title: tumor, VHH-PD-1-Fc, rep1

first: yan

last: chen

address: 163 Xianlin Road, Qixia District

institute: Nanjing university

description: Library name: VHH-PD-1-Fc1

data_processing:
Raw reads were quality filtered with fastp (v0.22.0) to remove adapters and low quality or ambiguous bases, discarding reads <75 bp after trimming; the remaining high quality clean reads were used for downstream bioinformatic analyses.
Assembly: Clean reads were aligned to the reference genome GRCh38 using HISAT2 (v2.2.1).
Supplementary files format and content: txt files include FPKM values for each sample

source_name: tumor

growth_protocol: The 4- to 5-week-old female BALB/c mice were housed in filter-topped cages with autoclaved food and water on a 12-hour light/dark cycle.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, 74136).
RNA was quantified on NanoDrop and RNA quality was assessed on an Agilent 2100 Bioanalyzer. First, poly(A)+ mRNA was enriched from total RNA using oligo(dT)-coated magnetic beads and fragmented. Reverse transcriptase was then used to synthesize the first and second strands of cDNA. The cDNA fragments underwent end repair and A-tailing at the 3' ends, followed by ligation of sequencing adapters. After purification to remove incompletely ligated adapters and adapter dimers, libraries were PCR-amplified using primers complementary to the adapter sequences. Finally, the sequencing libraries were purified using magnetic beads. RNA-seq (paired end 150 bp) was performed by illumina NovaSeq 6000.

treatment_protocol: mCherry-4T1 cells (5 × 10^6) were injected into the mammary fat pads of mice. Seven days later, mice were randomized into four groups and treated intraperitoneally with Ctrl-Fc (5mg/kg), VHH-OD-Fc (3.5mg/kg), VHH-PD-1-Fc (2.6 mg/kg), or VHH-OD-PD-1-Fc (4.3 mg/kg).

value: tumor


title: tumor, VHH-OD-PD-1-Fc, rep2

status: Public on Sep 20 2025

type: SRA

city: Nanjing

country: China

description: Library name: VHH-OD-PD-1-Fc2

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: treatment


title: tumor, VHH-OD-PD-1-Fc, rep1

description: Library name: VHH-OD-PD-1-Fc1


title: tumor, VHH-PD-1-Fc, rep2

description: Library name: VHH-PD-1-Fc2


title: tumor, VHH-PD-1-Fc, rep3

description: Library name: VHH-PD-1-Fc3


title: tumor, VHH-OD-PD-1-Fc, rep3

description: Library name: VHH-OD-PD-1-Fc3


title: tumor, OD-Fc, rep3

description: Library name: OD-Fc3

value: VHH-OD-Fc


title: tumor, OD-Fc, rep1

description: Library name: OD-Fc1


title: tumor, OD-Fc, rep2

description: Library name: OD-Fc2


title: tumor, Ctrl, rep3

description: Library name: Ctrl3

value: Ctrl


title: J.0.0.0.6h.gs025

city: Zeist

first: Marjolein

last: Meijerink

state: Utrecht

address: Utrechtseweg 48

department: RAPID

country: Netherlands

institute: TNO

data_processing:
Quality filtering and adapter-trimming of the Illumina NovaSeq6000 fastq files was performed by TRIMMOMATIC software
Trimmed Fastq files were merged (in case of Paired-end reads) and aligned to the ensembl reference genome using the STAR 2.5 algorithm with default settings (https://github.com/alexdobin/STAR).
Based on the mapped read locations and the gene annotation, Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count.files.
Assembly: GCF_000003025.6_Sscrofa11.1_genomic
Supplementary files format and content: The count files (.tsv) contain the # reads mapped per gene (not normalised per sample). These counts serve as input for the statistical analysis using DEseq2 package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).

organism: Sus scrofa domesticus

source_name: jejunum

growth_protocol: To be published in various papers

extract_protocol:
Total RNA was isolated from approximately 50 mg of porcine intestinal tissue with RNAqueous™ Total RNA Isolation Kit (Invitrogen). RNA concentrations were determined using Nanodrop 1000 (Isogen Life Science, De Meern, the Netherlands) and RNA integrity was assessed using RNA 6000 Nano LabChip 669 kit and a bioanalyzer 2100 (Agilent Technologies, Amstelveen, the Netherlands). NGS (NovaSeq6000) was performed at GenomeScan (Leiden, the Netherlands).
Total RNA was processed into tagged random sequence libraries (NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, NEB #E7760S/L , Biolabs) and sample quality was checked for proper size distribution (300-500 bp peak, Fragment Analyzer). The mixed (multiplex) sample libraries were sequenced on an Illumina NovaSeq6000 sequencer with a paired-read 150-cycle sequencing protocol at GenomeScan BV (Leiden, the Netherlands), resulting in ~20-40 million read counts per sample.
Illumina NovaSeq6000 v1.5
Clustering and DNA sequencing using the NovaSeq6000 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used yielding paired end reads (2x 150bp). NovaSeq control software NCS v1.7 was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.

treatment_protocol: To be published in various papers

value: jejunum

value: J


title: tumor, Ctrl, rep2

description: Library name: Ctrl2


title: LDN2, Input

city: Qingdao

first: xiaowei

middle: xiaowei

last: zhao

address: No.16 Jiangsu Road, Shinan District, Qingdao, China

institute: Qingdao University

description: Library name: sample 12

library_source: genomic

data_processing:
After obtaining the raw sequencing data (raw data), the first step is to filter the raw data to obtain high-quality sequencing data (clean data). The clean data is then aligned to the reference genome of the target species. Following alignment, genome-wide peak calling is performed to study the binding preferences of proteins across the genome. Finally, motif analysis is conducted on the binding sites.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for input sample)

molecule: genomic DNA

source_name: spinal cord

extract_protocol:
Formaldehyde crosslinking & quenching – Crosslink proteins to DNA in tissues/cells, then stop the reaction (forming covalent protein-DNA bonds). Cell lysis & nuclear isolation – Lyse tissues/cells to release cytoplasmic contents and collect nuclei. Nuclear lysis – Extract soluble chromatin (DNA-protein complexes). DNA fragmentation – Shear DNA into 200–1000 bp fragments (e.g., by sonication or enzymatic digestion). Immunoprecipitation (IP) – Precipitate target protein-DNA complexes using a specific antibody. Washing – Remove nonspecifically bound material by washing the immunoprecipitated complexes. Elution – Release the protein-DNA complexes from the beads. Reverse crosslinking & DNA purification – Separate DNA from proteins and extract the DNA. DNA quality control – Check the quantity and integrity of the precipitated DNA (e.g., by agarose gel or Bioanalyzer). Protein validation (Western Blot) – Verify immunoprecipitation efficiency by detecting the target protein. Library preparation – Construct a sequencing library from the immunoprecipitated DNA for downstream analysis (e.g., ChIP-seq).
End repair and A-tailing: Perform end repair on the immunoprecipitated (IP) DNA, followed by the addition of an 'A' base to the 3' ends. Adapter ligation: Ligate sequencing adapters to the end-repaired and A-tailed DNA. Size selection and PCR amplification: Use magnetic beads to recover DNA fragments of the desired size range, followed by PCR amplification to generate the sequencing library. Quality control by agarose gel electrophoresis: Assess the constructed library's quality using agarose gel electrophoresis. Library quantification using Qubit 2.0: Measure the library concentration with Qubit 2.0 to confirm suitability for sequencing. Sequencing: After passing quality control, pool multiple libraries based on their effective concentrations and desired sequencing depth, then load them onto the sequencer for high-throughput sequencing.

value: spinal cord

value: SNI+LDN193189 group

tag: replicate

value: replicate biosample 2

tag: Sex

value: male


title: SNI2, Input

description: Library name: sample 14

value: SNI group


title: SNI1, Input

description: Library name: sample 13

value: replicate biosample 1


title: sham2, Input

description: Library name: sample 10

value: sham group


title: SNI2, IP

description: Library name: sample 8


title: sham1, Input

description: Library name: sample 9


title: LDN1, IP

description: Library name: sample 4


title: LDN1, Input

description: Library name: sample 11


title: LDN2, IP

description: Library name: sample 5


title: sham2, IP

description: Library name: sample 2


title: sham1, IP

description: Library name: sample 1


title: SNI1, IP

description: Library name: sample 7


title: SUB40_4, humanASC, BMI≥40

city: Frankfurt

first: Nina-Naomi

last: Kreis

address: Theodor-Stern-Kai 7

department: Department of Gynecology and Obstetrics

country: Germany

institute: University Hospital Frankfurt, J. W. Goethe- University

description: Library name: Sample14

data_processing:
Quality Control (QC) of Raw Data
Trimming and Filtering
Alignment to Reference Genome, Tool: STAR
Quantification of Gene Expression, Tool: FeatureCounts
Differential Expression Analysis, Tool: DESeq2
Assembly: GRCh38
Supplementary files format and content: Gene Count Matrix CSV

organism: Homo sapiens

source_name: subcutaneous adipose tissue

growth_protocol: DMEM with pyruvate, 4.5 g/L D-glucose and L-glutamine containing 20% fetal bovine serum, 1% penicillin/streptomycin, and 1 µg/ml amphotericin-B, cultured under standard cell culture conditions.

extract_protocol:
EXTRACTME TOTAL RNA Kit (#EM09.2.-250, 7Bioscience, Neuenburg)
TruSeq Stranded mRNA Library Prep Kit

value: subcutaneous adipose tissue

tag: cell line

value: ASCs

tag: cell type

value: mesenchymal stromal/stem cells


title: SUB40_2, humanASC, BMI≥40

description: Library name: Sample12


title: SUB40_1, humanASC, BMI≥40

description: Library name: Sample11


title: SUB40_3, humanASC, BMI≥40

description: Library name: Sample13


title: SUB40_5, humanASC, BMI≥40

description: Library name: Sample15


title: SNI1

description: Library name: sample 7

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes gene counts for each sample
Supplementary files format and content: tab-delimited text file includes fpkm value for each sample

extract_protocol:
RNA was extracted from cell lines using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).


title: SNI3

description: Library name: sample 9

value: replicate biosample 3


title: LDN3

description: Library name: sample 6


title: LDN1

description: Library name: sample 4


title: LDN2

description: Library name: sample 5


title: tumor, Ctrl, rep1

description: Library name: Ctrl1


title: SUB35_4, humanASC, BMI≥35

description: Library name: Sample9


title: SNI2

description: Library name: sample 8


title: SUB35_5, humanASC, BMI≥35

description: Library name: Sample10


title: SUB35_2, humanASC, BMI≥35

description: Library name: Sample7


title: sham3

description: Library name: sample 3


title: SUB35_1, humanASC, BMI≥35

description: Library name: Sample6


title: SUB35_3, humanASC, BMI≥35

description: Library name: Sample8


title: SUB25_5, humanASC, BMI<25

description: Library name: Sample5


title: SUB25_1, humanASC, BMI<25

description: Library name: Sample1


title: sham1

description: Library name: sample 1


title: SUB25_2, humanASC, BMI<25

description: Library name: Sample2


title: XANTH2

city: Oxford

first: Klara

last: Piletic

address: Roosevelt Drive

country: United Kingdom

institute: University of Oxford

description: Library name: Sample 8

data_processing:
Quality control of raw reads was performed with a pipeline readqc.py (https://github.com/cgat-developers/cgat-flow) and mapped to GRCm38/Mm10.
Read counts were generated using Kallisto.
Assembly: Mm10
Supplementary files format and content: .tsv individual files for each sample provide gene abundances

molecule: polyA RNA

source_name: white adipose tissue

extract_protocol:
RNA was harvested from microbeads enriched cells using RNeasy Plus Micro Kit (Qiagen).
RNA libraries for RNA seq were prepared using NEBNext Ultra RNA Library Prep Kit following manufacturer's protocols.

