title: SARS-CoV2_NSP14-mut passage 11  in VERO-NP cells

description: Library name: P11_NSP14-mut-VERO-NP

value: Vero cells expressing Sars-CoV-2 NP

value: passage 11


title: Control primary mouse tubular epithelial cells under TNFα + IFNγ stimulation (replicate 1)

status: Public on Jun 16 2026

type: SRA

city: PHILADELPHIA

first: Yanjuan

last: Hou

state: PA

address: 3400 civic center blvd

department: Perelman School of Medicine, Department of Medicine

country: USA

institute: university of pennsylvania

description:
Library name: CTR_1
Bulk RNA-seq of primary mouse tubular epithelial cells under TNFα + IFNγ stimulation

library_source: transcriptomic

data_processing:
Raw sequencing reads were subjected to quality control and adaptor trimming.
Clean reads were aligned to the Mus musculus reference genome (mm10).
Gene-level counts were generated using featureCounts / Salmon quantification.
Expression values were normalized to TPM.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files containing raw gene counts and TPM-normalized expression values for all samples.

molecule: total RNA

organism: Mus musculus

source_name: primary culture

growth_protocol: Primary mouse renal tubular epithelial cells were isolated and cultured under standard conditions in appropriate growth medium at 37°C in a humidified atmosphere containing 5% CO₂.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA quality and concentration were assessed before library preparation.
RNA-seq libraries were prepared using an Illumina-compatible library preparation kit following the manufacturer’s protocol, including mRNA enrichment, cDNA synthesis, adaptor ligation, and PCR amplification.

treatment_protocol: Cells were infected with adenovirus expressing Cre recombinase (AdvCre) to induce ELF3 deletion or with control adenovirus. Following viral transduction, cells were stimulated with TNFα and IFNγ prior to RNA extraction.

tag: tissue

value: kidney

tag: cell type

value: renal tubular epithelial cells

tag: genotype

value: wild type

tag: treatment

value: TNFα + IFNγ

tag: batch

value: batch 1


title: C57BL/6J mouse liver,control,12 weeks,replicate 3

city: nanjing

first: xin

last: Qian

address: No. 24 Tongjia Lane, Gulou District, Nanjing, Jiangsu Province, P.R.China

country: China

institute: China Pharmaceutical University

description: Library name: C10

data_processing:
Raw paired-end reads were trimmed and quality controlled by fastp with default parameters to remove adapter sequences, low-quality reads, reads with high N content, and reads shorter than 20 bp after trimming, generating clean reads.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text file includes gene expression matrix for all samples.

source_name: liver tissue

growth_protocol: C57BL/6J mice were housed under standard laboratory conditions with free access to food and water. Mice were maintained under a 12 h light/12 h dark cycle before and during the experiment.

extract_protocol:
Total RNA was extracted from mouse liver tissues using TRIzol Reagent according to the manufacturer's instructions. RNA quality was assessed using an Agilent 5300 Bioanalyzer, and RNA concentration was quantified using a NanoDrop ND-2000 spectrophotometer. Only high-quality RNA samples were used for library construction.
RNA-seq libraries were prepared using the Illumina Stranded mRNA Prep, Ligation kit according to the manufacturer's instructions. Briefly, mRNA was enriched from total RNA using oligo(dT) beads, fragmented, reverse-transcribed into cDNA, end-repaired, adapter-ligated, size-selected, PCR-amplified, and purified. The qualified libraries were sequenced on the Illumina NovaSeq X Plus platform using paired-end 150 bp sequencing.

treatment_protocol: C57BL/6J mice were divided into four groups: normal control group, high-fat diet-induced MASH model group, Eleutheroside E-treated MASH group, and resmetirom-treated MASH group. After 8 weeks of model establishment, mice in the Eleutheroside E-treated group were orally administered Eleutheroside E at 100 mg/kg for 4 weeks, and mice in the resmetirom-treated group were orally administered resmetirom at 3 mg/kg for 4 weeks. Mice in the normal control group and MASH model group were orally administered 0.5% CMC-Na as vehicle control for 4 weeks. At the end of treatment, liver tissues were collected for RNA extraction, library construction, and high-throughput RNA sequencing.

value: liver tissue

value: normal chow diet


title: SARS-CoV2_NSP14-mut passage 9 in VERO-NP cells

city: San Antonio

first: Yan

last: Xiang

state: TX

address: 7703 FLOYD CURL DR

department: Microbiology, Immunology and Molecular Genetics

institute: UT Health San Antonio

description: Library name: P9_NSP14-mut-VERO-NP

data_processing:
Sequencing reads were mapped to the reference genome using minimap2
Per-position read depth was calculated using samtools
Variants were called from samtools mpileup by quantifying reference and alternate base counts at each position, followed by filtering based on sequencing quality, minimum coverage thresholds, and a minimum alternate allele frequency of 1.5%.
Assembly: recombinant SARS-CoV-2 genome included in the supplemental file
Supplementary files format and content: reference gemone in fasta format
Supplementary files format and content: reference GTF file
Supplementary files format and content: excel file containg read depth of every samples
Supplementary files format and content: excel file containg error rate per position of every samples
Supplementary files format and content: excel file containg SNP frequency of every samples

organism: Severe acute respiratory syndrome coronavirus 2

source_name: Vero cells expressing Sars-CoV-2 NP

growth_protocol: Five micrograms of SARS-CoV-2 BAC DNA was transfected into Vero-NP cells in 6-well plates using Lipofectamine 3000 transfection reagent (Invitrogen). After 4 hours, the transfection medium was replaced with DMEM containing 5% FBS. Cells were incubated at 37 °C with 5% CO₂ for 3–21 days, after which the tissue culture supernatant was collected and designated passage 0 (P0). Subsequent passages were generated by infecting fresh Vero-NP or Vero-AT cells with 500 µL of virus from the previous passage.

extract_protocol:
Culture supernatants from serial passages of recombinant SARS-CoV-2 in Vero-NP or Vero-AT cells were processed for RNA extraction using TRIzol LS reagent (Invitrogen) according to the manufacturer’s instructions.
The extracted RNA was converted into sequencing libraries and subjected to paired-end deep sequencing (100 or 150 bp reads) with NovaSeq 6000 system

tag: cell line

tag: timepoint

value: passage 9


title: MI2

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

description: Library name: Sample 4

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data(raw reads) of fastq format were firstly processed through in-houseperl scripts.In this step,clean data(clean reads) were obtained by removing reads containing adapter,reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly.Index of the reference genome was built using Hisat 2v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat 2v2.0.5.
Feature Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene.And then FPKM of each gene was calculated based on the length of the gene and readscount mapped to this gene.
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.8.3).
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab_delimited text files include Counts for each Sample
Supplementary files format and content: txt files include Counts for each Sample

organism: Mus

source_name: atria

growth_protocol: Rats were randomly assigned to four experimental groups: Sham + Vehicle, MI + Vehicle, and MI+ART.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA w as used for the construction of sequencing libraries.
RNA libraries for RNA-seq w ere prepared using SMARTER mRNA-Seq Library Prep Kitfollow ing manufacturer's protocols.

treatment_protocol: Male wild-type (WT) C57BL/6J mice (8–10 weeks old, 20–23 g) were purchased from SPF Biotechnology Co., Ltd. (Beijing, China). Myocardial infarction (MI) was induced by permanent ligation of the left anterior descending (LAD) coronary artery, as previously described. Sham-operated mice underwent identical surgical procedures except for LAD ligation. Artesunate (ART; MCE, Monmouth Junction, NJ, USA) was dissolved in dimethyl sulfoxide (DMSO) and administered intraperitoneally at a dose of 25 mg/kg body weight daily, beginning immediately after surgery and continuing for 7 consecutive days.

value: atria

value: WT

value: MI + Vehicle


title: CUT&RUN of NFKB2 in primary mouse tubular epithelial cells under TNFα + IFNγ stimulation

description:
Library name: NFKB2
CUT&RUN profiling of NFKB2 in primary mouse tubular epithelial cells under TNFα + IFNγ stimulation

library_source: genomic

data_processing:
Raw sequencing reads were quality-checked and adaptor-trimmed.
Trimmed reads were aligned to the Mus musculus reference genome (mm10).
Peak calling was performed using MACS2.
Summit regions were identified and exported as BED files.
Assembly: mm10
Supplementary files format and content: Processed CUT&RUN data include narrowPeak files representing enriched regions and BED files representing peak summit positions.
Library strategy: CUT&RUN

molecule: genomic DNA

extract_protocol:
CUT&RUN was performed according to established protocols. Briefly, antibody-bound chromatin complexes were targeted by micrococcal nuclease tethered to protein A/G, followed by controlled digestion and release of DNA fragments.
Sequencing libraries were prepared from released DNA fragments using an Illumina-compatible library preparation kit following the manufacturer’s instructions.

treatment_protocol: Cells were stimulated with TNFα and IFNγ prior to CUT&RUN experiments to model inflammatory activation.


title: CON3-AF

description: Library name: Sample 3

value: Sham+ Vehicle


title: 526MEL treated with supernatant and RSL3 replicate 2

city: Nagasaki

first: Daisuke

last: Ehara

address: 1-12-4 Sakamoto

department: Dermatology

country: Japan

institute: Nagasaki University Graduate School of Biomedical Sciences

description: Library name: supRSL3_2

data_processing:
Raw reads were generated on an Illumina sequencing platform by Novogene. Adapter-containing reads, reads containing >10% ambiguous bases (N), and low-quality reads containing >50% bases with Qscore ≤5 were removed to generate clean reads.
Gene expression matrices were generated from the sequencing data and exported in CSV format for downstream analyses. Ensembl-like gene identifiers were converted to gene symbols when applicable, and duplicate symbols were collapsed by mean expression values.
Group-wise Z-scores were calculated across experimental conditions. Statistical analyses were performed using two-sided Student’s t-tests with Benjamini–Hochberg correction.
Assembly: GRCh38/hg38
Supplementary files format and content: Processed data files consist of gene-level expression matrices in CSV format. Rows represent genes and columns represent individual samples. The files contain normalized expression values used for downstream analyses.

organism: Homo sapiens

source_name: tumor

extract_protocol:
Total RNA from two biological samples was individually isolated using the RNeasy Mini kit and treated with DNase I (Life Technologies, Gaithersburg, MD, USA), according to the manufacturer’s protocol. In addition, 0.5 μL of RNase inhibitor (Nippon Gene, Toyama, Japan) was added to each tube before the RNA purification.
RNA sequencing was performed by Novogene, where directional mRNA libraries were prepared using poly(A) enrichment and dUTP-based strand-specific library construction.

value: tumor

value: melanoma cells


title: SARS-CoV2_NSP14-mut passage 7 in VERO-NP cells

description: Library name: P7_NSP14-mut-VERO-NP

value: passage 7


title: CON2-AF

description: Library name: Sample 2


title: CUT&RUN of ELF3 in primary mouse tubular epithelial cells under TNFα + IFNγ stimulation

description:
Library name: ELF3
CUT&RUN profiling of ELF3 in primary mouse tubular epithelial cells under TNFα + IFNγ stimulation


title: SARS-CoV2_NSP14-mut passage 5 in VERO-NP cells

description: Library name: P5_NSP14-mut-VERO-NP

value: Vero cells expressing Sars-CoV-2 NP

value: passage 5


title: 526MEL untreated control replicate 2

description: Library name: control2


title: E11PA_WT_B9

city: Cincinnati

first: Jeffrey

middle: D

last: Steimle

email: jeffrey.steimle@cchmc.org, jeffrey.steimle@bcm.edu, jsteimle@uchicago.edu, jsteimle@alumni.nd.edu

state: OH

address: 240 Albert Sabin Way

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Medical Hospital Center

description: Library name: B9

data_processing:
FASTQ files were aligned to the mouse genome, mm10, using STAR (version 2.7.10a)
Differential expression analysis was performed using edgeR (version 3.40.2) and limma (version 3.54.2) using genotype and litter information as covariates. Significant changes were defined as an FDR less than 0.05.
Assembly: mm10
Supplementary files format and content: FeatureSummary.txt – Tab-delimited matrix of feature counts per gene (1st column) for each sample designated by library name (all other columns)
Supplementary files format and content: Fucci_edgeR_Results.txt – Differential gene expression analysis and columns represent Ensembl_ID, Gene, log2 fold change Heterozygote vs Wildtype, log2 fold change Homozygote vs Wildtype, p-value, false discovery rate, and all remaining columns are per sample normalized read count

molecule: polyA RNA

source_name: Pharyngeal arch

extract_protocol:
The pharyngeal arches of 18 embryonic day 11.5 embryos were collected from two litters by microdissection and stored in TRIzol. Following genotype confirmation (6 wild type, 7 Fucci-G1 heterozygotes, and 5 Fucci-G1 homozygotes), RNA was extracted using the manufacturer's protocol.
Purified total RNA were used for poly(A)-enriched, non-directional RNA-sequencing (Novogene Corporation, USA).

