title: SCC-25, RARG KO, 1μM Retinoic Acid, 6h, rep3

last: Hoxie

description:
Library name: RARGKO_6h_RA_3
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)

data_processing:
cDNA libraries were paired-end sequenced (2x100 cycles) on a NovaSeq X Plus instrument
raw sequencing reads were processed through Illumina bcl2fastq v.2.20 for demultiplexing and FASTQ conversion. Fastq files were merged per sample and further processed with low-quality (<Q30) base trimming and adaptor removal using Cutadapt v.3.5.
Reads were pseudoaligned with kallisto using the Homo_sapiens.GRCh38.cdna.all fasta file from Ensembl to generate an index for quantifying transcript abundances
A counts matrix of all samples was prepared using tximport from kallisto abundance files. Genes with fewer than 3/36 samples having raw counts > 10 were filtered out as low-abundance. The filtered counts matrix was used for DESeq2 input. DESeq2 in R was used for normalization and differential expression quantitation.
Assembly: GRCh38
Supplementary files format and content: tab delimited text file; DESeq2 normalized expression matrix

extract_protocol:
Total RNA was collected from the cells with 350μL Lysis Buffer RLT from RNeasy Plus Mini Kit (Qiagen, Cat. No. 74134) with 1:100 addition of β-mercaptoethanol, followed by gDNA removal and extraction according to the kit protocol.
Samples with RNA integrity number ≥ 9 were selected for cDNA library preparation with NEB Ultra II Directional RNA Library Prep (plus Poly A isolation module) according to the manufacturer’s instructions.

treatment_protocol: SCC-25 cells (3 x 105) were seeded in 6-well plates. Parental and RARG KO cells were each treated in triplicate with either Vehicle (DMSO, 0.01% final concentration), 1µM all-trans Retinoic Acid (RA), or 1µM CD1530 for 6 hours or 48 hours.

value: Head and Neck Cancer Cells

value: RARG knockout

value: 1 μΜ RA

tag: time


title: SCC-25, RARG KO, 1μM Retinoic Acid, 6h, rep1

status: Public on Dec 12 2025

type: SRA

city: New York

first: Helen

state: NY

address: 1300 York Avenue

department: Pharmacology

country: USA

institute: Weill Cornell Medical College

description:
Library name: RARGKO_6h_RA_1
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

growth_protocol: Human SCC-25 oral squamous carcinoma cells (CRL-1628 ATCC) were cultured in DMEM/F-12 (Thermo, Cat No. 11320033) supplemented with 100U/mL Pen Strep and hydrocortisone (400 ng/ml) and 10% FBS.

tag: cell line

tag: cell type

tag: genotype

tag: treatment

tag: batch


title: D600-JEPI1

first: Peter

middle: A

last: Sims

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

description: Library name: D600_001_ATAC_ABFNY-0157

library_source: genomic single cell

data_processing:
Alignment to the GRCh38 reference and demultiplexing of cell-identifying barcodes was performed using Cell Ranger ATAC (v.2.0.0, 10x Genomics).
Assembly: GRCh38
Supplementary files format and content: The processed files are gzip-compressed, tab-delimited files tabulating the alignment position (chromosome, start, end), cell-identifying barcode, and read count for each unique fragment sequenced in an snATAC-seq library.

molecule: genomic DNA

source_name: jejunum epithelium

extract_protocol:
Mononuclear cell suspensions were prepared from dissociated human lung tissue using the detailed protocol "Preparation of Single Cell Suspension from Human Lung Tissue" on protocols.io (dx.doi.org/10.17504/protocols.io.bwr9pd96). After dissection of the epithelium and lamina propria, mononuclear cell suspensions were prepared from dissociated human jejunum tissue using the detailed protocol "Preparation of Single Cell Suspensions of the Intra-Epithelial Layer and Lamina Propria from Human Intestinal Tissue" on protocols.io (dx.doi.org/10.17504/protocols.io.bwq7pdzn). The resulting single-cell suspensions from both tissue sites were cryopreserved and stored in liquid nitrogen. For snATAC-seq, cryopreserved cells were thawed rapidly at 37°C until small ice crystals remained. Cells were transferred into pre-warmed culture medium and gradually diluted to minimize shock. Following centrifugation, pellets were gently resuspended and treated with Benzonase (Millipore Sigma) to reduce cell clumping. Cells were washed in DPBS containing FBS and EDTA, and viability was assessed by fluorescence microscopy-based cell counting (Chemometec NC-3000). Finally, dead cells and contaminating populations (e.g., CD66b+, CD235ab+, and EpCAM+ cells) were removed using magnetic bead–based depletion (Miltenyi Biotec; BioMag Plus Streptavidin). Nuclei were prepared following the 10x Genomics protocol for single-cell ATAC sequencing (CG000169 Rev D) with minor adjustments. Briefly, 1 × 106 cells per sample were pelleted and resuspended in chilled lysis buffer containing detergents (Tween-20, NP-40 substitute, and digitonin) and BSA. After a brief incubation on ice, lysates were diluted in wash buffer and centrifuged to pellet intact nuclei.
Nuclei were resuspended in diluted nuclei buffer, counted by hemocytometer, and adjusted to a concentration corresponding to ~8,000 nuclei for loading into the 10x Genomics Chromium Controller for encapsulation and barcoding. Sequencing libraries were prepared using Chromium Next GEM Single Cell ATAC Reagent Kits v2 (10x Genomics) and sequenced on an Illumina NovaSeq X Plus with 2x100 paried-end reads.

tag: tissue

value: jejunum epithelium

tag: organ donor

value: Immune cells


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Pre-Splice, BiolRep 12

city: St. Louis

first: Joseph

middle: D

last: Dougherty

state: MO

address: 4370 Duncan Ave

department: Genetics

institute: Washington University in St. Louis

description: Library name: 3UTR.ms12.cortex.pre

data_processing:
Sequencing reads were aligned to reference libraries using custom scripts to identify exact matches, normalized with edgeR (TMM method) to CPM, filtered for low counts, and used to calculate log₂(RNA/DNA) expression or translational efficiency (TRAP), with variant pairs filtered to retain those with ≥4 measurements across conditions.
Assembly: hg38
Supplementary files format and content: raw files = fastq.gz , processed files = .txt

organism: Mus musculus

source_name: brain

growth_protocol: In Vitro: HEK cells were maintained in EMEMsupplemented with 10%FBS and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol Reagent and Zymo Clean and Concentrator Kit. 5ug of RNA per replicate were used for Library Preparation.
RNA libraries for RNA-seq were prepared using a targeted-RNA seq library preparation approach that followed similar paradigms to a Tru-Seq library construction for Illumina Sequencing.

treatment_protocol: In Vitro: Transfection was induced on 24 hours after plating and then cells were harvested 48hours after using Trizol. In Vivo: Mice were injected with AAV virus at PND1 and allowed to age until date of harvest; PND10 for Empra/eISOMPRA, PND21 for uISOMPRA

value: brain

value: uISOMPRA Library AAV Infection

tag: cre status

value: Homozygous

tag: Sex

value: F


title: C1_evolved

city: Hanover

first: Soni

last: Lacefield

state: New Hampshire

address: 74 College St

department: Biochemistry and Cell Biology

institute: Geisel School of medicine at Dartmouth

description: Library name: 174199_35

library_source: genomic

data_processing:
Raw reads were trimmed with Trimmomatic v0.39, with the following parameters, “ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:2:keepBothReads LEADING:3 TRAILING:3 MINLEN:36”.  Trimmed reads were aligned to the Yeast genome S288C, available at NCBI accession GCF_000146045.2, using BWA 0.7.17, with default parameters.  Duplicate reads were marked with “MarkDuplicates” from Picard tools v2.27.1, with default parameters.
SNPs and small indels were called with FreeBayes v1.3.4 and the following parameters “--min-coverage 5 --limit-coverage 200 --min-alternate-fraction .2 --min-mapping-quality 15 --min-alternate-count 2”.  SNPs were annotated using SNPEff v5.0e.
Copy number analysis was performed using the following commands from the Genome Analysis Tool Kit (GATK) v4.5.0.0. Genome intervals for calculating copy number were determined with the PreprocessIntervals command, with the following parameters, “--padding 0 -imr OVERLAPPING_ONLY”.  Reads counts for each sample and each interval were collected using the CollectReadCounts command, with default parameters.  Copy number per interval was standardized and denoised using the DenoiseReadCounts command, with the “--standardized-copy-ratios” and “--denoised-copy-ratios” parameters.  Genome-wide copy number graphs were created by plotting columns 2 (“START”) and 4 (“LOG2_COPY_RATIO”) of the denoised copy ratio output.
Assembly: GCF_000146045.2
Supplementary files format and content: The TSV files contain the processed data (log2 ratios) used for plotting the copy number variation graphs.
Library strategy:

organism: Saccharomyces cerevisiae

source_name: overnight grown culture of Saccharomyces cerevisiae

extract_protocol:
Genomic DNA was isolated from individual samples using the Phenol/Chloroform/Isoamyl alcohol method and washed with 70% ethanol to get good quality samples.
Input DNA was quantified by Qubit (Thermo Fisher) and 200ng was used as input into the Nextera DNA with tagmentation workflow (Illumina) to generate Illumina sequencing libraries according to the manufacturer’s protocol. Libraries were normalized and pooled for sequencing on a NextSeq2000 (Illumina), targeting 10 million, 150bp paired-end reads per sample.

tag: strain


title: iv AAV-Luc_Satellite cell

city: Muraoka-Higashi 2-chome Fujisawa, Kanagawa

first: Taisuke

last: Mochida

country: Japan

institute: Takeda Pharmaceutical Company Limited

description: Library name: TMs40_2-8

library_source: transcriptomic single cell

data_processing:
Sequenced reads were aligned to the mouse mm10 reference and quantified UMI counts using Cell Ranger v7.0.1 software.
Gene barcode matrices were generated from Cell Ranger software.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Skeletal muscle

extract_protocol: Single-cell RNA-seq libraries were generated using the 10x Genomics ChromiumTM controller and Chromium Single Cell 3' kits v3.1 (10x Genomics) according to the manufacturer’s instructions.

value: Skeletal muscle

value: Satellite cells

value: DMD mouse model

value: iv AAV-Luc_Satellite cell


title: SCC-25, PAR, 1μM Retinoic Acid, 6h, rep3

description:
Library name: PAR_6h_RA_3
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)

value: Parental


title: A3_evolved

description: Library name: 174199_31

value: overnight grown culture of Saccharomyces cerevisiae


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Post-Splice, BiolRep 11

description: Library name: 3UTR.ms11.exn.post


title: BAT, HFD+PTE, rep 1

city: Chongqing

first: Xiujuan

last: Jiang

address: Tiansheng road

country: China

institute: Southwest University

description:
Library name: BAT_HFD_T_1
HFD_T_1

data_processing:
Raw paired-end sequencing reads were quality-controlled and adapter-trimmed using fastp (v0.23.4) with default parameters to obtain clean reads.
The clean reads were aligned to the mouse reference genome (GRCm39) in orientation mode using HISAT2 (v2.2.1).
Transcript assembly and quantification were performed using StringTie (v2.2.1) with a reference-based approach. Gene expression levels were quantified as TPM (Transcripts Per Million) using RSEM (v1.3.3).
Differential gene expression analysis was performed using DESeq2 (v1.34.0). Genes with |log2(fold change)| ≥ 1 and a false discovery rate (FDR) < 0.05 were considered significantly differentially expressed.
Assembly: GRCm39 (GCF_000001635.27)
Supplementary files format and content: File: Exp_G_RSEM_TPM.csv is a tab-delimited text file containing gene expression levels quantified as TPM (Transcripts Per Million) by the RSEM software. The file includes data for all 623 genes across all 8 samples.

