title: TRA_F15_1N_MA_A80

description:
Library name: A80
TRA_F15_1N_MA_A80


title: brain, 687_PPC, posterior parietal cortex

status: Public on Jul 09 2026

type: SRA

city: Madison

first: Hasan

last: Khatib

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

country: USA

institute: University of Wisconsin Madison

description:
Library name: 687_PPC
687_PPC

library_source: transcriptomic

data_processing:
Alignment (STAR)
Read counts (Rsubread)
Differential expression analysis (DEseq2 R package)
Annotation
Assembly: ARS-UI_Ramb_v3.0
Supplementary files format and content: read counts

molecule: total RNA

organism: Ovis aries

source_name: Brain

extract_protocol:
RNA were extracted with either TRIzol reagent  (for sheep samples) or  Zymo Quick-RNA miniprep plus extraction kit (rat samples) followed by DNase I treatment before RNA sequencing.
RNA sequencing was performed for all samples using the NovaSeq X Plus platform with two 25B lanes, using V1.0 sequencing kits, and as 150 bp paired-end reads. Sheep RNA-Seq libraries were prepared with the Kapa Hyper Stranded mRNA library kit. Rat RNA-Seq libraries were prepared with the Watchmaker Stranded mRNA library kit. The libraries were pooled, quantified by qPCR, and sequenced on one 25B lane for 151 cycles from both ends of the fragments.

treatment_protocol: No specific treatment was applied.

tag: tissue

value: Brain


title: Control, 72 h, r1

type: genomic

city: Badalona

first: José

middle: Luis

last: Sardina

state: Barcelona

address: Ctra de Can Ruti, Camí de les Escoles, s/n

country: Spain

institute: Josep Carreras Leukaemia Research Institute

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium MethylationEPIC Bead-Chip arrays using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Methylation data were analyzed using the minfi package in R. Data was imported into R and normalized (noob and quantile normalization). Probes were removed if they did not pass the detection cut-off (p < 0.01), and if were associated with known SNPs or with the X and Y chromosomes
Normalized (preprocessNoob and preprocessQuantile) Beta-values

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: B-ALL cell line

label_protocol: Standard Illumina Protocol

growth_protocol: BlaER cells and subclones were grown in suspension in RPMI 1640 supplemented with 10% heat-inactivated FBS, 1X Penicillin-Streptomycin, 1X L-glutamine and 0,1X β-mercaptoethanol.

extract_protocol: DNA was isolated using Blood & Cell Culture DNA Mini Kit (QIAGEN).

treatment_protocol: BlaER cells with shTET2 and shCTRL were first pre-treated with doxycycline (1 µg/ml) for 48 hours. Next, to induce transdifferentiation cells were supplemented with 100 nM of 17-beta estradiol (E2), human IL-3 (10 ng/ml), and human M-CSF (10 ng/ml) during 7 days. Doxycycline (1 µg/ml) was re-added every 48 hours during the process. Cells were collected at 0, 72 and 144 hours post induction.

value: B-ALL cell line

tag: cell line

value: B-ALL cell line with shCTRL

tag: cell type

value: B cell intermediate to iMac

tag: genotype

value: Control

tag: time point

tag: treatment

value: Doxycycline (1 µg/ml)


title: NP1

city: Suzhou

first: Shuai

last: Yan

state: Jiangsu

address: 18 Yangsu Road

country: China

institute: Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine

data_processing:
Quality control: The quality of raw reads was first assessed using the FastQC. 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.
Genomic alignment and quantification: Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters. HTSeq v0.13.5 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:https://ftp.ensembl.org/pub/release-104/gtf/homo_sapiens/Homo_sapiens.GRCh38.104.gtf.gz. The CIRCexplorer program (v2.3.8) was used to identify both the circularizing junction and the spliced sequence of circRNAs. All circRNA candidates with junction reads less than 2 were discarded. The remaining circRNA candidates were considered bonafide circRNAs.
DESeq2 (v2) was applied for the detection of differentially expressed mRNAs/lncRNAs between two groups, the limma R package (3.40.6) was used for differentially expressed circRNAs.
Assembly: GRCh38
Supplementary files format and content: FileincludeFPKM/TPMvaluesforeachsample

source_name: colon

growth_protocol: This study comprised a total of 10 participants: 5 individuals diagnosed with STC who underwent subtotal colectomy, and 5 control subjects who underwent radical surgery for colon cancer. We chose patients with STC in strict accordance with international and national guidelines: (1) Meet the Rome IV STC diagnostic criteria; (2) Constipation symptoms are severe, defecation frequency is less than twice per week, there is no urge to defecate or there is no obvious desire to defecate, there is a high incidence of abdominal distension, laxatives must be used to maintain defecation or laxatives cannot maintain defecation; (3) Constipation sensations have been present for more than 5 years, substantially hurting quality of life, and medical treatment has been ineffective for more than two years, with a strong desire for surgery; (4) Colorectal organic lesions are excluded; (5) There was no evident stomach or intestinal motility impairment based on three colonic transit tests; (6) Hamilton anxiet scale < 14 points, no visible mental symptoms such as depression; (7) Excluding the constipation kind of irritable bowel syndrome.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Firstly,ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: Before the operation, all patients had a gastrointestinal transit test. The running track of the opaque marker was used to locate the intestinal segment of colonic transit dysfunction, and the normal intestinal segment of colon cancer patients was chosen as the control. Each sample was collected from the colon tissue within 3 min after surgery, and was divided into 1 cm3 samples, and then cryopreserved in liquid nitrogen at -80°C.

value: colon

value: Human

value: control


title: TRA_F15_2N_MH_A81

city: Nanjing

first: Xuan

last: Li

address: No. 666, Binjiang Avenue, Jiangbei New Area

institute: Nanjing Agricultural University

description:
Library name: A81
TRA_F15_2N_MH_A81

data_processing:
Alignment was performed with STAR (v2.7.11a) against the reference genome using a pre-built STAR genome index. STAR was run with “--outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts” to generate sorted alignment files and gene-level count profiles. Gene-level expression quantification was carried out using RSEM (v1.3.1) with STAR-generated transcriptome BAM files as input (--paired-end --no-bam-output --alignments).
Assembly: Nasonia vitripennis reference genome (RefSeq No. GCF_009193385.2, NCBI GenBank)
Supplementary files format and content: Tab-delimited text file includes raw counts and tpm value for each sample

molecule: polyA RNA

organism: Nasonia vitripennis

source_name: Head

extract_protocol:
RNA extraction was performed using Quick-RNATM Tissue/Insect Microprep (Catalogue No. R2030 Zymo Research, Germany) (without DNase treatment). For sequencing, RNA was resuspended in 10 µL DNase/RNase-free water and the RNA concentration and purity was measured using a fluorometer (Qubit 2.0, Life Technologies); poor quality samples judged by A260/A280 and A260/A230 ratios were discarded. The extracted RNA was sent to Novogene (UK) Company Limited for sequencing. Novogene Hongkong prepared the sample library.
Unique index codes were added to each sample using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, USA). mRNA was purified from total RNA using poly-T magnetic beads, and libraries were prepared according to the manufacturer's instructions (Illumina).

value: Head

tag: Sex

value: male

tag: age

value: 1 day after emergence

tag: strain

value: TRA


title: brain, 687_Pons, pons

description:
Library name: 687_Pons
687_Pons


title: Control, 0 h, r3

value: B cell

value: 0 h


title: THP1, Infected, PolII, ChIP-seq, Rep2

city: Bangalore

first: Bharath

last: Saravanan

state: Karnataka

address: Bellary Road

department: Genetics and Development

country: India

institute: National centre for Biological Sciences

library_source: genomic

data_processing:
Basecalls performed using standard illumina pipeline
ChIP-seq reads were aligned to the genome assembly using Bowtie 2 version 2.3.0 with default configurations
HOMER was used to build Tag directories using -unique -tbp 1
peaks were called using HOMER findPeaks
RNA-seq reads were aligned with hisat2. htseq was used to obtain raw counts. Deseq2 was used for differential analysis.
Assembly: hg19
Supplementary files format and content: Bigwig files
Supplementary files format and content: Gene expression counts

source_name: THP1 cells

growth_protocol: THP1 monocytes were cultured in RPMI 1640 (GibcoTM 31800022) supplemented with 10% fetal bovine serum (GibcoTM 16000-044) and 0.01% Antibiotic-Antimycotic (GibcoTM 15240- 062). THP1 monocytes were differentiated to macrophages by treatment with 20 ng/ml of phorbol-12-myristate-13-acetate (PMA, Sigma-Aldrich, P8139) for 16 hours followed by incubation in PMA-free RPMI 1640 medium for two days and used for infections.

extract_protocol:
ChIP-seq, H3K27ac marked regions were pull down using antibody
Libraries were prepared using standard ChIP-seq and RNA-seq library protocol

treatment_protocol: THP1 monocyte-derived macrophages were incubated with mycobacteria for 4 hours, followed by multiple washes with RPMI media to remove extracellular bacteria and incubated with fresh RPMI media for 48 hours

value: THP1 cells

value: Macrophages

value: Mycobacterium bovis infection


title: TRA_F15_2N_MH_A82

description:
Library name: A82
TRA_F15_2N_MH_A82


title: brain, 687_PC, prefrontal cortex

description:
Library name: 687_PC
687_PC

value: Brain


title: THP1, Infected, PolII, ChIP-seq, Rep1


title: TRA_F15_2N_MH_A83

description:
Library name: A83
TRA_F15_2N_MH_A83


title: Control, 0 h, r2

value: B-ALL cell line

value: B-ALL cell line with shCTRL


title: brain, 687_MC, motor cortex

description:
Library name: 687_MC
687_MC


title: RNA-seq in THP1 cells: IRF7 KO PolyIC Transfected Replicate 2

city: Cincinnati

first: Matthew

last: Weirauch

state: Ohio

address: 3333 Burnet Avenue

department: Center for Autoimmune Genomics and Etiology (CAGE)

institute: Cincinnati Children's Hospital Medical Center

description: Library name: RNA-seq_THP1_KOP32_E007046

data_processing:
RNA-seq reads were mapped to the hg19 genome using the nf-core RNA-seq pipeline with the default alignment options (STAR and Salmon).
Transcription abundance estimates generated by Salmon
Assembly: hg19
Supplementary files format and content: Aligned reads in bigWig format. Reads were normalized using deepTools bamCoverage with the parameters --normalizeUsing CPM --binSize 10. The reads aligned to the forward strand were processed separately from the reads aligned to the reverse strand. The parameter --scaleFactor -1 was used when generating the reads on the reverse strand.

