title: HaCaT cells, UVA 3

city: luzhou

first: yi

last: peng

address: xianglinlu

institute: 西南医科大学

description: TPM

data_processing:
Used the standard base calling software provided by Illumina HiSeq2500 to generate raw sequence reads in FASTQ format.
Circular RNAs were identified and quantified using find_circ and CIRCexplorer2.
Data filtering (Removed low quality reads, Removed reads with >10% N bases, Removed reads with adapter contamination, Removed reads <18 nt).
Used find_circ (version 1.2) to identify candidate circRNAs, Used CIRCexplorer2 (version 2.3.3) to further identify circRNAs.
Assembly: The human reference genome build/assembly used for read alignment was hg38/GRCh38.
Supplementary files format and content: Tab-delimited text files include expected counts and TPMs.

source_name: HaCaT

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer's protocol.
Ribosomal RNA was depleted from total RNA using RNase R.

value: HaCaT

value: human keratinocytes

value: WT

value: UVA irradiation


title: eWAT, Veh, biological replicate1

status: Public on Oct 02 2024

type: SRA

city: Los Angeles

first: Xia

last: Yang

state: California

address: 2000 Terasaki Life Sciences Bldg

department: Department of Integrative Biology and Physiology

country: USA

institute: University of California, Los Angeles

library_source: transcriptomic

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification. Quality control of raw sequencing data was conducted using FastQC, employing default parameters. Subsequently, sequencing reads were mapped to the mouse genome mm10 using Salmon. Differential gene expression analysis was then undertaken with DESeq2.
Assembly: mm10
Supplementary files format and content: Plain-text, tab-separated file that includes Salmon's quantification output  for each sample
Library strategy: Polysome-Seq

molecule: polyA RNA

organism: Mus musculus

source_name: epididymal adipose tissue

growth_protocol: DMEM (GIBCO) 10% FBS (Omega FB#11), 1% PenStrep (GIBCO), and 50ng/mL Primocin (Invivogen) - 37C incubator 5% CO2

extract_protocol:
Stromal vascular fractions were isolated as previously described. Briefly, entire WAT depots were cut into small pieces, suspended in DMEM (GIBCO) + 50 mM HEPES (GIBCO) + 1mg/mL type II collagenase (Sigma), + 1% BSA - low fatty acid (Gemini), and digested for 30 minutes at 37°C with agitation (120 rpm). The resulting dissociated tissue was passed through 100μm strainers, and adipocytes were removed from the supernatant by centrifugation (750g, 10min, 4C). After a second filtration with 40μm strainers, red blood cells were lysed using ACK lysis buffer (GIBCO). Cells were then treated to differentiate with complete adipogenic cocktail (0.5mM 3-isobutyl-1-methylxanthine (Sigma), 1μM dexamethasone (Sigma), 5μg/mL insulin (GIBCO) plus either 1μM rosiglitazone (Novo Nordisk) or vehicle (DMSO) for 2 days. After that, media was replaced for minimal maintenance media (Insulin/Rosi or Insulin/DMSO) for 2 days. At day 4 of differentiation cells were boosted with fresh media for one hour and for the last 5 minutes cycloheximide (Sigma) was added to the media (final concentration 100μg/mL). Cells were lysed and collected in hypotonic lysis buffer (5mM Tris HCl pH 7.5, 2.5 mM MgCl2, 1.5 mM KCl, 100 μg/mL cycloheximide, 2 mM DTT), and 0.5% Triton, 0.5% Sodium Deoxycholate were then added to the cell lysates after collection. The cytoplasmic extracts were resolved on 5-50% sucrose gradients by centrifugation in an SW40 rotor at 150,000 x g for 2 hours. The absorbance at 260 nm was measured using a Piston Gradient Fractionator Model 153 instrument (BioComp, Canada). RNA from polysomes or total RNA pool was resuspended in Trizol reagent (ThermoFisher), and RNA was isolated using Direct-zol RNA Microprep kits as described by the manufacture (Zymo research).
The RNA sample received was quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using TapeStation (Agilent Technologies, Palo Alto, CA, USA). The RNA sequencing library was prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First-strand and second-strand cDNA were subsequently synthesized. cDNA fragments were end-repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing library was clustered on three lanes of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq instrument (4000 or equivalent) according to the manufacturer’s instructions. The sample was sequenced using a 2x150bp Paired End (PE) configuration.

tag: tissue

value: epididymal adipose tissue

tag: Sex

value: male

tag: strain

value: Lepob/Lepob (The Jackson Laboratory #000632)

tag: cell type

value: stromal vascular fraction

tag: age

tag: treatment

value: Vehicle


title: PC3 cells, hsa_circ_0070512 Vector,Day9

city: kunming

first: Gao

last: hang

address: kunming

country: China

institute: Kunming Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM and count values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: prostate

growth_protocol: Human prostate cancer PC3 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics at 5% CO2 and 37℃.

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

treatment_protocol: hsa_cric_0070512 gene overexpression was transfected and compared with negative control group, and three groups of replicates were performed

value: prostate

tag: cell line

value: PC3 cells

value: Epithelioid cell

tag: genotype

value: Transfection 9 Days


title: HaCaT cells, UVA 2

description: TPM


title: MIA PaCa-2, 24hr, adagrasib (300nM), rep4

city: Palo Alto

first: Jin Hyun

last: Ju

state: CA

address: 3160 Porter Dr, Suite 250

institute: BridgeBio

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b to generate BAM files.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. If a strand-specific library preparation was performed, the reads were strand-specifically counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed.
Assembly: GRCh38
Supplementary files format and content: comma separated raw counts for all samples

source_name: MIA PaCa-2

growth_protocol: Mia PaCa-2 cells pancretic adenocarcinoma cells were maintined in DMEM supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin (Pen/Strep) in humidified atmosphere at 37C

extract_protocol:
RNA was extracted by Azenta life sciences' standard protocol.
cDNA libraries were constructed by Azenta life sciences' standard protocol

treatment_protocol: Cells were treated for 24 hours with DMSO,  30nM BBO-8520, 300nM adagrasib (MRTX-849) or 1μM sotorasib (AMG-510) with 5 replicates/condition. All had a final DMSO concentration of 0.1%.

value: MIA PaCa-2

value: Pancreatic Adenocarcinoma

tag: time

value: 24 hrs

value: adagrasib (300nM)


title: 5376

type: genomic

city: Bethesda

first: Alexander

middle: Christian

last: Harris

state: Maryland

address: 50 South Drive

department: National Human Genome Research Institute

institute: National Institutes of Health

description: LANC

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays and hybridized overnight at at 48oC.  Single-base extension and allele-specific staining was performed by hand.

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing:
Image data was analyzed using GenomeStudio with GT module (Illumina).
genotypes AA, AB, BB, NC=no call

molecule: genomic DNA

organism: Canis lupus familiaris

source_name: Unknown Source

label_protocol: 200ng of genomic DNA was amplified in an overnight reaction at 37oC. The amplified DNA was enzymatically fragmented, precipitated with isopropanol, and resuspended in hybridization buffer.

extract_protocol: Genomic DNA was extracted from whole blood or Buccal cells using Proteinase K and phenol/chloroform with standard protocols. Genomic DNA extracted from saliva using standard Performagene genotek DNA extraction protocols.

tag: breed

value: Lancashire Heeler


title: 5385

description: RWSE

value: Irish Red and White Setter


title: PC3 cells, hsa_circ_0070512 Vector,Day7

value: WT

value: Transfection 7 Days


title: HaCaT cells, UVA 1

description: TPM

value: HaCaT

value: human keratinocytes

value: UVA irradiation


title: MIA PaCa-2, 24hr, adagrasib (300nM), rep3


title: 5375

description: LANC


title: 5373

description: GBGV

value: Grande Basset Griffon Vendeen


title: HaCaT cells, Control 3

description: TPM

value: sham irradiated


title: 5372

description: GBGV


title: HaCaT cells, Control 2

description: TPM


title: 5370

description: GBGV


title: MIA PaCa-2, 24hr, adagrasib (300nM), rep1


title: BMDMs, AAV-SHISA3-2

city: Guangzhou

first: shimeng

last: zhang

address: 651 Dongfeng Road East, Yuexiu District

institute: Sun Yat-sen University Cancer Center

description:
shisa3-BMDM VS GFP-BMDM.txt
AAV-SHISA3-2

data_processing:
The data processing steps are as follows:
1) Remove the reads contaminated with the connector (the alkaline base of the connector contaminated in the reads is greater than 5bp. For dual end sequencing, if one end is contaminated with the connector, remove the reads at both ends);
2) Remove low-quality Reads (bases with a mass value of Q ≤ 19 account for more than 50% of the total base count in Reads. For dual end sequencing, if one end is low-quality Reads, both end Reads will be removed);
3) Remove Reads with a N content ratio greater than 5% (for dual end sequencing, if one end has a N content ratio greater than 5%, the Reads at both ends will be removed)
Assembly: MM9
Supplementary files format and content: tab-delimited txt file represent readcounts for each sample

source_name: BMDM

growth_protocol: BMDMs were cultured in RPMI 1640 (Gibco) supplemented with 10% FBS , 1% penicillin/ streptomycin  and 50 μM 2-mercaptoethanol in the presence of 20 ng ml–1 M-CSF at 37 °C with 5% CO2.

extract_protocol:
Total RNA from cells were extracted with Trizol reagent (Magen) according to the manufacturer’s instructions. The quantity and quality of RNA were measured by Nanodrop. 4 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina ® （NR604-01/02）following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample

treatment_protocol:
BMDMs were stimulated with 100 ng ml–1 LPS for 2 or 4 hours.
AAV infected BMDMs for 48h for overexpressing Shisa3 or GFP

value: BMDM

value: Shisa3 overexpression

value: AAV-Shisa3 transduced


title: 4812

description: FCR-

source_name: Whole Blood

value: Flat-Coated Retriever


title: MIA PaCa-2, 24hr, adagrasib (300nM), rep2

value: MIA PaCa-2


title: HaCaT cells, Control 1

description: TPM


title: BMDMs, AAV-SHISA3-1

description:
shisa3-BMDM VS GFP-BMDM.txt
AAV-SHISA3-1


title: MIA PaCa-2, 24hr, BBO-8520 (30nM), rep4

value: Pancreatic Adenocarcinoma


title: PC3 cells, hsa_circ_0070512 OE,Day9

value: prostate

value: PC3 cells

value: Epithelioid cell

value: hsa_circ_0070512 OE

value: Transfection 9 Days


title: BMDMs, AAV-GFP-2

description:
shisa3-BMDM VS GFP-BMDM.txt
AAV-GFP-2

value: WT

value: AAV-GFP transduced


title: non-irradiated control

city: suzhou

first: zhang

middle: shu

last: yu

address: No. 199, Ren'ai Road

department: soochow university

institute: Soochow University

description: mRNA Expression Profiling

data_processing:
The Cell Ranger software pipeline (version 5.0.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner.
the unique molecular identifier (UMI) count matrix using the R package Seurat(version 3.1.1)
Library size normalization was performed with NormalizeData function in Seurat to obtain the normalized count. Specifically, the global-scaling normalization method “LogNormalize” normalized the gene expression measurements for each cell by the total expression, multiplied by a scaling factor (10,000 by default), and the results were logtransformed.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: skin

