title: 42,Mithra,rep1,IgG

description: Library name: 42,Mithra,rep1,IgG


title: MitoRibo_C2C12_2

status: Public on Jun 05 2026

type: SRA

city: Wako city

first: Taisei

last: Wakigawa

state: Saitama prefecture

address: 2-1, Hirosawa

country: Japan

institute: RIKEN

description: Library name: L26

library_source: other

data_processing:
Basecalling with Illumina Casava 1.8 software
Base correction, filtering, 3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Assembly: Read quantitation using custom scripts
Supplementary files format and content: The human or mouse nuclear genomes (human, hg38; mouse, mm10) and custom-made mitochondrial transcript sequences
Supplementary files format and content: Fpframing text files contain nine columns:  1. the length of ribosome footprint; 2. the fraction of ribosome footprint; 3~5. the number of ribosome footprint at each frames;  6~8,the fraction of ribosome footprint at each frames; 9. the relative entropy of ribosome footprint.
Library strategy: MitoIP-Thor-Ribo-Seq

molecule: other

organism: Mus musculus

extract_protocol:
MitoIP-Thor-Ribo-Seq and MitoIP-Thor-Disome-Seq: Cells were cultured in 15-cm dishes, washed with ice-cold PBS, and lysed with 1200 µl of hypotonic buffer (10 mM HEPES-KOH pH 7.5, 10 mM KCl, 1.5 mM MgCl2, 1 mM DTT, 100 µg/ml cycloheximide, and 100 µg/ml chloramphenicol). The lysate was incubated with anti-TOM22 antibody-conjugated beads from Mitochondria Isolation Kit, Human (Miltenyi Biotec) for 60 min at 4°C. The subsequent wash and elution steps were performed with wash buffer (10 mM HEPES-KOH pH 7.5, 10 mM KCl, 15 mM MgCl2, 1 mM DTT, 100 µg/ml cycloheximide, and 100 µg/ml chloramphenicol), according to the manufacturer’s instructions. The eluted mitochondrial fraction was pelleted by centrifugation at 7,000 × g for 10 min at 4°C and resuspended in modified lysis buffer (20 mM Tris-HCl, pH 7.5, 150 mM NaCl, 15 mM MgCl2, 1 mM DTT, 1% Triton X-100, 100 µg/ml cycloheximide, 100 µg/ml chloramphenicol, and 2.5 U/ml TURBO DNase). After clarification by centrifugation at 20,000 × g for 10 min at 4°C, the supernatant was used for library preparation. Ribo-Seq and RNA-Seq: Cells in a 10-cm dish were lysed with 600 µl of lysis buffer (20 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1% Triton X-100, 1 mM DTT, 100 µg/ml cycloheximide, and 100 µg/ml chloramphenicol) and treated with 25 U/ml TURBO DNase (Thermo Fisher Scientific). Then, the lysate was clarified by centrifugation at 20,000 × g for 10 min at 4°C.
MitoIP-Thor-Ribo-Seq and MitoIP-Thor-Disome-Seq: preadenylated linkers with the antisense sequence of T7 promoter were ligated and footprints were amplified by in vitro transcription. RNA-seq: the libraries were prepared by a SEQuoia Express Standard RNA Library Prep Kit (Bio-Rad).

tag: cell line

tag: cell type

value: Naive


title: AL_054

city: Pittsburgh

first: Neil

last: Carleton

state: PA

address: 5051 Centre Ave

department: Pharmacology & Chemical Biology

country: USA

institute: University of Pittsburgh

library_source: transcriptomic

data_processing:
For processing, we used Rsubread (Bioconductor release 2.16) to align sequence reads to reference genome and used edgeR and limma R packages (Bioconductor release 4.0 and 3.58 respectively) to normalize gene expression level to log2 transcripts per million (TPM)
Assembly: We aligned sequence reads to GRCh38 release 14 human genome reference sequence and mapped the aligned sequences to Entrez Genes
Supplementary files format and content: After normalization, we removed genes of which expression level is zero across all samples to get 39,404 genes for further pathway analysis.

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
We used the standard procedure of RNeasy kit to extract total RNA from ER+ breast cancer samples of 83 tumor or 85 tumor-adjacent normal tissue obtained from Pitt Biospecimen Core (PBC) and grouped them by chronological age.
The NovaSeq 6000 library for DNA sequencing was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) following the protocol provided by the manufacturer.
Library size and quality were checked using Fragment Analyzer (Agilent) and fluorescent quantification on the Infinite F Nano + (Tecan). The libraries were normalized and pooled, and then sequenced using the NovaSeq 6000 Platform (Illumina) to an average of 25M 101 PE reads. Sequencing data was given as raw data with a Phred Q30 score of 80 or better.

tag: tumor or adjacent

tag: agerange

value: Middle

tag: chronologicalage

tag: read length


title: dose1_3h_MOD268_muscle

type: RNA

city: Lausanne

first: Gustavo

middle: Agustín

last: Ruiz Buendía

state: Vaud

address: Amphipôle, Quartier UNIL-Sorge

country: Switzerland

institute: Swiss Institute of Bioinformatics

description: See sample Dose, Time point, and Batch for experimenal condition.

hyb_protocol: Hybridization was performed per the manufacturer’s instructions for Gene Expression Panels with Panel Plus/CodeSet with CodeSet Plus. Briefly, Hybridization was set up with 5 mcL of sample (100 ng of RNA), which was added to 10 mcL of hybridization master mix (5 mcL of hybridization buffer + 3 mcL of Reporter CodeSet + 2 mcL of Reporter Plus) + 3 mcL of Capture Maser Mix. The total hybridization volume was 18uL per sample. Each cartridge was hybridized for 18 hours on a thermal cycler set to 65℃ with a lid heated to 70℃.

scan_protocol: Cartridges were then analyzed on the nCounter Pro Analysis System

data_processing: Nanostring Data was analyzed by ROSALIND (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step. Normalization, fold changes, and p-values were calculated using criteria provided by Nanostring.

label: NanoString

molecule: total RNA

source_name: Muscle

label_protocol: standard protocol

growth_protocol: Muscle samples were collected from mice, at multiple time points after 1 dose or 2 doses of a COVID-19 mRNA vaccine. Samples were snap-frozen and stored at -80ºC.

extract_protocol: Tissues were lysed and homogenized in Trizol using Precellys bead mill homogenizer and CK14 tubes (Bertin). RNA extraction was done using the Rneasy midi kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: C57BL/6J mice were vaccinated intramuscularly with 1 dose or 2 doses (21 days apart) of 1 µg of a COVID-19 mRNA vaccine.

tag: tissue

value: Muscle

tag: group

tag: dose

tag: time point

tag: batch


title: dose1_3h_MOD267_muscle


title: 42,DMSO,rep1,IgG

city: Miami

first: Felipe

last: Beckedorff

state: FL

address: 1501 NW 10th Avenue room 731.G , Miami, FL

institute: University of Miami

description: Library name: 42,DMSO,rep1,IgG

library_source: genomic

data_processing:
Paired-end FASTQ reads were trimmed with Trim Galore (version 0.6.10) using paired-end mode. Trimmed reads were aligned to the GENCODE human hg38/GRCh38 primary assembly genome using STAR (version 2.7.10b). Reads overlapping ENCODE blacklist regions were removed using bedtools intersect (version 2.31.1) with the hg38 blacklist BED file provided by ENCODE. BAM files were converted, sorted, and indexed with samtools (version 1.6). Read groups were added with Picard AddOrReplaceReadGroups, and duplicate reads were removed with Picard MarkDuplicates (version 3.3.0) using "REMOVE_DUPLICATES=true". Filtered BAM files were used for peak calling with MACS3 (version 3.0.1). Peaks were called as narrow peaks using paired-end BAM mode ("-f BAMPE"). Matched input BAM files were provided as controls for each ChIP sample using the MACS3 "-c" flag. BigWig tracks were generated from filtered BAM files using deepTools bamCoverage (version 3.5.5), with CPM normalization.
Assembly: hg38
Supplementary files format and content: bigwig

molecule: genomic DNA

growth_protocol: Lf-C2 and Lf-4-2 cells were grown in Fibroblast Basal Medium supplemented with Fibroblast Growth Kit-Low serum and were maintained at 37°C, 100% humidity, and 5% CO2

extract_protocol:
ChIP-seq was performed as per the manufacturer’s protocol (CST, catalog #: 9003) with modifications. Briefly, Lf-C2 and Lf-4-2 cells were treated with either DMSO or 300 nM Mithramycin A for 24 hours. Cells were crosslinked with Cross-link Gold (Diagenode, catalog #: C01019027), followed by 1% formaldehyde for 10 mins at room temperature. Fixed cells were enzymatically digested and sonicated. 750 µg of protein was incubated with anti-EGR1 (Bethyl, catalog #: A303-390A, 45 µg) or control IgG (CST, catalog #: 2729) overnight at 4°C with rotation. The antibody-bound chromatin was immunoprecipitated by protein G magnetic beads and eluted. After reversal of the crosslink, the DNA was purified, and sequencing was performed at the OncoGenomics Shared Resources (OGSR) of the Sylvester Comprehensive Cancer Center.
ChIP-seq libraries were prepared using the KAPA HyperPrep Kit (Roche, Cat # 07962363001). In brief, immunoprecipitated DNA fragments (IP frags) were quantified and qualitatively assessed on the ThermoFisher QuBit Fluorometer’s High Sensitivity DNA (cat. Q32855) and Agilent Femto Pulse Ultra Sensitivity NGS kits (cat. FP-1101-0275), respectively. Input of IP frags. were between 0.17 and 25 ng. HyperPrep kit was used for end repair, A-tailing and adapter ligation followed by PCR amplification. Finished libraries were quantified and qualitatively assessed on the ThermoFisher QuBit using Fluorometer’s High Sensitivity DNA (Cat #Q32855) and Agilent Fragment Analyzer High Sensitivity NGS kits (Cat # DNF-474-0500) prior to normalization and pooling in preparation for sequencing.. Pooled libraries were sequenced using paired-end 150 base pair chemistry on an Illumina NovaSeq X Plus instrument. Targeted average sequencing depth for ChIP-seq broad peak was 30 million clusters per library.

value: human lung fibroblast cell line

tag: genotype

tag: treatment

value: DMSO


title: MitoRibo_C2C12_1

description: Library name: L25


title: C2,Mithra,rep1,IgG

description: Library name: C2,Mithra,rep1,IgG

treatment_protocol: Lf-C2 and Lf-4-2 cells were treated with either DMSO or 300 nM Mithramycin A for 24 hours

value: WT

value: 300 nM Mithramycin


title: AL_053

source_name: BreastTumor

value: Tumor


title: dose1_3h_MOD266_muscle


title: AL_052


title: Aged HSPCs treated with uridine [C_3]

city: Hangzhou

first: Xiangjun

last: Zeng

address: Zhejiang univerisity

country: China

institute: Zhejiang univerisity

data_processing:
After quality control, paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Assembly: mm10
Supplementary files format and content: gene_count.xls: Excel file includes count values for each Sample.

source_name: bone marrow

extract_protocol:
RNA of cultured cells was extracted using Trizol.
Library construction and sequencing were performed by Novogene Corporation. In short, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads and Illumina NovaSeq 6000 was applied to generate the end reading of 150bp pairing.

