title: JU775_GFP_RNAi_22GRNA_Rep2

first: Germano

last: Cecere

address: Institut Pasteur, 28 Rue Du Docteur Roux, Batiment Monod, 5eme Etage

department: Development and stem cell biology

institute: Institut Pasteur

description:
Library name: JU775_GFP_RNAi_22GRNA_Rep2
small RNAs

data_processing:
Raw reads were demultiplexed using Illumina bcl2fastq (v2.17.1.14), and quality was assessed with FastQC (v0.11.5). Analyses followed the general framework of Barucci et al. (2020). The 3′ adapter sequence (TGGAATTCTCGGGTGCCAAGG) was trimmed using cutadapt (v4.9). UMIs consisting of 4-nt tags at both the 5′ and 3′ ends were removed using cutadapt with the parameters -u 4 -u -4. Reads of length 18–24 nt were retained using bioawk. Filtered reads were aligned to the C. elegans reference genome (WBcel235) using Bowtie2 (v2.5.4) with the following settings optimized for short RNA alignment: -L 6 -i S,1,0.8 -N 0. Mapped reads were quantified over structural RNA annotations (tRNA, snRNA, snoRNA, rRNA, and other non-coding RNAs from the iGenome WBcel235 distribution) using featureCounts (subread v2.0.0) with options -O -M --fraction. The abundance of non-structural small RNAs was obtained by subtracting structural RNA-derived reads from the total number of mapped reads. Mapped reads were classified using a custom Python script according to read length, sequence composition, and genomic annotation. Reads not corresponding to annotated miRNAs or piRNAs were considered candidate endogenous siRNAs. Candidate endo-siRNAs of 21–23 nt beginning with G were classified as 22G-RNAs if they mapped antisense to genomic features annotated as DNA transposons, retrotransposons, satellites, simple repeats, pseudogenes, or protein-coding genes (iGenome WBcel235). Coverage tracks (bigWig files) were generated using deepTools bamCoverage (v3.x), normalized to millions of non-structural small RNAs to avoid biases caused by highly abundant structural RNA fragments. Genome build: C. elegansce11 (WBcel235). To enable alignment of GFP-derived reads, the GFP coding sequence was added to the reference genome as an artificial chromosome (designated “CEGFP”). The augmented reference genome (WBcel235 + CEGFP) was indexed with Bowtie2 and used for all alignments described above.
Assembly: C. elegans ce11 (WBcel235)
Supplementary files format and content: normalized big wig files of 22G-RNAswill be provided for each libraries

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: All the different strains were maintained at 20°C, using standard methods (Brenner, 1974).

extract_protocol:
Synchronous populations of worms were grown at 20°C on NGM plates supplemented with a 2 µm filtered IPTG solution to obtain a final concentration of 1 mM and seeded with E. coli HT115 bacteria expressing GFP dsRNA or control E. coli bacteria OP50 (control) as concentrated food. Worms were grown at a density of maximum 40,000 animals per 15 cm Petri dish and harvested at Young Adult stage at 48 hours post hatching. The harvested animals were washed three times with M9 buffer and 40 µl of worm pellet was frozen in dry ice with TRI Reagent (MRC, Inc.). After five repetitions of freeze and thaw, total RNA was isolated according to the TRI Reagent protocol.
The small RNA library preparation was performed essentially as described previously by Barucci et al., 2020.

treatment_protocol: Stock populations of GFP+ nematodes were maintained for at least two generations at 20°C before starting an experiment. Two replicates were conducted in parallel for each. RNAi was initiated at 20°C using E. coli HT115 bacteria expressing dsRNA targeting the GFP sequence (GFP RNAi) or control E. coli bacteria OP50 (control). Empty 55 mm Petri dishes were poured with autoclaved NGM medium supplemented with a 2 µm filtered IPTG solution to obtain a final concentration of 1 mM. Plates were left to dry overnight and covered at room temperature. In parallel, liquid cultures of dsRNA vector containing-bacteria were incubated for ~16 hrs at 37°C with agitation at 220 rpm. The next day, the bacterial liquid cultures were used to seed now solidified NGM-ITPG plates with 100 µL and left to dry overnight covered at room temperature. This process was repeated for the two generations of exposure to RNAi (G-1 and G0).

value: whole worm

value: mfSi19[mex-5p::ce-GFP(2xNLS, non PATCs introns)::tbb-2 3'UTR + rps-0p::hygromycinR::rps-27 3'UTR] I

value: GFP RNAi


title: PHA treated rep 3

status: Public on Feb 01 2026

type: SRA

city: Rome

first: Daniela

last: Barilà

address: Via Cracovia, 90

department: Department of Biology

country: Italy

institute: Università Tor Vergata

description: Library name: TorV-MG713-PH4

library_source: transcriptomic

data_processing:
Data processed using the nf-core/rnaseq pipeline with default parameters
Assembly: hg19
Supplementary files format and content: comma-delimited text file including TPM values for each sample

molecule: total RNA

organism: Mus musculus

source_name: mammary gland tumor

growth_protocol: MGT cell lines, derived from MMTV-R26Met mice, were grown in DMEM/F12 (Dulbecco’s modified Eagle’s media/F12, 1/1, Sigma) supplemented with: 10% fetal bovine serum (FBS, Sigma), 100 U/mL penicillin, and 100 mg/mL streptomycin (P/S, Sigma), L-glutamine (2mM, Sigma), glucose (0,25%, Sigma), insulin (10 µg/mL, Sigma), transferrin (10 µg/mL, Sigma), sodium selenite (5 ng/mL, Sigma), hydrocortisone (0,5 µg/mL, Sigma), EGF (20 ng/mL, Sigma) and HGF (10 ng/mL, Thermo Fisher Scientific), at 37° in a 5% of CO₂ atmosphere. All MGT cells were routinely negative tested for Mycoplasma contamination

extract_protocol:
Total RNA was extracted using Qiazol (Qiagen, IT), purified from DNA contamination through a DNase I (Qiagen, IT) digestion step and further enriched by Qiagen RNeasy columns for gene expression profiling (Qiagen, IT). Quantity and integrity of the extracted RNA were assessed by NanoDrop Spectrophotometer (NanoDrop Technologies, DE) and by Agilent TapeStation (Agilent Technologies, CA), respectively
RNA libraries for sequencing were generated using the same amount of RNA for each sample according to the Illumina Stranded Total RNA Prep kit with an initial ribosomal depletion step using Ribo-Zero Plus (Illumina, CA). The libraries were quantified by qPCR and sequenced in paired-end mode (2x100 bp) with NovaSeq 6000 (Illumina, CA)

treatment_protocol: After 4h of serume deprivation, MGT-13 cells were treated for 24h with 1µM of PHA-665752 inhibitor

tag: tissue

value: mammary gland tumor

tag: cell line

tag: cell type

value: Epithelial cell

tag: treatment

value: Treated with PHA

tag: batch


title: PHA treated rep 2

description: Library name: TorV-MG713-PH3


title: JU775_GFP_RNAi_22GRNA_Rep1

city: Paris

country: France

description:
Library name: JU775_GFP_RNAi_22GRNA_Rep1
small RNAs

tag: genotype


title: Ant1(Tg)/+_female_quadricep_muscle_2

city: Syracuse

first: Nicholas

last: Brennan

state: New York

address: 766 Irving Ave

department: Biochemistry and Molecular Biology

country: USA

institute: SUNY Upstate Medical University

data_processing:
Illumina Bcl2FastQ software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, using Cutadapt-1.2.1 and low-quality (q < 25) sequence
Trimmed sequences were mapped to mm10 whole genome using STAR and quantified to Ensembl 100 annotation, using strict paired-end compatibility, with requirement of junction reads to match introns, minimum feature overlap of 95%, and minimum reads of 1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized alignment counts per gene for each sample

source_name: Quadricep skeletal muscle

growth_protocol: All the experiments were performed using age-matched controls. The animals were fed with a regular chow diet ad libitum and were housed at an ambient temperature.

extract_protocol:
Total RNA was extracted using Trizol/chloroform phase separation followed by RNeasy Mini kit column purification. The quality and quantity of RNA was assessed with the Bioanalyzer. 500ng RNA was used as input to the Illumina Stranded mRNA kit for the construction of sequencing libraries.
RNA libraries were prepared using the Illumina Stranded mRNA prep kit following the manufacturers protocol.

value: Quadricep skeletal muscle

tag: strain

tag: Sex

value: Female

tag: age

value: 2 months


title: granulosa cells, normal ovarian reserve, old, No76

city: Shanghai

first: Jiani

last: Lu

address: No.85 Wujin Rd.

country: China

institute: Shanghai General Hospital

description: Library name: NORH76

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Paired-end clean reads were aligned to mm10 using Hisat2 (v2.0.5). FeatureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene.
Assembly: hg38
Supplementary files format and content: xlsx file include raw counts for each sample

organism: Homo sapiens

source_name: ovarian follicle

extract_protocol:
The RNA was isolated using Trizol method.
Libraries were Fast RNA-seq Lib Prep Kit V2 following manufacturer's protocols

value: ovarian follicle

value: granulosa cells

tag: disease group

value: normal ovarian reserve

tag: age group


title: N2_GFP_RNAi_22GRNA_Rep1

description:
Library name: N2_GFP_RNAi_22GRNA_Rep1
small RNAs

value: mfSi13[mex-5p::ce-GFP(2xNLS, non PATCs introns)::tbb-2 3'UTR + rps-0p::hygromycinR::rps-27 3'UTR] I


title: granulosa cells, normal ovarian reserve, old, No71

description: Library name: NORH71


title: granulosa cells, normal ovarian reserve, old, No60

description: Library name: NORH60


title: N2_GFP_RNAi_22GRNA_Rep2

description:
Library name: N2_GFP_RNAi_22GRNA_Rep2
small RNAs


title: PHA treated rep 1

description: Library name: TorV-MG713-PH2


title: Ant1(Tg)/+_female_quadricep_muscle_1


title: Ant1(Tg)/+_female_quadricep_muscle_3


title: JU1395_GFP_RNAi_22GRNA_Rep2

description:
Library name: JU1395_GFP_RNAi_22GRNA_Rep2
small RNAs

value: mfSi27[mex-5p::ce-GFP(2xNLS, non PATCs introns)::tbb-2 3'UTR + rps-0p::hygromycinR::rps-27 3'UTR] I


title: Control rep 3

description: Library name: TorV-MG713-Ctr4

value: Control


title: granulosa cells, normal ovarian reserve, old, No56

description: Library name: NORH56


title: granulosa cells, normal ovarian reserve, old, No54

description: Library name: NORH54


title: JU1395_GFP_RNAi_22GRNA_Rep1

description:
Library name: JU1395_GFP_RNAi_22GRNA_Rep1
small RNAs


title: WT_female_quadricep muscle_3

value: Wildtype


title: WT_female_quadricep muscle_2


title: Control rep 1

description: Library name: TorV-MG713-Ctr2


title: granulosa cells, normal ovarian reserve, old, No49

description: Library name: NORH49


title: WT_female_quadricep muscle_1


title: WT_female_quadricep muscle_4


title: N2_OP50_22GRNA_Rep2

description:
Library name: N2_OP50_22GRNA_Rep2
small RNAs

value: OP50 (control)


title: JU1171_GFP_RNAi_22GRNA_Rep1

description:
Library name: JU1171_GFP_RNAi_22GRNA_Rep1
small RNAs

value: whole worm

value: mfSi8[mex-5p::ce-GFP(2xNLS, non PATCs introns)::tbb-2 3'UTR + rps-0p::hygromycinR::rps-27 3'UTR] I


title: GbaKOSNCA2_F815

city: Bethesda

first: Hannah

middle: B. D.