molecule: polyA RNA

source_name: brown adipose tissue

growth_protocol: Male C57BL/6J mice (6 weeks old) were fed a high-fat diet (60% kcal from fat) for 16 weeks to establish the obesity model. Mice were housed under specific pathogen-free conditions at 22±2°C with a 12-hour light/dark cycle.

extract_protocol:
Total RNA was extracted from brown adipose tissue using TRIzol® Reagent according to the manufacturer’s instructions. RNA quality was assessed using an ND-2000 spectrophotometer (NanoDrop Technologies) and a 5300 Bioanalyzer (Agilent Technologies). Only high-quality RNA samples (OD260/280=1.8-2.2, OD260/230≥2.0, RQN≥6.5, 28S:18S ratio≥1.0, total amount>1 μg) were used for subsequent library construction.
Sequencing libraries were constructed using the Illumina® Stranded mRNA Prep, Ligation kit. Briefly, mRNA was isolated by polyA selection using oligo(dT) beads, fragmented, and then used for double-stranded cDNA synthesis with random hexamer primers. The cDNA underwent end repair, phosphorylation, adapter ligation, size selection (targeting ~300 bp fragments), and PCR amplification (15 cycles). Library quantification was performed using Qubit 4.0.

treatment_protocol: The intervention group (HFD+PTE) received 0.25% (w/v) Pu-erh tea extract (PTE) ad libitum in drinking water for 16 weeks concurrently with high-fat diet feeding. PTE was prepared by hot-water extraction of ripened Pu-erh tea followed by lyophilization.

value: brown adipose tissue

value: high fat diet + Pu-erh tea extract


title: SCC-25, RARG KO, 1μM Retinoic Acid, 6h, rep2

description:
Library name: RARGKO_6h_RA_2
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)

value: Head and Neck Cancer Cells


title: SCC-25, PAR, 1μM Retinoic Acid, 6h, rep2

description:
Library name: PAR_6h_RA_2
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)


title: A3_non-evolved

description: Library name: 174199_04


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Pre-Splice, BiolRep 11

description: Library name: 3UTR.ms11.exn.pre


title: SCC-25, PAR, 1μM Retinoic Acid, 6h, rep1

description:
Library name: PAR_6h_RA_1
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Post-Splice, BiolRep 11

description: Library name: 3UTR.ms11.cortex.post


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Pre-Splice, BiolRep 11

description: Library name: 3UTR.ms11.cortex.pre


title: PBS_Satellite cell

description: Library name: TMs40-5

value: PBS_Satellite cell


title: PBS-2_Satellite cell

description: Library name: TMs40_2-7

value: PBS-2_Satellite cell


title: im LNP-Luc_Satellite cell

description: Library name: TMs40_2-6

value: im LNP-Luc_Satellite cell


title: A2_evolved

description: Library name: 174199_30


title: SCC-25, PAR, 1μM CD1530, 6h, rep3

description:
Library name: PAR_6h_CD1530_3
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)


title: SCC-25, PAR, 1μM CD1530, 6h, rep2

description:
Library name: PAR_6h_CD1530_2
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Pre-Splice, BiolRep 10

description: Library name: 3UTR.ms10.cortex.pre

value: M


title: iv LNP-Luc_Bulk

description: Library name: TMs40-4

value: Bulk

value: iv LNP-Luc_Bulk


title: A1_evolved

description: Library name: 174199_29


title: DE-DKO-Input

first: Julian

last: Pulecio

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

description: Library name: DE-DKO-Input

data_processing:
Paired-end reads were mapped to hg19 reference genome with bowtie2 using default parameters. Unmapped, duplicate and multi-mapping reads were removed using sambamba. Peaks were called using macs2 with p-value threshold of 0.01. Bigwig files were generated using the bamCoverage function in deepTools with CPM normalization.
Assembly: hg19
Supplementary files format and content: bigwig

source_name: Definitive Endoderm

growth_protocol: hESCs were cultured in Essential 8 (E8) medium (Thermo Fisher Scientific, A1517001) on vitronectin (VTN) (Thermo Fisher Scientific, A14700) pre-coated plates at 37 °C with 5% CO2. Medium was changed every day. Cells were passaged every 4-5 days at a ratio 1:15-20 using 0.5 mM EDTA (KD Medical, RGE-3130) or TrypLE Select (Gibco, 12563029) to dissociate cells. 5 μM Rho-associated protein kinase (ROCK) inhibitor Y-27632 (Selleck Chemicals, S1049) was added into the E8 media when passaging or thawing hESCs.

extract_protocol:
Cells were crosslinked by formaldehyde and lysated by SDS lysis buffer. Sonicated nuclei were incubated with antibody overnight and then pulled down by dynabeads. After washing, decrosslinking was performed to isolate DNA.
Libraries were generated by the NEBNext® Ultra II DNA Library Prep Kit (New England Biolabs; E7103S) and NEBNext® Multiplex Oligos for Illumina® (New England Biolabs Index Primers Set 1; NEB, E7335S). Samples were QC on a Bioanalyzer(Agilent) and sequenced on an Illumina NovaSeq X sequencer by the Integrated Genomic Operation(IGO) Core Facility at the MSKCC.

treatment_protocol: hESCs were seeded into VTN-coated 6well plates (4x105 per well), grown for 48 hours in E8 medium. After washing E8 away with PBS, cells were cultured in S1/2 medium, supplemented with Activin A (100ng/ml) and CHIR99021 (Stemgent, 04-0004-10) (5 µM on the 1st day and 0.5 µM on the 2nd day) for three days.  Cells reached early Definitive Endoderm (DE) at day 2 and were used for H3K27ac ChIP-Seq experiments.

value: Definitive Endoderm


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Post-Splice, BiolRep 9

description: Library name: 3UTR.ms9.exn.post

value: brain

value: uISOMPRA Library AAV Infection

value: Homozygous


title: SCC-25, PAR, 1μM CD1530, 6h, rep1

description:
Library name: PAR_6h_CD1530_1
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Pre-Splice, BiolRep 9

description: Library name: 3UTR.ms9.exn.pre


title: SCC-25, RARG KO, Vehicle, 6h, rep3

description:
Library name: RARGKO_6h_Veh_3
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)

value: RARG knockout

value: Vehicle


title: iv LNP-Luc_Satellite cell

description: Library name: TMs40-8

value: Skeletal muscle

value: Satellite cells

value: DMD mouse model

value: iv LNP-Luc_Satellite cell


title: SCC-25, RARG KO, 1μM CD1530, 6h, rep1

description:
Library name: RARGKO_6h_CD1530_1
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)

value: Head and Neck Cancer Cells


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Pre-Splice, BiolRep 9

description: Library name: 3UTR.ms9.cortex.pre


title: EPOP-WT EpiLCs, Elongin B KD, MTF2, Replicate 2, ChIP

city: Dallas

first: Xin

last: Liu

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

data_processing:
The raw sequencing reads were trimmed by Cutadapt
The trimmed reads were mapped by Bowtie 2 with the “--very-sensitive” parameter
The aligned reads were filtered by SAMtools using the “-F 1804 -f 2 -q 30” parameter. Duplicates were removed by Picard
Duplicates were removed by Picard. ChIP-seq peaks were called by MACS2 using the “-f BAMPE -q 0.05 --broad” parameter.
Genome browser tracks bigwig files were generated by bamCoverage from deepTools.
Assembly: mm10
Supplementary files format and content: BigWig

source_name: EpiLCs differentiated from E14 mESCs

growth_protocol: mESCs were cultured on 0.2% gelatin-coated plates in 2i/LIF medium (1:1 mix of DMEM/F-12 and Neurobasal medium supplemented with 1 × Pen/Strep, 0.05% BSA, 1 mM GlutaMAX, 100 μM β-mercaptoethanol, 0.5 × N2 supplement, 1 × B27 supplement, 1 μM MEK inhibitor PD0325901, 3 μM GSK3 inhibitor CHIR99021, and home-made LIF).  For the EpiLC differentiation, 1.5 million mESCs were plated on a 10 cm dish coated with human fibronectin (16.7 μg/ml) in N2B27 medium (1:1 mix of DMEM/F-12 and Neurobasal medium supplemented with containing 1 × Pen/Strep, 2 mM GlutaMAX, 50 μM β-mercaptoethanol, 0.5 × N2 supplement, 0.5 × B27 supplement, 20 ng/ml activin A, 12 ng/ml bFGF, and 1% KSR). The medium was replaced every day until 48 hours before cell collection.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 minutes. Formaldehyde was quenched with 0.125 M Glycine for 5 minutes before two PBS washes. Chromatin was prepared using the SimpleChIP kit from Cell Signalig Technology.
Libraries were constructed using the NEBNext Ultra II kit from NEB with 8 ng DNA from ChIP.

value: EpiLCs differentiated from E14 mESCs

value: Epiblast-like cells

value: Re-expression of WT EPOP with Elongin B KD


title: PBS_Bulk

description: Library name: TMs40-1


title: wildtype_LY1_evolved

description: Library name: 174199_28

value: overnight grown culture of Saccharomyces cerevisiae


title: SCC-25, RARG KO, Vehicle, 6h, rep2

description:
Library name: RARGKO_6h_Veh_2
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Post-Splice, BiolRep 9

description: Library name: 3UTR.ms9.cortex.post

value: M


title: DE-WT-Input

description: Library name: DE-WT-Input

value: WT


title: wildtype_LY1_non-evolved

description: Library name: 174199_01


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Post-Splice, BiolRep 10

description: Library name: 3UTR.ms10.cortex.post


title: SCC-25, RARG KO, 1μM CD1530, 6h, rep3

description:
Library name: RARGKO_6h_CD1530_3
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)


title: DE-DKO-H3K27ac-1

description: Library name: DE-DKO-H3K27ac-1

value: Definitive Endoderm


title: DE-WT-H3K27ac-2

description: Library name: DE-WT-H3K27ac-2


title: DE-DKO-H3K27ac-2

description: Library name: DE-DKO-H3K27ac-2


title: EPOP-WT EpiLCs, Elongin B KD, MTF2, Replicate 1, ChIP


title: ESC-DKO-Input

description: Library name: ESC-DKO-Input

source_name: Embryonic Stem Cells

value: Embryonic Stem Cells


title: iv AAV-Luc_Bulk

description: Library name: TMs40_2-4

value: Bulk

value: iv AAV-Luc_Bulk


title: SCC-25, RARG KO, Vehicle, 6h, rep1

description:
Library name: RARGKO_6h_Veh_1
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)

value: RARG knockout


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Post-Splice, BiolRep 8

description: Library name: 3UTR.ms8.cortex.post

value: brain

value: uISOMPRA Library AAV Infection

value: Homozygous


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Pre-Splice, BiolRep 8

description: Library name: 3UTR.ms8.exn.pre


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Pre-Splice, BiolRep 8

description: Library name: 3UTR.ms8.cortex.pre


title: SCC-25, PAR, Vehicle, 6h, rep1

description:
Library name: PAR_6h_Veh_1
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)

value: Parental

value: Vehicle


title: EPOP-WT EpiLCs, Elongin B KD, Input, Replicate 2, ChIP


title: A2_non-evolved

description: Library name: 174199_03


title: SCC-25, PAR, Vehicle, 6h, rep3

description:
Library name: PAR_6h_Veh_3
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)

value: Head and Neck Cancer Cells


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Post-Splice, BiolRep 8

description: Library name: 3UTR.ms8.exn.post


title: EPOP-WT EpiLCs, Control KD, MTF2, Replicate 1, ChIP

value: EpiLCs differentiated from E14 mESCs

value: Re-expression of WT EPOP with control KD


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Post-Splice, BiolRep 7

description: Library name: 3UTR.ms7.exn.post


title: EPOP-WT EpiLCs, Elongin B KD, Input, Replicate 1, ChIP

value: Epiblast-like cells

value: Re-expression of WT EPOP with Elongin B KD


title: SCC-25, RARG KO, 1μM CD1530, 6h, rep2

description:
Library name: RARGKO_6h_CD1530_2
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)


