title: Omaveloxolone treated well at 0.12 µM, biol repl 1

description:
Library name: K17_ATCACGACATGTCA
Omaveloxolone treated well at 0.12 µM. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: N2_48h_replicate3

status: Public on Aug 01 2026

type: SRA

city: Baltimore

first: John

last: Kim

state: MD

address: 3400 Charles Street

department: Department of Biology

country: USA

institute: Johns Hopkins University

description:
Library name: smallRNA2021-013-N2-48h-WW
N2 48h RT small RNA-seq replicate 3

library_source: other

data_processing:
One set of libraries was sequenced as 75-bp single-end reads, and two sets were sequenced as 150-bp paired-end reads on a NovaSeq 6000 platform (Illumina). For paired-end libraries, only R1 reads trimmed to 50 bp were used for downstream analysis. Raw reads were trimmed for Illumina adapters and quality using Trimmomatic v0.39 (SLIDING WINDOW: 4:25) (Bolger et al., 2014).
Reads between 19 and 30 nucleotides nt in length were retained. Reads 21–23 nucleotides nt in length were defined as piRNAs and aligned to the C. elegans reference genome (WBcel235) using Bowtie v1.1.1 with parameters -v 0 k 5 –best –strata –tryhard (Langmead et al., 2009).
piRNAs were quantified using a custom Python-based pipeline built upon the HTSeq framework. Read assignments were performed using the intersection-nonempty overlap resolution mode with the nonunique=fraction fractional counting setting, and putative novel piRNAs were identified by incorporating additional 5’ positional and nucleotide matching criteria to detect piRNAs absent from the reference annotation. Novel piRNAs were further defined based on expression support across wild-type samples, requiring a minimum raw read count of ≥5 per sample in at least half of the wild-type samples (n = 6) at either the spermatogenic or oogenic timepoint.
To identify differentially expressed piRNAs, an expression filter of counts per million (CPM) > 2 in at least 3 samples was applied to remove lowly expressed piRNAs. Differential expression analysis was performed using edgeR, comparing mutants to wild type, with thresholds of log2(fold-change) ≥ 0.26 and false discovery rate (FDR) ≤ 0.05 (Benjamini–Hochberg). To account for batch effects across four datasets, an additive model including source was incorporated into the design matrix.
For motif discovery, nucleotide sequences corresponding to the 60 nt upstream of each piRNA locus were extracted from the reference genome and analyzed using MEME Suite v5.1.1 (Bailey et al., 2009).
Assembly: WBcel235
Supplementary files format and content: tab-delimited txt file includes metadata for each sample
Supplementary files format and content: tab-delimited txt file includes read counts for each sample
Supplementary files format and content: tab-delimited txt file includes batch-adjusted log2(CPM) values for each sample

molecule: other

organism: Caenorhabditis elegans

source_name: whole worm

extract_protocol:
Animals were washed off plates in M9, washed repeatedly until the M9 was clear, and nutated for 15 min to clear intestinal contents. Animals were then washed three additional times in M9 and once in water. After centrifugation and removal of excess liquid, 100 µL of worm suspension was added to 1 mL of Trizol (Thermo Fisher). Samples were stored at -80°C until RNA isolation. RNA extraction was performed as previously described (Weiser et al., 2017). Samples were freeze-thawed three times in liquid nitrogen prior to addition of 100 µL of 1-bromo-3-chloropropane and incubation at room temperature for 15 min. Samples were centrifuged at 4°C for 15 min and the aqueous phase collected. An equal volume of 100% isopropanol and 0.5 µL glycogen (1 mg/mL) were added, followed by incubation at -80°C for 2 h and centrifugation for 30 min at 4°C. RNA pellets were washed three times with 75% ethanol, air-dried, and resuspended in nuclease-free water.
2 µg total RNA was pretreated with RNA 5’ polyphosphatase (Illumina) as described previously (Phillips et al., 2014). Pretreated RNA was used for small RNA library preparation with the NEBNext Multiplex Small RNA Library Prep kit according to the manufacturer’s instructions.

tag: tissue

value: whole worm

tag: age

tag: replicate

tag: genotype

value: wildtype


title: Omaveloxolone treated well at 0.04 µM, biol repl 4

city: Palo Alto

first: Drishti

last: Guin

state: CA

address: 1804 Embarcadero Rd Suite #201

institute: Transcripta Bio

description:
Library name: L8_ACACGACGATAGAG
Omaveloxolone treated well at 0.04 µM. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".

library_source: transcriptomic

data_processing:
Alignment was performed on plate-level fastq files using Kallisto bus 0.46.1. Bus files were demultiplexed and converted to count files using Bustools. For convenience, shared fastq files have been pre-demultiplexed into wells using barcode matching with a maximum tolerance of 1 base mismatch using sabre (https://github.com/najoshi/sabre). Read 1 contains a 14 base barcode and RNA reads are contained in read 2.
Assembly: GRCh38
Supplementary files format and content: gene_counts.csv contains well level gene counts.

molecule: polyA RNA

organism: Homo sapiens

source_name: Fibroblast

growth_protocol: Normal Human Dermal Fibroblasts (Lonza CC-2511) were maintained in DMEM (Thermo Scientific, 11965092) supplemented with 10% fetal bovine serum (Thermo Scientific, A5669701) and L-glutamime (Gibco, 25030081) at 37°C with 5% CO2. Cells were seeded in 384-well plates at a density of 1,250 cells per well.

extract_protocol:
Drug-treated fibroblasts in 384-well plates were processed using the Mercurius DRUG-seq Library Preparation 384 kit (Alithea Genomics, v.0.7.1.revA).
DRUG-seq libraries were constructed following the manufacturer’s protocol (Alithea Genomics, v.0.7.1.revA). Libraries were sequenced on an Illumina platform to a depth of approximately 3 billion raw reads per 384-well plate. Libraries were sequences across 4 lanes of a 25B flowcell.

treatment_protocol: Fibroblasts were treated with a selection of FDA-approved small molecule compounds added at one-third decreasing dose for 10 doses: 10µM, 3.33µM, 1.11µM, 0.37µM, 0.12µM, 40nM, 14nM, 5nM, 2nM, and 0.5nM in quadruplicate. Additionally, a total of 16 wells were treated with DMSO as control on each 384-well plate. Compounds and DMSO controls were dispensed directly into the 384-well cell culture plates using an Echo 650 Liquid Handler (Beckman Coulter). Cells were held at 37°C for 24 hours following drug treatment.

tag: cell line

value: Fibroblast

tag: cell type

value: normal human dermal fibroblasts

tag: treatment

value: Omaveloxolone, 0.04 µM


title: SKBR3- riGFP-HER2 CAR T, Mouse 3

city: Chicago

first: CRI

last: Bioinformatics

state: IL

address: 5801 S. Ellis Ave.

institute: University of Chicago

description:
Library name: RZ09
RZ09

data_processing:
Raw reads were processed using the nf-core/rnaseq v3.14.0 pipeline. Quality control was performed with FastQC, alignment was done using STAR v2.7.9a, and quantification was performed using Salmon v1.10.1. Duplicate reads were marked with Picard v3.0.0. Lowly expressed genes were filtered, and normalization was performed using trimmed mean of M-values (TMM) in EdgeR. Differential gene expression analysis was conducted with DESeq2.
Assembly: GRCh38
Supplementary files format and content: Processed data include gene-level count matrices and normalized expression values generated using Salmon, EdgeR (TMM), and DESeq2. Formats are consistent with nf-core/rnaseq v3.14.0 output (typically TSV or CSV). Additional files include PCA coordinates and metadata used for differential analysis and GSEA

molecule: total RNA

growth_protocol: SKBR3 cells were cultured in RPMI-1640 medium supplemented with 10% FBS and 1% penicillin-streptomycin at 37°C in a humidified 5% CO₂ incubator. Tumor xenografts were established in NSG mice by subcutaneous injection of 5×10⁶ SKBR3 cells mixed 1:1 with Matrigel.

extract_protocol:
Tumors were excised and enzymatically digested with Liberase TM (75 µg/mL) and DNase I (20 µg/mL) at 37°C for 40 minutes, followed by mechanical dissociation and filtration through a 70 µm strainer. Single-cell suspensions were stained for viability and surface markers. SKBR3 tumor cells were sorted by FACS based on positive staining for human EpCAM and exclusion of mouse cells (CD45⁻, CD31⁻, Podoplanin⁻). Viable tumor cells were sorted and RNA was extracted using the Qiagen RNeasy Micro Kit following the manufacturer’s protocol
RNA quality was assessed using an Agilent Bioanalyzer. Strand-specific mRNA-seq libraries were prepared using the TruSeq mRNA-SEQ Library Preparation Kit (Illumina), following the manufacturer’s instructions. Libraries were quantified and sequenced using the Illumina NovaSeq 6000 platform.

treatment_protocol: Mice bearing SKBR3 tumors received 1×10⁶ intraperitoneally injected radio-inducible TNF-expressing Her2 CAR T cells. Five days later, tumors were locally irradiated with two doses of 10 Gy (24 hours apart) using a Philips RT-250 X-ray irradiator. Tumors were harvested one day after the final irradiation.

value: Human epithelial breast cancer cells

tag: batch


title: P. promelas larvae, UP, biological replicate UP_B16, lane 2, time step = 4, analyzed on 20160927

city: Durham

first: Steven

middle: Thomas

last: Purucker

state: NC

address: 109 TW Alexander Dr

institute: US EPA

description: Library name: 20160927_ UP_4_B16_GCCAAT_L002_R1_001

data_processing:
Raw read quality assessment with FastQC 0.11.9 & MultiQC 1.12
Reads were processed with fastp 0.23.2 trimming with quality, length, and adapter trimming all enabled by default, and polyX trimming (flag: -x) enabled manually
Alignment with STAR 2.7.10a (--outSAMattributes NH HI AS NM MD --outSAMtype BAM SortedByCoordinate --outSAMheaderHD @HD VN 1.4 SO:sorted --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --outSAMunmapped Within --outFilterType BySJout)
Quantification with STAR 2.7.10a (--quantMode GeneCounts TranscriptomeSAM)
Assembly: P. promelas, GCF_016745375.1_EPA_FHM_2.0
Supplementary files format and content: Tab delimited text file with gene counts: all_counts_20220629.txt uploaded separately.

organism: Pimephales promelas

source_name: whole larvae

growth_protocol: Lab-reared individual fathead minnow larvae (Pimephales promelas) 2 days post-fertilization.

extract_protocol:
Total RNA was isolated from individual FHM using the MagMAX-96 Total RNA Isolation Kit (ThermoFisher Scientific) following manufacturer's protocols. RNA was quantified by spectrophotometric analysis with a Synergy HTX multi-mode plate reader (BioTek).
Neoprep Library Prep System (Illumina) and the TruSeq Stranded mRNA Library Prep for NeoPrep (Illumina). Library concentrations were determined using either the KAPA Library Quantification Kit (Kapa Biosystems) or Qubit dsDNA HS Assay (ThermoFisher Scientific), normalized to equimolar amounts, and then combined into pools of eight samples each. Sequencing was performed at Michigan State University’s RTSF Genomics Core on the Illumina HiSeq 2500 Rapid Run flow cell (v2) for 1x50 bp single-end reads with Rapid SBS reagents.

treatment_protocol: 48 hour lab exposures to moderately hard reconstituted water or river water grab samples collected in August 15 for 6 locations in the vicinity of a wastewater treatment plant (WWTP): upstream of WWTP, WWTP effluent discharging point, proximal location downstream WWTP outfall, distal location downstream of WWTP outfall, a downstream drinking water intake, and treated drinking water collected prior to discharge to the distribution system. Other exposures included 48 hour field fish deployments in exposure vessels secured to a minnow trap at 2 locations (upstream of a WWTP, WWTP effluent discharging point).

