol precipitation, the pellet was dissolved in 20 µl elution buffer (Qiagen, 1014609). DNA was denatured by 3 min incubation at 85°C. In the phosphorylation step, 5'-OH end generated after KOH hydrolysis at the ribonucleotide site was phosphorylated using a mix of 10 U 3'-phosphatase minus T4 polynucleotide kinase (BioLabs, M0236L), 2.5 µl of 10X reaction buffer (BioLabs, B0201S), and 2.5 µl of 10 mM adenosine 5'-triphosphate (BioLabs, P0756S) in a total volume of 25 µl. After 30 min incubation at 37°C, the reaction was stopped by 20 min incubation at 65°C. The samples were bead-washed using CleanPCR kit (GC biotech, CPCR-0050). In the ligation step, ARC140 adaptor was ligated to the 5'-OP. Denatured DNA was ligated using a mix of 10 U T4 RNA Ligase 1 (ssRNA Ligase) (BioLabs, M0204S), 5 µl of 10X reaction buffer (BioLabs, B0216S), 0.5 µl of 2 mM adenosine 5'-triphosphate (BioLabs, P0756S), 25 µl PEG8000(50%), 5 µl of 10 mM [Co(NH3)6]Cl3, and 0.5 µl of 100 µM oligo ARC140 in a total volume of 50 µl. After overnight incubation at the room temperature, the samples were twice beads-washed and dissolved in 14 µl elution buffer. In second strand synthesis step, denatured DNA was polymerized at the room temperature for 5 min using a mix of 4 U T7 DNA polymerase (unmodified) (BioLabs, M0274L), 2 µl of 10X reaction buffer (BioLabs, B0274A), 2 µl of 2 mM adenosine 5'-triphosphate (BioLabs, P0756S), 0.8 µl of BSA (1 mg/ml) (BioLabs, B9000S), and a heterodimer oligo, ARC76/77 in a total volume of 20 µl. After beads-wash and elution, the libraries were amplified by PCR reactions using KAPA HiFi hotstart readymix (2X) kit (KAPA biosystems, KK2602, 07958935001) with PCR parameters as follows: 95 °C for 45 s, followed by 18 cycles at 95 °C for 15 s, 65 °C for 30 s, and 72 °C for 30 s. The amplified libraries were beads-washed and eluted in 20 µl TE. The library concentration was measured using Qubit® dsDNA HS Assay Kit (Life technologies, molecular probes, Q32854). The library quality was checked by the Agilent 2100 bioanalyzer system (Agilent Technologies). Illumina NextSeq 500 system was used for paired-end sequencing.

value: blood

value: KOH


title: y1-mouse-muscle-KCl

source_name: muscle

value: muscle

value: KCl


title: EV71_S2


title: o3-mouse-muscle-KOH


title: Endometrial stromal cells from ESC_17

value: Amenorrheic


title: Sample_UJ-3100-z3; Conditioned medium (DOX-treated IHH)


title: y1-mouse-blood-KCl


title: Sample_UJ-3100-z1; Conditioned medium (DOX-treated IHH)


title: Sample_UJ-3100-z2; Conditioned medium (DOX-treated IHH)


title: o3-mouse-muscle-KCl


title: Endometrial stromal cells from ESC_18


title: Endometrial stromal cells from ESC_16

value: Secretory


title: Endometrial stromal cells from ESC_15


title: EV71_T4

source_name: thymus

value: thymus


title: o3-mouse-blood-KOH


title: EV71_T5


title: Sample_UJ-3100-y5; Conditioned medium (Ctrl)

value: liver

value: immortalized human hepatocytes (IHH)

value: Conditioned medium (Ctrl)


title: EV71_T3


title: Endometrial stromal cells from ESC_14

value: endometrial stromal cells


title: o3-mouse-blood-KCl


title: Sample_UJ-3100-y3; Conditioned medium (Ctrl)

value: hepatocytes


title: EV71_T2


title: Endometrial stromal cells from ESC_13

value: Proliferative


title: Sample_UJ-3100-y2; Conditioned medium (Ctrl)

value: WT


title: o2-mouse-muscle-KOH


title: o2-mouse-muscle-KCl


title: Endometrial stromal cells from ESC_12


title: Sample_UJ-3100-y1; Conditioned medium (Ctrl)


title: EV71_S1

value: spleen

value: EV71 infection


title: o2-mouse-blood-KOH


title: Endometrial stromal cells from ESC_11


title: EV71_M5


title: EV71_M4


title: Sample_UJ-3100-x5; DOX (2uM)

value: DOX (2uM)


title: Sample_UJ-3100-x4; DOX (2uM)


title: Endometrial stromal cells from ESC_10


title: Sample_UJ-3100-y4; Conditioned medium (Ctrl)


title: EV71_M3


title: o2-mouse-blood-KCl

value: blood


title: Endometrial stromal cells from ESC_9

value: Peri-ovulatory


title: Endometrial stromal cells from ESC_8


title: EV71_M2

value: muscle


title: Sample_UJ-3100-x2; DOX (2uM)


title: o1-mouse-muscle-KCl

value: KCl


title: Sample_UJ-3100-x3; DOX (2uM)


title: o1-mouse-blood-KOH

value: KOH


title: EV71_T1


title: Sample_UJ-3100-x1; DOX (2uM)


title: EV71_B5


title: o1-mouse-blood-KCl


title: Endometrial stromal cells from ESC_6


title: EV71_B4


title: Sample_UJ-3100-w5; Control

value: Control


title: y3-mouse-liver-KOH


title: Sample_UJ-3100-w4; Control


title: EV71_B3


title: o1-mouse-muscle-KOH


title: Endometrial stromal cells from ESC_4

value: Secretory


title: Sample_UJ-3100-w3; Control

value: liver


title: Sample_UJ-3100-w2; Control

value: immortalized human hepatocytes (IHH)


title: y3-mouse-liver-KCl


title: y3-mouse-kidney-KCl

source_name: kidney

value: kidney


title: Endometrial stromal cells from ESC_3

value: endometrial stromal cells


title: Endometrial stromal cells from ESC_2


title: EV71_M1


title: Endometrial stromal cells from ESC_7

value: Amenorrheic


title: EV71_B1


title: Endometrial stromal cells from ESC_1


title: NC_S5

value: Negative control


title: y2-mouse-liver-KOH


title: ML-2-overexpressing ZCCHC10 rep3 [ML2T3]

city: Changsha

first: Jianlin

last: Zhou

state: Hunan

address: 36 Lushan road

department: College of Life Science

institute: Hunan Normal University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo_sapiens.GRCh38.87 whole genome
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
DEGseq was used for differential gene expression analysis between two samples with non biological replicates. Under the assumption that the number of reads derived from a gene (or transcript isoform) follows abinomial distribution, DEGseq is proposed based on MA-plot and widely used for differential gene expression analysis. The P-value could be assigned to each gene and adjusted by the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with q≤0.05 and |log2_ratio|≥1 are identified as differentially expressed genes (DEGs).
Genome_build: Homo_sapiens.GRCh38.87
Supplementary_files_format_and_content: counts, FPKM

source_name: ML-2 cell

extract_protocol:
RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair,A-tailing and adapter added were implemented. The aimed products were retrieved and PCR was performed, then the library was completed.

value: acute myeloid leukemia (AML) cell line

tag: genotype/variation

value: overexpressing ZCCHC10


title: NC_S4

value: spleen

value: WT


title: Endometrial stromal cells from ESC_5

value: Proliferative


title: ML-2-overexpressing ZCCHC10 rep2 [ML2T2]


title: y2-mouse-liver-KCl


title: y2-mouse-kidney-KOH


title: ML-2-overexpressing ZCCHC10 rep1 [ML2T1]


title: NC_S3


title: y2-mouse-kidney-KCl


title: NC_S2


title: SSC-PAH + PDE5i 3

city: Pittsburgh

first: Satoshi

last: Okawa

state: PA

address: 200 Lothrop Street

country: USA

institute: University of Pittsburgh

library_source: transcriptomic single cell

data_processing:
The raw fastq reads were mapped against the human genome build hg38 and to generate raw counts using 10X Genomics Cell Ranger
Raw counts were normalized for the library size and log2 transformed
Then normalized counts were analyzed for potential batch effect corrections among different patient samples using SCTransform in Seurat v3
Assembly: hg38
Supplementary files format and content: Seurat object as R data serialization file

source_name: PBMC

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from peripheral venous blood drawn from patients seen at UPMC. Blood samples collected in EDTA purple top vacutainer were centrifuged at 2000 RPM for 15 minutes and plasma was removed for banking. Buffy coats were collected and used for Ficoll gradient to isolate PBMC which are used for the single cell RNA sequencing analysis.
RNA libraries were prepared using Chromium Single Cell 3’ Reagent Kits V2 per manufacturer’s guidelines (10x Genomics manual CG00052, cat# PN-12237). Single cell RNA-sequencing was performed using the GemCodeTM Single Cell Instrument (Chromium, 10X Genomics) which included at least 800 cells (~50K reads per cell).

tag: disease state

value: scleroderma PAH

value: PBMC

tag: time

value: 3 months post treatment


title: SSC-PAH + PDE5i + Macitentan 2

value: PDE5i, Macitentan


title: ML-2-overexpressing empty vector rep3 [ML2C3]

value: overexpressing empty vector


title: y3-mouse-kidney-KOH

value: KOH


title: SSC-PAH + PDE5i 2


title: y1-mouse-liver-KOH

value: liver


title: NC_S1


title: Sample_UJ-3100-w1; Control

value: immortalized human hepatocytes (IHH)

value: hepatocytes

value: Control


title: EV71_B2

value: blood

value: EV71 infection


title: ML-2-overexpressing empty vector rep1 [ML2C1]

value: acute myeloid leukemia (AML) cell line


title: NC_T5

value: thymus

value: Negative control


title: SSC-PAH + PDE5i + Macitentan 3


title: ML-2-overexpressing empty vector rep2 [ML2C2]


title: SSC-PAH 2


title: y1-mouse-liver-KCl

value: KCl


title: y1-mouse-kidney-KOH

value: kidney


title: SSC-PAH 1

value: scleroderma PAH


title: SSC-PAH + PDE5i + Macitentan 1

value: PBMC


title: NC_T4

value: WT


title: y1-mouse-kidney-KCl


title: male, 1mM, 48h, repl 2

city: Bloomington

first: Jason

middle: M

last: Tennessen

email: tennessenlab@gmail.com, tennlab@iu.edu, jtenness@iu.edu, tourigny@iu.edu

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University

data_processing:
Reads were quantified with Salmon psueodoaligner
Normalized counts were generated with DESeq2 using tximport and the Salmon quantification
Assembly: BDGP6.32
Supplementary files format and content: Salmon qunatification directories (including quant.sf, bootstrap, log files) as gzipped tar archives
Supplementary files format and content: supplemtental files containing sex-specific normalized log counts as output by vst() function of DESeq2

