title: PDOVCA_69

value: Ovarian cancer patient derived xenografts (PDX)


title: PDOVCA_54

status: Public on Dec 27 2024

type: SRA

city: Padova

first: Daniele

last: Boso

address: Via Gattamelata, 64

department: Basic and Translational Oncology Unit

country: Italy

institute: Veneto Institute of Oncology IOV - IRCCS

library_source: transcriptomic

data_processing:
data quality: FastQC and MultiQC(1.14)
trimming of the raw reads was carried out using cutadapt(1.18) with specific adapter sequences (AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT), and reads below a minimum length of 100 bases were discarded.
alignment and quantification of the high-quality human reads against the Gencode GRCh38.p13 reference genome were performed using Salmon(1.4.0)
Assembly: GRCh38.p13
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample

molecule: polyA RNA

organism: Homo sapiens

source_name: Ovarian cancer ascites

growth_protocol: Ovarian cancer PDX were propagated by injecting 1 million tumor cells intra-peritoneally into 8-week-old female NOD/SCID mice. Then, cells were harvested from developed ascites and used for RNAseq

extract_protocol:
RNA was harvested using Trizol® protocol. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit (NEB)

treatment_protocol: Ascites-derived cells were maintained in PBS until cell count was done and 1 million pellets were kept at -80°C until RNA extraction was performed

tag: tissue

value: Ovarian cancer ascites

tag: cell type


title: E14_d0_rep2

city: Cambridge

first: Simon

middle: Richard

last: Andrews

state: Cambs

address: Babraham Research Campus

department: Science Services

country: United Kingdom

institute: The Babraham Institute

data_processing:
Reads were mapped to the GRCm39 genome assemby using gene models from Ensembl v103 using hisat2 with options --no-softclip --no-discordant --no-mixed
Raw counts were calculated from merged mRNA isoforms in SeqMonk v1.48.1 using the RNA-Seq quantitation in opposing strand specific mode
Assembly: Mus musculus GRCm39
Supplementary files format and content: Tab delimited file of raw per gene exon overlap counts

molecule: total RNA

organism: Mus musculus

growth_protocol: E14 embryonic stem cells (ESCs) were grown on plates coated with gelatin (0.1%, Sigma) in DMEM containing 4.5 g/l glucose (Gibco) supplemented with 15% fetal bovine serum (Gibco, South American, A3160802), 2 mM l-glutamine, 1 mM pyruvate, 1x MEM nonessential amino acids, 50 units/ml penicillin and 50 µg/ml streptomycin (all Gibco), 0.2 mM β-mercaptoethanol (Sigma), and heterologously expressed recombinant LIF (made in-house and batch-tested for maintenance of self-renewal) at 37°C and 5% CO2.

extract_protocol:
Cells were resuspended in 1 ml TriPure isolation reagent (Roche) per 10-cm plate of ESCs or EBs (or per 2x 6-cm plate for plated neural cells). RNA was extracted following the manufacturer’s instructions and resuspended in BTE (10 mM Bis-Tris pH 6.7, 1 mM EDTA). Extracted RNA was treated with Turbo DNAse (Ambion) for 30 min at 37°C. RNA extraction was repeated using TriPure and purified RNA was resuspended in 50 μl BTE. Integrity of RNA was assessed using RNA 6000 Nano chips on a Bioanalyzer (Agilent).
Ribosomal RNA was depleted from 1 µg of RNA using the NEBNExt rRNA depletion kit v2 (NEB). Libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) and single index NEBNext multiplex oligos for Illumina (NEB). Following library preparation, library fragment size was determined using an Agilent Bioanalyzer 2100. Library concentration was assessed by qPCR using the NEBNext Library Quant kit for Illumina (NEB). Samples were sequenced on an S4 flow cell on an Illumina NovaSeq 6000 instrument as 150 bp paired-end reads (Novogene UK).

treatment_protocol: Neuronal differentiation was performed as previously described (Bibel et al., 2007). First, embryoid body (EB) formation was induced by removal of LIF. ESCs were plated onto non-adherent bacterial plates (Greiner) in 10 ml EB medium (ESC medium described above but without LIF and with 10% FBS instead of 15%) at a density of 4 x 10^6 cells per 10-cm plate. On day 2, the media was changed by gently transferring EBs to a 15-ml conical tube (Sarstedt), allowing EBs to settle for 5 min, then carefully aspirating the supernatant. EBs were then gently resuspended in 13 ml of fresh EB media using a 5-ml serological pipette (Sarstedt) and transferred to a fresh plate. On day 4 and day 6, media was changed in the same manner to 15 ml EB medium with 10 μM all-trans retinoic acid (Sigma). On day 8, EBs were washed 3 x in 20 ml PBS, trypsinised (Sigma, prepared at 0.5 mg/ml in 0.05% v/v EDTA/PBS) for approximately 3 min at 37°C with agitation and then quenched in 10 ml EB medium. Dissociated neural progenitor cells were then centrifuged for 5 min at 300 g, resuspended in 10 ml EB medium and passed through a 40-μm cell strainer (Thermo Fisher Scientific). Cells were counted, centrifuged again and resuspended in Advanced DMEM/F12 (Gibco) with 1x N2 supplement (Gibco) before being plated onto poly-D-lysine (Sigma) and laminin (Sigma) coated 6-cm dishes at a density of 3 x 10^6 cells/plate. On day 9, half of the media was replaced with Neurobasal medium (Gibco) containing 1x B27 supplement (Gibco). This was repeated on day 12.

