title: smallRNA_siLuc_Rep3

city: Vienna

first: Dominik

last: Handler

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences

description:
Library name: smallRNA_siLuc_Rep3
Sequencing of TraPR isolated Argonaute bound small RNAs isolated OSC cells

data_processing:
Illumina reads were processed by removing 3′ adapters with cutadapt {Martin, 2011 #646}, trimming 4 random nucleotides from each end and filtering for minimal length (>18 nt) and sequence complexity (bbduk, entropy = 0.35, entropy window = 18, k = 4) . Reads were first aligned to Drosophila rRNA precursor sequences and the mitochondrial genome using bowtie {Langmead, 2009 #656}. Remaining unmapped reads were mapped to the OSC_r1.01 genome using bowtie allowing for 1 mismatch. Alignments were separated into uniquely and all‑mapping fractions. For visualization, HOMER was used to generate tag directories (makeTagDirectory … -format bed -keepAll -single -fragLength given) and UCSC‑compatible tracks (makeUCSCfile … -fsize 1e20 -strand +/- -fragLength given -noadj -normLength 0) were generated per strand. Counts were normalized to 1M miRNAs and final BigWig tracks were created with bedGraphToBigWig (Kent Utilities), producing strand‑specific (sense and antisense) coverage profiles for genome browser display. For transposon histogram analysis, piRNA reads longer than 23 nucleotides were aligned to transposable element consensus sequences using bowtie (--best --strata -f -v 2 -a), permitting multiple mappings. Alignments were subsequently filtered to retain reads that mapped either uniquely or at most twice to a single transposon consensus, to account for long terminal repeat (LTR) redundancy. Reads mapping twice were assigned a fractional count of 0.5 to each location.
Assembly: OSC_r1.01.fa.gz
Supplementary files format and content: All mapping and unique mapping bigwig files for sense and antisense
Supplementary files format and content: TE-histogram data for sense and antisense

molecule: other

organism: Drosophila melanogaster

source_name: OSC

growth_protocol: Ovarian somatic cells (OSCs) were maintained at 27 °C in a humidified incubator with 2.5% CO₂, as previously described (Niki, Yamaguchi et al. 2006, Saito, Inagaki et al. 2009) Cells were cultured in M3 basal medium supplemented with 10% fetal bovine serum (FBS), insulin, glutathione, and fly extract.

extract_protocol:
sRNAseq libraries were prepared by first purifying Argonaute–sRNA complexes with TraPR resin columns. OSCs were harvested using trypsin, washed 2x with PBS and stored at -70°C after snap freezing cell-pellets in liquid nitrogen. OSCs were lysed by adding 330 µL of TraPR lysis buffer. OSC lysates were clarified, normalized to equal protein amounts (depending on the experiment 70-120 µg total protein) after Bradford measurements, applied to TraPR columns, and Argonaute-bound RNAs were eluted, followed by phenol–chloroform extraction and precipitation.
To minimize ligation bias and facilitate library multiplexing, adaptors were designed with random nucleotides placed adjacent to the ligating end. The 3′ adaptor carried six random bases at its 5′ terminus and contained sample barcodes (X) for multiplexing (5rApp/NNNNNNXXXX–Adaptor–/3ddC). The 5′ adaptor was an RNA oligo bearing four random nucleotides at its 3′ terminus (…UCUNNNN). After 3′ adaptor ligation with T4 RNA ligase 2, truncated KQ, samples were pooled as necessary, spiked with fluorescently labeled and ligation-blocked oligos as size controls, and gel-purified on a 12.5% polyacrylamide–urea gel. Small RNAs were isolated using the Zymo ZR small RNA PAGE Recovery kit and subjected to 5′ adaptor ligation with T4 RNA ligase 1. Following cleanup with Zymo RCC5 columns, reverse transcription was performed. Libraries were PCR-amplified with KAPA HiFi polymerase and dual-index barcoded primers. Amplification was monitored in real time with EvaGreen, and reactions were stopped upon reaching 3,500–4,000 RFU to prevent overamplification. Final libraries were size-selected on low-melt agarose gels, gel-purified (Zymo), quantified with Qubit, multiplexed and sequenced (SE50, Illumina NovaSeq6000).

value: OSC

value: ovarian somatic cells

value: wildtype

value: Transfection with siRNA at 0 and 48h. Harvested after 96h


title: smallRNA_siLuc_Rep2

status: Public on Nov 17 2025

type: SRA

description:
Library name: smallRNA_siLuc_Rep2
Sequencing of TraPR isolated Argonaute bound small RNAs isolated OSC cells

library_source: other

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: P209L Hnrnph2 ASO 8 weeks replicate 1 (3341183_TCF3005)

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

country: USA

institute: St. Jude Children's Research Hospital

description: Library name: 3341183_TCF3005

library_source: transcriptomic

data_processing:
Quality control filtering and adapter trimming of fastq files was performed with trim_galore
Paired-end reads were mapped by STAR(v2.7.1a)
Read duplication was marked with MarkDuplicates from GATK (v4.0.4.0)
RSEM was used to quantify read counts per gene
Assembly: mm10
Supplementary files format and content: gene-based TPM txt file for all 35 samples

molecule: total RNA

organism: Mus

source_name: brain

extract_protocol:
Cortex was dissected, flash frozen and stored at - 80 degrees. Frozen samples were treated with RNAlater-ICE (Thermo Fisher Scientific, AM7030), and total RNA was extracted with Qiagen’s RNeasy Universal plus mini kit (73404, Qiagen).
A sequencing library was prepared with a TruSeq Stranded Total RNA Kit (Illumina).

tag: tissue

value: brain

tag: treament

value: Hnrnph2 ASO

tag: strain

tag: Sex

value: Male

tag: age

value: 8 weeks


title: H4K20ac_WT biol rep1

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

library_source: genomic

data_processing:
Reads of the samples were trimmed for adapters using Cutadapt before alignment
Trimmed sequence reads were mapped to the reference genome (mm10) using Bowtie2
Peaks were called using Sicer and MACS2
ChIP-seq heatmap and plot profiles were generated using deeptool2 software
Assembly: mm10
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Mus musculus

growth_protocol: 4T1 cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Gibco), supplemented with 9% fetal bovine serum (FBS) (Gemini), 1% L-glutamine (Gibco), and 1% penicillin–streptomycin (Gemini).

extract_protocol:
Chromatin was prepared using ChIP-IT Express Enzymatic kit (Active Motif). Cells were fixed with 1% formaldehyde for appropriate time (5 minutes for H3K27ac, H3K27me3, H4K20ac and p300; 10 minutes for Nat10, Brd4-pan, Brd4-SF-V5 tag, Rrp1b endogenous, Rrp1b-HA tag and Sipa1). After lysis, chromatin was sheared using enzymatic digestion cocktail for 10 minutes.
Library was generated using SWIFT Accel-NGS 2s Plus DNA library prep kit according to manufacturer's instruction

value: Mouse mammary tumor cells

tag: chip antibody

value: H4K20ac (Millipore-Sigma, #SAB5600021)


title: H3K27me3_KO biol rep2


title: WT Hnrnph2 ASO 8 weeks replicate 3 (3341182_TCF3231)

description: Library name: 3341182_TCF3231

value: WT


title: HUVEC, siCTRL, 2

city: Kuopio

first: Nihay

last: Laham Karam

address: Neulaniementie 2

department: A.I. Virtanen Institute

country: Finland

institute: University of Eastern Finland

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. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences.
Assembly: human GRCh38/hg38
Supplementary files format and content: tab delimited text files contain raw counts for each sample

organism: Homo sapiens

source_name: HUVEC

growth_protocol: HUVECs at early passage were maintained in Endothelial Cell Growth Medium (PromoCell) supplemented with Endothelial Cell Growth Medium SupplementMix (PromoCell) with gentamicin (250 ng/mL)and amphotericin (10 ug/mL)   in cell culture flasks coated with 10 µg/ml fibronectin (Corning) and 0.05% gelatine (Sigma).

extract_protocol:
RNA was extracted using Qiagen RNeasy Plus Kit according to the manufacturer's instructions.
Library preparation was performed at Azenta Life Sciences using poly-A selection

treatment_protocol: HUVEC were either transfected with siRNA and cultured for 2 days or transduced with LV and cultured for 3 days.

value: HUVEC

value: endothelial cells

value: siRNA-CTRL

tag: time

value: 2 days


title: HUVEC, siCTRL, 1


title: smallRNA_siLuc_Rep1

description:
Library name: smallRNA_siLuc_Rep1
Sequencing of TraPR isolated Argonaute bound small RNAs isolated OSC cells


title: H3K27ac_KO biol rep2


title: WT Hnrnph2 ASO 8 weeks replicate 2 (3341181_TCF3179)

description: Library name: 3341181_TCF3179


title: HUVEC, siADAMTS18, 3


title: WT Hnrnph2 ASO 8 weeks replicate 1 (3341180_TCF3001)

description: Library name: 3341180_TCF3001


title: H3K27ac_KO biol rep1


title: HUVEC, siADAMTS18, 4


title: BEAS-2B with Nrf2 knockout, control, H3K4me1, ChIP

city: Stony Brook

first: Fei

last: Chen

state: NY

address: 101 Nicolls Road, MART 8M-0501

institute: Stony Brook University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Assembly: GRCh38/hg38
Supplementary files format and content: bigWig, narrowPeak (except for input sample)

growth_protocol: The human bronchial epithelial cell line BEAS-2B, obtained from the American Type Culture Collection (ATCC, Manassas, VA), was cultured at 37℃ in a humidified atmosphere with 5% CO2. The cells were grown in DMEM (Gibco, cat#11965092) supplemented with 5% fetal bovine serum (R&D Systems, cat#S11150), 1% penicillin-streptomycin (Gibco, cat#15140122), and 1% L-glutamine (Gibco, cat#25030081). The medium was refreshed every other day, and cells were passaged weekly.

extract_protocol:
Cells were fixed for 15 min at 25 °C with 4% formaldehyde, and the reaction was halted by adding 125 mM glycine for 5 min at room temperature. Fixed cells were washed with PBS, scraped from the culture surface, and chromatin was isolated using lysis buffer and disrupted with a Dounce homogenizer. The lysates were sonicated to shear DNA to an average length of 300–500 bp. Genomic DNA (Input) was prepared by treating chromatin with RNase and proteinase K, followed by heating for de-crosslinking and ethanol precipitation. The DNA was quantified using a NanoDrop spectrophotometer (Thermo Scientific) and the total chromatin yield was extrapolated. A 30 μg aliquot of chromatin was precleared with protein A agarose beads (Invitrogen).
ChIP was performed using 4 μg of antibodies against H3K4me1 (Thermofisher, cat#710795), H3K4me3 (Thermofisher, cat# 711958), H3K9me3 (CST, cat#4658), H3K27ac (CST, cat#8173), and KLF4 (R&D Systems, cat#AF3640). Complexes were washed, eluted with SDS buffer, treated with RNase and proteinase K, and crosslinks were reversed by overnight incubation at 65°C. ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Illumina sequencing libraries were prepared through end-polishing, dA-addition, and adapter ligation, followed by PCR amplification. Sequencing was performed using Illumina NextSeq 500, and 75-nt reads were aligned to the GRCh38/hg38 genome using the Burrows-Wheeler Aligner (BWA) with default settings.

treatment_protocol: BEAS-2B cells, with or without Nrf2 knockout, were treated with or without 1 μM As³⁺ for 6 hours, followed by ChIP-seq analysis.

value: normal human bronchial epithelial cells

value: Nrf2 Knockout

value: Control


title: HUVEC, siCTRL, 4


title: P209L Control ASO 8 weeks replicate 2 (3341178_AK302_6)

description: Library name: 3341178_AK302_6

value: Control ASO


title: P209L Control ASO 8 weeks replicate 3 (3341179_TCF3209)

description: Library name: 3341179_TCF3209


title: smallRNA_siArmi_Rep2

description:
Library name: smallRNA_siArmi_Rep2
Sequencing of TraPR isolated Argonaute bound small RNAs isolated OSC cells

value: OSC

value: ovarian somatic cells

value: wildtype


title: P209L Control ASO 8 weeks replicate 1 (3341177_TCF2973)

description: Library name: 3341177_TCF2973

value: brain


title: H3K27ac_WT biol rep1


title: smallRNA_flamenco-silencing_Gal4_Rep2

description:
Library name: smallRNA_flamenco-silencing_Gal4_Rep2
Sequencing of TraPR isolated Argonaute bound small RNAs isolated from FACS sorted OSC cells

value: wildtype besides a UAS-tethering construct integrated upstream of the flamenco promoter

value: Transfected with tethering plasmids encoding  Gal4. . Transfections were repeated after 48h to sustain tethering. At 6 and 7 days post transfection, cells were harvested by FACS, gated on reduced GFP reporter signal from the co-silenced selection cassette. For Gal4‑only controls, no FACS enrichment was applied.