value: whole larvae

value: 2 dpf

tag: treatment-replicate id

tag: treatment-time

tag: treatment-location

value: UP


title: P. promelas larvae, UP, biological replicate UP_B16, lane 1, time step = NA, analyzed on 20160927

description: Library name: 20160927_ UP_4_B16_GCCAAT_L001_R1_001


title: snp12null-snpc13null_72h_replicate2

description:
Library name: smallRNA2021-012-SNPC12null_SNPC13null-72h-WW
snpc-1.3(-) 72h RT small RNA-seq replicate 2

value: 72h gravid adult


title: Omaveloxolone treated well at 0.04 µM, biol repl 3

description:
Library name: L18_ATAGGCCACTTCAA
Omaveloxolone treated well at 0.04 µM. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: SKBR3- riGFP-HER2 CAR T, Mouse 2

description:
Library name: RZ08
RZ08


title: P. promelas larvae, EFP, biological replicate EFP_FIELD21, lane 2, time step = NA, analyzed on 20160927

description: Library name: 20160927_ EFP_FIELD_21_ATGTCA_L002_R1_001

value: EFP


title: snpc12null_72h_replicate2

description:
Library name: smallRNA2021-011-SNPC12null-72h-WW
snpc-1.2(-) 72h RT small RNA-seq replicate 2


title: Omaveloxolone treated well at 0.04 µM, biol repl 2

description:
Library name: K8_TAGCTACGATCACG
Omaveloxolone treated well at 0.04 µM. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: SKBR3- riGFP-HER2 CAR T, Mouse 1

description:
Library name: RZ07
RZ07


title: SKBR3- IR alone (10 Gy × 2), Mouse 3

description:
Library name: RZ06
RZ06

value: IR


title: N2_72h_replicate2

description:
Library name: smallRNA2021-010-N2-72h-WW
N2 72h RT small RNA-seq replicate 2


title: snp12null-snpc13null_48h_replicate2

description:
Library name: smallRNA2021-009-SNPC12null_SNPC13null-48h-WW
snpc-1.3(-) 48h RT small RNA-seq replicate 2


title: P. promelas larvae, EFP, biological replicate EFP_B12, lane 2, time step = 4, analyzed on 20160927

description: Library name: 20160927_ EFP_4_B12_ACAGTG_L002_R1_001


title: Omaveloxolone treated well at 0.04 µM, biol repl 1

description:
Library name: K18_AAGCCGAATCCTCC
Omaveloxolone treated well at 0.04 µM. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: Omaveloxolone treated well at 0.014 µM, biol repl 4

description:
Library name: L9_CACGCAGATCAGCA
Omaveloxolone treated well at 0.014 µM. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".

value: Omaveloxolone, 0.014 µM


title: SKBR3- IR alone (10 Gy × 2), Mouse 2

description:
Library name: RZ05
RZ05


title: P. promelas larvae, EFP, biological replicate EFP_B12, lane 1, time step = 4, analyzed on 20160927

description: Library name: 20160927_ EFP_4_B12_ACAGTG_L001_R1_001


title: snpc12null_48h_replicate2

description:
Library name: smallRNA2021-008-SNPC12null-48h-WW
snpc-1.2(-) 48h RT small RNA-seq replicate 2


title: Omaveloxolone treated well at 0.014 µM, biol repl 3

description:
Library name: L19_CAATGAATTCAAGG
Omaveloxolone treated well at 0.014 µM. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: SKBR3- IR alone (10 Gy × 2), Mouse 1

description:
Library name: RZ04
RZ04


title: P. promelas larvae, EFP, biological replicate EFP_B13, lane 2, time step = 3, analyzed on 20160927

description: Library name: 20160927_ EFP_3_B13_AGTTCC_L002_R1_001


title: N2_48h_replicate2

description:
Library name: smallRNA2021-007-N2-48h-WW
N2 48h RT small RNA-seq replicate 2


title: P. promelas larvae, EFP, biological replicate EFP_B13, lane 1, time step = 3, analyzed on 20160927

description: Library name: 20160927_ EFP_3_B13_AGTTCC_L001_R1_001


title: Omaveloxolone treated well at 0.014 µM, biol repl 2

description:
Library name: K9_TTACATTAGATGGC
Omaveloxolone treated well at 0.014 µM. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: SKBR3- UNTREATED, Mouse 3

description:
Library name: RZ03
RZ03

value: Untreated


title: snp12null-snpc13null_72h_replicate1

description:
Library name: smallRNA2021-006-SNPC12null_SNPC13null-72h-WW
snpc-1.3(-) 72h RT small RNA-seq replicate 1


title: Omaveloxolone treated well at 0.014 µM, biol repl 1

description:
Library name: K19_ACAATCCAACGCGG
Omaveloxolone treated well at 0.014 µM. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: P. promelas larvae, EFP, biological replicate EFP_FIELD21, lane 1, time step = NA, analyzed on 20160927

description: Library name: 20160927_ EFP_FIELD_21_ATGTCA_L001_R1_001


title: P. promelas larvae, EFP, biological replicate EFP_B17, lane 2, time step = 2, analyzed on 20160927

description: Library name: 20160927_ EFP_2_B17_CTTGTA_L002_R1_001


title: SKBR3- UNTREATED, Mouse 2

description:
Library name: RZ02
RZ02


title: Omaveloxolone treated well at 0.005 µM, biol repl 4

description:
Library name: L20_CATCTGACACGCGC
Omaveloxolone treated well at 0.005 µM. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".

value: Omaveloxolone, 0.005 µM


title: snpc12null_72h_replicate1

description:
Library name: smallRNA2021-005-SNPC12null-72h-WW
snpc-1.2(-) 72h RT small RNA-seq replicate 1


title: SKBR3- UNTREATED, Mouse 1

description:
Library name: RZ01
RZ01


title: P. promelas larvae, EFP, biological replicate EFP_B17, lane 1, time step = 2, analyzed on 20160927

description: Library name: 20160927_ EFP_2_B17_CTTGTA_L001_R1_001


title: N2_72h_replicate1

description:
Library name: smallRNA2021-004-N2-72h-WW
N2 72h RT small RNA-seq replicate 1


title: Omaveloxolone treated well at 0.005 µM, biol repl 3

description:
Library name: L10_CAGTACGTCAGACG
Omaveloxolone treated well at 0.005 µM. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: Mia-PaCa-2 cells, shEIF2B5, rep4

city: Montréal

first: Antonis

last: Koromilas

state: QC

address: 3755 Chem. de la Côte-Sainte-Catherine

country: Canada

institute: Lady Davis Institute - McGill University

description:
Library name: Sample 22
Column name in RNA_seq_raw_counts.csv: Miash5_MPS12351076_G05.quant.genes

data_processing:
For bulk RNA-seq, high-quality reads were then mapped to the hg38 (GRCh38.p12) human genome using the standard HISAT2 pipeline (v2.2.1). Transcript quantitation was performed using Salmon (v0.11.3) and summarized at gene level using the R package tximport (v1.22.0). Gene annotations were assigned using biomaRt (v2.50.3). RNA-seq experiment-wise data were managed and normalized using DESeq2 (v1.44.0).
Assembly: GRCh38
Supplementary files format and content: csv file includes raw counts for each sample

extract_protocol:
For Bulk RNA-seq, total RNA of H358, H1703 and MiaPaCa2 cells treated with scrambled siRNAs or eIF2Bε siRNAs (four replicates each) was isolated with Trizol (Thermo Fisher Scientific).
RNA-Seq libraries were prepared following the TruSeq Stranded Total RNA protocol (Illumina) according to the manufacturer’s instructions.

value: tumour cell line

value: EIF2B5 knockdown


title: P. promelas larvae, EFP, biological replicate EFP_B17, lane 2, time step = 1, analyzed on 20160927

description: Library name: 20160927_ EFP_1_B17_AGTCAA_L002_R1_001


title: snp12null-snpc13null_48h_replicate1

description:
Library name: smallRNA2021-003-SNPC12null_SNPC13null-48h-WW
snpc-1.3(-) 48h RT small RNA-seq replicate 1

value: whole worm


title: Omaveloxolone treated well at 0.005 µM, biol repl 2

description:
Library name: K20_TATGCCATGCCTAC
Omaveloxolone treated well at 0.005 µM. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".

value: wildtype


title: Mia-PaCa-2 cells, shEIF2B5, rep3

description:
Library name: Sample 21
Column name in RNA_seq_raw_counts.csv: Miash4_MPS12351076_C02.quant.genes


title: Omaveloxolone treated well at 0.005 µM, biol repl 1

description:
Library name: K10_AAGAACGGCCTGGC
Omaveloxolone treated well at 0.005 µM. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".

value: Fibroblast


title: P. promelas larvae, EFP, biological replicate EFP_B17, lane 1, time step = 1, analyzed on 20160927

description: Library name: 20160927_ EFP_1_B17_AGTCAA_L001_R1_001


title: snpc12null_48h_replicate1

description:
Library name: smallRNA2021-002-SNPC12null-48h-WW
snpc-1.2(-) 48h RT small RNA-seq replicate 1


title: Mia-PaCa-2 cells, shEIF2B5, rep2

description:
Library name: Sample 20
Column name in RNA_seq_raw_counts.csv: Miash3_MPS12351076_B02.quant.genes


title: P. promelas larvae, DSP, biological replicate DSP_B12, lane 2, time step = NA, analyzed on 20160927

description: Library name: 20160927_ DSP_B12_GTTTCG_L002_R1_001

value: DSP


title: N2_48h_replicate1

description:
Library name: smallRNA2021-001-N2-48h-WW
N2 48h RT small RNA-seq replicate 1


title: Omaveloxolone treated well at 0.002 µM, biol repl 4

description:
Library name: L21_CCTATGGAACTTGC
Omaveloxolone treated well at 0.002 µM. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".

value: normal human dermal fibroblasts

value: Omaveloxolone, 0.002 µM


title: Mia-PaCa-2 cells, shEIF2B5, rep1

description:
Library name: Sample 19
Column name in RNA_seq_raw_counts.csv: Miash2_MPS12351076_A02.quant.genes


title: P. promelas larvae, DSP, biological replicate DSP_B12, lane 1, time step = NA, analyzed on 20160927

description: Library name: 20160927_ DSP_B12_GTTTCG_L001_R1_001

value: whole larvae


title: snpc13null_72h_setA_replicate3

description:
Library name: smallRNA2022-115-snpc13null-72h-WW
snpc-1.3(-) 72h LKBsetA small RNA-seq replicate 3


title: Omaveloxolone treated well at 0.002 µM, biol repl 3

description:
Library name: L11_TATGTGACTGTACG
Omaveloxolone treated well at 0.002 µM. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: Mia-PaCa-2 cells, shControl, rep4

description:
Library name: Sample 18
Column name in RNA_seq_raw_counts.csv: MiaSCR4_MPS12351076_F05.quant.genes

value: WT


title: P. promelas larvae, UP, biological replicate UP_FIELD17, lane 2, time step = NA, analyzed on 20160927

description: Library name: 20160927_ UP_FIELD_17_ACTGAT_L002_R1_001

value: 2 dpf

value: UP


title: snpc12null_72h_setA_replicate3

description:
Library name: smallRNA2022-114-snpc12null-72h-WW
snpc-1.2(-) 72h LKBsetA small RNA-seq replicate 3

value: 72h gravid adult


title: Mia-PaCa-2 cells, shControl, rep3

description:
Library name: Sample 17
Column name in RNA_seq_raw_counts.csv: MiaSCR3_MPS12351076_H01.quant.genes


title: Omaveloxolone treated well at 0.002 µM, biol repl 2

description:
Library name: K21_TATGATGCTGACAC
Omaveloxolone treated well at 0.002 µM. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: P. promelas larvae, UP, biological replicate UP_FIELD17, lane 1, time step = NA, analyzed on 20160927

description: Library name: 20160927_ UP_FIELD_17_ACTGAT_L001_R1_001


title: N2_72h_setA_replicate3

description:
Library name: smallRNA2022-113-N2-72h-WW
N2 72h LKBsetA small RNA-seq replicate 3


title: Omaveloxolone treated well at 0.002 µM, biol repl 1

description:
Library name: K11_ACACAGTGTACTCG
Omaveloxolone treated well at 0.002 µM. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: Mia-PaCa-2 cells, shControl, rep2

description:
Library name: Sample 16
Column name in RNA_seq_raw_counts.csv: MiaSCR2_MPS12351076_G01.quant.genes


title: P. promelas larvae, UP, biological replicate UP_B02, lane 2, time step = 2, analyzed on 20160927

description: Library name: 20160927_ UP_2_B02_GAGTGG_L002_R1_001


title: snpc13null_48h_setA_replicate3

description:
Library name: smallRNA2022-109-snpc13null-48h-WW
snpc-1.3(-) 48h LKBsetA small RNA-seq replicate 3


title: Omaveloxolone treated well at 0.0005 µM, biol repl 4

description:
Library name: L22_ATGAAGTAACCAAG
Omaveloxolone treated well at 0.0005 µM. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".