title: ESC-WT-Input

description: Library name: ESC-WT-Input


title: ESC-DKO-H3K27ac-2

description: Library name: ESC-DKO-H3K27ac-2


title: SCC-25, PAR, Vehicle, 6h, rep2

description:
Library name: PAR_6h_Veh_2
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)


title: EPOP-WT EpiLCs, Control KD, MTF2, Replicate 2, ChIP


title: DE-WT-H3K27ac-1

description: Library name: DE-WT-H3K27ac-1


title: ESC-DKO-H3K27ac-1

description: Library name: ESC-DKO-H3K27ac-1


title: SCC-25, RARG KO, 1μM Retinoic Acid, 48h, rep3

description:
Library name: RARGKO_48h_RA_3
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)

value: 1 μΜ RA


title: SCC-25, RARG KO, 1μM Retinoic Acid, 48h, rep2

description:
Library name: RARGKO_48h_RA_2
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)


title: EPOP-WT EpiLCs, Control KD, Input, Replicate 2, ChIP


title: ESC-WT-H3K27ac-1

description: Library name: ESC-WT-H3K27ac-1

value: WT


title: SCC-25, RARG KO, 1μM Retinoic Acid, 48h, rep1

description:
Library name: RARGKO_48h_RA_1
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)


title: SCC-25, PAR, 1μM Retinoic Acid, 48h, rep2

description:
Library name: PAR_48h_RA_2
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Post-Splice, BiolRep 7

description: Library name: 3UTR.ms7.cortex.post

value: M


title: ESC-WT-H3K27ac-2

description: Library name: ESC-WT-H3K27ac-2

value: Embryonic Stem Cells


title: EPOP-Mutant EpiLCs, Elongin B KD, MTF2, Replicate 1, ChIP

value: Re-expression of mutant EPOP with Elongin B KD


title: DE-DKO-ATAC-2

description: Library name: DE-DKO-ATAC-2

extract_protocol:
200000 fresh cells were washed in cold PBS and lysed.
Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq) was performed as previously described (https://doi.org/10.1038/nmeth.2688). The transposition reaction containing TDE1 Tagment DNA Enzyme (Illumina; 20034198) was incubated at 37°C for 30 minutes. The DNA was purified with the MinElute PCR Purification Kit (QIAGEN; 28004) and amplified for 5 cycles using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs; M0541L). After evaluation by real-time PCR, 3-14 additional PCR cycles were done. The final product was cleaned by AMPure XP beads (Beckman Coulter; A63882) at a 1X ratio, and size selection was performed at a 0.5X ratio. Libraries were sequenced on a NovaSeq X platform (10B flow cell) in a PE100 run (200 Cycles) (Illumina).

value: Definitive Endoderm


title: EPOP-WT EpiLCs, Control KD, Input, Replicate 1, ChIP


title: EPOP-Mutant EpiLCs, Elongin B KD, Input, Replicate 2, ChIP


title: SCC-25, PAR, 1μM Retinoic Acid, 48h, rep3

description:
Library name: PAR_48h_RA_3
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Post-Splice, BiolRep 6

description: Library name: 3UTR.ms6.exn.post


title: EPOP-Mutant EpiLCs, Elongin B KD, Input, Replicate 1, ChIP


title: EPOP-Mutant EpiLCs, Elongin B KD, MTF2, Replicate 2, ChIP


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Pre-Splice, BiolRep 7

description: Library name: 3UTR.ms7.cortex.pre


title: DE-DKO-ATAC-1

description: Library name: DE-DKO-ATAC-1


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Pre-Splice, BiolRep 6

description: Library name: 3UTR.ms6.exn.pre


title: SCC-25, RARG KO, 1μM CD1530, 48h, rep2

description:
Library name: RARGKO_48h_CD1530_2
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)

value: RARG knockout


title: SCC-25, PAR, 1μM Retinoic Acid, 48h, rep1

description:
Library name: PAR_48h_RA_1
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)


title: SCC-25, RARG KO, 1μM CD1530, 48h, rep3

description:
Library name: RARGKO_48h_CD1530_3
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)


title: DE-WT-ATAC-1

description: Library name: DE-WT-ATAC-1


title: EPOP-Mutant EpiLCs, Control KD, MTF2, Replicate 2, ChIP

value: Re-expression of mutant EPOP with control KD


title: PBS-2_Bulk

description: Library name: TMs40_2-3

value: Skeletal muscle

value: Bulk

value: DMD mouse model


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Post-Splice, BiolRep 6

description: Library name: 3UTR.ms6.cortex.post

value: brain

value: uISOMPRA Library AAV Infection

value: Homozygous


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Pre-Splice, BiolRep 7

description: Library name: 3UTR.ms7.exn.pre


title: EPOP-Mutant EpiLCs, Control KD, MTF2, Replicate 1, ChIP

value: EpiLCs differentiated from E14 mESCs


title: A1_non-evolved

description: Library name: 174199_02

value: overnight grown culture of Saccharomyces cerevisiae


title: SCC-25, RARG KO, 1μM CD1530, 48h, rep1

description:
Library name: RARGKO_48h_CD1530_1
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)

value: Head and Neck Cancer Cells


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Pre-Splice, BiolRep 6

description: Library name: 3UTR.ms6.cortex.pre


title: EPOP-Mutant EpiLCs, Control KD, Input, Replicate 1, ChIP

value: Epiblast-like cells


title: A375 cells, DUS1L knockout, RNA-seq, replicate 3

city: Beijing

first: Jingkun

last: Yi

address: XueYuan Road No 38

department: School of Basic Medical Sciences

institute: Peking University

description:
Library name: DUS1LKO3
RNA-seq of DUS1L knockout A375 human melanoma cells, replicate 3

data_processing:
Raw reads were subjected to quality control, including adaptor trimming and removal of low-quality reads, using the standard BGISEQ-500 pipeline.
Assembly: Homo sapiens GRCh38 (hg38)
Supplementary files format and content: Gene-level expression matrix provided as a tab-delimited text file. Rows correspond to genes and are labeled by Ensembl gene IDs with version numbers (column "gene_id"). Columns correspond to samples (WT1, WT2, WT3, DUS1LKO1, DUS1LKO2, DUS1LKO3). Values represent gene-level expression values (normalized read counts) for each sample.

source_name: skin

growth_protocol: A375 human melanoma cells were maintained in DMEM supplemented with 10% fetal bovine serum and antibiotics at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. RNA concentration and purity were measured using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific), and RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies). Only samples with RNA integrity number (RIN) ≥ 7 were used for library preparation.
Indexed RNA-seq libraries were constructed after reverse transcription and cDNA synthesis following the standard protocol recommended by the sequencing provider. Libraries were quantified and pooled, and paired-end sequencing was performed on a BGISEQ-500 platform (Beijing Genomics Institute, Beijing, China).

treatment_protocol: A375 cells were engineered to generate DUS1L knockout and wild-type control lines. DUS1L knockout was achieved using CRISPR/Cas9-mediated gene editing targeting the DUS1L locus, followed by clonal selection and validation. Wild-type cells were maintained in parallel without DUS1L targeting.

value: skin

value: melanoma cells

value: DUS1L knockout


title: EPOP-Mutant EpiLCs, Control KD, Input, Replicate 2, ChIP


title: ESC-DKO-ATAC-1

description: Library name: ESC-DKO-ATAC-1

value: Embryonic Stem Cells


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Post-Splice, BiolRep 5

description: Library name: 3UTR.ms5.cortex.post

value: M


title: SCC-25, PAR, 1μM CD1530, 48h, rep1

description:
Library name: PAR_48h_CD1530_1
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)

value: Parental


title: SCC-25, PAR, 1μM CD1530, 48h, rep3

description:
Library name: PAR_48h_CD1530_3
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)


title: ESC-DKO-ATAC-2

description: Library name: ESC-DKO-ATAC-2


title: DE-WT-ATAC-2

description: Library name: DE-WT-ATAC-2

value: Definitive Endoderm

value: WT


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Pre-Splice, BiolRep 5

description: Library name: 3UTR.ms5.cortex.pre


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Post-Splice, BiolRep 5

description: Library name: 3UTR.ms5.exn.post


title: ESC-WT-ATAC-1

description: Library name: ESC-WT-ATAC-1


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Pre-Splice, BiolRep 10

description: Library name: 3UTR.ms10.exn.pre


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Post-Splice, BiolRep 4

description: Library name: 3UTR.ms4.exn.post


title: WES_sample

city: Cambridge

first: Gavin

middle: R

last: Schnitzler

state: Massachusetts

address: 415 Main St., Broad Institute

department: CVDi

institute: Broad Institute

description: Library name: WES_sample

data_processing:
Reads were mapped to the human hg38/GRCh38 genome build, and counts per gene tables assembled using kallisto
Differential expression calls were made using edgeR
To map sequences to all locations in the genome (not just known transcript exons), we used Bowtie2, with conversion from .sam to .bam format using Samtools
Assembly: hg38/GRCh38
Supplementary files format and content: text file with transcripts per million (TPM) values for each symbol for each sample

source_name: blood

growth_protocol: Fresh blood was collected from the proband and one control patient and peripheral blood mononuclear cells were isolated using Ficoll-Paque™ PLUS density gradient media (Cytiva).

extract_protocol:
Total RNA was harvested using the RNEasy kit (Qiagen) and mRNA was purified from 125ng of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation module (NEB)
PolyA+ RNA was prepared for RNA-seq using the NEBNext Ultra II RNA Library Kit for Illumina (NEB)

value: blood


title: SCC-25, RARG KO, Vehicle, 48h, rep3

description:
Library name: RARGKO_48h_Veh_3
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)

value: RARG knockout

value: Vehicle


title: JA_sample

description: Library name: JA_sample

value: CCM


title: A375 cells, DUS1L knockout, RNA-seq, replicate 2

description:
Library name: DUS1LKO2
RNA-seq of DUS1L knockout A375 human melanoma cells, replicate 2


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Pre-Splice, BiolRep 5

description: Library name: 3UTR.ms5.exn.pre

value: brain

value: uISOMPRA Library AAV Infection

value: Homozygous


title: A375 cells, DUS1L knockout, RNA-seq, replicate 1

description:
Library name: DUS1LKO1
RNA-seq of DUS1L knockout A375 human melanoma cells, replicate 1


title: ESC-WT-ATAC-2

description: Library name: ESC-WT-ATAC-2


title: HEK293 cells, ISOMPRA 3'UTR Mutated Control Library Transfected, Post-Splice BiolRep6

description: Library name: 3UTR.control.post.6

data_processing:
Sequencing reads were aligned to reference libraries using custom scripts to identify exact matches, normalized with edgeR (TMM method) to CPM, filtered for low counts, and used to calculate log₂(RNA/DNA) expression or translational efficiency (TRAP), with variant pairs filtered to retain those with ≥4 measurements across conditions.
Assembly: hg38

source_name: kidney

value: kidney

value: human embryonic kidney cells

value: ISOMPRA Library Transfection


title: SCC-25, PAR, 1μM CD1530, 48h, rep2

description:
Library name: PAR_48h_CD1530_2
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)

value: Head and Neck Cancer Cells


title: A375 cells, wild-type, RNA-seq, replicate 3

description:
Library name: WT3
RNA-seq of wild-type A375 human melanoma cells, replicate 3

value: skin

value: melanoma cells

value: wild-type


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Pre-Splice, BiolRep 4

description: Library name: 3UTR.ms4.exn.pre

value: M


title: SCC-25, RARG KO, Vehicle, 48h, rep1

description:
Library name: RARGKO_48h_Veh_1
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Post-Splice, BiolRep 4

description: Library name: 3UTR.ms4.cortex.post


title: SCC-25, RARG KO, Vehicle, 48h, rep2

description:
Library name: RARGKO_48h_Veh_2
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Pre-Splice, BiolRep 4

description: Library name: 3UTR.ms4.cortex.pre


title: A375 cells, wild-type, RNA-seq, replicate 2

description:
Library name: WT2
RNA-seq of wild-type A375 human melanoma cells, replicate 2


title: HEK293 cells, ISOMPRA 3'UTR Mutated Control Library Transfected, Post-Splice BiolRep4

description: Library name: 3UTR.control.post.4


title: SCC-25, PAR, Vehicle, 48h, rep1

description:
Library name: PAR_48h_Veh_1
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)

value: Parental


title: HEK293 cells, ISOMPRA 3'UTR Mutated Control Library Transfected, Post-Splice BiolRep3

description: Library name: 3UTR.control.post.3

value: WT


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Post-Splice, BiolRep 3

description: Library name: 3UTR.ms3.exn.post


title: Lung Cells, KO uninfected

city: Omaha

first: Sankarasubramanian

last: Jagadesan

state: NE

address: 42end and Emile st

department: Department of Genetics, Cell Biology & Anatomy

institute: University of Nebraska Medical Center

description:
Library name: KOPBS_2447
scRNASeq

data_processing:
The demultiplexing cell count were processed using Cell Ranger 7.1.0
Assembly: Mouse mm10
Supplementary files format and content: Processed data are provided in barcode, matrix, feature and H5 files.