last: Duffy

state: MD

address: 10 Center Drive

institute: National Institutes of Health

description:
Library name: Sample 11
KOSyn_Syn.csv
KOSyn_KO.csv
KOSyn_Ctr.csv

data_processing:
Adaptor sequences and low quality reads were filtered out
Reads were mapped to the reference genome (mm10) using Hisat2 v.2.0.5
Reads were counted with featureCounts v.1.5.0-p3
Limma trend was used to perform differential expression analysis
PCA, volcano plots, heat maps were generated in R
Assembly: mm10
Supplementary files format and content: Limma trend output: normalised read counts
Supplementary files format and content: Limma trend output: differential expression analysis

source_name: Brain (one hemisphere)

extract_protocol:
RNA harvested according to the manufacturer's instructions with the Qiagen miRNeasy mini kit
Library prep performed with the NEBNext II RNA Library Prep Kit for Illumina (New England BioLabs Inc.) according to the manufacturer's instructions

value: Brain (one hemisphere)

value: FloxGba, Thy1.2-CreERT2, hSNCAA53T

value: Tamoxifen citrate diet


title: GbaKOSNCA3_F822

description:
Library name: Sample 12
KOSyn_Syn.csv
KOSyn_KO.csv
KOSyn_Ctr.csv


title: granulosa cells, normal ovarian reserve, old, No386

description: Library name: NORH386


title: granulosa cells, normal ovarian reserve, old, No444

description: Library name: NORH444


title: JU1171_GFP_RNAi_22GRNA_Rep2

description:
Library name: JU1171_GFP_RNAi_22GRNA_Rep2
small RNAs

value: GFP RNAi


title: granulosa cells, normal ovarian reserve, old, No377

description: Library name: NORH377


title: N2_OP50_22GRNA_Rep1

description:
Library name: N2_OP50_22GRNA_Rep1
small RNAs


title: GbaKOSNCA1_F062

description:
Library name: Sample 10
KOSyn_Syn.csv
KOSyn_KO.csv
KOSyn_Ctr.csv

value: FloxGba, Thy1.2-CreERT2


title: granulosa cells, normal ovarian reserve, old, No339

description: Library name: NORH339


title: JU775_OP50_22GRNA_Rep2

description:
Library name: JU775_OP50_22GRNA_Rep2
small RNAs

value: mfSi19[mex-5p::ce-GFP(2xNLS, non PATCs introns)::tbb-2 3'UTR + rps-0p::hygromycinR::rps-27 3'UTR] I


title: JU775_OP50_22GRNA_Rep1

description:
Library name: JU775_OP50_22GRNA_Rep1
small RNAs


title: HCT116-3

type: RNA

city: weifang

first: Jiaqiu

last: Li

address: Baotong west street No.7166

institute: shandong second medical university

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human lncRNA Arrays (4x44K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing:
Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The lncRNAs that at least 7 out of 14 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed lncRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. The lncRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed lncRNAs were annotated  in detail with the lncRNA/miRNA interaction information. The lncRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed lncRNAs were annotated  in detail with the lncRNA/miRNA interaction information.
RNA normalized signal intensity

source_name: HCT116 cell

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

growth_protocol: HCT116 and FHC were cultured in McCOY’s 5A medium and DMEM medium supplemented with 10% bovine serum at 37ºC with 5% CO2.

extract_protocol: Total RNA was isolated using Trizol reagent. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: rna types

value: lncRNA and mRNA


title: granulosa cells, normal ovarian reserve, old, No334

description: Library name: NORH334

value: ovarian follicle


title: JU1395_OP50_22GRNA_Rep2

description:
Library name: JU1395_OP50_22GRNA_Rep2
small RNAs


title: GbaKO2_F060

description:
Library name: Sample 8
KOSyn_KO.csv
KO_Ctr.csv


title: HCT116-2


title: GbaKO3_F816

description:
Library name: Sample 9
KOSyn_KO.csv
KO_Ctr.csv


title: HCT116-1


title: FHC-3

source_name: FHC cell

value: FHC


title: granulosa cells, normal ovarian reserve, old, No306

description: Library name: NORH306

value: granulosa cells

value: normal ovarian reserve


title: granulosa cells, normal ovarian reserve, old, No325

description: Library name: NORH325


title: SNCA2_F065

description:
Library name: Sample 5
Syn_Ctr.csv
KOSyn_Syn.csv

value: FloxGba,  hSNCAA53T


title: JU1171_OP50_22GRNA_Rep2

description:
Library name: JU1171_OP50_22GRNA_Rep2
small RNAs


title: SNCA3_F814

description:
Library name: Sample 6
Syn_Ctr.csv
KOSyn_Syn.csv


title: JU1171_OP50_22GRNA_Rep1

description:
Library name: JU1171_OP50_22GRNA_Rep1
small RNAs


title: FHC-2


title: Control rep 2

description: Library name: TorV-MG713-C3

value: mammary gland tumor

value: Epithelial cell

value: Control


title: SNCA1_F064

description:
Library name: Sample 4
Syn_Ctr.csv
KOSyn_Syn.csv


title: JU1395_OP50_22GRNA_Rep1

description:
Library name: JU1395_OP50_22GRNA_Rep1
small RNAs

value: whole worm

value: mfSi27[mex-5p::ce-GFP(2xNLS, non PATCs introns)::tbb-2 3'UTR + rps-0p::hygromycinR::rps-27 3'UTR] I

value: OP50 (control)


title: E. coli, adaptive evolution, 40day, rep2

city: beijing

first: yueting

last: cui

address: xinjiekou street

institute: beijing normal university

description: Library name: WTevo_sample2

data_processing:
Sequencing libraries were subjected to quality control and pooled in appropriate proportions based on effective concentrations to achieve the desired sequencing output.
Raw sequencing data in FASTQ format were initially processed using Fastp (version 0.20.0).
Raw sequencing data in FASTQ format were initially processed using Fastp (version 0.20.0).
Quality metrics including Q20, Q30, and GC content were calculated to assess data quality.
All downstream transcriptomic analyses were conducted on high-quality clean reads. The clean data was mapped to the reference genome (escherichia_coli_k12_gcf_000005845_2_asm584v2) using Bowtie2 (version 2.2.3).
Assembly: reference genome: escherichia_coli_k12_gcf_000005845_2_asm584v2
Supplementary files format and content: Raw sequencing data are provided in compressed FASTQ format (.fq.gz)
Supplementary files format and content: csv files include FPKM values for each Sample

organism: Escherichia coli str. K-12 substr. MG1655

source_name: K-12 substr. MG1655

growth_protocol: E. coli K12 MG1655 was grown in tryptic soy broth at 37 °C

extract_protocol:
Total RNA was extracted from each sample using Trizol, followed by quantifying RNA concentration and purity using a NanoDrop spectrophotometer.
For library construction, ribosomal RNA was removed from total RNA, then precipitated using ethanol (Macklin, Beijing, China). The fragmented RNA served as a template for first-strand cDNA synthesis with random hexamer primers. To ensure strand specificity, second-strand cDNA was synthesized in the presence of deoxyuridine triphosphate (dUTP). Directional libraries were created through steps including end repair, A-tailing, adapter ligation, size selection, PCR amplification, and purification. These libraries were quantified with a Qubit 4 Fluorometer (Thermo Fisher Scientific Inc., USA) and a 7500 Fast Real-Time PCR System (Applied Biosystems, USA), while their size distributions were evaluated on an Agilent 2100 Bioanalyzer.

treatment_protocol: For treatment, the cultures were inoculated into fresh TSB medium with varying sertraline concentrations (0.1, 10, and 40 mg/L). After 24 h, they were transferred to new TSB with the same sertraline levels. TSB passages without sertraline served as controls. The serial passage lasted 40 days, resulting in the sertraline-evolved strain called WTevo.

value: K-12 substr. MG1655

value: adaptive evolution under 40 mg/L sertraline


title: GbaKO1_F059

description:
Library name: Sample 7
KOSyn_KO.csv
KO_Ctr.csv

value: Brain (one hemisphere)

value: Tamoxifen citrate diet


title: granulosa cells, normal ovarian reserve, old, No256

description: Library name: NORH256


title: granulosa cells, normal ovarian reserve, old, No299

description: Library name: NORH299


title: E. coli, adaptive evolution, 40day, rep1

description: Library name: WTevo_sample1


title: Sample_13MA-2_011

city: New Haven

first: Gianfilippo

last: Coppola

state: CT

address: 333 Cedar st

department: Pathology

institute: Yale University

description:
Library name: Sample_13MA-2_011
colname in geneExprMatrix.ctsSVA.csv: Sample_13MA-2_011

data_processing:
nf-core/rnaseq pipeline (v3.18.0)
STAR mapper and Salmon algo were used for quantification
Raw reads filtered by edgeR; filterByExpr
sva Bioconductor package was used to correct for latent variables
Differentially expressed genes were determined using edgeR and trended dispersion was used to estimate biological variance and GLM capability. FDR cut off =0.05
Assembly: GRCm39
Supplementary files format and content: comma separated value

molecule: polyA RNA

source_name: brain

extract_protocol:
RNA was immunoprecipitated using magnetic beads and extracted using Agilent RNAeasy Nanoprep Kit with DNAse treatment per the manufacturers instructions
Library proeparation using commercially available Kapa Library Quant Kit KK4854-07960298001 as per manufacturers instructions

value: brain

value: astrocyte

value: M

value: Males


title: E. coli, adaptive evolution, 40day, rep3

description: Library name: WTevo_sample3


title: E. coli, control,rep3

description: Library name: WT_sample3

value: control


title: FHC-1

value: FHC

value: lncRNA and mRNA


title: Sample_1MA-1_001

description:
Library name: Sample_1MA-1_001
colname in geneExprMatrix.ctsSVA.csv: Sample_1MA-1_001


title: Control3_F823

description:
Library name: Sample 3
Syn_Ctr.csv
KOSyn_Ctr.csv

value: FloxGba


title: Sample_25MA-3_020

description:
Library name: Sample_25MA-3_020
colname in geneExprMatrix.ctsSVA.csv: Sample_25MA-3_020


title: granulosa cells, normal ovarian reserve, old, No152

description: Library name: NORH152

value: ovarian follicle

value: granulosa cells

value: normal ovarian reserve


title: E. coli, control,rep2

description: Library name: WT_sample2


title: granulosa cells, normal ovarian reserve, old, No155

description: Library name: NORH155


title: Control1_F063

description:
Library name: Sample 1
Syn_Ctr.csv
KOSyn_Ctr.csv


title: E. coli, control,rep1

description: Library name: WT_sample1


title: granulosa cells, diminished ovarian reserve, young, No74

description: Library name: DORL74

value: diminished ovarian reserve


title: Sample_7FA-1_007

description:
Library name: Sample_7FA-1_007
colname in geneExprMatrix.ctsSVA.csv: Sample_7FA-1_007

value: F

value: Metestrus


title: Sample_37MA-4_008

description:
Library name: Sample_37MA-4_008
colname in geneExprMatrix.ctsSVA.csv: Sample_37MA-4_008


title: Multiomics, Gls cko, GEX

city: NEW HAVEN

first: Yiting

last: Xu

address: 111 Park St., Apt 9s

description: Library name: Sample 4

library_source: transcriptomic single cell

data_processing:
Analysis was performed using Signac and Seurat.  A multimodal Seurat object was creating with paired transcriptome and ATAC-seq profiles.  Filtering was done to exclude low quality cells.  Doublets were identified with Scrublet.  Maximum thresholds were set as follows: 0.2 for mitochondrial count ratio, 0.05 for hemoglobin count ratio, and 0.1 for blacklist sites count ratio.  Minimum thresholds were set as follows: 15 for fraction of reads in peaks, 2 for transcriptional start site (TSS) enrichment score and 0.65 for complexity score of a cell (log10 of the number of genes per number of UMIs).  Extreme outliers were filtered by dropping cells with fewer than 100 UMIs or more than 10,000 UMIs in both RNA and ATAC.  Peaks were recalculated after filtering using MACS2.  The gene expression data was normalized and mitochondrial variation was regressed out using SCTransform.  Linear dimensional reduction was performed using PCA.  The DNA accessibility assay was normalized using term frequency-inverse document frequency (TF-IDF).  Linear dimensional reduction was performed using singular value decomposition (SVD).  The combined steps of TF-IDF followed by SVD are known as latent semantic indexing (LSI).  Using the weighted nearest neighbor methods in Seurat, we computed a joint neighbor graph that represent both the gene expression and DNA accessibility measurements.  Multimodal clustering was performed using a weighted nearest neighbor approach with the first 50 dimensions of PCA and LSI reductions and using a resolution of 0.8. The resulting clusters were annotated using marker genes identified after using FindAllMarkers function.
Assembly: Mus_musculus.GRCm39
Supplementary files format and content: CellRanger output: Feature_bc_matrix.zip; fragments.tsv.gz

source_name: Skin

extract_protocol:
Wound bed tissue was excised, minced, and digested with a collagenase-containing enzyme mix to obtain a single-cell suspension. After filtration through a 70 µm cell strainer to remove debris, cells were washed. For  permeabilization, cells were treated with DIG lysis buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 3 mM MgCl2, 0.01% Digitonin and 2 U µl−1 of RNase inhibitor) for 5 min on ice, followed by adding 1 ml of chilled DIG wash buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 3 mM MgCl2 and 1 U µl−1 of RNAse inhibitor) and inversion before centrifugation at 500g for 5 min at 4 °C. The supernatant was discarded, and cells were resuspended in DIG wash buffer, followed by counting using trypan blue and a Countess II FL Automated Cell Counter. Cells were processed according to the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression user guide。
Multi-omics library constuction protocol described in Xu. et al.