value: Omaveloxolone, 0.0005 µM


title: Mia-PaCa-2 cells, shControl, rep1

description:
Library name: Sample 15
Column name in RNA_seq_raw_counts.csv: MiaSCR1_MPS12351076_F01.quant.genes


title: H358 cells, shEIF2B5, rep3

description:
Library name: Sample 14
Column name in RNA_seq_H358_raw_counts.csv: H358_shEIF2B5_rep3


title: snpc12null_48h_setA_replicate3

description:
Library name: smallRNA2022-108-snpc12null-48h-WW
snpc-1.2(-) 48h LKBsetA small RNA-seq replicate 3


title: P. promelas larvae, UP, biological replicate UP_B02, lane 1, time step = 2, analyzed on 20160927

description: Library name: 20160927_ UP_2_B02_GAGTGG_L001_R1_001


title: P. promelas larvae, UP, biological replicate UP_B11, lane 2, time step = 1, analyzed on 20160927

description: Library name: 20160927_ UP_1_B11_GTCCGC_L002_R1_001


title: N2_48h_setA_replicate3

description:
Library name: smallRNA2022-107-N2-48h-WW
N2 48h LKBsetA small RNA-seq replicate 3


title: Omaveloxolone treated well at 0.0005 µM, biol repl 2

description:
Library name: K22_ACATCCTAATACCG
Omaveloxolone treated well at 0.0005 µM. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: Omaveloxolone treated well at 0.0005 µM, biol repl 3

description:
Library name: L12_TTAGAATTCCGAAG
Omaveloxolone treated well at 0.0005 µM. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: H358 cells, shEIF2B5, rep2

description:
Library name: Sample 13
Column name in RNA_seq_H358_raw_counts.csv: H358_shEIF2B5_rep2


title: P. promelas larvae, UP, biological replicate UP_B11, lane 1, time step = 1, analyzed on 20160927

description: Library name: 20160927_ UP_1_B11_GTCCGC_L001_R1_001


title: Omaveloxolone treated well at 0.0005 µM, biol repl 1

description:
Library name: K12_ACGTCAGCATCGAC
Omaveloxolone treated well at 0.0005 µM. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: H358 cells, shEIF2B5, rep1

description:
Library name: Sample 12
Column name in RNA_seq_H358_raw_counts.csv: H358_shEIF2B5_rep1


title: snpc13null_72h_setA_replicate2

description:
Library name: smallRNA2022-103-snpc13null-72h-WW
snpc-1.3(-) 72h LKBsetA small RNA-seq replicate 2


title: P. promelas larvae, EMZ, biological replicate EMZ_B06, lane 2, time step = NA, analyzed on 20160927

description: Library name: 20160927_ EMZ_B06_ATCACG_L002_R1_001

value: EMZ


title: H358 cells, shControl, rep3

description:
Library name: Sample 11
Column name in RNA_seq_H358_raw_counts.csv: H358_PLKO_rep3


title: snpc12null_72h_setA_replicate2

description:
Library name: smallRNA2022-102-snpc12null-72h-WW
snpc-1.2(-) 72h LKBsetA small RNA-seq replicate 2


title: N2_72h_setA_replicate2

description:
Library name: smallRNA2022-101-N2-72h-WW
N2 72h LKBsetA small RNA-seq replicate 2


title: DMSO control well, biol repl 31

description:
Library name: P2_CAGCGACTACGCAG
DMSO control well. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".

value: DMSO control


title: P. promelas larvae, EMZ, biological replicate EMZ_B06, lane 1, time step = NA, analyzed on 20160927

description: Library name: 20160927_ EMZ_B06_ATCACG_L001_R1_001


title: DMSO control well, biol repl 32

description:
Library name: P23_CAACAGGAGGCTCC
DMSO control well. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: H358 cells, shControl, rep2

description:
Library name: Sample 10
Column name in RNA_seq_H358_raw_counts.csv: H358_PLKO_rep2


title: P. promelas larvae, EFP, biological replicate EFP_FIELD4, lane 2, time step = NA, analyzed on 20160927

description: Library name: 20160927_ EFP_FIELD_4_ACTTGA_L002_R1_001

value: EFP


title: snpc13null_48h_setA_replicate2

description:
Library name: smallRNA2022-097-snpc13null-48h-WW
snpc-1.3(-) 48h LKBsetA small RNA-seq replicate 2


title: DMSO control well, biol repl 30

description:
Library name: O23_CCTCGAGGTAGGAA
DMSO control well. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: H358 cells, shControl, rep1

description:
Library name: Sample 9
Column name in RNA_seq_H358_raw_counts.csv: H358_PLKO_rep1

value: tumour cell line


title: P. promelas larvae, DSP, biological replicate DSP_B06, lane 2, time step = NA, analyzed on 20160927

description: Library name: 20160927_ DSP_B06_TAGCTT_L002_R1_001


title: P. promelas larvae, EFP, biological replicate EFP_FIELD4, lane 1, time step = NA, analyzed on 20160927

description: Library name: 20160927_ EFP_FIELD_4_ACTTGA_L001_R1_001


title: DMSO control well, biol repl 29

description:
Library name: O2_CCTTATTGCGTTCC
DMSO control well. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: snpc12null_48h_setA_replicate2

description:
Library name: smallRNA2022-096-snpc12null-48h-WW
snpc-1.2(-) 48h LKBsetA small RNA-seq replicate 2


title: DMSO control well, biol repl 28

description:
Library name: N23_ATCATGCACTGCGA
DMSO control well. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: H1703 cells, shEIF2B5, rep3

description:
Library name: Sample 7
Column name in RNA_seq_raw_counts.csv: H1703SH4_MPS12351076_F07.quant.genes

value: EIF2B5 knockdown


title: H1703 cells, shEIF2B5, rep4

description:
Library name: Sample 8
Column name in RNA_seq_raw_counts.csv: H1703SH5_MPS12351076_A03.quant.genes


title: N2_48h_setA_replicate2

description:
Library name: smallRNA2022-095-N2-48h-WW
N2 48h LKBsetA small RNA-seq replicate 2

value: whole worm


title: P. promelas larvae, DSP, biological replicate DSP_B06, lane 1, time step = NA, analyzed on 20160927

description: Library name: 20160927_ DSP_B06_TAGCTT_L001_R1_001


title: snpc13null_72h_setA_replicate1

description:
Library name: smallRNA2022-091-snpc13null-72h-WW
snpc-1.3(-) 72h LKBsetA small RNA-seq replicate 1


title: DMSO control well, biol repl 27

description:
Library name: N2_CATCGCACGTATGC
DMSO control well. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".

value: wildtype


title: H1703 cells, shEIF2B5, rep2

description:
Library name: Sample 6
Column name in RNA_seq_raw_counts.csv: H1703SH3_MPS12351076_H02.quant.genes


title: DMSO control well, biol repl 26

description:
Library name: M23_CAATCTTGGCTTCA
DMSO control well. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".

value: Fibroblast


title: snpc12null_72h_setA_replicate1

description:
Library name: smallRNA2022-090-snpc12null-72h-WW
snpc-1.2(-) 72h LKBsetA small RNA-seq replicate 1


title: P. promelas larvae, MHW, biological replicate MHW_B06, lane 2, time step = NA, analyzed on 20160927

description: Library name: 20160927_ 15-08_B06_GTGGCC_L002_R1_001

value: MHW


title: H1703 cells, shEIF2B5, rep1

description:
Library name: Sample 5
Column name in RNA_seq_raw_counts.csv: H1703SH2_MPS12351076_G02.quant.genes


title: P. promelas larvae, MHW, biological replicate MHW_B06, lane 1, time step = NA, analyzed on 20160927

description: Library name: 20160927_ 15-08_B06_GTGGCC_L001_R1_001


title: N2_72h_setA_replicate1

description:
Library name: smallRNA2022-089-N2-72h-WW
N2 72h LKBsetA small RNA-seq replicate 1


title: DMSO control well, biol repl 25

description:
Library name: M2_ATAGGCTGGACCGG
DMSO control well. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".

value: normal human dermal fibroblasts


title: H1703 cells, shControl, rep4

description:
Library name: Sample 4
Column name in RNA_seq_raw_counts.csv: H1703SCR4_MPS12351076_E05.quant.genes


title: P. promelas larvae, MHW, biological replicate MHW_B02, lane 2, time step = NA, analyzed on 20160927

description: Library name: 20160927_ 15-07_B02_GGCTAC_L002_R1_001


title: snpc13null_48h_setA_replicate1

description:
Library name: smallRNA2022-085-snpc13null-48h-WW
snpc-1.3(-) 48h LKBsetA small RNA-seq replicate 1


title: DMSO control well, biol repl 24

description:
Library name: L23_ACGAGCACAGCTGA
DMSO control well. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: snpc12null_48h_setA_replicate1

description:
Library name: smallRNA2022-084-snpc12null-48h-WW
snpc-1.2(-) 48h LKBsetA small RNA-seq replicate 1


title: H1703 cells, shControl, rep2

description:
Library name: Sample 2
Column name in RNA_seq_raw_counts.csv: H1703SCR2_MPS12351076_E02.quant.genes


title: DMSO control well, biol repl 23

description:
Library name: L2_ACAGCAGACGATGC
DMSO control well. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: H1703 cells, shControl, rep3

description:
Library name: Sample 3
Column name in RNA_seq_raw_counts.csv: H1703SCR3_MPS12351076_F02.quant.genes


title: P. promelas larvae, UP, biological replicate UP_FIELD3, lane 2, time step = NA, analyzed on 20160926

description: Library name: 20160926_ UP_FIELD_3_GTGAAA_L002_R1_001


title: P. promelas larvae, MHW, biological replicate MHW_B02, lane 1, time step = NA, analyzed on 20160927

description: Library name: 20160927_ 15-07_B02_GGCTAC_L001_R1_001


title: N2_48h_setA_replicate1

description:
Library name: smallRNA2022-083-N2-48h-WW
N2 48h LKBsetA small RNA-seq replicate 1


title: DMSO control well, biol repl 22

description:
Library name: K23_TCGACTGCATGCGA
DMSO control well. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: H1703 cells, shControl, rep1

description:
Library name: Sample 1
Column name in RNA_seq_raw_counts.csv: H1703SCR1_MPS12351076_D02.quant.genes


title: P. promelas larvae, UP, biological replicate UP_FIELD3, lane 1, time step = NA, analyzed on 20160926

description: Library name: 20160926_ UP_FIELD_3_GTGAAA_L001_R1_001


title: DMSO control well, biol repl 21

description:
Library name: K2_CTTCATGGCTCCAC
DMSO control well. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: snpc12null-snpc13null_72h_setB_replicate3

description:
Library name: smallRNA2022-082-snpc12null_snpc13null-72h-WW
snpc-1.2(-); snpc-1.3(-) 72h LKBsetB small RNA-seq replicate 3


title: P. promelas larvae, UP, biological replicate UP_B06, lane 2, time step = 4, analyzed on 20160926

description: Library name: 20160926_ UP_4_B06_AGTCAA_L002_R1_001


title: H358 cells, shEIF2B5, Ribo-Seq,  rep3

description:
Library name: Sample 24
Column name in RIBO_seq_raw_counts.csv: AK123

data_processing:
For Ribo-Seq, Sequenced libraries were trimmed using Cutadapt 3.4 by removing the constant adapter (AGATCGGAAGAGCAC) from reads without allowing any mismatches. Any reads shorter than six nt and without the adapter were discarded. Trimmed reads were demultiplexed using the sample barcode anchored to the 5′ end of reads without allowing any mismatch in the barcodes. The multiplexed reads were then processed for alignments to the mouse transcriptome using the following criteria: First, low-quality reads and reads shorter than 25 were discarded, then reads were sequentially aligned to cytoplasmic and mitochondrion rRNA and tRNA using Bowtie 2 version 2.5.4 (PMID: 22388286) allowing three mismatches in the reads (parameters: −v 3 −norc −p 12). The remaining reads were aligned with the human GRCh38 whole transcriptome preset by Bowtie 2 version 2.5.4. SAM files were converted to BAM files, sorted, indexed.
Assembly: GRCh38
Supplementary files format and content: csv file includes raw counts for each sample
Library strategy: Ribo-Seq

extract_protocol:
For Ribo-Seq,  Cells were washed twice with ice-cooled PBS containing 100 μg/mL CHX, and lysed. Lysates were incubated on ice for 10 min, followed by centrifugation at 16000 x g for 10 min at 4°C. A portion of supernatants was saved for RNA-Seq. Ribo-Seq samples were digested with MNase or RNAse I (Epicenter) and digested polysomes were loaded on a 10-50% sucrose density gradient and centrifuged at 36,000 rpm for 3 hours at 4°C. Fractions corresponding to monosome peak fractions were collected, pooled, and RNAs were extracted using Trizol.
For Ribo-Seq library prep, we followed McGlincy and Ingolia 2017 ribosome profiling technique with some modification. RNA was electrochemically separated on a 15% TBU-Urea gel, and fragments of 25-40 nt were selected. After gel extraction, rRNA depletion, and dephosphorylation, ligation was performed with pre-adenylated linkers containing Unique Molecular Identifiers (UMIs) and barcodes. The ligated samples underwent gel purification, reverse transcription, and circularization using CircLigase I. Another rRNA depletion step was done before qPCR optimization. The final PCR product, confirmed for size and quantity, was sequenced on an Illumina NovaSeq 6000 System.