source_name: lung

extract_protocol:
Lungs were perfused with 10mL heparin-PBS, then removed. Lungs were then perfused with 500ul of digestion buffer ( HBSS, 0.3 mg/mL Liberase and 157 U/ul DNase I), and transferred to a C-tube (Miltenyi Biotech) for mechanical disassociation using gentleMACS (Miltenyi Biotech), default program m_lung_01. Samples were then placed in a shaking incubator for 15 minutes at 37oC. Mechanical disassociation was repeated using the gentleMACS using default program m_lung_2.  Reaction was neutralized with 6.5 mL of ice-cold FA3 buffer (PBS, 10mM HEPES, 2mM EDTA, 1% FBS).  Cells were filtered using a 70 um cell strainer.  Strainer was rinsed with 2mL FA3 buffer. Cells were then pelletted by centrifugation (300xg for 5 minutes at 4oC). Supernant was discarded and RBC lysis was performed by adding 1mL of 1x RBC Lysis buffer (BioLegend). Cells were mixed by pipetting and incubated at room temperature for 1 min.  Reaction was neutralized by adding 7 mL of FA3 buffer. Cell suspension was filtered over a 40 um cell strainer and rinsed with 2 mL FA3 buffer.  Cells were again pelleted and supernant discarded.  Dead cells were removed using Dead Cell Removal kit (Miltenyi Biotech) according to manufacture protocol.  Cells were transferred into FACS buffer (PBS, 2% FBS, 0.1% sodium azide). Viability and counts were assessed using TC-20 cell counter (BioRad) and 1x10^6 cells/mL were submitted for scRNA-seq.
Lungs from 1 mouse per treatment group were processed as previously described.Briefly, the lungs were perfused with 10 mL of heparin-PBS. The GentleMACS dissociator (Miltenyi Biotech) was used to separate the harvested lungs from the digesting solution (collagenase I, 0.2 μg/μL + DNase I, 75 U/mL + heparin, 1.5 U/mL) in Dulbecco's Modified Eagle’s Media (DMEM). Samples were shaken for 30 minutes at 37oC.  PBS with 4 mM EDTA was used to counteract the activity of the digestion solution. Red blood cells were lysed for 1 minute in 1 mL of lysis solution (BioLegend), and then neutralized with ice-cold Gibco DMEM. Dead cells were removed using the Dead Cell Removal Kit (Miltenyi Biotec). FACS buffer (2% fetal bovine serum (FBS) + 0.1% NaN3 in PBS) was used to prepare cells for RNAseq. All reagents, unless specified, were purchased from Sigma. The viability and quantification of single-cell suspensions obtained from the whole lung were determined using a LUNA-FLTM Dual Fluorescence Cell Counter (Logos Biosystems). Following manufacturer recommendations, single cells were extracted from cell suspensions (100–2,000 cells/μL) using a 10x Chromium controller (10x Genomics). The gel beads emulsion (GEM)/sample solution was collected and placed into strip tubes. Following cDNA amplification, reverse transcription was carried out using a thermocycler (C1000 TouchTM Thermal Cycler, Bio-Rad). Amplified products were solid phase reversible immobilization (SPRI) bead-purified and evaluated by a Fragment Analyzer (Agilent, Santa Clara, CA). Twenty-five percent of the cDNA volume was fragmented, and PCR purification and clean-up were carried out using double-sided SPRIselect (Beckman Coulter). Following adaptor ligation, each sample underwent SPRI clean-up and PCR amplification utilizing sample-specific indexes. The Fragment Analyzer was used to quantify, purify, and determine the library size distribution of PCR products. PCR products were purified, quantified and sequenced on an Illumina (San Diego, CA, USA) Novaseq6000. Libraries were sequenced to an average depth of 50,000 reads per cell following manufacturer-recommended conditions.

treatment_protocol: Intra-oral pharyngeal instillation of 4x10^8 CFU of S. pneumoniae, strain D39

value: lung

tag: gender

value: male

tag: age

value: 12-14 weeks

value: no infection


title: A375 cells, wild-type, RNA-seq, replicate 1

description:
Library name: WT1
RNA-seq of wild-type A375 human melanoma cells, replicate 1


title: HEK293 cells, ISOMPRA 3'UTR Mutated Control Library Transfected, Post-Splice BiolRep2

description: Library name: 3UTR.control.post.2


title: HEK293 cells, ISOMPRA 3'UTR Mutated Control Library Transfected, Post-Splice BiolRep5

description: Library name: 3UTR.control.post.5


title: SCC-25, PAR, Vehicle, 48h, rep2

description:
Library name: PAR_48h_Veh_2
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)

value: Vehicle


title: WT-CTX

city: shanghai

first: Qi

last: Cao

address: NO.325 Guohe Road

institute: Second Military Medical University

data_processing:
The demultiplexing，barcoded processing，gene counting and aggregation were using the Cell Ranger software v2.1.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: muscle

extract_protocol:
Dissect and wash the mouse gastrocnemius muscle in cold PBS, cut into small pieces, and digest in an enzyme solution at 37°C for 30-60 minutes with gentle agitation. Filter the digested tissue, centrifuge, and resuspend cells in cold PBS, then count and adjust the cell concentration to 700-1200 cells/μL.
Library was perfomed according to the manufacter instructions

value: muscle


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Pre-Splice, BiolRep 3

description: Library name: 3UTR.ms3.cortex.pre

value: brain

value: uISOMPRA Library AAV Infection

value: Homozygous


title: Lung Cells, WT-72hour post pneumococcal infection

description:
Library name: WT72hr_2439
scRNASeq

tag: bacterial strain

value: S. pneumoniae, D39

value: 72 hours post infection


title: GSDME-KO-CTX

value: GSDME-KO


title: im LNP-Luc_Bulk

description: Library name: TMs40_2-2

value: Skeletal muscle

value: Bulk

value: DMD mouse model

value: im LNP-Luc_Bulk


title: Lung Cells, KO-72 hour post pneumococcal infection

description:
Library name: KO72hr_2463
scRNASeq


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Pre-Splice, BiolRep 3

description: Library name: 3UTR.ms3.exn.pre

value: M


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Post-Splice, BiolRep 3

description: Library name: 3UTR.ms3.cortex.post


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Pre-Splice, BiolRep 2

description: Library name: 3UTR.ms2.exn.pre


title: shTOP3B_R2

city: Chiacgo

first: Arushi

last: Vats

state: Illinois

address: 320E Superior street

department: Microbiology-Immunology

institute: Northwestern University

description: Library name: shTOP3B_R2

data_processing:
DNBSEQ sequencing platform was used with sequencing length of SE50.
HISAT2 Alignment to align clean reads to reference genome for transcript mapping
Bowtie2 to align the clean reads to the reference genes
Dr. Tom (Analysis & Visualization) Performs differential expression, pathway analysis (KEGG/GO), and creates publication-ready figures
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: TOP1A/SCR_TPM_R1/R2 file remains in Microsoft Excel .txt format
Supplementary files format and content: TOP3B/SCR_TPM_R1/R2 file remains in Microsoft Excel .txt format

source_name: Cervical

growth_protocol: CIN 612 cells were maintained in E-media containing 10% FBS DMEM

extract_protocol:
RNA was extracted using an Rneasy mini plus kit (Qiagen).
RNAseq-PolyA technique was applied by NuCore aeq facility. Briefly, PolyA+RNA was captured and then fragmented and primed for cDNA synthesis. Following cDNA synthesis, 3' ends were adenylated and 5' ends repaired. DNA sequencing adapters were ligated and the ligated fragments were PCR amplified.

value: Cervical

value: CIN612 cells

value: Keratinocytes

value: Puromycin selection


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Post-Splice, BiolRep 2

description: Library name: 3UTR.ms2.exn.post


title: SCC-25, PAR, Vehicle, 48h, rep3

description:
Library name: PAR_48h_Veh_3
raw transcript counts (individual), DESeq normalized matrix for differential expression quantitation (all samples)

value: Head and Neck Cancer Cells

value: Parental

value: Vehicle


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Post-Splice, BiolRep 10

description: Library name: 3UTR.ms10.exn.post

value: brain

value: uISOMPRA Library AAV Infection


title: Lung Cells, WT uninfected

description:
Library name: WTPBS_2516
scRNASeq

value: lung

value: male

value: WT

value: 12-14 weeks

value: no infection


title: shTOP3B_R1

description: Library name: shTOP3B_R1


title: shTOP1A_R2

description: Library name: shTOP1A_R2


title: HEK293 cells, ISOMPRA 3'UTR Mutated Control Library Transfected, Post-Splice BiolRep1

description: Library name: 3UTR.control.post.1

value: kidney

value: human embryonic kidney cells

value: ISOMPRA Library Transfection


title: HEK293 cells, ISOMPRA 3'UTR Mutated Control Library Transfected, Pre-Splice BiolRep5

description: Library name: 3UTR.control.pre.5


title: HEK293 cells, ISOMPRA 3'UTR Mutated Control Library Transfected, Pre-Splice BiolRep6

description: Library name: 3UTR.control.pre.6


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Post-Splice, BiolRep 2

description: Library name: 3UTR.ms2.cortex.post

value: Homozygous

value: M


title: HEK293 cells, ISOMPRA 3'UTR Mutated Control Library Transfected, Pre-Splice BiolRep4

description: Library name: 3UTR.control.pre.4


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Post-Splice, BiolRep 1

description: Library name: 3UTR.ms1.exn.post


title: SCR_R2

description: Library name: SCR_R2

value: Cervical

value: CIN612 cells

value: Keratinocytes

value: SCRcontrol


title: HEK293 cells, ISOMPRA Library Transfected, Pre-Splice Rep24, Tet Inducing Experiment

description: Library name: rep24.pre.tet

treatment_protocol: In Vitro: Transfection was induced on 24 hours after plating and then cells were harvested 48hours after using Trizol. In Vivo: Mice were injected with AAV virus at PND1 and allowed to age until date of harvest; PND10 for Empra/eISOMPRA, PND21 for uISOMPRA, Tet Experiments: HEK cells were transfected 24 hours after plating and then cells were either treated with vehicle or 0.5mg.mL Doxycyline based on condition and then harvested another 24 hours after drug treatment.