value: Skin

value: Skin cells

value: Gls cko

tag: library type

value: mRNA


title: granulosa cells, diminished ovarian reserve, young, No72

description: Library name: DORL72


title: Control2_F821

description:
Library name: Sample 2
Syn_Ctr.csv
KOSyn_Ctr.csv

value: Brain (one hemisphere)

value: Tamoxifen citrate diet


title: granulosa cells, diminished ovarian reserve, young, No6

description: Library name: DORL6


title: shBGC823

city: Guiyang City

first: Haiyan

last: Wang

state: Guizhou

address: No. 9, Beijing Road, Yunyan District,

institute: Guizhou Meidical University

description: Library name: sample2

data_processing:
Raw sequencing reads were assessed for quality using FastQC (v0.11.9).
Adapter sequences and low-quality reads were removed using Trim Galore (v0.6.7).
Clean reads were aligned to the human reference genome using STAR (v2.7.10a).
Aligned reads were assigned to genes using featureCounts (v2.0.1).
Gene expression normalization and differential expression analysis were performed using DESeq2 (v1.34.0)
Assembly: GRCh38 (hg38)
Supplementary files format and content: Processed data include gene-level raw count matrices and normalized expression matrices for each sample. Differential expression results are provided as tab-delimited files containing gene symbols, Ensembl IDs, log2 fold changes, P values, and adjusted P values (FDR).

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) following the manufacturer’s instructions.
RNA libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs).

value: Human ovarian cancer cell line

value: CSN3 knockdown


title: Sample_43FA-4_013

description:
Library name: Sample_43FA-4_013
colname in geneExprMatrix.ctsSVA.csv: Sample_43FA-4_013

value: brain

value: astrocyte


title: granulosa cells, diminished ovarian reserve, young, No437

description: Library name: DORL437


title: Sample_67FA-6_001

description:
Library name: Sample_67FA-6_001
colname in geneExprMatrix.ctsSVA.csv: Sample_67FA-6_001


title: Multiomics, Control, ATAC

description: Library name: Sample 1

library_source: genomic single cell

molecule: genomic DNA

value: control

value: ATAC


title: granulosa cells, diminished ovarian reserve, young, No424

description: Library name: DORL424

value: ovarian follicle

value: granulosa cells


title: Sample_31FA-3_002

description:
Library name: Sample_31FA-3_002
colname in geneExprMatrix.ctsSVA.csv: Sample_31FA-3_002


title: HaCaT FLG enhancer knockout RNA-seq, replicate 2

city: Philadelphia

first: Yuanqing

last: Feng

state: Pennsylvania

address: 430 Clinical Research Building, 415 Curie Boulevard

department: Genetics

institute: University of Pennsylvania

description: Library name: FLG-EnKO-2

data_processing:
Raw RNA-seq FASTQ files were retrieved from the Genewiz server. Read quality was assessed using Falco v1.2.5
Adapter sequences and low-quality bases/reads were removed using fastp v1.0.1 with default parameters.
The hg38 reference transcriptome (refMrna.fa.gz) and gene annotation (refGene.txt.gz) were downloaded from the UCSC Genome Browser database. Transcript abundances were quantified using kallisto v0.51.1 with default settings.
Transcript-level estimates were summarized to gene-level counts using tximport v1.38.2, and genes with mean read count < 10 were excluded
ifferential expression was performed using DESeq2 v1.50.2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

growth_protocol: HaCaT human keratinocytes (RRID: CVCL_0038) were used for all experiments. This spontaneously immortalized epidermal keratinocyte line was derived from the skin of a 62-year-old male donor of European ancestry and obtained from Applied Biological Materials Inc. (Cat. No. T9145). Cells were cultured in complete growth medium consisting of Dulbecco’s Modified Eagle Medium (DMEM) with high glucose, L-glutamine, phenol red, and sodium pyruvate (Thermo Fisher, Cat. No. 11995073), supplemented with 10% fetal bovine serum (FBS; Thermo Fisher, Cat. No. A5670701) and 1% Penicillin–Streptomycin (Thermo Fisher, Cat. No. 15140122). Cells were maintained at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
Total RNA was purified from cultured HaCaT cells using Direct-zol RNA Miniprep Kits (Zymo, # R2052) following manufacturer’s instructions, and concentration was determined by Nanodrop 8000 spectrophotometer.
A total of 500 ng RNA was submitted to Genewiz. Briefly, mRNA was selected by Poly(A) enrichment, followed by fragmentation and reverse transcription, and the addition of sequencing adapters and amplification. The final library was sequenced on a NovaSeq X (150bp PE) at a depth of 20 million reads per library.

treatment_protocol: HaCaT cells were subjected to lentiviral CRISPR perturbation to generate FLG enhancer knockout cells and compared to control HaCaT cells. Cells were infected with lentiviruses carrying Cas9 (lentiCRISPR v2; Addgene 52961) and sgRNA (pLKO5 backbone), selected with puromycin, expanded, and harvested for RNA extraction. RNA-seq was performed on biological replicates of each condition. For CRISPR knockout of the FLG enhancer, HaCaT cells were infected with two lentiviruses: Cas9 (lentiCRISPR v2; Addgene, Cat. No. 52961) and sgRNA (pLKO5 backbone). Lentiviruses were produced using HEK293T packaging cells, HaCaT cells were seeded in 24-well plates at 5 × 10⁴ cells/well, allowed to attach for 24 h, and transduced with lentivirus (~10 MOI) in medium containing 8 µg/mL Polybrene (Sigma, Cat. No. H9268). Plates were centrifuged at 1,000 × g for 30 minutes at 32°C to enhance infection efficiency. After 24 h, media were replaced with fresh growth medium containing 2 µg/mL puromycin. Cells were selected for 2 days; medium was changed every 24 hours. Surviving cells were expanded and harvested for RNA extraction.

value: HaCaT

value: Keratinocytes

value: CRISPRKO

value: Enhancer KO


title: Sample_19FA-2_016

description:
Library name: Sample_19FA-2_016
colname in geneExprMatrix.ctsSVA.csv: Sample_19FA-2_016

value: F

value: Metestrus


title: CtrlBGC823

description: Library name: sample1

value: Ctrl

value: siCtrl


title: HaCaT FLG enhancer knockout RNA-seq, replicate 1

description: Library name: FLG-EnKO-1

value: Skin


title: Macrophages, Glscko1, Negative Control

description: Library name: Sample 5

library_source: genomic

data_processing:
Paired reads were trimmed with Trimmomatic for adapters and low quality.  They were then aligned using Bowtie2 with settings --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700 to UCSC's mm10 version of M. musculus. Mitochondrial reads, duplicate reads, and reads with quality score less than 30 were removed. The genome coverage is computed with  bedtools genomecov.  Then the peaks are calculated using SEACR. The negative control was used to generate an empirical threshold. Plus the settings "norm" and "stringent" were set.  In order to perform differential enriched peaks analysis with DESeq2, the fragment counts for each peak region was done with chromVAR's getCounts.  Various deepTools functions constructed the heatmap plots.
Assembly: TxDb.Mmusculus.UCSC.mm10.knownGene
Supplementary files format and content: big.Wig narrow peaks
Library strategy: CUT&Tag

extract_protocol:
Macrophages were isolated from wound bed skin tissue using the anti-F4/80 MicroBeads UltraPure, mouse (Miltenyi Biotec, Catalog #130-110-443) according to the manufacturer’s protocol. Briefly, 6 wounds from 3 mice were pooled for each sample and a total of 6 samples were used for each timepoint. Wound bed tissue was excised, minced, and digested with Collagenase IA and Collagenase II to obtain a single-cell suspension, as previously described. After filtration through a 70-µm cell strainer to remove debris, cells were washed and resuspended in MACS buffer (PBS containing 0.5% BSA and 2 mM EDTA). The single-cell suspension was incubated with anti-F4/80 MicroBeads for 15 minutes at 4°C. Labeled cells were then passed through an LS column (Miltenyi Biotec, Catalog #130-042-401) placed in a magnetic field using the QuadroMACS™ Separator (Miltenyi Biotec, Catalog #130-090-976) with MACS® MultiStand (Miltenyi Biotec, Catalog #130-042-303) according to manufacturer directions.
CUT&Tag libraries were prepared using the CUTANA™ CUT&Tag Kit (Epicypher, SKU: 14-1102) following the manufacturer’s instructions

value: Macrophages

value: Negative Control


title: HaCaT FLG enhancer knockout RNA-seq, replicate 3

description: Library name: FLG-EnKO-3


title: Multiomics, Control, GEX

description: Library name: Sample 3

value: Skin cells

value: mRNA


title: Sample_21-CTX_274_303

description:
Library name: Sample_21-CTX_274_303
colname in geneExprMatrix.ctsSVA.csv: Sample_21-CTX_274_303

value: brain

value: astrocyte


title: granulosa cells, diminished ovarian reserve, young, No423

description: Library name: DORL423

value: ovarian follicle

value: diminished ovarian reserve


title: granulosa cells, diminished ovarian reserve, young, No349

description: Library name: DORL349

value: granulosa cells


title: Macrophages, Glscko2, Negative Control

description: Library name: Sample 6


title: HaCaT control RNA-seq, replicate 3

description: Library name: FLG-con3

value: HaCaT

value: Keratinocytes

value: CRISPRKO-Control

value: Control


title: Sample_20-CTX_286_291

description:
Library name: Sample_20-CTX_286_291
colname in geneExprMatrix.ctsSVA.csv: Sample_20-CTX_286_291

value: F

value: Pro-Day


title: Macrophages, ctrl1, Negative Control

description: Library name: Sample 4


title: HaCaT control RNA-seq, replicate 2

description: Library name: FLG-con2


title: granulosa cells, diminished ovarian reserve, young, No322

description: Library name: DORL322


title: Sample_19-CTX_203_374

description:
Library name: Sample_19-CTX_203_374
colname in geneExprMatrix.ctsSVA.csv: Sample_19-CTX_203_374

value: Estrus


title: Macrophages, Glscko2, H3K4me3

description: Library name: Sample 3

value: Skin


title: HaCaT control RNA-seq, replicate 1

description: Library name: FLG-con1


title: Macrophages, Glscko1, H3K4me3

description: Library name: Sample 2

value: Macrophages


title: granulosa cells, diminished ovarian reserve, young, No318

description: Library name: DORL318


title: Sample_16-CTX_239_338

description:
Library name: Sample_16-CTX_239_338
colname in geneExprMatrix.ctsSVA.csv: Sample_16-CTX_239_338


title: Sample_17-CTX_227_350

description:
Library name: Sample_17-CTX_227_350
colname in geneExprMatrix.ctsSVA.csv: Sample_17-CTX_227_350


title: granulosa cells, diminished ovarian reserve, young, No301

description: Library name: DORL301


title: Sample_13-CTX_263_314

description:
Library name: Sample_13-CTX_263_314
colname in geneExprMatrix.ctsSVA.csv: Sample_13-CTX_263_314


title: Jurkat, sgRNA3, 2h TRAIL, No 4sU, biol rep 3

city: Berkeley

first: Britt

last: Glaunsinger

state: California

address: RM 565, 1951 Oxford St

department: PMB

institute: University of California, Berkeley

description:
Library name: Sample 24
Ribodepleted RNA, ERCC spike-in.