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: whole fly

growth_protocol: Flies were kept at 25°C, 60% humidity, 12h/12h light/dark cycle, on Bloomington food

extract_protocol:
Treated flies were frozen in bead tubes, followed by disruption and extraction in Trizol.  RNA was then cleaned with Qiagen RNeasy kit
Illumina Stranded mRNA prep, 96 index
Poly-A-selected total RNA prepared with TruSeq ligation for paired-end sequencing

treatment_protocol: 5-7 day old flies were anaesthetized with CO2 and sorted by sex into separate vials.  Two days later, flies were transferred to vials with sterile water and starved for 16h before transfer to exposure vials containing 0, 0.25, or 1mM sodium arseinite in liquid food (sucrose + yeast extract)  for 1h, 2h, 4h, 8h, 24h or 48h (see Holsopple et al doi:10.3791/65029 for treatment details)

value: whole fly

tag: Sex

value: male

tag: concentration

tag: replicate


title: NC_T2


title: o3-mouse-liver-KOH

value: KOH


title: male, 1mM, 48h, repl 1


title: NC_T1


title: SSC-PAH + PDE5i 1

value: 3 months post treatment


title: IPAH + PDE5i + Macitentan 3

value: IPAH

value: PDE5i, Macitentan


title: male, 0.25mM, 48h, repl 4


title: o3-mouse-liver-KCl

value: liver


title: IPAH + PDE5i 4


title: NC_M5

value: muscle


title: NC_M4


title: o3-mouse-kidney-KCl


title: o3-mouse-kidney-KOH


title: IPAH 2


title: male, 1mM, 48h, repl 4


title: male, 0.25mM, 48h, repl 3


title: male, 0.25mM, 48h, repl 1


title: NC_M3


title: NC_T3


title: IPAH + PDE5i + Macitentan 2


title: IPAH 1


title: male, 0mM, 48h, repl 3


title: NC_M2


title: male, 0mM, 48h, repl 2


title: NC_M1


title: IPAH + PDE5i 3


title: o2-mouse-kidney-KOH


title: o2-mouse-liver-KOH


title: male, 0mM, 48h, repl 1


title: NC_B5

value: blood


title: o2-mouse-kidney-KCl


title: male, 1mM, 24h, repl 4


title: NC_B4


title: male, 1mM, 24h, repl 3


title: IPAH + PDE5i + Macitentan 1


title: o1-mouse-liver-KOH


title: NC_B3


title: o1-mouse-liver-KCl


title: male, 1mM, 24h, repl 1


title: o2-mouse-liver-KCl


title: Control 3

value: normal


title: NC_B2


title: o1-mouse-kidney-KOH


title: male, 0.25mM, 24h, repl 3


title: o1-mouse-kidney-KCl


title: Control 1


title: NC_B1


title: Control 2


title: FF2_P_D2D2_C_S27 Female F2  (MaleDose2 x FemaleDose2) sample C

city: Montpellier

first: Brigitte

last: Boizet Bonhoure

address: 141 rue de la Cardonille

department: Human Genetic Institute

country: France

institute: CNRS UMR9002

description:
Female F2  (MaleDose2 x FemaleDose2) sample C
100 nt

data_processing:
Libraries were sequenced on a Novaseq 6000 (Illumina, San Diego, CA, USA) on one lane of a S4 flow cell in paired end 2*100nt mode according to the manufacturer’s instructions
For sequencing quality control, image analyses and base calling were performed using the NovaSeq Control Software and Real-Time Analysis component
Demultiplexing and trimming were performed using the Illumina's conversion software (bcl2fastq 2.20)
The raw data quality was assessed using FastQC (version 1.19) from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer). FastqScreen (version 0.15) was used to estimate the potential level of contamination
Assembly: For sequences alignment, the splice junction mapper, TopHat 2.1.1 and Bowtie 2.4.5 were used to align the RNA-Seq reads to the Mus musculus genome (NCBI mm39)
Supplementary files format and content: Samtools (v1.13) was used to sort the alignment files. Then, genes were counted with Featurecounts 2.0.3
Supplementary files format and content: Differentially expressed genes were identified using the Bioconductor, package DESeq2 1.32.0 ; Data were normalized using the DESeq2 normalization method

source_name: Ovary

extract_protocol:
RNA was extracted and purified using the TRIZOL technique (Invitrogen). RNA purity was confirmed by the A260/A280 and A260/A230 ratios of >1.8 and >2.0, respectively. RNA integrity of each sample was measured using an Agilent 2100 BioAnalyzer
RNA libraries were constructed using the Stranded mRNA Prep Ligation kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions

treatment_protocol: Two mixtures (doses 1, D1 and dose 2, D2) containing environmentally relevant doses of IBU/2hIBU + DCF + EE2 were added or not (control; C) to the drinking water of pregnant mice and their progeny from 8.5 days post-coitum (dpc) until animal sacrifice (30 days post-partum, dpp, for females and 35 dpp for males)

value: Ovary


title: y3-mouse-spleen-KOH

value: spleen


title: male, 0.25mM, 24h, repl 1


title: PBMC, HFpEF ADT

city: Nashville

first: Charles

middle: Duncan

last: Smart

address: 2201 West End Ave

department: Molecular Physiology and Biophysics

institute: Vanderbilt University

description:
Antibody-derived oligonucleotide library
Antibody-derived oligonucleotide (ADT)

library_source: other

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, ADT) was performed using the 10x genomics Cell Ranger pipeline (v6.1.1)
Further processing was done with Seurat in R
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: protein

source_name: Blood

extract_protocol:
PBMCs were isolated from whole blood using Ficoll density gradient centrifugation. RBCs were lysed and cells were stored in Bambanker freezing medium in liquid nitrogen until time of sequencing. Cells were thawed and stained with TotalSeq antibodies (Biolegend) prior to loading onto 10X controller
Library was prepared using Chromium Single Cell 5ʹ  protocol (10x Genomics)

value: Blood

tag: condition

value: heart failure with preserved ejection fraction

tag: library type

value: ADT


title: male, 0.25mM, 24h, repl 2


title: IPAH + PDE5i 2

tag: cell type

value: PBMC


title: y3-mouse-lung-KOH

source_name: lung

value: lung


title: male, 0mM, 24h, repl 3

value: whole fly


title: FF2_P_D2D2_A_S25 Female F2  (MaleDose2 x FemaleDose2) sample A

description:
Female F2  (MaleDose2 x FemaleDose2) sample A
100 nt


title: PBMC, HFpEF GEX

description:
5' mRNA library
poly A RNA

value: GEX


title: IPAH + PDE5i 1


title: PBMC, control ADT

value: non heart failure control


title: FF2_P_D2C_C_S24 Female F2  (MaleDose2 x FemaleCTL) sample C

description:
Female F2  (MaleDose2 x FemaleCTL) sample C
100 nt


title: FF2_P_D2C_B_S23 Female F2  (MaleDose2 x FemaleCTL) sample B

description:
Female F2  (MaleDose2 x FemaleCTL) sample B
100 nt


title: y2-mouse-spleen-KOH

value: KOH


title: male, 0mM, 24h, repl 2

value: male


title: male, 1mM, 8h, repl 3


title: y2-mouse-spleen-KCl

value: KCl


title: FF2_P_D2C_A_S22 Female F2  (MaleDose2 x FemaleCTL) sample A

description:
Female F2  (MaleDose2 x FemaleCTL) sample A
100 nt


title: y3-mouse-lung-KCl


title: CA12 knockout (KO) iCMs treated with doxorubicin 2

city: palo alto

first: Chun

last: Liu

state: CA

address: 1291 Welch Road BMI building, 3200-CVI Rm

institute: stanford

data_processing:
Adapter sequences were trimmed and low quality bases were filter out.
Processed reads were aligned to referrence genome (hg19) with TopHat and Cufflinks.
Assembly: hg19
Supplementary files format and content: csv file include raw counts for each Sample

source_name: iPSC differentiated cardiomyocytes

growth_protocol: iPSCs were routinely maintained using E8 medium (GIBCO, Life Technologies). Every 24 hr, medium was changed, and cells were kept at 37°C in a 5% CO2/95% air incubator. E8 medium was replaced with RPMI supplemented with B27 without insulin (Life Technologies) and 6 μM CHIR-99021 (Selleck Chemicals) to initiate cardiomyocyte differentiation when hiPSCs achieved 85% confluency in the dish. The medium was changed to RPMI supplement with insulin-free B27 for 24 hr, and for the next 48 hr, 5 μM IWR-1 (Selleck Chemicals) was added. After another 48 hr, cells were grown in RPMI supplement with B27 without insulin before switching to RPMI supplement with B27 for 72 hr. To metabolic purify beating hiPSC-CMs, the medium was changed to RPMI-B27 without D-glucose (Life Technologies) on day 11 for 48 hr. After that, cells were dissociated with TrypLE (Life Technologies) at 37°C, and then seeded into 6-well plates containing RPMI-B27 supplemented with 5% Knockout Serum Replacement (KOSR) (Thermo Fisher Scientific). 24 hr later, the medium was switched back to RPMI-B27 medium and changed every 2 days. On day 35, iCMs were ready to use.

extract_protocol:
Total RNA was extracted from the cells using the RNeasy Mini Plus Kit (Qiagen) following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using library construction NEBNext kit following the standard protocols.

treatment_protocol: doxorubicin (0.5 μM) or DMSO (vehicle control) was added in the medium and iCMs were treated for 72 hr.  Total RNA was harvested from all samples for library preparation.