value: white adipose tissue

value: macrophages

tag: genotype

value: WT

value: 100 µM xanthine


title: SUB25_3, humanASC, BMI<25

description: Library name: Sample3


title: SUB25_4, humanASC, BMI<25

description: Library name: Sample4


title: XANTH1

description: Library name: Sample 7


title: XANTH3

description: Library name: Sample 9


title: sham2

description: Library name: sample 2


title: XANTH4

description: Library name: Sample 10


title: HYPOX2

description: Library name: Sample 5

value: 100 µM hypoxanthine


title: HYPOX1

description: Library name: Sample 4


title: HCC009_001_OP_B

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

description: Library name: HCC009_001_OP_B

data_processing:
Reads were aligned to the human reference genome GRCh38 using STAR (v2.7.8a) with two-pass mode. Gene read counts were calculated using the intrinsic function of of STAR based on the GENCODE (v35) annotation.
Assembly: GRCh38
Supplementary files format and content: Gene count

source_name: Hepatocellular carcinoma

extract_protocol:
Total RNA was isolated from the FFPE tissue using the RNeasy FFPE Kit (Qiagen, Valencia, CA, USA).
Libraries were constructed using Illumina RNA Prep with Enrichment (Illumina, San Diego, CA, USA) and sequenced on the Illumina NovaSeq 6000 platform with a target of 25 million reads per sample.

value: Hepatocellular carcinoma

tag: Stage

value: post-treatment

value: Nivolumab plus ipilimumab


title: HCC006_001_OP_D

description: Library name: HCC006_001_OP_D


title: HCC701_001_OP_C

description: Library name: HCC701_001_OP_C


title: HCC006_001_OP_A

description: Library name: HCC006_001_OP_A


title: treated 3

city: Hradec Kralove

first: Josef

last: Skoda

state: Czech Republic

address: Akademika Heyrovského 1203

department: Department of Pharmacology and Toxicology

country: Czech Republic

institute: Faculty of Pharmacy in Hradec Kralove, Charles University, Czech Republic

description: Library name: KRDMI172_3

data_processing:
Aligned using STAR aligner and quantified using featureCounts with default settings. DESeq2 was used for differential expression.
Assembly: mm10
Supplementary files format and content: Individual sample files are in .tabular format containing transcript IDs and counts.

source_name: colon

growth_protocol: Mice were kept in 12-h cycle light and ventilation controled facility. Mice were fed HFD for 25 weeks

extract_protocol:
RNA from colon was extracted using phenol/chlorophorm extraction.
NEBNext Ultra II Directional RNA Library Prep Kit

treatment_protocol: Last 6 weeks of experiment were mice treated with vehicle or 7β-ipCDCA .

value: colon

value: whole tissue

tag: batch


title: TC_LPS

city: Indianapolis

first: Jade

last: Harkin

state: Indiana

address: NB Building, 320 W 15th St #414

country: USA

institute: Indiana University School of Medicine

description:
Library name: Sample2
10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software v7.2.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest/tutorials/cr-tutorial-in
Assembly: Human (GRCh38) 2020-A
Supplementary files format and content: 10x HDF5 Output (Cell Ranger software v7.2.0)

source_name: WTC11 iPSC cell line, H7 ES cell line

extract_protocol:
Single-cell suspensions were prepared from 1-week tri-cultures by adding 1 mL of Accutase per well and incubating for 15–20 minutes at 37 °C to achieve complete dissociation. Following dissociation, Accutase was diluted in 5 mL of BrainPhys medium supplemented with BDNF, GDNF, CNTF, IL-34, mCSF, and 10 μM ROCK inhibitor. The resulting suspension was passed through a 30-μm strainer to remove cell clumps, then centrifuged at 300 × g for 5 minutes. The cell pellet was resuspended in 70 μL of supplemented BrainPhys medium, kept on ice, and transferred to the core facility for downstream processing. Prior to sequencing, the suspension was washed at least three times with PBS containing 0.04% BSA, and cell viability was assessed to achieve a final concentration of 700–1200 cells/μL, following 10x Genomics guidelines.
Single-cell transcriptomic analysis was performed using the 10x Chromium Next GEM Single Cell 3’ Gene Expression v3.1 Dual Index platform (10x Genomics, Inc.) and sequenced on a NovaSeq 6000 system (Illumina, Inc.). Cell suspensions, reverse transcription reagents, gel beads, and partitioning oil were loaded onto a Next GEM Chip G (one sample per well), and GEM generation, barcoding, and reverse transcription were carried out on the 10x Chromium Controller. cDNA synthesis and library preparation followed the manufacturer’s protocol (CG000315). At each stage, cDNA and library quality were assessed using a Bioanalyzer and Qubit. Libraries were sequenced on an Illumina NovaSeq 6000 with paired-end 100 bp reads, achieving ~50,000 paired reads per cell, with 93% of reads at Q30 (corresponding to 99.9% base call accuracy). Sequencing data were processed with Cell Ranger (v7.2.0) using the GRCh38-2020-A human reference genome for alignment. The resulting feature-barcode matrices were used for downstream analysis.

treatment_protocol: Lipopolysaccaride

value: WTC11 iPSC cell line, H7 ES cell line

value: induced pluripotent and embryonic stem cell derived cells


title: TC_control

description:
Library name: Sample1
10X Genomics


title: IC_control

description:
Library name: Sample3
10X Genomics


title: CTRL3

description: Library name: Sample 3

value: no treatment


title: CTRL1

description: Library name: Sample 1


title: treated 4

description: Library name: KRDMI172_4


title: HCC701_001_OP_A

description: Library name: HCC701_001_OP_A


title: HCC004_013_OP_C

description: Library name: HCC004_013_OP_C


title: treated 2

description: Library name: KRDMI172_2


title: HCC004_012_OP_A

description: Library name: HCC004_012_OP_A


title: control 4

description: Library name: KRDctrl_4

value: vehicle


title: treated 1

description: Library name: KRDMI172_1


title: HCC004_011_OP_B

description: Library name: HCC004_011_OP_B


title: HCC004_009_OP_C

description: Library name: HCC004_009_OP_C


title: HCC004_010_OP_B

description: Library name: HCC004_010_OP_B


title: control 2

description: Library name: KRDctrl_2


title: control 3

description: Library name: KRDctrl_3


title: HYPOX4

description: Library name: Sample 6


title: control 1

description: Library name: KRDctrl_1


title: HCC004_008_OP_A

description: Library name: HCC004_008_OP_A


title: Untreated

city: Hangzhou

first: Yalin

last: Xiong

state: Zhejiang

address: No. 150, Dongfang Street, Xiasha Street, Qiantang District

institute: Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences

description:
Library name: PBS_control
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation weremade using the Cell Ranger toolkit (version 7.2.0) provided by 10x Genomics.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values fles and matrix files

extract_protocol:
After receiving AptCD4-LNT administration every 3 days with a dose of 5 × 10^6 cells, 4 × 10^6 cells, and 3 × 10^6 cells, sequentially, triple negative breast cancer  (4T1) bearing mice were sacrificed at 9 days, and tumor tissues were obtained. Mixing three parallel samples of tumor tissues for scRNA-Seq. The untreated mice bearing triple negative breast cancer received PBS as the control.
Library was performed according to the manufacter's instructions (10x Genomics). Briefly,Gel beads containing barcode information bind to a mixture of cells and enzymes and are then encapsulated by oil surfactant droplets located in a microfluidic system to form GEMs.The GEMs flow into a reservoir and are collected.The gel beads are lysed to release the Barcode sequence, reverse transcribe the cDNA fragments, and label the sample. The gel beads are crushed and the oil droplets are broken up and PCR amplification is performed using the cDNA as a template. The products of all GEMs were mixed to construct a standard sequencing library.

value: tumor

value: 4T1 tumor cell

value: tumor cell

value: BALB/c

value: Untreated


title: HCC004_007_OP_D

description: Library name: HCC004_007_OP_D


title: HCC004_007_OP_C

description: Library name: HCC004_007_OP_C


title: CTRL2

description: Library name: Sample 2

value: white adipose tissue

value: macrophages

value: WT


title: HCC004_006_OP_D

description: Library name: HCC004_006_OP_D

value: Hepatocellular carcinoma


title: B-cell depletion + anti-PD1 plus anti-CTLA4 (5)

data_processing:
Trimming adaptor sequences and removing reads of low quality were performed by cutadapt (v2.4).
Quantified reads were aligned to the mouse genome (GRCm38) by STAR (v2.7.2a) and then gene-level read counts were generated based on the annotations of Gencode (vM25)
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include read count values for each sample

extract_protocol:
Total RNA was extracted from frozen snaps using an AllPrep DNA/RNA mini kit (Qiagen, Hilden, Germany).
Libraries were constructed using Illumina TruSeq Stranded mRNA kit according to the manufacturers

value: Hepa1-6 cell

value: B-cell depletion

value: anti-PD1 + antiCTLA4


title: AptCD4-LNT

description:
Library name: high_CD4
10x Genomics


title: B-cell depletion + anti-PD1 plus anti-CTLA4 (3)


title: B-cell depletion + anti-PD1 plus anti-CTLA4 (4)


title: HCC004_001_OP_B

description: Library name: HCC004_001_OP_B

value: post-treatment

value: Nivolumab plus ipilimumab


title: HCC004_005_OP_C

description: Library name: HCC004_005_OP_C


title: HCC004_002_OP_D

description: Library name: HCC004_002_OP_D


title: HCC004_002_OP_C

description: Library name: HCC004_002_OP_C


title: B-cell depletion + Isotype (6)

value: Isotype


title: B-cell depletion + anti-PD1 plus anti-CTLA4 (1)


title: HCC003_002_OP_D

description: Library name: HCC003_002_OP_D


title: HCC002_017_OP_E

description: Library name: HCC002_017_OP_E


title: HCC002_017_OP_B

description: Library name: HCC002_017_OP_B


title: B-cell depletion + Isotype (1)


title: HCC002_014_OP_A

description: Library name: HCC002_014_OP_A


title: B-cell depletion + anti-PD1 plus anti-CTLA4 (2)


title: WT + anti-PD1 plus anti-CTLA4 (5)


title: HCC004_008_OP_D

description: Library name: HCC004_008_OP_D


title: HCC002_006_OP_A

description: Library name: HCC002_006_OP_A


title: WT + anti-PD1 plus anti-CTLA4 (4)


title: B-cell depletion + Isotype (4)


title: WT + anti-PD1 plus anti-CTLA4 (3)


title: B-IRI-PolgD257A-Biol rep 4

city: Dallas

first: Samir

last: Parikh

state: Texas

address: 5901 Forest Park Rd. ND9.300B

institute: UT Southwestern Medical Center

data_processing:
After demultiplexing the sequencing data, individual libraries were converted to the FASTQ format.
Raw results underwent quality control steps using FastQC and were aligned to the mouse genome GRCm38.p6 using STAR aligner.
The Gencode nucleotide sequence (gencode.vM22; regions: ALL) was used as the annotation reference.
The resulting output file was indexed using Samtools for read counting
Read counts for each gene were calculated using Feature Counts and normalized to the total mapped read counts.Statistical analysis of differential gene expression was performed using the DESeq2 package
Assembly: GRCm38.p6
Supplementary files format and content: normalized_featuredcounts_total24.csv
Supplementary files format and content: SurgBIR_Mut_ape_sig_winfo_total24.csv

source_name: Kidney

extract_protocol:
RNA were extracted by RNeasy kit  (QIAGEN) following manufactor's protocols. Total 2 ug of RNA were used for library constraction.
RNA library were prepared using NEBNext Ultra II RNA prep kit following manufactor's protocols.