growth_protocol: THP-1 IRF7 deficient and HEK Blue hTLR7 cells were purchased from InvivoGen. THP-1 cells were grown in RPMI 1640 medium supplemented with 10% FBS, 10,000 units/mL of penicillin, 10,000 ug/mL of streptomycin, and Normocin. Following transduction, THP-1 cell lines stably expressing IRF7 variants were also cultured in 1 ug/mL puromycin. HEK Blue hTLR7 cells were grown in DMEM medium supplemented with 10% FBS, 10,000 units/mL of penicillin, and 10,000 ug/mL of streptomycin. All cells were kept at 37°C and 5% CO2 and were determined to be mycoplasma free.

extract_protocol:
Total RNA was isolated using the mirVana RNA extraction kit
rRNA depleted, stranded libraries were generated by and sequenced at the Cincinnati Children’s Hospital Medical Center Genomics Sequencing Facility (CCHMC)

treatment_protocol: THP-1 cells were stimulated using 2.5ug/mL of low molecular weight Poly(I:C) transfected using Lipofectamine 2000. HEK Blue hTLR7 cells were stimulated using 1ug/mL of Resiquimod (R848).

tag: irf7 genotype

value: KO

tag: stimulation

value: PolyIC


title: Control, 0 h, r1

value: Control

value: Doxycycline (1 µg/ml)


title: THP1, Uninfected, PolII, ChIP-seq, Rep2


title: TRA_F15_2N_MH_A84

description:
Library name: A84
TRA_F15_2N_MH_A84


title: brain, 687_Hip, hippocampus

description:
Library name: 687_Hip
687_Hip


title: THP1, Uninfected, PolII, ChIP-seq, Rep1


title: Epidermis, Naked mole-rats, DMBA/TPA, Sample 2

city: Boston

first: Vladimir

last: Botchkarev

state: MA

address: 609 Albany Street

institute: Boston University

description:
Library name: Sample 6
Column name in raw Counts_NMR_Epidermis DMBA TPA Sample 2.xlsx

data_processing:
The bioinformatics analysis of the RNAseq data was performed by the LC Sciences (Houston, TX). Firstly, Cutadapt (Martin, 2011) and Perl scripts were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then, sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Bowtie2 (Langmead and Salzberg, 2012) and Tophat2 (Kim et al., 2013) were used to map reads to the genome of Heterocephalus glaber (https://useast.ensembl.org/Heterocephalus_glaber_female/Info/Index). The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with parametric F-test comparing nested linear models (p value < 0.05) by R package Ballgown. Ballgown was used to generate a list and heatmaps of differentially expressed genes, and in-house generated Perl scripts (LC Science, Houston, TX) were used for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses.
Assembly: Naked Mole-Rat genome (version Ensemble 104.1)
Supplementary files format and content: Excel files include FPKM values for each Sample

organism: Heterocephalus glaber

source_name: Skin epidermis

extract_protocol:
For RNA-Seq analysis of epidermis, skin was collected and cleaned thoroughly to remove any fat or muscle tissue and washed in PBS. Skin was then digested overnight in Dispase II (5mg/ml) in HBSS in +40C. After overnight digestion, epidermis was carefully separated from the dermis, homogenized in TRI Reagent and RNA was isolated using Direct-Zol Miniprep Kit following manufacturer’s protocol.
Libraries were prepared using Next Generation Sequencing Library Preparation kit from NEBNext® according to manufacturer protocol. Ribosomal RNAs (rRNAs) were depleted using NEBNext® rRNA Depletion Kit v2 and libraries were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®. After purifications, quality of the libraries was assessed on 5200 Fragment Analyzer with DNA Chip. For RNA-sequencing library preparation, concentration, quality and integrity of RNA was checked, and RNA with RIN>7 was used for the libraries.

treatment_protocol: Two-stage chemically induced carcinogenesis was performed as described previously (PMID: 19713956). 7,12-dimethylbenz[a]-anthracene (DMBA, 1mg/ml) and 12-O-tetra-decanoylphorbol-13-acetate (TPA, 0.1 mg/ml) were dissolved in acetone. In animals treated with DMBA only, single dose of DMBA (100µl) was applied on the back skin of animals, and skin was harvested on day 10 of experiment. In DMBA/TPA treated animals, after single DMBA application, TPA was applied to the back skin twice a week, and skin was harvested on day 46 after beginning of experiment. Skin of the control animals was treated by aceton.

value: Skin epidermis

value: Epidermis

value: WT

value: DMBA/TPA


title: TRA_F3_1N_MA_A8

description:
Library name: A8
TRA_F3_1N_MA_A8

source_name: Abdomen

value: Abdomen

value: male

value: 1 day after emergence

value: TRA


title: brain, 687_FC, frontal cortex

description:
Library name: 687_FC
687_FC


title: Epidermis, Naked mole-rats, DMBA/TPA, Sample 1

description:
Library name: Sample 5
Column name in raw Counts_NMR_Epidermis DMBA TPA Sample 1.xlsx


title: TRA_F15_2N_MH_A85

description:
Library name: A85
TRA_F15_2N_MH_A85

value: Head


title: brain, 687_EC, entorhinal cortex

description:
Library name: 687_EC
687_EC


title: THP1, Infected, H3K27ac, ChIP-seq, Rep2

value: THP1 cells

value: Macrophages

value: Mycobacterium bovis infection


title: TRA_F15_2N_MA_A86

description:
Library name: A86
TRA_F15_2N_MA_A86


title: THP1, Infected, H3K27ac, ChIP-seq, Rep1


title: Epidermis, Naked mole-rats, DMBA, Sample 2

description:
Library name: Sample 4
Column name in raw Counts_NMR_Epidermis DMBA Sample 2.xlsx

value: DMBA


title: brain, 687_CB, cerebellum

description:
Library name: 687_CB
687_CB

value: Brain


title: Epidermis, Naked mole-rats, DMBA, Sample 1

description:
Library name: Sample 3
Column name in raw Counts_NMR_Epidermis DMBA Sample 1.xlsx


title: THP1, Uninfected, H3K27ac, ChIP-seq, Rep2


title: brain, 687_BG, basal ganglia

description:
Library name: 687_BG
687_BG


title: Epidermis, Naked mole-rats, Controls DMBA/TPA

description:
Library name: Sample 2
Column names in raw Counts_NMR_Epidermis Controls DMBA TPA.xlsx

value: Aceton


title: TRA_F15_2N_MA_A87

description:
Library name: A87
TRA_F15_2N_MA_A87


title: TRA_F15_2N_MA_A88

description:
Library name: A88
TRA_F15_2N_MA_A88


title: THP1, Uninfected, H3K27ac, ChIP-seq, Rep1


title: Trim28 multiome: Trim28 knockout (Trim28-1 sgRNA): GEX

city: Cambridge

first: Nir

last: Hacohen

address: 415 Main Street, Room 6032

department: Cell Circuits Program / Center for Cell Circuits

institute: Broad Institute

description:
Library name: Tcf7_trim28_multiome_trim28_gex
GEX FASTQ files from mouse donor OT-I CD8 T cell sample from B16-OVA tumors profiled in the Trim28 multiome experiment. Cas9 x OT-I x CD45.1 Trim28-knockout donor cells and Cas9 x OT-I x CD45.2 NT donor cells were mixed 50:50 and transferred into Cas9 x CD45.1/CD45.2 recipient mice. Recipients were implanted subcutaneously with B16-OVA tumors 1 day after transfer, and NT and Trim28 donor populations were sorted from tumors 14 days after tumor implantation. Cells were profiled jointly by single-cell gene expression and chromatin accessibility using 10x Genomics Chromium Single Cell Multiome. Condition: Trim28 knockout (Trim28-1 sgRNA). All sequencing-lane files for this library are listed in the same run row. Sample description: Single-cell multiome sample from Trim28-1 gRNA donor cells recovered from B16-OVA tumors. Cas9 x OT-I x CD45.1 Trim28-knockout donor CD8 T cells and Cas9 x OT-I x CD45.2 NT donor CD8 T cells were mixed 50:50 and transferred into Cas9 x CD45.1/CD45.2 recipient mice. Recipient mice were implanted subcutaneously with B16-OVA tumors 1 day after transfer, and donor NT and Trim28 populations were sorted from tumors 14 days after tumor implantation into separate 10x Genomics Chromium Single Cell Multiome libraries for paired gene-expression and chromatin-accessibility profiling.

library_source: transcriptomic single cell

data_processing:
Single-cell multiome data were processed with Cell Ranger ARC and Scanpy; retained cells are included in RNA and ATAC AnnData objects with cell-level metadata, expression or peak-count layers, embeddings, and clustering results.
Assembly: GRCm38/mm10 mouse reference for gene-expression and chromatin-accessibility features.
Supplementary files format and content: H5AD AnnData archives containing cell-level gene-expression values or chromatin-accessibility peak values with matching cell metadata.

organism: Mus musculus

source_name: B16-OVA tumor

growth_protocol: Cas9 x OT-I x CD45.1 Trim28-knockout donor CD8 T cells and Cas9 x OT-I x CD45.2 NT donor CD8 T cells were mixed 50:50 and transferred into Cas9 x CD45.1/CD45.2 recipient mice. Recipient mice were implanted subcutaneously with B16-OVA tumors 1 day after transfer. Donor and recipient populations were distinguished using congenic CD45.1 and CD45.2 markers together with OT-I/TCR and Thy1.1 markers where applicable.

extract_protocol:
Tumors were excised, minced, and enzymatically dissociated using Miltenyi tumor dissociation reagents or an equivalent tumor-infiltrating lymphocyte dissociation workflow. Dissociated tumor material was filtered to remove debris and enrich viable lymphocytes. Depending on sample quality, lymphocytes were enriched by Lympholyte-M density-gradient separation and/or magnetic enrichment before flow sorting. Single-cell suspensions were stained with viability dye, Fc block, and surface antibodies to identify live CD8 T cells and distinguish donor NT and Trim28 populations by congenic markers.
Sorted donor cells were processed using the 10x Genomics Chromium Single Cell Multiome workflow to generate paired gene-expression and chromatin-accessibility libraries from the same captured cells. Gene-expression libraries captured cDNA, and ATAC libraries captured Tn5-accessibility fragments from the same sorted donor-cell populations. Libraries were sequenced on an Illumina NextSeq 2000.

treatment_protocol: The experimental conditions were NT sgRNA control and Trim28 knockout induced by Trim28-1 sgRNA. NT and Trim28 donor populations were recovered from B16-OVA tumors and sorted 14 days after tumor implantation, corresponding to 15 days after donor T cell transfer.