value: bone marrow

value: Aged HSPC

tag: strain

value: uridine


title: dose2_3h_MOD265_muscle


title: C2,DMSO,rep1,IgG

description: Library name: C2,DMSO,rep1,IgG


title: Aged HSPCs treated with uridine [C_2]


title: AL_051


title: 42,Mithra,rep3,EGR1

description: Library name: 42,Mithra,rep3,EGR1


title: dose2_3h_MOD264_muscle


title: AB789_Roi-thymo-3h-3_phago_3

city: Tel Aviv

first: Merav

last: Cohen

address: Chaim Levanon St 55

department: Clinical microbiology and immunology

country: Israel

institute: Tel Aviv University

description:
Library name: AB789
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad

library_source: transcriptomic single cell

data_processing:
We generated FASTQ files from the raw BCL files using the bcl2fastq software provided by Illumina (v.2.20.0.422) with default parameters.
Sequences were mapped to the mouse genome (GRCm39) using STAR (v.2.7.1a). Reads with multiple mapping positions were excluded. We then assigned gene names for exonic, genomic and mitochondrial regions using featureCounts (v.2.0.0), processed the resulting BAM file using samtools (v.1.10) and finally created gene-cell UMI matrices using the UMI-tools software package (v.1.1.2). Using the Scanpy package (v.1.9.8), we loaded these files to a unified data object.
We performed QC by excluding cells with <500 or >10,000 UMIs, >30% mitochondrial genes or >1 UMIs of hemoglobin genes. We also excluded cells from the in vitro model with any expression of T cell genes (Tcf7, Trbc2, Cd3d, Trbc1, Cd3g, Cd3e, Trac, Cd8b1) and from the in vivo lung model with >1 UMIs of endothelial genes (Pecam1, Cdh5, Col4a1, Plvap).
Assembly: GRCm39
Supplementary files format and content: h5ad files - unified post-QC scRNA-seq data, containing a gene-cell UMI matrix
Supplementary files format and content: csv files - flourescence intensity data where relevant (pHrodo+ cells)

source_name: in-vitro

growth_protocol: All mice were maintained under specific pathogen-free conditions

extract_protocol:
in-vitro: For macrophage-thymocyte co-culture, BM-derived macrophages were washed with cold PBS and seeded in 24-well plates at 2.5 x 105 cells per well in culture medium supplemented with 10 ng/ml M-CSF and incubated at 37 °C for 3 hours to settle. pHrodo-labeled apoptotic thymocytes were added to the BM-derived macrophages at 1.25 x 106 cells per well. Cells were co-cultured for 3 or 24 hours before they were collected by gentle scraping. in-vivo lung: To obtain single cell suspensions of lungs from mice inoculated with apoptotic thymocytes or PBS, the mice were perfused with PBS through the right ventricle. Lungs were dissociated using the mouse lung dissociation kit (Miltenyi Biotec) according to the manufacturer’s instructions with the following modifications: After mechanical dissociation using the gentleMACS dissociator program “m_lung_01”, lungs were incubated at 37 °C for 10 minutes with agitation. The sample was subsequently pipetted through 16G, 18G and 19G needles and then incubated again at 37 °C for 10 minutes with agitation and then washed with ice-cold sorting buffer (PBS supplemented with 0.2 mM EDTA, pH 8 and 0.5% BSA), filtered through a 100-µm cell strainer and pelleted. B16: To obtain single cell suspensions of B16 tumors, the tumors were removed and weighed using an analytical scale, and then placed in RPMI-1640 supplemented with DNase (28 μg/ml, Sigma-Aldrich) and collagenase IV (1 mg/ml, Worthington). Tissues were incubated at 37 °C for 10 minutes with agitation and then pipetted through 16G, 18G, 19G and 21G needles before they were incubated again at 37 °C for 10 minutes with agitation. Cell suspensions were then washed with cold sorting buffer and pelleted.
The library preparation was conducted following the previously reported protocol {Jaitin, 2014}. In brief, mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol {Jaitin, 2014}. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.

value: in-vitro

value: phago


title: Aged HSPCs treated with uridine [C_1]


title: AL_050


title: AL_070


title: Aged HSPCs treated with vehicle [A_3]

value: vehicle


title: dose2_3h_MOD263_muscle


title: 42,DMSO,rep3,EGR1

description: Library name: 42,DMSO,rep3,EGR1


title: AL_049


title: dose1_1h30_MOD262_muscle


title: C2,Mithra,rep3,EGR1

description: Library name: C2,Mithra,rep3,EGR1


title: Aged HSPCs treated with vehicle [A_2]


title: dose1_1h30_MOD261_muscle


title: AL_048


title: Control-2 Treatment

city: Chengdu

first: xiumei

last: luo

address: Shuangliu

department: Institute of Urban Agriculture

institute: Chinese Academy of Agricultural Sciences

description:
Library name: CK_2
Control rice leaves without Cd or SeNP exposure

data_processing:
StringTie v2.2.1 was used to assemble transcripts and estimate expression levels in transcripts per million (TPM) for each sample.
Differential gene expression between treatment groups was identified using DESeq2 v1.34.0 with a false discovery rate (FDR) cutoff of 0.05 and fold-change threshold of 2.
Clean reads were mapped to the Oryza sativa reference genome using HISAT2.
Differentially expressed genes were annotated using BLASTP against the NCBI non-redundant protein database and assigned GO terms using InterProScan.
Assembly: Oryza_sativa.IRGSP-1.0
Supplementary files format and content: Processed RNA-seq data are provided as gene-level expression matrices. Raw sequencing reads were quality-filtered, and clean reads were mapped to the Oryza sativa IRGSP-1.0 reference genome. Gene expression levels were quantified as normalized counts and FPKM values. The final processed dataset includes a tab-delimited matrix containing gene IDs, gene expression values across all samples, and corresponding sample annotations for control, Cd, SeNPs, and Cd + SeNP treatments. Differential expression results (log₂ fold change, p-values, and adjusted p-values) are also included for comparative analysis between treatment groups

organism: Oryza sativa

source_name: leaves

growth_protocol: Rice (Oryza sativa L. cv. Quan Youde Zhan) seeds were surface sterilized with 5% H₂O₂ for 10 min and rinsed thoroughly with sterile distilled water. Seeds were germinated in darkness at 25°C and transferred to hydroponic culture in 1/4 Kimura nutrient solution for 7 days, followed by 1/2 strength solution for another 7 days under controlled growth conditions (25°C, 16 h light/8 h dark photoperiod, 400 μmol m⁻² s⁻¹ light intensity, and 75% relative humidity, pH 6.0).

extract_protocol:
Total RNA was extracted from rice leaf tissues using a commercial plant RNA extraction kit following the manufacturer’s instructions. RNA quality and integrity were assessed using agarose gel electrophoresis and a NanoDrop spectrophotometer, and RNA concentration was further verified using a Qubit fluorometer. High-quality RNA samples were used for cDNA library construction and subsequent Illumina sequencing.
High-quality total RNA was used for cDNA library construction following the Illumina TruSeq RNA sample preparation protocol. mRNA was enriched using poly(A) selection and fragmented into short fragments. First-strand and second-strand cDNA were synthesized, followed by end repair, A-tailing, and adapter ligation. The ligated products were purified and amplified by PCR to generate sequencing-ready libraries. Library quality and fragment size distribution were assessed before sequencing on an Illumina platform.

treatment_protocol: Three-week-old rice seedlings were transferred to full-strength Kimura nutrient solution and exposed to cadmium and selenium nanoparticles under hydroponic conditions. Cadmium stress was applied using 10 mg/L CdCl₂·2.5H₂O after preliminary toxicity screening. Selenium nanoparticle (SeNPs) treatments were applied at 1, 3, and 5 mg/L, both alone and in combination with 10 mg/L Cd. Untreated plants served as the control. All treatments were maintained under controlled growth conditions, and leaf samples were collected at the 6-leaf stage (1.5 months) for RNA sequencing analysis.

value: leaves

value: whole leaf

value: Quan Youde Zhan

value: control (0 mg/L CdCl₂)


title: Aged HSPCs treated with vehicle [A_1]


title: C2,DMSO,rep3,EGR1

description: Library name: C2,DMSO,rep3,EGR1


title: AL_047

value: Middle


title: 200 aureobasidin, time 4

city: Indianapolis

first: David

last: Cooper

state: IN

address: 350 PHSB, 4600 Sunset Ave.

institute: Butler University

description:
Library name: LL-11
Sequenced by Novogene

data_processing:
Demultiplex bioreplicates, using cutadapt (parameters: --pair-adapters, -a biorep_bc.fa, -G biorepRev_bc.fa, -e 0.15, --max-ee 2)
Cut adapter sequences and filter by read length, using cutadapt (parameters: --pair-filter any, minimum-length 73)
Quantify sequence abundance using STAR (parameters: quantMode GeneCounts, --outFilterMismatchNmax 0)
Assembly: RulesLibrary.fasta (supplementary file, containing the designed TAD sequences)
Supplementary files format and content: tab-delimited TXT file, containing a matrix of pseudocounts of each sequence in each biorep

organism: Saccharomyces cerevisiae

source_name: Y2H Gold Yeast Cell Strain

growth_protocol: The cell culture was grown in -trp synthetic yeast growth medium containing 200 mig/mL aureobasidin, and grown for four days with daily 1/100 dilution to maintain the culture in mid-log phase.

extract_protocol:
Samples were taken at 0, 0.5, 1, 2, and 3 days. DNA was isolated with a Thermo Scientific Pierce Yeast DNA Extraction Reagent Kit, and the component from the library was isolated by PCR with the Invitrogen AccuPrime SuperMix I kit.
Designed sequences were provided as an Excel file to GenScript. The sequence pool was synthesized by massive parallel synthesis, stripped from the chip, amplified by PCR appending biorep barcodes, cloned into parental vector with estimation of library complexity by manual colony counting. DNA sequencing was conducted by NovoGene.

value: Y2H Gold Yeast Cell Strain

tag: time

value: 72 hours

value: Growth on 200 mM aureobasidin


title: dose1_1h30_MOD260_muscle

value: Muscle


title: AL_046


title: 42,DMSO,rep2,EGR1

description: Library name: 42,DMSO,rep2,EGR1

value: human lung fibroblast cell line

value: DMSO


title: dose2_1h30_MOD259_muscle


title: 200 aureobasidin, time 3

description:
Library name: LL-10
Sequenced by Novogene

value: 48 hours


title: 42,Mithra,rep2,EGR1

description: Library name: 42,Mithra,rep2,EGR1

value: 300 nM Mithramycin


title: dose2_1h30_MOD258_muscle


title: AL_045


title: C2,Mithra,rep2,EGR1

description: Library name: C2,Mithra,rep2,EGR1

value: WT


title: 200 aureobasidin, time 2

description:
Library name: LL-9
Sequenced by Novogene

value: 24 hours


title: AL_044

value: Tumor


title: dose2_1h30_MOD257_muscle


title: C2,DMSO,rep2,EGR1

description: Library name: C2,DMSO,rep2,EGR1


title: 200 aureobasidin, time 1

description:
Library name: LL-8
Sequenced by Novogene

value: 12 hours


title: AL_043


title: naive_0h_MOD280_DLN

data_processing:
Nanostring Data was analyzed by ROSALIND (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step. Normalization, fold changes, and p-values were calculated using criteria provided by Nanostring.
Normalized expression values after performing positive control normalization, background subtraction, and housekeeping gene adjustments.

source_name: Draining lymph node

growth_protocol: Draining lymph node samples were collected from mice, at multiple time points after 1 dose or 2 doses of a COVID-19 mRNA vaccine. Samples were snap-frozen and stored at -80ºC.

value: naive

value: Draining lymph node


title: 150 aureobasidin, time 4

description:
Library name: LL-7
Sequenced by Novogene

value: Growth on 150 mM aureobasidin


title: 42,Mithra,rep1,EGR1

description: Library name: 42,Mithra,rep1,EGR1


title: AL_042


title: naive_0h_MOD279_DLN


title: 42,DMSO,rep1,EGR1

description: Library name: 42,DMSO,rep1,EGR1


title: AL_041


title: C2,Mithra,rep1,EGR1

description: Library name: C2,Mithra,rep1,EGR1


title: baseline_0h_MOD277_DLN

value: baseline


title: whole larval P. promelas, 4-Chlorophenyl methyl sulfoxide, sample12

status: Public on Jun 06 2026

city: Duluth

first: Peter

last: Schumann

state: MN

address: 6201 Congdon Blvd

institute: United States Environmental Protection Agency

description:
Chem8_B_D4_D09
Chem8_counts_matrix.txt

data_processing:
*library strategy: TempO-Seq (Templated Oligo-Sequencing)
Sample-specific TempO-Seq libraries were pooled together and sequenced on an Illumina sequencer (NextSeq 500), 2 × 50 bp, single-end reads, NovaSeq X 10B reagent kits.
Sequence reads were then demultiplexed based on sample-specific barcodes, and a FASTQ file was generated for each sample using Illumina's bcl2fastq conversion software. Resulting TempO-Seq data were analyzed by Biospyder using TempO-SeqR software implemented in R.
The FASTQ files were aligned to the known transcript composition of the reduced transcriptome, and a count table (columns = samples, genes = rows) was generated.
Assembly: GCA_016745375.1
Supplementary files format and content: count matrices with rows as gene features and columns as samples

organism: Pimephales promelas

source_name: whole body

growth_protocol: not applicable

extract_protocol:
Samples were prepared for transcriptomics analysis by homogenization in a protease lysis buffer as directed by BioSpyder Technologies, Inc. Pimephales promelas were homogenized in 75 µL/well with a 2.3 mm stainless steel bead (BioSpec) at 30 Hz for 2 min using a well plate homogenizer (Bead Ruptor 96, OMNI International). Plates were centrifuged for 3 min at 1000 rpm. Homogenates were pooled (excluding any mortalities) by treatment concentration within each plate, resulting in n=3 replicates per treatment, each containing five pooled organisms (Supplementary Figure 2B). The final plates containing pool homogenates were stored at -80ºC until shipped on dry ice to BioSpyder Technologies, Inc. (Carlsbad, CA) for TempO-seq analysis. Test acceptability criteria were met if control survival was >90 %.
TempO-Seq libraries were prepared by ligating detector oligos to corresponding transcripts present in the whole-body homogenates. Quality control and sample quantification were performed with a DeNovix UV-visible spectrophotometer (DeNovix). Ligated transcripts were subjected to polymerase chain reaction amplification, which also introduces adaptors for sequencing and a sample-specific barcode.