treatment_protocol: IRI surgery

value: Kidney

value: B-IRI


title: HCC002_005_OP_D

description: Library name: HCC002_005_OP_D


title: B-cell depletion + Isotype (5)


title: B-IRI-PolgD257A-Biol rep 1


title: HCC002_003_OP_C

description: Library name: HCC002_003_OP_C


title: WT + anti-PD1 plus anti-CTLA4 (2)


title: HCC003_002_OP_A

description: Library name: HCC003_002_OP_A


title: B-IRI-PolgD257A-Biol rep 2


title: B-cell depletion + Isotype (3)


title: B-cell depletion + Isotype (2)


title: HCC002_001_OP_C

description: Library name: HCC002_001_OP_C


title: B-IRI-Polg+/+-Biol rep 5

value: Polg+/+


title: HCC002_001_OP_A

description: Library name: HCC002_001_OP_A


title: WT + anti-PD1 plus anti-CTLA4 (1)


title: B-IRI-Polg+/+-Biol rep 4


title: HCC001_003_OP_E

description: Library name: HCC001_003_OP_E


title: B-IRI-Polg+/+-Biol rep 3


title: WT + Isotype (5)


title: WT + Isotype (4)


title: B-IRI-PolgD257A-Biol rep 6


title: B-IRI-PolgD257A-Biol rep 5


title: B-IRI-Polg+/+-Biol rep 2


title: B-IRI-Polg+/+-Biol rep 1


title: HCC002_005_OP_B

description: Library name: HCC002_005_OP_B


title: Sham-PolgD257A-Biol rep 6

value: Sham


title: HCC001_003_OP_B

description: Library name: HCC001_003_OP_B


title: B-IRI-PolgD257A-Biol rep 3


title: Sham-PolgD257A-Biol rep 5


title: HCC701_001_PRE

description: Library name: HCC701_001_PRE

value: pre-treatment


title: WT + Isotype (3)


title: WT + Isotype (1)


title: Sham-PolgD257A-Biol rep 2


title: HCC401_002_PRE

description: Library name: HCC401_002_PRE


title: WT + Isotype (2)


title: Sham-PolgD257A-Biol rep 1


title: B-IRI-Polg+/+-Biol rep 6


title: Sham-PolgD257A-Biol rep 3


title: Sham-PolgD257A-Biol rep 4


title: Sham-Polg+/+-Biol rep 6


title: MO_31_WT_M

data_processing:
Quality control of raw reads was performed with a pipeline readqc.py (https://github.com/cgat-developers/cgat-flow) and mapped to GRCm38/Mm10.
Read counts were generated using Salmon.
Assembly: Mm10
Supplementary files format and content: excel file includes raw counts for each Sample

extract_protocol:
RNA was harvested from flow cytometry sorted cells using RNeasy Plus Micro Kit (Qiagen).
RNA libraries for RNA seq were prepared using NEBNext Ultra RNA Library Prep Kit following manufacturer's protocols.

value: high fat diet


title: HCC006_002_PRE

description: Library name: HCC006_002_PRE


title: Sham-Polg+/+-Biol rep 5


title: Sham-Polg+/+-Biol rep 4


title: HCC009_001_PRE

description: Library name: HCC009_001_PRE


title: MO_30_WT_M


title: HCC006_001_PRE

description: Library name: HCC006_001_PRE


title: Sham-Polg+/+-Biol rep 2


title: Sham-Polg+/+-Biol rep 3


title: MO_29_KO_M


title: HCC004_013_PRE

description: Library name: HCC004_013_PRE


title: Sham-Polg+/+-Biol rep 1


title: MO_28_KO_M


title: Rapalink1-2

city: Chicago

first: Sejeong

last: Shin

state: IL

address: 909 S Wolcott Ave.

institute: University of Illinois at Chicago

description: Library name: Sample11

data_processing:
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis.
Using DESeq2, a comparison of gene expression between the groups of samples was performed.
Assembly: GRCm38
Supplementary files format and content: Table formatted, Unique hit counts per each sample

growth_protocol: Cells were maintained in DMEM containing 10% FBS at 37°C with 5% CO2

extract_protocol:
Total RNA was isolated using the RNeasy mini kit (Qiagen)
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s instructions

treatment_protocol: Cells were treated with rapamycin (20 ng/ml), Torin1 (250 nM), and RapaLink-1 (10 nM) for 24 hours

value: Melanoma Cells


title: Rapalink1-3

description: Library name: Sample12


title: MO_27_KO_M

value: white adipose tissue


title: HCC004_011_PRE

description: Library name: HCC004_011_PRE


title: Rapalink1-1

description: Library name: Sample10


title: Torin1-2

description: Library name: Sample8


title: MO_26_WT_M

value: macrophages


title: Torin1-1

description: Library name: Sample7

value: WT


title: HCC004_010_PRE

description: Library name: HCC004_010_PRE

value: Hepatocellular carcinoma


title: MO_25_KO_M


title: Rapamycin3

description: Library name: Sample6

value: Rapamycin


title: HCC004_008_PRE

description: Library name: HCC004_008_PRE


title: Rapamycin2

description: Library name: Sample5


title: MO_72_WT_F


title: Control3

description: Library name: Sample3

value: DMSO


title: MO_71_KO_F


title: Rapamycin1

description: Library name: Sample4


title: HCC004_007_PRE

description: Library name: HCC004_007_PRE


title: Control2

description: Library name: Sample2


title: HCC004_006_PRE

description: Library name: HCC004_006_PRE


title: Control1

description: Library name: Sample1


title: c3h14c3h15 leaf replicate 3

city: Shanghai

first: Chenjiang

last: You

state: Shanghai

address: 2005 Songhu Rd

institute: Fudan University

description: Library name: c3h14c3h15_leaf_rep3

data_processing:
pRNASeqTools (https://github.com/ grubbybio/pRNASeqTools) was used for adaptor removal, mapping, and read count. To find genes with preferential expression in meiocytes compared with transcriptomes of IM, anther in stage 2, tapetum, and leaves, differentially expressed genes were identified based on the criteria of fold change ≥4 and p-value < 0.01. As for the analysis of meiocyte and leaves transcriptomes from WT, c3h14, c3h15, and c3h14 c3h15, differentially expressed genes were identified based on the criteria of fold change ≥2 and p-value < 0.01.
Assembly: Araport11
Supplementary files format and content: Tab-delimited text files including geneID, raw read count and transcript length

organism: Arabidopsis thaliana

source_name: leaf

extract_protocol:
Anthers of col-0, c3h14, c3h15 and c3h14 c3h15, during anther stage 4 to 7, were collected respectively and squeezed with forceps to release meiocytes. Recombinant RNase inhibitor (final concentration with 1 U/μL, Takara, 2313B) was used to prevent RNA degradation by adding to the collection buffer. Then RNA of meiocytes was extracted by TRIzol reagent (ThermoFisher, 15596026), facilitated by Dr. GenTLE™ Precipitation Carrier (Takara, 9094) for better precipitation of microscale RNA. As for inflorescence meristem (IM) and anthers at stage 2 from col-0, tissues were isolated and collected from Arabidopsis inflorescences. Leaves from col-0 and c3h14 c3h15 that had grown for 21 days were also collected for RNA-seq. All these tissue samples were used to extract RNA by using the TRIzol reagent (ThermoFisher, 15596026).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

value: leaf


title: MO_70_KO_F


title: siNUP153-3

city: Beijing

first: Qianqian

last: Jiang

address: No.11 Xizhimen South Street

institute: Peking University

data_processing:
To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. RSEM was used to quantify gene abundances. Essentially, differential expression analysis was performed using the DESeq2 or DEGseq.  In addition, functional-enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni-corrected P-value ≤0.05 compared with the whole-transcriptome background. GO functional enrichment and KEGG pathway analysis were carried out by Goatools and KOBAS, respectively.
Assembly: hg18
Supplementary files format and content: tab-delimited text files include TPM values for each sample

extract_protocol:
RNA was harvest using TRIzol (Invitrogen). 1ug of total RNA was used for the construction of sequencing libraries
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions (Illumina, San Diego, CA). The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNAwas subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by Qubit 4.0, paired-end RNA-seq sequencing library was sequenced with the NovaSeq 6000 sequencer (2 × 150bp read length).

value: hepatoma cell


title: HCC004_005_PRE

description: Library name: HCC004_005_PRE

value: Nivolumab plus ipilimumab


title: MO_69_WT_F


title: HCC004_004_PRE

description: Library name: HCC004_004_PRE


title: c3h14c3h15 leaf replicate 1

description: Library name: c3h14c3h15_leaf_rep1


title: c3h14c3h15 leaf replicate 2

description: Library name: c3h14c3h15_leaf_rep2


title: HCC004_012_PRE

description: Library name: HCC004_012_PRE


title: siNUP153-2


title: siNUP153-1


title: HCC004_003_PRE

description: Library name: HCC004_003_PRE


title: Torin1-3

description: Library name: Sample9


title: Col-0 leaf replicate 3

description: Library name: WT_leaf_rep3


title: sicontronl3

value: sicontronl


title: HCC004_002_PRE

description: Library name: HCC004_002_PRE


title: ethanol control

city: Houston

first: Hongjie

last: Li

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description:
Library name: Ru486-
10x Genomics

data_processing:
The sequencing fastq files were alligned and processed by Cell Ranger software v7.0.1
Assembly: dm6.31
Supplementary files format and content: .h5ad matrix file

molecule: nuclear RNA

organism: Drosophila melanogaster

source_name: Head

extract_protocol:
The heads of female flies were collected at day 50 (i.e., when the flies were 50 days old), placed into 1.5 mL Eppendorf tubes, flash-frozen in liquid nitrogen, and stored at -80C. In total, two samples (each containing 20 heads) were prepared for single-nucleus RNA sequencing: one where DIP-beta had been overexpressed in glial cells from day 5-50 and one where DIP-beta expression had not been manipulated (i.e., the flies received an ethanol control instead of the Ru486 drug used to induce overexpression of DIP-beta). Single-nucleus suspensions were prepared as described in the Fly Cell Atlas (H. Li et al. 2022). After nuclei dissociation, the nuclei were purified from debris using the SONY SH800 FACS sorter. Nuclei were stained with Hoechst-33342 (1:1000, >5 minutes). It is typical to observe separate cell populations during FACS since some cells have variable sizes of nuclei and ploidy numbers. All populations were included to ensure every cell would be captured from the samples. Nuclei were collected in a 1.5 mL Eppendorf tube containing 200uL 1X PBS with 0.5% BSA (RNase inhibitor added). For each of the 10X Genomics runs, 250-300k nuclei were collected. The nuclei were centrifuged for 10 minutes at 1000g in 4C. conditions and then resuspended using 40uL of 1X PBS with 0.5% BSA (RNase inhibitor added). 2uL of the nuclei suspension were allocated for counting under a hemocytometer to calculate the nuclei concentration. For the high-throughput single-cell sequencing kit from 10X Genomics, we loaded 50k cells into the Chromium Controller to target a final number of 20-30k nuclei.
Single-nucleus RNA-seq libraries were prepared using the 10X Genomics Chromium Single Cell 3’ HT v3.1 protocol. All PCR reactions were performed using the BioRad C1000 Touch Thermal Cycler with the 96-Deep Well Reaction Module. We used 11 cycles for the cDNA amplification and then we used 13 cycles for the sample index PCR. As per the 10X Genomics protocol, 1:10 dilutions of amplified cDNA and the final gene expression libraries were evaluated on the Agilent Tapestation Bioanalyzer. Each library was diluted to approximately 4nM and equal volumes of each library were pooled in a NovaSeq PE150 S4 sequencing run. Pools were sequenced with the dual index configuration Read 1 28 cycles, Index 1 (i7) 10 cycles, Index 2 (i5) 10 cycles, and Read 2 90 cycles. The sequencing depth was about 30-40k reads per nucleus.