title: DMSO control well, biol repl 20

description:
Library name: J23_TCTATAGAGTCGAG
DMSO control well. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: H358 cells, shEIF2B5, Ribo-Seq,  rep2

description:
Library name: Sample 23
Column name in RIBO_seq_raw_counts.csv: AK122


title: mut16_72h_setB_replicate3

description:
Library name: smallRNA2022-080-mut16-72h-WW
mut-16(-) 72h LKBsetB small RNA-seq replicate 3


title: DMSO control well, biol repl 19

description:
Library name: J2_CAGGATTATAGAAG
DMSO control well. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: P. promelas larvae, UP, biological replicate UP_B06, lane 1, time step = 4, analyzed on 20160926

description: Library name: 20160926_ UP_4_B06_AGTCAA_L001_R1_001


title: H358 cells, shEIF2B5, Ribo-Seq,  rep1

description:
Library name: Sample 22
Column name in RIBO_seq_raw_counts.csv: AK121


title: prg1_72h_setB_replicate3

description:
Library name: smallRNA2022-081-prg1-72h-WW
prg-1(-) 72h LKBsetB small RNA-seq replicate 3


title: P. promelas larvae, UP, biological replicate UP_B01, lane 2, time step = 3, analyzed on 20160926

description: Library name: 20160926_ UP_3_B01_GCCAAT_L002_R1_001


title: DMSO control well, biol repl 18

description:
Library name: I23_TTAATCGGCTGGCA
DMSO control well. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: hrde1_72h_setB_replicate3

description:
Library name: smallRNA2022-079-hrde1-72h-WW
hrde-1(-) 72h LKBsetB small RNA-seq replicate 3


title: H358 cells, shControl, Ribo-Seq,  rep3

description:
Library name: Sample 21
Column name in RIBO_seq_raw_counts.csv: AK120


title: N2_72h_setB_replicate3_resequenced

description:
Library name: smallRNA2022-078resequenced-N2-72h-WW
N2 72h LKBsetB small RNA-seq replicate 3


title: P. promelas larvae, UP, biological replicate UP_B01, lane 1, time step = 3, analyzed on 20160926

description: Library name: 20160926_ UP_3_B01_GCCAAT_L001_R1_001


title: DMSO control well, biol repl 17

description:
Library name: I2_ATACTTGCCGGACC
DMSO control well. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: snpc12null-snpc13null_48h_setB_replicate3

description:
Library name: smallRNA2022-077-snpc12null_snpc13null-48h-WW
snpc-1.2(-); snpc-1.3(-) 48h LKBsetB small RNA-seq replicate 3


title: H358 cells, shControl, Ribo-Seq,  rep2

description:
Library name: Sample 20
Column name in RIBO_seq_raw_counts.csv: AK119


title: DMSO control well, biol repl 16

description:
Library name: H23_ACTTAGTTCGGTAA
DMSO control well. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: P. promelas larvae, EFP, biological replicate EFP_FIELD3, lane 2, time step = NA, analyzed on 20160926

description: Library name: 20160926_ EFP_FIELD_3_GTTTCG_L002_R1_001


title: H358 cells, shControl, Ribo-Seq,  rep1

description:
Library name: Sample 19
Column name in RIBO_seq_raw_counts.csv: AK118


title: P. promelas larvae, EFP, biological replicate EFP_FIELD3, lane 1, time step = NA, analyzed on 20160926

description: Library name: 20160926_ EFP_FIELD_3_GTTTCG_L001_R1_001


title: prg1_48h_setB_replicate3

description:
Library name: smallRNA2022-076-prg1-48h-WW
prg-1(-) 48h LKBsetB small RNA-seq replicate 3


title: DMSO control well, biol repl 15

description:
Library name: H2_ATGTTGGCGGACAC
DMSO control well. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: H1703 cells, shEIF2B5, Ribo-Seq,  rep3

description:
Library name: Sample 18
Column name in RIBO_seq_raw_counts.csv: AK117


title: P. promelas larvae, EFP, biological replicate EFP_B02, lane 2, time step = 4, analyzed on 20160926

description: Library name: 20160926_ EFP_4_B02_ATGTCA_L002_R1_001


title: mut16_48h_setB_replicate3

description:
Library name: smallRNA2022-075-mut16-48h-WW
mut-16(-) 48h LKBsetB small RNA-seq replicate 3


title: H1703 cells, shEIF2B5, Ribo-Seq,  rep2

description:
Library name: Sample 17
Column name in RIBO_seq_raw_counts.csv: AK116


title: P. promelas larvae, EFP, biological replicate EFP_B02, lane 1, time step = 4, analyzed on 20160926

description: Library name: 20160926_ EFP_4_B02_ATGTCA_L001_R1_001


title: hrde1_48h_setB_replicate3

description:
Library name: smallRNA2022-074-hrde1-48h-WW
hrde-1(-) 48h LKBsetB small RNA-seq replicate 3


title: H1703 cells, shEIF2B5, Ribo-Seq,  rep1

description:
Library name: Sample 16
Column name in RIBO_seq_raw_counts.csv: AK115


title: DMSO control well, biol repl 14

description:
Library name: G23_ATGAACAGGCTCCG
DMSO control well. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: DMSO control well, biol repl 13

description:
Library name: G2_CAACCACTGAACCA
DMSO control well. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: P. promelas larvae, EFP, biological replicate EFP_B01, lane 2, time step = 3, analyzed on 20160926

description: Library name: 20160926_ EFP_3_B01_ACAGTG_L002_R1_001


title: N2_48h_setB_replicate3

description:
Library name: smallRNA2022-073-N2-48h-WW
N2 48h LKBsetB small RNA-seq replicate 3


title: DMSO control well, biol repl 12

description:
Library name: F23_CTTGCGAGGCAGCA
DMSO control well. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: H1703 cells, shControl, Ribo-Seq,  rep3

description:
Library name: Sample 15
Column name in RIBO_seq_raw_counts.csv: AK114


title: P. promelas larvae, EFP, biological replicate EFP_B01, lane 1, time step = 3, analyzed on 20160926

description: Library name: 20160926_ EFP_3_B01_ACAGTG_L001_R1_001


title: snpc12null-snpc13null_72h_setB_replicate2

description:
Library name: smallRNA2022-072-snpc12null_snpc13null-72h-WW
snpc-1.2(-); snpc-1.3(-) 72h LKBsetB small RNA-seq replicate 2


title: DMSO control well, biol repl 11

description:
Library name: F2_CAATTGTCTTATGG
DMSO control well. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: P. promelas larvae, EFP, biological replicate EFP_B06, lane 2, time step = 2, analyzed on 20160926

description: Library name: 20160926_ EFP_2_B06_AGTTCC_L002_R1_001


title: prg1_72h_setB_replicate2

description:
Library name: smallRNA2022-071-prg1-72h-WW
prg-1(-) 72h LKBsetB small RNA-seq replicate 2


title: H1703 cells, shControl, Ribo-Seq,  rep2

description:
Library name: Sample 14
Column name in RIBO_seq_raw_counts.csv: AK113


title: DMSO control well, biol repl 10

description:
Library name: E23_CACACGCGTACGAC
DMSO control well. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: H1703 cells, shControl, Ribo-Seq,  rep1

description:
Library name: Sample 13
Column name in RIBO_seq_raw_counts.csv: AK112


title: P. promelas larvae, EFP, biological replicate EFP_B06, lane 1, time step = 2, analyzed on 20160926

description: Library name: 20160926_ EFP_2_B06_AGTTCC_L001_R1_001


title: mut16_72h_setB_replicate2

description:
Library name: smallRNA2022-070-mut16-72h-WW
mut-16(-) 72h LKBsetB small RNA-seq replicate 2


title: DMSO control well, biol repl 9

description:
Library name: E2_TTGATAATACGCCA
DMSO control well. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: H358 cells, shEIF2B5, Ribo-Seq (RNaseI),  rep3

description:
Library name: Sample 12
Column name in RIBO_seq_raw_counts.csv: AK111


title: hrde1_72h_setB_replicate2

description:
Library name: smallRNA2022-069-hrde1-72h-WW
hrde-1(-) 72h LKBsetB small RNA-seq replicate 2


title: DMSO control well, biol repl 8

description:
Library name: D23_ACCATGGAGGATGG
DMSO control well. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: H358 cells, shEIF2B5, Ribo-Seq (RNaseI),  rep2

description:
Library name: Sample 11
Column name in RIBO_seq_raw_counts.csv: AK110


title: P. promelas larvae, EFP, biological replicate EFP_B02, lane 1, time step = 1, analyzed on 20160926

description: Library name: 20160926_ EFP_1_B02_CTTGTA_L001_R1_001


title: P. promelas larvae, EFP, biological replicate EFP_B02, lane 2, time step = 1, analyzed on 20160926

description: Library name: 20160926_ EFP_1_B02_CTTGTA_L002_R1_001


title: N2_72h_setB_replicate2

description:
Library name: smallRNA2022-068-N2-72h-WW
N2 72h LKBsetB small RNA-seq replicate 2


title: DMSO control well, biol repl 7

description:
Library name: D2_TTCTTGAACTCTGG
DMSO control well. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: H358 cells, shEIF2B5, Ribo-Seq (RNaseI),  rep1

description:
Library name: Sample 10
Column name in RIBO_seq_raw_counts.csv: AK109


title: P. promelas larvae, UP, biological replicate UP_FIELD30, lane 2, time step = NA, analyzed on 20160926

description: Library name: 20160926_ UP_FIELD_30_ACTGAT_L002_R1_001


title: DMSO control well, biol repl 6

description:
Library name: C23_CAACGGCCGGAAGA
DMSO control well. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: snpc12null-snpc13null_48h_setB_replicate2

description:
Library name: smallRNA2022-067-snpc12null_snpc13null-48h-WW
snpc-1.2(-); snpc-1.3(-) 48h LKBsetB small RNA-seq replicate 2


title: H358 cells, shControl, Ribo-Seq (RNaseI),  rep3

description:
Library name: Sample 9
Column name in RIBO_seq_raw_counts.csv: AK108


title: prg1_48h_setB_replicate2

description:
Library name: smallRNA2022-066-prg1-48h-WW
prg-1(-) 48h LKBsetB small RNA-seq replicate 2


title: P. promelas larvae, UP, biological replicate UP_FIELD30, lane 1, time step = NA, analyzed on 20160926

description: Library name: 20160926_ UP_FIELD_30_ACTGAT_L001_R1_001


title: DMSO control well, biol repl 5

description:
Library name: C2_TATATTAACGGTGG
DMSO control well. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: mut16_48h_setB_replicate2

description:
Library name: smallRNA2022-065-mut16-48h-WW
mut-16(-) 48h LKBsetB small RNA-seq replicate 2


title: P. promelas larvae, UP, biological replicate UP_FIELD16, lane 2, time step = NA, analyzed on 20160926

description: Library name: 20160926_ UP_FIELD_16_GTGGCC_L002_R1_001


title: H358 cells, shControl, Ribo-Seq (RNaseI),  rep2

description:
Library name: Sample 8
Column name in RIBO_seq_raw_counts.csv: AK107