title: HUVEC, siADAMTS18, 1


title: 8_Nat10_KO_c43_2_S8

description: Nat10-KO-c43 biol rep2

data_processing:
Reads of the samples were trimmed for adapters and low-qality bases using Cutadapt before alignment
Trimmed sequence reads were mapped to the reference genome (mm10) and annotated transcripts using STAR
Normalization was done in Partek Flow software
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized values for each Sample

extract_protocol:
RNA was isolated using RNEasy mini kit (Qiagen) with on column DNAse I digestion.
Library was generated using Illumina® Stranded Total RNA Prep kit and ligation with Ribo-Zero Plus according to manufacturer's instruction

value: Mouse mammary tumor cells

value: Knockout

value: 48 hours


title: 9_Nat10_KO_c43_3_S9

description: Nat10-KO-c43 biol rep3


title: WT Control ASO 8 weeks replicate 3 (3341173_TCF3299)

description: Library name: 3341173_TCF3299

value: WT

value: Male

value: 8 weeks


title: bonobo-iPS-0009M-B1

city: Inuyama

first: Yusuke

last: Hamazaki

state: Aichi

country: Japan

institute: Center for the Evolutionary Origins of Human Behavior, Kyoto University

data_processing:
Using the first reads of paired-end reads in all the datasets, adaptor and quality trimming were performed by Trim Galore. The preprocessed reads were mapped to all of the human (hg38), chimpanzee (panTro6), and bonobo (panPan3) reference genomes using STAR, regardless of species origin. Only reads that were successfully mapped to all three references were used for downstream analysis. After conversion from the bam format to bed format and removal of PCR duplicates, the intersectBed command in bedtools was used to sum up reads overlapping with exons. The Pandas was used to calculate transcripts per kilobase million (TPM) for normalization. Gene expression in humans, chimpanzees, and bonobos was calculated by the annotation of hg38. For the investigation of retrotransposon expression, the first 50 bp of the first reads were mapped onto the consensus sequences of 647 retrotransposons present in the Homo and/or Pan genomes using HISAT2. The same reads were also mapped to their respective genomes of origin (hg38, PanTro6, or PanPan3) using HISAT2. Reads that overlapped annotated exonic regions in the respective genomes were excluded from the retrotransposon counts.
Assembly: hg38, PanTro6, PanPan3
Supplementary files format and content: xlsx file including TPM value of gene expressions
Supplementary files format and content: xlsx file including RPM value of retrotransposon expressions

organism: Pan paniscus

source_name: iPSC

growth_protocol: Peripheral blood samples from two bonobos (GAIN-ID 0008; female, 0009; male) and one chimpanzee (0402; female) were collected for medical examination at Kumamoto Sanctuary Wildlife Research Center, Kyoto University and stored in liquid nitrogen for 5-10 years. PBMCs were isolated from the blood samples using BD Vacutainer CPT (362761; BD Biosciences, San Jose, CA, USA) and cultured in Advanced Roswell Park Memorial Institute (RPMI) 1640 medium (12633-012; Gibco, Waltham, MA, USA) supplemented with 10% fetal bovine serum (FBS), 1× GlutaMAX Supplement (35050061; Gibco), and 100 U/ml penicillin and 100 µg/ml streptomycin (168-23191; Wako, Osaka, Japan) at 37°C with 5% CO2. SRV transduction was performed using SRV iPSC-2 Vector (S1011694A; TOKIWA-Bio, Ibaraki, Japan) or SRV iPSC-4 Vector (S1011696A; TOKIWA-Bio) with a modified protocol. Briefly, 1 × 105 PBMCs were incubated with either SRV-2 or SRV-4 at a multiplicity of infection of 3 at 37°C for 2 or 6 hours, followed by washing with 10% FBS/RPMI medium and plating onto the iMatrix 511 (892024; Matrixome, Osaka, Japan)-coated 60-mm culture dishes. On day 1, 3, 5, and 7 after transduction, 1 ml of StemFit medium (AK02N; Ajinomoto, Tokyo, Japan) was added to the cell culture. Since day 9, the medium was changed to fresh StemFit medium change every other day. The iPSC-like colonies were mechanically isolated and dissociated with TrypLE Express (12604021; Gibco). The cells were expanded on mitomycin C-treated mouse embryonic fibroblasts (RCHEFC003; REPROCELL, Kanagawa, Japan) in StemFit medium supplemented with 2.5 µM IWR-1 (037-25131; Wako).

extract_protocol:
Total RNA of bonobo and chimpanzee iPSCs was extracted using ISOGEN (317-02503; Nippon Gene, Tokyo, Japan) and Direct-zol RNA Miniprep (R2050; Zymo Research, Irvine, USA).
cDNA libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420; New England Biolabs) and sequenced on Illumina NovaSeq with 2 x 150 bp paired-end read configuration.

value: iPSC


title: WT Control ASO 8 weeks replicate 2 (3341172_AK302_5)

description: Library name: 3341172_AK302_5


title: smallRNA_flamenco-silencing_Gal4_Rep1

description:
Library name: smallRNA_flamenco-silencing_Gal4_Rep1
Sequencing of TraPR isolated Argonaute bound small RNAs isolated from FACS sorted OSC cells


title: 7_Nat10_KO_c43_1_S7

description: Nat10-KO-c43 biol rep1


description:
Library name: smallRNA_flamenco-silencing_2x_Panx-IDR_7days
Sequencing of TraPR isolated Argonaute bound small RNAs isolated from FACS sorted OSC cells

value: Transfected with tethering plasmids encoding  Gal4 fused to the Panoramix IDR silencing domain . Transfections were repeated after 48h to sustain tethering. At 6 and 7 days post transfection, cells were harvested by FACS, gated on reduced GFP reporter signal from the co-silenced selection cassette. For Gal4‑only controls, no FACS enrichment was applied.


description:
Library name: smallRNA_flamenco-silencing_2x_Panx-IDR_6days
Sequencing of TraPR isolated Argonaute bound small RNAs isolated from FACS sorted OSC cells


title: 6_Nat10_KO_c19_3_S6

description: Nat10-KO-c19 biol rep3


title: WT Control ASO 8 weeks replicate 1 (3341171_TCF3169)

description: Library name: 3341171_TCF3169


title: bonobo-iPS-0008F-C1-6


title: H3K27ac_WT biol rep2


title: smallRNA_siArmi_Rep3

description:
Library name: smallRNA_siArmi_Rep3
Sequencing of TraPR isolated Argonaute bound small RNAs isolated OSC cells

value: Transfection with siRNA at 0 and 48h. Harvested after 96h


title: smallRNA_siArmi_Rep1

description:
Library name: smallRNA_siArmi_Rep1
Sequencing of TraPR isolated Argonaute bound small RNAs isolated OSC cells


title: HUVEC, siADAMTS18, 2

value: HUVEC

value: endothelial cells

value: 2 days


title: 5_Nat10_KO_c19_2_S5

description: Nat10-KO-c19 biol rep2


title: bonobo-iPS-0009M-C6


title: day 4 Erbb2d/d mouse endometrium; rep4

city: Cincinnati

first: Bo

last: Li

address: 240 Albert Sabin Way

institute: Cincinnati Children's Hospital Medical Center

description: Library name: RB2DD6

data_processing:
Reads were aligned to the mouse reference genome mm10 (GRCm38) using HISAT2 with default parameters (command: hisat2 -x mm10 -1 R1 -2 R2 -S sample.sam). Uniquely mapped reads were extracted, converted to BAM, sorted, and indexed with SAMtools. Gene-level counts were obtained using HTSeq-count with the NCBI annotation GTF file. Expression levels (FPKM) were estimated using StringTie.
Assembly: Mus musculus mm10 (GRCm38)
Supplementary files format and content: Count tables in plain text format (*.count_data.txt), containing gene-level read counts for each sample.

source_name: endometrium

extract_protocol:
Total RNA was extracted from mouse endometria using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.
mRNA was enriched using poly(A) selection, and RNA-seq libraries were prepared with the Plant and Animal Eukaryotic mRNA (WOBI) kit following the manufacturer’s protocol. Libraries were non-directional and sequenced on an Illumina NovaSeq X Plus platform with a paired-end 150 bp strategy (PE150). Each sample generated ~6 Gb of raw data with Q30 ≥ 85%.

value: endometrium

value: mouse endometrium

value: DD


title: 4_Nat10_KO_c19_1_S4

description: Nat10-KO-c19 biol rep1


title: ΔUhpTU + pBAD-UhpU-EC-G6P R1

city: Shanghai

first: Chuan

address: 131 # Dong An Road

country: China

institute: Fudan University

description:
Library name: deltaUhpTU + pBAD-UhpU-EC-G6P R1
The uhpTU-deleted E.coli strain carrying the pBAD-UhpU plasmid was cultured in M9CA medium supplemented with 0.1% (w/v) glucose-6-phosphate (G6P) at 37°C until reaching an OD₆₀₀ of approximately 0.5. L-arabinose was then added to a final concentration of 0.2% (w/v) to induce UhpU expression. After 10 minutes of induction, total RNA was extracted. This sample represents biological replicate 1 of the UhpU pulse-expression group.

data_processing:
RNA-seq was performed by BGI Group, Shenzhen, Guangdong, China. Briefly, a strand-specific cDNA library was constructed for each sample to keep the direction of RNA transcription. The obtained cDNA libraries were sequenced on an Illumina HiSeq 4000 machine.
SOAP (v2.21, -m 0 -x 1000 -s 28 -l 32 -v 5 -r 1 -p 3).The rest reads with adaptor，or with unknown bases more than 5%  ,or with more than 20% low-quality bases were cleared by a software developed by BGI group. After, clear reads were mapped to reference genome with Bowtie2： v2.2.5 -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --), and expression value was caculated  (http://deweylab.biostat.wisc.edu/RSEM）
Assembly: Salmonella Typhimurium LT2 Genome  (NC_003197) Chromosome (https://www.ncbi.nlm.nih.gov/nuccore/NC_003197.2) and plasmid (https://www.ncbi.nlm.nih.gov/nuccore/NC_003277.2) , E.coli K-12 MG1655 genome (NC_000913.3) chromosome, (https://www.ncbi.nlm.nih.gov/nuccore/556503834)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Escherichia coli

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

growth_protocol: M9CA broth plus 0.1% glucose-6-phosphate (G6P) or LB miller medium

extract_protocol:
Bacterial total RNA was isolated using the hot phenol method. Briefly, Cells were resuspended in lysozyme, 10% SDS and 3M sodium acetate (pH5.2). The cleared lysate was mixed with saturated phenol (pH4.5) and incubated at 64°C for 6 min with shaking. After mixing with chloroform and centrifugation in a Phase Lock Gel tube (#WM5-2302820, TIANGEN Biotech), the aqueous phase was collected and mixed the with 30:1 ethanol: sodium acetate (pH 6.5) and precipitated at -80°C overnight. RNA pellets were washed with 80% ethanol and dissolved in ultra-pure water (#10977, Thermo Fisher Scientific), and the RNA concentration was determined using NanoDrop 2000.
Ribosomal RNAs was removed by Biotin-labeled rRNA probe. RNA was fragmented with BGI fragmentation buffer and was reverse transcribed with random hexamer. Double chain cDNA was then blunted and phosphorylated for the 5’ end, and overhang A base in the 3’ end and ligated with T-overhang adapter. After PCR application, samples were sequenced in BGISeq-500 platform

treatment_protocol: UhpU expression was induced with 0.2% (w/v) L-arabinose for 10 minutes

value: {delta}UhpTU + pBAD-UhpU-EC-G6P


title: ΔUhpTU + pBAD-Ctr-EC-G6P R2

description:
Library name: deltaUhpTU + pBAD-Ctr-EC-G6P R2
The uhpTU-deleted E.coli strain carrying the empty pBAD plasmid was cultured in M9CA medium supplemented with 0.1% (w/v) glucose-6-phosphate (G6P) at 37°C until reaching an OD₆₀₀ of approximately 0.5. L-arabinose was then added to a final concentration of 0.2% (w/v) to induce expression. Cultures were incubated for an additional 10 minutes before total RNA was extracted. This sample represents biological replicate 2 of the control group.

