title: SBW25_noplasmid_dgacS_BR08

description:
Sample 18
CountsMatrix.csv
de_table_chr_vanc.csv
de_table_comp.csv
rpkm_chr.csv
18-BR08


title: sham+vehicle_2

status: Public on Apr 17 2021

type: SRA

city: Ulm

first: Tim

last: Eiseler

address: Albert-Einstein Allee 23

department: Internal Medicine 1

country: Germany

institute: Ulm University

library_source: transcriptomic

data_processing:
Expression profiling libraries were sequenced on HiSeq 3000/4000 instruments (Illumina, San Diego, CA, USA) in 50-base-pair, single-end mode. Base calls, provided by the real-time analysis (RTA) software (Illumina, San Diego, CA, USA), were subsequently converted into multiplexed, unaligned BAM format before demultiplexing into sample-specific, unaligned BAM files. For raw data processing off the instruments, custom programs, based on Picard tools (https://broadinstitute.github.io/picard/), were used
NGS reads were mapped to the Genome Reference Consortium GRCm38 assembly via “Spliced Transcripts Alignment to a Reference” (STAR) utilising the “basic” Ensembl transcript annotation from version e99 (January 2020) as reference transcriptome. Since the mm10 assembly flavour of the UCSC Genome Browser was preferred for downstream data processing with Bioconductor packages for entirely technical reasons, Ensembl transcript annotation had to be adjusted to UCSC Genome Browser sequence region names. STAR was run with options suggested by the ENCODE project. Aligned NGS reads overlapping Ensembl transcript features were counted with the Bioconductor GenomicAlignments::summarizeOverlaps() function, taking into account that the Illumina TruSeq stranded mRNA protocol leads to sequencing of the second strand so that all reads needed inverting before counting. Transcript-level counts were aggregated to gene-level counts and the Bioconductor DESeq2 package was used to test for differential expression based on a model using the negative binomial distribution
Genome_build: GRCm38
Supplementary_files_format_and_content: TSV files, FPKMS all samples

molecule: total RNA

organism: Mus musculus

source_name: Total lung

extract_protocol:
Total RNA was extracted from lung tissue using miRNAeasy mini kit (Qiagen)
RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina, San Diego, CA, USA) using Sciclone and Zephyr liquid handling workstations (PerkinElmer, Waltham, MA, USA) for pre- and post-PCR steps, respectively

treatment_protocol: mice were subjected to blast-wave induced thorax trauma (TxT) under anesthesia. 10-15 minutes after the insult the sEV biogenesis inhibitor GW4869 (2µg/g body weight) or NaCl (vehicle) was injected intravenously.

tag: tissue

value: Total lung

tag: strain

tag: genotype

value: wild type

tag: treatment

value: sham+vehicle

tag: age

value: 12 week-old

tag: gender

value: male


title: SBW25_pQBR57_dgacS_AR09

city: Liverpool

first: James

last: Hall

address: Crown Street

country: United Kingdom

institute: University of Liverpool

description:
Sample 9
CountsMatrix.csv
de_table_chr_vanc.csv
de_table_comp.csv
de_table_pQ57.csv
rpkm_chr.csv
rpkm_pQ57.csv
9-AR09

data_processing:
Trimmed using Cutadapt version 1.2.1 using the option -O 3
Trimmed using Sickle version 1.200 with a minimum window quality score of 20 and reads longer than 19 bp
Strand-specific alignment to the reference sequence(s) using HISAT 2.1.0 with options phred33, no-spliced-alignment, new-summary, and rna-strandness RF
Filtering using samtools to remove mapping with PHRED-scaled quality <10
Function featureCounts from Rsubread 1.30.9
Analysis using edgeR 3.22.5
Genome_build: Aligned to reference sequences AM181176, LN713926, AM235768
Supplementary_files_format_and_content: CountsMatrix.csv: raw counts for each feature for each sample. Output from Rsubread
Supplementary_files_format_and_content: CountsMatrix_stats.csv: statistics of the raw counts for each sample. Output from Rsubread
Supplementary_files_format_and_content: de_table_chr_vanc.csv: differential expression of chromosomal genes for each sample relative to the control. Output from edgeR
Supplementary_files_format_and_content: de_table_chr_comp.csv: differential expression of chromosomal genes for each sample relative to corresponding plasmid-bearing strains. Output from edgeR
Supplementary_files_format_and_content: de_table_pQ57.csv: differential expression for relevant samples relative to the wild-type pQBR57-bearer. Output from edgeR
Supplementary_files_format_and_content: de_table_pQ103.csv: differential expression for relevant samples relative to the wild-type pQBR103-bearer. Output from edgeR
Supplementary_files_format_and_content: edgeR_NormalizationFactors.csv: normalization factors for each sample. Output from edgeR
Supplementary_files_format_and_content: rpkm_*.csv: calculated RPKM values. Output from edgeR

organism: Pseudomonas [fluorescens] SBW25

source_name: Pseudomonas fluorescens SBW25

growth_protocol: Overnight cultures of bacteria were subcultured 1:50 into 6 ml prewarmed KB microcosms and grown at 28°C shaking at 180 rpm. Samples were harvested when cultures reached intermediate exponential phase (OD600 = 0.6, as assessed on a Tecan Spark plate reader).

extract_protocol:
Samples were harvested at 4.5 G for 10 minutes, resuspended in 1 ml TRI reagent, and incubated at room temperate for 5 minutes. Amylene-stabilised chloroform (400 µl, Sigma-Aldrich 34854-M) was added to each tube, and incubated for 2-15 minutes at room temperature. Samples were then transferred to 5Prime Phase Lock Gel 'Heavy' tubes (VWR 733-2478) and centrifuged at 17 G for 15 minutes at room temperature. The aqueous phase was collected into a fresh microfuge tube and 450 µl isopropanol was added to precipitate RNA. Samples were incubated at room temperature for 30 minutes before pelleting at 17 G for 30 minutes. The pellet was rinsed by gently adding 1 ml of 70% ethanol and pelleting at 7.5 G for 5 minutes. The supernatant was carefully removed and the pellet allowed to air dry before resuspension in RNase-free water at 65°C. To remove any residual contaminating DNA, RNA was diluted to ≤200 ng/µl and treated with TURBO DNA-free RNase-free DNase (Invitrogen AM1907) according to the manufacturer's instructions. Reaction products were purified with Agencourt RNAClean XP beads. Ribosomal RNA was removed using the Bacterial RiboZero rRNA depletion kit (Illumina).
NEBNext Ultra-Directional RNA library preparation kit (Illumina). Sequencing is 'reverse-stranded'.

treatment_protocol: 1 ml samples were added to 0.4 volumes of ice-cold 95% ethanol 5% phenol 'stop solution' [@Colgan2016-mu], mixed gently, and incubated on ice for at least 30 minutes. Each of the three replicates was processed separately as a block.

tag: taxid

tag: amelioration/genotype

value: dgacS

tag: plasmid


title: PBS 10ml/Kg [189748]

type: RNA

city: Frederick

first: RAJAA

last: EL MESKINI

state: MD

address: 1050, Boyles Street

department: Center for Advanced Preclinical Research

country: USA

institute: Leidos Biomedical Research, Inc

description:
Study#3
PBS 10ml/Kg [189748]

hyb_protocol: A total of 20 ug of biotinylated cRNA was then fragmented for hybridization on the Affymetrix GeneChip Mouse Genome 430 2.0 Array.

scan_protocol: GeneChip Operating Software Tool was used for data capture and quality

data_processing: Raw CEL files from the scan were analyzed using a microarray pipeline written in ‘R’.  Data were normalized using the Robust Multichip Average (RMA) method.  Linear modeling was performed using Limma’s lmFit function (LIMMA, RRID:SCR_010943, Limma powers differential expression analyses for RNA-sequencing and microarray studies), and differential gene expression was determined using the contrasts.fit and eBayes functions. Top pathways for each comparison (Non-responders, Responders, and Relapse;  normalized with control IgG treatment samples) were determined using (Gene Set Enrichment Analysis) GSEA (SeqGSEA, RRID:SCR_005724, http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Gsea_Citation). The top 10 up and down regulated pathways were generated from Reactome (Reactome diagram viewer: data structures and strategies to boost performance) based on NES scores if Q-value meets threshold of less than 0.1. The top genes from Reactome were then used to run GSVA (Gene Set Variation Analysis for microarray and RNA-seq data) to find enrichment for each sample. Heatmaps were generated for the GSVA analysis, columns (samples) were sorted by group and rows (pathways) were clustered by Euclidean distance. Individual sample differential expression heatmap was analyzed by computing the log fold-change between a sample against the mean expression of the IgG samples, upper and lower limits shown on the heat map are log values from -2 to 2. Gene expression data from this report is available through the Collaborative Bioinformatics Resource of NIH, Center for Cancer Research (CCR). https://zenodo.org/record/3770853#.X9PmhhNKg_N.

label: Biotin

source_name: Subcutaneous tumor

label_protocol: A total input of 800ng of isolated RNA was applied to the Message Amp II-Biotin Enhanced aRNA Amplification Kit according to manufacture protocol for first and second Strand cDNA synthesis followed by in-vitro transcription (IVT) reaction to synthesize the complementary RNA (cRNA) for transcriptional amplification and biotin labeling.

growth_protocol: See publication Materials and Methods: Melanoma allograft model

extract_protocol: Tumor samples were lysed and homogenized for RNA isolation using the RNeasy Mini Kit following manufacturer’s protocol for purification of total RNA with on-column DNase digestion (Qiagen). RNA purity and concentration were determined spectrophotometrically, and RNA quality was assessed using the Agilent Technology Tape Station RNA Screen Tape.

treatment_protocol: See publication Materials and Methods: Immunotherapy treatment

tag: disease

value: Melanoma


title: PBS 10ml/Kg [189749]

description:
Study#3
PBS 10ml/Kg [189749]


title: SBW25_noplasmid_dgacS_AR08

description:
Sample 8
CountsMatrix.csv
de_table_chr_vanc.csv
de_table_comp.csv
rpkm_chr.csv
8-AR08


title: PT10_4

data_processing:
Expression profiling libraries were sequenced on HiSeq 3000/4000 instruments (Illumina, San Diego, CA, USA) in 50-base-pair, single-end mode. Base calls, provided by the real-time analysis (RTA) software (Illumina, San Diego, CA, USA), were subsequently converted into multiplexed, unaligned BAM format before demultiplexing into sample-specific, unaligned BAM files. For raw data processing off the instruments, custom programs, based on Picard tools (https://broadinstitute.github.io/picard/), were used
NGS reads were mapped to the Genome Reference Consortium GRCm38 assembly via “Spliced Transcripts Alignment to a Reference” (STAR) utilising the “basic” Ensembl transcript annotation from version e99 (January 2020) as reference transcriptome. Since the mm10 assembly flavour of the UCSC Genome Browser was preferred for downstream data processing with Bioconductor packages for entirely technical reasons, Ensembl transcript annotation had to be adjusted to UCSC Genome Browser sequence region names. STAR was run with options suggested by the ENCODE project. Aligned NGS reads overlapping Ensembl transcript features were counted with the Bioconductor GenomicAlignments::summarizeOverlaps() function, taking into account that the Illumina TruSeq stranded mRNA protocol leads to sequencing of the second strand so that all reads needed inverting before counting. Transcript-level counts were aggregated to gene-level counts and the Bioconductor DESeq2 package was used to test for differential expression based on a model using the negative binomial distribution
Supplementary_files_format_and_content: TSV files, FPKMS all samples

organism: Homo sapiens

source_name: HUVEC treated with plasma sEVs from Polytrauma patient 4hrs after trauma

