title: P20

city: chengdu

first: yujie

last: xie

address: No. 37 Guoxue Lane, Wuhou District, Chengdu City, Sichuan Province

institute: West China Hospital, Sichuan University

description:
Library name: sample20
Column name in raw_counts_All_Samples.txt: P20

data_processing:
Raw Data Quality Control and Trimming: Raw paired-end sequencing reads were processed using fastp (v 0.23.2) to remove adapter sequences (auto-detected), trim low-quality bases (Phred score <20 at read ends), and discard reads containing >5% poly-N nucleotides or shorter than 50 bp. Quality metrics (Q20, Q30, GC content) were calculated for both raw and clean data.
Alignment to Reference Genome: Clean reads were aligned to the human reference genome GRCh38 using HISAT2 (v 2.2.1)
Gene Expression Quantification: Gene-level read counts were generated using featureCounts (v 2.0.6), Final outputs included raw count matrix and FPKM-normalized expression matrix.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Esophageal squamous cell carcinoma

extract_protocol:
Total RNA was extracted from esophageal squamous cell carcinoma tissue using TRIzol reagent (Invitrogen, Catalog #: 15596026) following the manufacturer's protocol. RNA concentration and purity (A260/A280 ratio > 1.9, A260/A230 ratio > 2.0) were measured using a NanoDrop 2000 spectrophotometer. RNA integrity was confirmed by 1% agarose gel electrophoresis showing distinct 18S and 28S rRNA bands.
Stranded RNA sequencing libraries were prepared from total RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer's instructions.

value: Esophageal squamous cell carcinoma

value: primary tumor stage T2 patients with lymph node metastasis


title: Patient 02, Primary prostate cancer, PSMA high tumor area

status: Public on Aug 01 2026

type: SRA

city: Vienna

first: Gerda

last: Egger

address: Waehringer Guertel 18-20

department: Pathology

country: Austria

institute: Medical University of Vienna

description: Library name: p02_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

organism: Homo sapiens

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.

tag: tissue

value: Primary Prostate Cancer

tag: cell type

value: bulk


title: P. promelas larvae, EFP, biological replicate EFP_B06, lane 1, time step = 4, analyzed on 20161003

city: Durham

first: Steven

middle: Thomas

last: Purucker

state: NC

address: 109 TW Alexander Dr

country: USA

institute: US EPA

description: Library name: 20161003_ EFP_4_B06_CTTGTA_L001_R1_001

library_source: transcriptomic

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.

molecule: total RNA

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

tag: age

value: 2 dpf

tag: treatment-replicate id

tag: treatment-time

tag: treatment-location

value: EFP

tag: batch


title: HepG2_B2_minus_AhRinh_Day12_H3K27ac_ChIP_rep2

city: Palo Alto

first: Yohei

last: Abe

state: California

address: 3181 Porter Dr

institute: Arc Institute

description: Library name: Sample 54

data_processing:
FASTQ files were processed to assess quality by determining general sequencing bias, clonality and adapter sequence contamination.
FASTQ files were mapped to the hg38 human or mm10 mouse reference genome with Bowtie2 using default parameters. Alignment files were processed using HOMER. Peaks were called by combining replicate conditions and using HOMER (findPeaks) using parameters “-style factor -size 200”.
Assembly: hg38 or mm10
Supplementary files format and content: Peak files (BED format)

extract_protocol:
For ChIP-seq, crosslinked cells were resuspended in ice-cold hypotonic buffer (10 mM HEPES-KOH (pH 7.9), 85 mM KCl, 1 mM EDTA, 1% NP-40, 1× protease inhibitor cocktail), and centrifuged at 1,000 × g for 5 min at 4°C to obtain a nuclear fraction.
Chromatin immunoprecipitation (ChIP) was performed in biological replicates as previously described58 with modifications as follows. For H3K27ac ChIP assays, cells were cross-linked with 1% (vol/vol) formaldehyde in PBS for 10 min at room temperature. For AhR and C/EBPα ChIP assays, cells were cross-linked with 2 mM disuccinimidyl glutarate (DSG) (ProteoChem) in PBS for 30 min at room temperature, and then directly a second crosslinking was performed by the addition of 1% (vol/vol) formaldehyde in PBS for 10 min. The crosslinking reaction was quenched by 0.125 M glycine (Sigma-Aldrich). Cells were washed once with ice-cold PBS and pelleted at 1,000 × g for 5 min at 4°C. Crosslinked cells were resuspended in ice-cold hypotonic buffer (10 mM HEPES-KOH (pH 7.9), 85 mM KCl, 1 mM EDTA, 1% NP-40, 1× protease inhibitor cocktail), and centrifuged at 1,000 × g for 5 min at 4°C to obtain a nuclear fraction. Nuclear pellets were resuspended in 100 µl of either LB3 buffer (10 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-laurosylsarcosine, 1× protease inhibitor cocktail, for H3K27ac ChIP) or PIPA-NR buffer (20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.4% sodium deoxycholate, 0.1% SDS, 1% NP-40, 0.5 mM DTT, 1× protease inhibitor cocktail, for AhR and C/EBPα ChIPs). Chromatin DNA was sonicated in a 0.2 ml microtube (Diagenode) using a Bioruptor® Pico sonication device (30 sec ON / 30 sec OFF cycles) for 10 min at 4°C. Samples were centrifuged at 15,000 rpm for 10 min at 4C, and the supernatant was used for immunoprecipitation. LB3 lysate was diluted 1.1-fold with 10% Triton X-100. 1% of the lysate was kept as ChIP input. The lysates were rotated with each antibody pre-bound to 20 µl of beads (10 µl of Dynabeads protein A (Thermo Fisher Scientific) + 10 µl of Dynabeads protein G (Thermo Fisher Scientific)) overnight at 4°C. After the immunoprecipitation, beads were collected on a magnet and washed three times each with wash buffer I (20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA, 1× protease inhibitor cocktail), wash buffer III (10 mM Tris-HCl (pH 7.5), 250 mM LiCl, 1% Triton X-100, 0.7% sodium deoxycholate, 1 mM EDTA, 1× protease inhibitor cocktail) and twice with TET (10 mM Tris-HCl (pH 7.5), 1 mM EDTA, 0.2% Tween-20, 1× protease inhibitor cocktail), and then resuspended in 25 µl of TT (10mM Tris-HCl (pH 7.5), 0.05% Tween-20). The immunoprecipitated chromatin samples were used for library preparation with NEBNext Ultra II Library kit (NEB) according to the manufacturer’s instructions. DNA in 46.5 µl of NEB reactions was revers crosslinked by adding 4 µl of 10% SDS, 4.5 µl of 5 M NaCl, 3 µl of 500 mM EDTA, 1 µl of 20 mg/ml proteinase K and 20 µl of water by incubation for 1 hr at 55°C, and then 30 min at 65°C. DNA was purified with 2 µl of SpeedBeads in 20% PEG 8000/1.5 M NaCl (Final 12% PEG 8000), and eluted with 25 µl of TT. The eluted DNA was amplified for 14 cycles in 50 µl of PCR reactions using NEBNext High-Fidelity 2× PCR Master Mix (NEB) and 0.5 mM each of primers Solexa 1GA and Solexa 1GB. The amplified libraries were purified with 2 µl of SpeedBeads in 20% PEG 8000/2.5 M NaCl (Final 13% PEG 8000), eluted with 20 µl of TT, size selected using PAGE/TBE gel for 225-325 bp fragments by gel extraction, and single-end sequenced on NextSeq 2000 or NovaSeq X Plus (Illumina). ChIP input material (1% of sheared DNA) in 46.5 µl of TE was revers crosslinked by adding 4 µl of 10% SDS, 4.5 µl of 5 M NaCl, 3 µl of 500 mM EDTA, 1 µl of 20 mg/ml proteinase K and 20 µl of water by incubation for 1 hr at 55°C, and then 30 min at 65°C. The input DNA was purified with SpeedBeads as described above, and eluted with 25 µl of TT. The eluted input DNA was prepared for libraries and amplified as described for ChIP samples.

treatment_protocol: Control vs. Vitamin B2 deficiency

tag: cell line

tag: treatment


title: Patient 01, Primary prostate cancer, PSMA low tumor area

description: Library name: p01_low


title: P. promelas larvae, EFP, biological replicate EFP_B07, lane 2, time step = 3, analyzed on 20161003

description: Library name: 20161003_ EFP_3_B07_AGTCAA_L002_R1_001


title: P19

country: China

description:
Library name: sample19
Column name in raw_counts_All_Samples.txt: P19


title: HepG2_B2_minus_AhRinh_Day12_H3K27ac_ChIP_rep1

description: Library name: Sample 53


title: Patient 01, Primary prostate cancer, PSMA high tumor area

description: Library name: p01_high


title: P. promelas larvae, UP, biological replicate UP_B03, lane 2, time step = 2, analyzed on 20161004

description: Library name: 20161004_ UP_2_B03_ACTGAT_L002_R1_001

value: UP


title: control 3

city: Qingdao

first: yunfeng

last: yang

address: State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P.R. China

institute: shandong university

description: Library name: Sample 9

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: REY15A
Supplementary files format and content: aCcrK OE gene FPKM.xlsx

organism: Saccharolobus islandicus REY15A

source_name: S. islandicus REY15A

growth_protocol: Strains of Sis/pSeSD(Cont) and Sis/pSeSD-aCcrK were cultured in ATV medium