value: Pharyngeal arch

tag: developmental stage

value: Wildtype

tag: litter

value: B


title: ELF3 knockout primary mouse tubular epithelial cells under TNFα + IFNγ stimulation (replicate 2)

description:
Library name: KO_2
Bulk RNA-seq of primary mouse tubular epithelial cells under TNFα + IFNγ stimulation

value: kidney

value: renal tubular epithelial cells

value: ELF3 knockout

value: TNFα + IFNγ


title: CON1-AF

description: Library name: Sample 1


title: SARS-CoV2_NSP14-mut passage 3 in VERO-NP cells

description: Library name: P3_NSP14-mut-VERO-NP

value: passage 3


title: SARS-CoV2_NSP14-WT passage 13 in VERO-AT cells

description: Library name: P13_NSP14-WT-VERO-AT

source_name: Vero cells expressing ACE2 and Tmprss2

value: Vero cells expressing ACE2 and Tmprss2

value: passage 13


title: Liver, High-fat diet, rep4

city: Santa Cruz

first: Andrew

middle: David

last: Holmes

state: California

address: 1156 High Street

department: Molecular, Cell, and Developmental Biology

institute: UC Santa Cruz

description: Library name: LIVER_HF_4

data_processing:
Sequences were trimmed with  "cutadapt --no-indels -O 15 -m 2 -a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC" ,"cutadapt -u 7" , and then "cutadapt -u -1" to remove the adapter, the UMI, and the TPRT base (the UMI was not used for removing duplicates)  Only reads >65 bases were used for most analyses
Data was mapped and counted using TRAX, which uses an all-best mapping approach and uses Deseq2 for normalization and detection of differential expression
Assembly: mm10
Supplementary files format and content: tab-delimited raw counts for calculated by tRAX, with mitochondrial tRNA counts appended

source_name: Liver

growth_protocol: Mice were group-housed (maximum of 5 per cage) with a 12-hour light-dark cycle (lights off at 6 pm) and free access to food and water ad libitum.

extract_protocol:
Samples were vortexed for 5 minutes to ensure complete breakdown of the sperm, followed by centrifugation at 12,000 RCF for 4 minutes. The aqueous phase was then removed and transferred to a low-binding RNase/DNase-free microcentrifuge tube, followed by the addition of 20 µg of glycoblue (Invitrogen) and 1 volume of Isopropanol. The RNA was then precipitated for 30 minutes or greater at -20°C, followed by centrifugation at 18,000 RCF for 30 minutes at 4°C, and one wash with 70% cold ethanol followed by centrifugation at 12,000 RCF for 10 minutes at 4°C. Finally, the RNA was reconstituted in nuclease-free water.
Library was constructed using Ottr-seq protocol.  Input RNA was PNK treated and labelled at the 3’ end by incubation in buffer containing ddATP for 90 minutes in 30˚C, followed by an addition of ddGTP and another incubation at 30˚C for 30 minutes. The reaction was stopped by incubating at 65°C for 5 minutes, followed by the addition of 5 mM MgCl2 and 0.5 units of shrimp alkaline phosphatase (NEB, cat# M0371S) at 37°C for 15 minutes, then stopped by the addition of 5 mM EGTA, and incubated at 65°C for 5 minutes. Samples were then incubated in templated cDNA synthesis buffer, adaptors, and dNTPs at 37˚C for 20 minutes, followed by heat inactivation at 65˚C for 5 minutes and RNase A/H treatment. cDNA was size selected on a 10% PAGE urea gel to minimize adaptor dimers. Size selected cDNA was PCR amplified for 12 cycles with Q5 high fidelity polymerase (NEB, cat# M0491S). The final PCR product was cleaned up with AMPure XP beads (Beckman, cat # A63881) and finally separated by 6% TBE gel to remove adaptor dimers. The desired product was excised from the gel and eluted in 400ul elution buffer (300 mM NaCl, 10 mM Tris pH 8, 1 mM EDTA) overnight at -20, followed by isopropanol precipitation and resuspension in 9µl nuclease-free H2O.

treatment_protocol: Animals were raised on one of four diets – a low protein diet (LP; 10% of protein rather than 18%, remaining mass made up with sucrose, BioServ, cat# S3156), control for low protein diet (C; BioServ AIN-93g, cat# F3156), a high fat diet (HF; 60% of fat calories rather than 16%, BioServ, cat# S3282) , or control for high-fat diet  (C_HF; 7.2% fat calories, BioServ, cat# S4031)

value: Liver

value: High-fat diet


title: 526MEL untreated control replicate 1

description: Library name: control1

value: tumor


title: LPFC8

city: Philadelphia

first: Stephanie

last: Daws

address: 3500 N Broad St

institute: Temple University

description: 10 days of saline self-administration

data_processing:
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean data (clean reads) were obtained by removing reads containing poly-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing poly A or T or G or C and low quality reads from raw data.
The small RNA tags were mapped to reference sequence by Bowtie
Mapped small RNA tags were used to look for known miRNA. miRBase22.0 was used as reference, and mirdeep2  and srna-tools-cli were used to obtain the potential miRNA. Custom scripts were used to obtain the miRNA counts
To remove tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA, small RNA tags were mapped to RepeatMasker, Rfam database or those types of datas from the specified species itself
miRNA expression levels were estimated by TPM (transcript per million) through the following criteria: Normalization formula: Normalized expression = mapped readcount/Total reads*1000000
Assembly: rn6
Supplementary files format and content: TPM in .xls format

organism: Rattus norvegicus

source_name: prefrontal cortex

extract_protocol:
Total RNA was extracted from prefrontal cortex and nucleus accumbens tissue samples with Trizol, according to manufacter's protocols. Exosomal RNA was extracted from blood serum using the SeraMir kit, using manufacturer's protocols.
Small RNA sequencing was performed on six biological replicate samples per treatment group, per region of interest (prefrontal cortex, nucleus accumbens, or serum). 3’ and 5’ adaptors were ligated to 3’ and 5’ end of small RNA, respectively. Then the first strand cDNA was synthesized after hybridization with reverse transcription primer. The double-stranded cDNA library was generated through PCR enrichment. After purification and size selection, libraries with insertions between 18~40 bp were ready for sequencing

treatment_protocol: Adult male Sprague Dawley rats were aged 8 weeks on arrival. Forheroin exposure, animals were acclimited to the animal facility for 1 week then underwent jugular vein catheterization. Following 1 week of recovery, animals self-administered  heroin at a dose of 0.075mg/kg/infusion for 6 hours per day in 10 daily sessions. Saline animals underwent the same surgical procedures but self-administered saline for 10 days. Following the last self-administration session, animals were euthanized with 60 minutes and their brains were frozen in ice cold isopentane. Trunk blood was collected during decapitation. Blood was collected into sterile tubes, allowed to clot, and then spun at 2g for 10 min to collect serum. Prefrontal cortex and nucleus accumbens tissue was dissected from each animal on dry ice then RNA extraction proceeded.

value: prefrontal cortex

tag: strain

value: Sprague-Dawley

tag: Sex

value: male

tag: age

value: adult

value: saline self-administration for 10 days


title: E11PA_WT_B8

description: Library name: B8

value: Pharyngeal arch

value: Wildtype


title: Human ileal enteroid line 1013, HME_POOL

city: Houston

first: Mary

last: Estes

address: 1 Baylor Plaza

department: Microbiology and Virology

institute: Baylor College of Medicine

description: Library name: IL1013DifPol

data_processing:
Fastq files were trimmed using Trim Galore!.
Trimmed reads were aligned to the GRCh38 genome using HISAT2.
Aligned reads were quantified using featureCounts.
Assembly: GRCh38
Supplementary files format and content: Raw count and Differentially expressed gene list

source_name: ileum

growth_protocol: Enteroids were generated from intestinal tissue samples using standard protocols. Enteroids were then grown in enteroid growth media during proliferation. Growth factors were withdrawn for differentiation.

extract_protocol:
RNA was isolated with the Qiagen RNeasy Micro kit according to the manufacturer's protocol.
Libraries were created from the cDNA by first blunt ending the fragments, attaching an adenosine to the 3′ end, and finally ligating unique adapters to the ends for PCR amplification. Paired end sequencing (2 × 150 bp) was performed on an Illumina NovaSeq 6000  for a depth of 30 million paired end reads (a total of 60 million reads) per RNA sample.

treatment_protocol: Enteroids were treated with either PBS or human milk derived exosomes from a pool of human milk samples for 72 hours.

value: ileum

value: enteroid

value: Differentiated


title: TNFα + IFNγ 12 h replicate 3

description:
Library name: TaIF12H-3
Bulk RNA-seq analysis of human RPTECs following TNFα and IFNγ stimulation

data_processing:
Raw sequencing reads were quality-checked and trimmed prior to alignment.
Reads were aligned to the Homo sapiens reference genome (hg38).
Gene-level counts were generated using featureCounts / Salmon quantification.
Expression values were normalized to TPM.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files containing raw counts and TPM-normalized gene expression values for all samples.

source_name: RPTEC

growth_protocol: Immortalized human renal proximal tubule epithelial cells (hTERT-RPTECs) were maintained in DMEM/F12 medium supplemented with the RPTEC Growth Kit (ATCC) and 0.5% fetal bovine serum at 37°C in a humidified atmosphere with 5% CO₂.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA quality and concentration were assessed prior to library preparation.
RNA-seq libraries were prepared using a poly(A) selection / rRNA depletion strategy followed by cDNA synthesis and Illumina-compatible library construction according to standard protocols.

treatment_protocol: Cells were treated with TNFα, IFNγ, or TNFα + IFNγ for 3 h or 12 h prior to RNA extraction. Untreated cells served as controls.

value: RPTEC

value: renal proximal tubule epithelial cells

value: WT

value: TNFα + IFNγ

value: batch 1


title: SARS-CoV2_NSP14-mut passage 1 in VERO-NP cells

description: Library name: P1_NSP14-mut-VERO-NP

value: Vero cells expressing Sars-CoV-2 NP

value: passage 1


title: E11PA_G1Het_B7

description: Library name: B7

value: Heterozygote

value: B


title: Human ileal enteroid line 1013, PBS

description: Library name: IL1013DifPBS

value: PBS


title: PA3321, mutant, rep 3

city: Honolulu

first: Hung

last: Vo

state: Hawaii

address: 1800 East-West Road Life Sciences Building, Rm 318

department: Microbiology

institute: University of Hawaii at Manoa

description:
Library name: PA3321R3
RNA-seq of PA3321::Tn mutant in staticbiofilm formation growth, replication 3

data_processing:
Rockhopper version 2.03
Follow the protocol of Rockhopper
https://cs.wellesley.edu/~btjaden/Rockhopper/user_guide.html
Assembly: NC_002516.2
Supplementary files format and content: tab delimited text file include raw data of each sample
Supplementary files format and content: txt sample include RKPM value compared sample 1 and sample 2

organism: Pseudomonas aeruginosa

source_name: Bacteria

growth_protocol: The mutant PA3321::Tn and the wt PA01 strain were grown overnight in LB broth, diluted 100-fold into fresh LB broth, and grown in the same biofilm growth condition (30oC, no shake, 48 hours)

extract_protocol:
Bacteria were harvested, and total RNA was isolated using the Qiagen RNeasy Mini Kit (Qiagen), with on-column DNase I treatment; rRNA was depleted using RiboZero (Epicentre®)
Total mRNA was sent to TUCF (Tufts University Core Facility) for RNA-seq. Illumina® NGS libraries were created and sequenced at TUCF Genomics (http://tucf-genomics.tufts.edu/)

treatment_protocol: RNA-seq profiles of the mutant of regulator PA3321 compared to Pa wt PA01 in static biofilm condition

value: Bacteria

value: P. aeruginosa

value: mutant PA3321::Tn

value: Static biofilm grow, 30 oC


title: Human ileal enteroid line 1010, HME_POOL

description: Library name: IL1010DifPol

value: ileum


title: TNFα + IFNγ 12 h replicate 1

description:
Library name: TaIF12H-1
Bulk RNA-seq analysis of human RPTECs following TNFα and IFNγ stimulation