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). cDNA was then amplified by PCR with appropriate cycles which depend on the recovery cells. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed, and index adaptor ligated and library amplification. Then these libraries were sequenced on the Illumina sequencing platform and 150 bp paired-end reads were generated.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

tag: sample preparation

value: scRNA-seq

tag: protocol

value: non-irradiated


title: MIA PaCa-2, 24hr, BBO-8520 (30nM), rep2

value: 24 hrs


title: IR

description: mRNA Expression Profiling

value: irradiated


title: MIA PaCa-2, 24hr, BBO-8520 (30nM), rep5


title: 3036

description: BRUS

value: Brussels Griffon


title: PC3 cells, hsa_circ_0070512 OE,Day5

value: Transfection 5 Days


title: PC3 cells, hsa_circ_0070512 OE,Day7

value: Transfection 7 Days


title: BMDMs, AAV-GFP-1

description:
shisa3-BMDM VS GFP-BMDM.txt
AAV-GFP-1

value: BMDM


title: 3300

description: WELT

source_name: Buccal cells

value: Welsh Terrier


title: whole spleen, unfractionated, biological replicate 3

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

library_source: transcriptomic single cell

data_processing:
Demultiplexing: Cell Ranger (v.5.0.0)`cellranger mkfastq`
Trimming, filtering, alignment: Cell Ranger (v.5.0.0) `cellranger count`
Assembly: channel catfish assembly Coco_2.0, Accession number GCF_001660625.3
Supplementary files format and content: .h5, filtered feature-barcode matrices

organism: Ictalurus punctatus

source_name: spleen

extract_protocol:
Three channel catfish (~ 1 kg) were euthanized in a solution of buffered MS-222 for 10 min. The individual spleens were removed and placed into Petri dishes containing Leibovitz’s L-15 medium adjusted to catfish tonicity (cL-15) with PenStrep glutamine solution and 5% FBS.  The spleens were first processed through 70 µM and then 40 µM cell sieves into a 50 mL Falcon tube and cL-15 was added up to 10 mL. The splenic cell suspensions were washed 3 times in 10 mL cL-15 and centrifuged at 350 x g for 5 min. The final cell pellet was resuspended in 15 mL cL-15. Cells were counted, and cell viability was assessed. Cells were pelleted and resuspended in 1 mL of freezing medium (90% FBS, 10% DMSO) and placed into a Mr. Frosty freezing container at -80°C for 24 h. The cryogenic vials were then moved into a liquid nitrogen storage until shipping to a sequencing vendor.
The single-nuclei RNA-seq libraries were prepared and constructed using the Chromium X Instrument (10x Genomics) and the Chromium Next GEM Single Cell 3’ GEM Kit v3.1 (10x Genomics) following the manufacturer’s protocol.

value: spleen

tag: developmental stage

value: adult

value: delta select


title: 2998

description: PTWD

value: Portuguese Water Dog


title: BMDMs, LPS 4h

description:
BMDM LPS.txt
LPS 4h

value: LPS 4h


title: whole spleen, unfractionated, biological replicate 2


title: BMDMs, LPS 2h

description:
BMDM LPS.txt
LPS 2h

value: LPS 2h


title: PC3 cells, hsa_circ_0070512 Vector,Day5

value: prostate

value: PC3 cells

value: Epithelioid cell

value: WT


title: 2039

description: GOLD

value: Golden Retriever


title: MIA PaCa-2, 24hr, DMSO, rep5

value: MIA PaCa-2

value: Pancreatic Adenocarcinoma

value: 24 hrs

value: DMSO


title: BMDMs, WT

description:
BMDM LPS.txt
LPS 0h

value: BMDM

value: without treatment


title: 2010

description: LAB-

value: Labrador Retriever


title: Sorgum_U

city: Godollo

first: Eva

last: Varallyay

address: 4 Szent-Györgyi Albert Street

department: Institute of Plant Protection

country: Hungary

institute: Hungarian University of Agriculture and Life Sciences

description: small RNA

data_processing:
The quality check of the sequenced small RNA libraries was done by FastQC program, embedded in CLC
Trimming of raw reads was performed using the CLC
Removing redundant reads using CLC
Supplementary files format and content: tab-delimited counts of all unique read with its number of repeats
Assembly: as small RNAs were sequences as one read no assembly was needed

organism: Sorghum halepense

source_name: plant leaf

extract_protocol:
Phenol-Kloroform extraction White and Karper (White, J.L.; Kaper, J.M. A simple method for detection of viral satellite rnas in small plant tissue samples. J. Virol. Methods 1989, 23, 83–93.)
modified Illumina Trueseq small RNA kit protocol: https://doi.org/10.1007/978-1-4939-7683-6_9

value: plant leaf

tag: species

value: pool of 5 individual plants

value: July 2021


title: MIA PaCa-2, 24hr, DMSO, rep3


title: 1257

description: MALT

value: Maltese


title: whole spleen, unfractionated, biological replicate 1

value: spleen

value: adult

value: delta select


title: MIA PaCa-2, 24hr, DMSO, rep1


title: S8

city: Philadelphia

first: Makarand

middle: V

last: Risbud

address: 1025 Walnut St.

institute: Thomas Jefferson University

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Rattus_norvegicus.Rnor_6.0_ERCC reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.
Assembly: Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Rattus_norvegicus.Rnor_6.0_ERCC reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.
Supplementary files format and content: S6 ShKD vs ShCtrl Differential_expression_analysis_table.csv

organism: Rattus norvegicus

source_name: primary rat nucleus pulposus cells

growth_protocol: Primary nuclues pulposus cells were maintained in DMEM with 10%FBS and antibiotics in humidified atmosphere with 5%CO2 at 37C

extract_protocol:
RNA was extracted using RNA easy kit (Qiagen) and used for construction of sequencing libraries.
RNA libraries were prepared as per standard library prep kit as per manufacturer's protocol (Azenta).

value: primary rat nucleus pulposus cells

value: nuclues pulposus cells

value: Lentiviral ShRNA transduction


title: Echinocloa_US

description: small RNA

organism: Echinochloa crus-galli

value: pool of 8 individual plants


title: MIA PaCa-2, 24hr, DMSO, rep2

value: MIA PaCa-2

value: Pancreatic Adenocarcinoma


title: 1024

description: WELT

value: Welsh Terrier


title: 1124

description: AHRT

value: American Hairless Terrier


title: PATH3-2

city: Nedlands

first: Kevin

middle: Guangxing

last: Chen

address: Hospital Avenue

country: Australia

institute: The Kids Research Institute Australia

description: Molecule: PCR amplicon

library_source: other

data_processing:
Raw sequencing reads were processed using the ENCODE/DCC pipeline (https://github.com/ENCODE-DCC/rna-seq-pipeline)
Reads were aligned to GRCh38 and quantified using kallisto.
Kallisto quantificiation files were read into edgeR/limma using the tximport package in R to generate counts matrices
Amplicon sequencing: reads were aligned to either WT or HDR amplicon using CRISPResso2
Assembly: GRCh38
Supplementary files format and content: RawCountsMatrix.tsv contains the Kallisto-quantified counts of all genes for each sample
Library strategy: Amplcon-seq

molecule: other

source_name: KOLF2, Day 0

growth_protocol: KOLF2 cells were grown on Matrigel-coated plates in TeSR-E8 media. The STEMdiff SMADi Neural Induction Kit (STEMCELL technologies) were used to induce differentiation into NPCs.

extract_protocol:
Cells were collected on day 0 and 24 for RNA extraction using RNeasy (Thermo Fisher). gDNA for amplicon sequencing was extracted using PureLinkTM Genomic DNA Mini Kit (Life Technologies)
RNA integrity was determined using the Agilent TapeStation system (Genomics WA). RNA sequencing was performed according to SureSelect Strand-Specific RNA Library preparation for Illumina Multiplexed sequencing, paired-end, 100 bp, 30 M read RNA sequencing on the NOVAseq 6000 platform (Illumina, USA) at Genomics WA (Perth, Australia). PCR amplicon products corresponding to the SNV sites in SETBP1, PATH2, PATH3 and VUS2, were prepared from extracted gDNA with forward and reverse amplicon primers and Phusion High-Fidelity PCR Master Mix with HF Buffer (Thermo Scientific). Purified samples were barcoded with TruSeq primers (IDT) and SETBP1 sequences determined with paired-end, 250bp DNA amplicon sequencing with a MiniSeq Mid-Output Kit, 300 cycles.

value: KOLF2, Day 0

value: induced pluripotent stem cells


title: S7


title: PATH3-1

description: Molecule: PCR amplicon


title: S6


title: 988

description: AMWS

value: American Water Spaniel


title: S5


title: MIA PaCa-2, 24hr, BBO-8520 (30nM), rep1

value: 24 hrs


title: Lm208 at 5°C with C18:1 (FA37)_replicate_3

city: Jouy En Josas

first: Maud

last: Darsonval

state: State/Province

address: Domaine de Vilvert, bâtiment 440

department: Institue Micalis

country: France

institute: Université Paris-Saclay, INRAE, AgroParisTech

data_processing:
Raw reads were demultiplexed with bcl2fastq2 v.2.18.12 and quality control wad done with FastQC v.0.11.5.
Adapter were trimmed with Cutadapt v.1.15
Trimmed reads were mapped against Listeria monocytogenes Lm208 strain genome (BioProject PRJNA1074122) using BWA 0.6.2-r126 R package
FeatureCounts (v.1.5.2) was used to assign sequence reads to genomic features
Raw count were normalized according to gene length and the total number of mapped reads by calculating FPKM (Fragments per Kilobase per Million Mapped reads)
Read counts were extracted with R package DESeq2 (v.1.30.1)
Assembly: Listeria monocytogenes Lm208 genome (BioProject PRJNA1074122)
Supplementary files format and content: tab-delimited text fil includes raw counts for each sample
Supplementary files format and content: First 4 columns : locus tag in L. monocytogenes Lmo208 genome (PRJNA1074122) ; corresponding locus tag in L. monocytogenes EGD-e reference genome (NC_003210, PRJNA61583), ORF lenght in bp and corresponding putative protein lenght in aa.
Supplementary files format and content: Next 12 columns (2 growth conditions x 2 temperatures x 3 replicates) labelled from C5.R1.rawcount to FA37.R3.rawcount : raw count of the number of reads mapped in each gene.
Supplementary files format and content: Last 12 columns (2 growth conditions x 2 temperatures x 3 replicates) labelled from C5.R1.log2fpkm to FA37.R3.log2fpkm : log2(fpkm) for each gene.

organism: Listeria monocytogenes

source_name: planktonic cell at early exponential phase

growth_protocol: Listeria monocytogenes lmo2058 strain was grown in TSB (Tryptone Soy Broth) with or without fatty acid supplementation (C18:1, 0.045 mM  in 0.05% bovine serum albumin (w/v) ) at 5°C or 37°C.

extract_protocol:
Cells were harvested at early exponential growth phase (OD600nm=0.1) by centrifugation and then freezed in liquid nitrogen until furtur experiment.
Total RNA was extracted from thawed pellets by the Trizol™ reagent method (Invitrogen™, Thermo Fisher Scientific) with some adaptations (Toledo-Arana et al., 2009). Pellets were re-suspended in 1mL of Trizol™ and transferred into a screw-cap tube containing 0-50µm glass beads for cell disruption by bead beating for 40sec at 6m/s (FastPrep-24 instrument, MP Biomedicals). RNA contained in the upper aqueous phase were washed with chloroform, then precipitated with cold isopropanol, and finally washed twice with 75% ethanol. RNA pellet was dried for 30sec at 63°C and re-suspended in 20µL of nuclease free water. Total RNA was treated by DNase I and purified using the Monarch® RNA Cleanup kit (New England BioLabs® Inc., Evry-Courcouronnes, France)
RNA libraries for RNA-seq were prepared using Truseq total RNA stranded and and Ribo-Zero Bacteria Illumina kits following the manufacturer's protocols.

value: strain Lm0208, wild-type


title: PATH2-3

description: Molecule: PCR amplicon


title: MIA PaCa-2, 24hr, DMSO, rep4

value: DMSO


title: Lm208 at 5°C with C18:1 (FA37)_replicate_2

value: planktonic cell at early exponential phase


title: 987

description: AMWS


title: MIA PaCa-2, 24hr, BBO-8520 (30nM), rep3


title: 947

description: EFOX

value: English Foxhound


title: Lm208 at 5°C with C18:1 (FA37)_replicate_1


title: S3


title: WT-6

description: Molecule: PCR amplicon

value: WT


title: 311

description: LAB-

value: Labrador Retriever


title: 310

description: LAB-


title: Lm208 at 5°C without C18:1 (C5)_replicate_2


title: S1

value: primary rat nucleus pulposus cells

value: nuclues pulposus cells


title: S2

value: Lentiviral ShRNA transduction


title: WT-5

description: Molecule: PCR amplicon


title: Lm208 at 5°C without C18:1 (C5)_replicate_1


title: Lm208 at 37°C with C18:1 (FA37)_replicate_3


title: PATH2-1

description: Molecule: PCR amplicon


title: 176

description: SAMO

value: Samoyed


title: WT lowPi 3

city: Richardson

first: Joseph

middle: Michael

last: Boll

state: TX

address: 800 W Campbell

department: Biological Sciences

institute: University of Texas at Dallas

data_processing:
CLC genomic workbench software (Qiagen) was used to process reads
Reads were aligned  to the A. baumannii ATCC 17978 genome annotation.
The RPKM expression values and the weighted proportions fold change of expression values between meropenem treated and treated samples at the same timepoint were calcualted.
Baggerley’s test on proportions was used to generate a false discovery rate adjusted P-value.
Assembly: GCA_000015425.1
Supplementary files format and content: Each processed file is in MS Excel format and show the gene expresion levels.