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For transcriptomic analysis, culture was inoculated with an initial OD600 of 0.05. The cells were pelleted at 6,000 g for 10 min after 12 h of cultivation when the OD600 reached approximately 0.2. The pellet was resuspended in 1 ml PBS buffer. The cells were pelleted again and stored at -80°C.

tag: strain

value: S. islandicus REY15A

tag: genotype

value: empty plasmid control

value: Arabinose induction


title: P. promelas larvae, EFP, biological replicate EFP_B07, lane 1, time step = 3, analyzed on 20161003

description: Library name: 20161003_ EFP_3_B07_AGTCAA_L001_R1_001


title: P. promelas larvae, EFP, biological replicate EFP_B02, lane 2, time step = 2, analyzed on 20161003

description: Library name: 20161003_ EFP_2_B02_GCCAAT_L002_R1_001


title: HepG2_B2_minus_DMSO_Day12_H3K27ac_ChIP_rep2

description: Library name: Sample 52


title: P17

description:
Library name: sample17
Column name in raw_counts_All_Samples.txt: P17


title: Human macrophages, Donor H3, IFNy stimulated

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_IFNy

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: IFNy stimulated


title: control 2

description: Library name: Sample 8


title: P18

description:
Library name: sample18
Column name in raw_counts_All_Samples.txt: P18


title: P16

description:
Library name: sample16
Column name in raw_counts_All_Samples.txt: P16


title: Control_rep2

city: Beijing

first: jun

last: Huang

address: No.16, Nanxiao Street, Dongzhimen, Dongcheng District, Beijing, China.

institute: Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing

description: Library name: Control2

data_processing:
Step 1: Quality Control and Preprocessing Raw sequencing reads in FASTQ format were first processed through FastQC (v0.11.9) to assess read quality. Low-quality reads, adapter sequences, and poly-N sequences were trimmed using Trimmomatic (v0.39) (or Cutadapt/fastp) to obtain clean reads.  Step 2: Read Alignment The cleaned reads were mapped to the mouse reference genome (Mus musculus, e.g., GRCm39/mm10) using STAR (v2.7.9a) (or HISAT2) with default parameters. The alignment files (BAM format) were generated for downstream quantification.  Step 3: Quantification of Gene Expression The number of reads mapped to each gene was counted using featureCounts (v2.0.1) (or HTSeq-count) based on the corresponding GTF annotation file.  Step 4: Normalization and Differential Expression Analysis Differential expression analysis between groups (Control, Model, and HBG doses L/M/G) was performed using the DESeq2 (v1.34.0) R package. Read counts were normalized using the median-of-ratios method. Genes with an adjusted p-value < 0.05 and |log2FoldChange| > 1 were identified as differentially expressed genes (DEGs).  Step 5: Functional Enrichment Analysis Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted using the clusterProfiler R package to explore the biological functions and signaling pathways (e.g., TGF-β/Smad, PI3K-Akt) associated with the therapeutic effects of HBG.
Assembly: mm10
Supplementary files format and content: The processed data file (e.g., all_counts_matrix.txt) is a tab-delimited text file containing raw read counts and FPKM/TPM values for each sample. Each row represents a gene and each column represents a sample.
Supplementary files format and content: The processed data file (expression_matrix.xls) contains normalized expression values for all samples. Rows represent Ensembl gene IDs and columns represent biological replicates.

molecule: polyA RNA

organism: Mus musculus

source_name: Lung tissue

growth_protocol: Male C57BL/6 mice (6-8 weeks old) were housed under standard pathogen-free conditions with a 12h light/dark cycle and free access to food and water. Pulmonary fibrosis was induced by a single intratracheal instillation of bleomycin

extract_protocol:
Total RNA was extracted from fresh lung tissues using TRIzol reagent (Invitrogen) following the manufacturer’s instructions. RNA integrity and concentration were assessed using the Agilent 2100 Bioanalyzer.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Libraries were constructed using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit. Sequencing was performed on the Illumina NovaSeq 6000 platform with 150 bp paired-end reads.

treatment_protocol: Starting from day 7 post-modeling, mice in the HBG groups were orally administered HBG daily at doses of L, M, or G (specify doses, e.g., 7g/kg for G) for 14 consecutive days. The control and model groups received an equal volume of distilled water.

value: Lung tissue


title: anti-CD3 antibody stimulated, day1, rep1

first: Qi

last: Tang

address: Chengfu Road #292

institute: Peking University

description:
Library name: CD3_day1_rep1
polyA RNA

data_processing:
Raw FASTQ data were filtered by TrimGalore v0.6.5 (https://www.bioinformatics.babraham-.ac.uk/projects/trim_galore/). Reads with a mapping quality score Q < 30 were removed. Reference mouse genome (GRCm38) and gene annotation files were downloaded from Gencode. Paired-end clean reads were aligned to the reference genome using STAR v2.7.6a with default parameters. The mapped reads were then counted to different genes by featureCounts v1.6.3.
Assembly: GRCm38
Supplementary files format and content: featureCounts output txt file

source_name: CD8+T cells

extract_protocol:
Total RNA was extracted using TRIzol™ (Thermo), according to the manufacturer’s instructions. For input cells less than 100,000, the aqueous phase of the TRIZol/chloroform extraction was carefully transferred into a new tube and the RNAs were cleaned and concentrated by using the ZYMO RNA Clean & Concentrator following the manufacturers’ instructions. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer (5X). First-strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure was ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with the AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers, and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library was sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

treatment_protocol: For in vitro stimulated CD8+ T cells, naïve splenic CD8+ T cells form OT-1 mice were either left unstimulated (considered naïve) or stimulated under various conditions: treated with antigen peptides for 24 or 48 hours, activated with immobilized anti-CD3 antibody, or anti-CD3/CD28-coated microbeads for 24 hours.

value: CD8+T cells

value: Anti-CD3 antibody stimulation for 1 day

tag: library type

value: mRNA


title: SAMPLE 64

city: Little Rock

first: Roopa

last: Siddaiah

state: AR

address: 1 Children's way

department: Pediatrics

institute: Arkansas Children's Hospital

description:
Library name: G984-6
Small RNA library prepared using QIAseq miRNA kit with UMI

data_processing:
The libraries were pooled and diluted to 3 nM using 10 mM Tris-HCl, pH 8.5 and denatured. The denatured libraries were then loaded onto an SP flow cell on an Illumina® NovaSeq 6000 instrument and run for 68 cycles according to the manufacturer’s instructions.
Assembly: Fitlered reads were aligned to the human reference genome (GRCh38 using HISAT2 (version 2.1.0) and the resulting ded-duplicated reads were summarized to each gene using HTSeq.
Supplementary files format and content: XLS

source_name: Tracheal Aspirate

extract_protocol:
Frozen tracheal aspirate (TA) samples were thawed on ice, and mixed by pipetting. For each sample, 300 uL of the aspirate was transferred to a 1.5 ml tube and 75 ul of ExoQuick Exosome Precipitation Solution (System biosciences, cat # EXOQ5A-1) was added. Sample and solution were mixed well by inverting, incubated upright and undisturbed at 4 C overnight. Sample mixture was then centrifuged at 1550 x g for 30 min at 4 C. After centrifugation, supernatant was discarded without disturbing the pellet. Pellet was then resuspended in 100 uL 1x PBS. All 100 uL of the sample was used for RNA extraction. RNA was extracted using Zymo Research Quick-RNA Micro Prep Kit following manufacturer's protocol. The typical size distribution for the small RNA ranged between 13.14 and 283.50 ng. Frozen saliva (SA) samples were thawed on ice. RNA was extracted using Quick-RNA Microprep purification kits (Zymo Research). RNA Pico BioAnalyzer (Agilent technologies) was used to determine the RNA quality and quantity. The typical size distribution for the small RNA and quantities for saliva ranged between 33.90 and 922.50 ng
Small RNA libraries were prepared from 5–250 ng total RNA using the QIAseq miRNA Library Kit (QIAGEN) as per the manufacturer’s instructions.

value: Tracheal Aspirate

value: PH

tag: Sex

value: F


title: HepG2_B2_minus_DMSO_Day12_H3K27ac_ChIP_rep1

description: Library name: Sample 51


title: H9_Day10 CD43/CD34

city: Kalamazoo

first: Momoko

last: Yoshimoto

state: MI

address: 300 Portage St.

