title: Neurons derived from patient iPSC cells treated with 125 nM Omaveloxolone replicate 1

description:
Library name: RL130
Column names mean the following in the processed data file: target ID - ensembl transcript ID, length: transcript length, eff_length: effective transcript length (the adjusted transcript length used in abundance estimation, taking into account the fragment length distribution), est_counts - transcript counts, tpm - transcript counts normalized by effective length


title: Huh7 cells, FLAG, replicate 3

status: Public on Aug 01 2026

type: SRA

city: Hong Kong

first: Qinglin

last: Zhang

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

country: China

institute: The University of Hong Kong

description: Library name: Sample3

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

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

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

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

tag: cell line

tag: cell type

value: human hepato cellular carcinoma cell line

tag: genotype

value: WT

tag: treatment

value: lentivirus infection


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

city: Durham

first: Steven

middle: Thomas

last: Purucker

state: NC

address: 109 TW Alexander Dr

country: USA

institute: US EPA

description: Library name: 20160923_ UP_1_B06_AGTCAA_L001_R1_001

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

organism: Pimephales promelas

source_name: whole larvae

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

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

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

tag: tissue

value: whole larvae

tag: age

value: 2 dpf

tag: treatment-replicate id

tag: treatment-time

tag: treatment-location

value: UP

tag: batch


title: Huh7 cells, FLAG, replicate 2

description: Library name: Sample2


title: P. promelas larvae, MHR, biological replicate MHR_B01, lane 2, time step = NA, analyzed on 20160923

description: Library name: 20160923_ MHR_B01_GCCAAT_L002_R1_001

value: MHR


title: Neurons derived from patient iPSC cells treated with DMSO replicate 3

city: Palo Alto

first: Drishti

last: Guin

state: CA

address: 1804 Embarcadero Rd Suite #201

institute: Transcripta Bio

description:
Library name: RL129
Column names mean the following in the processed data file: target ID - ensembl transcript ID, length: transcript length, eff_length: effective transcript length (the adjusted transcript length used in abundance estimation, taking into account the fragment length distribution), est_counts - transcript counts, tpm - transcript counts normalized by effective length

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)

molecule: polyA RNA

source_name: NGN2-driven glutamatergic neurons

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

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

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

value: NGN2-driven glutamatergic neurons

value: Neurons

value: DMSO


title: ET0584163

type: genomic

city: Reus

first: Dorota

last: Komar

address: avenida univeritat 1

country: Spain

institute: center for omic sciences, Eurecat

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

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

data_processing: SeSAMe package in R environment

label: Cy3 and Cy5

molecule: genomic DNA

source_name: PBMCs

label_protocol: standard Illumina protocol

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

value: PBMCs

value: highcardio

tag: age at menopause


title: Huh7 cells, FLAG, replicate 1

description: Library name: Sample1


title: ET0584162

value: hepatic


title: Neurons derived from patient iPSC cells treated with DMSO replicate 2

description:
Library name: RL128
Column names mean the following in the processed data file: target ID - ensembl transcript ID, length: transcript length, eff_length: effective transcript length (the adjusted transcript length used in abundance estimation, taking into account the fragment length distribution), est_counts - transcript counts, tpm - transcript counts normalized by effective length


title: Neurons derived from patient iPSC cells treated with DMSO replicate 1

description:
Library name: RL127
Column names mean the following in the processed data file: target ID - ensembl transcript ID, length: transcript length, eff_length: effective transcript length (the adjusted transcript length used in abundance estimation, taking into account the fragment length distribution), est_counts - transcript counts, tpm - transcript counts normalized by effective length


title: P. promelas larvae, MHR, biological replicate MHR_B01, lane 1, time step = NA, analyzed on 20160923

description: Library name: 20160923_ MHR_B01_GCCAAT_L001_R1_001


title: HepG2, 10uM 5-azacytidine, rep3, RNA-seq

city: 강남구

first: Wonjin

last: Woo

state: 서울 — Seoul

address: 서울시 강남구 도곡로237 강남세브란스 의생명연구센터 1층 김락균 교수님 실험실

country: South Korea

institute: Yonsei University

description:
Library name: HepG2_10uM_rep3_RNA
HepG2 cells treated with 10 μM 5-azacytidine for 4 days (RNA-seq)

data_processing:
ATAC-seq raw FASTQ files were processed using PEPATAC pipeline (v0.10.2) for quality control, alignment, and peak calling.
ATAC-seq consensus peak sets were generated using iterative peak merging approach.
ATAC-seq read counts were quantified and differential accessibility analysis was performed using DiffBind (v3.12.0) with DESeq2 normalization.
RNA-seq raw FASTQ files were aligned to hg38 genome using HISAT2 (v2.2.1).
RNA-seq gene-level read counts were generated using HTSeq (v2.0.4).
RNA-seq differential expression analysis was performed using DESeq2 (v1.42.1).
RNA-seq variance-stabilized transformation was applied for data visualization.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files containing normalized count matrices for RNA-seq and peak count matrices for ATAC-seq with gene/peak annotations.
Supplementary files format and content: BED format file containing consensus peak coordinates for ATAC-seq analysis.

source_name: liver

growth_protocol: HepG2 cells were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C in a humidified incubator with 5% CO2. Cells were seeded at 70-80% confluence.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, 74104) according to manufacturer's protocol. For ATAC-seq, nuclei were extracted and processed according to standard ATAC-seq protocol using Nextera DNA Library Prep Kit.
RNA libraries were prepared with the TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina). ATAC-seq libraries were prepared using the Nextera DNA Library Prep Kit (Illumina).

treatment_protocol: DNA methyltransferase inhibition was induced using 5-azacytidine (Sigma-Aldrich) at concentrations of 0, 2, or 10 μM for 4 days, with daily medium replacement.

value: liver

value: hepatocyte

value: 10 μM 5-azacytidine for 4 days


title: ET0584154


title: P. promelas larvae, EFP, biological replicate EFP_B01, lane 2, time step = 3, analyzed on 20160923

description: Library name: 20160923_ EFP_3_B01_GTTTCG_L002_R1_001

value: EFP


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

description:
Library name: RL126
Column names mean the following in the processed data file: target ID - ensembl transcript ID, length: transcript length, eff_length: effective transcript length (the adjusted transcript length used in abundance estimation, taking into account the fragment length distribution), est_counts - transcript counts, tpm - transcript counts normalized by effective length

value: 500 nM Omaveloxolone


title: HepG2, 10uM 5-azacytidine, rep2, RNA-seq

description:
Library name: HepG2_10uM_rep2_RNA
HepG2 cells treated with 10 μM 5-azacytidine for 4 days (RNA-seq)

value: WT


title: ET0584150

value: lipid


title: P. promelas larvae, EFP, biological replicate EFP_B01, lane 1, time step = 3, analyzed on 20160923

description: Library name: 20160923_ EFP_3_B01_GTTTCG_L001_R1_001

value: whole larvae


title: HepG2, 10uM 5-azacytidine, rep1, RNA-seq

description:
Library name: HepG2_10uM_rep1_RNA
HepG2 cells treated with 10 μM 5-azacytidine for 4 days (RNA-seq)


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

description:
Library name: RL124
Column names mean the following in the processed data file: target ID - ensembl transcript ID, length: transcript length, eff_length: effective transcript length (the adjusted transcript length used in abundance estimation, taking into account the fragment length distribution), est_counts - transcript counts, tpm - transcript counts normalized by effective length


title: P. promelas larvae, EFP, biological replicate EFP_B01, lane 2, time step = 2, analyzed on 20160923

description: Library name: 20160923_ EFP_2_B01_GTGAAA_L002_R1_001

value: 2 dpf


title: ET0584149


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

description:
Library name: RL125
Column names mean the following in the processed data file: target ID - ensembl transcript ID, length: transcript length, eff_length: effective transcript length (the adjusted transcript length used in abundance estimation, taking into account the fragment length distribution), est_counts - transcript counts, tpm - transcript counts normalized by effective length


title: P. promelas larvae, EFP, biological replicate EFP_B01, lane 1, time step = 2, analyzed on 20160923

description: Library name: 20160923_ EFP_2_B01_GTGAAA_L001_R1_001


title: ET0584146


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

description:
Library name: RL123
Column names mean the following in the processed data file: target ID - ensembl transcript ID, length: transcript length, eff_length: effective transcript length (the adjusted transcript length used in abundance estimation, taking into account the fragment length distribution), est_counts - transcript counts, tpm - transcript counts normalized by effective length

value: 250 nM Omaveloxolone


title: HepG2, 2uM 5-azacytidine, rep2, RNA-seq

description:
Library name: HepG2_2uM_rep2_RNA
HepG2 cells treated with 2 μM 5-azacytidine for 4 days (RNA-seq)

value: 2 μM 5-azacytidine for 4 days


title: HepG2, 2uM 5-azacytidine, rep3, RNA-seq

description:
Library name: HepG2_2uM_rep3_RNA
HepG2 cells treated with 2 μM 5-azacytidine for 4 days (RNA-seq)


title: P. promelas larvae, EFP, biological replicate EFP_B01, lane 2, time step = 1, analyzed on 20160923

description: Library name: 20160923_ EFP_1_B01_ATGTCA_L002_R1_001


title: ET0584144


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

description:
Library name: RL122
Column names mean the following in the processed data file: target ID - ensembl transcript ID, length: transcript length, eff_length: effective transcript length (the adjusted transcript length used in abundance estimation, taking into account the fragment length distribution), est_counts - transcript counts, tpm - transcript counts normalized by effective length

value: NGN2-driven glutamatergic neurons


title: HepG2, 2uM 5-azacytidine, rep1, RNA-seq

description:
Library name: HepG2_2uM_rep1_RNA
HepG2 cells treated with 2 μM 5-azacytidine for 4 days (RNA-seq)


title: P. promelas larvae, EFP, biological replicate EFP_B01, lane 1, time step = 1, analyzed on 20160923