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

value: {delta}UhpTU + pBAD-Ctr-EC-G6P


title: day 4 Erbb2d/d mouse endometrium; rep2

description: Library name: RB2DD3


title: day 4 Erbb2d/d mouse endometrium; rep3

description: Library name: RB2DD5


title: RGECO_5

city: Cambridge

first: Ritu

last: Raman

state: MA

address: 77 Massachusetts Avenue

department: Mechanical Engineering

institute: Massachusetts Institute of Technology

description:
Library name: D25-216016
Singular G4

data_processing:
Fastq files were generated with the Illumina off-line basecaller (olb) v. 1.9.4.
Reads were aligned against mm10 (Feb., 2009) using bwa mem v. 0.7.12-r1039 with flags –t 16 –f, and mapping rates, fraction of multiply-mapping reads, number of unique 20-mers at the 5´ end of the reads, insert size distributions and fraction of ribosomal RNAs were calculated using bedtools v. 2.25.0. In addition, each resulting bam file was randomly down-sampled to a million reads, which were aligned against hg19, and read density across genomic features were estimated for RNA-Seq-specific quality control metrics
Fastq files were processed using the nf-core/rnaseq v 3.11.1 pipeline [https://zenodo.org/records/10171269] in the Nextflow 22.10.4 environment, using the GRCm39 reference genome and ENSEMBL GRCm39.110 murine annotation.
Gene-level expression tables of counts and transcript-per-million (TPM) generated by STAR/Salmon processing were retrieved [Dobin2013, Soneson2015, Patro2017] .
Assembly: GRCm39 / ENSEMBL 110 annotation
Supplementary files format and content: Gene-level raw counts and transcript per million (TPM) data generated by Salmon, tab-separated format

source_name: muscle

growth_protocol: High glucose DMEM w/ l-glutamine, 4.5g/L sodium pyruvate and glucose as the base, with 10% fetal bovine serum and 1% pen-strep for growth of these myoblasts. Differentiated using the same DMEM but with 10% inactivated horse serum, 1mg/mL of aminocaproic acid and 50 ng/ml IGF-1.

extract_protocol:
Followed the Rneasy Mini Kit for RNA extraction
Ten microliters of undiluted total RNA was incubated with 10ul of NEB Dynabeads for polyaA+ RNA selection, eluted, and fragmented in 20ul. Illumina libraries were constructed using NEB Ultra II protocol; 5ul of the fragmented solution using half the amount of reagent and 1,2 PrD instead of enhancer in the ligation step, with 14 PCR cycles of final amplification and TS Singular index barcoding.Library sizes were quantified and verified by QPCR and on a Fragment Analyzer before loading for sequencing on a Singular G4 instrument in a 50-base paired-end configuration.

value: muscle

value: myoblast

value: RGECO


title: ΔUhpTU + pBAD-Ctr-EC-G6P R1

description:
Library name: deltaUhpTU + pBAD-Ctr-EC-G6P R1
The uhpTU-deleted E.coli strain carrying the empty pBAD plasmid was cultured in M9CA medium supplemented with 0.1% (w/v) glucose-6-phosphate (G6P) at 37°C until reaching an OD₆₀₀ of approximately 0.5. L-arabinose was then added to a final concentration of 0.2% (w/v) to induce expression. Cultures were incubated for an additional 10 minutes before total RNA was extracted. This sample represents biological replicate 1 of the control group.


title: 2_4T1_WT_2_S2

description: WT biol rep2

value: Mouse mammary tumor cells

value: WT

value: 48 hours


title: RGECO_1

description:
Library name: D25-216012
Singular G4


title: day 4 Erbb2f/f mouse endometrium; rep4

description: Library name: RB2FF6

value: FF


title: day 4 Erbb2f/f mouse endometrium; rep3

description: Library name: RB2FF5


title: ΔUhpTU + pBAD-UhpU-EC-LB R2

description:
Library name: deltaUhpTU + pBAD-UhpU-EC-LB R2
The uhpTU-deleted E.coli strain carrying the pBAD-UhpU plasmid was cultured in LB miller medium at 37°C until reaching an OD₆₀₀ of approximately 0.5. L-arabinose was then added to a final concentration of 0.2% (w/v) to induce UhpU expression. After 10 minutes of induction, total RNA was extracted. This sample represents biological replicate 2 of the UhpU pulse-expression group.

value: {delta}UhpTU + pBAD-UhpU-EC-LB


title: plt345-RNA_seq-3

city: Wuhan

first: Qi

address: Lion Rock Street

department: Hongshan District

institute: Huazhong Agricultural University

data_processing:
The RNA-seq clean data were mapped against the rice genome(MSU version 7.0) with the corre_x0002_sponding annotation by hisat2 using default parameters
FeatureCounts (version 2.0.0) and DESeq2 (version 1.38.3) were used to calculate DEGs
Assembly: MSU version 7.0 rice genome
Supplementary files format and content: output from DESeq

organism: Oryza sativa Japonica Group

source_name: root tip

growth_protocol: Seedlings were grown in one-half-strength Murashige and Skoog medium under 14-h light/10-h dark cycles at 28/24 °C

extract_protocol:
Total RNA was extracted from the indicated tissues using TRIzol reagent (Invitrogen, USA) according to the manufac_x0002_turer’s protocol.
RNA-seq libraries were prepared using rolling circle replication of BGISEQ-500 and sequenced (paired-end, 2 x 150bp) on the BGISEQ-500 platform.

value: root tip

value: triple mutant of PLT3, PLT4 and PLT5


title: 1_4T1_WT_1_S1

description: WT biol rep1


title: RGECO_2

description:
Library name: D25-216013
Singular G4


title: ΔUhpTU + pBAD-UhpU-EC-G6P R2

description:
Library name: deltaUhpTU + pBAD-UhpU-EC-G6P R2
The uhpTU-deleted E.coli strain carrying the pBAD-UhpU plasmid was cultured in M9CA medium supplemented with 0.1% (w/v) glucose-6-phosphate (G6P) at 37°C until reaching an OD₆₀₀ of approximately 0.5. L-arabinose was then added to a final concentration of 0.2% (w/v) to induce UhpU expression. After 10 minutes of induction, total RNA was extracted. This sample represents biological replicate 2 of the UhpU pulse-expression group.


title: RGECO_4

description:
Library name: D25-216015
Singular G4


title: plt345-RNA_seq-2


title: ΔUhpTU + pBAD-Ctr-EC-LB R2

description:
Library name: deltaUhpTU + pBAD-Ctr-EC-LB R2
The uhpTU-deleted E.coli strain carrying the empty pBAD plasmid was cultured in LB miller medium at 37°C until reaching an OD₆₀₀ of approximately 0.5. L-arabinose was then added to a final concentration of 0.2% (w/v) to induce expression. Cultures were incubated for an additional 10 minutes before total RNA was extracted. This sample represents biological replicate 2 of the control group.

value: {delta}UhpTU + pBAD-Ctr-EC-LB


title: day 4 Erbb2f/f mouse endometrium; rep2

description: Library name: RB2FF4

value: endometrium


title: RGECO_6

description:
Library name: D25-216017
Singular G4


title: 3_4T1_WT_3_S3

description: WT biol rep3


title: WT_5

description:
Library name: D25-216010
Singular G4

value: wild type


title: WT_4

description:
Library name: D25-216009
Singular G4


title: plt345-RNA_seq-1


title: day 4 Erbb2f/f mouse endometrium; rep1

description: Library name: RB2FF3

value: mouse endometrium


title: day 4 Erbb2d/d mouse endometrium; rep1

description: Library name: RB2DD1

value: DD


title: adrenal gland 2, SeekOne

city: Moscow

first: Alesya

last: Maluchenko

address: Kulakova str. 20

country: Russia

institute: Moscow Center for Advanced Studies

description:
Library name: AG2_SeekOne
SurfSeq 5000

library_source: transcriptomic single cell

data_processing:
In each tissue type, fastq files were subsetted to have an equal number of reads in data from each sample using seqtk. ScRNA-seq reads from 10x Genomics samples were mapped to human GRCh38 (GENCODE v32/Ensembl98) or mouse mm10 (GENCODE vM23/Ensembl98) reference genome using 10x Genomics Cell Ranger v9.0.1 software with default parameters. ScRNA-seq reads from SeekOne samples were mapped to human GRCh38 reference genome downloaded from seeksoultools v1.2.2 documentation site or mouse mm10 (GENCODE vM23/Ensembl98) reference genome built by Cell Ranger. Mapping was conducted using seeksoultools v1.2.2 with chemistry DDV2 and including introns. ScRNA-seq reads from MobiDrop samples were mapped to human GRCh38 (GENCODE v32/Ensembl98) or mouse mm10 (GENCODE vM23/Ensembl98) reference genome created by mobivision mkindex. Mapping was conducted using MobiVision v3.2 software. Count matrices were filtered using the R package pagoda2 v1.0.12. with minimal UMI count per cell was 1,000, maximal UMI count was 50,000, minimal number of genes per cell was 500 and minimal cells per gene number was 3. Doublets were identified using Scrublet v0.2.3. Decontamination was performed using DecontX from celda package v1.16.1. The following analysis was performed using the Seurat library. Seurat objects of PBMC samples were filtered with maximum percent of mitochondrial genes per cell set to 15%, maximum percent of hemoglobin genes per cell set to 2%, scrublet score lower than 0.2, number of total RNA count for each cell lower than 12,000, number of RNA features between 1,000 and 6,000. Cluster contaminated with neutrophil genes was removed. For murine adrenal samples and pancreatic neuroendocrine tumor samples cells having percent of mitochondrial genes more than 25%, percent of ribosomal genes more than 40%, scrublet score greater than 0.2, number of total RNA count greater than 50,000 and less than 500, number of RNA features lower than 250 were filtered out.
Assembly: GRCh38 (GENCODE v32/Ensembl98), mm10 (GENCODE vM23/Ensembl98)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: adrenal gland

extract_protocol:
A patient's whole blood sample was diluted in PBS at a ratio of 1:1. Ficoll solution was added to a clean 15 ml falcon. The diluted blood sample was carefully layered on the Ficoll layer, preventing their mixing. Then, the sample was centrifuged with the following parameters: 450 g, 30 minutes, without brake. After that, the mononuclear cell ring was carefully collected from the Ficoll surface with a dispenser, and transferred to a clean 15 ml tube. The sample volume was brought to 10 ml using PBS. The sample was centrifuged at the parameters: 300 g for 10 minutes, after which the supernatant was removed. These steps were performed twice. Cryopreservation of the isolated cells was carried out according to the manufacturer's protocol. The samples were defrosted, washed, samples from 4 patients were pooled with 1 million cells from each patient for further loading onto the chip. Murine adrenal glands were excised and placed in PBS 1X with 10% fetal bovine serum (FBS) on ice. Under a binocular microscope, adipose tissue was removed with two tweezers/scalpel, and adrenal glands were mechanically homogenized with a scalpel on ice. Next, the adrenal gland homogenates were placed in a dissociating solution (HBSS buffer, Ca2+ 1.26 mM, collagenase IV 20 mg/mL, DNAse I 0.7 mg/ul, 0.5% BSA, RNase inhibitor) followed by 30-minute incubation at 37°C in a shaker-incubator (100 RPM). During the incubation, the suspension was pipetted every 10 minutes. Following the incubation, it was carefully pipetted, and 800 μl of PBS 1X with 10% FBS were added. The suspension was centrifuged 450 rcf for 6 min at +4◦C, then the supernatant was decanted, and the pellet was resuspended in 700 μl PBS 1X with 10% bovine serum and passed through a 70 μm filter. Then it was centrifuged 450 rcf 6 min at +4◦C, the supernatant was collected, the pellet was resuspended in 450 μl 1x PBS-0.05% BSA. The cell suspensions were gently mixed with cooled methanol in a ratio of 1:10 and placed for long-term storage at −80°C. For further work, the samples were defrosted on ice and rehydrated using a citrate buffer. Human pancreatic neuroendocrine tumor tissue was dissociated for single cell RNA sequencing using the Multi Tissue Dissociation Kit 2 by Miltenyi Biotec (cat. no. 130-110-203). Briefly, the tissue was placed in a petri dish on ice and cut into small pieces of 2–4 mm. The pieces were infused with the RPMI/enzyme mix (Miltenyi Biotec), transferred to a gentleMACS C tube containing RPMI/enzyme mix, attached to the sleeve of the single cell suspension dissociator (DSC-400) and run using the standard “H_Tumor_heater_1” program. After the termination of the program, the cells were centrifuged at 650 x g for 6 min at +4°C, resuspended in PBS 1X with 0.04 % bovine serum, passed through a 70 µm strainer and centrifugation was repeated. The supernatant was collected, the pellet was resuspended in 1 ml 1x PBS-0.04% BSA. Next, the cell suspension was fixed in cooled methanol. The cell suspension obtained in the previous step was mixed with methanol in a ratio of 1:10 and placed for long-term storage at −80°C. For further work, the samples were defrosted on ice and rehydrated using a citrate buffer.
The Chromium Next GEM Single Cell 5′ v2 Kit, Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10× Genomics, Pleasanton, CA, USA) and the Chromium Single Cell Controller Instrument were used to generate 10× single-cell libraries according to the manufacturer’s instructions. The SeekOne DD Single Cell 3’ Transcriptome-seq Kit v1.1 and the SeekOne Digital Droplet System Instrument were used to generate single-cell libraries according to the manufacturer’s instructions. The MobiCube Single-Cell 3’ RNA-seq Kit v2.0, MobiCube Single-Cell 5’ V(D)J Kit v1.0 and the MobiNovaSP-100 Instrument were used to generate single-cell libraries according to the manufacturer’s instructions.