department: Investigative Medicine

institute: WMU Homer Stryker MD School of Medicine

description:
Library name: H9_Day10_10X 3v3.1
10X genomics

library_source: transcriptomic single cell

data_processing:
The data were processed through Cell Ranger (10X Genoomics)
Assembly: hg38
Supplementary files format and content: tab-separated values files and matrix files

source_name: Day10 differentiation EC and HPC

growth_protocol: Human H9 ESCs that were transduced Runx1+23 enhancer reporter construct (H9 with DsRed reporter) were differentiated onto Laminin 511 coated plates. Undifferentiated clusters were plated into 6 well plate at a density of five to ten clusters per well in mTeSR. Once the colonies became >700 um, we started differentiation as follows. Day 0: CHIR 2uM, BMP4 80ng/mL, VEGF 80ng/mL in Essential 8, Day2: VEGF 80ng/mL, SCF 50ng/mL, SB431542 1uM, and bFGF 25ng/mL in Essential 6, Day4: VEGF 15ng/mL and SCF 100ng/mL in Essential 6, Day6 and later: VEGF 5ng/mL, SCF 50ng/mL, TPO 50ng/mL, Flt3-L 10ng/mL, IL-6 10ng/mL, IL-11 5ng/mL, IGF-1 25ng/mL, EPO 2u/mL, and IL-3 10ng/mL in StemSpanII.

extract_protocol:
On day of differentiation culture, all cells were harvested using Accutase and cells were stained with anti-CD43 and CD34 antibodies. CD43+ and/or CD34+ cells were sorted using FACS Melody. About 10^5 cells were sorted and applied to 10X chrominium.
Library prep was conducted by Baylor Single cell core according to the manufactual instruction, 10X chromium 3V3.1

value: Day10 differentiation EC and HPC

value: H9 Runx1+23

value: ECs and HPCs

value: Runx1+23 enh Trangenic


title: P. promelas larvae, UP, biological replicate UP_B07, lane 2, time step = 1, analyzed on 20161004

description: Library name: 20161004_ UP_1_B07_ACTTGA_L002_R1_001

value: whole larvae

value: 2 dpf

value: UP


title: HepG2_Cont_DMSO_Day12_H3K27ac_ChIP_rep2

description: Library name: Sample 50


title: HepG2_Kyn_AhRinh_Day12_RNA_EX4_rep1

description: Library name: Sample 138

data_processing:
FASTQ files were processed to assess quality by determining general sequencing bias, clonality and adapter sequence contamination.
RNA sequencing reads were aligned to the hg38 human or mm10 mouse reference genome using STAR using default parameters.  Gene expression levels were calculated using HOMER by counting all strand specific reads within exons.  Only the most abundant transcripts, including multiple alternative variants, were selected for each gene, and the genes with a length smaller than 250 bp were removed.  Transcripts per million (TPM) were used to evaluate the correlation among replicates.
FASTQ files were mapped to the hg38 human or mm10 mouse reference genome with Bowtie2 using default parameters.
Assembly: hg38 or mm10
Supplementary files format and content: TPM expression matrices

extract_protocol:
For RNA-seq, total RNA was isolated from culture cells and purified using a Direct-zol RNA MicroPrep Kit (Zymo Research) as described by the manufacturer.
RNA-seq library preparation was performed according to the manufacturer’s instructions of the QuantSeq 3’ mRNA-Seq V2 Library Prep Kit (Lexogen Inc). In detail, RNA-seq libraries were prepared from 500 ng of total RNA using a reverse transcription–based workflow incorporating Illumina-compatible adapter sequences. First-strand cDNA synthesis was performed using an oligo(dT) primer containing an Illumina-compatible sequence at its 5′ end. The primer was annealed to polyadenylated RNA, and reverse transcription was carried out according to the manufacturer’s instructions to generate first-strand cDNA. Following first-strand synthesis, the RNA template was enzymatically degraded to enable efficient second-strand synthesis. Reaction plates were briefly centrifuged prior to removal of the sealing film to ensure complete recovery of reaction volume. Second-strand synthesis was initiated using a random primer harboring an Illumina-compatible linker sequence at its 5′ end, resulting in double-stranded cDNA (dsDNA) libraries. Double-stranded cDNA libraries were purified using magnetic beads to remove residual enzymes, primers, nucleotides, and buffer components. Beads were equilibrated to room temperature for 30 min prior to use and thoroughly resuspended before addition to samples. Libraries were washed and eluted in an elution buffer according to the manufacturer’s protocol. Purified dsDNA libraries were PCR-amplified (14–16 cycles) to introduce full-length Illumina adapter sequences required for cluster generation, as well as unique dual indices for multiplexed sequencing. Amplified libraries were purified using magnetic beads to remove residual PCR components that may interfere with downstream applications. Final libraries were quantified using a QubitTM 1× dsDNA HS Assay Kit (Thermo Fisher Scientific) and subjected to quality control prior to sequencing.


title: P15

description:
Library name: sample15
Column name in raw_counts_All_Samples.txt: P15

value: Esophageal squamous cell carcinoma

value: primary tumor stage T2 patients with lymph node metastasis


title: control 1

description: Library name: Sample 7

value: S. islandicus REY15A

value: empty plasmid control

value: Arabinose induction


title: P. promelas larvae, DWIP, biological replicate DWIP_B02, lane 2, time step = NA, analyzed on 20161003

description: Library name: 20161003_ DWIP_B02_ATGTCA_L002_R1_001

value: DWIP


title: aCcrK overexpressed 3

description: Library name: Sample 3

value: aCcrK overexpressed


title: P14

description:
Library name: sample14
Column name in raw_counts_All_Samples.txt: P14


title: HepG2_Cont_DMSO_Day12_H3K27ac_ChIP_rep1

description: Library name: Sample 49


title: P. promelas larvae, DWIP, biological replicate DWIP_B02, lane 1, time step = NA, analyzed on 20161003

description: Library name: 20161003_ DWIP_B02_ATGTCA_L001_R1_001


title: aCcrK overexpressed 2

description: Library name: Sample 2


title: P13

description:
Library name: sample13
Column name in raw_counts_All_Samples.txt: P13


title: HepG2_Day12_B2_minus_CEBPa_ChIP_rep2

description: Library name: Sample 68

value: CEBPa


title: aCcrK overexpressed 1

description: Library name: Sample 1


title: HepG2_Day12_B2_minus_H3K27ac_ChIP_rep5

description: Library name: Sample 48


title: P. promelas larvae, UP, biological replicate UP_FIELD50, lane 2, time step = NA, analyzed on 20161003

description: Library name: 20161003_ UP_FIELD_50_GTGGCC_L002_R1_001


title: P. promelas larvae, UP, biological replicate UP_FIELD50, lane 1, time step = NA, analyzed on 20161003

description: Library name: 20161003_ UP_FIELD_50_GTGGCC_L001_R1_001


title: P12

description:
Library name: sample12
Column name in raw_counts_All_Samples.txt: P12


title: control 2

description: Library name: Sample 8

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: REY15A
Supplementary files format and content: CCTF1 OE gene FPKM.xlsx

growth_protocol: Strains of Sis/pSeSD(Cont) and Sis/pSeSD-CCTF1 were cultured in ATV medium


title: HepG2_Day12_B2_minus_H3K27ac_ChIP_rep4

description: Library name: Sample 47


title: P10

description:
Library name: sample10
Column name in raw_counts_All_Samples.txt: P10

value: primary tumor stage T2 patients without lymph node metastasis


title: HepG2_Day12_Cont_H3K27ac_ChIP_rep4

description: Library name: Sample 45

value: Control


title: control 1

description: Library name: Sample 7


title: Patient Control(Sample Tag 12)

city: Longmata District, Luzhou City, Sichuan Province.

first: zheng

last: ran

address: No. 1, Xianglin Road, Section 1

institute: Southwest Medical University

description:
Library name: Sample 3
Sample multiplexing: Lesion and patient-matched control (pControl) samples from the same patient were pooled and sequenced together on the Illumina NovaSeq X Plus platform. The two samples were distinguished using BD Rhapsody Sample Tags (ST). WTA library represents whole-transcriptome amplified cDNA, while ST library contains sample tag-derived reads for sample demultiplexing.

data_processing:
Raw sequencing reads were generated on Illumina NovaSeq XPlus platform with NovaSeq S4 reagent kit.
Raw FASTQ files were demultiplexed and quality-filtered to remove low-quality reads and adapter sequences.
Cell barcode, UMI and Sample Tag sequences were identified and corrected.
Gene expression matrices were generated after reads alignment and UMI deduplication.
Basic quality control including cell filtering, gene count statistics and cell viability assessment was performed.
Assembly: Homo sapiens (GRCh38/hg38)
Supplementary files format and content: Compressed MEX format files: barcodes.tsv.gz (list of cell barcode sequences), genes.tsv.gz (list of gene identifiers), matrix.mtx.gz (sparse matrix of molecule counts per cell per gene).

source_name: Colonic

growth_protocol: Human colonic tissues were collected from clinical specimens. All samples were kept on ice and processed immediately after collection to maintain cell viability.