description: Library name: 20160923_ EFP_1_B01_ATGTCA_L001_R1_001


title: ET0584141


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

description:
Library name: RL121
Column names mean the following in the processed data file: target ID - ensembl transcript ID, length: transcript length, eff_length: effective transcript length (the adjusted transcript length used in abundance estimation, taking into account the fragment length distribution), est_counts - transcript counts, tpm - transcript counts normalized by effective length

value: Neurons


title: ET0584136


title: P. promelas larvae, UP, biological replicate UP_Field52, lane 2, time step = NA, analyzed on 20160809

description: Library name: 20160809_ Up_Field_52_GGCTAC_L002_R1_001

value: UP


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

description:
Library name: RL120
Column names mean the following in the processed data file: target ID - ensembl transcript ID, length: transcript length, eff_length: effective transcript length (the adjusted transcript length used in abundance estimation, taking into account the fragment length distribution), est_counts - transcript counts, tpm - transcript counts normalized by effective length

value: 125 nM Omaveloxolone


title: HepG2, 0uM 5-azacytidine, rep3, RNA-seq

description:
Library name: HepG2_0uM_rep3_RNA
HepG2 cells treated with 0 μM 5-azacytidine for 4 days (RNA-seq)

value: 0 μM 5-azacytidine for 4 days


title: HepG2, 0uM 5-azacytidine, rep2, RNA-seq

description:
Library name: HepG2_0uM_rep2_RNA
HepG2 cells treated with 0 μM 5-azacytidine for 4 days (RNA-seq)


title: P. promelas larvae, UP, biological replicate UP_Field52, lane 1, time step = NA, analyzed on 20160809

description: Library name: 20160809_ Up_Field_52_GGCTAC_L001_R1_001


title: ET0584132

value: PBMCs

value: highcardio


title: HepG2, 0uM 5-azacytidine, rep1, RNA-seq

description:
Library name: HepG2_0uM_rep1_RNA
HepG2 cells treated with 0 μM 5-azacytidine for 4 days (RNA-seq)

value: liver

value: hepatocyte


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

description:
Library name: RL119
Column names mean the following in the processed data file: target ID - ensembl transcript ID, length: transcript length, eff_length: effective transcript length (the adjusted transcript length used in abundance estimation, taking into account the fragment length distribution), est_counts - transcript counts, tpm - transcript counts normalized by effective length


title: P. promelas larvae, UP, biological replicate UP_Field2-d, lane 2, time step = NA, analyzed on 20160809

description: Library name: 20160809_ Up_Field_2-d_GAGTGG_L002_R1_001


title: ET0584128

value: hepatic


title: Neurons derived from familial control iPSC cells treated with 125 nM Omaveloxolone replicate 1

description:
Library name: RL118
Column names mean the following in the processed data file: target ID - ensembl transcript ID, length: transcript length, eff_length: effective transcript length (the adjusted transcript length used in abundance estimation, taking into account the fragment length distribution), est_counts - transcript counts, tpm - transcript counts normalized by effective length


title: P. promelas larvae, UP, biological replicate UP_B28, lane 2, time step = 4, analyzed on 20160809

description: Library name: 20160809_ Up_4_B28_ATCACG_L002_R1_001


title: A549 cells, shRAD21, Input

city: Beijing

first: Chu

last: Xiao

state: Beijing

address: Nanli panjiayuan, Chaoyang District, Beijing

department: Thoracic Surgery

institute: Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

description: Library name: A549_shRAD21, Input

library_source: genomic

data_processing:
The connector-including reads and low-quality reads were removed by Trimmomatic and clean data was obtained. Clean data was mapped to the human genome hg38 by Bowtie2 with default filtering criteria. PCR duplicates were further deleted using SAMtools (v1.9) and only high-quality reads were retained. Peak calling for ChIP-Seq data of H3K4me3 and RAD21 was performed with MACS3 and Input samples as reference controls for background correction.
Assembly: hg38
Supplementary files format and content: bw file (except for input sample)

growth_protocol: A549 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 ℃.

extract_protocol:
The chromatin immunoprecipitation was conducted with the simpleChIP Enzymatic Chromatin IP kit (#9003, CST) following the manufacturer's protocol.
ChIP-seq libraries were constructed with Ultra II DNA Library Kits (NEB, #E7645)according to the manufacturer’s instructions and sequenced on Illumina NovaSeq 6000 using the 150bp paired-end option.

value: lung adenocarcinoma cells

value: RAD21 knockdown

tag: chip antibody


title: P. promelas larvae, UP, biological replicate UP_Field2-d, lane 1, time step = NA, analyzed on 20160809

description: Library name: 20160809_ Up_Field_2-d_GAGTGG_L001_R1_001


title: ET0584122

value: healthy


title: ET0584127


title: A549 cells, shNC, Input

description: Library name: A549_shNC, Input

value: wild type


title: Neurons derived from familial control iPSC cells treated with DMSO replicate 3

description:
Library name: RL117
Column names mean the following in the processed data file: target ID - ensembl transcript ID, length: transcript length, eff_length: effective transcript length (the adjusted transcript length used in abundance estimation, taking into account the fragment length distribution), est_counts - transcript counts, tpm - transcript counts normalized by effective length

value: DMSO


title: Neurons derived from familial control iPSC cells treated with DMSO replicate 2

description:
Library name: RL116
Column names mean the following in the processed data file: target ID - ensembl transcript ID, length: transcript length, eff_length: effective transcript length (the adjusted transcript length used in abundance estimation, taking into account the fragment length distribution), est_counts - transcript counts, tpm - transcript counts normalized by effective length


title: A549 cells, shRAD21, H3K4me3(ChIP)

description: Library name: A549_shRAD21, ChIP of H3K4me3


title: ET0584119


title: P. promelas larvae, UP, biological replicate UP_B28, lane 1, time step = 4, analyzed on 20160809

description: Library name: 20160809_ Up_4_B28_ATCACG_L001_R1_001

value: whole larvae

value: 2 dpf


title: Neurons derived from familial control iPSC cells treated with DMSO replicate 1

description:
Library name: RL115
Column names mean the following in the processed data file: target ID - ensembl transcript ID, length: transcript length, eff_length: effective transcript length (the adjusted transcript length used in abundance estimation, taking into account the fragment length distribution), est_counts - transcript counts, tpm - transcript counts normalized by effective length

value: NGN2-driven glutamatergic neurons


title: ET0584174


title: P. promelas larvae, EFP, biological replicate EFP_Field48, lane 2, time step = NA, analyzed on 20160809

description: Library name: 20160809_ EFP_Field_48_ACTGAT_L002_R1_001

value: EFP


title: ADT expression CD34 cells samples treated by pan-cancer-exosomes and one untreated CD34 cells sample, Well6

city: Indiana University

first: Reza

last: Shahbazi

address: 980 W Walnut st

institute: Indiana University

description:
Library name: Well 6_FB
Anti-body expression of CD34 cells  samples treated by exosomes extracted from different cancers cell-lines and one untreated CD34 cells sample, Well6

library_source: other

data_processing:
All raw input data were distributed across 6 wells, meaning each well contained a portion of the sequencing data for all samples. The Cell Ranger pipeline (version 7.2.0) from 10x Genomics was used to process the raw sequencing data, including quality filtering, alignment to the human reference genome (GRCh38), cell barcode assignment, and generation of unique molecular identifier (UMI) counts to produce the gene expression matrix. Data from all wells were then aggregated to generate a unified H5 gene expression file for each individual sample.
Assembly: hg38
Supplementary files format and content: h5 files includes gene expression
Library strategy: CITE-seq

molecule: protein

source_name: CD34 cell

growth_protocol: Leukemia cell lines (HL60, MOLM-14, Jurkat, K562, RS4;11, CCRF-CEM, and MOLT-4) were cultured in RPMI-1640 medium (Gibco) supplemented with 10% exosome-depleted fetal bovine serum (Gibco) and 1% penicillin-streptomycin (Gibco) at 37°C in a humidified incubator with 5% CO₂. Cells were maintained in suspension and passaged every 2–3 days to maintain optimal density between 0.2–1 × 10⁶ cells/mL. For exosome collection, cells were grown to mid-log phase, and conditioned media was harvested after 48 hours for exosome isolation.

extract_protocol:
After incubation with exosomes, cells were harvested, washed, and stained with the TotalSeq™-C anti-human Hashtag antibodies (BioLegend), following the manufacturer’s recommended titration and staining protocol.The isolated RNA, was quantified using a NanoDrop spectrophotometer (Thermo Fisher Scientific), and RNA quality was assessed with an Agilent Bioanalyzer 2100 (Agilent Technologies).
For single cell RNA-seq, following staining, cells were counted and loaded onto the Chromium X system (10x Genomics) using the Chromium Single Cell 5′ High Throughput (HT) Immune Profiling Kit. Single-cell Gel Bead-In-Emulsions (GEMs) were generated, and barcoded cDNA libraries, including gene expression and antibody-derived tag (ADT) libraries, were constructed according to the manufacturer’s instructions. The resulting libraries were sequenced on an Illumina NovaSeq 6000 platform using an S4 flow cell to a targeted depth of ~50,000 reads per cell. For noncoding RNAs, library preparation was performed using the NEXTFLEX® Small RNA-Seq Kit v4 with Unique Dual Indices (UDIs) (Revvity), which includes 3′ and 5′ adapter ligation, reverse transcription, PCR amplification, and size selection steps optimized for non-coding RNA capture. Prepared libraries were quantified using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and validated for size distribution using the Agilent Bioanalyzer. Sequencing was conducted on an Illumina platform following standard procedures for small RNA libraries.