title: E11PA_G1Hom_B5

description: Library name: B5

value: Pharyngeal arch

value: Homozygote


title: Human ileal enteroid line 1010, PBS

description: Library name: IL1010DifPBS

value: enteroid

value: Differentiated


title: PA3321, mutant, rep 1

description:
Library name: PA3321R1
RNA-seq of PA3321::Tn mutant in staticbiofilm formation growth, replication 1


title: TNFα + IFNγ 3 h replicate 3

description:
Library name: TaIF3H-3
Bulk RNA-seq analysis of human RPTECs following TNFα and IFNγ stimulation

value: RPTEC

value: renal proximal tubule epithelial cells

value: WT


title: E11PA_WT_B4

description: Library name: B4

value: Wildtype


title: Human ileal enteroid line 1004 HME_POOL

description: Library name: IL1004DifPol


title: TNFα + IFNγ 3 h replicate 2

description:
Library name: TaIF3H-2
Bulk RNA-seq analysis of human RPTECs following TNFα and IFNγ stimulation

value: TNFα + IFNγ

value: batch 1


title: E11PA_G1Het_B3

description: Library name: B3

value: Heterozygote

value: B


title: Human ileal enteroid line 1004, PBS

description: Library name: IL1004DifPBS

value: PBS


title: PA01, wt control, rep 2

description:
Library name: WTR2
RNA-seq of PA01 in staticbiofilm formation growth, replication 1

value: Bacteria

value: P. aeruginosa

value: wild type PA01


title: TNFα + IFNγ 3 h replicate 1

description:
Library name: TaIF3H-1
Bulk RNA-seq analysis of human RPTECs following TNFα and IFNγ stimulation


title: E11PA_G1Hom_B2

description: Library name: B2


title: H23 T6 unInfected Replicate 3

city: Saskatoon

first: Franco

middle: J

last: Vizeacoumar

state: Saskatchewan

address: 4D40 Health Sciences Building, 107 Wiggins Road

department: Oncology

country: Canada

institute: University of Saskatchewan

description:
Library name: Sample 12
H23_Raw_read_counts_matrix.txt

data_processing:
Sequenced files were demultiplexed from illumina
Read counts were calculated using the package from Li, et al. Genome Biology 15:554 (2014). MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens.
Assembly: GRCh38
Supplementary files format and content: Matrix table with gene raw counts for every gene and every sample
Library strategy: CRISPR Screen

source_name: Lung Adenocarcinoma

growth_protocol: As explained in Khan et al manuscript

extract_protocol:
genomic DNA was extracted using the QIAamp Blood Maxi kit (Qiagen #51194)
libraries were constructed following the previously described method in Shalem O et al Science 2014

treatment_protocol: As explained in Khan et al manuscript

value: Lung Adenocarcinoma

value: ACE Over expression

value: Uninfected


title: TNFα 12 h replicate 2

description:
Library name: Ta12H-2
Bulk RNA-seq analysis of human RPTECs following TNFα and IFNγ stimulation

value: TNFα


title: E11PA_G1Het_B1

description: Library name: B1

value: Pharyngeal arch


title: H23 T6 unInfected Replicate 2

description:
Library name: Sample 11
H23_Raw_read_counts_matrix.txt


title: TNFα 12 h replicate 1

description:
Library name: Ta12H-1
Bulk RNA-seq analysis of human RPTECs following TNFα and IFNγ stimulation

value: RPTEC


title: E11PA_G1Hom_A9

description: Library name: A9

value: Homozygote

value: A


title: H23 T6 uninfected Replicate 1

description:
Library name: Sample 10
H23_Raw_read_counts_matrix.txt


title: UHRF1_2

type: genomic

city: Guangzhou

first: Bo

last: Xuan

address: No.280, Outer Ring East Road, Higher Education Mega Center, Panyu District, Guangzhou City

department: School of Basic Medical Science

institute: Guangdong Pharmaceutical University

description: UHRF1 knockdown group, replicate biosample 2

hyb_protocol: DNA was bisulfite treated using the Zymo Research EZ DNA methylaiton-Glod Kits (Zymo Research, Irvine, CA, USA).  Bisulfite-converted DNA was analysed on an Illumina Infinium MethylationEPIC(850K) BeadChip (Illumina).

scan_protocol: Illumina iSCAN was used to scan the chip to get the Idat files.

data_processing:
Idat files were imported and then preprocessed with ChAMP(version 2.12.4) package in R to get raw data. Next, the raw data was  normalized with BMIQ method. Statistical differences in continuing variables between two groups were compared by  t-test. The significantly DMS(differential methylation Sites) were identified by a threshold of |deltaBeta| > 0.1  and P.Value < 0.05. Gene ontology(GO, http://www.geneontology.org) and the Kyoto Encyclopedia of Genes and Genomes  (KEGG, http://www.kegg.jp/) pathway enrichment analysis were performed using the scripts in Python to clarify the  function and biological pathways of differentially expressed methylation loci‐related genes. The GO terms and KEGG  pathways with p < 0.05 are considered the significant enrichment of genes related to differentially methylated sites.
Processed data: normalized signal intensity values used for downstream analysis

label: Cy3 and Cy5

label_protocol: standard Illumina protocol

extract_protocol: Genomic DNA was isolated from DU145 cells and bisulfite conversion was performed. Add 0.1 N NaOH to the sample to denature the DNA to single-stranded DNA.  After neutralization, add the whole genome amplification reagent, and incubate overnight at 37 °C.  The DNA fragments were precipitated by adding isopropanol, and the fragmented DNA was enriched by centrifugation at 4 °C and purified.

treatment_protocol: DU145 cells were divided into two groups: the control group (without any treatment) and the UHRF1 knockdown group. Each group consisted of three biological replicates. Following cell culture, DNA methylation sequencing was conducted on all samples.

value: cell culture

value: not applicable

value: UHRF2 knockdown


title: TNFα 3 h replicate 2

description:
Library name: Ta3H-2
Bulk RNA-seq analysis of human RPTECs following TNFα and IFNγ stimulation

value: renal proximal tubule epithelial cells

value: WT

value: batch 1


title: E11PA_WT_A8

description: Library name: A8

value: Wildtype


title: H23 T6 Infected Replicate 3

description:
Library name: Sample 9
H23_Raw_read_counts_matrix.txt

value: Infected with SARS CoV2


title: UHRF1_1

description: UHRF1 knockdown group, replicate biosample 1

value: UHRF1 knockdown


title: TNFα 3 h replicate 1

description:
Library name: Ta3H-1
Bulk RNA-seq analysis of human RPTECs following TNFα and IFNγ stimulation


title: E11PA_G1Hom_A7

description: Library name: A7


title: IFNγ 12 h replicate 2

description:
Library name: IF12H-2
Bulk RNA-seq analysis of human RPTECs following TNFα and IFNγ stimulation

value: IFNγ


title: UHRF1_3

description: UHRF1 knockdown group, replicate biosample 3

value: UHRF3 knockdown


title: E11PA_G1Het_A6

description: Library name: A6

value: Heterozygote


title: H23 T6 Infected Replicate 1

description:
Library name: Sample 7
H23_Raw_read_counts_matrix.txt

value: Lung Adenocarcinoma

value: ACE Over expression


title: NC_2

description: control group, replicate biosample 2


title: IFNγ 12 h replicate 1

description:
Library name: IF12H-1
Bulk RNA-seq analysis of human RPTECs following TNFα and IFNγ stimulation

value: RPTEC


title: 526MEL treated with IFN-γ replicate 1

description: Library name: IFNg1

value: tumor

value: melanoma cells


title: 526MEL treated with RSL3 replicate 2

description: Library name: RSL3_2


title: E11PA_G1Hom_A5

description: Library name: A5

value: Pharyngeal arch

value: Homozygote

value: A


title: H23 T0 Replicate 3

description:
Library name: Sample 6
H23_Raw_read_counts_matrix.txt

value: Uninfected


title: NC_1

description: control group, replicate biosample 1

value: cell culture

value: not applicable


title: IFNγ 3 h replicate 2

description:
Library name: IF3H-2
Bulk RNA-seq analysis of human RPTECs following TNFα and IFNγ stimulation

value: renal proximal tubule epithelial cells

value: WT

value: batch 1


title: E11PA_WT_A4

description: Library name: A4

value: Wildtype


title: NC_3

description: control group, replicate biosample 3


title: H23 T6 Infected Replicate 2

description:
Library name: Sample 8
H23_Raw_read_counts_matrix.txt

value: Infected with SARS CoV2


title: 526MEL treated with RSL3 replicate 1

description: Library name: RSL3_1


title: H23 T0 Replicate 2

description:
Library name: Sample 5
H23_Raw_read_counts_matrix.txt


title: KO3

city: Baltimore

first: Akira

last: Sawa

state: Maryland

address: 600 N Wolfe St Meyer 3-166

institute: Johns Hopkins University

description: Library name: A7N56_2

data_processing:
FastQC was used to check the quality of reads. Reads were aligned to the mouse genome (mm10) using STAR with the following optional parameters: --runThreadN 8 --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts. Count from ReadsPerGene table generated from STAR was used for further analysis
Assembly: mm10
Supplementary files format and content: csv file includes raw count of each sample

source_name: brain tissue homogenate of the cerebral cortex

extract_protocol:
Cortical tissue was dissected from mice and RNA was extracted using the RNeasy kit (Qiagen).
Total RNA was assessed for quality via Agilent bioanalyzer and Thermo nanodrop, and RNA libraries were prepared using Illumina TruSeq Stranded RNA LT Kit with Ribo-Zero Gold rRNA depletion. Barcoded libraries were quality-controlled using the Kappa PCR kit and pooled in equimolar ratios for subsequent cluster generation and sequencing on an Illumina HiSeq 2000 instrument to yield >50,000,000 paired end 100x100 bp tags for each sample.

value: male

value: ALDH7A1 KO


title: IFNγ 3 h replicate 1

description:
Library name: IF3H-1
Bulk RNA-seq analysis of human RPTECs following TNFα and IFNγ stimulation

value: IFNγ


title: E11PA_G1Het_A3

description: Library name: A3

value: Heterozygote


title: H23 T0 Replicate 1

description:
Library name: Sample 4
H23_Raw_read_counts_matrix.txt

value: Lung Adenocarcinoma

value: ACE Over expression


title: Control 12 h replicate 3

description:
Library name: CRT12H-3
Bulk RNA-seq analysis of human RPTECs following TNFα and IFNγ stimulation

value: RPTEC

value: untreated


title: KO2

description: Library name: A7N55_1

value: brain tissue homogenate of the cerebral cortex


title: E11PA_G1Het_A2

description: Library name: A2

value: Pharyngeal arch

value: A


title: HEK293 T6 uninfected

description:
Library name: Sample 3
HEK293T_Raw_read_counts_matrix.txt

source_name: embryonic kidney cell line

value: embryonic kidney cell line

value: Uninfected


title: KO1

description: Library name: A7N20_1


title: Control 12 h replicate 2

description:
Library name: CRT12H-2
Bulk RNA-seq analysis of human RPTECs following TNFα and IFNγ stimulation

value: renal proximal tubule epithelial cells

value: WT


title: E11PA_G1Het_A1

description: Library name: A1


title: WT4

description: Library name: A7N55_3

value: Wild-type


title: HEK293 T6 Infected

description:
Library name: Sample 2
HEK293T_Raw_read_counts_matrix.txt

value: Infected with SARS CoV2


title: TNFα + IFNγ 12 h replicate 2

description:
Library name: TaIF12H-2
Bulk RNA-seq analysis of human RPTECs following TNFα and IFNγ stimulation

value: TNFα + IFNγ

value: batch 1


title: Control 12 h replicate 1

description:
Library name: CRT12H-1
Bulk RNA-seq analysis of human RPTECs following TNFα and IFNγ stimulation


title: E11PA_WT_B5

description: Library name: B6

value: Wildtype

value: B


title: LeprCre_aged

first: Yuki

last: Matsushita

state: Nagasaki

address: Sakamoto 1-7-1

institute: Nagasaki University

description:
Library name: geo_submission_scRNAseq_Aged
Uninjured  aged stroma at 18 months

library_source: transcriptomic single cell

data_processing:
The sequencing data was first pre-processed using the BD software Seven Bridges.
For alignment purposes, we generated and used a custom genome fasta and index file by including the sequences of EGFP and tdTomato-WPRE to the mouse genome (GRCm39).
Further downstream analysis steps were performed using the Seurat R package (v.5.1).
We filtered out cells with less than 2,000 genes per cell and more than 20% mitochondrial read content.
The downstream analysis steps include normalization (LogNormalize), identification of highly variable genes across the single cells (vst method), scaling with default settings, dimensionality reduction (PCA and UMAP), unsupervised clustering, and the discovery of differentially expressed cell-type specific markers.
Assembly: GRCm39
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz & matrix.mtx.gz