value: B16-OVA tumor

value: CD8 T cells

value: Trim28 knockout

tag: library type

value: mRNA


title: Epidermis, Naked mole-rats, Controls DMBA

description:
Library name: Sample 1
Column names in raw Counts_NMR_Epidermis Controls DMBA.xlsx

value: Skin epidermis

value: Epidermis

value: WT


title: THP1, Infected, RNA-seq, Rep2


title: TRA_F15_2N_MA_A89

description:
Library name: A89
TRA_F15_2N_MA_A89

value: Abdomen

value: male


title: Trim28 multiome: Trim28 knockout (Trim28-1 sgRNA): ATAC

description:
Library name: Tcf7_trim28_multiome_trim28_atac
ATAC FASTQ files from mouse donor OT-I CD8 T cell sample from B16-OVA tumors profiled in the Trim28 multiome experiment. Cas9 x OT-I x CD45.1 Trim28-knockout donor cells and Cas9 x OT-I x CD45.2 NT donor cells were mixed 50:50 and transferred into Cas9 x CD45.1/CD45.2 recipient mice. Recipients were implanted subcutaneously with B16-OVA tumors 1 day after transfer, and NT and Trim28 donor populations were sorted from tumors 14 days after tumor implantation. Cells were profiled jointly by single-cell gene expression and chromatin accessibility using 10x Genomics Chromium Single Cell Multiome. Condition: Trim28 knockout (Trim28-1 sgRNA). All sequencing-lane files for this library are listed in the same run row. Sample description: Single-cell multiome sample from Trim28-1 gRNA donor cells recovered from B16-OVA tumors. Cas9 x OT-I x CD45.1 Trim28-knockout donor CD8 T cells and Cas9 x OT-I x CD45.2 NT donor CD8 T cells were mixed 50:50 and transferred into Cas9 x CD45.1/CD45.2 recipient mice. Recipient mice were implanted subcutaneously with B16-OVA tumors 1 day after transfer, and donor NT and Trim28 populations were sorted from tumors 14 days after tumor implantation into separate 10x Genomics Chromium Single Cell Multiome libraries for paired gene-expression and chromatin-accessibility profiling.

library_source: genomic single cell

value: ATAC


title: Epidermal keratinocytes, Naked mole-rats Sample 3

description:
Library name: Sample 3
Column name in raw Counts_NMR_Epid_KCs 441 Sample 3.xlsx

data_processing:
The bioinformatics analysis of the RNAseq data was performed by the LC Sciences (Houston, TX). Firstly, Cutadapt (Martin, 2011) and Perl scripts were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then, sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Bowtie2 (Langmead and Salzberg, 2012) and Tophat2 (Kim et al., 2013) were used to map reads to the genome of Heterocephalus glaber (https://useast.ensembl.org/Heterocephalus_glaber_female/Info/Index). The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with parametric F-test comparing nested linear models (p value < 0.05) by R package Ballgown. Ballgown was used to generate a list and heatmaps of differentially expressed genes, and in-house generated Perl scripts (LC Science, Houston, TX) were used for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses.
Assembly: Naked Mole-Rat genome (version Ensemble 104.1)
Assembly: mm10
Supplementary files format and content: Excel files include FPKM values for each Sample

extract_protocol:
For RNA-Seq analysis of epidermal keratinocytes, NMR and mouse skin was digested overnight with Dispase II (5mg/ml) and separated epidermis was then digested with TrypLE Express. Detached keratinocytes were washed, labelled with anti-CD49f antibody and FACS-sorted. Keratinocytes were lysed in TRI Reagent and RNA was isolated using Direct-Zol Microprep Kit.
Libraries were prepared using Next Generation Sequencing Library Preparation kit from NEBNext® according to manufacturer protocol. Ribosomal RNAs (rRNAs) were depleted using NEBNext® rRNA Depletion Kit v2 and libraries were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®. After purifications, quality of the libraries was assessed on 5200 Fragment Analyzer with DNA Chip. For RNA-sequencing library preparation, concentration, quality and integrity of RNA was checked, and RNA with RIN>7 was used for the libraries.

value: Keratinocytes

value: normal homeostatic 6-7 month-old Naked mole-rat


title: THP1, Infected, RNA-seq, Rep1

value: THP1 cells

value: Macrophages


title: TRA_F15_2N_MA_A90

description:
Library name: A90
TRA_F15_2N_MA_A90

value: 1 day after emergence

value: TRA


title: Epidermal keratinocytes, Naked mole-rats Sample 2

description:
Library name: Sample 2
Column name in raw Counts_NMR_Epid_KCs 440 Sample 2.xlsx


title: TRA_F3_1N_MA_A9

description:
Library name: A9
TRA_F3_1N_MA_A9


title: Trim28 multiome: NT sgRNA: GEX

description:
Library name: Tcf7_trim28_multiome_control_gex
GEX FASTQ files from mouse donor OT-I CD8 T cell sample from B16-OVA tumors profiled in the Trim28 multiome experiment. Cas9 x OT-I x CD45.1 Trim28-knockout donor cells and Cas9 x OT-I x CD45.2 NT donor cells were mixed 50:50 and transferred into Cas9 x CD45.1/CD45.2 recipient mice. Recipients were implanted subcutaneously with B16-OVA tumors 1 day after transfer, and NT and Trim28 donor populations were sorted from tumors 14 days after tumor implantation. Cells were profiled jointly by single-cell gene expression and chromatin accessibility using 10x Genomics Chromium Single Cell Multiome. Condition: NT sgRNA. All sequencing-lane files for this library are listed in the same run row. Sample description: Single-cell multiome sample from NT control donor cells recovered from B16-OVA tumors. Cas9 x OT-I x CD45.1 Trim28-knockout donor CD8 T cells and Cas9 x OT-I x CD45.2 NT donor CD8 T cells were mixed 50:50 and transferred into Cas9 x CD45.1/CD45.2 recipient mice. Recipient mice were implanted subcutaneously with B16-OVA tumors 1 day after transfer, and donor NT and Trim28 populations were sorted from tumors 14 days after tumor implantation into separate 10x Genomics Chromium Single Cell Multiome libraries for paired gene-expression and chromatin-accessibility profiling.

value: NT sgRNA


title: THP1, Uninfected, RNA-seq, Rep2


title: Epidermal keratinocytes, Naked mole-rats Sample 1

description:
Library name: Sample 1
Column name in raw Counts_NMR_Epid_KCs 439 Sample 1.xlsx


title: Trim28 multiome: NT sgRNA: ATAC

description:
Library name: Tcf7_trim28_multiome_control_atac
ATAC FASTQ files from mouse donor OT-I CD8 T cell sample from B16-OVA tumors profiled in the Trim28 multiome experiment. Cas9 x OT-I x CD45.1 Trim28-knockout donor cells and Cas9 x OT-I x CD45.2 NT donor cells were mixed 50:50 and transferred into Cas9 x CD45.1/CD45.2 recipient mice. Recipients were implanted subcutaneously with B16-OVA tumors 1 day after transfer, and NT and Trim28 donor populations were sorted from tumors 14 days after tumor implantation. Cells were profiled jointly by single-cell gene expression and chromatin accessibility using 10x Genomics Chromium Single Cell Multiome. Condition: NT sgRNA. All sequencing-lane files for this library are listed in the same run row. Sample description: Single-cell multiome sample from NT control donor cells recovered from B16-OVA tumors. Cas9 x OT-I x CD45.1 Trim28-knockout donor CD8 T cells and Cas9 x OT-I x CD45.2 NT donor CD8 T cells were mixed 50:50 and transferred into Cas9 x CD45.1/CD45.2 recipient mice. Recipient mice were implanted subcutaneously with B16-OVA tumors 1 day after transfer, and donor NT and Trim28 populations were sorted from tumors 14 days after tumor implantation into separate 10x Genomics Chromium Single Cell Multiome libraries for paired gene-expression and chromatin-accessibility profiling.

value: B16-OVA tumor


title: TRA_F3_1N_MA_A10

description:
Library name: A10
TRA_F3_1N_MA_A10


title: THP1, Uninfected, RNA-seq, Rep1


title: ESKO.3

status: Public on Jul 08 2026

city: 3601 Spruce Street

first: Yan

last: Zhou

state: PA

address: 333 Cottman Ave

department: Bioinformatics

institute: Fox Chase Cancer Center

data_processing:
Raw reads were aligned to mm10 genome using STAR
Raw counts in each known gene from the Ensembl database were enumerated using htseq-count from the HTSeq package
Assembly: mm10
Supplementary files format and content: raw count in tab-delimited format

source_name: spleen and lymph nodes

growth_protocol: naïve CD4 T cells were stimulated with anti-CD3/CD28 beads and grown in IMDM + 10% FBS+ 10 ng/ml IL2 + 10ng/ml IL12 + 10 ug/ml anti-IL4 for 4 days.

extract_protocol:
Qiagen RNeasy Mini Kit
Truseq stranded total RNA Library Prep Gold

value: spleen and lymph nodes

value: cultured primary CD4 T cells

value: Ezh2 and Stim1 knuckout


title: ESKO.2


title: ESKO.1


title: WT.2

value: wild type


title: WT.1


title: SKO.2

data_processing:
Raw sequence reads were aligned to the mouse genome (mm10) using the Tophat algorithm
Cufflinks was implemneted to assemble transcripts and estimate their abundance.
Cuffdiffwas used to statistically assess expression changes in quantified genes in different conditions
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for all Sample ...

source_name: spleen

growth_protocol: Donor CD4 T cells were infused into Balb/c recipients and FACS-purified from the spleens of recipients 14 days post-HSCT.