treatment_protocol: High-throughput in vivo exposures were conducted in 1 mL 96-well deep well plates (NEST, Catalog #502162) for 24 h. Each exposure consisted of two chemicals tested in a 1/2 log dilution series with five replicates per treatment concentration on each of three plates (15 organisms exposed per concentration). Final exposure concentrations ranged from 66.67 – 0.021 µM for all data poor chemicals, except fipronil amide (56.43- 0.018 µM) and fexofenadine hydrochloride (32.2 – 0.011 µM). All chemical stocks were prepared in DMSO and had purities > 95%. For each exposure, a Tecan D300e Bioprinter (Corvallis, OR, USA) was used to prepare an initial chemical dosing plate containing 1800 µL/well of test solution diluted in UV-treated, filtered Lake Superior Water in a 2 mL 96-well deep well plate (NEST, Catalog #503162). The concentration of DMSO was normalized across all wells to match those of the highest % DMSO obtained with the chemical delivery (i.e., the highest exposure concentration; generally 0.34% DMSO). Using the bioprinter, the dosing solutions were arranged to evenly distribute replicate exposure groups along the edges of the plate to avoid confounding any edge effects, if present, with treatment. For each exposure, one organism was loaded with 150 µL of control water (UV-treated, filtered Lake Superior Water) to each well of the three 96-well plates. A multi-channel pipette was used to deliver 550 µL of dosing solution to each well for a final volume of 700 µL per well. Each assay included DMSO controls, with final in-well DMSO concentrations never exceeding 0.34% in the exposure plate wells.

value: whole body

tag: developmental stage

value: larval

value: 4-Chlorophenyl methyl sulfoxide


title: 150 aureobasidin, time 3

description:
Library name: LL-6
Sequenced by Novogene

value: Y2H Gold Yeast Cell Strain


title: AL_040

value: Young


title: 150 aureobasidin, time 2

description:
Library name: LL-5
Sequenced by Novogene


title: 150 aureobasidin, time 1

description:
Library name: LL-4
Sequenced by Novogene


title: AL_039


title: C2,DMSO,rep1,EGR1

description: Library name: C2,DMSO,rep1,EGR1

value: human lung fibroblast cell line


title: baseline_0h_MOD276_DLN


title: PDO-296, Flex Pool 2 (E2, E2+ICI, E2+HSD17B7i)

description:
Library name: FlexPool2
10x Chromium Flex, multiplexed samples OS05, OS06, OS07 (probe barcodes BC001, BC002, BC003)
AL2_FlexPool_5-7

data_processing:
Cell Ranger multi v9.0.1 was used for demultiplexing, alignment, and per-sample gene counting with filter-probes set to false to retain all probes including HSD17B7.
Quality control filtering: cells with <500 genes, <1000 UMIs, or >15% mitochondrial reads were removed. Doublets were detected and removed using Scrublet.
Normalization and log-transformation (scanpy pp.normalize_total, pp.log1p). HVG selection (2000 genes), PCA (50 components), Harmony batch correction across pools, UMAP visualization, and Leiden clustering.
Pseudobulk differential expression analysis using PyDESeq2 across treatment contrasts.
Assembly: GRCh38-2024-A (custom, with HSD17B7 probe retention)
Supplementary files format and content: MEX format: per-sample filtered feature-barcode matrices (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz) from Cell Ranger multi per_sample_outs.

source_name: breast

growth_protocol: PDO-296 patient-derived breast cancer organoids were maintained in Matrigel domes with organoid culture media as previously described.

extract_protocol:
Organoids were dissociated to single cells, fixed, and processed according to the 10x Genomics Chromium Fixed RNA Profiling (Flex) protocol. Probe hybridization and ligation were performed per manufacturer instructions.
Single-cell gene expression libraries were prepared using the 10x Genomics Chromium Fixed RNA Profiling (Flex) kit with probe set v1.1.0 (GRCh38-2024-A). Samples were multiplexed using probe barcode-based sample indexing. Pool 1 contained samples OS01-OS04 (probe barcodes BC001-BC004) and Pool 2 contained samples OS05-OS07 (probe barcodes BC005-BC007). Libraries were sequenced on an Illumina NovaSeq X Plus with 101 PE reads.

treatment_protocol: Organoids were treated with the following conditions: Vehicle (DMSO), E1 (estrone), E1 + ICI 182,780 (fulvestrant), E1 + HSD17B7 inhibitor, E2 (estradiol), E2 + ICI 182,780, or E2 + HSD17B7 inhibitor.

value: breast

value: organoid

value: E2, E2+ICI, E2+HSD17B7i


title: dose1_4h30_MOD274_DLN


title: Untreated sample, time 2

description:
Library name: LL-3
Sequenced by Novogene

value: Growth on 0 mM aureobasidin


title: dose1_4h30_MOD273_DLN


title: AL_038


title: PDO-296, Flex Pool 1 (Vehicle, E1, E1+ICI, E1+HSD17B7i)

description:
Library name: FlexPool1
10x Chromium Flex, multiplexed samples OS01, OS02, OS03, OS04 (probe barcodes BC001, BC002, BC003, BC004)
AL1_FlexPool_1-4

value: Vehicle, E1, E1+ICI, E1+HSD17B7i


title: Untreated sample, time 1

description:
Library name: LL-2
Sequenced by Novogene


title: AL_037


title: dose2_4h30_MOD271_DLN


title: MitoRibo_HeLa_mtRRF_KO_2

description: Library name: L36

source_name: HeLa

value: HeLa


title: Untreated sample, time 0

description:
Library name: LL-1
Sequenced by Novogene

value: 0 hours


title: AL_036

value: Tumor


title: MitoRibo_HeLa_mtRRF_KO_1

description: Library name: L35


title: IRF8

first: Jesus

last: Corria-Osorio

address: Chemin des Boveresses 155

department: Department of Fundamental Oncology

institute: Ludwig Institute for Cancer Research. Lausanne Branch. UNIL

description:
Library name: IRF8
CUT&RUN antibody: anti-IRF8

data_processing:
CUT&RUN: Raw sequencing reads were quality-checked using FastQC. Reads were aligned to the mouse reference genome (GRCm38/mm10) using Bowtie2. Aligned reads were sorted and indexed using samtools, and low-quality reads were filtered. Genome coverage tracks were generated using deepTools (bamCoverage) with CPM normalization. Peak calling was performed using SEACR (norm, stringent mode) using IgG as control. Replicate bigWig files were merged for visualization using deepTools or UCSC tools. GRCm38 bigWig files represent CPM-normalized genome-wide coverage tracks for visualization.
scRNA-seq: Raw FASTQ files were aligned to the mm10 reference genome (10x Genomics mm10-2020-A) using Cell Ranger count (10x Genomics) with default parameters.
Hashtag oligo (HTO) libraries (TILH samples) were demultiplexed using HTODemux in Seurat to assign cells to individual samples.
Low-quality cells were filtered based on number of detected genes, total UMI counts, and percentage of mitochondrial reads. Doublets were identified and removed.
mm10 (GRCm38)
scRNA-seq: Standard 10x Genomics MEX format output by Cell Ranger count: barcodes.tsv.gz (cell barcodes), features.tsv.gz (gene names and Ensembl IDs), matrix.mtx.gz (UMI count matrix in sparse Matrix Exchange format). One set of three files per sample.
CUT&RUN: bigWig files represent CPM-normalized genome-wide coverage tracks for visualization.
Assembly: mm10 (GRCm38)
Supplementary files format and content: scRNA-seq: Standard 10x Genomics MEX format output by Cell Ranger count: barcodes.tsv.gz (cell barcodes), features.tsv.gz (gene names and Ensembl IDs), matrix.mtx.gz (UMI count matrix in sparse Matrix Exchange format). One set of three files per sample.
Supplementary files format and content: CUT&RUN: bigWig files represent CPM-normalized genome-wide coverage tracks for visualization.
Library strategy: CUT&Run

source_name: CD8 T cells

growth_protocol: Primary T cells were cultured in complete RPMI 1640 GlutaMAXTM-I.

extract_protocol:
scRNA-seq: Mouse P14 Cas9 control transduced or transduced with a sgRNA targeting IRF2, IRF4 or IRF8 were flow sorted from B16-gp33 tumors in Cas9-expressing host mice 14 days after tumor engraftment and 7 days after adoptive co-transfer of control and KO. Single cell suspensions from each tumor were labelled with a hashtagging antibody prior sorting and sequencing (APC-Streptavidin-oligonucleotide conjugates, Biolegend).
CUT&RUN: Post antibody incubation, samples were processed following manufacturer's instruction (EpiCypher)
scRNA-seq: Chromium Single Cell 5' Kit v2 (Dual Index) - 5'RNA-seq
CUT&RUN: Libraries were prepared following the manufactures instruction (EpiCypher) with the modification of increasing the concentration of the beads to ensure smaller fragments were not lost during the purification process. Libraries were pooled and subjected to 3 further rounds of bead purification to exclude the adapter dimers present in the libraries.

treatment_protocol: Samples were incubated with antiIRF2, antiIRF4, antiIRF8 or IgG control antibody.

value: CD8 T cells

value: In vitro chronic TCR stimulation (in vitro induced exhaustion)


title: AL_035


title: dose2_4h30_MOD270_DLN

description: See sample Dose, Time point, and Batch for experimenal condition.

value: Draining lymph node


title: MitoRibo_HeLa_10

description: Library name: L34

value: Naive


title: dose1_3h_MOD268_DLN


title: IRF4

description:
Library name: IRF4
CUT&RUN antibody: anti-IRF4


title: MitoRibo_HeLa_9

description: Library name: L33


title: dose2_3h_MOD265_DLN


title: IRF2

description:
Library name: IRF2
CUT&RUN antibody: anti-IRF2


title: AL_034


title: dose1_1h30_MOD262_DLN


title: AL_033


title: lncRNA2- Replicate 3

city: Murcia

first: Carlos

last: Lax

address: Facultad de Biología

department: Genetics and Microbiology

country: Spain

institute: University of Murcia

description: Library name: N16C

data_processing:
Raw paired-end (PE)   from R. microsporus RNA-seq datasets were quality-checked using FastQC v0.11.9
Adapters were removed with Trim Galore! V.0.4.3.1
Reads with a Phred quality score (q) ≤32 and/or a total length < 20 nt were removed from the analysis
Assembly: Rhizopus microsporus ATCC11559 v2.0 (https://mycocosm.jgi.doe.gov/Rhimi59_2/Rhimi59_2.home.html)
Supplementary files format and content: Spreadsheet including counts, log2FC, differential expression statistics and functional annotation for every gene

organism: Rhizopus microsporus

source_name: Spores

growth_protocol: UM6 and lncRNA2::pyrF and lncRNA4::pyrF mutant spores were incubated in MMC media for 24 hours at 30°C.