value: ISOMPRA Library Transfection, 0.5mg/mL Doxycycline Treatment


title: BMDM, WT Untreated rep 2

city: Nashville

first: Kristin

middle: L

last: Patrick

state: Tennessee

department: Pathology, Microbiology, and Immunology (PMI)

institute: Vanderbilt University Medical Center

description: Library name: WTUN rep2

data_processing:
FASTA files were subject to quality control and trimming using fastp (v1.0.1) standard parameters.
Trimmed paired-end reads were aligned to the mouse reference genome (GRCm39) using STAR (v2.7.11b). STAR was run in single-pass mode with splice-aware alignment against a genome index built with an overhang of 149 bp. STAR used its default filtering criteria, including removal of reads mapping to more than 10 genomic locations and requiring a minimum alignment score and matched length relative to read length (0.66). Low-quality bases at read ends were soft-clipped, and reads were aligned across annotated exon-exon junctions. Output files were generated as coordinate-sorted BAM files suitable for downstream differential expression and splicing analyses.
Gene-level read counts were quantified using featureCounts (v 2.1.1) from STAR-aligned BAM files. Raw count matrices were imported in DESeq2 (v1.46.0), where normalization was performed using the media-of-ratios method to account for library size differences. Differential expression analysis was carried out using DESeq2's negative binomial model with Benjamini-Hochberg correction.
Assembly: GRCm39

source_name: cell line

growth_protocol: DMEM supplemented with 20% FBS and 2% Hepes. Cells cultured at 37C and 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent. Zymo Research Direct-zol kits were used to isolate RNA with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BMDMs were infected with low passage Erdman strain Mycobacterium tuberculosis at an MOI = 5 via spinfect. 0 or 8 hours post-infection, RNA was collected.

value: bone marrow derived macrophages (BMDM)

value: macrophage

value: Untreated


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Post-Splice, BiolRep 1

description: Library name: 3UTR.ms1.cortex.post

value: brain

value: uISOMPRA Library AAV Infection


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Pre-Splice, BiolRep 1

description: Library name: 3UTR.ms1.cortex.pre


title: A375 cells, DUS1L knockout, tRF-seq, replicate 1

description:
Library name: DUS1LKO1
tRF-seq of DUS1L knockout A375 human melanoma cells, replicate 1

data_processing:
Raw reads were assessed for sequencing quality using FastQC, and 3' adaptor sequences were trimmed with cutadapt. Low-quality reads and very short reads were removed.
Assembly: Homo sapiens GRCh38 (hg38); tRNA genomic coordinates as implemented in MINTmap.
Supplementary files format and content: Processed tRF-seq data are provided as a tab-delimited text file named "A375_tRFseq_counts.txt". The first column ("tRF_ID") lists the identifier of each tRNA-derived fragment (tRF), and the second column ("tRF_type") annotates the fragment class (e.g. 5'-half, 5'-tRF). Subsequent columns correspond to individual small RNA libraries (WT1, WT2, WT3, DUS1LKO1, DUS1LKO2, DUS1LKO3). Entries represent read counts mapped to each tRF in each sample, and these count values were used as input for DESeq2-based differential expression analysis between DUS1L knockout and wild-type A375 cells.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions and used as input for small RNA library preparation.
Small RNA sequencing libraries were prepared using the NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs) according to the manufacturer’s protocol. Adapter-ligated small RNAs were reverse-transcribed, PCR-amplified and size-selected to enrich for tRNA-derived fragments (tRFs). Libraries were quality-controlled on an Agilent 2100 Bioanalyzer and sequenced on an Illumina NextSeq 500 platform to generate single-end reads.

value: skin

value: melanoma cells

value: DUS1L knockout


title: shTOP1A_R1

description: Library name: shTOP1A_R1

value: Puromycin selection


title: BMDM, A2B1 KO Untreated rep 4

description: Library name: A2B1KOUN rep4

value: A2B1 KO


title: BMDM, A2B1 KO Untreated rep 2

description: Library name: A2B1KOUN rep2


title: BMDM, WT Untreated rep 3

description: Library name: WTUN rep3

value: WT


title: HEK293 cells, ISOMPRA 3'UTR Mutated Control Library Transfected, Pre-Splice BiolRep2

description: Library name: 3UTR.control.pre.2

value: kidney

value: human embryonic kidney cells

value: ISOMPRA Library Transfection


title: HEK293 cells, ISOMPRA 3'UTR Mutated Control Library Transfected, Pre-Splice BiolRep3

description: Library name: 3UTR.control.pre.3


title: HEK293 cells, ISOMPRA Library Transfected, Post-Splice Rep23, Tet Inducing Experiment

description: Library name: rep23.post.tet


title: BMDM, A2B1 KO +Mtb rep 3

description: Library name: A2B1KO8HMTB rep3

value: 8h Mtb


title: BMDM, WT Untreated rep 4

description: Library name: WTUN rep4


title: Mouse Brain, eMPRA Library AAV Infected Pre-Splice, BiolRep16.1

description: Library name: ms16.1.empra

value: eMPRA Library AAV Infection

value: F


title: HEK293 cells, ISOMPRA 3'UTR Mutated Control Library Transfected, Pre-Splice BiolRep1

description: Library name: 3UTR.control.pre.1


title: BMDM, A2B1 KO Untreated rep 1

description: Library name: A2B1KOUN rep1

value: bone marrow derived macrophages (BMDM)


title: BMDM, WT Untreated rep 1

description: Library name: WTUN rep1

value: macrophage


title: BMDM, A2B1 KO Untreated rep 3

description: Library name: A2B1KOUN rep3

value: Untreated


title: Mouse Brain, eMPRA Library AAV Infected Pre-Splice, BiolRep14.1

description: Library name: ms14.1.empra

value: brain


title: HEK293 cells, ISOMPRA Library Transfected, Pre-Splice Rep23, Tet Inducing Experiment

description: Library name: rep23.pre.tet

value: ISOMPRA Library Transfection, 0.5mg/mL Doxycycline Treatment


title: Mouse Brain, eMPRA Library AAV Infected Pre-Splice, BiolRep13.1

description: Library name: ms13.1.empra

value: M


title: Mouse Brain, eMPRA Library AAV Infected Pre-Splice, BiolRep17.1

description: Library name: ms17.1.empra


title: A375 cells, DUS1L knockout, tRF-seq, replicate 2

description:
Library name: DUS1LKO2
tRF-seq of DUS1L knockout A375 human melanoma cells, replicate 2

value: skin

value: melanoma cells


title: HEK293 cells, ISOMPRA Library Transfected, Post-Splice Rep21, Tet Inducing Experiment

description: Library name: rep21.post.tet


title: BMDM, WT +Mtb rep 3

description: Library name: WT8HMTB rep3


title: HEK293 cells, ISOMPRA Library Transfected, Pre-Splice Rep20, Tet Inducing Experiment

description: Library name: rep20.pre.tet


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-ON (Excitatory Neuron), Pre-Splice, BiolRep 1

description: Library name: 3UTR.ms1.exn.pre

value: uISOMPRA Library AAV Infection

value: Homozygous


title: SCR_R1

description: Library name: SCR_R1

value: Cervical

value: CIN612 cells

value: Keratinocytes

value: SCR control

value: Puromycin selection


title: A375 cells, DUS1L knockout, tRF-seq, replicate 3

description:
Library name: DUS1LKO3
tRF-seq of DUS1L knockout A375 human melanoma cells, replicate 3

value: DUS1L knockout


title: BMDM, A2B1 KO +Mtb rep 4

description: Library name: A2B1KO8HMTB rep4

value: A2B1 KO

value: 8h Mtb


title: Mouse Brain, uISOMPRA Library AAV Infected, Cre-OFF (Whole Cortex), Pre-Splice, BiolRep 2

description: Library name: 3UTR.ms2.cortex.pre


title: A375 cells, wild-type, tRF-seq, replicate 3

description:
Library name: WT3
tRF-seq of wild-type A375 human melanoma cells, replicate 3

value: wild-type


title: HEK293 cells, ISOIMPRA Library Transfected, Post-Splice Rep20, Tet Inducing Experiment

description: Library name: rep20.post.tet

value: kidney

value: human embryonic kidney cells

value: WT


title: HEK293 cells, ISOMPRA Library Transfected, Post-Splice Rep24 Tet Inducing Experiment

description: Library name: rep24.post.tet

value: ISOMPRA Library Transfection, 0.5mg/mL Doxycycline Treatment


title: A375 cells, wild-type, tRF-seq, replicate 2

description:
Library name: WT2
tRF-seq of wild-type A375 human melanoma cells, replicate 2

value: skin


title: A375 cells, wild-type, tRNA-seq, replicate 2

description:
Library name: WT2
tRNA-seq of wild-type A375 human melanoma cells, replicate 2

data_processing:
Raw reads were assessed for quality using FastQC and trimmed with cutadapt to remove adapters and low-quality bases.
Assembly: Homo sapiens GRCh38 (hg38); tRNA reference sequences compiled from GtRNAdb.
Supplementary files format and content: Processed tRNA-seq data are provided as a tab-delimited text file named "A375_tRNAseq_isodecoder_counts.txt". Each row corresponds to a single tRNA isodecoder, annotated by the columns "Isodecoder", "Isotype", "Isoacceptor", "Strand" and "Sequence". The "Isodecoder" column lists the unique identifier for each tRNA isodecoder, "Isotype" indicates the amino acid, "Isoacceptor" specifies the anticodon, "Strand" indicates the mapped strand, and "Sequence" contains the tRNA sequence used as the reference. Subsequent columns correspond to individual tRNA-seq libraries (WT1, WT2, WT3, DUS1LKO1, DUS1LKO2, DUS1LKO3), and entries represent the read counts mapped to each tRNA isodecoder in each sample. These count values were used as input for differential expression analysis of tRNA isodecoders between DUS1L knockout and wild-type A375 cells.

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. Approximately 20 μg RNA per sample was used for tRNA-seq library preparation.

value: melanoma cells


title: Mouse Brain, eMPRA Library AAV Infected Pre-Splice, BiolRep15.1

description: Library name: ms15.1.empra

value: brain

value: eMPRA Library AAV Infection

value: M


title: BMDM, A2B1 KO +Mtb rep 2

description: Library name: A2B1KO8HMTB rep2

value: bone marrow derived macrophages (BMDM)

value: macrophage


title: BMDM, WT +Mtb rep 1

description: Library name: WT8HMTB rep1


title: HEK293 cells, ISOMPRA Library Transfected, Pre-Splice Rep22, Tet Inducing Experiment

description: Library name: rep22.pre.tet


title: HEK293 cells, ISOMPRA Library Transfected, Post-Splice Rep22, Tet Inducing Experiment

description: Library name: rep22.post.tet


title: Control5

city: hefei

first: Yajun

last: Chen

state: anhui

address: No.1688, Lianhua Road, Hefei 230601, Anhui, China.

institute: Hefei Normal University

description: Library name: Sample 10

data_processing:
Basecalling is performed by Illumina RTA software in sequencer.
Raw data (raw reads) of FASTQ format were firstly processed through fastp to generate clean reads.
Paired-end clean reads were mapped to the reference genome using HISAT2 software.
Differential expression analysis of two conditions/groups (five biological replicates per condition) was performed using the DESeq2 R package (1.16.1).Genes with an  P-value <0.05 found by DESeq2 were assigned as differentially expressed.
GO and KEGG enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package.
Assembly: GRCh38
Supplementary files format and content: processed data file.txt

source_name: tissue liver

extract_protocol:
After sacrifice, mouse liver samples were likewise snap-frozen in liquid nitrogen and stored at −80℃. After the tissues were homogenized, total RNA was extracted employing Trizol reagent (Invitrogen, CA, USA). A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries  for lncRNA-seq were prepared as rRNA depletion and stranded method. Briefly, the ribosomal RNA was depleted from total RNA using the rRNA Removal Kit following manufacturer’s instruction. RNA was then fragmented into 250~300 bp fragments, and first strand cDNA was reversetranscribed using fragmented RNA and dNTPs . RNA was degraded using RNase H, and second strand cDNA was synthesised using DNA polymerase I and dNTPs. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/ polymerase activities. After adenylation of 3’ ends of DNA fragments,sequencing adaptors were ligated to the cDNA. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system. Uridine digestion was performed using Uracil-N-Glycosylase, which was followed by the cDNA amplification using PCR.