treatment_protocol: Human G-CSF-mobilized peripheral blood leukopaks (BIOIVT) were processed to isolate CD34⁺ hematopoietic stem and progenitor cells (HSPCs) using density gradient centrifugation and EasySep™ CD34 positive selection (Stem Cell Technologies). Isolated cells (>80% CD34⁺, >90% viability) were treated with leukemia-derived exosomes for 48 hours. Post-treatment, cells were stained with TotalSeq™-C antibodies and hashtags (BioLegend) and processed using the 10X Genomics 5’ HT Immune Profiling workflow. Libraries were sequenced on an Illumina NovaSeq S4 platform and aligned to the GRCh38 reference genome using CellRanger v7.2.0.

value: CD34 cell


title: ADT expression CD34 cells samples treated by pan-cancer-exosomes and one untreated CD34 cells sample, Well5

description:
Library name: Well 5_FB
Anti-body expression of CD34 cells  samples treated by exosomes extracted from different cancers cell-lines and one untreated CD34 cells sample, Well5


title: A549 cells, shNC, H3K4me3(ChIP)

description: Library name: A549_shNC, ChIP of H3K4me3


title: ET0584115

value: lipid


title: Patient12, MPR

city: Hangzhou

first: Yi

last: Xu

address: Qiutao Street 166

institute: Zhejiang University

description: Library name: Patient12

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: Female

tag: history

value: Yes

tag: smoking

value: No

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: A549 cells, shNC, RAD21(ChIP)

description: Library name: A549_shNC, ChIP of RAD21

tag: cell line

tag: cell type

value: lung adenocarcinoma cells

tag: genotype


title: ET0584118

value: PBMCs

tag: treatment

value: hepatic

tag: age

tag: age at menopause


title: ET0584116


title: A549 cells, shRAD21, RAD21(ChIP)

description: Library name: A549_shRAD21, ChIP of RAD21

value: RAD21 knockdown

tag: chip antibody

tag: batch


title: P. promelas larvae, EFP, biological replicate EFP_Field48, lane 1, time step = NA, analyzed on 20160809

description: Library name: 20160809_ EFP_Field_48_ACTGAT_L001_R1_001

tag: tissue

tag: treatment-replicate id

tag: treatment-time

tag: treatment-location


title: P. promelas larvae, EFP, biological replicate EFP_B28, lane 1, time step = 3, analyzed on 20160809

description: Library name: 20160809_ EFP_3_B28_ACTTGA_L001_R1_001


title: Patient05,non-MPR

description: Library name: Patient05

tag: individual

tag: ID

tag: gender

value: Male

tag: history

tag: smoking

tag: drinking

tag: site

tag: t stage

tag: n statge


title: ADT expression CD34 cells samples treated by pan-cancer-exosomes and one untreated CD34 cells sample, Well4

description:
Library name: Well 4_FB
Anti-body expression of CD34 cells  samples treated by exosomes extracted from different cancers cell-lines and one untreated CD34 cells sample, Well4

tag: cell type


title: P. promelas larvae, EFP, biological replicate EFP_B23, lane 2, time step = 2, analyzed on 20160809

description: Library name: 20160809_ EFP_2_B23_GTGGCC_L002_R1_001

value: whole larvae

tag: age


title: ET0584112

tag: treatment

tag: age at menopause


title: Patient04,non-MPR

description: Library name: Patient04

tag: tissue

tag: m stage

tag: clinical stage

tag: orr

tag: mpr


title: ET0584109

value: highcardio


title: ADT expression CD34 cells samples treated by pan-cancer-exosomes and one untreated CD34 cells sample, Well1

description:
Library name: Well 1_FB
Anti-body expression of CD34 cells  samples treated by exosomes extracted from different cancers cell-lines and one untreated CD34 cells sample, Well1


title: P. promelas larvae, EFP, biological replicate EFP_B28, lane 2, time step = 1, analyzed on 20160809

description: Library name: 20160809_ EFP_1_B28_TAGCTT_L002_R1_001

value: 2 dpf

tag: treatment-replicate id

tag: treatment-time

tag: treatment-location

tag: batch


title: ET0584107


title: Patient03,non-MPR

description: Library name: Patient03

tag: individual

tag: ID

tag: gender

tag: history

tag: smoking

tag: drinking


title: Gene expression of CD34 cells samples treated by pan-cancers-exosomes and one untreated CD34 cells sample, Well6

description:
Library name: Well 6_gex
Gene expression of CD34 cells  samples treated by exosomes extracted from different cancers cell-lines and one untreated CD34 cells sample, Well6

tag: cell type


title: Patient02,non-MPR

description: Library name: Patient02

tag: age

tag: site

tag: t stage

tag: n statge


title: ET0584105

tag: treatment

tag: age at menopause


title: Gene expression of CD34 cells samples treated by pan-cancers-exosomes and one untreated CD34 cells sample, Well5

description:
Library name: Well 5_gex
Gene expression of CD34 cells  samples treated by exosomes extracted from different cancers cell-lines and one untreated CD34 cells sample, Well5


title: Patient01,non-MPR

description: Library name: Patient01

tag: tissue

tag: m stage

tag: clinical stage

tag: orr

tag: mpr


title: P. promelas larvae, EFP, biological replicate EFP_B23, lane 1, time step = 2, analyzed on 20160809

description: Library name: 20160809_ EFP_2_B23_GTGGCC_L001_R1_001

tag: treatment-replicate id

tag: treatment-time

tag: treatment-location

value: EFP

tag: batch


title: ET058495

value: healthy


title: P. promelas larvae, DWIP, biological replicate DWIP_B27, lane 2, time step = NA, analyzed on 20160809

description: Library name: 20160809_ DWIP_B27_GTCCGC_L002_R1_001

value: DWIP


title: Gene expression of CD34 cells samples treated by pan-cancers-exosomes and one untreated CD34 cells sample, Well4

description:
Library name: Well 4_gex
Gene expression of CD34 cells  samples treated by exosomes extracted from different cancers cell-lines and one untreated CD34 cells sample, Well4

value: CD34 cell


title: HSC-3 cells, Microgravity (RCCS), biol rep3

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. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count. PCA analysis were performed using R(v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq2. Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) 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 3.2.0), respectively. R (v 3.2.0) 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

growth_protocol: HSC-3 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 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 OE Biotech Co., Ltd. (Shanghai, China). The libraries were sequenced on an llumina Novaseq 6000 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×.

treatment_protocol: Rotary Cell Culture System (RCCS) was used to simulate microgravity (as SMG group)

tag: cell line

value: Human Tumor cells of OSCC

value: Microgravity(RCCS)


title: ET058493

tag: cell type


title: P. promelas larvae, DWIP, biological replicate DWIP_B27, lane 1, time step = NA, analyzed on 20160809

description: Library name: 20160809_ DWIP_B27_GTCCGC_L001_R1_001

tag: age


title: Gene expression of CD34 cells samples treated by pan-cancers-exosomes and one untreated CD34 cells sample, Well3

description:
Library name: Well 3_gex
Gene expression of CD34 cells  samples treated by exosomes extracted from different cancers cell-lines and one untreated CD34 cells sample, Well3


title: HSC-3 cells, Microgravity (RCCS), biol rep2


title: P. promelas larvae, UP, biological replicate UP_Field2-c, lane 2, time step = NA, analyzed on 20160805

description: Library name: 20160805_ Up_Field_2-c_ACAGTG_L002_R1_001

value: UP


title: Gene expression of CD34 cells samples treated by pan-cancers-exosomes and one untreated CD34 cells sample, Well2

description:
Library name: Well 2_gex
Gene expression of CD34 cells  samples treated by exosomes extracted from different cancers cell-lines and one untreated CD34 cells sample, Well2


title: ET058485

value: lipid


title: ET058482


title: HSC-3 cells, Microgravity (RCCS), biol rep1


title: Gene expression of CD34 cells samples treated by pan-cancers-exosomes and one untreated CD34 cells sample, Well1

description:
Library name: Well 1_gex
Gene expression of CD34 cells  samples treated by exosomes extracted from different cancers cell-lines and one untreated CD34 cells sample, Well1

library_source: transcriptomic single cell

data_processing:
All raw input data were distributed across 6 wells, meaning each well contained a portion of the sequencing data for all samples. The Cell Ranger pipeline (version 7.2.0) from 10x Genomics was used to process the raw sequencing data, including quality filtering, alignment to the human reference genome (GRCh38), cell barcode assignment, and generation of unique molecular identifier (UMI) counts to produce the gene expression matrix. Data from all wells were then aggregated to generate a unified H5 gene expression file for each individual sample.
Assembly: hg38
Supplementary files format and content: h5 files includes gene expression


title: HSC-3 cells, Normal Gravity, biol rep 3

value: Normal Gravity


title: P. promelas larvae, UP, biological replicate UP_B17, lane 2, time step = 2, analyzed on 20160805

description: Library name: 20160805_ Up_2_B17_GTTTCG_L002_R1_001


title: ET058479


title: P. promelas larvae, UP, biological replicate UP_Field2-c, lane 1, time step = NA, analyzed on 20160805

description: Library name: 20160805_ Up_Field_2-c_ACAGTG_L001_R1_001


title: HSC-3 cells, Normal Gravity, biol rep 2


title: Huh7 cell line, FLAG tag knock-in, infected with lenti-VPS72-FLAG virus, H3K4me1 (ChIP)

description: Library name: VPS72-H3K4me1

data_processing:
Fastqc and Trimmomatic were applied for quality control and reads trimming. Then the trimmed reads were mapping to hg19 genome by BWA MEM. Finally chipseq peaks were called by MACS2. Bed/narrow peak results of five antibodies in two conditions (VPS72/FLAG) were put in the result folder.
Assembly: hg38
Supplementary files format and content: bigwig, narrowPeak (expect for Input Sample)