extract_protocol:
Total RNA was extracted using the Qiagen kit and treated with DNase (Sigma, On-Column DNaseI treatment set)
NEBNext® Ultra™ Directional RNA Library Prep Kit

value: Spores

value: Mutant strain (lncRNA2::pyrF)


title: AL_032


title: IgG

description:
Library name: IgG negative control
CUT&RUN antibody: IgG


title: lncRNA2 - Replicate 2

description: Library name: N16B


title: dose2_1h30_MOD259_DLN


title: KO IRF4 or IRF8_Hashtag_batch2

description: Library name: kIRF48TILH

data_processing:
CUT&RUN: Raw sequencing reads were quality-checked using FastQC. Reads were aligned to the mouse reference genome (GRCm38/mm10) using Bowtie2. Aligned reads were sorted and indexed using samtools, and low-quality reads were filtered. Genome coverage tracks were generated using deepTools (bamCoverage) with CPM normalization. Peak calling was performed using SEACR (norm, stringent mode) using IgG as control. Replicate bigWig files were merged for visualization using deepTools or UCSC tools. GRCm38 bigWig files represent CPM-normalized genome-wide coverage tracks for visualization.
scRNA-seq: Raw FASTQ files were aligned to the mm10 reference genome (10x Genomics mm10-2020-A) using Cell Ranger count (10x Genomics) with default parameters.
Hashtag oligo (HTO) libraries (TILH samples) were demultiplexed using HTODemux in Seurat to assign cells to individual samples.
Low-quality cells were filtered based on number of detected genes, total UMI counts, and percentage of mitochondrial reads. Doublets were identified and removed.
mm10 (GRCm38)
scRNA-seq: Standard 10x Genomics MEX format output by Cell Ranger count: barcodes.tsv.gz (cell barcodes), features.tsv.gz (gene names and Ensembl IDs), matrix.mtx.gz (UMI count matrix in sparse Matrix Exchange format). One set of three files per sample.
CUT&RUN: bigWig files represent CPM-normalized genome-wide coverage tracks for visualization.
Assembly: mm10 (GRCm38)
Supplementary files format and content: scRNA-seq: Standard 10x Genomics MEX format output by Cell Ranger count: barcodes.tsv.gz (cell barcodes), features.tsv.gz (gene names and Ensembl IDs), matrix.mtx.gz (UMI count matrix in sparse Matrix Exchange format). One set of three files per sample.
Supplementary files format and content: CUT&RUN: bigWig files represent CPM-normalized genome-wide coverage tracks for visualization.

source_name: TILs

value: TILs

value: P14-Cas9 CD8 T cells

value: CD45.1 and CD45.1.2 P14 CD4-CRE STOPfl/fl-Cas9-eGFP


title: naive_0h_MOD278_DLN

value: naive


title: AL_031

value: Young


title: lncRNA2- Replicate 1

description: Library name: N16A


title: Control IRF4 or IRF8_Hashtag_batch2

description: Library name: cIRF48TILH


title: AL_030


title: UM6 - Replicate 3

description: Library name: UM6C

value: Wild-type strain (UM6)


title: baseline_0h_MOD275_DLN

value: baseline


title: KO IRF4 or IRF8_batch2

description: Library name: kIRF48TILG


title: UM6 - Replicate 2

description: Library name: UM6B


title: dose1_4h30_MOD272_DLN


title: AL_029


title: Control IRF4 or IRF8_batch2

description: Library name: cIRF48TILG


title: AL_028


title: dose2_4h30_MOD269_DLN


title: KO IRF2 or IRF8_Hashtag_batch1

description: Library name: kIRF28TILH


title: UM6 - Replicate 1

description: Library name: UM6A


title: AL_027


title: lncRNA4- Replicate 3

description: Library name: R5C

value: Mutant strain (lncRNA4::pyrF)


title: dose1_3h_MOD267_DLN


title: Control IRF2 or IRF8_Hashtag_batch1

description: Library name: cIRF28TILH


title: AL_026


title: lncRNA4 - Replicate 2

description: Library name: R5B


title: dose1_3h_MOD266_DLN


title: AL_025


title: lncRNA4 - Replicate 1

description: Library name: R5A


title: KO IRF2 or IRF8_batch1

description: Library name: kIRF28TILG


title: dose2_3h_MOD264_DLN


title: AL_024


title: dose2_3h_MOD263_DLN


title: Control IRF2 or IRF8_batch1

description: Library name: cIRF28TILG


title: BMDM negative control Bulk RNA [control_1]

city: Boston

first: Yen

last: Nguyen

state: MA

address: 11 Myrtle St, unit 2

department: Center of Systems Biology

institute: Mass General Brigham

description: Library name: Control samples

data_processing:
Novogene customized bioinformatics analysis provides gene count files from the original fastq data. Specifically, they performed Data QC- filtering reads containing adapter or low quality, Statistics analysis of Data QC, and Mapping reads to reference genome. Then, we normalized for raw gene count data using R (as described in the manuscript) to get logCPM.
Assembly: mm10
Supplementary files format and content: raw gene count, logCPM

source_name: Bone-marrow derived macrophage

extract_protocol:
Rneasy Kit for RNA Purification
mRNA library_preparation (poly A_enrichment)

value: Bone-marrow derived macrophage

value: Macrophages

value: PBS


title: AL_023


title: dose1_1h30_MOD261_DLN


title: PAM3CSK4_3_Biological Replicate3 [M_PAM3CSK4_3_M60]

first: Michele

middle: Joana

last: Alves

address: 11200 SW 8th Street,  AHC1- 417B

department: Cellular and Molecular Medicine

institute: Florida International University

description:
Gene expression data from isolated cells of brainstem tissue following 3h after inflammatory or saline stimulus. Isolated cells were kept in -80C until further processing with all samples for RNA extraction
Clariom_S_Mouse.r1.na36.mm10
M_PAM3CSK4_3_M60

hyb_protocol: Affymetrix GeneChip Mouse Gene ST 2.0 arrays for 16 h, 45 °C, at 60 RPM

scan_protocol: The arrays were washed, and readings obtained by Affymetrix Expression Console

data_processing:
The Affymetrix Clarion S Mouse microarrays were analyzed with Affymetrix Expression Console  version 1.3.1. TAC (Affymetrix Transcriptome Analysis Console) was used was used with default parameters following the annotation : Clariom_S_Mouse.r1.na36.mm10
Differential gene expression was obtained in TAC software by using a cutoff of 2-fold change and P-value of 0.05 and t-test in comparison to control group.

label: Biotin

source_name: CD11b+ Microglia from Brainstem of PD5 pups

label_protocol: Clariom™ S Assay mouse and Affymetrix Gene Chip Mouse Gene ST 2.0 arrays was performed per  The Ohio State University Comprehensive Cancer Center Genomics Shared Resource protocol..

extract_protocol: Total RNA was isolated using trizol and PureLink® RNA Mini Kit per manufacture’s recommendations.

treatment_protocol: Tissue was dissected out after euthanasia and further processed for total RNA. Cells were isolated from brainstem tissue and processed for total RNA

value: CD11b+ Microglia

tag: litter

value: Litter 7, 8 and 9

tag: pooling samples of same litter

value: 10 pooled brainstem of 3 different litters


title: BMDM CANDI470 treated Bulk RNA

description: Library name: CANDI470 treated sample

tag: cell type


title: PAM3CSK4_2_Biological Replicate2 [M_PAM3CSK4_2_M57]

description:
Gene expression data from isolated cells of brainstem tissue following 3h after inflammatory or saline stimulus. Isolated cells were kept in -80C until further processing with all samples for RNA extraction
Clariom_S_Mouse.r1.na36.mm10
M_PAM3CSK4_2_M57

value: Litter 4, 5 and 6


title: dose1_1h30_MOD260_DLN

value: Draining lymph node


title: dose2_1h30_MOD258_DLN


title: AL_021

tag: tumor or adjacent

value: Tumor


title: Muc2hom_ENU_DWAC18.1G distal 2

city: Cambridge

first: Matthew

last: Eldridge

address: Robinson Way

department: Cancer Research UK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

description: Library name: SITSH2

data_processing:
Fastq files were processed using the Spaceranger command line tool (10x Genomics v3.0.1) and mapped to the pre-built mm10 reference genome.
Assembly: mm10
Supplementary files format and content: cytassist_image.tiff: CytAssist slide image
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scale factors in JSON format
Supplementary files format and content: spatial_enrichment.csv: table of Morans's I values for each feature
Supplementary files format and content: tissue_hires_image.png: high resolution downsampled image of the tissue sample
Supplementary files format and content: tissue_lowres_image.png: low resolution downsampled image of the tissue sample
Supplementary files format and content: tissue_positions.csv: spot coordinates
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market exchange format
Supplementary files format and content: filtered_feature_bc_matrix.h5: feature barcode expression count matrices in HDF5 format
Library strategy: Spatial Transcriptomics

source_name: Colon

extract_protocol:
Colons were flushed with PBS before whole-mounting and fixation in 4% PFA at 4 degrees Celsius overnight. After 24h in 70% Ethanol, sections were cut.
Libraries were processed by the CRUK Cambridge Institute Genomics Core according to the manufacturer’s instructions and sequenced on Illumina’s NovaSeqX Plus to an average depth of 8 million mapped reads per sample.

value: Colon

value: ENU


title: PAM3CSK4_1_Biological Replicate1 [M_PAM3CSK4_1_M51]

description:
Gene expression data from isolated cells of brainstem tissue following 3h after inflammatory or saline stimulus. Isolated cells were kept in -80C until further processing with all samples for RNA extraction
Clariom_S_Mouse.r1.na36.mm10
M_PAM3CSK4_1_M51

value: Litter 1, 2 and 3


title: Muc2hom_ENU_DWAC18.1G distal 1

description: Library name: SITSG2


title: dose2_1h30_MOD257_DLN


title: Muc2hom_ENU_DWAC18.1G proximal 2

description: Library name: SITSF2


title: Col0_3

city: Wako

first: Asanga

middle: Deshappriya

last: Nagalla

address: 2-1 Hirosawa

department: RIKEN Nishina Center for Accelerator-Based Science

description: Library name: Sample6

data_processing:
Quality control was conducted using Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1)
Clean reads of each biological sample were aligned to the Arabidopsis genome assembly (TAIR10) by using Hisat2
The HTSeq (v0.6.1) software package (Anders et al. 2010) was used to count the reads mapped to genomic features
Assembly: Arabidopsis genome assembly (TAIR10)
Supplementary files format and content: The .csv files contained the raw counts and FPKM values

organism: Arabidopsis thaliana

source_name: Leaf tissues

extract_protocol:
The total RNA was extracted using the RNeasy Plant Mini Kit
library preparation was conducted by using VAHTS Universal V8 RNA-seq Library Prep kit

value: Leaf

tag: line


title: AL_019

data_processing:
For processing, we used Rsubread (Bioconductor release 2.16) to align sequence reads to reference genome and used edgeR and limma R packages (Bioconductor release 4.0 and 3.58 respectively) to normalize gene expression level to log2 transcripts per million (TPM)
Assembly: We aligned sequence reads to GRCh38 release 14 human genome reference sequence and mapped the aligned sequences to Entrez Genes
Supplementary files format and content: After normalization, we removed genes of which expression level is zero across all samples to get 39,404 genes for further pathway analysis.