value: iPSC differentiated cardiomyocytes

value: iPSC

value: cardiomyocytes

value: CA12 KO

value: doxorubicin


title: male, 1mM, 8h, repl 2


title: PBMC, control GEX

description:
5' mRNA library
poly A RNA


title: FF2_P_D1C_C_S21 Female F2  (MaleDose1 x FemaleCTL) sample C

description:
Female F2  (MaleDose1 x FemaleCTL) sample C
100 nt

value: Ovary


title: male, 1mM, 8h, repl 1


title: CA12 knockout (KO) iCMs treated with doxorubicin 1


title: y2-mouse-lung-KCl


title: FF2_P_D1C_B_S20 Female F2  (MaleDose1 x FemaleCTL) sample B

description:
Female F2  (MaleDose1 x FemaleCTL) sample B
100 nt


title: CA12 knockout (KO) iCMs treated with DMSO 2

value: DMSO


title: y3-mouse-spleen-KCl

value: spleen


title: FF2_P_D2D2_B_S26 Female F2  (MaleDose2 x FemaleDose2) sample B

description:
Female F2  (MaleDose2 x FemaleDose2) sample B
100 nt


title: male, 0.25mM, 8h, repl 3


title: CA12 knockout (KO) iCMs treated with DMSO 1


title: male, 0.25mM, 8h, repl 2


title: FF2_P_D1C_A_S19 Female F2  (MaleDose1 x FemaleCTL) sample A

description:
Female F2  (MaleDose1 x FemaleCTL) sample A
100 nt


title: y1-mouse-spleen-KOH


title: y2-mouse-lung-KOH


title: male, 0mM, 24h, repl 1


title: FF2_P_CD2_C_S18 Female F2  (MaleCTL x FemaleDose2) sample C

description:
Female F2  (MaleCTL x FemaleDose2) sample C
100 nt


title: Wildtype (WT) iCMs treated with doxorubicin and indisulam 2

value: WT

value: doxorubicin and indisulam


title: y1-mouse-lung-KOH

value: lung


title: FF2_P_CD2_B_S17 Female F2  (MaleCTL x FemaleDose2) sample B

description:
Female F2  (MaleCTL x FemaleDose2) sample B
100 nt


title: Wildtype (WT) iCMs treated with doxorubicin and indisulam 1


title: y1-mouse-lung-KCl


title: male, 0.25mM, 8h, repl 1

value: whole fly


title: FF2_P_CD2_A_S16 Female F2  (MaleCTL x FemaleDose2) sample A

description:
Female F2  (MaleCTL x FemaleDose2) sample A
100 nt


title: male, 0mM, 8h, repl 2


title: Wildtype (WT) iCMs treated with doxorubicin 2


title: y1-mouse-spleen-KCl


title: male, 0mM, 8h, repl 3


title: o3-mouse-spleen-KOH


title: male, 0mM, 8h, repl 1


title: FF2_P_CD1_B_S14 Female F2  (MaleCTL x FemaleDose1) sample B

description:
Female F2  (MaleCTL x FemaleDose1) sample B
100 nt


title: male, 1mM, 4h, repl 3


title: FF2_P_CD1_C_S15 Female F2  (MaleCTL x FemaleDose1) sample C

description:
Female F2  (MaleCTL x FemaleDose1) sample C
100 nt


title: o3-mouse-spleen-KCl


title: Wildtype (WT) iCMs treated with DMSO 2


title: FF2_P_CD1_A_S13 Female F2  (MaleCTL x FemaleDose1) sample A

description:
Female F2  (MaleCTL x FemaleDose1) sample A
100 nt


title: o3-mouse-lung-KOH


title: Wildtype (WT) iCMs treated with doxorubicin 1


title: Wildtype (WT) iCMs treated with DMSO 1


title: o3-mouse-lung-KCl


title: FF2_P_CC_C_S12 Female F2  (MaleCTL x FemaleCTL) sample C

description:
Female F2  (MaleCTL x FemaleCTL) sample C
100 nt


title: AR INPUT

city: Worcester

first: Junhui

state: MA

address: 364 Plantation St

institute: University of Massachusetts Medical School

data_processing:
FastQC (version 0.11.5) and MultiQC (version 1.4) were used for raw reads quality assessment.
ChIPQC (version 1.26.0) and plotFingerprint were employed to generate ChIP-seq specific quality metrics and diagnostic plots.
Reads were trimmed with Trim Galore (version 0.6.6)
Trimmed reads were aligned to the reference human genome assembly hg38 using bowtie2 (version 2.4.1) with default parameters.
Aligned reads were further processed with duplicates removed using samtools (version 1.9) and picard (version 2.23.3)
bamCoverage (version 3.5.1) was used to generate bigwig files with default settings except the following parameters: --binSize 20 –normallizeUsing RPKM –smoothLength 60 –extendReads 150 –centerReads.
Peak calling with default settings except the following parameters: -f BAMPE -g hs --nolambda -q 0.2 , annotation, and visualization were carried out with MACS2 (version 2.2.7.1), ChIPpeakAnno (version 3.24.2)  and trackViewer (version 1.26.2) respectively.
Genome_build: hg38
Supplementary_files_format_and_content: biwig files were generated using bamCoverage(version 3.5.1); Scores represent reads coverage
Supplementary_files_format_and_content: peak text files

source_name: Human lung cell line A549

growth_protocol: A549 cells were grown in RPMI-1640 medium supplemented with 10 % FBS, 100 units/ml penicillin, and 100 µg/ml streptomycin.

extract_protocol:
Chromatin was obtained from sonicated nuclei and AR-bound DNA fragments were isolated with antibody.
Library was constructed for illumina sequencing using KAPA HyperPrep kit (Roche, #07962347001). Briefly, fragmented dsDNA was used for end repair and A-tailing. Illumina sequencing adapter was ligated to the end of DNA. Adapter-ligated library was PCR-amplified and purified using bead-based cleanup. Libraries were sequenced on the HiSeq 4000 to generate 50-bp paired end reads according to manufacturer's protocol.

value: Human lung cell line A549

value: Human lung adenocarcinoma

tag: endogenous tag

value: AR C-terminal HA tag

tag: chip antibody


title: male, 1mM, 4h, repl 2

value: male


title: male, 1mM, 4h, repl 1


title: FF2_P_CC_B_S11 Female F2  (MaleCTL x FemaleCTL) sample B

description:
Female F2  (MaleCTL x FemaleCTL) sample B
100 nt


title: o2-mouse-spleen-KOH

value: KOH


title: male, 0.25mM, 4h, repl 4


title: AR IP

value: HA (abcam, ab9110)


title: FF2_P_CC_A_S10 Female F2  (MaleCTL x FemaleCTL) sample A

description:
Female F2  (MaleCTL x FemaleCTL) sample A
100 nt


title: o2-mouse-spleen-KCl

value: KCl


title: HOX lung, scRNA-seq

city: Milwaukee

first: Ru-Jeng

last: Teng

state: WI

address: 9200 W. Wisconsin Ave.

department: Pediatrics

institute: Medical College of Wisconsin

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: rn6
Supplementary files format and content: Tab-separated values files and matrix files

organism: Rattus norvegicus

extract_protocol:
Freshly obtained rat whole lungs were finely chopped before treatment with 0.1 mg/mL collagenase-D in DMEM and 100ug/mL DNase-I for 1 h. The treated tissue was mashed through a 100 µm cell strainer and washed with 20 mL DMEM containing 10% FBS and 1% antibiotics. The cell suspension was centrifuged for 5 min at 300g to pellet the cells. Red cells were removed by the lysis buffer at room temperature for 60 seconds. The suspension was then serially washed with PBS containing 0.01% BSA before centrifuging at 300 g for 5 min and went through a 70 µm cell strainer once and 40 µm cell strainers twice.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics)

value: all lung cell types

tag: age

tag: strain

value: Outbred


title: male, 0.25mM, 4h, repl 1

tag: tissue


title: male, 0.25mM, 4h, repl 3


title: FF1_P_D2B_S8 Female F1  Dose 2 sample B

description:
Female F1  Dose 2 sample B
100 nt

value: Dose 2


title: o2-mouse-lung-KOH


title: o2-mouse-lung-KCl


title: NOX lung, scRNA-seq

description: 10x Genomics


title: SNI-3, replicate3

city: Jinan

first: chuanxin

last: wang

address: 247 Beiyuan Street, Jinan 250033, Shandong, China,

institute: The Second Hospital of Shandong University

description: Spared nerve injury (SNI) induced NP rats, replicate3

data_processing:
Raw reads in fastq format were processed to remove contaminating adapter sequences using Trimmomatics
Quality distribution plot and base content distribution were generated by FASTQC
RNAseq reads were aligned to the Rat6_Ensemblusing STAR.
Read counts for individual gene of each sample were produced with HTSeq-count
Assembly: Rat6_Ensembl
Supplementary files format and content: xls(gene expression of all sample)

source_name: spinal cord

extract_protocol:
RNA was extracted using Trizol following the manufacturer's protocol.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: spinal cord

value: spared nerve injury


title: FF1_P_D2C_S9 Female F1  Dose 2 sample C

description:
Female F1  Dose 2 sample C
100 nt

value: Ovary


title: FF1_P_D1C_S6 Female F1  Dose 1 sample C

description:
Female F1  Dose 1 sample C
100 nt

value: Dose 1


title: SNI-2, replicate2

description: Spared nerve injury (SNI) induced NP rats, replicate2


title: male, 0mM, 4h, repl 3


title: FF1_P_D2A_S7 Female F1  Dose 2 sample A

description:
Female F1  Dose 2 sample A
100 nt


title: FF1_P_D1B_S5 Female F1  Dose 1 sample B

description:
Female F1  Dose 1 sample B
100 nt


title: male, 0mM, 4h, repl 2


title: Control-3, replicate3

description: sham rats (control), replicate3

value: sham


title: o1-mouse-lung-KOH

value: lung


title: male, 1mM, 2h, repl 3

value: whole fly


title: FF1_P_D1A_S4 Female F1  Dose 1 sample A

description:
Female F1  Dose 1 sample A
100 nt


title: Control-2, replicate2

description: sham rats (control), replicate2


title: male, 1mM, 2h, repl 2


title: o1-mouse-lung-KCl


title: Control-1, replicate1

description: sham rats (control), replicate1


title: male, 1mM, 2h, repl 1


title: FF1_P_CtrlC_S3 Female F1  Control sample C

description:
Female F1  Control sample C
100 nt


title: y3-mouse-bonemarrow-KOH

source_name: bonemarrow

value: bonemarrow


title: y3-mouse-bonemarrow-KCl


title: male, 0mM, 4h, repl 1


title: SNI-1, replicate1

description: Spared nerve injury (SNI) induced NP rats , replicate1


title: o1-mouse-spleen-KCl

value: spleen


title: male, 0.25mM, 2h, repl 4


title: y2-mouse-bonemarrow-KOH


title: input -CON-1

data_processing:
Raw reads in fastq format were processed to remove contaminating adapter sequences using Trimmomatics
Quality distribution plot and base content distribution were generated by FASTQC
ChIP-seq reads were aligned to the Rat6_Ensembl using BWA（0.7.13-r1126） . Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.2 with the significance cut-off q-value <=0.05
bigWig files were generated using the deeptools. Peak files were generated using MACS v2 with default settings.
Assembly: Rat6_Ensembl
Supplementary files format and content: bw

extract_protocol:
ChIP assays were performed by Shanghai Jiayin Biotechnology Co., Ltd, according to the standard crosslinking ChIP protocol with modifications.
The ChIP-Seq library was prepared using ChIP-Seq DNA sample preparation kit (NEBNext® Ultra™II DNA) according to the manufacturer’s instructions.

tag: genotype

tag: antibody


title: input -SNI-1

value: NP


title: o1-mouse-spleen-KOH

tag: treatment


title: FF1_P_CtrlB_S2 Female F1  Control sample B

description:
Female F1  Control sample B
100 nt


title: FF1_P_CtrlA_S1 Female F1  Control sample A

description:
Female F1  Control sample A
100 nt


title: male, 0.25mM, 2h, repl 3

value: male


title: y2-mouse-bonemarrow-KCl


title: Anti-H3K27ac -SNI-1


title: MF2_P_D2D2_C_S81 Male F2  (MaleDose2 x FemaleDose2) sample C

description:
Male F2  (MaleDose2 x FemaleDose2) sample C
100 nt

source_name: Testis

value: Testis


title: Anti-H3K27ac-CON-1


title: MF2_P_D2D2_B_S80 Male F2  (MaleDose2 x FemaleDose2) sample B

description:
Male F2  (MaleDose2 x FemaleDose2) sample B
100 nt


title: y1-mouse-bonemarrow-KCl


title: MF2_P_D2D2_A_S79 Male F2  (MaleDose2 x FemaleDose2) sample A

description:
Male F2  (MaleDose2 x FemaleDose2) sample A
100 nt


title: B4_240min-arrest_RNA-rRNAdep

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

institute: STANFORD UNIVERSITY

description:
Cells were arrested with a 1N DNA content via induction of CRISPRi against the origin of replication (oriC) for 240 minutes.
2023-06-18-MS230511L08_exp230502_B4_CJW7357_240min-arrest_RNA-rRNAdep

data_processing:
Read alignment: Bowtie 1.0.1
bigWig file generation: Custom code
Assembly: Custom index, combining the Caulobacter crescentus_NA1000 (ASM2200v1) and Escherichia_coli_str._K-12_substr._MG1655 (ASM584v2) assemblies.
Supplementary files format and content: bigWig of read coverage, normalized to RPM.