value: Head


title: MO_68_WT_F


title: HCC003_002_PRE

description: Library name: HCC003_002_PRE


title: Col-0 leaf replicate 2

description: Library name: WT_leaf_rep2


title: HCC003_001_PRE

description: Library name: HCC003_001_PRE


title: sicontronl1


title: glial DIP-β overexpression treatment

description:
Library name: Ru486+
10x Genomics


title: Col-0 anther S2 replicate 1

description: Library name: WT_S2_rep1

source_name: anther

value: anther


title: Col-0 leaf replicate 1

description: Library name: WT_leaf_rep1


title: S5

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

description: Library name: Sample16

data_processing:
Utilize the bcl2fastq software to perform Base Calling on the original image files from Illumina high-throughput sequencing and convert them into original sequencing reads.
Use the FastQC software to analyze the base quality from 5' to 3' of the sequencing reads and assess the content of A, T, C, and G bases in the sequencing data, evaluating the base type ratio at each position from an overall level.
Utilize the fastp software to filter the raw data, removing reads that do not meet the analysis criteria, in order to obtain clean reads that can be used for subsequent alignment, statistics, and further analysis.
After quality control of the raw sequencing data, clean data is obtained. The clean data is then assessed to review the effectiveness of the quality control, and ultimately, the clean data is used for analysis.
Read count extraction and normalization were performed using RseQC software
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Cardiac

extract_protocol:
RNA was harvested using TRIzol® Reagent (invitrogen.). 1 µgof total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using Nebnext ultra-RNA library preparation kit following manufacturer's protocols.

value: Cardiac

value: ModelSwimming

value: Swimming exercise intervention


title: S6

description: Library name: Sample17


title: sicontronl2


title: S4

description: Library name: Sample15


title: Col-0 anther S2 replicate 2

description: Library name: WT_S2_rep2


title: Col-0 anther S2 replicate 3

description: Library name: WT_S2_rep3


title: LP09020

city: Vienna

first: Reinhard

last: Gruber

address: Sensengasse 2a

country: Austria

institute: Medical University Vienna

description:
Library name: Sample12
Column name in raw_counts_All_Samples.tsv: LP09020

data_processing:
Reads in FASTQ format were generated using the Illumina bcl2fastq command-line tool (v2.19.1.403) and the Lexogen idemux tool for optimal demultiplexing of long, unique, dual indices. Reads were trimmed and filtered using cutadapt version 2.8 to trim polyA tails, remove reads with N's, and trim bases with a quality of less than 30 from the 3' ends of the reads. On average, 8.9 million reads were left after this procedure. Trimmed reads in fastq format were aligned to the human reference genome version GRCh38 with Gencode 29 annotations using the STAR aligner version 2.6.1a in 2-pass mode. STAR counted raw reads per gene. Differential gene expression was calculated using DESeq2 version 1.44.0.
Assembly: Reads in fastq format were aligned to the human reference genome version GRCh38 with Gencode 29 annotations using STAR aligner version 2.6.1a in 2-pass mode
Supplementary files format and content: raw_counts_All_Samples.tsv contains a matrix with raw gene counts, gene symbols, and gene types for each sample.

source_name: human gingiva

growth_protocol: Gingival fibroblasts were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Sigma-Aldrich, St. Louis, MO, USA) containing penicillin, streptomycin (Sigma Aldrich, St. Louis, MO), and 10% fetal bovine serum (Bio&Sell GmbH, Nuremberg, Germany).

extract_protocol:
Total RNA was extracted using the GeneMATRIX Universal RNA Purification Kit (EURX, Gdańsk, Poland) with rDNase set (Macherer-Nagel, Düren, Germany ).
Sequencing libraries from total RNA were prepared at the Core Facility Genomics, Medical University of Vienna, using the QuantSeq 3' FWD protocol version 2 with unique dual indices (Lexogen GmbH, Vienna, Austria). Seventeen PCR cycles were used for library preparation, as determined by quantitative PCR (qPCR) according to the library preparation manual.

treatment_protocol: Gingival fibroblasts were exposed to the lysates of platelet-poor plasma (PPP) and heated PPP (Alb-gel/hPPP), buffy coat (C-PRF/BC) in a serum-free medium for 24 h at 37 °C, 5% CO2, and 95% humidity.

value: human gingiva

value: gingival fibroblast

value: treated with BC


title: HCC002_017_PRE

description: Library name: HCC002_017_PRE

value: pre-treatment


title: S3

description: Library name: Sample14


title: LP09004

description:
Library name: Sample10
Column name in raw_counts_All_Samples.tsv: LP09004


title: HCC002_015_PRE

description: Library name: HCC002_015_PRE


title: HCC002_013_PRE

description: Library name: HCC002_013_PRE


title: Col-0 IM replicate 2

description: Library name: WT_IM_rep2

source_name: inflorescence meristem

value: inflorescence meristem


title: Col-0 IM replicate 1

description: Library name: WT_IM_rep1


title: M6

description: Library name: Sample11

value: Model

value: Transplantation of tumor implants


title: LP09012

description:
Library name: Sample11
Column name in raw_counts_All_Samples.tsv: LP09012


title: S2

description: Library name: Sample13


title: S1

description: Library name: Sample12


title: LP09003

description:
Library name: Sample7
Column name in raw_counts_All_Samples.tsv: LP09003

value: treated with hPPP


title: Col-0 IM replicate 3

description: Library name: WT_IM_rep3


title: HCC002_014_PRE

description: Library name: HCC002_014_PRE

value: Hepatocellular carcinoma


title: HCC002_016_PRE

description: Library name: HCC002_016_PRE


title: LP09018

description:
Library name: Sample6
Column name in raw_counts_All_Samples.tsv: LP09018

value: treated with PPP


title: HCC002_011_PRE

description: Library name: HCC002_011_PRE

value: Nivolumab plus ipilimumab


title: Col-0 meiocyte replicate 5

description: Library name: WT_meio_rep5

source_name: meiocyte

value: meiocyte


title: M4

description: Library name: Sample9


title: M5

description: Library name: Sample10


title: HCC002_012_PRE

description: Library name: HCC002_012_PRE


title: Col-0 meiocyte replicate 4

description: Library name: WT_meio_rep4


title: LP09019

description:
Library name: Sample9
Column name in raw_counts_All_Samples.tsv: LP09019


title: M3

description: Library name: Sample8


title: c3h14c3h15 meiocyte replicate 2

description: Library name: c3h14c3h15_meio_rep2


title: HCC002_009_PRE

description: Library name: HCC002_009_PRE


title: LP09017

description:
Library name: Sample3
Column name in raw_counts_All_Samples.tsv: LP09017

value: untreated


title: Col-0 meiocyte replicate 3

description: Library name: WT_meio_rep3


title: LP09002

description:
Library name: Sample4
Column name in raw_counts_All_Samples.tsv: LP09002


title: LP09011

description:
Library name: Sample8
Column name in raw_counts_All_Samples.tsv: LP09011


title: HCC002_010_PRE

description: Library name: HCC002_010_PRE


title: c3h14c3h15 meiocyte replicate 1

description: Library name: c3h14c3h15_meio_rep1


title: M2

description: Library name: Sample7


title: HCC002_008_PRE

description: Library name: HCC002_008_PRE


title: C5

description: Library name: Sample5

value: CON

value: Blank group no tumors


title: LP09009

description:
Library name: Sample2
Column name in raw_counts_All_Samples.tsv: LP09009


title: HCC002_007_PRE

description: Library name: HCC002_007_PRE


title: M1

description: Library name: Sample6

value: Cardiac


title: c3h15 meiocyte replicate 2

description: Library name: c3h15_meio_rep2


title: LP09001

description:
Library name: Sample1
Column name in raw_counts_All_Samples.tsv: LP09001


title: c3h15 meiocyte replicate 1

description: Library name: c3h15_meio_rep1


title: HCC002_005_PRE

description: Library name: HCC002_005_PRE


title: C4

description: Library name: Sample4


title: HCC002_006_PRE

description: Library name: HCC002_006_PRE


title: LP09010

description:
Library name: Sample5
Column name in raw_counts_All_Samples.tsv: LP09010


title: c3h14 meiocyte replicate 2

description: Library name: c3h14_meio_rep2


title: HCC002_004_PRE

description: Library name: HCC002_004_PRE


title: C3

description: Library name: Sample3


title: c3h14 meiocyte replicate 1

description: Library name: c3h14_meio_rep1


title: C1

description: Library name: Sample1


title: Col-0 meiocyte replicate 2

description: Library name: WT_meio_rep2


title: HCC002_002_PRE

description: Library name: HCC002_002_PRE


title: Col-0 meiocyte replicate 1

description: Library name: WT_meio_rep1


title: HepG2 cell, a-tomatine treatment 24h 4

first: Tianzhen

last: Wang

address: No.500, Dongchuan Road

institute: East China Normal University

description: Library name: Sample 16

data_processing:
Reads were trimmed using cutadapt
Reads were aligned to the Homo sapiens genome build GRCh38_p13 using STAR (2.7.3a)
Deduplication was carried out by flagging all reads  that were mapped to the same gene and had the same UMI using UMI-Tools (version 1.1.2) (read 2 has the UMI)
Reads were counted using Ensembl annotations, build 106 (1000 bases of the 3’ UTR), using HTSeq-Counts (version 2.0.2)
Normalization and differential expression analysis were performed using DESeq2 (1.38.3)
Assembly: GRCh38_p13
Supplementary files format and content: Text file includes raw counts for each sample

growth_protocol: HepG2 cell were maintained in DMEM supplemented by 10% FBS and antibiotics in humidified atomosphere with 5% CO2 at 37C.

extract_protocol:
RNA was extracted by using NucleoSpin® RNA, MACHEREY-NAGEL kit following instruments.
Libraries were prepared by using 1 μg of RNA per samples measured with Qubit 2.0 fluorometer (Thermo Fisher Scientific) by the KAPA stranded mRNA-seq Kit Illumina platform KR0960.

treatment_protocol: 2uM a-tomatine were applied for indicated time points.

value: Hepatocelular carcinoma

value: WT

value: a-tomatine treatment 24h

value: no batch effect


title: HCC002_001_PRE

description: Library name: HCC002_001_PRE

value: pre-treatment


title: rSVA-III-B

first: Fuxiao

last: Liu

address: 700 Changcheng Road, Chengyang District

institute: Qingdao Agricultural University

description:
Library name: Sample 5
Ribo-seq of SVA-GFP with synonymous mutations in 3D region, 24 hpi

data_processing:
First, perform raw data quality control using Q30 values. Employ cutadapt software (v1.9.3) to trim adapters and remove low-quality reads, yielding high-quality clean reads. Use Tophat2 software to align clean reads to the reference genome. Subsequently, obtain raw count data using HTSeq software (v0.9.1), followed by normalization with edgeR or DESeq2.
Assembly: KX751945.1
Supplementary files format and content: count
Library strategy: Ribo-Seq

organism: Senecavirus A

source_name: BHK-21 cells

growth_protocol: The BHK-21 cell line was cultured at 37°C with 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (VivaCell, Shanghai, China), penicillin (100 U/mL), streptomycin (100 µg/mL), amphotericin B (0.25 µg/mL), and G418 (500 µg/mL).