tag: cell line

value: embryonic stem cell (E14 line)

tag: genotype

value: E14 wildtype

tag: treatment

tag: time point


title: 20

city: Grenoble

first: Anouk

last: Emadali

address: Allée des Alpes, Site Santé La Tronche, BP170, Cedex 9

department: Institute for Advanced Biosciences

country: France

institute: Grenoble University Hospital

data_processing:
Reads were quality-checked using FastQC. (Dobin 226 et al., 2013).
Reads were then aligned to H. sapiens genome build hg38 using STAR 2.7.1a
Raw read counts for each gene were calculated using HTSeqCount 0.11.2.
Read counts were normalized using log2 of RPM normalization
Assembly: hg38
Supplementary files format and content: Normalized counts (log2 RPM) for each sample

growth_protocol: NUDUL-1, OCI-Ly18, RAMOS cell lines were 143 cultured in RPMI 1640 medium supplemented with 20% fetal bovine serum (FBS), 1% 144 glutamine, 100 mg/mL penicillin/streptomycin. SUDHL-4, SUDHL-6, HT, B593 and RAJI cell 145 lines were cultured in RPMI Glutamax supplemented with 20% FBS, 1 mM sodium pyruvate, 146 1% minimum essential medium non-essential amino acids (MEM NEAA) and 100 mg/mL 147 penicillin/streptomycin. OCI-Ly1 cell line was grown in IMDM medium with 20 % FBS and 100 148 mg/mL penicillin/streptomycin.

extract_protocol:
RNA was extracted from 3 million cells with NucleoSpin 210 RNA extraction kit (Macherey-Nagel) according to manufacturer's instructions.
(Samples 1-36) RNA-Seq libraries were generated according to manufacturer's instructions from 500 ng of total RNA using the Illumina Stranded mRNA Prep, Ligation kit and IDT for Illumina RNA UD Indexes Ligation (Illumina, San Diego, USA). Briefly, Oligo(dT) magnetic beads were used to purify and capture the mRNA molecules containing polyA tails.The purified mRNA were then fragmented at 94oC for 8 min and copied into first strand complementary DNA (cDNA) using reverse transcriptase and random primers. Second strand cDNA synthesis further generated blunt-ended double-stranded cDNA and incorporated dUTP in place of dTTP to achieve strand specificity by quenching the second strand during amplification. Following A-tailing of DNA fragments and ligation of pre-index anchors, PCR amplification was used to add indexes and primer sequences and to enrich DNA libraries (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x12cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using SPRIselect beads (Beckman-Coulter, Villepinte, France) and the final libraries were checked for quality and quantified using capillary electrophoresis. (Samples 37-60) Librairies were prepared according to BGI procedures.

treatment_protocol: Cells cere treated for 24h with 500 nM JQ1 and compared to DMS0-treated counterparts.

value: High-grade B-Cell Lymphoma

value: JQ1 replicat 1


title: ORG11HS-control-1

city: Boston

first: Kung-Chi

last: Chang

state: MA

address: 240 Longwood Avenue, Building C/Rom 501

department: Cell Department

country: USA

institute: Harvard medical School

description:
Sample 9
HS71490
sample1-12_count_matrix

data_processing:
Data was processed and analyzed at Partek.com using Partek Flow Genomic Analysis Software
Alignment using STAR; hg38 for assembly (whole genome)
Quantify to an annotation model (Partek E/M)
Noise reduction for low expression genes by applying fliter exclude features where maximum <= 50.0.
DESeq2 (Median ratio DESeq2 only) for normalization
Assembly: hg38
Supplementary files format and content: matrix table text files include sample reads and gene counts

source_name: Breast

growth_protocol: Organoid culture medium from dekker et. Al, 2021 (PMID: 33692550)

extract_protocol:
RNA was extracted using Trizol/Chloroform method and isopropanol precipitation
RNA samples were sent to Novogene co. for library preparation

treatment_protocol:
Cells isolated from human breast organoids
Hormone sensing (HS) treated w/wo Estrogen 1nM for 7 days
luminal adaptive secretory precursor fate (LASP), Basal (BA)

value: Breast

value: Primary epithelial cells

value: HS

value: WT

value: Control


title: PDOVCA_62


title: 17

value: Diffuse Large B-Cell Lymphoma

value: JQ1 replicat 3


title: Amh-cre Hdac3 KO rep3

city: Nanjing

first: Qing

last: He

state: Jiangsu

address: 101 Longmian Avenue

department: State Key Laboratory of Reproductive Medicine and Offspring Health

country: China

institute: Nanjing Medical University

data_processing:
Clean data were obtained by trimming the adaptor sequence and removing sequences with low quality.
Clean reads were mapped to the mouse genome (mm10) with HISAT2 (v.2.1.0; Johns Hopkins University, Baltimore, MD, USA) with a GTF file download from the UCSC database (University of California, Santa Cruz).
The aligned reads of genes were counted using HTSeq followed by DESeq2 normalization to evaluate gene expression as normalized counts per million.
Assembly: mm10
Supplementary files format and content: Gene counts for every gene and every sample
Supplementary files format and content: bigwig

source_name: Testis

extract_protocol:
Sertoli cells were isolated from wild-type and  Amh-cre Hdac3 KO mice at P10, and RNA was harvested using Trizol reagent.
Strand-specific libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation kit (Illumina).