extract_protocol: RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina, San Diego, CA, USA) using Sciclone and Zephyr liquid handling workstations (PerkinElmer, Waltham, MA, USA) for pre- and post-PCR steps, respectively

tag: cell type

value: Human umbilical vein endothelial cells (HUVEC)


title: SBW25_pQBR57_V100A_AR07

description:
Sample 7
CountsMatrix.csv
de_table_chr_vanc.csv
de_table_comp.csv
de_table_pQ57.csv
rpkm_chr.csv
rpkm_pQ57.csv
7-AR07


title: PT10_24

source_name: HUVEC treated with plasma sEVs from Polytrauma patient 24hrs after trauma


title: PBS 10ml/Kg [189746]

description:
Study#3
PBS 10ml/Kg [189746]


title: SBW25_pQBR103_d4242_AR06

description:
Sample 6
CountsMatrix.csv
de_table_chr_vanc.csv
de_table_comp.csv
de_table_pQ103.csv
rpkm_chr.csv
rpkm_pQ103.csv
6-AR06


title: SBW25_pQBR57_d4242_AR04

description:
Sample 4
CountsMatrix.csv
de_table_chr_vanc.csv
de_table_comp.csv
de_table_pQ57.csv
rpkm_chr.csv
rpkm_pQ57.csv
4-AR04


title: SBW25_pQBR103_dgacS_AR10

description:
Sample 10
CountsMatrix.csv
de_table_chr_vanc.csv
de_table_comp.csv
de_table_pQ103.csv
rpkm_chr.csv
rpkm_pQ103.csv
10-AR10


title: PT09_24

value: treated with plasma sEVs from Polytrauma patient 24hrs after trauma


title: PT09_4

value: treated with plasma sEVs from Polytrauma patient 4hrs after trauma


title: SBW25_pQBR57_wt_AR03

description:
Sample 3
CountsMatrix.csv
de_table_chr_vanc.csv
de_table_comp.csv
de_table_pQ57.csv
rpkm_chr.csv
rpkm_pQ57.csv
3-AR03

value: wt


title: SBW25_noplasmid_d4242_AR02

description:
Sample 2
CountsMatrix.csv
de_table_chr_vanc.csv
de_table_comp.csv
rpkm_chr.csv
2-AR02


title: SBW25_noplasmid_wt_AR01

description:
Sample 1
CountsMatrix.csv
de_table_chr_vanc.csv
de_table_comp.csv
rpkm_chr.csv
1-AR01


title: PT07_24


title: sham+vehicle_1


title: SBW25_pQBR103_wt_AR05

description:
Sample 5
CountsMatrix.csv
de_table_chr_vanc.csv
de_table_comp.csv
de_table_pQ103.csv
rpkm_chr.csv
rpkm_pQ103.csv
5-AR05


title: PT07_4


title: U2OS Input (1)

city: Lund

first: Maria

last: Alvarado-Kristensson

address: 59 Jan Waldenstr ms street

country: Sweden

institute: Lund University

library_source: genomic

data_processing:
SOLiD XSQ files were converted into color based fastq file using XSQConvertor version v10:03-07-2013
ChIP-seq reads were aligned to the hg19 genome assembly using BFAST version 0.70a
Peaks were called using PeakSeq version 1.31 with FDR cutoff of 0.01.
Genome_build: hg19
Supplementary_files_format_and_content: BedGraph files were generated; Scores represent signal values

molecule: genomic DNA

source_name: osteosarcoma

growth_protocol: U2OS osteosarcoma epitelial cells were grown in McCoy'5A medium supplemented with 5% fetal calf serum and 1% PEST.

extract_protocol:
Nuclei were lysed and sonicated. Nuclei were cleared and gamma-tubulin-DNA-complexes or PCNA-DNA-complexes were isolated with antibody.
Libraries were prepared according to AB libray builder system instructions accompanying the DNA Sample Kit.

treatment_protocol: Cells were subjected to dubble thymidine syncronization and released for 0h, 3h, 5h, 7h, 9h prior to harvest. Alternatively, cells were kept in confluency 48 h before harvesting.

value: bone

tag: cell line

tag: developmental stage

value: exponentially growing

tag: antibody


title: Relapse to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [197463]

description:
Study#3
Relapse to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [197463]


title: Relapse to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [197461]

description:
Study#3
Relapse to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [197461]


title: 5h PCNA (2)

value: PCNA


title: Stabilization to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [197456]

description:
Study#3
Stabilization to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [197456]


title: PT05_24


title: Stabilization to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [197454]

description:
Study#3
Stabilization to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [197454]


title: Stabilization to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [197442]

description:
Study#3
Stabilization to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [197442]


title: 5h PCNA (1)


title: Relapse to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [197446]

description:
Study#3
Relapse to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [197446]


title: 3h PCNA (2)


title: 3h PCNA


title: Non-responders to 10mg/kg anti-mousePD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [197409]

description:
Study#3
Non-responders to 10mg/kg anti-mousePD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [197409]


title: PT05_4


title: 5h MH2A (1)


title: PT04_24


title: 3h MH2A (2)


title: 5h MH2A (2)


title: 3h MH2A


title: U2OS Input (2)


title: PT04_4


title: G0/G1 (1)

value: Cell confluence arrested cells

value: gamma tubulin


title: G0/G1 (2)


title: 9h (2)


title: 9h (1)


title: PT03_24


title: PT03_4


title: Non-responders to 10mg/kg anti-mousePD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [197436]

description:
Study#3
Non-responders to 10mg/kg anti-mousePD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [197436]


title: HC06

source_name: HUVEC treated with plasma sEVs from healthy control


title: 7h (1)


title: U2OS 7h IPgtub


title: Non-responders to 10mg/kg anti-mousePD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [197429]

description:
Study#3
Non-responders to 10mg/kg anti-mousePD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [197429]


title: Non-responders to 10mg/kg anti-mousePD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [197434]

description:
Study#3
Non-responders to 10mg/kg anti-mousePD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [197434]


title: Non-responders to 10mg/kg anti-mousePD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [197444]

description:
Study#3
Non-responders to 10mg/kg anti-mousePD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [197444]


title: Non-responders to 10mg/kg anti-mousePD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [197437]

description:
Study#3
Non-responders to 10mg/kg anti-mousePD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [197437]


title: Non-responders to 10mg/kg anti-mousePD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [197441]

description:
Study#3
Non-responders to 10mg/kg anti-mousePD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [197441]


title: 5h gtub


title: 3h gTub


title: HC04

value: treated with plasma sEVs from healthy control


title: Non-responders to 10mg/kg anti-mousePD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [197404]

description:
Study#3
Non-responders to 10mg/kg anti-mousePD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [197404]


title: 0h (1)


title: 0h (2)


title: U2OS 3h IPgtub (1)


title: HC02


title: HC03


title: 5h gtub (2)


title: Non-responders to 10mg/kg anti-mousePD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [197420]

description:
Study#3
Non-responders to 10mg/kg anti-mousePD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [197420]


title: HC05


title: Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [197462]

description:
Study#3
Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [197462]


title: HC01


title: REDS15_day23_SLC_TKO_2

city: Vienna

first: Kai-Chun

last: Li

address: Lazarettgasse 14, AKH BT 25.3

country: Austria

institute: CeMM

data_processing:
Raw sequencing reads were demultiplexed, and after barcode, adaptor and quality trimming with cutadapt
Quality control was performed using FastQC
The remaining reads were mapped to the GRCh38/h38 human genome assembly using genomic short-read RNA-Seq aligner STAR version 2.5
Transcripts were quantified using End Sequence Analysis Toolkit (ESAT)
Differential expression analysis was performed using independent triplicates with DESeq2 (1.24.0) on the basis of read counts.
Genome_build: GRCh38/h38
Supplementary_files_format_and_content: Matrix table with gene counts

source_name: BRD4 reporter KBM7 cells (REDS15 clone)

growth_protocol: BRD4 reporter KBM7 cells (REDS1 and REDS15 clones) were grown in IMDM supplemented with 10% FBS and 1% PS

extract_protocol:
Total RNA was extracted using RNeasy Mini kit (Qiagen 74106) including a DNase I digest step according to manufacturer's instructions
The Illumina compatible library was prepared with QuantSeq 3’mRNA-seq Library Prep kit (Lexogen 015.96) according to manufacturer's instructions

treatment_protocol: 23 days after lentivirus delivered sgRNA in cells

value: SLC35F5/SLC29A4/SLC28A3 triple knockout

tag: replicate

value: BRD4 reporter KBM7 cells (REDS15 clone)


title: Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [197438]

description:
Study#3
Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [197438]


title: REDS15_day23_SLC_TKO_1


title: Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [197432]

description:
Study#3
Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [197432]


title: b.end3 - Ep2_3_fpkm

city: Kaifeng

first: Haigang

last: wu

state: Henan province

address: dongjing Road

department: School of Life Sciences

country: China

institute: Henan University

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimed for adaptor sequence, and masked for low-complexity or low quality sequence, then mapped to the mm8 hole genome using bowtie v0.12.2 with parameters set as defaults.
Reads for kilobased of exon per megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: mm8

source_name: b.end3 cells

growth_protocol: Rat endothelial cell b.end3 was obtained from the cell bank of Chinese Academy of Sciences. Cells were cultured in DMEM medium (SH30022.01B, Gibco) with 10% FBS (SH30084.03, HyClone) and 100 U/mL Penicillin-Streptomycin (Gibco, Cat.15140122) under 5% CO2 at 37 °C.

extract_protocol:
Cell samples ere lyzed and harvested using Trizol reagent. THe purification of RNA was performed using protocol provided by extracting kits (Total RNA Extraction Kit, Cat. R1200, Solarbio life science, China).
RNA library were prepared for sequencnig using standard illumina protocols

treatment_protocol: When the b.end3 formed the monolayer, the photosensitizer Porfimer sodium (300 μg/mL) was added to the medium and incubated for 90 min. Then the b.end3 cells received the laser exposure (635 nm with 100 mW/cm2) and the light dosages are 10 J/cm2 and 20 J/cm2, respectively.

value: Brain microvessel endothelial cells

value: treated with PDT with 20 J/cm2


title: b.end3 - Ep2_1_fpkm


title: b.end3 - Ctrl_3_fpkm

value: untreated


title: b.end3 - Ep1_1_fpkm

value: treated with PDT with 10 J/cm2


title: b.end3 - Ep2_2_fpkm


title: b.end3 - Ctrl_2_fpkm


title: b.end3 - Ep1_2_fpkm


title: b.end3 - Ctrl_1_fpkm


title: b.end3 - Ep1_3_fpkm


title: REDS1_day23_SLC_TKO_2

source_name: BRD4 reporter KBM7 cells (REDS1 clone)

value: BRD4 reporter KBM7 cells (REDS1 clone)


title: Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [197426]

description:
Study#3
Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [197426]

value: Melanoma


title: p53control_untreated2

city: Zurich

first: Tanja

last: Rothgangl

address: Winterthurerstrasse, 190

department: Pharmacology and Toxicology

country: Switzerland

institute: UZH Zurich

data_processing:
Library strategy: targeted amplicon sequencing
CHANGE-seq pipeline (https://github.com/tsailabSJ/changeseq)
For all targeted amplicon sequencing files, we used CRISPRESSO2 for the analysis: https://crispresso.pinellolab.partners.org/submission . This platform directly reads in a fastq.gz file and provides a summary about editing rates and allele frequency.
Genome_build: macFas5
Supplementary_files_format_and_content: CHANGE-seq: text files containing identified off-target sites

source_name: whole liver lysate

growth_protocol: DMEM growth medium supplemented with 10% FBS and 1% P/S for HEK293T and Hepa1-6 cells; EMEM with same supplements for HepG2 cells

extract_protocol:
Detachment with TryplE, wash with PBS, lysis and DNA isolation for cell lines and whole tissue or primary hepatocyte isolation for in vivo samples.
targeted amplicon sequencing; CHANGE-seq  library preparation

treatment_protocol: per 48 well plate: 1 ug total DNA with 1.5 ul Lipofectamine2000, cells were treated with the respective base-editor targeting the indicated locus. For HepG2 cells, the base editor and sgRNA was inroduced by NEON electroporation. In vivo treatment was delivery by AAV or LNP mediated delivery via tail vein injection.