extract_protocol:
The CHX-treated cells were lysed with lysis buffer and digested with nuclease. Digested samples were purified with size exclusion chromatography to obtain ribosome footprints. Ribosome protected fragments were size-selected with polyacrylamide gel electrophoresis (PAGE), and subjected to rRNA removal. Then, purified RNA fragments were end-repaired, ligated with 3' adapters and reverse-transcribed to cDNA. The cDNA was PAGE gel purified, circularized, and amplified by PCR.
RNA libraries for Ribo-seq were prepared using GenSeq® Ribo Profile Kit following manufacturer's protocols.

treatment_protocol: Cell monolayers at 80% confluency were infected with rSVA-GFP (MOI = 0.1), followed by treatment with cycloheximide (CHX) at 0.1 mg/ml for 1 minute at 24 hours post-infection (hpi).

value: BHK-21 cells

value: synonymously mutated

value: viral infection


title: HCC001_003_PRE

description: Library name: HCC001_003_PRE


title: HepG2 cell, a-tomatine treatment 24h 3

description: Library name: Sample 15


title: rSVA-III-C

description:
Library name: Sample 6
Ribo-seq of SVA-GFP with synonymous mutations in 3D region, 24 hpi


title: rSVA-III-A

description:
Library name: Sample 4
Ribo-seq of SVA-GFP with synonymous mutations in 3D region, 24 hpi


title: HepG2 cell, a-tomatine treatment 24h 1

description: Library name: Sample 13


title: rSVA-GFP-C

description:
Library name: Sample 3
Ribo-seq of wild-type virus SVA-GFP, 24 hpi


title: HepG2 cell, a-tomatine treatment 24h 2

description: Library name: Sample 14


title: HepG2 cell, a-tomatine treatment 12h 4

description: Library name: Sample 12

value: a-tomatine treatment 12h


title: HCC001_002_PRE

description: Library name: HCC001_002_PRE

value: Hepatocellular carcinoma


title: HepG2 cell, a-tomatine treatment 12h 3

description: Library name: Sample 11


title: rSVA-GFP-A

description:
Library name: Sample 1
Ribo-seq of wild-type virus SVA-GFP, 24 hpi


title: HepG2 cell, a-tomatine treatment 12h 2

description: Library name: Sample 10


title: HCC001_001_PRE

description: Library name: HCC001_001_PRE


title: dCCTM target-1

city: Tianjin

first: Shu-Lin

address: No.94 of Weijin Road

institute: Nankai University

description: Library name: dCCTM target-1

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Assembly: GRCh38.112
Supplementary files format and content: Excel file includes readcount value for each sample.

extract_protocol:
RNA was purified using the Trizol Kit. RNA was used for library construction.
The extracted and purified mRNA is subjected to quality control. Samples that pass the quality control are then used for library construction with a kit.

value: Epithelial cell

tag: construct expression

value: dCCTM

tag: grna

value: EGFP-targeting


title: HCC002_003_PRE

description: Library name: HCC002_003_PRE

value: Nivolumab plus ipilimumab


title: C2

description: Library name: Sample2

value: CON


title: cHiC of element C2,C3, and A deletion in mouse NPC at the Zfp608 locus R2

city: Montpellier

first: Ivana

last: Jerkovic

state: Occitanie

address: 141 rue de la Cardonille

country: France

institute: IGH, CNRS

description: Library name: cHiC_NPC_dAC2C3_R2

data_processing:
Data were mapped using bowtie2, the duplicated reads were discarded and bigwigs were produced directly from deduplicated bam files. For detailed protocol see the methods section of the adjoining paper.
Assembly: mm10
Supplementary files format and content: ATAC-seq rocessed files are given as a bigwig file of the two merged replicates.
Supplementary files format and content: Each cHi-C processed file represent pairwise information of the observed genome contacts. For score files: the data was analyzed with "misha" (https://github.com/tanaylab/misha) database entry and scores were generated using the "shaman" pipeline (https://github.com/tanaylab/shaman). The .mcool files were produced using the cooler package (https://cooler.readthedocs.io/en/latest/index.html).

source_name: E14tg2a differentiated into neuronal progenitor cells (NPCs)

growth_protocol: ESC were grown in FBS+LIF media with standard conditions. NPCs were differentiated using retinoic acid between days 4 and 8 when the cells were harvested. For detailed protocol see adjoning paper.

extract_protocol:
ATAC-seq was performed as in Active Motif #53150 kit with no modifications. For cHi-C, cell lysis, digestion, ligation, sonication and biotin labeling was preformed as in in-situ Hi-C protocol from Rao et al 2014. The rest of the protocol was done with SureSelect Agilent capture kit and custom capture library. For detailed protocol see adjoning paper.
ATAC-seq libraries were prepared as designated in Active Motif #53150 with no modifications. cHi-C libraries were prepared with the SureSelect Agilent kit. For detailed protocol see adjoning paper.

value: triple deletion of elements C2, C3 and A


title: HepG2 cell, a-tomatine treatment 12h 1

description: Library name: Sample 9


title: dCCTM control-1

description: Library name: dCCTM control-1

value: non-targeting


title: cHiC of element C2,C3, and A deletion in mouse NPC at the Zfp608 locus R1re

description: Library name: cHiC_NPC_dAC2C3_R1re

value: E14tg2a differentiated into neuronal progenitor cells (NPCs)


title: dCCTM control-2

description: Library name: dCCTM control-2


title: HepG2 cell, a-tomatine treatment 6h 4

description: Library name: Sample 8

value: Hepatocelular carcinoma

value: WT

value: a-tomatine treatment 6h


title: WT Cas13 target-2

description: Library name: WT Cas13 target-2

value: WT Cas13d


title: WT Cas13 target-1

description: Library name: WT Cas13 target-1


title: dCCTM target-2

description: Library name: dCCTM target-2


title: HepG2 cell, a-tomatine treatment 6h 3

description: Library name: Sample 7

value: no batch effect


title: WT Cas13 control-2

description: Library name: WT Cas13 control-2


title: rSVA-GFP-B

description:
Library name: Sample 2
Ribo-seq of wild-type virus SVA-GFP, 24 hpi

value: BHK-21 cells


title: cHiC of element C2 and C3 deletion in mouse NPC at the Zfp608 locus R2

description: Library name: cHiC_NPC_dC2C3_R2

value: double deletion of elements C2 and C3


title: HepG2 cell, a-tomatine treatment 6h 2

description: Library name: Sample 6


title: ATAC-seq in CTCF motif deletion at element A NPC R2

description: Library name: ATAC_NPC_dCTCF_R2

value: NPC dCTCF

value: deletion of CTCF motif at element A


title: HepG2 cells, PBS control 4

description: Library name: Sample 4

value: PBS


title: AML_2_CR_Untreated

city: Köln

first: Stuart

middle: James

last: Blakemore

state: NRW

address: Robert-Koch-Str. 21

department: TRIO

institute: University Hospital Cologne

description: 10X Genomics

data_processing:
Samples were analyzed with the M3K in-house processing pipeline (unpublished). For each sample, barcodes and UMIs were extracted from sequences in file1 and concatenated to corresponding sequence names in file2.
Barcodes having a mismatch at a single nucleotide position compared to the reference list of barcodes provided by 10x Genomics were corrected, where possible. Next, sequences from file2 were mapped to altered human genome (hg19) using STAR Aligner (version 2.5.2b) only keeping uniquely mapped reads 1.
Duplicate reads were identified as sequences within the same cell with the same UMI and same or slightly variable start position (between 1 and 3 nucleotides), and were excluded from further analysis 2. In addition, UMIs at each exonic region with 1 nucleotide mismatch from a set of UMIs residing at that exon were considered as duplicate reads and were consequently removed.
First and second derivatives in combination with curve smoothing were used to identify a point where the number of quantified reads per cell drastically drops marking it a cutoff for the number of viable cells.
Assembly: hg19
Supplementary files format and content: .Rdata files containing Seurat objects
Supplementary files format and content: .hd5 files containing dynamical RNA Velocity analyses

source_name: Bone Marrow

growth_protocol: AML bone marrow (BM) samples were obtained from patients at the City of Hope National Medical Center (COHNMC), under one of four City of Hope Institutional Review Board approved banking protocol #18067 in accordance with assurances filed with and approved by the Department of Health and Human Services, and meeting all requirements of the Declaration of Helsinki.

extract_protocol:
AML biopsies were checked for viability via Trypan Blue using a Neubauer chamber. If the viability was <70%, the cells were negatively sorted for viable cells using the Miltenyi Dead Cell Removal kit (Miltenyi Biotech). The cell concentration for each sample was adjusted to allow for a target output of ~10000 cells/sample.
Single cells from all samples using the Chromium Controller were encapsulated into emulsion droplets (10x Genomics). The Chromium Single Cell 3’ v2 Reagent Kit was used to construct the scRNA-Seq libraries, according to the manufacturer’s protocol. Libraries were sequenced using the NovoSeq 6000 (Illumina).

treatment_protocol: Bone marrow specimens from two AML patients who initially achieved a complete remission to the combination of hypomethylating agents with the Bcl-2 inhibitor venetoclax (HMA-VEN), (CR, defined as less than 5% marrow blasts by morphology) then became refractory to HMA-VEN (HMA-VEN-Refractory) were analyzed by scRNA-Seq.

value: Bone Marrow

tag: patient id

value: Acute Myeloid Leukemia hematopoietic cells

value: Untreated


title: WT Cas13 control-1

description: Library name: WT Cas13 control-1

value: Epithelial cell


title: ATAC-seq in CTCF motif deletion at element A NPC R1

description: Library name: ATAC_NPC_dCTCF_R1


title: cHiC of element C2 and C3 deletion in mouse NPC at the Zfp608 locus R1

description: Library name: cHiC_NPC_dC2C3_R1


title: HepG2 cells, PBS control 3

description: Library name: Sample 3


title: AML_1_HMA-VEN_Refractory

description: 10X Genomics

value: HMA-VEN


title: ATAC-seq in wt NPC R2

description: Library name: ATAC_NPC_wt_R2

value: NPC wt

value: Wild type


title: HepG2 cells, PBS control 2

description: Library name: Sample 2

value: Hepatocelular carcinoma


title: ATAC-seq in wt NPC R1

description: Library name: ATAC_NPC_wt_R1

value: E14tg2a differentiated into neuronal progenitor cells (NPCs)


title: AML_1_CR_Untreated

description: 10X Genomics


title: HepG2 cells, PBS control 1

description: Library name: Sample 1

value: WT


title: H01B_NICA

status: Public on Sep 19 2025

city: New York

first: Patrick

last: Wilson

state: NY

address: 413 E 69th St

department: Drukier Institute

institute: Weill Cornell Medicine

description:
Library name: NICA
10x Genomics

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger (v7.1.0) functions (mkfastq, count, vdj)
Assembly: GRCh3
Supplementary files format and content: consenus.fasta: the consensus sequence of each assembled contig in FASTA format
Supplementary files format and content: filtered_contig_annotations.csv: high-level annotations of each high-confidence contigs from cell associated barcodes

source_name: B cells

extract_protocol:
Single-cell suspensions of FACS-sorted B cells were processed using the 10x Genomics Chromium Single Cell 5' Immune Profiling workflow. Cells were loaded onto the Chromium Controller for partitioning and barcoding, followed by reverse transcription, cDNA amplification, and library construction according to the manufacturer’s protocol [10x Genomics Single Cell V(D)J Reagent Kits v2].
The sorted single cells were processed according to 10x Genomics 5’ gene expression and B cell Immunoglobulin (Ig) enrichment protocol to prepare the libraries for sequencing.