organism: Acinetobacter baumannii

growth_protocol: An overnight culture of A. baumannii strain ATCC 17978 was backdiluted 1:10 in fresh, in minimal medium supplemented with excess (1 mM) vs. limiting (50 μM) phosphate at OD600 of ~0.5 in triplicate.

extract_protocol:
RNA was extracted with the Direct-Zol RNA miniprep kit (Zymo Research).
Done at SeqCenter - Samples were DNAse treated with Invitrogen DNAse (RNAse free). Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices (UDI). Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v4.2.4)1.

treatment_protocol: Cutltures were upplemented with excess (1 mM) or limiting (50 μM) phosphate.

value: 50 uM phosphate


title: WT lowPi 2


title: WT-4

description: Molecule: PCR amplicon


title: WT-3

description: Molecule: PCR amplicon


title: Lm208 at 37°C with C18:1 (FA37)_replicate_2


title: WT-2

description: Molecule: PCR amplicon


title: nol_563

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

data_processing:
Raw reads were processed for quality trimming and adaptors removal using fastx_toolkit v0.0.14 and cutadapt v2.10 (ref 1). The processed reads were aligned to the Caenorhabditis elegans transcriptome and genome version WBcel235 with annotations from Ensembl release 106 using TopHat v2.1.1. Counts per gene quantification was done with htseq-count v2.01. Normalization and differential expression analysis were done with the DESeq2 package v 1.36.0.
Assembly: WBcel235
Supplementary files format and content: txt table with DESeq2 raw and normalized counts per gene (rows) per sample(column)
Supplementary files format and content: DESeq2_raw_norm_counts.txt

organism: Caenorhabditis elegans

source_name: pool of whole worms

growth_protocol: Synchronized CL2006 worms were grown at 20C on EV plates until L4 larva stage, and then treated with the indicated RNAi (EV or nol-56), washed and transferred onto new plates every day to remove progeny. The nematodes were harvested at day 6 of adulthood.

extract_protocol:
RNA was extracted using the NucleoSpin® RNA kit (MACHEREY-NAGEL; 740955) according to the manufacturer instructions.
PolyA-selection, mRNA libraries were prepared using KAPA Stranded mRNA kit with mRNA Capture Beads (KAPA Biosystems, KK8421). In brief, 1µg was used for the library construction; library was eluted in 20µl of elution buffer. All DNA samples libraries were pooled to 10nM sample. Multiplex samples Pool were loaded on NovaSeq 6000 (Illumina), using NovaSeq 6000 SP Reagent Kit v1.5 100 cycles (cat# 20028401), with 122 cycles

treatment_protocol: After L4 larva stage, worms were treated with EV (as control) or nol-56 RNAi until day 6 of harvesting

value: pool of whole worms

tag: harvest time

value: day 6 of adulthood

value: grown on nol-56 RNAi


title: WT lowPi 1


title: Lm208 at 37°C with C18:1 (FA37)_replicate_1


title: nol_561


title: WT highPi 3

value: 1 mM phosphate


title: PATH2-2

description: Molecule: PCR amplicon

value: KOLF2, Day 0

value: induced pluripotent stem cells


title: Lm208 at 37°C without C18:1 (C37)_replicate_3

value: strain Lm0208, wild-type


title: WT-1

description: Molecule: PCR amplicon


title: untreated EV3

value: Untreated worms


title: WT highPi 2


title: VUS2-3

description: Molecule: PCR amplicon


title: S4


title: Lm208 at 37°C without C18:1 (C37)_replicate_2

value: planktonic cell at early exponential phase


title: Lm208 at 5°C without C18:1 (C5)_replicate_3


title: untreated EV2


title: WT highPi 1


title: VUS2-2

description: Molecule: PCR amplicon


title: Lm208 at 37°C without C18:1 (C37)_replicate_1


title: Setaria_Cynodon_US

description: small RNA

organism:
Setaria viridis
Cynodon dactylon

value: plant leaf

value: pool of 11 individual plants

value: July 2021


title: VUS2-1

description: Molecule: PCR amplicon


title: VQPS107

status: Public on Oct 01 2024

city: Illkirch

first: Stephane

middle: D

last: VINCENT

address: 1 rue Laurent Fries

department: Development and Stem Cells

institute: IGBMC

library_source: genomic

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bclconvert 3.8.4.
Reads were mapped to mouse genome (mm10) using Bowtie2 v2.5.0 with default parameters except for “--mm”. Reads which mapping quality is below 10 were removed using samtools v1.15.1 with the command line "samtools view -b -q 10". Then, reads falling into Encode blacklisted regions v2 were removed using BEDtools intersect v2.30.0
BigWig files were generated using Deeptools bamCoverage v3.5.4 with the following parameters “-bs 10 -p 10–skipNonCoveredRegions –extendReads”. Deeptools bamCoverage was used  2r with “—scaleFactor” and scale factors determined based on the background signals calculated on the 30% least enriched regions
Assembly: mm10
Supplementary files format and content: BigWigs files normalized to the background

growth_protocol: cells plated at day -1, treatment starts at day 0

extract_protocol:
MicroPlex Library Preparation kit v3 (Diagenode)
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
MicroPlex Library Preparation kit v3 (Diagenode)

treatment_protocol: 3 days treatment with EtOH or 100 nM of 4-OHT

value: mESCs


title: VQPS108


title: VQPS105

value: EtOH


title: VQPS104


title: VQPS103


title: VQPS102


title: VQPS101


title: 223_mouse_DMBA_TPA_sorted_ctr_bio_rep1

city: Heidelberg

first: Rebecca

middle: Emma

last: Wagner

address: Inf 280 im Neuenheimer Feld

department: Cell Biology and Tumor Biology

country: Germany

institute: DKFZ

data_processing:
Reads were aligned to the GRCm38mm10 reference genome using STAR aligner
FeatureCounts was used for gene specific quantification fo reads on the appropriate gene annotation
Raw gene count values were then used as input for a differential gene expression analysis using DESeq2 within R
Assembly: Grcm38mm10
Supplementary files format and content: res_p95h_het_ctr_annotation.txt

source_name: reporter positive cells from back skin

extract_protocol:
RNA was extracted with Trizol following manufacturer's instructions
For SRSF2 knock out mice and controls RNA sequencing libraries were prepared using TruSeq Stranded Total RNA Gold library prep kit. For SRSF2 P95H mutant mice and controls RNA sequencing libraries were prepared using stranded Total RNA prep with Ribo-zero plus kit.

treatment_protocol: mouse back skin was treated topically every other day for a given period of time with 4-hydroxy tamoxifen

value: reporter positive cells from back skin

value: ctr

value: 3x tamoxifen injection and DMBA/TPA

value: 20 weeks


title: 246_mouse_DMBA_TPA_sorted_P95H_het_bio_rep3


title: 214_mouse_DMBA_TPA_sorted_P95H_het_bio_rep2


title: 222_mouse_DMBA_TPA_sorted_P95H_het_bio_rep1


title: RT10 EtOH IgG

description:
IgG CUT&RUN
SNVT268

data_processing:
Image analysis and base calling were performed using RTA version 2.7.7 and BCL Convert version 3.8.4
Data were preprocessed with Cutadapt (Martin 2011) v4.0 to trim adapter sequences (Nextera Transposase Sequence) from 3’ end of reads. Cutadapt was used with the following parameters ‘-a AGATCGGAAGAG -A AGATCGGAAGAG -m 25:25
Reads were mapped to Mus musculus genome (assembly mm10) using Bowtie2 (Langmead and Salzberg 2012) v2.4.4 with default parameters except for “–end-to-end –very-sensitive –no-mixed –no-discordant -I 10 -X 700”. Reads which mapping quality is below 10 were removed using samtools v1.15.1 (Li et al. 2009) with the command line “samtools view -b -q 10”. Reads falling into Encode blacklisted regions v2 (Amemiya, Kundaje, and Boyle 2019) were removed using BEDtools intersect v2.30.0 (Quinlan and Hall 2010).
Bigwig files of mean signal per condition were generated using Deeptools bamCompare (Ramírez et al. 2016) v3.5 with the following parameters “-of bigwig –operation mean –effectiveGenomeSize 2652783500 –normalizeUsing CPM –scaleFactorsMethod None –extendReads”.
The peak calling was done with Macs2 v2.2.7.1 with default parameters except “-f BAMPE -q 0.1”.
Assembly: mm10
Supplementary files format and content: bigwig files
Supplementary files format and content: TBP peak calling bed files
Library strategy: CUT&Run

growth_protocol: cells were cultured on plates coated with 0.1% gelatin solution in 1x PBS (Dutcher, Cat# P06-20410) using DMEM medium supplemented with 15% fetal calf serum ES-tested (ThermoFisher Scientific, Cat# 10270-106), 2 mM ʟ-glutamine (ThermoFisher Scientific, Cat# 25030-024), 0.1% β-mercaptoethanol (ThermoFisher Scientific, Cat# 31350-010), 100 UI/ml penicillin and 100 μg/ml streptomycin (ThermoFisher Scientific, Cat# 15140-122), 0.1 mM non-essential amino acids (ThermoFisher Scientific, Cat# 11140-035) and 1,500 U/ml leukemia inhibitory factor (home-made),  3 μM CHIR99021 (Axon Medchem, Cat# 1386) and 1 μM PD0325901 (Axon Medchem, Cat# 1408) were added freshly to the medium. Cells were grown at 37°C in a humidiﬁed, 5% CO2 incubator.

extract_protocol:
Cells were washed and resuspended in wash buffer and incubated for 10 min at room temperature with 10 µl of concanavalin A-coated beads (Bangs Laboratories, BP531). Cells bound to beads were permeabilized using 0.05% digitonin and incubated with the appropriate antibody at 4°C overnight. Protein A-MNAse (pA-MN) was added to a final concentration of 700 ng/ml and incubated at 4°C for 1 hr on a tube rotator. After washing, pA-MN was activated with 2 µl of 100 mM CaCl2 and digestion was performed for 30 min at 0°C. The reaction was stopped with 100 µl of stop buffer containing 2 pg/ml of heterologous spike-in DNA from yeast. Release of the DNA fragments was achieved by incubating samples at 37°C during 15 min. DNA was extracted using NucleoSpin columns (Macherey-Nagel) and eluted in 30 µl of NE buffer.
CUT&RUN-seq libraries were generated using the MicroPlex library preparation kit v3 (Diagenode), following the manufacturer’s instructions, except that the stage 4 of the library amplification PCR was performed with a combined annealing-extension step for 10 s at 60°C, and stage 5 with an extension step for 10 s at 60°C for 7 cycles. Yield and size distribution were quantified on a 2100 Bioanalyzer instrument (Agilent).