value: Testis

value: Sertoli cells

value: Amh-cre Hdac3 Knockout


title: PDOVCA_52


title: ORG5HS_E21nM-1

description:
Sample 7
HS7216E27
sample1-12_count_matrix


title: Amh-cre Hdac3 KO rep1


title: PDOVCA_53


title: ORG5HS-control-1

description:
Sample 5
HS72160
sample1-12_count_matrix


title: ORG5HS_E21nM-2

description:
Sample 8
HS7216E27_2
sample1-12_count_matrix

value: Estrogen 1nM 7days


title: 16

value: DMSO replicat 3


title: PDOVCA_41

value: Ovarian cancer ascites

value: Ovarian cancer patient derived xenografts (PDX)


title: Hdac3fl/+ rep2

value: Wild-type


title: ORG5HS-control-2

description:
Sample 6
HS72160_2
sample1-12_count_matrix


title: Amh-cre Hdac3 KO rep2


title: Hdac3fl/+ rep1


title: 8

value: High-grade B-Cell Lymphoma


title: 7


title: PDOVCA_15


title: 14

value: JQ1 replicat 2


title: Hdac3fl/+ rep3


title: Hepatic organoid2, rep3

city: Jinan

first: Shule

last: Zhang

address: 107 Wenhua Xilu

institute: Qilu Hospital of Shandong University

data_processing:
Remove the reads without 3' adapter. Remove the reads without insert fragment. Remove the reads contain too much A/T. Remove the reads which length is out of range. Remove the low-quality reads. Then obtain the clean reads.
The clean reads were mapped to reference genome.
Map reads to mature miRNA and hairping which recorded in miRBase(release 21) to identiy known-miRNA.
DEGseq was used for differential gene expression analysis.
Assembly: hg38
Supplementary files format and content: fpkm.csv
Supplementary files format and content: count.csv

source_name: Hepatic organoid

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

value: Hepatic organoid


title: Ribo-seq, nohs, siSrp72, rep2

first: Hun-Goo

last: Lee

address: 185 Cambridge St

department: Molecular Biology

institute: Mass General Hospital

library_source: other

data_processing:
Preprocessing for the raw fastq files including adaptor sequence removal was performed by Trim Galore v0.4.1 software
Trimmed sequences were aligned to rRNA sequence to filter out reads from rRNA and collected non-rRNA sequence reads were aligned to mouse genome (mm10) by TopHat2 with the parameters “—no-novel-juncs” and “—b2-very-sensitive”.
Meta-analysis for coding-sequence regions was conducted by utilizing deepTools2 and the lengths of CDS regions for all genes were normalized to 100 for the meta-analysis.
featureCounts (Liao et al., 2014)  was used for analyzing the differentially enriched genes.
Assembly: mm10
Supplementary files format and content: Bigwig coverage files were generated by using bamCoverage software with the parameter --normalizeUsingRPKM
Supplementary files format and content: read count table for all the Ribo-seq samples
Library strategy: Ribo-seq

molecule: other

source_name: cell line

growth_protocol: NIH3T3 cells were cultured in DMEM medium supplemented with 10% fetal bovine serum, 1% Penicilin- Streptomycin-Neomycin (PSN) antibiotic mixture and 1% non-essential amino acids from GibcoTM.

extract_protocol:
After the treatment, plates were placed on ice, medium was removed, and the cells were washed in 2ml per well in cold 1X PBS without cycloheximide (CHX). PBS was removed and cells were lysed in 450μl of lysis buffer. (*Polysome buffer: 20mM Tris pH 7.5, 150mM NaCl, 100μg/ml CHX, 5mM MgCl2, 1mM DTT. *Lysis buffer: Polysome buffer + 25U/ml TURBOTM DNase + 1% Triton X-100. Cells were spun for 10min at 20000g and supernatant was collected. 300μl of the lysate was used for ribosome footprinting. After RNAseI treatment, samples were layered on top of 900μl of 1M sucrose in polysome buffer in Beckman polycarbonate tubes (No. 343778) and ultracentrifugation was performed for 30min at 120000rpm using TLA120.2 rotor @ 4 ̊C. Subsequently, supernatant was removed, and pellet was resuspended in 700μl of Qiazol. RNA from ribosomal pellet was extracted using miRneasy kit and eluted in 50μl of RNAse free water.
Ribo-Seq library was constructed according to Ingolia et al., 2012. Forward library DNA primer was used as a lower marker for footprint excision. Following each precipitation step, pellets were additionally washed with 500μl of 70% EtOH to remove residual salts. Circularized cDNA libraries were amplified 8 cycles and 3 reactions were pooled together for sequencing.

treatment_protocol: Briefly, 800 x 103 NIH3T3 cells were plated per well in a 6 well plate and transfected either with siScr or siSrp72. 24h later medium was replaced, and transfection was repeated. 24h later medium was removed, and cells were exposed to heat shock (45 ̊C, 10min) or not (37 ̊C, 10min) in 1ml medium pre-warmed to 37 ̊C or 45 ̊C.

