title: QX569

description: Library name: E16


title: Z0684_CiPSC-4 rep2

status: Public on Jul 30 2025

type: SRA

city: Beijing

first: Ruoqi

last: Cheng

state: Beijing

address: NO.5, Yiheyuan Road, Haidian District

department: School of Life Sciences

country: China

institute: Peking University

description:
Library name: Z0684_CiPSC-4 rep2
column name in counts.csv: Z0684_CiPSC-4#-2

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low quality data by Trimmomatic v0.39, then mapped to hg38 whole genome using STAR v2.7.10b and annotated using gencode v47 gtf file.
sam file generated by STAR was converted to bam and counts were generated using featureCounts v2.0.6.
Assembly: hg38
Supplementary files format and content: csv file with raw gene counts for every gene and every sample.

molecule: total RNA

organism: Homo sapiens

source_name: induced from EPC

extract_protocol:
Total RNA was extracted utilizing the TGuide S32 Blood/Cell/Tissue RNA kit in conjunction with the TGuide S32 nucleic acid extractor.
For the preparation of RNA-seq libraries, the NEBNext Ultra RNA Library Prep Kit for Illumina (provided by New England BioLabs, catalog number E7775) was used. The resultant libraries, comprising fragmented and randomly primed RNA molecules, were sequenced as paired-end reads of 2 x 150 base pairs

tag: tissue

value: induced from EPC

tag: cell line

tag: cell type

value: EPC derived hCiPSC

tag: genotype

value: WT


title: 261304

type: protein

city: San Francisco

first: Denise

middle: M

last: Wolf

state: CA

address: 2340 Sutter st

country: USA

institute: University of California, San Francisco

data_processing: Samples from the Ganitumab arm, and a subset the control arm patients, were assayed on a new RPPA array (RPPA.4).  three different RPPA arrays (RPPA.1, RPPA.2 and RPPA.3) under GPL28470.  This RPPA array (containing over 100 samples across HR/HER2 subtypes) was standardized as follows: (1) sample w/out replacement 5000 times, maintaining a receptor subtype balance equal to that of the first ~1000 patients (HR+HER2-: 0.384, TN:0.368, HR+HER2+:0.158, HR-HER2+:0.09); (2) calculate the mean(mean) and mean(sd) for each RPPA endpoint over the samples; (3) standardize each endpoint of the array, as y=(x-mean(mean))/mean(sd).  These standardized data were then combined with controls assayed on RPPA arrays RPPA.1, RPPA.2, and RPPA.3, each normalized in the same way.  This procedure resulted in removal of batch effects, without 'warping' due to mismatches in subtype prevalence.

molecule: protein

source_name: primary breast cancer

value: primary breast cancer

tag: arm (short name)

value: Ganitumab

tag: arm

value: Paclitaxel + Ganitumab

tag: hr

tag: pcr


title: Z0684_CiPSC-1 rep2

description:
Library name: Z0684_CiPSC-1 rep2
column name in counts.csv: Z0684_CiPSC-1#-2


title: 955035


title: 890372


title: 212307


title: Z0684_CiPSC-1 rep1

description:
Library name: Z0684_CiPSC-1 rep1
column name in counts.csv: Z0684_CiPSC-1#-1


title: QX500

city: Lausanne

first: Xiaoxu

last: Li

address: Station 15 - CH

country: Switzerland

institute: EPFL

description: Library name: D4

data_processing:
FastQC (default parameters) was used to verify the quality of the reads. No low-quality reads were present and no trimming was needed.
Alignment was performed against worm genome (WBcel235 sm-toplevel) following the STAR (version 2.73a) manual guidelines
Counts for each sample features (outputed by STAR) where read into R
Assembly: WBcel235 sm-toplevel
Supplementary files format and content: processed_data_GEO_upload.xlsx

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans

growth_protocol: For both the RIAILs and wild-type N2 validation experiments, 5–10 L4-stage worms were transferred onto RNAi plates (containing 2 mM IPTG and 25 µg/mL carbenicillin) seeded with E. coli HT115, with 15 µg/mL doxycycline (Dox; Sigma, Cat. D9891). Once F1 progeny reached the L4 stage, worms were transferred to corresponding plates supplemented with 10 µM 5-fluoro-2’-deoxyuridine (5FU) to prevent progeny production. The L4 stage was defined as day 2 of life

extract_protocol:
On the day of the extraction, 1 mL of TriPure Isolation Reagent was added to each tube. The samples were then frozen and thawed quickly eight times with liquid nitrogen and 37ºC water bath to rupture cell membranes. RNA was then extracted by using a column-based kit from Macherey-Nagel.
BGISeq-500 library construction Protocol

value: Caenorhabditis elegans

tag: treatment

value: Doxycycline


title: Z0684-EPC rep2

description:
Library name: Z0684-EPC rep2
column name in counts.csv: Z0684-EPC-1

source_name: human blood cells

value: human blood cells

value: erythroid progenitor cells (EPC)


title: 277888


title: QX495

description: Library name: E10


title: 100899


title: N2_batch2

description: Library name: D38


title: YB3272-EPC rep2

description:
Library name: YB3272-EPC rep2
column name in counts.csv: YB3272-EPC-2


title: QX520

description: Library name: D36


title: 318407


title: QX518

description: Library name: D32


title: YB3272-CiPSC-4 rep2

description:
Library name: YB3272-CiPSC-4 rep2
column name in counts.csv: YB3272_CiPSC-4#-2


title: YB3272-EPC rep1

description:
Library name: YB3272-EPC rep1
column name in counts.csv: YB3272-EPC-1


title: 516834


title: 435279


title: QX517

description: Library name: D28


title: 564701


title: YB3272-CiPSC-4 rep1

description:
Library name: YB3272-CiPSC-4 rep1
column name in counts.csv: YB3272_CiPSC-4#-1


title: QX516

description: Library name: D30


title: YB3272-CiPSC-3 rep2

description:
Library name: YB3272-CiPSC-3 rep2
column name in counts.csv: YB3272_CiPSC-3#-2


title: QX514

description: Library name: D24


title: YB3272-CiPSC-3-15 rep2

description:
Library name: YB3272-CiPSC-3-15 rep2
column name in counts.csv: YB3272-CiPSC-3-15-2

value: teratoma derived from hCiPSC


title: 928446


title: QX512

description: Library name: D22


title: 317131


title: YB3272-CiPSC-3 rep1

description:
Library name: YB3272-CiPSC-3 rep1
column name in counts.csv: YB3272_CiPSC-3#-1


title: 524170


title: QX510

description: Library name: D18


title: 898618


title: 804979


title: QX509

description: Library name: D16


title: YB3271-EPC rep1

description:
Library name: YB3271-EPC rep1
column name in counts.csv: YB3271-EPC-1


title: QX506

description: Library name: D14


title: YB3271-CiPSC-7 rep2

description:
Library name: YB3271-CiPSC-7 rep2
column name in counts.csv: YB3271_CiPSC-7#-2


title: QX511

description: Library name: D20


title: QX505

description: Library name: D12


title: 165925


title: 296123


title: 870077


title: YB3272-CiPSC-3-15 rep1

description:
Library name: YB3272-CiPSC-3-15 rep1
column name in counts.csv: YB3272-CiPSC-3-15-1


title: YB3271-CiPSC-7-14 rep2

description:
Library name: YB3271-CiPSC-7-14 rep2
column name in counts.csv: YB3271-CiPSC-7-14-2


title: QX504

description: Library name: D10


title: 412772


title: YB3271-CiPSC-7-14 rep1

description:
Library name: YB3271-CiPSC-7-14 rep1
column name in counts.csv: YB3271-CiPSC-7-14-1


title: 760901


title: YB3271-CiPSC-7-13 rep2

description:
Library name: YB3271-CiPSC-7-13 rep2
column name in counts.csv: YB3271-CiPSC-7-13-2


title: 531988


title: CB4856_batch1

description: Library name: C2


title: QX539

description: Library name: C6


title: YB3271-CiPSC-7-13 rep1

description:
Library name: YB3271-CiPSC-7-13 rep1
column name in counts.csv: YB3271-CiPSC-7-13-1


title: 264305


title: YB3271-CiPSC-6-8 rep2

description:
Library name: YB3271-CiPSC-6-8 rep2
column name in counts.csv: YB3271-CiPSC-6-8-2


title: WT Experiment (no-sgRNA) sample 4, Soma Fraction

city: Rockville

first: Veronica

last: Ryan

state: MD

address: 9000 Rockville Pike

department: Center for Alzheimer's and Related Dementias, Alzheimer's and Related Dementias Independent Scholar

institute: National Institute on Aging

description: Library name: soma.4

data_processing:
WT sample reads were deduplicated based on the entire read sequence; RBP KD samples were deduplicated using the 8-nt UMI at the start of R2. Following deduplication, the remaining 6 nt linker on R2 was then trimmed. Reads were aligned using STAR v2.7.11b  to GENCODE release 45 with primary assembly annotation. Optical duplicates were marked using picardtools MarkDuplicates v3.2.0. Gene counts were quantified using the featureCounts module of subread v 2.0.6 with the following parameters: counting paired-end reads as a single entity instead of fragments (-p --countReadPairs); ignoring marked duplicates (--ignoreDup); including multimapping reads with fractional count assignment (-M --fraction); assign to exon features (-t exon); summarize at gene-level meta feature (-g gene_id). Fractional read counts were rounded to the nearest integer.
Assembly: hg38 GENCODE v45
Supplementary files format and content: csv, ENSEMBL gene-level feature counts per sample

growth_protocol: iPSCs were grown as established in Essential 8 media. As appropriate, sgRNAs were transduced and iPSCs were selected for cells with successful transduction. Cells were split with accutase and replated in doxycyline-containing induction media to initiate neuronal differentation, as established. on d3 post dox induction, neurons were split to PLO and laminin coated 6-well cell culture inserts with 1 µm pore size transparent PET membranes. On day 17 post dox induction, neurons were harvested.

extract_protocol:
RNA was collected using the Qiagen RNeasy Miniprep kit following manufacterers instructions.
10 ng of RNA per sample was used with the Takara Total RNA-seq Kit v2 - Pico Input Mammalian (634413) for WT samples and Takara Total RNA-seq Kit v3 - Pico Input Mammalian (634485) for RBP KD samples and followed manufacturer instructions.

tag: fraction

value: Soma

value: no-sgRNA


title: 130580


title: QX564

description: Library name: C24


title: YB3271-CiPSC-7 rep1

description:
Library name: YB3271-CiPSC-7 rep1
column name in counts.csv: YB3271_CiPSC-7#-1


title: QX538

description: Library name: C4


title: QX563

description: Library name: C22


title: YB3271-CiPSC-6-8 rep1

description:
Library name: YB3271-CiPSC-6-8 rep1
column name in counts.csv: YB3271-CiPSC-6-8-1


title: 800447


title: QX562

description: Library name: C20


title: YB3271-CiPSC-6-7 rep2

description:
Library name: YB3271-CiPSC-6-7 rep2
column name in counts.csv: YB3271-CiPSC-6-7-2


title: 417474


title: QX540

description: Library name: C8


title: YB3271-EPC rep2

description:
Library name: YB3271-EPC rep2
column name in counts.csv: YB3271-EPC-2


title: Dorsal skin, sample 6

city: Davis

first: Robert

last: Rice

state: California

address: 4139 Meyer Hall, One Shields Avenue

department: Environmental Toxicology

institute: UC Davis

description:
Library name: WDS1
Column name in Rice_Sturgeon_Isoseq_transcript_counts.filtered.txt: 6_WDS1_bc1019
White_Species_Consensus_Transcripts.fasta

data_processing:
Raw sequencing data were analyzed according to the IsoSeq3 pipeline (v3.4.0, https://isoseq.how/) and aligned to the Sterlet genome (ASM1064508v1).
Resulting transcripts were classified and filtered using the default criteria within Sqanti3 (v4.1) with the exception of the splice junction coverage filter, which was replaced by a minimum supporting reads filter (>= 3).
The command line implementation of blastp (v2.14.1+) was used to align the translated transcripts to the protein sequences of the Sterlet genome for functional annotation.
Alignments with an e-value less than 0.01 and at least 80% sequence identity were considered significant.
Assembly: ASM1064508v1
Supplementary files format and content: Fasta
Supplementary files format and content: counts table in .txt format

molecule: polyA RNA

organism: Acipenser transmontanus

source_name: Dorsal Skin

growth_protocol: Tissue explants were permitted to expand to confluence in DMEM/F12 with 5% FBS plus Y27632, EGF, hydrocortisone, insuliin, transferrin, adenine, amphotericin B, ciprofloxicin.