value: tissue liver

value: Solvent administration


title: HEK293 cells, ISOMPRA Library Transfected, Post-Splice Rep19, Tet Inducing Experiment

description: Library name: rep19.post.tet

value: ISOMPRA Library Transfection, Vehicle Treatment


title: A375 cells, wild-type, tRF-seq, replicate 1

description:
Library name: WT1
tRF-seq of wild-type A375 human melanoma cells, replicate 1


title: A375 cells, DUS1L knockout, tRNA-seq, replicate 2

description:
Library name: DUS1LKO2
tRNA-seq of DUS1L knockout A375 human melanoma cells, replicate 2

value: DUS1L knockout


title: A375 cells, DUS1L knockout, tRNA-seq, replicate 3

description:
Library name: DUS1LKO3
tRNA-seq of DUS1L knockout A375 human melanoma cells, replicate 3


title: Mouse Brain, eMPRA Library AAV Infected Pre-Splice, BiolRep10.1

description: Library name: ms10.1.empra


title: Mouse Brain, eMPRA Library AAV Infected Pre-Splice, BiolRep9.1

description: Library name: ms9.1.empra


title: Mouse Brain, eMPRA Library AAV Infected Pre-Splice, BiolRep12.1

description: Library name: ms12.1.empra


title: Mouse Brain, eMPRA Library AAV Infected Pre-Splice, BiolRep7.1

description: Library name: ms7.1.empra


title: A375 cells, wild-type, tRNA-seq, replicate 3

description:
Library name: WT3
tRNA-seq of wild-type A375 human melanoma cells, replicate 3


title: Control1

description: Library name: Sample 6


title: HEK293 cells, ISOMPRA Library Transfected, Pre-Splice Rep19, Tet Inducing Experiment

description: Library name: rep19.pre.tet


title: BMDM, A2B1 KO +Mtb rep 1

description: Library name: A2B1KO8HMTB rep1

value: A2B1 KO

value: 8h Mtb


title: HEK293 cells, ISOMPRA Library Transfected, Post-Splice Rep6, Tet Inducing Experiment

description: Library name: rep6.post.tet

value: kidney


title: HEK293 cells, ISOMPRA Library Transfected, Pre-Splice Rep5, Tet Inducing Experiment

description: Library name: rep5.pre.tet

value: human embryonic kidney cells


title: BMDM, WT +Mtb rep 4

description: Library name: WT8HMTB rep4

value: WT


title: Mouse Brain, eMPRA Library AAV Infected Pre-Splice, BiolRep6.1

description: Library name: ms6.1.empra


title: A375 cells, wild-type, tRNA-seq, replicate 1

description:
Library name: WT1
tRNA-seq of wild-type A375 human melanoma cells, replicate 1

value: wild-type


title: HEK293 cells, ISOMPRA Library Transfected, Pre-Splice Rep21, Tet Inducing Experiment

description: Library name: rep21.pre.tet

value: ISOMPRA Library Transfection, 0.5mg/mL Doxycycline Treatment


title: BMDM, WT +Mtb rep 2

description: Library name: WT8HMTB rep2


title: A375 cells, DUS1L knockout, tRNA-seq, replicate 1

description:
Library name: DUS1LKO1
tRNA-seq of DUS1L knockout A375 human melanoma cells, replicate 1

value: skin

value: melanoma cells


title: HEK293 cells, ISOMPRA Library Transfected, Pre-Splice Rep4, Tet Inducing Experiment

description: Library name: rep4.pre.tet


title: 81_LS

city: Torino

first: Giovanni

last: Birolo

state: TO

address: Via Santena 19

department: Medical Sciences

country: Italy

institute: University of Turin

description: Library name: 81_LS

data_processing:
read cleaning with cutadapt
alignment to sncRNA reference with bwa
alignment filtering and counting with custom script
sncRNA and sample filtering with custom script
Assembly: mature sncRNA sequences from various sources
Supplementary files format and content: the raw count matrix with all sncRNA and samples with at least one alignment after filtering
Supplementary files format and content: the clean count matrix with a subset of sncRNA and samples that were retained for analysis

source_name: Urine

extract_protocol:
Qiazol reagent and miRNeasy Mini Kit (Qiagen, #217004)
NEBNext Multiplex Small RNA Library Prep Set for Illumina (Protocol E7330

value: Urine

tag: diet

value: LS


title: Treatment3

description: Library name: Sample 3

value: Gigantol administration


title: 86_LS

description: Library name: 86_LS


title: 83_LS

description: Library name: 83_LS


title: Control3

description: Library name: Sample 8


title: Mouse Brain, eMPRA Library AAV Infected Pre-Splice, BiolRep8.1

description: Library name: ms8.1.empra

data_processing:
Sequencing reads were aligned to reference libraries using custom scripts to identify exact matches, normalized with edgeR (TMM method) to CPM, filtered for low counts, and used to calculate log₂(RNA/DNA) expression or translational efficiency (TRAP), with variant pairs filtered to retain those with ≥4 measurements across conditions.
Assembly: hg38
Supplementary files format and content: raw files = fastq.gz , processed files = .txt

extract_protocol:
RNA was harvested using Trizol Reagent and Zymo Clean and Concentrator Kit. 5ug of RNA per replicate were used for Library Preparation.
RNA libraries for RNA-seq were prepared using a targeted-RNA seq library preparation approach that followed similar paradigms to a Tru-Seq library construction for Illumina Sequencing.

value: brain

value: eMPRA Library AAV Infection

value: F


title: Control4

description: Library name: Sample 9

value: tissue liver

value: Solvent administration


title: Control2

description: Library name: Sample 7


title: HEK293 cells, ISOMPRA Library Transfected, Pre-Splice Rep6, Tet Inducing Experiment

description: Library name: rep6.pre.tet

value: ISOMPRA Library Transfection, Vehicle Treatment


title: Mouse Brain, eMPRA Library AAV Infected Pre-Splice, BiolRep11.1

description: Library name: ms11.1.empra

value: M


title: 86_HS

description: Library name: 86_HS

value: HS


title: Mouse Brain, ISOMPRA Library AAV Infected Post-Splice, BiolRep16.1

description: Library name: ms17.1.post

value: ISOMPRA Library AAV Infection


title: Mouse Brain, eMPRA Library AAV Infected Pre-Splice, BiolRep3.1

description: Library name: ms3.1.empra

value: WT


title: Treatment1

description: Library name: Sample 1


title: 77_LS

description: Library name: 77_LS


title: 80_LS

description: Library name: 80_LS


title: HEK293 cells, ISOMPRA Library Transfected, Post-Splice Rep5, Tet Inducing Experiment

description: Library name: rep5.post.tet

value: kidney

value: human embryonic kidney cells


title: Treatment5

description: Library name: Sample 5


title: HEK293 cells, ISOMPRA Library Transfected, Post-Splice Rep4, Tet Inducing Experiment

description: Library name: rep4.post.tet


title: 83_HS

description: Library name: 83_HS


title: Mouse Brain, eMPRA Library AAV Infected Pre-Splice, BiolRep5.1

description: Library name: ms5.1.empra


title: Treatment2

description: Library name: Sample 2


title: HEK293 cells, ISOIMPRA Library Transfected, Post-Splice Rep2, Tet Inducing Experiment

description: Library name: rep2.post.tet


title: Mouse Brain, eMPRA Library AAV Infected Pre-Splice, BiolRep2.1

description: Library name: ms2.1.empra


title: Mouse Brain, ISOMPRA Library AAV Infected Post-Splice, BiolRep14.1

description: Library name: ms15.1.post


title: HEK293 cells, ISOMPRA Library Transfected, Pre-Splice Rep1, Tet Inducing Experiment

description: Library name: rep1.pre.tet


title: Mouse Brain, ISOMPRA Library AAV Infected Post-Splice, BiolRep13.1

description: Library name: ms14.1.post


title: Mouse Brain, eMPRA Library AAV Infected Pre-Splice, BiolRep4.1

description: Library name: ms4.1.empra


title: Pooled colon tumor cells from control Hmox1 fl/fl mouse B

city: Aurora

last: Onyiah

state: CO

institute: University of Colorado

description:
Library name: Hmox1 fl/fl B
10X Genomics

data_processing:
Processing and aggregation were performed using Cell Ranger software version 7.0 (10X Genomics)
Assembly: Mouse mm10
Supplementary files format and content: Hierarchical Data Format version 5 matrix files

source_name: Colon tumor

extract_protocol:
Colonic tumors were pooled per mouse, minced,and cells enzymatically dissociated with 3 mg/mL collagenase type IV and Dnase I 75 U/mL in complete RPMI media for 30 minutes at 37 degrees celcius. Live cells were then stained with a viability dye (7AAD) and sorted uing a FACSAria.
Library construction was performed according to the manufacturer's instructions (Next GEM 3' Gene Expression v3, 10X Genomics)

treatment_protocol: AOM-DSS protocol ending at day 80

value: Colon tumor

value: Hmox1 fl/fl

value: AOM-DSS


title: Mouse Brain, ISOMPRA Library AAV Infected Post-Splice, BiolRep12.1

description: Library name: ms13.1.post

source_name: brain


title: 81_HS

description: Library name: 81_HS

value: Urine


title: Pooled colon tumor cells from control Hmox1 fl/fl mouse A

description:
Library name: Hmox1 fl/fl A
10X Genomics


title: HEK293 cells, ISOMPRA Library Transfected, Post-Splice Rep1, Tet Inducing Experiment

description: Library name: rep1.post.tet


title: Treatment4

description: Library name: Sample 4

value: Gigantol administration


title: Pooled colon tumor cells from epithelial Hmox1 knockout mouse A

description:
Library name: Hmox1 IEC KO A
10X Genomics

value: Hmox1 fl/fl /Vil1 Cre


title: Mouse Brain, ISOMPRA Library AAV Infected Post-Splice, BiolRep11.1

description: Library name: ms12.1.post

value: brain


title: HEK293 cells, ISOMPRA Library Transfected, Pre-Splice Rep2, Tet Inducing Experiment

description: Library name: rep2.pre.tet


title: 3_HS

description: Library name: 3_HS


title: Mouse Brain, eMPRA Library AAV Infected Pre-Splice, BiolRep1.1

description: Library name: ms1.1.empra

value: eMPRA Library AAV Infection


title: HEK293 cells, ISOMPRA Library Transfected, Post-Splice Rep3, Tet Inducing Experiment

description: Library name: rep3.post.tet


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, TRAP Capture BiolRep6.1

description: Library name: 3UTR.hek.trap.capture6.1

value: ISOMPRA Library Transfection


title: HEK293 cells, ISOMPRA Library Transfected, Pre-Splice Rep3, Tet Inducing Experiment

description: Library name: rep3.pre.tet


title: Mouse Brain, ISOMPRA Library AAV Infected Post-Splice, BiolRep15.1

description: Library name: ms16.1.post

value: F


title: 5_LS

description: Library name: 5_LS

value: LS


title: 30_LS

description: Library name: 30_LS


title: Mouse Brain, ISOMPRA Library AAV Infected Post-Splice, BiolRep9.1

description: Library name: ms10.1.post


title: 77_HS

description: Library name: 77_HS


title: 80_HS

description: Library name: 80_HS


title: 30_HS

description: Library name: 30_HS


title: Pooled colon tumor cells from epithelial Hmox1 knockout mouse B

description:
Library name: Hmox1 IEC KO B
10X Genomcis


title: 5_HS

description: Library name: 5_HS


title: Mouse Brain, ISOMPRA Library AAV Infected Post-Splice, BiolRep8.1

description: Library name: ms9.1.post


title: Mouse Brain, ISOMPRA Library AAV Infected Post-Splice, BiolRep7.1

description: Library name: ms8.1.post


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, TRAP Capture BiolRep7.1

description: Library name: 3UTR.hek.trap.capture7.1


title: Distal colon, HSCR mouse, rep 2

city: Charlottesville

first: Lily

middle: S.