extract_protocol:
Human colonic tissue samples were obtained from surgery. Tissue was washed with DPBS, minced into small pieces (approx. 1-3 mm³) in a petri dish, and further cut in a 5 mL centrifuge tube. Tissue pieces were washed twice with DPBS. Single-cell suspensions were prepared by sequential enzymatic digestion using MasterAim® Tissue Digestion Solution I at 37°C for 30 min with shaking, followed by Digestion Solution II for 10 min. Digestion was terminated by centrifugation at 2000 rpm for 5 min. Red blood cells were lysed using Beyotime Red Blood Cell Lysis Buffer. Cell viability and count were assessed using an automated counter (Countstar) with AOPI staining or BD Rhapsody™ Scanner with Calcein AM and DRAQ7 staining. For samples "123" and "45", cells were labeled with BD™ Sample Tags (sample tag 8 and 12, respectively) by incubating with 20 μL of Sample Tag in 180 μL BD Pharmingen Stain Buffer (FBS) for 20 min at room temperature, followed by two washes with Stain Buffer.
Single-cell libraries were constructed using the BD Rhapsody™ Enhanced Cartridge Reagent Kit and BD Rhapsody™ cDNA Kit. Briefly, the single-cell suspension was loaded onto a BD Rhapsody™ 8-Lane Cartridge, allowing cells to settle into microwells. Barcoded magnetic beads were loaded to capture polyadenylated RNA from individual cells. On-cartridge cell lysis was performed, and beads were retrieved. Captured mRNA was reverse-transcribed into cDNA on the beads using a custom reverse transcription mix (containing RT Buffer, dNTP, DTT, RT/PCR Enhancer, RNase Inhibitor, and Reverse Transcriptase) at 37°C for 20 min with shaking (1200 rpm). Exonuclease I treatment (Exonuclease I Mix) was performed at 37°C for 30 min followed by inactivation at 80°C for 20 min. Whole Transcriptome Amplification (WTA) libraries were generated via a two-round Random Priming Extension (RPE) process, involving template switching, extension, and PCR amplification. Sample Tag libraries (for multiplexed samples "123" and "45") were constructed separately using two rounds of PCR. Final indexed libraries (WTA and Sample Tag) were prepared using index PCR with Illumina-compatible primers, followed by double-sided or single-sided size selection using AMPure XP beads.

treatment_protocol: No special drug treatment was performed on the collected tissues. Tissue dissociation, cell staining and sample multiplexing were carried out according to standard single-cell experimental procedures. Two samples were labeled with Custom BD Single-Cell Multiplexing Set for pooled loading.

value: Colonic

value: T cells, B cells , Endothelial Cells,Intestinal Epithelial Cells, Epithelial Cells , Macrophages, Mast cells, Smooth muscle cells , Neurons , Neutrophils, Plasma cells , and Stromal cells.


title: P. promelas larvae, UP, biological replicate UP_B22, lane 2, time step = 4, analyzed on 20161003

description: Library name: 20161003_ UP_4_B22_GAGTGG_L002_R1_001


title: HepG2_Day12_Cont_H3K27ac_ChIP_rep5

description: Library name: Sample 46


title: P. promelas larvae, UP, biological replicate UP_B16, lane 2, time step = 3, analyzed on 20161003

description: Library name: 20161003_ UP_3_B16_GTCCGC_L002_R1_001


title: Lesion (Sample Tag 8)

description:
Library name: Sample 2
Sample multiplexing: Lesion and patient-matched control (pControl) samples from the same patient were pooled and sequenced together on the Illumina NovaSeq X Plus platform. The two samples were distinguished using BD Rhapsody Sample Tags (ST). WTA library represents whole-transcriptome amplified cDNA, while ST library contains sample tag-derived reads for sample demultiplexing.

value: T cells, B cells , Endothelial Cells, Intestinal Epithelial Cells, Epithelial Cells, Macrophages, Mast cells, Smooth muscle cells , Neurons , Neutrophils, Plasma cells , and Stromal cells.


title: CCTF1 overexpressed 2

description: Library name: Sample 2

value: CCTF1 overexpressed


title: P. promelas larvae, UP, biological replicate UP_B16, lane 1, time step = 3, analyzed on 20161003

description: Library name: 20161003_ UP_3_B16_GTCCGC_L001_R1_001

value: whole larvae


title: P7

description:
Library name: sample7
Column name in raw_counts_All_Samples.txt: P7


title: P. promelas larvae, UP, biological replicate UP_B30, lane 2, time step = 2, analyzed on 20161003

description: Library name: 20161003_ UP_2_B30_GGCTAC_L002_R1_001

value: 2 dpf


title: Normal Control colon sample

description: Library name: Sample 1


title: P6

description:
Library name: sample6
Column name in raw_counts_All_Samples.txt: P6


title: Ovary of mated Plutella xylostella biol rep 3

city: fuzhou

first: junhao

last: zheng

state: --- Select One ---

address: Cangshan District, Fuzhou City, Fujian Province, China

institute: Fujian Agriculture and Forestry University

description:
Library name: FRAS220302513-1r
H3

data_processing:
Hisat2 v2.0.5; StringTie (v1.3.3b); featureCounts v1.5.0-p3
Clean reads were aligned with the reference genome using HISAT2 with default parameters and assembled using Trinity v2.11.0.
Gene quantitative analysis was performed using RSEM v1.3.3 and Feature Counts v1.5.0-p3.
Differentially expressed genes (DEGs) were identified using DESeq2 v1.20.0.
Assembly: GCF_932276165.1
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

organism: Plutella xylostella

source_name: Ovary

extract_protocol:
RNA was harvested using Eastep® Super Total RNA Extraction Kit (Promega). 10 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® in accordance with the protocol of Novogene Bioinformatics Technology Co. Ltd. (Beijing, China)

value: Ovary

value: WT

value: Mated


title: P4

description:
Library name: sample4
Column name in raw_counts_All_Samples.txt: P4

value: Esophageal squamous cell carcinoma


title: Donor 2, octanoic acid

city: Chicago

first: Mariana

last: Bustamante Eduardo

state: IL

address: 303 E. Superior St. Lurie 4-220

department: Department of Surgery

institute: Northwestern University

description:
Library name: MBE-4_296-OA
llumina Single Cell 3′ RNA Prep, T10 kit

data_processing:
Raw sequencing data were processed using PIPseeker (version 3.3.0). Sequencing reads were aligned to the GRCh38 human genome using the corresponding gene model from the Ensembl database, and a digital expression matrix containing unique molecular identifiers (UMIs) was generated. scRNA-seq analysis was performed using Seurat (version 5.3.1) in R (version 4.4.0).
Assembly: hg 38
Supplementary files format and content: scRNA-seq matrix files generated by pipseeker

source_name: breast

growth_protocol: Breast microstructures were plated in Corning Primaria cell culture plates in vehicle or octanoic acid media, and primary cells were allowed to migrate from the microstructures onto the plate surface over 48 hours.

extract_protocol:
Migratory cells were incubated in 0.05% Trypsin-EDTA (Gibco, #25300054) for 15 minutes, then passed through a 40 µm cell strainer.
A total of 3,400 viable cells/μL were resuspended in Cell Suspension Buffer for library preparation using the Illumina Single Cell 3' RNA Prep, T10 kit (Illumina, #20135691) following the manufacturer’s protocol.

value: breast

value: octanoic acid


title: P3

description:
Library name: sample3
Column name in raw_counts_All_Samples.txt: P3


title: Donor 2, vehicle

description:
Library name: MBE-3_296-VE
llumina Single Cell 3′ RNA Prep, T10 kit

value: vehicle


title: P. promelas larvae, EFP, biological replicate EFP_FIELD52, lane 2, time step = NA, analyzed on 20161003

description: Library name: 20161003_ EFP_FIELD_52_TAGCTT_L002_R1_001

value: EFP


title: Ovary of unmated Plutella xylostella biol rep 3

description:
Library name: FRAS220302510-1r
Q3

value: Unmated


title: Donor 1, octanoic acid

description:
Library name: MBE-2_292-OA
llumina Single Cell 3′ RNA Prep, T10 kit


title: P2

description:
Library name: sample2
Column name in raw_counts_All_Samples.txt: P2

value: primary tumor stage T2 patients without lymph node metastasis


title: P. promelas larvae, EFP, biological replicate EFP_FIELD52, lane 1, time step = NA, analyzed on 20161003

description: Library name: 20161003_ EFP_FIELD_52_TAGCTT_L001_R1_001


title: Ovary of unmated Plutella xylostella biol rep 2

description:
Library name: FRAS220302509-1r
Q2


title: P. promelas larvae, DWIP, biological replicate DWIP_B26, lane 2, time step = NA, analyzed on 20161003

description: Library name: 20161003_ DWIP_B26_ATCACG_L002_R1_001

value: DWIP


title: P. promelas larvae, EFP, biological replicate EFP_B02, lane 1, time step = 2, analyzed on 20161003