extract_protocol:
RNA was harvested in RLT Plus lysis buffer (Qiagen) and extracted with the RNeasy Plus Mini kits (Qiagen) using gDNA eliminator columns. RNA was extracted from tissue in the same way after disruption with an Omni Bead Ruptor 24. RNA integrity was verified by Nanodrop 1000 befor library contsruction.
cDNA and SMRTbell libraries were constructed using 300 ng of total RNA for cDNA construction with the NEBNext® Single Cell/Low Input cDNA Synthesis & Amplification Module (New England Biolabs, Ipswich, MA; Cat. #E6421L). After 15 cycles of PCR amplification, cDNA was purified using 0.86X SMRTbell cleanup beads. cDNA libraries were pooled for SMRTbell library construction using the SMRTbell prep kit 2.0 or 3.0 (Pacific Biosciences, Menlo Park, CA) with repair and A-tailing, overhang adapter ligation, and nuclease treatment. The Iso-Seq SMRTbell library was sequenced at UC Davis DNA Technologies Core (Davis, CA) using one 8M SMRT cell (Pacific Biosciences, Menlo Park, CA; Cat #101-389-001), Sequel II sequencing chemistry 2.0, and 24-hour movies on a PacBio Sequel II sequencer. cDNA preparation, amplification, and library prep were performed with the Iso-Seq Express Oligo Kit (PacBio) and SMRTbell Prep Kit 3.0 (PacBio).

value: Dorsal Skin

value: Octoploid

tag: batch


title: Esophagus-White, sample 5

description:
Library name: WE1
Column name in Rice_Sturgeon_Isoseq_transcript_counts.filtered.txt: 5_WE1_bc1018
White_Species_Consensus_Transcripts.fasta

source_name: Esophagus

value: Esophagus


title: CB4856_batch2

description: Library name: E2


title: YB3271-CiPSC-6-7 rep1

description:
Library name: YB3271-CiPSC-6-7 rep1
column name in counts.csv: YB3271-CiPSC-6-7-1


title: Mouth, sample 4

description:
Library name: WM2
Column name in Rice_Sturgeon_Isoseq_transcript_counts.filtered.txt: 4_WM2_bc1012
White_Species_Consensus_Transcripts.fasta

source_name: Mouth

value: Mouth


title: 145777


title: YB3271-CiPSC-6-3 rep1

description:
Library name: YB3271-CiPSC-6-3 rep1
column name in counts.csv: YB3271-CiPSC-6-3-1

value: induced from EPC


title: 987728


title: Oral (inside mouth, upper palate), sample 3

description:
Library name: WI1
Column name in Rice_Sturgeon_Isoseq_transcript_counts.filtered.txt: 3_WI1_bc1008
White_Species_Consensus_Transcripts.fasta

source_name: Oral (upper palate)

value: Oral (upper palate)


title: 875089


title: 882538


title: YB3271-CiPSC-6 rep2

description:
Library name: YB3271-CiPSC-6 rep2
column name in counts.csv: YB3271_CiPSC-6#-2

value: EPC derived hCiPSC

value: WT


title: 280375

value: primary breast cancer

value: Ganitumab


title: Ampullae of Lorenini, sample 2

description:
Library name: WA2
Column name in Rice_Sturgeon_Isoseq_transcript_counts.filtered.txt: 2_WA2_bc1006
White_Species_Consensus_Transcripts.fasta

source_name: Ampullae of Lorenini

value: Ampullae of Lorenini


title: Barbel, sample 1

description:
Library name: WB2
Column name in Rice_Sturgeon_Isoseq_transcript_counts.filtered.txt: 1_WB2_bc1005
White_Species_Consensus_Transcripts.fasta

source_name: Barbel

value: Barbel


title: QX543

description: Library name: C14

value: Caenorhabditis elegans

value: Doxycycline


title: S1-NIBR rep2

description:
Library name: S1-NIBR rep2
column name in counts.csv: S1-NIBR-2

source_name: human blood cells during chemical reprogramming

value: without NIBR


title: YB3271-CiPSC-6 rep1

description:
Library name: YB3271-CiPSC-6 rep1
column name in counts.csv: YB3271_CiPSC-6#-1


title: QX546

description: Library name: C18


title: Mouth, Epithelial sample 5

description:
Library name: W8
Column name in Rice_Sturgeon_Isoseq_transcript_counts.filtered.txt: 5_12W8_bc1020
White_Species_Consensus_Transcripts.fasta

value: Epithelial


title: QX542

description: Library name: C12


title: 691753

value: Paclitaxel + Ganitumab


title: S1-NIBR rep1

description:
Library name: S1-NIBR rep1
column name in counts.csv: S1-NIBR-1

value: human blood cells during chemical reprogramming


title: YB3271-CiPSC-6-3 rep2

description:
Library name: YB3271-CiPSC-6-3 rep2
column name in counts.csv: YB3271-CiPSC-6-3-2

value: teratoma derived from hCiPSC


title: QX541

description: Library name: C10


title: QX548

description: Library name: B8


title: 917762


title: Mouth, Epithelial sample 4

description:
Library name: W12
Column name in Rice_Sturgeon_Isoseq_transcript_counts.filtered.txt: 4_9W12_bc1019
White_Species_Consensus_Transcripts.fasta

value: Dodecaploid


title: S1-NC rep2

description:
Library name: S1-NC rep2
column name in counts.csv: S1NC-2

value: S1 control


title: QX547

description: Library name: B6


title: QX544

description: Library name: C16


title: CB4856_batch

description: Library name: B4


title: Skin, Epithelial sample 2

description:
Library name: WS1
Column name in Rice_Sturgeon_Isoseq_transcript_counts.filtered.txt: 2_2WS_bc1012
White_Species_Consensus_Transcripts.fasta

source_name: Skin

value: Skin

value: Octoploid


title: N2_batch1

description: Library name: B2


title: S1-NC rep1

description:
Library name: S1-NC rep1
column name in counts.csv: S1NC-1


title: S1-BI-NIBR rep2

description:
Library name: S1-BI-NIBR rep2
column name in counts.csv: S1-BI-NIBR-2

value: without BI-7273, NIBR


title: QX560

description: Library name: B24


title: miRNA_FLV1

city: Guelph

first: Sonja

last: Fonfara

state: Ontario

address: 36 College Ave W

department: Clinical Studies

country: Canada

institute: University of Guelph

data_processing:
The raw trimmed reads are aligned to the reference genome using the STAR aligner.After sequencing, the quality of the data was assessed using FastQC v.0.11.5. The adaptors were trimmed using Trim Galore v.0.4.4. After trimming, the quality of reads was re-assessed with FastQC.
Raw trimmed reads were aligned to reference genome using the STAR aligner, followed by HTSeq- count v.0.6.1p2 to obtain uniquely mapped gene counts.
The identification of differentially expressed genes between different comparison groups was performed using edgeR R package v.3.22.3
For miRNA, sequencing libraries were generated for all samples using the NEBNext small RNA Library Prep Kit from Illumina. Total RNA from each sample was ligated to 3’ and 5’ adaptors, and poly (A) tails were added using poly (A) polymerase. RNA was reverse transcribed and amplified by PCR with primers specific to the adaptor sequences. MicroRNA enrichment was completed by extracting the 15-30 nucleotide fraction of the polyacrylamide gel. Sequencing was performed on the Hiseq 2500 SR50 bp (Illumina) platform, with 150M reads total. Quality of sequencing data was assessed using fastq.gzC v.0.11.2 (https://www.bioinformatics.babraham.ac.uk/projects/fastq.gzc/).
Assembly: The Felis_Catus_9.0.96 (Ensembl gene models) with annotations was used as the reference genome.
Supplementary files format and content: Excel files containing counts for each gene in FPKM (Fragments per kilobase per million mapped reads)

organism: Felis catus

source_name: Left ventricle

extract_protocol:
The miRNeasy Mini Kit (Qiagen, Toronto, ON, Canada) was used to isolate total RNA.RNA purity was assessed using the Nanodrop 2000 spectrophotometer. Samples with a 260/280 ratio of >1.9 and RNA integrity number of >5.7 were used for sequencing.
A stranded, paired-end poly-A mRNA library was prepared for each sample. Sequencing libraries were generated using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, USA) as per manufacturer’s instructions. Briefly, mRNA was isolated, fragmented and primed from total RNA and cDNA synthesis were performed. The cDNA fragments were adapter ligated and PCR amplification was done according to Illumina instructions.  The libraries were sequenced on the NovaSeq 6000 system, SP flowcell 2 x 150 bp (Illumina).

value: Left ventricle

value: Young healthy female


title: Skin, Epithelial sample 3

description:
Library name: WS2
Column name in Rice_Sturgeon_Isoseq_transcript_counts.filtered.txt: 3_5WS_bc1018
White_Species_Consensus_Transcripts.fasta


title: miRNA_FLV2


title: QX557

description: Library name: B20


title: S1-BI rep2

description:
Library name: S1-BI rep2
column name in counts.csv: S1-BI-2

value: WT

value: without BI-7273


title: QX559

description: Library name: B22


title: S1-BI rep1

description:
Library name: S1-BI rep1
column name in counts.csv: S1-BI-1


title: QX555

description: Library name: B16


title: QX556

description: Library name: B18


title: miRNA_FLV9


title: miRNA_FLV8


title: S1-BI-NIBR rep1

description:
Library name: S1-BI-NIBR rep1
column name in counts.csv: S1-BI-NIBR-1


title: QX554

description: Library name: B14


title: 6665_CiPSC-2 rep2

description:
Library name: 6665_CiPSC-2 rep2
column name in counts.csv: 6665-CiPSC-2#-2

source_name: induced from ASF

value: induced from ASF

value: ASF derived hCiPSC


title: HDF6665-P6 rep1

description:
Library name: HDF6665-P6 rep1
column name in counts.csv: ASF6665-2

source_name: human adult skin fibroblast

value: human adult skin fibroblast

value: human adult skin fibroblast (ASF)


title: 6665_CiPSC-2 rep1

description:
Library name: 6665_CiPSC-2 rep1
column name in counts.csv: 6665-CiPSC-2#-1


title: miRNA_FLV10


title: QX552

description: Library name: B12

value: Caenorhabditis elegans

value: Doxycycline


title: QX597

description: Library name: F38


title: 6665_CiPSC-1 rep2

description:
Library name: 6665_CiPSC-1 rep2
column name in counts.csv: 6665-CiPSC-1#-2


title: QX550

description: Library name: B10


title: miRNA_FLV7


title: miRNA_FLV11


title: miRNA_FLA11

source_name: Left atrium

value: Left atrium


title: 6665_CiPSC-1 rep1

description:
Library name: 6665_CiPSC-1 rep1
column name in counts.csv: 6665-CiPSC-1#-1


title: HDF6665-P6 rep2

description:
Library name: HDF6665-P6 rep2
column name in counts.csv: ASF6665-1


title: miRNA_FLA10


title: QX530

description: Library name: A6


title: 148357

value: primary breast cancer

value: Ganitumab

value: Paclitaxel + Ganitumab


title: 105286


title: 411950


title: 567907


title: 5034CBMC-EPC rep2

description:
Library name: 5034CBMC-EPC rep2
column name in counts.csv: 5034CBMC-EPC-2

value: human blood cells

value: erythroid progenitor cells (EPC)


title: 188700


title: 851488


title: 774840


title: 241705


title: QX536

description: Library name: A8


title: 563681


title: 407539


title: 745633


title: 884011


title: 376676


title: 628788


title: miRNA_FLA9


title: Mouth, Epithelial sample 1

description:
Library name: WM
Column name in Rice_Sturgeon_Isoseq_transcript_counts.filtered.txt: 1_1WM_bc1008
White_Species_Consensus_Transcripts.fasta

value: Mouth

value: Epithelial

value: Octoploid


title: QX528

description: Library name: A4


title: miRNA_FLA8

value: Young healthy female


title: 5034CBMC-EPC rep1

description:
Library name: 5034CBMC-EPC rep1
column name in counts.csv: 5034CBMC-EPC-1

value: WT


title: 663144


title: 5034CBMC-CiPSC-14 rep2

description:
Library name: 5034CBMC-CiPSC-14 rep2
column name in counts.csv: 5034_CiPSC-14#-2

value: induced from EPC

value: EPC derived hCiPSC


title: miRNA_FLA7


title: 769972


title: 5034CBMC-CiPSC-14 rep1

description:
Library name: 5034CBMC-CiPSC-14 rep1
column name in counts.csv: 5034_CiPSC-14#-1