library_source: other

data_processing:
Data was preprocessed (PhiX removal, deduplication, N-remover, adaptor trimming, etc.) using the standard HTStream version 1.3.0 workflow
Human GRCh38.p13, ERCC Spike-In genomes were concatenated and indexed using STAR version 2.7.1a. Gencode annotation v43 were used.
Preprocessed reads were aligned with STAR version 2.7.1a and counts tables were exported for bulk RNA
Separately, the same genome and annotation was prepared for GRAND-SLAM analysis with gedi and mapped using GRAND-SLAM default parameters to generate a counts table for nascent transcripts by multiplying total counts by the nascent-to-total ratio MAP statistic.
Assembly: Human genome GRCh38.p13 + Gencode v43; ERCC Spike-In sequences (Invitrogen)
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample bulk RNA
Supplementary files format and content: Tab-delimited text file includes nascent RNA count estimates from GRAND-SLAM for nascent RNA from 4sU-containing samples.
Supplementary files format and content: Tab-delimited text file includes ERCC spike-in counts for 4sU-containing samples.

molecule: other

source_name: Jurkat

growth_protocol: Jurkat cells base-edited for at least 10 days with ABE8e base editor RNA and indicated sgRNA pools were maintained in RPMI 1640 media (Gibco) supplemented with 10% Tet-free fetal bovine serum, 1X GlutaMAX (Gibco), 1x Pen-Strep (Gibco) and 1 mM sodium pyruvate (Gibco)  in a humidified chamber at 37℃ and 5% CO2. Cells were kept at densities between 0.5-2x10^6 cells/mL.

extract_protocol:
2 h post-TRAIL treatment, total RNA was extracted in the dark using TRIzol (Invitrogen) and phenol-chloroform extraction. ERCC Spike-In (Invitrogen) and mixed 4sU unlabelled/labelled spike-in was added. RNA was then alkylated, DNase-treated, and cleaned. General protocol from Lexogen's SLAM-seq Anabolic labelling kit.
RNA libraries for SLAM-seq/RNA-seq were prepared using KAPA RNA Hyperprep Kit with RiboErase (HMR) with KAPA Unique Dual Index Adaptors according to the manufacturer's protocols and include ERCC Spike-In mix for normalization. Sequencing on NovaSeq X Plus 25B.

treatment_protocol: SLAM-sequencing was performed: Each Jurkat genotype/guide pool was treated with 250 ng/mL SUPERKILLER TRAIL ligand (Enzo) or mock diluant for 2 h. 300 uM of 4-thiouridine (4sU) was also added simultaneously to all samples to label nascent RNA synthesized before the harvesting endpoint of 2 h (except those indicated No 4sU as a control).

value: Jurkat

value: Immortalized T cell lymphocyte

tag: genotype/sgrna/sgrna code

tag: replicate

value: 2h TRAIL

value: No 4sU


title: Jurkat, sgRNA3, 2h Mock,No  4sU, biol rep 3

description:
Library name: Sample 23
Ribodepleted RNA, ERCC spike-in.

value: 2h Mock


title: granulosa cells, diminished ovarian reserve, young, No3

description: Library name: DORL3

value: ovarian follicle


title: granulosa cells, diminished ovarian reserve, young, No324

description: Library name: DORL324

value: diminished ovarian reserve


title: Jurkat, sgRNA3, 2h TRAIL, 4sU, biol rep 3

description:
Library name: Sample 22
Ribodepleted RNA, ERCC spike-in.


title: granulosa cells, diminished ovarian reserve, young, No295

description: Library name: DORL295

value: granulosa cells


title: Macrophages, ctrl1, H3K4me3

description: Library name: Sample 1


title: Sample_12-CTX_275_302

description:
Library name: Sample_12-CTX_275_302
colname in geneExprMatrix.ctsSVA.csv: Sample_12-CTX_275_302

value: brain

value: astrocyte


title: Sample_11-CTX_287_290

description:
Library name: Sample_11-CTX_287_290
colname in geneExprMatrix.ctsSVA.csv: Sample_11-CTX_287_290


title: granulosa cells, diminished ovarian reserve, young, No290

description: Library name: DORL290


title: Jurkat, sgRNA3, 2h Mock, 4sU, biol rep 3

description:
Library name: Sample 21
Ribodepleted RNA, ERCC spike-in.


title: 11566-JG-22

city: Nashville

first: Matthew

middle: A

last: Cottam

state: TN

address: 2301 Vanderbilt Place

department: Surgical Sciences

institute: Vanderbilt University Medical Center

description:
Library name: 11566-JG-22
Single Cell RNAseq of C57Bl/6J mice: CD70KO; Lean; Adipose Tissue

data_processing:
Raw reads were processed using CellRanger v7.1.0
Droplets were detected and filtered using DropKick.
Ambient RNA was corrected using SoupX
Doublets were detected and filtered using scDblFinder
Transcript counts were normalized using Seurat::NormalizeData with default settings
Samples were integrated using harmony to correct for batch effects.
Assembly: GRCm39-2024-A
Supplementary files format and content: data_integrated.rds; Seurat object for integrated and batch corrected data.

source_name: Adipose

growth_protocol: Mice were maintained on low fat or high fat diet for 27 weeks before immune cells were extracted from the epididymal adipose tissue.

extract_protocol:
Epididymal AT depots were excised, minced and digested in 6 mL of collagenase for 30 min at 37°C. For flow cytometry applications AT was digested in 2 mg/mL type II collagenase (Sigma C6885; St. Louis, MO) and for single cell applications AT was digested in 2 mg/mL type IV collagenase (Worthington LS004189; Lakewood, NJ, USA). Digested AT was then vortexed, filtered through 100 mm filters, lysed with ACK buffer and filtered through 35 mm filters. The SVF was incubated with anti-mouse Fc Block (BD Biosciences) at 1:200 for 10 min. For animals in obese and WC groups, the CD45+ fraction of the epididymal AT was isolated for scRNAseq. Cells from each mouse were labeled with unique hashtag antibodies (1:200) (Biolegend TotalSeq-C) and anti-CD45 microbeads (10 μL/ sample) (Miltenyi #130-110-608). Biological replicates were pooled and sorted on a manual Miltenyi OctoMACS Separator. CD45+ cells were then labeled for CITE-sequencing using TotalSeq-C antibodies (Biolegend) for cell surface markers to identify major cell types. All immunolabeling was completed at a 1:200 dilution for 20 min at 4°C in the dark. Next, cells were stained with 0.25 μg/mL DAPI for FACS sorting and DAPI- viable cells were collected for downstream processing and sequencing. All samples from the obese and WC groups were submitted and processed for sequencing on the same day to minimize batch effects. Another round of single cell sequencing was performed on CD45+ cells isolated from the epididymal AT of lean and WL animals. The same procedure for isolating the SVF was followed as described above however, SVF was stained with CD45 (1:200) (Biolegend; clone 30-F11; catalogue #: 103137) antibody and 0.25 μg/mL DAPI. The live CD45+ cells were isolated by gating on the DAPI- CD45+ fraction on the 4-laser FACSAria III, Bioprotect IV Baker Hood Enclosure. Furthermore, in the WL AT, SVF was also stained with CD4+ (1:200) (Biolegend clone RM4-4; catalogue #: 116022) and CD8+ (1:200) (Biolegend clone 53-6.7; catalogue#: 100707) antibody. Following the DAPI- CD45+ sort, sample was also sorted for DAPI-, CD45+, CD8+, CD4+ cells.
Sample preparation for obese and weight cycled samples was conducted using the 5’ assay for the 10X Chromium platform (10X Genomics) targeting 20,000 cells per diet group. In all, 50,000 reads per cell were targeted for PE-150 sequencing on an Illumina NovaSeq6000. The Chromium Next GEM Single Cell 5’ HT v2 kit from 10X Genomics was implemented for both lean and WL samples and run on the NovaSeq 6000. All samples were run at the VUMC VANTAGE core facility.

treatment_protocol: Mice were maintained on WT or CD70-/- background.

value: Adipose

value: KO

tag: diet

value: Lean


title: 11566-JG-21

description:
Library name: 11566-JG-21
Single Cell RNAseq of C57Bl/6J mice: CD70KO; Lean; Adipose Tissue


title: 11566-JG-23

description:
Library name: 11566-JG-23
Single Cell RNAseq of C57Bl/6J mice: CD70KO; Lean; Adipose Tissue


title: 11566-JG-24

description:
Library name: 11566-JG-24
Single Cell RNAseq of C57Bl/6J mice: CD70KO; Lean; Adipose Tissue


title: Sample_10-CTX_204_373

description:
Library name: Sample_10-CTX_204_373
colname in geneExprMatrix.ctsSVA.csv: Sample_10-CTX_204_373

value: F

value: Metestrus


title: granulosa cells, diminished ovarian reserve, young, No286

description: Library name: DORL286


title: Jurkat, sgRNA2, 2h Mock, 4sU, biol rep 3

description:
Library name: Sample 19
Ribodepleted RNA, ERCC spike-in.

value: TFIIB D207G/D207G-#2/sgRNA2


title: 11566-JG-20

description:
Library name: 11566-JG-20
Single Cell RNAseq of C57Bl/6J mice: Wild-type; Lean; Adipose Tissue

value: WT


title: Multiomics, Gls cko, ATAC

description: Library name: Sample 2

value: Skin

value: Skin cells

value: Gls cko

value: ATAC


title: Sample_8-CTX_216_361

description:
Library name: Sample_8-CTX_216_361
colname in geneExprMatrix.ctsSVA.csv: Sample_8-CTX_216_361


title: granulosa cells, diminished ovarian reserve, young, No285

description: Library name: DORL285


title: Jurkat, sgRNA1, 2h TRAIL, 4sU, biol rep 3

description:
Library name: Sample 18
Ribodepleted RNA, ERCC spike-in.

value: Jurkat

value: Immortalized T cell lymphocyte

value: TFIIB D207G/D207G-#1/sgRNA1

value: 2h TRAIL


title: 11566-JG-19

description:
Library name: 11566-JG-19
Single Cell RNAseq of C57Bl/6J mice: Wild-type; Lean; Adipose Tissue


title: Jurkat, sgRNA2, 2h TRAIL, 4sU, biol rep 3

description:
Library name: Sample 20
Ribodepleted RNA, ERCC spike-in.


title: Jurkat, sgRNA1, 2h Mock, 4sU, biol rep 3

description:
Library name: Sample 17
Ribodepleted RNA, ERCC spike-in.

value: 2h Mock


title: Luminal-induced_Upk2 [BLA_1108_S6]

city: Santa Cruz

last: Chu

address: 1156 High Street

department: MCD Biology

institute: University of California, Santa Cruz

description:
Library name: BLA_1108_S6
10x Genomics

data_processing:
Demultiplexing of samples was performed at the UC Davis Genomics Core. Barcode processing, gene alignment and couting was done using STARSolo (https://doi.org/10.1101/2021.05.05.442755)
Assembly: Mouse mm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bladder Urothelium

extract_protocol:
For collection of 13-month Bas-induce and Lum-induce bladder tumor cells, the urothelium was separated from the muscle layer using tweezers, and tumor lesions were identified based on GFP signal under a fluorescent microscope and excised from the  epithelium with a scalpel before being transferred to a Collagenase/Hydrogenase digestion solution (F12/MEMD + 4.5%FBS + 10%C/H) to obtain single cell suspension.
Library preparation was performed using 10x Genomics Chromium Single Cell 3’ Solution with v3.1 chemistry following the manufacturer’s protocol (10x Genomics). The library  purity, size, and quantity were validated by capillary electrophoresis using 2,100  Bioanalyzer (Agilent Technologies).

treatment_protocol: Mice were tamoxifen-induced at 7-week of age, and the bladder was delivered with plasmids expressing Pten and Trp53 sgRNAs by electroporation 2 weeks later.