value: cell line

value: fibroblast

value: wt

value: no hs, siSrp72


title: PDOVCA_6


title: PDOVCA_49


title: PDOVCA_5


title: 13

value: Diffuse Large B-Cell Lymphoma

value: DMSO replicat 2


title: 1

value: DMSO replicat 1


title: 5


title: Ribo-seq, hs, siCtrl, rep1

value: hs, siCtrl


title: PDOVCA_1


title: Hepatic organoid1, rep2


title: NNML36

value: JQ1 replicat 3


title: 11

value: JQ1 replicat 1


title: PDOVCA_24


title: ORG1HS_E21nM-2

description:
Sample 4
HS6555E27_2
sample1-12_count_matrix

value: Breast

value: Primary epithelial cells

value: HS

value: WT

value: Estrogen 1nM 7days


title: Ribo-seq, hs, siSrp72, rep1

value: hs, siSrp72


title: ORG1HS_E21nM-1

description:
Sample 3
HS6555E27
sample1-12_count_matrix

value: Control


title: Hepatic organoid1, rep3

value: Hepatic organoid


title: EB_GFP-yki-ss_biol rep 04

city: London

first: Nicola

middle: Laura

last: Diny

address: 1 Midland Rd

institute: The Francis Crick Institute

description:
salmon.merged.gene_counts.tsv
varianceStabilizedCounts.txt

data_processing:
Libraries were sequenced to a depth of at least 25M reads on an Illumina NovaSeq 6000 run in 101-8-8-101 configuration.
Sequencing runs were concatenated into single gzipped fastq files. These were then aligned to genome BDGP6 using nf-core/rnaseq 3.1
The resulting counts file salmon.merged.gene_counts.tsv was used to create a SummarizedExperiment
This was then analysed using DESeq2 to produce tables of differentially expressed genes and rnk files. PCA plots were made using the DESeq2 function varianceStabilizingTransformation(). R computations were carried out using R version 4.2.3 (2023-03-15), "Shortstop Beagle".
Assembly: BDGP6
Supplementary files format and content: raw counts
Supplementary files format and content: variance stabilized counts

organism: Drosophila melanogaster

source_name: midgut

growth_protocol: fly crosses were set up at 18C and adult females aged 0-4 days were transferred to 29C for 2 days

extract_protocol:
RNA from 5,000-30,000 cells was isolated using the Qiagen RNeasy Plus Micro Kit and eluted in 15µl water. RNA quality and concentration was analysed on a Bioanalyzer and only samples with RIN>7 were used for sequencing.
NEBNext Low Input RNA libraries were prepared manually following the manufacturer’s protocol (NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® Instruction Manual Version 5.0_5/20, NEB #E6420L). Samples were normalized to 1ng total RNA material per library in 8μl of nuclease-free water. RNA samples underwent reverse transcription, and the resulting cDNA was amplified by 10 cycles of PCR (according to the manufacturer recommendation for 1 ng input DNA). Amplified cDNA was subjected to two consecutive bead clean-ups with a 0.6X and 0.9X ratio of SPRISelect beads [B23318; Beckman Coulter] to sample volume. cDNA was fragmented enzymatically to target an insert size of ~200bp. Adaptors (diluted to 0.6µM) were ligated to the cDNA fragments and adaptor-ligated samples were cleaned up with SPRISelect beads (ratio: 0.8x). For the amplification of the sequencing library, 25µl of Q5 Master Mix was added, plus 10µl of a unique index (NEBNext Multiplex Oligos for Illumina [NEB #E6609]). Libraries were amplified by 8 PCR cycles. Final libraries were cleaned up with SPRISelect beads (ratio: 0.9x). The quality of the purified libraries was assessed using an Agilent D1000 ScreenTape Kit on an Agilent 4200 TapeStation.

treatment_protocol: Midguts were dissected and 10-30 midguts per sample were digested in 100-300µl digestion buffer (30µL PBS, 10µL of 4mg/mL Elastase, 0.4µL of 5mg/mL DNase I) at 27°C with shaking for 1h, followed by pipetting 20 times for mechanical separation. Cells were washed in wash buffer (PBS, 2mM EDTA, 0.2% BSA), centrifuged and incubated with Live/Dead nIR stain (Thermofisher) at 4°C for 30 minutes, washed in PBS resuspended in wash buffer with DAPI and filtered through 40µm filters. Live cells were sorted through a 70µm nozzle on a BD Fusion instrument (BD Biosciences) using BD Diva software. GFP positive ISC and EB were gated according to Fig. S2B-D.

value: midgut

value: enteroblast

value: esgts> GFP.NLS,ykiact, ssHA

tag: Sex

value: female

tag: developmental stage

value: adult


title: NNML35

value: High-grade B-Cell Lymphoma

value: JQ1 replicat 2


title: E14_d0_rep1

value: embryonic stem cell (E14 line)

value: E14 wildtype


title: EB_GFP-yki-ss_biol rep 03


title: 10

value: Diffuse Large B-Cell Lymphoma

value: DMSO replicat 1


title: ORG1HS-control-2

description:
Sample 2
HS65550_2
sample1-12_count_matrix

value: Breast

value: Primary epithelial cells

value: HS


title: Ribo-seq, hs, siSrp72, rep2

value: cell line

value: fibroblast

value: wt

value: hs, siSrp72


title: NNML34

value: JQ1 replicat 1


title: ORG1HS-control-1

description:
Sample 1
HS65550
sample1-12_count_matrix

value: WT

value: Control


title: PDOVCA_14

value: Ovarian cancer ascites

value: Ovarian cancer patient derived xenografts (PDX)