title: QX594

description: Library name: A16


title: miRNA_LV8

value: Left ventricle

value: Adult healthy female


title: QX531

description: Library name: A14

value: Caenorhabditis elegans


title: 5034CBMC-CiPSC-1 rep2

description:
Library name: 5034CBMC-CiPSC-1 rep2
column name in counts.csv: 5034_CiPSC-1#-2


title: CB4856

description: Library name: A2

value: Doxycycline


title: miRNA_LV7


title: 5034CBMC-CiPSC-1 rep1

description:
Library name: 5034CBMC-CiPSC-1 rep1
column name in counts.csv: 5034_CiPSC-1#-1


title: 1217_CiPSC-3 rep2

description:
Library name: 1217_CiPSC-3 rep2
column name in counts.csv: 1217-CiPSC-3#-2

source_name: induced from hADSC

value: induced from hADSC

value: ADSC derived hCiPSC


title: QX588

description: Library name: A10


title: 928170

value: primary breast cancer

value: Ganitumab


title: 1217_CiPSC-3 rep1

description:
Library name: 1217_CiPSC-3 rep1
column name in counts.csv: 1217-CiPSC-3#-1


title: miRNA_LA7

value: Left atrium


title: Healhty rat plus 1 cycle on LS-FMD (72 hours refeeding)

city: West Hollywood

first: AGCT

last: Core

address: 8687 Melrose Ave, PDC B230

department: BMS

institute: Cedars Sinai Medical Center

description: 10X Genomics

data_processing:
Raw sequencing data were processed using the 10X Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to Rnor6.0 (Rat) genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantifies using Space Ranger's default settings
Assembly: Rnor6.0
Supplementary files format and content: barcodes.tsv.gz : list of spatial barcodes
Supplementary files format and content: features.tsv.gz : list of gene IDs
Supplementary files format and content: matrix.mtx.gz : gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: sample.tif : images captured of the samples
Library strategy: Spatial transcriptomics

organism: Rattus norvegicus

source_name: Kidney

extract_protocol:
Kidneys were embedded in OCT, frozen, cryosectioned at 10 um, and sections placed onto 10x Genomics Visium gene expression slides.
Spatial transcriptome sequencing libraries were prepared as per the 10x Genomics Visium Spatial Gene Expression Reagent Kit user guide.

tag: strain

value: Sprague-Dawley

value: Kidney

value: all renal cell types

value: LS-FMD


title: 1217_CiPSC-2 rep2

description:
Library name: 1217_CiPSC-2 rep2
column name in counts.csv: 1217-CiPSC-2#-2


title: PAN plus 6 cycles of LS-FMD

description: 10X Genomics

value: puromycin plus LS-FMD


title: miRNA_LA12


title: miRNA_LV10


title: Healhty rat

description: 10X Genomics

value: no treatment


title: QX589

description: Library name: A12


title: miRNA_LV21


title: PAN

description: 10X Genomics

value: puromycin injection


title: miRNA_LA21


title: miRNA_LA10


title: 1013_CiPSC-D rep2

description:
Library name: 1013_CiPSC-D rep2
column name in counts.csv: 1013-CiPSC-D#-2

value: WT


title: Kidney, healhty control, rep4

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger software version 7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Rnor6.0
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Kidneys were harvested and a small section (< 50 mg) was collected per each animal and immediately frozen and stored in liquid nitorgen until further processing. Nuclei from fresh frozen tissue were isolated using the 10x Genomics Chromium Nuclei Isolation kit. The frozen tissue was homogenized in lysis buffer using a pestle and microcentrifuge tube, filtered to remove any remaining pieces of tissue and large debris, then the nuclei suspension was cleaned up using the debris removal solution.  The nuclei were then washed and resuspended in Wash and Resuspension Buffer, followed by counting using AOPI.  The nuclei suspension concentration was adjusted as needed for capture.
Single-nucleus RNA-Seq libraries were prepared per the Single Cell 3′ v3.1 Reagent Kits User Guide. Nuclear suspensions were loaded on a Chromium Controller instrument to generate single-cell Gel Bead-In-EMulsions (GEMs). After GEM-RT, cDNA was amplified and cleaned up. Indexed sequencing libraries were constructed using the Chromium Single-Cell 3′ Library Kit for enzymatic fragmentation, end-repair, A-tailing, adapter ligation, ligation cleanup, sample index PCR, and PCR cleanup. The barcoded sequencing libraries were quantified by quantitative PCR.

value: No treatment


title: 629606

source_name: primary breast cancer

value: Paclitaxel + Ganitumab


title: 910188


title: 1013_CiPSC-D rep1

description:
Library name: 1013_CiPSC-D rep1
column name in counts.csv: 1013-CiPSC-D#-1


title: 1217_CiPSC-2 rep1

description:
Library name: 1217_CiPSC-2 rep1
column name in counts.csv: 1217-CiPSC-2#-1


title: miRNA_LV1162

value: Left ventricle

value: Hypertrophic Cardiomyopathy female


title: 1013_CiPSC-A rep2

description:
Library name: 1013_CiPSC-A rep2
column name in counts.csv: 1013-CiPSC-A#-2

value: induced from hADSC


title: Kidney, healhty control, rep3

description: 10x Genomics


title: miRNA_FLVD7


title: 1013_CiPSC-A rep1

description:
Library name: 1013_CiPSC-A rep1
column name in counts.csv: 1013-CiPSC-A#-1

value: ADSC derived hCiPSC


title: Kidney, healhty control, rep2

description: 10x Genomics


title: 0618_CiPSC-2 rep2

description:
Library name: 0618_CiPSC-2 rep2
column name in counts.csv: 0618-CiPSC-2#-1


title: Kidney, healhty control, rep1

description: 10x Genomics


title: miRNA_FLVD5


title: 0618_CiPSC-2 rep1

description:
Library name: 0618_CiPSC-2 rep1
column name in counts.csv: 0618-CiPSC-2#-1


title: Kidney, PAN/72 hr RF, rep3

description: 10x Genomics

value: Puromycin 14 days plus LS-FMD (72hr RF)


title: miRNA_FLVD4


title: miRNA_FLVD6


title: miRNA_FLVD3


title: Kidney, PAN/72 hr RF, rep2

description: 10x Genomics


title: 454808

value: primary breast cancer

value: Ganitumab


title: 229328


title: Kidney, PAN/72 hr RF, rep1

description: 10x Genomics


title: miRNA_FLVD1


title: 0618_CiPSC-1 rep1

description:
Library name: 0618_CiPSC-1 rep1
column name in counts.csv: 0618-CiPSC-1#-1


title: PBMC hCiPSC rep2

description: Library name: PBMC hCiPSC rep2

library_source: genomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low quality data by Trimmomatic v0.39, then mapped to hg38 whole genome using bwa v0.7.19.
sam file generated by bwa was converted to bam and sorted using samtools v1.21. Duplicated reads were removed using sambamba markdup v1.0.1. Then, bam files were convert to bigwig files with ‘--normalizeUsing RPKM’ with bamCoverage in deeptools v3.5.6
Assembly: hg38
Supplementary files format and content: bigwig files for every sample.

molecule: genomic DNA

extract_protocol:
Approximately 50,000 cells of each sample were collected, washed once with cold PBS and re-suspended in 50 m L Lysis buffer containing 10 mM Tris-HCl (pH7.4), 10 mM NaCl, 3 mM MgCl 2 , and 0.5% NP-40.
DNA library constructions were prepared by TurePrepDNA Library Prep Kit V2 for Illumina (TD501-02, Vazyme) and PCR ampliﬁed by TruePrep Index Kit V2 for Illumina (TD202 96rxn, Vazyme). Libraries were sequenced on a Hiseq X Ten using PE150.

treatment_protocol: blood cells were treatment by the chemical reprogramming protocol

value: human blood cells during chemical reprogramming

value: self-derived hCiPSC


title: miRNA_FLAD7

value: Left atrium


title: miRNA_LA1162


title: PBMC hCiPSC rep1

description: Library name: PBMC hCiPSC rep1


title: 0618_CiPSC-1 rep2

description:
Library name: 0618_CiPSC-1 rep2
column name in counts.csv: 0618-CiPSC-1#-2


title: Kidney, PAN/24 hr RF, rep2

description: 10x Genomics

value: Kidney

value: all renal cell types

value: Puromycin 14 days plus LS-FMD (24hr RF)


title: miRNA_FLAD6


title: S1-BI-7273 rep2

description: Library name: S1-BI-7273 rep2

value: self-derived S1-BI-7273

value: without BI-7273


title: Kidney, PAN/EoD, rep3

description: 10x Genomics

value: Puromycin 14 days plus LS-FMD (EoD)


title: miRNA_FLAD5


title: 542392

value: Paclitaxel + Ganitumab


title: 115638


title: Kidney, PAN/24 hr RF, rep1

description: 10x Genomics


title: S1-BI-7273 rep1

description: Library name: S1-BI-7273 rep1

value: WT


title: Kidney, PAN/24 hr RF, rep3

description: 10x Genomics


title: Kidney, PAN/EoD, rep2

description: 10x Genomics


title: S1 rep2

description: Library name: S1 rep2

value: self-derived S1


title: miRNA_FLAD4

value: Hypertrophic Cardiomyopathy female


title: Kidney, PAN/EoD, rep1

description: 10x Genomics


title: 289420


title: 509012


title: 239061


title: 511851


title: 580632


title: S1 rep1

description: Library name: S1 rep1


title: 962827


title: 520471


title: miRNA_FLAD3


title: Kidney, PAN, rep3

description: 10x Genomics

value: Puromycin 14 days


title: miRNA_FLAD1


title: PBMC EPC rep2

description: Library name: PBMC EPC rep2

value: human blood cells

value: Z0684 PBMC EPC

value: erythroid progenitor cells (EPC)


title: miRNA_MLV16

value: Left ventricle

value: Young healthy male


title: PBMC EPC rep1

description: Library name: PBMC EPC rep1


title: Kidney, PAN, rep2

description: 10x Genomics


title: S. anginous KH1 grown in artificial saliva medium, sample 2

city: Taoyuan

first: RUEILIN

last: Chiang

address: No.259, Wenhua 1st Rd

country: Taiwan

institute: CGU

description:
Library name: 4
KH1_SV_2

data_processing:
The sequences were determined using Illumina's sequencing-by-synthesis (SBS) technology (Illumina, USA). Reads were assessed through a Phred quality score (Q score of 20) and trimmed using Trimmomatic v0.36. The trimmed reads were mapped to the genome sequence of KH1 by using HISAT2.
Assembly: CP117042
Supplementary files format and content: Excl files include the TPM of all samples, the statistic analysis, and the ratio of TPM between the two growth conditions.

organism: Streptococcus anginosus

source_name: bacterial cells

growth_protocol: KH1 was cultivated in either artificial saliva medium or modified serum medium. The artificial saliva medium contains 0.25% mucin, 1% proteose peptone,1% trypticase peptone,1% yeast extract, 0.25% KCl, and 0.25% glucose. To prepare the modified serum medium, venous blood samples were collected from healthy human volunteers in BD Vacutainer™ SST™ II Advance Tubes (BD). The blood samples were subjected to centrifugation at 2,500×g, 25°C for 10 min to remove the blood cells. The recovered plasma was heated at 56oC for 30 min to inactivate complement. HEPES and glucose were added to the plasma to final concentrations of 40 mM and 0.5%, respectively, to make modified serum medium.

extract_protocol:
Total cellular RNA was isolated from KH1 cultures at OD600 = 0.3  and further purified using the RNeasy kit (Qiagen). Ribosomal RNA was removed from the RNA preparation using RiboMinus transcriptome isolation kits (Invitrogen). PCR was performed with primers specific for SAGKH1_01193 to ensure the preparations were free of chromosomal DNA.
The RNA library was constructed using a SureSelect XT HS2 mRNA library preparation kit (Agilent, USA).

value: bacterial cells


title: Kidney, PAN, rep1

description: 10x Genomics

value: Kidney


title: prostate_Large_B766

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

institute: Purdue University

description:
Library name: B766
column B766 in readcount.txt

data_processing:
STAR aligner v2.6.1d was used to align reads to the human reference genome, allowing 2 mismatches.
FeatureCounts v1.5.0-p3 was used with default parameters to generate the count matrix
DESeq2 v1.20.0 was used to identify differentially expressed genes (padj<0.05).
Assembly: GRCh38.p12
Supplementary files format and content: readcount.txt - count matrix generated by FeatureCounts in xls format

source_name: prostate

extract_protocol:
Frozen TZ tissue from 10 small and 7 large prostates were placed in Trizol and homogenized using a tissue shredder. The same patient cohort as the scRNA-seq analysis plus 4 additional large (>90 grams) specimens were included. After isolation of RNA following the Trizol protocol, cleanup was conducted using the RNeasy Plus mini kit (Qiagen). RNA concentration and quality were determined using a Nanodrop 2000 spectrophotometer (ThermoFisher) and Qubit 4 fluorometer using RNA BR reagents (Invitrogen).
Bulk RNA-seq paired-end 150 bp reads were sequenced by NovogeneRNA was sent to Novogene Corporation Inc. for quality control and strand-specific cDNA library preparation.