extract_protocol:
When the cells reached 90–100% confluency, they were washed twice with PBS and treated with DMEM containing 1% formaldehyde, followed by a 5 min incubation on a shaker. After this step, 900 µL of 2.5 M glycine was added, and the cells were incubated for an additional 5 min on a shaker. The cells were then washed twice with PBS, scraped off, and collected by centrifugation at 500 g for 5 min at 4 °C. They were resuspended in lysis buffer (85 mM KCl, 0.5% CA-630, 5 mM PIPES pH 8, 1 mM PMSF, and Pierce Protease and Phosphatase Inhibitor from Thermo) and sonicated for 150 s using the M220 Focused-ultrasonicator (Covaris, Woburn, MA, USA) at a peak power of 75 W, duty factor of 2%, 200 cycles/burst, and temperature maintained at 4 °C. Following sonication, the lysate was centrifuged at 1000 g for 5 min at 4 °C. The nuclear pellet was then resuspended in shearing buffer (10 mM Tris-HCl pH 8, 0.1% SDS, 1 mM EDTA pH 8, 1 mM PMSF, and Protease and Phosphatase Inhibitor) and subjected to sonication for 1560 s under the same conditions as before. After another centrifugation at 10,000 g for 10 min at 4 °C, the supernatant was collected. This supernatant was either stored as input or mixed with antibodies and incubated overnight on a shaker at 4 °C. After incubation, pre-blocked ChIP-grade Protein A/G Magnetic Beads (Thermo) were added and incubated on a shaker at 4 °C for 4 h. After this step, the beads were precipitated, and the supernatant was discarded. The beads were washed three times with sequential wash buffers: wash buffer I (150 mM NaCl, 20 mM Tris-HCl pH 8, 2 mM EDTA pH 8, 0.1% SDS, 1% Triton), wash buffer II (500 mM NaCl, 20 mM Tris-HCl pH 8, 2 mM EDTA pH 8, 0.1% SDS, 1% Triton), and wash buffer III (250 mM LiCl, 10 mM Tris-HCl pH 8, 1 mM EDTA pH 8, 1% sodium deoxycholate, 1% CA-630). The proteins were then eluted using elution buffer (1% SDS, 100 mM NaHCO3). All samples received a 5 M NaCl solution to achieve a final concentration of 0.2 M and were incubated overnight at 65 °C. After this incubation, the samples were treated with RNase A and Proteinase K, purified using the Monarch PCR & DNA Cleanup Kit (NEB)
DNA libraries were prepared by using NEBNext Ultra II DNA Library Prep Kit for Illu minaandlibrarysizewasselectedbyusingPromegaProNexSize-Selective Purification System.

treatment_protocol: For lentivirus packaging, psPAX2, pMD2.G to gether with the carrier plasmid were co-transfected into HEK293T cells in  a 2:1:2 mass ratio. Lentivirus was harvested 48 and 72h after transfection  by centrifuging at 500g for 5 min and filtering through a 0.45 um filter and preserved at -80 ℃.For infection, lentivirus was added into cell media and maintained for 24h. sgRNA targeting the end of protein-coding sequence of VPS72 gene was cloned into px459 vector for sgRNA and Cas9 expression. The neomycin resistant gene on pFETCh_Donor (EMM0021) (63 934, Addgene) was replaced by a Blasticidin (BSD) resistance gene, and the −800 and + 800 sequences flanking the stop codon of VPS72 were amplified by PCR and inserted into the upstream and downstream of FLAG-FLAG-FLAG-BSD cassette respectively to serve as the template for homology directed repair. The modified px459 and pFETCh plasmids were transfected into Huh7 cells at a 2:1 mass ratio with GenJet transfection reagent. A control group was included with the modified px459 and original pFETCh plasmids. BSD selection at a concentration of 2.5ug/ml was conducted from 72 h post-transfection and lasted for 14 days. Wild type Huh7 conditioned medium was used during BSD selection to support the growth of single cells, medium and BSD were replaced every 3 days. After BSD selection, the colonies that survived were transferred into 24-well plates for amplification and genotyping. The cells were maintained in 1ug/ml BSD.

value: human hepato cellular carcinoma cell line

tag: genotype

value: VPS77 overexpression with FLAG tag knock-in

value: FLAG tag knock-in, lentivirus infection

tag: antibody


title: P. promelas larvae, UP, biological replicate UP_B17, lane 1, time step = 2, analyzed on 20160805

description: Library name: 20160805_ Up_2_B17_GTTTCG_L001_R1_001


title: ET058476

value: PBMCs


title: Huh7 cell line, FLAG tag knock-in, infected with lenti-VPS72-FLAG virus, H3K27ac (ChIP)

description: Library name: VPS72-H3K27ac

value: VPS76 overexpression with FLAG tag knock-in


title: P. promelas larvae, EFP, biological replicate EFP_B28, lane 2, time step = 3, analyzed on 20160809

description: Library name: 20160809_ EFP_3_B28_ACTTGA_L002_R1_001

value: whole larvae


title: HSC-3 cells, Normal Gravity, biol rep 1


title: ET058475

value: highcardio


title: P. promelas larvae, UP, biological replicate UP_B23, lane 2, time step = 1, analyzed on 20160805

description: Library name: 20160805_ Up_1_B23_GTGAAA_L002_R1_001

value: 2 dpf


title: Huh7 cell line, FLAG tag knock-in, infected with lenti-VPS72-FLAG virus, H2A.Zac (ChIP)

description: Library name: VPS72-H2AZac

value: VPS75 overexpression with FLAG tag knock-in


title: PHLDA2_4

city: Irvine

first: Hannah

last: Savage

address: 839 Health Sciences Road

institute: University of California Irvine

data_processing:
Initial quality control of raw sequencing reads was conducted using FastQC
Sequence reads were aligned to the Homo sapiens reference genome (hg38) using HISAT2
Gene-level read counts were generated using featureCounts, counting only exonic regions
Differential gene expression analysis was performed with DESeq2, identifying differentially expressed genes (DEGs) with an FDR-corrected adjusted p-value < 0.05 and log2 fold change ≥ 0.5 for the PHLDA2 overexpression samples compared to GFP control samples
Low-count genes were filtered out before calculating reads per kilobase per million mapped reads (RPKM)
Only protein-coding genes with an average RPKM above 2 were included in volcano plots
Assembly: hg38
Supplementary files format and content: tab delimited text file including raw counts for each sample
Supplementary files format and content: tab delimited text file including RPKM and TPM values for each sample

source_name: HCI010 PDX cells

growth_protocol: HCI010 GFP or PHLDA2-GFP PDX cells were established with lentivirus transduction. Cell lines were maintained in NSG mice. Cells were injected into mammary fat pads to allow tumors to form. Passaging was performed approximately every 2 months.

extract_protocol:
Tumors were extracted from mice and digested into a single cell suspension. GFP+ tumor cells were isoalted with FACS. RNA isolation and bulk sequecing preparations were performed on sorted tumor cells.
Library construction was performed according to the Illumina TruSeq mRNA stranded protocol.  The input quantity for total RNA within the recommended range and mRNA was enriched using oligo dT magnetic beads. The enriched mRNA was chemically fragmented. First strand synthesis used random primers and reverse transcriptase to make cDNA. After second strand synthesis the ds cDNA was cleaned using AMPure XP beads and the cDNA was end repaired and then the 3’ ends were adenylated. Illumina barcoded adapters were ligated on the ends and the adapter ligated fragments were enriched by nine cycles of PCR. The resulting libraries were validated by qPCR and sized by Agilent Bioanalyzer DNA high sensitivity chip. The concentrations for the libraries were normalized and then multiplexed together. The multiplexed libraries were sequenced using paired end 100 cycles chemistry for the Illumina NovaSeq 6000.

value: HCI010 PDX cells

value: breast cancer

value: PHLDA2 overexpression + GFP


title: ET0584113

value: healthy


title: ET058418

value: hepatic


title: ET058470


title: PHLDA2_3


title: P. promelas larvae, UP, biological replicate UP_B23, lane 1, time step = 1, analyzed on 20160805

description: Library name: 20160805_ Up_1_B23_GTGAAA_L001_R1_001

value: UP


title: Huh7 cell line, FLAG tag knock-in, infected with lenti-VPS72-FLAG virus, H2A.Z (ChIP)

description: Library name: VPS72-H2AZ

value: VPS74 overexpression with FLAG tag knock-in


title: ADT expression CD34 cells samples treated by pan-cancer-exosomes and one untreated CD34 cells sample, Well3

description:
Library name: Well 3_FB
Anti-body expression of CD34 cells  samples treated by exosomes extracted from different cancers cell-lines and one untreated CD34 cells sample, Well3

value: CD34 cell


title: P. promelas larvae, EMZ, biological replicate EMZ_B27, lane 2, time step = NA, analyzed on 20160805

description: Library name: 20160805_ EMZ_B27_CTTGTA_L002_R1_001

value: EMZ


title: Huh7 cell line, FLAG tag knock-in, infected with lenti-VPS72-FLAG virus, FLAG (ChIP)

description: Library name: VPS72-Flag

value: human hepato cellular carcinoma cell line

value: VPS73 overexpression with FLAG tag knock-in

value: FLAG


title: ADT expression CD34 cells samples treated by pan-cancer-exosomes and one untreated CD34 cells sample, Well2

description:
Library name: Well 2_FB
Anti-body expression of CD34 cells  samples treated by exosomes extracted from different cancers cell-lines and one untreated CD34 cells sample, Well2


title: P. promelas larvae, EMZ, biological replicate EMZ_B27, lane 1, time step = NA, analyzed on 20160805

description: Library name: 20160805_ EMZ_B27_CTTGTA_L001_R1_001


title: PHLDA2_2


title: PBMC; SeqWell; Animal T625; Timepoint chronic; Array A2

city: Cambridge

first: Alex

last: Shalek

state: MA

address: 77 Massachusetts Ave

institute: Massachusetts Institute of Technology

description:
Library name: T625_chronic_A2
T625_chronic_A2

data_processing:
BCL files were converted to fastQs via Terra cumulus/bcl2fastq/5
For processed data: A custom genome combining  mmul10 and SIVmac251 was created using jgould/dropseq_bundle/10 (Terra). Alignment was performed using cumulus/dropseq_workflow/11 (Terra).
Assembly: custom mmul10 + SIVmac251
Supplementary files format and content: RDS, a seurat object of all cells combined from all samples directly following alignment (untrimmed, filtered)