extract_protocol:
Total RNA was extracted with Qiagen RNeasy Mini Kit.
SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

value: spleen

value: CD4 T cell

value: Stim1 knockout


title: SKO.3


title: EKO.3

value: Ezh2 knockout


title: SKO.1


title: EKO.1


title: EKO.2


title: WT.4


title: WT.3


title: WT.2


title: WT.1


title: GBM17 BG1, PANX1 CRISPR KO

city: London

first: Silvia

last: Penuela

state: Ontario

address: 1151 Richmond St DSB00066

country: Canada

institute: University of Western Ontario

description: Library name: Sample 6

data_processing:
Partek Flow Version 11.0.24.022 was used for subsequent analysis of Fastq Files, including alignment of the data to the Homo sapiens genome with STAR
A filtered list of detected genes was generated in Partek Flow to include features that exhibited a fold change greater than absolute 1.5 and a false discovery rate (FDR) step-up of less than 0.05
Assembly: hg38 Ensembl Transcripts release
Supplementary files format and content: Partek Normalized Counts (approx 19000 entries).xlsx, excel file of all normalized counts of detected genes in all samples
Supplementary files format and content: gene_list FDRsu 0.05 FC1.5.xlsx, excel file of differentially expressed genes with fold change 1.5 and FDR of less than 0.05
Supplementary files format and content: Partek Gene List.xlsx, excel file of total counts of genes for all samples

growth_protocol: patient-derived GBM17 cells were maintained in DMEM supplemented with 10% FBS and 1% Pen/Strep in a humidified environment at 37 degrees C and 5% CO2

extract_protocol:
Total RNA was harvested using Qiagen Rneasy Mini plus kit.
Library preparation for sequencing, including rRNA reduction was completed using a Vazyme VAHTS V8 RNA-seq Library Prep Kit for Illumina. cDNA from each sample was prepared by rRNA depletion and fragmentation, followed by indexing, before amplification via PCR

treatment_protocol: Cells were transfected using Lipofectamine 3000 with either a plasmid containing PANX1 gRNA/CRISPR Cas9 or SCR control gRNA/CRISPR Cas9. Cells were selected with puromycin for 72 hours and then single colony selection was performed. 3 control clones and 3 KO clones were selected for RNA-Seq

value: patient derived GBM cells

value: PANX1 CRISPR KO


title: GBM17 BD6, PANX1 CRISPR KO

description: Library name: Sample 5


title: GBM17 BC12, PANX1 CRISPR KO

description: Library name: Sample 4


title: GBM17 H5, SCR CRISPR control

description: Library name: Sample 3

value: WT

value: SCR control CRISPR


title: GBM17 G11, SCR CRISPR control

description: Library name: Sample 2


title: GBM17 G9, SCR CRISPR control

description: Library name: Sample 1


title: A549 cell, Spike protein, 24 h, replicate 2

city: Seoul

first: Hyo-Jeong

last: Lee

state: --- Select One ---

address: 26, Kyungheedae-ro,Dondaemun-gu, Seoul, 02447, Korea

country: South Korea

institute: Kyung Hee University

description:
Library name: A549-4
Gene-level read counts for A549 cells.

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: lung

growth_protocol: A549 cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum and 1% antibiotics in humidified atmosphere with 5% CO2 at 37 °C

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: A549 cells were treated with 10 ng/mL recombinant SARS-CoV-2 S1 subunit protein for 24 h

value: lung

value: lung adenocarcinoma epithelial cell

value: SARS-CoV-2 spike protein

tag: batch


title: A549 cell, Spike protein, 24 h, replicate 1

description:
Library name: A549-2
Gene-level read counts for A549 cells.


title: A549 cell, control, 24 h,  replicate 2

description:
Library name: A549-3
Gene-level read counts for A549 cells.

value: untreatment


title: A549 cell, control, 24 h, replicate 1

description:
Library name: A549-1
Gene-level read counts for A549 cells.


title: OCI-AML-3 H1-3 cells, clone 1 replique 3

city: Marseille

first: Estelle

middle: Anna

last: Duprez

address: 23 bvd lei roure

department: OHIO

country: France

institute: CRCM-INSERM

description: Library name: RNAseq_OCI3_H1.3_KO1_rep3

data_processing:
paired-end reads were aligned to the human GRCh38 reference genome using Subread-align (v1.5.0) with default parameters. Gene expression quantification was performed by counting mapped tags at gene levels using featureCounts. Differentially expressed genes were identified using DESeq2 (v1.26.0)
Assembly: GRCh38 genome
Supplementary files format and content: RPKM

source_name: OCI-AML-3 H1-3KO clone 1

growth_protocol: Cells were growth in MEMα medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin and 100 U/mL streptomycin under standard culture conditions (37°C, 5% CO2)

extract_protocol:
Total RNA was extracted from one the OCI-AML3 parental cell line and two KOs (KO clone #1 and KO clone #2). Each experimental condition includes three biological replicates using the RNeasy® Mini Kit (Qiagen; 74104)
Libraries were prepared with rRNA depletion with a Kapa mRNA HyperPrep kit (Roche, #KR1352-v7.21) and sequenced using the Illumina Novaseq6000 platform, 100-bp paired-end reads, at 50 million reads per sample and Nextseq500, 75-bp paired-end reads, 30 million reads per sample.

value: OCI-AML-3 H1-3KO clone 1

value: Acute myeloid leukemia

value: OCI-AML-3 H1-3 KO clone 1


title: OCI-AML-3 H1-3 cells, clone 1 replique 2

description: Library name: RNAseq_OCI3_H1.3_KO1_rep2


title: OCI-AML-3 H1-3 cells, clone 1 replique 1

description: Library name: RNAseq_OCI3_H1.3_KO1_rep1


title: OCI-AML-3 H1.3-V5 + dox cells, (Input)

description: Library name: ChIPseq_OCI3_H1.3-V5dox_Input

data_processing:
Sequencing quality control was determined using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and aggregated across samples using MultiQC (v1.7)
Reads with a Phred quality score of less than 30 were filtered out and mapped to a human (Hg38) genome using using default parameters of Bowtie2 (v2.3.4.3) Only mapped reads were filtered in using samtools (v1.9). Duplicate tags were removed using Picard Tools
Peaks were called  using MACS2 callpeak (v2.1.2)  in broad mode (--broad broad-cutoff=0.05 -q 0.01 --nomodel)
bigWigs files were generated  using the deepTools suite (v3.2.1)
Assembly: GRCh38 reference genome
Supplementary files format and content: Bigwig

source_name: OCI-AML-3 H1.3-V5 + Doxycycline

extract_protocol:
Cells were fix with 1% formaldehyde. Cell lysates were clarified from sonicated nuclei using a Diagenode Bioruptor, and histone-DNA complexes were isolated with antibody incubated over-night. Rabit IgG (Cell signaling; #2729S) was used as a control. Genomic DNA was purified using the i-Pure V2 kit (Diagenode)
Libraries were generated using the MicroPlex Library Preparation Kit (Diagenode) following the manufacturer's instructions and analyzed on a 2100 Bioanalyzer system (Agilent) prior sequencing

treatment_protocol: H1.3-V5 DNA was cloned into a doxycycline-inducible plasmid pLix-403 (Addgene) using the GATEWAY strategy. The plasmid (pLix403-H1.3-V5) was transfected into OCI-AML3 cells by electroporation using the Amaxa Kit V (program X-001) according to the manufacturer’s protocol. Transfected cells were selected 48 h after electroporation with puromycin 2 µg/mL, which was kept in the culture medium to maintain pressure selection. Expression of the H1.3-V5 construct was obtained with 1 µg/mL doxycycline and induction of expression was assessed by Western blot

value: OCI-AML-3 H1.3-V5 + Doxycycline

value: OCI-AML-3 expressing H1-3

value: doxycycline

tag: chip antibody


title: OCI-AML-3 H1.3-V5 + dox cells, V5 antibody (ChIP)

description: Library name: ChIPseq_OCI3_H1.3-V5dox_V5


title: OCI-AML-3 WT1 + dox cells, (Input)

description: Library name: ChIPseq_OCI3_WTdox_Input

source_name: OCI-AML-3 parental + Doxycycline

value: OCI-AML-3 parental + Doxycycline

value: non


title: OCI-AML-3 WT1 + dox cells, H3K27ac antibody (ChIP)

description: Library name: ChIPseq_OCI3_WTdox_H3K27ac

value: H3K27ac (Active Motif; #39133)


title: T190127

city: Taipei

first: Yu-Hung

last: Wang

address: N0 7, Chung-Shan South Rd

country: Taiwan

institute: National Taiwan University Hospital

description: MDS

data_processing:
Reads were then aligned to the human genome (GRCh38) and gene annotated with its corresponding GTF files (GENCODE GRCh38) using STAR version 2.4.2a with the settings –outFilterMultimapNmax 20 –outFilterType BySJout –alignSJoverhangMin 8 –quantMode GeneCounts.
Assembly: GRCh38
Supplementary files format and content: Read counts in .csv format

source_name: human BM Mononuclear cells

extract_protocol:
RNA was extracted from fresh BM samples of patients and healthy donors and sent for RNA sequencing.
The purified RNA was used to prepare the sequencing library using the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) following the manufacturer’s recommendations. Briefly, mRNA was purified from total RNA (1 μg) using oligo(dT)-coupled magnetic beads and fragmented into small pieces at elevated temperatures.
First-strand cDNA was synthesized using reverse transcriptase and random primers. After the generation of double-strand cDNA and adenylation on the 3’ ends of DNA fragments, the adaptors were ligated and purified with the AMPure XP system (Beckman Coulter, Beverly, USA). The quality of the libraries was assessed using an Agilent Bioanalyzer 2100 system and a real-time polymerase chain reaction (PCR) system. The qualified libraries were then sequenced on an Illumina NovaSeq 6000 platform with 150 bp paired-end reads generated by Genomics, BioSci & Tech Co., New Taipei City, Taiwan. The bases with low quality and sequences from adapters in the raw data were removed using Cutadapt (v 3.0).

value: human BM Mononuclear cells


title: T190124

description: MDS


title: T190122

description: MDS


title: T180288

description: MDS


title: T180254

description: MDS


title: T190123

description: MDS


title: T180208

description: MDS


title: T180127

description: MDS


title: T180123

description: MDS


title: T180122

description: MDS


title: S180196

description: MDS


title: S180195

description: MDS


title: S180191

description: MDS


title: S180188

description: MDS


title: S180187

description: MDS


title: S180180

description: MDS


title: S180181

description: MDS


title: S180167

description: MDS


title: R160206

description: MDS


title: R160130

description: MDS


title: R160193

description: MDS


title: R160128

description: MDS


title: Myeloid059

description: MDS


title: Myeloid092

description: MDS


title: MDS981

description: MDS


title: MDS979

description: MDS


title: Myeloid048

description: MDS


title: MDS971

description: MDS


title: MDS970

description: MDS


title: MDS967

description: MDS


title: C_3

city: guangzhou

first: Jinyan

last: Guo

state: guangdong

address: No. 600, Tianhe Road, Tianhe District

department: The Third Affiliated Hospital

institute: Sun Yat-sen University

description:
Library name: sample 6
Oxy@Lipo/Gel group, replicate biosample 3

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 GrCM38 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: RheMac8 / Mmul_8.0.1 (2017)
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

organism: Macaca mulatta

source_name: Lubricated catheter

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).

treatment_protocol: Control Group: Treatment: Normal saline Sample: Tracheal tissue of rhesus monkeys Sampling Site: Guangdong Landau Biotechnology Co., Ltd. Sampling Date: March 17, 2025 Oxy@Lipo/Gel Material Group: Treatment: Oxy@Lipo/Gel-coated tracheal lubricant Model: General anesthesia endotracheal intubation Sample: Tracheal tissue of rhesus monkeys Sampling Site: Guangdong Landau Biotechnology Co., Ltd. Sampling Date: March 17, 2025

value: Lubricated catheter


title: C_2

description:
Library name: sample 5
Oxy@Lipo/Gel group, replicate biosample 2


title: MDS966

description: MDS


title: C_1

description:
Library name: sample 4
Oxy@Lipo/Gel group, replicate biosample 1


title: MDS964

description: MDS


title: A_3

description:
Library name: sample 3
control group, replicate biosample 3


title: MDS962

description: MDS


title: A_2

description:
Library name: sample 2
control group, replicate biosample 2


title: MDS961

description: MDS


title: A_1

description:
Library name: sample 1
control group, replicate biosample 1


title: MDS959

description: MDS


title: Rai1-wt_d60_rep4

city: Ann Arbor

first: Shigeki

last: Iwase

state: MI

address: 1241 E. Catherine St., 5815 Medical Science II

department: Department of Human Genetics

institute: University of Michigan Medical School

description:
Library name: WTc2t4D
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.