value: adrenal gland


title: RGECO_3

description:
Library name: D25-216014
Singular G4


title: ZH11-RNA_seq-3

value: wild-type


title: WT_3

description:
Library name: D25-216008
Singular G4

value: muscle


title: EC ΔUhpTU-R2

description:
Library name: EC deltaUhpTU-R2
E. coli ΔUhpTU strain was grown in standard LB (Miller) medium at 37°C until the culture reached an OD₆₀₀ of approximately 1.0. Total RNA was extracted for sequencing. This sample corresponds to biological replicate 2

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

value: EC {delta}UhpTU


title: adrenal gland 2, 10x

description:
Library name: AG2_10x
SurfSeq 5000


title: ZH11-RNA_seq-2


title: WT_2

description:
Library name: D25-216007
Singular G4

value: myoblast


title: ΔUhpTU + pBAD-UhpU-EC-LB R1

description:
Library name: deltaUhpTU + pBAD-UhpU-EC-LB R1
The uhpTU-deleted E.coli strain carrying the pBAD-UhpU plasmid was cultured in LB miller medium at 37°C until reaching an OD₆₀₀ of approximately 0.5. L-arabinose was then added to a final concentration of 0.2% (w/v) to induce UhpU expression. After 10 minutes of induction, total RNA was extracted. This sample represents biological replicate 1 of the UhpU pulse-expression group.


title: EC ΔUhpTU-R1

description:
Library name: EC deltaUhpTU-R1
E. coli ΔUhpTU strain was grown in standard LB (Miller) medium at 37°C until the culture reached an OD₆₀₀ of approximately 1.0. Total RNA was extracted for sequencing. This sample corresponds to biological replicate 1


title: WT_6

description:
Library name: D25-216011
Singular G4


title: ZH11-RNA_seq-1


title: adrenal gland 1, MobiDrop

description:
Library name: AG1_MobiDrop
SurfSeq 5000


title: EC WT-R1

description:
Library name: EC WT-R1
Wild-type E. coli strain was grown in standard LB (Miller) medium at 37°C until the culture reached an OD₆₀₀ of approximately 1.0. Total RNA was extracted for sequencing. This sample corresponds to biological replicate 1

value: EC WT


title: WT_1

description:
Library name: D25-216006
Singular G4


title: adrenal gland 1, 10x

description:
Library name: AG1_10x
SurfSeq 5000


title: siControl, Sample 3

status: Public on Nov 16 2025

city: Urbana

first: Erik

middle: Russell

last: Nelson

state: IL

address: 407 S. Goodwin Ave

department: Molecular and Integrative Physiology

description: Library name: M_siCntrl3

data_processing:
ATAC-seq fastq files were trimmed using Trim Galore (paired-end, quality score ≥ 30). Trimmed reads were aligned to the mouse genome (GRCm39) using Bowtie2, and the sorted and indexed BAM files created using Samtools. Peak calling was performed with MACS2 using the parameters --bdg --nomodel --g mm to identify accessible chromatin regions in each sample. To combine peaks across all samples, Bedtools merge was used to create a merged peak set, and coverage signal across all merged peaks was quantified with Bedtools coverage. Read counts were normalized to reads per million mapped reads (RPM), with the total number of mapped reads calculated using Samtools view (-c -F 256). Differential accessibility analysis was carried out using DESeq2 on three biological replicates of macrophage control and treatment samples, to identify differentially accessible regions. For motif enrichment analysis, peaks were divided into upregulated and downregulated groups based on the SWFC (significance weight fold change) score (-log10(p_adj) * log2(Fold Change)), with thresholds of -1 and 1 for upregulated and downregulated peaks, respectively. Genomic sequences of these peak groups were extracted using Bedtools getfasta, and motif enrichment was assessed using SEA (- - thresh 10.0 - -align center) from the MEME Suite with the HOCOMOCOv11_full_mouse_mono motif database . Non-differential peaks (SFW between -1 and 1) were used as a control for motif enrichment analysis.
Assembly: GRCm39, NCBI Annotation Release 0.9
Supplementary files format and content: MACS2, Peak Called

source_name: Bone marrow derived macrophages

extract_protocol:
The libraries were prepared using the ATAC-seq Kit (Active Motif) following the manufacturer’s protocol. Briefly, cell viability was assessed by AO/PI staining with bright-field microscopy, and all samples had a viability of 80 percent or higher. Fresh cells were lysed, followed by tagmentation with Tn5 transposase to fragment accessible chromatin and to insert partial sequencing adapters. The resulting DNA fragments were purified, PCR-amplified to add unique dual barcodes to each library and cleaned up with magnetic beads to remove adapter dimers.
Construction of the ATACSeq libraries and sequencing on the Illumina NovaSeq 6000 were performed at the Roy J. Carver Biotechnology Center at the University of Illinois at Urbana-Champaign. The final libraries were quantitated with Qubit (ThermoFisher) and the average cDNA fragment sizes were determined on a Fragment Analyzer. The libraries were diluted to 5nM and further quantitated by qPCR on a CFX Connect Real-Time qPCR system (BioRad) for accurate pooling of barcoded libraries and maximization of number of clusters in the flowcell.  The pooled barcoded ATACseq libraries were loaded on one SP lane on a NovaSeq 6000 for cluster formation and sequencing. The libraries were sequenced from both ends of the fragments for 150 cycles per end. The fastq read files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina).

value: Bone marrow derived macrophages

value: Wildtype

value: siRNA - control


title: siABCA1, Sample 2

institute: University of Illinois at Urbana-Champaign

description: Library name: M_siABCA1_2

value: siRNA ABCA1


title: siABCA1, Sample 1

description: Library name: M_siABCA1_1


title: ΔUhpTU + pBAD-Ctr-EC-LB R1

description:
Library name: deltaUhpTU + pBAD-Ctr-EC-LB R1
The uhpTU-deleted E.coli strain carrying the empty pBAD plasmid was cultured in LB miller medium at 37°C until reaching an OD₆₀₀ of approximately 0.5. L-arabinose was then added to a final concentration of 0.2% (w/v) to induce expression. Cultures were incubated for an additional 10 minutes before total RNA was extracted. This sample represents biological replicate 1 of the control group.


title: siABCA1, Sample 3

description: Library name: M_siABCA1_3


title: siControl, Sample 1

description: Library name: M_siCntrl1


title: myotubes, nuc, RNA-seq

city: shanghai

first: hong

last: cheng

address: yueyang road

institute: ucas

description: Library name: Samples12

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using catadapt.
Trimed reads from WT and Zfc3h1 KO MSCs and MTs were aligned to a combined mm10 genome and ERCC RNA spike-ins using STAR. Trimed reads from other samples were mapped solely to the mm10 genome.
Gene read counts were quantified using featureCounts from the Subread package.
Assembly: mm10
Supplementary files format and content: bigwig

molecule: polyA RNA

extract_protocol:
RNA was extracted in Trizol and purified.
Approximately 1 µg of total RNA was used for either polyA RNA enrichment or rRNA depletion. Stranded cDNA libraries were then constructed using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina, following the manufacturer’s guidelines.

value: myotube


title: siControl, Sample 2

description: Library name: M_siCntrl2


title: myotubes, cyto, RNA-seq

description: Library name: Samples11


title: siABCA1, sample 5

description:
Library name: M_si5
M_si5 in logcpm

data_processing:
Salmon (v 1.4.0) was used to quasi-map reads to the transcriptome and quantify the abundance of each transcript. The transcriptome was first indexed using the decoy-aware method in Salmon with the entire genome as the decoy sequence. Then quasi-mapping was performed to map reads to transcriptome with additional arguments --seqBias and --gcBias to correct sequence-specific and GC content biases, --numBootstraps=30 to compute bootstrap transcript abundance estimates and --validateMappings to help improve the accuracy of mappings.
Gene-level counts were then estimated based on transcript-level counts using the “bias corrected counts without an offset” method from the tximport package (v1.24.0) in R (4.2.0) . This method provides more accurate gene-level counts estimates and keeps multi-mapped reads in the analysis compared to traditional alignment-based method
Assembly: GRCm39, NCBI Annotation Release 0.9
Supplementary files format and content: Excel files containing gene level counts for the samples

extract_protocol:
700,000 BMDMs were seeded in each well of a 6-well plate. 48 hrs post-transfection RNA was extracted using the RNeasy Kits from Qiagen (Cat No 74104) using RNA isolation columns as per the manufacturer’s instructions. DNA was removed using an on-column DNase treatment. Pure, concentrated RNA was eluted in nuclease free-water.
Kapa Hyper Stranded mRNA library kit (Roche)

value: wildtype

value: siRNA ABCA5


title: siABCA1, sample 2

description:
Library name: M_si2
M_si2 in logcpm

value: siRNA ABCA2


title: siABCA1, sample 3

description:
Library name: M_si3
M_si3 in logcpm

value: siRNA ABCA3


title: satellite cells, nuc, RNA-seq

description: Library name: Samples10

value: satellite cell


title: siABCA1 sample 1

description:
Library name: M_si1
M_si1 in logcpm


title: satellite cells, cyto, RNA-seq

description: Library name: Samples9


title: siCon, sample 5

description:
Library name: M_cntrl5
M_cntrl5 in logcpm


title: siCon, sample 4

description:
Library name: M_cntrl4
M_cntrl4  in logcpm


title: MDA-MB-231 cell, Paclitaxe

city: Beijing

first: Yuqi

last: Xing

state: Beijing

address: Peking University

institute: Peking University

description: Library name: X231-L-2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork. Trimmed sequence reads were mapped to hg38 using CLC genomic benchwork. Read count extraction and normalization were performed using CLC genomic benchwork.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes TF

source_name: MDA-MB-231 cell

extract_protocol:
The total RNA was isolated from cells using Trizol reagent (Invitrogen) according to the manufacture’s instruction, followed by being fragmented into shorter fragments with buffer.
The resulting cDNA was performed with complex method according to the manufacture’s protocol.

value: MDA-MB-231 cell

value: Human breast cancer cell

value: Paclitaxe


title: EC WT-R2

description:
Library name: EC WT-R2
Wild-type E. coli strain was grown in standard LB (Miller) medium at 37°C until the culture reached an OD₆₀₀ of approximately 1.0. Total RNA was extracted for sequencing. This sample corresponds to biological replicate 2

