title: biol rep 6 liver Male

description:
Foie_212
Raw_counts_Liver.txt


title: biol rep 7 liver Male

status: Public on Jun 09 2024

type: SRA

city: Québec

first: Florent

last: Sylvestre

state: Québec

address: 2325, rue de l'Université

country: Canada

institute: Université Laval

description:
Foie_213
Raw_counts_Liver.txt

library_source: transcriptomic

data_processing:
Read quality: filter low quality read with fastp (v0,15,0), also removes poly-A tail, illumina adapters and first 12bp. Only keep reads >12bp
Read aligment: STAR v2,7,2b two pass mode, followed by quantification using HTSeq v0,11,3 in union mode after discarding multi-mapping reads
Read counts from each samples were merged Per tissus using a custom R script
Assembly: Stickleback reference genome on NCBI, RefSeq assembly GCF_016920845.1. Fisr 0,32Mb were removed from the Y chromosome (pseudo-autosomal region)
Supplementary files format and content: All processed data files contains raw read counts for each gene (row) and each individual (column). Individual are labelled with library lane (Cerveau = Brain, Foie = Liver and Branchie = Gills)

molecule: total RNA

organism: Gasterosteus aculeatus

source_name: Liver

growth_protocol: Natural population

extract_protocol:
Rneasy Mini kit (Qiagen)
Dual indexing  Quant seq 3' mRNAq Seq library prep Kit FWD
Quant-Seq

treatment_protocol: No treatment (Sex was our explanatory variable)

tag: tissue

value: Liver

tag: Sex

value: male


title: biol rep 1 liver Male

description:
Foie_10
Raw_counts_Liver.txt


title: biol rep 38 liver Female

description:
Foie_B2
Raw_counts_Liver.txt

value: female


title: biol rep 37 liver Female

description:
Foie_B1
Raw_counts_Liver.txt


title: biol rep 14 liver Male

description:
Foie_230
Raw_counts_Liver.txt


title: biol rep 13 liver Male

description:
Foie_224
Raw_counts_Liver.txt


title: biol rep 35 liver Female

description:
Foie_75
Raw_counts_Liver.txt


title: biol rep 5 liver Male

description:
Foie_211
Raw_counts_Liver.txt


title: biol rep 33 liver Female

description:
Foie_6
Raw_counts_Liver.txt


title: biol rep 36 liver Female

description:
Foie_79
Raw_counts_Liver.txt


title: biol rep 32 liver Female

description:
Foie_57
Raw_counts_Liver.txt


title: biol rep 34 liver Female

description:
Foie_68
Raw_counts_Liver.txt


title: biol rep 30 liver Female

description:
Foie_51
Raw_counts_Liver.txt


title: biol rep 29 liver Female

description:
Foie_35
Raw_counts_Liver.txt


title: biol rep 28 liver Female

description:
Foie_34
Raw_counts_Liver.txt


title: biol rep 27 liver Female

description:
Foie_31
Raw_counts_Liver.txt


title: biol rep 26 liver Female

description:
Foie_267
Raw_counts_Liver.txt


title: biol rep 24 liver Female

description:
Foie_263
Raw_counts_Liver.txt


title: biol rep 25 liver Female

description:
Foie_264
Raw_counts_Liver.txt


title: biol rep 20 liver Female

description:
Foie_256
Raw_counts_Liver.txt


title: biol rep 21 liver Female

description:
Foie_257
Raw_counts_Liver.txt


title: biol rep 22 liver Female

description:
Foie_259
Raw_counts_Liver.txt


title: biol rep 23 liver Female

description:
Foie_261
Raw_counts_Liver.txt


title: biol rep 19 liver Female

description:
Foie_255
Raw_counts_Liver.txt


title: biol rep 18 liver Female

description:
Foie_251
Raw_counts_Liver.txt


title: biol rep 17 liver Female

description:
Foie_250
Raw_counts_Liver.txt


title: biol rep 16 liver Female

description:
Foie_244
Raw_counts_Liver.txt


title: biol rep 14 liver Female

description:
Foie_240
Raw_counts_Liver.txt


title: biol rep 15 liver Female

description:
Foie_243
Raw_counts_Liver.txt


title: biol rep 13 liver Female

description:
Foie_233
Raw_counts_Liver.txt


title: biol rep 11 liver Female

description:
Foie_229
Raw_counts_Liver.txt


title: biol rep 10 liver Female

description:
Foie_226
Raw_counts_Liver.txt


title: biol rep 7 liver Female

description:
Foie_207
Raw_counts_Liver.txt


title: biol rep 31 liver Female

description:
Foie_55
Raw_counts_Liver.txt


title: AFF4_KD RNA-seq rep2

status: Public on Jun 10 2024

city: Shang Hai

first: Zimei

last: Yang

address: Dongchuan road 800

country: China

institute: Shang Hai Jiaotong University

data_processing:
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters. RNA-seq read were aligned using hisat2 v2.1.0 with parameter --rna-strandness RF.
Fragment count were obtained using featureCounts v1.6.1.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include fragment count values of genes for each sample.

molecule: polyA RNA

organism: Homo sapiens

source_name: HEL cell line

growth_protocol: Human cells HEL were cultured in 90% RPMI-1640 + 10% FBS + 2% Penicillin/Streptomycin.

extract_protocol:
RNA was extracted from cells using RNeasy Plus Mini Kit (Qiagen, cat. no. 74134) and Quick-RNA MiniPrep Kit (Zymo Research, cat. no. R1054)
the Illumina TruSeq RNA Library preparation protocol: PolyA RNA is captured by oligodT beads and fragmented when eluted from the beads. The first-strand cDNA was synthesized by reverse transcriptase using dNTP, whereas the second-strand cDNA was generated using a dUTP mix . After end-repair, dA-tailing and adapter ligation, the dUTP-containing second strand is digested by uracil DNA glycosylase, rendering it unamplifiable in the subsequent PCR step. Hence the resulting library contains only PCR product of the first-strand cDNA. And then, the barcoded DNA was amplified by 15-cycle PCR.  Libraries were sequenced on Illumina Genome Analyzer II, HiSeq 2000, or HiSeq 2500.