value: Bladder Urothelium

value: Upk2-CreERT2; R26-LSL-Cas9-eGFP

value: Tamoxifen induced, bladder electroporation with Pten and Trp53 gRNA plasmid


title: 11566-JG-18

description:
Library name: 11566-JG-18
Single Cell RNAseq of C57Bl/6J mice: Wild-type; Lean; Adipose Tissue

value: Adipose

value: Lean


title: granulosa cells, diminished ovarian reserve, young, No254

description: Library name: DORL254

value: ovarian follicle

value: granulosa cells

value: diminished ovarian reserve


title: Luminal-induced_Upk2 [BLA_7838_S4]

description:
Library name: BLA_7838_S4
10x Genomics


title: Jurkat, sgRNA3, 2h TRAIL, No 4sU, biol rep 2

description:
Library name: Sample 16
Ribodepleted RNA, ERCC spike-in.

value: No 4sU


title: 11566-JG-16

description:
Library name: 11566-JG-16
Single Cell V(D)J Sequencing of C57Bl/6J mice: CD70KO; Weight Loss; Adipose Tissue

data_processing:
Raw reads were processed using CellRanger v7.1.0
Droplets were detected and filtered using DropKick.
Ambient RNA was corrected using SoupX
Doublets were detected and filtered using scDblFinder
Transcript counts were normalized using Seurat::NormalizeData with default settings
Samples were integrated using harmony to correct for batch effects.
Assembly: GRCm39-2024-A
Supplementary files format and content: data_integrated.rds; Seurat object for integrated and batch corrected data.
Library strategy: TCR-Seq

value: KO

value: Weight loss


title: 11566-JG-17

description:
Library name: 11566-JG-17
Single Cell RNAseq of C57Bl/6J mice: Wild-type; Lean; Adipose Tissue

value: WT


title: Luminal-induced_Upk2 [BLA_7828_S5]

description:
Library name: BLA_7828_S5
10x Genomics


title: granulosa cells, diminished ovarian reserve, young, No242

description: Library name: DORL242


title: 11566-JG-15

description:
Library name: 11566-JG-15
Single Cell V(D)J Sequencing of C57Bl/6J mice: CD70KO; Weight Loss; Adipose Tissue


title: granulosa cells, diminished ovarian reserve, young, No270

description: Library name: DORL270


title: Jurkat, sgRNA3, 2h Mock,No  4sU, biol rep 2

description:
Library name: Sample 15
Ribodepleted RNA, ERCC spike-in.

value: Jurkat


title: Jurkat, sgRNA3, 2h TRAIL, 4sU, biol rep 2

description:
Library name: Sample 14
Ribodepleted RNA, ERCC spike-in.

value: Immortalized T cell lymphocyte


title: Basal-induced_CK5 [BLA_7843_S2]

description:
Library name: BLA_7843_S2
10x Genomics

value: CK5-CreERT2; R26-LSL-Cas9-eGFP


title: granulosa cells, diminished ovarian reserve, young, No247

description: Library name: DORL247


title: granulosa cells, diminished ovarian reserve, young, No2

description: Library name: DORL2


title: Basal-induced_CK5 [BLA_1229_S8]

description:
Library name: BLA_1229_S8
10x Genomics


title: Jurkat, sgRNA3, 2h Mock, 4sU, biol rep 2

description:
Library name: Sample 13
Ribodepleted RNA, ERCC spike-in.


title: Jurkat, sgRNA2, 2h TRAIL, 4sU, biol rep 2

description:
Library name: Sample 12
Ribodepleted RNA, ERCC spike-in.

value: TFIIB D207G/D207G-#2/sgRNA2

value: 2h TRAIL


title: 11566-JG-14

description:
Library name: 11566-JG-14
Single Cell V(D)J Sequencing of C57Bl/6J mice: CD70KO; Weight Loss; Adipose Tissue


title: Basal-induced_CK5 [BLA_1228_S7]

description:
Library name: BLA_1228_S7
10x Genomics

value: Bladder Urothelium


title: granulosa cells, diminished ovarian reserve, young, No20

description: Library name: DORL20


title: granulosa cells, diminished ovarian reserve, young, No17

description: Library name: DORL17


title: 11566-JG-11

description:
Library name: 11566-JG-11
Single Cell V(D)J Sequencing of C57Bl/6J mice: Wild-type; Weight Loss; Adipose Tissue


title: Macrophages, Glscko3

description: Library name: Sample 6

data_processing:
Paired reads were trimmed with Trimmomatic for adapters and low quality.
Trimmed sequence reads were aligned using Star to the mouse genome Mus_musculus.GRCm39.
Mapped reads to genomic features were summarized by featureCounts
The differential gene expression analysis was performed with DeSeq2
The significant results used cutoffs of adjusted p-value of 0.05 and log2 fold change of +/-1
Assembly: Mus_musculus.GRCm39
Supplementary files format and content: Tab-delimited text file including raw counts for each sample

extract_protocol:
Macrophages were isolated from wound bed skin tissue using the anti-F4/80 MicroBeads UltraPure, mouse (Miltenyi Biotec, Catalog #130-110-443) according to the manufacturer’s protocol. Briefly, 6 wounds from 3 mice were pooled for each sample and a total of 6 samples were used for each timepoint. Wound bed tissue was excised, minced, and digested with Collagenase IA and Collagenase II to obtain a single-cell suspension, as previously described. After filtration through a 70-µm cell strainer to remove debris, cells were washed and resuspended in MACS buffer (PBS containing 0.5% BSA and 2 mM EDTA). The single-cell suspension was incubated with anti-F4/80 MicroBeads for 15 minutes at 4°C. Labeled cells were then passed through an LS column (Miltenyi Biotec, Catalog #130-042-401) placed in a magnetic field using the QuadroMACS™ Separator (Miltenyi Biotec, Catalog #130-090-976) with MACS® MultiStand (Miltenyi Biotec, Catalog #130-042-303) according to manufacturer directions.
RNA was harvested using RNeasy mini plus kit (Qiagen)

value: Skin

value: Macrophages

tag: time point

value: day 3 post injury


title: Macrophages, Glscko2

description: Library name: Sample 5

tag: tissue


title: granulosa cells, diminished ovarian reserve, young, No16

description: Library name: DORL16


title: Jurkat, sgRNA2, 2h Mock, 4sU, biol rep 2

description:
Library name: Sample 11
Ribodepleted RNA, ERCC spike-in.

tag: cell line

value: 2h Mock


title: 11566-JG-13

description:
Library name: 11566-JG-13
Single Cell V(D)J Sequencing of C57Bl/6J mice: CD70KO; Weight Loss; Adipose Tissue

value: Adipose


title: Jurkat, sgRNA1, 2h TRAIL, 4sU, biol rep 2

description:
Library name: Sample 10
Ribodepleted RNA, ERCC spike-in.

tag: cell type

value: TFIIB D207G/D207G-#1/sgRNA1


title: Macrophages, Glscko1

description: Library name: Sample 4


title: 11566-JG-10

description:
Library name: 11566-JG-10
Single Cell V(D)J Sequencing of C57Bl/6J mice: Wild-type; Weight Loss; Adipose Tissue


title: 11566-JG-9

description:
Library name: 11566-JG-9
Single Cell V(D)J Sequencing of C57Bl/6J mice: Wild-type; Weight Loss; Adipose Tissue


title: Jurkat, sgRNA1, 2h Mock, 4sU, biol rep 2

description:
Library name: Sample 9
Ribodepleted RNA, ERCC spike-in.

tag: treatment


title: Jurkat, sgRNA3, 2h TRAIL, No 4sU, biol rep 1

description:
Library name: Sample 8
Ribodepleted RNA, ERCC spike-in.


title: granulosa cells, diminished ovarian reserve, young, No156

description: Library name: DORL156

value: ovarian follicle

value: granulosa cells

value: diminished ovarian reserve


title: 11566-JG-7

description:
Library name: 11566-JG-7
Single Cell RNAseq of C57Bl/6J mice: CD70KO; Weight Loss; Adipose Tissue

value: KO

value: Weight loss

tag: batch


title: granulosa cells, diminished ovarian reserve, young, No127

description: Library name: DORL127


title: granulosa cells, diminished ovarian reserve, old, No8

description: Library name: DORH8


title: Macrophages, ctrl3

description: Library name: Sample 3

tag: genotype

value: control


title: Macrophages, ctrl2

description: Library name: Sample 2


title: Jurkat, sgRNA3, 2h Mock, 4sU, biol rep 1

description:
Library name: Sample 5
Ribodepleted RNA, ERCC spike-in.

value: Jurkat

value: Immortalized T cell lymphocyte


title: 11566-JG-6

description:
Library name: 11566-JG-6
Single Cell RNAseq of C57Bl/6J mice: CD70KO; Weight Loss; Adipose Tissue


title: Jurkat, sgRNA3, 2h TRAIL, 4sU, biol rep 1

description:
Library name: Sample 6
Ribodepleted RNA, ERCC spike-in.

value: No 4sU


title: Jurkat, sgRNA3, 2h Mock, No 4sU, biol rep 1

description:
Library name: Sample 7
Ribodepleted RNA, ERCC spike-in.


title: Macrophages, D3e

description:
Library name: Sample 8
D3e_S7

value: isolated from mouse wounds day 3 post injury


title: granulosa cells, diminished ovarian reserve, old, No73

description: Library name: DORH73


title: 11566-JG-8

description:
Library name: 11566-JG-8
Single Cell RNAseq of C57Bl/6J mice: CD70KO; Weight Loss; Adipose Tissue


title: 11566-JG-5

description:
Library name: 11566-JG-5
Single Cell RNAseq of C57Bl/6J mice: CD70KO; Weight Loss; Adipose Tissue


title: Macrophages, ctrl1

description: Library name: Sample 1


title: granulosa cells, diminished ovarian reserve, old, No448

description: Library name: DORH448


title: 11566-JG-4

description:
Library name: 11566-JG-4
Single Cell RNAseq of C57Bl/6J mice: Wild-type; Weight Loss; Adipose Tissue

value: WT


title: granulosa cells, diminished ovarian reserve, old, No65

description: Library name: DORH65


title: Macrophages, D3c

description:
Library name: Sample 6
D3c_S5

value: Skin


title: granulosa cells, diminished ovarian reserve, old, No438

description: Library name: DORH438


title: Macrophages, D3d

description:
Library name: Sample 7
D3d_S6

value: Macrophages


title: Jurkat, sgRNA2, 2h Mock, 4sU, biol rep 1

description:
Library name: Sample 3
Ribodepleted RNA, ERCC spike-in.

value: TFIIB D207G/D207G-#2/sgRNA2


title: Jurkat, sgRNA2, 2h TRAIL, 4sU, biol rep 1

description:
Library name: Sample 4
Ribodepleted RNA, ERCC spike-in.

value: 2h TRAIL


title: Jurkat, sgRNA1, 2h TRAIL, 4sU, biol rep 1

description:
Library name: Sample 2
Ribodepleted RNA, ERCC spike-in.


title: Jurkat, sgRNA1, 2h Mock, 4sU, biol rep 1

description:
Library name: Sample 1
Ribodepleted RNA, ERCC spike-in.