organism:
Escherichia coli K-12
Caulobacter vibrioides

growth_protocol: E. coli was grown at 37°C in M9glyCAAT media.

extract_protocol:
Cells in PBS as mixed with 250 ul TRI Reagent (Zymo Research) and lysed by bead beating on a Fastprep 24 (MPbio). Cell debris was pelleted (14k rpm, 2 min) and the supernatant was recovered. RNA was then extracted using the direct-zol RNA microprep kit (Zymo Research).
rRNA was depleted using the NEBNextrRNA Depletion Kit for Bacteria (NEB, #E7850) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, #E7760) was then used to prepare libraries for paired-end (2x150bp) Illumina sequencing (Novogene).

tag: sample

value: cDNA from E. coli arrested with 1N DNA content for 240 minutes.


title: male, 0mM, 2h, repl 2


title: male, 0mM, 2h, repl 3


title: o3-mouse-bonemarrow-KOH

value: KOH


title: y1-mouse-bonemarrow-KOH


title: B3_200min-arrest_RNA-rRNAdep

description:
Cells were arrested with a 1N DNA content via induction of CRISPRi against the origin of replication (oriC) for 200 minutes.
2023-06-18-MS230511L07_exp230502_B3_CJW7357_200min-arrest_RNA-rRNAdep

value: cDNA from E. coli arrested with 1N DNA content for 200 minutes.


title: MF2_P_D2C_B_S77 Male F2  (MaleDose2 x FemaleCTL) sample B

description:
Male F2  (MaleDose2 x FemaleCTL) sample B
100 nt


title: B2_120min-arrest_RNA-rRNAdep

description:
Cells were arrested with a 1N DNA content via induction of CRISPRi against the origin of replication (oriC) for 120 minutes.
2023-06-18-MS230511L06_exp230502_B2_CJW7357_120min-arrest_RNA-rRNAdep

value: cDNA from E. coli arrested with 1N DNA content for 120 minutes.


title: MF2_P_D2C_C_S78 Male F2  (MaleDose2 x FemaleCTL) sample C

description:
Male F2  (MaleDose2 x FemaleCTL) sample C
100 nt


title: MF2_P_D2C_A_S76 Male F2  (MaleDose2 x FemaleCTL) sample A

description:
Male F2  (MaleDose2 x FemaleCTL) sample A
100 nt


title: male, 1mM, 1h, repl 3


title: male, 0.25mM, 2h, repl 2


title: B1_060min-arrest_RNA-rRNAdep

description:
Cells were arrested with a 1N DNA content via induction of CRISPRi against the origin of replication (oriC) for 60 minutes.
2023-06-18-MS230511L05_exp230502_B1_CJW7357_060min-arrest_RNA-rRNAdep

value: cDNA from E. coli arrested with 1N DNA content for 60 minutes.


title: MF2_P_D1C_C_S75 Male F2  (MaleDose1 x FemaleCTL) sample C

description:
Male F2  (MaleDose1 x FemaleCTL) sample C
100 nt


title: male, 1mM, 1h, repl 1


title: o2-mouse-bonemarrow-KOH


title: o2-mouse-bonemarrow-KCl

value: KCl


title: A3_200min-arrest_RNA-rRNAdep

description:
Cells were arrested with a 1N DNA content via induction of CRISPRi against the origin of replication (oriC) for 200 minutes.
2023-06-18-MS230511L03_exp230501_A3_CJW7357_200min-arrest_RNA-rRNAdep


title: A4_240min-arrest_RNA-rRNAdep

description:
Cells were arrested with a 1N DNA content via induction of CRISPRi against the origin of replication (oriC) for 240 minutes.
2023-06-18-MS230511L04_exp230501_A4_CJW7357_240min-arrest_RNA-rRNAdep


title: MF2_P_D1C_A_S73 Male F2  (MaleDose1 x FemaleCTL) sample A

description:
Male F2  (MaleDose1 x FemaleCTL) sample A
100 nt


title: male, 0.25mM, 1h, repl 2


title: male, 0.25mM, 1h, repl 3


title: A2_120min-arrest_RNA-rRNAdep

description:
Cells were arrested with a 1N DNA content via induction of CRISPRi against the origin of replication (oriC) for 120 minutes.
2023-06-18-MS230511L02_exp230501_A2_CJW7357_120min-arrest_RNA-rRNAdep


title: y3-mouse-heart-KCl

source_name: heart

value: heart


title: y3-mouse-brain-KOH

source_name: brain

value: brain


title: MF2_P_CD2_C_S72 Male F2  (MaleCTL x FemaleDose2) sample C

description:
Male F2  (MaleCTL x FemaleDose2) sample C
100 nt


title: A1_060min-arrest_RNA-rRNAdep

description:
Cells were arrested with a 1N DNA content via induction of CRISPRi against the origin of replication (oriC) for 60 minutes.
2023-06-18-MS230511L01_exp230501_A1_CJW7357_060min-arrest_RNA-rRNAdep


title: male, 0.25mM, 1h, repl 1


title: male, 0mM, 2h, repl 1


title: o3-mouse-bonemarrow-KCl


title: y3-mouse-brain-KCl


title: MF2_P_CD2_B_S71 Male F2  (MaleCTL x FemaleDose2) sample B

description:
Male F2  (MaleCTL x FemaleDose2) sample B
100 nt


title: male, 0mM, 1h, repl 3


title: MF2_P_CD2_A_S70 Male F2  (MaleCTL x FemaleDose2) sample A

description:
Male F2  (MaleCTL x FemaleDose2) sample A
100 nt


title: male, 1mM, 1h, repl 2


title: MF2_P_D1C_B_S74 Male F2  (MaleDose1 x FemaleCTL) sample B

description:
Male F2  (MaleDose1 x FemaleCTL) sample B
100 nt


title: y3-mouse-heart-KOH


title: T17-02230

type: RNA

city: Amsterdam

first: Charlotte

last: Stroes

address: Meibergdreef 9

department: Medical Oncology

country: Netherlands

institute: Amsterdam UMC

hyb_protocol: Samples were hybridized for 20 hours in 65 degrees Celsius.

scan_protocol: The NanoString nCounter PanCancer IO360 panel (XT-CSO-HIO360-12) was used to profile the samples. The hybridized samples were analysed using the NanoString nCounter SPRINT profiler with 12 samples per run.

data_processing: Images were processed with the nCounter instrument, and the reporter probe counts are tabulated in a comma separated value format. The assay performance of the data was assessed through quality control metrics using imaging quality control, binding density quality control, positive control linearity quality control and limit of detection. Second, raw data were normalized using the nCounter Advanced Analysis 2.0 module of NanoString normalizing for technical variability using positive control normalization and assay input variability using codeset content normalization with the housekeeping genes. Data with low expression below the set threshold were filtered. Finally, the Advanced Analysis module of Nanostring and the R2 platform for gene expression (http://r2.amc.nl) were used for data analyses. For pathway analysis, we used the Hallmark (2020 and the KEGG signatures.

source_name: primary esophageal adenocarcinoma

label_protocol: Hybridization buffer (70 uL) was added to the reporter codeset tube (from NanoString) to create the Master Mix. Master Mix was than added in each tube of a labeled 12-tube strip. A total of 50ng/5 µL RNA was added to each tube.

extract_protocol: Formalin-fixed paraffin embedded pre-treatment biopsies from the primary tumor were cut into slides of 4 µm. RNA was isolated using the RNease FFPE kit (Qiagen, Hilden, Germany) as per the instructions, and stored at -80°C. RNA concentration and integrity were determined using Nanodrop (ThermoFisher, Waltham, MA) and a 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA).

tag: included

value: Included

tag: cohort

value: Match

tag: gender

value: M


title: T18-03524


title: y2-mouse-heart-KCl


title: y2-mouse-heart-KOH


title: male, 0mM, 1h, repl 2

value: whole fly

tag: Sex

tag: concentration

tag: time


title: y2-mouse-brain-KOH


title: male, 0mM, 1h, repl 1

tag: replicate


title: T17-01209


title: male, 0mM, 0h, repl 3


title: T16-07495


title: T15-10458


title: MF2_P_CD1_B_S68 Male F2  (MaleCTL x FemaleDose1) sample B

description:
Male F2  (MaleCTL x FemaleDose1) sample B
100 nt


title: y2-mouse-brain-KCl


title: MF2_P_CC_C_S66 Male F2  (MaleCTL x FemaleCTL) sample C

description:
Male F2  (MaleCTL x FemaleCTL) sample C
100 nt


title: MF2_P_CD1_A_S67 Male F2  (MaleCTL x FemaleDose1) sample A

description:
Male F2  (MaleCTL x FemaleDose1) sample A
100 nt


title: male, 0mM, 0h, repl 2


title: T15-04546

value: Excluded


title: y1-mouse-heart-KOH


title: male, 0mM, 0h, repl 1


title: y1-mouse-heart-KCl


title: T15-03552

value: F


title: MF2_P_CC_B_S65 Male F2  (MaleCTL x FemaleCTL) sample B

description:
Male F2  (MaleCTL x FemaleCTL) sample B
100 nt


title: female, 1mM, 48h, repl 4

value: female


title: y1-mouse-brain-KOH


title: MF2_P_CC_A_S64 Male F2  (MaleCTL x FemaleCTL) sample A

description:
Male F2  (MaleCTL x FemaleCTL) sample A
100 nt


title: MF2_P_CD1_C_S69 Male F2  (MaleCTL x FemaleDose1) sample C

description:
Male F2  (MaleCTL x FemaleDose1) sample C
100 nt


title: T15-01087


title: y1-mouse-brain-KCl


title: T15-00758


title: MF1_P_D2B_S62 Male F1  Dose 2 sample B

description:
Male F1  Dose 2 sample B
100 nt

value: Dose 2


title: female, 1mM, 48h, repl 1


title: female, 1mM, 48h, repl 3


title: o3-mouse-heart-KOH


title: T15-00435


title: MF1_P_D2C_S63 Male F1  Dose 2 sample C

description:
Male F1  Dose 2 sample C
100 nt

value: Testis


title: female, 0.25mM, 48h, repl 3


title: T14-07218


title: T13-05747


title: MF1_P_D2A_S61 Male F1  Dose 2 sample A

description:
Male F1  Dose 2 sample A
100 nt


title: o3-mouse-heart-KCl


title: female, 0.25mM, 48h, repl 2


title: T10-09848


title: MF1_P_D1B_S59 Male F1  Dose 1 sample B

description:
Male F1  Dose 1 sample B
100 nt

value: Dose 1


title: o3-mouse-brain-KCl


title: female, 0.25mM, 48h, repl 1


title: female, 0mM, 48h, repl 3


title: o2-mouse-heart-KOH

value: KOH


title: T10-04745


title: MF1_P_D1A_S58 Male F1  Dose 1 sample A

description:
Male F1  Dose 1 sample A
100 nt


title: o2-mouse-heart-KCl


title: female, 0mM, 48h, repl 2


title: 9003


title: female, 0mM, 48h, repl 1


title: MF1_P_CtrlC_S57 Male F1  Control sample C

description:
Male F1  Control sample C
100 nt


title: 7010


title: MF1_P_CtrlB_S56 Male F1  Control sample B

description:
Male F1  Control sample B
100 nt


title: 7009


title: MF1_P_CtrlA_S55 Male F1  Control sample A

description:
Male F1  Control sample A
100 nt


title: female, 1mM, 24h, repl 2


title: o2-mouse-brain-KCl


title: o1-mouse-heart-KOH


title: MF1_P_D1C_S60 Male F1  Dose 1 sample C

description:
Male F1  Dose 1 sample C
100 nt


title: 7007


title: female, 1mM, 24h, repl 1


title: 7006


title: ventricle, Rad knockout, TAC TKO4

city: Lexington

first: Jonathan

last: Satin

state: KY

address: 741 S. Limestone St.