tag: agerange

value: Young

tag: chronologicalage


title: LPS3_Biological Replicate3 [M_LPS_3_M59]

description:
Gene expression data from isolated cells of brainstem tissue following 3h after inflammatory or saline stimulus. Isolated cells were kept in -80C until further processing with all samples for RNA extraction
Clariom_S_Mouse.r1.na36.mm10
M_LPS_3_M59


title: LPS2_Biological Replicate2 [M_LPS_2_M56]

description:
Gene expression data from isolated cells of brainstem tissue following 3h after inflammatory or saline stimulus. Isolated cells were kept in -80C until further processing with all samples for RNA extraction
Clariom_S_Mouse.r1.na36.mm10
M_LPS_2_M56


title: Muc2hom_ENU_DWAC18.1D distal 1

description: Library name: SITSE2

tag: tissue


title: LPS1_Biological Replicate1 [M_LPS_1_M50]

description:
Gene expression data from isolated cells of brainstem tissue following 3h after inflammatory or saline stimulus. Isolated cells were kept in -80C until further processing with all samples for RNA extraction
Clariom_S_Mouse.r1.na36.mm10
M_LPS_1_M50


title: AL_018

tag: read length


title: Col0_2

description: Library name: Sample5


title: Col0_1

description: Library name: Sample4


title: Muc2hom_ENU_DWAC18.1F distal 2

description: Library name: SITSB2


title: AL_017


title: Muc2hom_ENU_DWAC18.1F distal 1

description: Library name: SITSD1


title: C30-81-as6_3

description: Library name: Sample3


title: CTR3_Biological Replicate3 [M_Control_3_M58]

description:
Gene expression data from isolated cells of brainstem tissue following 3h after inflammatory or saline stimulus. Isolated cells were kept in -80C until further processing with all samples for RNA extraction
Clariom_S_Mouse.r1.na36.mm10
M_Control_3_M58


title: AL_016


title: CTR2_Biological Replicate2 [M_Control_2_M55]

description:
Gene expression data from isolated cells of brainstem tissue following 3h after inflammatory or saline stimulus. Isolated cells were kept in -80C until further processing with all samples for RNA extraction
Clariom_S_Mouse.r1.na36.mm10
M_Control_2_M55


title: CTR1_Biological Replicate1 [M_Control_1_M49]

description:
Gene expression data from isolated cells of brainstem tissue following 3h after inflammatory or saline stimulus. Isolated cells were kept in -80C until further processing with all samples for RNA extraction
Clariom_S_Mouse.r1.na36.mm10
M_Control_1_M49


title: Muc2hom_ENU_DWAC18.1F proximal 2

description: Library name: SITSH1


title: C30-81-as6_2

description: Library name: Sample2


title: AL_015


title: C30-81-as6_1

description: Library name: Sample1


title: AL_014


title: Muc2hom_ENU_DWAC18.1D distal 2

description: Library name: SITSD2


title: PAM3CSK4_3_Biological Replicate3 [N_PAM3CSK4_3_N45]

description:
Gene expression data from isolated cells of brainstem tissue following 3h after inflammatory or saline stimulus. Isolated cells were kept in -80C until further processing with all samples for RNA extraction
Clariom_S_Mouse.r1.na36.mm10
N_PAM3CSK4_3_N45

source_name: Neurons from brainstem of PD5 pups

value: Neurons


title: Muc2hom_ENU_DWAC18.1D proximal 1

description: Library name: SITSC1


title: MEP diploid acc1 S1157A Pgpd SAK1 overexpression (A2A), 48h, rep 3

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

institute: The Babraham Institute

description: Library name: A2A 48h 3

data_processing:
After adapter and quality trimming using Trim Galore (v0.6.6), RNA-seq data was mapped to yeast genome R64-1-1 using HISAT2 v2.1.0 (Kim et al., 2019) by the Babraham Institute Bioinformatics Facility. Mapped data was imported into SeqMonk v1.48.1
Assembly: R64-1-1
Supplementary files format and content: Supplementary files format and content: Quantified for log2 total reads mapping to the antisense strand of annotated open reading frames (opposite strand specific libraries) including probes to the rDNA intergrenic regions. Read counts were adjusted by Size Factor normalisation for the full set of quantified probes.
Supplementary files format and content: tsv

source_name: Whole organism

growth_protocol: All cells were grown in YPD media (2% peptone, 1% yeast extract, 2% glucose) at 30°C with shaking at 200 rpm. Media components were purchased from Formedium and media was sterilised by filtration. MEP experiments were performed as described with modifications (Cruz et al., 2018): cells were inoculated in 4 ml YPx (where x is the sugar) and grown for 6-8 hours then diluted in 25 ml YPD and grown for 16-18 hours to 0.2-0.6x107 cells/ml in 50 ml Erlenmeyer flasks. 0.125x107 cells per aged culture were harvested by centrifugation (15 s at 13,000 g), washed twice with 125 µl PBS and re-suspended in 125 µl of PBS containing ~3 mg/ml Biotin-NHS (Pierce 10538723). Cells were incubated for 30 min on a wheel at room temperature, washed once with 125 µl PBS and re-suspended in 125 µl YPD then inoculated in 125 ml YPD at 1x104 cells/ml in a 250 ml Erlenmeyer flask (FisherBrand FB33132) sealed with Parafilm. 1 µM β-estradiol (from stock of 1 mM Sigma E2758 in ethanol) was added after 2 hours. An additional 0.125x107 cells were harvested from the log phase culture while biotin labelling reactions were incubating at room temperature. Cells were harvested by centrifugation for 1 min, 4600 rpm, immediately fixed by resuspension in 70% ethanol and stored at -80°C.

extract_protocol:
Percoll gradients (1-2 per sample depending on harvest density) were formed by vortexing 1 ml Percoll (Sigma P1644) with 110 µl 10x PBS in 2 ml tubes and centrifuging 15 min at 15,000 g, 4 °C. Ethanol fixed cells were defrosted and washed once with 1 volume of cold PBSE (PBS + 2 mM EDTA) before resuspension in ~100 µl cold PBSE per gradient and layering on top of the pre-formed gradients. Gradients were centrifuged for 4 min at 2,000 g, 4 °C, then the upper phase and brown layer of cell debris removed and discarded. 1 ml PBSE was added, mixed by inversion and centrifuged 1 min at 2,000 g, 4 °C to pellet the cells, which were then re-suspended in 1 ml PBSE per time point (re-uniting samples where split across two gradients). 25 µl Streptavidin microbeads (Miltenyi Biotech 1010007) were added and cells incubated for 5 min on a wheel at room temperature. Meanwhile, 1 LS column per sample (Miltenyi Biotech 1050236) was loaded on a QuadroMACS magnet and equilibrated with cold PBSE in 4 °C room. Cells were loaded on columns and allowed to flow through under gravity, washed with 1 ml cold PBSE and eluted with 1 ml PBSE using plunger. Cells were re-loaded on the same columns after re-equilibration with ~500 µl PBSE, washed and re-eluted, and this process repeated for a total of three successive purifications. After addition of Triton X-100 to 0.01% to aid pelleting, cells were split into 2 fractions in 1.5 ml tubes, pelleted 30 s at 20,000 g, 4 °C, frozen on N2 and stored at -70 °C. Cells were re-suspended in 50 µl Lysis/Binding Buffer (from mirVANA kit, Life Technologies AM1560), and 50 µl 0.5 µm zirconium beads (Thistle Scientific 11079105Z) added. Cells were lysed with 5 cycles of 30 s 6500 ms-1 / 30 s ice in an MP Fastprep bead beater or for 3 min at power 12 in a Bullet Blender (ThermoFisher) in cold room, then 250 µl Lysis/Binding buffer added followed by 15 µl miRNA Homogenate Additive and cells were briefly vortexed before incubating for 10 minutes on ice. 300 µl acid phenol : chloroform was added, vortexed and centrifuged 5 min at 13,000 g, room temperature before extraction of the upper phase. 400 µl room temperature ethanol and 2 µl glycogen (Sigma G1767) were added and mixture incubated for 1 hour at -30 °C before centrifugation for 15 minutes at 20,000 g, 4 °C. The pellet was washed with cold 70% ethanol and re-suspended in 10 µl water. 1 µl RNA was glyoxylated and analysed on a BPTE mini-gel, and RNA was quantified using a PicoGreen RNA kit (Life Technologies R11490) or Qubit® RNA HS Assay Kit. 150 ng RNA was used to prepare libraries using the NEBNext Ultra II Directional mRNAseq kit with poly(A)+ purification module (NEB E7760, E7490) as described with modifications: Reagent volumes for elution from poly(T) beads, reverse transcription, second strand synthesis, tailing and adaptor ligation were reduced by 50%; libraries were amplified for 13 cycles using 2 µl each primer per 50 µl reaction before two rounds of AMPure bead purification at 0.9x and elution in 11 µl 0.1x TE prior to quality control using a Bioanalyzer HS DNA ChIP (Agilent) and quantification using a KAPA Library Quantification Kit (Roche).
NEBNext Ultra II Direction RNA-seq kit

value: Whole organism


title: AL_013


title: PAM3CSK4_2_Biological Replicate2 [N_PAM3CSK4_2_N33]

description:
Gene expression data from isolated cells of brainstem tissue following 3h after inflammatory or saline stimulus. Isolated cells were kept in -80C until further processing with all samples for RNA extraction
Clariom_S_Mouse.r1.na36.mm10
N_PAM3CSK4_2_N33


title: AL_012

source_name: BreastTumor


title: Muc2hom_ENU_DWAC18.1C distal 2

description: Library name: SITSC2


title: MEP diploid acc1 S1157A Pgpd SAK1 overexpression (A2A), 48h, rep 2

description: Library name: A2A 48h 2


title: PAM3CSK4_1_Biological Replicate1 [N_PAM3CSK4_1_N21]

description:
Gene expression data from isolated cells of brainstem tissue following 3h after inflammatory or saline stimulus. Isolated cells were kept in -80C until further processing with all samples for RNA extraction
Clariom_S_Mouse.r1.na36.mm10
N_PAM3CSK4_1_N21


title: MEP diploid acc1 S1157A Pgpd SAK1 overexpression (A2A), 48h, rep 1

description: Library name: A2A 48h 1


title: AL_011


title: LPS3_Biological Replicate3 [N_LPS_3_N44]

description:
Gene expression data from isolated cells of brainstem tissue following 3h after inflammatory or saline stimulus. Isolated cells were kept in -80C until further processing with all samples for RNA extraction
Clariom_S_Mouse.r1.na36.mm10
N_LPS_3_N44


title: Muc2hom_ENU_DWAC18.1C distal 1

description: Library name: SITSB1


title: MEP diploid acc1 S1157A Pgpd SAK1 overexpression (A2A), 40h, rep 2

description: Library name: A2A 40h 2


title: Muc2hom_ENU_DWAC18.1A proximal 1

description: Library name: SITSA2


title: AL_010


title: LPS2_Biological Replicate2 [N_LPS_2_N32]

description:
Gene expression data from isolated cells of brainstem tissue following 3h after inflammatory or saline stimulus. Isolated cells were kept in -80C until further processing with all samples for RNA extraction
Clariom_S_Mouse.r1.na36.mm10
N_LPS_2_N32


title: MEP diploid acc1 S1157A Pgpd SAK1 overexpression (A2A), 40h, rep 1

description: Library name: A2A 40h 1


title: AL_009


title: LPS1_Biological Replicate1 [N_LPS_1_N20]

description:
Gene expression data from isolated cells of brainstem tissue following 3h after inflammatory or saline stimulus. Isolated cells were kept in -80C until further processing with all samples for RNA extraction
Clariom_S_Mouse.r1.na36.mm10
N_LPS_1_N20


title: Muc2hom_ENU_DWAC18.1C proximal 1

description: Library name: SITSG1


title: AL_008


title: MEP diploid acc1 S1157A Pgpd SAK1 overexpression (A2A), 24h, rep 3

description: Library name: A2A 24h 3


title: MEP diploid acc1 S1157A Pgpd SAK1 overexpression (A2A), 24h, rep 2

description: Library name: A2A 24h 2


title: Muc2hom_ENU_DWAC18.1A distal 2

description: Library name: SITSA1


title: AL_007


title: CTR2_Biological Replicate2 [N_Control_2_N31]

description:
Gene expression data from isolated cells of brainstem tissue following 3h after inflammatory or saline stimulus. Isolated cells were kept in -80C until further processing with all samples for RNA extraction
Clariom_S_Mouse.r1.na36.mm10
N_Control_2_N31


title: CTR3_Biological Replicate3 [N_Control_3_N43]

description:
Gene expression data from isolated cells of brainstem tissue following 3h after inflammatory or saline stimulus. Isolated cells were kept in -80C until further processing with all samples for RNA extraction
Clariom_S_Mouse.r1.na36.mm10
N_Control_3_N43


title: Muc2hom_ENU_DWAC18.1A distal 1

description: Library name: SITSF1


title: CTR1_Biological Replicate1 [N_Control_1_N19]

description:
Gene expression data from isolated cells of brainstem tissue following 3h after inflammatory or saline stimulus. Isolated cells were kept in -80C until further processing with all samples for RNA extraction
Clariom_S_Mouse.r1.na36.mm10
N_Control_1_N19


title: MEP diploid acc1 S1157A Pgpd SAK1 overexpression (A2A), 24h, rep 1

description: Library name: A2A 24h 1


title: AL_006


title: Muc2hom_ENU_DWAC18.1A proximal 2

description: Library name: SITSE1


title: MEP diploid acc1 S1157A Pgpd SAK1 overexpression (A2A), log, rep 2

description: Library name: A2A log 2

value: log


title: Muc2hom_3

description: Library name: SITSD12


title: PAM3CSK4_3_Biological Replicate3 [A_PAM3CSK4_3_A39]

description:
Gene expression data from isolated cells of brainstem tissue following 3h after inflammatory or saline stimulus. Isolated cells were kept in -80C until further processing with all samples for RNA extraction
Clariom_S_Mouse.r1.na36.mm10
A_PAM3CSK4_3_A39