value: 2h Mock


title: granulosa cells, diminished ovarian reserve, old, No435

description: Library name: DORH435


title: Macrophages, D3b

description:
Library name: Sample 5
D3b_S4


title: 11566-JG-2

description:
Library name: 11566-JG-2
Single Cell RNAseq of C57Bl/6J mice: Wild-type; Weight Loss; Adipose Tissue

value: Adipose


title: granulosa cells, diminished ovarian reserve, old, No434

description: Library name: DORH434

value: ovarian follicle


title: Macrophages, D3a

description:
Library name: Sample 4
D3a_S3


title: 9213-HCF-4_TCR

description:
Library name: 9213-HCF-4_TCR
Single Cell RNAseq of C57Bl/6J mice: CD70KO; Obese; Adipose Tissue

value: Obese


title: granulosa cells, diminished ovarian reserve, old, No429

description: Library name: DORH429

value: granulosa cells

value: diminished ovarian reserve


title: Macrophages, D1c

description:
Library name: Sample 3
D1c_S10

value: isolated from mouse wounds day 1 post injury


title: Macrophages, D1b

description:
Library name: Sample 2
D1b_S2


title: 11566-JG-1

description:
Library name: 11566-JG-1
Single Cell RNAseq of C57Bl/6J mice: Wild-type; Weight Loss; Adipose Tissue

value: Weight loss


title: granulosa cells, diminished ovarian reserve, old, No431

description: Library name: DORH431


title: 9213-HCF-3_TCR

description:
Library name: 9213-HCF-3_TCR
Single Cell RNAseq of C57Bl/6J mice: Wild-type; Obese; Adipose Tissue


title: HAP1_wt_1

city: Chicago

first: Gemma

last: Carvill

state: IL

address: 303 E Chicago, Ward 9-183

department: Neurology

institute: Northwestern University

description: Library name: exon21-B4

data_processing:
nf-core/rnaseq v3.18.0
Reads aligned with STAR and quantified using RSEM
Assembly: hg38
Supplementary files format and content: tsv files containing gene counts and TPM for each sample

extract_protocol:
RNA was harvested using TRIzol reagent (15596026), extracting the aqueous phase and purifying the RNA using Zymo RNA Clean & Concentrator-25 (R1017)
RNA libraries for RNAseq were constructed with the mRNA library prep kit per manufacturers protocols

value: engineered haploid cell line derived  from chronic myeloid leukemia (CML) patient's KBM-7 leukemia cell line

value: wildtype

tag: edit

value: no edit


title: Macrophages, D1a

description:
Library name: Sample 1
D1a_S1


title: 11566-JG-3

description:
Library name: 11566-JG-3
Single Cell RNAseq of C57Bl/6J mice: Wild-type; Weight Loss; Adipose Tissue


title: HAP1_path_8

description: Library name: exon21_A2

value: pathogenic


title: HAP1_wt_3

description: Library name: exon21_A5


title: granulosa cells, diminished ovarian reserve, old, No425

description: Library name: DORH425


title: HAP1_path_9

description: Library name: exon21_B5


title: Stacc_FGO_KO_2

city: Nanning

first: liu

last: shaoyuan

address: Guangxi province of china

institute: Guangxi university

description:
Library name: Stacc_seq_8
Stacc-seq

data_processing:
Raw reads were removed adapters and low-quality fragments using Trim-galore (version 0.6.7). The paired-end Stacc–seq reads were aligned to the mouse genome (mm10) with the parameters: -local --very-sensitive-local --phred33 --no-unal by Bowtie2 (version 2.3.5.1). All unmapped reads, on-uniquely mapped reads and PCR duplicates were removed by using the Samtlools (version 1.9) and Sambamba (version 0.7.1). For downstream analysis, we normalized the read counts by computing the number of reads per kilobase of bin per million reads sequenced (RPKM) and generate bigwig files by deeTools (version 3.5.1) with the parameters: bamCoverage -bs 10 --effectiveGenomeSize mm10 --normalizeUsing RPKM using merged replicate bam files.
Assembly: mm10
Supplementary files format and content: bw

source_name: oocyte

extract_protocol:
Antibody and Hyperactive pAG-Tn5 Transposon (Vazyme, S614-01) complexes were prepared 20 minutes prior to the sample lysis step. One microlitre fully dissolved 5% digitonin (Sigma, D141) was added to 1 ml buffer 1 (10 mM Tris-HCl pH = 7.4, 150 mM NaCl, 0.5 mM spermidine, 1 × EDTA-free Roche complete protease inhibitor) to prepare DB-1 buffer. Seven microlitres of DB-1 buffer, 0.5 μl pAG–Tn5, and 0.5 μg antibody were added to a 200-μl low-binding tube and mixed by vortex. The mixture was incubated at 4 °C for 30 min. At the same time samples were transfer from the culture medium to wash buffer (DNase/RNase-free 0.01% BSA) with three washes and collected in DNA-lowing binding tubes (Each sample contains 50 oocytes)
After removing the zona pellucida the samples were lysed in DB-1 buffer at 4℃ on the Thermo Mixer (TS100) at 500 rpm for 10 minutes, with vortexing every 2.5 minutes, three times. Thirty-five microlitres of DB-1 buffer, the pA/G–Tn5 mixture and 12.5 μl pre-warmed (37 °C) 5 × TTBL (Vazyme, TD502) were added into the resulting samples and then incubated in an Eppendorf Thermo mixer at 37 °C for 30 min at 400 rpm. Followed by the addition of 2 μl of 10% SDS and 40 ng of carrier RNA to the reacted samples in an Eppendorf Thermo Mixer at 55 °C for 30 minutes at 400 rpm. DNA was purified by 2x AMPure beads (Beckman, A63882). Then PCR was performed to amplify the libraries (Vazyme, TD601) using the following PCR conditions: 72 °C for 3 min; 98 °C for 30 s; thermocycling for 16 cycles at 98 °C for 15 s, 60 °C for 30 s and 72 °C for 3 min; followed by 72 °C for 5 min. After the PCR reaction, libraries were purified using 0.4×–1.7× AMPure beads (Beckman, A63882) for size selection and were subjected to next-generation sequencing.

value: oocyte


title: granulosa cells, diminished ovarian reserve, old, No428

description: Library name: DORH428


title: 9213-HCF-2_TCR

description:
Library name: 9213-HCF-2_TCR
Single Cell RNAseq of C57Bl/6J mice: CD70KO; Weight Cycled; Adipose Tissue

value: Weight cycled


title: HAP1_path_7

description: Library name: exon16_C6


title: 9213-HCF-1_TCR

description:
Library name: 9213-HCF-1_TCR
Single Cell RNAseq of C57Bl/6J mice: Wild-type; Weight Cycled; Adipose Tissue

value: WT


title: granulosa cells, diminished ovarian reserve, old, No42

description: Library name: DORH42


title: Stacc_FGO_KO_1

description:
Library name: Stacc_seq_7
Stacc-seq


title: Stacc_FGO_WT_2

description:
Library name: Stacc_seq_6
Stacc-seq


title: granulosa cells, diminished ovarian reserve, old, No36

description: Library name: DORH36


title: 9213-HCF-3

description:
Library name: 9213-HCF-3
Single Cell RNAseq of C57Bl/6J mice: Wild-type; Obese; Adipose Tissue

data_processing:
Raw reads were processed using CellRanger v7.1.0
Droplets were detected and filtered using DropKick.
Ambient RNA was corrected using SoupX
Doublets were detected and filtered using scDblFinder
Transcript counts were normalized using Seurat::NormalizeData with default settings
Samples were integrated using harmony to correct for batch effects.
Assembly: GRCm39-2024-A
Supplementary files format and content: data_integrated.rds; Seurat object for integrated and batch corrected data.
Library strategy: CITE-seq


title: 9213-HCF-4

description:
Library name: 9213-HCF-4
Single Cell RNAseq of C57Bl/6J mice: CD70KO; Obese; Adipose Tissue


title: HAP1_path_6

description: Library name: exon16_C4


title: Stacc_FGO_WT_1

description:
Library name: Stacc_seq_5
Stacc-seq


title: granulosa cells, diminished ovarian reserve, old, No353

description: Library name: DORH353

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Paired-end clean reads were aligned to mm10 using Hisat2 (v2.0.5). FeatureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene.
Assembly: hg38
Supplementary files format and content: xlsx file include raw counts for each sample


title: 9213-HCF-1

description:
Library name: 9213-HCF-1
Single Cell RNAseq of C57Bl/6J mice: Wild-type; Weight Cycled; Adipose Tissue


title: HAP1_path_5

description: Library name: exon16_B3


title: Stacc_GO_WT_2

description:
Library name: Stacc_seq_4
Stacc-seq


title: HAP1_path_4

description: Library name: exon16_B2


title: HAP1_path_3

description: Library name: exon16_B1


title: granulosa cells, diminished ovarian reserve, old, No335

description: Library name: DORH335


title: EMPP_Lmo4_rep3

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: Weatheral Institute of Molecular Medicine

data_processing:
Adaptor sequences were removed from fastq file using Trim Galore ! (version 0.6.5)
Reads were quantified with Salmon (version 1.2.0)
Assembly: mm10
Supplementary files format and content: tab-delimited text file including raw counts for each sample

source_name: Bone marrow cells

extract_protocol:
SMART-seq 2 based protocol
Dual index Nextera

value: Bone marrow cells

value: EMPP


title: Stacc_GO_WT_1

description:
Library name: Stacc_seq_3
Stacc-seq


title: granulosa cells, diminished ovarian reserve, old, No333

description: Library name: DORH333


title: Stacc_NGO_WT_2

description:
Library name: Stacc_seq_2
Stacc-seq


title: granulosa cells, diminished ovarian reserve, old, No327

description: Library name: DORH327


title: HAP1_path_2

description: Library name: exon21-D3


title: EMPP_Lmo4_rep1


title: Stacc_NGO_WT_1

description:
Library name: Stacc_seq_1
Stacc-seq


title: HAP1_path_1

description: Library name: exon37-D2


title: granulosa cells, diminished ovarian reserve, old, No326

description: Library name: DORH326


title: EMPP_Ctrl_rep3

value: Ctrl


title: ATAC_FGO_KO_2

description:
Library name: ATAC_seq_4
ATAC-seq

extract_protocol:
Each sample contains 50 oocytes collected from mated female mice at 44 hours after PMSG injection. Oocytes were washed with DNase/RNase-free 0.01% BSA and collected in DNA-lowing binding tubes. Lysis buffer (0.05% digitonin, 0.5% NP-40, and 0.5% Tween20) were added immediately after sample collection.
Tn5 enzyme in Chromatin Profile Kit for Illumina (Novoprotein; N248) was used to fragment chromatin at 37℃ on Thermo Mixer (TS100) with 1000 rpm for 30 minutes and stopped by stop buffer immediately. After extraction with DNA extract beads, DNA fragments were amplified for 15 cycles using the following PCR conditions: 72℃ for 3min; 98℃ for 30 s; and thermocycling at 98℃ for 15 s, 60℃ for 15 s and 72℃ for 8 s; following by 72℃ 2 min. After the PCR reaction, libraries were purified with the 1.2x DNA clean beads following with fragment selection with 0.5x/0.7x AMPure beads (Beckman, A63882). Barcoded libraries were pooled and sequenced on the Illumina HiSeq X Ten platform using 150 bp paired-end reads


title: EMPP_Lmo4_rep2


title: 9213-HCF-2

description:
Library name: 9213-HCF-2
Single Cell RNAseq of C57Bl/6J mice: CD70KO; Weight Cycled; Adipose Tissue

value: Adipose


title: HAP1_benign_5

description: Library name: exon37-D3

value: benign


title: granulosa cells, diminished ovarian reserve, old, No319

description: Library name: DORH319

extract_protocol:
The RNA was isolated using Trizol method.
Libraries were Fast RNA-seq Lib Prep Kit V2 following manufacturer's protocols

value: ovarian follicle


title: granulosa cells, diminished ovarian reserve, old, No316

description: Library name: DORH316

value: granulosa cells


title: HAP1_benign_4

description: Library name: exon37-D1


title: granulosa cells, diminished ovarian reserve, old, No310

description: Library name: DORH310

value: diminished ovarian reserve


title: EMPP_Ctrl_rep2


title: ATAC_FGO_WT_2

description:
Library name: ATAC_seq_2
ATAC-seq


title: ATAC_FGO_KO_1

description:
Library name: ATAC_seq_3
ATAC-seq


title: ATAC_FGO_WT_1

description:
Library name: ATAC_seq_1
ATAC-seq


title: HAP1_benign_2

description: Library name: exon37-B5


title: granulosa cells, diminished ovarian reserve, old, No305

description: Library name: DORH305


title: granulosa cells, diminished ovarian reserve, old, No304

description: Library name: DORH304


title: HAP1_benign_1

description: Library name: exon37-A5


title: EMPP_52c_IL33


title: PreMegE_Lmo4_rep2

value: PreMegE


title: EMPP_Ctrl_rep1


title: granulosa cells, diminished ovarian reserve, old, No300

description: Library name: DORH300


title: HAP1_benign_3

description: Library name: exon37-C3


title: PreMegE_Lmo4_rep1


title: Mm48-3

city: Ann Arbor

first: Stephen

middle: J

last: Weiss

state: MI

address: 210 Washtenaw Ave

institute: University of Michigan

description: Library name: 9982-AO-30

data_processing:
BCL Convert Conversion Software (v4.0, Illumina) was used to generate de-multiplexed FASTQ files. Reads were trimmed using Cutadapt (v2.3) (132). FastQC (v0.11.8) (133) was used to ensure the quality of data. Fastq Screen (v0.13.0) was used to screen for various types of contamination (134).
Assembly: Reads were mapped to the reference genome GRCh38 (ENSEMBL), using STAR v2.7.8a (135) and assigned count estimates to genes with RSEM (v1.3.3) (136). Alignment options followed ENCODE standards for RNA-seq. Multiqc (v1.7) compiled the results from several of these tools and provided a detailed and comprehensive quality control report (137).
Supplementary files format and content: Samples had an average of ~35 million reads each and were analyzed in R (4.3.2) using DESeq2 (1.42.0).