treatment_protocol: 4-OHT to induce the deletion of the floxed alleles: cells were plated at day 0, treated with EthOH or 100 mM 4-OHT from day1 to day 3

value: mouse ES cells

value: Ethanol


title: RT7 4-OHT IgG

description:
IgG CUT&RUN
SNVT267


title: nol_562

value: pool of whole worms

value: day 6 of adulthood

value: grown on nol-56 RNAi


title: RT10 4-OHT IgG

description:
IgG CUT&RUN
SNVT269


title: RT7 EtOH IgG

description:
IgG CUT&RUN
SNVT266


title: RT10 4-OHT TAF12 rep1

description:
TAF12 CUT&RUN
SNVT264


title: RT10 EtOH TAF12 rep2

description:
TAF12 CUT&RUN
SNVT263


title: RT10 EtOH TAF12 rep1

description:
TAF12 CUT&RUN
SNVT262


title: RT10 4-OHT TAF12 rep2

description:
TAF12 CUT&RUN
SNVT265


title: untreated EV1


title: RT7 4-OHT TAF12 rep2

description:
TAF12 CUT&RUN
SNVT261


title: RT7 EtOH TAF12 rep2

description:
TAF12 CUT&RUN
SNVT259


title: RT10 4-OHT TAF10 rep1

description:
TAF10 CUT&RUN
SNVT256


title: RT7 EtOH TAF12 rep1

description:
TAF12 CUT&RUN
SNVT258


title: RT10 EtOH TAF10 rep2

description:
TAF10 CUT&RUN
SNVT255


title: VQPS106


title: RT7 4-OHT TAF10 rep2

description:
TAF10 CUT&RUN
SNVT253


title: 259_mouse_DMBA_TPA_sorted_ctr_bio_rep3


title: RT7 4-OHT TAF10 rep1

description:
TAF10 CUT&RUN
SNVT252


title: RT7 EtOH TAF10 rep1

description:
TAF10 CUT&RUN
SNVT250


title: RT10 4-OHT TAF7 rep2

description:
TAF7 CUT&RUN
SNVT249


title: RT10 4-OHT TAF7 rep1

description:
TAF7 CUT&RUN
SNVT248


title: RT7 4-OHT TAF7 rep2

description:
TAF7 CUT&RUN
SNVT245


title: RT10 EtOH TAF7 rep2

description:
TAF7 CUT&RUN
SNVT247


title: RT10 EtOH TAF7 rep1

description:
TAF7 CUT&RUN
SNVT246


title: RT7 4-OHT TAF7 rep1

description:
TAF7 CUT&RUN
SNVT244


title: RT10 4-OHT TBP rep2

description:
TBP CUT&RUN
SNVT241


title: RT7 EtOH TAF7 rep2

description:
TAF7 CUT&RUN
SNVT243


title: RT7 EtOH TAF7 rep1

description:
TAF7 CUT&RUN
SNVT242


title: RT10 EtOH TBP rep2

description:
TBP CUT&RUN
SNVT239


title: RT7 4-OHT TAF12 rep1

description:
TAF12 CUT&RUN
SNVT260


title: RT7 4-OHT TBP rep2

description:
TBP CUT&RUN
SNVT237


title: RT10 4-OHT TBP rep1

description:
TBP CUT&RUN
SNVT240


title: 4L_RESTKD_sh87_rep2

city: New York

first: Elena

last: Grossi

state: NY

address: 1470 Madison Ave

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Libraries were prepared using the NEXTFLEX Rapid Directional RNA-seq Kit 2.0
Single-end 75-bp reads were aligned to hg38/GRCh38 with STAR
The featureCounts function of the Rsubread R package was used to assign reads to genes
Assigned reads were normalized and differential expression analysis was performed using the R package DESeq2
Assembly: hg38
Supplementary files format and content: tab-delimited text file including normalized counts for all samples within an experiment

growth_protocol: Melanoma cells were maintained in DMEM, 10% FBS and 1X penicillin-streptomycin. Primary normal human epithelial melanocytes (NHEM - batches SW5, SW11 and NHM1) were cultured in Melanocyte Growth Media 254, 1X HMGS, 0.2 mM CaCl2 and 10 ng/mL PMA.

extract_protocol:
2-4M cells were used for total RNA extraction using the RNeasy Mini Kit (Qiagen) according to manufacturer’s protocol.
1-2 ug of total RNA was used to isolate poly-A RNA with NEXTFLEX Poly(A) beads 2.0

value: skin

value: melanoma

value: BRAFV600E subtype

tag: disease stage

value: metastatic


title: RT10 EtOH TAF10 rep1

description:
TAF10 CUT&RUN
SNVT254


title: RT7 EtOH TBP rep2

description:
TBP CUT&RUN
SNVT235


title: 258_mouse_DMBA_TPA_sorted_ctr_bio_rep2


title: RT10 4-OHT TAF10 rep2

description:
TAF10 CUT&RUN
SNVT257


title: 4L_RESTKD_sh87_rep1


title: 4L_shSCR_rep1


title: RT7 EtOH TAF10 rep2

description:
TAF10 CUT&RUN
SNVT251


title: 4L_shSCR_rep2


title: SW11_ARID2KO_sg5_rep2

source_name: neonatal foreskin

value: neonatal foreskin

value: NHEM

value: normal


title: SW11_ARID2KO_sg1_rep2


title: SW11_ARID2KO_sg5_rep1


title: SW11_ARID2KO_sg1_rep1


title: SW11_sgNTC_rep2


title: 4L_ARID2KO_sg5.11_rep1


title: 4L_ARID2KO_sg5.11_rep2


title: 4L_ARID2KO_sg1.17_rep2


title: 4L_ARID2KO_sg1.17_rep1


title: 4L_sgNTC_rep1


title: RT10 EtOH TBP rep1

description:
TBP CUT&RUN
SNVT238


title: SW11_sgNTC_rep1


title: RT7 EtOH TBP rep1

description:
TBP CUT&RUN
SNVT234


title: 4L_Parental_rep2


title: 4L_sgNTC_rep2


title: RT7 4-OHT TBP rep1

description:
TBP CUT&RUN
SNVT236


title: NHEM_REST_ChIP_ARID2_KO5

data_processing:
Single-end reads were trimmed with Trimmomatic, paired reads with NGmerge.
Reads were aligned to GRCh38/hg38 using Bowtie2 with standard parameters and quality was assessed using fastQC.
samtools was used to generate bam files and filter out low quality, mitochondrial and duplicated reads.
bigwig files were generated from filtered bam files using deepTools bamCoverage.
Assembly: hg38
Supplementary files format and content: bigwig

extract_protocol:
For ChIP-seq: For histone modifications, 10-15M cells were crosslinked with 1% Formaldehyde; For chromatin remodelers and TFs, 10-40M cells were double cross-linked with 0.25 M disuccinimidyl glutarate (DSG), followed by 1% formaldehyde. Nuclei were isolated and lysed, and chromatin was fragmented by sonication. Extracts were incubated with specific antibodies O/N, followed by 2h incubation with magnetic Protein A+G beads. After extensive washes, DNA was eluted from the beads and reverse crosslinked. For ChIC: Chromatin Immuno Cleavage (ChIC or CUT&RUN) was performed using CUTANA ChIC/CUT&RUN kit following manufacturer’s protocol.
Libraries for ChIP-seq were prepared according to Carcamo et al., Cell Rep 39, 110637. 10.1016/j.celrep.2022.110637. Libraries for ChIC were prepared using NEBNext Ultra II DNA library kit, following manufacturer’s recommendations.
ChIP-seq
CUT&Run (ChIC)

tag: chip antibody

value: REST - Millipore #07-579


title: 4L_Parental_rep1

tag: tissue


title: 4L_RESTKD_sh3_rep2


title: 4L_RESTKD_sh3_rep1


title: NHEM_CTCF_ChIP

value: CTCF - Millipore #07-729


title: NHEM_REST_ChIP_NTC1


title: NHEM_H3K4me3_ChIP

value: H3K4me3 - Abcam #ab8580


title: NHEM_REST_ChIP_ARID2_KO1


title: NHEM_REST_ChIP_NTC2


title: NHEM_REST_ChIP


title: NHEM_SS18_ChIP

value: SS18 - Cell Signaling #21792 D6I4Z


title: NHEM_ARID2_ChIP

value: ARID2 - Cell signaling #82342 D8D8U


title: NHEM_H3K27ac_ChIP

value: H3K27ac - Abcam #ab4729


title: 4L_REST_ChIP_ARID2_KO1-17


title: HHEM_H3K9me3_ChIP

value: H3K9me3 - Abcam #ab176916


title: NHEM_Input_ChIP


title: 4L_REST_ChIP


title: 4L_BRG1_ChIP

value: BRG1 - Abcam #ab110641


title: 4L_H3K4me3_ChIP


title: 4L_SS18_ChIP


title: 4L_ARID2_ChIP


title: 4L_Input_ChIP


title: PBMC, replicate 1, viably frozen, single-cell, 3' workflow

city: Darlinghurst

first: Taopeng

last: Wang

state: New South Wales

address: 384 Victoria St

department: Cancer ecosystem

institute: Garvan institute of medical research

data_processing:
Demultiplexing and reads alignment were performed using Cell Ranger v7.0.1 or v2023.0415.0 as documented in https://www.biorxiv.org/content/10.1101/2023.12.07.570700v1.
raw count matrix generated using 10X Genomics cellranger v7.0.1
filtered count matrix generated using 10X Genomics cellranger v7.0.1
Assembly: hg38
Supplementary files format and content: Unfiltered counts in .h5 format generated by 10X Genomics cellranger (v2023.0415.0 / v7.0.1)
Supplementary files format and content: 10X Genomics cellranger v3 format .h5 files for counts filtered using cellranger v7.0.1 (PBMC data) or cellbender v2.0.0 (all other data)

source_name: Peripheral blood mononuclear cells

extract_protocol:
Samples were processed for 3' or Flex chemistry (10x Genomics) using establihsed protocols as mentioned in https://www.biorxiv.org/content/10.1101/2023.12.07.570700v1.
libraries were prepared accoridng to the manufacturer's instructions (3' V3.1 chemistry & Flex chemistry, 10x Genomics).

value: Peripheral blood mononuclear cells

tag: sample type

value: viably frozen sample

tag: workflow

value: 10X 3p workflow

tag: library protocol

value: 10X Genomics 3' v3.1


title: Kidney_k48, FFPE, single-cell, scFFPE workflow

data_processing:
Demultiplexing and reads alignment were performed using Cell Ranger v7.0.1 or v2023.0415.0 as documented in https://www.biorxiv.org/content/10.1101/2023.12.07.570700v1.
raw count matrix generated using 10X Genomics cellranger v7.0.1
filtered count matrix gnerated using cellbender v0.2.0
Assembly: hg38
Supplementary files format and content: Unfiltered counts in .h5 format generated by 10X Genomics cellranger (v2023.0415.0 / v7.0.1)
Supplementary files format and content: 10X Genomics cellranger v3 format .h5 files for counts filtered using cellranger v7.0.1 (PBMC data) or cellbender v2.0.0 (all other data)

source_name: Kidney

value: Kidney

value: FFPE sample

value: 10X scFFPE workflow

value: 10X Genomics FLEX


title: Kidney_k48, FFPE, single-nucleus, snPATHO-seq workflow

molecule: nuclear RNA

value: snPATHO-seq workflow


title: PBMC, replicate 1, viably frozen, single-cell, FLEX workflow

value: 10X FLEX workflow


title: PBMC, replicate 2, viably frozen, single-cell, FLEX workflow


title: 4399, FFPE, single-nucleus, snPATHO-seq workflow

source_name: Breast cancer liver metastasis

value: Breast cancer liver metastasis


title: PLC/PRF/5 on ovo rep2 [PLC-B]

city: Grenoble

first: Anouk

last: Emadali

address: Allée des Alpes, Site Santé La Tronche, BP170, Cedex 9

department: Institute for Advanced Biosciences

institute: Grenoble University Hospital

data_processing:
Data processing has been performed using the default parameters of the DriverMap™ Human Genome-Wide Targeted RNA Expression Profiling (EXP) Platform-Read count
Assembly: hg38
Supplementary files format and content: table summarizing read count across samples for targeted sequencing of 19000 protein-coding genes

extract_protocol:
RNA was extracted from cells lines (samples in vitro) using Mini RNeasy (#74104, QIAGEN) and from xenografted tumors (samples on ovo) using Midi RNeasy (#75144, QIAGEN)
500 ng of total RNA was used for the construction of sequencing libraries using the DriverMap Targeted Expression Profiling kits (#DM2-HGW-96, CELLECTA)

tag: cell type

value: hepatoma cell line

value: grown in ovo


title: PLC/PRF/5 in vitro rep1 [PLC-1]

tag: treatment

value: grown in vitro


title: PLC/PRF/5 in vitro rep2 [PLC-2]

tag: cell line


title: PLC/PRF/5 on ovo rep1 [PLC-A]


title: HuH7 on ovo rep1 [HUH7-B]


title: PLC/PRF/5 on ovo rep3 [PLC-D]


title: 4L_REST_ChIP_NTC

value: skin

value: melanoma

tag: genotype

value: BRAFV600E subtype

value: metastatic

value: REST - Millipore #07-579


title: HuH7 on ovo rep3 [HUH7-D]


title: PLC/PRF/5 in vitro rep3 [PLC-3]


title: PLC/PRF/5 on ovo rep4 [PLC-E]