title: Ribo-seq, hs, siCtrl, rep2

value: hs, siCtrl


title: PDOVCA_9


title: Hepatic organoid2, rep2

value: Hepatic organoid


title: Ribo-seq, nohs, siCtrl, rep2

value: no hs, siCtrl


title: RNA, hs, siCtrl, rep2

data_processing:
Preprocessing for the raw fastq files including adaptor sequence removal was performed by Trim Galore v0.4.1 software
Preprocessed fastq files were aligned to mm10 genome by TopHat v2.0.10 with the following parameters: --read-edit-dist 3 --read-mismatches 3 --read-gap-length 3 --b2-very-sensitive --mate-inner-dist 100 --mate-std-dev 100
DEseq2 (Love et al., 2014), featureCounts (Liao et al., 2014), and enhancedVolcano were used for analyzing the differentially expressed genes.
Assembly: mm10
Supplementary files format and content: Bigwig coverage files were generated by using bamCoverage software with the parameter --normalizeUsingRPKM
Supplementary files format and content: read count table for all the RNA-seq samples

extract_protocol:
After the treatment, plates were placed on ice, medium was removed, and the cells were washed in 2ml per well in cold 1X PBS without cycloheximide (CHX). PBS was removed and cells were lysed in 450μl of lysis buffer. (*Polysome buffer: 20mM Tris pH 7.5, 150mM NaCl, 100μg/ml CHX, 5mM MgCl2, 1mM DTT. *Lysis buffer: Polysome buffer + 25U/ml TURBOTM DNase + 1% Triton X-100. Cells were spun for 10min at 20000g and supernatant was collected.
mRNA was isolated from 100-200 ng of total RNA with NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB, E7490S). cDNA libraries were prepared according to the protocol for NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina (NEB, E7760S). Libraries were amplified 12 cycles and sent for Illumina sequencing. Experiment was performed using 2 biological replicates.


title: Hepatic organoid2, rep1


title: PDOVCA_17


title: 2

value: High-grade B-Cell Lymphoma


title: Ribo-seq, nohs, siCtrl, rep1


title: Foregut, rep3

source_name: Foregut

value: Foregut


title: NNML31

value: DMSO replicat 1


title: 4

value: DMSO replicat 2


title: RNA, nohs, siCtrl, rep2


title: Hepatic organoid1, rep1


title: EB_GFP-yki_biol rep 03

value: midgut

value: enteroblast

value: esgts> GFP.NLS,ykiact

value: female

value: adult


title: Ribo-seq, nohs, siSrp72, rep1

value: cell line

value: fibroblast

value: wt

value: no hs, siSrp72


title: Hepatoblast, rep3

source_name: Hepatoblast

value: Hepatoblast


title: RNA, hs, siSrp72, rep1

value: hs, siSrp72


title: NNML29

source_name: HT

value: HT

value: Diffuse Large B-Cell Lymphoma

value: JQ1 replicat 2


title: EB_GFP-yki_biol rep 01


title: RNA, hs, siSrp72, rep2


title: Hepatoblast, rep1


title: EB_GFP-yki-ss_biol rep 02

value: esgts> GFP.NLS,ykiact, ssHA


title: Hepatoblast, rep2


title: NNML33

value: High-grade B-Cell Lymphoma

value: DMSO replicat 3


title: EB_GFP-yki-ss_biol rep 01

value: midgut


title: cerebral cortex of gestational week 12 and 13

city: Xiamen

first: Xueyu

last: Guo

state: Fujian

address: 668 Jimei Avenue, Jimei District

department: Center for Precision Medicine

institute: Huaqiao University

description: Fresh frozen tissue Spatial transcriptome sequencing.

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline (v2.0.0) to generate FASTQ files.
Sequences were aligned to GRCh38_release95 genome to gene expression count using Space Ranger's default settings.
Assembly: GRCh38
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.tsv.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions.csv.gz: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: filtered_feature_bc_matrix.h5.gz: the h5 format of spatial data
Library strategy: Spatial Transcriptomics

source_name: cerebral cortex of fetal brain

extract_protocol:
The fresh fetal cerebral cortices were embedded into suitable tissue block sizes. After passing the RNA quality inspection, the tissue sections (10 µm cut thickness) were placed on a spatial transcriptomics slide. The optimal incubation time for permeabilization of the tissue sections were determined, and then the tissue sections were fixed, stained, imaged, permeabilized, reverse transcribed, and finally the spatial library and sequencing were prepared.
Spatial transcriptome sequencing library was prepared with 10x Genomics Visium Spatial Gene Expression Slide & Reagent Kit according to manufacturer's construction.

value: cerebral cortex of fetal brain

value: geatational week 12 and 13

value: Four sections from geatational week 12 and 13 were processed on the same spatial transcriptome slide.