source_name: Breast Cancer

growth_protocol: MDA-MB-231 spheroids were generated (2000cell/spheroid, 100,000 total cells/sample) and RNA was prepared either following 5 days of spheroid formation in hanging droplets, 24 hours post-embedding in collagen hydrogels or 48 hours post-embedding in collagen hydrogels.

extract_protocol:
At the designated time point, media were aspirated, and collagen hydrogels were gently removed from their well and transferred to a 1.7ml tube. Using small surgical scissors, gels were cut into pieces before adding sterilized digestion buffer (2mg/ml Type 7 Collagenase (Worthington) in HBSS) at a 2:1 buffer to gel ratio. Samples were incubated at 37°C for 10 minutes before lightly vortexing and pipetting the samples. After an additional 5-10 minutes, when collagen was no longer visible, cells were pelleted in a microcentrifuge at 300g. Samples isolated directly from droplets were washed off of the plate and centrifuged at 300g. From there all samples were washed with PBS and spun back down before RNA isolation. RNA samples were extracted using RNeasy Mini Kit (Qiagen, 74104).
RNA-seq libraries were prepared using standard Poly-A Library Prep (Illumina) and subjected to 151bp paired-end sequencing according to manufacturer’s protocols (Illumina NovaSeqXPlus).

value: Breast Cancer

value: Triple Negative Breast Cancer

value: 48 Hours embedded in collagen hydrogel


title: EMPP_52b_IL33


title: EMPP_52a_IL33


title: granulosa cells, diminished ovarian reserve, old, No298

description: Library name: DORH298


title: PreMegE_Ctrl_rep3


title: EMPP_51c_PBS

value: PBS


title: PreMegE_Lmo4_rep3


title: granulosa cells, diminished ovarian reserve, old, No27

description: Library name: DORH27


title: Mm48-2

description: Library name: 9982-AO-29


title: PreMegE_Ctrl_rep2


title: Mm48-1

description: Library name: 9982-AO-28


title: EMPP_51a_PBS


title: M48-3

description: Library name: 9982-AO-27

value: Wildtype


title: granulosa cells, diminished ovarian reserve, old, No249

description: Library name: DORH249


title: M48-2

description: Library name: 9982-AO-26


title: BEMP_Lmo4_rep3

value: BEMP


title: M48-1

description: Library name: 9982-AO-25


title: granulosa cells, diminished ovarian reserve, old, No246

description: Library name: DORH246


title: HP_Day11_3

value: Day 11


title: Mm24-3

description: Library name: 9982-AO-24

value: 24 Hours embedded in collagen hydrogel


title: BEMP_Lmo4_rep1

value: Bone marrow cells


title: granulosa cells, diminished ovarian reserve, old, No258

description: Library name: DORH258


title: granulosa cells, diminished ovarian reserve, old, No19

description: Library name: DORH19


title: EMPP_51b_PBS

value: EMPP


title: HP_Day11_5


title: granulosa cells, diminished ovarian reserve, old, No165

description: Library name: DORH165


title: BEMP_Lmo4_rep2


title: HP_Day11_2


title: BEMP_Ctrl_rep3

value: Ctrl


title: PreMegE_Ctrl_rep1


title: Mm24-1

description: Library name: 9982-AO-22


title: granulosa cells, diminished ovarian reserve, old, No151

description: Library name: DORH151


title: granulosa cells, diminished ovarian reserve, old, No149

description: Library name: DORH149


title: HP_Day4_5

value: Day 4


title: BEMP_Ctrl_rep2


title: HP_Day11_1


title: M24-3

description: Library name: 9982-AO-21


title: Mm24-2

description: Library name: 9982-AO-23


title: BEMP_Ctrl_rep1


title: HP_Day4_3


title: HP_Day4_2


title: granulosa cells, diminished ovarian reserve, old, No13

description: Library name: DORH13


title: EMPP_Lmo4_rep2

data_processing:
Reads were aligned with Bowtie2 (version 2.4.1)
SAM files were converted to BAM files and PCR duplicate reads were filtered out using SAMtools (version 1.17)
Peak calling was performed using MACS2 (version 2.1.2)
Unique reads mapped to these regions were quantified using featuresCounts (version 2.0.1)
Assembly: mm10
Supplementary files format and content: tab-delimited text file including raw counts for each sample

extract_protocol:
ATAC-seq based protocol
Dual index Nextera


title: granulosa cells, diminished ovarian reserve, old, No123

description: Library name: DORH123


title: EMPP_Lmo4_rep3


title: M24-1

description: Library name: 9982-AO-19


title: granulosa cells, diminished ovarian reserve, old, No120

description: Library name: DORH120


title: MmSph-3

description: Library name: 9982-AO-18

value: Spheroid Formed in Hanging Droplet


title: HP_Naive4

value: Naive


title: EMPP_Lmo4_rep1


title: MmSph-2

description: Library name: 9982-AO-17


title: EMPP_Ctrl_rep3


title: MmSph-1

description: Library name: 9982-AO-16


title: M24-2

description: Library name: 9982-AO-20


title: Systemic lupus erythematosus-04

city: Weifang

first: Wenchang

last: Sun

state: Shandong

address: No.151，Guangwen street

institute: The First Affiliated Hospital of Weifang Medical University

description:
OES19442150-04
one sample of human peripheral blood mononuclear cell

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: PBMC

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: PBMC

tag: disease state

value: Systemic lupus erythematosus


title: HP_Naive3


title: HP_Naive2


title: EMPP_Ctrl_rep2


title: Systemic lupus erythematosus treated with belimumab

description: one sample of human peripheral blood mononuclear cell


title: EMPP_Ctrl_rep1


title: Msph-3

description: Library name: 9982-AO-15


title: Systemic lupus erythematosus-03

description:
OES19442150-03
one sample of human peripheral blood mononuclear cell


title: Systemic lupus erythematosus-02

description:
OES19442150-02
one sample of human peripheral blood mononuclear cell


title: HP_Naive1


title: HP_Day4_1


title: preMegE_WT_rep3

value: preMegE

value: WT


title: PreMegE_Lmo4_rep3

value: PreMegE


title: Msph-1

description: Library name: 9982-AO-13

value: Breast Cancer

value: Triple Negative Breast Cancer


title: Rheumatoid arthritis-04

description:
OES19443150-04
one sample of human peripheral blood mononuclear cell

value: Rheumatoid arthritis


title: Msph-2

description: Library name: 9982-AO-14

value: Wildtype


title: preMegE_WT_rep2


title: hMDMs, siADAR1, rep 5

city: Huddinge

first: Niklas

last: Björkström

address: Alfreds Nobel Alle 8

country: Sweden

institute: Karolinska Institutet

description: Library name: Sample 14

data_processing:
Alignment, variant calling, and quality control were performed using the RNA-seq pipeline within the bcbio-nextgen framework (1.2.9). Briefly, RNA-seq data were aligned to the hg38 human reference genome using the STAR aligner. Quality control was performed with MultiQC, and transcript quantification was conducted using Salmon. Gene-level counts were generated from the Salmon counts using the tximport package for downstream analysis. Differential expression between siADAR1, siADAR1-p150, and negative control silenced macrophages was calculated using DESeq2 (1.36.0), with a significance threshold set at adjusted p-values < 0.05.
Assembly: hg38
Supplementary files format and content: csv file includes raw counts for each sample
Supplementary files format and content: csv file includes TPM for each sample

source_name: Blood

growth_protocol: Monocytes were isolated using a Pan-Monocyte isolation kit from healthy PBMCs, seeded at 1 million/ml density and differentiated into macrophages by culturing with 50 ng/ml MCSF1 for 7 days. Cells were maintained in RPMI 1640 supplemented with 1% Pen/Strep and 10% heat-inactivated FBS.

extract_protocol:
RNA was extracted from cells using the Direct-Zol RNA Micro Kit (Zymo Research) following the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA kit following manufacturer's protocol.

treatment_protocol: Macrophages were transfected with their respective siRNAs using Lipofectamine RNAiMax in Opti-MEM overnight. Following transfection, the medium was replaced with complete RPMI, and cells were allowed to rest for an additional 24 hours.At 48 hours post-transfection, cells were harvested for RNAseq analyses.

value: Blood

value: Primary macrophages

value: monocyte-derived macrophages


title: hMDMs, siADAR1-p150, rep 5

description: Library name: Sample 15


title: PreMegE_Ctrl_rep3

value: Bone marrow cells


title: preMegE_G320D_rep3


title: Healthy control-04

description:
OES19441150-04
one sample of human peripheral blood mononuclear cell

value: Healthy control


title: PreMegE_Lmo4_rep2


title: preMegE_WT_rep1


title: hMDMs, siADAR1-p150, rep 4

description: Library name: Sample 12


title: Healthy control-03

description:
OES19441150-03
one sample of human peripheral blood mononuclear cell


title: BEMP_Lmo4_rep3

value: BEMP


title: Rheumatoid arthritis-02

description:
OES19443150-02
one sample of human peripheral blood mononuclear cell


title: PreMegE_Ctrl_rep1

value: Ctrl


title: Rheumatoid arthritis-01

description:
OES19443150-01
one sample of human peripheral blood mononuclear cell


title: hMDMs, Negative control, rep 5

description: Library name: Sample 13

value: Negative control


title: Healthy control-02

description:
OES19441150-02
one sample of human peripheral blood mononuclear cell

value: PBMC


title: preMegE_G320D_rep1


title: Healthy control-01

description:
OES19441150-01
one sample of human peripheral blood mononuclear cell


title: EMPP_WT_rep3

value: EMPP


title: hMDMs, Negative control, rep 4

description: Library name: Sample 10


title: EMPP_WT_rep2


title: TRExRTA BCBL-1,D207A, DOX, 48h, biol rep 4

description:
Ribodepleted RNA, ERCC spike-in. Note "WT" refers to cells expressing exogenous TFIIB-2xStrep, and "D207A" refers to cells expressing exogenous TFIIB(D207A)-2xStrep.
BN_D207A_DOX_48h

data_processing:
Data was preprocessed (PhiX removal, deduplication, N-remover, adaptor trimming, etc.) using the standard HTStream version 1.3.0 workflow
Human GRCh38.p13, KSHV BAC16, ERCC Spike-In genomes were concatenated and indexed using STAR version 2.7.1a
Preprocessed reads were aligned with STAR version 2.7.1a and counts tables were exported
Assembly: Human genome GRCh38.p13; KSHV BAC16 genome; ERCC Spike-In sequences
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: TRExRTA BCBL-1 cells

growth_protocol: Cells harbor latent KSHV and were maintained in RPMI 1640 media (Gibco) supplemented with 10% Tet-free fetal bovine serum, 1X GlutaMAX (Gibco), and 10 ug/mL hygromycin B in a humidified chamber at 37℃ and 5% CO2. TFIIB-2xStrep or TFIIB(D207A)-2xStrep expression constructs were integrated via transposon delivery, then selected for and maintained in 1 ug/mL puromycin.