source_name: Glast1+ Astrocytes from PD5 pups brainstem

value: Glast1+ Astrocytes


title: AL_005


title: Muc2hom_2

description: Library name: SITSG12


title: AL_004


title: MEP diploid acc1 S1157A Pgpd SAK1 overexpression (A2A), log, rep 1

description: Library name: A2A log 1


title: MEP diploid acc1 S1157A, 48h, rep 3

description: Library name: acc1 48h 3

value: acc1 S1157A


title: Muc2hom_1

description: Library name: SITSF12


title: PAM3CSK4_2_Biological Replicate2 [A_PAM3CSK4_2_A27]

description:
Gene expression data from isolated cells of brainstem tissue following 3h after inflammatory or saline stimulus. Isolated cells were kept in -80C until further processing with all samples for RNA extraction
Clariom_S_Mouse.r1.na36.mm10
A_PAM3CSK4_2_A27


title: AL_003


title: PAM3CSK4_1_Biological Replicate1 [A_PAM3CSK4_1_A15]

description:
Gene expression data from isolated cells of brainstem tissue following 3h after inflammatory or saline stimulus. Isolated cells were kept in -80C until further processing with all samples for RNA extraction
Clariom_S_Mouse.r1.na36.mm10
A_PAM3CSK4_1_A15


title: LPS3_Biological Replicate3 [A_LPS_3_A38]

description:
Gene expression data from isolated cells of brainstem tissue following 3h after inflammatory or saline stimulus. Isolated cells were kept in -80C until further processing with all samples for RNA extraction
Clariom_S_Mouse.r1.na36.mm10
A_LPS_3_A38


title: MEP diploid acc1 S1157A, 48h, rep 2

description: Library name: acc1 48h 2


title: AL_002


title: DSS_D7_3

description: Library name: SITSH12

value: DSS+ENU


title: MEP diploid acc1 S1157A, 48h, rep 1

description: Library name: acc1 48h 1


title: DSS_D7_2

description: Library name: SITSE12


title: AL_001


title: LPS2_Biological Replicate2 [A_LPS_2_A26]

description:
Gene expression data from isolated cells of brainstem tissue following 3h after inflammatory or saline stimulus. Isolated cells were kept in -80C until further processing with all samples for RNA extraction
Clariom_S_Mouse.r1.na36.mm10
A_LPS_2_A26


title: 3_0.5Q+

city: shanghai

first: Yinrui

last: Lei

state: 固态

address: 800 Dong chuan Road

department: Shanghai Center for Systems Biomedicine

institute: shanghai jiaotong university

data_processing:
Read mapping by SeqPrep and Sickle.
Differential expression genes was calculated according to the transcript per million reads (TPM) method.
Assembly: hg38
Supplementary files format and content: txt, RNA-seq RPKM

growth_protocol: A549 cells were cultured in RPMI1640 supplemented with 10% FBS at 37C in a 5% CO2 container.

extract_protocol:
RNA was extracted with TRIzol Reagent (Invitrogen). 1ug of total RNA was used to construct the library.
RNA-seq transcriptome library was prepared according to TruSeq TM RNA sample preparation kit of Illumina.

treatment_protocol: The cells were treated with or without TGFbeta in 0.5% dialyzed FBS under different concentrations of glutamine for 24 hours.

tag: cell line

value: human non small cell lung cancer cell

value: WT

value: 0.5 mM Q,TGFbeta


title: MEP diploid acc1 S1157A, 24h, rep 3

description: Library name: acc1 24h 3


title: DSS_D7_1

description: Library name: SITSA12


title: CTR3_Biological Replicate3 [A_Control_3_A37]

description:
Gene expression data from isolated cells of brainstem tissue following 3h after inflammatory or saline stimulus. Isolated cells were kept in -80C until further processing with all samples for RNA extraction
Clariom_S_Mouse.r1.na36.mm10
A_Control_3_A37

value: Litter 7, 8 and 9

value: 10 pooled brainstem of 3 different litters


title: DSS_D21_3

description: Library name: SITSB12


title: MEP diploid acc1 S1157A, 24h, rep 2

description: Library name: acc1 24h 2


title: 3_0.5Q

value: 0.5 mM Q


title: LPS1_Biological Replicate1 [A_LPS_1_A14]

description:
Gene expression data from isolated cells of brainstem tissue following 3h after inflammatory or saline stimulus. Isolated cells were kept in -80C until further processing with all samples for RNA extraction
Clariom_S_Mouse.r1.na36.mm10
A_LPS_1_A14


title: DSS_D21_2

description: Library name: SITSC12

value: Colon


title: 3_0.2Q+

value: 0.2 mM Q,TGFbeta


title: MEP diploid acc1 S1157A, 24h, rep 1

description: Library name: acc1 24h 1


title: CTR2_Biological Replicate2 [A_Control_2_A25]

description:
Gene expression data from isolated cells of brainstem tissue following 3h after inflammatory or saline stimulus. Isolated cells were kept in -80C until further processing with all samples for RNA extraction
Clariom_S_Mouse.r1.na36.mm10
A_Control_2_A25

value: Litter 4, 5 and 6


title: 3_0.2Q

value: 0.2 mM Q


title: DSS_D21_1

description: Library name: SITSH11


title: MEP diploid acc1 S1157A, log, rep 3

description: Library name: acc1 log 3


title: CTR1_Biological Replicate1 [A_Control_1_A13]

description:
Gene expression data from isolated cells of brainstem tissue following 3h after inflammatory or saline stimulus. Isolated cells were kept in -80C until further processing with all samples for RNA extraction
Clariom_S_Mouse.r1.na36.mm10
A_Control_1_A13

value: Litter 1, 2 and 3


title: Apc_4

description: Library name: SITSE11

value: ENU


title: MEP diploid acc1 S1157A, log, rep 2

description: Library name: acc1 log 2

value: Whole organism


title: 3_0Q+


title: MEP diploid acc1 S1157A, log, rep 1

description: Library name: acc1 log 1

value: log


title: Apc_3

description: Library name: SITSG11


title: 3_0Q


title: MitoDiso_HeLa_mtRF1L_KO_2

first: Taisei

last: Wakigawa

address: 2-1, Hirosawa

description: Library name: L48

data_processing:
Basecalling with Illumina Casava 1.8 software
Base correction, filtering, 3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Assembly: Read quantitation using custom scripts
Supplementary files format and content: The human or mouse nuclear genomes (human, hg38; mouse, mm10) and custom-made mitochondrial transcript sequences
Supplementary files format and content: Fpframing text files contain nine columns:  1. the length of ribosome footprint; 2. the fraction of ribosome footprint; 3~5. the number of ribosome footprint at each frames;  6~8,the fraction of ribosome footprint at each frames; 9. the relative entropy of ribosome footprint.
Library strategy: MitoIP-Thor-Disome-Seq

extract_protocol:
MitoIP-Thor-Ribo-Seq and MitoIP-Thor-Disome-Seq: Cells were cultured in 15-cm dishes, washed with ice-cold PBS, and lysed with 1200 µl of hypotonic buffer (10 mM HEPES-KOH pH 7.5, 10 mM KCl, 1.5 mM MgCl2, 1 mM DTT, 100 µg/ml cycloheximide, and 100 µg/ml chloramphenicol). The lysate was incubated with anti-TOM22 antibody-conjugated beads from Mitochondria Isolation Kit, Human (Miltenyi Biotec) for 60 min at 4°C. The subsequent wash and elution steps were performed with wash buffer (10 mM HEPES-KOH pH 7.5, 10 mM KCl, 15 mM MgCl2, 1 mM DTT, 100 µg/ml cycloheximide, and 100 µg/ml chloramphenicol), according to the manufacturer’s instructions. The eluted mitochondrial fraction was pelleted by centrifugation at 7,000 × g for 10 min at 4°C and resuspended in modified lysis buffer (20 mM Tris-HCl, pH 7.5, 150 mM NaCl, 15 mM MgCl2, 1 mM DTT, 1% Triton X-100, 100 µg/ml cycloheximide, 100 µg/ml chloramphenicol, and 2.5 U/ml TURBO DNase). After clarification by centrifugation at 20,000 × g for 10 min at 4°C, the supernatant was used for library preparation. Ribo-Seq and RNA-Seq: Cells in a 10-cm dish were lysed with 600 µl of lysis buffer (20 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1% Triton X-100, 1 mM DTT, 100 µg/ml cycloheximide, and 100 µg/ml chloramphenicol) and treated with 25 U/ml TURBO DNase (Thermo Fisher Scientific). Then, the lysate was clarified by centrifugation at 20,000 × g for 10 min at 4°C.
MitoIP-Thor-Ribo-Seq and MitoIP-Thor-Disome-Seq: preadenylated linkers with the antisense sequence of T7 promoter were ligated and footprints were amplified by in vitro transcription. RNA-seq: the libraries were prepared by a SEQuoia Express Standard RNA Library Prep Kit (Bio-Rad).

value: HeLa


title: PAM3CSK4_2_Biological Replicate2 [BS_PAM3CSK4_2_A8]

description:
Gene expression data from postnatal day 5 pups- brainstem tissue following 3h after inflammatory or saline stimulus
Clariom_S_Mouse.r1.na36.mm10
BS_PAM3CSK4_2_A8

source_name: Brainstem from PD5 pups

value: Brainstem tissue

value: Litter 2

value: Pooled Total RNA Samples 5-6-7-8


title: 2_0.5Q+

value: human non small cell lung cancer cell

value: WT


title: Apc_2

description: Library name: SITSF11


title: 362C-2_VDJ - HC - CITEseq

city: London

first: Jo

last: Spencer

state: Kent

address: Guy’s Hospital Campus

institute: King's College London

description: Library name: 362C-2_VDJ

data_processing:
Raw reads were processed using CellRanger (pipeline version cellranger-arc-2.0.2)
Assembly: hg38
Supplementary files format and content: Tab separated files for gene IDs, cell barcodes and count matrix per sample
Library strategy: BCR-Seq

source_name: appendix

extract_protocol:
Live single CD19+ B cells were stained with ADT antibodies and anti-CD19 antibody used for FACS. Cells were sorted into 200ml 100% FBS, washed with ice-cold 1xPBS and then centrifuged at 500 g for 5 min at 4°C. They were resuspended in FACS buffer (2% FBS in DPBS).
Cells were loaded onto a 10X Genomics Chromium controller for library generation.

value: appendix

value: B cell


title: PAM3CSK4_1_Biological Replicate1 [BS_PAM3CSK4_1_A7]

description:
Gene expression data from postnatal day 5 pups- brainstem tissue following 3h after inflammatory or saline stimulus
Clariom_S_Mouse.r1.na36.mm10
BS_PAM3CSK4_1_A7

value: Litter 1

value: Pooled Total RNA Samples 1-2-3-4


title: Apc_1

description: Library name: SITSB11

value: Colon


title: PAM3CSK4_3_Biological Replicate3 [BS_PAM3CSK4_3_A9]

description:
Gene expression data from postnatal day 5 pups- brainstem tissue following 3h after inflammatory or saline stimulus
Clariom_S_Mouse.r1.na36.mm10
BS_PAM3CSK4_3_A9

value: Litter 3

value: Pooled Total RNA Samples 9-10-11-12


title: 2_0.5Q

value: 0.5 mM Q


title: 362C-2_GEX - HC - CITEseq

description: Library name: 362C-2_GEX

data_processing:
Raw reads were processed using CellRanger (pipeline version cellranger-arc-2.0.2)
Assembly: hg38
Supplementary files format and content: Tab separated files for gene IDs, cell barcodes and count matrix per sample


title: LPS3_Biological Replicate3 [BS_LPS_3_A6]

description:
Gene expression data from postnatal day 5 pups- brainstem tissue following 3h after inflammatory or saline stimulus
Clariom_S_Mouse.r1.na36.mm10
BS_LPS_3_A6


title: Muc2het_3

description: Library name: SITSD11


title: 362C-2_CSP - HC - CITEseq

description: Library name: 362C-2_CSP

data_processing:
Raw reads were processed using CellRanger (pipeline version cellranger-arc-2.0.2)
Assembly: hg38
Supplementary files format and content: Tab separated files for gene IDs, cell barcodes and count matrix per sample
Library strategy: CITE-seq

molecule: protein


title: 2_0.2Q+

value: 0.2 mM Q,TGFbeta


title: Muc2het_2

description: Library name: SITSA11


title: LPS2_Biological Replicate2 [BS_LPS_2_A5]

description:
Gene expression data from postnatal day 5 pups- brainstem tissue following 3h after inflammatory or saline stimulus
Clariom_S_Mouse.r1.na36.mm10
BS_LPS_2_A5