data_processing:
Adapter trimming and quality filtering were performed using Cutadapt v4.8.
Sequencing quality was assessed using FastQC v0.11.8 and summarized with MultiQC v1.20.
Trimmed reads were aligned to the human reference genome using STAR v2.7.8a.
Gene-level expression estimates were generated using RSEM v1.3.3.
Differential expression and downstream analyses were performed using count matrices generated from the RNA-seq workflow.
Assembly: GRCh38 (Ensembl release 109)
Supplementary files format and content: Gene-level raw read count matrix generated from RNA-seq data. Rows correspond to genes and columns correspond to individual biological samples.
Supplementary files format and content: Raw count values were generated using RSEM following alignment to the GRCh38 (Ensembl release 109) reference genome and are provided as tab-delimited text files.

source_name: In vitro differentiated cortical neuron culture

growth_protocol: Isogenic wild-type (RAI1+/+), heterozygous (RAI1+/-), and homozygous (RAI1-/-) CRISPR/Cas9-edited H9 human embryonic stem cells were maintained on Geltrex-coated culture plates in TeSR-E8 medium. Cells were differentiated into cortical neurons using a dual-SMAD inhibition protocol. Neural induction was initiated using dorsomorphin and SB431542, followed by sequential supplementation with FGF2, vitamin A, Compound E, GDNF, BDNF, dbcAMP, and laminin during neuronal maturation. Cells were collected at differentiation days 0, 20, 34, and 60 for RNA isolation.

extract_protocol:
RNA was extracted using TRIzol reagent and purified using the RNeasy Mini kit according to the manufacturer’s protocol.
Bulk mRNA-seq libraries were prepared from total RNA using oligo-dT priming to enrich for polyadenylated transcripts.

treatment_protocol: Neuronal differentiation was initiated by plating 1 million cells per well. From day 0–11, cells were cultured in 3N medium without vitamin A supplemented with dorsomorphin and SB431542. Cells were passaged at day 12 and cultured with continued dual-SMAD inhibition. FGF2 was added when rosettes appeared. Cells were further passaged at days 20, 27, and 34, then maintained in 3N medium with vitamin A and neuronal survival factors including GDNF, BDNF, dbcAMP, and Compound E according to differentiation stage.

value: H9 human embryonic stem cells

value: hESC-derived cortical neural progenitors / neurons

value: Dual-SMAD inhibition cortical neuron differentiation

value: clone2 duplicate


title: MDS955

description: MDS


title: Rai1-wt_d60_rep3

description:
Library name: WTc2t4
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.

value: In vitro differentiated cortical neuron culture


title: MDS944

description: MDS


title: MDS938

description: MDS


title: Rai1-wt_d60_rep1

description:
Library name: WTc1t4
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: Rai1-wt_d60_rep2

description:
Library name: WTc1t4D
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.

value: clone1 duplicate


title: MDS932

description: MDS


title: Rai1-wt_d34_rep3

description:
Library name: WTc2t3
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: MDS926

description: MDS


title: MDS921

description: MDS


title: Rai1-wt_d34_rep4

description:
Library name: WTc2t3D
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: Rai1-wt_d34_rep2

description:
Library name: WTc1t3D
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: MDS920

description: MDS


title: Rai1-wt_d34_rep1

description:
Library name: WTc1t3
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: MDS918

description: MDS


title: Rai1-wt_d20_rep4

description:
Library name: WTc2t2D
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: Rai1-wt_d20_rep3

description:
Library name: WTc2t2
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: MDS906

description: MDS


title: MDS905

description: MDS


title: Rai1-wt_d20_rep2

description:
Library name: WTc1t2D
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: MDS903

description: MDS


title: Rai1-wt_d20_rep1

description:
Library name: WTc1t2
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: MDS893

description: MDS


title: Rai1-wt_d0_rep4

description:
Library name: WTc2t1D
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: MDS887

description: MDS


title: Rai1-wt_d0_rep3

description:
Library name: WTc2t1
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: MDS882

description: MDS


title: Rai1-wt_d0_rep2

description:
Library name: WTc1t1D
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: MDS875

description: MDS


title: MDS867

description: MDS


title: Rai1-wt_d0_rep1

description:
Library name: WTc1t1
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: Rai1-ko_d60_rep4

description:
Library name: KOc2t4D
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: MDS866

description: MDS


title: Rai1-ko_d60_rep3

description:
Library name: KOc2t4
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: Rai1-ko_d60_rep2

description:
Library name: KOc1t4D
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: MDS862

description: MDS


title: MDS861

description: MDS


title: Rai1-ko_d60_rep1

description:
Library name: KOc1t4
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: MDS856

description: MDS


title: Rai1-ko_d34_rep4

description:
Library name: KOc2t3D
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: MDS851

description: MDS


title: Rai1-ko_d34_rep3

description:
Library name: KOc2t3
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: MDS849

description: MDS


title: MDS847

description: MDS


title: Rai1-ko_d34_rep1

description:
Library name: KOc1t3
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: Rai1-ko_d34_rep2

description:
Library name: KOc1t3D
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: MDS838

description: MDS


title: Rai1-ko_d20_rep4

description:
Library name: KOc2t2D
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: Rai1-ko_d20_rep3

description:
Library name: KOc2t2
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: Rai1-ko_d20_rep2

description:
Library name: KOc1t2D
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: MDS836

description: MDS


title: MDS837

description: MDS


title: Rai1-ko_d20_rep1

description:
Library name: KOc1t2
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: MDS833

description: MDS


title: MDS834

description: MDS


title: Rai1-ko_d0_rep4

description:
Library name: KOc2t1D
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: MDS832

description: MDS


title: Rai1-ko_d0_rep3

description:
Library name: KOc2t1
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: Rai1-ko_d0_rep2

description:
Library name: KOc1t1D
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: MDS821

description: MDS


title: MDS826

description: MDS


title: MDS818

description: MDS


title: Rai1-ko_d0_rep1

description:
Library name: KOc1t1
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: Rai1-het_d60_rep4

description:
Library name: HYc2t4D
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: MDS813

description: MDS


title: Rai1-het_d60_rep3

description:
Library name: HYc2t4
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: MDS804

description: MDS


title: Rai1-het_d60_rep1

description:
Library name: HYc1t4
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: Rai1-het_d60_rep2

description:
Library name: HYc1t4D
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: MDS801

description: MDS


title: MDS795

description: MDS


title: Rai1-het_d34_rep4

description:
Library name: HYc2t3D
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: MDS794

description: MDS


title: Rai1-het_d34_rep3

description:
Library name: HYc2t3
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: MDS787

description: MDS


title: MDS782

description: MDS


title: Rai1-het_d34_rep2

description:
Library name: HYc1t3D
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: Rai1-het_d34_rep1

description:
Library name: HYc1t3
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: MDS781

description: MDS


title: Rai1-het_d20_rep4

description:
Library name: HYc2t2D
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: MDS777

description: MDS


title: Rai1-het_d20_rep3

description:
Library name: HYc2t2
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: MDS771

description: MDS


title: Rai1-het_d20_rep2

description:
Library name: HYc1t2D
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: MDS770

description: MDS


title: Rai1-het_d20_rep1

description:
Library name: HYc1t2
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: MDS768

description: MDS


title: Rai1-het_d0_rep4

description:
Library name: HYc2t1D
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: MDS763

description: MDS


title: Rai1-het_d0_rep3

description:
Library name: HYc2t1
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: MDS759

description: MDS


title: MDS757

description: MDS


title: Rai1-het_d0_rep1

description:
Library name: HYc1t1
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: Rai1-het_d0_rep2

description:
Library name: HYc1t1D
Bulk RNA-seq was performed on WT, RAI1 heterozygous, and RAI1 homozygous mutant H9 hESC-derived cortical neuron cultures collected across dual SMAD inhibition differentiation.


title: MDS747

description: MDS


title: MDS724

description: MDS


title: RAI1 WT, HET and KO cortical differentiation scRNA-seq library

description:
Library name: 11534-BZ-Pool01-GEX_S4
Chromium Fixed RNA Profiling (10x Genomics Flex) library containing multiplexed WT, RAI1+/− and RAI1−/− cortical differentiation samples collected at day 20 and day 60.

data_processing:
BCL files were converted to FASTQ files using Illumina BCL Convert Conversion Software v4.0.
FASTQ files were processed using the 10x Genomics Chromium Fixed RNA Profiling analysis pipeline to generate gene-cell count matrices.
Cells with greater than 20% mitochondrial transcript counts were removed during quality control.
Downstream analyses, including normalization, dimensionality reduction, clustering, and cell-type annotation, were performed using Seurat in R.
Differential expression analysis, pseudobulk analysis, and pseudotime trajectory analysis were performed using Seurat and Monocle 3 in R.
Assembly: GRCh38
Supplementary files format and content: Gene-by-cell count matrices generated from the 10x Genomics Chromium Fixed RNA Profiling pipeline, together with accompanying cell barcode and gene annotation files.
Supplementary files format and content: Processed Seurat objects and accompanying cell metadata containing sample identity, genotype, differentiation time point, quality control metrics, cluster assignments, cell-type annotations, and dimensionality reduction coordinates (UMAP).

source_name: H9 human embryonic stem cells

growth_protocol: Human H9 embryonic stem cells (WT, RAI1+/−, and RAI1−/− CRISPR-edited lines) were maintained on Geltrex-coated plates in TeSR-E8 medium. Cortical differentiation was induced using a dual-SMAD inhibition protocol. Cells were cultured in 3N medium supplemented with dorsomorphin and SB431542 during neural induction, followed by sequential supplementation with FGF2, vitamin A, Compound E, GDNF, BDNF, dbcAMP, and laminin during neuronal maturation. Cells were harvested at differentiation days 20 and 60 for single-cell RNA sequencing.