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


title: BT549 cell, DMSO

description: Library name: BT549-1

source_name: BT549 cell

value: BT549 cell

value: DMSO


title: SUM159 cell, Paclitaxe

description: Library name: sum159-2

source_name: SUM159 cell

value: SUM159 cell


title: CD45+ sorted, Healthy 6 (control); frozen. TCR library

city: Boston

first: Stephanie

last: Dougan

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

description: Library name: Frozen3-VDJ

data_processing:
Cellranger v7.0.0 was used to align and count FASTQ reads (including aligning TCR sequences using cellranger multi)
The count matrices were imported for downstream analysis into R using the Seurat (v4.3.0) package. Cells were called from barcodes using the Seurat R package
Count normalization, integration, and clustering was performed using Seurat
Assembly: GRCh38
Assembly: cellranger-vdj-GRCh38-alts-ensembl-7.1.0 (downloaded from 10x Genomics website)
Supplementary files format and content: CG_raw_feature_bc_matrix.tar: Tar file of count/feature matrices (raw_feature_bc_matrix) output from Cellranger
Supplementary files format and content: TCR_contigs.tar: Tar of raw TCR alignments (all_contig_annotations) output from Cellranger
Supplementary files format and content: CG_Seurat_metadata.csv: Comma-separated values of Seurat object metadata with cell annotations/clusters
Library strategy: scTCR-Seq

source_name: Stomach (fundus)

extract_protocol:
Biopsy bites were immediately collected into DMEM media on ice, or put into freezing media (10% DMSO; 40% RPMI; 50% FBS) and frozen (for later CD45-enrichment). Fresh or frozen and thawed tissue was then manually dissociated with a sterile razor and transferred to pre-warmed 37°C digestion enzyme mix in RPMI (Miltenyi tumor dissociation kit, cat. 130-095-929). In a 37°C water bath, tissue digestion was agitated every 2 minutes, and pipetted up and down every 10 minutes for a total of 30 minutes. Digested tissue was filtered through a 70μM strainer, washed with RPMI containg 10% FBS, and the single-cell suspension was collected and processed for scRNAseq. Fresh samples were loaded immediately while frozen samples were sorted for CD45+ Live (Zombie-NIR-) cells.
Library preparation was performed with the 10x Genomics Chromium Single Cell 5’ v2 library kit (for both GEX and TCR libraries)

value: Stomach (fundus)

tag: type

value: Biopsy

tag: disease

value: Healthy


title: KO Zfc3h1, myotubes, biol replicate 1, RNA-seq

description: Library name: Samples7

value: muscle

value: Zfc3h1 knockout


title: WT, myotubes, biol replicate 2, RNA-seq

description: Library name: Samples6

value: myotube

value: WT


title: siCon, sample 3

description:
Library name: M_cntrl3
M_cntrl3 in logcpm

value: Bone marrow derived macrophages

value: wildtype

value: siRNA - control


title: CD45+ sorted, Patient G (CG); frozen. TCR library

description: Library name: Frozen4-VDJ

value: CG


title: KO Zfc3h1, satellite cells, biol replicate 2, RNA-seq

description: Library name: Samples4

value: satellite cell


title: siCon, sample 2

description:
Library name: M_cntrl2
M_cntrl2 in logcpm


title: CD45+ sorted, Patient D (CG) biopsy #2; frozen. TCR library

description: Library name: D2-CD45-TCR


title: WT, satellite cells,biol replicate 2, RNA-seq

description: Library name: Samples2


title: MDA-MB-231 cell, DMSO

description: Library name: X231-L-1

value: MDA-MB-231 cell

value: Human breast cancer cell


title: Unsorted Healthy 6 (control); fresh

description: Library name: Fresh3-GEX

data_processing:
Cellranger v7.0.0 was used to align and count FASTQ reads (including aligning TCR sequences using cellranger multi)
The count matrices were imported for downstream analysis into R using the Seurat (v4.3.0) package. Cells were called from barcodes using the Seurat R package
Count normalization, integration, and clustering was performed using Seurat
Assembly: GRCh38
Assembly: cellranger-vdj-GRCh38-alts-ensembl-7.1.0 (downloaded from 10x Genomics website)
Supplementary files format and content: CG_raw_feature_bc_matrix.tar: Tar file of count/feature matrices (raw_feature_bc_matrix) output from Cellranger
Supplementary files format and content: TCR_contigs.tar: Tar of raw TCR alignments (all_contig_annotations) output from Cellranger
Supplementary files format and content: CG_Seurat_metadata.csv: Comma-separated values of Seurat object metadata with cell annotations/clusters


title: Atf6-/- liver tumor, rep3

city: La Jolla

first: Randal

middle: J.

last: Kaufman

state: CA

address: 10901 North Torrey Pines Road

department: Cancer Metabolism and Microenvironment Program, Center for Genetic Disorders and Aging Research NCI-Designated Cancer Center

institute: Sanford Burnham Prebys Medical Discovery Institute

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 Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
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.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include counts values for each Sample.

source_name: liver

extract_protocol:
According to the manufacturer’s protocol, total RNA isolation from snap-frozen liver tissue was performed with RNeasy Mini Kit (Qiagen, 74106). RNA samples were treated with TURBO DNase (ThermoFisher Scientific, AM1907) to remove genomic DNA.
Library preparation, Illumina, RNA with PolyA selection, Illumina HiSeq 2x150 bp sequencing, single index

treatment_protocol: Mice were intraperitoneally injected with diethylnitrosamine (DEN) at two weeks of age prior to high-fat diet (HFD) feeding and sacrifice at 38 weeks of age.

value: liver

value: Diethylnitrosamine (DEN) + high fat diet


title: siCon, sample 1

description:
Library name: M_cntrl1
M_cntrl1 in logcpm


title: CD45+ sorted, Healthy 5 (control); frozen

description: Library name: Frozen1214-GEX


title: Atf6-/- liver tumor, rep1


title: SUM159 cell, DMSO

description: Library name: sum159-1

value: SUM159 cell

value: DMSO


title: Atf6+/+ liver tumor, rep3


title: KO Zfc3h1, myotubes, biol replicate 2, RNA-seq

description: Library name: Samples8


title: CD45+ sorted, Healthy 4 (control); frozen

description: Library name: Frozen1213-GEX

value: Stomach (fundus)

value: Biopsy


title: CD45+ sorted, Healthy 5 (control); frozen. TCR library

description: Library name: Frozen1214-VDJ

value: Healthy


title: CD45+ sorted, Healthy 4 (control); frozen. TCR library

description: Library name: Frozen1213-VDJ


title: siABCA1, sample 4

description:
Library name: M_si4
M_si4 in logcpm

value: siRNA ABCA4


title: Atf6+/+ liver tumor, rep2


title: KO Zfc3h1, satellite cells, biol replicate 1, RNA-seq

description: Library name: Samples3

value: muscle

value: Zfc3h1 knockout


title: CD45+ sorted, Patient F (CG); frozen. TCR library

description: Library name: CG-F-CD45-TCR


title: WT, myotubes, biol replicate 1, RNA-seq

description: Library name: Samples5

value: myotube

value: WT


title: TG liver TG-AAV-CRE tumoral, rep5

data_processing:
Raw reads were preprocessed by trimming Illumina Truseq adapters, polyA, and polyT sequences using cutadapt v2.3 with parameters “cutadapt -j 4 -m 20 --interleaved -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT Fastq1 Fastq2 | cutadapt --interleaved -j 4 -m 20 -a "A{100}" -A "A{100}" - | cutadapt -j 4 -m 20 -a "T{100}" -A "T{100}" -”.
Trimmed reads were subsequently aligned to mouse genome version mm10 using STAR aligner  v2.7.0d_0221 with parameters according to ENCODE long RNA-seq pipeline.
Gene expression levels were quantified using RSEM v1.3.1. Ensembl v84 gene annotations were used for the alignment and quantification steps. RNA-seq sequence, alignment, and quantification qualities were assessed using FastQC v0.11.5 and MultiQC v1.8. Lowly expressed genes were filtered out by retaining genes with estimated counts (from RSEM) ≥ number of samples times 5.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample.

extract_protocol:
According to the manufacturer’s protocol, total RNA isolation from snap-frozen liver tissue was performed with RNeasy Mini Kit (Qiagen, 74106). RNA samples were treated with TURBO DNase (ThermoFisher Scientific, AM1907) to remove genomic DNA.
Library preparation, Illumina, RNA with PolyA selection, Illumina HiSeq 2x150 bp sequencing, single index.

treatment_protocol: Mice were intraperitoneally injected with diethylnitrosamine (DEN) at two weeks of age prior to high-fat diet (HFD) feeding and sacrifice at 30 weeks of age.

value: TG Atf6p50

value: Diethylnitrosamine (DEN) high fat diet


title: WT, satellite cells,biol replicate 1, RNA-seq

description: Library name: Samples1

value: satellite cell


title: TG liver TG-AAV-CRE tumoral, rep4


title: TG liver TG-AAV-CRE tumoral, rep3


title: CD45+ sorted, Patient E (CG); frozen. TCR library

description: Library name: CG-E-CD45-TCR

value: CG


title: Unsorted Patient F (CG); fresh

description: Library name: CG-F-total-GEX


title: BT549 cell, Paclitaxe

description: Library name: BT549-2

value: BT549 cell

value: Human breast cancer cell

value: Paclitaxe


title: CD45+ sorted, Healthy 6 (control); frozen

description: Library name: Frozen3-GEX


title: Atf6-/- liver tumor, rep2

value: liver

value: Diethylnitrosamine (DEN) + high fat diet


title: Unsorted Healthy 5 (control); fresh

description: Library name: Fresh2-GEX

value: Stomach (fundus)


title: Unsorted Healthy 4 (control); fresh

description: Library name: Fresh1-GEX

value: Biopsy


title: TG liver TG-AAV-CRE non-tumoral, rep4


title: Atf6+/+ liver tumor, rep1


title: CD45+ sorted, Patient G (CG); frozen

description: Library name: Frozen4-GEX


title: TG liver TG-AAV-CRE non-tumoral, rep2


title: Transcriptomic effects of PFHxA exposure on RPMI2650 cells 3/4

first: Ting

last: Xu

address: No. 1239 Road Siping

institute: Tongji University

data_processing:
Hisat2 (version: 2.0.4)
Assembly: GRCh38 (hg38)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Nasal epithelium

extract_protocol:
0.05 -4 μg total RNA was dissolved in Nuclease-free ddH2O to a total volume of 50 μl
Total RNA was extracted from exposed cells and libraries were prepared according to Illumina standard instructions (VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina®). The concentration and size distribution of the cDNA libraries was assessed using an Agilent 4200 Bioanalyzer before sequencing and sequenced using an Illumina novaseq 6000.

value: Nasal epithelium

value: Epithelium cell

value: Wild Type

value: PFHxA expsoure


title: TG liver TG-AAV-CRE non-tumoral, rep1


title: Unsorted Patient G (CG); fresh

description: Library name: Fresh4-GEX


title: TG liver TG-AAV-CRE tumoral, rep2


title: WT liver TG-AAV-GFP tumoral, rep2


title: TG liver TG-AAV-CRE tumoral, rep1


title: Transcriptomic effects of PFBA exposure on RPMI2650 cells 3/4

value: PFBA exposure


title: TG liver TG-AAV-CRE non-tumoral, rep5


title: WT liver TG-AAV-GFP non-tumoral, rep3

value: WT


title: Unsorted Patient E (CG); fresh

description: Library name: CG-E-total-GEX


title: Unsorted Patient D (CG) biopsy #2; fresh

description: Library name: D2-total-GEX


title: TG liver TG-AAV-CRE non-tumoral, rep3

value: TG Atf6p50


title: Transcriptomic effects of PFHxA exposure on RPMI2650 cells 4/4


title: Transcriptomic effects of PFHxA exposure on RPMI2650 cells 2/4


title: CD45+ sorted, Patient F (CG); frozen

description: Library name: CG-F-CD45-GEX


title: Transcriptomic status of RPMI2650 cells 4/4

value: Control


title: Transcriptomic effects of PFHxA exposure on RPMI2650 cells 1/4


title: Transcriptomic effects of PFBA exposure on RPMI2650 cells 1/4


title: WT liver TG-AAV-GFP tumoral, rep1

value: Diethylnitrosamine (DEN) high fat diet


title: Transcriptomic effects of PFBA exposure on RPMI2650 cells 4/4


title: CD45+ sorted, Patient E (CG); frozen

description: Library name: CG-E-CD45-GEX

value: CG


title: WT liver TG-AAV-GFP tumoral, rep3


title: CP3G

city: ChunCheon-si

first: Jun Won

last: Park

address: Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Kangwondaehak-gil

country: South Korea

institute: kangwon national univercity

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to mm10 whole genome by using HISAT2 version 2.1.0 with parameter -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
FPKM were calculated by using StringTie version 2.1.3b, with parameter --rf -l -o -G -A -e
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Gastric organoid

growth_protocol: CP, CPS organoid were maintained in advanced DMEM/F12 with L-WRN cell line supernatent supplemented with 5% fetal bovine serum (FBS) and reagent in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 0.5 ug of total RNA was used for the construction of sequencing libraries.
A library was independently prepared using 0.5ug of total RNA from each sample using the Illumina TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina; Cat# 20020599).