value: AAV-mediated delivery

value: tail vein

value: targeted amplicon sequencing

value: base-edited PCSK9


title: REDS15_day23_SLC_TKO_3


title: REDS1_day23_SLC_TKO_3


title: REDS1_day23_SLC_TKO_1


title: Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [197435]

description:
Study#3
Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [197435]


title: Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [197431]

description:
Study#3
Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [197431]


title: Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [197460]

description:
Study#3
Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [197460]


title: PTC_04

hyb_protocol: Agilent protocol

scan_protocol: Slides were scanned using a G2565CA microarray scanner (Agilent Technologies, Santa Clara, CA, USA).

data_processing: Pre-processing of expression data was performed according to Agilent's standard workflow. Using 5 quality flags (gIsPosAndSignif, gIsFeatNonUnifOL, gIsWellAboveBG, gIsSaturated, and gIsFeatPopnOL) from the Feature Extraction software output, probes were labelled as detected, not detected, or compromised. Gene expression levels were background corrected, and signals for duplicated probes were summarized by the geometric mean of non-compromised probes. After log2 transformation, a percentile shift normalization at the 75% level was performed.

source_name: sEVs isolated from HUVEC supernatant after 24hrs treatment with PTC

label_protocol: Samples were processed with the miRNA Complete Labeling & Hybridization Kit (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer's guidelines

growth_protocol: Human umbilical vein endothelial cells (HUVEC, ATCC, CRL-1730) were maintained at 37°C and 5% CO2 in endothelial cell growth medium MV2 (PromoCell, #C-22022)

extract_protocol: For purification of total RNA including miRNA 700µl QIAzol was added to sEVs derived from cell culture supernatants or serum/plasma. Subsequently, isolation was performed using the miRNeasy mMicro Kkit (Qiagen, #217084)

treatment_protocol: After cells reached confluency, cells were washed several times with serum-free DMEM and then incubated in serum-free media for 24h to accumulate sEVs at 37°C, 5% CO2. Culture mediums were collected and centrifuged for 15min at 1000 rpm at 4°C. Subsequently, the culture supernatants were centrifuged for 45min at 4000rpm (4°C) and then passed through 0.2µm syringe filters (Filtropur S, #83.1826.001, Sarstedt). The supernatant was concentrated by ultrafiltration at 2000 rpm and 4°C using Vivaspin Turbo 15 (100,000 MWCO) units (Sartorius, #VS15T41) until a volume of 1ml was reached. The concentrated supernatant was transferred into Lo-Bind 1.5ml tubes and 0.5 volumes (V) of supplied buffer A was added. After incubation overnight at 4°C the samples were centrifuged for 1hr at 14000 rpm and 4°C. The supernatant was discarded, and the pellet was resolved in 100µl sterile (0.2µm) filtered PBS. For size exclusion chromatography Exo-spin columns were centrifuged for 30 seconds at 500 rpm after cap and stopper were removed. The columns were equilibrated by centrifugation at 500 rpm for 30sec using 200µl sterile filtered PBS. The sEV pellet solved in PBS was pipetted onto the column and centrifuged for 1min at 500rpm. The eluate was discarded, and the column was placed in a fresh 1.5ml-Lo-Bind tube. For elution, 200µl sterile filtered PBS was added to the column and centrifuged for 1min at 500 rpm. The sEV eluate was stored at -80°C. The surface protein concentration was determined using Bradford Protein Assay (Bio-Rad, #5000006).

value: HUVEC (human umbilical vein endothelial cells)

value: after 24hrs treatment with PTC


title: PTC_03


title: Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [197425]

description:
Study#3
Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [197425]


title: PTC_01


title: PTC_02


title: H2O_01

source_name: sEVs isolated from HUVEC supernatant after 24hrs treatment with H2O

value: after 24hrs treatment with H2O


title: H2O_04


title: REDS15_day23_sgRen_2

value: control Renilla guide RNA


title: Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [197451]

description:
Study#3
Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [197451]


title: Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [197443]

description:
Study#3
Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [197443]


title: REDS1_day23_sgRen_3


title: epi_c18_rep4

city: Toronto

first: Aaron

last: Wong

state: Ontario

address: 101 College Street

department: TGHRI

country: Canada

institute: University Health Network

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: R oligo package, annotations from brain array v19, RMA normalization

label: biotin

label_protocol: Affymetrix protocol

growth_protocol: Normal human bronchial epithelial cell line (BEAS-2B) was obtained from ATCC (Manassas, VA), and cells were cultured in low glucose Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS, GIBCO, Carlsbad, CA).  Human pulmonary microvascular endothelial cell line (HPMEC) was obtained from Kirkpatrick’s research lab, and cultured in flasks or on plates precoated with 0.2% gelatin. The culture medium used was medium M199 supplemented with 20% FBS, Glutamax (2 mM), endothelial cell growth supplement from bovine neural tissue (ECGS 50 μg/ml, Sigma Aldrich), heparin (50 U/ml) and Penicillin/Streptomycin solution (100 U/100 μg/ml)

extract_protocol: Total RNA was purified using RNeasy Mini Kit (Qiagen; Hilden, Germany). RNA quality was tested using Nanodrop spectrophotometer (VWR) and Bioanalyzer (Agilent; Santa Clara, CA).

treatment_protocol: Cold ischemia was simulated by replacing cell culture medium with cold Perfadex® solution, a clinically used solution for donor lung preservation, and stored in a 4ºC chamber for 6 h, 12 h, 18 h, 24 h. Clinically, donor lungs are inflated with 50% O2 during hypothermic preservation, thus, the chamber was filled with room air mixed with 50% O2. To simulate reperfusion, the cold Perfadex® solution was changed back to warm serum-containing culture medium and cultured at 37ºC for 2 h or 4 h.

value: 18 hours cold ischemia


title: epi_c18_rep2


title: Normal IgG 10 mg/kg [200377]

description:
Study#3
Normal IgG 10 mg/kg [200377]


title: epi_c18_rep3


title: REDS1_day23_sgRen_2


title: REDS15_day23_sgRen_1


title: epi_c6r2_rep5

value: 6 hours cold ischemia + 2 hours reperfusion


title: epi_c6r2_rep3


title: epi_c6r2_rep4


title: Normal IgG 10 mg/kg [200375]

description:
Study#3
Normal IgG 10 mg/kg [200375]


title: Normal IgG 10 mg/kg [200381]

description:
Study#3
Normal IgG 10 mg/kg [200381]


title: REDS15_day23_sgRen_3

value: BRD4 reporter KBM7 cells (REDS15 clone)


title: REDS1_day23_sgRen_1


title: epi_c6r2_rep2


title: H2O_02


title: epi_c6_rep5

value: 6 hours cold ischemia


title: epi_c6_rep3


title: REDS1_6MP_10uM_rep2

treatment_protocol: Cells with compound treatment for 72 hours or 12 days after lentivirus delivered sgRNA in cells

value: 10 uM 6-mercaptopurine treatment for 72 hours

value: rep 2


title: epi_c18_rep5


title: Normal IgG 10 mg/kg [200373]

description:
Study#3
Normal IgG 10 mg/kg [200373]


title: epi_c6_rep2


title: Normal IgG 10 mg/kg [200372]

description:
Study#3
Normal IgG 10 mg/kg [200372]


title: REDS1_6MP_10uM_rep1

value: rep 1


title: Normal IgG 10 mg/kg [200378]

description:
Study#3
Normal IgG 10 mg/kg [200378]


title: REDS15_sgRen_rep2

value: control Renilla guide RNA transudction for 12 days


title: epi_con_rep2

value: untreated


title: epi_con_rep4


title: epi_con_rep5


title: epi_con_rep3


title: REDS15_sgRen_rep1


title: Normal IgG 10 mg/kg [200370]

description:
Study#3
Normal IgG 10 mg/kg [200370]

value: Melanoma


title: Normal IgG 10 mg/kg [200376]

description:
Study#3
Normal IgG 10 mg/kg [200376]


title: endo_c18r2_rep4

value: 18 hours cold ischemia + 2 hours reperfusion

value: HPMEC


title: Growth Delay to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223331]

description:
Study#2
Growth Delay to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223331]


title: endo_c18r2_rep2


title: epi_c6_rep4


title: REDS1_JQ1_1uM_rep1

value: 1 uM (+)-JQ1 treatment for 72 hours

value: BRD4 reporter KBM7 cells (REDS1 clone)


title: REDS1_JQ1_1uM_rep2


title: endo_c18_rep3


title: endo_c18_rep4


title: REDS15_sgSLC35F5_sgSLC28A3_sgSLC29A4_rep1

value: SLC35F5/SLC29A4/SLC28A3 triple knockout for 12 days


title: endo_c18r2_rep3


title: REDS1_DMSO_rep2

value: control DMSO treatment for 72 hours


title: endo_c18r2_rep5


title: Relapse to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223274]

description:
Study#2
Relapse to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223274]


title: endo_c18_rep2


title: Relapse to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223305]

description:
Study#2
Relapse to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223305]


title: endo_c6r2_rep5


title: REDS1_DMSO_rep1


title: endo_c6_rep5


title: endo_c6r2_rep2


title: REDS15_JQ1_1uM_rep2


title: endo_c6r2_rep3


title: endo_c6_rep3


title: REDS15_JQ1_1uM_rep1


title: endo_c6_rep4


title: endo_c6_rep2


title: Growth Delay to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223262]

description:
Study#2
Growth Delay to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223262]


title: Relapse to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223308]

description:
Study#2
Relapse to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223308]


title: Non-responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223323]

description:
Study#2
Non-responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223323]


title: Non-responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223298]

description:
Study#2
Non-responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223298]


title: Non-responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223320]

description:
Study#2
Non-responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223320]


title: epi_c18r2_rep4


title: endo_c6r2_rep4


title: Non-responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223282]

description:
Study#2
Non-responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223282]


title: epi_c18r2_rep3


title: endo_con_rep5


title: epi_c18r2_rep5


title: REDS1_sgSLC35F5_sgSLC28A3_sgSLC29A4_rep2


title: REDS1_sgSLC35F5_sgSLC28A3_sgSLC29A4_rep1


title: endo_con_rep4


title: REDS1_sgRen_rep2


title: endo_con_rep3


title: epi_c18r2_rep2


title: Perirenal1828

city: Tjele

first: Mette

middle: Olaf

last: Nielsen

address: Blichers Alle 20

department: Animal Science

country: Denmark

institute: Aarhus University

data_processing:
The adapter sequences and low quality reads were removed using Trimmomatic v0.39 software. The rRNA contamination of the paired-end reads were done using the database from SILVA v132, and the BWA v0.7.17-r1188 software was used to build the BWA index file.
The clean paired-end reads were mapped to Oar v3.1.99 gtf using STAR v2.7.3a software.
A post-alignment quality control was assessed using Qualimap v2.2 software.
The gene expression counts were computed using HTSeq v0.11.8 software.
Low count genes were filtered by excluding less than 1 count per million (cpm) and the DEGs were identified using DESeq2 v1.26.0 package in RStudio (v1.2.5042)
Genome_build: Oar V3.1
Supplementary_files_format_and_content: _.HTSeqCount_exon.txt Files of the raw count for each samples computed by HTSeq v0.11.8 software