last: Cheng

state: VA

address: 409 Lane Rd

department: Surgery

institute: University of Virginia

description: Library name: KDI12

data_processing:
RNA-seq data were mapped using hisat2 (version 2.2.1) to the mouse genome bulid UCSC mm39
Gene expression quantifcation was performed using featurecounts (version 2.0.6)
Differential gene expression was evaluated using the R package EdgeR and normalized using the R package RUVr4(LRT RUVr)
GO and KEGG enrichment analysis were performed using cluster prolifer (version 4.8.1)
Assembly: mm39
Supplementary files format and content: excel file containing raw counts and FPKM for all samples

source_name: longitudinal muscle and myenteric plexus of proximal colon

extract_protocol:
RNA was extracted from longitudinal muscle and myenteric plexus tissues isolated from the proximal and distal colon segments of Ednrb -/- and wildtype mice using the RNeasy Kit (Qiagen)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library.For the non strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: Ednrb -/-


title: Mouse Brain, ISOMPRA Library AAV Infected Post-Splice, BiolRep6.1

description: Library name: ms7.1.post

value: M


title: Distal colon, HSCR mouse, rep 1

description: Library name: KDI07

value: longitudinal muscle and myenteric plexus of proximal colon


title: 2_HS

description: Library name: 2_HS

value: HS


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, TRAP Input BiolRep8.1

description: Library name: 3UTR.hek.trap.input8.1

value: kidney

value: WT


title: AK2 Androgenetic mESC  (Hi-C)

city: Gif-sur-Yvette

first: Benoit

last: Moindrot

address: 1, avenue de la terrasse

country: France

institute: Institute for Integrative Biology of the Cell

description: Library name: Hi-C in AK2 mESC

data_processing:
The reads were processed using Hi-C pro. The resulting ValidPairs tables was converted into mcool files, using Hi-C pro hicpro2higlass.sh script, using --res 10000 and --norm parameters
Assembly: mm10
Supplementary files format and content: mcool

source_name: mouse embryonic stem cells

growth_protocol: ESGRO Complete PLUS Clonal Grade Medium (Merck)

extract_protocol:
Hi-C experiment in mono-parental mESCs (AK2 and PR8) was performed using the Arima Hi-C+ kit (Arima Genomics), following the manufacturer’s instruction.
Hi-C libraries were sequenced on the Illumina NovaSeq 6000 system (2 x 150).

value: mouse embryonic stem cells

value: Androgenetic


title: Mouse Brain, ISOMPRA Library AAV Infected Post-Splice, BiolRep4.1

last: Dougherty

institute: Washington University in St. Louis

description: Library name: ms4.1.post

value: ISOMPRA Library AAV Infection


title: Mouse Brain, ISOMPRA Library AAV Infected Post-Splice, BiolRep5.1

description: Library name: ms5.1.post


title: 25_LS

description: Library name: 25_LS

value: Urine


title: Distal colon, wildtype mouse, rep 4

description: Library name: LC423

value: Ednrb +/+


title: Mouse Brain, ISOMPRA Library AAV Infected Post-Splice, BiolRep3.1

description: Library name: ms3.1.post


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, TRAP Capture BiolRep4.1

description: Library name: 3UTR.hek.trap.capture4.1

value: human embryonic kidney cells


title: Mouse Brain, ISOMPRA Library AAV Infected Post-Splice, BiolRep10.1

description: Library name: ms11.1.post

value: brain


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, TRAP Capture BiolRep5.1

description: Library name: 3UTR.hek.trap.capture5.1


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, TRAP Capture BiolRep2.1

description: Library name: 3UTR.hek.trap.capture2.1


title: 3_LS

description: Library name: 3_LS


title: 2_LS

description: Library name: 2_LS


title: PR8 Parthenogenetic mESC  (Hi-C)

description: Library name: Hi-C in PR8 mESC

value: Parthenogenetic


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, TRAP Input BiolRep4.1

description: Library name: 3UTR.hek.trap.input4.1

value: ISOMPRA Library Transfection


title: Distal colon, HSCR mouse, rep 4

description: Library name: LC421


title: 1_HS

description: Library name: 1_HS


title: Proximal colon, HSCR mouse, rep 4

description: Library name: CM03


title: Mouse Brain, eMPRA Library AAV Infected Pre-Splice, BiolRep17

description: Library name: ms17.empra

value: eMPRA Library AAV Infection

value: F


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, TRAP Input BiolRep7.1

description: Library name: 3UTR.hek.trap.input7.1


title: Proximal colon, HSCR mouse, rep 3

description: Library name: LC371

value: Ednrb -/-


title: 23_HS

description: Library name: 23_HS


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, TRAP Input BiolRep1.1

description: Library name: 3UTR.hek.trap.input1.1


title: Mouse Brain, eMPRA Library AAV Infected Pre-Splice, BiolRep16

description: Library name: ms16.empra


title: Distal colon, wildtype mouse, rep 3

description: Library name: LC372


title: Distal colon, HSCR mouse, rep 3

description: Library name: LC422


title: 25_HS

description: Library name: 25_HS


title: 23_LS

description: Library name: 23_LS

value: LS


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, TRAP Input BiolRep6.1

description: Library name: 3UTR.hek.trap.input6.1


title: Mouse Brain, eMPRA Library AAV Infected Pre-Splice, BiolRep15

description: Library name: ms15.empra

value: M


title: Distal colon, wildtype mouse, rep 1

description: Library name: WDI07

value: longitudinal muscle and myenteric plexus of proximal colon


title: 18_LS

description: Library name: 18_LS


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, TRAP Input BiolRep3.1

description: Library name: 3UTR.hek.trap.input3.1

value: kidney


title: Mouse Brain, ISOMPRA Library AAV Infected Post-Splice, BiolRep1.1

description: Library name: ms1.1.post

value: WT


title: Mouse Brain, eMPRA Library AAV Infected Pre-Splice, BiolRep14

description: Library name: ms14.empra


title: 1_LS

description: Library name: 1_LS


title: Distal colon, wildtype mouse, rep 2

description: Library name: WDI12


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, TRAP Input BiolRep2.1

description: Library name: 3UTR.hek.trap.input2.1


title: Mouse Brain, ISOMPRA Library AAV Infected Post-Splice, BiolRep2.1

description: Library name: ms2.1.post


title: Proximal colon, wildtype mouse, rep 4

description: Library name: CM02


title: 18_HS

description: Library name: 18_HS

value: HS


title: 19_HS

description: Library name: 19_HS


title: 19_LS

description: Library name: 19_LS


title: 17_HS

description: Library name: 17_HS


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Post-Splice BiolRep3.1

description: Library name: 3UTR.hek.post3.1


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, TRAP Input BiolRep5.1

description: Library name: 3UTR.hek.trap.input5.1


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Post-Splice BiolRep7.1

description: Library name: 3UTR.hek.post7.1


title: Astrocyte Hevin OE, replicate 2, scRNAseq

city: Durham

first: Cagla

last: Eroglu

state: NC

address: 307 Research Dr

institute: Duke University

description:
Library name: output_R4
PIPseq v4.0PLUS

data_processing:
demultiplexing, barcode processing, gene counting, and aggregation were made using PIPseeker 3.3.0 (https://www.fluentbio.com/products/pipseeker-software-for-data-analysis/)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain (cortex)

extract_protocol:
P15 mice were perfused with 15 mM HEPES pH7 + 0.5% Glucose + 1xHBSS supplemented with 5ug/mL Actinomycin D and 10 uM Triptolide. Brains were extracted and cortices were dissected off in ice cold 1X HBSS supplemented with 5ug/mL Actinomycin D, 10 uM Triptolide, and 27.1 ug/mL Anisomycin. Cortices were then dissociated using the MIltenyi GentleMACS system in Miltenyi Neural Tissue Dissociation kit supplemented with 5ug/mL Actinomycin D, 10 uM Triptolide, and 27.1 ug/mL Anisomycin. Enzymes were washed off and single cell suspension was generated by passing cells through a 70 um cell strainer. Single cell suspension was then resuspended in MACS buffer and cells were incubated with CD11b selection beads. Excess beads were washed off with MACS buffer and cells were then passed through a 30 um cell strainer into LS columns. CD11b+ fraction was collected and cells were resuspended in Cell suspension buffer following PIPseq kit instructions. Up to 40,000 cells were added to PIP reaction and processed for library preparation as instructed by the PIPseq kit.
Library construction was performed following manufacturer's instructions from PIPseq v4.0PLUS kit.

treatment_protocol: Mice were injected intracortically at P0 or P1 with adeno-associated viruses expressing mCherry or Hevin, under the control of the astrocyte-specific promoter GfaABC1D.

value: Brain (cortex)

value: Astrocyte Hevin overexpression


title: 16_HS

description: Library name: 16_HS

value: Urine


title: Mouse Brain, eMPRA Library AAV Infected Pre-Splice, BiolRep13

city: St. Louis

first: Joseph

description: Library name: ms13.empra


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Pre-Splice BiolRep8.1

description: Library name: 3UTR.hek.pre8.1


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Post-Splice BiolRep6.1

description: Library name: 3UTR.hek.post6.1


title: Mouse Brain, eMPRA Library AAV Infected Pre-Splice, BiolRep9

description: Library name: ms9.empra


title: Proximal colon, HSCR mouse, rep 1

description: Library name: KPO07


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Pre-Splice BiolRep7.1

description: Library name: 3UTR.hek.pre7.1


title: Mouse Brain, eMPRA Library AAV Infected Pre-Splice, BiolRep8

description: Library name: ms8.empra


title: Proximal colon, HSCR mouse, rep 2

description: Library name: KPO12


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Post-Splice BiolRep4.1

description: Library name: 3UTR.hek.post4.1


title: Proximal colon, wildtype mouse, rep 1

description: Library name: WPO07

value: Ednrb +/+


title: Proximal colon, wildtype mouse, rep 3

description: Library name: CM01


title: Astrocyte Hevin OE, replicate 1, scRNAseq

description:
Library name: output_R2
PIPseq v4.0PLUS


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Pre-Splice BiolRep6.1

description: Library name: 3UTR.hek.pre6.1

value: human embryonic kidney cells


title: Proximal colon, wildtype mouse, rep 2

description: Library name: WPO12


title: Mouse Brain, eMPRA Library AAV Infected Pre-Splice, BiolRep10

description: Library name: ms10.empra

value: brain


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Post-Splice BiolRep8.1

description: Library name: 3UTR.hek.post8.1.1


title: Astrocyte mCherry OE, replicate 1, scRNAseq

description:
Library name: output_J1
PIPseq v4.0PLUS

value: Astrocyte mCherry overexpression


title: Mouse Brain, eMPRA Library AAV Infected Pre-Splice, BiolRep12

description: Library name: ms12.empra


title: 11_LS

description: Library name: 11_LS


title: 12_LS

description: Library name: 12_LS


title: 16_LS

description: Library name: 16_LS


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Post-Splice BiolRep1.1

description: Library name: 3UTR.hek.post1.1

value: ISOMPRA Library Transfection


title: 17_LS

description: Library name: 17_LS


title: 12_HS

description: Library name: 12_HS


title: Mouse Brain, eMPRA Library AAV Infected Pre-Splice, BiolRep7

description: Library name: ms7.empra

value: eMPRA Library AAV Infection


title: Mouse Brain, eMPRA Library AAV Infected Pre-Splice, BiolRep11

description: Library name: ms11.empra


title: 11_HS

description: Library name: 11_HS


title: Astrocyte mCherry OE, replicate 2, scRNAseq

description:
Library name: output_J3
PIPseq v4.0PLUS


title: PDO from MOSR12

city: Milan

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

institute: OSR - San Raffaele Scientific Institute

description: Patient Derived Organonids from biopsy MOSR12

data_processing:
Single cell gene-count matrices were obtained with CellRanger
Assembly: hg38
Supplementary files format and content: Tab-separated value files and matrix in gz

source_name: Pdo

extract_protocol:
The tumoral biopsies and non-tumoral pleura tissues were minced mechanically into small pieces of 1 cm2 using sterile scalpels in sterile conditions. Further tissue dissociation into single-cell suspension was performed using Multi Tissue Dissociation Kit 2 (Cat No. 130-110-203) combining mechanical with enzymatic dissociation, according to the manufacturer´s datasheet. GentleMACS Dissociators were used for the mechanical dissociation steps. After dissociation, each sample was applied to a filter supplied in the kit to remove any remaining larger particles from the single-cell suspension
Cell suspensions were prepared and vitality was assessed for each individual scRNA-seq experiment. Cells were loaded onto a single-cell chip for GEM generation using the 10x Genomics Chromium Controller (10× Genomics, Pleasanton, CA). 3′mRNA-seq gene expression libraries were constructed using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 (10x Genomics) according to the manufacturer’s guidelines.