treatment_protocol: The next day after culturing the cells, they were replaced with Advanced DMEM/F12 supplemented with B27,N2 without FBS, L-WRN conditional media and grown for 2 days.

value: Gastric organoid

value: CPG

value: organoid


title: CD45+ sorted, Patient D (CG) biopsy #2; frozen

description: Library name: D2-CD45-GEX


title: Transcriptomic effects of PFBA exposure on RPMI2650 cells 2/4


title: WT liver TG-AAV-GFP non-tumoral, rep2

value: liver


title: iPSC  Cardiomyocytes Tbx2del/del  Day:10 Replicate:2

city: Cardiff

first: Peter

last: Kille

state: Caerdydd

address: The Sir Martin Evans Building, Museum Avenue

department: School of Biosciences

country: United Kingdom

institute: Cardiff University

description:
Library name: Tbx2del/delDay10R2
TBX2_B10_Day10_R1

data_processing:
Data filtering fastp - v0.20
Read alignment Star - 2.7.6a
Gene quantification - Subread - v2.03
DEG generation SARTools / DESeq2
Assembly: Data was processed against Ensembl GRCh38.p14
Supplementary files format and content: Normalised counts in csv format - headers represent library name

growth_protocol: iPSCs provided by **doi**

extract_protocol:
RNA was extracted using the acid-guanidinium thiocyanate phenol chloroform method (Chomczynski and Sacchi 1987)
RNASeq Library construction used Illumina Trueseq2

treatment_protocol: iPSCs were cultured on Corning™ cell culture plates coated with Geltrex™ at 30-45 µg/mL in DMEM/F12 Media and maintained with B8 media formulated as described by ( doi:10.1016/j.stemcr.2019.12.007). Passaging was carried out when cultures reached 75-80% confluency. ReLeSR™ was used to dissociate iPSC colonies as per the manufacturer’s instructions (StemCell Technologies), following this the cells were replated and fed with B8 2.5 μM Y27632 (HelloBio) for 24 hours following passaging before being switched to B8 for regular feeding every other day. All cells were maintained at 37°C in a humidified atmosphere with 5% CO2. Differentiation of iPSCs into CMs was carried out using two commonly utilised Wnt modulation protocols (doi:10.1038/nmeth.2999)(doi:10.1073/pnas.1200250109)

value: iPSC

value: Cardiomyocytes

tag: replicate

tag: batch


title: WT liver TG-AAV-GFP non-tumoral, rep1


title: iPSC  Cardiomyocytes Tbx2del/del  Day:10 Replicate:1

description:
Library name: Tbx2del/delDay10R1
TBX2_B10_Day10_R2


title: iPSC  Cardiomyocytes WT  Day:7 Replicate:1

description:
Library name: WTDay7R1
WT_Day7_R2


title: iPSC  Cardiomyocytes WT  Day:7 Replicate:2

description:
Library name: WTDay7R2
WT_Day7_R1


title: CP3S4

value: Smad4 Knockout


title: Transcriptomic status of RPMI2650 cells 3/4

value: Nasal epithelium


title: CP3S1


title: iPSC  Cardiomyocytes WT  Day:10 Replicate:1

description:
Library name: WTDay10R1
WT_Day10_R2


title: CD45+ sorted, Patient B (CG); frozen. TCR library

value: Stomach (fundus)

tag: specimen

value: Biopsy


title: Transcriptomic status of RPMI2650 cells 2/4

value: Epithelium cell

value: Wild Type


title: iPSC  Cardiomyocytes WT  Day:10 Replicate:2

description:
Library name: WTDay10R2
WT_Day10_R1

value: WT


title: Transcriptomic status of RPMI2650 cells 1/4


title: CD45+ sorted, Patient A (CG) Post Steroids; frozen. TCR library

value: Steroids


title: iPSC  Cardiomyocytes PRDM1-/-  Day:7 Replicate:1

description:
Library name: PRDM1-/-Day7
PRMD1_B12_Day7


title: iPSC  Cardiomyocytes PRDM1-/-  Day:3 Replicate:1

description:
Library name: PRDM1-/-Day3
PRDM1_B12_Day3


title: iPSC  Cardiomyocytes WT  Day:10 Replicate:4

description:
Library name: WTDay10R4
WT_Day10_R2


title: Control_CTB5_40.0weeks

type: RNA

city: Auckland

first: Teena

last: Gamage

state: Scotland

country: New Zealand

institute: Grafton

hyb_protocol: Affymetrix GeneChip PrimeView microarrays using the3' IVT PLUS kit

scan_protocol: Standard Affymetrix protocol

data_processing: Microarray data were quality cheked and lacked obvious outliers (Bolstad et al. 2003; Irizarry et al 2003a; Irizarry et al 2003b). Preprocessing and normalaisation of the data using RMA was conducted using R package affy (Gautier et al. 2004). Side-population trophoblast gene expression was compared to that of cytotrophoblasts from the same placenta.  In oder to determine differentially expressed transcripts, the statistical program R and the R package limma were used. (Ritchie et al 2015). Linear models were used to determine Log fold changes between side-population trophoblasts and cytotrophoblast populations from FGR and gestation-matched control placentae and an emperical Bayes method was used to moderate the standard deviation of the estimated Log fold changes.

label: biotin

source_name: Placental Villi

label_protocol: Standard Affymetrix protocol

growth_protocol: Uncultured

extract_protocol: FACS sorting live MHC Class I negative  Hoechst 33342-low side-population trophoblasts and bete4-integrin positive cytotrophoblasts

tag: sample type

value: Gestation-matched control

tag: time point

value: 40.0 weeks

value: Cytotrophoblast


title: iPSC  Cardiomyocytes WT  Day:10 Replicate:3

description:
Library name: WTDay10R3
WT_Day10_R1

tag: cell line

tag: cell type


title: CD45+ sorted, Patient C (CG); frozen. TCR library

value: CG


title: CP3E

value: Gastric organoid

value: CPE

tag: genotype

value: Control


title: iPSC  Cardiomyocytes Tbx2del/del  Day:7 Replicate:1

description:
Library name: Tbx2del/delDay7R1
TBX2c.700_761del__Day7_R2

value: iPSC


title: iPSC  Cardiomyocytes Tbx2del/del  Day:7 Replicate:2

description:
Library name: Tbx2del/delDay7R2
TBX2c.700_761del_Day7_R1

value: Cardiomyocytes


title: iPSC  Cardiomyocytes WT  Day:3 Replicate:1

description:
Library name: WTDay3R1
WT_Day3_R1


title: CD45+ sorted, Healthy 3 (control); frozen. TCR library

tag: tissue

value: Healthy


title: CD45+ sorted, Patient D (CG); frozen. TCR library


title: iPSC  Cardiomyocytes GATA4 -/-  Day:10 Replicate:2

description:
Library name: GATA4-/-Day10R2
GATA4_B1_Day10_R2

value: GATA4 -/-


title: iPSC  Cardiomyocytes WT  Day:5 Replicate:2

description:
Library name: WTDay5R2
WT_Day5_R2


title: Control_CTB4_36.6weeks

value: 36.6 weeks


title: CD45+ sorted, Healthy 2 (control); frozen. TCR library

value: Stomach (fundus)

value: Biopsy


title: iPSC  Cardiomyocytes GATA4 -/-  Day:10 Replicate:1

description:
Library name: GATA4-/-Day10R1
GATA4_B1_Day10_R1


title: iPSC  Cardiomyocytes WT  Day:2 Replicate:1

description:
Library name: WTDay2
WT_Day2


title: iPSC  Cardiomyocytes GATA4 -/-  Day:2 Replicate:1

description:
Library name: GATA4-/-Day2
GATA4-/-_Day2


title: CD45+ sorted, Healthy 1 (control); frozen. TCR library


title: iPSC  Cardiomyocytes WT  Day:5 Replicate:1

description:
Library name: WTDay5R1
WT_Day5_R1


title: AAV CRE/FBP1 liver, rep3

extract_protocol:
PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module
Barcoded libraries were made using the NEBNext® Ultra II™ Directional RNA Library Prep Kit for Illumina®(NEB, Ipswich MA).  Libraries were pooled and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2 kit (Illumina Inc., San Diego CA).

treatment_protocol: Mice were intravenously injected with the corresponding AAV8 at 9 weeks of age prior to sacrifice after an overnight 16h fast at 12 weeks of age.

value: liver

value: Transgenic Atf6p50

tag: treatment

value: AAV CRE/FBP1


title: iPSC  Cardiomyocytes GATA4 -/-  Day:5 Replicate:2

description:
Library name: GATA4-/-Day5R2
GATA4-/-_Day5_R2


title: AAV CRE/FBP1 liver, rep2


title: Control_CTB3_36.2weeks

value: Gestation-matched control

value: 36.2 weeks


title: Control_SP5_40.0weeks

value: 40.0 weeks

value: Side-population


title: CD45+ sorted, Patient A (CG); frozen. TCR library

value: CG


title: iPSC  Cardiomyocytes GATA4 -/-  Day:5 Replicate:1

description:
Library name: GATA4-/-Day5R1
GATA4-/-_Day5_R1


title: CD45+ sorted, Patient C (CG); frozen


title: Unsorted Patient D (CG); fresh


title: Control_CTB2_34.4weeks

value: 34.4 weeks

value: Cytotrophoblast


title: AAV CRE liver, rep3

value: AAV CRE


title: AAV CRE/FBP1 liver, rep4


title: CD45+ sorted, Patient D (CG); frozen


title: AAV CRE liver, rep2


title: AAV FBP1 liver, rep4

value: WT

value: AAV FBP1


title: AAV CRE liver, rep4


title: AAV CRE/FBP1 liver, rep1


title: Control_SP1_38weeks

value: 38 weeks


title: CD45+ sorted, Patient B (CG); frozen


title: Control_CTB1_38weeks


title: CD45+ sorted, Healthy 3 (control); frozen

value: Healthy


title: CD45+ sorted, Patient A (CG) Post Steroids; frozen

value: Stomach (fundus)

value: Steroids


title: AAV CRE liver, rep1

value: liver


title: AAV FBP1 liver, rep3


title: AAV FBP1 liver, rep1


title: CD45+ sorted, Healthy 2 (control); frozen

value: Biopsy


title: AAV FBP1 liver, rep2


title: Unsorted Healthy 3 (control); fresh


title: AAV GFP liver, rep3

value: AAV GFP


title: AAV GFP liver, rep4


title: Unsorted Healthy 2 (control); fresh


title: CD45+ sorted, Healthy 1 (control); frozen


title: Unsorted Healthy 1 (control); fresh


title: AAV GFP liver, rep2


title: AAV GFP liver, rep1


title: KO Zfc3h1, myotubes, biol replicate 1, QuantSeq

description: Library name: Z1KOD2-R1

data_processing:
QuantSeq FWD reads were trimmed using Cutadapt to remove adapters, polyT sequences from the 5′ end of Read1, and polyA sequences from the 3′ end of Read2.The trimmed reads were then aligned to the mouse reference genome (mm10) using the STAR aligner (version 2.7.10b) with the following parameters: --outFilterMismatchNoverReadLmax 0.05, --alignIntronMin 20, --alignIntronMax 1000000, and --outSAMattributes Standard.Read1 was extracted from the BAM file using samtools, followed by removal of internally primed alignments using a custom script.Strand-specific bigWig coverage tracks, limited to a single base at the 3′ end of the RNA, were generated using deepTools' bamCoverage function. For the forward strand, the following parameters were used: --filterRNAstrand forward --offset -1 --binSize 1, and for the reverse strand: --filterRNAstrand reverse --offset -1 --binSize 1.The alignment ends within ±6 bp of each annotated polyadenylation site (PAS) in the polyA_DB database were counted using a custom script.
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
RNA was harvested using Trizol reagent and purified
For Quant-seq, approximately 500 ng of total RNA was used for library preparation using the Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit REV following the manufacturer’s guidelines