extract_protocol:
Approximately 3 × 10^5 cells per sample were washed with ice-cold PBS containing 0.04% BSA and fixed using the Chromium Next GEM Cell Fixed RNA Sample Preparation Kit (10x Genomics). Cells were incubated overnight at 4°C in Fixation Buffer, quenched, treated with Enhancer, supplemented with glycerol for storage, and submitted for Chromium Fixed RNA Profiling library preparation.
Single-cell RNA sequencing libraries were prepared using the Chromium Fixed RNA Profiling (Flex) platform (10x Genomics) according to the manufacturer's protocol. Libraries were sequenced on an Illumina NovaSeq 6000 platform using 28 × 91 bp paired-end sequencing.

treatment_protocol: No chemical treatment was applied beyond the differentiation protocol. Samples consisted of isogenic wild-type (WT), heterozygous (RAI1+/−), and homozygous (RAI1−/−) RAI1 knockout human embryonic stem cell-derived cortical cultures collected at differentiation day 20 and day 60.

value: Differentiating cortical cells

value: Dual-SMAD inhibition cortical differentiation


title: MDS721

description: MDS


title: PHH cells POLA 5

city: Oxford

first: Leanne

last: Hodson

address: OCDEM, Churchill Hospital

department: OCDEM

country: United Kingdom

institute: University of Oxford

description: Library name: EC5P8

data_processing:
Novogene carried out the initial data processing which involved the following: Removal of low-quality reads or reads containing poly-N regions using in-house perl scripts, indexing and alignment of clean reads to a downloaded reference genome using Hisat2 (version 2.0.5) and finally counting reads mapped to each gene using featureCounts (version 1.5.0-p3).
Assembly: Hg38
Supplementary files format and content: Text file contains raw counts for each sample

source_name: Liver

growth_protocol: Huh7 and PHH cells were used. Huh7 cells were kindly provided by Dr Camilla Pramfalk (Karolinska Institute) and were cultured as previously described. PHH cells were obtained from Thermofisher (ThermoFisher, HMCPSQ) originating from both male and female donors (see supplementary data, Table 1 for donor characteristics. Frozen PHH cells were thawed in a 37°C water bath rapidly. 500µL of warm plating media (500mL Williams E Medium (ThermoFisher, A1217601) supplemented with a Primary Hepatocyte Thawing and Plating Supplements (ThermoFisher, CM3000) which contained FBS, dexamethasone, and a cocktail of penicillin-streptomycin, insulin, GlutaMAX™ and HEPES solution, was then added to the cryovial. Cells were then suspended and transferred to a falcon tube containing 4.5mL of warm plating media. Cell number and viability was then quantified using Trypan blue stain (ThermoFisher, 15250061) and a Cellometer Auto T4 Bright Field Cell Counter. Cells were then diluted with plating media and seeded into plates which had been pre-coated with collagen type I (ThermoFisher, A1048301) at a density of 35,000 cells/well for 96-well plates, 150,000 cells/well for 24-well plates or 50,000 cells/well for 12mm diameter glass cover slips for microscopy experiments. Both Huh7 and PHH cells were maintained at 37°C in 5% CO2.

extract_protocol:
RNA was extracted using the RNEasy® Plus mini kit (QIAGEN Sciences) according to manufacturer's instructions. The resulting RNA was treated with DNase (QIAGEN Sciences) and quality checked with an Agilent Bioanalyzer.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. cDNA was then synthesised from this mRNA. The library was checked with Qubit and RT PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: Huh7 cells were seeded into relevant plates and cultured in experimental media comprised of 2% HS, 5.5mM glucose and 800µM of 4 FAs (oleic acid (O), palmitic acid (P), linoleic acid (L) and alpha-linoleic acid (A)) in one of two physiological ratios: OPLA (45:30:24:1) or POLA (44:45:10:1), or a no fat control as previously described. Huh7 cells were cultured in experimental media for seven days with media changes every other day as previously described. Following seeding, PHHs were cultured in plating media overnight then cultured in experimental media which consisted of Williams E Medium (ThermoFisher, A1217601) and Primary Hepatocyte Maintenance Supplements (ThermoFisher, CM4000) containing dexamethasone and a cocktail of penicillin-streptomycin, insulin, transferrin, selenium complex, BSA, GlutaMAX™, and HEPES solution, supplemented with 2% HS. PHH cells were cultured in 800µM OPLA and POLA or no fat control experimental media for four days with media changes every other day.

value: Liver

value: PHH

value: Hepatocytes

value: POLA


title: RNAseq, Patient 50

first: Sarah

middle: J.

last: Hill

address: 450 Brookline Ave., Dana Building, Room 1410C

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Library name: Patient 50

data_processing:
Exome-capture RNA sequencing data were processed through the nf-core rnaseq pipeline version 3.14.0.
Quality control of raw reads was performed using FastQC version 0.12.1 (RRID: SCR_014583) and adapter and quality trimming was performed using cutadapt version 3.4 (RRID: SCR_011841) and Trim Galore version 0.6.7 (RRID: SCR_011847).
Trimmed reads were aligned to human genome (GRCh38.p14) using STAR version 2.7.9a (RRID:SCR_004463) and quantified using Salmon version 1.10.1 (RRID:SCR_017036).
Alignments were checked for evenness of coverage, rRNA content, genomic content of alignments, complexity, and other quality checks using a combination of FastQC (RRID:SCR_014583), Qualimap version 2.3 (RRID:SCR_001209), Samtools version 1.17 (RRID:SCR_002105), MultiQC version 1.19 (RRID:SCR_014982), and bcbioR version 0.4.5.
Lowly expressed genes (total counts ≤10 or expressed in <80% of samples) were filtered out.
Assembly: GRCh38.p14
Supplementary files format and content: Raw counts for non-lowly-expressed genes in CSV format.

source_name: Endometrial cancer

growth_protocol: There was no growth or treatment. Tissue was scraped from FFPE slides and used to prepare RNA

extract_protocol:
Methods are provided directly from the linked manuscript. For additional details, please see the linked manuscript.
For each patient, tumor was identified and circled on an H&E stained slide. Matched unstained slides for that patient were then held up to the circled H&E stained slide, and the tumor-containing region was circled on the unstained slide. Tissue within the circled area on the unstained slide or slides for each individual patient was scraped from the slide and collected into one mL of xylene (Fisher Cat. #447240010) in a microcentrifuge tube for each patient sample. Depending on the size of the tumor section, one to four slides were processed for each patient. The sample collected was vortexed vigorously for 10 seconds and spun at 13,500 rpm for two minutes in a tabletop microcentrifuge. The supernatant was removed, followed by the addition of one mL of ≥99.45% ethanol (Sigma-Aldrich Cat. #E7023-500mL). The tube was vortexed and spun again at 13,500 rpm for two minutes in a tabletop microcentrifuge, the supernatant was removed, and residual ethanol was evaporated completely by allowing the tube to stand open at room temperature. The resulting pellet was then processed for RNA extraction. Total RNA extraction was performed using the RNeasy FFPE Kit (Qiagen, Cat. #73504) following the manufacturer’s protocol, with DNase I digestion performed to remove genomic DNA. RNA samples were snap frozen and stored at -80°C until all samples were ready for sequencing as described below.
The exome-capture RNA sequencing was performed by the Molecular Biology Core Facilities (MBCF) at Dana-Farber Cancer Institute, and the methodological details were provided by the MBCF as described below. Purified total RNA was evaluated for quality and quantity using the Agilent Fragment Analyzer RNA assay. Samples were prepared from 200ng of RNA using Roche Kapa RNA Hyper reagents without any prior enrichment or depletion according to the manufacturer’s protocol on a Beckman Coulter Biomek i7. Following library preparation, samples were characterized by Qubit fluorometer and Agilent TapeStation 4200. Libraries were pooled in 10 or 11 plex reactions based on available material. Pools were then hybridized to Twist Exome 2.0 probes for target enrichment. Post capture library pools were quantified by Qubit fluorometer and Agilent TapeStation 4200. Pre-pooled, uniquely dual indexed libraries were shallowly sequenced on an Illumina MiSeq to further evaluate overall library quality and pool balance. Final library pools were sequenced on an Illumina NovaSeqX+ targeting 35 million reads per library with 150bp paired-end reads at the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

value: Endometrial cancer


title: Human TS cells (CT27), IP PPARG, replicate 1

city: Kansas City

first: Esteban

middle: Mauricio

last: Dominguez

state: Kansas

address: 3901 Rainbow Blvd.

department: Pathology

institute: University of Kansas Medical Center

description: Library name: IP_PPARG_1

data_processing:
The sequence quality of the raw FASTQ files was evaluated by fastqc (version 0.11.9). Quality control for the FASTQ files was performed by HTStream (version 1.3.3).
For each biological replicate, peaks were independently identified using  MACS3 (version 3.0.0b1) with fold enrichment >1.5 and q-value <0.01.
Bigwig files were created by deeptools (version 3.5.1) to visualize peaks in the UCSC genome browser (https://genome.ucsc.edu/s/kchen7/hg38_p14_Pparg_ChIPseq).
Genomic features of the peak regions and motif analysis were performed using HOMER (version 5.1) scripts annotatePeaks.pl and findMotifsGenome.pl
Assembly: GRCh38.p14
Supplementary files format and content: Bigwig files

source_name: human trophoblast stem cells- CT27 (Okae et.al)

growth_protocol: Human Triophoblast Stem cells  were grown and differentiated in the dish for 8 days into extravillous trophoblast cells media

extract_protocol:
EVT cells were fixed with 1% Formaldehyde for 10 minutes at RT, following Simple ChIP Enzymatic Chromatin IP Kit (9003, Cell Signaling Technology) protocol.
ChIP-seq library was constructed using the Tecan Ovation Ultralow DNA System V2 (NuGEN Technologies, Redwood City, CA)

value: PPARG (2435S, Cell Signaling Technology)