value: Pdo

tag: tissue source


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Pre-Splice BiolRep3.1

description: Library name: 3UTR.hek.pre3.1


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Pre-Splice BiolRep5.1

description: Library name: 3UTR.hek.pre5.1


title: Mouse Brain, eMPRA Library AAV Infected Pre-Splice, BiolRep5

description: Library name: ms5.empra


title: Gpx4 KO biol rep 3

city: Innsbruck

first: Christina

last: Plattner

address: Innrain 80

department: Institute of Bioinformatics

country: Austria

institute: Medical University of Innsbruck

description:
Library name: FG5
10X Genomics

data_processing:
Bulk fastq sequencing files of MODE-K cells were processed with the nf-core/rnaseq pipeline v3.8.1.
10X single-cell fastq sequencing files were processed with cellranger v7.1.0 using the nf-core/scRNA-seq pipeline v2.4.1
Assembly: Mouse mm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: small intestine

extract_protocol:
After stimulation at 37°C for 8h, cell culture medium was discarded and cells were rinsed once with PBS. RNA isolation was performed according to manufacturer’s instructions using a RNeasy mini kit (Qiagen, 74104).
For single cell isolation, the small intestine (SI) was cleaned of adhering stool/tissue. Afterwards the middle 60 % of the SI was flushed with ice cold PBS. The SI was then opened longitudinally and washed again with ice cold PBS. Thereafter, the tissue was cut into small pieces and digested in 50ml PBS containing 2mM EDTA. Samples were shaken regularly for the next 30min. The supernatant was collected and remaining tissue pieces were dissolved in ice cold PBS and shaken again. This step was repeated 4 times. Supernatant was then centrifuged for 5 min at 300 g at 4°C and the resulting cell pellet was dissolved in trypsin + PBS (1:1), vortexed gently and dissolved in DMEM containing FCS. Accordingly, cells were counted and incubated with beads for live dead separation using a dead cell removal kit (Miltenyi Biotec, 130-090-101) according to the manufacturer’s recommendations. The viable cells were collected and centrifuged at 300 g and 4°C for 5 min. Pellets were dissolved in 100 µl ice-cold PBS containing 0,4 % BSA.
Bulk RNA-seq: Purified total RNA was processed using the QuantSeq 3' mRNA-Seq Library Prep method (Lexogen, Vienna Biocenter).
Single cell suspensions were processed with a Chromium single cell controller (10xGenomics) and Chromium Next GEM Single Cell 3' Kit v3.1 chemistry, targeting 8000 cells per sample.

treatment_protocol: Stimulation of MODE-K IECs was performed for 8 hours with either arachidonic acid (AA) or docosahexaenoic acid (DHA).

value: small intestine

value: PUFA-enriched Western diet for 3 months


title: PDO from MOSR11

description: Patient Derived Organonids from biopsy MOSR11


title: Mouse Brain, eMPRA Library AAV Infected Pre-Splice, BiolRep6

description: Library name: ms6.empra

value: M


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, TRAP Capture BiolRep7

description: Library name: 3UTR.hek.trap.capture7


title: Gpx4 KO biol rep 4

description:
Library name: FG7
10X Genomics


title: PDO from MOSR9

description: Patient Derived Organonids from biopsy MOSR9


title: Mouse Brain, eMPRA Library AAV Infected Pre-Splice, BiolRep3

description: Library name: ms3.empra


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Pre-Splice BiolRep1.1

description: Library name: 3UTR.hek.pre1.1


title: Gpx4 KO biol rep 2

description:
Library name: FG3
10X Genomics


title: WT biol rep 3

description:
Library name: FG8
10X Genomics


title: Mouse Brain, eMPRA Library AAV Infected Pre-Splice, BiolRep4

description: Library name: ms4.empra

value: F


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, TRAP Capture BiolRep6

description: Library name: 3UTR.hek.trap.capture6

value: kidney


title: WT biol rep 2

description:
Library name: FG6
10X Genomics

value: WT


title: WT biol rep 1

description:
Library name: FG4
10X Genomics


title: Mouse Brain, eMPRA Library AAV Infected Pre-Splice, BiolRep1

description: Library name: ms1.empra


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, TRAP Capture BiolRep3

description: Library name: 3UTR.hek.trap.capture3


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, TRAP Capture BiolRep2

description: Library name: 3UTR.hek.trap.capture2


title: Mouse Brain, ISOMPRA Library AAV Infected Post-Splice, BiolRep16

description: Library name: ms17.post

value: ISOMPRA Library AAV Infection


title: Mouse Brain, eMPRA Library AAV Infected Pre-Splice, BiolRep2

description: Library name: ms2.empra


title: siGpx4 DHA biol rep 2

description: Library name: MM200_3_C4

value: MODE-K

value: IEC

value: stimulation with docosahexaenoic acid


title: Mouse Brain, ISOMPRA Library AAV Infected Post-Splice, BiolRep14

description: Library name: ms15.post


title: siGpx4 DHA biol rep 3

description: Library name: MM200_4_C4


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, TRAP Capture BiolRep1

description: Library name: 3UTR.hek.trap.capture1


title: Mesothelioma tumor biposy MOSR8

description: Tumoral Biopsy from patient MOSR8

source_name: Mesothelioma

value: Mesothelioma


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, TRAP Capture BiolRep5

description: Library name: 3UTR.hek.trap.capture5

value: human embryonic kidney cells


title: Mesothelioma tumor biposy MOSR3

description: Tumoral Biopsy from patient MOSR3


title: Mouse Brain, ISOMPRA Library AAV Infected Post-Splice, BiolRep15

description: Library name: ms16.post

value: brain


title: siCtrl DHA biol rep 3

description: Library name: MM200_3_A4

value: siCtrl


title: Mesothelioma tumor biposy MOSR9

description: Tumoral Biopsy from patient MOSR9


title: Non tumoral pleura from pleurisy patient

description: Non tumoral pleura from a biopsy of a pleurisy patient

source_name: Pleura

value: Pleura

value: pleurisy patient


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, TRAP Capture BiolRep4

description: Library name: 3UTR.hek.trap.capture4

value: ISOMPRA Library Transfection


title: Mesothelioma tumor biposy MOSR12

description: Tumoral Biopsy from patient MOSR12


title: Mouse Brain, ISOMPRA Library AAV Infected Post-Splice, BiolRep11

description: Library name: ms12.post


title: Mouse Brain, ISOMPRA Library AAV Infected Post-Splice, BiolRep12

description: Library name: ms13.post


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, TRAP Input BiolRep7

description: Library name: 3UTR.hek.trap.input7


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, TRAP Input BiolRep8

description: Library name: 3UTR.hek.trap.input8


title: Mouse Brain, ISOMPRA Library AAV Infected Post-Splice, BiolRep13

description: Library name: ms14.post


title: siGpx4 DHA biol rep 1

description: Library name: MM200_2_C4

value: small intestine


title: siCtrl DHA biol rep 2

description: Library name: MM200_2_A4


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, TRAP Input BiolRep6

description: Library name: 3UTR.hek.trap.input6


title: Non tumoral pleura from pneumothorax sample

description: Non tumoral pleura from a biopsy of a pneumothorax patient

value: pneumothorax sample


title: Non tumoral pleura from adenocarcinoma of the lung

description: Non tumoral pleura sample from a biopsy of adenocarcinoma of the lung

value: adenocarcinoma of the lung


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, TRAP Input BiolRep5

description: Library name: 3UTR.hek.trap.input5


title: Mouse Brain, ISOMPRA Library AAV Infected Post-Splice, BiolRep10

description: Library name: ms11.post

value: M


title: rnamap.trim.UF-UI-23_S13.geneAbundanceHisat2

city: Chicago

first: Ayman

last: Al-Hendy

address: 5841 S Maryland Ave

department: OBGyN

institute: University of Chicago

data_processing:
Sequenced reads were trimmed for adaptor sequence using TrimGalore
Reads were mapped to the UCSC human reference genome hg38 using STAR.
featureCounts was used to evaluate gene expression level as read counts
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: uterus

extract_protocol:
We used the Qiagen RNeasy kit (74106) to isolate total RNA, with DNAseI treatment (Qiagen 79254).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue type

value: UF:uterine fibroid

tag: race

value: black


title: siCtrl DHA biol rep 1

description: Library name: MM200_1_A4

tag: cell line


title: Mouse Brain, ISOMPRA Library AAV Infected Post-Splice, BiolRep9

address: 4370 Duncan Ave

description: Library name: ms10.post

tag: cell type

value: WT

value: ISOMPRA Library AAV Infection

value: F


title: Gpx4 KO biol rep 1

description:
Library name: FG1
10X Genomics

tag: genotype

value: PUFA-enriched Western diet for 3 months


title: rnamap.trim.UF-UI-13_S15.geneAbundanceHisat2


title: Mouse Brain, ISOMPRA Library AAV Infected Post-Splice, BiolRep8

description: Library name: ms9.post

tag: treatment


title: Mouse Brain, ISOMPRA Library AAV Infected Post-Splice, BiolRep6

description: Library name: ms7.post

tag: batch


title: Mouse Brain, ISOMPRA Library AAV Infected Post-Splice, BiolRep7

description: Library name: ms8.post

tag: tissue


title: rnamap.trim.UF-428_S17.geneAbundanceHisat2

value: white


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, TRAP Input BiolRep4

description: Library name: 3UTR.hek.trap.input4

source_name: kidney

value: kidney

value: human embryonic kidney cells


title: rnamap.trim.UF-526_S16.geneAbundanceHisat2


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, TRAP Input BiolRep3

description: Library name: 3UTR.hek.trap.input3


title: rnamap.trim.UF-372_S18.geneAbundanceHisat2


title: rnamap.trim.UF-483_S14.geneAbundanceHisat2


title: siGpx4 AA biol rep 3

description: Library name: MM200_4_C2

value: MODE-K

value: IEC

value: stimulation with arachidonic acid


title: Mouse Brain, ISOMPRA Library AAV Infected Post-Splice, BiolRep5

description: Library name: ms5.post

value: brain


title: siCtrl AA biol rep 2

description: Library name: MM200_2_A2

value: small intestine

value: siCtrl


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, TRAP Input BiolRep1

description: Library name: 3UTR.hek.trap.input1

value: ISOMPRA Library Transfection


title: rnamap.trim.MyoN-UI-8_S6.geneAbundanceHisat2

value: MyoF:myometrium adjacent to UF


title: Mouse Brain, ISOMPRA Library AAV Infected Post-Splice, BiolRep4

description: Library name: ms4.post


title: siCtrl AA biol rep 1

description: Library name: MM200_1_A2


title: siGpx4 AA biol rep 1

description: Library name: MM200_2_C2


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Post-Splice BiolRep8

description: Library name: 3UTR.hek.post8


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, TRAP Input BiolRep2

description: Library name: 3UTR.hek.trap.input2


title: siCtrl AA biol rep 3

description: Library name: MM200_3_A2


title: siGpx4 AA biol rep 2

description: Library name: MM200_3_C2