value: muscle

value: myotube

value: Zfc3h1 knockout


title: KO Zfc3h1, myotubes, biol replicate 2, QuantSeq

description: Library name: Z1KOD2-R2


title: WT, myotubes, biol replicate 2, QuantSeq

description: Library name: WTD2-R2


title: Unsorted Patient A (CG); fresh


title: Gh_cond_pH2_rep2

status: Public on Nov 15 2025

city: Hickory Corners

first: Kadeem

last: Gilbert

state: MI

address: 3700 E Gull Lake Dr

department: Plant Biology

institute: Michigan State University

description:
Gh_salmon.gene.counts.txt
Gh_salmon.gene.TPM.txt
Gh_Trinity.fasta
Gh_Trinity_map.txt
annotatedCounts_G_hirsutum.txt

data_processing:
Each RNAseq analysis was performed for each species separately. The raw read quality of each paired-end library was tested by FastQC v0.11.9 (Andrews, 2010).
Adapters and low-quality bases were removed with Trimmomatic (Bolger et al., 2014).
Transcriptome de novo assembly was performed using Trinity v2.9.1 (Grabherr et al., 2011) with default settings for each species to treat them all the same.
Reads counts were done with Salmon v1.5.0. Low counts (< 3 TPM) were filtered out and the most highly expressed isoform for each gene was kept. Transdecoder (Haas and Papanicolaou, 2017) was used to identify ORF coding region in all the assemblies.
Annotation was done with Trinotate v4.0.2 (Haas et al., 2013) and EnTAP v1.0.1 using Swissprot and PFAM protein database mainly. Salmon counts were filtered by taxonomy, only genes that were annotated for Viridiplantae taxa were considered.
Assembly: De novo transcriptome assembly without reference genome
Supplementary files format and content: tab-delimited text file includes all raw counts by sample for each species: _salmon.gene.counts.txt
Supplementary files format and content: tab-delimited text file including all normalized TPM gene expression by sample for each species: _salmon.gene.TPM.txt
Supplementary files format and content: fasta file of whole transcript sequence by species: _Trinity.fasta
Supplementary files format and content: tab-delimited text file with transcript to gene map by species: _Trinity_map.txt
Supplementary files format and content: tab-delimited text file with whole annotation of transcripts by species: annotatedCounts_Species.txt

organism: Gossypium hirsutum

source_name: Leaf blade

growth_protocol:
We acquired seeds of G. arboreum (accession PI 615701), G. hirsutum (accession PI 529181), and B. vulgaris (accession Ames 3060) from the United States Department of Agriculture (USDA) Germplasm Resources Information Network (GRIN). The seeds were planted in Sunshine #4 Soil Mix (Professional growing mix, Sungro horticulture)  and grown in the Pennsylvania State University Department of Entomology headhouse greenhouse under ambient conditions
Because it was not feasible to grow Nepenthes from seed, we attained small adult plants (clonally propagated) of N. bicalcarata (accession BE-3031) and N. rafflesiana (accession BE-3722)  from Borneo Exotics ltd. Supplied by Carnivero (Austin, TX, USA). The Nepenthes were potted in a sphagnum medium and grown in a Conviron reach-in growth chamber with the following settings: 12-hour day-night cycle, daytime temp = 28°C, nighttime temp = 26°, relative humidity = 80%, fluorescent/ incandescent levels = 250 uMol. The Nepenthes pots were also treated with imidacloprid to clear a scale infestation before the start of the experiment. For Nepenthes, we exposed to the pH treatments, two tissues, leaf blade and pitcher leaves separately. In this paper we only used the transcriptome of the leaf lamina for our comparative transcriptomics analysis.
For the plants grown from seed, they were all planted in October 2020 and grown until all species had germinated, emerged, and produced the first two nodes of true leaves (4-6 weeks from being sown).

extract_protocol:
We conducted total RNA extractions using the Spectrum Plant Total RNA kit, according to manufacturer’s protocol with some modifications. First, the leaves were transferred into clean tubes and centrifuged at max speed for 30 seconds to remove remnant RNALater. For the mechanical lysis step, we used a single large steel bead (autoclaved and sterilized with RNAse Away) to homogenize the leaf sample in lysis buffer using a FastPrep machine set to 5.5 m/s for 20 s. Following homogenization, the sample was incubated in a heatblock at 56 C for 5 minutes, and the remaining steps proceeded as per the original protocol.
Our extracted RNA was sent to Novogene for library prep, quality control, and sequencing on an Illumina NovaSeq 6000 PE150 platform.

treatment_protocol: For the pH manipulation experiments, the leaf was sprayed with one of three pH treatments: pH 6.5, 4.0, and 2.0. These sprays were created by mixing distilled deionized water (ddH2O) with the appropriate volume of HCl to reach the target pH level. These pH solutions were stored in inert glass spray bottles to avoid leaching of material or change in pH due to CO2 diffusion. The leaf was sprayed until thoroughly wet (~15 sprays) and collected directly into 2.0 mL DNAse/RNAse-free tubes of RNALater after 5 minutes of exposure.

value: Leaf blade

value: Gossypium hirsutum L.

tag: accession

tag: grin plant_name

value: pH 2

tag: time (min)


title: Control_SP3_36.2weeks

value: Gestation-matched control

value: 36.2 weeks

value: Side-population


title: Gh_cond_pH2_rep1


title: Gh_cond_pH4_rep2

value: pH 4


title: Control_SP4_36.6weeks

value: 36.6 weeks


title: WT, myotubes, biol replicate 1, QuantSeq

description: Library name: WTD2-R1

value: WT


title: KO Zfc3h1, satellite cells, biol replicate 2, QuantSeq

description: Library name: Z1KOP1-R2

value: satellite cell


title: FGR_CTB1_38.3weeks

value: Fetal Growth Restricted

value: 38.3 weeks

value: Cytotrophoblast


title: FGR_SP4_37.2weeks

value: 37.2 weeks


title: Gh_cond_pH6_rep1


title: Gh_cond_pH6_rep2


title: CD45+ sorted, Patient A (CG); frozen

value: Stomach (fundus)

value: Biopsy

value: CG


title: FGR_SP5_39.6weeks

value: 39.6 weeks


title: FGR_CTB4_37.2weeks


title: FGR_CTB5_39.6weeks


title: FGR_CTB2_30.2weeks

value: 30.2 weeks


title: FGR_SP3_37weeks

value: 37 weeks


title: Control_SP2_34.4weeks

value: Gestation-matched control

value: 34.4 weeks


title: KO Zfc3h1, satellite cells, biol replicate 1, QuantSeq

description: Library name: Z1KOP1-R1

value: muscle

value: Zfc3h1 knockout


title: WT, satellite cells, biol replicate 2, QuantSeq

description: Library name: WTP1-R2


title: FGR_SP2_30.2weeks

value: Side-population


title: C4-2 Cell line ILF2_CLIP_rep2

first: Yanqiang

address: 300 Longwood Ave.

department: Cardiology Department

institute: Boston Children's Hospital

data_processing:
The raw reads with fastq format were aligned to the human reference genome hg19 from iGenome (https://support.illumina.com/sequencing/sequencing_software /igenome.html) using STAR aligner (v2.7.9a) (1). The count number of mapped reads were calculated by htseq-count (v0.11.2) software (2). After mapping, the software REDItoolDnaRna.py from REDItools (v1.3) (3) was used to detect the RNA editing with the C4-2 genome information using the parameters provided by the published protocol (4). For the whole genome sequencing, the raw fastq files were mapped to the human reference genome hg19 with BWA. Sorted bam file was used as the corresponding genome reference of C4-2 for delectation of RNA editing events.
For eCLIP-seq analysis, both STAR (v2.7.9a)[57] with default parameters and UCSC known genes were firstly employed to map the genome hg19, followed by peak calling using CLIP-seq peak caller Piranha with default parameters and bin size=20[64]. To define the RBP binding peaks in each sample, a P-value cutoff of 0.01 was set up. The homer (v4.8.3) annotatePeaks.pl script[65] was then applied to annotate the peaks from the eCLIP-seq data.
Assembly: hg19
Supplementary files format and content: abundance measurements for each sample
Supplementary files format and content: bigwig for each sample

source_name: C4-2 Cell line

growth_protocol: The human prostate cancer cell line C4-2 was a gift from L. Chung at Cedars-Sinai Medical Center and were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS). The cells were maintained at 37 °C and 5% CO2 in a humidified atmosphere and were authenticated and routinely screened for Mycoplasma.

extract_protocol:
Total RNA (n=4 for siCTRL, n=4 for siEZH2, n=6 for siADAR1 and n=5 for siADAR2) was isolated from C4-2 cells using RNeasy Plus Mini Kit (Qiagen) and subjected to BGI for library preparation and sequencing using the DNBseq platform. Meanwhile, the genomic DNA was extracted from C4-2 cells using Quick-DNA Kit (Zymo Research) and subjected to BGI for human true PCR-free 30x coverage WGS.
The eCLIP-seq experiment was performed in duplicates following the method described previously[63]. For each sample, a total of 50 million C4-2 cells were crosslinked, lysed and partially digested by RNase I (Thermo Fisher). The resulting lysates were incubated with the antibody of interested RBP and Protein A/G magnetic beads (Pierce) at 4 ºC overnight, followed by washing, end repair and 3′ adaptor ligation. The protein-RNA complexes were then eluted from the beads, resolved by denaturing gel electrophoresis and transferred to a nitrocellulose membrane. Subsequently, the region of interest was cut from membrane and subjected to RNA extraction, cDNA synthesis and library preparation. The cDNA library was further amplified using Q5 PCR Master Mix (NEB) and sent to BGI for sequencing using the DNBseq platform.
For high-throughput sequencing of RNA-seq, DNA-seq, input and CLIP RNA samples were shipped to BGI for library preparation and sequencing using the DNBseq platform.

value: C4-2 Cell line

value: prostate cancer

tag: antibody


title: C4-2 Cell line ILF2_input_rep1

value: input


title: Gh_cond_pH4_rep3

value: Leaf blade

value: Gossypium hirsutum L.

value: pH 4


title: FGR_CTB3_37weeks

value: Fetal Growth Restricted

value: Cytotrophoblast


title: C4-2 Cell line EZH2_CLIP_rep2


title: Gh_cond_pH4_rep1


title: Gh_cond_pH2_rep3

value: pH 2


title: WT, satellite cells, biol replicate 1, QuantSeq

description: Library name: WTP1-R1

value: satellite cell

value: WT


title: Gh_cond_Control_rep2

value: Dry control


title: Gh_cond_Control_rep1


title: C4-2 Cell line ADAR_input_rep1


title: C4-2 Cell line siCTRL_rep2

description: CTRL_2rep_EZH2_2rep_ADAR1_4rep_ADAR2_5rep.count.txt

value: siCTRL


title: C4-2 Cell line ADAR_CLIP_rep1

value: anti-ADAR


title: C4-2 Cell line siCTRL_rep1


title: C4-2_genome

data_processing:
The raw reads with fastq format were aligned to the human reference genome hg19 from iGenome (https://support.illumina.com/sequencing/sequencing_software /igenome.html) using STAR aligner (v2.7.9a) (1). The count number of mapped reads were calculated by htseq-count (v0.11.2) software (2). After mapping, the software REDItoolDnaRna.py from REDItools (v1.3) (3) was used to detect the RNA editing with the C4-2 genome information using the parameters provided by the published protocol (4). For the whole genome sequencing, the raw fastq files were mapped to the human reference genome hg19 with BWA. Sorted bam file was used as the corresponding genome reference of C4-2 for delectation of RNA editing events.
For eCLIP-seq analysis, both STAR (v2.7.9a)[57] with default parameters and UCSC known genes were firstly employed to map the genome hg19, followed by peak calling using CLIP-seq peak caller Piranha with default parameters and bin size=20[64]. To define the RBP binding peaks in each sample, a P-value cutoff of 0.01 was set up. The homer (v4.8.3) annotatePeaks.pl script[65] was then applied to annotate the peaks from the eCLIP-seq data.
Assembly: hg19
Supplementary files format and content: abundance measurements for each sample
Supplementary files format and content: bigwig for each sample
Library strategy: DNA-seq