title: PHH cells OPLA 5

description: Library name: EC5O8

value: OPLA


title: PHH cells Control 5

description: Library name: EC5C

value: Control


title: PHH cells POLA 4

description: Library name: EC4P8


title: MDS716

description: MDS

value: human BM Mononuclear cells


title: MDS717

description: MDS


title: PHH cells OPLA 4

description: Library name: EC4O8


title: MDS719

description: MDS


title: MDS708

description: MDS


title: PHH cells Control 4

description: Library name: EC4C


title: MDS699

description: MDS


title: PHH cells POLA 3

description: Library name: EC3P8


title: MDS694

description: MDS


title: PHH cells OPLA 3

description: Library name: EC3O8


title: MDS693

description: MDS


title: PHH cells Control 3

description: Library name: EC3C


title: MDS672

description: MDS


title: MDS662

description: MDS


title: PHH cells OPLA 2

description: Library name: EC2O8


title: MDS661

description: MDS


title: PHH cells Control 2

description: Library name: EC2C


title: MDS660

description: MDS


title: PHH cells POLA 2

description: Library name: EC2P8


title: PHH cells POLA 1

description: Library name: EC1P8


title: MDS653

description: MDS


title: RNAseq, Patient 46

description: Library name: Patient 46


title: MDS650

description: MDS


title: PHH cells Control 1

description: Library name: EC1C


title: PHH cells OPLA 1

description: Library name: EC1O8


title: MDS644

description: MDS


title: Huh7 cells POLA 5

description: Library name: FBSN_15


title: Huh7 cells POLA 4

description: Library name: FBSN_14


title: MDS638

description: MDS


title: MDS636

description: MDS


title: Huh7 cells POLA 3

description: Library name: FBSN_13


title: MDS612

description: MDS


title: Huh7 cells POLA 2

description: Library name: FBSN_12


title: MDS607

description: MDS


title: MDS606

description: MDS


title: Huh7 cells OPLA 5

description: Library name: FBSN_10


title: MDS600

description: MDS


title: Huh7 cells POLA 1

description: Library name: FBSN_11


title: Huh7 cells OPLA 4

description: Library name: FBSN_09


title: MDS596

description: MDS


title: Huh7 cells OPLA 3

description: Library name: FBSN_08


title: Huh7 cells OPLA 2

description: Library name: FBSN_07


title: MDS576

description: MDS


title: MDS577

description: MDS


title: Huh7 cells OPLA 1

description: Library name: FBSN_06


title: MDS569

description: MDS


title: Huh7 cells Control 5

description: Library name: FBSN_05


title: Huh7 cells Control 4

description: Library name: FBSN_04


title: MDS574

description: MDS


title: MDS567

description: MDS


title: Huh7 cells Control 3

description: Library name: FBSN_03


title: MDS560

description: MDS


title: Huh7 cells Control 1

description: Library name: FBSN_01


title: MDS561

description: MDS


title: Huh7 cells Control 2

description: Library name: FBSN_02


title: MDS558

description: MDS


title: BA807NGQ-11

type: RNA

city: Portland

first: Julie

middle: A

last: Saugstad

state: Oregon

address: 3181 SW Sam Jackson Park Road

department: Anesthesiology & Perioperative Medicine

institute: Oregon Health & Science University

scan_protocol: Each card was assayed on a QuantStudio 7K Flex (TFS) by automatic loading of the cards using an Orbitor R2 robot to increase throughput.

data_processing:
For each RT-qPCR well, we examined a variety of quality control (QC) metrics exported by ExpressionSuite software. Cq values for miRNA amplifications were included in statistical analysis if they had an AmpScore ≥1.0 with CqConf ≥0.8. MiRNA amplifications (e.g., let-7b-5p) that showed performance slightly below those thresholds (either AmpScore ≥0.9 with CqConf ≥0.8, or CqConf ≥0.75 with AmpScore ≥1.0) had Cq values accepted for statistical analysis conditional on meeting other criteria for good amplification (strong consistency of Cq values across triplicate wells). For accepted amplifications we examined the appropriateness of the baseline separation from the recorded Cq value and compared our QC assessments with other quality flags exported by QuantStudio, finding nothing unusual. Amplifications with acceptable QC but Cq >35 were considered censored values and given special handling using censoring-aware methods in the analysis. Amplifications that did not meet the QC standards for accepted or censored amplifications were considered missing measurements, regardless of Cq value. Amplifications labeled "Undetermined" by QuantStudio were also considered missing measurements. As a final fidelity check we 1) examined the amplifications for the two negative control miRNAs (miR-1293 and miR-647) to verify that no sample had a Cq value recorded for either of those with acceptable QC, and 2) verified that the spike-in positive control (cel-miR-39-3p) and primary endogenous normalization control (miR-16-5p) were both completely observed with acceptable QC in all replicates for all samples. The other endogenous normalizer control miRNAs (miR-24-3p, miR-92a-3p, miR-204-5p) showed good performance, with expression of miR-24-3p and miR-92a-3p in 100% of samples and miR-204-5p in 77% of samples. Given our built-in redundancy of normalizer control miRNAs and model-based methods of normalization that can handle noninformative missing data, we considered this amount of normalizer measurement dropout acceptable.
For technical calibration, all raw Cq values were adjusted for RNA isolation differences via median-alignment of the cel‑miR‑39‑3p spike‑in control reactions as an exogenous calibration factor. This adjustment represented the largest contribution to the overall normalization, with 57% of the technical variance explained by differences in spike-in control values (Note that we define technical variance as the variance in average Cq values across samples.) After technical calibration, all Cq values for the cel‑miR‑39‑3p spike-in (being exactly aligned by median) were removed from the dataset and did not contribute to later normalization steps. Next, these technical calibrated Cq values were batch calibrated to remove residual artifacts attributed to processing order. We fit a linear mixed-effects regression model including the same 5-knot restricted cubic spline of the RT-qPCR run order as above, plus indicators for known abnormal sample or processing events (e.g., visible hemolysis), with PCR run batches entered as random intercepts. Fitted values from this regression were subtracted from the corresponding Cq values for all miRNAs as the adjustment for batch and order-related effects. Batch calibration adjustments were relatively minor for our dataset, accounting for 10% of the technical variance.
Calibrated Cq values were normalized using a mixed-effects model on the endogenous miRNA normalizer Cq values only. The model included quadratic effects of age (interaction effect of age with itself, to model the effect of age at differing ages rather than assuming the effect is linear for all ages), fully-interacted indicators for sex and diagnosis group to adjust out study factors (because we wish to retain these factors for analysis), and crossed random effects of miRNA and sample to model the miRNA-sample interaction. We used this model to estimate the residual differences between samples as BLUPs (best linear unbiased predictions). The BLUP values were subtracted from the fully calibrated Cq values as endogenous normalizer level effects across samples. The resulting normalized Cq values were recentered to the global median of the input Cq value distribution. This final normalization step accounted for 26% of the technical variance in the data. The remaining 7% of technical variance was unexplained. After normalization, 83% of the total Cq variance (expected between-miRNA variance plus signal and residual technical and noise variance) was attributable to differences in mean expression across miRNAs (expected variance), 9% was attributable to sample-miRNA interactions (the biological signal), and <1% to differences in mean expression across samples (the residual technical variance, meaning the normalization was highly successful); the remainder of ~7% is residual variance (the measurement noise). We verified that the normalized Cq values of the normalizer miRNAs themselves had essentially flat profiles and noted that the normalization achieved substantial variance reduction.
Censored Cq values are quantitatively unreliable because their measurement falls outside the linear range of the assay. These were treated as interval observations, defined as an unobserved value falling between an upper and a lower limit. For the purposes of regression on the Cq values as an outcome predicted by diagnosis status these can be handled as interval observations directly via modeling. However, when the Cq values are used as predictors of diagnosis status the interval observation must be collapsed to a single most-likely value falling within the interval. To accomplish this, we used a Bayesian multilevel interval regression model that considers all replicate wells for the sample jointly and naturally accounts for the different character of censored values in the context of non-censored values for the same miRNA. For the Bayesian prior distribution on the mean level for the miRNA, we used a Student's t distribution with 4 degrees of freedom and a (wide and uninformative) scale of 10, and for the log of the root mean square error we used a (similarly uninformative) half-Cauchy distribution with the same scale of 10. Random effects for individual samples were assigned a zero-centered prior normal distribution with default conjugate inverse-gamma hyperprior (shape and scale parameters both 1/100) for the random-effect variance. The imputed value for a censored observation was taken as the posterior grand mean for the miRNA plus the posterior mean of the random effect, based on 10000 Markov chain Monte Carlo draws from the posterior distribution, following a burn-in run of 2500 draws. Note that the rank correlation between the predictions from this model and the naïve means of the corresponding replicate wells was 0.98, reflecting almost complete preservation of rank ordering among samples, but the model prediction is less biased because it accounts for censoring, which prevents it from overestimating the expression level. (The mean overestimate was 0.95 Cq.)
Prior to imputation the normalized Cq values, both censored and uncensored, are converted to an expression scale using inverted Cq units so that positive values mark higher expression. Non-censored Cq values with acceptable QC were used as exact measurements (both bounds of the interval are the same normalized Cq value). Censored Cq values with acceptable QC were treated as falling between the censoring threshold of 35 (lower bound) and the average (upper bound) of the normalized Cq value and the maximum normalized Cq value across all observations on all miRNAs (the "observed maximum", a value that will be strictly less than the maximum cycle number of 40, specified as a machine setting). Missing Cq values were treated as falling between the observed maximum (lower bound) and the maximum cycle number (upper bound of 40). Non-missing Cq values with unacceptable QC were treated as missing measurements for most purposes, but in this context the recorded Cq (with all normalization adjustments) was used as the lower bound and the maximum cycle number (40) as the upper bound. Finally, all the interval bounds were subtracted from the maximum cycle number of 40 to invert the scale.

label: FAM

source_name: total cell-free biofluid RNA

label_protocol: MiRNA was converted to cDNA as previously described using the TaqMan Advanced miRNA cDNA Synthesis kit (TFS). Briefly, 3 μL of total RNA was 3’ poly-adenylated, followed by a 5’ adaptor ligation step and reverse transcription. The resulting cDNA (5 μL) was added to a 14-cycle universal miR-amplification step. The miR-amplification reaction was diluted 1:10 with nuclease free water, 220 µL of the diluted cDNA was mixed with 220 µL of nuclease free water and 440 µL of TaqMan Fast Advanced master mix (TFS). The RT-qPCR mix (100 µL) was loaded into custom TaqMan Advanced Human miRNA Custom Cards.

extract_protocol: Total RNA was isolated from 100 μL of plasma using the MagMax Mirvana Total RNA Isolation Kit (Thermo Fisher Scientific, TFS) using a KingFisher Apex System (TFS) automated purification instrument following the manufacturer’s protocol. For the RNA isolation, the 289 plasma samples were processed in a total of 4 batches (3 plates x 80 samples = 240, 1 plate x 49 samples). On the first day, plasma samples were mixed with 5 µL of proteinase K and 45 µL of digestion buffer and incubated for 30 minutes at 65°C. 100 µL of lysis buffer containing 1% β-mercaptoethanol was added to each well, mixed and stored at -20°C overnight. The following day, the plate was thawed to room temperature and an exogenous cel-miR-39-3p spike-in control (TFS) was added at a final concentration of 3 pM, followed by the addition of 20 µL of magnetic isolation beads. Samples were mixed for 5 minutes using a plate shaker followed by the addition of 270 µL of isopropanol and brief mix. The sample plate as well as 4 wash plates (each containing 150 µL of wash buffer), a DNase plate containing 45 µL of Turbo DNase buffer and 2 µL of DNase, and an elution plate containing 50 µL of nuclease free water were all processed using the KingFisher Apex instrument. Following the DNase step, 50 µL re-binding buffer and 100 µL of isopropanol was added to each well and automation was resumed for the washing and elution steps. All isolations were completed within two consecutive days. Following the elution step, the miRNA concentration of a subset of samples from each batch (minimum of 30% of samples per batch across each plate) was measured using the Qubit miRNA Assay kit (TFS) and read using a Qubit 4.0 fluorometer (TFS) to ensure the isolation was consistent across the batch. Prior to the eluted RNA being frozen at -80°C until RT-qPCR, each plate of 80 RNA samples was divided into 2 plates of 40 RNA samples, as 40 is the maximum number of miRNA RT-qPCR assays that can be processed in a day, and the plate with 49 RNA samples was divided into 1 plate of 40 samples and 1 plate of 9 samples. Thus, the RT-qPCR was performed with the 289 eluted RNA samples in a total of 8 batches (7 x 40 RNA = 280, 1 x 9 RNA), with one batch being completed per day in unbroken succession to mitigate time drift in measurements.