organism: Macaca mulatta

source_name: PBMC

extract_protocol:
PBMC samples from rhesus macaque were processed for single-cell analysis using SeqWellS3 as described in Hughes, et al; Immunity 2020.
scRNAseq libraries were prepared via NexteraXT as described in Hughes, et al; Immunity 2020

value: PBMC

tag: animalid

tag: timepoint

value: chronic

tag: array

tag: assay

value: SeqWell

tag: hassiv

value: yes

tag: onart

value: no

tag: weekssinceinfection

tag: weeksonart


title: PHLDA2_1

value: HCI010 PDX cells


title: Huh7 cell line, FLAG tag knock-in, infected with lenti-VPS72-FLAG virus (Input)

description: Library name: VPS72-Input

value: VPS72 overexpression with FLAG tag knock-in

tag: treatment

value: FLAG tag knock-in, lentivirus infection

value: none; input


title: P. promelas larvae, EFP, biological replicate EFP_Field36, lane 1, time step = NA, analyzed on 20160805

description: Library name: 20160805_ EFP_Field_36_GCCAAT_L001_R1_001

tag: tissue

value: whole larvae

value: 2 dpf

tag: treatment-replicate id

tag: treatment-time

value: EFP


title: GFP_control_4

tag: cell line

value: breast cancer

value: GFP


title: P. promelas larvae, EFP, biological replicate EFP_Field36, lane 2, time step = NA, analyzed on 20160805

description: Library name: 20160805_ EFP_Field_36_GCCAAT_L002_R1_001

tag: treatment-location

tag: batch


title: PBMC; SeqWell; Animal T625; Timepoint chronic; Array A1

description:
Library name: T625_chronic_A1
T625_chronic_A1


title: GFP_control_3

tag: cell type

tag: genotype


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

description: Library name: 20161003_ UP_1_B26_ACTGAT_L001_R1_001

tag: age

value: UP


title: P. promelas larvae, EFP, biological replicate EFP_B28, lane 1, time step = 1, analyzed on 20160809

description: Library name: 20160809_ EFP_1_B28_TAGCTT_L001_R1_001


title: Ovary of mated Plutella xylostella biol rep 1

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: FRAS220302511-1r
H1

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: P. promelas larvae, UP, biological replicate UP_B30, lane 1, time step = 2, analyzed on 20161003

description: Library name: 20161003_ UP_2_B30_GGCTAC_L001_R1_001


title: P. promelas larvae, UP, biological replicate UP_B22, lane 1, time step = 4, analyzed on 20161003

description: Library name: 20161003_ UP_4_B22_GAGTGG_L001_R1_001


title: P11

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: sample11
Column name in raw_counts_All_Samples.txt: P11

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: Huh7 cell line, FLAG tag knock-in, infected with lenti-HA virus, H3K27ac (ChIP)

description: Library name: HA-H3K27ac

value: human hepato cellular carcinoma cell line

value: WT with FLAG tag knock-in

tag: antibody


title: CCTF1 overexpressed 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 3

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

organism: Saccharolobus islandicus REY15A

source_name: S. islandicus REY15A

growth_protocol: Strains of Sis/pSeSD(Cont) and Sis/pSeSD-CCTF1 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

value: CCTF1 overexpressed

value: Arabinose induction


title: Huh7 cell line, FLAG tag knock-in, infected with lenti-HA virus, H3K4me1 (ChIP)

description: Library name: HA-H3K4me1

value: FLAG tag knock-in, lentivirus infection


title: PBMC; SeqWell; Animal T625; Timepoint acute; Array A4

description:
Library name: T625_acute_A4
T625_acute_A4

value: PBMC

tag: animalid

tag: timepoint

value: acute

tag: array

tag: assay

value: SeqWell

value: yes

value: no


title: PBMC; SeqWell; Animal T625; Timepoint acute; Array A3

description:
Library name: T625_acute_A3
T625_acute_A3

tag: hassiv

tag: onart

tag: weekssinceinfection

tag: weeksonart


title: P. promelas larvae, DWIP, biological replicate DWIP_B22, lane 2, time step = NA, analyzed on 20160805

description: Library name: 20160805_ DWIP_B22_AGTCAA_L002_R1_001

tag: tissue

value: whole larvae

value: 2 dpf

tag: treatment-replicate id

tag: treatment-time

value: DWIP


title: Huh7 cell line, FLAG tag knock-in, infected with lenti-HA virus, H2A.Zac (ChIP)

description: Library name: HA-H2AZac

tag: cell line

tag: treatment


title: GFP_control_2

value: HCI010 PDX cells

tag: cell type

value: breast cancer

tag: genotype

value: GFP


title: PBMC; SeqWell; Animal T625; Timepoint ART2; Array A4

description:
Library name: T625_ART2_A4
T625_ART2_A4


title: P. promelas larvae, DWIP, biological replicate DWIP_B22, lane 1, time step = NA, analyzed on 20160805

description: Library name: 20160805_ DWIP_B22_AGTCAA_L001_R1_001

tag: age

tag: treatment-location

tag: batch


title: PBMC; SeqWell; Animal T625; Timepoint ART2; Array A3

description:
Library name: T625_ART2_A3
T625_ART2_A3

tag: animalid

tag: timepoint


title: Huh7 cell line, FLAG tag knock-in, infected with lenti-HA virus, FLAG (ChIP)

description: Library name: HA-Flag

value: human hepato cellular carcinoma cell line

tag: antibody

value: FLAG


title: PBMC; SeqWell; Animal T625; Timepoint ART1; Array A4

description:
Library name: T625_ART1_A4
T625_ART1_A4

tag: array

tag: assay

tag: hassiv


title: 93

city: Maastricht

first: Julian

last: Krauskopf

address: Universiteitssingel 50

country: Netherlands

institute: Maastricht University

data_processing:
Raw sequence reads were assessed for quality using FastQC. Low-quality reads and adapter sequences were trimmed using Trimmomatic with a quality score threshold of 20.
miRNA read counts were extracted using miRge2.
Assembly: miRBase v. 22
Supplementary files format and content: comma separated text files include raw counts for each sample.

molecule: other

source_name: plasma

extract_protocol:
RNA was harvested from plasma samples using the miRNeasy Serum/Plasma kit (Qiagen). A minimum of 1 ng RNA with a distinct 21-nucleotide peak was used for library construction.
RNA libraries for small RNA sequencing were prepared using the RealSeq®-small RNA sequencing library preparation kit (Somagenics) according to the manufacturer's protocols.

value: plasma

tag: Sex

value: Female

tag: exposure

value: High Exposure

value: 40 or Above

tag: bmi

value: Under weight


title: P. promelas larvae, MHW, biological replicate MHW_B22, lane 2, time step = NA, analyzed on 20160805

description: Library name: 20160805_ 15-07_B22_ATGTCA_L002_R1_001

tag: tissue

tag: treatment-replicate id

tag: treatment-time

value: MHW


title: P. promelas larvae, MHW, biological replicate MHW_B22, lane 1, time step = NA, analyzed on 20160805

description: Library name: 20160805_ 15-07_B22_ATGTCA_L001_R1_001


title: Huh7 cell line, FLAG tag knock-in, infected with lenti-HA virus, H2A.Z (ChIP)

description: Library name: HA-H2AZ

tag: cell line

tag: cell type

value: WT with FLAG tag knock-in

tag: treatment

value: FLAG tag knock-in, lentivirus infection


title: Ribosome protected fragments, MDA-MB-231 cells, AZD0095, replicate 3

first: Yichen

address: Yuhangtang Road 866

description: Library name: Sample 12

data_processing:
Low quality reads were filtered by fastp.61 Raw reads containing over 50% of low quality bases or over 10% of N bases were removed. Adapter sequences were trimmed and reads with length between 20-40bp were retained for subsequent analysis. Reads alignment tool Bowtie2 was used for mapping reads to ribosome RNA (rRNA) database, GenBank, Rfam database. The reads mapped to rRNAs, transfer RNAs (tRNA), small nuclear RNAs (snRNA), small nucleolar RNAs (snoRNA), and miRNA were removed. Processed RNA-seq reads were aligned to the genome using whole genome alignment by STAR with 2- pass setting enabled. The reads mapped to classical noncoding RNAs were abandoned. Remaining RFs were assigned to different genomic features (5’UTR, CDS, 3’UTR and intron) based on the position of the 5’ end of the alignment.
Assembly: hg38
Supplementary files format and content: Tab-delimited files containing ensembl ID, gene name and FPKM value for each sample
Library strategy: Ribo-Seq

growth_protocol: Cells were cultured in a 37°C 5% CO2 humidified incubator. The MDA-MB-231cells were cultured in DMEM medium supplemented with 10% FBS, GlutaMAX (1x) (Gibco), and Penicillin-Streptomycin (100 U/mL) (Gibco).