source_name: Femur bone marrow

extract_protocol:
Femurs were dissected, distal epiphyseal growth plates were removed and proximal ends were cut off. Remaining bones were cut roughly, and cells were enzymatically dissociated. tdTomato+ cells were FACS-isolated. ~30,000 cells per each group were loaded onto the BD Rhapsody HT Xpress (BD Biosciences).
BD Rhapsody HT Xpress (BD Biosciences)

value: Femur bone marrow

value: Bone marrow stromal cells

value: Lepr-cre; R26R-tdTomato


title: PA3321, mutant, rep 2

description:
Library name: PA3321R2
RNA-seq of PA3321::Tn mutant in staticbiofilm formation growth, replication 2

value: Bacteria

value: P. aeruginosa

value: mutant PA3321::Tn

value: Static biofilm grow, 30 oC


title: HEK293 T0

description:
Library name: Sample 1
HEK293T_Raw_read_counts_matrix.txt

value: embryonic kidney cell line

value: ACE Over expression


title: LeprCre_exhausted

description:
Library name: geo_submission_scRNAseq_Ab2
Exhausted stroma at 15 weeks (surgeries at 9 and 13 weeks)

value: 2x bone marrow ablation surgery


title: WT3

description: Library name: A7N25_4

value: brain tissue homogenate of the cerebral cortex

value: male


title: Control 3 h replicate 3

description:
Library name: CRT3H-3
Bulk RNA-seq analysis of human RPTECs following TNFα and IFNγ stimulation

value: RPTEC

value: renal proximal tubule epithelial cells

value: WT

value: untreated


title: db_D10

city: Chicago

first: Timothy

middle: Jon

last: Koh

state: IL

address: 1919 W Taylor Room 650

institute: University of Illinois at Chicago

description: Library name: db_D10

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Skin wound

extract_protocol:
Monocytes and macrophages isolated from skin wounds on male BKS.Cg-Dock7m+/+Leprdb/J on day 3, 6, and 10 post-injury, subjected to enzymatic digestion to obtain single cells and pooled from two mice per time point. Fresh cells with viability over 70% processed using the 10x Chromium platform. Libraries sequenced on HiSeq with paired-end reads. Fastq files were generated and demultiplexed into single cells using Cell Ranger software
10X genomics 3' RNA-seq

value: Skin wound

tag: time point

value: day 10 post-injury


title: WT2

description: Library name: A7N25_3

value: Wild-type


title: LeprCre_naive

description:
Library name: geo_submission_scRNAseq_Ab1
Naive stroma at 15weeks (surgery at 13 weeks)

value: Femur bone marrow

value: Bone marrow stromal cells

value: Lepr-cre; R26R-tdTomato

value: 1x bone marrow ablation surgery


title: db_D6

description: Library name: db_D6

value: day 6 post-injury


title: Control 3 h replicate 2

description:
Library name: CRT3H-2
Bulk RNA-seq analysis of human RPTECs following TNFα and IFNγ stimulation

value: batch 1


title: WT1

description: Library name: A7N20_6


title: Control 3 h replicate 1

description:
Library name: CRT3H-1
Bulk RNA-seq analysis of human RPTECs following TNFα and IFNγ stimulation


title: PA01, wt control, rep 3

description:
Library name: WTR3
RNA-seq of PA01 in staticbiofilm formation growth, replication 1

value: Bacteria

value: P. aeruginosa

value: wild type PA01

value: Static biofilm grow, 30 oC


title: LeprCre_control

description:
Library name: geo_submission_scRNAseq_Cont
Uninjured control stroma at 15 weeks


title: db_D3

description: Library name: db_D3

value: day 3 post-injury


title: Turmeric ELN 1

status: Public on Jun 15 2026

city: Louisville

first: Huang-Ge

last: Zhang

state: KY

address: 505 S Hancock Street

department: James Graham Brown Cancer Center

institute: University of Louisville

data_processing:
Illumina Casava v1.8.4 software used for basecalling.
Raw fastqs were adapter and quality score trimmed with cutadapt v1.10. with a minimum length of 15 nt.
MicroRNAs were identified using the sRNABench Pipeline (version 05/14).
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Curcuma longa

source_name: Turmeric root

extract_protocol:
Total RNA exptracted with miRNeasy Mini Kit (Qiagen)
Small RNA libraries were generated with 100ng of total RNA and TruSeq Small RNA library Prep Reference Guide (illumina) according to the manufacturer’s instructions. Equal amounts of libraries were pooled and sequenced on the Illumina HiSeq 2500 using NextSeq Sequencing Kit (illumina).

value: Turmeric nanoparticle


title: Turmeric ELN 2


title: 2-GEX

city: Suita

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
Sequencing was performed on DNBSEQ-G400 (MGI Tech) platform in a 28+100 base paired-end mode.
Generated reads were input into the cellranger pipeline (Cell Ranger v.6.0.0, 10x Genomics) for UMI counting for each gene - cell (barcode) combination.
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: genematrix.csv: comma-delimited text files including UMI counts for all cells detected

source_name: Peripheral blood

extract_protocol:
Sinlge cell droplets were generated by 10x Genomics Chromium Controller, and cDNAs with UMIs were generated at single-cell level.
The single cell libraries were prepared following the protocol outlined in the Chromium Single Cell 5' Reagent Kits v2 User Guide and using MGI Universal Library Conversion kit (App-A).

value: Peripheral blood

value: sample cocultured with KO tumor


title: 1-GEX

value: sample cocultured with WT tumor


title: RNA-Seq of Danio rerio: adult female FG follicle, FSHB-LHCGR-Mut. (Rep.4)

city: Macau

first: Chu

last: ZENG

address: Avenida da Universidade Taipa

country: Macau

institute: University of Macau

description:
Library name: fshb_lhcgr_5
raw_counts.xls
gene_fpkm.xls
fshb_lhcgrvsCtrl.xls

data_processing:
Differential expression analysis was performed using the DESeq2 R package (1.20.0). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach to control the false discovery rate. Genes with an adjusted P-value < 0.05 were considered differentially expressed genes (DEGs) with statistical significance. DEGs were then subjected to Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses.
Assembly: Not involved
Supplementary files format and content: Excel table includes raw counts for each Sample
Supplementary files format and content: Excel table includes differential expression results for each Sample

organism: Danio rerio

source_name: ovary

growth_protocol: The zebrafish (180 dpf) were maintained under controlled conditions in the ZebTEC Multilinking Zebrafish system (Tecniplast, Buguggiate, Italy), with a temperature of 28 ± 1 °C, a pH of 7.3, and a photoperiod of 14-h light and 10-h darkness (light on at 8:30 am). They were fed with Otohime fish diet (Marubeni Nisshin Feed, Tokyo, Japan) twice daily.

extract_protocol:
RNA was harvested using Trizol reagent.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads and the sequencing libraries were prepared using the TruSeq RNA Library Prep Kit (Illumina, San Diego, CA)

treatment_protocol: The sampled ovaries from each fish were placed in a microtube containing 1 mL L15 medium (Sigma-Aldrich). Fat tissues and ligaments surrounding the ovaries were removed using the BD Microlance 26G needle (BD, San Diego, CA). The ovarian fragments were then gently pipetted multiple times with a transfer pipette (JET Biofil, Guangzhou, China) to disperse the follicles. FG follicles (> 650 μm) were enriched by passing the suspended follicles through a 600 μm filter (SPL Lifesciences, Waunakee, WI) and manually selected for subsequent transcriptome (RNA-seq) analysis.

value: ovary

value: FSHB-LHCGR-Mut.


title: RNA-Seq of Danio rerio: adult female FG follicle, FSHB-LHCGR-Mut. (Rep.3)

description:
Library name: fshb_lhcgr_4
raw_counts.xls
gene_fpkm.xls
fshb_lhcgrvsCtrl.xls


title: RNA-Seq of Danio rerio: adult female FG follicle, FSHB-LHCGR-Mut. (Rep.2)

description:
Library name: fshb_lhcgr_3
raw_counts.xls
gene_fpkm.xls
fshb_lhcgrvsCtrl.xls


title: RNA-Seq of Danio rerio: adult female FG follicle, FSHB-LHCGR-Mut. (Rep.1)

description:
Library name: fshb_lhcgr_2
raw_counts.xls
gene_fpkm.xls
fshb_lhcgrvsCtrl.xls


title: RNA-Seq of Danio rerio: adult female FG follicle, LHB-LHCGR-Mut. (Rep.4)

description:
Library name: lhb_lhcgr_5
raw_counts.xls
gene_fpkm.xls
lhb_lhcgrvsCtrl.xls

value: LHB-LHCGR-Mut.


title: RNA-Seq of Danio rerio: adult female FG follicle, LHB-LHCGR-Mut. (Rep.3)

description:
Library name: lhb_lhcgr_4
raw_counts.xls
gene_fpkm.xls
lhb_lhcgrvsCtrl.xls


title: RNA-Seq of Danio rerio: adult female FG follicle, LHB-LHCGR-Mut. (Rep.1)

description:
Library name: lhb_lhcgr_2
raw_counts.xls
gene_fpkm.xls
lhb_lhcgrvsCtrl.xls


title: RNA-Seq of Danio rerio: adult female FG follicle, Ctrl (Rep. 3)

description:
Library name: C5
raw_counts.xls
gene_fpkm.xls

value: Ctrl


title: PA01, wt control, rep 1

description:
Library name: WTR1
RNA-seq of PA01 in staticbiofilm formation growth, replication 1


title: RNA-Seq of Danio rerio: adult female FG follicle, LHB-LHCGR-Mut. (Rep.2)

description:
Library name: lhb_lhcgr_3
raw_counts.xls
gene_fpkm.xls
lhb_lhcgrvsCtrl.xls


title: RNA-Seq of Danio rerio: adult female FG follicle, Ctrl (Rep. 2)

description:
Library name: C3
raw_counts.xls
gene_fpkm.xls


title: Cutntag_Ovaries 512c, MTD-GAL4_piwi_sh H3K27me3, rep 1

city: Risskov

first: Thomas

middle: Høgsbro

last: Grønbæk

address: Broloftet 5, 4.tv

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

description: Library name: Sample_85

data_processing:
RNA and sRNAseq: RNA reads were demultiplexed and trimmed for standard illumina adapter sequences including 4 random nucleotides from each end.
cutntag: Paired-end illumina reads were adapter-trimmed using Trim Galore for standard illumina adapters.
Assembly: dm6, r6.63
Supplementary files format and content: SLX-19644_totalRNA_RNAseq_GeTMM_TE_sense.xlsx, R17585_TOsK_MZ-piwiaub_dKD_TE_GeTMM_sense.xlsx, R18168_GeTMM_gene.xlsx,  R18168_GeTMM_TE_sense.xlsx, SLX-17461_GeTMM_gene.xlsx. All xlsx file with RNAseq reads mapping to TE consensus sequences in sense orientation or to whole transcriptiome. Mapped to the Drosophila transcriptome using STAR, allowing 2 mismatches and uniquely mapped reads were used for downstream analysis. Gene expression quantification was normalized using Gene length corrected TMM using edgeR (v3.34.0).
Supplementary files format and content: R16775_1kb_tiles_RNA_mappers_sum-PlusMinus.xlsx. xlsx file, Small RNAseq mapping to 1kb tiles. Not accounting for orientation (summed). Reads were mapped to the Drosophila genome using Bowtie allowing 0 MM and only uniquely mapping reads. Read coverage was quantified over non-overlapping 1 kb genomic windows using bedtools and normalized to 10 million uniquely mapping reads.
Supplementary files format and content: CutnTag_avg_GeTMM_TE_consensus_unistrand.xlsx. Xlsx file, cutntag reads mapping to TE consensus sequence unistrand. Mapped to the Drosophila transcriptome using Bowtie, allowing 0 mismatches and uniquely mapped reads were used for downstream analysis. Gene expression quantification was normalized using Gene length corrected TMM using edgeR (v3.34.0).
Supplementary files format and content: CutnTag_bam_Table_for_heatmap_log2CPMadd1_single_TE_insertions.xlsx. Xlsx table of cutntag reads mapping to 50bp windows 500bp +/- to all identified single TE insertions in log2 counts per million (CPM). Reads were mapped to in-house ONT long-read assembled D. melanogaster genome from MTD-GAL4; white-sh fly cross using Bowtie2 with concordant-only alignment. The resulting alignments were coordinate-sorted and duplicate marking was done using samtools. Finally reads were filtered for only paired alignments with MAPQ ≥ 30 and no duplicates. Bigwig tracks (all mappers and unique mappers) were generated per sample using deeptools bamCoverage (bin size 10 bp, CPM normalization). Bigwig tracks were intersected with TE insertion coordinates (CutnTag_single_TE_insertions_table.xlsx) from long read DNA sequencing and Cut&Tag data for info on how these were called).
Supplementary files format and content: CutnTag_single_TE_insertions_table.xlsx. Xlsx file of single TE insertions and genome coordinates. TE annotation in long-read genome assembly was done using EDTA v. 2.2 with Drosophila consensus TE library supplied as the reference. TE annotation with CUT&Tag data was done using ngs_te_mapper2 v. 1.0.2. Briefly, the reads from CUT&Tag experiments were used to search for TE insertions by means of finding reads spanning TE consensus sequence and flanking long-read genome assembly sequence at candidate insertion sites. To call an insertion, we required the detection of reads spanning the TE and the flanking genome at both ends of the TE. Insertions identified this way were then pooled for the same fly line and then we analyzed only TE insertions present – but not necessarily homozygous – across every experimental cross in our CUT&Tag analyses.
Library strategy: CUT&Tag