tag: donor id

value: Plasma

tag: disease

value: NC

value: Female

tag: mmse

tag: anatomical location

value: Circulating blood

tag: sample collection method

value: Venous

tag: starting amount

tag: holding temperature


title: MCF7-IgG (Tube_CUT&RUN)

city: Houston

first: Yue

last: Lu

state: TX

address: 1881 East Road

department: Epigenetics & Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

description: Library name: IgG_Tube

data_processing:
Adapter sequences were removed from the 3' ends of reads using Trim Galore! (version 0.6.7) and cutadapt (version 4.1).
The reads were then mapped to the human genome (hg38) using Bowtie (version 1.1.2) with the following parameters: "--allow-contain --maxins 2000 -v 2 -m 1 --best --strata".
To avoid PCR bias, only one copy of multiple fragments mapped to the same genomic position was retained for further analysis. Fragments longer than 1000 bp (less than 1% of the total) were excluded from subsequent analysis.
For signal track to display in genome browser, each fragment was resized to a length of 151 bp, spanning from -75 bp to +75 bp around its midpoint. The count of fragments covering each genomic position was normalized to 10M total number of fragments. These values were then averaged over a 10 bp resolution.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Run

extract_protocol:
Fresh harvested and counted cells were bound to magnetic Concavilin A beads and subjected to CUT&RUN following the protocol
Library preparation from CUT&RUN DNA was carried out using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (New England Biolabs) according to the manufacturer's instructions with some modifications. Libraries were purified using SPRIselect beads (Beckman Coulter) and fragment size was confirmed on Agilent TapeStation 4200.

tag: cell line

tag: cell type

value: ER+ breast cancer cell line

tag: protocol

value: CUT&RUN in tube

tag: cut&run antibody

value: IgG (EpiCypher, # 13-0042)


title: MCF7-IgG (Plate_CUT&RUN)

description: Library name: IgG_Plate

value: CUT&RUN in 96-well plate


title: MDS551

description: MDS


title: MDS549

description: MDS


title: MCF7-H3K4me3 (Tube_CUT&RUN)

description: Library name: H3K4me3_Tube


title: Capture Hi-C in wild type mouse bone marrow derived macrophages treated with 100 uM heme (rep1)

city: Debrecen

first: Laszlo

last: Nagy

address: Egyetem ter 1.

country: Hungary

institute: University of Debrecen

data_processing:
library strategy: cHi-C
Reads were aligned and quality controlled using Hicup (v0.6.1). Interactions between virtual restriction fragments were detected using Chicago (v1.6.0) using custom weights calculated from high confidence interactions in the data.
Assembly: mm10

source_name: mouse bone marrow derived macrophages

growth_protocol: Isolation and differentiation were completed as described earlier (Daniel et al., 2014). Isolated bone marrow-derived cells were differentiated for 6 days in the presence of L929 supernatant.

extract_protocol:
Mouse bone marrow-derived macrophages were cross-linked using formaldehyde-based cross-linking method and processed to Hi-C using the Arima Hi-C kit. A capture enrichment step was applied to the generated Hi-C libraries using sustom-designed probes (SureSelect, Agilent Tier 2 -2,9Mb ). Our design has two components combined in the same probe set : a. The Hmox1 genomic locus (tiled probescovering a 500kb area). The coordinates of this area arechr8:74850001-75350000. b.9127 sites covering the top BACH1’s ChIP-seqsites (in untreated BMDMs) sorted based on the RPKM.
Hi-C and cHi-C libraries were prepared with the Arima Hi-C kit and Agilent SureSelect library systems according to the manufacturer protocol.

treatment_protocol: Treatments of mouse bone marrow-derived macrophages occurred at Day7 of differentiation after an overnight incubation in fresh medium.

value: bone marrow derived macrophages

tag: strain

tag: genotype

value: Bach1 fl/fl (Control)

tag: cell treatment

value: 100μΜ Hemin (Sigma 51280)

tag: duration of_treatment_(hours)

tag: capture selection_probes

value: Custom-designed selection probes (SureSelect- Agilent) against BACH1-bound genomic sites


title: MDS539

description: MDS


title: MCF7-H3K4me3 (Plate_CUT&RUN)

description: Library name: H3K4me3_Plate


title: MDS537

description: MDS


title: MCF7-H3K4me1 (Tube_CUT&RUN)

description: Library name: H3K4me1_Tube

value: H3K4me1 (Abcam, # ab8895)


title: MDS541

description: MDS


title: MCF7-H3K4me1 (Plate_CUT&RUN)

description: Library name: H3K4me1_Plate


title: MCF7-H3K27ac (Tube_CUT&RUN)

description: Library name: H3K27ac_Tube

value: H3K27ac (Active Motif, #39133)


title: MDS530

description: MDS


title: MDS520

description: MDS


title: MCF7-H3K27ac (Plate_CUT&RUN)

description: Library name: H3K27ac_Plate


title: MDS525

description: MDS


title: MDS518

description: MDS


title: MCF7-CTCF (Plate_CUT&RUN)

description: Library name: CTCF_Plate

value: CTCF (Milipore, #07-729)


title: HCT116, treated with 20 µM 5FdUR, replicate 2,short RNA

city: Budapest

first: Angela

last: Bekesi

address: Műegyetem rakpart 3.

department: Department of Applied Biotechnology and Food Science

institute: Budapest University of Technology and Economics, Faculty of Chemical Technology and Biotechnology

description:
Library name: 5FdUR_HCT116_rep2.sRNA
FdUR_sRNA_2

data_processing:
For lRNA-seq data, quality was checked using fastQC, residual rRNA-related reads were removed in silico, then polyG, adapter, and low-quality sequences were trimmed using the fastp tool. For sRNA-seq data, quality was checked using fastQC, and adapter and low-quality sequences were trimmed using the Trimmomatic tool.
Clean reads were aligned to the human reference genome GRCh38  using HiSAT2, or STAR aligners for lRNA and sRNA data, respectively.
Aligned data were filtered for the core chromosomes.
For lRNA-seq data, treated samples were compared to the corresponding non-treated ones using the Cufflinks package (cuffnorm and cuffdiff), and the two drug treatments were also directly compared. For sRNA-seq data, FeatureCounts was used to count reads on annotated mature miRNA genes (miRBase) as well as on sRNA, snRNA, and snoRNA genes as defined by Gencode v34, and samples were compared using the deseq2 R package.
Read coverage tracks were calculated for the forward and reverse strands, respectively, using bamCoverage of the deeptools package.
Assembly: GRCh38
Supplementary files format and content: The *forward.filtered.bw and *reverse.filtered.bw files contain the strand-selective coverage tracks in bigwig format.
Supplementary files format and content: The *cuffdiff.gene_exp.tsv files  (9) are tab-separated text files, which contain the results of differential expression analysis (cuffdiff output for lRNAs).
Supplementary files format and content: The lRNA_genes_cuffnorm.FPKM_table.annot.tsv file is a tab-separated text file, which contains all the FPKM values and the annotation details of the lRNAs, calculated using cuffnorm.
Supplementary files format and content: The ALL_sRNA_counts.tsv file is a tab-separated text file, which contains all the count values and several identifiers of the sRNAs and miRNAs. Counts were calculated with featureCounts.
Supplementary files format and content: The *deseq2.tsv files (9) are tab-separated text files, which contain the results of differential expression analysis for sRNAs and miRNAs calculated by deseq2.

growth_protocol: Cells were maintained in McCoy’s 5A medium supplemented with 10% FBS and 1% PenStrep.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer's protocol. RNA quality was assessed by agarose gel electrophoresis, and concentration was measured using a NanoDrop 2000C UV-Vis spectrophotometer (Thermo Fisher Scientific).
Stranded RNA sequencing libraries for short RNAs (<200 nt) and long RNAs (>200 nt) were prepared separately. Library preparations, including rRNA depletion and quality control, as well as the sequencing, were performed by Novogene Co., Ltd. (China) as a whole-transcriptome sequencing service. The small RNA library was sequenced using the Illumina 50 pb single-end protocol, which yielded 20 M reads. The long RNA library was sequenced on a Novaseq 6000 platform using Illumina 150 paired-end protocol, which resulted in approximately 150 M reads for each sample.

treatment_protocol: Cells were cultured in 6-well plates, treated with 100 nM RTX or 20 µM 5FdUR for 48 hours.

value: colon adenocarcinoma

value: MMR deficient

tag: treatment

value: 20 µM 5FdUR


title: MDS514

description: MDS

value: human BM Mononuclear cells


title: HCT116, treated with 20 µM 5FdUR, replicate 1, short RNA

description:
Library name: 5FdUR_HCT116_rep1.sRNA
FdUR_sRNA_1


title: MDS512

description: MDS


title: MDS509

description: MDS


title: HCT116, treated with 100 nM RTX, replicate 2, short RNA

description:
Library name: RTX_HCT116_rep2.sRNA
RTX_sRNA_2

value: 100 nM RTX


title: HCT116, treated with 100 nM RTX, replicate 1, short RNA

description:
Library name: RTX_HCT116_rep1.sRNA
RTX_sRNA_1


title: MDS504

description: MDS


title: HCT116, non-treated, replicate 2, short RNA

description:
Library name: NT_HCT116_rep2.sRNA
NT_sRNA_2


title: MDS483

description: MDS


title: HCT116, non-treated, replicate 1, short RNA

description:
Library name: NT_HCT116_rep1.sRNA
NT_sRNA_1


title: MDS428

description: MDS


title: HCT116, treated with 20 µM 5FdUR, replicate 2, long RNA

description:
Library name: 5FdUR_HCT116_rep2.lRNA
5FdUR_lRNA_2


title: MDS393

description: MDS


title: HCT116, treated with 20 µM 5FdUR, replicate 1, long RNA

description:
Library name: 5FdUR_HCT116_rep1.lRNA
5FdUR_lRNA_1


title: MDS389

description: MDS