organism: Ovis aries

source_name: LOW_CONV_Perirenal adipose tissue

extract_protocol:
The RNA was extracted using Trizol reagent
cDNA library was constructed using NEB Next Ultra Directional RNA Library PrepKit for Illumina

tag: Sex

value: Female

tag: prenatal nutrition

value: LOW

tag: early postnatal diet

value: CONV

value: Perirenal adipose tissue

tag: molecule subtype

value: mRNA/lncRNA


title: Perirenal1826

tag: tissue


title: Perirenal1821

source_name: LOW_HCHF_Perirenal adipose tissue

value: Male

value: HCHF


title: Perirenal1822


title: REDS15_DMSO_rep2

tag: treatment

value: rep 2

value: BRD4 reporter KBM7 cells (REDS15 clone)


title: Perirenal1823

source_name: HIGH_HCHF_Perirenal adipose tissue

value: HIGH


title: REDS15_DMSO_rep1

value: rep 1


title: Perirenal1818


title: REDS1_sgRen_rep1

value: control Renilla guide RNA transudction for 12 days


title: Perirenal1816


title: Non-responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223256]

description:
Study#2
Non-responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223256]

value: Melanoma

tag: genotype

tag: strain


title: Perirenal1810


title: Non-responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223254]

description:
Study#2
Non-responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223254]


title: Non-responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223324]

description:
Study#2
Non-responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223324]


title: Perirenal1807


title: Non-responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223261]

description:
Study#2
Non-responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223261]


title: REDS15_6MP_10uM_rep1

value: 10 uM 6-mercaptopurine treatment for 72 hours


title: Perirenal1804

source_name: NORM_CONV_Perirenal adipose tissue

value: NORM


title: Non-responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223315]

description:
Study#2
Non-responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223315]


title: REDS15_6MP_10uM_rep2


title: REDS15_sgSLC35F5_sgSLC28A3_sgSLC29A4_rep2

value: SLC35F5/SLC29A4/SLC28A3 triple knockout for 12 days


title: Perirenal1799


title: Perirenal1802


title: Non-responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223310]

description:
Study#2
Non-responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223310]


title: Perirenal1789

source_name: NORM_HCHF_Perirenal adipose tissue


title: Perirenal1792


title: Non-responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223299]

description:
Study#2
Non-responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223299]


title: NHP_CHANGE3_Treated2

organism: Macaca fascicularis

value: LNP-mediated delivery

value: intravenous

value: targeted amplicon sequencing

value: base-edited PCSK9


title: NHP_CHANGE3_Treated3


title: Perirenal1784

value: LOW

value: CONV

value: Perirenal adipose tissue


title: Perirenal1785

value: Male

value: HCHF

value: mRNA/lncRNA


title: Perirenal1787

value: HIGH


title: Non-responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223294]

description:
Study#2
Non-responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223294]


title: Non-responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223290]

description:
Study#2
Non-responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223290]


title: Perirenal1783


title: NHP_CHANGE3_Treated1


title: NHP_CHANGE3_Control3

value: untreated control


title: Perirenal1796

source_name: HIGH_CONV_Perirenal adipose tissue


title: Perirenal1782


title: Perirenal1778

value: Female


title: Perirenal1777


title: Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223296]

description:
Study#2
Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223296]

source_name: Subcutaneous tumor

value: Melanoma


title: Perirenal1774


title: Non-responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223307]

description:
Study#2
Non-responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223307]


title: Perirenal1770


title: Perirenal1788


title: Perirenal1772


title: Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223330]

description:
Study#2
Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223330]


title: NHP_CHANGE3_Control1


title: NHP_CHANGE3_Control2


title: Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223277]

description:
Study#2
Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223277]


title: Perirenal1769


title: Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223301]

description:
Study#2
Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223301]


title: Perirenal1767


title: NHP_CHANGE2_Treated2


title: Perirenal1775


title: Perirenal1768


title: Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223267]

description:
Study#2
Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223267]


title: NHP_CHANGE2_Treated3


title: Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223266]

description:
Study#2
Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223266]


title: Perirenal1766


title: NHP_CHANGE2_Treated1


title: Perirenal1764


title: Perirenal1763


title: NHP_CHANGE2_Control3


title: Perirenal1761


title: Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223280]

description:
Study#2
Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223280]


title: NHP_CHANGE2_Control2


title: Perirenal1759


title: Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223273]

description:
Study#2
Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223273]


title: Subcutaneous1828

source_name: LOW_CONV_Subcutaneous adipose tissue

value: Subcutaneous adipose tissue


title: Perirenal1755


title: Subcutaneous1823

source_name: HIGH_HCHF_Subcutaneous adipose tissue


title: Subcutaneous1818


title: Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223337]

description:
Study#2
Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223337]


title: NHP_CHANGE1_Treated3


title: Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223334]

description:
Study#2
Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223334]


title: Subcutaneous1816


title: Subcutaneous1810


title: NHP_CHANGE1_Treated2


title: NHP_CHANGE1_Treated1


title: Subcutaneous1807

source_name: LOW_HCHF_Subcutaneous adipose tissue


title: Subcutaneous1799


title: Subcutaneous1796

source_name: HIGH_CONV_Subcutaneous adipose tissue


title: NHP_CHANGE1_Control3


title: Subcutaneous1788


title: Subcutaneous1789

source_name: NORM_HCHF_Subcutaneous adipose tissue

value: NORM


title: NHP_CHANGE2_Control1


title: Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223317]

description:
Study#2
Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223317]


title: Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223312]

description:
Study#2
Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223312]


title: Subcutaneous1787


title: Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223327]

description:
Study#2
Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223327]


title: Subcutaneous1785


title: Subcutaneous1784


title: CHANGE-seq control NHP

description: Processed data file: Macaca_identified_matched.txt

data_processing:
Library strategy: CHANGE-seq
CHANGE-seq pipeline (https://github.com/tsailabSJ/changeseq)
For all targeted amplicon sequencing files, we used CRISPRESSO2 for the analysis: https://crispresso.pinellolab.partners.org/submission . This platform directly reads in a fastq.gz file and provides a summary about editing rates and allele frequency.
Genome_build: macFas5
Supplementary_files_format_and_content: CHANGE-seq: text files containing identified off-target sites

source_name: NHP untreated PBMCs

value: in situ gDNA digest

value: Cas9 digest without sgRNA-hP01

value: CHANGE-seq

value: Cas9-KO PCSK9


title: NHP_CHANGE1_Control1

value: LNP-mediated delivery

value: intravenous

value: targeted amplicon sequencing


title: Subcutaneous1802

source_name: NORM_CONV_Subcutaneous adipose tissue

value: CONV


title: Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223326]

description:
Study#2
Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223326]


title: Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223291]

description:
Study#2
Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223291]


title: Subcutaneous1782

value: Male


title: Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223281]

description:
Study#2
Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223281]


title: Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) [223263]

description:
Study#2
Responders to 10mg/kg anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS [223263]


title: Heart-1_C01

city: Beijing

first: Qi

middle: Trinity

last: Peng

state: Beijing

address: No.5 Yiheyuan Road Haidian District

department: Institute of Molecular Medicine

institute: Peking University

description: heart.uniq.sorted.bw

data_processing:
Library strategy: Iso-seq
ROI (Reads-Of-Insert) reads were extracted and primer sequences flanking ROI reads were then trimmed
Primer-trimmed reads were further processed to scan the PA tail and trimmed to get PA-trimmed reads which represents reads with a PA tail trimmed.
PA-trimmed reads were then mapped to the reference genome (rheMac8 for macaque; mm9 for mouse) by GMAP and the low-quality reads were filtered to get the final processed alignments.
Genome_build: rheMac8, mm9
Supplementary_files_format_and_content: bigWig files were generated using DeepTools (version 3.3.0) with default parameters; scores represented coverage of uniquely-mapped Iso-seq reads；

organism: Macaca mulatta

source_name: Heart

extract_protocol:
Total RNAs were extracted using the Trizol Reagent (Invitrogen, catalog #15596018) and analyzed on an Agilent 2100 Bioanalyzer to access the quality. The quantity of total RNA was measured by Qubit. cDNA was synthesized using the SMARTer PCR cDNA Synthesis Kit (Clotech, catalog #634925) and PrimeSTAR GXL DNA Polymerase (Clontech, catalog #R050B).
SMRT bell libraries were generated by using SMRTbellTM Template prep kit 1.0-SPv3 (PN 100-991-900)

value: Heart


title: Subcutaneous1775

value: LOW

value: HCHF

value: mRNA/lncRNA


title: Subcutaneous1777

value: Female

value: HIGH


title: Subcutaneous1774

value: Subcutaneous adipose tissue


title: NHP_CHANGE1_Control2

source_name: whole liver lysate

value: untreated control


title: Normal IgG 10 mg/kg [223234]

description:
Study#2
Normal IgG 10 mg/kg [223234]

value: Melanoma


title: Subcutaneous1770

value: NORM


title: Heart-1_E03

description: heart.uniq.sorted.bw


title: Subcutaneous1783


title: Subcutaneous1769


title: CHANGE-seq target NHP

value: in situ gDNA digest

value: Cas9 digest with sgRNA-hP01

value: CHANGE-seq


title: Subcutaneous1778


title: Normal IgG 10 mg/kg [223239]

description:
Study#2
Normal IgG 10 mg/kg [223239]


title: Subcutaneous1772


title: Subcutaneous1767


title: Subcutaneous1764


title: Subcutaneous1766


title: Subcutaneous1768


title: Heart-1_B01

description: heart.uniq.sorted.bw


title: Heart-1_B03

description: heart.uniq.sorted.bw


title: Subcutaneous1763


title: Testis-1_A01_180202

description: testis.uniq.sorted.bw

source_name: Testis

value: Testis


title: Normal IgG 10 mg/kg [223235]

description:
Study#2
Normal IgG 10 mg/kg [223235]


title: Normal IgG 10 mg/kg [223252]

description:
Study#2
Normal IgG 10 mg/kg [223252]


title: endo_con_rep2

value: untreated

value: HPMEC


title: Testis-1_A01_181224

description: testis.uniq.sorted.bw


title: Subcutaneous1759

value: Male


title: Testis-1_A01_180130

description: testis.uniq.sorted.bw

data_processing:
Library strategy: Iso-seq
ROI (Reads-Of-Insert) reads were extracted and primer sequences flanking ROI reads were then trimmed
Primer-trimmed reads were further processed to scan the PA tail and trimmed to get PA-trimmed reads which represents reads with a PA tail trimmed.
PA-trimmed reads were then mapped to the reference genome (rheMac8 for macaque; mm9 for mouse) by GMAP and the low-quality reads were filtered to get the final processed alignments.
Genome_build: rheMac8, mm9
Supplementary_files_format_and_content: bigWig files were generated using DeepTools (version 3.3.0) with default parameters; scores represented coverage of uniquely-mapped Iso-seq reads;


title: Subcutaneous1755


title: Normal IgG 10 mg/kg [223237]

description:
Study#2
Normal IgG 10 mg/kg [223237]


title: Normal IgG 10 mg/kg [223251]

description:
Study#2
Normal IgG 10 mg/kg [223251]