description: Library name: 20161003_ EFP_2_B02_GCCAAT_L001_R1_001


title: Ovary of unmated Plutella xylostella biol rep 1

description:
Library name: FRAS220302508-1r
Q1


title: LA3

city: Hangzhou

first: Min

last: Li

address: Yuhang

department: School of Public health and Nursing

institute: HangZhouNomal University

description:
Library name: sample6
count.LA3

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Homo sapiens reference genome using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: GRCm39
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

source_name: connective tissue

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

value: connective tissue

value: Fibrosarcoma cells

value: cell line

value: LA


title: P. promelas larvae, DWIP, biological replicate DWIP_B26, lane 1, time step = NA, analyzed on 20161003

description: Library name: 20161003_ DWIP_B26_ATCACG_L001_R1_001

value: whole larvae


title: Patient10, MPR

first: Yi

last: Xu

address: Qiutao Street 166

institute: Zhejiang University

description: Library name: Patient10

data_processing:
Raw reads for each sample were generated. Raw reads of fastq format were firstly processed using fastp and the low-quality reads were removed to obtain the clean reads. Then clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the reference genome using HISAT. PCA analysis were performed using R(v 4.3.1) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq2. P value < 0.05 and foldchange > 1 or foldchange < -1 was set as the threshold for significantly differential expression gene (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 4.3.1) to demonstrate the expression pattern of genes in different groups and samples.
Based on the hypergeometric distribution, GO, KEGG pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 4.3.1), respectively. R (v 4.3.1) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Tumors of mucosa

extract_protocol:
Biopsy tissue was obtained from patients prior to neoadjuvant chemotherapy combined with PD-1 monoclonal antibody therapy, and preserved in RNAlater (Servicebio, China). The screened specimens would undergo RNA sequencing (RNAseq)Tissues were Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by Hongsun Co., Ltd (Shanghai, China) ,Biomarkers Technologies Co., Ltd (Beijing, China) and Biotech Co., Ltd. (Shanghai, China). The libraries were sequenced on an llumina Novaseq 6000 and DNBSEQ-T7 platform and 150 bp paired-end reads were generated.
Sequencing libraries were prepared, and the quality of the libraries was assessed by Qubit (Thermo Fischer Scientific), 2100 Bioanalyzer (Aligent), and qPCR. Qualifying samples were sequenced by HiSeq (Illumina), and 150-bp paired-end reads were generated at a depth of 20×.

value: Tumors of mucosa

tag: individual

tag: ID

tag: gender

value: Male

tag: history

value: Yes

tag: smoking

tag: drinking

tag: site

value: Tougue

tag: t stage

tag: n statge

tag: m stage

tag: clinical stage

value: IVa

tag: orr

tag: mpr


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

first: Drishti

last: Guin

state: CA

address: 1804 Embarcadero Rd Suite #201

institute: Transcripta Bio

description:
Library name: treated_3mo_3
plasma_oma_conc.csv
Plasma omaveloxolone concentration for this timepoint is in row with timepoint = 3

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 12 year old male patient diagnosed with Leigh Syndrome caused by heterozygous NM_003172.4(SURF1):c.312_321delinsAT (p.Pro104_Leu105insTer); NM_003172.4(SURF1):c.574C>T (p.Arg192Trp) 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 July 2024 to November 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 50 mg PO, daily and dose was increased to 100 mg PO, daily after 2 months. Concentration of Omaveloxolone in plasma was estimated using mass spectrometry.

tag: tissue

value: blood

tag: treatment

value: 100 mg Omaveloxolone

tag: time

value: 3 months


title: LA1

description:
Library name: sample4
count.LA1

tag: cell line

tag: cell type

tag: genotype

tag: batch


title: P. promelas larvae, MHW, biological replicate MHW_B26, lane 1, time step = NA, analyzed on 20161003

description: Library name: 20161003_ 15-07_B26_ACTTGA_L001_R1_001

tag: age

value: 2 dpf

tag: treatment-replicate id

tag: treatment-time

tag: treatment-location

value: MHW


title: P9

description:
Library name: sample9
Column name in raw_counts_All_Samples.txt: P9

data_processing:
Raw Data Quality Control and Trimming: Raw paired-end sequencing reads were processed using fastp (v 0.23.2) to remove adapter sequences (auto-detected), trim low-quality bases (Phred score <20 at read ends), and discard reads containing >5% poly-N nucleotides or shorter than 50 bp. Quality metrics (Q20, Q30, GC content) were calculated for both raw and clean data.
Alignment to Reference Genome: Clean reads were aligned to the human reference genome GRCh38 using HISAT2 (v 2.2.1)
Gene Expression Quantification: Gene-level read counts were generated using featureCounts (v 2.0.6), Final outputs included raw count matrix and FPKM-normalized expression matrix.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Total RNA was extracted from esophageal squamous cell carcinoma tissue using TRIzol reagent (Invitrogen, Catalog #: 15596026) following the manufacturer's protocol. RNA concentration and purity (A260/A280 ratio > 1.9, A260/A230 ratio > 2.0) were measured using a NanoDrop 2000 spectrophotometer. RNA integrity was confirmed by 1% agarose gel electrophoresis showing distinct 18S and 28S rRNA bands.
Stranded RNA sequencing libraries were prepared from total RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer's instructions.

value: Esophageal squamous cell carcinoma

value: primary tumor stage T2 patients without lymph node metastasis


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

description:
Library name: treated_3mo_2
plasma_oma_conc.csv
Plasma omaveloxolone concentration for this timepoint is in row with timepoint = 3


title: R3

description:
Library name: sample3
count.R3

value: connective tissue


title: CCTF1 overexpressed 1

description: Library name: Sample 1

tag: strain

value: S. islandicus REY15A

value: CCTF1 overexpressed

value: Arabinose induction


title: P. promelas larvae, UP, biological replicate UP_FIELD31, lane 2, time step = NA, analyzed on 20160930

description: Library name: 20160930_ UP_FIELD_31_ACAGTG_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.

value: whole larvae

value: UP


title: Patient08, MPR

description: Library name: Patient08

value: Tumors of mucosa

tag: individual

tag: ID

tag: gender

value: Male

tag: history

value: No

tag: smoking

tag: drinking

tag: site

tag: t stage

tag: n statge


title: P5

description:
Library name: sample5
Column name in raw_counts_All_Samples.txt: P5

tag: tissue

tag: treatment


title: Ovary of mated Plutella xylostella biol rep 2

description:
Library name: FRAS220302512-1r
H2

value: Ovary

tag: genotype

value: WT

value: Mated


title: P. promelas larvae, UP, biological replicate UP_B26, lane 2, time step = 1, analyzed on 20161003

description: Library name: 20161003_ UP_1_B26_ACTGAT_L002_R1_001

tag: age

tag: batch


title: Donor 3, vehicle

description:
Library name: MBE-5_298-VE
llumina Single Cell 3′ RNA Prep, T10 kit

value: breast

value: vehicle


title: R2

description:
Library name: sample2
count.R2

tag: cell line

tag: cell type

value: Fibrosarcoma cells

value: cell line


title: Patient07,non-MPR

description: Library name: Patient07

value: Yes

value: Tougue

tag: m stage

tag: clinical stage

value: IVa

tag: orr

tag: mpr


title: R1

description:
Library name: sample1
count.R1

value: connective tissue


title: Patient06, MPR

description: Library name: Patient06

tag: individual

tag: ID

tag: gender

tag: history


title: P. promelas larvae, EFP, biological replicate EFP_FIELD51, lane 2, time step = NA, analyzed on 20160930

description: Library name: 20160930_ EFP_FIELD_51_ATGTCA_L002_R1_001

value: 2 dpf

tag: treatment-replicate id

tag: treatment-time

tag: treatment-location

value: EFP


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

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

tag: tissue

value: blood

tag: treatment

value: 50 mg Omaveloxolone

tag: time

value: 2 months


title: Patient11,non-MPR

description: Library name: Patient11

value: Tumors of mucosa

value: Male

tag: age

tag: smoking

tag: drinking

tag: site

tag: t stage

tag: n statge

value: No


title: T cells CLL, patient 5 and 17, IVE stimulated, Month3, Hash Library

city: Freiburg

first: Ariane

last: Lehmann

address: Breisacher Strasse 153

department: IBSM

institute: Medical Center Freiburg

description:
Library name: 05_17_M3_IVE_Hash
Multiplex

data_processing:
Cellranger count (version 8.0.0) was used for the alignment of sequence reads to the reference genome, filtering, barcode counting, and UMI counting.
Assembly: GRCh38
Supplementary files format and content: Hierarchical Data Format (H5) of filterd feature-count matrix for the GEX and Hash, csv format for the VDJ

source_name: PBMCs

extract_protocol:
T cells were enriched by magnetic cell separation using the Pan T Cell Isolation Kit, human (Miltenyi, Cat# 130-096-535)
10× Genomics protocol ‘Cell surface protein labeling for single cell RNA sequencing protocols with Feature Barcode technology’ (CG000149) was used

treatment_protocol: T cells at baseline and after third vaccination were expanded with the patient-individual HLA class I- and II-restricted peptide pool

value: PBMCs

value: in vitro expaned with the patient-individual vaccine cocktail


title: P. promelas larvae, EFP, biological replicate EFP_FIELD51, lane 1, time step = NA, analyzed on 20160930

description: Library name: 20160930_ EFP_FIELD_51_ATGTCA_L001_R1_001

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.