value: B cells


title: cHiC of element C2,C3, and A deletion in mouse NPC at the Zfp608 locus R1

description: Library name: cHiC_NPC_dAC2C3_R1

value: triple deletion of elements C2, C3 and A


title: cHiC of element C2 and C3 deletion in mouse NPC at the Zfp608 locus R2re

description: Library name: cHiC_NPC_dC2C3_R2re


title: H01A

description:
Library name: Human
10x Genomics


title: H01C_lib1

description:
Library name: LIB1
10x Genomics


title: MatKIP3

city: Berlin

first: Jose

middle: M.

last: Muino

address: Max-Dohrn-Str. 8-10

institute: German Federal Institute for Risk Assessment

description: plastid RNA

data_processing:
Basecalls performed using"Bcl to FastQ" version: 2.19
Data trimming was done with Trimmomatic version 0.36 with the next parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:5; Unpaired reads were eliminated
RIP-seq paired-end reads were aligned to the tobacco organelle genomes (NC_001879.2, NC_006581.1) using bowtie2 version 2.2.9 using default parameter values
peaks were called using CSAR  with the following setting: backg=10 , norm=10^9, w=75, considerStrand="Sum"
Assembly: NC_001879.2, NC_006581.1
Supplementary files format and content: wig file was generated using CSAR and it represents the ratios of IP/control; bed file was generated using CSAR and it represents significant regions (FDR<0.05)

organism: Nicotiana tabacum

source_name: seedlings without root

growth_protocol: Nicotiana tabacum seeds were sown on polyamide nets (mesh size 500 μM, Franz Eckert GmbH) on soil. Plants were grown under long day conditions (16 hours light, 8 hours dark) at 27°C with light intensities of approximately 300 μmol. m-2. s -1. Both seed sowing and seedling harvesting were performed at 10:00 am.

extract_protocol:
Stroma fraction was prepared from isolated chloroplasts, MatK-RNA complex was isolated with antibody
Libraries were prepared according to the instructions accompanying the RNA Sample Kit (NEBNext Multiplex Small RNA Library Prep Set for Illumina, E7300s)

tag: cultivar

value: Petit Havana

value: seedlings without root

tag: developmental stage

value: 7 days old

tag: rip antibody

value: HA (Sigma, H3663)

value: Nicotiana tabacum with aada selection marker and HA tagged MatK


title: HepG2 cell, a-tomatine treatment 6h 1

description: Library name: Sample 5

value: a-tomatine treatment 6h

value: no batch effect


title: H01B_IASO

description:
Library name: IASO
10x Genomics


title: MatKIP2

description: plastid RNA


title: control1

description: plastid RNA

value: Nicotiana tabacum with aada selection marker


title: MatKIP1

description: plastid RNA


title: control2

description: plastid RNA


title: Pistil of which floral buds diameter greater between 1.6-2.0mm of  H. bodinieri female flower. C2_C_R3

city: nanning

first: tianfeng

last: liu

address: Xixiangtang Street

institute: guangxi university

description:
Pistil of which floral buds diameter greater between 1.6-2.0mm of  H. bodinieri female flower.
Handeliodendron bodinieri（Levl.）Rehd

data_processing:
The samples were sequenced using a BGISEQ-500 Analyzer (BGI Genomics, Shenzhen, China).
Clean reads were assembled by using Trinit.
Tgicl was used to cluster the transcripts to obtain Unigene
Clean reads of each sample were compared to Unigene using Bowtie2 software.
The fragments per Kilobase of transcript per Million mapped reads (FPKM) were calculated was calculated by RSEM.
Supplementary files format and content: Microsoft Office Excel files include FPKM values for each Sample.
Supplementary files format and content: fasta files include the sequence and length of genes.

organism: Handeliodendron bodinieri

source_name: Flower

extract_protocol:
Total RNA was isolated from samples using TRIzol reagent according to the manufacturer’s protocol (Invitrogen).
The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligationoftheadapter.Theproducts are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the BGISEQ-500 platform for the following data analysis study. For this step, the BGISEQ-500 platform combines the DNA nanoball-based nanoarrays andstepwisesequencingusingCombinationalProbe-AnchorSynthesis SequencingMethod.

value: female

tag: pistil development stage

value: stage two of pistil development

value: pistil


title: Pistil of which floral buds diameter greater between 1.6-2.0mm of  H. bodinieri female flower. C2_C_R1


title: Pistil of which floral buds diameter between 1.3~1.6mm of  H. bodinieri female flower. C1_C_R3

description:
Pistil of which floral buds diameter between 1.3~1.6mm of  H. bodinieri female flower.
Handeliodendron bodinieri（Levl.）Rehd

value: stage one of pistil development


title: Pistil of which floral buds diameter between 1.3~1.6mm of  H. bodinieri female flower. C1_C_R2


title: Pistil of which floral buds diameter greater between 1.6-2.0mm of  H. bodinieri male flower. X2_C_R1

description:
Pistil of which floral buds diameter greater between 1.6-2.0mm of  H. bodinieri male flower.
Handeliodendron bodinieri（Levl.）Rehd

value: male


title: AML_2_HMA-VEN_Refractory

description: 10X Genomics

value: Bone Marrow

value: Acute Myeloid Leukemia hematopoietic cells

value: HMA-VEN


title: H01C_lib2

description:
Library name: LIB2
10x Genomics

value: B cells


title: Pistil of which floral buds diameter between 1.3~1.6mm of  H. bodinieri female flower. C1_C_R1


title: Pistil of which floral buds diameter between 1.3~1.6mm of  H. bodinieri male flower. X1_C_R1

description:
Pistil of which floral buds diameter between 1.3~1.6mm of  H. bodinieri male flower.
Handeliodendron bodinieri（Levl.）Rehd


title: Pistil of which floral buds diameter greater between 1.6-2.0mm of  H. bodinieri male flower. X2_C_R3


title: Mouse brain, H3K27me3, LPC lesion, 21 days post lesion, replicate 1

city: New Haven

first: Di

last: Zhang

address: 55 Prospect St

institute: Yale University

description: Library name: Epigenomic_10_LPC21S1_H3K27me3

data_processing:
Base-calling and demultiplexing were performed using Illumina standard software.
Reads were quality filtered with fastp and aligned to the mouse genome (mm10) using STAR (RNA) or BWA (ATAC).
RNA counts were generated with featureCounts, and ATAC peaks were called with MACS2.
Final processed matrices were compiled with genes/peaks as rows and samples as columns.
Assembly: mm10
Supplementary files format and content: fragments.tsv.gz, fragments file (bgzipped)
Supplementary files format and content: fragments.tsv.gz.tbi, Tabix index for fragments file
Library strategy: CUT&Tag

source_name: brain

extract_protocol:
Mouse brains were embedded in OCT, cryosectioned at 10 µm thickness, and processed for spatial multi-omic library preparation using DBiT-seq.
Spatial barcoding was performed on 10 µm brain cryosections using DBiT-seq. Barcoded RNA/cDNA (and/or ATAC fragments) were then converted into Illumina-compatible sequencing libraries following standard protocols.

value: brain


title: Mouse brain, LPC lesion, 5 days post lesion, Saggital

description: Library name: Epigenomic_LPC5_Saggital

data_processing:
Base-calling and demultiplexing were performed using Illumina standard software.
Reads were quality filtered with fastp and aligned to the mouse genome (mm10) using STAR (RNA) or BWA (ATAC).
RNA counts were generated with featureCounts, and ATAC peaks were called with MACS2.
Final processed matrices were compiled with genes/peaks as rows and samples as columns.
Assembly: mm10
Supplementary files format and content: fragments.tsv.gz, fragments file (bgzipped)
Supplementary files format and content: fragments.tsv.gz.tbi, Tabix index for fragments file


title: Mouse brain, H3K27me3, LPC lesion, 5 days post lesion, replicate 2

description: Library name: Epigenomic_09_LPC5S2_H3K27me3


title: Pistil of which floral buds diameter between 1.3~1.6mm of  H. bodinieri male flower. X1_C_R3


title: Mouse brain, H3K27me3, LPC lesion, 21 days post lesion, replicate 2

description: Library name: Epigenomic_10_LPC21S2_H3K27me3


title: Pistil of which floral buds diameter greater between 1.6-2.0mm of  H. bodinieri male flower. X2_C_R2


title: Mouse brain, LPC lesion, 21 days post lesion, replicate 2

description: Library name: Epigenomic_08_LPC21S2


title: Mouse brain, LPC lesion, 21 days post lesion, replicate 1

description: Library name: Epigenomic_08_LPC21S1


title: Mouse brain, LPC lesion, 10 days post lesion, replicate 2

description: Library name: Epigenomic_07_LPC10S2


title: Pistil of which floral buds diameter between 1.3~1.6mm of  H. bodinieri male flower. X1_C_R2


title: Pistil of which floral buds diameter greater between 1.6-2.0mm of  H. bodinieri female flower. C2_C_R2


title: Mouse brain, LPC lesion, 5 days post lesion, replicate 1

description: Library name: Epigenomic_06_LPC5S1


title: Mouse brain, LPC lesion, 10 days post lesion, replicate 1

description: Library name: Epigenomic_07_LPC10S1


title: Mouse brain, LPC lesion, 5 days post lesion, replicate 2

description: Library name: Epigenomic_06_LPC5S2


title: Mouse brain, postnatal day 21, replicate 3

description: Library name: Epigenomic_05_P21S3


title: Mouse brain, postnatal day 21, replicate 1

description: Library name: Epigenomic_05_P21S1


title: Mouse brain, postnatal day 10, replicate 3

description: Library name: Epigenomic_04_P10S3


title: Mouse brain, postnatal day 10, replicate 2

description: Library name: Epigenomic_04_P10S2


title: Mouse brain, postnatal day 7

description: Library name: Epigenomic_03_P7S2


title: Mouse brain, postnatal day 21, replicate 2

description: Library name: Epigenomic_05_P21S2


title: Mouse brain, postnatal day 5, replicate 3

description: Library name: Epigenomic_02_P5S3


title: Mouse brain, postnatal day 10, replicate 1

description: Library name: Epigenomic_04_P10S1


title: Mouse brain, postnatal day 5, replicate 2

description: Library name: Epigenomic_02_P5S2


title: Mouse brain, postnatal day 5, replicate 1

description: Library name: Epigenomic_02_P5S1


title: Mouse brain, postnatal day 2, replicate 1

description: Library name: Epigenomic_01_P2S1


title: Mouse brain, postnatal day 2, replicate 3

description: Library name: Epigenomic_01_P2S3


title: Mouse brain, H3K27me3, LPC lesion, 5 days post lesion, replicate 1

description: Library name: Epigenomic_09_LPC5S1_H3K27me3


title: Mouse brain, postnatal day 2, replicate 2

description: Library name: Epigenomic_01_P2S2


title: Mouse brain, postnatal day 0, replicate 3

description: Library name: Epigenomic_00_P0S3


title: Mouse brain, postnatal day 0, replicate 4

description: Library name: Epigenomic_00_P0S4


title: Mouse brain, postnatal day 0, replicate 1

description: Library name: Epigenomic_00_P0S1


title: Mouse brain, LPC lesion, 5 days post lesion, Saggital

description: Library name: RNA_LPC5_Saggital

data_processing:
Base-calling and demultiplexing were performed using Illumina standard software. Reads were quality filtered with fastp and aligned to the mouse genome (mm10) using STAR (RNA) or BWA (ATAC). RNA counts were generated with featureCounts, and ATAC peaks were called with MACS2. Final processed matrices were compiled with genes/peaks as rows and samples as columns.
Assembly: mm10
Supplementary files format and content: RNA_matrix.csv.gz: gene expression count matrix
Supplementary files format and content: scalefactors_json.json: scalefactors in JSON format
Supplementary files format and content: tissue_hires_image.png: high-resolution image of tissue section
Supplementary files format and content: tissue_lowres_image.png: low-resolution image of tissue section
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