tag: cell line

value: HEL cell line

tag: cell type

value: Human erythroblast

tag: genotype

value: AFF4 knockdown


title: biol rep 8 liver Female

description:
Foie_21
Raw_counts_Liver.txt


title: biol rep 1 liver Female

description:
Foie_13
Raw_counts_Liver.txt


title: biol rep 4 liver Female

description:
Foie_17
Raw_counts_Liver.txt


title: biol rep 3 liver Female

description:
Foie_16
Raw_counts_Liver.txt


title: biol rep 5 liver Female

description:
Foie_20
Raw_counts_Liver.txt


title: biol rep 34 brain Male

description:
Cerveau_61
Raw_counts_Brain.txt

source_name: Brain

value: Brain


title: biol rep 38 brain Male

description:
Cerveau_70
Raw_counts_Brain.txt


title: biol rep 33 brain Male

description:
Cerveau_60
Raw_counts_Brain.txt


title: biol rep 37 brain Male

description:
Cerveau_7
Raw_counts_Brain.txt


title: biol rep 36 brain Male

description:
Cerveau_67
Raw_counts_Brain.txt


title: biol rep 31 brain Male

description:
Cerveau_53
Raw_counts_Brain.txt


title: biol rep 9 liver Female

description:
Foie_216
Raw_counts_Liver.txt


title: biol rep 12 liver Female

description:
Foie_231
Raw_counts_Liver.txt


title: biol rep 28 brain Male

description:
Cerveau_42
Raw_counts_Brain.txt


title: biol rep 27 brain Male

description:
Cerveau_40
Raw_counts_Brain.txt


title: biol rep 35 brain Male

description:
Cerveau_63
Raw_counts_Brain.txt


title: biol rep 29 brain Male

description:
Cerveau_43
Raw_counts_Brain.txt


title: biol rep 32 brain Male

description:
Cerveau_54
Raw_counts_Brain.txt


title: biol rep 25 brain Male

description:
Cerveau_3
Raw_counts_Brain.txt


title: biol rep 26 brain Male

description:
Cerveau_38
Raw_counts_Brain.txt


title: biol rep 24 brain Male

description:
Cerveau_279
Raw_counts_Brain.txt


title: biol rep 22 brain Male

description:
Cerveau_270
Raw_counts_Brain.txt


title: biol rep 2 liver Female

description:
Foie_15
Raw_counts_Liver.txt


title: biol rep 6 liver Female

description:
Foie_203
Raw_counts_Liver.txt


title: biol rep 39 brain Male

description:
Cerveau_73
Raw_counts_Brain.txt


title: biol rep 21 brain Male

description:
Cerveau_269
Raw_counts_Brain.txt


title: biol rep 20 brain Male

description:
Cerveau_25
Raw_counts_Brain.txt


title: biol rep 19 brain Male

description:
Cerveau_241
Raw_counts_Brain.txt


title: biol rep 30 brain Male

description:
Cerveau_50
Raw_counts_Brain.txt


title: biol rep 18 brain Male

description:
Cerveau_238
Raw_counts_Brain.txt


title: biol rep 13 brain Male

description:
Cerveau_224
Raw_counts_Brain.txt


title: biol rep 17 brain Male

description:
Cerveau_237
Raw_counts_Brain.txt


title: biol rep 10 brain Male

description:
Cerveau_22
Raw_counts_Brain.txt


title: biol rep 11 brain Male

description:
Cerveau_222
Raw_counts_Brain.txt


title: biol rep 14 brain Male

description:
Cerveau_230
Raw_counts_Brain.txt


title: biol rep 16 brain Male

description:
Cerveau_235
Raw_counts_Brain.txt


title: biol rep 9 brain Male

description:
Cerveau_218
Raw_counts_Brain.txt


title: biol rep 8 brain Male

description:
Cerveau_217
Raw_counts_Brain.txt


title: biol rep 15 brain Male

description:
Cerveau_232
Raw_counts_Brain.txt


title: biol rep 23 brain Male

description:
Cerveau_274
Raw_counts_Brain.txt


title: biol rep 12 brain Male

description:
Cerveau_223
Raw_counts_Brain.txt


title: biol rep 2 brain Male

description:
Cerveau_12
Raw_counts_Brain.txt


title: biol rep 6 brain Male

description:
Cerveau_212
Raw_counts_Brain.txt


title: biol rep 7 brain Male

description:
Cerveau_213
Raw_counts_Brain.txt


title: biol rep 5 brain Male

description:
Cerveau_211
Raw_counts_Brain.txt


title: biol rep 3 brain Male

description:
Cerveau_204
Raw_counts_Brain.txt


title: biol rep 4 brain Male

description:
Cerveau_205
Raw_counts_Brain.txt


title: biol rep 37 brain Female

description:
Cerveau_79
Raw_counts_Brain.txt


title: biol rep 39 brain Female

description:
Cerveau_B2
Raw_counts_Brain.txt


title: biol rep 38 brain Female

description:
Cerveau_B1
Raw_counts_Brain.txt


title: biol rep 36 brain Female

description:
Cerveau_75
Raw_counts_Brain.txt


title: biol rep 35 brain Female

description:
Cerveau_68
Raw_counts_Brain.txt


title: biol rep 34 brain Female

description:
Cerveau_6
Raw_counts_Brain.txt


title: biol rep 33 brain Female

description:
Cerveau_57
Raw_counts_Brain.txt


title: biol rep 32 brain Female

description:
Cerveau_55
Raw_counts_Brain.txt


title: biol rep 31 brain Female

description:
Cerveau_51
Raw_counts_Brain.txt


title: biol rep 30 brain Female

description:
Cerveau_35
Raw_counts_Brain.txt


title: biol rep 29 brain Female

description:
Cerveau_34
Raw_counts_Brain.txt


title: biol rep 27 brain Female

description:
Cerveau_267
Raw_counts_Brain.txt


title: biol rep 25 brain Female

description:
Cerveau_263
Raw_counts_Brain.txt


title: biol rep 21 brain Female

description:
Cerveau_256
Raw_counts_Brain.txt


title: biol rep 23 brain Female

description:
Cerveau_259
Raw_counts_Brain.txt


title: biol rep 1 brain Male

description:
Cerveau_10
Raw_counts_Brain.txt


title: biol rep 24 brain Female

description:
Cerveau_261
Raw_counts_Brain.txt


title: biol rep 18 brain Female

description:
Cerveau_250
Raw_counts_Brain.txt


title: biol rep 20 brain Female

description:
Cerveau_255
Raw_counts_Brain.txt


title: biol rep 16 brain Female

description:
Cerveau_243
Raw_counts_Brain.txt


title: biol rep 22 brain Female

description:
Cerveau_257
Raw_counts_Brain.txt


title: biol rep 13 brain Female

description:
Cerveau_231
Raw_counts_Brain.txt


title: biol rep 17 brain Female

description:
Cerveau_244
Raw_counts_Brain.txt


title: biol rep 14 brain Female

description:
Cerveau_233
Raw_counts_Brain.txt


title: biol rep 15 brain Female

description:
Cerveau_240
Raw_counts_Brain.txt


title: biol rep 9 brain Female

description:
Cerveau_21
Raw_counts_Brain.txt


title: biol rep 11 brain Female

description:
Cerveau_226
Raw_counts_Brain.txt


title: biol rep 8 brain Female

description:
Cerveau_203
Raw_counts_Brain.txt


title: biol rep 5 brain Female

description:
Cerveau_17
Raw_counts_Brain.txt


title: biol rep 7 brain Female

description:
Cerveau_20
Raw_counts_Brain.txt


title: biol rep 6 brain Female

description:
Cerveau_18
Raw_counts_Brain.txt


title: biol rep 26 brain Female

description:
Cerveau_264
Raw_counts_Brain.txt


title: biol rep 28 brain Female

description:
Cerveau_31
Raw_counts_Brain.txt


title: biol rep 4 brain Female

description:
Cerveau_16
Raw_counts_Brain.txt


title: biol rep 3 brain Female

description:
Cerveau_15
Raw_counts_Brain.txt


title: biol rep 19 brain Female

description:
Cerveau_251
Raw_counts_Brain.txt


title: biol rep 31 gills Male

description:
Branchie_61
Raw_counts_Gills.txt

source_name: Gills

value: Gills


title: biol rep 1 brain Female

description:
Cerveau_13
Raw_counts_Brain.txt


title: biol rep 36 gills Male

description:
Branchie_73
Raw_counts_Gills.txt


title: biol rep 2 brain Female

description:
Cerveau_14
Raw_counts_Brain.txt


title: biol rep 35 gills Male

description:
Branchie_70
Raw_counts_Gills.txt


title: biol rep 33 gills Male

description:
Branchie_67
Raw_counts_Gills.txt


title: biol rep 32 gills Male

description:
Branchie_63
Raw_counts_Gills.txt


title: biol rep 26 gills Male

description:
Branchie_50
Raw_counts_Gills.txt


title: biol rep 10 brain Female

description:
Cerveau_216
Raw_counts_Brain.txt


title: biol rep 29 gills Male

description:
Branchie_56
Raw_counts_Gills.txt


title: biol rep 28 gills Male

description:
Branchie_54
Raw_counts_Gills.txt


title: biol rep 12 brain Female

description:
Cerveau_229
Raw_counts_Brain.txt


title: biol rep 30 gills Male

description:
Branchie_60
Raw_counts_Gills.txt


title: biol rep 21 gills Male

description:
Branchie_279
Raw_counts_Gills.txt


title: biol rep 23 gills Male

description:
Branchie_40
Raw_counts_Gills.txt


title: biol rep 25 gills Male

description:
Branchie_43
Raw_counts_Gills.txt


title: biol rep 22 gills Male

description:
Branchie_38
Raw_counts_Gills.txt


title: biol rep 27 gills Male

description:
Branchie_53
Raw_counts_Gills.txt


title: biol rep 19 gills Male

description:
Branchie_269
Raw_counts_Gills.txt


title: biol rep 15 gills Male

description:
Branchie_235
Raw_counts_Gills.txt


title: biol rep 18 gills Male

description:
Branchie_25
Raw_counts_Gills.txt


title: biol rep 12 gills Male

description:
Branchie_224
Raw_counts_Gills.txt


title: biol rep 16 gills Male

description:
Branchie_238
Raw_counts_Gills.txt


title: biol rep 17 gills Male

description:
Branchie_241
Raw_counts_Gills.txt


title: biol rep 11 gills Male

description:
Branchie_223
Raw_counts_Gills.txt


title: biol rep 13 gills Male

description:
Branchie_230
Raw_counts_Gills.txt


title: biol rep 14 gills Male

description:
Branchie_232
Raw_counts_Gills.txt


title: biol rep 8 gills Male

description:
Branchie_218
Raw_counts_Gills.txt


title: biol rep 7 gills Male

description:
Branchie_213
Raw_counts_Gills.txt


title: biol rep 10 gills Male

description:
Branchie_222
Raw_counts_Gills.txt


title: biol rep 9 gills Male

description:
Branchie_22
Raw_counts_Gills.txt


title: biol rep 24 gills Male

description:
Branchie_42
Raw_counts_Gills.txt


title: biol rep 5 gills Male

description:
Branchie_211
Raw_counts_Gills.txt


title: biol rep 20 gills Male

description:
Branchie_274
Raw_counts_Gills.txt


title: biol rep 2 gills Male

description:
Branchie_12
Raw_counts_Gills.txt


title: biol rep 4 gills Male

description:
Branchie_205
Raw_counts_Gills.txt


title: biol rep 35 gills Female

description:
Branchie_B1
Raw_counts_Gills.txt


title: biol rep 1 gills Male

description:
Branchie_10
Raw_counts_Gills.txt


title: biol rep 33 gills Female

description:
Branchie_68
Raw_counts_Gills.txt


title: biol rep 32 gills Female

description:
Branchie_6
Raw_counts_Gills.txt


title: biol rep 36 gills Female

description:
Branchie_B2
Raw_counts_Gills.txt


title: biol rep 34 gills Male

description:
Branchie_7
Raw_counts_Gills.txt


title: biol rep 3 gills Male

description:
Branchie_204
Raw_counts_Gills.txt


title: biol rep 31 gills Female

description:
Branchie_57
Raw_counts_Gills.txt


title: biol rep 30 gills Female

description:
Branchie_55
Raw_counts_Gills.txt


title: biol rep 29 gills Female

description:
Branchie_51
Raw_counts_Gills.txt


title: biol rep 34 gills Female

description:
Branchie_75
Raw_counts_Gills.txt


title: biol rep 25 gills Female

description:
Branchie_267
Raw_counts_Gills.txt


title: biol rep 28 gills Female

description:
Branchie_35
Raw_counts_Gills.txt


title: biol rep 24 gills Female

description:
Branchie_264
Raw_counts_Gills.txt


title: biol rep 27 gills Female

description:
Branchie_34
Raw_counts_Gills.txt


title: biol rep 26 gills Female

description:
Branchie_31
Raw_counts_Gills.txt


title: biol rep 21 gills Female

description:
Branchie_259
Raw_counts_Gills.txt


title: biol rep 6 gills Male

description:
Branchie_212
Raw_counts_Gills.txt


title: biol rep 20 gills Female

description:
Branchie_257
Raw_counts_Gills.txt


title: biol rep 23 gills Female

description:
Branchie_263
Raw_counts_Gills.txt


title: biol rep 22 gills Female

description:
Branchie_261
Raw_counts_Gills.txt


title: biol rep 19 gills Female

description:
Branchie_256
Raw_counts_Gills.txt


title: biol rep 16 gills Female

description:
Branchie_250
Raw_counts_Gills.txt


title: biol rep 15 gills Female

description:
Branchie_244
Raw_counts_Gills.txt


title: biol rep 18 gills Female

description:
Branchie_255
Raw_counts_Gills.txt


title: biol rep 11 gills Female

description:
Branchie_229
Raw_counts_Gills.txt


title: biol rep 17 gills Female

description:
Branchie_251
Raw_counts_Gills.txt


title: biol rep 13 gills Female

description:
Branchie_240
Raw_counts_Gills.txt


title: biol rep 12 gills Female

description:
Branchie_233
Raw_counts_Gills.txt


title: biol rep 10 gills Female

description:
Branchie_226
Raw_counts_Gills.txt


title: biol rep 9 gills Female

description:
Branchie_216
Raw_counts_Gills.txt


title: biol rep 5 gills Female

description:
Branchie_20
Raw_counts_Gills.txt


title: biol rep 8 gills Female

description:
Branchie_21
Raw_counts_Gills.txt


title: biol rep 7 gills Female

description:
Branchie_207
Raw_counts_Gills.txt


title: biol rep 3 gills Female

description:
Branchie_16
Raw_counts_Gills.txt


title: biol rep 2 gills Female

description:
Branchie_15
Raw_counts_Gills.txt


title: biol rep 1 gills Female

description:
Branchie_13
Raw_counts_Gills.txt


title: AA

city: Seoul

first: Mi-Ock

last: Lee

address: 1 Gwanak-ro

department: College of Pharmacy

country: South Korea

institute: Seoul National University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw BCL files produced by the Illumina platform were demultiplexed into FASTQ files using Cell Ranger v7.2.0 (10x Genomics). Then, cellranger count pipeline was used to align the reads onto the mouse reference genome ‘mm10’, and to perform filtering, barcode counting, and unique molecular identifier (UMI) counting. The sequencing data quality was assessed using FastQC v0.11.7.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: dorsal skin

extract_protocol:
The dorsal skin of 25-week-old C3H/HeN mice was collected from the backs of 7-8 mice per group. The skin samples were pooled, mechanically minced, and enzymatically digested with 0.7 mg/mL collagenase D solution (Sigma-Aldrich) at 37°C for 1 hour. The digested tissue was then passed through 70 µm and 40 µm meshes. Red blood cells were lysed using ACK Lysing Buffer (Gibco), and debris was removed through density gradient-based separation using Percoll (Sigma-Aldrich) media with a 30%-37%-70% gradient. The resulting cell suspension was immediately processed for single-cell RNA sequencing.
Prepared single-cell suspensions were processed using the Chromium Next GEM Single Cell 3’ RNA library v3.1 protocol (10x Genomics) according to the manufacturer’s instructions. Briefly, cells were encapsulated into nanoliter-scale Gel Beads-in-emulsion (GEMs) containing barcoded oligonucleotides. The poly(dT) primers in the GEMs captured polyadenylated mRNA from each cell, allowing for the generation of barcoded, full-length cDNA. The cDNA was amplified to construct 3’ gene expression libraries, which were sequenced on an Illumina sequencing system (Illumina) at Macrogen.

value: dorsal skin

tag: strain

value: whole skin

tag: age

value: 25 weeks old

tag: treatment

value: Alopecia areata model


title: AA+Ab

description: 10x Genomics

value: Alopecia areata model treated with CXCL12-neutralizing antibody


title: Neg

description: 10x Genomics

value: Negative (vehicle) control


title: E15_rep_2_scMultiome_chromatin

city: Beijing

first: Yiming

last: Sun

state: Beijing

address: NO.5, Yiheyuan Road, Haidian District

department: School of Life Sciences

institute: Peking University

description: 10x Genomics scMultiome chromatin accessibility part

library_source: genomic

data_processing:
The demultiplexing, barcode processing and fragment generation were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest?). Peak calling and insertion counts were made in ArchR.
Assembly: Mmul_10
Supplementary files format and content: bed format, peak called using scMultiome data from all samples
Supplementary files format and content: Tab-seperated table format, gene counts matrix
Supplementary files format and content: Matrix market format, Tn5 insertion counts matrix
Supplementary files format and content: Tab-seperated table format, meta data for each cell

molecule: genomic DNA

source_name: prefrontal cortex

extract_protocol:
Transfer fresh frozen tissue sample to a pre-chilled 1.5 mL Eppendorf tube, add 500 μL of chilled Nuclei Lysis Buffer, and then transfer to a Douncer. Dounce the tissue with A and B pestle for complete homogenization, filter with a 40 μm strainer, and add 500 μL of chilled Nuclei Lysis Buffer. Mix gently and incubate on ice for 5 min. Centrifuge the nuclei at 500 x g for 5 min at 4°C. Remove supernatant without disturbing the pellet. Isolate pure nuclei using gradient centrifugation, and quantify the nuclei using Trypan blue staining on a hemocytometer.
For single-nucleus multi-omics library construction, the isolated nuclei were resuspended with 500 μL diltuted nuclei buffer (1 x nuclei buffer (10X Genomics, PN-2000207), 1mM DTT, 1U/μL RNase inhibitor, nuclease-free Water). The nuclei were counted using Trypan blue staining on a hemocytometer, and 6,000 nuclei were loaded per lane. All libraries were constructed based on the user guide of Chromium Next GEM Single Cell Multiome ATAC + GEX kit (10X Genomics). Libraries were sequenced on the Illumina NovaSeq 6000 platform.