title: NHEM_H3K27me3_ChIP

value: neonatal foreskin

value: NHEM

value: normal

value: H3K27me3 - Millipore #07-449


title: HuH7 on ovo rep2 [HUH7-C]


title: HuH7 on ovo rep4 [HUH7-E]


title: HuH7 in vitro rep3 [HUH7-3]


title: HuH7 in vitro rep2 [HUH7-2]


title: 4L_H3K27ac_ChIP

value: H3K27ac - Abcam #ab4729


title: HuH7 in vitro rep1 [HUH7-1]


title: Hep3B on ovo rep4 [Hep3B-E]


title: Hep3B on ovo rep3 [Hep3B-D]


title: PBMC, replicate 2, viably frozen, single-cell, 3' workflow

value: Peripheral blood mononuclear cells

value: viably frozen sample

value: 10X 3p workflow

value: 10X Genomics 3' v3.1


title: Hep3B on ovo rep2 [Hep3B-C]

value: hepatoma cell line


title: Hep3B on ovo rep1 [Hep3B-B]

value: grown in ovo


title: Hep3B in vitro rep3 [Hep3B-3]

value: grown in vitro


title: HepG2 on ovo rep4 [HepG2-E]


title: Hep3B in vitro rep1 [Hep3B-1]


title: HepG2 on ovo rep1 [HepG2-A]


title: HepG2 on ovo rep3 [HepG2-D]


title: Hep3B in vitro rep2 [Hep3B-2]


title: HepG2 in vitro rep3 [HepG2-3]


title: HepG2 in vitro rep1 [HepG2-1]


title: HepG2 in vitro rep2 [HepG2-2]


title: 4L_H3K9me3_ChIC

data_processing:
Single-end reads were trimmed with Trimmomatic, paired reads with NGmerge.
Reads were aligned to GRCh38/hg38 using Bowtie2 with standard parameters and quality was assessed using fastQC.
samtools was used to generate bam files and filter out low quality, mitochondrial and duplicated reads.
bigwig files were generated from filtered bam files using deepTools bamCoverage.
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&Run

value: skin

value: H3K9me3 - Abcam #ab176916


title: 4L_H3K4me1_ChIC

value: melanoma

value: BRAFV600E subtype

value: H3K4me1 - Epicypher #13-0040


title: 4L_H3K27me3_ChIC

value: metastatic

value: H3K27me3 - Epicypher #13-0055


title: 4L_EZH2_ChIC

value: EZH2 - Cell Signaling #3147 AC22


title: OVCAR4 P7i replicate 2

city: Dallas

first: W. Lee

last: Kraus

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated with 500 nM RBN-2397.

data_processing:
The RNA-seq reads were aligned to the hg38 human reference genome using star aligner.
Mapped reads were sorted and represented in bam files for differential gene expression analysis. Bigwig files were generated for visualization on genome browser using custom R scripts.
Assembly: hg38
Supplementary files format and content: BigWig - Browser Tracks showing normalized count for visualization on UCSC geneome browser

source_name: high-grade serous ovarian adenocarcinoma

growth_protocol: OVCAR3 and OVCAR4 serous ovarian cancer cell lines were purchased from the American Type Culture Collection (OVCAR3: ATCC; RRID: CVCL_0465, OVCAR4: ATCC; RRID: CVCL_1627). They were maintained in RPMI media (Sigma-Aldrich, R8758) supplemented with Glutamax, 10% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol:
OVCAR3 and OVCAR4 cells were seeded at at density of 0.5x10^6 cells per well in a 6-well plate and treated as described above. Total RNA was isolated using the Qiagen RNeasy Plus Mini kit (Qiagen, 74136) according to the manufacturer's protocol.
Total RNA was isolated from OVCAR3 and OCVAR4 cells treated with RBN-2397, paclitaxel, combination, or vehicle. Total RNA was isolated using the RNeasy kit (Qiagen, 74106) according to the manufacturer’s instructions. The NEBNext Ultra II Directional RNA Library Prep (NEB, E7765L) in conjunction with Poly(A) mRNA Magnetic Isolation Module kit (NEB, E7490L) was then used to prepare libraries according to the manufacturer’s instructions. The RNA-seq libraries were subjected to QC analyses [final library yields as assessed by Qubit 2.0 (Invitrogen) and size distribution of the final library DNA fragments as assessed by TapeStation (Illumina)] and sequenced using an Illumina NextSeq 2000.

treatment_protocol: OVCAR3 and OVCAR4 cells were treated with  DMSO, RBN-2397 (500 nM), pacliaxel (0.4 nM) or combination of  RBN-2397 (500 nM) and pacliaxel (0.4 nM) for 24 hours.

value: epithelial cells

value: 500 nM RBN-2397 for 24 hours


title: 4L_PBRM1_ChIP

value: PBRM1 - Bethyl #A700-019


title: OVCAR4 P7i replicate 3

value: high-grade serous ovarian adenocarcinoma


title: OVCAR4 combination replicate 3

description: cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated with 0.4 nM paclitaxel and 500 nM RBN-2397.

value: 0.4 nM paclitaxel and 500 nM RBN-2397 for 24 hours


title: OVCAR4 combination replicate 1


title: OVCAR4 taxol replicate 2

description: cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated with o.4 nM paclitaxel.

value: 0.4 nM paclitaxel for 24 hours


title: OVCAR4 taxol replicate 3


title: OVCAR3 combination replicate 3


title: OVCAR4 DMSO replicate 3

description: cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated with DMSO

value: DMSO (control)


title: OVCAR4 DMSO replicate 1


title: HepG2 on ovo rep2 [HepG2-C]

value: hepatoma cell line

value: grown in ovo


title: OVCAR3 combination replicate 1


title: OVCAR3 taxol replicate 3


title: OVCAR3 DMSO replicate 2

description: cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated  with DMSO


title: OVCAR3 taxol replicate 1


title: OVCAR3 P7i replicate 2


title: OVCAR3 P7i replicate 1


title: OVCAR3 DMSO replicate 3


title: OVCAR3 P7i replicate 3


title: OVCAR4 P7i replicate 1


title: OVCAR3 taxol replicate 2


title: NC059 aCM+cond biol rep 3

city: Leiden

first: Thomas

last: Hutschalik

address: Galileiweg 8

country: Netherlands

institute: Ncardia Services B.V.

description: #24 aCM+cond s3 N

data_processing:
Performed by Singe Cell Discoveries (Netherlands)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Cell line 2 (NC-059)

growth_protocol: Cells were cultured in PCM (Ncardia) at 37C and 5% CO2 until 8 days after seeding

extract_protocol:
NucleoSpin RNA, Mini kit for RNA purification (According to manufacturer protocol), (Machery-Nagel)
Performed by Single Cell Discoveries (Netherlands) 1. Pre-quality checks to measure RNA concentration and RNA quality 2. Performing RT to generate cDNA 3. Pooling of all samples (barcodes are now integrated within the cDNA molecules) 4. Amplification of the material through an IVT reaction (linear amplification), which generates amplified RNA 5. QC: bioanalyzer of the amplified RNA 6. Library preparation to generate a sequenceable cDNA library (aRNA) 7. QC: bioanalyzer of the final cDNA library

treatment_protocol: For M1 coculture and M1 conditioned medium: Maturation of monocytes towards M1 macrophages was performed by supplementing culture medium with 20 ng/mL GM-CSF (Gibco) for 6 days, with medium being refreshed at d3. Matured M1 macrophages were activated by adding 100 ng/mL IFN-γ (Peprotech) and 50 ng/mL LPS (InvivoGen) at d6 for 20h, followed by a change of medium with 100 ng/mL LPS added for 4h. For Hydrocortisone Treatment: Hydrocortisone 10 µM was added to cells. Cocultures were seeded and cultured as previously described and hydrocortisone added during medium changes at d6, d6+20h, d7 and d8 after seeding. For conditioned medium samples: For conditioned medium samples, 125 ul supernatant from M1 monocultures (24 well plate, 500,000 cells/well in 0.5 mL PCM) was added to appropriate samples.

value: Cell line 2 (NC-059)

value: hiPSC-derived atrial cardiomyocyte

value: WT

value: M1 Conditioned Medium


title: OVCAR4 combination replicate 2


title: NC059 aCM+cond biol rep 2

description: #23 aCM+cond s2 N


title: NC059 aCM only biol rep 1

description: #19 aCM only s1 N


title: NC059 aCM+cond biol rep 1

description: #22 aCM+cond s1 N


title: NC059 aCM+M1+H biol rep 3

description: #18 aCM+M1+H s3 N

value: M1 coculture

value: + Hydrocortisone 10 µM


title: OVCAR3 DMSO replicate 1


title: NC059 aCM+M1+H biol rep 2

description: #17 aCM+M1+H s2 N


title: NC059 aCM+M1+H biol rep 1

description: #16 aCM+M1+H s1 N


title: OVCAR4 DMSO replicate 2


title: OVCAR3 combination replicate 2


title: NHEM_H3K4me1_ChIC

value: neonatal foreskin

value: NHEM

value: normal

value: H3K4me1 - Epicypher #13-0040


title: NC059 aCM only biol rep 2

description: #20 aCM only s2 N


title: NC059 aCM+M1 biol rep 1

description: #13 aCM+M1 s1 N


title: NC030 aCM+cond biol rep 3

description: #12 aCM+cond s3

source_name: Cell line 1 (NC-030)

value: Cell line 1 (NC-030)


title: NC030 aCM+cond biol rep 2

description: #11 aCM+cond s2


title: NC030 aCM+M1+H biol rep 3

description: #6 aCM+M1+H s3


title: NC030 aCM only biol rep 2

description: #8 aCM only s2


title: NC030 aCM only biol rep 1

description: #7 aCM only s1


title: NC030 aCM+M1+H biol rep 2

description: #5 aCM+M1+H s2


title: NC059 aCM only biol rep 3

description: #21 aCM only s3 N


title: NC030 aCM+M1 biol rep 1

description: #1 aCM+M1 s1


title: NC030 aCM+M1+H biol rep 1

description: #4 aCM+M1+H s1


title: NC030 aCM+M1 biol rep 2

description: #2 aCM+M1 s2


title: 48-4-totalPolii

data_processing:
Reads were aligned to the hs37d5 reference genome using STAR aligner
FeatureCounts was used for gene specific quantification fo reads on the appropriate gene annotation
Raw gene count values were then used as input for a differential gene expression analysis using DESeq2 within R
Bedtools were used to generate bedGraph files and bedGraphToBigWig was used to produce BigWig files.
Assembly: hs37d5
Library strategy: Cut&Run

source_name: FaDu

growth_protocol: Keratinocytes were cultured with KBM-Gold (Lonza) medium  supplemented with 0.06mM CaCl and the essential growth factors supplied. FaDu cells were cultured with EMEM supplemented with 10% FBS and pen/strep. SCC25 cells were cultured in DMEM/F12 HEPES with 10% FBS and pen/strep. All cells were kept at 37 with 5% CO2

extract_protocol:
Total RNA was extracted using Trizol reagent, following manufacturer's instructions. DNA was purified using spin columns following manufacturer's instructions.
Total RNA from keratinocytes was rRNA depleted and RNA-sequencing libraries were prepped using NEB Ultra II directional kit (NEB). Total RNA from FaDu cells was used to prepare libraries using TruSeq stranded total RNA kit (Illumina). RNA from SCC25 cells and clones was used to generate RNA-sequencing libraries using stranded total RNA prep with Ribo-zero plus kit (Illumina). SLAM-sequencing libraries were prepared using Quant-seq 3' mRNA library prep kit (Lexogen). Libraries were prepared from purified DNA using the SimpleChIP, ChIP-seq DNA library prep kit for illumina (CST).