organism: Drosophila melanogaster

source_name: Sorted 512C nurse cell nuclei

growth_protocol: D. melanogaster strains were crossed and reared for experiments at 25°C and 70% humidity with 12:12 hrs light/dark cycle in vials containing standard medium. Before dissection, the flies were fed extra yeast and kept with 3-5 males to support ovary development. The day before dissection, the flies were transferred to a fresh vial to provide the females ample space for egg-laying, preventing egg accumulation in the ovaries.

extract_protocol:
Bulk ovary RNA and small-RNA: 6-8 Ovary pairs from 3-4 days old females were dissected into ice-cold Phosphate-buffered saline (PBS) for bam mutant flies. Bam mutant and heat-shock bam ovarian cysts: 30 ovarian cysts were collected for each sample to compensate for their significantly smaller size.  RNA isolation for RNAseq and small-RNAseq: Samples were subjected to homogenization in TRIzolTM using handheld elecrtric pestle. After 5 minutes incubation Chloroform was added and samples were shaken vigorously and incubated for 3 minutes at RT, then centrifuged at 12,000g and 4°C for 15 minutes. The aqueous phase was transferred to a clean tube and the RNA was subsequently purified first using isopropanol and pelleting the RNA then 75% ethanol. The RNA was resuspended in Rnase-free water and concentrations were measured by spectrophotometry. The samples were stored at -70°C if not immediately used for RNA or small-RNA sequencing library preparation.  Cut&tag: approximately 150 whole ovaries were dissected into Drosophila Ringers buffer for 512C nurse cell nuclei FACS sorting. the ovaries were digested in 5mg/mL collagenase for 15 minutes at RT with continous shaking and intermittent pipetting. Cell suspension was collected by centrifugation 3min at 500rcf and rinced buffort adding nuclear isolation buffer. We disrupted cells with 10 strokes in a Dounce homogenizer with the B pestle and the homogenate was filtered twice through 100µM Nitex mesh. The filtered homogenate was placed on a sucrose step gradient of 2.2 M, 1.6 M, and 0.8 M sucrose and centrifuged for 20 min at 20,000 x g. After centrifugation the sucrose gradient was removed and the pellet was resuspended in nuclear isolation buffer. Hoechst was added to the homogenate at a concentration of 0.5 mg/ml. Nuclei were stored on ice until FACS. Approximately 400 ovaries from Vasa-GFP, bam-/- ovarian cysts, were dissected into Schneider’s insect medium supplemented with 10% fetal bovine serum. GSC-like cells were collected based GFP positive staining. Vasa-GFP, bam –/– ovaries were dissociated in 0,5% trypsin–0,05% EDTA and 5 mg/mL collagenase for 15 min at room temperature, with continuous shaking and intermittent pipetting. Ovarian cell suspension is then filtered through a 70µM Nitex mesh to remove aggregates or debris. The filter was rinsed with S-FBS and cells were collected by centrifugation 5min at 400g, 4ºC. Cells were stored on ice and GFP-positive germline cells were elected from the suspension via fluorescence-activated cell sorting (FACS).
RNAseq: RNA Sample of 2 µg were DNaseI treated and purified using the RNA clean & ConcentratorTM-5 kit (ZYMO #R1013). mRNA were isolated by polyA-RNA enrichment using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760S). For total RNAseq, Ribosomal RNA was removed by hybridisation to standard 50nt DNA oligos covering relevant regions in the rRNA precursor and mitochrondrial genome in ratio 1µg RNA : 4µg oligomix and subsequent digestion using thermostable RNAse H (NEB #M0523S). Libraries were cloned using the NEBNextTM Ultra II directional RNA library prep kit for illumina (NEB # E7760) following the instructions. libraries were amplified by PCR using Q5 high-fidelity DNA polymerase with unique dual barcoded primers. Amplified libraries were purified using homemade SPRI (“Ampure”)-beads. Samples were multiplexed in equal amounts and sequenced by VBCF NGS facility on an illumina NovaSeq X flowcell single- or paried-end or an illumina HiSeq 4000 flowcell paired-end or at the CRUK facility in cambridge on an illumina NovaSeq 6000 flowcell singleRead.  Small-RNA: Argonaute bound small RNAs were isolated using the Trans-kingdom, rapid, affordable Purification of RISCs (TRAPR) isolation technique specified in the punlication: Grentzinger et al. 2020. “A Universal Method for the Rapid Isolation of All Known Classes of Functional Silencing Small RNAs.” Nucleic Acids Research 48 (14): e79. sRNA libraries were generated based on protocol from:  Jayaprakash et al. 2011. “Identification and Remediation of Biases in the Activity of RNA Ligases in Small-RNA Deep Sequencing.” Nucleic Acids Research 39 (21): e141. In brief, 3’ linker ligation was performed by adding uniquely barcoded 3’RNA linkers to the samples. Ligation was performed O/N using T4 RNA ligase 2, truncated K227Q (NEB #M0242). The samples were then multiplexed into sub-multiplexes of individually barcoded samples (biological replicates together), and purified using ZYMO RNA clean and concentrator-5 kit (ZYMO #R1013).  Then the samples were recovered and size selected for 52-63 nt reads (18-29nt RNAs + 3’linker) using PAGE purification. To follow exact size selection on the gel, fluorescently labeled oligos migrating similar to 40 and 60-nucleotide single-stranded RNA was added to samples prior to gel electrophoresis. PAGE purification was performed using ZYMO small-RNATM PAGE Recovery Kit (ZYMO #R1070). 5’ RNA linkers were added to samples, and ligation was performed O/N using T4 RNA ligase (NEB #M0204). The samples were subjected to SPRI purification. The sRNA libraries were then reverse transcribed using Superscript II (InvitrogenTM #18064014) following the manufacturer's instructions using the illumina_RvnTxn primer. Libraries were amplified by PCR using Q5 High-Fidelity DNA Polymerases (NEB #M0491) and unique dual-barcoded primers. Samples were then inspected and purified from a 2% low-melt agarose gel using the Zymoclean gel DNA recovery kit (ZYMO #D4001). Concentrations were measured using QubitTM DNA HS kit (InvitrogenTM Q32851) and sub-multiplexes were multiplexed in equal amounts and sequenced by VBCF NGS facility on a NovaSeqX XP flowcell singleRead.  Cut&tag: Library preparation were conduced on freshly FACS-isolated cells or nuclei in duplicates following the published protocol with minor modifications Kaya-Okur et al. 2019. “CUT&Tag for Efficient Epigenomic Profiling of Small Samples and Single Cells.” Nature Communications 10 (1): 1930. Around 40,000 GSCs sorted-cells (40,000 2C cells) and 500-800 512C sorted-nuclei  (128,000-200,000 2c nuclei) were used for each CUT&Tag reaction. The cells or nuclei were bound to 10µL of concanavalin A-coated beads (Polysciences,  86057-10) by incubation 15min at room temperature . The unbound supernatant was removed and bead-bound cells/nuclei were resuspended in Wash Buffer (WB150 : 20 mM HEPES pH 7.9; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail; 0.05% Digitonin) containing 2 mM EDTA and 0,1% BSA with the appropriate primary antibody (listed in the Reagent Table). Primary antibody incubation was performed on a rotating platform overnight at 4 °C. Secondary antibodies were then added (1:100 dilution in WB150) and incubate for 1h at room temperature. Protein A–Tn5 transposase (gift from the Joan Barau laboratory), pre-loaded with MEDS adaptors (see Oligonucleotide Table), was added at a 1:200 dilution in WB150 with adapted 0,01% Digitonin (WB300). Following an incubation of 1h at room temperature, cells/nuclei and beads were washed with WB300 and mixed in a tagmentation buffer (10 mM MgCl2 in WB300). The tagmentation was performed 1h at 37ºC and stoped by adding 10µL a Digest solution ( 90mM EDTA, 1,2% SDS, 3mg/mL Proteinase K) and incubate 1h at 55ºC. DNA was extracted using the DNA Clean & Concentrator kit and libraries were amplified by Q5 high-fidelity DNA polymerase with unique dual barcoded primers for 10-15 amplification cycles. Amplified libraries were purified using homemade SPRI (“Ampure”)-beads and DNA quality was assessed using the 5200 Fragment Analyzer system. Pooled  libraries  were  sequenced by the VBCF NGS facility on an Illumina NextSeq 2000 sequencing device.

treatment_protocol: For heat-shock bam experiments: Heat-shock treatment was performed on 3-4 day old females as described in (Samuels et al. 2024). The treatment involved 1 hour at 37°C followed by 2 hours at 34°C. The 'hours after HS' is defined as starting immediately after this 3-hour treatment.

value: Sorted 512C nurse cell nuclei

value: nuclei 512c nurse cell

value: Cog-GAL4 / w; internalGT-GAL4/+ ; nos-GAL4/pGLKD>piwi_sh2[attP2];

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit Monoclonal Antibody #9733 (Cell Signaling Technology)


title: Cutntag_Ovaries 512c, MTD-GAL4_piwi_sh H3K4me3, rep 2

description: Library name: Sample_84

value: Tri-Methyl-Histone H3 (Lys4) (C42D8) Rabbit Monoclonal Antibody #9751 (Cell signaling technology)


title: Cutntag_Ovaries 512c, MTD-GAL4_piwi_sh H3K27me3, rep 2

description: Library name: Sample_86


title: RNA-Seq of Danio rerio: adult female FG follicle, Ctrl (Rep. 1)

description:
Library name: C1
raw_counts.xls
gene_fpkm.xls


title: Cutntag_Ovaries 512c, MTD-GAL4_piwi_sh H3K4me3, rep 1

description: Library name: Sample_83


title: Cutntag_Ovaries 512c, MTD-GAL4_piwi_sh H3K9me3, rep 2

description: Library name: Sample_82

value: Anti-Histone H3 (tri methyl K9) rabbit monoclonal antibody #ab176916 (abcam)


title: Cutntag_Ovaries 512c, MTD-GAL4_piwi_sh H3K9me3, rep 1

description: Library name: Sample_81


title: Cutntag_Ovaries 512c, MTD-GAL4_white_sh H3K27me3, rep 2

description: Library name: Sample_80

value: Cog-GAL4 / w; internalGT-GAL4/+; nos-GAL4/pW20>w_sh[attP2];


title: Cutntag_Ovaries 512c, MTD-GAL4_white_sh H3K27me3, rep 1

description: Library name: Sample_79


title: Cutntag_Ovaries 512c, MTD-GAL4_white_sh H3K4me3, rep 1

description: Library name: Sample_77


title: Cutntag_Ovaries 512c, MTD-GAL4_white_sh H3K4me3, rep 2

description: Library name: Sample_78


title: Cutntag_Ovaries 512c, MTD-GAL4_white_sh H3K9me3, rep 2

description: Library name: Sample_76


title: Cutntag_Ovaries 512c, MTD-GAL4_white_sh H3K9me3, rep 1

description: Library name: Sample_75


title: Cutntag_BamMut GSCs, Nos-GAL4_piwi_sh H3K27me3, rep 2

description: Library name: Sample_74

source_name: Sorted GSCs from bam mutant

value: Sorted GSCs from bam mutant

value: GSCs

value: w ;  bam[delta86], nos>GAL4_VP16, GFP_Vas [attP2]/ e[1] bam[Delta86], pGLKD>piwi_sh2[attP2]