department: Physiology

institute: University of Kentucky

description: ventricle, Rad knockout, TAC

data_processing:
Quality control steps;  1) remove reads containing adaptors; 2) remove reads containing N > 10% (N represents base that could not be determined); 3) remove low quality reads: The Qscore (Quality value) of over 50% bases of the read is <=5
mapping with HISAT2 (divided in 3 parts: (1) whole sequence aligned to a single exon; (2) sequencing sequence was peicewise aligned to 2 exons of the genome; (3) sequencing sequence  was segmented and aligned to >=3 exons
Assembly: mm10
Supplementary files format and content: tab delinimited text files with headings for columns: (1) gene_id; (2) normalized read counts; (3) avg normalized readcount; (4) log2 fold change (performed by DESeq2 R/EdgeR; (5) p-value; (6) adjusted p-value; (7) gene name: (8) chromosome; (9, 10) start, end position of gene on chromosome; (11) gene strand; (12) gene length; (13) gene type; (14) gene function description; (15) family name of transcription factor; (16) raw readcount; (17) FPKN

source_name: heart, ventricle

extract_protocol:
RNA was harvested using Qiagen RNAeasy Fibrous Tissue Mini Kit (cat. 74704)
polyA enrichment library preparation in construction of 250-300bp insert cDNA library

treatment_protocol: TAC performed 4 weeks prior to tamoxifen administration

value: heart, ventricle


title: o3-mouse-brain-KOH


title: ventricle, Rad knockout, TAC TKO3

description: ventricle, Rad knockout, TAC


title: o1-mouse-heart-KCl


title: 7005


title: female, 0.25mM, 24h, repl 2


title: ventricle, Rad knockout, TAC TKO2

description: ventricle, Rad knockout, TAC


title: ventricle, Rad knockout, TAC TKO1

description: ventricle, Rad knockout, TAC


title: o1-mouse-brain-KCl


title: o2-mouse-brain-KOH


title: ventricle, Rad knockout, sham SKO3

description: ventricle, Rad knockout, sham


title: 3044


title: female, 0.25mM, 24h, repl 1


title: MT1_D21_rep2

city: CHENNAI

first: SOWMYA

last: PARAMESWARAN

address: 41 COLLEGE ROAD

country: India

institute: VISION RESEARCH FOUNDATION

data_processing:
The raw reads were processed using FastQC for quality assessment and pre-processing using TrimGalore.
Hisat2 was used to align the pre-processed high quality data to Homo sapiens reference(GRCh38.p13) genome from Ensembl database with default parameters..
Featurecounts tool was used to estimate and calculate transcript and gene abundance. Absolute counts were estimated and used in differential expression analysis.
DESeq was used to calculate the differentially expressed transcripts
Assembly: Homo sapiens (GRCh38.p13)
Supplementary files format and content: tab-delimited text file format of normalized count for each sample

source_name: Mesenchymal stem cells

growth_protocol: The orbital adipose derived mesenchymal stem cells (OAMSCs) from retinoblastoma patients were cultured in DMEM-F12 with 10% FBS and maintained in MesenPRO RS medium (Gibco) at 37Cin 5% CO2 incubator.

extract_protocol:
Total RNA was isolated from cells at the various stages of osteogenic differentiation using TRIZOL reagent (sigma).
RNA sequencing library was prepared using Illumina-compatible NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England BioLabs) following manufacturer's protocol. 500 ng of total RNA was taken for mRNA isolation, fragmentation and priming. Fragmented and primed mRNA was further subjected to first strand synthesis followed by second strand synthesis. The double stranded cDNA was purified using JetSeq magnetic beads and was end-repaired, adenylated and ligated to Illumina adapters as per NEBNext® Ultra™ II Directional RNA Library Prep protocol followed by second strand excision. Adapter ligated cDNA was purified using JetSeq Beads and was subjected to 11 cycles for Indexing and to enrich the adapter-ligated fragments. Final PCR products (sequencing library) were purified with JetSeq Beads, followed by library quality control check. Illumina-compatible sequencing libraries were quantified by Qubit fluorometer and fragment size distribution was analyzed on Agilent 2200 TapeStation. The Illumina-compatible sequencing libraries showed an average fragment length of 496 bp and sufficient concentration to obtain the desired amount of sequencing data. The libraries were paired-end sequenced on Illumina Sequencer

treatment_protocol: To induce osteogenic differentiation, OAMSCs were cultured in osteogenic differentiation medium (Life Technologies) for different time intervals (7, 14 and 21days) with medium replenished every three days.

tag: cell type

value: Mesenchymal stem cells

value: RB+/-MUT

value: Osteogenic differentiation

value: Day 21


title: female, 1mM, 24h, repl 3


title: female, 0mM, 24h, repl 3


title: ventricle, Rad knockout, sham SKO2

description: ventricle, Rad knockout, sham


title: 3042


title: MT1_D14_rep2

value: Day 14


title: female, 0mM, 24h, repl 2


title: 3041

value: Included


title: female, 0mM, 24h, repl 1


title: female, 0.25mM, 24h, repl 3


title: ventricle, WT, TAC TWT4

description: ventricle, WT, TAC


title: MT1_D14_rep1


title: female, 1mM, 8h, repl 3


title: MT1_D21_rep1


title: o1-mouse-brain-KOH

value: brain


title: 3039

value: Match

value: M


title: 3047


title: 3038


title: female, 1mM, 8h, repl 2

value: whole fly


title: MT1_D7_rep1

value: Day 7


title: MT1_D7_rep2


title: 3035


title: ventricle, WT, TAC TWT2

description: ventricle, WT, TAC


title: female, 1mM, 8h, repl 1

value: female


title: MT1_D0_rep2

value: Day 0


title: ventricle, WT, TAC TWT1

description: ventricle, WT, TAC


title: 3034


title: MT1_D0_rep1


title: ventricle, WT, sham SWT3

description: ventricle, WT, sham


title: ventricle, Rad knockout, sham SKO1

description: ventricle, Rad knockout, sham


title: 3030


title: female, 0.25mM, 8h, repl 2


title: WT1_D21_rep2

value: WT


title: ventricle, WT, TAC TWT3

description: ventricle, WT, TAC


title: ventricle, WT, sham SWT1

description: ventricle, WT, sham


title: ventricle, WT, sham SWT2

description: ventricle, WT, sham


title: female, 0.25mM, 8h, repl 1


title: WT1_D21_rep1


title: 3025


title: female, 0mM, 8h, repl 3


title: Flt3L_HI_3

city: Braunschweig

first: Carolin

last: Wiechers

state: Niedersachsen

address: Inhoffenstraße 7

department: Experimental Immunology

country: Germany

institute: Helmholtz Centre for Infection Research

data_processing:
Sequencing reads were mapped to mouse genome (mm10) using STAR and aligned reads to annotated genes were quantified with htseq-count
calculated read counts were further processed with DESeq2 for quantiﬁcation of differential gene expression. Raw read counts were converted to RPKM (reads per kilobase of exon length per million mapped reads) values.
Genome_build: mm10
Supplementary_files_format_and_content: comma separated values (.csv) file of DESeq2 results

source_name: in vitro cultured DC-like cells

growth_protocol: FSCs were isolated from pooled mLNs or pLN samples and 2,000 LN FSCs per well were directly sorted by flow cytometry into the prepared plates. At the same time, pre DCs were isolated from whole bone marrow of the same mice as described above and sorted by flow cytometry into Eppendorf tubes. After cell sorting, the plates containing LN FSCs were centrifuged for 1 min at 200 x g at RT in order to gently spin-down the cells. Then, 3,000 pre-DCs were added to each culture well containing either mLN or pLN FSCs or they were added to empty wells. In addition, wells containing only pre-DCs received either 50 ng/ml CSF1 or 200 ng/ml FLT3L.

extract_protocol:
At day 3 of the respective cultures, cells were harvested and wells from each condition were pooled. Single-cell suspensions were washed with PBS before dead cells were labeled. For staining of surface antigens, cells were washed and then incubated with the corresponding antibodies dissolved in PBS/0.2% BSA (Sigma-Aldrich) for 15 min on ice. The antibodies targeting CD3 (17A2), CD4 (RM4 5), CD8α (53-6.7), CD11b (M1/70), CD11c (N418), CD19 (6D5), CD24 (M1/69), CD31 (390), CD45 (30-F11), CD45R (RA3-6B2), CD49b (DX5), CD135 (A2F10), CD172a (P84), gp38 (8.1.1), TER-119 (TER-119) and MHCII (M5/114.15.2) were used for sorting. Subsequently, both viable CD45+CD11c+MHCIIlow and CD45+CD11c+MHCIIhigh DC-like cells were sorted by flow cytometry for RNAseq library preparation. An aliquot of sorted Lin-MHCII-CD11c+CD11b-CD135+CD172α- pre-DCs isolated during the seeding of the respective cell culture was used as an input control. Cell sorting for  RNAseq analyses was performed  on FACS Aria IIu (BD Bioscience), FACS Aria II SORP (BD Bioscience) and FACS Aria-Fusion (BD Bioscience).
Cells were directly FACS sorted into RLT+ lysis buffer (Qiagen) containing 10 µl/ml β-Mercaptoethanol (Roth). Total RNA was extracted with the RNeasy Plus Micro kit (Qiagen) according to manufactures instructions. cDNA conversion was carried out using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Clontech Laboratories) according to manufacturer’s instructions, followed by PCR product purification with Agencourt AMPure XP magnetic beads (Beckman Coulter). Libraries were prepared with the Nextera XT DNA Library Prep Kit (Illumina) employing enzymatic tagmentation and simultaneous adapter ligation before subsequent indexing and fragment amplification. PCR product clean-up and size selection was performed with the Agencourt AMPure XP magnetic beads. RNA and cDNA quality and content as well as the correct sizing of cDNA library fragments was verified using the Agilent Technologies Fragment Analyzer 5200 profiles and Qubit measurements after each step.
Sequencing of libraries was carried out at the sequencing facility on Illumina NovaSeq6000 using 50 bp paired-end reads and quality of sequenced libraries was verified with FastQC.