value: prostate

tag: prostate zone

value: Transition Zone

tag: size

value: Large


title: miRNA_MLV15


title: S. anginous KH1 grown in artificial saliva medium, sample 1

description:
Library name: 3
KH1_SV_1


title: 467622

value: primary breast cancer

value: Ganitumab


title: 973837

value: Paclitaxel + Ganitumab


title: 666147


title: 299962


title: 345460


title: S. anginous KH1 grown in modified serum medium, sample 2

description:
Library name: 2
KH1_SE_2

value: WT


title: prostate_Large_B1338

description:
Library name: B1338
column B1338 in readcount.txt


title: miRNA_MLV14


title: prostate_Large_B1344

description:
Library name: B1344
column B1344 in readcount.txt


title: S. anginous KH1 grown in modified serum medium, sample 1

description:
Library name: 1
KH1_SE_1


title: miRNA_MLV12


title: BT3xHuBL liver 3

city: Stockholm

first: Anton

last: Gisterå

address: Bioclinicum J8:20, Visionsgatan 4, Karolinska University Hospital, Solna

department: Medicine Solna

country: Sweden

institute: Karolinska Institutet

description: Library name: 138615.tsv

data_processing:
Data processing according to HTSeq 2.0 by Putri et al (Bioinformatics, Volume 38, Issue 10, 15 May 2022, Pages 2943–2945).
Assembly: Sequence reads were aligned to a mouse reference genome (Mus_musculus.GRCm38.95).
Supplementary files format and content: Tab-delimited data files contain raw counts for each sample.

organism: Mus musculus

source_name: Liver

extract_protocol:
RNA was isolated using Qiagen Rneasy mini kit.
Sequencing libraries were prepared with Lexogen QuantSeq V2.

value: Liver

value: Normal laboratory diet

tag: time

value: 52 weeks


title: prostate_Small_B1196

description:
Library name: B1196
column B1196 in readcount.txt

value: Small


title: BT3xHuBL liver 2

description: Library name: 138613.tsv


title: miRNA_MLV5


title: Granulosa, rep2

city: Antwerp

first: Valeriya

last: Malysheva

state: Select State

address: Universiteitsplein 1, Building V

country: Belgium

institute: VIB Center for Molecular Neurology

description:
Library name: Granulosa_rep2
column name in Sertoli_Granulosa_chicago_5kb_original_baits_score5.txt: Granulosa

data_processing:
*library strategy: Capture Hi-C
Read processing, alignment and filtering was performed using a modified version of the Hi-C User Pipeline (HiCUP) v0.7.4, HiCUP Combinations (https://github.com/StevenWingett/HiCUP/tree/combinations), which first creates all possible combinations of ditags from the paired reads prior to mapping, then performs standard filtering for common Hi-C artefacts. To generate the consensus interaction calling per cell type (Granulosa and Sertoli cells), CHiCAGO input (.chinput) files were generated per biological replicate, using bam2chicago.sh from chicagoTools v1.13 and then CHiCAGO pipeline was run at 5 kb bins resolution taking the variation across replicates into account (Cairs & Freire-Pritchett et al., 2016). The pipeline was run in two complementary modes. One where we only considered chromosomoal interactions with the original baited fragment (termed "original bait") and another where the baited fragment was expanded to a 5 kb bin resolution (termed "5 kb extended bait"), as we have previously described (Freire-Pritchett & Ray-Jones et al., 2021). We performed tests for epigenetic marker enrichment at promoter interacting regions in both modes, using the peakEnrichment4Features function in CHiCAGO. For the enrichment analysis ChIP-seq data for H3K4me3, H3K27ac and H3H27me3 from E13.5 pre-granulosa and Sertoli cells was obtained from GSE118755 and GSE130749 and reanalysed using the nf-core/chipseq v2.0.0 as previously described (Stévant et al., 2024).
Assembly: mm10
Supplementary files format and content: Bam files contain aligned and filtered reads, containing, at least in one of the interacting regions, the region of interest (i.e. promoter of a protein-coding gene)
Supplementary files format and content: Sertoli_Granulosa_chicago_5kb_original_baits_score5.txt and Sertoli_Granulosa_chicago_5kb_extended_baits_score5.txt are CHiCAGO peakmatix files containing interaction coordinates, read count and p-values for significant interactions as identified by CHiCAGO, in "original bait" and "extended bait" modes, respectively. The columns "Sertolli" and "Granulosa" in these files refer to joint calling of interactions per cell type, taking the variance of the read counts across biological replicates into account.

source_name: gonads

extract_protocol:
Following dissection, gonads were separated from the mesonephros using a G25 needle and dissociated into single cells by culture in 0.045% trypsin- EDTA (Thermo, cat. 25300062) along with 0.25% collagenase (Wortington, cat. LS004176) in a total volume of 500 µl  for 8 min at 37°C in a 24-well plate. 200 µl of DPBS (without Calcium and Magnesium) containing 3% Bovine serum albumin (BSA) (Sigma-Aldrich, cat. A3311) were added to quench the trypsin action and immediately aspirated to remove the trypsin. Gonads were then resuspended in 300µl of DPBS containing 3% BSA and mechanically dissociated by gentle pipetting. Cells were filtered through a 30µm strainer (Miltenyi Biotec, cat. 130-041-407) and collected into a Polypropylene FACS tube (BD Falcon, cat. 352063). The well and filter are washed with additional 200µl of DPBS containing 3% BSA. Cells were sorted using the BD FACS Aria III cell sorter with an 85-micron nozzle. Texas Red filter (excitation 561 nm, emission 610 nm) was used to detect mCherry and FITC (excitation 495 nm, emission 519 nm) filters to detect GFP. For ATAC sequencing, positive cells were sorted into Eppendorf tubes containing 150µl of DPBS + 3% BSA. For RNA sequencing positive cells were collected into 150µl QIAzol lysis reagent (Qiagen, 79306). FACS raw data were analysed using FlowJo v10 for visualization.
Capture Hi-C libraries (3 libraries of E13.5 Sox9IRES-GFP Sertoli cells and 2 libraries of E13.5 Enh8-mCherry pre-granulosa cells) were generated from 100,000 sorted cells, crosslinked as previously described (92, 93). Following lysis, the nuclei were permeabilized and digested with DpnII (NEB) overnight. The restriction overhangs were filled in using a biotinylated dATP (Jena Bioscience) and ligation was performed for 4 hours at 16°C (T4 DNA ligase; Life Technologies). The crosslinks were reversed using proteinase K and overnight incubation at 65°C, followed by purification with SPRI beads (AMPure XP; Beckman Coulter). Short fragments up to 1000 bp were produced via tagmentation and the biotinylated restriction junctions were then pulled down using MyOne C1 streptavidin beads (Life Technologies). PCR amplification (5 cycles) was performed on the libraries directly bound to the C-1 beads and the libraries were purified using SPRI beads as before. Promoter Capture was performed using the mouse custom-designed Agilent SureSelect system, following the manufacturer’s protocol, followed by 7 PCR cycles. The libraries were sequenced using 150 bp paired-end sequencing on an Illumina NovaSeq (Novogene UK) with a sequencing depth of 1bln paired reads for each biological replicate.

value: gonads

value: Granulosa

value: E13.5 Enh8-mCherry pre-granulosa cells


title: BT3xHuBL liver 1

description: Library name: 138612.tsv


title: prostate_Large_B1195

description:
Library name: B1195
column B1195 in readcount.txt


title: Granulosa, rep1

description:
Library name: Granulosa_rep1
column name in Sertoli_Granulosa_chicago_5kb_original_baits_score5.txt: Granulosa


title: miRNA_MLV4

value: Left ventricle

value: Young healthy male


title: HuBL liver 4

description: Library name: 138611.tsv

value: HuBL


title: prostate_Large_B1157

description:
Library name: B1157
column B1157 in readcount.txt

value: prostate


title: BT3xHuBL liver 4

description: Library name: 138616.tsv


title: miRNA_MLV3


title: Sertoli, rep3

description:
Library name: Sertoli_rep3
column name in Sertoli_Granulosa_chicago_5kb_original_baits_score5.txt: Sertoli

value: Sertoli

value: E13.5 Sox9IRES-GFP Sertoli cells


title: HuBL liver 3

description: Library name: 138610.tsv


title: 783764

value: primary breast cancer


title: 780272

value: Ganitumab


title: prostate_Small_B013

description:
Library name: B013
column B013 in readcount.txt

value: Transition Zone


title: HuBL aorta 3

description: Library name: 187384.tsv

source_name: Aorta

value: Aorta


title: Sertoli, rep2

description:
Library name: Sertoli_rep2
column name in Sertoli_Granulosa_chicago_5kb_original_baits_score5.txt: Sertoli


title: prostate_Large_B012

description:
Library name: B012
column B012 in readcount.txt

value: Large


title: prostate_Large_B0118

description:
Library name: B0118
column B0118 in readcount.txt


title: Sertoli, rep1

description:
Library name: Sertoli_rep1
column name in Sertoli_Granulosa_chicago_5kb_original_baits_score5.txt: Sertoli


title: 1x IFN-g 24h,replicate2,bulk_RNA-seq

first: Eneritz

last: Agirre

address: Solnavägen 9

department: MBB

description:
Library name: sample14
RNA-seq

data_processing:
A total of 3 replicates per condition were sequenced for both bulk RNA-seq. Raw FastQ files were aligned and processed using the NextFlow core RNA pipeline, nextflow version 24.04.2, to the genome assembly GRCm38. After QC we discarded replicate 1 for downstream analyses.
Gene level integer raw counts tables from nf-core Salmon output were loaded into R and used as input for edgeR 4.2.0 together with their associated metadata. The combined counts table was used to estimate the library size, perform CalcNormFactors with trimmed mean of M values (TMM) method and to perform the fit of genewise common dispersion (glmFit) followed by likelihood ratio test (glmLRT). Benjamini and Hochberg's algorithm (BH) test was used to control false discovery rate (FDR).
Output bam files fron nf-core RNA-seq were processed with Deeptools v.2 bamCoverage with CPM normalization.
Assembly: mm10
Supplementary files format and content: tab delimited txt raw count genes tables from each sample, output nf-core RNA-seq
Supplementary files format and content: Strand specific BigWig files for each sample

source_name: brain

growth_protocol: Primary OPC cell culture. Mice brains from P3-6 pups were dissociated using the Neural Tissue Dissociation Kit (Miltenyi Biotec, 130-092-628) according to the manufacturer’s protocol. OPCs were obtained with MACS with CD140a microbeads following the manufacturer’s protocol (CD140a Microbead kit, Miltenyi Biotec, 130-101-547). Cells were seeded in Poly-L-lysine (Sigma, P4707)-coated dishes and grown on OPC proliferation media comprising DMEM/F-12/GlutaMAX (ThermoFisher, 10565018), N2 media (ThermoFisher, 17502048), penicillin–streptomycin (ThermoFisher, 15140122), NeuroBrew (Miltenyi, 130-097-263), bFGF 40 ng/ml (R&D, 233-FB) and PDGF-AA 20 ng/ml (Peprotech, 315-17).

extract_protocol:
RNA extraction was performed using the RNeasy Kit (Qiagen, 74106)
RNA-seq libraries were prepared using Stranded Total RNA Prep, Ligation with Ribo-Zero Plus (Illumina, 20040525) according to the manufacturer’s protocol.
Libraries were sequenced on an Illumina NovaSeq X, with a 75-10-10-75 read setup.

tag: timepoint

value: 1x IFN 24h

tag: sequencing id

value: brain

value: Primary OPC cell culture

tag: replicate


title: miRNA_MLV2

tag: tissue


title: prostate_Small_B010

description:
Library name: B010
column B010 in readcount.txt

value: Small


title: HuBL aorta 2

description: Library name: 187383.tsv

value: Normal laboratory diet

value: 52 weeks


title: HuBL liver 1

description: Library name: 138608.tsv

value: Liver


title: 1x IFN-g 24h,replicate3,bulk_RNA-seq

description:
Library name: sample15
RNA-seq

treatment_protocol: 17502048), penicillin–streptomycin (ThermoFisher, 15140122), NeuroBrew (Miltenyi, 130-097-263), bFGF 40 ng/ml (R&D, 233-FB) and PDGF-AA 20 ng/ml (Peprotech, 315-17).