title: Cutntag_BamMut GSCs, Nos-GAL4_piwi_sh H3K4me3, rep 2

description: Library name: Sample_72


title: Cutntag_BamMut GSCs, Nos-GAL4_piwi_sh H3K4me3, rep 1

description: Library name: Sample_71


title: Cutntag_BamMut GSCs, Nos-GAL4_piwi_sh H3K27me3, rep 1

description: Library name: Sample_73


title: Cutntag_BamMut GSCs, Nos-GAL4_piwi_sh H3K9me3, rep 1

description: Library name: Sample_69


title: Cutntag_BamMut GSCs, Nos-GAL4_white_sh H3K27me3, rep 2

description: Library name: Sample_68

value: w ;  bam[delta86], nos>GAL4_VP16, GFP_Vas [attP2]/ e[1] bam[Delta86], pW20>w_sh[attP2]


title: Cutntag_BamMut GSCs, Nos-GAL4_piwi_sh H3K9me3, rep 2

description: Library name: Sample_70


title: Cutntag_BamMut GSCs, Nos-GAL4_white_sh H3K4me3, rep 2

description: Library name: Sample_66


title: Cutntag_BamMut GSCs, Nos-GAL4_white_sh H3K27me3, rep 1

description: Library name: Sample_67


title: Cutntag_BamMut GSCs, Nos-GAL4_white_sh H3K9me3, rep 2

description: Library name: Sample_64


title: Cutntag_BamMut GSCs, Nos-GAL4_white_sh H3K4me3, rep 1

description: Library name: Sample_65


title: LPFC1

description: 10 days of heroin self-administration (0.075mg/kg)

value: prefrontal cortex

value: Sprague-Dawley

value: male

value: adult

value: heroin self-administration for 10 days


title: Cutntag_BamMut GSCs, Nos-GAL4_white_sh H3K9me3, rep 1

description: Library name: Sample_63


title: sRNA_Ovaries, MTD-GAL4_piwi_sh, rep 2

description: Library name: Sample_62

library_source: other

data_processing:
RNA and sRNAseq: RNA reads were demultiplexed and trimmed for standard illumina adapter sequences including 4 random nucleotides from each end.
cutntag: Paired-end illumina reads were adapter-trimmed using Trim Galore for standard illumina adapters.
Assembly: dm6, r6.63
Supplementary files format and content: SLX-19644_totalRNA_RNAseq_GeTMM_TE_sense.xlsx, R17585_TOsK_MZ-piwiaub_dKD_TE_GeTMM_sense.xlsx, R18168_GeTMM_gene.xlsx,  R18168_GeTMM_TE_sense.xlsx, SLX-17461_GeTMM_gene.xlsx. All xlsx file with RNAseq reads mapping to TE consensus sequences in sense orientation or to whole transcriptiome. Mapped to the Drosophila transcriptome using STAR, allowing 2 mismatches and uniquely mapped reads were used for downstream analysis. Gene expression quantification was normalized using Gene length corrected TMM using edgeR (v3.34.0).
Supplementary files format and content: R16775_1kb_tiles_RNA_mappers_sum-PlusMinus.xlsx. xlsx file, Small RNAseq mapping to 1kb tiles. Not accounting for orientation (summed). Reads were mapped to the Drosophila genome using Bowtie allowing 0 MM and only uniquely mapping reads. Read coverage was quantified over non-overlapping 1 kb genomic windows using bedtools and normalized to 10 million uniquely mapping reads.
Supplementary files format and content: CutnTag_avg_GeTMM_TE_consensus_unistrand.xlsx. Xlsx file, cutntag reads mapping to TE consensus sequence unistrand. Mapped to the Drosophila transcriptome using Bowtie, allowing 0 mismatches and uniquely mapped reads were used for downstream analysis. Gene expression quantification was normalized using Gene length corrected TMM using edgeR (v3.34.0).
Supplementary files format and content: CutnTag_bam_Table_for_heatmap_log2CPMadd1_single_TE_insertions.xlsx. Xlsx table of cutntag reads mapping to 50bp windows 500bp +/- to all identified single TE insertions in log2 counts per million (CPM). Reads were mapped to in-house ONT long-read assembled D. melanogaster genome from MTD-GAL4; white-sh fly cross using Bowtie2 with concordant-only alignment. The resulting alignments were coordinate-sorted and duplicate marking was done using samtools. Finally reads were filtered for only paired alignments with MAPQ ≥ 30 and no duplicates. Bigwig tracks (all mappers and unique mappers) were generated per sample using deeptools bamCoverage (bin size 10 bp, CPM normalization). Bigwig tracks were intersected with TE insertion coordinates (CutnTag_single_TE_insertions_table.xlsx) from long read DNA sequencing and Cut&Tag data for info on how these were called).
Supplementary files format and content: CutnTag_single_TE_insertions_table.xlsx. Xlsx file of single TE insertions and genome coordinates. TE annotation in long-read genome assembly was done using EDTA v. 2.2 with Drosophila consensus TE library supplied as the reference. TE annotation with CUT&Tag data was done using ngs_te_mapper2 v. 1.0.2. Briefly, the reads from CUT&Tag experiments were used to search for TE insertions by means of finding reads spanning TE consensus sequence and flanking long-read genome assembly sequence at candidate insertion sites. To call an insertion, we required the detection of reads spanning the TE and the flanking genome at both ends of the TE. Insertions identified this way were then pooled for the same fly line and then we analyzed only TE insertions present – but not necessarily homozygous – across every experimental cross in our CUT&Tag analyses.

molecule: other

source_name: bam mutant ovarian cysts

value: bam mutant ovarian cysts

value: Bulk ovarian cysts


title: sRNA_Ovaries, MTD-GAL4_piwi_sh, rep 1

description: Library name: Sample_61


title: sRNA_Ovaries, MTD-GAL4_white_sh, rep 2

description: Library name: Sample_60


title: Liver, Low-protein diet, rep4

description: Library name: LIVER_LP_4

value: Liver

value: Low-protein diet


title: sRNA_BamMut 68h-Heat-Shock, nos-GAL4_piwi_sh, rep 3

description: Library name: Sample_58

value: w ; nosP-GAL4-NGT40/+ ; e[1] bam[Delta86], pGLKD>piwi_sh2[attP2]/ bam[Delta86], P{w[+mC]=hs-bam.O}11d


title: sRNA_BamMut No-Heat-Shock, nos-GAL4_piwi_sh, rep 3

description: Library name: Sample_57


title: sRNA_Ovaries, MTD-GAL4_white_sh, rep 1

description: Library name: Sample_59


title: sRNA_BamMut 68h-heat-shock, nos-GAL4_white_sh, rep 3

description: Library name: Sample_56

value: w ; nosP-GAL4-NGT40/+ ; e[1] bam[Delta86], pW20>w_sh[attP2] / bam[Delta86], P{w[+mC]=hs-bam.O}11d


title: sRNA_BamMut No-Heat-Shock, nos-GAL4_white_sh, rep 3

description: Library name: Sample_55


title: sRNA_BamMut No-Heat-Shock, nos-GAL4_piwi_sh, rep 2

description: Library name: Sample_53


title: sRNA_BamMut 68h-heat-shock, nos-GAL4_white_sh, rep 2

description: Library name: Sample_52


title: sRNA_BamMut 68h-Heat-Shock, nos-GAL4_piwi_sh, rep 2

description: Library name: Sample_54


title: sRNA_BamMut No-Heat-Shock, nos-GAL4_white_sh, rep 2

description: Library name: Sample_51


title: sRNA_BamMut 68h-Heat-Shock, nos-GAL4_piwi_sh, rep 1

description: Library name: Sample_50


title: sRNA_BamMut No-Heat-Shock, nos-GAL4_piwi_sh, rep 1

description: Library name: Sample_49


title: sRNA_BamMut 68h-heat-shock, nos-GAL4_white_sh, rep 1

description: Library name: Sample_48


title: sRNA_BamMut No-Heat-Shock, nos-GAL4_white_sh, rep 1

description: Library name: Sample_47


title: PolyA-RNA_Ovaries, TOsK-GAL4_piwi_sh, rep 3

description: Library name: Sample_38

source_name: Ovaries

value: Ovaries

value: Bulk ovaries

value: w ; matalpha-GAL4-VP16, osk-GAL4-VP16 / + ; pGLKD>piwi_sh2[attP2] / +


title: PolyA-RNA_Ovaries, TOsK-GAL4_piwi_sh, rep 2

description: Library name: Sample_37


title: PolyA-RNA_Ovaries, TOsK-GAL4_piwi_sh, rep 1

description: Library name: Sample_36


title: PolyA-RNA_Ovaries, TOsK-GAL4_white_sh, rep 3

description: Library name: Sample_35

value: w ; matalpha-GAL4-VP16, osk-GAL4-VP16 / + ; pW20>w_sh[attP2] / +


title: PolyA-RNA_Ovaries, TOsK-GAL4_white_sh, rep 2

description: Library name: Sample_34


title: PolyA-RNA_Ovaries, TOsK-GAL4_white_sh, rep 1

description: Library name: Sample_33


title: SARS-CoV2_NSP14-mut passage 5 in VERO-AT cells

last: Xiang

address: 7703 FLOYD CURL DR

institute: UT Health San Antonio

description: Library name: P5_NSP14-mut-VERO-AT

data_processing:
Sequencing reads were mapped to the reference genome using minimap2
Per-position read depth was calculated using samtools
Variants were called from samtools mpileup by quantifying reference and alternate base counts at each position, followed by filtering based on sequencing quality, minimum coverage thresholds, and a minimum alternate allele frequency of 1.5%.
Assembly: recombinant SARS-CoV-2 genome included in the supplemental file
Supplementary files format and content: reference gemone in fasta format
Supplementary files format and content: reference GTF file
Supplementary files format and content: excel file containg read depth of every samples
Supplementary files format and content: excel file containg error rate per position of every samples
Supplementary files format and content: excel file containg SNP frequency of every samples

source_name: Vero cells expressing ACE2 and Tmprss2

extract_protocol:
Culture supernatants from serial passages of recombinant SARS-CoV-2 in Vero-NP or Vero-AT cells were processed for RNA extraction using TRIzol LS reagent (Invitrogen) according to the manufacturer’s instructions.
The extracted RNA was converted into sequencing libraries and subjected to paired-end deep sequencing (100 or 150 bp reads) with NovaSeq 6000 system

value: Vero cells expressing ACE2 and Tmprss2

value: passage 5


title: PolyA-RNA_BamMut 68h-heat-shock, nos-GAL4_moon_sh, rep 2

description: Library name: Sample_32

value: w ; nosP-GAL4-NGT40/+ ; e[1] bam[Delta86], pW20>moon_sh3[attP2]/ bam[Delta86], P{w[+mC]=hs-bam.O}11d


title: PolyA-RNA_BamMut 68h-heat-shock, nos-GAL4_moon_sh, rep 1

description: Library name: Sample_31


title: PolyA-RNA_BamMut 68h-heat-shock, nos-GAL4_piwi_sh, rep 2

description: Library name: Sample_30


title: PolyA-RNA_BamMut 68h-heat-shock, nos-GAL4_piwi_sh, rep 1

description: Library name: Sample_29


title: PolyA-RNA_BamMut 68h-heat-shock, nos-GAL4_white_sh, rep 1

description: Library name: Sample_27


title: PolyA-RNA_BamMut 68h-heat-shock, nos-GAL4_white_sh, rep 2

description: Library name: Sample_28


title: PolyA-RNA_BamMut 42h-heat-shock, nos-GAL4_moon_sh, rep 2

description: Library name: Sample_26


title: PolyA-RNA_BamMut 42h-heat-shock, nos-GAL4_moon_sh, rep 1

description: Library name: Sample_25


title: PolyA-RNA_BamMut 42h-heat-shock, nos-GAL4_piwi_sh, rep 2

description: Library name: Sample_24


title: PolyA-RNA_BamMut 42h-heat-shock, nos-GAL4_piwi_sh, rep 1

description: Library name: Sample_23


title: PolyA-RNA_BamMut 42h-heat-shock, nos-GAL4_white_sh, rep 1

description: Library name: Sample_21


title: PolyA-RNA_BamMut 42h-heat-shock, nos-GAL4_white_sh, rep 2

description: Library name: Sample_22


title: PolyA-RNA_BamMut No-Heat-Shock, nos-GAL4_moon_sh, rep 2

description: Library name: Sample_20


title: PolyA-RNA_BamMut No-Heat-Shock, nos-GAL4_piwi_sh, rep 2

description: Library name: Sample_18


title: PolyA-RNA_BamMut No-Heat-Shock, nos-GAL4_piwi_sh, rep 1

description: Library name: Sample_17


title: PolyA-RNA_BamMut No-Heat-Shock, nos-GAL4_moon_sh, rep 1

description: Library name: Sample_19


title: PolyA-RNA_BamMut No-Heat-Shock, nos-GAL4_white_sh, rep 2

description: Library name: Sample_16


title: PolyA-RNA_BamMut No-Heat-Shock, nos-GAL4_white_sh, rep 1

description: Library name: Sample_15


title: PolyA-RNA_Ovaries, MTD-GAL4_piwi_sh, rep 2

description:
Library name: Sample_14
piwiKD_2 polyA-TNA_MTD-GAL4_run18168

value: Cog-GAL4 / w; internalGT-GAL4/+ ; nos-GAL4/pGLKD>piwi_sh2[attP2];