title: RNA, nohs, siSrp72, rep2


title: EB_GFP-yki_biol rep 04

value: enteroblast

value: esgts> GFP.NLS,ykiact

value: female

value: adult


title: NNML32

value: DMSO replicat 2


title: RNA, nohs, siSrp72, rep1

value: cell line

value: fibroblast

value: wt

value: no hs, siSrp72


title: Foregut, rep2

value: Foregut


title: NNML30

value: HT

value: Diffuse Large B-Cell Lymphoma

value: JQ1 replicat 3


title: Foregut, rep1


title: EB_GFP-ss_biol rep 03

value: midgut

value: esgts> GFP.NLS,ssHA


title: EB_GFP-yki_biol rep 02


title: NNML28

value: JQ1 replicat 1


title: RNA, hs, siCtrl, rep1

value: hs, siCtrl


title: EB_GFP-ss_biol rep 04

value: enteroblast


title: NNML27

value: DMSO replicat 3


title: RNA-seq_RPE_USP39_KD_rep3

city: Frankfurt am Main

first: Michaela

last: Müller-McNicoll

address: Max-von-Laue-Str. 13

country: Germany

institute: Goethe University Frankfurt

description: RNA-seq

data_processing:
RNA-seq: Reads were mapped to the human genome hg38 using STAR (v2.6.1d) with default parameters. Mapped reads were counted with htseq-count or featureCounts (v2.0.1) using GENCODE gene annotation (version 44).
Mapped reads were analysed with DESeq2 for differential expression. Alternative splicing was analyzed with the MAJIQ framework (version 2.3). BAM files of Ctrl and KD experiments together with the GENCODE gene annotation (version 38) served as input. majiq build and majiq deltapsi were executed with default parameters while for voila modulize the following parameters were adjusted: --changing-between-group-dpsi 0.05, --non-changing-between-group-dpsi 0.02, --changing-between-group-dpsi-secondary 0.025, --probability-changing-threshold 0.9, --probability-non-changing-threshold 0.5 and --show-all.
Assembly: hg38
Supplementary files format and content: Count tables in .txt format.

source_name: RPE

growth_protocol: Cells were grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum and 1% penicilin at 37˚C with 5% CO2.

extract_protocol:
Total RNA was isolated using the Trizol method.
For RNA-seq, total RNA was subjected to polyA selection and Illumina library preparation following standard procedures. RNA-seq libraries were sequenced on an Illumina NovaSeq6000 instrument (paired-end 150-nt reads).

treatment_protocol: Cells were transfected 24 h postseeding with 20 nM siRNAs ON TARGETplus anti-USP39 siRNA (Horizon Discovery) and AllStars Negative Control siRNA (Qiagen) using Lipofectamine RNAiMAX (Life Technologies) according to the manufacture protocol. Experiments were performed 72 h post transfection. Transfection efficiency was verified by Western blotting.

value: KD


title: EB_GFP-ss_biol rep 01

value: female

value: adult


title: RNA-seq_RPE_USP39_KD_rep2

description: RNA-seq


title: RNA-seq_RPE_Ctrl_rep2

description: RNA-seq

value: Ctrl


title: RNA, nohs, siCtrl, rep1

value: cell line

value: fibroblast

value: no hs, siCtrl


title: EB_GFP-ss_biol rep 02


title: NNML23

value: High-grade B-Cell Lymphoma

value: JQ1 replicat 2


title: Batf3_CD62L_neg_T_rep3

first: Hua

last: Tang

state: Shandong

address: Qingdao Road 6699

institute: Shandong First Medical University &Shandong Academy of Medical Sciences

description: Primed donor CD62L- CD44hiCD45.1+CD4+ T cells

data_processing:
Raw data were assessed using FastQC, and were filtered using Trimmomatic (version 0.36).
Clean reads were mapped to mm10 Mus musculus reference genome using STAR software (version 2.7.3a) with default parameters, and were counted by featureCounts (Subread-1.6.5).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: mediastinal lymph node

extract_protocol:
All cell subsets were sorted into microcentrifuge tubes containing 500 μl of RLT buffer supplemented with β-mercaptoethanol. RNAs were extracted with the RNeasy Micro Kit (QIAGEN) following the manufacturer’s instructions.
All RNA samples were amplified by 13 cycles using RNALib Single cell WTA Kit (Lifeint). Libraries were constructed using Lifeint Transpose DNA Library Prep Kit for Illumina. The library quality was assessed using a Bioptic Qsep 100 analyzer.

treatment_protocol: Naive CD45.1+CD4+OT-II T cells, specifically recognize Ovalbumin323-339, were sorted from superficial lymph nodes and spleens of un-treated CD45.1×OT-II mice by BD Aria II cell sorter. Twenty-four hours after injection with naive CD45.1+OT-II cells, WT and Batf3-/- recipient mice were intranasally immunized with 60 μg OVA (Grade VI, Sigma Aldrich) plus 30 μg papain (Sigma Aldrich) 3 times every 6-8 hours. Activated donor CD44hiCD62L+ and CD44hiCD62L- CD45.1+T cells were sorted from mediastinal lymph nodes 5 days after immunization.

value: CD4+ OT-II T cells

tag: recipient mice

value: Batf3-/- mice

tag: state

value: primed


title: Batf3_CD62L_pos_T_rep3

description: Primed donor CD62L+ CD44hiCD45.1+CD4+ T cells


title: Batf3_CD62L_pos_T_rep2


title: NNML25

value: HT

value: Diffuse Large B-Cell Lymphoma

value: DMSO replicat 1


title: NNML26

value: DMSO replicat 2


title: RNA-seq_RPE_Ctrl_rep1

description: RNA-seq


title: RNA-seq_RPE_USP39_KD_rep1

description: RNA-seq


title: Mac, cxcl10, rep4

city: Shanghai

first: Zhe

last: Wang

state: Shanghai

address: Siping Road, Shanghai

institute: Tongji university

description: instrument model: illumina novaseq x plus

data_processing:
trim_galore software was used to trim adapters of FastQ files
RNA-seq reads were then aligned to the hg38 with STAR
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount
Assembly: hg38
Supplementary files format and content: Raw counts