title: DMSO control well, biol repl 4

description:
Library name: B23_CCTCATACAACACG
DMSO control well. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: P. promelas larvae, UP, biological replicate UP_FIELD16, lane 1, time step = NA, analyzed on 20160926

description: Library name: 20160926_ UP_FIELD_16_GTGGCC_L001_R1_001


title: H358 cells, shControl, Ribo-Seq (RNaseI),  rep1

description:
Library name: Sample 7
Column name in RIBO_seq_raw_counts.csv: AK106


title: hrde1_48h_setB_replicate2

description:
Library name: smallRNA2022-064-hrde1-48h-WW
hrde-1(-) 48h LKBsetB small RNA-seq replicate 2


title: H1703 cells, shEIF2B5, Ribo-Seq (RNaseI),  rep3

description:
Library name: Sample 6
Column name in RIBO_seq_raw_counts.csv: AK105


title: DMSO control well, biol repl 3

description:
Library name: B2_TAGACGTGGACCAG
DMSO control well. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: P. promelas larvae, EMZ, biological replicate EMZ_B01, lane 2, time step = NA, analyzed on 20160926

description: Library name: 20160926_ EMZ_B01_GGCTAC_L002_R1_001


title: DMSO control well, biol repl 2

description:
Library name: A23_ATAACCTCTCGCCA
DMSO control well. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: N2_48h_setB_replicate2

description:
Library name: smallRNA2022-063-N2-48h-WW
N2 48h LKBsetB small RNA-seq replicate 2


title: H1703 cells, shEIF2B5, Ribo-Seq (RNaseI),  rep2

description:
Library name: Sample 5
Column name in RIBO_seq_raw_counts.csv: AK104


title: P. promelas larvae, EMZ, biological replicate EMZ_B01, lane 1, time step = NA, analyzed on 20160926

description: Library name: 20160926_ EMZ_B01_GGCTAC_L001_R1_001


title: snpc12null-snpc13null_72h_setB_replicate1

description:
Library name: smallRNA2022-062-snpc12null_snpc13null-72h-WW
snpc-1.2(-); snpc-1.3(-) 72h LKBsetB small RNA-seq replicate 1


title: DMSO control well, biol repl 1

description:
Library name: A2_AACTATATGTTGCG
DMSO control well. Library name contains well id and barcode separated by "_". Counts file "raw_counts.csv.gz" contain gene counts corresponding to well in column "well_id".


title: H1703 cells, shEIF2B5, Ribo-Seq (RNaseI),  rep1

description:
Library name: Sample 4
Column name in RIBO_seq_raw_counts.csv: AK103


title: P. promelas larvae, EFP, biological replicate EFP_FIELD33, lane 2, time step = NA, analyzed on 20160926

description: Library name: 20160926_ EFP_FIELD_33_ACTTGA_L002_R1_001


title: prg1_72h_setB_replicate1

description:
Library name: smallRNA2022-061-prg1-72h-WW
prg-1(-) 72h LKBsetB small RNA-seq replicate 1


title: Blood from patient 10 month post-treatment with Omaveloxolone at a dose of 100 mg PO daily, replicate 3

description:
Library name: treated_10mo_3
Plasma omaveloxolone concentration for this timepoint is in row with timepoint = 10

data_processing:
Raw reads were aligned using Kallisto with bootstrapping (number of bootstraps = 100).
Assembly: GRCh38
Supplementary files format and content: Tab separated files containing transcript ID, transcript length, effective length (the adjusted transcript length used in abundance estimation, taking into account the fragment length distribution), est_counts (raw counts) and tpm (counts normalized by eff_length)

source_name: Blood

growth_protocol: Blood samples were collected from a 19 year old female patient diagnosed with Leigh Syndrome caused by heterozygous NM_003172.4(SURF1):c.312_321delinsAT (p.Pro104_Leu105insTer); NM_003172.4(SURF1):c.-11_13del (p.Met1_Ala5del) mutations in the SURF1 gene. The patient was  enrolled in an approved research protocol (WCG IRB Protocol #2001-01). Blood was collected in PAXgene tubes and shipped at room temperature to the sequencing facility for processing within 24 hours for RNA sequencing. Whole blood samples were collected at approximately 1 month intervals between November 2023 to May 2024.

extract_protocol:
The RNA was extracted using the PAXgene RNA extraction kit.
Barcoded libraries for RNA-seq were prepared with 100 ng of RNA using NEBNext Ultra II RNA Library Prep Kit (NEB, Ipswich, MA) for Illumina with QIAGEN QIAseq FastSelect -rRNA HMR Kit (QIAGEN, Germany) per manufacturer’s protocol.

treatment_protocol: Omaveloxolone was originally prescribed at 100 mg PO, daily. The prescribed dose (100 mg PO, daily) of Omaveloxalone was reduced by half (50 mg PO, daily) after two post-treatment blood samples were collected, and two additional blood samples were collected following this reduction of dose. Concentration of Omaveloxolone in plasma was estimated using mass spectrometry.

value: Blood

value: 100 mg Omaveloxolone


title: H1703 cells, shControl, Ribo-Seq (RNaseI),  rep3

description:
Library name: Sample 3
Column name in RIBO_seq_raw_counts.csv: AK102

value: WT


title: P. promelas larvae, EFP, biological replicate EFP_FIELD33, lane 1, time step = NA, analyzed on 20160926

description: Library name: 20160926_ EFP_FIELD_33_ACTTGA_L001_R1_001

value: whole larvae

value: 2 dpf


title: mut16_72h_setB_replicate1

description:
Library name: smallRNA2022-060-mut16-72h-WW
mut-16(-) 72h LKBsetB small RNA-seq replicate 1

value: 72h gravid adult


title: H1703 cells, shControl, Ribo-Seq (RNaseI),  rep2

description:
Library name: Sample 2
Column name in RIBO_seq_raw_counts.csv: AK101


title: P. promelas larvae, EFP, biological replicate EFP_FIELD28, lane 2, time step = NA, analyzed on 20160926

description: Library name: 20160926_ EFP_FIELD_28_ATCACG_L002_R1_001


title: Blood from patient 10 month post-treatment with Omaveloxolone at a dose of 100 mg PO daily, replicate 1

description:
Library name: treated_10mo_1
Plasma omaveloxolone concentration for this timepoint is in row with timepoint = 10


title: Blood from patient 10 month post-treatment with Omaveloxolone at a dose of 100 mg PO daily, replicate 2

description:
Library name: treated_10mo_2
Plasma omaveloxolone concentration for this timepoint is in row with timepoint = 10


title: hrde1_72h_setB_replicate1

description:
Library name: smallRNA2022-059-hrde1-72h-WW
hrde-1(-) 72h LKBsetB small RNA-seq replicate 1


title: H1703 cells, shControl, Ribo-Seq (RNaseI),  rep1

description:
Library name: Sample 1
Column name in RIBO_seq_raw_counts.csv: AK100


title: P. promelas larvae, EFP, biological replicate EFP_FIELD28, lane 1, time step = NA, analyzed on 20160926

description: Library name: 20160926_ EFP_FIELD_28_ATCACG_L001_R1_001


title: N2_72h_setB_replicate1

description:
Library name: smallRNA2022-058-N2-72h-WW
N2 72h LKBsetB small RNA-seq replicate 1


title: Blood from patient 9 month post-treatment with Omaveloxolone at a dose of 100 mg PO daily, replicate 3

description:
Library name: treated_9mo_3
Plasma omaveloxolone concentration for this timepoint is in row with timepoint = 9


title: ALS patient Motor Neuros,treated with 500nM peptide,48h,rep3

city: Shanghai

first: Xiaoyang

last: Chen

state: Shanghai

address: No. 393, Huaxia Middle Road, Pudong New Area, Shanghai

department: School of life science and technology

country: China

institute: shanghaitech university

description:
Library name: CMF48500-3
RNA seq of human IPS-derived MNs, ALS Patient,treated by 500nM peptides 48h,replication3

data_processing:
Raw sequencing reads in FASTQ format were processed using Cutadapt (v1.9.1) to remove technical sequences and low-quality bases. Phred quality cutoff: 20, Error rate: 0.1, Minimum read length: 75 bp, Maximum proportion of ambiguous (N) bases: 0.1
Read quality was confirmed using FastQC (v0.11.9) to ensure compliance with standard metrics
Clean reads were aligned to the reference genome HISAT2 (v2.2.1)
Gene-level counts were quantified using HTSeq (v0.6.1). Reads overlapping exons were counted, and multi-mapping reads or reads overlapping multiple genes were excluded.
Assembly: GRCh38.107
Supplementary files format and content: txt file include FPKM values and raw counts for each Sample

source_name: IPS-derived motor neuros

growth_protocol: The IPS-derived MNs culture medium, as common articles described

extract_protocol:
After being washed with PBS,the cells were directly treated with pre-cooled Trizol RNA isolation reagent (Thermo Fisher Scientific; Cat No.15596026) in the well plates for 3min, RT.
1 μg total RNA was used for the following library preparation. For mRNA enrichment, poly(A) mRNA isolation was performed using Oligo(dT) beads. Alternatively, when the sample quality or experimental design necessitated, ribosomal RNA was depleted using rRNA removal methods to enrich for coding and non-polyadenylated transcripts. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA synthesis was carried out using reverse transcriptase, followed by second-strand cDNA synthesis. For strand-specific library construction, during the second-strand synthesis the standard dTTP was replaced with dUTP; subsequent treatment with USER enzyme selectively degrades the second strand prior to PCR amplification, thereby preserving strand information. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tail in a single reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers, and the PCR products were validated. Finally, libraries with different indexes were multiplexed and loaded on an Illumina Nove instrument for sequencing using a 2×150 paired-end (PE) configuration according to the manufacturer’s instructions.

treatment_protocol: The peptides were dissolved by culture medium and directly treated the cells

tag: disease state

value: ALS patient

value: IPS-derived motor neurons

value: FUS mutation

value: 500nM peptide,48h


title: Blood from patient 9 month post-treatment with Omaveloxolone at a dose of 100 mg PO daily, replicate 2

description:
Library name: treated_9mo_2
Plasma omaveloxolone concentration for this timepoint is in row with timepoint = 9


title: P. promelas larvae, DWIP, biological replicate DWIP_B12, lane 2, time step = NA, analyzed on 20160926

description: Library name: 20160926_ DWIP_B12_TAGCTT_L002_R1_001

value: DWIP


title: ALS patient Motor Neuros,treated with 500nM peptide,48h,rep2

description:
Library name: CMF48500-2
RNA seq of human IPS-derived MNs, ALS Patient,treated by 500nM peptides 48h,replication2


title: P. promelas larvae, DWIP, biological replicate DWIP_B12, lane 1, time step = NA, analyzed on 20160926

description: Library name: 20160926_ DWIP_B12_TAGCTT_L001_R1_001


title: prg1_48h_setB_replicate1

description:
Library name: smallRNA2022-056-prg1-48h-WW
prg-1(-) 48h LKBsetB small RNA-seq replicate 1


title: Blood from patient 9 month post-treatment with Omaveloxolone at a dose of 100 mg PO daily, replicate 1

description:
Library name: treated_9mo_1
Plasma omaveloxolone concentration for this timepoint is in row with timepoint = 9


title: ALS patient Motor Neuros,treated with 500nM peptide,48h,rep1

description:
Library name: CMF48500-1
RNA seq of human IPS-derived MNs, ALS Patient,treated by 500nM peptides 48h,replication1


title: snpc12null-snpc13null_48h_setB_replicate1

description:
Library name: smallRNA2022-057-snpc12null_snpc13null-48h-WW
snpc-1.2(-); snpc-1.3(-) 48h LKBsetB small RNA-seq replicate 1


title: P. promelas larvae, DSP, biological replicate DSP_B28, lane 2, time step = NA, analyzed on 20160926

description: Library name: 20160926_ DSP_B28_GTCCGC_L002_R1_001

value: DSP


title: mut16_48h_setB_replicate1

description:
Library name: smallRNA2022-055-mut16-48h-WW
mut-16(-) 48h LKBsetB small RNA-seq replicate 1

value: whole worm


title: Blood from patient 7 month post-treatment with Omaveloxolone at a dose of 100 mg PO daily, replicate 3

description:
Library name: treated_7mo_3
Plasma omaveloxolone concentration for this timepoint is in row with timepoint = 7