title: PolyA-RNA_Ovaries, MTD-GAL4_piwi_sh, rep 1

description:
Library name: Sample_13
piwiKD_1 polyA-TNA_MTD-GAL4_run18168


title: PolyA-RNA_Ovaries, MTD-GAL4_white_sh, rep 2

description:
Library name: Sample_12
control_2 polyA-RNA_MTD-GAL4_run18168

value: Cog-GAL4 / w; internalGT-GAL4/+; nos-GAL4/pW20>w_sh[attP2];


title: PolyA-RNA_Ovaries, MTD-GAL4_white_sh, rep 1

description:
Library name: Sample_11
control_1 polyA-RNA_MTD-GAL4_run18168


title: RNA_Ovaries, TOsK-GAL4_MZ_piwiAub_sh, rep 1

description:
Library name: Sample_10
post-mitotic and pre-GSC piwiaubKD RNA_run17585

value: ; pV20>piwi_sh3[attP40] / matalpha-GAL4-VP16, osk-GAL4-VP16 ; pGLKD>aub_sh[attP2] / +

value: P0-male:shRNAs, P0-female:GAL4


title: RNA_Ovaries, TOsK-GAL4_M_piwiAub_sh, rep 1

description:
Library name: Sample_9
pre-GSC_piwiaubKD RNA_run17585

value: ; pV20>piwi_sh3[attP40] / CyO ; pGLKD>aub_sh[attP2 / +


title: RNA_Ovaries, TOsK-GAL4_Z_piwiAub_sh, rep 1

description:
Library name: Sample_8
post-mitotic_piwiaubKD RNA_run17585

value: p0-male:GAL4 , P0-female:shRNAs


title: RNA_Ovaries, TOsK-GAL4_O-Ctrl, rep 1

description:
Library name: Sample_7
control for piwiaub RNA_run17585

value: ; pV20>piwi_sh3[attP40] / CyO ; pGLKD>aub_sh[attP2]/+

value: P0-male:GAL4 , P0-female:shRNAs


title: WGS ΔaddAB Plus IPTG-2

city: Nashville

first: Juan

last: Carvajal Garcia

state: TN

address: 2215 Garland Avenue

institute: Vanderbilt University

description: Library name: Sample 14

data_processing:
Data processing with fastp
Data alignment with bowtie2
Assembly: Bacillus subtilis subsp. subtilis str. JH642 substr. AG174
Supplementary files format and content: Genomic coordinate (position in the B. subtilis chromosome) for each read in the whole genome sequencing file (txt files)

organism: Bacillus subtilis

extract_protocol:
Phenol-Chloroform
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®

value: Bacteria


title: WGS ΔaddAB Plus IPTG-1

description: Library name: Sample 13


title: WGS ΔaddAB Minus IPTG-2

description: Library name: Sample 12


title: WGS ΔaddAB Minus IPTG-1

description: Library name: Sample 11


title: WGS WT Plus IPTG-1

description: Library name: Sample 9


title: WGS WT Minus IPTG-2

description: Library name: Sample 8


title: WGS WT Plus IPTG-2

description: Library name: Sample 10


title: WGS WT Minus IPTG-1

description: Library name: Sample 7


title: Tn-seq. Plus IPTG-3

description: Library name: Sample 6

data_processing:
Data processing with fastp
Data alignment with bowtie2
Assembly: Bacillus subtilis subsp. subtilis str. JH642 substr. AG174
Supplementary files format and content: Genomic coordinate (position in the B. subtilis chromosome) of each transposon insertion (csv files)

extract_protocol:
Phenol-Chloroform
For Tn-seq: custom method derived from Dobihal et al., 2022.


title: Tn-seq. Plus IPTG-2

description: Library name: Sample 5


title: Tn-seq. Plus IPTG-1

description: Library name: Sample 4


title: Tn-seq. Minus IPTG-3

description: Library name: Sample 3


title: Tn-seq. Minus IPTG-2

description: Library name: Sample 2


title: Tn-seq. Minus IPTG-1

description: Library name: Sample 1


title: T84 shRNA targeting HCF2 #449 rep3

city: Omaha

first: M

middle: Jordan

last: Rowley

state: NE

address: 601 S Saddle Creek Rd

department: GCBA

institute: Univ of Nebraska Medical Center

description: Library name: T84_HCF2KD_2_rep3

data_processing:
Reads aligned to GRCh38 with STAR using GENCODE v49 basic annotation. Per-gene expression quantified with StringTie -e against GENCODE v49 (TPM and read counts; gene_count_matrix.csv via prepDE).
Assembly: GRCh38 / GENCODE v49 (basic)
Supplementary files format and content: gene_count_matrix.csv: genes x samples raw read counts.

growth_protocol: Colorectal cancer cell lines SW620 and T84 were purchased from the American Type Culture Collection (ATCC) and maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin. Cells were cultured at 37°C with 5% CO₂ and ambient O₂.

extract_protocol:
Total RNA was extracted (2/21/25); RNA integrity and purity confirmed (A260/A280 ~2.1). Libraries prepared and sequenced by Novogene.
PolyA-selected stranded mRNA libraries, Illumina, paired-end 150 bp.

treatment_protocol: SW620 and T84 cells were plated at 2.5 × 10⁶ cells per 60-mm dish. Cells were transduced with lentiviral shRNA constructs targeting HCF-2 (HCF-2 287 and HCF-2 449) or a non-targeting mission control shRNA (shMC1). The lentiviral plasmid expressed GFP, allowing transduction to be visually confirmed by fluorescence microscopy. Each condition was prepared in biological triplicate.

value: colorectal cancer

value: shRNA 449 for HCF-2


title: T84 shRNA targeting HCF2 #449 rep2

description: Library name: T84_HCF2KD_2_rep2


title: T84 shRNA targeting HCF2 #449 rep1

description: Library name: T84_HCF2KD_2_rep1


title: T84 shRNA targeting HCF2 #287 rep3

description: Library name: T84_HCF2KD_1_rep3

value: shRNA 287 for HCF-2


title: T84 shRNA targeting HCF2 #287 rep2

description: Library name: T84_HCF2KD_1_rep2


title: T84 shRNA targeting HCF2 #287 rep1

description: Library name: T84_HCF2KD_1_rep1


title: T84 non-targeting control (mc1) rep3

description: Library name: T84_WT_rep3

value: non-targeting control shRNA


title: T84 non-targeting control (mc1) rep2

description: Library name: T84_WT_rep2


title: T84 non-targeting control (mc1) rep1

description: Library name: T84_WT_rep1


title: SW620 shRNA targeting HCF2 #449 rep3

description: Library name: SW620_HCF2KD_2_rep3


title: SW620 shRNA targeting HCF2 #449 rep2

description: Library name: SW620_HCF2KD_2_rep2


title: SW620 shRNA targeting HCF2 #449 rep1

description: Library name: SW620_HCF2KD_2_rep1


title: SW620 shRNA targeting HCF2 #287 rep3

description: Library name: SW620_HCF2KD_1_rep3


title: Caput,  Low-protein diet, rep5

description: Library name: CP_LP_5

data_processing:
Sequences were trimmed with  "cutadapt --no-indels -O 15 -m 2 -a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC" ,"cutadapt -u 7" , and then "cutadapt -u -1" to remove the adapter, the UMI, and the TPRT base (the UMI was not used for removing duplicates)  Only reads >65 bases were used for most analyses
Data was mapped and counted using TRAX, which uses an all-best mapping approach and uses Deseq2 for normalization and detection of differential expression
Assembly: mm10
Supplementary files format and content: tab-delimited raw counts for calculated by tRAX, with mitochondrial tRNA counts appended

source_name: Caput

extract_protocol:
Samples were vortexed for 5 minutes to ensure complete breakdown of the sperm, followed by centrifugation at 12,000 RCF for 4 minutes. The aqueous phase was then removed and transferred to a low-binding RNase/DNase-free microcentrifuge tube, followed by the addition of 20 µg of glycoblue (Invitrogen) and 1 volume of Isopropanol. The RNA was then precipitated for 30 minutes or greater at -20°C, followed by centrifugation at 18,000 RCF for 30 minutes at 4°C, and one wash with 70% cold ethanol followed by centrifugation at 12,000 RCF for 10 minutes at 4°C. Finally, the RNA was reconstituted in nuclease-free water.
Library was constructed using Ottr-seq protocol.  Input RNA was PNK treated and labelled at the 3’ end by incubation in buffer containing ddATP for 90 minutes in 30˚C, followed by an addition of ddGTP and another incubation at 30˚C for 30 minutes. The reaction was stopped by incubating at 65°C for 5 minutes, followed by the addition of 5 mM MgCl2 and 0.5 units of shrimp alkaline phosphatase (NEB, cat# M0371S) at 37°C for 15 minutes, then stopped by the addition of 5 mM EGTA, and incubated at 65°C for 5 minutes. Samples were then incubated in templated cDNA synthesis buffer, adaptors, and dNTPs at 37˚C for 20 minutes, followed by heat inactivation at 65˚C for 5 minutes and RNase A/H treatment. cDNA was size selected on a 10% PAGE urea gel to minimize adaptor dimers. Size selected cDNA was PCR amplified for 12 cycles with Q5 high fidelity polymerase (NEB, cat# M0491S). The final PCR product was cleaned up with AMPure XP beads (Beckman, cat # A63881) and finally separated by 6% TBE gel to remove adaptor dimers. The desired product was excised from the gel and eluted in 400ul elution buffer (300 mM NaCl, 10 mM Tris pH 8, 1 mM EDTA) overnight at -20, followed by isopropanol precipitation and resuspension in 9µl nuclease-free H2O.

value: Caput

value: Low-protein diet


city: Shanghai

first: Zhu

last: Ming

address: No. 500, Dongchuan Road

institute: East China Normal University

description: Library name: Cas9_VEGFA2_48h_HEK293T_500k_PEI_IBR2_rep2

data_processing:
Data were mapped to hg38 (human) using chromap.
Reads overlaped the ENCODE blacklist are removed
Bedtools was used to generate bedGraph files, which were then normalized and converted to BigWig files by bedGraphToBigWig
Assembly: hg38
Supplementary files format and content: BigWig of genome-editing signals

extract_protocol:
Cells were fixed with Concanavalin A bead, washed, and resuspended with buffer containing RPA2/MRE11/IgG antibodies. pA-MNase was added to cleavage the DNA. Cleavaged fragments were collected and then digested with DNase. For Tracking-seq, DNA was purified with DNA Clean Beads and then HL-dsDNase was added to remove dsDNA.
The strand-specific ssDNA libraries were constructed using VAHTS ssDNA Library Prep Kit. CUT&RUN-MRE11 library was constructed using NEBNext® Ultra™ II DNA Library Prep Kit.


title: SW620 shRNA targeting HCF2 #287 rep1

description: Library name: SW620_HCF2KD_1_rep1


title: HO211

city: Rochester

first: Martin

last: Fernandez-Zapico

state: MN

address: 200 1st St SW

institute: Mayo Clinic

description: Library name: Sample 9

data_processing:
Libraries were combined across flow cells and trimmed using Cutadapt 1.16.5 to remove the Nextera adapters. Trimmed reads were aligned to Hg38 using Bowtie2 2.5.0 with the preset --very sensitive end-to-end. Reads were filtered for mapQuality (phred scale) ≥ 30, properly paired reads, and removal of mitochondrial reads. Duplicates were removed using Picard 2.26.10 MarkDuplicates.
BAM files were converted to bigwig using Deeptools 3.3.2 bamCoverage with a bin size of 50 bases and RPKM normalization.
Assembly: GRCh38
Supplementary files format and content: BAM files were converted to bigwig using Deeptools 3.3.2 bamCoverage with a bin size of 50 bases and RPKM normalization.
Supplementary files format and content: Narrow Peaks were called using MACS2 2.2.9 Callpeak with a set extension size of 200 and a set shift size of -100. Peak detection was based on a minimum FDR cutoff of ≤0.01.