tag: cell line


title: miRNA_MLA15

value: Left atrium

tag: genotype

value: Young healthy male


title: miRNA_MLA16


title: 1x IFN-g 24h,replicate1,bulk_RNA-seq

description:
Library name: sample13
RNA-seq


title: miRNA_MLA13


title: HuBL liver 2

description: Library name: 138609.tsv

value: HuBL


title: prostate_Small_B009

description:
Library name: B009
column B009 in readcount.txt

value: prostate


title: miRNA_MLA9


title: prostate_Small_B1144

description:
Library name: B1144
column B1144 in readcount.txt


title: 2x IFN-g 24h,replicate3,bulk_RNA-seq

description:
Library name: sample12
RNA-seq

value: 2x IFN 24h


title: miRNA_MLA6


title: prostate_Small_B008

description:
Library name: B008
column B008 in readcount.txt


title: 2x IFN-g 24h,replicate2,bulk_RNA-seq

description:
Library name: sample11
RNA-seq


title: miRNA_MLA5


title: BT3xHuBL aorta 1

description: Library name: 187380.tsv


title: BT3xHuBL aorta 3

description: Library name: 187382.tsv


title: miRNA_MLA1


title: prostate_Small_B006

description:
Library name: B006
column B006 in readcount.txt


title: 2x IFN-g 24h,replicate1,bulk_RNA-seq

description:
Library name: sample10
RNA-seq


title: miRNA_MLA4


title: miRNA_LV6

value: Left ventricle

value: Adult healthy male


title: HuBL aorta 1

description: Library name: 187378.tsv


title: IFN-g 24h (+96),replicate3,bulk_RNA-seq

description:
Library name: sample9
RNA-seq


title: 6752lung

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

data_processing:
The reads that fail to align to the mouse genome were subsequently mapped to the complete collection of all available virus genomes (https://www.ncbi.nlm.nih.gov/genome/) with Kraken2 for exact alignment of k-mers and accurate viral read classification.
Relative abundances and differential analysis was performed with DESeq2 upon variance-stabilizing transformation.
Assembly: mm10 mouse genome
Supplementary files format and content: normalized_counts_unique.tsv contain DESeq2 normalized counts

source_name: Lung

extract_protocol:
RNA was extracted with the RNeasy Kits for RNA Purification according to manufacturer's instructions.
Libraries were produced by Azenta Life Sciences

value: Lung

value: WT


title: 248255

value: primary breast cancer

tag: arm (short name)

value: Ganitumab

value: Paclitaxel + Ganitumab


title: 6752colon

source_name: Colon

value: Colon


title: IFN-g 24h (+96),replicate1,bulk_RNA-seq

description:
Library name: sample7
RNA-seq

value: brain

value: Primary OPC cell culture


title: prostate_Small_B004

description:
Library name: B004
column B004 in readcount.txt

value: Transition Zone

value: Small


title: 6747colon

value: HO


title: miRNA_LV23B


title: IFN-g 24h (+96),replicate2,bulk_RNA-seq

description:
Library name: sample8
RNA-seq


title: miRNA_LV9


title: BT3xHuBL aorta 2

description: Library name: 187381.tsv

value: Aorta

value: Normal laboratory diet

value: 52 weeks


title: miRNA_LV22


title: prostate_Small_B007

description:
Library name: B007
column B007 in readcount.txt

value: prostate


title: IFN-g 24h (+0),replicate2,bulk_RNA-seq

description:
Library name: sample5
RNA-seq


title: prostate_Small_B003

description:
Library name: B003
column B003 in readcount.txt


title: miRNA_LV15

value: Left ventricle


title: IFN-g 24h (+0),replicate3,bulk_RNA-seq

description:
Library name: sample6
RNA-seq


title: 6684lung


title: 6683lung


title: miRNA_LA6

value: Left atrium

value: Adult healthy male


title: 6683colon


title: IFN-g 24h (+0),replicate1,bulk_RNA-seq

description:
Library name: sample4
RNA-seq


title: Ctrl,replicate3,bulk_RNA-seq

description:
Library name: sample3
RNA-seq

value: Ctrl


title: Ctrl,replicate2,bulk_RNA-seq

description:
Library name: sample2
RNA-seq


title: miRNA_LA23


title: miRNA_LA20


title: DB_ZHX2_Mut4_3

city: Jinan

first: Chunyan

last: Ji

address: Wenhua West Road

institute: Qilu Hospital

description: Library name: sample6

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens GRCh38. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: GRch38
Supplementary files format and content: xlsx,gz,Gene_differential_expression

source_name: cell line

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA.

value: cell line

value: DB

tag: cell type

value: B-lymphoma


title: 5842lung

value: Lung

value: WT


title: 5839lung


title: DB_ZHX2_Mut4_2

description: Library name: sample5


title: 5842colon

value: Colon


title: miRNA_LA15


title: 6684colon


title: 1x IFN-g 24h,replicate3,bulk_ATAC-seq

description:
Library name: sample15
bulk ATAC-seq

data_processing:
A total of 3 replicates per condition were sequenced for both bulk ATAC-seq. Raw FastQ files were aligned and processed using the NextFlow core ATAC pipeline, nextflow version 24.04.2, to the genome assembly GRCm38. After QC we discarded replicate 1 for downstream analyses.
Assembly: mm10
Supplementary files format and content: broad peaks called with MACS2 tab delimited txt files for each sample. As part of nf-core ATACseq pipeline
Supplementary files format and content: BigWig files for each sample.

extract_protocol:
For each condition, 50,000 primary OPCs were collected, washed with PBS, and lysed with 50 μL of lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL (CA-630), 0.1% Tween-20, 0.01% Digitonin) on ice for 3 minutes. After lysis, 1 mL of wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20) was added, and the nuclei were pelleted by centrifugation at 500g for 10 minutes at 4°C. After aspirating the supernatant, the nuclei were resuspended in 50 μL of transposition mix (25 μL 2x TD buffer (Tagment DNA Buffer), 16.5 μL PBS, 0.5 μL 1% Digitonin, 0.5 μL 10% Tween-20, 2.5 μL Tn5 Transposase (final 100 nM), and 5 μL nuclease-free H2O) and incubated for 30 minutes at 37°C in a thermomixer with 1000 RPM mixing.
The DNA was purified both pre- and post-PCR using the Zymo DNA Clean and Concentrator-5 kit (Zymo Research).
Libraries were sequenced on an Illumina NovaSeq X with a 51-8-8-50 read setup.

value: 1x IFN 24h

value: brain

value: Primary OPC cell culture


title: 1x IFN-g 24h,replicate2,bulk_ATAC-seq

description:
Library name: sample14
bulk ATAC-seq


title: 5837colon

value: HO


title: DB_ZHX2_Mut4_1

description: Library name: sample4


title: miRNA_LA22


title: Ctrl,replicate1,bulk_RNA-seq

description:
Library name: sample1
RNA-seq


title: 5806lung


title: 1x IFN-g 24h,replicate1,bulk_ATAC-seq

description:
Library name: sample13
bulk ATAC-seq


title: miRNA_MLVD22

value: Hypertrophic Cardiomyopathy male


title: miRNA_MLVD20


title: 5806colon


title: DB_ZHX2_2

description: Library name: sample2


title: DB_ZHX2_1

description: Library name: sample1


title: 5680lung


title: 2x IFN-g 24h,replicate3,bulk_ATAC-seq

description:
Library name: sample12
bulk ATAC-seq

value: 2x IFN 24h


title: miRNA_MLVD23


title: 2x IFN-g 24h,replicate2,bulk_ATAC-seq

description:
Library name: sample11
bulk ATAC-seq


title: 5680colon


title: miRNA_LV0061


title: SU4_KD3

description: Library name: sample6


title: 2x IFN-g 24h,replicate1,bulk_ATAC-seq

description:
Library name: sample10
bulk ATAC-seq


title: 5678lung


title: IFN-g 24h (+96),replicate3,bulk_ATAC-seq

description:
Library name: sample9
bulk ATAC-seq


title: SU4_KD2

description: Library name: sample5


title: DB_ZHX2_3

description: Library name: sample3


title: IFN-g 24h (+96),replicate2,bulk_ATAC-seq

description:
Library name: sample8
bulk ATAC-seq


title: miRNA_LV0045


title: miRNA_MLVD24


title: S_cerevisiae_WT_3

city: Sherbrooke

first: Michelle

middle: S

last: Scott

state: QC

address: 3201 Jean-Mignault

institute: Université de Sherbrooke

description:
Library name: Sample 10
Ribodepleted total RNA

data_processing:
Base callings were converted to fastq using bcl2fastq v2.20.0 with the following parameters for S. pombe, S. cerevisiae and M. musculus: --minimum-trimmed-read-length 13 --mask-short-adapter-reads 13 --no-lane-splitting -p 32. Base callings were converted to fastq using bases2fastq v1.2.0 with the following parameters for G. gallus and M. mulatta: -p 36 –detect-adapters --filter-mask R1:N*-R2:N*.
Trimming of paired-end reads was performed using Trimmomatic v0.36 (parameters: ILLUMINACLIP:<fastaWithAdaptersEtc>:2:12:10:8, TRAILING:30, LEADING:30, MINLEN:20) in order to remove adapters and low-quality reads.
FastQC v0.11.5 was used before and after trimming to assess the quality of the reads.
Alignment of reads to the reference genome was performed using STAR v2.6.1a (parameters: --runMode alignReads, --outSAMunmapped None, --outSAMtype BAM SortedByCoordinates, outFilterScoreMinOverLread 0.3, --outFilterMatchNminOverLread 0.3, --outFilterMultimapNmax 100, --winAnchorMultimapNmax 100, --alignEndsProtrude 5 ConcordantPair). The index needed to align reads was generated using STAR v2.6.1a (parameters: --runMode genomeGenerate, --sjdbOverhang 74)
Gene expression normalized in transcript per million (TPM) was obtained using CoCo v0.2.1p4 (parameters: cc, --countType both, --strand 1 --paired)
Assembly: GRCg7b (G. gallus), Mmul_10 (M. mulatta), GRCm39 (M. musculus), R64-1-1 (S. cerevisiae), ASM294v2 (S. pombe)
Supplementary files format and content: A tab-separated (.tsv) file showing the gene id, gene name and abundance (in TPM) of all annotated genes for each sample in the given species.

organism: Saccharomyces cerevisiae

growth_protocol: Wild type 10H3 S. cerevisiae cultures were grown in Yeast Extract Peptone Dextrose (YEPD) rich media at 26°C. Wild type yAS99 S. pombe cultures were grown to mid-log phase in 25 mL of YES media at 32°C.

extract_protocol:
Phenol-chloroform RNA extraction was performed for M. musculus, S. cerevisiae and S. pombe, whereas no RNA extraction was needed for the Biochain-purchased RNA for G. gallus and M. mulatta.
TGIRT-Seq libraries were constructed as described previously (Boivin et al., RNA, 2018) using ribodepleted total RNA (S. cerevisiae and M. musculus) or gel-purified and size-selected small RNAs (S. pombe, M. mulatta and G. gallus).