extract_protocol:
For RNA-seq samples, RNA were extracted directly using RNA Clean & Concentrator-25™ kit (Zymo Research, R1017); for Ribo-seq samples, after removing the nuclei and mitochondria from the 2 min 100 µg/ml cycloheximide treated cell lysate, to prepare ribosome footprints (RFs), 10 μL of RNase I (NEB) and 6 μL of DNase I (NEB) were added to 400μL of lysate for 45 min to digest mRNAs that are not protected by the ribosome. The digestion was stopped by adding 10 μL SUPERase-In RNase Inhibitor (Ambion, AM2696), followed by centrifuging to pellet ribosomes. Ribosome-protected fragments were purified by the RNA Clean & Concentrator-25™ kit (Zymo Research, R1017). rRNA was removed using the method reported previously. Briefly, short (50 - 80 bases) antisense DNA probes complementary to rRNA sequences was added to solution containing RFs, then RNase H (NEB) and DNase I (NEB) was added to digest rRNA and residual DNA probes. Finally, RFs were further purified using magnet beads (Vazyme).
Ribo-seq libraries were constructed using NEBNext® Multiple Small RNA Library Prep Set for Illumina® (catalog no.E7300S, E7300L). The 140-160bp size PCR products were enriched to generate a cDNA library

treatment_protocol: 10nM AZD0095 or DMSO were supplied to the cells for 4-hour before harvesting

value: human triple-negative breast cancer cell line


title: Huh7 cell line, FLAG tag knock-in, infected with lenti-HA virus (Input)

description: Library name: HA-Input

tag: genotype

value: none; input


title: PBMC; SeqWell; Animal T625; Timepoint ART1; Array A3

description:
Library name: T625_ART1_A3
T625_ART1_A3

value: PBMC

value: SeqWell

value: yes

tag: onart

tag: weekssinceinfection

tag: weeksonart


title: GFP_control_1

value: HCI010 PDX cells

value: breast cancer


title: P. promelas larvae, MHW, biological replicate MHW_B26, lane 1, time step = NA, analyzed on 20160805

description: Library name: 20160805_ 15-08_B26_AGTTCC_L001_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

tag: age

value: 2 dpf

tag: treatment-location

tag: batch


title: 89

value: plasma

value: Normal Weight


title: 8

value: Male

value: Medium Exposure

value: 16-25 years


title: ET0584166

value: PBMCs

value: highcardio

tag: age at menopause


title: Ribosome protected fragments, MDA-MB-231 cells, AZD0095, replicate 2

description: Library name: Sample 11


title: 87

tag: Sex

value: Female

value: High Exposure

value: 26-39 years


title: P. promelas larvae, UP, biological replicate UP_Field2-b, lane 2, time step = NA, analyzed on 20160804

description: Library name: 20160804_ Up_Field_2-b_GAGTGG_L002_R1_001

value: UP


title: liver/anterior intestine/gill, Day 14, 28 ppt, rep c

city: Fort Pierce

first: David

last: Bradshaw

state: FL

department: Aquaculture & Stock Enhancement

institute: Florida Atlantic University at Harbor Branch Oceanographic Institute

data_processing:
Qiagen CLC Genomics Step - The resulting paired-end reads were processed through Qiagen’s CLC Genomics Workbench for adapter trimming and elimination of low-quality reads (Qiagen, 2021). The filtered reads were then merged and mapped to a reference genome of a related species, the greater amberjack (Seriola dumerili; RefSeq: GCF_002206705.1), with > 75% mapping success. Gene expression values were calculated as transcripts per million (TPM) and identification of differentially expressed genes (DEGs) were conducted in the CLC Genomics Workbench.  DEGs were defined as biologically significant with an absolute fold change ≥2 and statistically significant with an FDR p-value ≤0.05 when compared to expression under control conditions (Day 0 or 28 ppt).
R Data Processing and Statistical Analysis -  Abundance tables and DEGs from CLC Genomics were uploaded into RStudio. Gene and transcript counts were variance stabilizing transformed for beta diversity analysis. These tables were converted into a Bray-Curtis dissimilarity matrix which was analyzed with principal coordinates of analysis (PCoA) and permutational analysis of variance (PERMANOVA). PRIMER7/PERMANOVA+ was used to conduct PERMANOVA analysis with Monte Carlo (MC) p-value. In order to discover general functional trends, DEGs underwent Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses via clusterProfiler.
Assembly: Seriola dumerili; RefSeq: GCF_002206705.1
Supplementary files format and content: VST_TX_Table.csv is the DESeq2 variance stabilizing transformed counts for transcripts
Supplementary files format and content: VST_GN_Table.csv is the DESeq2 variance stabilizing transformed counts for genes

organism: Trachinotus carolinus

source_name: Florida pompano

growth_protocol: Prior to initiation of the experiment, a total of 300 juvenile pompano (~5g) were transferred from their larviculture facility (Proaquatix, Vero Beach, FL) to a recirculating aquaculture system (RAS) tanks at 28 ppt at FAU-HBOI facilities. Salinity treatments included marine control (28 ppt), estuarine (20 ppt), isosmotic (12 ppt), and hypoosmotic (8 ppt) treatments. Each treatment was run in triplicate (n= 3, total 12 tanks) in a 300 L RAS tanks. In each tank, 25 fish were stocked to replicate production stocking densities. In order to avoid undue stress on the fish, salinities in the estuarine, isosmotic, and hypoosmotic tanks were lowered from marine (28 ppt) to their target salinities over the course of 4 days at the rate of -2 ppt, -4 ppt, and -5 ppt per day in estuarine, isosmotic, and hypoosmotic tanks, respectively. During this time, the 28 ppt marine control tanks underwent partial water changes to mimic water exchanges occurring in the estuarine, isosmotic, and hypoosmotic tanks. Target salinities were achieved and maintained through a combination of treated marine water and dechlorinated freshwater. Fish were fed commercially available fish pellets (provided by Proaquatix) at a rate of approximately 2% body weight per day.

extract_protocol:
In order to ensure sufficient RNA yields for transcriptomic analysis, the liver, anterior intestine, and gill lamellae (removed from three gill arches on the left side of the fish) were dissected and pooled in 1 mL cryovials, then flash frozen at -80oC. All samples were stored at -80oC until RNA extraction. RNA extractions were conducted on pooled gill lamellae, immune organs, and liver samples using Qiagen RNeasy kits (Qiagen, Hilden, Germany) according to manufacturer protocols. RNA quality and concentrations were determined using a Qubit Fluorometer 3 (Thermo Fisher Scientific, Waltham, MA) and a ThermoFisher NanoDrop Spectrophotometer 2000 (Thermo Fisher Scientific Inc., Waltham, MA). Extracted RNA for transcriptomics was flash frozen and shipped overnight on dry ice to Novogene (Sacramento, CA) for high throughput RNA sequencing.
Total RNA was used to create 21 poly-A enriched libraries that were then sequenced on an Illumina NovaSeq to generate 2 x 150 bp paired-ends sequencing reads.

treatment_protocol: In order to avoid undue stress on the fish, salinities in the estuarine, isosmotic, and hypoosmotic tanks were lowered from marine (28 ppt) to their target salinities over the course of 4 days at the rate of -2 ppt, -4 ppt, and -5 ppt per day in estuarine (20 ppt), isosmotic (12 ppt), and hypoosmotic (8 ppt) tanks, respectively. During this time, the 28 ppt marine control tanks underwent partial water changes to mimic water exchanges occurring in the estuarine, isosmotic, and hypoosmotic tanks. Target salinities were achieved and maintained through a combination of treated marine water and dechlorinated freshwater.

value: liver/anterior intestine/gill

value: Day 14, 28 ppt


title: liver/anterior intestine/gill, Day 14, 28 ppt, rep b


title: Ribosome protected fragments, MDA-MB-231 cells, AZD0095, replicate 1

description: Library name: Sample 10

value: human triple-negative breast cancer cell line


title: 85

tag: exposure

value: 40 or Above

value: Obese


title: P. promelas larvae, UP, biological replicate UP_Field2-b, lane 1, time step = NA, analyzed on 20160804

description: Library name: 20160804_ Up_Field_2-b_GAGTGG_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

value: 2 dpf


title: P. promelas larvae, UP, biological replicate UP_Field2-a, lane 2, time step = NA, analyzed on 20160804

description: Library name: 20160804_ Up_Field_2-a_ACTTGA_L002_R1_001


title: 84

value: plasma

tag: bmi


title: liver/anterior intestine/gill, Day 14, 20 ppt, rep c

tag: tissue

value: Day 14, 20 ppt


title: Ribosome protected fragments, MDA-MB-231 cells, DMSO, replicate 2

description: Library name: Sample 8

value: DMSO


title: liver/anterior intestine/gill, Day 14, 20 ppt, rep b


title: liver/anterior intestine/gill, Day 14, 28 ppt, rep a


title: Ribosome protected fragments, MDA-MB-231 cells, DMSO, replicate 1

description: Library name: Sample 7


title: liver/anterior intestine/gill, Day 14, 20 ppt, rep a


title: 83

value: Medium Exposure


title: P. promelas larvae, UP, biological replicate UP_Field1, lane 2, time step = NA, analyzed on 20160804

description: Library name: 20160804_ Up_Field_1_TAGCTT_L002_R1_001

tag: treatment-replicate id


title: 81

value: Normal Weight


title: total RNA, MDA-MB-231 cells, AZD0095, replicate 3

description: Library name: Sample 6

data_processing:
Low quality reads were filtered by fastp.61 Raw reads containing over 50% of low quality bases or over 10% of N bases were removed. Adapter sequences were trimmed and reads with length between 20-40bp were retained for subsequent analysis. Reads alignment tool Bowtie2 was used for mapping reads to ribosome RNA (rRNA) database, GenBank, Rfam database. The reads mapped to rRNAs, transfer RNAs (tRNA), small nuclear RNAs (snRNA), small nucleolar RNAs (snoRNA), and miRNA were removed. Processed RNA-seq reads were aligned to the genome using whole genome alignment by STAR with 2- pass setting enabled. The reads mapped to classical noncoding RNAs were abandoned. Remaining RFs were assigned to different genomic features (5’UTR, CDS, 3’UTR and intron) based on the position of the 5’ end of the alignment.
Assembly: hg38
Supplementary files format and content: Tab-delimited files containing ensembl ID, gene name and FPKM value for each sample


title: Ribosome protected fragments, MDA-MB-231 cells, DMSO, replicate 3

description: Library name: Sample 9


title: P. promelas larvae, UP, biological replicate UP_Field1, lane 1, time step = NA, analyzed on 20160804

description: Library name: 20160804_ Up_Field_1_TAGCTT_L001_R1_001

tag: treatment-time


title: liver/anterior intestine/gill, Day 14, 12 ppt, rep b

value: Day 14, 12 ppt


title: 80

value: Female


title: 7

value: Male

value: 16-25 years


title: P. promelas larvae, EFP, biological replicate EFP_Field2, lane 2, time step = NA, analyzed on 20160804