treatment_protocol: LNs were digested for FSC isolation and pre-DC were isolated from bone marrow and all cells were FACS sorted for culturing.

value: DC-like cells

tag: cell population

value: MHCII high expressing


title: WT1_D14_rep1


title: WT1_D14_rep2


title: 3023


title: Flt3L_HI_2


title: 3022


title: female, 0mM, 8h, repl 1


title: Flt3L_HI_1


title: WT1_D7_rep2


title: 3032


title: female, 0.25mM, 8h, repl 3


title: female, 1mM, 4h, repl 3


title: WT1_D7_rep1


title: Flt3L_LO_3

value: MHCII low expressing


title: WT1_D0_rep2

value: Mesenchymal stem cells


title: 3019


title: 3020


title: WT1_D0_rep1


title: 3027


title: Flt3L_LO_2


title: female, 1mM, 4h, repl 2


title: female, 0mM, 8h, repl 2


title: female, 1mM, 4h, repl 1


title: Flt3L_LO_1


title: 3013


title: 3015


title: hCiLB-1013,RNA-seq

city: Beijing

first: Jingxiao

last: Cao

state: Beijing

address: No.5 Yiheyuan Road, Yanyuan Street, Haidian District, Beijing

department: School of Life Sciences, Center for Bioinformatics, Center for Statistical Science, Peking University, Beijing, China.

institute: Peking University

data_processing:
Raw sequencing data were performed quality control using FastQC.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (parameter- ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:7:1:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)
Trimmed sequence reads were mapped to hg19 using STAR (parameters- --readFilesCommand zcat --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical)
Read count extraction were calculated using program featureCounts of Subread package
The gene count matrix was normalized for visualization using R package DESeq2
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: induced from hADSC

extract_protocol:
The Direct-zol RNA MiniPrep Kit (Zymo Research, R2053) was used to extract total RNA.
The NEBNext Ultra RNA Library Prep Kit was used for RNA sequencing library construction. Fragmented and randomly primed 2 × 150 bp paired-end libraries were sequenced using the Illumina HiSeq X Ten system.

value: induced from hADSC

tag: cell line


title: female, 0.25mM, 4h, repl 3


title: female, 0.25mM, 4h, repl 2


title: hCiLB-0618,RNA-seq


title: MCSF_HI_3

value: MCSF


title: MCSF_HI_2


title: 3007


title: 3008


title: hADSC-0618,RNA-seq

source_name: Adipose tissue

value: Adipose tissue

value: hADSC


title: MCSF_HI_1


title: 3006

value: Included


title: MCSF_LO_3


title: female, 0mM, 4h, repl 2

source_name: whole fly


title: female, 0mM, 4h, repl 3


title: hADSC-0325,RNA-seq


title: 3005


title: hCiLB-0721,RNA-seq

source_name: induced from skin fibroblats

value: induced from skin fibroblats


title: 3004

value: Match


title: MCSF_LO_1


title: female, 0mM, 4h, repl 1


title: female, 1mM, 2h, repl 3


title: hASF-0721,RNA-seq

source_name: Skin

value: Skin

value: dermal fibrobalsts


title: 9009004

value: TRAP

value: F


title: hADSC-1013,RNA-seq


title: female, 1mM, 2h, repl 2

value: whole fly

value: female


title: female, 1mM, 2h, repl 1


title: 1087

value: M


title: hCiLB-0325,RNA-seq


title: female, 0.25mM, 4h, repl 1


title: mLN_HI_3

value: DC-like cells

value: mLN

value: MHCII high expressing


title: 9009002


title: mLN_HI_1


title: head, scarb2a mut, rep 3

city: Rehovot

first: Karina

last: Yaniv

state: Israel

address: Hertzel 234

department: Immunology and Regenerative Biology

country: Israel

institute: Weizmann Institute of Science

description: mut rep 3

data_processing:
done using the User-friendly Transcriptomic Analysis Pipeline
Assembly: danRer11
Supplementary files format and content: countsMatrix_normalized.txt: expression dataset - txt file contaning normalized UMI counts table for all samples.

organism: Danio rerio

source_name: head

extract_protocol:
For each experimental condition, a pool of 50 heads (3 biological replicates) was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single-cell suspension. After a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 (Roche), trypsin B (BI), and DNAseI (Roche), the cell suspension was strained through a 70µm filter and stained with SYTOXTM blue (ThermoFisher) for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl of lysis/binding buffer solution (ThermoFisher) containing RNase inhibitor RNasinTM (Promega). FACS analysis and sorting were performed on a (BD FACS Aria III) using a 70µm nozzle.
RNA was captured using Dynabeads™ mRNA DIRECT™ Purification Kit (ThermoFisher) prior to library preparation. A bulk adaptation of the MARS-seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing-ready library by tagging the samples with Illumina sequences during ligation, RT, and PCR.  The final library concentration was measured by Qubit, TapeStation, and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles (Illumina; paired-end sequencing), and each sample was sequenced for 6M reads.

value: head

value: scarb2a+ cells

value: scarb2a mut


title: female, 0.25mM, 2h, repl 3


title: 9009001


title: mLN_HI_2


title: mLN_LO_3

value: MHCII low expressing


title: mLN_LO_2


title: head, scarb2a mut, rep 1

description: mut rep 1


title: MCSF_LO_2

value: MCSF


title: female, 0.25mM, 2h, repl 1


title: mLN_LO_1


title: head, wt, rep 4

description: wt rep 4

value: wt


title: 6001

value: Included


title: female, 0mM, 2h, repl 3


title: head, wt, rep 3

description: wt rep 3


title: pLN_HI_3

value: pLN


title: 5004


title: female, 0mM, 2h, repl 2


title: head, wt, rep 1

description: wt rep 1


title: pLN_HI_2


title: 5003


title: head, scarb2a mut, rep 2

description: mut rep 2


title: 4005


title: female, 0mM, 2h, repl 1


title: pLN_HI_1


title: female, 0.25mM, 2h, repl 2


title: MTZ3

city: Liège

first: Isabelle

last: Manfroid

address: Avenue de l'Hopital 1

department: GIGA-Stem Cell

country: Belgium

institute: Université de Liège

data_processing:
sequenced with Illumina NextSeq500
obtained 20million 100bp paired end reads
Mapped to zebrafish genome GRCz11 using  STAR version 2.6.1
Gene expression levels calculated with featureCounts
Assembly: GRCz11
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: pancreas

extract_protocol:
Lysis buffer : pure nuclease free water, triton 0,28%, dNTP 2,38mM , oligo dT primer 2,38uM
cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations (Picelli et.al 2014); Nextera XT DNA Library Prep Kit (Illumina FC-131-1024)

treatment_protocol: Adult zebrafish were treated with 10mM metronidazole and DMSO overnight. Control fish were only treated with DMSO

value: pancreas

value: ductal

value: Tg(ins:NTR-mcherry); Tg(nkx6.1:GFP)

value: metronidazole


title: female, 1mM, 1h, repl 4

value: whole fly

value: female


title: 4003

value: TRAP

value: M


title: MTZ1


title: pLN_LO_2

value: DC-like cells


title: pLN_LO_3


title: 3046


title: MTZ2


title: 6002


title: female, 1mM, 1h, repl 3


title: Ductal3

value: DMSO


title: pLN_LO_1


title: Ductal2


title: female, 0.25mM, 1h, repl 3


title: 3045

value: F


title: female, 1mM, 1h, repl 2


title: preDC_input_3

value: preDC

value: input


title: preDC_input_2


title: 3043


title: Ductal1


title: female, 0.25mM, 1h, repl 2


title: 3031


title: female, 0.25mM, 1h, repl 1


title: 3033


title: BSC, Term, rep8

city: Boston

first: Xingbin

last: Ai

address: 55 Fruit St

institute: MASSACHUSETTS GENERAL HOSPITAL

data_processing:
The paired-end 42 bp sequencing reads are mapped to the human hg38 reference genome using the STAR algorithm with default settings.
The number of fragments overlapping predefined genomic genes is counted. Only read pairs that have both ends aligned are counted.
Read pairs that have their two ends mapping to different chromosomes or mapping to same chromosome but on different strands are discarded.
The gene annotations were obtained from Subread R package. These annotations were originally from NCBI RefSeq database and then adapted by merging overlapping exons from the same gene to form a set of disjoint exons for each gene.
Genes with the same Entrez gene identifiers were also merged into one gene.
Assembly: hg38
Supplementary files format and content: csv

source_name: Basal stem cell

extract_protocol:
Total RNA isolation using a RNeasy kit (QIAGEN, Cat# 74104).
For each sample, 2 µg of total RNA was used in library construction using TruSeq Stranded mRNA Library kit (Illumina, Cat# 20020594).

tag: source

value: Tracheal aspirate

value: Basal stem cell

tag: group

value: term


title: preDC_input_1


title: AltChe8

type: genomic

city: Tartu

first: Alena

last: Kushniarevich

address: Riia 23b

department: Institute of Genomics

country: Estonia

institute: UNIVERSITY OF TARTU

description: Genomic DNA extracted from blood was genotyped using InfiniumOmniExpress-24v1.3 (Illumina).