tag: treatment/time point


title: Mouse brain, H3K27me3, LPC lesion, 21 days post lesion, replicate 1

description: Library name: RNA_10_LPC21S1_H3K27me3

tag: tissue


title: Mouse brain, H3K27me3, LPC lesion, 21 days post lesion, replicate 2

description: Library name: RNA_10_LPC21S2_H3K27me3


title: Mouse brain, H3K27me3, LPC lesion, 5 days post lesion, replicate 2

description: Library name: RNA_09_LPC5S2_H3K27me3


title: Mouse brain, postnatal day 0, replicate 2

description: Library name: Epigenomic_00_P0S2


description: Library name: RNA_09_LPC5S1_H3K27me3

value: H3K27me3, LPC lesion, 5 days post lesion


title: Mouse brain, LPC lesion, 21 days post lesion, replicate 2

description: Library name: RNA_08_LPC21S2

value: LPC lesion, 21 days post lesion


title: Mouse brain, LPC lesion, 5 days post lesion, replicate 1

description: Library name: RNA_06_LPC5S1

value: LPC lesion, 5 days post lesion


title: Mouse brain, LPC lesion, 21 days post lesion, replicate 1

description: Library name: RNA_08_LPC21S1


title: Mouse brain, LPC lesion, 10 days post lesion, replicate 1

description: Library name: RNA_07_LPC10S1

value: LPC lesion, 10 days post lesion


title: Mouse brain, LPC lesion, 10 days post lesion, replicate 2

description: Library name: RNA_07_LPC10S2


title: Mouse brain, LPC lesion, 5 days post lesion, replicate 2

description: Library name: RNA_06_LPC5S2


title: Mouse brain, postnatal day 21, replicate 1

description: Library name: RNA_05_P21S1

value: postnatal day 21


title: Mouse brain, postnatal day 21, replicate 3

description: Library name: RNA_05_P21S3


title: Mouse brain, postnatal day 10, replicate 2

description: Library name: RNA_04_P10S2

value: postnatal day 10


title: Mouse brain, postnatal day 10, replicate 1

description: Library name: RNA_04_P10S1


title: Mouse brain, postnatal day 7

description: Library name: RNA_03_P7S2

value: postnatal day 7


title: Mouse brain, postnatal day 21, replicate 2

description: Library name: RNA_05_P21S2


title: Mouse brain, postnatal day 10, replicate 3

description: Library name: RNA_04_P10S3


title: Mouse brain, postnatal day 5, replicate 3

description: Library name: RNA_02_P5S3

value: postnatal day 5


title: Mouse brain, postnatal day 5, replicate 2

description: Library name: RNA_02_P5S2


title: Mouse brain, postnatal day 2, replicate 3

description: Library name: RNA_01_P2S3

value: postnatal day 2


title: Mouse brain, postnatal day 5, replicate 1

description: Library name: RNA_02_P5S1


title: Mouse brain, postnatal day 2, replicate 1

description: Library name: RNA_01_P2S1


title: Mouse brain, postnatal day 2, replicate 2

description: Library name: RNA_01_P2S2


title: Mouse brain, postnatal day 0, replicate 3

description: Library name: RNA_00_P0S3

value: postnatal day 0


title: Mouse brain, postnatal day 0, replicate 4

description: Library name: RNA_00_P0S4


title: Mouse brain, postnatal day 0, replicate 2

description: Library name: RNA_00_P0S2


title: MEF, HSV-1, FLAG-input, 3 [B319096]

city: Oxford

first: Aleksandr

last: Fedorov

address: John Radcliffe Hospital/Headley Way

department: Radcliffe Department of Medicine

institute: University of Oxford

description: Library name: B319096+2691159

data_processing:
All samples were aligned to a chimeric reference composed of the host (GRCm39) and viral reference sequences (HSV-1 and IAV) using a custom fork of the nf-core 'rnaseq' pipeline (https://github.com/alnfedorov/rnaseq, commit 41e95d6a4a24d1f4fe4f2c50bb4d9a4744158c9b). Briefly, reads were trimmed using fastp (v0.23.4), aligned using STAR (v2.7.10a), duplicates were marked with Picard (v3.1.1), and the abundance of individual RNAs was quantified using Salmon (v1.10.1).
Peak calling and dsRNA reconstruction of endogenous RNAs were performed using biobit (https://github.com/biomancy/biobit, v0.0.4). Inferred dsRNA clusters were tested for induction and enrichment using DESeq2 (v1.46.0) and apeglm (v1.28.0).
Aberrant transcription was analyzed with DEXSeq (v1.52.0) by treating each mRNA with a matched aberrant transcription region, or each intron with its matched 5′ constitutive exon, as regions belonging to the same group in DEXSeq.
Enrichment of viral RNAs was visualized using pyCirclize (v1.7.1). ViennaRNA (v2.7.0) and Z-Hunt[rs] (https://github.com/biomancy/zhuntrs, v0.0.4) were used to predict putative Z-prone RNA stems within the minimum free energy structures of individual vRNAs.
All code used to analyze sequencing data in this study is publicly available at https://github.com/alnfedorov/Z-DoTT.
Assembly: GRCm39, GCF_000865725.1, NC_001806.2
Supplementary files format and content: The counts.tsv.gz file includes five index columns followed by count columns, with column names corresponding to the library names provided in the submission. The index columns define the region being assessed: its unique ID, type, and localization (sequence ID, strand, and location). For split regions (e.g., exons), multiple coordinates are separated by semicolons. Each region represents either a normalization bin (used exclusively for library normalization) or a putative dsRNA cluster predicted from RIP data. This table can be used to identify dsRNA clusters that are strongly induced during infection and reproducibly enriched in RIP experiments from infected cells.

source_name: MEF

growth_protocol: MEFs were maintained in DMEM supplemented with 15% FBS, 1 mM sodium pyruvate, 1x GlutaMAX, and 1% penicillin/streptomycin. All cells were cultured at 37°C in 5% CO2, and routinely tested for mycoplasma.

extract_protocol:
RIP was conducted using the EZ-Magna RIP (Cross-Linked) RNA-Binding Protein Immunoprecipitation Kit (Millipore) following the manufacturer’s instructions. Briefly, cross-linked cell pellets were lysed in RIP lysis buffer, followed by incubation with RIP Buffer containing magnetic beads conjugated with anti-Z-NA antibody (clone Z22, Absolute Antibody), anti-FLAG antibody (F1804, Sigma-Aldrich) or their respective isotype control antibodies, at 4°C overnight. Samples were then incubated with proteinase K and immunoprecipitated RNAs were recovered by phenol:chloroform:isoamyl alcohol purification.  Ten percent of the cell lysate was used for total RNA extraction as the input, and the remaining ninety percent was used for immunoprecipitation.
Libraries were prepared from RIP or input RNA using the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions (Illumina). Libraries were analyzed for insert size distribution using the 2100 BioAnalyzer High Sensitivity kit (Agilent), 4200 TapeStation D1000 ScreenTape assay (Agilent), or 5300 Fragment Analyzer NGS fragment kit (Agilent). Libraries were quantified using the Quant-iT PicoGreen ds DNA assay (Thermo Fisher Scientific) or by low pass sequencing with a MiSeq nano kit (Illumina). Paired-end 150 cycle sequencing was performed on a NovaSeq 6000 (Illumina).

treatment_protocol: FLAG-ZBP1 and FLAG-ZBP1 ΔZα MEFs were generated via stable retroviral transduction (pRetroX, Clontech) of immortalized Zbp1-/- MEFs with expression vectors encoding either FLAG-tagged full-length mouse ZBP1 or ZBP1 lacking both Zα domains (ΔZα). Cells were infected (MOI=2) with or without HSV-1 (F strain[VR-733]) or IAV (A/Puerto Rico/8/1934) for 8h.

value: MEF

value: mouse embryonic fibroblast

tag: treatment

value: HSV-1 infection

tag: rip

value: FLAG-input


title: MEF, HSV-1, FLAG-input, 4 [B319096]

description: Library name: B319096+2691160


title: MEF, HSV-1, FLAG-input, 1 [B319096]

description: Library name: B319096+2691157


title: Mouse brain, postnatal day 0, replicate 1

description: Library name: RNA_00_P0S1


title: MEF, HSV-1, FLAG-input, 2 [B319096]

description: Library name: B319096+2691158


title: MEF, mock, FLAG-input, 1 [B319096]

description: Library name: B319096+2691155

value: Mock


title: MEF, HSV-1, FLAG, 4 [B319096]

description: Library name: B319096+2691154

library_source: other

molecule: other

value: FLAG


title: MEF, HSV-1, FLAG, 2 [B319096]

description: Library name: B319096+2691152


title: MEF, mock, FLAG, 1 [B319096]

description: Library name: B319096+2691149


title: MEF, mock, FLAG, 2 [B319096]

description: Library name: B319096+2691150


title: MEF, HSV-1, FLAG, 1 [B319096]

description: Library name: B319096+2691151


title: MEF, HSV-1, FLAG, 3 [B319096]

description: Library name: B319096+2691153


title: MEF, HSV-1, RIP-input, 2 [B261790]

description:
Library name: B261790+2393138
An extra control RIP input library.

value: RIP-input


title: MEF, HSV-1, Z22-input, 2 [B261790]

description: Library name: B261790+2393137


title: MEF, HSV-1, IgG-input, 2 [B261790]

description: Library name: B261790+2393136

value: IgG-input


title: MEF, mock, Z22-input, 2 [B261790]

description: Library name: B261790+2393134


title: MEF, HSV-1, IgG-input, 1 [B261790]

description: Library name: B261790+2393130


title: MEF, mock, IgG-input, 2 [B261790]

description: Library name: B261790+2393133


title: MEF, HSV-1, Z22-input, 1 [B261790]

description: Library name: B261790+2393131


title: MEF, mock, RIP-input, 1 [B261790]

description:
Library name: B261790+2393129
An extra control RIP input library.


title: MEF, mock, RIP-input, 2 [B261790]

description:
Library name: B261790+2393135
An extra control RIP input library.


title: MEF, mock, IgG-input, 1 [B261790]

description: Library name: B261790+2393127


title: MEF, HSV-1, IgG, 2 [B261790]

description: Library name: B261790+2393124

value: IgG


title: MEF, mock, IgG, 2 [B261790]

description: Library name: B261790+2393121


title: MEF, mock, FLAG-input, 2 [B319096]

description: Library name: B319096+2691156


title: MEF, mock, Z22, 2 [B261790]

description: Library name: B261790+2393122


title: MEF, HSV-1, Z22, 1 [B261790]

description: Library name: B261790+2393119


title: MEF, HSV-1, Z22, 2 [B261790]

description: Library name: B261790+2393125


title: MEF, HSV-1, RIP-input, 1 [B261790]

description:
Library name: B261790+2393132
An extra control RIP input library.