title: SU4_KD1

description: Library name: sample4


title: miRNA_MLVD1


title: IFN-g 24h (+96),replicate1,bulk_ATAC-seq

description:
Library name: sample7
bulk ATAC-seq


title: S_cerevisiae_WT_2

description:
Library name: Sample 9
Ribodepleted total RNA


title: SU4_CON2

description: Library name: sample2


title: S_cerevisiae_WT_1

description:
Library name: Sample 8
Ribodepleted total RNA


title: miRNA_X0457LV


title: ME/CFS RRBS, patient #030

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

country: New Zealand

institute: University of Otago

description: Library name: ME030_PBMC_RRBS

data_processing:
The quality check and processing of the sequenced RRBS reads were performed using in-house developed bioinformatics tools.  Processed sequence reads were then aligned to the reference human genome (GRCh37) using Bismark with stringent mapping criteria by allowing only one mismatch (default = 2) in the seed. The median non-CpG DNA methylation of all samples was 1.30%, indicating effective bisulfite conversion and low levels of true non-CpG methylation.  Analyses were conducted using the updated version of the DMAP pipeline, namely the DMAP2 analysis pipeline on a macOS computer to examine methylation changes across fragments ranging from 40–220 bp. DMAP2 employed an ANOVA F-test to compare patient and control groups, ensuring that only fragments with data available for all individuals in each group were included. A raw p-value threshold of <0.05 was applied. We have used a stringent P value threshold without false discovery rate correction in order not to lose true positives from this analysis, considering our sample size is low. Genomic features overlapping with these fragments were identified using the in-built Geneloc function of DMAP2.  R packages were used for analysing the DMAP2 output.Principal Component Analysis (PCA) using default parameters (prcomp), unsupervised hierarchical clustering of CpG site methylation, using pheatmap package and cluster rows, venn diagram was drawn using venn diagram package, the plots were drawn using ggplot2. Sankey Plot was drawn with network D3 and htmlwidgets.
Assembly: GRCh37 (hg19)
Supplementary files format and content: .txt format (contains Chr, Start, End, Len, CpGs, Pr, Test, >Meth, Control_count, LongCovid_count, ME_count, Controls_meth, LongCovid_meth, ME_meth, C010, C018, C037, C038, C039, COV01, COV02, COV03, COV04, COV05,  ME007, ME027, ME028, ME029, ME030, Enddist, Overlap, CpGIs_range, CpGIs_dist, CpGI_relation, Strand, GeneID, GeneRange)

source_name: Blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood by layering it onto Ficoll-Paque, followed by centrifuging at 400×g to separate plasma from PBMCs and the PBMCs from other cells. The removed PBMC layer was diluted with PBS and then pelleted at 100×g. The pellet was washed in PBS and stored at −80°C in a solution of FCS containing 10% DMSO. DNA was extracted from 200 μL of the PBMC fraction using the Illustra Blood Genomic Prep Mini Spin Kit, following the manufacturer’s instructions. Elution was performed using the kit’s EB buffer, and DNA concentration was measured with a Qubit 2.0 fluorometer according to the Qubit dsDNA HS Assay Kit protocol.
500 µg of genomic DNA was digested using 160 U of the MspI restriction enzyme. After end repair and adenylation of the 3′ ends, adaptors were ligated to the DNA fragments. Bisulfite conversion was carried out using the EZ DNA Methylation Kit (Zymo Research Corp, USA) according to the manufacturer’s instructions. A semi-quantitative PCR was performed on the bisulfite-converted DNA to determine the optimal number of amplifi-cation cycles required for the final large-scale PCR of the complete library. Following PCR amplification, DNA was size-selected using magnetic beads (AMPure XP beads from the TruSEq DNA nanokit -Beckman Coulter USA), isolating fragments between 40–220 bp to construct the RRBS libraries while minimizing adaptor contamination. The purified DNA was assessed for quality using a BioAnalyzer (Agilent, USA) and Qubit (Thermofisher Scientific, USA) measurements, followed by further purification with AMPure XP Beads (Beckman Coulter, USA).

value: Blood

value: PBMC


title: miRNA_MLVD2

source_name: Left ventricle

value: Left ventricle


title: SU4_CON1

description: Library name: sample1


title: IFN-g 24h (+0),replicate1,bulk_ATAC-seq

description:
Library name: sample4
bulk ATAC-seq


title: NC_2

city: Urumqi

first: daniyaer

last: nuerdebieke

state: 新疆

address: Urumqi

department: Urology Center

institute: People's Hospital of Xinjiang Uygur Autonomous Region

description: Library name: sample 2

data_processing:
Raw sequencing reads containing more than 2-N bases were first discarded. Subsequently, the raw reads were trimmed of adaptors and low-quality bases using a FASTX-Toolkit (v.0.0.13; http://hannonlab.cshl.edu/fastx toolkit/).
In addition, short reads of less than 16 nt were dropped to retain clean reads, which were subsequently aligned to the GRch38 genome by HISAT2 . Uniquely mapped reads were ultimately used to calculate read number and paired-end fragments per kilobase of exon per million fragments mapped (FPKM) for each gene.
The software DEseq2, which is specifically used to analyze the differential expression of genes, was applied to screen the RNA-seq data for DEGs. The results were analyzed based on the fold change (FC≥2 or ≤0.5) and false discovery rate (FDR<0.05) to determine whether a gene was differentially expressed.
The alternative splicing events (***-AS) and regulated alternative splicing events (***-RAS) between ***-OE and control samples were defined and quantified using the SUVA pipeline described previously . The frequency and proportion of reads of SUVA AS events (pSAR) were calculated.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: HUVEC cells

extract_protocol:
RNAs were converted into double strand cDNA. Following end repair and A tailing, the DNAs were ligated to VAHTS RNA Multiplex Oligos Set 1 for Illumina (N323,Vazyme,China)，the ligated products were amplified，purified，quantified and stored at -80℃ before sequencing. The strand marked with dUTP (the 2nd cDNA strand) is not amplified, allowing strand-specific sequencing. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina Novaseq 6000 system for 150 nt paired-end sequencing.
A total of 10 μg total RNA from each sample was used to prepare a directional RNA-seq library. First, the polyadenylated mRNAs were concentrated with oligo (dT)-conjugated magnetic beads (Invitrogen; Thermo Fisher Scientific, Inc.). The concentrated mRNAs were then iron-fragmented at 95˚C, end-repaired and ligated to a 5′ adaptor. RT was performed with RT primer harboring a 3′ adaptor sequence and randomized hexamer. The purified cDNAs were amplified and stored at -80˚C until they were used for sequencing. Following the manufacturer’s instructions, the libraries were prepared for high-throughput sequencing. The Illumina Novaseq 6000 (Illumina, Inc.) was used to collect data from 150-bp pair-end sequencing (Illumina, Inc).

value: HUVEC cells

value: HUVEC cell (control plasmid)


title: 672734

data_processing: Samples from the Ganitumab arm, and a subset the control arm patients, were assayed on a new RPPA array (RPPA.4).  three different RPPA arrays (RPPA.1, RPPA.2 and RPPA.3) under GPL28470.  This RPPA array (containing over 100 samples across HR/HER2 subtypes) was standardized as follows: (1) sample w/out replacement 5000 times, maintaining a receptor subtype balance equal to that of the first ~1000 patients (HR+HER2-: 0.384, TN:0.368, HR+HER2+:0.158, HR-HER2+:0.09); (2) calculate the mean(mean) and mean(sd) for each RPPA endpoint over the samples; (3) standardize each endpoint of the array, as y=(x-mean(mean))/mean(sd).  These standardized data were then combined with controls assayed on RPPA arrays RPPA.1, RPPA.2, and RPPA.3, each normalized in the same way.  This procedure resulted in removal of batch effects, without 'warping' due to mismatches in subtype prevalence.

value: primary breast cancer

value: Ganitumab

tag: arm

value: Paclitaxel + Ganitumab

tag: hr


title: OE_CELF2_3

description: Library name: sample 6

value: CELF2 overexpressed in HUVEC cell


title: NC_1

description: Library name: sample 1


title: OE_CELF2_1

description: Library name: sample 4


title: ME/CFS RRBS, patient #029

description: Library name: ME029_PBMC_RRBS


title: OE_CELF2_2

description: Library name: sample 5


title: NC_3

description: Library name: sample 3


title: miRNA_MLAD20

value: Left atrium


title: Ctrl,replicate3,bulk_ATAC-seq

description:
Library name: sample3
bulk ATAC-seq

value: Ctrl

tag: treatment


title: IFN-g 24h (+0),replicate3,bulk_ATAC-seq

description:
Library name: sample6
bulk ATAC-seq


title: ChIP_DB_ZHX2_Mut4

description: Library name: sample3

data_processing:
Raw reads were filtered to obtain high-quality clean reads by removing sequencing adapters, short reads (length <35 bp) and low-quality reads using trim-galore (v0.6.4). Then FastQC (v0.11.9) and Multiqc (v1.8) were used to ensure high reads quality. The clean reads were mapped to the human genome (assembly human genome hg38) using the Burrow-Wheeler Aligner (BWA v0.7.17) software. PCR duplicates were removed using Picard (v2.22.2-0). Peak detection was performed using the MACS2 (v2.2.6) peak finding algorithm with 0.05 set as the q-value cutoff. Annotation of peak sites to gene features was performed using the homer annotatePeaks.pl (v4.10). Pearson correlation coefficient between biological replicates was calculated using deeptools (v3.4.3) multiBamSummary with default parameters. The resulting histograms (genomic ‘signal maps’) were stored in bigWig files using deeptools (v3.4.3) bamCoverage (paramters: --normalizeUsing RPKM --extendReads 200 --ignoreForNormalization chrX chrY --ignoreDuplicates)
Assembly: hg38
Supplementary files format and content: xlsx,gz

extract_protocol:
5 million DB cells were fixed with 1% formaldehyde at room temperature for 10 minutes, quenched with 125 mM glycine and harvested. The harvested cells were sent to Active Motif China (Shanghai, China) for ChIP-Seq.
Active Motif prepared chromatin, performed ChIP reactions, generated the libraries and performed basic data analysis. In brief, chromatin was isolated by adding lysis buffer and fragmented by sonication. DNA was sheared to an average length of 200–500bp with Active Motif's PIXUL® Multi-Sample Sonicator (Cat# 53130). Genomic DNA (Input) was prepared by de-crosslinking at 65°C for 4 hours followed by RNase A (Thermo Fisher) and Proteinase K (Thermo Fisher) digestion. The Input DNA was purified with QIAGEN PCR Purification Kit and quantified by Onedrop (Wins). Fragmented chromatin (for IP) was incubated with 15 μl of anti-ZHX2 (CST, Cat #43035) at 4℃ for overnight. 25 ul of rProtein A Magarose Beads (smart-lifesciences) were added to the samples and incubated at 4°C for 2 hours. Complexes were washed, eluted from the beads with SDS buffer, then de-crosslinked at 65°C for overnight. The de-crosslinked chromatin was subjected to RNase A and proteinase K treatment. ChIP DNA was purified with QIAGEN PCR Purification Kit and quantified with Qubit (Thermo Fisher). Illumina sequencing libraries were prepared from the ChIP-DNA and input DNAs with VAHTS Universal DNA Library Prep Kit for Illumina V4.

value: cell line

value: DB

value: B-lymphoma


title: miRNA_MLAD6

data_processing:
The raw trimmed reads are aligned to the reference genome using the STAR aligner.After sequencing, the quality of the data was assessed using FastQC v.0.11.5. The adaptors were trimmed using Trim Galore v.0.4.4. After trimming, the quality of reads was re-assessed with FastQC.
Raw trimmed reads were aligned to reference genome using the STAR aligner, followed by HTSeq- count v.0.6.1p2 to obtain uniquely mapped gene counts.
The identification of differentially expressed genes between different comparison groups was performed using edgeR R package v.3.22.3
For miRNA, sequencing libraries were generated for all samples using the NEBNext small RNA Library Prep Kit from Illumina. Total RNA from each sample was ligated to 3’ and 5’ adaptors, and poly (A) tails were added using poly (A) polymerase. RNA was reverse transcribed and amplified by PCR with primers specific to the adaptor sequences. MicroRNA enrichment was completed by extracting the 15-30 nucleotide fraction of the polyacrylamide gel. Sequencing was performed on the Hiseq 2500 SR50 bp (Illumina) platform, with 150M reads total. Quality of sequencing data was assessed using fastq.gzC v.0.11.2 (https://www.bioinformatics.babraham.ac.uk/projects/fastq.gzc/).
Assembly: The Felis_Catus_9.0.96 (Ensembl gene models) with annotations was used as the reference genome.
Supplementary files format and content: Excel files containing counts for each gene in FPKM (Fragments per kilobase per million mapped reads)


title: ME/CFS RRBS, patient #028

description: Library name: ME028_PBMC_RRBS


title: SU4_CON3

description: Library name: sample3


title: Ctrl,replicate1,bulk_ATAC-seq

description:
Library name: sample1
bulk ATAC-seq

value: brain

value: Primary OPC cell culture


title: miRNA_LA0061

value: Hypertrophic Cardiomyopathy male


title: ME/CFS RRBS, patient #027

description: Library name: ME027_PBMC_RRBS

value: Blood


title: ME/CFS RRBS, patient #007

description: Library name: ME007_PBMC_RRBS

value: PBMC


title: miRNA_X0552LV

value: Left ventricle


title: miRNA_X0552 LA


title: Ctrl,replicate2,bulk_ATAC-seq

description:
Library name: sample2
bulk ATAC-seq


title: spinal cord organoid, 30-days-old, infected with EVA71, 48hpi, rep1

city: Bethesda

first: Philip

last: Murphy

address: 10 CENTER DR RM 11N111

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

description:
Library name: Sample_14_EVA71_org
10Xgenomics

data_processing:
The fastQ files were submitted to Cell Ranger version 7.0.0 ‘mkref’, ‘mkfastq’ and ‘count’ functions with a custom genome of GRCh38 human reference genome and the enterovirus genome corresponding to the specific strain identity of the sample.
Assembly: GRCh38 human reference (hg38_gex-GRCh38-2024-A). EVD68_18952 genome acession number - KM851230.1. EVD68_23089 genome acession number - MN245983.1. EVA71 genome acession number - AF304458.1.
Supplementary files format and content: H5 files.