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on an iSCAN System (Illumina).

data_processing:
Image data was analyzed using Genomestudio 2.0.5 (Illumina).
Genotype: AA,AB,BB,or NC (no call)

label: Biotin (C, G), Dinitrophenyl (A, T)

source_name: blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master, according to the manufacturer's protocol. After incubation the amplified DNA was fragmented with fragmentation mix, precipitated with isopropanol and precipitation mix and resuspended in hybridization buffer.

extract_protocol: Extraction of genomic DNA from blood was performed using standard extraction protocols.

tag: project

tag: samplewell

tag: population

value: Altai Chelkan

tag: geographic location

value: Russia


title: female, 0mM, 1h, repl 2

city: Bloomington

first: Jason

address: 1001 E 3rd St

institute: Indiana University

data_processing:
Reads were quantified with Salmon psueodoaligner
Normalized counts were generated with DESeq2 using tximport and the Salmon quantification
Assembly: BDGP6.32
Supplementary files format and content: Salmon qunatification directories (including quant.sf, bootstrap, log files) as gzipped tar archives
Supplementary files format and content: supplemtental files containing sex-specific normalized log counts as output by vst() function of DESeq2

extract_protocol:
Treated flies were frozen in bead tubes, followed by disruption and extraction in Trizol.  RNA was then cleaned with Qiagen RNeasy kit
Illumina Stranded mRNA prep, 96 index
Poly-A-selected total RNA prepared with TruSeq ligation for paired-end sequencing

tag: tissue


title: female, 0mM, 1h, repl 3


title: AltKum9

value: Altai Kumandin


title: 3028

tag: included

value: Included


title: BSC, Term, rep5


title: CDA294V

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using bcltofastQ (Illumina).
Sequencing adapter contaminations were removed using cutadapt, discarding those reads that were shorter than 30 nt after trimming.
Resulting reads were aligned against the GRCm38_91 mouse transcriptome, with RSEM v1.3.1, to obtain expression estimates at gene level.
Assembly: GRCm38_91
Supplementary files format and content: TMM-normalized counts for 16118 expressed genes (at least 1 CPM, in at least 3 samples), in each sample.

source_name: Heart ventricle

growth_protocol: Meis1flox/flox; Meis2flox/flox females were crossed with Meis1flox/wt; Meis2flox/flox; α-MHC-Cre tg/wt males in order to obtain 25% of dKO embryos Meis1flox/flox; Meis2flox/flox; aMHC tg/wt.   Meis1flox/flox; Meis2flox/flox mice females were crossed with Meis1flox/flox; Meis2flox/flox; α-MHC-MerCreMer tg/wt to obtain 50% of Meis1flox/flox; Meis2flox/flox; α-MHC-MerCreMer tg/wt idKO) and 50% of Meis1flox/flox; Meis2flox/flox; α-MHC-MerCreMer wt/wt (Control).

extract_protocol:
RNA was extracted with the Qiagen RNeasy mini and midi kit and was treated with DNase.
Total RNA (20 ng) was used to generate libraries with the NEBNext Ultra RNA Library preparation kit (New England Biolabs). Libraries were sequenced in a HiSeq2500 next-generation sequencer (Illumina) to generate 60-base single reads.

treatment_protocol: Fetuses were harvested at E15.5 from four independent litters and a Control and a dKO were selected from each litter. Hearts were dissected in ice-cold sterile PBS. Atria and ventricles were separated and OFT removed, to be immediately frozen with liquid nitrogen and stored at -80ºC until all the samples were collected. Tissue lysis was performed with TissueLyser LT (Quiagen).  Adult hearts from 8 male littermates were harvested two weeks after tamoxifen induction and cannulated to clean the blood with ice-cold sterile PBS. Atria and ventricles were separated and OFT removed before  being frozen at -80ºC. Tissue lysis was done with TriReagent (Trizol; Sigma-T9424) using TissueLyser LT (Quiagen).

tag: organ

value: Heart

tag: genotype

value: Meis1flox/flox; Meis2flox/flox;alpha-MHC-MerCreMer wt/wt (Control)


title: female, 0mM, 1h, repl 1

last: Tennessen

value: whole fly

tag: Sex

value: female


title: 3009

tag: cohort

value: TRAP

tag: gender

value: M


title: BSC, Adult, rep3

value: adult


title: CDA294Au

source_name: Heart atrium


title: AltKum6


title: AltChe16


title: female, 0mM, 0h, repl 3

tag: concentration

tag: time

tag: replicate


title: 1104

value: F


title: 1105


title: female, 0mM, 0h, repl 2


title: AltChe14


title: CDA293V


title: 1103


title: female, 0mM, 0h, repl 1


title: 1102


title: CDA293Au


title: AltTub1

value: Altai Tubalar


title: AltTub4


title: late recovery (12h), mutant, replicate 3

data_processing:
QC with FastQC and MultiQC
Quantification with salmon
Quantifications imported with tximport
Normalization and transformed log counts with DESeq2
Assembly: BDGP6.32
Supplementary files format and content: salmon quantification directories as gzip'd archives
Supplementary files format and content: supplementary file contained transformed log counts of all samples

growth_protocol: Flies were maintained at 25°C, 60% humidity, 12h/12h light/dark cycle, on Bloomington food, except during hypoxia treatment

extract_protocol:
Flies were homogenized in trizol + ceramic beads
Illumina Stranded mRNA prep, 96 index
Poly-A-selected total RNA prepared with TruSeq ligation for paired-end sequencing

treatment_protocol: Flies were kept in a hypoxic environment of 1% oxygen for 12 hours before being allowed to recover for 1 or 12 hours in a normoxic environment

value: het L2HGDH mutant (12/14)

tag: treatment


title: CDA292V


title: 1094


title: AltTub61


title: CDA292Au


title: late recovery (12h), mutant, replicate 2


title: late recovery (12h), mutant, replicate 1


title: AltKum24


title: 1093


title: AltTl208

value: Altai Teles


title: 1077


title: CDA291Au

value: Meis1flox/flox; Meis2flox/flox;alpha-MHC-MerCreMer tg/wt (idKO)


title: AltTl166


title: late recovery (12h), wild type, replicate 2

value: het control (12/+)


title: 1070


title: AltTub170


title: late recovery (12h), wild type, replicate 1


title: CDA290Au


title: 1055


title: early recovery (1h), mutant, replicate 3


title: 1054


title: AltTl170


title: CDA289V


title: early recovery (1h), mutant, replicate 2


title: CDA289Au


title: 1081


title: AltTub225


title: early recovery (1h), mutant, replicate 1


title: AltTl169


title: CDA291V


title: 1037


title: CDA288V


title: late recovery (12h), wild type, replicate 3


title: CDA288Au


title: CDA290V


title: early recovery (1h), wild type, replicate 3


title: CDA287V


title: Tartary buckwheat,20%PEG-6000,8 h-3

city: Lanzhou

first: Qi

last: Lu

state: Gansu

address: Tianshui South Road 222

institute: lanzhou University

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Differential expression analysis was performed using the DESeq2.
Assembly: PRJCA009237
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample

organism: Fagopyrum tataricum

source_name: seedings(leaf,stem)

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

treatment_protocol: Soak the seeds uniformly in water in a glass petri dish for about 2-3 days to germinate until the roots are 1-2 cm long, then transplant into soil or black hydroponic boxes for subsequent processing. When the Tartary buckwheat grows normally to the 2-leaf stage under long-day conditions. The Tartary buckwheat in the soil is treated with water shortage and drought for 10-14 days. The tartary buckwheat seedlings in the hydroponic box are treated with 20% PEG-6000 for 0 h, 2 h, 4 h, and 8 h.

value: seedings(leaf,stem)

tag: cultivar


title: 1034


title: early recovery (1h), wild type, replicate 2


title: 1030


title: Tartary buckwheat,20%PEG-6000,8 h-2


title: Tartary buckwheat,20%PEG-6000,8 h-1


title: CDA287Au


title: 1029


title: hypoxic control (0h recovery), mutant, replicate 3


title: early recovery (1h), wild type, replicate 1


title: 1041


title: Tartary buckwheat,20%PEG-6000,4 h-3


title: 648E9Auricula

growth_protocol: Meis1flox/flox; Meis2flox/flox females were crossed with Meis1flox/wt; Meis2flox/flox; α-MHC-Cre tg/wt males in order to obtain 25% of dKO embryos Meis1flox/flox; Meis2flox/flox; aMHC tg/wt.

treatment_protocol: Fetuses were harvested at E15.5 from four independent litters and a Control and a dKO were selected from each litter. Hearts were dissected in ice-cold sterile PBS. Atria and ventricles were separated and OFT removed, to be immediately frozen with liquid nitrogen and stored at -80ºC until all the samples were collected. Tissue lysis was performed with TissueLyser LT (Quiagen).

value: Meis1flox/flox; Meis2flox/flox; aMHC tg/wt (dKO)


title: hypoxic control (0h recovery), mutant, replicate 2


title: Tartary buckwheat,20%PEG-6000,4 h-2


title: 1027


title: hypoxic control (0h recovery), mutant, replicate 1


title: 648E3Ventriculo

value: Meis1flox/flox; Meis2flox/flox;aMHC +/+ (Control)


title: Tartary buckwheat,20%PEG-6000,4 h-1


title: 648E3Auricula


title: 1022

value: Included


title: hypoxic control (0h recovery), wild type, replicate 2


title: 648E10Ventriculo

value: Heart


title: hypoxic control (0h recovery), wild type, replicate 3


title: 1016


title: 1021


title: hypoxic control (0h recovery), wild type, replicate 1


title: 648E9Ventriculo


title: Tartary buckwheat,20%PEG-6000,2 h-2


title: normoxic control, mutant, replicate 3

value: normox


title: Tartary buckwheat,20%PEG-6000,2 h-1


title: 627E5Ventriculo


title: normoxic control, mutant, replicate 2

value: whole fly


title: 627E5Auricula


title: Tartary buckwheat,control,0 h-3

value: Hoagland's nutrient


title: 1012

value: TRAP


title: 1028

value: M


title: Tartary buckwheat,control,0 h-2


title: 1002


title: normoxic control, mutant, replicate 1


title: 1025


title: Tartary buckwheat,control,0 h-1


title: Tartary buckwheat,20%PEG-6000,2 h-3


title: Nrf2-KO-3

city: Xi'an

first: Siyu

last: Li

address: 1 Xinsi Road

institute: Tangdu Hospital, Fourth Military Medical University

data_processing:
The Qubit 4.0 fluorimeter and Agilent 2100 bioanalyzer were utilized for monitoring mRNA concentration and assessing fragment integrity in the library.
paired-end reads were obtained by sequencing on the DNBSEQ-T7 platform.
Data underwent filtering and QC analysis utilizing fastp software and FastQC software.
Comparison with reference genome sequences was conducted employing hisat2 software. The FPKM method was employed to quantify the expression of individual genes. The Benjamini-Hochberg procedure was applied for multiple correction of P-value to generate FDR value.
DEGs was conducted using DESeq2 (Version 1.34.0).
Assembly: hg18
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes raw counts for each Group

source_name: Nrf2 KO

growth_protocol: HEI-OC1 cells and Nrf2 KO HEI-OC1 cells were cultured in DMEM medium supplemented with 10% FBS and 1% penicillin-streptomycin solution, at a temperature of 33°C and under a CO2 concentration of 10%.

extract_protocol:
Total RNA from the Control group and Nrf2_ KO group were extracted using Trizol reagent.
For the construction of RNA-seq libraries, mRNA samples were initially enriched using Oligo (dT) magnetic beads. Subsequently, fragmentation buffer was added to break down the mRNA into shorter fragments. The first cDNA strand was then synthesized with mRNA as a template using six-base random primers, followed by synthesis of the second cDNA strand through addition of buffer, dNTPs, RNase H, and DNA polymer double-stranded cDNA was generated using a six-base random primer. Next, end-repairing of the double-stranded cDNA was performed along with addition of poly(A), connection of sequencing junctions, purification via magnetic beads, and library generation by selecting suitable fragments for PCR amplification.

tag: cell line

value: Nrf2 KO

tag: cell type

value: Cochlear stem cell

value: Nrf2 knockout


title: normoxic control, wild type, replicate 3


title: normoxic control, wild type, replicate 2


title: 627E4Auricula


title: 648E10Auricula


title: 627E2Ventriculo


title: Nrf2-KO-2

value: Nrf2 KO HEI-OC1 cells were cultured in DMEM medium supplemented with 10% FBS and 1% penicillin-streptomycin solution, at a temperature of 33°C and under a CO2 concentration of 10%.