title: ALS patient Motor Neuros,treated with 250nM peptide,48h,rep3

description:
Library name: CMF48250-3
RNA seq of human IPS-derived MNs, ALS Patient,treated by 250nM peptides 48h,replication3

value: 250nM peptide,48h


title: P. promelas larvae, DSP, biological replicate DSP_B28, lane 1, time step = NA, analyzed on 20160926

description: Library name: 20160926_ DSP_B28_GTCCGC_L001_R1_001


title: hrde1_48h_setB_replicate1

description:
Library name: smallRNA2022-054-hrde1-48h-WW
hrde-1(-) 48h LKBsetB small RNA-seq replicate 1


title: P. promelas larvae, MHW, biological replicate MHW_B11, lane 2, time step = NA, analyzed on 20160926

description: Library name: 20160926_ 15-07_B11_GAGTGG_L002_R1_001


title: Blood from patient 7 month post-treatment with Omaveloxolone at a dose of 100 mg PO daily, replicate 2

description:
Library name: treated_7mo_2
Plasma omaveloxolone concentration for this timepoint is in row with timepoint = 7


title: ALS patient Motor Neuros,treated with 250nM peptide,48h,rep2

description:
Library name: CMF48250-2
RNA seq of human IPS-derived MNs, ALS Patient,treated by 250nM peptides 48h,replication2


title: Blood from patient 7 month post-treatment with Omaveloxolone at a dose of 100 mg PO daily, replicate 1

description:
Library name: treated_7mo_1
Plasma omaveloxolone concentration for this timepoint is in row with timepoint = 7


title: N2_48h_setB_replicate1

description:
Library name: smallRNA2022-053-N2-48h-WW
N2 48h LKBsetB small RNA-seq replicate 1

value: wildtype


title: P. promelas larvae, MHW, biological replicate MHW_B11, lane 1, time step = NA, analyzed on 20160926

description: Library name: 20160926_ 15-07_B11_GAGTGG_L001_R1_001

value: MHW


title: Z3-C-3

city: luzhou

first: chun

last: li

state: sichuan

address: No. 182 Chunhui Road, Longmatan District

institute: the Affiliated Traditional Chinese Medicine  Hospital of Southwest Medical University

description: Library name: Sample 9

data_processing:
Raw sequencing data in FASTQ format were processed using fastp (v0.23.2) to remove adapter sequences, reads with >5% unknown bases (N), and reads with more than 60% low-quality bases (quality score ≤25). Clean reads were then aligned to the C. elegans reference genome (WBcel235) using HISAT2 (v2.2.1). Gene-level quantification was performed using FeatureCounts (v2.0.3), and expression levels were calculated as FPKM.
Assembly: WBcel235
Supplementary files format and content: Processed data includes FPKM expression matrices in CSV format, with gene IDs and corresponding FPKM values for each sample.

source_name: whole organism

growth_protocol: All strains were maintained at 20°C on nematode growth medium agar plates seeded with Escherichia coli OP50.

extract_protocol:
Total RNA was extracted using TRIzol® Reagent (Magen) according to the manufacturer’s protocol. RNA purity was assessed with a Nanodrop ND-2000 spectrophotometer (ThermoFisher), and RNA integrity was determined using an Agilent 4150 Bioanalyzer (Agilent Technologies Inc.). Only samples with acceptable RIN values were used for library construction.
Paired-end libraries were constructed using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (ABclonal) following the manufacturer’s instructions. mRNA was purified using oligo(dT) magnetic beads, fragmented, and reverse-transcribed to synthesize first and second strand cDNA. After end-repair and adapter ligation, libraries were PCR amplified and purified with AMPure XP beads (Beckman Coulter). Library quality was assessed using the Agilent 4150 Bioanalyzer. Sequencing was performed on an Illumina NovaSeq 6000 or MGISEQ-T7 platform.

value: whole organism

value: WLZ3 wlzIs3 [snb-1p::Hsa-LRRK2(G2019S)+ lin15(+)]

value: total RNA


title: Blood from patient 5 month post-treatment with Omaveloxolone at a dose of 50 mg PO daily, replicate 3

description:
Library name: treated_5mo_3
Plasma omaveloxolone concentration for this timepoint is in row with timepoint = 5

value: Blood

value: 50 mg Omaveloxolone


title: P. promelas larvae, UP, biological replicate UP_B25, lane 2, time step = 4, analyzed on 20160923

description: Library name: 20160923_ UP_4_B25_AGTTCC_L002_R1_001

value: whole larvae

value: 2 dpf

value: UP


title: ALS patient Motor Neuros,negtive control,48h,rep3

description:
Library name: CMF480-3
RNA seq of human IPS-derived MNs, ALS Patient,treated by 0nM peptides 48h,replication3

value: ALS patient

value: IPS-derived motor neurons


title: Z3-C-2

description: Library name: Sample 8


title: P. promelas larvae, UP, biological replicate UP_B25, lane 1, time step = 4, analyzed on 20160923

description: Library name: 20160923_ UP_4_B25_AGTTCC_L001_R1_001


title: Z3-C-1

description: Library name: Sample 7


title: Blood from patient 5 month post-treatment with Omaveloxolone at a dose of 50 mg PO daily, replicate 2

description:
Library name: treated_5mo_2
Plasma omaveloxolone concentration for this timepoint is in row with timepoint = 5


title: ALS patient Motor Neuros,negtive control,48h,rep2

description:
Library name: CMF480-2
RNA seq of human IPS-derived MNs, ALS Patient,treated by 0nM peptides 48h,replication2

value: FUS mutation


title: Blood from patient 5 month post-treatment with Omaveloxolone at a dose of 50 mg PO daily, replicate 1

description:
Library name: treated_5mo_1
Plasma omaveloxolone concentration for this timepoint is in row with timepoint = 5


title: ALS patient Motor Neuros,treated with 250nM peptide,48h,rep1

description:
Library name: CMF48250-1
RNA seq of human IPS-derived MNs, ALS Patient,treated by 250nM peptides 48h,replication1


title: ALS patient Motor Neuros,negtive control,48h,rep1

description:
Library name: CMF480-1
RNA seq of human IPS-derived MNs, ALS Patient,treated by 0nM peptides 48h,replication1


title: P. promelas larvae, UP, biological replicate UP_B11, lane 2, time step = 3, analyzed on 20160923

description: Library name: 20160923_ UP_3_B11_CTTGTA_L002_R1_001


title: Z1-C-3

description: Library name: Sample 6

value: WLZ1 wlzIs1 [snb-1p::Hsa-LRRK2 + lin15(+)]


title: Blood from patient 4 month post-treatment with Omaveloxolone at a dose of 50 mg PO daily, replicate 3

description:
Library name: treated_4mo_3
Plasma omaveloxolone concentration for this timepoint is in row with timepoint = 4


title: Healthy donor Motor Neuros,treated with 500nM peptide,48h,rep3

description:
Library name: LJH48500-3
RNA seq of human IPS-derived MNs, healthy donor,treated by 500nM peptides 48h,replication3

value: Healthy donor

value: WT

value: 500nM peptide,48h


title: P. promelas larvae, UP, biological replicate UP_B11, lane 1, time step = 3, analyzed on 20160923

description: Library name: 20160923_ UP_3_B11_CTTGTA_L001_R1_001


title: Z1-C-2

description: Library name: Sample 5


title: Blood from patient 4 month post-treatment with Omaveloxolone at a dose of 50 mg PO daily, replicate 2

description:
Library name: treated_4mo_2
Plasma omaveloxolone concentration for this timepoint is in row with timepoint = 4


title: P. promelas larvae, UP, biological replicate UP_B13, lane 2, time step = 2, analyzed on 20160923

description: Library name: 20160923_ UP_2_B13_AGTCAA_L002_R1_001


title: Z1-C-1

description: Library name: Sample 4


title: Healthy donor Motor Neuros,treated with 500nM peptide,48h,rep2

description:
Library name: LJH48500-2
RNA seq of human IPS-derived MNs, healthy donor,treated by 500nM peptides 48h,replication2


title: Blood from patient 4 month post-treatment with Omaveloxolone at a dose of 50 mg PO daily, replicate 1

description:
Library name: treated_4mo_1
Plasma omaveloxolone concentration for this timepoint is in row with timepoint = 4


title: P. promelas larvae, UP, biological replicate UP_B13, lane 1, time step = 2, analyzed on 20160923

description: Library name: 20160923_ UP_2_B13_AGTCAA_L001_R1_001


title: Human macrophages, Donor H3, untreated control

city: Greifswald - Insel Riems

first: Björn

last: Corleis

state: Mecklenburg-Western Pomerania

address: Südufer 10

department: Institute of immunology

country: Germany

institute: Friedrich-Loeffler-Institut

description: Library name: H3_CTR

data_processing:
STAR (version 2.7.9a) read alignment
Subread featureCounts (version 2.0.3) read counting
Assembly: GRCh38.p14, GRCm39
Supplementary files format and content: tab delimeted .txt file containing raw read counts for each gene

source_name: monocyte derived macrophages

growth_protocol: For transcriptomic analysis, macrophages were differentiated in 48-well plates at a density of 1 × 10⁶ cells per well in RPMI 1640 supplemented with 10% FCS, 2 mM L-glutamine, and 1 mM sodium pyruvate.

extract_protocol:
RNA was extracted from 1 ml Trizol™ using PhaseMaker tubes and chloroform. After phase separation by centrifugation (12,000 × g, 15 min, 4°C), the aqueous phase was precipitated with glycogen and isopropanol (–20°C, 60 min), pelleted, washed with 75% ethanol, and air-dried. RNA was resuspended in 20 µl nuclease-free water and incubated at 60°C for 15 min.
TotTotal RNA was purified with RNA-SPRI beads and ethanol washes. Whole-transcriptome amplification was performed using Smart-seq2. cDNA was synthesized, amplified, and purified with DNA-SPRI beads. Quality was assessed via Qubit and Bioanalyzer. Libraries were prepared using Nextera XT for tagmentation and adapter ligation, PCR-amplified, bead-purified, and stored at –20 °C

treatment_protocol: Cells were pre-treated with 500 ng/ml recombinant IFNγ for 24 hours, followed by infection with M. tuberculosis (Mtb) at a multiplicity of infection (MOI) of 1 for an additional 24 hours

value: monocyte derived macrophages

value: untreated control


title: Patient 10, Primary prostate cancer, PSMA high tumor area

city: Vienna

first: Gerda

last: Egger

address: Waehringer Guertel 18-20

department: Pathology

country: Austria

institute: Medical University of Vienna

description: Library name: p10_high

library_source: genomic

data_processing:
RRBS pools were sequenced on a HiSeq 3000 instrument (Illumina, San Diego, CA, USA) following a 50-base-pair, single-end recipe. Raw data acquisition (HiSeq Control Software, HCS, HD 3.4.0.38) and base calling (Real-Time Analysis Software, RTA, 2.7.7) was performed on-instrument, while the subsequent raw data processing off the instruments involved two custom programs based on Picard tools (2.19.2). In a first step, base calls were converted into lane-specific, multiplexed, unaligned BAM files suitable for long-term archival (IlluminaBasecallsToMultiplexSam, 2.19.2-CeMM), thereby annotating an eventual start of NGS adapter sequences in XT tags. In a second step, archive BAM files were demultiplexed into sample-specific, unaligned BAM files (IlluminaSamDemux, 2.19.2-CeMM).
Custom scripts were used to calculate the digestion metrics for the TaqI and MspI restriction enzymes. Unaligned BAM files were converted into FASTQ files and pre-processed with Trimmomatic using options ILLUMINACLIP:RRBS_adapters.fa:2:40:7 SLIDINGWINDOW:4:15 MAXINFO:20:0.50 MINLEN:18. Trimmed NGS reads were aligned to the reference genome with the methylation-aware BSMAP aligner in RRBS mode for MspI (-D C-CGG) and TaqI (-D T-CGA) restriction sites, a filter of 5 Ns (-f 5), a quality threshold of 0 (-q 0), a seed size of 12 (-s 12), a mismatch rate of 0.08 (-v 0.08, or 4 mismatches in 50), a minimal inset size of 20 (-m 20), a maximal insert size of 500 (-x 500) mapping to forward strands only (-n 0). (Options: -D C-CGG -D T-CGA -f 5 -m 20 -n 0 -p 4 -q 0 -r 1 -s 12 -S 0 -u -v 0.08 -V 2 -w 100 -x 500). Methylated bases were called with the biseqMethCalling script and the resulting UCSC Genome Browser BED files were converted into BigBed files for integration into a UCSC Genome Browser Track Hub for visual inspection. Internal standards comprised of fully methylated and unmethylated double stranded synthetic oligo sequences were added to each sample to determine the rates of conversion and over-conversion, respectively. The internal standards were aligned with Bismark and methylation calls were evaluated with a custom script.
Assembly: hg38
Supplementary files format and content: bigwig