source_name: spinal cord organoids

growth_protocol: Human iPSC line SCTi003A (Stem Cell, 200-0511) was maintained in mTeSRTM Plus medium (Stem Cell, 100-0276), supplemented with 10 µM Y-27632 (Tocris, 1254). They were seeded and passaged in flasks coated with 150 µg/mL Cultrex (R&D Systems, 3434-005-02).  For patterning, on days 0–3, 10 µM Y-27632 (Tocris, 1254), 20 ng/mL bFGF (ThermoFisher, 13256-029), and 3 µM CHIR 99021 were added. From day 0 to day 6, 10 µM SB431542 (Tocris, 1614) and 0.2 µM LDN 193189 (Tocris, 6053) were added. From day 3 to day 15, 100 nM retinoic acid (Tocris, 302-79-4) and 500 nM smoothened agonist (SAG) (Tocris, 912545-86-9) were added. For 3-DiSC hSCO, 10% (vol/vol) knockout serum replacement (KSR, Invitrogen) was added to differentiation medium, and LDN193189 and SAG were removed. After 14 days, organoids were transferred to a 24-well plate and cultured in suspension in N2B27 medium supplemented to contain 1 mM L-glutamine, 0.1 mM 2-ME, 0.5 µM ascorbic acid, 10 ng/mL BDNF (ThermoFisher, PHC7074), 10 ng/mL GDNF (ThermoFisher, PHC7041), and 100 nM RA.

extract_protocol:
After 48hpi, the pools were dissociated to a single-cell suspension with Accumax (Invitrogen). They were incubated for 15 minutes in the water bath at 37℃, gently mixed, and then proceeded with the proposed 10X Genomics protocol (Cell Preparation Guide - CG00053 Rev C). Once the cell's concentration were achieved the cells were moved to ice.
For the preparation of the cDNA and sequencing library generation, we followed manufacturer instructions from the Chromium Next GEM Single Cell 5’ Reagent Kit v2 (Dual index) User Guide with one modification: primers were spiked-in during the cDNA synthesis to enrich the capture viral RNA (Step 1.1) only in samples 5, 6 and 13. The virus-specific primer concentration added to each RT reaction was ~15 pmoles. All the other reagents were added according to the protocol, except the nuclease-free water, which was reduced to accommodate the primer spike-in volume. The Illumina library quality, yield, and size distribution was assessed by TapeStation D1000 high sensitivity assay, and by Qubit High Sensitivity dsDNA kit. The molar concentrations of the libraries were determined and diluted for sequencing according to Illumina sequencing protocol. We aimed to sequence each library to achieve >50,000 reads per cell.

treatment_protocol: hSCOs were infected in pools of 8-12 organoids each and inoculated with virus at 10^5 PFU/pool or media (Mock_control). After 1 hour of incubation at room temperature, hSCOs were washed 3X with PBS and moved to new wells before incubation with fresh medium. No further media changes were performed for the rest of the experiment. The EV-D68 infected pool was incubated at 33oC and EV-A71 at 37oC for 48 hours post infection (hpi).

value: spinal cord organoids

tag: developmental stage

value: 100000 PFU/per pool of 8-12 organoids - EVA71 Tainan/4643/1998 (BEI)


title: IFN-g 24h (+0),replicate2,bulk_ATAC-seq

description:
Library name: sample5
bulk ATAC-seq


title: Long COVID RRBS, patient #05

description: Library name: LC05_PBMC_RRBS


title: miRNA_X0457

source_name: Left atrium

extract_protocol:
The miRNeasy Mini Kit (Qiagen, Toronto, ON, Canada) was used to isolate total RNA.RNA purity was assessed using the Nanodrop 2000 spectrophotometer. Samples with a 260/280 ratio of >1.9 and RNA integrity number of >5.7 were used for sequencing.
A stranded, paired-end poly-A mRNA library was prepared for each sample. Sequencing libraries were generated using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, USA) as per manufacturer’s instructions. Briefly, mRNA was isolated, fragmented and primed from total RNA and cDNA synthesis were performed. The cDNA fragments were adapter ligated and PCR amplification was done according to Illumina instructions.  The libraries were sequenced on the NovaSeq 6000 system, SP flowcell 2 x 150 bp (Illumina).


title: hM vs. WT: KO biol rep 2

city: Houston

first: Zixiu

last: Cheng

state: Texas

address: TX 77030 one baylor plaza, ABBR R631

institute: BCM

data_processing:
The resultant clean reads were obtained and stored in FASTQ format and mapped to the reference genome GRCm38.p6 using HISAT2 (v2.0.4). Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set, and the expression level of genes was calculated with RSEM (v1.2.12). The differential expression analysis was performed using the DESeq2 (v1.4.5). A gene was considered differentially expressed if the adjusted p-value was < 0.05. We carried out functional annotation analysis using DAVID Bioinformatics Resources 6.7. Differentially expressed genes were used as input gene lists, and all genes expressed in the heart were used as the background. We looked for enrichment for genetic association with biological processes in Gene Ontology (GO) and KEGG pathways.
Assembly: GRCm38.p6
Supplementary files format and content: xlsx files includes FPKM values for each samples and DEGs between WT vs. KO/NS-DAD

source_name: heart

extract_protocol:
TRIzol (Sigma) and RNeasy Mini Kit (Qiagen)
RNA-seq was performed using total RNA (n = 3 in each group). The sequence was done on the BGI MGISEQ-2000 platform to an average depth of 60 million reads per sample. The sequencing data was filtered with SOAPnuke (v1.5.2) by removing reads containing the sequencing adapter.

value: heart

value: HDAC3 KO


title: Input_DB_ZHX2_Mut4

description: Library name: sample4


title: miRNA_MLAD2


title: spinal cord organoid, 24-days-old, infected with 23089_EVD68, 48hpi, rep1

description:
Library name: Sample_8_23089_org
10Xgenomics

value: Human iPSC line SCTi003A (Stem Cell, 200-0511)

value: 100000 PFU/per pool of 8-12 organoids - US/CO/18-23089 (CDC)


title: hM vs. WT: KO biol rep 1


title: Long COVID RRBS, patient #04

description: Library name: LC04_PBMC_RRBS


title: spinal cord organoid, 30-days-old, Mock_control, 48hpi, rep1

description:
Library name: Sample_13_EVA71_Mock
10Xgenomics

value: Mock control


title: mRNA_FLV11

value: Young healthy female


title: Long COVID RRBS, patient #03

description: Library name: LC03_PBMC_RRBS


title: Long COVID RRBS, patient #02

description: Library name: LC02_PBMC_RRBS


title: ChIP_DB_ZHX2

description: Library name: sample1

value: cell line


title: mRNA_FLV10


title: mRNA_FLV9


title: Input_DB_ZHX2

description: Library name: sample2

value: DB


title: spinal cord organoid, 24-days-old, infected with 23089_EVD68, 48hpi, rep2

description:
Library name: Sample_6_23089_org_SEARCH
10Xgenomics


title: Long COVID RRBS, patient #01

description: Library name: LC01_PBMC_RRBS


title: hM vs. WT: WT biol rep 1

value: WT


title: spinal cord organoid, 24-days-old, Mock_control, 48hpi, rep1

description:
Library name: Sample_7_Mock_org
10Xgenomics


title: spinal cord organoid, 24-days-old, Mock_control, 48hpi, rep2

description:
Library name: Sample_5_Mock_org_SEARCH
10Xgenomics


title: hM vs. WT: KO biol rep 3


title: hM vs. WT: WT biol rep 3


title: Healthy Controls RRBS, patient #038

description: Library name: C038_PBMC_RRBS


title: mRNA_FLV8


title: NS-DADm vs. WT: NS-DADm biol rep 3

value: NS-DADm


title: mRNA_FLV7


title: spinal cord organoid, 24-days-old, infected with 18952_EVD68, 48hpi, rep1

description:
Library name: Sample_4_18952_org
10Xgenomics

value: 100000 PFU/per pool of 8-12 organoids - EV-D68 US/IL/14-18952 (CDC)


title: NS-DADm vs. WT: NS-DADm biol rep 2


title: Healthy Controls RRBS, patient #037

description: Library name: C037_PBMC_RRBS


title: mRNA_FLV2


title: LNCaP cells, siSLC38A1, repeat3

city: Dresden

first: Vasyl

last: Lukiyanchuk

address: Handelallee 26

country: Germany

institute: OncoRay

description: Library name: Sample 24

data_processing:
Performed by RNAseq service provider Genewiz (Standard RNA-Seq analysis, value package)
Assembly: hg38
Supplementary files format and content: Raw counts in tab-delimeted txt format

source_name: Prostate

growth_protocol: DMEM (for DU145) or RPMI-1640 (for LNCaP) supplemented with 10%FBS, 2mM l-glutamine, 10mM HEPES, 1mM sodium piruvate and 1x MEM-NEAA

extract_protocol:
NucleoSpin RNA Plus
Performed by RNAseq service provider Genewiz (Illumina, RNA with PolyA selection, value package)

treatment_protocol: 200 000 (for DU145) or 300 000 (for LNCaP) cells per well of 6-well plate were transfected with 40pmol of siRNA and 9ul Lipofectamine RNAiMax in 300 ul of OptiMEM.

value: Prostate

value: LNCaP

value: Prostate carcinoma


title: NS-DADm vs. WT: NS-DADm biol rep 1


title: Healthy Controls RRBS, patient #018

description: Library name: C018_PBMC_RRBS

value: Blood

value: PBMC


title: mRNA_FLV1

value: Left ventricle


title: NS-DADm vs. WT: WT biol rep 3

value: heart


title: Healthy Controls RRBS, patient #010

description: Library name: C010_PBMC_RRBS


title: mRNA_FLA11

value: Left atrium


title: hM vs. WT: WT biol rep 2


title: Healthy Controls RRBS, patient #039

description: Library name: C039_PBMC_RRBS


title: mRNA_FLA10


title: NS-DADm vs. WT: WT biol rep 2


title: Before_5

city: Oslo

first: Andrea

last: Dalmao-Fernandez

address: Gaustadveien 9

country: Norway

institute: University of Oslo

description:
Library name: BB5
Column name in After_5vsBefore_5_deg.txt: Before_5

data_processing:
The library preparation and RNA-seq analysis were carried out at Novogene Co., LTD. (Milton, United Kingdom).
To identify differentially expressed genes Novomagic (https://magic.novogene.com) online platform was used. This allowed us to test for statistical enrichment of differentially expressed genes, and p-values less than 0.05 was considered as statistically significant.
Data filtering step: only differentially expressed protein-coding DEGs were taken into account for comparison analyses
Assembly: Assembly: hg38
Supplementary files format and content: AftervsBefore_deg_all_samples.txt is the processed/analyzed file (differential gene expression between groups Before (BB) and After (AA)) provided by Novogen

source_name: skeletal muscle

growth_protocol: Human satellite cells were isolated cultured and proliferated in DMEM-GlutaMAX (5.5 mM glucose) supplemented with 10% FBS, HEPES (25 mM), gentamicin (50 ng/ml), penicillin (25 IU), streptomycin (25 μg/ml), amphotericin B (1.25 μg/ml), hEGF (10 ng/ml), dexamethasone (0.39 μg/ml) and 0.05% BSA.

extract_protocol:
TRIzol was added to the samples and they were homogenized by IKA® Ultra-Turrax® tissue homogenizer (Sigma-Aldrich, St. Louis, MO, US) for the complete RNA isolation. According to the manufacturer´s protocol, 0.2 ml of chloroform added directly to 1 ml of TRIzol was used for lysis and separation of the aqueous phase containing RNA. 0.5 ml of isopropanol was mixed to precipitate RNA. The RNA pellet was washed with 75% ethanol and resuspended in 15 µl of RNase-free water before the quantity and quality of the RNA were assessed.
The RNA library preparation and transcriptome sequencing processes were outsourced to Novogene Co., LTD. (Milton, United Kingdom), utilizing their Illumina platform for paired-end sequencing.