title: gill,hypoxia,3 [EG6]

city: Dalian

first: Zhongming

last: Fu

state: Liaoning

address: Heishijiao Street

institute: Dalian Ocean University

data_processing:
Raw reads of fastq format were firstly processed using fastp 1 and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2.
FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: NCBI_Mizuhopecten_yessoensis_v2.0
Supplementary files format and content: txt file includes raws counts for each sample

organism: Mizuhopecten yessoensis

source_name: gill

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the instructions. The purity and quality of RNA were identified using a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA), and the integrity of RNA was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
RNA libraries were constructed using VAHTS Universal V5 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: gill


title: gill,hypoxia,2 [EG3]


title: Nrf2-KO-1


title: normoxic control, wild type, replicate 1


title: gill,hypoxia,1 [EG2]


title: 627E2Auricula


title: 627E1Ventriculo


title: DL03

city: Yangling

first: Zehui

last: Wei

address: No.3 Taicheng Road

institute: Northwest A&F University

data_processing:
The quality of the RNA samples was evaluated in an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). After the quality control, the library preparations were sequenced on an Illumina Hiseq2000 platform (Illumina, San Diego, CA, USA) and paired-end reads were generated.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Bos_taurus.ARS-UCD1.2 whole genome using HISAT2 v2.0.4 with parameters -p 8 --dta -x -S
Genome_build: Bos_taurus.ARS-UCD1.2
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Bos frontalis

source_name: The longissimus dorsi muscle

extract_protocol:
All the samples were frozen in liquid nitrogen immediately and stored at -80℃ until further processing.Total RNA of each muscle sample was extracted from approximately 50 mg of frozen tissue using TRIzol Reagent (Invitrogen Corporation, Carlsbad, CA, USA) according to manufacturer recommendations. The quality of the RNA samples was evaluated in an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). After the quality control, the library preparations were sequenced on an Illumina Hiseq2000 platform (Illumina, San Diego, CA, USA) and paired-end reads were generated.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: 3.5 ± 0.5-year-old

value: m. longissimus dorsi

tag: species

value: Gayal


title: OC1-3

value: WT

value: HEI-OC1 cells were cultured in DMEM medium supplemented with 10% FBS and 1% penicillin-streptomycin solution, at a temperature of 33°C and under a CO2 concentration of 10%.


title: gill,normal,3 [CG6]


title: gill,normal,2 [CG5]


title: OC1-2


title: DL02


title: DL01


title: 627E1Auricula

value: Meis1flox/flox; Meis2flox/flox;aMHC +/+ (Control)


title: OC1-1


title: 605E2Ventriculo

value: Heart

value: Meis1flox/flox; Meis2flox/flox; aMHC tg/wt (dKO)


title: 627E4Ventriculo


title: 605E2Auricula


title: Hippocampal neuron culture, HT_rep2

city: Ann Arbor

first: Shigeki

last: Iwase

address: 1241 E. Catherine St.

institute: University of Michigan

data_processing:
confirming the quality of sequencing data by FastQC
reads were mapped to rn6 reference genome using Bowtie2
and annotated with Tophat 2
Adaptors were trimmed using BBDUK
Bru-seq signals of genes were quantified by FeatureCounts
Genome_build: RN6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Hippocampal neuron culture

growth_protocol: To achieve enough neurons, both cortical and hippocampal tissue were isolated as described. Neurons were plated onto poly-D-lysine-coated 6-well cell culture plates at a density of ~3 million cells/well. Cells were plated with ~1mL NGM per well and then supplemented with ~1mL of NGM-GC 2hrs after plating. Prior to experimental treatments, neurons were maintained at 5% CO2 and 37°C and fed NGM-GC every 4 days until DIV14.

extract_protocol:
RNA was purified using phenol-chloroform extraction and isopropanol precipitation, treated with DNase-I (NEB, M0303) then fragmented by high-magnesium, high temperature incubation.
Enrichment of BrU-containing RNA and library preparation were performed as previously described (PMID: 32783930).

treatment_protocol: At the start of the experiment, each well contained ~3mL of media. Similarly, to our electrophysiology experiments, 1mL of initial conditioned media is removed and saved for the drug-washout period. After removal, neurons were treated with either TTX or Veh (1:1000; 1µM TTX) for 24hrs. The initial TTX/Veh treatment was thoroughly removed via 2x washes (leaving ~500µL of media to cover the cells each wash) and lastly maintained with a final 50:50 saved media and fresh NGM solution for 48hrs before secondary treatment. On DIV17, cells were treated with TTX or Veh. 3.5hrs post-treatment, bromouridine (BrU, Sigma, 18670, dissolved in PBS) was added to cultures at 2mM final concentration and incubated at 5% CO2 and 37°C for the final .5hrs. Cultures were harvested in Tri-reagent BD (Sigma, T3809) and frozen immediately.

value: Cultured neurons from newborn rat pups

tag: strain

value: Sprague Dawley

tag: fraction

value: Nascent RNA


title: Integument of 32DAP in WT rep3

city: Wuhan

first: Liqing

state: Hubei

address: No.1 of Shizishan street, Hongshan District

institute: Huazhong Agricultural University

data_processing:
Cutadapt was used to remove the 3’ sequencing adapters (at least 10bp overlap) and allow 20% mismatches
The full-length isoform produced by pacbio sequencing were used to establish index using bowtie2 with default parameters
The software RSEM were used to calculate readcount of each transcript and transform into FPKM (Fragments Per Kilobase of transcript per Million mapped reads) value
The differential expression analysis was performed by DESeq R package with a criterion of |log2FoldChange| > 1 and P value < 0.05
Supplementary_files_format_and_content: Tab-delimited text files include read count and FPKM values for each sample

organism: Citrus reticulata

source_name: Integument

extract_protocol:
RNA was extracted from cell mass captured by laser capture microdissection following the manufacturer’s suggested protocol (Arcturus Picopure kit, Kit0204). About 10-20ng total RNA of 36 samples (contained three biological replications) was used for cDNA synthesis and amplification using an Ovation RNA-seq System V2 Kit (Nugen Technologies).
The first strand cDNA were synthesized using random hexamer primers and dNTPs, and the second strand cDNA were synthesized using the first strand cDNA as a template with same reaction mix as above. The purification steps were carried out in accordance with the protocol. The product was used to SPIA cDNA amplification following by the purification again with QIAGEN MinElute Reaction Cleanup Kit to guarantee no primer and dNTP remains. The cDNA libraries were sequenced with the paired-end (PE, 2 x 150bp) strategy on the Hiseq X ten platform / NovaSeq 6000 (Illumina)

tag: development stage

value: 32 day after pollening

value: Egan No.1 ponkan


title: mouse, high E2 prenatal exposure, male, rep3

city: Shanghai

first: Xiaoguo

last: Zheng

address: 145 Guangyuan Road

institute: Shanghai Jiaotong University

data_processing:
fastp 0.20.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp 0.20.1 with default parameters
Clean read were aligned to reference genome with hisat2 version 2.1.0 (--rna-strandness rf --fr)
htseq-count (version 0.11.2;-s reverse) was used to analysis FPKM values
DESeq2 (Version 1.22.2)was used to analyze differentially expressed genes (cutoff qvalue(pvalue)<0.05, |log2FoldChange|>1)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: placenta

extract_protocol:
Three male and three female placenta samples per group were randomly selected for RNA isolation, which was performed by using TRIzol Reagent (Invitrogen) under the manufacturer’s instructions. Extracted RNA was dissolved in RNase-free water and quantified using Qubit○R RNA Assay Kit in Qubit○R 2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 3 μg RNA per sample was used as input material for RNA sample preparations. Sequencing libraries were generated using NEBXext○R UltraTM RNA Library Prep Kit for Illumina○R (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNest First Strand Synthesis Reaction Buffer (5×). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37℃ for 15 min followed by 5 min at 95℃ before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent bioanalyzer 2100 system.

tag: tissue

value: placenta

value: male

value: high E2 prenatal exposure


title: Integument of 32DAP in WT rep2


title: mouse, high E2 prenatal exposure, male, rep2


title: dKO_2_V

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using bcltofastQ (Illumina).
Sequencing adapter contaminations were removed using cutadapt, discarding those reads that were shorter than 30 nt after trimming.
Resulting reads were aligned against the GRCm38_91 mouse transcriptome, with RSEM v1.3.1, to obtain expression estimates at gene level.
Assembly: GRCm38_91
Supplementary files format and content: TMM-normalized counts for 14549 expressed genes (at least 1 CPM, in at least 3 samples), in each sample.

source_name: Epicardium+Subepicardium

growth_protocol: Conditional Meis1 and Meis2 double-deficient  recombined with WT1-Cre (Meis1fl/fl;Meis2fl/fl;WT1-Cre) were retrieved at E16.5

extract_protocol:
RNA was then purified from each pool using RNeasy Micro kit (Qiagen 74004).
40 ng of total RNA were used to generate barcoded RNA-seq libraries using the NEBNext Ultra RNA Library preparation kit (New England Biolabs). Briefly, poly A+ RNA was purified using poly-T oligo- attached magnetic beads followed by fragmentation and then first and second cDNA strand synthesis. Next, cDNA 3’ ends were adenylated and the adapters were ligated followed by PCR library amplification. Finally, the size of the libraries was checked using the Agilent 2100 Bioanalyzer DNA 1000 chip and their concentration was determined using the Qubit® fluorometer (Life Technologies).

treatment_protocol: The epicardium/subepicardium was dissected as previously described (Lioux et al., 2020) and quickly frozen in separate 1.5 ml Eppendorf tubes on dry ice. For mRNA isolation, samples from at least three different litters were used. As low RNA amount from one single epicardial layer was expected, two dissected epicardia of the same genotype were pooled together. Therefore, the three biological replicates per genotype represent six different hearts pooled by pairs.

value: Epicardium+Subepicardium

tag: organ

value: Epicardial+Subepicardial cells

tag: genotype

value: Meis1-Meis2 KO


title: mouse, high E2 prenatal exposure, male, rep1

tag: Sex


title: Hippocampal neuron culture, TH_rep2


title: Hippocampal neuron culture, HH_rep2


title: gill,normal,1 [CG4]

value: gill


title: Hippocampal neuron culture, TT_rep2


title: dKO_3_V


title: dKO_1_V


title: mouse, high E2 prenatal exposure, female, rep3

value: female


title: Integument of 28DAP in WT rep3

value: 28 day after pollening


title: Hippocampal neuron culture, TT_rep1


title: Integument of 28DAP in WT rep2


title: Integument of 32DAP in WT rep1


title: C_4_V

value: Wild-type


title: mouse, high E2 prenatal exposure, female, rep2


title: Integument of 28DAP in WT rep1


title: Hippocampal neuron culture, HT_rep1


title: Integument of 18DAP in WT rep3

value: 18 day after pollening


title: C_1_V

value: Heart