source_name: Tumor

growth_protocol: PDOs were grown in PaTOM media

extract_protocol:
100,000 cells were collected in a 1.5 mL low-binding microcentrifuge tube and brought to a total volume of 1 mL in ice-cold PBS and mixed gently. Cells were pelleted and resuspended in 100 µL of ice-cold anti-freezing buffer (10% DMSO, 10% FBS in DMEM) and mixed gently. Approximately 50 – 100K cells were subjected to ATAC following the Omni-ATAC protocol.
Libraries were purified by AMPure XP magnetic beads (Beckman Coulter, A63881) and the size distribution of library DNA was determined by Fragment Analyzer (Advanced Analytical Technologies) using a High Sensitivity NGS Fragment Analysis Kit (Advanced Analytical Technologies, DNF-486). Real-time PCR analysis was performed using SYBR Green universal PCR mixes (Bio-Rad) to measure enrichment of accessible regions in the library DNAs. The following primers were used: for accessible regions, Fam86fp-F: 5’-GGCATTAGGGCGGGGATAAA-3’, Fam86fp-R: 5’-TAAGACCTGTCTCCTGGGCT-3’; Ccdc146-F: 5’-GCTCCGCCTCTTAGAAACCA-3’, Ccdc146-R: 5’-GCGATTCTAACACCTGCCCT-3’; for inaccessible region, hATAC-C19 inter-F: 5’-GCTTGTCTTTCCCAAGTTTACTC-3’, hATAC-C19 inter-R: 5’-TAGCTGTCGCACTTCAGAGGA-3’. The libraries were sequenced to 51 base pairs from both ends on an Illumina NovaSeq 6000 SP platform. The concentration and fragmentation profile of submitted ATAC libraries were determined using Qubit fluorometry (Invitrogen) and the Agilent Bioanalyzer. The libraries were sequenced using Illumina's standard protocol for the NovaSeq 6000. The flow cells were sequenced as 50 X 2 paired end reads using the NovaSeq SP sequencing kit and NovaSeq Control Software v1.8.0. Base-calling was performed using Illumina’s RTA version 3.4.4.

treatment_protocol: No treatment

value: Tumor

value: peritoneal metastsis

value: Colorectal cancer


title: SW620 non-targeting control (mc1) rep3

description: Library name: SW620_WT_rep3


title: SW620 shRNA targeting HCF2 #287 rep2

description: Library name: SW620_HCF2KD_1_rep2


title: SW620 non-targeting control (mc1) rep2

description: Library name: SW620_WT_rep2


title: SW620 non-targeting control (mc1) rep1

description: Library name: SW620_WT_rep1


title: RC77TE_H3K27ac_R1

city: Los Angeles

first: Suhn

middle: K

last: Rhie

state: CA

address: 1450 Biggy Street NRT 3504

department: Cancer Biology

institute: University of Southern California

description:
Library name: RC77TE H3K27ac R1
ChIP-seq

data_processing:
ChIP-seq data were processed following ENCODE3 guidelines (PMID: 22955616). Briefly, BWA (PMID: 19451168) was used to align the raw sequencing reads to the human reference genome (hg38). Library complexity was computed to determine the PCR bottleneck coefficients, non-redundant fraction, normalized strand cross-correlation coefficient, and relative strand cross-correlation coefficient. PCR duplicates and unaligned reads were removed using Picard (https://github.com/broadinstitute/picard) and samtools (PMID: 19505943). Uniquely mapped reads were used to call peaks using MACS2 (PMID: 18798982) (narrowPeak format).
Assembly: hg38
Supplementary files format and content: .bw

source_name: Prostate

growth_protocol: 22Rv1 (CRL-2505) and RWPE-1 (CRL-11609) cells were obtained from the American Type Culture Collection (ATCC). RC-77N/E and RC77T/E cells were received from Johng Sik Rhim. Cells were cultured according to the suggested protocols at 37°C with 5% CO2. 22Rv1 cells were cultured in RPMI 1640 (Corning, #10-040-CV) supplemented with 10% FBS (Avantor Seradigm, #89510-188) and 1% penicillin/streptomycin. RWPE-1, RC-77N/E, and RC77T/E cells were cultured in the Keratinocyte Serum Free Medium kit (Thermo Fisher Scientific, #17005-042).

extract_protocol:
For ChIP-seq, cells were grown to 70%-90% confluence and cross-linked with 1% formaldehyde for 10 minutes and quenched with 125nM glycine for 5 minutes at RT. Nuclei were lysed in nuclei lysis buffer, and performed snap-freeze using liquid nitrogen. Chromain was sonicated to an approximate length of 200 bp - 500 bp using bioruptor sonicator.
ChIP-seq library: Libraries were prepared using the KAPA Hyper Prep Kit from KAPA Biosystems. End-Repair and A-Tailing Buffers, DNA ligase, and ligation buffer were used. Ampure beads were used for post-ligation clean up, and KAPA HiFi HotStart Ready Mix and Nextflex Primer Mix were used for amplification of adapter modified DNA fragments.

value: Prostate

value: prostate cells


title: RC77TE_H3K27ac_R2

description:
Library name: RC77TE H3K27ac R2
ChIP-seq


title: RC77NE_H3K27ac_R2

description:
Library name: RC77NE H3K27ac R2
ChIP-seq


title: Alveolus-on-chip, butyrate treated, infected

city: Jena

first: Marc Thilo

last: Figge

state: Thuringen

address: Adolf-Reichwein-Straße 23

department: Applied System Biology

country: Germany

institute: HKI-Leibniz

description:
Library name: Infected_butyrate
10xGenomics

data_processing:
Raw sequencing data from four iPSC-derived lung-on-chip conditions (Control, butyrate-treated control, IAV-infected and IAV-infected butyrate-treated) were processed using Cell Ranger (10x Genomics) against the GRCh38 genome
Assembly: GRCh38
Supplementary files format and content: Cell ranger filtered feature matrices .h5 for each sample

source_name: lung

growth_protocol: The iAT2s were first seeded onto the apical side of the membrane and cultured under static conditions until confluence. Once a confluent epithelial monolayer formed, on day 3, endothelial cells were seeded on the basal side of the membrane. Media were exchanged daily, and both cell layers remained under static conditions. As the final cell type, iPSC-derived macrophages were added to the endothelial surface on day 7.

extract_protocol:
At 24 hours post-infection, cells from the chip were washed with PBS -/- and enzymatically dissociated using Accutase, incubated for 15 minutes at 37 °C, then processed for single-cell RNA sequencing on the 10x Genomics Chromium platform. After dissociation, the cells were assessed for viability, and based on cell number and viability, approximately 10,000 cells per condition were pipetted for further experiments.
Single-cell RNA sequencing libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 protocol (10xGenomics, PN-1000268). The workflow included three main steps: Step 1 – GEM Generation & Barcoding: A reaction mix was prepared and loaded onto a Chromium Next GEM Chip. The chip was then operated on the Chromium Controller to produce Gel Bead-In-Emulsions (GEMs), which enable cell barcoding. After GEM formation, GEMs were carefully transferred for reverse transcription (GEM-RT) incubation. GEM-RT reactions were incubated as recommended, with interim storage at 4°C for up to 72 hours or at −20°C for up to a week if necessary. Step 2 – Post GEM-RT Cleanup & cDNA Amplification: Following incubation, GEMs were disrupted, and post-GEM-RT cleanup was performed using Dynabeads. Amplification of cDNA was conducted to generate enough material for downstream applications. The amplified cDNA was purified using SPRIselect beads (Beckman Coulter, B23318) and then subjected to quality control (QC) and quantification. cDNA samples could be stored at 4°C for up to 72 hours or at −20°C for up to four weeks before further use. Step 3 – 3ʹ Gene Expression Library Construction: The amplified cDNA was fragmented, end-repaired, and A-tailed. After fragmentation, a double-sided size selection was performed using SPRIselect beads. Adaptors were ligated to the fragmented cDNA, followed by a cleanup with SPRIselect. Samples were then indexed by PCR amplification, and a final double-sided size selection was performed to purify the libraries. The final libraries underwent quality control and quantification before sequencing. Libraries were sequenced on an Illumina NovaSeq 6000, according to the recommendations of 10x Genomics.

treatment_protocol: On day 12, all infected chips were exposed to Influenza A virus A/Wisconsin/588/2019 (H1N1) at an MOI of 0.1. The virus was applied apically for 2 hours under static conditions. Following incubation, the virus was removed, the chips were washed with serum-free medium, and ALI was re-established. Medium containing butyrate (10 µM) was maintained in the vascular channel of the treated group throughout the post-infection period.

value: lung

value: epithelial, endothelial, macrophages

value: IAV, butyrate


title: Alveolus-on-chip, infected

description:
Library name: Infected
10xGenomics

value: IAV


title: Alveolus-on-chip, uninfected, replicate_2

description:
Library name: Control_2
10xGenomics


title: Alveolus-on-chip, butyrate treated, uninfected, replicate_1

description:
Library name: Control_butyrate
10xGenomics

value: butyrate


title: Alveolus-on-chip, uninfected, replicate_1

description:
Library name: Control
10xGenomics


title: KG1a, PRMT2 WT, replicate 2

city: Dijon

first: Laurent

last: DELVA

address: 7 boulevard Jeanne d’Arc

department: Inserm U1231 (CTM)

country: France

institute: Université de Bourgogne

description: Library name: KG1a_PRMT2_WT_2

data_processing:
Raw paired-end FASTQ reads were quality-controlled before alignment.
Reads were aligned to the human reference genome GRCh38 using STAR in two-pass mode.
Gene-level read counts were generated from aligned reads.
Differential gene expression analysis was performed in R using DESeq2.
Low-count genes were filtered before analysis, and log₂ fold changes were estimated using apeglm shrinkage. Differentially expressed genes were defined using adjusted statistical thresholds.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file containing raw gene-level read counts for each sample (STAR2 count).
Supplementary files format and content: Comma-separated values file containing RNA-seq expression values as raw counts and TPM values offset by 1 × 10⁻⁴ for each gene.

growth_protocol: KG-1a human acute myeloid leukemia cells were cultured in RPMI 1640 medium supplemented with 20% fetal bovine serum at 37°C in a humidified incubator with 5% CO₂. Cells were routinely tested for mycoplasma contamination.

extract_protocol:
Total RNA was extracted from KG-1a PRMT2 wild-type and PRMT2 knockout cells using TRIzol reagent according to the manufacturer’s instructions. RNA quality and quantity were assessed before library preparation.
RNA-seq libraries were prepared from total RNA using an Illumina-compatible library preparation workflow GENEWIZ (Azenta Life Sciences). Libraries were sequenced on an Illumina NovaSeq 6000 platform using a paired-end 2 × 150 bp configuration.

treatment_protocol: PRMT2 knockout KG-1a cell lines were generated using CRISPR/Cas9-mediated genome editing. Independent PRMT2 knockout clones and wild-type control cells were expanded under identical culture conditions before RNA extraction. No drug treatment was applied.

value: Acute myeloid leukemia cell line

value: PRMT2 wild type


title: KG1a, PRMT2 WT, replicate 3

description: Library name: KG1a_PRMT2_WT_3


title: KG1a, PRMT2 WT, replicate 1

description: Library name: KG1a_PRMT2_WT_1


title: KG1a, PRMT2 KO, clone 2, replicate 3

description: Library name: KG1a_PRMT2_KO2_3

value: PRMT2 knockout clone 2


title: KG1a, PRMT2 KO, clone 2, replicate 1

description: Library name: KG1a_PRMT2_KO2_1


title: KG1a, PRMT2 KO, clone 1, replicate 3

description: Library name: KG1a_PRMT2_KO1_3

value: PRMT2 knockout clone 1


title: KG1a, PRMT2 KO, clone 1, replicate 2

description: Library name: KG1a_PRMT2_KO1_2


title: KG1a, PRMT2 KO, clone 1, replicate 1

description: Library name: KG1a_PRMT2_KO1_1