treatment_protocol:
human participants received a daily krill oil supplement (1 g/day, equivalent to four servings of fatty fish per week [8] ) for 7 weeks, containing 0.12 g EPA, 0.065 g DHA, in total 0.24 g omega-3 polyunsaturated fatty acids, 0.03 g palmitoleic acid (16:1, omega-7), > 42% phospholipids, and > 0.2 mg of astaxanthin. Krill oil was provided by Rimfrost AS (Ålesund, Norway). Skeletal muscle biopsies were obtained from the musculus vastus lateralis on both the first and last days of the study.
Cells underwent differentiation for 10 days in a 3D format with DMEM-Glutamax™ (5.5 mmol/L glucose) containing 2% FBS, 25 p.m. insulin, HEPES (25 mmol/l), amphotericin B (1.25 μg/ml), gentamicin (50 ng/ml), penicillin (25 IU), and streptomycin (25 μg/ml).

value: skeletal muscle

value: Before krill oil intervention


title: LNCaP cells, siSLC38A1, repeat2

description: Library name: Sample 20


title: NS-DADm vs. WT: WT biol rep 1


title: Before_2

description:
Library name: BB2
Column name in After_2vsBefore_2_deg.txt: Before_2


title: LNCaP cells, siSCR, repeat3

description: Library name: Sample 21

value: siSCR


title: LNCaP cells, siSLC7A5, repeat2

description: Library name: Sample 19


title: mRNA_FLA8

value: Young healthy female


title: mRNA_FLA9


title: Before_4

description:
Library name: BB4
Column name in After_4vsBefore_4_deg.txt: Before_4


title: whole body larval fathead minnow, 6PPD-Q, biol rep5 [6PPD_C_H12]

city: RTP

first: Monique

last: Hazemi

state: NC

address: 109 T.W. Alexander Dr

institute: US EPA

data_processing:
Sequencing was performed in a 2x150bp paired end format using a NovaSeq 6000 v1.5 300 cycle reagent cartridge.
Base calling was done by Illumina Real Time Analysis (RTA) v3.4.4 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0.
The fathead minnow reference genome (assembly GCA_016745375.1; Martinson et al. 2022) was indexed with STAR v2.7.10a and concurrently had in-house gene annotations loaded. The following sample specific parameters were used to generate the genome index: --genomeSAindexNbases 13 --sjdbOverhang 149.
After performing quality control on the raw FASTQ data using FastQC and MultiQC v1.12, raw reads were trimmed using Trim Galore! v0.6.6 to remove sequencing adapters and low-quality bases and filter out trimmed reads shorter than 20 bp.
Trimmed reads were then mapped with STAR v2.7.10a to the indexed genome using the default parameters except for the use of: --outSAMattributes NH HI AS NM XS.
Samtools v1.13 was used to sort (via the command: samtools view -buS [.sam_file] | samtools sort -m 1G -@ 100 -o [orted.bam_file] -O bam) and index (via the command: samtools index [sorted.bam_file]) the alignment files.
HTSeq v0.13.5 was used to assign counts to each gene with the following parameters: -f bam -r pos -s no.
FastQC and MultiQC v1.12 were used to assess quality control metrics of the processed reads.
Counts to each gene were parsed, and raw count data for each exposure condition written to a single tab-delimited matrix file with samples arranged as columns and genes arranged in rows.
Quality control screening and filter steps were applied to each raw count matrix using the R statistical computing software. Samples were first screened to see if any exhibited total counts <2M, and a boxplot of log10 raw counts (+1) for each sample was generated to look for samples with unusual counts distribution. Lowly expressed genes were removed from the raw count matrices using edgeR’s built-in filtering function, filterByExpr(), in version 3.40.2; namely, genes with < 15 reads across all samples and < 10 reads in the smallest group (treatment or control) sample size were filtered out. Normalization factors for the filtered count matrices were calculated using the trimmed mean of M-values method via the edgeR function calcNormFactors(). Filtered counts were then normalized by applying a log2 transformation to the counts per million (CPM) read with a pseudo-count of 1 added (to prevent occurrence of any negative count values for downstream analyses, i.e., log2(CPM+1)). Any sample with a filtered, normalized count distribution (assessed via boxplot) that markedly deviated from the rest of the samples within an individual chemical dataset was removed. Multidimensional scaling (MDS) plots were generated to look for possible outliers. Overall, quality control procedures resulted in the removal of samples 6PPD_C_D12 and 6PPD_C_H11 from the normalized count matrix for 6PPD-Q.
Assembly: RefSeq GCF_016745375.1 (EPA_FHM_2.0; NCBI Annotation Release 100)
Supplementary files format and content: tab-delimited text file providing raw counts for each Sample (both 6PPD and 6PPD-Q exposures together + controls)
Supplementary files format and content: tab-delimited text file providing log2(CPM+1) counts for each Sample for 6PPD exposure and controls
Supplementary files format and content: tab-delimited text file providing log2(CPM+1) counts for each Sample for 6PPD-Q exposure and controls

organism: Pimephales promelas

source_name: whole body fathead minnow

growth_protocol: Fathead minnows (Pimephales promelas) used for the present were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division. Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  At five-day post-fertilization  , larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use.

extract_protocol:
Exposure media was removed from each well, 100 ul of Omega Biotek MagBind Total RNA homogenization buffer was added and individual fish were homogenized using a bead mill at 30 Hz for 2 min. Whole-body homogenates were extracted using MagMAX-96 Total RNA Isolation kits (ThermoFischer Scientific AM1830) and RNA quality verified using an Agilent Tapestation (Agilent, Santa Clara, CA).
Complementary DNA libraries were prepared from 250 ng total RNA using SENSE mRNA-Seq Library Prep kits (Lexogen).

treatment_protocol: Larval (five day post hatch) fathead minnow were exposed for 24 hr in 1-mL, 96-well plate format to 600 uL of either the tire rubber antioxidant chemical 6ppd (n=30) or its quinone transformation product, 6ppd-quinone (6ppd-q; n=40). Exposures were conducted without feeding (reliant on yolk and not independently feeding at this age) in a total volume of 700 µl with 0.3% DMSO per well. Fish were exposed to either six (6ppd) or eight (6ppd-q) concentrations, with 5 replicate fish exposed per plate and triplicate plates (A, B, C). Plates were sealed and placed in a 25°C incubator under a 16:8h light routine for 24 h.

value: whole body fathead minnow

value: larval (5-day post hatch)

tag: biological replicate

tag: dose (mg/l)


title: Before_1

description:
Library name: BB1
Column name in After_1vsBefore_1_deg.txt: Before_1


title: LNCaP cells, siSLC1A5, repeat2

description: Library name: Sample 18


title: mRNA_FLA7

first: Sonja

last: Fonfara

address: 36 College Ave W


title: whole body larval fathead minnow, 6PPD-Q, biol rep5 [6PPD_C_H10]


title: LNCaP cells, siSLC1A5, repeat3

description: Library name: Sample 22


title: After_5

description:
Library name: AA5
Column name in After_5vsBefore_5_deg.txt: After_5

value: After krill oil intervention


title: whole body larval fathead minnow, 6PPD-Q, biol rep5 [6PPD_C_H11]


title: LNCaP cells, siSCR, repeat2

description: Library name: Sample 17


title: After_4

description:
Library name: AA4
Column name in After_4vsBefore_4_deg.txt: After_4


title: mRNA_LV8

value: Adult healthy female


title: whole body larval fathead minnow, 6PPD-Q, biol rep5 [6PPD_C_H08]


title: LNCaP cells, siSLC38A1, repeat1

description: Library name: Sample 16


title: After_2

description:
Library name: AA2
Column name in After_2vsBefore_2_deg.txt: After_2


title: mRNA_LV10


title: LNCaP cells, siSLC7A5, repeat3

description: Library name: Sample 23


title: LNCaP cells, siSLC7A5, repeat1

description: Library name: Sample 15


title: mRNA_LV7


title: whole body larval fathead minnow, 6PPD-Q, biol rep5 [6PPD_C_H09]


title: After_1

description:
Library name: AA1
Column name in After_1vsBefore_1_deg.txt: After_1


title: mRNA_LV21


title: whole body larval fathead minnow, 6PPD-Q, biol rep5 [6PPD_C_H06]


title: LNCaP cells, siSLC1A5, repeat1

description: Library name: Sample 14


title: whole body larval fathead minnow, 6PPD-Q, biol rep5 [6PPD_C_H05]


title: Uninfected, #3

city: Chapel Hill

first: xiaojing

last: zheng

address: 111 Mason Farm Road

institute: UNC-CH

description: Library name: sample14

data_processing:
Sequenced on an Illumina HiSeq2500 platform in the High Throughput Sequencing Facility (HTSF) at the University of North Carolina. Gene expression quantification used BBMap (v37.25) and samtools (v1.4.1).
Assembly: hg38
Supplementary files format and content: Comma-separated values (csv) file includes counts for each sample.

source_name: Endometrial tissue

extract_protocol:
mRNA Extraction and Profiling: Total RNA was extracted from endometrial biopsies stored at -80°C in tubes containing RNA/DNA Shield (Zymo Research, Irvine, CA). After thawing, samples were weighed, minced, and processed for simultaneous DNA and RNA extraction using the Quick DNA/RNA™ isolation kit according to the manufacturer's protocol (Zymo) with on column DNase I treatment prior to total RNA elution. Libraries were prepared using the Ovation SoLo RNA-Seq kit (NuGen Technologies) and sequenced on an Illumina HiSeq2500 platform in the High Throughput Sequencing Facility (HTSF) at the University of North Carolina.
Libraries were prepared using the Ovation SoLo RNA-Seq kit (NuGen Technologies).

value: Endometrial tissue

tag: infection group

value: Uninfected

tag: Sex

value: Female


title: mRNA_LA12

city: Guelph

institute: University of Guelph


title: DU145 cells, siSLC38A1, repeat3

description: Library name: Sample 12

value: Prostate

value: Prostate carcinoma


title: mRNA_LA10


title: Uninfected, #4

description: Library name: sample15


title: whole body larval fathead minnow, 6PPD-Q, biol rep4 [6PPD_C_H04]


title: Uninfected, #2

description: Library name: sample13


title: whole body larval fathead minnow, control, biol rep10 [6PPD_C_H03]

value: control


title: mRNA_LA21


title: DU145 cells, siSLC7A5, repeat3

description: Library name: Sample 11


title: DU145 cells, siSLC1A5, repeat3

description: Library name: Sample 10


title: mRNA_LA7


title: whole body larval fathead minnow, control, biol rep9 [6PPD_C_H02]


title: mRNA_FLVD7

value: Left ventricle

value: Hypertrophic Cardiomyopathy Female


title: Endo-, #4

description: Library name: sample11

value: Endo-


title: whole body larval fathead minnow, 6PPD-Q, biol rep5 [6PPD_C_H07]


title: whole body larval fathead minnow, 6PPD, biol rep5 [6PPD_C_H01]


title: Endo-, #3

description: Library name: sample10


title: DU145 cells, siSLC38A1, repeat2

description: Library name: Sample 8


title: LNCaP cells, siSCR, repeat1

description: Library name: Sample 13

value: LNCaP


title: DU145 cells, siSCR, repeat3

description: Library name: Sample 9


title: mRNA_FLVD6


title: whole body larval fathead minnow, 6PPD-Q, biol rep4 [6PPD_C_G12]


title: Endo-, #2

description: Library name: sample9


title: whole body larval fathead minnow, 6PPD-Q, biol rep3 [6PPD_C_G10]


title: mRNA_FLVD5


title: whole body larval fathead minnow, 6PPD-Q, biol rep4 [6PPD_C_G08]


title: DU145 cells, siSLC7A5, repeat2

description: Library name: Sample 7


title: mRNA_FLVD3


title: Endo+, Clinical PID-, #3

description: Library name: sample7

value: Endo+, Clinical PID-


title: DU145 cells, siSLC1A5, repeat2

description: Library name: Sample 6


title: Endo-, #1

description: Library name: sample8


title: Uninfected, #1

description: Library name: sample12


title: DU145 cells, siSLC38A1, repeat1

description: Library name: Sample 4


title: Endo+, Clinical PID-, #2

description: Library name: sample6


title: mRNA_FLVD1


title: Endo+, Clinical PID+, #4

description: Library name: sample4

value: Endo+, Clinical PID+


title: Endo+, Clinical PID-, #1

description: Library name: sample5


title: mRNA_FLAD7

value: Left atrium


title: mRNA_FLAD6


title: whole body larval fathead minnow, 6PPD-Q, biol rep4 [6PPD_C_G07]

value: whole body fathead minnow


title: whole body larval fathead minnow, 6PPD-Q, biol rep3 [6PPD_C_G02]

value: larval (5-day post hatch)


title: Endo+, Clinical PID+, #3

description: Library name: sample3