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen) and phenol-chloroform extraction
RNA libraries were prepared using KAPA RNA Hyperprep Kit with RiboErase (HMR) with KAPA Unique Dual Index Adaptors according to the manufacturer's protocols and include ERCC Spike-In mix for normalization

treatment_protocol: TFIIB-2xStrep or TFIIB(D207A)-2xStrep expressing TRExRTA BCBL-1 cells were treated with 660 ng/mL Superkiller TRAIL (Enzo) for 7 h or reactivated to lytic KSHV infection for 24 or 48 h by addition of 1 ug/mL doxycycline, which induces expression of the viral lytic transactivator RTA.

value: TRExRTA BCBL-1 cells

value: B cell lymphoma

value: DOX

tag: time


title: BEMP_Lmo4_rep1


title: PreMegE_Ctrl_rep2

value: PreMegE


title: preMegE_G320D_rep2

value: preMegE


title: hMDMs, siADAR1-p150, rep 3

description: Library name: Sample 9


title: hMDMs, siADAR1, rep 4

description: Library name: Sample 11


title: hMDMs, siADAR1, rep 3

description: Library name: Sample 8


title: TRExRTA BCBL-1,D207A, DOX, 24h, biol rep 4

description:
Ribodepleted RNA, ERCC spike-in. Note "WT" refers to cells expressing exogenous TFIIB-2xStrep, and "D207A" refers to cells expressing exogenous TFIIB(D207A)-2xStrep.
BM_D207A_DOX_24h


title: BEMP_Lmo4_rep2


title: BEMP_Ctrl_rep3


title: EMPP_G320D_rep3


title: BEMP_Ctrl_rep1


title: BEMP_Ctrl_rep2


title: hMDMs, Negative control, rep 3

description: Library name: Sample 7


title: hMDMs, siADAR1-p150, rep 2

description: Library name: Sample 6


title: TRExRTA BCBL-1,D207A, TRAIL, 24h, biol rep 4

description:
Ribodepleted RNA, ERCC spike-in. Note "WT" refers to cells expressing exogenous TFIIB-2xStrep, and "D207A" refers to cells expressing exogenous TFIIB(D207A)-2xStrep.
BL_D207A_TRAIL_24h

value: TRAIL


title: BEMP_WT_rep3

value: WT


title: EMPP_WT_rep1


title: EMPP_G320D_rep2


title: S8384

city: Rochester

first: Gagandeep

last: Kaur

address: 601 Elmwood Ave

department: Environmental Medicine

institute: University of Rochester Medical Center

description:
10X Genomics
integrated_ecig_0.5resolution_corrected.rds
General_Umap_annotated.rds
Detailed_Umap_annotated.rds

data_processing:
demultiplexing: cellranger 7.0.1 mkfastq ran using default parameters
cell and gene counting: cellranger 7.0.1count ran using default parameters
Seurat package and basic workflow used for filtering.
scTransform and CCA used for normalization and integration of data.
Assembly: 10X provided mm10-2020-A reference
Supplementary files format and content: compressed folders containing barcode, feature, and matrix files for each sample. Generated as part of the outputs via cellranger count

source_name: Lung

extract_protocol:
Extraction is included within the 10X genomics scRNA protocol
Cell suspensions were processed to generate single-cell RNA-Seq libraries using Chromium Next GEM Single Cell 3′ GEM, Library and Gel Bead Kit v3.1 (10x Genomics), per the manufacturer’s recommendations, as summarized below. Samples were loaded on a Chromium Single-Cell Instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell GEMs (Gel Bead-in-Emulsions). GEM reverse transcription (GEM-RT) was performed to produce a barcoded, full-length cDNA from poly-adenylated mRNA. After incubation, GEMs were broken, the pooled GEM-RT reaction mixtures were recovered, and cDNA was purified with silane magnetic beads (DynaBeads MyOne Silane Beads, ThermoFisher Scientific). The purified cDNA was further amplified by PCR to generate sufficient material for library construction.  Enzymatic fragmentation and size selection was used to optimize the cDNA amplicon size and indexed sequencing libraries were constructed by end repair, A-tailing, adaptor ligation, and PCR.

treatment_protocol: The inExpose nose-only inhalation system from SCIREQ (SCIREQ, Montreal, Canada) for mouse exposures. A puffing profile of two puffs per minute with a puff volume of 51 mL, puff duration of 3 seconds, and an inter puff interval of 27 seconds with a 2 L/min bias flow between puffs was used to expose the mouse to air, PGVG, mango, menthol or tobacco flavored e-cig aerosol based on their groups.

tag: strain

tag: sac date

tag: Sex

value: Male

value: Tobacco

value: Lung


title: TRExRTA BCBL-1,WT, DOX, 48h, biol rep 4

description:
Ribodepleted RNA, ERCC spike-in. Note "WT" refers to cells expressing exogenous TFIIB-2xStrep, and "D207A" refers to cells expressing exogenous TFIIB(D207A)-2xStrep.
BI_WT_DOX_48h


title: hMDMs, siADAR1, rep 2

description: Library name: Sample 5

value: Blood

value: Primary macrophages

value: monocyte-derived macrophages


title: EMPP_G320D_rep1

value: Bone marrow cells


title: S8889

value: Female


title: S6869

value: MentholMint


title: hMDMs, Negative control, rep 2

description: Library name: Sample 4

value: Negative control


title: TRExRTA BCBL-1,WT, DOX, 24h, biol rep 4

description:
Ribodepleted RNA, ERCC spike-in. Note "WT" refers to cells expressing exogenous TFIIB-2xStrep, and "D207A" refers to cells expressing exogenous TFIIB(D207A)-2xStrep.
BH_WT_DOX_24h

value: TRExRTA BCBL-1 cells


title: hMDMs, siADAR1-p150, rep 1

description: Library name: Sample 3


title: TRExRTA BCBL-1,WT, TRAIL, 24h, biol rep 4

description:
Ribodepleted RNA, ERCC spike-in. Note "WT" refers to cells expressing exogenous TFIIB-2xStrep, and "D207A" refers to cells expressing exogenous TFIIB(D207A)-2xStrep.
BG_WT_TRAIL_24h

value: B cell lymphoma


title: BEMP_WT_rep2

value: BEMP


title: TRExRTA BCBL-1,WT, Mock, 24h, biol rep 4

description:
Ribodepleted RNA, ERCC spike-in. Note "WT" refers to cells expressing exogenous TFIIB-2xStrep, and "D207A" refers to cells expressing exogenous TFIIB(D207A)-2xStrep.
BE_WT_Mock_24h

value: Mock


title: TRExRTA BCBL-1,D207A, Mock, 24h, biol rep 4

description:
Ribodepleted RNA, ERCC spike-in. Note "WT" refers to cells expressing exogenous TFIIB-2xStrep, and "D207A" refers to cells expressing exogenous TFIIB(D207A)-2xStrep.
BJ_D207A_Mock_24h


title: BEMP_WT_rep1


title: S6364


title: BEMP_G320D_rep3


title: S4344

value: Mango


title: BEMP_G320D_rep2


title: hMDMs, Negative control, rep 1

description: Library name: Sample 1


title: J.gamma1 cells, NUDT21 antibody, replicate 2

city: suzhou

first: yang

last: yang

address: zhongnan road

institute: soochow university

description: Library name: Sample 2

data_processing:
Filtering: Raw reads were filtered using fastp (verion 0.23.4)
Mapping: Clean reads were mapped to hg38 using bowtie2 (version 2.2.5)
Peak calling: MACS3 (version 3.0.1) was used to call peak with the significance cut-off q-value <= 0.01
Assembly: hg38
Supplementary files format and content: Read coverage in BigWig format; Narrow peaks in bed format.
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag was performed with Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) according to the manufacturer’s protocol.
Library construction was performed using TruePrep® DNA Library Prep Kit V2 for Illumina (Vazyme) and TruePrep® Index Kit V2 for Illumina (Vazyme).

value: T-ALL cells

tag: antibody

value: NUDT21 (Proteintech, #10322-1-AP)


title: TRExRTA BCBL-1,D207A, DOX, 48h, biol rep 3

description:
Ribodepleted RNA, ERCC spike-in. Note "WT" refers to cells expressing exogenous TFIIB-2xStrep, and "D207A" refers to cells expressing exogenous TFIIB(D207A)-2xStrep.
BD_D207A_DOX_48h

value: DOX


title: S1617

value: Air


title: TRExRTA BCBL-1,D207A, DOX, 24h, biol rep 3

description:
Ribodepleted RNA, ERCC spike-in. Note "WT" refers to cells expressing exogenous TFIIB-2xStrep, and "D207A" refers to cells expressing exogenous TFIIB(D207A)-2xStrep.
BC_D207A_DOX_24h


title: hMDMs, siADAR1, rep 1

description: Library name: Sample 2


title: J.gamma1 cells, NUDT21 antibody, replicate 1

description: Library name: Sample 1


title: S4849

value: Lung


title: BEMP_G320D_rep1


title: J-Gammal cells, control, replicate 2 [PAS-seq]

description: Library name: Sample 4

data_processing:
Filtering: Only read 2 was used to determine PAS sites. Raw reads were trimmed to remove adapters, low-quality bases with a score below 20, more than 3 consecutive "G"s at the end of the sequence, as well as "N"s and all subsequent sequences. Reads containing no less than 30% of the bases with a quality score below 20 were filtered out. Processed reads with a remaining length greater than 20 were retained.
Removing poly(A) tract: To remove poly(A) tract, we first search for at least 8 consecutive A's from the end of the reads. If more than 2 consecutive non-A bases are encountered, the poly(A) tract and all subsequent bases are removed, retaining only those reads with a length of 12 bases or more. Next, we scan for A's starting from the 5' end of the reads; if more than 9 consecutive A's are present, the poly(A) tract and all subsequent bases are removed, with reads of 12 bases or longer retained.
Alignment: These two sets of processed reads above are then simultaneously aligned to hg38 genome and Gencode.v45 using HISAT2. For reads that align successfully under both conditions, priority is given to the alignment result corresponding to the read with a poly(A) tract at the end.
Assembly: hg38
Supplementary files format and content: BigWig files containing read coverage normalized to CPM (read count per million)

source_name: J-Gammal

extract_protocol:
Total RNA was extracted using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme, RC112-01).
For each sample, 5 μg of total RNA was treated with RQ1 DNase (M6101,Promega, USA) to remove DNA, fragmented RNAs were used for PAS-seq library preparation. mRNAs were captured with mRNA Capture Beads kit （N401,Vazyme,Chian）. Fragmented mRNAs were used for directional PAS-seq library preparation by KAPA Stranded mRNA-Seq Kit for Illumina® Platforms (KK8544, Roche, USA). Fragmented mRNAs were converted into double strand cDNA. Following end repair and A tailing, the DNAs were ligated to Diluted Roche Adaptor (KK8726, Roche, USA). After purification of ligation product and size fractioning to 300-500 bp, the ligated products were amplified and purified, quantified and stored at -80℃ before sequencing. The strand marked with dUTP (the 2nd cDNA strand) is not amplified, allowing strand-specific sequencing. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina Novaseq Xplus system for 150 nt paired-end sequencing.

value: J-Gammal

value: control


title: TRExRTA BCBL-1,D207A, TRAIL, 24h, biol rep 3

description:
Ribodepleted RNA, ERCC spike-in. Note "WT" refers to cells expressing exogenous TFIIB-2xStrep, and "D207A" refers to cells expressing exogenous TFIIB(D207A)-2xStrep.
BB_D207A_TRAIL_24h

value: TRAIL


title: J-Gammal cells, control, replicate 1 [PAS-seq]

description: Library name: Sample 3


title: S1112

value: Male


title: TRExRTA BCBL-1,D207A, Mock, 24h, biol rep 3

description:
Ribodepleted RNA, ERCC spike-in. Note "WT" refers to cells expressing exogenous TFIIB-2xStrep, and "D207A" refers to cells expressing exogenous TFIIB(D207A)-2xStrep.
AZ_D207A_Mock_24h


title: preMegE_WT_rep3

value: Bone marrow cells

value: preMegE

value: WT


title: S0102

value: PGVG


title: preMegE_WT_rep1


title: S0607

value: Female


title: TRExRTA BCBL-1,WT, DOX, 24h, biol rep 3

description:
Ribodepleted RNA, ERCC spike-in. Note "WT" refers to cells expressing exogenous TFIIB-2xStrep, and "D207A" refers to cells expressing exogenous TFIIB(D207A)-2xStrep.
AX_WT_DOX_24h

value: TRExRTA BCBL-1 cells

value: B cell lymphoma


title: preMegE_G320D_rep3


title: TRExRTA BCBL-1,WT, TRAIL, 24h, biol rep 3

description:
Ribodepleted RNA, ERCC spike-in. Note "WT" refers to cells expressing exogenous TFIIB-2xStrep, and "D207A" refers to cells expressing exogenous TFIIB(D207A)-2xStrep.
AW_WT_TRAIL_24h


title: preMegE_WT_rep2