molecule: genomic DNA

source_name: Primary Prostate Cancer

extract_protocol:
DNA was extracted automated with the Qiagen EZ1 using the Qiagen EZ1 DNA FFPE Kit following manufacturers instruction for sample preparation.
Reduced Representation Bisulphite Sequencing (RRBS) libraries were generated as described previously. Briefly, up to 100 ng of genomic DNA were digested for 12 hours at 37 °C with 20 U of MspI (R0106L, New England Biolabs, Inc., Ipswich, MA, USA) in 30 μl of 1 x NEB buffer 2. To retain even the smallest fragments and to minimize the loss of material, end preparation and adaptor ligation were performed in a single-tube setup. End fill-in and A-tailing were performed by addition of Klenow Fragment 3’ > 5’ exo-mix (P7010-LC-L, Enzymatics) and dNTP mix (10 mM dATP, 1 mM dCTP, 1 mM dGTP, N0446S, New England Biolabs). After ligation to methylated Illumina TruSeq LT v2 adaptors using T4 DNA Ligase rapid (L6030-HC-L, Enzymatics), the libraries were size selected via a 0.75 x clean-up with AMPure XP beads (A63881, Beckman Coulter). The libraries were pooled based on qPCR data and subjected to bisulfite conversion using the EZ DNA Methylation Direct Kit (D5020, Zymo Research) with changes to the manufacturer’s protocol: conversion reagent was used at 0.9 x concentration, incubation performed for 20 cycles of 1 min at 95 °C, 10 min at 60 °C and the desulfonation time was extended to 30 min. These changes increase the number of CpG dinucleotides covered, by reducing double strand break formation in larger library fragments. Bisulfite-converted libraries were enriched via KAPA HiFi HS Uracil+ RM (07959079001, Roche Molecular Systems, Inc.). The minimum number of enrichment cycles was estimated based on a qPCR experiment. After a 1 x AMPure XP clean-up, library concentrations were quantified with the Qubit Fluorometric Quantitation system (Q32854, Thermo Fisher Scientific, Waltham, MA, USA) and the size distribution was assessed using the High Sensitivity DNA Kit (5067-4626, Agilent, Santa Clara, CA, USA) on a 2100 Bioanalyzer (Agilent) instrument. Sample-specific RRBS libraries were diluted and pooled in equimolar amounts.

value: Primary Prostate Cancer

value: bulk


title: N2-C-3

description: Library name: Sample 3

value: whole organism

value: wild-type N2 (Bristol)

value: total RNA


title: Healthy donor Motor Neuros,treated with 500nM peptide,48h,rep1

description:
Library name: LJH48500-1
RNA seq of human IPS-derived MNs, healthy donor,treated by 500nM peptides 48h,replication1


title: P. promelas larvae, EFP, biological replicate EFP_B08, lane 2, time step = 1, analyzed on 20161004

description: Library name: 20161004_ EFP_1_B08_GAGTGG_L002_R1_001

value: whole larvae

value: EFP


title: Blood from patient 2 month post-treatment with Omaveloxolone at a dose of 100 mg PO daily, replicate 3

description:
Library name: treated_2mo_3
Plasma omaveloxolone concentration for this timepoint is in row with timepoint = 2

value: Blood

value: 100 mg Omaveloxolone


title: Healthy donor Motor Neuros,treated with 250nM peptide,48h,rep3

description:
Library name: LJH48250-3
RNA seq of human IPS-derived MNs, healthy donor,treated by 250nM peptides 48h,replication3

value: IPS-derived motor neurons

value: 250nM peptide,48h


title: P. promelas larvae, UP, biological replicate UP_B12, lane 2, time step = 1, analyzed on 20160923

description: Library name: 20160923_ UP_1_B12_GCCAAT_L002_R1_001

value: 2 dpf

value: UP


title: N2-C-2

description: Library name: Sample 2


title: Blood from patient 2 month post-treatment with Omaveloxolone at a dose of 100 mg PO daily, replicate 2

description:
Library name: treated_2mo_2
Plasma omaveloxolone concentration for this timepoint is in row with timepoint = 2


title: Healthy donor Motor Neuros,treated with 250nM peptide,48h,rep2

description:
Library name: LJH48250-2
RNA seq of human IPS-derived MNs, healthy donor,treated by 250nM peptides 48h,replication2

value: Healthy donor

value: WT


title: P. promelas larvae, UP, biological replicate UP_B12, lane 1, time step = 1, analyzed on 20160923

description: Library name: 20160923_ UP_1_B12_GCCAAT_L001_R1_001


title: N2-C-1

description: Library name: Sample 1


title: Blood from patient 2 month post-treatment with Omaveloxolone at a dose of 100 mg PO daily, replicate 1

description:
Library name: treated_2mo_1
Plasma omaveloxolone concentration for this timepoint is in row with timepoint = 2


title: P. promelas larvae, EFP, biological replicate EFP_B08, lane 2, time step = 4, analyzed on 20160923

description: Library name: 20160923_ EFP_4_B08_GTTTCG_L002_R1_001


title: Healthy donor Motor Neuros,treated with 250nM peptide,48h,rep1

description:
Library name: LJH48250-1
RNA seq of human IPS-derived MNs, healthy donor,treated by 250nM peptides 48h,replication1


title: Blood from patient 1 month post-treatment with Omaveloxolone at a dose of 100 mg PO daily, replicate 3

description:
Library name: treated_1mo_3
Plasma omaveloxolone concentration for this timepoint is in row with timepoint = 1


title: P. promelas larvae, EFP, biological replicate EFP_B08, lane 1, time step = 4, analyzed on 20160923

description: Library name: 20160923_ EFP_4_B08_GTTTCG_L001_R1_001


title: ET0584187B

type: genomic

city: Reus

first: Dorota

last: Komar

address: avenida univeritat 1

country: Spain

institute: center for omic sciences, Eurecat

hyb_protocol: bisulfite converted DNA was amplified, fragmented and hybridized  to human Infinium MethylationEPICv2 BeadChip using standard illumina protocol

scan_protocol: BeadArray reader (HiScan) with standard Illumina recommended scanning seetings

data_processing: SeSAMe package in R environment

label: Cy3 and Cy5

source_name: PBMCs

label_protocol: standard Illumina protocol

extract_protocol: DNA from human PBMCs has been extracted with the use of NucleoSpin™ TriPrep Mini kit (11972392, Macherey-Nagel™) following manufacturer’s instruction. Purity was determined using the NanoDrop™ 2000 spectophotometer and quantity by Qubit 4 Fluorometer.

value: PBMCs

value: highcardio

tag: age at menopause


title: ET0584CN

value: control


title: Healthy donor Motor Neuros,negtive control,48h,rep3

description:
Library name: LJH480-3
RNA seq of human IPS-derived MNs, healthy donor,treated by 0nM peptides 48h,replication3


title: Blood from patient 1 month post-treatment with Omaveloxolone at a dose of 100 mg PO daily, replicate 2

description:
Library name: treated_1mo_2
Plasma omaveloxolone concentration for this timepoint is in row with timepoint = 1


title: P. promelas larvae, EFP, biological replicate EFP_B12, lane 2, time step = 3, analyzed on 20160923

description: Library name: 20160923_ EFP_3_B12_GTGAAA_L002_R1_001


title: Blood from patient 1 month post-treatment with Omaveloxolone at a dose of 100 mg PO daily, replicate 1

description:
Library name: treated_1mo_1
Plasma omaveloxolone concentration for this timepoint is in row with timepoint = 1


title: Healthy donor Motor Neuros,negtive control,48h,rep2

description:
Library name: LJH480-2
RNA seq of human IPS-derived MNs, healthy donor,treated by 0nM peptides 48h,replication2


title: ET0584187A


title: P. promelas larvae, EFP, biological replicate EFP_B12, lane 1, time step = 3, analyzed on 20160923

description: Library name: 20160923_ EFP_3_B12_GTGAAA_L001_R1_001


title: Healthy donor Motor Neuros,negtive control,48h,rep1

description:
Library name: LJH480-1
RNA seq of human IPS-derived MNs, healthy donor,treated by 0nM peptides 48h,replication1


title: P. promelas larvae, EFP, biological replicate EFP_B11, lane 2, time step = 2, analyzed on 20160923

description: Library name: 20160923_ EFP_2_B11_ATGTCA_L002_R1_001


title: scRNA profiling of CD8+ T cells from donor 4

city: Seoul

first: Yunjung

last: Cho

address: 73, Goryeodae-ro, Seoulbuk-gu

department: Department of Laboratory Medicine

country: South Korea

institute: Korea University Medicine

description: Library name: CD8_sample4

library_source: transcriptomic single cell

data_processing:
Raw base call files were processed using Cell Ranger (10x Genomics, v7.1.0).
Gene expression matrices were generated using cellranger count with default parameters.
Reads were aligned to the GRCh38 reference genome provided by 10x Genomics.
Low-quality cells were filtered and downstream analysis performed using Seurat (v4).
Assembly: GRCh38 (10x Genomics reference package: refdata-gex-GRCh38-2020-A)
Supplementary files format and content: Processed data include gene expression matrices (.h5 and .mtx formats), barcode and feature annotation files generated by Cell Ranger.
Supplementary files format and content: Each sample includes three matrix files (matrix.mtx, features.tsv, barcodes.tsv) and/or a combined .h5 file.

source_name: blood

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from fresh blood of healthy adult donors using Ficoll-Paque density gradient centrifugation.

extract_protocol:
CD4⁺ and CD8⁺ T cells were isolated from PBMCs using MACS (magnetic-activated cell sorting). Cells were immediately processed for single-cell RNA library preparation without prior stimulation.
Single-cell suspensions were loaded onto the 10x Genomics Chromium Controller to generate Gel Bead-in-Emulsions (GEMs). Libraries were prepared using the 10x Genomics Chromium Single Cell 5’ v2 kit following the manufacturer’s protocol. Gene expression libraries were constructed.

value: blood

value: T cell

value: CD8+ T cell

tag: donor

value: donor 4


title: Pre-treated blood, replicate 3

description:
Library name: pre-treated_3
Plasma omaveloxolone concentration for this timepoint is in row with timepoint = 0


title: scRNA profiling of CD8+ T cells from donor 3

description: Library name: CD8_sample3

value: donor 3


title: Pre-treated blood, replicate 2

description:
Library name: pre-treated_2
Plasma omaveloxolone concentration for this timepoint is in row with timepoint = 0


title: ET0584198

value: lipid


title: ET0584200

value: hepatic


title: P. promelas larvae, EFP, biological replicate EFP_B11, lane 1, time step = 2, analyzed on 20160923

description: Library name: 20160923_ EFP_2_B11_ATGTCA_L001_R1_001

value: whole larvae

value: EFP


title: Pre-treated blood, replicate 1

description:
Library name: pre-treated_1
Plasma omaveloxolone concentration for this timepoint is in row with timepoint = 0

value: Blood


title: ET0584197

value: healthy


title: P. promelas larvae, EFP, biological replicate EFP_B08, lane 1, time step = 1, analyzed on 20161004

description: Library name: 20161004_ EFP_1_B08_GAGTGG_L001_R1_001

value: 2 dpf


title: scRNA profiling of CD8+ T cells from donor 2

description: Library name: CD8_sample2

value: donor 2


title: P. promelas larvae, EFP, biological replicate EFP_B07, lane 2, time step = 1, analyzed on 20160923

description: Library name: 20160923_ EFP_1_B07_ACAGTG_L002_R1_001


title: ET0584190


title: Neurons derived from patient iPSC cells treated with 500 nM Omaveloxolone replicate 3

description:
Library name: RL138
Column names mean the following in the processed data file: target ID - ensembl transcript ID, length: transcript length, eff_length: effective transcript length (the adjusted transcript length used in abundance estimation, taking into account the fragment length distribution), est_counts - transcript counts, tpm - transcript counts normalized by effective length