treatment_protocol: SRSF2 depletion was achieved by transfecting an siRNA pool using Lipofectamine RNAiMax

value: FaDu

value: squamous cell carcinoma cells

value: siRNA transfection


title: NC030 aCM+M1 biol rep 3

description: #3 aCM+M1 s3


title: Ctr-4-totalPolii


title: NC059 aCM+M1 biol rep 2

description: #14 aCM+M1 s2 N


title: Ctr-3-totalPolii


title: NC059 aCM+M1 biol rep 3

description: #15 aCM+M1 s3 N


title: Ctr-5-totalPolii


title: 48-3-totalPolii


title: 48-5-totalPolii


title: NC030 aCM+cond biol rep 1

description: #10 aCM+cond s1


title: J-Lat-Mock-m6A-SACseq-rp3

city: Chicago

first: Chuan

last: He

state: IL

address: 929 E 57th St

department: Chemistry Department

institute: University of Chicago

description:
SACseq-Mock-label-3
Drug_vs_Mock_cellular_mRNA_m6A.xlsx
SACseq-Drug-m6a_site.HIV.txt

data_processing:
RNA-seq data was analyzed by following pipeline discribed: The adaptor sequences were trimmed with Cutadapt (v4.2) using the parameter "cutadapt -j 15 -m 26 --nextseq-trim=20 -O 6 -n 3 --pair-filter=any  -a AGATCGGAAGAGCACACGTCTG -A AGATCGGAAGAGCGTCGTG". The trimmed reads were deduplicated by BBMap tools. The deduplicated reads were mapped to both HIV genome (AF033819.3) and hg38 genome using STAR(v2.7.9a) with parameters "--alignEndsType Local --outFilterMatchNminOverLread 0.66 --outFilterMatchNmin 15 --outFilterMismatchNmax 5 --outFilterMismatchNoverLmax 0.2 --outFilterMultimapNmax 10".
SAC-seq data was analyzed according to the reported protocol (Nat Protoc 18, 626–657 (2023)).
Assembly: hg38, HIV-1 (AF033819.3)
Supplementary files format and content: "Mock_vs_Drug.DEresults.RNAseq.txt" shows the differentially expression levels of cellular genes with or without lonomycin treatment; "HIV-1.RPKM.txt" shows the expression levels of  HIV-1 proteins with or without lonomycin treatment; "Drug_vs_Mock_cellular_mRNA_m6A.xlsx" shows the differential fraction of each m6A site with or without lonomycin treatment; "SACseq-Drug-m6a_site.HIV.txt" shows the HIV-1 m6A methylome by SAC-seq.
Library strategy: m6A-SAC-seq

source_name: Peripheral blood

growth_protocol: Cell were grown in RPMI-1640, with 10% FBS and 1% penicillin-streptomycin. Cells were maintained at 37°C with 5% CO2.

extract_protocol:
RNA was isolated using Trizol method and precipitated using ethanol.
RNA-seq libraries were prepared using SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit. SAC-seq libraries were prepared according to the reported protocol (Nat Protoc 18, 626–657 (2023)).

treatment_protocol: J-Lat 10.6 cells were treated with either DMSO or combination of PMA+Ionomycin for 6 hours.

value: Peripheral blood

value: T-lymphoblast

value: pseudodiploid

value: DMSO


title: J-Lat-PMA-m6Ainput-SACseq-rp1

description:
SACseq-Drug-input-1
Drug_vs_Mock_cellular_mRNA_m6A.xlsx
SACseq-Drug-m6a_site.HIV.txt

value: PMA+Ionomycin


title: J-Lat-Mock-m6Ainput-SACseq-rp1

description:
SACseq-Mock-input-1
Drug_vs_Mock_cellular_mRNA_m6A.xlsx
SACseq-Drug-m6a_site.HIV.txt


title: J-Lat-PMA-m6A-SACseq-rp3

description:
SACseq-Drug-label-3
Drug_vs_Mock_cellular_mRNA_m6A.xlsx
SACseq-Drug-m6a_site.HIV.txt


title: J-Lat-PMA-m6A-SACseq-rp2

description:
SACseq-Drug-label-2
Drug_vs_Mock_cellular_mRNA_m6A.xlsx
SACseq-Drug-m6a_site.HIV.txt


title: J-Lat-Mock-m6Ainput-SACseq-rp3

description:
SACseq-Mock-input-3
Drug_vs_Mock_cellular_mRNA_m6A.xlsx
SACseq-Drug-m6a_site.HIV.txt


title: J-Lat-PMA-m6A-SACseq-rp1

description:
SACseq-Drug-label-1
Drug_vs_Mock_cellular_mRNA_m6A.xlsx
SACseq-Drug-m6a_site.HIV.txt


title: J-Lat-PMA-m6Ainput-SACseq-rp3

description:
SACseq-Drug-input-3
Drug_vs_Mock_cellular_mRNA_m6A.xlsx
SACseq-Drug-m6a_site.HIV.txt


title: J-Lat-Mock-m6Ainput-SACseq-rp2

description:
SACseq-Mock-input-2
Drug_vs_Mock_cellular_mRNA_m6A.xlsx
SACseq-Drug-m6a_site.HIV.txt


title: NC030 aCM only biol rep 3

description: #9 aCM only s3

value: hiPSC-derived atrial cardiomyocyte

value: WT


title: J-Lat-Mock-m6A-SACseq-rp1

description:
SACseq-Mock-label-1
Drug_vs_Mock_cellular_mRNA_m6A.xlsx
SACseq-Drug-m6a_site.HIV.txt


title: J-Lat-Mock-m6A-SACseq-rp2

description:
SACseq-Mock-label-2
Drug_vs_Mock_cellular_mRNA_m6A.xlsx
SACseq-Drug-m6a_site.HIV.txt


title: J-Lat-PMA-RNAseq-rp3

description:
Drug-3-RNAseq
Mock_vs_Drug.DEresults.RNAseq.txt
HIV-1.RPKM.txt

data_processing:
RNA-seq data was analyzed by following pipeline discribed: The adaptor sequences were trimmed with Cutadapt (v4.2) using the parameter "cutadapt -j 15 -m 26 --nextseq-trim=20 -O 6 -n 3 --pair-filter=any  -a AGATCGGAAGAGCACACGTCTG -A AGATCGGAAGAGCGTCGTG". The trimmed reads were deduplicated by BBMap tools. The deduplicated reads were mapped to both HIV genome (AF033819.3) and hg38 genome using STAR(v2.7.9a) with parameters "--alignEndsType Local --outFilterMatchNminOverLread 0.66 --outFilterMatchNmin 15 --outFilterMismatchNmax 5 --outFilterMismatchNoverLmax 0.2 --outFilterMultimapNmax 10".
SAC-seq data was analyzed according to the reported protocol (Nat Protoc 18, 626–657 (2023)).
Assembly: hg38, HIV-1 (AF033819.3)
Supplementary files format and content: "Mock_vs_Drug.DEresults.RNAseq.txt" shows the differentially expression levels of cellular genes with or without lonomycin treatment; "HIV-1.RPKM.txt" shows the expression levels of  HIV-1 proteins with or without lonomycin treatment; "Drug_vs_Mock_cellular_mRNA_m6A.xlsx" shows the differential fraction of each m6A site with or without lonomycin treatment; "SACseq-Drug-m6a_site.HIV.txt" shows the HIV-1 m6A methylome by SAC-seq.


title: J-Lat-PMA-RNAseq-rp2

description:
Drug-2-RNAseq
Mock_vs_Drug.DEresults.RNAseq.txt
HIV-1.RPKM.txt


title: J-Lat-PMA-m6Ainput-SACseq-rp2

description:
SACseq-Drug-input-2
Drug_vs_Mock_cellular_mRNA_m6A.xlsx
SACseq-Drug-m6a_site.HIV.txt


title: J-Lat-Mock-RNAseq-rp3

description:
Mock-3-RNAseq
Mock_vs_Drug.DEresults.RNAseq.txt
HIV-1.RPKM.txt


title: J-Lat-PMA-RNAseq-rp1

description:
Drug-1-RNAseq
Mock_vs_Drug.DEresults.RNAseq.txt
HIV-1.RPKM.txt


title: J-Lat-Mock-RNAseq-rp2

description:
Mock-2-RNAseq
Mock_vs_Drug.DEresults.RNAseq.txt
HIV-1.RPKM.txt


title: J-Lat-Mock-RNAseq-rp1

description:
Mock-1-RNAseq
Mock_vs_Drug.DEresults.RNAseq.txt
HIV-1.RPKM.txt


title: LS

city: Hefe

first: sheng

last: zhang

state: Anhui Province

address: Shushan District

institute: anhui agriculture university

description: 10x Genomics

data_processing:
Raw reads were aligned against the S. marcescens FY Lactobacillus plantarum FY1.Then, genome and counted by StarSolo. Sequencing data was further analyzed using the Scanpy software.
We initially reduced dimensionality of the dataset using principal components analysis (PCA), retaining 20 principal components.
Subsequent steps, like low-dimensional UMAP visualization and cell clustering via Leiden algorithm, were based on the initial PCA.
Finally, Wilcoxon rank sum was used to analyze the difference between different cluster cells.
Assembly: Serratia marcescens with the Genbank accession number CP053378 and Lactobacillus plantarum with the Genbank accession number KY038178
Supplementary files format and content: tsv files include gene counts for each Sample

organism:
Serratia marcescens
Lactiplantibacillus plantarum

source_name: WT

extract_protocol:
Up to half a million cells were collected by centrifuging at 4000 rpm for 5 min at 4℃.The supernatant was removed and cell pellets were resuspended in 2 mL ice-cold 4% formaldehyde (Sigma, 47608) and incubated with shaking overnight at 4℃. The fixative was removed by centrifuging at 4000 rpm for 5 min at 4℃ and cells were washed twice by 1 mL PBS-TRI (1x PBS supplemented with 0.1% Tween-20 and 0.1 U/mL Murine RNase inhibitor (Vazyme, R 301)). The supernatant was removed and cells were resuspended in 200 μL PBS-TRI (1x PBS supplemented with 0.1% Tween-20 and 0.2 U/mL Murine RNase inhibitor (Vazyme, R 301)).
The cell suspensions were counted with a Moxi cell counter (ORFLO Technologies, Ketchum, Idaho) and diluted according to the manufacturer’s instructions to obtain 2000-4000 single-cell per sample. Random primers were added to amplify the full length of RNA, and the resulting cDNA fragment was added with adaptor. The microbeads with cell barcode, UMI, and the cDNA fragments linked to the adaptor were combined with the mixture of enzymes and extended in the microfluidic system to obtain the labeled cDNA chain. The beads were lysed and the cDNA was used as a template for PCR amplification. All products were pooled to construct a standard sequencing library.

tag: strain

value: Serratia marcescens FY,Lactobacillus plantarum FY1

value: bacteria  co-cultured


title: LFS4

description: replicate=LFS group biological replicate 4

data_processing:
For annotation, the genome of S. marcescens (GCF_013122155.1) and L. plantarum (GCF_032436005.1) was used as reference.
The significant differentially expressed genes were determined in different groups using the DESeq software, with the standards of P-value ≤0.05, and fold change |log2FC| ≥1.
KEGG B class database was used to classify the genes with significantly differential expression based on their functions using the tool Omicshare.
Assembly: Serratia marcescens with the Genbank accession number CP053378 and Lactobacillus plantarum with the Genbank accession number KY038178
Supplementary files format and content: txt files include gene count values for each Sample

source_name: Serratia marcescens FY and Lactobacillus plantarum FY1

extract_protocol:
RNA was harvested using Bacteria RNA Extraction Kit (Vazyme). 1 ug of total RNA was used for the construction of sequencing libraries.
With Ribo-off rRNA Depletion Kit (Vazyme), the total bacterial RNA was subjected to rRNA removing to obtain mRNA.And then RNA libraries for RNA-seq were prepared using VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme) following manufacturer's protocols.