value: prefrontal cortex

value: WT


title: E14_rep_2_scMultiome_chromatin


title: E14_rep_1_scMultiome_chromatin


title: E15_rep_3_scMultiome_chromatin


title: E16_rep_1_scMultiome_chromatin


title: E15_rep_1_scMultiome_chromatin


title: biol rep 14 gills Female

description:
Branchie_243
Raw_counts_Gills.txt


title: E16_rep_1_scMultiome_RNA

description: 10x Genomics scMultiome transcriptom part

molecule: nuclear RNA


title: E15_rep_3_scMultiome_RNA


title: E15_rep_2_scMultiome_RNA


title: biol rep 6 gills Female

description:
Branchie_203
Raw_counts_Gills.txt


title: E15_rep_1_scMultiome_RNA


title: E14_rep_2_scMultiome_RNA


title: 16 weeks_maternal high-fat diet_ZT21_replicate 2

city: St Lucia

first: Benjamin

middle: D

last: Weger

state: QLD

address: 306 Carmody Road

department: IMB

country: Australia

institute: University of Queensland

description:
gene_count_liver_16weeks.txt
OH21_2

data_processing: Reads were trimmed from adapters and mapped with Hisat2 (v2.0.5) to align the reads to the mouse reference genome (GRCm38/mm10). Uniquely mapped reads per genes were counted using FeatureCounts (v1.5.0-p3) based on the annotation from Ensembl release 94.

source_name: liver

growth_protocol: Mice at 4 weeks old were maintained in a specific pathogen-free (SPF) environment at a controlled temperature of 22±2℃ and subjected to a 12:12 light/dark cycle (lights on at 06:00 h, ZT0 = 06:00).

extract_protocol: Total RNA was extracted from liver tissues using the E.Z.N.A. Total RNA Kit II (OMEGA, R6934). Briefly, 500 µL of RNA-Solv Reagent was added to approximately 50 mg of frozen liver tissue. We then added 3-4 mm zirconia beads. This mixture was subjected to homogenization in two 30-second cycles, interspersed with a 10-second interval, at 4°C using a KZ-III-F homogenizer (Servicebio). Following this, 200 µL of chloroform was added, and the solution was vigorously shaken for 20 seconds. The mixture was then allowed to settle for 3 minutes at room temperature before being centrifuged at 12,000 x g for 15 minutes at 4°C. The resulting RNA supernatant was collected and subsequently purified using the columns provided with the kit, in accordance with the manufacturer’s protocol. RNA integrity of all samples was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies). Only RNA with a RIN above 8.0 were further processed. mRNA was purified from total RNA (3 μg of total RNA) using poly-T oligo-attached magnetic beads. Sequencing libraries were obtained using the NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer’s instructions.

treatment_protocol: Female C57BL/6 mice at 4 weeks old were maintained in a specific pathogen-free (SPF) environment at a controlled temperature of 22±2℃ and subjected to a 12:12 light/dark cycle (lights on at 06:00 h, ZT0 = 06:00). After acclimation for 7 days, 5-week-old mice with similar body weight were randomly assigned into two groups: the control group (Ctr), which were fed a standard chow diet (AIN-93G) (15.8% of the calories as fat), and the HFD group (HF), which were fed an HFD (D12492) (60% of the calories as fat). After 5 weeks of intervention, female mice were mated with normal control 9-week-old C57BL/6 male mice by housing 2 females and 1 male per cage for 5 days. The pregnant mice continued their respective diets throughout the pregnancy. To avoid nutritional bias between litters, the litter sizes were homogenized to 6 pups for each dam within the first 3 post-natal days. Male offspring were weaned at postnatal 21 days on a standard chow diet until 16 weeks of age.

value: liver

value: 16 week

value: maternal high-fat diet

tag: replicate

value: replicate 2


title: 16 weeks_maternal high-fat diet_ZT21_replicate 3

description:
gene_count_liver_16weeks.txt
OH21_3

value: replicate 3


title: 16 weeks_maternal high-fat diet_ZT17_replicate 2

description:
gene_count_liver_16weeks.txt
OH17_2


title: 16 weeks_maternal high-fat diet_ZT13_replicate 3

description:
gene_count_liver_16weeks.txt
OH13_3


title: 16 weeks_maternal high-fat diet_ZT21_replicate 1

description:
gene_count_liver_16weeks.txt
OH21_1

value: replicate 1


title: 16 weeks_maternal high-fat diet_ZT13_replicate 2

description:
gene_count_liver_16weeks.txt
OH13_2


title: E14_rep_1_scMultiome_RNA


title: 16 weeks_maternal high-fat diet_ZT17_replicate 3

description:
gene_count_liver_16weeks.txt
OH17_3


title: biol rep 4 gills Female

description:
Branchie_17
Raw_counts_Gills.txt

value: female


title: 16 weeks_maternal high-fat diet_ZT17_replicate 1

description:
gene_count_liver_16weeks.txt
OH17_1


title: 16 weeks_maternal high-fat diet_ZT9_replicate 2

description:
gene_count_liver_16weeks.txt
OH9_2


title: 16 weeks_maternal high-fat diet_ZT9_replicate 1

description:
gene_count_liver_16weeks.txt
OH9_1


title: 16 weeks_maternal high-fat diet_ZT9_replicate 3

description:
gene_count_liver_16weeks.txt
OH9_3


title: 16 weeks_maternal high-fat diet_ZT13_replicate 1

description:
gene_count_liver_16weeks.txt
OH13_1


title: 16 weeks_maternal high-fat diet_ZT5_replicate 1

description:
gene_count_liver_16weeks.txt
OH5_1


title: 16 weeks_maternal high-fat diet_ZT5_replicate 2

description:
gene_count_liver_16weeks.txt
OH5_2


title: 16 weeks_maternal high-fat diet_ZT5_replicate 3

description:
gene_count_liver_16weeks.txt
OH5_3


title: 16 weeks_maternal high-fat diet_ZT1_replicate 3

description:
gene_count_liver_16weeks.txt
OH1_3


title: 16 weeks_maternal high-fat diet_ZT1_replicate 1

description:
gene_count_liver_16weeks.txt
OH1_1


title: 16 weeks_maternal high-fat diet_ZT1_replicate 2

description:
gene_count_liver_16weeks.txt
OH1_2


title: 16 weeks_maternal control diet_ZT21_replicate 2

description:
gene_count_liver_16weeks.txt
OC21_2

value: maternal control diet


title: 16 weeks_maternal control diet_ZT21_replicate 3

description:
gene_count_liver_16weeks.txt
OC21_3


title: 16 weeks_maternal control diet_ZT21_replicate 1

description:
gene_count_liver_16weeks.txt
OC21_1


title: 16 weeks_maternal control diet_ZT17_replicate 2

description:
gene_count_liver_16weeks.txt
OC17_2


title: 16 weeks_maternal control diet_ZT17_replicate 3

description:
gene_count_liver_16weeks.txt
OC17_3


title: 16 weeks_maternal control diet_ZT13_replicate 3

description:
gene_count_liver_16weeks.txt
OC13_3


title: 16 weeks_maternal control diet_ZT13_replicate 2

description:
gene_count_liver_16weeks.txt
OC13_2


title: 16 weeks_maternal control diet_ZT17_replicate 1

description:
gene_count_liver_16weeks.txt
OC17_1


title: 16 weeks_maternal control diet_ZT13_replicate 1

description:
gene_count_liver_16weeks.txt
OC13_1


title: 16 weeks_maternal control diet_ZT9_replicate 3

description:
gene_count_liver_16weeks.txt
OC9_3


title: 16 weeks_maternal control diet_ZT9_replicate 1

description:
gene_count_liver_16weeks.txt
OC9_1


title: 16 weeks_maternal control diet_ZT5_replicate 3

description:
gene_count_liver_16weeks.txt
OC5_3


title: 16 weeks_maternal control diet_ZT9_replicate 2

description:
gene_count_liver_16weeks.txt
OC9_2


title: 16 weeks_maternal control diet_ZT5_replicate 1

description:
gene_count_liver_16weeks.txt
OC5_1


title: 16 weeks_maternal control diet_ZT5_replicate 2

description:
gene_count_liver_16weeks.txt
OC5_2


title: 16 weeks_maternal control diet_ZT1_replicate 2

description:
gene_count_liver_16weeks.txt
OC1_2


title: 16 weeks_maternal control diet_ZT1_replicate 1

description:
gene_count_liver_16weeks.txt
OC1_1


title: 4 weeks_maternal high-fat diet_ZT21_replicate 2

description:
gene_count_liver_4weeks.txt
H62

value: 4 week


title: 4 weeks_maternal high-fat diet_ZT21_replicate 1

description:
gene_count_liver_4weeks.txt
H61


title: 4 weeks_maternal high-fat diet_ZT17_replicate 3

description:
gene_count_liver_4weeks.txt
H53


title: 4 weeks_maternal high-fat diet_ZT17_replicate 1

description:
gene_count_liver_4weeks.txt
H51


title: 4 weeks_maternal high-fat diet_ZT13_replicate 3

description:
gene_count_liver_4weeks.txt
H43


title: 4 weeks_maternal high-fat diet_ZT9_replicate 3

description:
gene_count_liver_4weeks.txt
H33


title: 4 weeks_maternal high-fat diet_ZT13_replicate 2

description:
gene_count_liver_4weeks.txt
H42


title: 4 weeks_maternal high-fat diet_ZT13_replicate 1

description:
gene_count_liver_4weeks.txt
H41


title: 4 weeks_maternal high-fat diet_ZT9_replicate 1

description:
gene_count_liver_4weeks.txt
H31


title: 4 weeks_maternal high-fat diet_ZT9_replicate 2

description:
gene_count_liver_4weeks.txt
H32


title: 4 weeks_maternal high-fat diet_ZT5_replicate 3

description:
gene_count_liver_4weeks.txt
H23


title: 4 weeks_maternal high-fat diet_ZT5_replicate 2

description:
gene_count_liver_4weeks.txt
H22


title: 4 weeks_maternal high-fat diet_ZT1_replicate 2

description:
gene_count_liver_4weeks.txt
H12


title: 16 weeks_maternal control diet_ZT1_replicate 3

description:
gene_count_liver_16weeks.txt
OC1_3


title: 4 weeks_maternal high-fat diet_ZT1_replicate 1

description:
gene_count_liver_4weeks.txt
H11


title: 4 weeks_maternal high-fat diet_ZT1_replicate 3

description:
gene_count_liver_4weeks.txt
H13


title: 4 weeks_maternal control diet_ZT21_replicate 2

description:
gene_count_liver_4weeks.txt
C62


title: 4 weeks_maternal control diet_ZT17_replicate 3

description:
gene_count_liver_4weeks.txt
C53


title: 4 weeks_maternal control diet_ZT21_replicate 3

description:
gene_count_liver_4weeks.txt
C63


title: 4 weeks_maternal high-fat diet_ZT5_replicate 1

description:
gene_count_liver_4weeks.txt
H21


title: 4 weeks_maternal control diet_ZT13_replicate 3

description:
gene_count_liver_4weeks.txt
C43


title: 4 weeks_maternal high-fat diet_ZT21_replicate 3

description:
gene_count_liver_4weeks.txt
H63


title: 4 weeks_maternal control diet_ZT13_replicate 2

description:
gene_count_liver_4weeks.txt
C42


title: 4 weeks_maternal control diet_ZT9_replicate 2

description:
gene_count_liver_4weeks.txt
C32


title: 4 weeks_maternal control diet_ZT17_replicate 1

description:
gene_count_liver_4weeks.txt
C51


title: 4 weeks_maternal control diet_ZT21_replicate 1

description:
gene_count_liver_4weeks.txt
C61


title: 4 weeks_maternal control diet_ZT9_replicate 1

description:
gene_count_liver_4weeks.txt
C31


title: 4 weeks_maternal control diet_ZT17_replicate 2

description:
gene_count_liver_4weeks.txt
C52


title: 4 weeks_maternal control diet_ZT5_replicate 3

description:
gene_count_liver_4weeks.txt
C23


title: 4 weeks_maternal control diet_ZT5_replicate 2

description:
gene_count_liver_4weeks.txt
C22


title: 4 weeks_maternal high-fat diet_ZT17_replicate 2

description:
gene_count_liver_4weeks.txt
H52


title: 4 weeks_maternal control diet_ZT1_replicate 2

description:
gene_count_liver_4weeks.txt
C12


title: 4 weeks_maternal control diet_ZT5_replicate 1

description:
gene_count_liver_4weeks.txt
C21


title: E92_rep_2_snRNA-seq

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest?)
Assembly: Mmul_10
Supplementary files format and content: Tab-seperated table format, gene counts matrix
Supplementary files format and content: Tab-seperated table format, meta data for each cell