title: SLC TKO_BRD4_IP_rep3

data_processing:
Read trimming was performed using Skewer
Read mapping was performed to GRCh38/hg38 using Bowtie2 and the “-very sensitive” parameter. Only unique reads with a mapping quality >30 and alignment to the nuclear genome were included in the downstream analyses.
Peak calling was performed using MACS2 using respective IgG ChIP samples as control.
Peaks overlapping blacklisted features defined in the ENCODE project38 were discarded from the analyses.
Consensus peak set generation of ChIP-seq peaks across samples per ChIP-seq dataset, read count quantification per peak and read count normalization across samples using reads per million normalization (rpm) was performed as implemented in ngs.toolkit
ChIP-seq consensus peaks were annotated to their closest gene body as implemented in ngs.toolkit
Principal component analysis (PCA) was performed using the R package factoextra
Differential expression analysis was performed using DESeq2 using raw count data
Differential regions were defined as having an FDR-adjusted p-value <0.01 and an absolute log2 fold change >= 1
Genome_build: GRCh38/hg38

source_name: BRD4 reporter KBM7 cells (REDS15)

growth_protocol: BRD4 reporter KBM7 cells (REDS15) were grown in IMDM supplemented with 10% FBS and 1% PS

extract_protocol:
50 million cells were crosslinked with 1% formaldehyde for 10 min at room temperature followed by quenching with 125 mM glycine (pH 2.5) for 5 min on ice. After two times washing with cold PBS, cell pellet was lysed and then the chromatin was sheared using a Covaris S2X (duty cycle: 5%; intensity: 4; power: 10 W; cycles per burst: 200; time: 40 min). The fragmented chromatin was incubated with antibodies overnight at 4 °C, followed by a 3 h incubation with Dynabeads Protein G (Thermal Fisher Scientific) at 4 °C. After washing the beads twice with low-salt RIPA buffer, twice with high-salt RIPA buffer and twice with RIPA-LiCl buffer, the antibody-bound chromatin was eluted, and treated with RNase for 30 min at 37 °C, with proteinase K for 2.5 h at 55°C, and then decrosslinked overnight at 65 °C. DNA was then extracted using phenol-chloroform, precipitated and then dissolved in Tris-EDTA buffer.
NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, E7645S) with NEBNext Multiplex Oligos for Illumina (New England Biolabs, E7335S and E7500S)

treatment_protocol: (+)-JQ1 or 6-MP treatment: 48h; sgRen or SLC TKO: 12 days after lentivirus delivered sgRNA in cells

value: SLC35F5/28A3/29A4 triple knockout, day 12

tag: chip-ab

value: BRD4 (ab128874, Abcam)


title: Normal IgG 10 mg/kg [223241]

description:
Study#2
Normal IgG 10 mg/kg [223241]


title: Testis-2_C02

description: testis.uniq.sorted.bw


title: SLC TKO_BRD4_IP_rep2


title: SLC TKO_BRD4_IP_rep1


title: Normal IgG 10 mg/kg [223240]

description:
Study#2
Normal IgG 10 mg/kg [223240]


title: SLC TKO_IgG_IP

value: rabbit polyclonal IgG (sc-66931, Santa Cruz)


title: sgRen_BRD4_IP_rep3

value: control Renilla sgRNA , day 12


title: Brain-3_D01

description: brain.uniq.sorted.bw

source_name: Brain

value: Brain


title: sgRen_BRD4_IP_rep2


title: Brain-4_E01

description: brain.uniq.sorted.bw


title: sgRen_BRD4_IP_rep1


title: sgRen_IgG_IP


title: Normal IgG 10 mg/kg [223248]

description:
Study#2
Normal IgG 10 mg/kg [223248]


title: Normal IgG 10 mg/kg [223253]

description:
Study#2
Normal IgG 10 mg/kg [223253]


title: Normal IgG 10 mg/kg [223244]

description:
Study#2
Normal IgG 10 mg/kg [223244]


title: JQ1_BRD4_IP_rep1

value: (+)-JQ1 1 micromolar, 48h


title: Brain-2_F03

description: brain.uniq.sorted.bw


title: JQ1_IgG_IP


title: Brain-2_C03

description: brain.uniq.sorted.bw


title: 6MP_BRD4_IP_rep3

value: 6-MP 1 micromolar, 48h


title: 6MP_BRD4_IP_rep2


title: Normal IgG 10 mg/kg [223238]

description:
Study#2
Normal IgG 10 mg/kg [223238]


title: Testis-1_G02

description: testis.uniq.sorted.bw


title: 6MP_BRD4_IP_rep1


title: JQ1_BRD4_IP_rep3


title: JQ1_BRD4_IP_rep2


title: Normal IgG 10 mg/kg [223245]

description:
Study#2
Normal IgG 10 mg/kg [223245]


title: PBS 10ml/Kg [223226]

description:
Study#2
PBS 10ml/Kg [223226]


title: Normal IgG 10 mg/kg [223246]

description:
Study#2
Normal IgG 10 mg/kg [223246]


title: Kif3aΔTub

city: Hamburg

first: Yu

last: Zhao

address: Falkenried 94

department: Institute of Medical Systems Biology

institute: University Medical Center Hamburg-Eppendorf

description: Disease

data_processing:
10x Genomics raw sequencing data were processed using CellRanger software (version 3.0.2, 10x Genomics, Pleasanton, CA) and the 10x mouse genome mm10 3.0.0 release as the reference (function cellranger count). The matrices of cells and the unique molecular identifier (UMI) count were obtained and further processed by the R package Seurat (version 3.1.1)
As a quality-control (QC) step, we first filtered out genes detected in less than 3 cells and those cells in which less than 200 genes had nonzero counts. To remove potential doublets, cutoff values for number of expressed genes (nGene) were determined for samples following visual inspection of the distribution of nGene and nUMI for each cell. The cells with higher nGene values (6000) were excluded. We further removed low-quality cells with more than 50% mitochondrial genes of all detected genes
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: kidney

growth_protocol: Single cell suspension was prepared using a cold active protease (CAP). Briefly, one kidney per mouse was minced into pieces on ice, transferred to 2 hard tissue homogenizing tube (CK28, Percells) filled with 1ml ice-cold PBS and homogenized using Minilys® (Bertin-instruments) at highest speed for 15 s. The homogenized kidney was centrifuged at 400 g for 4 min at 4ºC.  Kidney pellet was suspended in 2 ml red blood lysis buffer (R7757, Sigma-Aldrich) for 2 min to remove red blood cells. After spin down kidney pellet was suspended in 2 ml CAP solution (10 mg/ml Bacillus Licheniformis protease (P5380, Sigma-Aldrich), 5 mM CaCl2, 100 U/ml DNAse (04536282001, Roche) in PBS) for 20 min on ice with repeated trituration steps for 20 s every 5 min. The digestion was neutralized by 15 ml PBS supplemented with 10% fetal bovine serum (FBS) and passed through a 40 μm Corning® cell strainer.

extract_protocol:
Cells were loaded on a 10x Chromium single cell instrument.
All steps were performed according to standard protocol of the Chromium single cell 3’ v3 kit to generate high-quality cDNA libraries.

treatment_protocol: Cells were centrifuged at 400 g for 4 min at 4°C and washed twice in 20 ml PBS supplemented with 0.5% bovine serum albumin (BSA). Dead cells were removed by dead cell removal kit (130-090-101, Miltenyi Biotec) according to the manufacturer’s protocol. The living cells were passed through a 30 µm cell strainer (04-004-2326, Sysmex) and cell concentration was determined using a TC20™ automated cell counter (Bio-Rad).

tag: age

value: 5 weeks

value: KO

tag: tissue/cell type

value: kidney cells


title: WT

description: Control

value: WT


title: 6MP_IgG_IP


title: SAMPLE_76

status: Public on Apr 16 2021

city: New York

first: Eric

last: Vornholt

state: NY

address: 800 E. Leigh St. Box 980126

institute: Icahn School of Medicine

description:
Random primer labeling coupled with RNase R sample pretreatment to ensure specific and efficient labeling of circular RNAs.
circRNA

hyb_protocol: Not availible through manufacturer

scan_protocol: Not availible through manufacturer

data_processing: Not availible through manufacturer

source_name: Postmortem Nucleus Accumbens

growth_protocol: Not Used

extract_protocol: Total RNA containing the small RNA fraction was isolated from 100mg fresh frozen tissue from the prefrontal cortex (PFC) using the mirVana-PARIS kit (Life Technologies, Carlsbad, CA) following manufacturer's protocols. RNA concentration was measured using the Quant-iT Broad Range RNA Assay kit (Life Technologies) and the RNA Integrity Number (RIN) was measured on the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA).

treatment_protocol: Not Used

tag: diagnosis

value: Alcohol

tag: rin

tag: brain weight

tag: ph

tag: pmi

tag: hemisphere

tag: neuropathology

tag: hepatology

tag: toxicology

tag: smoking


title: SAMPLE_77

label_protocol: Random primer labeling coupled with RNase R sample pretreatment to ensure specific and efficient labeling of circular RNAs.

value: Control


title: SAMPLE_80


title: SAMPLE_73


title: SAMPLE_64


title: PBS 10ml/Kg [223228]

description:
Study#2
PBS 10ml/Kg [223228]

tag: disease

value: Melanoma


title: SAMPLE_82


title: SAMPLE_69


title: SAMPLE_66


title: SAMPLE_54


title: SAMPLE_51


title: SAMPLE_74


title: SAMPLE_57


title: SAMPLE_70


title: SAMPLE_46


title: SAMPLE_56


title: SAMPLE_60


title: SAMPLE_61


title: PBS 10ml/Kg [223232]

description:
Study#2
PBS 10ml/Kg [223232]


title: SAMPLE_48


title: SAMPLE_30


title: SAMPLE_40


title: SAMPLE_42


title: SAMPLE_27


title: SAMPLE_26


title: anti-PDL1 3

city: Nantong

first: zhao

last: yu

address: qixiu road 19

institute: Nantong university

data_processing:
Sequencing by BGISEQ500 platform
filtering low quality readers  for the reliability of the results.
HISAT was used to align the clean reads to the reference genome
Align clean reads to the reference genes by using Bowtie2 to get the alignment result.
Genome_build: GCF_000001635.26_GRCm38.p6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: MC38 cells

extract_protocol: RNA was extracteded using Trizol reagent

tag: tissue

value: tumor grafted subcutaneously


title: exercise with anti-PDL1 2


title: control 4


title: exercise 1


title: anti-PDL1 1


title: exercise 3


title: anti-PDL1 2


title: control 3


title: exercise with anti-PDL1 4


title: exercise with anti-PDL1 1


title: anti-PDL1 4


title: exercise 4


title: SAMPLE_45


title: SAMPLE_33


title: SAMPLE_25


title: SAMPLE_18


title: control 2


title: SAMPLE_20


title: SAMPLE_35


title: exercise 2


title: SAMPLE_13


title: control 1


title: exercise with anti-PDL1 3


title: SAMPLE_24


title: Z6_Zfp541-KO_lP_360h_rep2

city: Hangzhou

first: Li

state: Zhejiang

address: Shilongshan ST #18, Xihu District

institute: Westlake University

data_processing:
For plate-based scRNA-seq by SMART-Seq2, UMI-tools (version 1.0.0) extract subcommand was used to extract barcode and UMI from the read 2 (Smith et al., 2017). Next, read 1 was trimmed to remove TSO sequence, polyA tail, adaptor contaminants, and low-quality bases from the 3’ end with flexbar (version 3.4.0) (Roehr et al., 2017). The clean reads were aligned to mm10 mouse reference genome merged with ERCC spike-in sequences using STAR (version 2.5.3a) with default parameters (Dobin et al., 2013). The uniquely aligned reads were further assigned to gencode.vM21 gene annotation merged with ERCC spike-in by featureCounts (version 1.6.4) and then distinct UMIs per gene in each cell are counted with UMI-tools count subcommand with defined parameters (--per-gene --gene-tag=XT --assigned-status-tag=XS --per-cell) to generate final digital gene expression matrix (Liao et al., 2014). Raw counts matrix were normalized to log(CPM/10+1). Cells fulfill with any of the following criteria were removed from the following analysis: (1) < 2,000 genes; (2) < 50,000 UMIs; (3) percentage of ERCC UMIs > 20%; (4) percentage of mitochondria > 5%. To remove germ cells contaminated by somatic cell, cells with log normalized expression level of Vim > 3 or Clu > 4 were excluded. Only protein coding genes expressed at least in 10 cells were kept for further analysis. Finally, the plate-based scRNA-seq generated 929 profiles in Fig. 3a.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include gene informations
Supplementary_files_format_and_content: tab-delimited text files include cell metadata
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