description: Library name: 20160804_ EFP_Field_2_GTCCGC_L002_R1_001

value: EFP


title: liver/anterior intestine/gill, Day 14, 12 ppt, rep a

value: liver/anterior intestine/gill


title: liver/anterior intestine/gill, Day 14, 8 ppt, rep c

value: Day 14, 8 ppt


title: total RNA, MDA-MB-231 cells, AZD0095, replicate 1

description: Library name: Sample 4

tag: cell line

value: human triple-negative breast cancer cell line


title: total RNA, MDA-MB-231 cells, DMSO, replicate 3

description: Library name: Sample 3

tag: cell type


title: 78

value: 40 or Above


title: P. promelas larvae, EFP, biological replicate EFP_Field1, lane 2, time step = NA, analyzed on 20160804

description: Library name: 20160804_ EFP_Field_1_GTGGCC_L002_R1_001


title: total RNA, MDA-MB-231 cells, DMSO, replicate 2

description: Library name: Sample 2

tag: treatment


title: 74

description: 74_ChahFatehwala_M_I5_L4_S55_R1_001.trim1


title: 76


title: P. promelas larvae, EFP, biological replicate EFP_Field1, lane 1, time step = NA, analyzed on 20160804

description: Library name: 20160804_ EFP_Field_1_GTGGCC_L001_R1_001


title: liver/anterior intestine/gill, Day 14, 8 ppt, rep a


title: P. promelas larvae, EFP, biological replicate EFP_B1, lane 2, time step = 4, analyzed on 20160804

description: Library name: 20160804_ EFP_4_B1_ATCACG_L002_R1_001


title: liver/anterior intestine/gill, Day 0, 20 ppt, rep c

value: Day 0, 20 ppt


title: liver/anterior intestine/gill, Day 0, 20 ppt, rep b


title: LDH mutant, bloomington food, repl LB3

city: Bloomington

first: Jason

middle: M

last: Tennessen

email: tennessenlab@gmail.com, tennlab@iu.edu, jtenness@iu.edu, tourigny@iu.edu

state: IN

address: 1001 E 3rd St

department: Biology

description:
Library name: GSF3528-MR12-mut-bloomington-repl-LB3
GSF3528_MR12_mut_bloomington_repl_LB3

data_processing:
Quantification via Salmon pseudoaligner
Normalization and differential expression via DESeq2
Assembly: BDGP6.32
Supplementary files format and content: tab-separated, transformed log counts from DESeq2

organism: Drosophila melanogaster

source_name: whole animal

growth_protocol: Control (Impl317/+) and Ldh (Impl317/16) mutant eggs were collected on M+Y food. After 40-44hrs, 50 larvae were transferred to each M+Y food plate and BDSC-F Cubes plate, kept at 25ºC.

extract_protocol:
Three biological replicates containing 25 mid-L2 (~60 hours AEL after egg-laying) larvae were collected from both plates and washed twice with ice-cold 1X PBS. Total RNA was extracted from homogenized samples using a RNeasy kit (Qiagen; 74104).
Illumina TruSeq Stranded mRNA Library Kit

value: whole animal

tag: genotype

value: LDH mutant (Impl3 17/16)

value: bloomington food

tag: replicate


title: H358 cells, shNC, rep2

description:
Library name: Control H358 cells of shRNA, rep2
column name in raw_counts_shRAD21_shNC_samples.xls: H358_NC_2

data_processing:
Raw data of fastq format was processed by fastp to remove low quality reads and adaptor reads. The clean data was mapped to the hg38 reference genome by HISAT2 (v2.0.5). Then the read counts of genes were obtained by featureCounts (v1.5.0-p3).
Assembly: hg38
Supplementary files format and content: xls files include raw count values for each sample

growth_protocol: A549 and H358 lung adenocarcinoma cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 ℃.

extract_protocol:
The total RNA of cells was extracted with TRIzol regent (Invitrogen) and the qualities of RNA were evaluated with Qubit3.0 and Agilent 2100 bioanalyzer.
RNA libraries for RNA-seq were constructed using a VAHTS Universal V6 RNA-seq Library Prep Kit (Vazyme) following manufacturer's protocols.

value: lung adenocarcinoma cells

value: wild type

value: April, 2024


title: LDH mutant, bloomington food, repl LB2

description:
Library name: GSF3528-MR11-mut-bloomington-repl-LB2
GSF3528_MR11_mut_bloomington_repl_LB2


title: liver/anterior intestine/gill, Day 0, 20 ppt, rep a


title: LDH mutant, bloomington food, repl LB1

description:
Library name: GSF3528-MR10-mut-bloomington-repl-LB1
GSF3528_MR10_mut_bloomington_repl_LB1


title: P. promelas larvae, DWIP, biological replicate DWIP_B1, lane 1, time step = NA, analyzed on 20160804

description: Library name: 20160804_ DWIP_B1_GGCTAC_L001_R1_001

value: whole larvae

value: 2 dpf

value: DWIP


title: P. promelas larvae, DWIP, biological replicate DWIP_B1, lane 2, time step = NA, analyzed on 20160804

description: Library name: 20160804_ DWIP_B1_GGCTAC_L002_R1_001


title: P. promelas larvae, EFP, biological replicate EFP_B1, lane 1, time step = 4, analyzed on 20160804

description: Library name: 20160804_ EFP_4_B1_ATCACG_L001_R1_001


title: LDH mutant, molasses + yeast, repl LM3

description:
Library name: GSF3528-MR09-mut-molasses-repl-LM3
GSF3528_MR09_mut_molasses_repl_LM3

value: molasses + yeast


title: H358 cells, shRAD21, rep3

description:
Library name: RAD21 knockdown in H358, rep3
column name in raw_counts_shRAD21_shNC_samples.xls: H358_SH_6

value: RAD21 knockdown


title: H358 cells, shRAD21, rep2

description:
Library name: RAD21 knockdown in H358, rep2
column name in raw_counts_shRAD21_shNC_samples.xls: H358_SH_5


title: liver/anterior intestine/gill, Day 0, 8 ppt, rep c

value: Day 0, 8 ppt


title: H358 cells, shRAD21, rep1

description:
Library name: RAD21 knockdown in H358, rep1
column name in raw_counts_shRAD21_shNC_samples.xls: H358_SH_4


title: het ctrl, bloomington food, repl CB3

description:
Library name: GSF3528-MR06-ctrl-bloomington-repl-CB3
GSF3528_MR06_ctrl_bloomington_repl_CB3

value: heterozygous control (Impl3 17/+)


title: liver/anterior intestine/gill, Day 0, 8 ppt, rep a

value: liver/anterior intestine/gill


title: A549 cells, EV, rep2

description:
Library name: Control A549 cells of OE, rep2
column name in raw_counts_RAD21OE_EV_samples.xls: A549_Ctrl_2


title: het ctrl, bloomington food, repl CB2

description:
Library name: GSF3528-MR05-ctrl-bloomington-repl-CB2
GSF3528_MR05_ctrl_bloomington_repl_CB2


title: kidney, HPC,renal ischemia–reperfusion injury,rep1

city: Xining

first: Drolma

last: Gomchok

address: No. 16 Kunlun Road

institute: Qinghai university

description: Library name: HR1

data_processing:
Raw sequencing reads were subjected to quality control to remove adaptor sequences, low-quality reads, and reads containing ambiguous bases. Clean reads were then mapped to the mouse reference genome using a standard RNA-seq alignment pipeline.
Gene-level read counts were generated using HTSeq-count, and gene expression abundance was calculated as fragments per kilobase of transcript per million mapped reads (FPKM).
Principal component analysis (PCA) was performed to evaluate sample clustering and biological reproducibility among groups. Differential gene expression analysis was conducted using DESeq2. Genes with an adjusted P value (q value) < 0.05 and a fold change > 2.0 or < 0.5 were considered differentially expressed genes.
Hierarchical clustering was performed to visualize expression patterns of differentially expressed genes across experimental groups.
Functional enrichment analysis of differentially expressed genes was performed using Gene Ontology, Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, and WikiPathways databases. Gene set enrichment analysis (GSEA) was further performed to evaluate coordinated pathway-level changes.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: kidney

extract_protocol:
Total RNA was extracted from frozen renal tissues using TRIzol reagent according to the manufacturer's instructions. RNA purity and concentration were assessed using a NanoDrop 2000 spectrophotometer, and RNA integrity was evaluated using an Agilent 2100 Bioanalyzer. Only RNA samples meeting the quality-control criteria were used for library construction.
RNA-seq libraries were prepared using the VAHTS Universal V10 RNA-seq Library Prep Kit according to the manufacturer's protocol. Sequencing was performed on a DNBSEQ-T7 platform.