organism: Macaca mulatta


title: E84_rep_2_snRNA-seq

description: 10x Genomics


title: E92_rep_1_snRNA-seq

description: 10x Genomics


title: E84_rep_1_snRNA-seq

description: 10x Genomics


title: E90_rep_2_snRNA-seq

description: 10x Genomics


title: E80_rep_1_snRNA-seq

description: 10x Genomics


title: Populus qamdoensis, White, replicate 2

city: Kunming

first: Xiaolin

last: Zhang

address: qingyun street

institute: southwest forestry university

data_processing:
Populus yunnanensis [242124]
Based on sequencing-by-synthesis (Sequencing By Synthesis, SBS) technology, cDNA libraries were sequenced on Illumina high-throughput platform.
Populus yunnanensis Reference genome was pre-defined for the mapping RNA-seq reads with HISAT2，StringTie was applied to assemble the mapped reads.（--merge -F 0.1 -T 0.1）
Discovery of novel transcripts and genes was achieved by StringTie on base of Populus yunnanensis reference genome.  Excluding short transcripts(coding peptides with less than 50 amino acids) or those containing only one exons, 1,917 novel genes were discovered in this project.
Assembly: PRJNA886471
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Populus qamdoensis

source_name: leaf

extract_protocol:
Cultivation of two poplars under different light qualities
The mRNA was collected from the leaves of cuttings under different light quality cultures, respectively.

value: leaf

value: growth stage

value: cutting

value: white quality


title: Populus qamdoensis, White, replicate 3


title: Populus qamdoensis, White, replicate 1


title: E90_rep_2_scMultiome_chromatin


title: E80_rep_2_scMultiome_chromatin


title: Populus qamdoensis, Green, replicate 1

value: green quality


title: Populus qamdoensis, Green, replicate 3


title: E90_rep_1_scMultiome_chromatin


title: E80_rep_1_scMultiome_chromatin


title: 4 weeks_maternal control diet_ZT1_replicate 3

description:
gene_count_liver_4weeks.txt
C13


title: Populus qamdoensis, Green, replicate 2


title: Populus qamdoensis, Blue, replicate 3

value: blue quality


title: E90_rep_2_scMultiome_RNA

value: prefrontal cortex


title: E80_rep_2_scMultiome_RNA

value: WT


title: INPUT_CTRL

city: Chennai

first: Samson

last: Mani

state: Tamilnadu

address: 38, Sardar Patel Road

department: Molecular Oncology

country: India

institute: Cancer Institute (WIA)

data_processing:
Raw reads obtained from the sequencing were quality checked with FASTQC and the reads of low quality lesser than 30 phred score were discarded. Adapter content were trimmed with cutadapt.
The reads were aligned against the hg19 human reference genome using the BWA-mem algorithm and obtained more than 95% effective alignment.
The bam files obtained were sorted using samtools sort and then converted it into bigwig files with 20bp bin size for visualization.
The aligned reads were processed with MACS2 peak caller with p-value of 0.05.
Assembly: hg19
Supplementary files format and content: narrow peak file

growth_protocol: MCF-7 cells were cultured in Dulbecco’s modified Eagle medium (DMEM) with high glucose and sodium bicarbonate contents (HiMedia, India), 10% heat-inactivated fetal bovine serum (FBS) (Gibco, USA), and 1X antibiotic solution (HiMedia, India).  Cells maintained in the humidified incubators at 37° C supplemented with 5% CO2. Cells were washed with 1X Phosphate buffered saline (HiMedia, India) under confluency and detached using 0.25% Trypsin-EDTA solution (HiMedia, India). The desired seeding density of the cells was followed based on the standard seeding density chart (Thermo Fischer, USA), and the cells were counted using an automated cell counter Countess II FL (Life Technologies, Thermo Fischer, USA) with 0.4% trypan blue. All the cell lines were routinely checked for mycoplasma contamination using the Lookout® Mycoplasma PCR detection kit (Cat.no: MP0035, Sigma-Aldrich, USA).

extract_protocol:
BC cells were harvested and washed with 1X PBS. Approximately 1X106 cells were used per ChIP reaction. The siRNA transfected and the control cells were collected and crosslinked with 1% v/v formaldehyde followed by 0.125M glycine treatment. The cells were washed with 1XPBS containing 1mM phenyl methyl sulfonate (PMSF) (Sigma) and 1X protease inhibitor cocktail (Sigma). The cell pellets were further processed for nuclei preparation. Chromatin shearing was performed by sonication in 15-sec pulse ON and 45-sec pulse OFF for 15 cycles to get the sheared chromatin fragments in the size range of 200-800bp. The size-selected sheared chromatin was further immunoprecipitated with H3K4me1antibody (Invitrogen, Thermo Scientific, USA) and H3K27ac antibody (Invitrogen, Thermo Scientific, USA). The magnetic protein A beads were used to collect the chromatin immunoprecipitated complex. Other clean-up and purification steps were performed per the manufacturer’s instruction (Zymo Spin ChIP kit, Zymo Research, USA).
The ChIP input DNA was size verified with tape station profiling followed by low-input ChIP library preparation.
ChIP-sequencing 150*2 PE chemistry

treatment_protocol: TET1, and TET2 genes targeting siRNA were purchased from Santa Cruz Technologies, USA. Breast cancer cells were cultured for 16-18h at 75-80% confluency and incubated in serum-free DMEM for 3 h before transfection. The optimal concentration of siRNA was added to the 1.5 mL tube along with the required volume of serum-free medium and INTERFERin (Polyplus Transfection, SA, France). The siRNA-INTERFERin complex was incubated at room temperature (RT) for 20 min. The cells were replaced with a complete DMEM medium and the siRNA-INTERFERin complex was added. The cells were incubated for 24 h, and 48 h after transfection required for the experimental protocol. Scrambled siRNA was used as control siRNA in all experiments

value: Breast cancer

value: Control cells


title: E90_rep_1_scMultiome_RNA


title: E80_rep_1_scMultiome_RNA


title: Input_mES_HG_ChIP-seq

city: Bunkyo-ku

first: Daisuke

last: Nara

state: Tokyo

address: 1-1-1 Yayoi

department: Dep. of Animal resource sciences

country: Japan

institute: The uniersity of Tokyo

data_processing:
ChIP-seq reads were mapped to mm10 assembly of mouse genome or hg38 assembly of human genome using Bowtie2 (v2.3.4.2).
The peaks of all samples were detected using MACS (v1.0.1). The following parameter was used: input-seq aligned reads as a control file, 25 bp tag size, 300 bp bandwidth, and 10e-03 (for mouse) or 10e-05 (for human) p-value cutoff for peak detection.
The H4T71Gc coverage track normalized by input-seq in mESCs was generated by BamCompare (v3.1.2.0.0) using mapping data of H4T71Gc and input.
Genome_build: mm10 (Mus musculus), hg38 (Homo sapiens)
Supplementary_files_format_and_content: Bam files were generated by Bowtie2 (v2.3.4.2) analysis using each fastq data. Bed files and Bigwig files were generated by MACS (v1.0.1) and BamCompare (v3.1.2.0.0) analysis using each bam data of H4T71Gc ChIP-seq and Input-seq, respectively.

growth_protocol: mESCs line J1, derived from 129S4/SvJae mouse embryos, were maintained the stemness on the gelatin-coated dish in D-MEM (Wako) supplemented 20% fetal bovine serum, 2 mM L-glutamine (Wako), 1 mM Na-pyruvate (Wako), Non-essential amino acid (Wako), 0.1 mM 2-Mercaptoethanol (Wako), Penicillin-Streptomycin (Wako) and 1,500 U/mL LIF (ESGRO; Millipore). Glucose concentration was adjusted using 2.5 M glucose solution (Sigma-Aldrich) to 1 or 25 mM. hiPSCs line 201B7  were also maintained the stemness on feeder layers of mitomycin C-treated STO/Neo resistant/LIF (SNL) feeder cells in ReproStem medium (ReproCELL) supplemented with 5 ng/mL bFGF (Wako). The pellets of fixed hESCs line H9 maintained the stemness was provided by Dr. Suzuki (University of Wisconsin, Madison).

extract_protocol:
ChIP-enriched DNA was obtaind by using ChIP-IT Express Enzymatic (Active Motif, 53009) and H4T71Gc specific antibody (20H3) according to the manufacturer’s instructions.  For repairing the ends of DNA fragments isolated by ChIP (50 ng each), adding a single “A” base to the 3’-end of them, and ligating TruSeq DNA adapters (illumina) to them,KAPA hyper Prep kit (KAPA Biosystems) was used according to the manufacturer’s instructions. Ligation products were purified on KAPA pure beads (KAPA Biosystems) to remove unligated adapters and subjected to eight cycles of PCR amplification. Completed libraries were quantified using Library Quantification Kit (Takara bio).
In this study, all of data processing for ChIP-seq was performed by using Galaxy platform (https://usegalaxy.org/).   ChIP-seq reads were mapped to mm10 assembly of mouse genome or hg38 assembly of human genome using Bowtie2.  The peaks of all samples were detected using MACS. The following parameter was used: input-seq aligned reads as a control file, 25 bp tag size, 300 bp bandwidth, and 10e-03 (for mouse) or 10e-05 (for human) p-value cutoff for peak detection.

treatment_protocol: mESCs were cultured in ES medium containing 25 mM (normal condition, HG-mESCs) or 1 mM glucose (LG-mESCs) for 96 hrs.