molecule: polyA RNA

source_name: late pachytene spermatocytes

extract_protocol:
Testicular tissues were disassociated enzymatically using enzyme mixtures comprising of 1 mg/mL collagenase IV (GIBCO,17104-019), 1.5 mg/mL hyaluronidase (SIGMA，H2126), 1 mg/mL trypsin (SIGMA，T1426), and 1 mg/mL DNase I (SIGMA, DN25), dissolved in DMEM medium at 35℃ with gentle agitation for 20 mins. Subsequently, the cell suspension was filtered through a 40 μm cell strainer, centrifuged at 250×g for 5 min at 4 °C, the supernatant was removed and cells in the pellet were resuspended in cold PBS (Phosphate buffer saline) containing 0.05% BSA carefully.
Single-cell RNA-seq by Smart-seq2 were performed as previously reported (Chen et al., 2018b; Li et al., 2017; Picelli et al., 2013). Briefly, the single spermatogenic cells were picked into lysis buffer containing reverse transcription primers by mouth pipette. After the first-strand synthesis, the second-strand cDNAs were synthesized, and the cDNAs were amplified by 17 cycles of PCR. Samples with different barcodes were pooled together. Biotinylated pre-indexed primers were used to amplify the PCR product by an additional 4 cycles of PCR to introduce biotin tags to the 3′ ends of the amplified cDNA. cDNA was sheared to approximately 300 bp by Covaris S2, and the 3′ terminal of the cDNA was captured by Dynabeads® MyOne Streptavidin C1 beads (Thermo Fisher). The RNA-seq library was constructed using a Kapa Hyper Prep Kit (Kapa Biosystems) and subjected to 150 bp paired-end sequencing on an Illumina HiSeq 4000 platform (sequenced by Novogene).

treatment_protocol: 2-dpp mice were pipette fed WIN 18,446 (MP) for 7 consecutive days. At Day 8 of WIN 18,446 treatments, these animals were received an injection of RA (Sigma), and then left to recover. We collected testes enriched for early (260 hours after retinoic acid treatment) and late pachytene (360 hours after retinoic acid treatment) cells from WT and Zfp541-KO mice.

tag: cell type

value: germ cells

value: testis

tag: genotype

tag: developmental stage

value: late pachytene

tag: treatment

value: 360h after RA restoration


title: Z2_Zfp541-KO_lP_360h_rep1

tag: strain


title: Z8_Zfp541-KO_lP_360h_rep3


title: Z5_WT_lP_360h_rep3


title: Z3_Zfp541-KO_eP_260h_rep2

source_name: early pachytene spermatocytes

value: early pachytene

value: 260h after RA restoration


title: Z4_WT_lP_360h_rep2


title: Z10_WT_lP_360h_rep1


title: Z7_Zfp541-KO_eP_260h_rep3


title: C-TA replicate 2

city: Kashiwa

first: Fumihito

last: Miura

state: Chiba

address: Kashiwanoha 5-1-5

department: Graduate School of Frontier Sciences

country: Japan

institute: The University of Tokyo

data_processing:
Reads were mapped on mixed reference of human genome hg19 and lammbda phage genome using in-house program BMap.
Alignments exported from BMap were summarized into a binary file in graph format using in-house program MPTC.
The methylation levels and coverage were exported from the file in graph format using in-hose program MethExport
Genome_build: Mouse mm10
Supplementary_files_format_and_content: bedGraph

source_name: Tibialis anterior satellite cells replicate 2

extract_protocol:
Protease K treated muscle tissues are extracted with phenol, phenol/chloroform, and chloroform. DNA was ethanol precipitated, dissolved in 10 mM Tris-buffer (pH8.0)
tPBAT method as described in Miura F et al (2019), NAR, 47, e85

value: Tibialis anterior

tag: sample type

value: Satellite cells


title: Fetal liver HSC scRNA sequencing

city: Zhengzhou

first: Yanfang

last: Lu

state: Henan

address: Weiwu road 7th

institute: Zhengzhou University

data_processing:
The FASTQ format results were analyzed using Cell Ranger pipeline (3.0.2) for sample demultiplexing, barcode processing and gene counting.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: Fetal liver

extract_protocol:
For whole fetal liver single cell RNA sequencing, fetal liver tissues were isolated from E14.5 C57BL/6 pregnant mice and digested by dissociation enzyme (Accutase) for 10 min at room temperature. Red blood cells were removed using 1×RBC lysis buffer at 4 °C. Then, cells were passed through a 40 μm strainer and re-suspended in cold DPBS with 0.04% (wt/vol) BSA. For sorted HSC single cell RNA sequencing, fetal liver tissues were isolated from E14.5 C57BL/6 pregnant mice and in cold 1×PBS dissociated into single cell suspension by pipetting up and down through 15 mL pipette. Red blood cells were removed using 1×RBC lysis buffer at room temperature for 5 min. Cells were incubated for 5 minutes at room temperature and mixed constantly by inverting the tube. After that, cells were centrifuged for 5 minutes then the supernatant was carefully removed without disturbing the pellet cells. Cells were resuspended in cold 1×PBS with 0.5% BSA, passed through a 40 μm strainer.
RNA libraries were prepared with Chromium Single Cell 3′ Reagent Kits (v2) Kits according to the manufacturer's protocol.

value: wild type

value: liver

value: hematopoietic stem cell (HSC)


title: WT E14.5 fetal liver

data_processing:
Paired-end reads were aligned to the mouse genome (Gencode vM14) with Tophat and transcripts were assembled with Cufflinks.
Genome_build: Gencode vM14
Supplementary_files_format_and_content: tab-delimited file include FPKM values

extract_protocol:
Total RNA was extracted from E14.5 fetal liver using RNeasy Mini Kit (QIAGEN, 74104). mRNA was isolated using the Dynabeads mRNA Purification Kit.
The cDNA libraries were produced with a NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® and NEBNext® Multiplex Oligos for Illumina® according to the manufacturer’s description.


title: Z9_WT_eP_260h_rep3


title: Z11_Zfp541-KO_eP_260h_rep1


title: Whole fetal liver scRNA sequencing


title: Z1_WT_eP_260h_rep1


title: Z12_WT_eP_260h_rep2


title: C-TA replicate 1

source_name: Tibialis anterior satellite cells replicate 1


title: C-TA replicate 3

source_name: Tibialis anterior satellite cells replicate 3


title: C-MAS replicate 2

source_name: Masseter satellite cells replicate 2

value: Masseter


title: C-MAS replicate 3

source_name: Masseter satellite cells replicate 3


title: T-TA replicate 3

source_name: Tibialis anterior muscle tissue replicate 3

value: Muscle tissue


title: T-TA replicate 2

source_name: Tibialis anterior muscle tissue replicate 2


title: T-TA replicate 1

source_name: Tibialis anterior muscle tissue replicate 1


title: T-MAS replicate 1

source_name: Masseter muscle tissue replicate 1


title: C-MAS replicate 1

source_name: Masseter satellite cells replicate 1


title: Spleen CD32+ T4 cells from CM #3

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

description:
Mac.PvsM.complete.txt
MACp3

data_processing:
Reads were cleaned of adapter sequences, and low-quality sequences were removed using cutadapt version 1.11.Only sequences ≥ 25 nucleotides (nt) in length were considered for further analysis.
STAR version 2.5.0a, with default parameters, was used for alignment on the reference genome
Genes were counted using featureCounts version 1.4.6-p3 from Subreads package (parameters: -t gene, -g ID and -s 1).
Data were analyzed using R version 3.4.3 and the Bioconductor package DESeq2 version 1.18.185. Normalization and dispersion estimation were performed with DESeq2, using the default parameters, and statistical tests for differential expression were performed by applying the independent filtering algorithm. A generalized linear model, including the monkey identifier as a blocking factor, was used to test for the differential expression between the biological conditions. For each pairwise comparison, raw p values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure86. Genes with an adjusted p value <0.05 were considered differentially expressed.
Genome_build: Chlorocebus sabaeus, and macaca fascicularis from Ensembl release 90
Supplementary_files_format_and_content: Matrix from DESeq2

source_name: Spleen from cynomolgus macaque

extract_protocol:
RNA was isolated from the sorted CD4 populations cells using the RNeasy® Mini Kit (205113, Qiagen)
RNA integrity was verified with the Agilent Bioanalyser. DNase-treated RNA was treated for library preparation using the Truseq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA), according to manufacturer’s instructions. An initial poly(A) RNA isolation step (included in the Illumina protocol) is performed on 10 ng of total RNA to keep only the polyadenylated RNA fraction and remove the ribosomal RNA. A step of fragmentation is then performed on the enriched fraction, by divalent ions at high temperature. The fragmented RNA samples were randomly primed for reverse transcription followed by second-strand synthesis to create double-stranded cDNA fragments. No end repair step was necessary. An adenine was added to the 3'-end and specific Illumina adapters were ligated. Ligation products were submitted to PCR amplification. The obtained oriented libraries were controlled by Bioanalyzer DNA1000 Chips (Agilent, # 5067-1504) and quantified by spectrofluorimetry (Quant-iT™ High-Sensitivity DNA Assay Kit, #Q33120, Invitrogen). Sequencing was performed on the Illumina Hiseq2500 platform to generate single-end 100 bp reads bearing strand specificity.

treatment_protocol: A 6-color panels was used to sort CD32+/- CD4+ T cells from the spleen of 3 chronically infected AGM and 3 chronically infected cynomolgus macaques. Cells were thawed in 20% FBS-containing media supplemented with benzonase nuclease, and counts and viabilities were performed (Life Technologies).  Cells were  incubated with Fcγ receptor blocker for 10 minutes. Antibody cocktail mix was added and incubated for 20 minutes. Following surface staining, cells were washed and resuspended in complete medium and kept in the dark at 4°C until acquisition. Cells were sorted on a FACSAria II (BD Biosciences)  in purity mode. For RNA extraction cells  were directly collected in a lysis buffer that contained TCEP. The purity of the cells was >97%.