extract_protocol:
After incubation, we washed cells twice with PBS, then used TRIzol (ambion) to extract RNA following the manufacturer's recommended protocol.
RNA-Seq libraries were prepared with Ilhumina® Stranded mRNA Prep, Ligation

value: CXCL10 (100ng/mL)


title: Batf3_CD62L_pos_T_rep1


title: NNML24

value: JQ1 replicat 3


title: EB_GFP_biol rep 02

value: midgut

value: enteroblast

value: esgts> GFP.NLS

value: female


title: NNML22

value: JQ1 replicat 1


title: Batf3_CD62L_neg_T_rep2


title: RNA-seq_RPE_Ctrl_rep3

description: RNA-seq

value: Ctrl


title: EB_GFP_biol rep 01

value: adult


title: NNML21

value: High-grade B-Cell Lymphoma

value: DMSO replicat 3


title: Batf3_CD62L_neg_T_rep1

value: CD4+ OT-II T cells

value: Batf3-/- mice


title: EB_GFP_biol rep 03


title: Mac, cxcl10, rep1


title: ISC_GFP-yki-ss_biol rep 01

value: intestinal stem cell

value: esgts> GFP.NLS,ykiact, ssHA


title: ISC_GFP-yki-ss_biol rep 03


title: Mac, cxcl10, rep3


title: NNML20


title: WT_CD62L_pos_T_rep2

value: C57BL/6 mice

value: primed


title: WT_CD62L_pos_T_rep3


title: NNML18

source_name: Raji

value: Raji

value: Burkitt Lymphoma


title: ISC_GFP-yki-ss_biol rep 02

value: midgut


title: NNML19

value: DMSO replicat 1


title: WT_CD62L_pos_T_rep1


title: ISC_GFP-yki_bio rep 02

value: esgts> GFP.NLS,ykiact


title: Mac, con, rep4

value: control


title: ISC_GFP-yki_bio rep 03

value: female


title: acRIP_siTDP_IgG_3

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

data_processing:
Raw reads were cleaned by Trim Galore v0.6.7, and the clean reads were further mapped to the mouse genome (mm10) by STAR v2.7.10a. Uniquely mapped reads were quantified by FeatureCounts v2.0.2.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes the read count list of each sample.
Library strategy: acRIP-seq

extract_protocol:
Polyadenylated RNAs were isolated from total RNAs by Oligo(dT)25 Dynabeads.
Libraries were constructed by following the Smart-seq2 procedure.