value: 25 mM glucose (normal condition)

value: Undifferentiated embryonic stem cells

tag: chip-antibody

value: 20H3 (mouse monoclonal antibody, prepared in-house)


title: Populus qamdoensis, Blue, replicate 1


title: H4T71Gc_mES_LG_ChIP-seq

value: 1 mM glucose


title: INPUT_TET2

value: Tet2 knockdown


title: 4 weeks_maternal control diet_ZT1_replicate 1

description:
gene_count_liver_4weeks.txt
C11

value: liver

value: maternal control diet

value: replicate 1


title: INPUT_TET1

value: Tet1 knockdown


title: H4T71Gc_mES_HG_ChIP-seq


title: COPD4

first: xiqian

last: xing

state: Yunnan

address: No. 176, Qingnian Road

department: Department of Respiratory Medicine

institute: The Affiliated Hospital of Yunnan University, The Second People's Hospital of Yunnan Province

data_processing:
Illumina HiSeq sequencing platform was used
After extracting total RNA from peripheral blood mononuclear cells (PBMCs) involed five stable COPD patients and five healthy controls using TRIzol (Invitrogen, CA, USA), the rRNA in the total RNA was removed by a ribosomal RNA removal kit, and the RNA was interrupted to 200-300 bp fragments by ion interruption.
Subsequently, using RNA as a template, the first and second strands of cDNA. After the library is constructed, PCR amplification is used to enrich the library fragments, and the library size is 300-400bp.
Then, the Agilent 2100 Bioanalyzer was used for quality inspection of the library, including total concentration and effective concentration.
After the quality inspection results were passed, next-generation sequencing technology (Next-Generation Sequencing, NGS) was used to perform paired-end sequencing of these libraries based on the Illumina HiSeq sequencing platform
Assembly: Ensembl, Homo_sapiens.GRCh38.dna.primary_assembly.fa
Supplementary files format and content: After data filtering (Cutadapt) and quality evaluation (FastQC), the RNA-Seq data was compared to the reference genome (Tophat2), and the data source for the reference genome is the Ensembl database (http://www.ensembl.org/, Homo_sapiens.GRCh38.dna.primary_assembly.fa).
Supplementary files format and content: Then, we use HTSeq to compare the Read Count value of each gene as the original expression of the gene, and use FPKM, CPM, TPM to normalize the expression. Matrix table with raw gene counts for every gene and every sample

source_name: Peripheral blood

extract_protocol:
PBMCs were isolated, and total RNA was harvested using Trizol reagent. The long  RNAs using Illumina, Poly-A enrichment, Illumina TrueSeq paired-end library construction, and short RNAs using Illumina, Poly-A enrichment, Illumina TrueSeq single-end library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Peripheral blood

value: PBMCs

value: COPD


title: E92_rep_1_scATAC-seq

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing and fragment generation were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest?). Peak calling and insertion counts were made in ArchR.
Assembly: Mmul_10
Supplementary files format and content: bed format, peak called using scATAC-seq data from all samples
Supplementary files format and content: Matrix market format, Tn5 insertion counts matrix
Supplementary files format and content: Tab-seperated table format, meta data for each cell


title: K4_CTRL

tag: chip antibody


title: COPD2


title: Populus qamdoensis, Blue, replicate 2

value: leaf

value: growth stage

value: cutting

value: blue quality


title: COPD1


title: K4_TET2

value: Breast cancer


title: E84_rep_1_scATAC-seq

description: 10x Genomics

value: prefrontal cortex

value: WT


title: COPD3


title: Input_mES_LG_ChIP-seq

value: Undifferentiated embryonic stem cells

value: 20H3 (mouse monoclonal antibody, prepared in-house)


title: Con4

value: healthy control


title: K4_TET1


title: Con3


title: Con1


title: E90_rep_2_scATAC-seq

description: 10x Genomics


title: Input_hiPS_ChIP-seq

value: normal condition

value: Undifferentiated induced-pluripotent stem cells


title: K27_CTRL

value: Control cells


title: COPD5


title: H4T71Gc_hiPS_ChIP-seq


title: E84_rep_2_scATAC-seq

description: 10x Genomics


title: E80_rep_1_scATAC-seq

description: 10x Genomics


title: E92_rep_2_scATAC-seq

description: 10x Genomics


title: H4T71Gc_hES_ChIP-seq


title: Input_hES_ChIP-seq


title: Populus schneideri, White, replicate 3

organism: Populus schneideri

value: white quality


title: Ythdf3-/- -3

city: Tianjin

first: Jianwei

last: Wang

address: 10 Yuexin Street, Binhai New Area

institute: HAIHE LABORATORY OF CELL ECOSYSTEM

data_processing:
The trimmed RNA sequencing reads were mapped to the mouse reference mm10 from UCSC database through hisat2 (v2.2.1).
The reads were quantified by HTSeq (v0.12.4).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table include raw gene counts for every gene and each sample.

source_name: hematopoietic stem cells

growth_protocol: hematopoietic stem cells were sorted from bone marrow of Ythdf3-/- and WT mice

extract_protocol:
Lysates were clarified from FACS-sorted  hematopoietic stem cells
First, 30 HSCs ( Lineage- Sca-1+ c-kit+ CD34- CD150+) from Ythdf3-/- and WT mice were sorted into lysis buffer directly. The transcriptome libraries were prepared using Smart-seq2 method. Then, Agilent Bioanalyzer 2100 system (Agilent Technologies) was used to assess the insertion size, and HiSeq PE Cluster Kit v4-cBot-HS (Illumina) was used to perform the clustering of the index-coded samples according the manufacturer’s instructions. Finally, the libraries were sequenced using an Illumina Hiseq platform with 150-bp paired-end.

treatment_protocol: Ythdf3-/- and WT mice

value: mouse-derived hematopoietic stem cells


title: Ythdf3-/- -2


title: Populus schneideri, White, replicate 1


title: Con5

value: Peripheral blood

value: PBMCs


title: MKN-45 cells, Six2_2

city: Nanjing

first: Lufeng

last: Zheng

state: Jiangsu

address: Tongjia Xiang 24

department: School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention

institute: China Pharmaceutical University

description: MKN-45 cells with SIX2 overexpression

data_processing:
Illumina casav2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell
Assembly: mm9
Supplementary files format and content: Excel files include readcount values for each sample

growth_protocol: Cells were cultured in DMEM medium (Gibco, Grand Island, NY, USA) at 37 °C under a humidified atmosphere with 5% CO2, and supplemented with 10% FBS (Gibco), 80 U/ml penicillin, and 0.08 mg/ml streptomycin.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MKN-45 cells were infected with Six2 overexpression lentivirus and the control lenvirus. Cells with stable-infectin were screened using puromycin, and subjected to  deep sequencing, in triplicate, using  Illumina NovaSeq 6000.

value: gastric cancer cell

value: SIX2 overexpression


title: Populus schneideri, Green, replicate 3

value: leaf

value: growth stage

value: cutting

value: green quality


title: Populus schneideri, White, replicate 2


title: K27_TET2

value: Breast cancer

value: Tet2 knockdown


title: K27_TET1

value: Tet1 knockdown


title: Ythdf3-/- -1


title: Populus schneideri, Green, replicate 2


title: Populus schneideri, Blue, replicate 3

value: blue quality


title: WT-2

value: WT


title: Populus schneideri, Green, replicate 1


title: MKN-45 cells, NC_1

description: MKN-45 cells with NC expression

value: control


title: MKN-45 cells, Six2_1

description: MKN-45 cells with SIX2 overexpression


title: MKN-45 cells, NC_2

description: MKN-45 cells with NC expression


title: Populus schneideri, Blue, replicate 2


title: E90_rep_1_scATAC-seq

description: 10x Genomics

value: prefrontal cortex


title: WT-1


title: cKO_3

status: Public on Jun 08 2024

city: hangzhou

first: wang

last: pengfei

address: yuhangtang road 866

institute: zhejiang university

description: Hspa9 cKO DN3 thymocytes

data_processing:
Cutadapt (V1.9.1)
Assembly: mm10
Supplementary files format and content: txt file includes raw counts for each sample

source_name: DN3 thymocytes

extract_protocol:
The total RNA of each sample was extracted using an RNA extraction kit (ESscience) according to the manufacturer’s instructions.One microgram of total RNA was used for the subsequent library preparation
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol. The poly(A) mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module or rRNA removal Kit. The mRNA fragmentation and priming was performed using First Strand Synthesis Reaction Buffer and Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double- stranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dA- tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor- ligated DNA was then performed using beads, and fragments of ~420 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 13 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic，Taiwan， China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

value: DN3 thymocytes

value: Hspa9 cKO

value: no treatment


title: cKO_1

description: Hspa9 cKO DN3 thymocytes


title: WT_2

description: WT DN3 thymocytes


title: Populus schneideri, Blue, replicate 1


title: WT_3

description: WT DN3 thymocytes


title: Vehicle, Spatial Transcriptomics

city: Greifswald

first: Yao

last: Xu

state: State

address: Felix-Hausdorff-Straße 3

country: Germany

institute: University Medicine Greifswald

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Assembly: mm10
Supplementary files format and content: barcodes.tsv: lust of spatial barcodes
Supplementary files format and content: genes.tsv: list of gene IDs
Supplementary files format and content: matrix.mtx: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: kidney

extract_protocol:
Fresh frozen tissue were OCT embedded, and 10 μm frozen sections were cut with cryostat
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction

value: kidney

tag: condition

value: unilateral ureteral obstruction (UUO) surgery

value: Vehicle


title: WT_1

description: WT DN3 thymocytes


title: DFO_24h, scRNAseq

city: Shanghai

first: Jun

state: --- Select One ---

address: siping Rd.1239

institute: School of Medicine, Tongji University

data_processing:
Cellranger standard processing
**Cell filter** Seurat allows to easily explore QC metrics and filter cells, we can visualize gene and molecule counts, plot their relationship, and exclude cells with a clear outlier number of genes detected as potential multiplets. Followed criteria were used to filter cells: 1.gene counts 500-Inf per cell. 2.UMI counts 3. the percentage of mitochondrial genes < 25% %(customized). 4.DoubletFinder for detecting doublets.
**Cell clustering** Cell clustering contains the following steps: 1)Normalizing the data After removing unwanted cells from the dataset, the next step is to normalize the data. By default, we employ a global-scaling normalization method “LogNormalize” that normalizes the gene expression measurements for each cell by the total expression.
PCA(Principal component analysis): To overcome the extensive technical noise in any single gene for scRNA-seq data, Seurat clusters cells based on their PCA scores, with each PC essentially representing a ‘metagene’ that combines information across a correlated gene set.
t-SNE (t-distributed Stochastic Neighbor Embedding) visualization: Seurat continues to use t-SNE as a powerful tool to visualize and explore these datasets. The tSNE aims to place cells with similar local neighborhoods in high-dimensional space together in low-dimensional space.
Assembly: Plasmodium falciparum 3D7 (assembly GCA_000002765); Plasmodium yoelii (assembly GCA_900002385)
Supplementary files format and content: cellranger; features.tsv.gz, barcodes.tsv.gz, matrix.mtx,gz

organism: Plasmodium falciparum

source_name: P. falciparum 3D7

growth_protocol: In vivo experiment, when the infection rate of P. yoelii yoelii 17XNL reached 25 % - 35 %, artemether (100 mg/kg) was fed to the mice. After different time points of treatment, blood samples were collected, respectively. In vitro iron sucrose and zinc protoporphyrin IX (ZnPPIX) assay, the P. falciparum parasites (3D7 strain) were cultured in human O+ erythrocytes at 2 % haematocrit in RPMI 1640 medium supplemented with 0.5 % (w/v) Albumax I (Gibco), 0.2 mmol/L hypoxanthine (Sigma), 25 mmol/L HEPES (Gibco), 0.2 % NaHCO3, and 20 μg/mL gentamicin, and incubated under a controlled atmosphere of 5 % CO2 and 5 % O2 at 37 °C, as previously described.