title: MEF, mock, Z22, 1 [B261790]

description: Library name: B261790+2393116


title: MEF, HSV-1, IgG, 1 [B261790]

description: Library name: B261790+2393118


title: MEF, mock, IgG, 1 [B261790]

description: Library name: B261790+2393115


title: MEF, IAV, FLAG-input, 2 [B256178]

description: Library name: B256178+2360326

value: IAV infection


title: MEF, mock, Z22-input, 1 [B261790]

description: Library name: B261790+2393128


title: MEF, mock, FLAG-input, 2 [B256178]

description: Library name: B256178+2360323


title: MEF, IAV, IgG-input, 2 [B256178]

description: Library name: B256178+2360324


title: MEF, IAV, Z22-input, 1 [B256178]

description: Library name: B256178+2360319


title: MEF, IAV, FLAG-input, 1 [B256178]

description: Library name: B256178+2360320


title: MEF, mock, Z22-input, 1 [B256178]

description: Library name: B256178+2360316


title: MEF, mock, FLAG-input, 1 [B256178]

description: Library name: B256178+2360317


title: MEF, IAV, FLAG, 2 [B256178]

description: Library name: B256178+2360314


title: MEF, IAV, IgG-input, 1 [B256178]

description: Library name: B256178+2360318


title: MEF, IAV, Z22, 2 [B256178]

description: Library name: B256178+2360313


title: MEF, IAV, IgG, 2 [B256178]

description: Library name: B256178+2360312


title: MEF, IAV, Z22-input, 2 [B256178]

description: Library name: B256178+2360325


title: MEF, mock, FLAG, 2 [B256178]

description: Library name: B256178+2360311


title: MEF, mock, Z22, 2 [B256178]

description: Library name: B256178+2360310


title: MEF, IAV, Z22, 1 [B256178]

description: Library name: B256178+2360307


title: MEF, IAV, IgG, 1 [B256178]

description: Library name: B256178+2360306


title: MEF, mock, IgG-input, 2 [B256178]

description: Library name: B256178+2360321


title: MEF, mock, Z22-input, 2 [B256178]

description: Library name: B256178+2360322


title: Apc Colon Tum EGFRi Rep1

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

institute: CRUK Scotland Institute

description:
Library name: Colon_tum1
10x genomics GEMX-flex

data_processing:
Pooled sequencing data was demultiplexed, UMIs counted and count tables produced using CellRanger 9.0.0
Assembly: GRCm39
Supplementary files format and content: h5 matrix files

source_name: Colon

extract_protocol:
Tumours were processed to single cells using a GEM-X Flex Sample preparation kit, before being incubated overnight at 4 degrees celcius in GEM-X flex Fixation Buffer B. Samples were washed in PBS then resuspended in GEM-X flex Quench Buffer, then dissiciated in RPMI and 5mg/ml Liberase TH. Homogenisation was then performed on a GentleMACS Octo Dissociator, cells were filtered with a 30 um strainer, pelleted and resuspended in GEM-X flex Quench buffer, then counted using equal parts of cell suspension and ReadyCount Green/Red Viability Stain on a CellDrop Automated Cell Counter.
Libraries were prepared using a 10X Genomics Gem-X Flex Gene Expression kit with the Mouse Transcriptome Probe panel, according to the manufacturer’s protocol

value: Colon


title: MEF, mock, Z22, 1 [B256178]

description: Library name: B256178+2360304


title: Multiplexed GEMX flex data Tumour Organoids

description:
Library name: GEMX flex Tumour Organoids
10x genomics GEMX-flex

source_name: Tumour Organoid

growth_protocol: Murine tumour organoids were derived from the intestinal tumours and/or sychronous liver metastasis. Tumour organoids were grown in base media consiting of Advanced DMEM/F12 (ADMEM), L-Glutamine (2mM), HEPES (010mM) and Penicillin + Steptomycin (100U/ml + 100ug/ml) supplemented with N2 and B27 supplements, Recombinant Human Epidermal Growth Factor (50ng/ml) and Recombinant Murine Noggin (100ng/ml). Organoid lines were passaged 3 times per week.

extract_protocol:
Tumour organoids were harvested 72-hours after seeding, digested using TrpLE + Rocki and manually discociated into a single cell suspension. Tumour organoids were processed using a GEM-X Flex Sample preparation kit, before being incubated overnight at 4 degrees celcius in GEM-X flex Fixation Buffer B. Samples were washed in PBS then resuspended in GEM-X flex Quench Buffer, then dissiciated in RPMI and 5mg/ml Liberase TH. Homogenisation was then performed on a GentleMACS Octo Dissociator, cells were filtered with a 30 um strainer, pelleted and resuspended in GEM-X flex Quench buffer, then counted using equal parts of cell suspension and ReadyCount Green/Red Viability Stain on a CellDrop Automated Cell Counter.
Libraries were prepared using a 10X Genomics Gem-X Flex Gene Expression kit with the Mouse Transcriptome Probe panel, according to the manufacturer’s protocol

value: Tumour Organoid


title: MEF, mock, FLAG, 1 [B256178]

description: Library name: B256178+2360305


title: BPRNF SI Tum d3 Multiplex

description:
Library name: BPRNF_d3
10x genomics GEMX-flex

source_name: Small Intestine

extract_protocol:
Tumours were processed to single cells using a GEM-X Flex Sample preparation kit, before being incubated overnight at 4 degrees celcius in GEM-X flex Fixation Buffer B. Samples were washed in PBS then resuspended in GEM-X flex Quench Buffer, then dissiciated in RPMI and 5mg/ml Liberase TH. Homogenisation was then performed on a GentleMACS Octo Dissociator, cells were filtered with a 30 um strainer, pelleted and resuspended in GEM-X flex Quench buffer, then counted using equal parts of cell suspension and ReadyCount Green/Red Viability Stain on a CellDrop Automated Cell Counter.
Libraries were constructed using a 10X Genomics Gem-X flex Gene Expression kit using the MouseTranscriptome Probe panel, as per the manufacturer’s instructions.

value: Small Intestine

tag: sample type

value: Primary Tumour

value: VilCreER BrafV600E/+ p53 fl/fl RNF43 fl/fl

tag: time point

value: Day 3


title: MEF, mock, IgG-input, 1 [B256178]

description: Library name: B256178+2360315

tag: cell line

tag: cell type


title: WT

first: yumeng

address: Changchun street.

department: Xuanwu hospital

institute: Capital Medical University

description:
Library name: Symbol 1
BG

data_processing:
The BD pipeline filtered feature/barcode tables were processed with a custom script to create a Seurat object (Seurat package, v4.3.1)[14]. To recover platelets from the BD raw data, the top 5000 droplets with the most detected genes were extracted from the original BAM file for each sample, and all droplets were merged for further processing. The following steps were implemented to retain platelet-size droplets:MK/Platelet-related signature genes were obtained from the “m5.go.bp.v2023.1.Mm.symbols.gmt” file, and for each droplet, a “MKPP score” was calculated using the Seurat function “AddModuleScore.” A “cell-to-mean correlation” metric was then calculated, following the approach described in the paper (DOI: 10.1186/s13059-016-0888-1), to distinguish real cells from empty droplets. Based on the distribution of these two metrics, the top 25% MKPP-scoring droplets with a cell-to-mean correlation greater than 0.3 were retained for further integration with the BD-filtered dataset. The resulting cells were considered valid and used for subsequent analysis.
Assembly: Mouse mm10
Supplementary files format and content: Helicobacter pylori ASM2599845v1
Supplementary files format and content: Tab-separeted values files and matrix files

source_name: bone marrow

extract_protocol:
The mice were divided into four groups: The BMF group (experimental group) n=4, the whole-body irradiation (TBI) group (control group) n=3, the normal young mouse group (WT), and the normal aged mouse group (Aged). Specifically, first-generation hybrid B6D2F1 mice were bred by crossing C57BL/6 and DBA/2 mice. These male mice, aged 8-12 weeks, were used as test subjects for the BMF mouse model. Male C57BL/6 mice, aged 8-12 weeks, were used as lymphocyte donors. Male B6D2F1 mice, aged 8 weeks, served as the normal young mouse group, while male B6D2F1 mice, aged 104 weeks, served as the normal aged mouse group. All mice were provided by Beijing Weitong Lihua Experimental Animal Technology Co., Ltd. and were housed in a standard highly hygienic environment. The study was approved by the Experimental Animal Welfare Ethics Committee of Xuanwu Hospital, Capital Medical University (approval number: XW-20210531-1).
Cells were first stained with two fluorescent dyes, Calcein AM and Draq7, to precisely determine cell concentration and viability using the BD Rhapsody™ Scanner (BD Biosciences) before antibody-based labeling. Each sample was stained for 30 minutes on ice with 25 AbSeq antibodies targeting major mouse immune markers from the BD Abseq immune discovery panel (Cat. No. 940320, 940107, 940110, 940119, 940132, 940130, 940127, 940168, 940109, 940163, 940131, 940108, 940345, 940137, 940417, 940116, 940496, 940329, 940357, 940437, 940128, 940134, 940165, 940209, 940151). Afterward, the cells were labeled with the respective AbSeq antibodies, washed three times with Stain Buffer (FBS) (BD Biosciences, Cat. No. 554656), and loaded into a BD Rhapsody micro-well cartridge for single-cell capture.Excessive cell capture beads were added to ensure nearly every micro-well contained a bead, and any excess beads were washed away. After cell lysis with lysis buffer, cell capture beads were retrieved, washed, and reverse transcription was performed. The microbeads captured single-cell transcriptomes, along with Ab-tagged index sequences targeting 25 immune cell-associated surface antigens, generating separate cDNA libraries for transcriptome and AbSeq, each containing cell labels and unique molecular identifier (UMI) information. The entire process followed the manufacturer's protocols using the BD Rhapsody cDNA Kit (BD Biosciences, Cat. No. 633773) and the BD Rhapsody WTA Amplification Kit (BD Biosciences, Cat No. 633802). The libraries were sequenced using the PE150 mode (Pair-End for 150 bp read) on the NovaSeq 6000 platform (Illumina).

value: bone marrow

value: primary and differentiation cells

value: bone marrow cells

tag: group

value: WT


title: TBI

description:
Library name: Symbol 2
BG

value: TBI


title: Ripply1ΔHep-3

first: Guangyan

last: Zhangyuan

address: 197 Ruijin Er Road

department: Department of General Surgery, Pancreatic Disease Center

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

description: Library name: Sample 6

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Assembly: mm10
Supplementary files format and content: raw counts for each sample

source_name: Liver cancer

growth_protocol: SPF (specific pathogen free)

extract_protocol:
RNA was harvested using Trizol reagent from primary hepatocytes of DEN/PB-induced liver tumors .1 ug of total RNA was used for the construction of sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The male Ripply1F/F and Ripply1ΔHep mice were intraperitoneally injected with a single dose of DEN (90 μg/g) at 6 weeks of age. After a treatment-free interval of 3 weeks, mice were kept on a diet containing 0.05% PB for 27 weeks

value: Liver cancer

value: Hepatocyte

tag: genotype

value: Hepatocte specific Ripply1 Knockout

value: DEN/PB


title: Ripply1ΔHep-1

description: Library name: Sample 4


title: Aged

description:
Library name: Symbol 4
BG

value: Aged


title: Ripply1ΔHep-2

description: Library name: Sample 5


title: BMF

description:
Library name: Symbol 3
BG

value: BMF


title: Ripply1F/F-3

description: Library name: Sample 3

value: Ripply1 Flox


title: Ripply1F/F-1

description: Library name: Sample 1


title: MEF, mock, IgG, 2 [B256178]

description: Library name: B256178+2360309

value: MEF

value: mouse embryonic fibroblast

value: Mock

value: IgG

tag: batch


title: Ripply1F/F-2

description: Library name: Sample 2