source_name: NGN2-driven glutamatergic neurons

growth_protocol: SURF1-mediated Leigh Syndrome patient-derived primary cell models were prepared alongside control cells prepared from an immediate family member. The patient was identified as having one allele with a truncating mutation NM_003172.4(SURF1):c.312_321del10insAT (p.Leu105X) and the other allele with a missense mutation NM_003172.4(SURF1):c.574C>T (p.Arg192Trp). The healthy parent is a heterozygous carrier with the truncating mutation.  Somatic cells were collected from the peripheral blood of both individuals and reprogrammed to iPSCs using established protocols detailed in the CytoTuneTM-iPS Reprogramming Kit (Gibco, Life Technologies, Publication Part Number MAN0006712) and banked in cryogenic storage. iPSCs were cultured on Matrigel (Corning, #354277)-coated plates using mTeSR Plus medium (STEMCELL,#100-0276). Patient and control iPSCs were stably transduced with a doxycycline-inducible NGN2 expression system. 10 cm dishes for NGN2-induced neural differentiation were coated with Matrigel according to the manufacturer's manual and incubated overnight at 37°C. On the day of induction, iPSCs were removed using Accutase (StemCell, Cat# 07920), centrifuged at 300 xg for 5 mins and resuspended in NGN2 Neural Induction Media containing 10 µM Y-27632 (StemCell, Cat# 72304). NGN2 Neural Induction Media was made using a base of Knockout DMEM/F12 (Gibco, Cat# 12660012) with the addition of 1x N2 Supplement-B (StemCell, Cat# 07156), 1x MEM Non-Essential Amino Acids (Gibco, Cat# 11140050), 1ug/mL Natural Mouse Laminin (1 mg/mL stock Life Technologies, Cat# 23017-015), 10 ng/mL NT-3 in sterile distilled water (StemCell, Cat# 78074), 10 ng/mL BDNF in sterile distilled water (StemCell, Cat# 78133) and 2 µg/mL doxycycline (stock concentration 20 mg/mL, Fisher Scientific, Cat# AAJ67043AD). Cells were counted using Trypan Blue (Invitrogen, Cat# T10282) on the Invitrogen Countess and plated at 5X106 cells/10 cm dish. Daily media changes were performed on days 2–3 with NGN2 Neural Induction Medium. One day prior to replating cells for neuronal maturation, two 384-well PerkinElmer Pheno Plates were coated with 0.1mg/mL Poly-D-Lysine (Gibco, cat# A3890401) at 37°C overnight. The next morning, the plates were washed 3x with sterile water and dried under a BSC with the fan turned on. At least 2 hours prior to replating, 10 µg/mL Natural Mouse Laminin (Gibco, Cat# 23017015) diluted in DMEM/F12 (Gibco, Cat#11320033) was added to the plates and returned to a 37°C incubator. On day 4, cells were replated at 600000 cells/well in 12-well plates for neuronal maturation in NGN2 Neuronal Medium containing 2 µg/mL doxycycline (Fisher Scientific, Cat# AAJ67043AD) and 5 µM of U-FdU. NGN2 Neuronal Medium was made using 1:1 DMEM/F12 (Gibco, Cat#11320033) and Neurobasal-A Medium (Gibco, Cat# 10888022) as the base with the addition of 1x MEM Non-Essential Amino Acids (Gibco, Cat# 11140050), 0.5x GlutaMAX Supplement (Gibco, Cat# 35050061), 1x N2 Supplement-B (StemCell, Cat# 07156), 1x B-27 Plus Supplement (Gibco, Cat# A3582801), 10 ng/mL NT-3 (StemCell, Cat# 78074), 10ng/mL BDNF (StemCell, Cat# 78133) and 1 µg/mL Natural Mouse Laminin (Gibco, Cat# 23017015). Half media changes were performed every 3–4 days from Day 7-Day 15 using NGN2 Neuronal Medium.

extract_protocol:
Neurons were lysed and RNA was extracted from each sample using the Qiagen RNeasy Plus Mini Kit protocol (Qiagen, Cat: 74134). RNA concentration was determined by using the Qubit Fluorometer (Invitrogen) and quality was measured using an RNA High Sensitivity screentape with the Agilent Tapestation.
200ng of RNA from each sample was prepared using Illumina Stranded Total RNA prep with Ribo-Zero Plus kit. Quality of the final Bulk RNA Sequencing library was determined using a DNA High Sensitivity D1000 screentape, and concentration was quantified by qPCR using Roche’s KAPA Universal Illumina Library Quantification Kit.

treatment_protocol: Matured neurons in the 12-well plates were treated with omaveloxolone at 3 doses: 125 nM, 250nM and 500nM. Additionally DMSO was used as vehicle control for the drug treatment. Starting at Day 15 of differentiation, cells were treated every 24 hours for a total of 72 hours before processing for downstream assays.

value: NGN2-driven glutamatergic neurons

value: Neurons

value: 500 nM Omaveloxolone


title: scRNA profiling of CD8+ T cells from donor 1

description: Library name: CD8_sample1

value: donor 1


title: P. promelas larvae, EFP, biological replicate EFP_B07, lane 1, time step = 1, analyzed on 20160923

description: Library name: 20160923_ EFP_1_B07_ACAGTG_L001_R1_001


title: Neurons derived from patient iPSC cells treated with 500 nM Omaveloxolone replicate 2

description:
Library name: RL137
Column names mean the following in the processed data file: target ID - ensembl transcript ID, length: transcript length, eff_length: effective transcript length (the adjusted transcript length used in abundance estimation, taking into account the fragment length distribution), est_counts - transcript counts, tpm - transcript counts normalized by effective length


title: P. promelas larvae, UP, biological replicate UP_B11, lane 2, time step = 4, analyzed on 20160923

description: Library name: 20160923_ UP_4_B11_ACAGTG_L002_R1_001

value: UP


title: ET0584183

value: PBMCs


title: scRNA profiling of CD4+ T cells from donor 4

description: Library name: CD4_sample4

value: blood

value: T cell

value: CD4+ T cell


title: ET0584182

value: lipid


title: Neurons derived from patient iPSC cells treated with 500 nM Omaveloxolone replicate 1

description:
Library name: RL136
Column names mean the following in the processed data file: target ID - ensembl transcript ID, length: transcript length, eff_length: effective transcript length (the adjusted transcript length used in abundance estimation, taking into account the fragment length distribution), est_counts - transcript counts, tpm - transcript counts normalized by effective length


title: ET0584186


title: scRNA profiling of CD4+ T cells from donor 3

description: Library name: CD4_sample3

value: donor 3


title: P. promelas larvae, UP, biological replicate UP_B11, lane 1, time step = 4, analyzed on 20160923

description: Library name: 20160923_ UP_4_B11_ACAGTG_L001_R1_001

value: whole larvae


title: Neurons derived from patient iPSC cells treated with 250 nM Omaveloxolone replicate 3

description:
Library name: RL135
Column names mean the following in the processed data file: target ID - ensembl transcript ID, length: transcript length, eff_length: effective transcript length (the adjusted transcript length used in abundance estimation, taking into account the fragment length distribution), est_counts - transcript counts, tpm - transcript counts normalized by effective length

value: 250 nM Omaveloxolone


title: scRNA profiling of CD4+ T cells from donor 2

description: Library name: CD4_sample2


title: P. promelas larvae, UP, biological replicate UP_B06, lane 2, time step = 3, analyzed on 20160923

description: Library name: 20160923_ UP_3_B06_AGTTCC_L002_R1_001


title: ET0584181

value: highcardio


title: Neurons derived from patient iPSC cells treated with 250 nM Omaveloxolone replicate 2

description:
Library name: RL134
Column names mean the following in the processed data file: target ID - ensembl transcript ID, length: transcript length, eff_length: effective transcript length (the adjusted transcript length used in abundance estimation, taking into account the fragment length distribution), est_counts - transcript counts, tpm - transcript counts normalized by effective length


title: scRNA profiling of CD4+ T cells from donor 1

description: Library name: CD4_sample1


title: P. promelas larvae, UP, biological replicate UP_B06, lane 1, time step = 3, analyzed on 20160923

description: Library name: 20160923_ UP_3_B06_AGTTCC_L001_R1_001


title: Neurons derived from patient iPSC cells treated with 250 nM Omaveloxolone replicate 1

description:
Library name: RL133
Column names mean the following in the processed data file: target ID - ensembl transcript ID, length: transcript length, eff_length: effective transcript length (the adjusted transcript length used in abundance estimation, taking into account the fragment length distribution), est_counts - transcript counts, tpm - transcript counts normalized by effective length


title: Huh7 cells, VPS72, replicate 3

city: Hong Kong

first: Qinglin

last: Zhang

address: Room 7N07, Kadoorie Biological Sciences Building, The University of Hong Kong, Sai Ying Pun

institute: The University of Hong Kong

description: Library name: Sample6

data_processing:
The raw sequence reads were aligned against the reference genome (human genome build 37, hg19) by standard STAR pipeline. The gene expression was imputed by RSEM with default parameters to generate the log 2 TPM value for each gene. Differential gene expression analysis was conducted by the limma empirical Bayes moderation for each gene and each contrast.8 The gene set enrichment analysis (GSEA) was performed on a collection of functional gene sets (Hallmark gene sets, KEGG pathways, Gene Ontology Biological Process, Molecular Function, Cellular Component). Then the gene ranks by t-statistics between test condition and control were projected into the functional gene set to get the enrichment score and adjusted P-value.9 Finally, enriched gene sets were ranked based on the adjusted p-value and the top-ranked gene sets were listed according to a normalized enrichment score (NES), from positive enrichment to negative enrichment.
Assembly: hg38
Supplementary files format and content: text file document includes raw counts for each sample

growth_protocol: All cells were cultured in Dulbecco’s  modified Eagle medium (DMEM, Gibco). 10% fetal bovine serum (FBS,  Gibco) and antibiotic-antimycotic mixture (Gibco) were added into the  culture media. Cells were maintained at 37 °C in a CO2 incubator with  5% CO2.

extract_protocol:
Total RNA was isolated using RNAzol (Molecular Research Center).
The library was prepared by using KAPA RNA HyperPrep Kit (Roche)

treatment_protocol: For lentivirus packaging, psPAX2, pMD2.G to gether with the carrier plasmid were co-transfected into HEK293T cells in  a 2:1:2 mass ratio. Lentivirus was harvested 48 and 72h after transfection  by centrifuging at 500g for 5 min and filtering through a 0.45 um filter and preserved at -80 ℃.For infection, lentivirus was added into cell media and maintained for 24h.

value: human hepato cellular carcinoma cell line

value: VPS72 overexpression

value: lentivirus infection


title: ET0584176


title: P. promelas larvae, UP, biological replicate UP_B01, lane 2, time step = 2, analyzed on 20160923

description: Library name: 20160923_ UP_2_B01_CTTGTA_L002_R1_001

value: 2 dpf


title: P. promelas larvae, UP, biological replicate UP_B01, lane 1, time step = 2, analyzed on 20160923

description: Library name: 20160923_ UP_2_B01_CTTGTA_L001_R1_001


title: Huh7 cells, VPS72, replicate 1

description: Library name: Sample4


title: ET0584172

value: healthy


title: Huh7 cells, VPS72, replicate 2

description: Library name: Sample5


title: Neurons derived from patient iPSC cells treated with 125 nM Omaveloxolone replicate 3

description:
Library name: RL132
Column names mean the following in the processed data file: target ID - ensembl transcript ID, length: transcript length, eff_length: effective transcript length (the adjusted transcript length used in abundance estimation, taking into account the fragment length distribution), est_counts - transcript counts, tpm - transcript counts normalized by effective length

value: NGN2-driven glutamatergic neurons

value: Neurons

value: 125 nM Omaveloxolone


title: Neurons derived from patient iPSC cells treated with 125 nM Omaveloxolone replicate 2

description:
Library name: RL131
Column names mean the following in the processed data file: target ID - ensembl transcript ID, length: transcript length, eff_length: effective transcript length (the adjusted transcript length used in abundance estimation, taking into account the fragment length distribution), est_counts - transcript counts, tpm - transcript counts normalized by effective length


title: P. promelas larvae, UP, biological replicate UP_B06, lane 2, time step = 1, analyzed on 20160923

description: Library name: 20160923_ UP_1_B06_AGTCAA_L002_R1_001

value: UP


title: ET0584169

value: PBMCs