value: kidney

value: WT

value: Hypoxic preconditioning followed by renal ischemia–reperfusion injury


title: H358 cells, shNC, rep1

description:
Library name: Control H358 cells of shRNA, rep1
column name in raw_counts_shRAD21_shNC_samples.xls: H358_NC_1


title: P. promelas larvae, MHW, biological replicate MHW_B1, lane 2, time step = NA, analyzed on 20160804

first: Steven

description: Library name: 20160804_ 15-08_B1_ACTGAT_L002_R1_001

value: MHW


title: liver/anterior intestine/gill, Day 0, 12 ppt, rep b

value: Day 0, 12 ppt


title: kidney, HPC, sham control, rep3

description: Library name: HS3

value: Hypoxic preconditioning sham control


title: liver/anterior intestine/gill, Day 0, 8 ppt, rep b


title: kidney, HPC,renal ischemia–reperfusion injury,rep3

description: Library name: HR3


title: kidney, HPC,renal ischemia–reperfusion injury,rep2

description: Library name: HR2


title: het ctrl, molasses + yeast, repl CM3

description:
Library name: GSF3528-MR03-ctrl-molasses-repl-CM3
GSF3528_MR03_ctrl_molasses_repl_CM3

value: whole animal


title: Kupffer cells, 2h post Sham (control), replicate 2

city: Gent

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

description: Library name: SHAM-2

data_processing:
Reads were quality checked with fastQC and no further processing was required
Reads were mapped to the mm39 reference genome with STAR (2.7.10b) and the gencode M30. Read counts were directly obtained using the the featurecounts package
Differential expression analysis was done using the DESeq2 package, with the FDR set at 5%
Assembly: mm39
Supplementary files format and content: tab delimited count matrix with the raw counts per sample

growth_protocol: All mice were housed in individually ventilated cages at conventional housing conditions (22°C, 14/10h light/dark cycle, dark phase starting at 9 p.m.) in a specific pathogen-free facility. Food (chow diet consisting of 18% proteins, 4.5% fibers, 4.5% fat and 6.3% ashes, Provimi Kliba SA) and water were given at libitum

extract_protocol:
Total RNA was isolated with Aurum Total RNA mini Kit (Bio-Rad) following the manufacturer’s instructions
Library preparation was done using the illumina truseq stranded library kit for sequencing with a Cloudbreak sequencing kit on the element AVITI according the the manufacturer's instructions

treatment_protocol: Mice were subject to CLP or sham surgery and 2 hours later livers were isolated and prepared for FACS to isolate KCs

value: liver

value: Kupffer cell

value: WT C57BL/6J

value: Sham


title: A549 cells, RAD21OE, rep2

description:
Library name: RAD21 overexpression in A549, rep2
column name in raw_counts_RAD21OE_EV_samples.xls: A549_OE_2

value: lung adenocarcinoma cells

value: RAD21 overexpression


title: het ctrl, molasses + yeast, repl CM2

description:
Library name: GSF3528-MR02-ctrl-molasses-repl-CM2
GSF3528_MR02_ctrl_molasses_repl_CM2

value: molasses + yeast


title: kidney, HPC, sham control, rep1

description: Library name: HS1


title: Kupffer cells, 2h post Sham (control), replicate 1

description: Library name: SHAM-1


title: A549 cells, RAD21OE, rep1

description:
Library name: RAD21 overexpression in A549, rep1
column name in raw_counts_RAD21OE_EV_samples.xls: A549_OE_1


title: Kupffer cells, 2h post Sham (control), replicate 3

description: Library name: SHAM-3


title: A549 cells, RAD21OE, rep3

description:
Library name: RAD21 overexpression in A549, rep3
column name in raw_counts_RAD21OE_EV_samples.xls: A549_OE_3


title: P. promelas larvae, MHW, biological replicate MHW_B26, lane 2, time step = NA, analyzed on 20160805

city: Durham

last: Purucker

address: 109 TW Alexander Dr

description: Library name: 20160805_ 15-08_B26_AGTTCC_L002_R1_001

value: whole larvae

value: 2 dpf


title: A549 cells, shNC, rep3

description:
Library name: Control A549 cells of shRNA, rep3
column name in raw_counts_shRAD21_shNC_samples.xls: A549_NC_3

value: wild type

value: April, 2024


title: kidney, HPC, sham control, rep2

description: Library name: HS2

value: kidney

value: WT


title: PBMC; SeqWell; Animal T627; Timepoint chronic; Array A2

description:
Library name: T627_chronic_A2
T627_chronic_A2

value: PBMC

tag: animalid

tag: timepoint

value: chronic

tag: array

tag: assay

value: SeqWell

tag: hassiv

value: yes

tag: onart

value: no

tag: weekssinceinfection


title: kidney,no HPC,renal ischemia–reperfusion injury,rep2

description: Library name: NR2

value: renal ischemia–reperfusion injury

tag: batch


title: P. promelas larvae, UP, biological replicate UP_Field2-a, lane 1, time step = NA, analyzed on 20160804

description: Library name: 20160804_ Up_Field_2-a_ACTTGA_L001_R1_001

tag: age

tag: treatment-location

value: UP


title: Kupffer cells, 2h post CLP, replicate 3

description: Library name: CLP-3

tag: tissue

value: liver

value: Kupffer cell

value: WT C57BL/6J

value: CLP


title: total RNA, MDA-MB-231 cells, AZD0095, replicate 2

description: Library name: Sample 5

value: human triple-negative breast cancer cell line


title: PBMC; SeqWell; Animal T627; Timepoint chronic; Array A1

description:
Library name: T627_chronic_A1
T627_chronic_A1

tag: weeksonart


title: kidney,no HPC,renal ischemia–reperfusion injury,rep1

description: Library name: NR1


title: A549 cells, shNC, rep2

description:
Library name: Control A549 cells of shRNA, rep2
column name in raw_counts_shRAD21_shNC_samples.xls: A549_NC_2

tag: cell line

value: lung adenocarcinoma cells


title: liver/anterior intestine/gill, Day 14, 8 ppt, rep b

value: liver/anterior intestine/gill

value: Day 14, 8 ppt


title: Kupffer cells, 2h post CLP, replicate 2

description: Library name: CLP-2

tag: cell type


title: P. promelas larvae, EFP, biological replicate EFP_Field2, lane 1, time step = NA, analyzed on 20160804

description: Library name: 20160804_ EFP_Field_2_GTCCGC_L001_R1_001

value: whole larvae

value: 2 dpf

tag: treatment-replicate id

tag: treatment-time

value: EFP


title: 59

value: plasma

tag: Sex

value: Male

tag: exposure

value: Medium Exposure

value: 40 or Above

tag: bmi

value: Normal Weight


title: total RNA, MDA-MB-231 cells, DMSO, replicate 1

description: Library name: Sample 1

tag: treatment

value: DMSO


title: het ctrl, molasses + yeast, repl CM1

description:
Library name: GSF3528-MR01-ctrl-molasses-repl-CM1
GSF3528_MR01_ctrl_molasses_repl_CM1

value: whole animal

tag: genotype

value: heterozygous control (Impl3 17/+)

value: molasses + yeast

tag: replicate


title: A549 cells, shNC, rep1

description:
Library name: Control A549 cells of shRNA, rep1
column name in raw_counts_shRAD21_shNC_samples.xls: A549_NC_1

value: wild type

value: April, 2024


title: H358 cells, shNC, rep3

description:
Library name: Control H358 cells of shRNA, rep3
column name in raw_counts_shRAD21_shNC_samples.xls: H358_NC_3

value: lung adenocarcinoma cells


title: kidney, no HPC, sham control, rep3

description: Library name: NS3

value: kidney

value: WT

value: sham control


title: Kupffer cells, 2h post CLP, replicate 1

description: Library name: CLP-1

value: liver

value: Kupffer cell

value: WT C57BL/6J

value: CLP


title: A549 cells, shRAD21, rep3

description:
Library name: RAD21 knockdown in A549, rep3
column name in raw_counts_shRAD21_shNC_samples.xls: A549_SH_6

value: RAD21 knockdown


title: PBMC; SeqWell; Animal T627; Timepoint acute; Array A1

description:
Library name: T627_acute_A1
T627_acute_A1

value: PBMC

tag: animalid

tag: timepoint

value: acute

tag: array

tag: assay

value: SeqWell

tag: hassiv

value: yes

tag: onart

value: no


title: kidney, no HPC, sham control, rep2

description: Library name: NS2

tag: tissue

tag: batch


title: RPM, 2h post Sham (control), replicate 4

description: Library name: Sham-4

source_name: spleen

treatment_protocol: Mice were subject to CLP or sam surgery and 2 hours later spleend were isolated and prepared for FACS to isoate RPMs

value: spleen

tag: cell type

value: red pulp macrophage

value: Sham


title: A549 cells, shRAD21, rep2

description:
Library name: RAD21 knockdown in A549, rep2
column name in raw_counts_shRAD21_shNC_samples.xls: A549_SH_5

tag: cell line

value: lung adenocarcinoma cells

value: April, 2024


title: PBMC; SeqWell; Animal T627; Timepoint ART2; Array A4

description:
Library name: T627_ART2_A4
T627_ART2_A4

tag: weekssinceinfection

tag: weeksonart


title: RPM, 2h post Sham (control), replicate 3

description: Library name: Sham-3


title: RPM, 2h post Sham (control), replicate 2

description: Library name: Sham-2


title: Leaves, pip2-7 KO, Rep2

city: Bengaluru

first: Shivaprasad

last: Padubidri V.

state: Karnataka

address: GKVK Campus, Bellary Road

country: India

institute: National Centre for Biological Sciences, TIFR

description: Indica Rice, Pusa Basmati-1 (PB-1)

data_processing:
The raw reads were quality and adapter trimmed using TrimGalore (-q 20 -length 30)
Single-end RNA-seq reads were aligned to the rice IRGSP-1.0 genome using Hisat2 (--dta-cufflinks --max-intronlen 20000 --secondary --phred33 -k 20 -q -U).
Differetial expression analysis was performed using Cuffdiff (v2.2.1) as mentioned in Cole Trapnell et al, 2012.
Raw read counts per gene was calculated using featureCounts (Liao Y et al., 2013)
Supplementary files format and content: FPKM values of the genes obtained using Cuffdiff and featureCounts output are provided in tsv format

organism: Oryza sativa

source_name: 2.5-month-old PIP2-7 KO Leaves

growth_protocol: Regenerated and rooted transgenics were transferred to soil and kept for acclimatization for 3-5 days in plant growth chamber (16/8 hr light /Dark cycle, 70% RH, 24°C Temperature). The plants were then transferred to bigger pots in transgenic green house with the same conditions.

extract_protocol:
Total RNA from vegetative leaves were extracted using Trizol (Invitrogen) reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Samples were collected equally at 2.5 months post transfer to Green house.

tag: variety

value: Pusa Basmati-1 (PB-1)

value: pip2-7 KO

value: Leaves


title: Leaves, pip2-7 KO, Rep1

description: Indica Rice, Pusa Basmati-1 (PB-1)


title: RPM, 2h post Sham (control), replicate 1

description: Library name: Sham-1