extract_protocol:
The aorta tissue was dissected into five segments and the single cell suspension was obtained by enzymatic digestion. The cell pellet was resuspended in 50 μl of 1× PBS (0.04% BSA). The overall cell viability was confirmed by trypan blue exclusion , which needed to be above 85%, single cell suspensions were counted using a haemocytometer/ Countess II Automated Cell Counter and concentration adjusted to 700-1200 cells/μl.
Single-cell suspensions were loaded to 10x Chromium to capture 5000 single cell according to the manufacturer’s instructions of 10X Genomics Chromium Single-Cell 3’ kit (V3) .The following cDNA amplification and library construction steps were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run,150bp)

treatment_protocol: (A)After 0, 3, 9 and 24 h of artemether treatment, a blood sample containing 2-4 drops was collected from mice infected with P. yoelii yoelii 17XNL-EGFP parasites and placed in a 15 ml tube containing 10 ml RPMI 1640 media. The samples were immediately transferred onto ice along with the controls for cell sorting. Cell samples from the test and control groups were sorted on a BD FACS-Aria II cell sorter (BD Biosciences) by using UV, blue and red lasers at the wavelengths of 355, 488 and 633 nm, respectively. Positive cells were collected in RPMI 1640 medium containing 5 % BSA. After sorting, the collected erythrocytes (parasites) were used for the scRNA experiment.  (B) For the examination of the impact of DHA, DHA and iron sucrose or DFO on asynchronized P. falciparum 3D7 at 3, 9 and 24 h post-treatment, erythrocytes infected by P. falciparum 3D7 with a parasitemia of 1.5%-2% were divided into four groups as follows: (1) DHA was added to 5000 µL of asynchronized P. falciparum 3D7 culture at a final concentration of 150 nmol/L; (2) DHA and iron sucrose were added to the same culture at the final concentrations of 150 nmol/L and 0.3 mmol/L, respectively; (3) DFO was added to the same culture at the final concentration of 500 µmol/L and (4) asynchronized P. falciparum 3D7 culture without any treatment as a control. Then, 500 µL of the parasite-infected erythrocytes were mixed with 2000 µL of RPMI 1640 medium and 25 µL of Hochest 33342, and sorted and analyzed by flow cytometry on a BD FACSAria II cell sorter (BD Biosciences), as previously described. After sorting, the collected erythrocytes (parasites) were used for the scRNA experiment.

value: P. falciparum 3D7

value: P. falciparum 3D7 sample 24 h after DFO action


title: Patient6

type: RNA

city: Ulsan

first: Hongtae

last: Kim

address: 50 UNIST-gil, Ulju-gun

department: Department of Biological Sciences

institute: Ulsan National Institute of Science and Technology

description: replicate 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: BeadStation Plarform/iSCAN system, standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: Biotin

source_name: PBMC

label_protocol: Biotin cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: For microarray analysis, mononuclear cells (MNC) were prepared from PBMCs using Lymphoprep™ (AXIS-SHIELD, Oslo, Norway) and total RNA was extracted from the prepared MNC using the Trizol reagent (Invitrogen, Carlsbad, USA) according to manufacturer's instruction. Two micrograms of total RNA was reverse transcribed into first-strand cDNA using Transcriptor First Strand cDNA Synthesis kit (Roche, Mannheim, Germany). QC with gel electrophoresis, spectrophotometer, Agilent Bioanalyzeror RiboGreen. Ratio of 28S to 18S = 2:1, OD 260/280 range = 1.7-2.1, OD 260/230 > 2.0

value: PBMC

value: chronic phase CML (CML-CP)


title: SH045, Spatial Transcriptomics


title: Patient3

description: replicate 3


title: Vehicle, replicate 3, scRNAseq

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CeleScope softwere v1.6.1 (www.github.com/singleron-RD/CeleScope; Singleron Biotechnologies GmbH)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Tissue was washed with 1x PBS (phosphate-buffered saline, Gibco, cat. nr. 10010-23) and dissociated with ophthalmic scissors to pieces of 1-2 mm. The pieces were digested in 2 ml sCellLive™ Tissue Dissociation Solution (Singleron Biotechnologies, cat. nr. 1190062) at 37°C for 15 minutes in a 15-ml centrifuge tube (Sarstedt, cat. nr. 62.5544.003) with continuous agitation on a thermal shaker. The state of dissociation was checked at regular intervals under a light microscope. Following digestion, the suspension was filtered using a 40-µm sterile strainer (Greiner, cat nr. 542040). The cells were centrifuged at 350xg for 5 minutes at 4°C and the cell pellets were resuspended in 1 ml PBS. Cells were stained with a 0.4% w/v solution of Trypan Blue (Gibco, cat nr. 15250-061) and the cell number and viability were calculated in a hemacytometer under a light microscope.
The single cell RNA-seq libraries were constructed using (GEXSCOPE™ Single Cell RNAseq Library Kit, Singleron Biotechnologies, cat nr. 4161031) according to manufacturer´s instructions. Briefly, for each library, the concentration of the single-cell suspension was adjusted to 3x105 cells/ml with PBS and the suspension was loaded onto an SD microfluidic chip to capture 6000 cells. Paramagnetic beads conjugated to oligodT probes that carry a unique molecular identifier (UMI) and a barcode unique to each bead (from the same kit) were loaded, after which the cells were lysed. The beads bound to polyadenylated mRNA were extracted from the chip and reverse transcribed into cDNA at 42°C for 1.5 hours, and the cDNA amplified by PCR. The cDNA was then fragmented and ligated to indexed Illumina adapters. The fragment size distribution of the final amplified library was obtained on an Agilent Fragment Analyzer.


title: DHA_Fe_24h, scRNAseq

value: P. falciparum 3D7 sample 24 h after DHA and iron sucrose action


title: Con2

value: Peripheral blood

value: PBMCs

value: healthy control


title: Patient4

description: replicate 4


title: Vehicle, replicate 2, scRNAseq


title: Patient1

description: replicate 1


title: DHA_24h, scRNAseq

value: P. falciparum 3D7 sample 24 h after DHA action


title: Healthy3

description: replicate 3

value: healthy


title: cKO_2

description: Hspa9 cKO DN3 thymocytes


title: Patient2

description: replicate 2


title: Patient5

description: replicate 5


title: DHA_Fe_9h, scRNAseq

value: P. falciparum 3D7 sample 9 h after DHA and iron sucrose action


title: DFO_9h, scRNAseq

value: P. falciparum 3D7 sample 9 h after DFO action


title: Healthy1

description: replicate 1


title: Healthy6

description: replicate 6


title: Healthy2

description: replicate 2


title: Vehicle, replicate 1, scRNAseq


title: SH045, replicate 3, scRNAseq


title: Healthy5

description: replicate 5


title: SH045, replicate 1, scRNAseq


title: DHA_3h, scRNAseq

value: P. falciparum 3D7 sample 3 h after DHA action


title: SH045, replicate 2, scRNAseq


title: CH_no_drug_3, scRNAseq

value: P. falciparum 3D7 sample (control group)


title: DFO_3h, scRNAseq

value: P. falciparum 3D7 sample 3 h after DFO action


title: DHA_Fe_3h, scRNAseq

value: P. falciparum 3D7 sample 3 h after DHA and iron sucrose action


title: DHA_9h, scRNAseq

value: P. falciparum 3D7 sample 9 h after DHA action


title: Healthy4

description: replicate 4


title: HUVEC, FA treat, rep2

city: Guangzhou

first: Shanshui

last: Zeng

address: Bsogao Road

institute: Southern medical university

data_processing:
To get high quality clean reads, reads were further filtered by fastp (version 0.18.0). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides(N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome (Ensembl_release104) using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: Ensembl_release104
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: Primary HUVEC cells

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according  to the manufacturer’s protocol
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT)  beads.Then the enriched  mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB  #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The  ligation reaction was purified with the AMPure XP Beads(1.0X).Ligated fragments were  subjected to size selection by agarose gel electrophoresis and polymerase chain reaction  (PCR) amplified.

value: Primary HUVEC cells

value: wild type

value: FA treat


title: HUVEC, PBS treat, rep3

value: PBS treat


title: control left ventricle 4

first: Mingxuan

last: Zhou

state: China

address: No. 2 Nanwei Road, Tianqiao Street

institute: Institute of Materia Medica, Chinese Academy of Medical Sciences

data_processing:
Fastp software was used to process raw reads in fastq format. Clean reads were obtained after low-quality reads were removed for subsequent data analysis. We use Bowtie2 to map clean reads to reference gene and use HISAT to reference genome. RSEM was used for gene qualification and FPKM values.
Assembly: mm35
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample

source_name: left ventricle

growth_protocol: Mice were anesthetized following experimental treatment, and then the heart was punctured and flushed with 20 ml of saline to remove blood from systemic circulation.

extract_protocol:
Total RNA was extracted from CRC cells using the RNeasy kit (Beyotime, Shanghai, China, R0027) and subjected to reverse transcription using the SuperScript II reverse transcriptase. (TaKaRa, Japan, RR047) according to the manufacturer´s instructions.
The samples were tested by Nanodrop for RNA concentration, OD260/280, OD260/230, and Agilent 2100 for RNA fragment length. Then, mRNA was enriched using Oligo (dT) magnetic beads, and the enriched mRNA was interrupted and split into two pieces. After enrichment, the mRNA was broken into fragments and synthesized into one-stranded cDNA by adding six-base random primers, and then two-stranded cDNA was synthesized by adding buffer, dNTPs, and DNA polymerase I. The synthesized double-stranded cDNA was purified, end-repaired, A-added, spliced, and screened for fragment size by using AMPure XP beads. Finally, a cDNA library was constructed by polymerase chain reaction (PCR) amplification.

treatment_protocol: Mice were infused for 7 days with saline or a “pressor dose” of Ang II (1500 ng/kg/min) by osmotic mini-pumps (Alzet MODEL 1007D; DURECT, Cupertino, CA, USA) implanted subcutaneously.

value: left ventricle

value: WT

value: Saline infusion for 7 days


title: control left ventricle 3


title: control left ventricle 11


title: ANG II-induced hypertensive left ventricle 3

value: ANG II infusion (1500 ng/kg/min) for 7 days


title: control left ventricle 10


title: HUVEC, FA treat, rep3


title: HUVEC, FA treat, rep1


title: ANG II-induced hypertensive left ventricle 2


title: control left ventricle 12


title: HUVEC, PBS treat, rep2


title: HUVEC, PBS treat, rep1


title: ANG II-induced hypertensive left ventricle 1


title: control left ventricle 9


title: BM2, WT83, 0.1%rGO, Unstimulated

city: La Jolla

first: Adam

middle: Jeffrey

last: Engler

state: CA

address: 9500 Gilman Drive, MC 0412

department: Bioengineering

country: USA

institute: UC San Diego

data_processing:
Sequencing quality was assessed using FASTQC and adapters were trimmed using Trim Galore!.
Reads were transcriptionally mapped to the human reference genome hg38 using kallisto and feature aggregation was preformed using tximport.
Assembly: GRCh38.108
Supplementary files format and content: csv file includes TPM values for each sample

source_name: brain organoid

growth_protocol:
PSCs were cultured on Matrigel-coated 6-well plates, fed every other day with mTeSR Plus (Stemcell Technologies, 100-0276), and chemically passaged using ReLeSR (Stemcell Technologies, 100-0483). The brain organoid differentiation was modified from the cortical organoid protocol described in Trujillo et al. and Fitzgerald et al.. A 24-well AggreWell 800 plate (Stemcell Technologies, 34811) was prepared by adding Anti-Adherence Rinsing Solution (Stemcell Technologies, 07010) to each well, centrifuging the plate at 1300 xg for 5 minutes, and rinsing each well with D-PBS.
On Day 1, PSCs were dissociated into single cells Accutase (Stemcell Technologies, 07920) in D-PBS at a 1:1 ratio for 10 minutes at 37 °C. The cells were then centrifuged for 3 minutes at 150 xg and the pellet was resuspended in mTeSR Plus supplemented + 10 μM SB431542 (SB; Stemgent, 04-0010-base) + 1 μM Dorsomorphin (Dorso; R&D Systems, 3093) + 5 μM ROCKi). 2.5×106cells were transferred to each well of the prepared AggreWell 800 plate, and the plate was centrifuged at 1300 xg for 5 minutes. The AggreWell plate was incubated at 37 °C overnight. On day 2, embryonic bodies were transferred from each used well of the AggreWell plate to each well of a 6-well plate in fresh mTeSR Plus + 10 μM SB + 1 μM Dorso and kept in suspension on an orbital shaker (90 rpm rotation) for the duration of the brain organoid differentiation. Media was changed daily through day 6. From days 7-11, media was changed every other day with M1 media [Neurobasal Medium (Life Technologies, 21103049) + 1% GlutaMAX (ThermoFisher Scientific, 35050061) + 1% Gem21 NeuroPlex (Gemini Bio, 400-160-010) + 1% N2 NeuroPlex (Gemini Bio, 400-163-005) + 1% NEAA (ThermoFisher Scientific, 11140050) + 1% PS (ThermoFisher Scientific, 15140122) + 10 μM SB + 1 μM Dorso] and embryoid bodies were split between new wells approximately once during this period to prevent overcrowding. From days 12-18, media was changed every day with M2 media [Neurobasal Medium + 1% GlutaMAX + 1% Gem21 NeuroPlex + 1% NEAA + 1% PS] + 20 ng/mL FGF2 (Peprotech, 100-25). From days 19-25, media was changed every other day with M2 + 20 ng/mL FGF2 + 20 ng/mL EGF (PeproTech, AF-100-15). From days 26-29, half media changes were performed with M3 media [M2 medium + 10 ng/mL BDNF (PeproTech, 450-02) + 10 ng/mL GDNF (PeproTech, 450-10) + 10 ng/mL NT-3 (PeproTech, 450-03) + 200 μM L-ascorbic acid (Sigma-Aldrich, A4403) + 1 mM dibutyryl-cAMP (Stemcell Technologies, 100-0244)] + 20 ng/mL FGF2. From days 30-35, media was changed every 3-4 days with M3 media. From days 36-42, media was changed every 3-4 days with M2.5 media [M3 medium with half the concentration of factors]. From day 43 on, brain organoids were maintained in M2 media, media changes every 3-4 days.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen, 74104). RNA quality was measured using an Agilent TapeStation 4200 and only RNA with RINe values greater than 7.0 were used for sequencing.
Illumina Stranded mRNA bulk RNA sequencing libraries were sequenced on an Illumina NovaSeq 6000 with paired end reads (PE150).