value: bacteria and larvae were co-cultured


title: LFS

description: 10x Genomics


title: LFS1

description: replicate=LFS group biological replicate 1

value: Serratia marcescens FY and Lactobacillus plantarum FY1


title: LFS2

description: replicate=LFS group biological replicate 2


title: LFS3

description: replicate=LFS group biological replicate 3


title: LS4

description: replicate=LS group biological replicate 4


title: LS3

description: replicate=LS group biological replicate 3


title: LS2

description: replicate=LS group biological replicate 2


title: LS1

description: replicate=LS group biological replicate 1


title: PA28_Strs01

city: La Plata

first: Leónidas

middle: Hernán

last: Olivera

state: Buenos Aires

department: IGEVET

country: Argentina

institute: CONICET-UNLP

data_processing:
The NovaSeq Xp output files with base calls and qualities were converted into FASTQ file format and demultiplexed. Sequence reads were trimmed using fastp program v0.12.5.
Quality of sequencing data was checked and combined in one FASTQ file using FastQC within the nf-core/RNAseq project pipeline.
All reads that passed quality control were mapped to the bos taurus reference genome ARS-UCD1.2 with STAR aligner within the nf-core/RNAseq project pipeline .
The read abundance was calculated using the featureCounts algorithm as part of the nf-core/RNAseq project pipeline .
DESeq2 package in R was used to read the featureCounts data. The count data were subjected to a regularized-logarithm transformation. DESeq2 v1.26.0 to assess differential expression between groups.
Assembly: reference bovine genome ARS-UCD1.2
Supplementary files format and content: txt file with a matrix table with normalized gene counts for every expressed gene in every skin sample

organism: Bos taurus

source_name: skin biopsy

extract_protocol:
RNA was isolated from RNAlater stored skin by Novogene Sequencing facility (Sacramento, CA, USA).
From each sample 1 ug of high quality RNA (RNA integrity number (RIN) > 8) was used for non-stranded, paired-end cDNA library preparation (kits selected by Novogene Sequencing facility (Sacramento, CA, USA).
Multiplexed total cDNA libraries were sequenced using the NovaSeq 6000 instrument with 2x150 bp paired-end sequencing cycles (Novogene Sequencing facility (Sacramento, CA, USA).

value: Brangus

tag: disease state

value: control animals (control group)

value: skin


title: PA31_Strs03


title: PA32_Strs04


title: PA29_Strs02


title: PA02_Ctrl02

value: heat stress (case group)


title: N354, scRNAseq

first: Raghavi

last: Sudharsan

address: 3900 Delancey Street

institute: University of Pennsylvania

data_processing:
Sequencing data were processed using the Cell Ranger pipeline
Assembly: Dog10K_Boxer_Tasha/canFam6
Supplementary files format and content: Compressed Tab-separated value files and matrix market exchange format files

source_name: Neuroretina

extract_protocol:
Five mm diameter neuretinal punches were collected and pretreated with 0.25% trypsin for 10 min at 37C. The tissue was then dissociated into single cells using the Miltenyi Biotec Neural Tissue Dissociation kit - Postnatal neurons. Cells were washed in PBS and resuspended in PBS supplemented 0.5% BSA.
Libraries were prepared using 10X Single Cell 3' v3.1 following manufacterer's protocol.

value: Neuroretina

tag: Sex

value: male

tag: age

value: 40 weeks

value: Normal or Wild-type


title: PA16_Ctrl05


title: PA01_Ctrl01


title: N350, scRNAseq


title: Yki-WT male accessory gland 10days rep3

city: Ann Arbor

first: Laura

last: Buttitta

state: Michigan

address: 5218 BSB, University of Michigan

department: MCDB

institute: University Of Michigan

description:
Bulk_TPM_genes.csv
Bulk_TPM_transcripts.csv

data_processing:
Used module Bioinformatics , Cutadapt v 1.18,  and Kallisto
Sequence reads were trimmed from adapter/low-quality sequences using Cutadapt v 1.18. Trim low-quality bases with quality score less than 20. Discard reads shorter than 25 bases after trimming. Discards a pair of reads if either read is too short.
Assembly: Trimmed sequance reads were mapped to Drosophila Melanogaster BDGP6.32 using Kallisto (parameter setting using 100 bootstrap sampling)
Read count extracted and normalized using Sleuth
Supplementary files format and content: comma-separated values files include TPM counts for each sample Bulk_TPM_genes.csv
Supplementary files format and content: comma-separated values files include TPM counts for each sample Bulk_TPM_transcripts.csv

organism: Drosophila melanogaster

source_name: male accessory gland

growth_protocol: Flies were reared at 25ºC for 10 days

extract_protocol:
Their accessory glands were extracted and immediately placed in TRIzol (Invitrogen 15596026) for RNA preservation. Following the manufacturer's instructions, we isolated RNA from these samples
RNA  libraries for RNA-Seq were prapaired using TruSeq Stranded mRNA library prep kit from Illumina, with poly-A selection to enrich for mRNA.

value: male accessory gland

value: y,w,hs-flp12; Uas-P35; UAS-yki/Act>CD2>gal4, Uas-GFP(nls)

tag: time

value: 10 days


title: PA05_Ctrl04


title: dMyc, E2F, Dp  male accessory gland 10days rep2

value: y,w,hs-flp12; UAS E2F1, UAS-Dp/Uas-P35; UAS-dMyc/Act>CD2>gal4, Uas-GFP(nls)


title: PA03_Ctrl03


title: dMyc, E2F, Dp  male accessory gland 10days rep3


title: YWHS, male accessory gland10days rep3

value: y,w,hs-flp12; Uas-P35; Act>CD2>gal4, Uas-GFP(nls)


title: Yki-WT male accessory gland 10days rep1


title: YWHS, male accessory gland10days rep1


title: dMyc, E2F, Dp  male accessory gland 10days rep1


title: F-3

city: Nanjing

first: Jiaqi

last: Zhou

address: NO.1 WeiGang

institute: Nanjing Agricultural University

data_processing:
Filtering of Clean Reads.Reads obtained from the sequencing machines includes raw reads containing adapters or low   quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp [1] (version 0.18.0). The parameters were as 1) removing reads containing adapters;2) removing reads containing more than 10% of unknown nucleotides (N);3) removing low qualityreads containing more than 50% of low quality(Q-value≤20) bases.
Alignment with Ribosome RNA (rRNA)  Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome   RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean  reads were further used in assembly and gene abundance calculation.
Alignment with Reference Genome  An index of the reference genome was built, and paired-end clean reads were mapped to the   reference genome using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as   a default.
Quantification of Gene Abundance  The mapped reads of each sample were assembled by using StringTie v1.3.1[4][5] in a   reference-based approach. For each transcription region, a FPKM (fragment per kilobase of   transcript per million mapped reads) value was calculated to quantify its expression   abundance and variations, using StringTie software.  The FPKM formula is shown as follows: FPKM=106C/NL/103  Given FPKM(A) to be the expression of gene A, C to be number of fragments mapped to   gene A, N to be total number of fragments that mapped to reference genes, and L to be   number of bases on gene A. The FPKM method is able to eliminate the influence of different   gene lengths and sequencing data amount on the calculation of gene expression. Therefore,   the calculated gene expression can be directly used for comparing the difference of gene   expression among samples.
RNAs differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes/transcripts with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change≥2 were considered differentially expressed genes/transcripts.
Assembly: Sscrofa11.1
Supplementary files format and content: processed data.xls

organism: Sus scrofa

source_name: ovary

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according   to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer   (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel   electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT)   beads, while prokaryotic mRNA was enriched by removing rRNA by Ribo-ZeroTM Magnetic   Kit (Epicentre, Madison, WI, USA).
Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters.
The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina HiSeq2500 by Gene Denovo Biotechnology Co.   (Guangzhou, China)

value: ovary

value: primary cell

value: granulosa cell

value: WT

value: FSH


title: S-2

value: sulforaphane


title: S-3


title: F-1


title: YWHS, male accessory gland10days rep2


title: PA33_Strs05

value: Brangus

value: control animals (control group)

value: skin


title: C-3

value: control


title: F-2


title: S-1


title: Yki-WT male accessory gland 10days rep2


title: C-1


title: Dlk1+ hepatoblasts, siLuc, replicate2

city: Dresden

first: Lenka

last: Belicova

state: Saxony

address: Pfotenhauerstr. 108

institute: MPI-CBG Dresden

data_processing:
Basic quality control of raw sequencing data was performed with FastQC v0.11.2
Reads were mapped to the mouse genome reference assembly GRCm38 and genes of the Ensembl release v92
Reads were quantified using STAR v2.5.2b
The read duplication level was assessed using MarkDuplicates from Picard tools v2.10.2 and dupRadar v1.8.0
The counts were normalized using DESeq2
Assembly: GRCm38
Supplementary files format and content: tab-delimited txt file includes raw counts

source_name: liver

growth_protocol: DLK+ positive hepatoblasts were isolated from time-pregnant (E13.5) mice. Hepatoblasts were plated in matrigel-coated wells in expansion media: DMEM/F-12, GlutaMAX supplement (Thermo Fisher Scientific; cat. no. 31331028), 10% FBS, 1× ITS-X (GIBCO BRL; cat. no. 51500–056), 0.1 µM dexamethasone (Sigma-Aldrich; cat. no D1756-25MG), 10 mM nicotinamide (Sigma-Aldrich; cat. no. N0636-100G), 10 ng/ml human HGF (in-house production), and 10 ng/ml mouse EGF (in-house production). After 24h, the cells were overlaid with differentiation media: MCDB131 (Thermo Fisher Scientific: cat. No. 10372019), 2 mM L-glutamine (Thermo Fisher Scientific: cat. No. M11-004) 0.25x ITS-X and 0.1 µM dexamethasone, containing Matrigel (Corning; cat. no. 356231) to a final concentration of 5% v/v. Cells were cultured for 5 d at 37°C, 5% CO2.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen, Cat. No. 74104 50) including the DNase I treatment step (Qiagen, cat. No. 79254).
RNA libraries for RNA-seq were prepared using 300 ng input total RNA, mRNA was enriched by poly-dT pull down with NEBNext Poly(A), libraries were prepared withNEBNext Ultra II Directional RNA Library Prep kit for Illumina following manufacturer's protocols. 75bp single read sequencing on Illumina NextSeq 500.

treatment_protocol: Hepatoblasts were reverse-transfected with siRNAs targetting control (Luciferase) or Rab35 mRNA. Transfection was performed using Lipofectamine RNAiMAX and a final concentration of 10 nM siRNA.

value: liver

tag: developmental stage

value: E13.5 embryonic

value: hepatoblats/hepatocytes

value: siLuc


title: Dlk1+ hepatoblasts, siRab35, replicate1

value: Rab35 knockdown


title: Dlk1+ hepatoblasts, siRab35, replicate2


title: Dlk1+ hepatoblasts, siLuc, replicate3


title: C-2


title: PK mammary gland injected intraductally 12x with 4NQO

city: Boston

first: Joshua

last: Rivera

state: MA

address: 110 William T Morrisey Blvd

institute: University of Massachusetts, Boston

description: 10x genomics

data_processing:
Data demultiplexing was performed with 10x Genomics' Cell Ranger sofrware v3.1.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: mm10-1.2.0
Supplementary files format and content: tab-separated value files for counts matriax, barcode assignment, and features counts.

source_name: mammary gland

extract_protocol:
Removed post-mortem glands were divested of lymph nodes and processed into single cells. Glands were mechanically dissociated in 1x PBS (Gibco Cat. No. 10010023) into a pulpous mass before being enzymatically digested with 2mg/ml collagenase XI (Milipore-Sigma Cat. No. C9407) and 0.1 mg/ml hyaluronidase (Milipore-Sigma Cat. No. H3506). Cell suspensions were further digested by 100ug/mL DNAse I (StemCell Tech Cat. No. 07900) and 5U/mL Dispase II (Milipore-Sigma Cat. No. D4693) to generate single cell suspensions. Suspension was filtered through 40mm filter (puriSelect Cat. No. 43-50040-01) and washed in PBS, counted, and submitted for scRNA-seq
Single cell librarier were generated according to the manufacturer's instructions for 10x Genomics single cell 3' v2 chemistry protocol.
10x Genomics scRNA-seq library preparation.

value: mammary gland

value: Brca1 wt/wt, Trp53 flox/flox, Krt14cre

value: 12x 600mg/mL 4NQO


title: BPK mammary tumor formed after 24x injections of 4NQO

description: 10x genomics

source_name: mammary tumor

value: mammary tumor

value: Brca1 wt/flox, Trp53 flox/flox, Krt14cre

value: 24x 600mg/mL 4NQO


title: BPK mammary gland injected intraductally 12x with 4NQO

description: 10x genomics


title: Dlk1+ hepatoblasts, siLuc, replicate1


title: BPK mammary gland injected intraductally 12x with PBS/PEG

description: 10x genomics

value: Vehicle (PBS/PEG)


title: OVCAR4 taxol replicate 1

description: cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated with o.4 nM paclitaxel.