title: 362C-1_VDJ - HC - CITEseq

description: Library name: 362C-1_VDJ


title: 2_0.2Q

value: 0.2 mM Q


title: CTR3_Biological Replicate3 [BS_Control_3_A3]

description:
Gene expression data from postnatal day 5 pups- brainstem tissue following 3h after inflammatory or saline stimulus
Clariom_S_Mouse.r1.na36.mm10
BS_Control_3_A3


title: 362C-1_GEX - HC - CITEseq

description: Library name: 362C-1_GEX


title: Muc2het_1

description: Library name: SITSC11


title: 2_0Q+


title: LPS1_Biological Replicate1 [BS_LPS_1_A4]

description:
Gene expression data from postnatal day 5 pups- brainstem tissue following 3h after inflammatory or saline stimulus
Clariom_S_Mouse.r1.na36.mm10
BS_LPS_1_A4


title: ATDC5 Day 21 rep4

city: Freiburg

first: Anna

last: Klawonn

address: Hugstetter Str. 55

country: Germany

institute: University Hospital Freiburg

description: Library name: D214

data_processing:
Raw data were processed on Galaxy platform (usegalaxy.eu). Quality control was performed using FastQC (version 0.74+galaxy1)
Adapter trimming with Trim Galore! (version 0.6.7+galaxy0)
Mapping of trimmed reads to mouse genome mm39 with RNA STAR (version 2.7.11a+galaxy1) as paired end data and “length of the genomic sequence around annotated junctions” set to 149
Read counts per gene were quantified using featureCounts (version 2.0.6+galaxy0)
Assembly: mm39
Supplementary files format and content: tabular file containing read counts gene for each sample (feature counts output)

growth_protocol: Up to day 0 ATDC5 cells were maintained in growth medium composed of Dulbecco’s modified eagle medium and Ham´s F-12 in a ratio of 1:1, supplemented with 10 % fetal calf serum, 1% Sodium Pyruvate, 100 U/ml penicillin and 100 µg/ml streptomycin at 37°C and 5% CO2. After day 0 cells were maintained in differentiation medium, similar to growth medium but with 5% FCS and supplemented with 10µg/ml insulin, 30nM sodium selenite, 50µg/ml ascorbic acid and 10µg/ml transferrin. The medium was changed every other day.

extract_protocol:
RNA was extracted with Qiagen Rneasy Fibrous Tissue Kit according to manufacturers instruction
Novogene in house protocol: Purification: mRNA was isolated from total RNA using poly‑T oligo‑attached magnetic beads. cDNA synthesis: Fragmented mRNA was reverse transcribed using random hexamer primers to generate first-strand cDNA, followed by second-strand synthesis. Library construction: Libraries were prepared by end repair, A‑tailing, adapter ligation, size selection, amplification, and purification. Quality control: Libraries were quantified using Qubit and qPCR; size distribution was assessed with a Bioanalyzer.

value: wild type

value: day 21


title: 2_0Q


title: CTR2_Biological Replicate2 [BS_Control_2_A2]

description:
Gene expression data from postnatal day 5 pups- brainstem tissue following 3h after inflammatory or saline stimulus
Clariom_S_Mouse.r1.na36.mm10
BS_Control_2_A2

value: Brainstem tissue


title: 343B-2_VDJ - HC - CITEseq

description: Library name: 343B-2_VDJ


title: 362C-1_CSP - HC - CITEseq

description: Library name: 362C-1_CSP


title: ATDC5 Day 21 rep3

description: Library name: D213


title: 1_0.5Q+

value: 0.5 mM Q,TGFbeta


title: XY at D6 under testicular condition

city: Suita

first: Katsuhiko

last: Hayashi

state: Osaka

address: 2-2 Yamadaoka

department: Graduate School of Medicine

institute: The University of Osaka

description: Library name: D6 XY/Tes

data_processing:
Transcriptome reads from 10x Genomics were mapped to the mouse genome (GRCm38) using CellRanger v6.0.1 with the --exclude-introns option. The mapped reads were then summarized into raw UMI count matrices. For quality control, cells were filtered using the following thresholds: more than 8,000 total UMIs, more than 2,000 detected genes, and less than 20% of UMIs mapped to mitochondrial genes (percentMT < 0.2). In addition, potential multiplets were removed based on predictions by Scrublet v0.2.3 (Wolock et al., 2019, doi:10.1016/j.cels.2018.11.005). Datasets were applied to RECODE v0.2.1 (Imoto et al., 2022; Life Science Alliance, DOI: 10.26508/lsa.202201591), implemented in Python (https://github.com/yusuke-imoto-lab/RECODE). UMI counts were normalized by the total UMI count per cell, scaled to 100,000, and log₂-transformed with a pseudo-count of 1 [log₂(ss100k + 1)]. To account for technical variation across batches, we then applied fastMNN implemented in batchelor v1.20.0　(Haghverdi et al., 2018; doi:10.1038/nbt.4091), using the following options: cos.norm = FALSE, correct.all = TRUE, and d = 200.
Assembly: GRCm38
Supplementary files format and content: Comma-separated value files and matrix files

organism: Mus

source_name: Mouse ES cells

extract_protocol:
Differentiated cells cultured under each condition were dissociated by incubation with 0.05% trypsin/EDTA for 7 minutes at 37 °C, followed by gentle pipetting with an equal volume of DMEM supplemented with 10% FBS, 2 mM glutamine, and 1× penicillin-streptomycin. The resulting single-cell suspension was incubated with BV421-conjugated anti-hCD271 antibody, and hCD271-positive cells were subsequently sorted using a BD FACSAria Fusion. The sorted cells were centrifuged and resuspended in XXXXX buffer.
cDNA libraries were constructed using the Chromium Single Cell 3ʹ v3 Reagent Kits (10x Genomics). FACS-sorted cells were mixed with the Single Cell Master Mix to generate gel bead-in-emulsions (GEMs). Within each GEM, RNA was reverse-transcribed, and the resulting cDNAs were amplified by PCR. Sequencing libraries, adapted for the Illumina platform, were then prepared from the amplified cDNAs. The single-cell RNA-seq libraries were sequenced using paired-end reads on an Illumina HiSeq X Ten platform.

value: Induced cells

value: ES cell-derived gonadal cells

value: Male


title: MitoDiso_HeLa_ICT1_KO_1

city: Wako city

institute: RIKEN

description: Library name: L41

value: HeLa


title: CTR1_Biological Replicate1 [BS_Control_1_A1]

description:
Gene expression data from postnatal day 5 pups- brainstem tissue following 3h after inflammatory or saline stimulus
Clariom_S_Mouse.r1.na36.mm10
BS_Control_1_A1


title: AL_137

city: Pittsburgh

first: Neil

last: Carleton

address: 5051 Centre Ave

institute: University of Pittsburgh

extract_protocol:
We used the standard procedure of RNeasy kit to extract total RNA from ER+ breast cancer samples of 83 tumor or 85 tumor-adjacent normal tissue obtained from Pitt Biospecimen Core (PBC) and grouped them by chronological age.
The NovaSeq 6000 library for DNA sequencing was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) following the protocol provided by the manufacturer.
Library size and quality were checked using Fragment Analyzer (Agilent) and fluorescent quantification on the Infinite F Nano + (Tecan). The libraries were normalized and pooled, and then sequenced using the NovaSeq 6000 Platform (Illumina) to an average of 25M 101 PE reads. Sequencing data was given as raw data with a Phred Q30 score of 80 or better.

value: Tumor

value: Elderly


title: 343B-2_GEX - HC - CITEseq

description: Library name: 343B-2_GEX

value: appendix

value: B cell


title: 1_0.5Q

value: human non small cell lung cancer cell

value: WT


title: XY at D6 under ovarian condition

description: Library name: D6 XY/Ova


title: ATDC5 Day 21 rep1

description: Library name: D211


title: 343B-2_CSP - HC - CITEseq

description: Library name: 343B-2_CSP


title: 1_0.2Q+


title: XX at D6 under testicular condition

description: Library name: D6 XX/Tes

value: Female


title: ATDC5 Day 14 rep4

description: Library name: D144

value: day 14


title: XX at D6 under ovarian condition

description: Library name: D6 XX/Ova


title: 1_0.2Q

value: 0.2 mM Q


title: ATDC5 Day 14 rep3

description: Library name: D143

value: wild type


title: 318B-2_GEX - HC - CITEseq

description: Library name: 318B-2_GEX


title: 1_0Q+


title: XY at D5 under testicular condition

description: Library name: D5 XY/Tes


title: ATDC5 Day 14 rep2

description: Library name: D142


title: 318B-2_CSP - HC - CITEseq

description: Library name: 318B-2_CSP


title: 1_0Q


title: XY at D5 under ovarian condition

description: Library name: D5 XY/Ova


title: ATDC5 Day 14 rep1

description: Library name: D141


title: Whole blood RNA-seq from control participants with reported reactogenicity

city: Lausanne

first: Gustavo

last: Ruiz Buendía

address: Amphipôle, Quartier UNIL-Sorge

institute: Swiss Institute of Bioinformatics

description: Library name: ICoVax_control_reacto_whole_blood

data_processing:
nfcore rnaseq pipeline (release 3.17.0) using a modified version of the human genome (GRCh38.p13) from ensembl where the sequences corresponding to the BioNTech/Pfizer BNT-162b2 and Moderna mRNA-1273 SARS-CoV-2 spike-encoding mRNA vaccine transcripts were added.
Pseudoalignment and quantification was performed with Salmon (1.10.3). Gene-level quantification was obtained with the tximport R package (1.20.1).
Assembly: GRCh38.p13
Supplementary files format and content: Tab-delimited text file includes raw gene-level counts for each sample.

source_name: Blood

growth_protocol: Venous blood was collected in PAXgene Blood RNA Tubes (BD) for transcriptomic analysis. Blood samples were processed less than 3 hours after collection. PAXgene tubes were stored at -80ºC until RNA extraction.  Venous blood was collected in CPT tubes (BD) for peripheral blood monocuclear cell (PBMC) isolation. PBMCs were isolated by density gradient centrifugation. Red blood cells were lysed (ACK lysis buffer, Lonza) and PBMCs were resuspended in FCS containing 10% DMSO and cryopreserved in liquid nitrogen. PBMCs were thawed and cell-surface stained for 30 minutes at 4ºC and draq7 (1:500, Invitrogen) was added to exclude dead cells. Classical monocytes were sorted with a FACSAria (BD) as CD3- CD19- CD15- CD56- HLA-DR+ CD14+ CD16- cells, wheras intermediate monocytes were sorted as CD3- CD19- CD15- CD56- HLA-DR+ CD14+ CD16+.

extract_protocol:
Whole blood RNA extraction was performed with the PAXgene Blood miRNA Kit (PreAnalytix) on a QIAcube instrument following the manufacturer's instructions.  RNA extraction for sorted monocyte samples was performed with the Rneasy kit (Qiagen) following the manufacturer's instructions.  After extraction, RNA concentration and quality were assessed with a Qubit (Invitrogen) and 2100 Bioanalyzer (Agilent) respectively.
RNA libraries for whole blood samples were prepared with the Stranded Total RNA Ribo-Zero Plus kit (Illumina) with 250 ng of total RNA as input.  RNA libraries for sorted monocytes were prepared with the SMARTer + Nextera XT kit (Illumina) with 1 to 5 ng of total RNA as input.  Library molarity and quality were assessed with a Qubit and Tapestation using a DNA High sensitivity chip (Agilent). Libraries from the same biological source were pooled at equimolar amounts and sequenced on an Illumina HiSeq 4000 sequencer (whole blood) or NovaSeq 6000 (sorted monocytes) for a minimum of 30 million single-end reads per sample.

treatment_protocol: Participants were vaccinated with the Spikevax or Comirnaty COVID-19 mRNA vaccine.

value: Blood


title: uts2r3 rep 6

city: Eugene

first: Samuel

last: Bertrand

state: OR

address: 1318 Franklin Blvd

department: IMB

institute: University of Oregon

description: Library name: uts_6

data_processing:
Trimming of adaptors and low-quality reads was performed by Cutadapt
Alignment, quantification, and analysis of RNA sequencing data was performed using the Rsubread
Reads were aligned to a comprehensive transcript annotation for zebrafish in R (Lawson et al., 2020)
Read counts and differential gene expression analysis were performed using the Deseq2 Bioconductor R package
Assembly: Lawson lab transcriptome assembly (Lawson et al., 2020) and GRCz11 [danRer11.primary.fa.txt]
Supplementary files format and content: tab delimited file with all BAM files

organism: Danio rerio

source_name: whole body

extract_protocol:
Total RNA extraction was performed using a DirectZol RNA kit following manufacturer instructions for n = 5 controls and n = 5 mutants for RNA seq and n = 1 control and mutant for whole genome sequencing
Libraries were sequenced on a HiSeq 2500 using a P3 flow cell according to the manufacturer’s instructions for paired end reads.