title: FGR_SP1_38.3weeks

value: 38.3 weeks


title: C4-2 Cell line ILF2_input_rep2


title: C4-2 Cell line ILF2_CLIP_rep1


title: C4-2 Cell line EZH2_input_rep2


title: C4-2 Cell line EZH2_input_rep1


title: Gh_cond_Control_rep3


title: C4-2 Cell line EZH2_CLIP_rep1


title: C4-2 Cell line siADAR1_rep2


title: C4-2 Cell line siEZH2_rep2_6h


title: C4-2 Cell line ADAR_input_rep2


title: C4-2 Cell line ADAR_CLIP_rep2


title: C4-2 Cell line siADAR2_rep3


title: C4-2 Cell line siEZH2_rep2


title: C4-2 Cell line siEZH2_rep1


title: C4-2 Cell line siADAR2_rep5


title: C4-2 Cell line siCTRL_rep2_6h


title: C4-2 Cell line siADAR2_rep4


title: C4-2 Cell line siADAR2_rep2


title: C4-2 Cell line siCTRL_rep2_3h


title: C4-2 Cell line siADAR2_rep1


title: C4-2 Cell line siCTRL_rep2_0h


title: C4-2 Cell line siEZH2_rep2_3h


title: C4-2 Cell line siADAR1_rep1


title: C4-2 Cell line siADAR1_rep3


title: Gh_cond_pH6_rep3


title: C4-2 Cell line siEZH2_rep2_24h


title: C4-2 Cell line siCTRL_rep1_24h


title: C4-2 Cell line siEZH2_rep2_0h


title: C4-2 Cell line siEZH2_rep1_6h


title: C4-2 Cell line siEZH2_rep1_12h


title: C4-2 Cell line siEZH2_rep1_3h


title: C4-2 Cell line siEZH2_rep1_24h


title: C4-2 Cell line siCTRL_rep1_0h


title: C4-2 Cell line siADAR1_rep2_24h


title: C4-2 Cell line siEZH2_rep1_0h


title: C4-2 Cell line siADAR1_rep1_6h


title: C4-2 Cell line siADAR1_rep4


title: C4-2 Cell line siCTRL_rep2_24h


title: C4-2 Cell line siADAR1_rep1_3h


title: C4-2 Cell line siADAR1_rep1_12h


title: C4-2 Cell line siCTRL_rep1_6h


title: C4-2 Cell line siADAR1_rep1_0h


title: C4-2 Cell line siEZH2_rep2_12h


title: C4-2 Cell line siCTRL_rep1_12h


title: C4-2 Cell line siCTRL_rep1_3h


title: NIH/3T3, Sox5 KO, Serum starvation 24 h, rep2

first: Weihua

last: Wang

address: No.8, Sanjiaohu Rd

institute: Jianghan University

description: Library name: Sample 10

data_processing:
The raw sequencing reads were mapped to the Mus musculus reference genome (GRCm39/mm39) using HISAT2 (v2.1.0).
StringTie (v1.3.3b) was subsequently used to assemble the mapped reads.
Gene expression levels were quantified as fragments per kilobase of transcript per million fragments mapped (FPKM).
Differential expression analysis between experimental groups was performed using DESeq2 (v1.12.4).
Assembly: GRCm39/mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: The NIH/3TT3 was cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% calf serum (CS) and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was extracted from the samples using the TRIzol reagent (Invitrogen).
RNA libraries for sequencing were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions.

treatment_protocol: NIH/3T3 cells were seeded at a low density and grown for 24 hours in standard medium, after which the medium was switched to serum-free DMEM for an additional 24 hours of culture.

value: mouse embryonic fibroblast

value: Sox5 KO

value: Serum Starvation for 24 h


title: NIH/3T3, Nono KO, Serum starvation 24 h, rep1

description: Library name: Sample 6

value: Nono KO


title: NIH/3T3, Xap5 KO, Serum starvation 24 h, rep1

description: Library name: Sample 3

value: Xap5 KO


title: NIH/3T3, WT, Serum starvation 24 h, rep1

description: Library name: Sample 1


title: C4-2 Cell line siADAR1_rep2_3h

value: C4-2 Cell line

value: prostate cancer


title: C4-2 Cell line siADAR1_rep2_0h


title: C4-2 Cell line siADAR1_rep2_6h


title: C4-2 Cell line siADAR1_rep2_12h


title: WT lung, 7 days after bleomycin administration-01-03

city: Hiroshima

first: Arisa

last: Hamada

state: Hiroshima

address: Kasumi, Minami-ku,

department: Department of Molecular and Internal Medicine

institute: Graduate School of Biomedical and Health Sciences, Hiroshima University

description: Library name: WT-d7-01-03

data_processing:
Read1 (barcode read) was extracted by using UMI-tools (ver.1.1.1) with the following command “umi_tools extract -I read1.fastq --read2-in=read2.fastq --bc-pattern=NNNNNNNNNNCCCCCCCCC --read2-stdout ”.
Adaptor sequence and low quality sequence were removed and read length below 20bp were discarded by using Trim Galore (ver. 0.6.7).
Reads were mapped to the GRCm39 reference using HISAT2 (ver. 2.2.1).
Gene count was obtaind by featureCounts(ver.2.0.1) and UMI duplication was ramoved by using UMI tools (ver.1.1.1).
Assembly: GRCm39
Supplementary files format and content: compressed tab separated files(.tsv.gz, .txt.gz)

source_name: lung

extract_protocol:
Total lung RNA of WT and KO mice  were homogenized using 1 mL TRIzol reagent (Life Technologies) and total RNA was extracted using the RNeasy Mini Kit (Qiagen). 180ng of total RNA was used for the construction of sequencing libraries.
Libraries were prepared by BRB-Seq(Alpern D, et al.) method. Individual samples were reverse transcribed using dT primer with unique cell barcodes. Then replicate were mixed and amplified by PCR. 10nt of UMI followedby 9nt of cell barcode are in read1 and 81nt of RNA insert reads are in read2.

value: lung

value: bleomycin administration


title: C4-2 Cell line siCTRL_rep2_12h


title: miR26a-KO lung, 7 days after bleomycin administration-01-03

description: Library name: KO-d7-01-03

value: miR-26a KO


title: CD4+ Treg cells extracted from the CD4+ full dataset

city: Prague

first: Veronika

last: Niederlova

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the Czech Academy of Science

description:
Library name: cd4_l3_treg.rds
ScRNAseq data from multiple batches and multiple participants. For details please see the metadata of the .rds file or the associated Zenodo and Github repositories.

data_processing:
The count matrices were generated by 10x Cell Ranger 5.0.1 Software (count tool) and pre-processed using Seurat 4.3.1 package 114 on R 4.2.1. Any cell that was not marked by any expected combination of hashtags was removed. All cells with more than 10% of genes mapping to mitochondrial genes, those expressing less than 200 genes and those that were marked as doubles according to the V(D)J (more than 2 TCRα or more than 1 productive TCRβ sequence present) were excluded during initial object creation. Mitochondrial genes, ribosomal genes, genes encoding TCR variable segments (any gene symbol containing the TR[AB][VDJ] substring) and genes present in less than 3 cells were removed. Batches were integrated using STACAS. Detailed methods can be found in the publication, all scripts are available on Github: https://github.com/Lab-of-Adaptive-Immunity/dia.
Assembly: GRCh38
Supplementary files format and content: Processed data contain Seurat objects with all metadata.

source_name: PBMC

extract_protocol:
Three to ten mL of peripheral blood were collected into EDTA-coated tubes, kept on ice, and transferred from Motol University Hospital to the Institute of Molecular Genetics within two hours. PBMCs were separated using Ficoll-Paque (GE Healthcare) and immediately frozen following a cryopreservation protocol (10x Genomics). PBMCs were then gently thawed by slow, sequential dilution in RPMI medium containing 10% FBS. Cells were labeled with TotalSeq-C hashtags and flow cytometry antibodies. In initial experiments, we sorted CD4+ and CD8+ T cells. In final experiments, non-naïve cells were enriched as follows: from each sample 1 000 naïve (CCR7+ CD45RA+) and 5 000 antigen-experienced cells were sorted into two tubes, one for CD4+ T cells and one for CD8+ T cells. For detailed methods please refer to the publication.
10x Chromium Single Cell 5’ Library & Gel Bead and Chromium Single Cell 5' Feature Barcode Library kits (10x Genomics, #PN-1000014, #PN-1000020, #PN-1000080, #PN-1000009, #PN-1000084)

value: PBMC

value: T cell

value: CD4+ T cell


title: NIH/3T3, Sox5 KO, Serum starvation 24 h, rep3

description: Library name: Sample 11


title: Nnt-wt mouseID=MYW22

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

data_processing:
RNA preparation, library construction, sequencing on NovaSeq 6000 platform and raw data filtering was performed by Novogene (China).
Reads were aligned to the mouse genome (Mus_musculus.GRCm39.108) using STAR  (-runThreadN 2 --genomeDir --readFilesIn  --readFilesCommand gunzip -c --outFileNamePrefix  --outSAMtype BAM SortedByCoordinate --outSAMunmapped None --outSAMattrIHstart 0 --outFilterType BySJout --sjdbGTFfile /Mus_musculus.GRCm39.108.gtf --quantMode TranscriptomeSAM
Reads were quantified using HTSeq
Assembly: Mus_musculus.GRCm39.108
Supplementary files format and content: Raw counts using HTSeq

source_name: Gastrocnemius muscle

extract_protocol:
Mice were killed by cervical dislocation. Gastrocnemius was isolated, snap frozen in liquid nitrogen and stored at -80°C until further analysis. Total RNA was extracted by grinding frozen muscle tissue and dissolving approximately 15 mg in 1 ml Trizol. Further RNA isolation was performed according to manufacture's  instructions (Thermo Fisher). RNA concentration was measured using NanoDrop one spectrophotometer (Thermo Fisher). RNA integrity was measured using RNA Screentape on the 2200 Tapestation (Agilent).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dUTP for directional library. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification(In-house kit: Novogene NGS Stranded RNA Library Prep Set (PT044)). The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms (NovaSeq 6000 platform using S4 flow cells), according to effective library concentration and data amount.

treatment_protocol: Gene expression profiles from gastrocnemius of 24-day-old Nnt-wt and Nnt-mut male mice were compared. Mice were weaned on 21 days and had ad libitum access to chow diet and water. Mice were killed in the first half light phase.

value: Gastrocnemius muscle

tag: Sex

value: male

tag: strain

value: Nnt-wt

tag: age

value: 24 days


title: CD4+ T cells sorted from PBMC of children with T1D and healthy donors

description:
Library name: cd4_l1_full_filt.rds
ScRNAseq data from multiple batches and multiple participants. For details please see the metadata of the .rds file or the associated Zenodo and Github repositories.


title: NIH/3T3, Nono KO, Serum starvation 24 h, rep2

description: Library name: Sample 7

value: mouse embryonic fibroblast


title: NIH/3T3, Xap5 KO, Serum starvation 24 h, rep3

description: Library name: Sample 5


title: NIH/3T3, Nono KO, Serum starvation 24 h, rep3

description: Library name: Sample 8


title: NIH/3T3, Sox5 KO, Serum starvation 24 h, rep1

description: Library name: Sample 9

value: Sox5 KO


title: Nnt-wt mouseID=MYW21


title: CD8+ T cells sorted from PBMC of children with T1D and healthy donors

description:
Library name: cd8_l1_full_filt.rds
ScRNAseq data from multiple batches and multiple participants. For details please see the metadata of the .rds file or the associated Zenodo and Github repositories.

value: CD8+ T cell


title: NIH/3T3, Xap5 KO, Serum starvation 24 h, rep2

description: Library name: Sample 4

value: Serum Starvation for 24 h


title: Nnt-wt mouseID=MYW20


title: NIH/3T3, WT, Serum starvation 24 h, Nono

description: Library name: SAMPLE 2

data_processing:
Raw reads were assessed for quality with FastQC (v0.11.9) and trimmed with fastp (v0.20.0; parameters: --length_required 15, --n_base_limit 6).
Clean reads were aligned to the Mus musculus reference genome (mm39) using BWA-MEM (v0.7.12; parameters: -k 32, -T 30, -M).
Peak calling was performed using MACS2 (v2.1.0) with a q-value threshold of 0.05 and the following parameters: -f AUTO --call-summits --nomodel --shift -100 --extsize 200 --keep-dup all.
Peak annotation and association with the nearest genes were performed using the ChIPseeker R package.
Assembly: GRCm39
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

extract_protocol:
Following a 24-hour starvation period, NIH/3T3 cells were harvested using 0.25% Trypsin-EDTA. Cell viability was assessed using a hemocytometer with Trypan Blue staining. Only cell suspensions with a viability of 90% or greater were carried forward for CUT&Tag library preparation. A total of 100,000 viable cells were used as input for each CUT&Tag reaction.
CUT&Tag libraries for sequencing were prepared according to the manufacturer’s protocol using Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme).

value: Nono


title: NIH/3T3, WT, Serum starvation 24 h, rep2

description: Library name: Sample 2

value: WT