value: whole larvae

tag: batch


title: TS_3

first: Xiaoying

last: Lin

state: Asia

address: 3 East Qingchun Road

institute: Sir Run Run Shaw Hospital, Zhejiang University School of Medicine

description: Library name: TS_3

data_processing:
Raw reads were filtered to remove adapter sequences, low-quality reads, and reads with >5% N bases using SOAPnuke (v1.5.2).
Assembly: GCF_000001635.27_GRCm39
Supplementary files format and content: Expression matrix in .csv format, containing gene symbols and TPM values for all samples.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) following the manufacturer’s protocol. RNA integrity was assessed by Agilent 2100 Bioanalyzer.
RNA-seq libraries were constructed using the MGIEasy RNA Library Prep Kit (BGI, China). Poly-A mRNA was enriched, fragmented, and reverse-transcribed into cDNA, followed by end repair, adaptor ligation, and PCR amplification.

tag: cell line

tag: cell type

value: Mouse embryonic fibroblast

value: STC-1 and TGF-β1


title: P. promelas larvae, MHW, biological replicate MHW_B26, lane 2, time step = NA, analyzed on 20161003

description: Library name: 20161003_ 15-07_B26_ACTTGA_L002_R1_001

value: MHW


title: T cells CLL, patient 5 and 17, unstimulated, Month3, Hash Library

description:
Library name: 05_17_M3_us_Hash
Multiplex

value: unstimulated


title: P. promelas larvae, EFP, biological replicate EFP_B21, lane 2, time step = 4, analyzed on 20160930

description: Library name: 20160930_ EFP_4_B21_AGTTCC_L002_R1_001


title: Blood from patient 1 month post-treatment with Omaveloxolone at a dose of 50 mg PO daily, replicate 3

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

tag: genotype

value: 1 month


title: T cells CLL, patient 5 and 17, IVE stimulated, Day1, Hash Library

description:
Library name: 05_17_d1_IVE_Hash
Multiplex


title: P. promelas larvae, EFP, biological replicate EFP_B21, lane 1, time step = 4, analyzed on 20160930

description: Library name: 20160930_ EFP_4_B21_AGTTCC_L001_R1_001


title: Blood from patient 1 month post-treatment with Omaveloxolone at a dose of 50 mg PO daily, replicate 2

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


title: Patient09,non-MPR

description: Library name: Patient09

tag: individual

tag: ID

tag: gender

tag: history

value: Yes

value: Tougue

tag: m stage

tag: clinical stage

value: IVa

tag: orr

tag: mpr


title: TS_1

description: Library name: TS_1

tag: treatment


title: P. promelas larvae, EFP, biological replicate EFP_B26, lane 2, time step = 3, analyzed on 20160930

description: Library name: 20160930_ EFP_3_B26_CTTGTA_L002_R1_001

tag: tissue

tag: age

value: 2 dpf

tag: treatment-replicate id

tag: treatment-time

tag: treatment-location

value: EFP


title: TGFb1_3

description: Library name: TGFb1_3

tag: cell line


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

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

value: blood

value: 50 mg Omaveloxolone

tag: time


title: Pre-treated blood,  replicate 3

description: Library name: pre-treated_3

tag: genotype

value: 0 months


title: P. promelas larvae, EFP, biological replicate EFP_B28, lane 2, time step = 2, analyzed on 20160930

description: Library name: 20160930_ EFP_2_B28_AGTCAA_L002_R1_001

tag: batch


title: P8

first: yujie

last: xie

address: No. 37 Guoxue Lane, Wuhou District, Chengdu City, Sichuan Province

institute: West China Hospital, Sichuan University

description:
Library name: sample8
Column name in raw_counts_All_Samples.txt: P8

value: Esophageal squamous cell carcinoma

value: primary tumor stage T2 patients without lymph node metastasis


title: Donor 3, octanoic acid

description:
Library name: MBE-6_298-OA
llumina Single Cell 3′ RNA Prep, T10 kit

value: breast

value: octanoic acid


title: Pre-treated blood,  replicate 2

description: Library name: pre-treated_2


title: T cells CLL, patient 3 and 8, IVE stimulated, Day1, Hash Library

description:
Library name: 03_08_d1_IVE_Hash
Multiplex

value: PBMCs

value: in vitro expaned with the patient-individual vaccine cocktail


title: P. promelas larvae, EFP, biological replicate EFP_B28, lane 1, time step = 2, analyzed on 20160930

first: Steven

last: Purucker

address: 109 TW Alexander Dr

institute: US EPA

description: Library name: 20160930_ EFP_2_B28_AGTCAA_L001_R1_001

value: whole larvae


title: STC1_3

description: Library name: STC1_3

tag: cell type

value: Mouse embryonic fibroblast


title: Pre-treated blood,  replicate 1

description: Library name: pre-treated_1


title: P. promelas larvae, EFP, biological replicate EFP_B26, lane 2, time step = 1, analyzed on 20160930

description: Library name: 20160930_ EFP_1_B26_GCCAAT_L002_R1_001


title: STC1_2

description: Library name: STC1_2


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

description:
Library name: treated_3mo_1
plasma_oma_conc.csv
Plasma omaveloxolone concentration for this timepoint is in row with timepoint = 3

value: 100 mg Omaveloxolone

value: 3 months


title: APACT12

city: Augsburg

first: Victoria

middle: Elisabeth

last: Fincke

address: Stenglinstraße 2

institute: Childens Cancer Center - University hospital Augsburg

description: Library name: D1_w2921

data_processing:
Data was rocessed with the Space Ranger software provided by 10x Genomics
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of Gene Ids
Supplementary files format and content: matrix.mtx.gz: Count Matrix
Library strategy: Spatial Transcriptomics

source_name: adrenocortical carcinoma

extract_protocol:
FFPE slides were prepared according to Visium HD protocol from 10x Genomics
Library was constructed according to 10x Genomics Visium HD protocol

value: adrenocortical carcinoma


title: T cells CLL, patient 5 and 17, IVE stimulated, Month3, GEX Library

description:
Library name: 05_17_M3_IVE_GEX
Multiplex


title: P. promelas larvae, EFP, biological replicate EFP_B26, lane 1, time step = 1, analyzed on 20160930

description: Library name: 20160930_ EFP_1_B26_GCCAAT_L001_R1_001


title: Blood from patient 2 month post-treatment with Omaveloxolone at a dose of 50 mg PO daily, replicate 1

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

value: 2 months


title: STC1_1

description: Library name: STC1_1


title: APACT4

description: Library name: D1_w2911


title: T cells CLL, patient 3 and 8, unstimulated, Day1, Hash Library

description:
Library name: 03_08_d1_us_Hash
Multiplex

value: unstimulated


title: TS_2

description: Library name: TS_2

value: STC-1 and TGF-β1


title: T cells CLL, patient 5 and 17, unstimulated, Month3, GEX Library

description:
Library name: 05_17_M3_us_GEX
Multiplex


title: P. promelas larvae, DSP, biological replicate DSP_B21, lane 2, time step = NA, analyzed on 20160930

description: Library name: 20160930_ DSP_B21_GTGAAA_L002_R1_001

value: 2 dpf

value: DSP


title: T cells CLL, patient 5 and 17, unstimulated, Day1, Hash Library

description:
Library name: 05_17_d1_us_Hash
Multiplex


title: Con_3

description: Library name: Con_3

value: Con


title: APACT19

description: Library name: A1-w2941


title: T cells CLL, patient 5 and 17, IVE stimulated, Day1, GEX Library

description:
Library name: 05_17_d1_IVE_GEX
Multiplex


title: P. promelas larvae, DSP, biological replicate DSP_B21, lane 1, time step = NA, analyzed on 20160930

description: Library name: 20160930_ DSP_B21_GTGAAA_L001_R1_001


title: Con_2

description: Library name: Con_2


title: T cells CLL, patient 3 and 8, IVE stimulated, Month3, Hash Library

description:
Library name: 03_08_M3_IVE_Hash
Multiplex


title: APACT27

description: Library name: A1-w2931


title: T cells CLL, patient 5 and 17, unstimulated, Day1, GEX Library

description:
Library name: 05_17_d1_us_GEX
Multiplex


title: Con_1

description: Library name: Con_1


title: Omaveloxolone treated well at 10.0 µM, biol repl 4

description:
Library name: L3_TACATATGCATGAC
Omaveloxolone treated well at 10.0 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".