tag: animal status

value: SIVmac251 chronically infected

value: spleen

value: CD4+ T lymphocytes

tag: cell phenotype


title: T-MAS replicate 3

source_name: Masseter muscle tissue replicate 3


title: Spleen CD32+ T4 cells from CM #2

description:
Mac.PvsM.complete.txt
MACp2


title: Spleen CD32+ T4 cells from CM #1

description:
Mac.PvsM.complete.txt
MACp1


title: Spleen CD32- T4 cells from CM #3

description:
Mac.PvsM.complete.txt
MACm3


title: Spleen CD32- T4 cells from CM #2

description:
Mac.PvsM.complete.txt
MACm2


title: Spleen CD32- T4 cells from CM #1

description:
Mac.PvsM.complete.txt
MACm1


title: SAMPLE_43

source_name: Postmortem Nucleus Accumbens

tag: diagnosis

value: Alcohol

tag: age

tag: rin

tag: brain weight

tag: ph


title: WT_input_rep1

data_processing:
Adaptors were trimmed and low-quality reads were removed from raw reads by cutadapt (version 2.6) with defined parameters (-a AGATCGGAAGAG –A AGATCGGAAGAG –q 30 –m 16) (Martin, 2011). Then clean reads were aligned to the mouse genome (mm10) using bowtie2 (version 2.3.5) with default parameters and transform into bam format with samtools (version 1.10) (Langmead and Salzberg, 2012; Li et al., 2009). Duplicated reads were filtered using picard MarkDuplicates (version 2.23.4) subcommand with defined settings (REMOVE_DUPLICATES=true). To identify ZFP541’s binding sites, MACS2 (version 2.2.6) subcommand callpeak was used with defined parameters (-f BAMPE -g mm -q 0.9 -m 2 50). To reduce the false positive binding sites (Zhang et al., 2008), the peaks overlapped with blacklist regions were removed from the following analysis (Amemiya et al., 2019). Deeptools subcommand bamCoverage (version 3.5.0) was used to produce bigWig track for data visualization with defined parameters (-bs 10 --normalizeUsing RPGC --effectiveGenomeSize 2652783500 --extendReads) from bam files excluding blacklist regions (Ramirez et al., 2016).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated using deeptools subcommand bamCoverage (version 3.5.0)
Supplementary_files_format_and_content: peak text files

source_name: Wild type pachytene/diplotene spermatocytes

extract_protocol:
The enriched pachytene and diplotene spermatocytes were cross-linked with 1% formaldehyde for 10 min and then stopped by adding 10× glycine solution. Chromatin samples were prepared with Chromatin IP Kit (CST, 9005S) according to the manufacturer’s guidelines. Specific antibodies were incubated with chromatin samples overnight at 4 °C. Antibodies used are: Control rabbit IgG (from ChIP kit) and rabbit-ZFP541 (Epitope: 1-300 aa). The protein-DNA complexes were immobilized on 30μL protein A/G beads at 4℃ for 4 hrs, and then washed sequentially in low salt buffer for three times, high salt buffer for one time, and then eluted with Elution buffer at 65℃ for 30 mins. De-crosslinking was carried out in elution buffer (with proteinase K) at 65 °C overnight. DNA samples were purified with DNA Purification Buffers and Spin Columns (CST, 14209S). Immunoprecipitated and input DNAs were analyzed by deep sequencing.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit

treatment_protocol: Single testicular cells from adult mice were prepared by enzyme mixture digestion as described above, pachytene and diplotene spermatocytes were then isolated and enriched using the STA-PUT method as previously reported (Bryant et al., 2013; Jiang et al., 2017).

value: Pachytene/diplotene spermatocytes

value: Testis

value: WT

value: Adult

tag: antibody


title: WT_input_rep2


title: WT_ZFP541_rep2


title: ZFP541-KO_ZFP541_rep1


title: WT_ZFP541_rep1


title: PEG18_4

city: Shihezi

first: Hong

state: Xinjiang

address: Beisi road

department: School of Pharmacy

institute: Shihezi University

description: Chlorella cells PEG2 rep2

data_processing:
Illumina Casava1.8 software used for basecalling.
Clean data were filtered after the removal of adapters, poly-N strands, and low-quality reads. There was no reference genomes for Chlorella sp. TLD6B, and de novo assembly for clean reads was performed by using Trinity (Grabherr et al, 2011).
The sequences were compared with databases such as NR, NT, Swiss-Pro, GO, KEGG, PFAM, and KOG using Blast X (e-value ≤ 10-5). The GO annotation of Unigenes was obtained using BLast2GO (Götz al., 2008).
FPKM method was used for the analysis of gene expression levels (Trapnell et al., 2010)
DESeq (Anders et al, 2010) was used to analyze differently expressed genes, with |log2FC|≥1 and P < 0.05 as the threshold. The DEGs with P value and FDR lower than 0.05, were mapped to terms in databases GO and KEGG for functional and pathway analysis.
Genome_build: mm9

organism: Chlorella sp.

source_name: Chlorella cells

growth_protocol: The algae cells in the logarithmic growth phase were inoculated into Erlenmeyer flask containing 500 ml BBM medium. With the light intensity of 4000 lx,  light-dark cycle of 12h/12h, and temperature of 23 ℃, flasks were shaken three times a day at regular intervals and cultured for 24 days.

extract_protocol:
Chlorella were cleaned and quickly stored at - 80℃ for RNA extraction.Total RNA was isolated using TRIzol reagent (Invitrogen, USA). RNA quality was measured using Agilent Bioanaylzer 2100 (Agilent Technologies, Palo Alto, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: NaCl was added into the BBM medium, making the NaCl concentrations for the salt stress treatments reaching 0.1 M, 0.8 M. PEG-6000 was added into the BBM medium, making the PEG-6000 concentrations for the drought stress treatments reaching 0.05 g/mL, 0.1 g/mL.  The NaCl or PEG-6000 concentration for the control was 0.0 M.

value: Chlorella cells

value: treated with 0.1g/mL PEG-6000 for 18 days


title: PEG18_3

description: Chlorella cells PEG2 rep1


title: PEG18_2

description: Chlorella cells PEG1 rep2

value: treated with 0.05g/mL PEG-6000 for 18 days


title: Subcutaneous1761

source_name: NORM_HCHF_Subcutaneous adipose tissue

tag: Sex

value: Female

tag: prenatal nutrition

value: NORM

tag: early postnatal diet

value: HCHF

value: Subcutaneous adipose tissue

tag: molecule subtype

value: mRNA/lncRNA


title: Capture-C of Hoxa1 in Mus musculus: Halr1-KO-RA-1d

city: Tianjin

first: Niannian

state: Tianjin

address: No. 94 Weijin Road, Nankai District, Tianjin

department: college of Life Sciences

institute: Nankai University

data_processing:
Library strategy: Capture-C
Clean reads of RNA-seq were mapped to mm10 using HISAT2(2.1.0)
Expression levels of all genes were counted and expression profile matrix was constructed with HTSeq (0.9.1)
Differential expression analysis was calculated in R using DESeq2(1.18.1), with p value < 0.05 and fold change > 2 or < 1/2
Clean reads of Capture-C were cut into two pieces in the DpnII sites
All the reads were mapped to mm10 with Bowtie2(2.3.1)
Report all the reads that contains the Bait sequence
Genome_build: mm10
Supplementary_files_format_and_content: Text files include genes counts values and Capture-C signal peaks for each Sample

source_name: Embryonic stem cell

growth_protocol: Mouse ESCs E14 was cultured as the previous scheme with a few modifications. ESCs were grown in culture dishes coated with 0.1% gelatin (Sigma, Lot # SLBQ9498V) in Dulbecco's Modified Eagle's Medium (DMEM, Gibco, Lot # 8119213) supplemented with 15% fetal bovine serum (FBS, AusGeneX, Lot # FBS00717-1), 100 nM nonessential amino acids (100x, Gibco, Lot # 2027433), 200 mM L-Glutamate (100x, Gibco, Lot # 2085472), 1% Penicillin-streptomycin (Gibco, Lot # 2029632), 50 μM β-mercaptoethanol (Sigma, Cas # 60-24-2), 10 ng/mL LIF (ESGRO, Lot # ESG1107), 1 μM PD0325901 (a MEK inhibitor, MedChemExpress, Lot # HY-10254) and 3 μM CHIR99021 (a GSK inhibitor, MedChemExpress, Lot # HY-10182). The medium was replaced every 1 - 2 days. All cells are maintained at 37 °C in a 5% CO2 incubator.

extract_protocol:
1. For RNA -seq: cells were lysed with Trizol reagent (Life Technologies) and RNA was extracted according to the manufacturer's instructions. 2. For Capture-C：Briefly, cells were fixed with 1% (vol/vol) formaldehyde for 10 min at room temperature, quenched with 125 mM glycine in PBS, and then lysed in cold lysis buffer (10 mM Tris–HCl, pH7.5, 10 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 0.2% NP-40, 1× complete protease inhibitor cocktail (Roche)). Chromatin was digested with DpnII (New England Biolabs) at 37°C overnight. Fragments were then diluted and ligated with T4 DNA ligase (Takara) at 16°C overnight. Cross-linking was reversed by overnight incubation at 60°C with proteinase K (Bioline). Then 3C libraries were purified by phenol-chloroform followed by chloroform extraction and ethanol-precipitated at −80°C overnight. Sequencing libraries were prepared from 10μg of the 3C library by sonication to an average size of 200 ~300 bp and indexed using NEBnext reagents (New England Biolabs), according to the manufacturer's protocol. Enrichment of 2μg of an indexed library incubated with 3uM of a pool of biotinylated oligonucleotides (probe sequences are listed in Supplementary Table 7) was performed using the SeqCap EZ Hybridization reagent kit (#05634261001, Roche/NimbleGen), following the manufacturer's instructions. Two rounds of capture employing 48~72 and 24 hr hybridizations, respectively, were used. Correct library size was confirmed by agarose gel electrophoresis, and DNA concentrations were determined using a Qubit 2.0 Fluorometer (Thermo Fisher Scientific). All sequencing was performed on Hi-Seq 2500 platforms using paired 150 bp protocols (Illumina).
The Capture-C libraray was constructed with NEBNext DNA Library Prep Master Mix Set for Illumina (NEB).

treatment_protocol: To induce ESCs differentiation, cells were gently washed with 1x phosphate buffer saline solution (PBS), dissociated and replanted at an appropriate density on gelatin-coated plates in LIF/2i withdrawal medium supplemented with 2µm RA (Solarbio®, Lot # 1108F031). The culture medium was replaced at the given point-in-time.

tag: cell line

tag: tissue

value: embryo, blastocyst embryo, blastocyst

tag: cell type

value: Embryonic stem cell

value: RA induced differentiation


title: T-MAS replicate 2

source_name: Masseter muscle tissue replicate 2

value: Masseter

value: Muscle tissue


title: Capture-C of Enhancer1/2/3 and Halr1 Hoxa1 in Mus musculus: WT-RA-1d

tag: treatment


title: Zfp541-KO whole testis

data_processing:
For droplet-based scRNA-seq by 10x Chromium, CellRanger (version 3.1.0) was used to aligned reads to the mm10 mouse reference genome. Raw counts matrix was imported into Seurat (version 3.2.0) for preprocessing (Stuart et al., 2019). Cells were excluded based on either one of the following criteria: (1) fewer than 1,000 genes; (2) percentage of mitochondria UMIs > 10%. Finally, 21,185 cells were kept for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: cell barcodes
Supplementary_files_format_and_content: gene information
Supplementary_files_format_and_content: digital expression matrix
Supplementary_files_format_and_content: cell metadata includes cell type, pseudotime, UMAP embeddings

source_name: tetraploid germ cells

extract_protocol:
Droplet-based scRNA-seq (10x Chromium) was performed by Genergy Bio-Technology (Shanghai) Co., Ltd. Testicular tissues were disassociated enzymatically using enzyme mixtures comprising of 1 mg/mL collagenase IV (GIBCO,17104-019), 1.5 mg/mL hyaluronidase (SIGMA，H2126), 1 mg/mL trypsin (SIGMA，T1426), and 1 mg/mL DNase I (SIGMA, DN25), dissolved in DMEM medium at 35℃ with gentle agitation for 20 mins. Subsequently, the cell suspension was filtered through a 40 μm cell strainer, centrifuged at 250×g for 5 min at 4 °C, the supernatant was removed and cells in the pellet were resuspended in cold PBS (Phosphate buffer saline) containing 0.05% BSA carefully. Tetraploid germ cell populations were then isolated by flow cytometry as previously described (Jung et al., 2019). Single tetraploid germ cells were stained with trypan blue (Invitrogen) and counted using light microscopy and then loaded onto a 10x Chromium microfluidics system according to the manufacturer’s guidelines.
Libraries were generated using Single Cell 3′ library and Gel Bead Kit v.3 according to the protocol guidelines. The final library pools were sequenced on an Illumina Novo 6000 platform instrument using 150-base-pair paired-end reads.