treatment_protocol:
CytoView MEA 48 plates (Axion Biosystems, M768-tMEA-48B) were first sterilized by incubating the wells with 1% Terg-a-zyme (Sigma-Aldrich, 7273287) in sterile DI water for 2 hours. Terg-a-zyme was removed from the wells and the wells rinsed with sterile DI water. The wells were sterilized a second time by incubating 70% ethanol (Sigma-Aldrich, E7023) in sterile DI water for 30 minutes. Ethanol was removed from the wells and the wells rinsed with sterile DI water. M2 media was added to the wells and incubated for at least 48 hours at 37 °C to pre-condition the surface. After pre-conditioning, wells were rinsed with sterile DI water, air-dried, and a solution 0.07% PEI (Sigma-Aldrich, P3143) in 1X borate buffer (ThermoFisher Scientific, 28341) sterilized through a 0.22 μm filter (Millipore Sigma, SCGP00525) was added to the wells and incubated at 37 °C for 1 hour. Then the wells were rinsed with sterile DI water, air-dried, and coated with 0.4 mg/mL laminin (Life Technologies, 23017015) in D-PBS by pipetting a small volume directly onto the electrodes, without allowing the solution to spread to the edges of the well. The plates were then incubated at 37 °C for 1 hour. M2 media was added to the wells, followed by 2-4 organoids between 60-90 days of differentiation and then 100 μg of sterilized, Matrigel-coated nanofibers were added to each well. Micropipette tips were used the move the organoids onto the electrodes, taking care not to scratch the wells’ surfaces. The plates were then incubated at 37 °C for 5 days to allow organoids to attach. Half media changes were performed every 4-5 days, taking care not to disturb the brain organoids as networks were forming.
MEA recordings were performed on the Meastro Pro (Axion Biosystems) approximately 2 weeks after seeding the brain organoids on MEA plates, every 4-5 days (the day after media change) for 8 weeks. 1 hour of daily light stimulation was produced using the Lumos (Axion Biosystems) with the following parameters: both blue and green lights at 100% intensity, 1-2 Hz pulse frequency 1 ms pulse rise, 10 ms pulse duration, 5 ms pulse off. Light frequency was increased from 1 to 2 Hz in 0.3 Hz intervals over the 8 weeks of light training. Control plates were never exposed to light stimulation and a single 5 minute recording was made on recording day for these plates.

value: brain organoid

value: induced pluripotent stem cell

tag: biorep

value: 0.1%rGO, Unstimulated


title: BM2, WT83, 0%rGO, Unstimulated

value: 0%rGO, Unstimulated


title: ANG II-induced hypertensive left ventricle 4


title: BM2, WT83, 0%rGO, Light-Trained

value: 0%rGO, Light-Trained


title: control left ventricle 8


title: BM2, WT83, 0.1%rGO, Light-Trained

value: 0.1%rGO, Light-Trained


title: control left ventricle 1


title: control left ventricle 2


title: ELS71P556

city: Philadelphia

first: Mathieu

last: Wimmer

state: PA

address: 1701 N 13th Street

institute: Temple University

data_processing:
none provided by the submitter
Supplementary_files_format_and_content: FPKM, TPM

organism: Rattus norvegicus

source_name: Orbitofrontal cortex brain tissue

extract_protocol:
Orbitofrontal cortex tissue was dissected and flash frozen on dry ice. RNA was extracted using trizol reagent followed by the Qiagen micro RNAeasy kit
Library preps were created using the NEBNext Ultra library prep kit for illumina

value: Long evans

value: Female

value: Control Female


title: BM2, WT83, 0.01%rGO, Unstimulated

value: 0.01%rGO, Unstimulated


title: ELS69P598

value: LBN Female


title: control left ventricle 7


title: 12P95

value: Male

value: LBN  male


title: control left ventricle 6

value: left ventricle


title: control left ventricle 5

value: WT


title: ELS70P547


title: ELS74P585


title: BM1, H9, 0%rGO, Light-Trained

value: embryonic stem cell


title: control left ventricle 4

value: Saline infusion for 7 days


title: 226

value: Control Male


title: BM1, H9, 0.1%rGO, Unstimulated

value: brain organoid


title: ELS70P546


title: control left ventricle 3


title: ELS74P584


title: BM1, H9, 0.01%rGO, Unstimulated


title: ELS74P583


title: 230


title: ELS63P524


title: ELS71P557


title: control left ventricle 2


title: control left ventricle 1


title: B39, WT83, 0.1%rGO, Unstimulated

value: induced pluripotent stem cell

value: 0.1%rGO, Unstimulated


title: ELS74P582


title: ANG II-induced hypertensive left ventricle 12

value: ANG II infusion (1500 ng/kg/min) for 7 days


title: BM2, WT83, 0.01%rGO, Light-Trained

value: 0.01%rGO, Light-Trained


title: BM1, H9, 0.01%rGO, Light-Trained


title: 1P4

value: Long evans


title: B39, WT83, 0.01%rGO, Unstimulated


title: P17

value: Female


title: BM1, H9, 0%rGO, Unstimulated

value: 0%rGO, Unstimulated


title: 2P11


title: ANG II-induced hypertensive left ventricle 11


title: ELS63P523


title: ELS69P590


title: B38, H9, 0%rGO, Unstimulated


title: B38, H9, 0.1%rGO, Unstimulated


title: ELS71P552


title: ANG II-induced hypertensive left ventricle 9


title: WT rep2

city: shanghai

first: meng

last: liu

address: 1239,SiPing Road

institute: TongJi University

data_processing:
Low-quality and adaptor sequences were trimmed using cut adapt (v1.18) with the parameters: -a AGATCGGAAGAGC -A AGATCGGAAGAGC --trim-n -m 50 -q 20,20. RNA sequencing reads were aligned using hisat2 (v2.1.0) to the Arabidopsis ThalianaTAIR10 genome. Mapped reads were subsequently assembled into transcripts using feature Counts (v1.6.1) with parameters: -p -C -B to calculate read counts. RNA-seq for atbmi1a/b/c was obtained from previously published data14, and was performed as described above. Our data and public data were normalized using DEseq2.Differentially expressed genes (DEGs) were calculated using. The threshold for DEGs is fold change >4 and p adjusted value < 0.05.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample ...

organism: Arabidopsis thaliana

source_name: WT rep2

growth_protocol: Plants were grown at 21°C in long day condition (16 h light and 8 h dark cycles) on Murashige&Skoog (MS) medium supplemented with 1.5% sucrose and 0.8% agar.

extract_protocol:
The total RNAs were extracted from 7-day-old Arabidopsis seedlings using Trizol reagent (TIANGEN)
After the RNA samples were qualified, the magnetic beads with oligo (DT) were used to enrich the eukaryotic mRNA (in the case of prokaryotes, the rRNA was removed by the kit to enrich the mRNA). After that, the fragment buffer was added to break the mRNA into short fragments. Using the mRNA as the template, random hexamers were used to synthesize a strand of cDNA. Then the buffer solution, dNTPs, DNA polymerase I and RNase H were added to synthesize the two strand cDNA. Then the double strand cDNA was purified by ampere XP beads. The purified double stranded cDNA was repaired at the end, added a tail and connected to the sequencing connector, and then ampure XP beads was used to select the fragment size. Finally, the PCR products were amplified by PCR and purified by ampure XP beads to obtain the final library. After the library was constructed, qubit 2.0 was used for preliminary quantification, and the library was diluted. Then, Agilent 2100 was used to detect the insert size of the library. After the insert met the expectation, Q-PCR method was used to accurately quantify the effective concentration of the library to ensure the quality of the library.

treatment_protocol: No treatment

tag: ecotype

value: whole seedlings

value: wild type


title: ANG II-induced hypertensive left ventricle 10


title: WT rep3

source_name: WT rep3


title: B38, H9, 0.1%rGO, Light-Trained

value: 0.1%rGO, Light-Trained


title: WT rep1

source_name: WT rep1


title: ELS69P591

value: Male

value: LBN  male


title: ANG II-induced hypertensive left ventricle 8

value: left ventricle

value: WT


title: AHR KO 3

city: Galveston

first: Cornelis

middle: Johan

last: Elferink

state: TX

address: 301 University Boulevard

department: Pharmacology and Toxicology

institute: University of Texas Medical Branch

data_processing:
Base calling was using Illumina's bcl2fastq2-v2.20 converter
A genome index was built with STAR (v2.5.4b) using the mouse mm10 genome .
Reads were aligned to the mouse reference using the STAR software version 2.6.0c with the parameters recommended for the ENCODE consortium.
Read counts per gene were produced with the --quantMode GeneCounts function of STAR. Small non-coding RNAs were not counted.
Differential gene expression was analyzed with the R (version 3.5.1) software DESeq2 (version 1.20.0)
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited table of raw read counts per gene

source_name: AHR KO_liver

extract_protocol:
Total cellular RNA was extracted using  Trizol Reagent (Life Technologies, CA) according to the manufacturer’s recommendations.
Poly-A plus RNA was enriched from  ~0.1 ug of total RNA and used to generate libraries using the NEBNext Ultra II Kit.

tag: strain background

value: adult (6 months old)

tag: genotype/variation

value: AHR KO

value: female

value: high-fat diet for 13 weeks

value: liver


title: B38, H9, 0.01%rGO, Unstimulated

value: brain organoid

value: embryonic stem cell

value: 0.01%rGO, Unstimulated


title: Wildtype2, CMT167 cell, scRNA-seq

city: Boston

first: David

middle: H

last: Sherr

state: MA

address: 72 East Concord St

department: Environmental Health

institute: Boston University

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were done using the Cell ranger software v2.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files

source_name: Lung

growth_protocol: DMEM + 10% FBS

extract_protocol:
Single cell suspensions of tumor-infiltrating leukocytes were obtained by digesting tumors in 1.25 mg/mL collagenase IV (STEMCELL Technologies, Cambridge, MA), 0.025 mg/mL hyaluronidase (Sigma-Aldrich), and 0.01 mg/mL DNAse I (Sigma- Aldrich) followed by processing with the Miltenyi GentleMACS system (Miltenyi, Bergisch Gladbach, Germany). For single cell RNA sequencing or intracellular cytokine staining digests were further cleaned by magnet bead isolation of live cells using Miltenyi’s Dead Cell Removal Kit.
Barcoding and scRNA-seq cDNA library preparation were done using the Chromium platform from 10X Genomics.