value: whole body


title: XX at D5 under testicular condition

description: Library name: D5 XX/Tes


title: ATDC5 Day 7 rep4

description: Library name: D74

value: day 7


title: Cite-seq, old ,GEX 4

city: New York City

first: Eduardo

last: Esteva

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

description:
Library name: Old Arch mRNA sample 4
samples are 81,84, and 88 weeks old with reads split across fastqs
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz

data_processing:
Sequencing was performed on an Illumina HiSeq 4000 platform using 2 × 150 bp paired-end reads with >90% sequencing saturation. Raw sequencing data were processed using Cell Ranger Single Cell Software Suite v3.1 (10x Genomics) for demultiplexing, barcode processing, UMI counting, and generation of gene expression matrices. Downstream analyses were performed using Seurat v4.0.5 in R/RStudio. Quality control, normalization, scaling, batch correction, dimensionality reduction, neighborhood graph construction, and clustering analyses were performed using Seurat. Mitochondrial transcript content was regressed using the SCTransform function, and clustering was performed based on principal component analysis.
Assembly: mm10
Supplementary files format and content: Cellranger filtered barcode output: gene x cell matrix (.mtx.gz); features.tsv.gz; barcodes.tsv.gz
Supplementary files format and content: feature reference CSV
Library strategy: CITE-seq

source_name: Ascending thoracic aorta

extract_protocol:
Aged ATA tissues were enzymatically digested for 60 min at 37°C in a solution containing type II collagenase (10 mg/mL; Sigma Aldrich, C6885) and elastase (1 mg/mL; Worthington Biochemistry, LS002292). Digested tissues were filtered through a 70 μm cell strainer to obtain single-cell suspensions. Viable cells were enriched using a Dead Cell Removal Kit (Miltenyi Biotech, 130-090-101). Cell viability was assessed by Trypan Blue staining (0.4%; Bio-Rad, 1450013) using a TC20 automated cell counter (Bio-Rad).
Approximately 15,000 viable cells per sample were loaded onto a 10x Genomics Chromium Controller to generate gel beads-in-emulsion (GEMs). Single-cell 3′ gene expression libraries were prepared using the Chromium Single Cell 3′ Reagent Kits v2 (10x Genomics; PN-120237, PN-120236, PN-120262) according to the manufacturer’s instructions.

value: Ascending thoracic aorta


title: uts2r3 rep 5

description: Library name: uts_5


title: AL_022

value: Young


title: XY at D4 under bipotential condition

description: Library name: D4 XY

value: Induced cells

value: ES cell-derived gonadal cells

value: Male


title: uts2r3 rep 4

description: Library name: uts_4


title: ATDC5 Day 7 rep2

description: Library name: D72


title: ATDC5 Day 7 rep3

description: Library name: D73


title: Cite-seq, old ,GEX 2

description:
Library name: Old Arch mRNA sample 2
samples are 81,84, and 88 weeks old with reads split across fastqs
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz


title: uts2r3 rep 3

description: Library name: uts_3


title: XX at D4 under bipotential condition

description: Library name: D4 XX


title: ATDC5 Day 7 rep1

description: Library name: D71


title: uts2r3 rep 2

description: Library name: uts_2


title: Rep_3_rodo_high

city: Tel Aviv

first: Merav

last: Cohen

address: Chaim Levanon St 55

institute: Tel Aviv University

description: Library name: Rep_3_rodo_high

data_processing:
We generated FASTQ files from the raw BCL files using the bcl2fastq software provided by Illumina (v.2.20.0.422) with default parameters.
Next, we perfrormed QC on the fastq files using fastp with --detect-adapter-for-pe
Sequences were mapped to the mouse genome (GRCm39) using STAR (v.2.7.1a).
We processed the resulting BAM files with samtools (v.1.10) to remove duplicate mapping and mappings with low quality, as well as remove mitochondrial reads.
BigWig files were created using the bamCoverage function from deepTools (v.3.3.2)
Using bedtools (v2.27.1) we excluded established blacklist regions of the genome.
Peaks were identified, labelled and quantified using MACS3 (v.3.0.3) and featureCounts (v.2.0.0).
Assembly: GRCm39
Supplementary files format and content: BigWig files containing chromatin accessibility information for each sample.

extract_protocol:
B16: To obtain single cell suspensions of B16 tumors, the tumors were removed and weighed using an analytical scale, and then placed in RPMI-1640 supplemented with DNase (28 μg/ml, Sigma-Aldrich) and collagenase IV (1 mg/ml, Worthington). Tissues were incubated at 37 °C for 10 minutes with agitation and then pipetted through 16G, 18G, 19G and 21G needles before they were incubated again at 37 °C for 10 minutes with agitation. Cell suspensions were then washed with cold sorting buffer and pelleted. Finally, cells were bulk sorted into 4 bins according to pHrodo intensity.
The library preparation was performed…

value: Rodo high


title: Cite-seq, old ,GEX 1

description:
Library name: Old Arch mRNA sample 1
samples are 81,84, and 88 weeks old with reads split across fastqs
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz


title: ATDC5 Day 4 rep4

description: Library name: D44

value: day 4


title: Cite-seq, old ,HTO 4

description:
Library name: Old Arch HT sample 8
samples are 81,84, and 88 weeks old with reads split across fastqs
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz
feature-ref1.csv

tag: hto


title: ATDC5 Day 4 rep3

description:
Library name: D43
sample failed in processing and was therefore excluded from further analysis


title: Rep_3_rodo_int

description: Library name: Rep_3_rodo_int

value: Rodo intermediate

tag: batch


title: uts2r3 rep 1

description: Library name: uts_1

tag: genotype


title: Cite-seq, old ,HTO 3

description:
Library name: Old Arch HT sample 7
samples are 81,84, and 88 weeks old with reads split across fastqs
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz
feature-ref1.csv


title: wt rep 4

description: Library name: abc-4


title: Rep_3_rodo_low

description: Library name: Rep_3_rodo_low

value: Rodo low


title: ATDC5 Day 4 rep2

description: Library name: D42


title: Cite-seq, old ,HTO 2

description:
Library name: Old Arch HT sample 6
samples are 81,84, and 88 weeks old with reads split across fastqs
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz
feature-ref1.csv


title: wt rep 3

description: Library name: abc-3


title: ATDC5 Day 4 rep1

description: Library name: D41


title: Cite-seq, old ,HTO 1

description:
Library name: Old Arch HT sample 5
samples are 81,84, and 88 weeks old with reads split across fastqs (GEX and HTO)
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz
feature-ref1.csv


title: wt rep 2

description: Library name: abc-2


title: ATDC5 Day 0 rep4

description: Library name: D04

value: day 0


title: Cite-seq, Young ,GEX 4

description:
Library name: Young Arch mRNA sample 16
sampes are 11,12,13 weeks old with reads spread over HT and GEX fastqs; there are 3 hashtags with each one mapping to one age group
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz

extract_protocol:
Young ATA tissues were enzymatically digested for 60 min at 37°C in a solution containing type II collagenase (10 mg/mL; Sigma Aldrich, C6885) and elastase (1 mg/mL; Worthington Biochemistry, LS002292). Digested tissues were filtered through a 70 μm cell strainer to obtain single-cell suspensions. Viable cells were enriched using a Dead Cell Removal Kit (Miltenyi Biotech, 130-090-101). Cell viability was assessed by Trypan Blue staining (0.4%; Bio-Rad, 1450013) using a TC20 automated cell counter (Bio-Rad).
Approximately 15,000 viable cells per sample were loaded onto a 10x Genomics Chromium Controller to generate gel beads-in-emulsion (GEMs). Single-cell 3′ gene expression libraries were prepared using the Chromium Single Cell 3′ Reagent Kits v2 (10x Genomics; PN-120237, PN-120236, PN-120262) according to the manufacturer’s instructions.


title: Rep_2_rodo_hi

description: Library name: Rep_2_rodo_hi


title: Rep_2_rodo_int

description: Library name: Rep_2_rodo_int


title: ATDC5 Day 0 rep3

description: Library name: D03


title: Cite-seq, Young ,GEX 3

description:
Library name: Young Arch mRNA sample 15
sampes are 11,12,13 weeks old with reads spread over HT and GEX fastqs; there are 3 hashtags with each one mapping to one age group
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz


title: Rep_2_rodo_low

description: Library name: Rep_2_rodo_low


title: HeLa S3 WT METTL4 rep3

city: Pushchino

first: Andrey

middle: Igorevich

last: Buyan

state: Moskovskaya obl.

address: Institutskaya st., 4

country: Russia

institute: Institute of Protein Research

description:
Library name: WT_mRNA_3
Processed data on this series is identical to GSE299981.

data_processing:
Sequence reads were trimmed for universal illumina adapter and low-quality sequence using cutadapt (parameters -q 20 -a AGATCGGAAGAGC).
Trimmed sequence reads were mapped to GRCh38/hg38 or GRCm38/mm10 using STAR 2-pass mapping with other parameters set according to ENCODE standard long RNA-seq pipeline and STAR-Fusion default parameters.
The resulting bam files were used as input for featureCounts with gencode comprehensive v.42 or v.M20 annotation in order to calculate gene-level coverages. Next, they were used in edgeR for differential expression estimation of 13813 (human data) or 11390 (mouse data) genes with at least 3 cpm in 3 or more samples. For that, counts were normalized with calcNormFactors, followed by estimateDisp, glmQLFit and glmQLFTest.
Alternative splicing events were identified using rMATS with -t single --variable-read-length --readLength 120 options and gencode v.42 (human data) or v.M20 (mouse data) annotation.
Assembly: hg38, mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample, edgeR differential expression results for METTL4 KO vs WT (control) and the alternative splicing events from rMATS for METTL4 KO (group 2) vs WT (group 1).

source_name: HeLa S3

growth_protocol: HeLa S3 сells were cultured in DMEM/F12 medium (Gibco™: 11320033), containing 10% FBS (Gibco™: 16000044), 100 U/mL of penicillin and 100 µg/mL of streptomycin (Gibco™: 15140122) with 1% glutaMAX (Gibco™: 35050061) at 37oC, 5% CO2. Animals were kept in individually ventilated cages (IVC system, TECNIPLAST S.p.A., Italy) with free access to food and water purified by reverse osmosis, in an environment free of specific pathogens, with light regime 12/12 (light on at 09:00), in rooms with air exchange rate more than 15 r/h, at 20-24°C, humidity 30-70%. Wood chips with minimal dust formation were used as bedding. Shelters and building materials for nests made of natural materials were used as enrichment of the environment. All materials supplied to the animals were sterilized by autoclaving.

extract_protocol:
RNA was extracted using QIAzol lysis reagent (QIAGEN:79306) following the manufacturer's instructions.
NEB NEBNext Ultra II RNA Library Prep Kit for Illumina (E7770) was used for library preparation. Beads were mixed with first strand buffer, random primer and water according to the protocol provided by the manufacturer and incubated at 94°C for 12 min to get longer RNA fragments. The following steps were performed according to the protocol provided by the manufacturer, the resulting cDNA library was sequenced using HiSeq 1500.

treatment_protocol: Inactivation of METTL4 gene was done by CRISPR/Cas9 system.

value: HeLa S3

value: epithelial

value: WT


title: Cite-seq, Young ,GEX 2

description:
Library name: Young Arch mRNA sample 14
sampes are 11,12,13 weeks old with reads spread over HT and GEX fastqs; there are 3 hashtags with each one mapping to one age group
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz


title: ATDC5 Day 0 rep2

description: Library name: D02

value: wild type


title: ATDC5 Day 0 rep1

description: Library name: D01


title: Rep_2_rodo_neg

description: Library name: Rep_2_rodo_neg

value: Rodo negative


title: HeLa S3 WT METTL4 rep1

description:
Library name: WT_mRNA_1
Processed data on this series is identical to GSE299981.


title: Rep_1_rodo_hi

description: Library name: Rep_1_rodo_hi