value: high-grade serous ovarian adenocarcinoma

value: epithelial cells

value: 0.4 nM paclitaxel for 24 hours


title: BPK mammary gland injected intraductally 12x with 4NQO replicate 2

description: 10x genomics


title: mOCcKO_HMD201207003_DP18

city: Fukuoka

first: Tappei

last: Mishina

address: 744 Motooka Nishi-ku

country: Japan

institute: Kyushu University

data_processing:
Adaptor sequences and low quality bases were trimmed using Fastq-mcf v1.1.2 in the ea-utils package.
The RamDA-seq reads were mapped to the mouse genome (GRCm38) using Hisat2 v2.2.0.
The gene count table was obtained using the featureCounts v2.0.1 tool in the Subread package with the option ‘-t exon -g gene_id’ and the annotation gtf file from GENCODE (vM25).
We evaluated the quality control metrics and filtered out low quality samples based on the RNA integrity assessed by coverage profile along the gene body and the number of detected genes ≤ 8,000.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw counts or TPM values for each sample.

growth_protocol: mouse lines used for this study were maintained on a mixed genetic background

extract_protocol:
At postnatal day (PD) 7, ovaries from euthanized control mice (n=3) and from Wls cKO mice (n=8) were collected. Ovaries were treated with a CTK solution (consisting of 0.25% trypsin (Thermo), 0.1% collagenase type IV (Gibco), 20% KSR (Invitrogen) and 1 mM CaCl2 in PBS) for 30 min at 37°C, then further treated with Accutase (Nacalai) at 37°C for 15 min. The reaction was halted by adding L-15 medium with 0.1% penicillin-streptomycin and 5% FBS, and the cells were dissociated by pipetting. The cell suspension was filtered through 70 μm cell strainers, followed by centrifugation at 400 g for 5 min and resuspension in sorting buffer (7.5% BSA (Life Technologies) in PBS). Blocking was performed with rat IgG (5 mg/mL, I8015, Sigma-Aldrich) for 15 min on ice. Subsequently, cell surface staining was conducted using anti-ckit-APC (1:50, 105812, BioLegend) and anti-CD45-Alexa Fluor 488 (1:200, 103122, BioLegend) for 15 min on ice. After centrifugation at 400 g for 5 min, cells were resuspended in sorting buffer. Prior to single-cell sorting by flow cytometry, samples were passed through 40 μm cell strainers, and DAPI (1:10,000) was added. Control and Wls cKO samples were each sorted using MoFlo Astrios EQ with Summit v 6.3.0. software (Beckman Coulter) into 384-well plates containing 286 tdTomato-positive somatic cells and 95 ckit-positive oocytes. DAPI-positive dead cells and CD45-positive leukocytes were excluded.
Library preparation for RamDA-seq was performed according to a previously report. However, to reduce reagent costs and rRNA-derived sequencing reads, the method was modified as follows: To suppress rRNA-derived cDNA synthesis, 0.008 units/µl XRN-1 (NEB) was added to the genomic DNA digestion mix, and the reaction was performed at 30°C for 5 min. To reduce reagent costs, a liquid dispenser Mantis (Formulatrix) was used to perform the reaction up to second strand synthesis at 1/10 the reaction volume. After that, 2.5 μl 0.8 X Tagment DNA Buffer (Illumina) diluted with RNase-free water was added to 0.5 μl of the second strand synthesis products for dilution. Then, 0.5 μl Amplicon Tagment Mix (Illumina) was added to 1.5 μl of the diluted product, and tagmentation was performed at 55°C for 10 min. After that, the library was prepared using 1/10 the reaction volume according to the Nextera XT DNA Library Prep Kit (Illumina) procedure. Twelve PCR cycles were performed. Somatic and oocyte library products were collected separately in equal volumes of 1 μl/well. Subsequently, 50 μl of each sample was fractionated from the equal mixed library, purified with 1.2X AMPureXP (Beckman Coulter), and eluted with 25 μl TE. To prevent large discrepancies in the number of sequencing reads per cell between somatic and oocyte cells, purified libraries were mixed to ensure a constant average molar per cell type using the quantitative results from the Bioanalyzer Agilent High-Sensitivity DNA Kit and the ratio of the number of cells sorted (somatic cells: oocytes = 286:95). The pooled library of 2.3 pM was sequenced in single end read 76 cycles using NextSeq 500 High Output Kit v2.5.

value: ovary

value: altered oocytes

tag: subpopulation gc

tag: subpopulation oocyte

value: Sf1-Cre;Wls flox/del;Ai9 (Wls cKO)

tag: marker expression_tdtomato

tag: marker expression_kit-apc

tag: cell size_(fsc1_area)

tag: intron ratio


title: mOCcKO_HMD201207003_DL24

tag: tissue

value: oocytes


title: mOCcKO_HMD201207003_DD20

tag: cell type


title: mGCcKO_HMD201207003_CH21

value: ovarian surface epithelial cells


title: mGCcKO_HMD201207003_CF09


title: mGCcKO_HMD201207003_BA06


title: mGCcKO_HMD201207003_CH19

value: pre-granulosa cells


title: mOCcKO_HMD201207003_DN12


title: mGCcKO_HMD201207003_AO21

value: altered granulosa cells


title: mGCcKO_HMD201207003_AK07


title: mOCcKO_HMD201207003_DD22


title: mOCcKO_HMD201207003_DB20


title: mGCcKO_HMD201207003_BO20


title: mGCcKO_HMD201207003_CD19

value: granulosa cells


title: mGCcKO_HMD201207003_CD15


title: Dlk1+ hepatoblasts, siRab35, replicate3

value: liver

value: E13.5 embryonic

value: hepatoblats/hepatocytes

tag: treatment

value: Rab35 knockdown


title: mGCcKO_HMD201207003_AA13


title: mGCcKO_HMD201207003_CN07

value: interstitial cells


title: mOCcKO_HMD201207003_DL14


title: mOCcKO_HMD201207003_DB24


title: mGCcKO_HMD201207003_CL09


title: mGCcKO_HMD201207003_AA07


title: mGCcKO_HMD201207003_AO07


title: mGCcKO_HMD201207003_AK03


title: mGCcKO_HMD201207003_BO08


title: mGCcKO_HMD201207003_AA05


title: mGCcKO_HMD201207003_CH11


title: mOCcKO_HMD201207003_DL18


title: mGCcKO_HMD201207003_BM10


title: mGCcKO_HMD201207003_CF23


title: mGCcKO_HMD201207003_BE02


title: mGCcKO_HMD201207003_AO09


title: mOCcKO_HMD201207003_DH08


title: mGCcKO_HMD201207003_AG01


title: mGCcKO_HMD201207003_AC19


title: mGCcKO_HMD201207003_BA04


title: mGCcKO_HMD201207003_BO06


title: mGCcKO_HMD201207003_AM21


title: mGCcKO_HMD201207003_BK02


title: mOCcKO_HMD201207003_DN04


title: mGCcKO_HMD201207003_BI08


title: mGCcKO_HMD201207003_BC02


title: mGCcKO_HMD201207003_CD21


title: mGCcKO_HMD201207003_CF01


title: mOCcKO_HMD201207003_DB12


title: mGCcKO_HMD201207003_AA01


title: mGCcKO_HMD201207003_AE05


title: mOCcKO_HMD201207003_DD14


title: mOCcKO_HMD201207003_DP10


title: mGCcKO_HMD201207003_AC07


title: mGCcKO_HMD201207003_BE10


title: mGCcKO_HMD201207003_BM06


title: mGCcKO_HMD201207003_AE11


title: mGCcKO_HMD201207003_AM19


title: mGCcKO_HMD201207003_AM11


title: mOCcKO_HMD201207003_DH16


title: mGCcKO_HMD201207003_BE04


title: mGCcKO_HMD201207003_CB13


title: mGCcKO_HMD201207003_BM18


title: mOCcKO_HMD201207003_DF12


title: mGCcKO_HMD201207003_AM07


title: mOCcKO_HMD201207003_DL12

value: excluded by low quality


title: mGCcKO_HMD201207003_BM20


title: mGCcKO_HMD201207003_CD23


title: mGCcKO_HMD201207003_CL01


title: mGCcKO_HMD201207003_BI24


title: mGCcKO_HMD201207003_CB21


title: mOCcKO_HMD201207003_DD18


title: mOCcKO_HMD201207003_DL22


title: mOCcKO_HMD201207003_DP20


title: mGCcKO_HMD201207003_CP03


title: mGCcKO_HMD201207003_CJ21


title: mGCcKO_HMD201207003_CN09


title: mGCcKO_HMD201207003_AI21


title: mGCcKO_HMD201207003_BM02


title: mGCcKO_HMD201207003_CJ07


title: mGCcKO_HMD201207003_CF05


title: mGCcKO_HMD201207003_CL17


title: mGCcKO_HMD201207003_CN21


title: mOCcKO_HMD201207003_DJ22


title: mGCcKO_HMD201207003_AG09


title: mOCcKO_HMD201207003_DP14


title: mGCcKO_HMD201207003_BA16


title: mGCcKO_HMD201207003_AC05


title: mGCcKO_HMD201207003_CH03


title: mOCcKO_HMD201207003_DF16


title: mGCcKO_HMD201207003_AM03


title: mGCcKO_HMD201207003_CJ09


title: mGCcKO_HMD201207003_CJ03


title: mGCcKO_HMD201207003_AE01


title: mGCcKO_HMD201207003_BM24


title: mGCcKO_HMD201207003_AA03


title: mGCcKO_HMD201207003_BI20


title: mGCcKO_HMD201207003_CP07


title: mOCcKO_HMD201207003_DJ14


title: mGCcKO_HMD201207003_CH07


title: mGCcKO_HMD201207003_BG18


title: mGCcKO_HMD201207003_AO17


title: mGCcKO_HMD201207003_BC24


title: mGCcKO_HMD201207003_BA22


title: mGCcKO_HMD201207003_AK13


title: mGCcKO_HMD201207003_AA09


title: mGCcKO_HMD201207003_CN23


title: mOCcKO_HMD201207003_DH12


title: mGCcKO_HMD201207003_BA02


title: mGCcKO_HMD201207003_AI23


title: mGCcKO_HMD201207003_BA18


title: mGCcKO_HMD201207003_BI22


title: mGCcKO_HMD201207003_BO18


title: mGCcKO_HMD201207003_CH05


title: mGCcKO_HMD201207003_BG08


title: mGCcKO_HMD201207003_AM01


title: mOCcKO_HMD201207003_DD02


title: mGCcKO_HMD201207003_AO19


title: mOCcKO_HMD201207003_DF20


title: mGCcKO_HMD201207003_BG10


title: mGCcKO_HMD201207003_AG19


title: mGCcKO_HMD201207003_BM04


title: mGCcKO_HMD201207003_BA08


title: mOCcKO_HMD201207003_DP08


title: mGCcKO_HMD201207003_BO16


title: mGCcKO_HMD201207003_AC17


title: mGCcKO_HMD201207003_CD09


title: mOCcKO_HMD201207003_DD06


title: mGCcKO_HMD201207003_BG24


title: mGCcKO_HMD201207003_AA21


title: mGCcKO_HMD201207003_AA15


title: mOCcKO_HMD201207003_DH14


title: mGCcKO_HMD201207003_BK16


title: mGCcKO_HMD201207003_CF19


title: mGCcKO_HMD201207003_CH01


title: mGCcKO_HMD201207003_BA24


title: mGCcKO_HMD201207003_BI06


title: mGCcKO_HMD201207003_AM05


title: mGCcKO_HMD201207003_AO13


title: mOCcKO_HMD201207003_DP04


title: mGCcKO_HMD201207003_AI07


title: mGCcKO_HMD201207003_BC10


title: mOCcKO_HMD201207003_DF24


title: mGCcKO_HMD201207003_BK12


title: mGCcKO_HMD201207003_AK17


title: mGCcKO_HMD201207003_BM22


title: mOCcKO_HMD201207003_DL04


title: mGCcKO_HMD201207003_AM23


title: mGCcKO_HMD201207003_CF15


title: mOCcKO_HMD201207003_DF06


title: mOCcKO_HMD201207003_DJ10


title: mOCcKO_HMD201207003_DB02


title: mGCcKO_HMD201207003_CJ17


title: mGCcKO_HMD201207003_BK06


title: mGCcKO_HMD201207003_CJ19


title: mGCcKO_HMD201207003_BC12


title: mGCcKO_HMD201207003_CP17


title: mGCcKO_HMD201207003_AC09