treatment_protocol: AhR was deleted from CMT167 cells by CRISPR/Cas9 gene editing

value: Lung

value: Epithelial Cells

value: Not Applicable

tag: gender

value: male


title: B33, H9, 0%rGO, Unstimulated

tag: tissue

value: 0%rGO, Unstimulated


title: ANG II-induced hypertensive left ventricle 6

city: Beijing

value: ANG II infusion (1500 ng/kg/min) for 7 days


title: AhR knockout3,CMT167 cell, scRNA-seq

description: 10x Genomics

value: AhR knockout


title: Wildtype1, CMT167 cell, scRNA-seq

description: 10x Genomics


title: AHR KO 2

tag: Sex


title: B33, H9, 0%rGO, Light-Trained

tag: cell line

value: 0%rGO, Light-Trained


title: AhR knockout2,CMT167 cell, scRNA-seq

description: 10x Genomics

tag: cell type


title: ANG II-induced hypertensive left ventricle 5

value: left ventricle

tag: genotype

value: WT


title: B33, H9, 0.1%rGO, Unstimulated

value: 0.1%rGO, Unstimulated


title: AhR knockout1,CMT167 cell, scRNA-seq

description: 10x Genomics


title: AHR Flox 3

source_name: AHR Flox_liver

value: adult (6 months old)

value: AHR Flox

value: female


title: B33, H9, 0.1%rGO, Light-Trained

value: brain organoid

value: 0.1%rGO, Light-Trained


title: AHR Flox 2

value: high-fat diet for 13 weeks

value: liver


title: AhR control2,CMT167 cell, bulkRNA-seq

data_processing:
A custom workflow was used to perform the following tasks: • Assess the quality of each sample using FastQC and RSeQC
• Align each sample to the genome with STAR
• Count proper pairs of reads aligning to mitochondrial or ribosomal RNA using SAMtools
• Count proper pairs of reads aligning uniquely to non-mitochondrial Ensembl Genes using featureCounts
This workflow produces the following output: • A matrix of Ensembl Genes (rows) and samples (columns), containing the number of proper read pairs that aligned uniquely to each locus
Assembly: mm10
Supplementary files format and content: Excel file with counts with matrix of Ensembl Genes (rows) and samples (columns)

extract_protocol:
RNA was extracted from three sets of CMT167Cas9 control, CMT167AhR-KO, reversed transcribed, and cDNA sequenced using the Illumina NextSeq 2000. Triplicate wells of each subline were harvested separately, and total RNA was extracted using the RNeasy Plus Mini Kit (QIAGEN, Hilden, Germany), according to the manufacturer’s instructions. cDNA was generated using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems, Waltham, MA) following the manufacturer’s instructions. cDNA was sequenced using the Boston University Microarray and Sequencing Core Facility. Between 18 and 28 million total read pairs (CMT167 lines) were obtained per sample. Quality metrics were similar across all samples with no technical outliers.
RNA libraries for RNA-seq were prepared folllowing manufacturer's protocols. cDNA was generated using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems, Waltham, MA) following the manufacturer’s instructions.

value: Lung

value: Epithelial Cells


title: B33, H9, 0.01%rGO, Unstimulated

value: embryonic stem cell

value: 0.01%rGO, Unstimulated


title: AhR control3,CMT167 cell, bulkRNA-seq

value: Not Applicable

value: male


title: AHR Flox 1


title: AHR KO 1

value: AHR KO


value: left ventricle

value: ANG II infusion (1500 ng/kg/min) for 7 days


title: B33, H9, 0.01%rGO, Light-Trained

value: WT

value: 0.01%rGO, Light-Trained


title: AhR control1,CMT167 cell, bulkRNA-seq


title: ANG II-induced hypertensive left ventricle 7


title: CCLF_dup3

city: Jiangsu

first: Boxiang

last: Qi

address: 18 Sudi north road, Xuzhou, Jiangsu

institute: Xuzhou Children Hospital

description: both CLP-operation and CCLF administration (200mg/kg)group, biological duplication#3

data_processing:
The obtained sequencing data fastq files were subjected to quality control: filtering to remove low-quality reads and trimming adapter sequences using fastp software (https://github.com/OpenGene/fastp) under the default parameters.
The clean raw data were quantified to generate an expression matrix by Salmon software (https://salmon.readthedocs.io/en/latest/salmon.html) using an index (made by salmon index command) based on the well-annotated Mus musculus transcriptome (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001635.27/) from NCBI.
Assembly: Genome assemblyGRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: hippocampus

extract_protocol:
High-quality total RNA from hippocampus tissues of sham, SAE, and CCLF mice were extracted using RNeasy Micro Kit (Cat: 74004, Qiagen) following the manufacturer’s instructions
For bulk sequencing libraries, the ribosomal RNAs were removed using Ribo-off rRNA Depletion Kit (Cat:#N406, Vazyme), and 200 ng obtain products were used as the input of VAHTS Universal V10 RNA-seq Library Prep Kit for Illumina (Cat: NR606, Vazyme)

value: hippocampus


title: ARNT Flox 2

source_name: ARNT Flox_liver

value: adult (6 months old)

value: ARNT Flox

value: female


title: AhR knockout3,CMT167 cell, bulkRNA-seq

value: AhR knockout


title: ARNT Flox 1

value: high-fat diet for 13 weeks

value: liver


title: AhR control3,A549 cell, bulkRNA-seq

data_processing:
A custom workflow was used to perform the following tasks: • Assess the quality of each sample using FastQC and RSeQC
• Align each sample to the genome with STAR
• Count proper pairs of reads aligning to mitochondrial or ribosomal RNA using SAMtools
• Count proper pairs of reads aligning uniquely to non-mitochondrial Ensembl Genes using featureCounts
This workflow produces the following output: • A matrix of Ensembl Genes (rows) and samples (columns), containing the number of proper read pairs that aligned uniquely to each locus
Assembly: hg38
Supplementary files format and content: Excel file with counts with matrix of Ensembl Genes (rows) and samples (columns)

extract_protocol:
RNA was extracted from three sets of A549Cas9 control, or A549AhR-KO cells, reversed transcribed, and cDNA sequenced using the Illumina NextSeq 2000. Triplicate wells of each subline were harvested separately, and total RNA was extracted using the RNeasy Plus Mini Kit (QIAGEN, Hilden, Germany), according to the manufacturer’s instructions. cDNA was generated using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems, Waltham, MA) following the manufacturer’s instructions. cDNA was sequenced using the Boston University Microarray and Sequencing Core Facility. Between 50 to 71 million total read pairs (A549 lines) were obtained per sample. were obtained per sample. Quality metrics were similar across all samples with no technical outliers.
RNA libraries for RNA-seq were prepared folllowing manufacturer's protocols. cDNA was generated using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems, Waltham, MA) following the manufacturer’s instructions.

value: Lung

value: Epithelial Cells


title: Extracellular exoxomes, non-AKI group. NO.4. 4 hours after surgery

first: Pengtao

last: Liu

address: 1678th, Dongfang Road

department: Urology

institute: Shanghai Children's Medical Center

description: exosomal microRNAs

data_processing:
Raw data were processed with Cutadapt(version 2.7) . The raw data were cleaned by removing reads containing adaptors, contaminants, and low-quality reads. Additionally, the Q30, and GC content were calculated to estimate the quality of clean reads. Next, the clean reads were aligned to the reference Database of miRBase(version22.1), piRNABank and RfamV14.1 using bowtie(version 1.2.2) . The UMI Counts of miRNA , piRNA and SmallRNA were calculated by perl5(version 26). And the expression of miRNA , piRNA and SmallRNA was normalized to CPM. CPM refers to the number of miRNA, piRNA or SmallRNA counts-per-million, descriptive measures for the expression level of a gene. Differential expression miRNA's target genes of mRNA come from miRTarBase database.
Assembly: Database of miRBase22.1, piRNABank and RfamV14.1 using bowtie-1.2.2.
Supplementary files format and content: processed data files is an excel document which contains the CPM values of 8 serum samples and it's statistical result.

source_name: Extracellular exosomal-microRNA

extract_protocol:
The exosomes were isolated and total RNA was extracted using exoRNeasy Midi Kit (Cat#77144, Qiagen).
Sequencing libraries were constructed by QIAseq miRNA Library Kit for Illumina (Cat #331505, Qiagen)

value: serum

tag: disease

value: transposition of conducting arteries

value: cardiac surgery


title: AhR knockout1,CMT167 cell, bulkRNA-seq

value: male


title: CCLF_dup2

description: both CLP-operation and CCLF administration (200mg/kg)group, biological duplication#2


title: SAE_dup3

description: Cecal ligation and puncture (CLP) operation only group, biological duplication#3


title: Extracellular exoxomes, non-AKI group. NO.3. 4 hours after surgery

description: exosomal microRNAs


title: Extracellular exoxomes, AKI group. NO.4. 4 hours after surgery

description: exosomal microRNAs

value: double outlet right ventricle


title: AhR knockout2,CMT167 cell, bulkRNA-seq


title: Extracellular exoxomes, non-AKI group. NO.2. 4 hours after surgery

description: exosomal microRNAs

value: pulmonary subvalvular stenosis


title: CCLF_dup1

description: both CLP-operation and CCLF administration (200mg/kg)group, biological duplication#1


title: Extracellular exoxomes, AKI group. NO.3. 4 hours after surgery

description: exosomal microRNAs

value: Ebstein anomaly


title: ARNT KO 3

source_name: ARNT KO_liver

tag: age

value: ARNT KO


title: AhR control1,A549 cell, bulkRNA-seq

tag: treatment

value: Not Applicable


title: Extracellular exoxomes, non-AKI group. NO.1. 4 hours after surgery

description: exosomal microRNAs


title: ANG II-induced hypertensive left ventricle 3

value: left ventricle

value: WT

value: ANG II infusion (1500 ng/kg/min) for 7 days


title: ARNT KO 1

value: adult (6 months old)

value: female


title: CTL_dup3

description: sham group, biological duplication#3

value: hippocampus

value: sham group


title: AhR knockout2,A549 cell, bulkRNA-seq

value: Lung

value: Epithelial Cells

value: AhR knockout


title: SAE_dup1

description: Cecal ligation and puncture (CLP) operation only group, biological duplication#1


title: ARNT Flox 3

value: ARNT Flox

value: high-fat diet for 13 weeks

value: liver


title: SAE_dup2

description: Cecal ligation and puncture (CLP) operation only group, biological duplication#2


title: AhR knockout1,A549 cell, bulkRNA-seq

value: male


title: twenty_four_h, scRNAseq

last: Sun

organism: Plasmodium yoelii

source_name: P. yoelii yoelii 17XNL

value: P. yoelii yoelii 17XNL

value: P. yoelii yoelii 17XNL sample 24 h after artemetner action


title: Extracellular exoxomes, AKI group. NO.1. 4 hours after surgery

description: exosomal microRNAs

value: serum

value: mitral valve insufficiency

value: cardiac surgery


title: AhR knockout3,A549 cell, bulkRNA-seq


title: nine_h, scRNAseq

value: P. yoelii yoelii 17XNL sample 9h after artemetner action


title: CTL_dup2

description: sham group, biological duplication#2


title: Extracellular exoxomes, AKI group. NO.2. 4 hours after surgery

description: exosomal microRNAs

value: double outlet right ventricle


title: ITGB4-EX3_raw

status: Public on Jun 07 2024

city: changsha

first: ruijiang

address: No.139 Renmin Road Central

institute: The Second Xiangya Hospital of Central South University

data_processing:
Total RNA qualification
mRNA enrichment
Double-strand cDNA synthesis
End repair, ploy-A & adaptor addition
Fragment selection and PCR
Library qualty assessement
illumina sequencing
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: bladder

growth_protocol: RT4 cells were cultured in Mycoy' s 5A medium supplemented with 10% fetal bovine serum (FBS) and incubated at 37 °C in 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: bladder

value: RT4 cells

value: bladder cancer cells

tag: group

value: the treat group of overexpression of ITGB6 by plasmid

value: transfection infection


title: ITGB4-EX2_raw

value: the treat group of overexpression of ITGB5 by plasmid


title: zero_h, scRNAseq

value: P. yoelii yoelii 17XNL sample 0 h after artemetner action


title: AhR control2,A549 cell, bulkRNA-seq

value: Lung

value: Epithelial Cells

value: Not Applicable