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.

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.

value: Fibroblast

value: normal human dermal fibroblasts

value: wildtype

value: Omaveloxolone, 10.0 µM


title: TGFb1_2

description: Library name: TGFb1_2


title: P. promelas larvae, EFP, biological replicate EFP_B26, lane 1, time step = 3, analyzed on 20160930

description: Library name: 20160930_ EFP_3_B26_CTTGTA_L001_R1_001

value: EFP


title: P. promelas larvae, MHW, biological replicate MHW_B21, lane 2, time step = NA, analyzed on 20160930

description: Library name: 20160930_ 15-08_B21_GTTTCG_L002_R1_001

value: MHW


title: T cells CLL, patient 3 and 8, IVE stimulated, Month3, GEX Library

description:
Library name: 03_08_M3_IVE_GEX
Multiplex

value: PBMCs

value: in vitro expaned with the patient-individual vaccine cocktail


title: T cells CLL, patient 3 and 8, unstimulated, Month3, Hash Library

description:
Library name: 03_08_M3_us_Hash
Multiplex


title: P. promelas larvae, MHW, biological replicate MHW_B21, lane 1, time step = NA, analyzed on 20160930

description: Library name: 20160930_ 15-08_B21_GTTTCG_L001_R1_001

value: whole larvae


title: Omaveloxolone treated well at 10.0 µM, biol repl 3

description:
Library name: L13_CTCGCTGATAGCAC
Omaveloxolone treated well at 10.0 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: SW48 cells levofloxacin-3

city: Wuhan

first: Jiangyang

last: Chi

address: Youyi street

institute: Hubei University

description: Library name: Sample 6

data_processing:
Raw reads were quality-filtered (SOAPnuke). Clean reads were aligned to GRCh38.p13 using HISAT2. Gene counts were obtained using featureCounts. Differential expression was analyzed using DESeq2 (FDR<0.05, |log2FC|>1). Functional enrichment (GO/KEGG) was performed using clusterProfiler.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file (gene_counts) contains raw read counts for all genes across the 6 samples.
Supplementary files format and content: tab-delimited text file (gene_TPM) contains FPKM values for all genes across the 6 samples.
Supplementary files format and content: tab-delimited text file (DEG_vs_pbs) listing significantly differentially expressed genes.

source_name: Colon

growth_protocol: SW48 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen) according to the manufacturer’s protocol, followed by DNase I treatment to remove genomic DNA. RNA integrity was verified by Bioanalyzer (RIN > 8.0).
Stranded mRNA-seq libraries were constructed from poly(A)+ RNA using the BGI MGI Easy RNA Library Prep Kit and sequenced on a BGISEQ platform with 150 bp paired-end reads.

treatment_protocol: SW48 cells were treated with 100 μM Levofloxacin or vehicle control for 5 days, with medium refreshed every 48 hours. Total RNA was isolated from harvested cells post-treatment.

value: Colon

value: colorectal cancer cells

value: Levofloxacin


title: T cells CLL, patient 3 and 8, unstimulated, Month3, GEX Library

description:
Library name: 03_08_M3_us_GEX
Multiplex

value: unstimulated


title: P. promelas larvae, UP, biological replicate UP_Field2, lane 2, time step = NA, analyzed on 20160928

description: Library name: 20160928_ Up_Field_2_ACTTGA_L002_R1_001

source_name: whole larvae

value: UP


title: Omaveloxolone treated well at 10.0 µM, biol repl 2

description:
Library name: K3_CCGCAACCAAGGCA
Omaveloxolone treated well at 10.0 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: T cells CLL, patient 3 and 8, IVE stimulated, Day1, GEX Library

description:
Library name: 03_08_d1_IVE_GEX
Multiplex


title: SW48 cells levofloxacin-2

description: Library name: Sample 5


title: P. promelas larvae, UP, biological replicate UP_Field2, lane 1, time step = 3, analyzed on 20160928

description: Library name: 20160928_ Up_Field_2_ACTTGA_L001_R1_001

value: 2 dpf


title: SW48 cells levofloxacin-1

description: Library name: Sample 4


title: Omaveloxolone treated well at 10.0 µM, biol repl 1

description:
Library name: K13_ACTACTCGTGTCGA
Omaveloxolone treated well at 10.0 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: T cells CLL, patient 3 and 8, unstimulated, Day1, GEX Library

description:
Library name: 03_08_d1_us_GEX
Multiplex


title: P. promelas larvae, UP, biological replicate UP_B12, lane 2, time step = 3, analyzed on 20160928

description: Library name: 20160928_ UP_3_B12_GAGTGG_L002_R1_001


title: SW48 cells pbs-3

description: Library name: Sample 3

value: vehicle


title: Omaveloxolone treated well at 3.33 µM, biol repl 4

description:
Library name: L4_ACATAGCCTGGCGG
Omaveloxolone treated well at 3.33 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, 3.33 µM


title: P. promelas larvae, UP, biological replicate UP_B12, lane 1, time step = 2, analyzed on 20160928

description: Library name: 20160928_ UP_3_B12_GAGTGG_L001_R1_001


title: T cells CLL, patient 5 and 17, IVE stimulated, Month3, VDJ Library

description:
Library name: 05_17_M3_IVE_VDJ
Multiplex


title: SW48 cells pbs-2

description: Library name: Sample 2


title: TGFb1_1

description: Library name: TGFb1_1

value: Mouse embryonic fibroblast


title: P. promelas larvae, UP, biological replicate UP_B21, lane 2, time step = 2, analyzed on 20160928

description: Library name: 20160928_ UP_2_B21_GTCCGC_L002_R1_001


title: T cells CLL, patient 5 and 17, unstimulated, Month3, VDJ Library

description:
Library name: 05_17_M3_us_VDJ
Multiplex


title: Omaveloxolone treated well at 3.33 µM, biol repl 2

description:
Library name: K4_AACCTGAGGCAAGA
Omaveloxolone treated well at 3.33 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

value: normal human dermal fibroblasts


title: SW48 cells pbs-1

description: Library name: Sample 1


title: T cells CLL, patient 5 and 17, IVE stimulated, Day1, VDJ Library

description:
Library name: 05_17_d1_IVE_VDJ
Multiplex


title: P. promelas larvae, UP, biological replicate UP_B21, lane 1, time step = 1, analyzed on 20160928

description: Library name: 20160928_ UP_2_B21_GTCCGC_L001_R1_001


title: K562, AW1-51, rep 2

city: Boston

first: Annalisa

last: Di Ruscio

state: Massachusetts

address: 3 Blackfan Circle

institute: Harvard Medical School Initiative for RNA Medicine

description:
Library name: Sample 8
K562_reads.txt
K562-MIX72_203

data_processing:
Optical duplicates were removed using clumpify from the BBTools suite using the flag “dedupe spany addcount”.
quality trimming was performed using Trimmomatic (version 0.36) in paired end mode with the flags “LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36”
Trimmed sequences were aligned to hg38 genome using STAR (version 2.5.4a) and reads were generated using FeatureCounts of the Subreads package (version 2.0.0)
Normalization and differential expression analysis were performed using DESeq2 (version 1.22.0)
Assembly: hg38
Supplementary files format and content: 2 tab delimited file containing the raw counts for the samples, one for each cell line

growth_protocol: K562 and A549 cell lines were grown in RPMI medium supplemented with 10% fetal bovine serum (FBS; Gibco, Thermo Fisher Scientific) in humidified incubator at 37ºC with 5% CO2

extract_protocol:
Total RNA was isolated by phenol chloroform purification using the commercially available TriReagent (Ambion, Thermo Fisher Scientific) according to manufacturer’s recommendations. After 1:1 isopropanol precipitation of the aqueous phase, the RNA pellet was treated with DNAse I (Roche; 15 U per sample) at 37° C for one hour in the presence of RNase Inhibitor (Promega). DNase was inactivated with the addition of 10 mM EDTA pH 8 (Sigma-Aldirch) and RNA was then recovered by acidic phenol (Sigma, pH 4.3) extraction and 3:1 ethanol precipitation in the presence of 200 mM NaCl. RNA was resuspended in RNAse-free water.
Poly A RNA fraction was extracted and RNA libraries for sequencing were prepared using Stranded total RNA libraryIllumina Truseq stranded kit / MGI’s directional kits,

treatment_protocol: saRNAs (50 nM) were transfected into K562 cells with Kit V program T-016 by Amaxa Nucleofector Device II (Lonza). In A549, saRNAs (50 nM) were transfected using DharmaFECT 1 (DF1, Horizon Discovery). Following Voutila et al protocol, cells were first reverse transfected and then forward transfected 24h later

value: Chronic Myeloid Leukemia

value: WT

value: AW1-51 saRNA


title: T cells CLL, patient 5 and 17, unstimulated, Day1, VDJ Library

description:
Library name: 05_17_d1_us_VDJ
Multiplex

value: PBMCs


title: Omaveloxolone treated well at 3.33 µM, biol repl 1

description:
Library name: K14_TAAGCCTACACAGG
Omaveloxolone treated well at 3.33 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: P. promelas larvae, UP, biological replicate UP_B17, lane 2, time step = 1, analyzed on 20160928