value: germ cells

tag: strain

value: testis

tag: genotype

tag: developmental stage


title: WT whole testis

value: WT


title: QHMM rep2 microRNA

city: Changchun

first: Limin

last: Sun

state: Jilin

address: Xincheng Street 2888,Jingyue Distric

institute: Jilin Agricultural University

data_processing:
We applied the reads filtration to filter the reads with lower quality and short sequence under following criteria: read length > 50; over 30% base quality >13.
We applied the miRNA-seq mapping using Mapsplice software to the Sheep miRbase,  Sheep genome, Human miRbase,Mouse miRbase,Rat miRbase and Rfam for further study.
The differentially expressed miRNAs were achieved by Using DEseq program(｜log2FoldChange｜was >0.585 and FDR was<0.05),The miRanda database was used to predict the target genes of  DEmiRNAs.
Gene Ontology (GO) terms were assigned to target genes
pathway analysis was used to find out the significant pathway of the target genes according to KEGG database.
Genome_build: Oar_v3.1
Supplementary_files_format_and_content: tab-delimited text files include all counts values for each Sample

source_name: longissimus muscle

growth_protocol: Natural conditions

extract_protocol:
Total RNA was extracted from muscle tissue samples by Trizol Reagent (Life technologies, USA). The RNA quality was checked by NanoDrop 2000(Thermo scientific, USA) and Agilent 2200(Agilent, USA) instruments.
The cDNA libraries were prepared for single-end sequencing by using Ion Total RNA-Seq Kit v2.0 (Life technologies, USA) and had been size selected by PAGE Gel electrophoresis for miRNA sequencing. Samples were diluted and processed on a OneTouch 2 instrument(Life Technologies, USA) and enriched on a OneTouch 2 ES station(Life Technologies, USA) for preparing the template-positive Ion PI™ Ion Sphere™ Particles(Life Technologies, USA)according to Ion PI™ Template OT2 200 Kit v2.0(Life Technologies, USA).

treatment_protocol: Two breeds of sheep

value: longissimus muscle

tag: breed

value: Qianhua Mutton Merino


title: STH rep3 microRNA

value: Small Tail Han


title: QHMM rep3 microRNA


title: STH rep2 microRNA


title: PEG18_1

description: Chlorella cells PEG1 rep1

value: Chlorella cells

value: treated with 0.05g/mL PEG-6000 for 18 days


title: Nacl18_3

description: Chlorella cells NaCl2 rep1

value: treated with 0.8M NaCl for 18 days


title: Nacl18_4

description: Chlorella cells NaCl2 rep2


title: RNA-Seq of Mus musculus: DKO(Hoxa1-Halr1)-RA-1d rep-3

data_processing:
Clean reads of RNA-seq were mapped to mm10 using HISAT2(2.1.0)
Expression levels of all genes were counted and expression profile matrix was constructed with HTSeq (0.9.1)
Differential expression analysis was calculated in R using DESeq2(1.18.1), with p value < 0.05 and fold change > 2 or < 1/2
Clean reads of Capture-C were cut into two pieces in the DpnII sites
All the reads were mapped to mm10 with Bowtie2(2.3.1)
Report all the reads that contains the Bait sequence
Genome_build: mm10
Supplementary_files_format_and_content: Text files include genes counts values and Capture-C signal peaks for each Sample


title: Capture-C of Enhancer1/2/3 in Mus musculus: WT-RA-0d


title: STH rep1 microRNA


title: QHMM rep1 microRNA


title: Nacl18_1

description: Chlorella cells NaCl1 rep1

value: treated with 0.1M NaCl for 18 days


title: CK18_2

description: Chlorella cells CK18 rep2

value: untreated for 18 days


title: RNA-Seq of Mus musculus: DKO(Hoxa1-Halr1)-RA-1d rep-1


title: CK18_1

description: Chlorella cells CK18 rep1


title: RNA-Seq of Mus musculus: Hoxa1-KO-RA-1d rep-3


title: CK0_2

description: Chlorella cells CK0 rep2

value: untreated for 0 days


title: RNA-Seq of Mus musculus: Hoxa1-KO-RA-1d rep-2

value: embryo, blastocyst embryo, blastocyst


title: CK0_1

description: Chlorella cells CK0 rep1


title: WFMD232A - Control

city: Hamilton

first: Jocelyn

middle: M

last: Wessels

address: 1280 Main Street West

department: Obstetrics and Gynecology

institute: McMaster University

data_processing:
Paired-end alignment using PANDAseq
FASTQ Trimming using Cutadept/sickle
FASTQ Culling using Chimera checking
OTU picking - de novo (AbundantOTU+, CD-HIT, DNACLUST, UCLUST, UPARSE) and closed reference (BLAST, UCLUST-ref, UCLUST-ref-strict)
Genome_build: Taxon Assignment - assigment algorithm (BLAST, RDP) and reference database (Greengenes 2011, Greengenes 2013, Silva 111)
Supplementary_files_format_and_content: otu_table_rdp-training_gg2011_n1_noRoot_L6.xlsx (Relative abundance table)

source_name: Endometrial biopsy

extract_protocol:
Genomic DNA was extracted from the endometrial biopsies using the RNeasy Mini Kit (Qiagen, Hilden, Germany), omitting the DNase treatment, and following the manufacturer’s protocol. The quantity and purity of nucleic acids was assessed using the Nanodrop 2000. In order to retain bacterial DNA and eliminate the RNA that might inhibit the PCR reaction, RNase A (Qiagen Hilden, Germany) was added to the first PCR mastermix. The hypervariable V3 region of the 16S rRNA gene was amplified by using a two-stage (nested) PCR approach.
sl1p pipeline (Whenlan and Surette, 2017, BMC Microbiome)
16S rRNA gene sequencing

tag: group

value: control

value: Endometrial biopsy

tag: material sequenced

value: 16S rRNA gene


title: RNA-Seq of Mus musculus: Hoxa1-KO-RA-1d rep-1

value: Embryonic stem cell

value: RA induced differentiation


title: WFMD227A - Control


title: RNA-Seq of Mus musculus: Hoxa1-WT-RA-1d rep-3


title: WFMD222B - Control


title: RNA-Seq of Mus musculus: Hoxa1-WT-RA-1d rep-2


title: WFMD215B - Control


title: RNA-Seq of Mus musculus: DKO(Hoxa1-Halr1)-RA-1d rep-2


title: WFMD206A - Control


title: Nacl18_2

description: Chlorella cells NaCl1 rep2


title: WFMD202B - Control


title: RNA-Seq of Mus musculus: Halr1-KO-RA-1d rep-3


title: RNA-Seq of Mus musculus: Hoxa1-WT-RA-1d rep-1


title: WFMD190B - Control


title: RNA-Seq of Mus musculus: Halr1-KO-RA-1d rep-1


title: WFMD177B - Control


title: RNA-Seq of Mus musculus: Halr1-WT-RA-1d rep-3


title: WFMD176B - Case

value: endometriosis


title: Mg-treated Hypoxia-ischemia vs Mg-treated naive mice + 12h  [RV Mg 12h c]

city: Rouen cedex

first: Celine

last: Derambure

address: 22 Bvd Gambetta

institute: INSERM U905

description: Biological replicate 3 of 3. 5 day-old brain harvested 12h after hypoxia-ischemia.

hyb_protocol: Hybridization was performed according to the Agilent instructions for Gene Expression Hybridization Kit (catalog number 5188-5242). Samples were applied to microarrays enclosed in Agilent SureHyb hybridization chambers (65°C, 17H). After hybridization, slides were washed and dried in acetonitril.

scan_protocol: Scanned on an Agilent G2565CA scanner. Images were quantified using Agilent Feature Extraction Software (v 10.5.1.1)

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for data extraction and LOWESS normalization.

source_name: Brain Mg treated mice

label_protocol: Agilent Low input QuickAmp Labeling kit was used according to the manufacturer instructions (catalog number 5190-2306) with 100ng  of total starting RNA.

growth_protocol: Naval Medical Resarch Institute (NMRI)-mice housed in our laboratory. Day of birth was noted 1.

extract_protocol: Total RNA from brain hemisphere (deleted of olfactory bulb and sectionned anterior to colliculus) were extracted using Nucleospin RNA plus kit (Ref 740984-250; Macherey-Nagel) following manufacturer's instructions. RNA Integrity Number was obtained by BioAnalyzer 2100 (Agilent).

treatment_protocol: Animals at day 5 received sub-cutaneous injection of MgSO4 (600 mg/kg) in Phosphate buffered saline or saline alone. Right carotid was ligatured permanently. After 1h30, 3h, 6h 12h or 24h 6 animals (3 males and 3 females) were sacrificed and forebrain tissues were collected. Controls were obtained from the same liters and were collected at the same time.

value: Naval Medical Resarch Institute (NMRI)-mouse

value: MgSO4 (600 mg/kg)

tag: sublocalization

value: Forebrain

tag: time point

source_name: 5 day-old brain harvested 12h after MgSO4-treated hypoxia-ischemia

tag: hypoxia-ischemia (rv) or none

value: Hypoxia-ischemia (RV)

tag: delay for observation

value: forebrain


title: Hypoxia-ischemia vs naive mice + 12h  [RV PBS 12h c]

source_name: Brain Naive mice

value: PBS

source_name: 5 day-old brain harvested 12h after hypoxia-ischemia


title: Hypoxia-ischemia vs naive mice + 12h  [RV PBS 12h b]

description: Biological replicate 2 of 3. 5 day-old brain harvested 12h after hypoxia-ischemia.


title: Mg-treated Hypoxia-ischemia vs Mg-treated naive mice + 12h  [RV Mg 12h b]


title: Mg-treated Hypoxia-ischemia vs Mg-treated naive mice + 12h  [RV Mg 12h a]

description: Biological replicate 1 of 3. 5 day-old brain harvested 12h after hypoxia-ischemia.


title: Hypoxia-ischemia vs naive mice + 12h  [RV PBS 12h a]


title: Mg-treated Hypoxia-ischemia vs Mg-treated naive mice + 3h  [RV Mg 3h c]

description: Biological replicate 3 of 3. 5 day-old brain harvested 3h after hypoxia-ischemia.

source_name: 5 day-old brain harvested 3h after MgSO4-treated hypoxia-ischemia


title: Mg-treated Hypoxia-ischemia vs Mg-treated naive mice + 3h  [RV Mg 3h a]

description: Biological replicate 1 of 3. 5 day-old brain harvested 3h after hypoxia-ischemia.


title: RNA-Seq of Mus musculus: Halr1-WT-RA-1d rep-2


title: WFMD153B - Case


title: WFMD172B - Case


title: RNA-Seq of Mus musculus: Halr1-KO-RA-1d rep-2


title: RNA-Seq of Mus musculus: Halr1-WT-RA-1d rep-1