description: Library name: 20160928_ UP_1_B17_GGCTAC_L002_R1_001

value: whole larvae


title: K562, AW1-51, rep 1

description:
Library name: Sample 7
K562_reads.txt
K562-MIX72_195


title: Omaveloxolone treated well at 1.11 µM, biol repl 4

description:
Library name: L5_TATTAACTGGATGG
Omaveloxolone treated well at 1.11 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, 1.11 µM


title: T cells CLL, patient 3 and 8, IVE stimulated, Month3, VDJ Library

description:
Library name: 03_08_M3_IVE_VDJ
Multiplex

value: in vitro expaned with the patient-individual vaccine cocktail


title: P. promelas larvae, UP, biological replicate UP_B17, lane 1, time step = NA, analyzed on 20160928

description: Library name: 20160928_ UP_1_B17_GGCTAC_L001_R1_001


title: Omaveloxolone treated well at 1.11 µM, biol repl 3

description:
Library name: L15_ACAGTCATACGACA
Omaveloxolone treated well at 1.11 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 3.33 µM, biol repl 3

description:
Library name: L14_ACGACATCGCGCAC
Omaveloxolone treated well at 3.33 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: T cells CLL, patient 3 and 8, unstimulated, Month3, VDJ Library

description:
Library name: 03_08_M3_us_VDJ
Multiplex


title: P. promelas larvae, EMZ, biological replicate EMZ_B24, lane 2, time step = NA, analyzed on 20160928

description: Library name: 20160928_ EMZ_B24_TAGCTT_L002_R1_001

value: EMZ


title: K562, NC, rep 2

description:
Library name: Sample 6
K562_reads.txt
K562-NC72_202

value: non targetting saRNA


title: K562, NC, rep 1

description:
Library name: Sample 5
K562_reads.txt
K562-NC72_194


title: Omaveloxolone treated well at 1.11 µM, biol repl 2

description:
Library name: K5_ACTCCATATTCGGC
Omaveloxolone treated well at 1.11 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: T cells CLL, patient 3 and 8, IVE stimulated, Day1, VDJ Library

description:
Library name: 03_08_d1_IVE_VDJ
Multiplex


title: P. promelas larvae, EMZ, biological replicate EMZ_B24, lane 1, time step = NA, analyzed on 20160928

description: Library name: 20160928_ EMZ_B24_TAGCTT_L001_R1_001


title: A549, AW1-51, rep 2

description:
Library name: Sample 4
A549_reads.txt
A549-273_Mix72

value: lung adenocarinoma


title: Omaveloxolone treated well at 1.11 µM, biol repl 1

description:
Library name: K15_ATACAGCTACTAGC
Omaveloxolone treated well at 1.11 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: T cells CLL, patient 3 and 8, unstimulated, Day1, VDJ Library

description:
Library name: 03_08_d1_us_VDJ
Multiplex

value: unstimulated


title: P. promelas larvae, EFP, biological replicate EFP_FIELD34, lane 2, time step = NA, analyzed on 20160928

description: Library name: 20160928_ EFP_FIELD_34_ATCACG_L002_R1_001

value: 2 dpf

value: EFP


title: Omaveloxolone treated well at 0.37 µM, biol repl 4

description:
Library name: L6_CCTCCTAATGACGG
Omaveloxolone treated well at 0.37 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, 0.37 µM


title: A549, AW1-51, rep 1

description:
Library name: Sample 3
A549_reads.txt
A549-263_Mix72


title: P. promelas larvae, EFP, biological replicate EFP_FIELD34, lane 1, time step = NA, analyzed on 20160928

description: Library name: 20160928_ EFP_FIELD_34_ATCACG_L001_R1_001


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

first: CRI

last: Bioinformatics

address: 5801 S. Ellis Ave.

institute: University of Chicago

description:
Library name: RZ19
RZ19

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

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


title: A549, NC, rep 2

description:
Library name: Sample 2
A549_reads.txt
A549-272_NC72


title: Omaveloxolone treated well at 0.37 µM, biol repl 3

description:
Library name: L16_AATGTCGATACGAA
Omaveloxolone treated well at 0.37 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

value: normal human dermal fibroblasts


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

description:
Library name: RZ18
RZ18


title: P. promelas larvae, DWIP, biological replicate DWIP_B06, lane 2, time step = NA, analyzed on 20160928

description: Library name: 20160928_ DWIP_B06_GTGGCC_L002_R1_001

value: DWIP


title: A549, NC, rep 1

description:
Library name: Sample 1
A549_reads.txt
A549-262_NC72

value: WT


title: Omaveloxolone treated well at 0.37 µM, biol repl 2

description:
Library name: K6_AATACATACCTTCC
Omaveloxolone treated well at 0.37 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 0.37 µM, biol repl 1

description:
Library name: K16_AAGAAGTCGGAGAA
Omaveloxolone treated well at 0.37 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, DWIP, biological replicate DWIP_B06, lane 1, time step = NA, analyzed on 20160928

description: Library name: 20160928_ DWIP_B06_GTGGCC_L001_R1_001


title: snp12null-snpc13null_72h_replicate3

city: Baltimore

first: John

last: Kim

state: MD

address: 3400 Charles Street

department: Department of Biology

institute: Johns Hopkins University

description:
Library name: smallRNA2021-018-SNPC12null_SNPC13null-72h-WW
snpc-1.3(-) 72h 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.

value: whole worm

value: 72h gravid adult

tag: replicate


title: SKBR3- riTNF-HER2 CAR T+IR (10 Gy × 2) , Mouse 2

description:
Library name: RZ15
RZ15


title: SKBR3- riTNF-HER2 CAR T+IR (10 Gy × 2) , Mouse 3

description:
Library name: RZ16
RZ16


title: P. promelas larvae, MHW, biological replicate MHW_B16, lane 2, time step = NA, analyzed on 20160928

description: Library name: 20160928_ 15-07_B16_ACTGAT_L002_R1_001

value: whole larvae

value: MHW


title: snpc12null_72h_replicate3

description:
Library name: smallRNA2021-017-SNPC12null-72h-WW
snpc-1.2(-) 72h RT small RNA-seq replicate 3


title: Omaveloxolone treated well at 0.12 µM, biol repl 4

description:
Library name: L7_CCTGATACACGTAA
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".

value: wildtype

value: Omaveloxolone, 0.12 µM


title: SKBR3- riTNF-HER2 CAR T+IR (10 Gy × 2) , Mouse 1

description:
Library name: RZ14
RZ14


title: P. promelas larvae, MHW, biological replicate MHW_B16, lane 1, time step = NA, analyzed on 20160928

description: Library name: 20160928_ 15-07_B16_ACTGAT_L001_R1_001


title: N2_72h_replicate3

description:
Library name: smallRNA2021-016-N2-72h-WW
N2 72h RT small RNA-seq replicate 3


title: P. promelas larvae, UP, biological replicate UP_FIELD18, lane 2, time step = NA, analyzed on 20160927

description: Library name: 20160927_ UP_FIELD_18_GTGAAA_L002_R1_001

value: UP


title: SKBR3- riGFP-HER2 CAR T+IR (10 Gy × 2) , Mouse 3

description:
Library name: RZ13
RZ13


title: Omaveloxolone treated well at 0.12 µM, biol repl 3

description:
Library name: L17_CTATCGCATCTGAC
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: Omaveloxolone treated well at 0.12 µM, biol repl 2

description:
Library name: K7_CAACTAATCCGGAA
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: snp12null-snpc13null_48h_replicate3

description:
Library name: smallRNA2021-015-SNPC12null_SNPC13null-48h-WW
snpc-1.3(-) 48h RT small RNA-seq replicate 3


title: SKBR3- riGFP-HER2 CAR T+IR (10 Gy × 2) , Mouse 2

description:
Library name: RZ12
RZ12


title: control 3

first: yunfeng

last: yang

address: State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P.R. China

institute: shandong university

description: Library name: Sample 9

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: REY15A
Supplementary files format and content: CCTF1 OE gene FPKM.xlsx

source_name: S. islandicus REY15A

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: S. islandicus REY15A

value: empty plasmid control

value: Arabinose induction


title: P. promelas larvae, UP, biological replicate UP_FIELD18, lane 1, time step = 4, analyzed on 20160927

description: Library name: 20160927_ UP_FIELD_18_GTGAAA_L001_R1_001

value: 2 dpf


title: snpc12null_48h_replicate3

description:
Library name: smallRNA2021-014-SNPC12null-48h-WW
snpc-1.2(-) 48h RT small RNA-seq replicate 3


title: SKBR3- riGFP-HER2 CAR T+IR (10 Gy × 2) , Mouse 1

description:
Library name: RZ11
RZ11