value: siTARDBP

tag: antibody

value: IgG


title: WT_CD62L_neg_T_rep1


title: NNML17

value: JQ1 replicat 2


title: acRIP_siTDP_IgG_2


title: WT_CD62L_neg_T_rep3


title: Mac, con, rep1


title: NNML16

value: JQ1 replicat 1


title: ISC_GFP-yki_bio rep 01

value: adult


title: NNML15

value: DMSO replicat 3


title: ISC_GFP-ss_biol rep 04

value: intestinal stem cell

value: esgts> GFP.NLS,ssHA


title: NNML14

value: DMSO replicat 2


title: WT_CD62L_neg_T_rep2

value: CD4+ OT-II T cells

value: C57BL/6 mice

value: primed


title: ISC_GFP-ss_biol rep 03

value: midgut


title: Mac, con, rep3


title: ISC_GFP-ss_biol rep 02


title: NNML13

value: Raji

value: Burkitt Lymphoma

value: DMSO replicat 1


title: NaiveT_rep1

description: Naïve CD44loCD62L+CD45.1+CD4+TCRVα2+TCRVβ5.1/5.2+ OT-II T cells

source_name: superficial lymph node and spleen

value: not transferred

value: naive


title: acRIP_siTDP_IgG_1

value: siTARDBP

value: IgG


title: NNML11

source_name: Riva

value: Riva

value: Diffuse Large B-Cell Lymphoma

value: JQ1 replicat 2


title: ISC_GFP_biol rep 03

value: intestinal stem cell

value: esgts> GFP.NLS

value: female

value: adult


title: NaiveT_rep2

value: CD4+ OT-II T cells


title: Ovary miRNA, Pregnancy, rep2

city: Chengdu

first: Binyun

last: Pan

address: No. 211 Huimin Road, Wenjiang District

institute: Sichuan Agricultural University

data_processing:
Small RNA data processing step Data filtering The raw sequencing data are called raw tags. We obtained clean tags using the SOAPnuke[1]. The filtering rules were as follows: removed low quality tags; removed tags with 5’ primer contaminants; remove tags without 3’ primer; removed tags without insertion; removed tags with poly A; removed tags shorter than 15nt.  Small RNA Annotation and miRNA Identification After filtering, the clean tags were mapped to the reference genome and other sRNA database including miRbase, siRNA, piRNA and snoRNA with Bowtie2[2]. Particularly, cmsearch[3] was performed for Rfam  mapping. In the annotation information of different RNAs, to ensure that each small RNA was mapped to a unique category, we set the following rules: MiRbase(v22) > pirnabank(v1.0) > snoRNA(v1.2 human/plant ) > Rfam (v12.1)> other sRNA. The miRDeep-P2 [4] or miRDeep2[5] package was used to identify potentially novel miRNAs. The potentially novel miRNAs and were named novel_mirXXX, in which XXX is a unique number specified for each novel miRNA candidate. Target Gene Prediction RNAhybrid [6], miRanda[7] and TargetScan [8] were used to predict target genes of miRNAs . miRNA quantification The small RNA expression level is calculated by counting absolute numbers of molecules using unique molecular identifiers. The expression formula is: C is the number of UMIs of reads that were mapped to the small RNA, T is the UMI number of total clean reads of the sample.    Differential Expression Analysis  Differential expression analysis was performed using the DEGseq2  on Dr. Tom Multi-omics Data Mining System (https://biosys.bgi.com). Q value≤ 0.05 (or FDR value≤0.001) was used to judge the significance of expression difference.  Target Genes Annotation To annotate gene functions, all target genes were aligned against the Kyoto Encyclopedia of Genes KEGG and Gene Ontology database. GO enrichment analysis and KEGG enrichment analysis of target genes were performed using phyper, a function of R on Dr. Tom Multi-omics Data Mining System (https://biosys.bgi.com). The P-value was corrected using the Bonferroni method, and a corrected P-value ≤ 0.05 was taken as a threshold. GO terms or KEGG terms fulfilling this condition were defined as significantly enriched terms. [1]SOAPnuke(1.5.0) -p 0.7 -z 18 [2]Bowtie2 (2.2.9) -L 16 [3]cmsearch (1.1.2)  [4]miRDeep-P2  [5]miRDeep2 (0.0.8) mapper.pl reads.fa -c -i -j -n -l 17 -r 20 -o 6; miRDeep2.pl -g -1 -v -u -P -c [6]RNAhybrid(0.1) -b 100 -c -f 2,8 -m 100000 -v 3 -u 3 -e -20 -p 1 -s 3utr_human [7]miRanda (3.3a) -en -20 -strict [8]TargetScan (7.1)
Assembly: GCF_000003025.6_Sscrofa11.1
Supplementary files format and content: Microsoft Excel 97-2003 (.xls) core_table.xls:gene_id mirbase_id mature_seq mature_chr mature_seq_length exp read_count average_exp average_read_count diffexp_deseq2_qvalue diffexp_deseq2_pvalue diffexp_log2fc
Supplementary files format and content: Microsoft Excel 97-2003 (.xls) core_table_gene.xls:st_gene_id  gene_id  gene_symbol  fpkm tpm read_coun  norm_read_count average average_tpm average_read_count  norm_average_read_count  diffexp_deseq2_qvalue diffexp_deseq2_pvalue diffexp_log2fc gene_symbol  gene_other_symbol gene_type gene_tran_num  gene_tran_list gene_coding_capacity  gene_known_novel  gene_chr  gene_start  gene_end  gene_strand  gene_map_loc  url_ncbi_gene_id  url_hgnc_gene_id  url_ensembl_gene_id  url_genecard_gene_id  url_mirbase_gene_id  gene_kegg_k_id  cog  eggnog  genebank  go_c  go_f go_p  interpro  kegg_disease  kegg_module  kegg_pathway  kegg_reaction  pfam  reactome  tf  tf_cofactors  uniprot primary_seq

organism: Sus scrofa

source_name: ovary

extract_protocol:
Small RNA Library Construction Protocol 1 Sample QC Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 Adapter Ligation Take a certain amount of RNA sample,The purified RNA is combined with 3’ Adapter, and incubated. Then combine 5’ Adapter, and incubate.  3 RT - PCR Prepare the Reverse Transcription Reaction Mixture, into the thermocycler and run the program. Prepare the PCR Reaction Mixture, into the thermocycler and run the program. 4 Purify PCR products Then the PCR products are purified with PAGE gel, dissolve the recylced products in EB solution. 5 Library QC The corresponding library quality control protocol will be selected depending upon product requirements. 6 Circularization Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. 7 Sequencing Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).
1 Tissue Sample Fragmentation and Lysis 1.1 Grinding Machine 1.1.1 Transfer appropriate sample to corresponding grinding tube, 1.1.2 Add 1.5 mL TRIzol lysis buffer, transfer to the grinding machine, grind 30 s, stay at 5 min 1.2 Liquid Nitrogen Grinding and Crushing 1.2.1 Dispense 1.5 mL of TRIzol lysis buffer to a 2 mL tube. 1.2.2 Take appropriate amount of tissue samples, grind the tissue samples into powder with liquid nitrogen and transfer into the lysis buffer. Stand flat for 5 min for the fully lysis of tissue cells. 1.3 Cell Sample Lysis Add appropriate TRIzol lysis buffer into the cell sample tube (1 mL TRIzol for 1×106 cells) 2 Sample Purification 2.1 Centrifuge the tissue samples after grinding and crushing at 12000×g for 5 min in 4℃. 2.2 Transfer the supernatant to the centrifuge tube with 300 µL Chloroform/isoamyl alcohol (24:1) mix thoroughly by upside down violent shaking； 2.3 Centrifuge at 12000×g for 8 min in 4℃ (optional extraction with equal supernatant volume of chloroform/isoamyl alcohol (24:1) could be used if the middle layer is thick and the water phase turbidity). 2.4 Transfer the supernatant to the 1.5 mL centrifuge tube, add 2/3 volume of Isopropyl alcohol, (optional 2µL 5 mg/mL glycogen for low-input tissue and cell sample to help precipitation). Gently invert and mix, place in -20℃ refrigerator for more than 2 h. 2.5 Centrifuge at 17500×g for 25 min in 4℃. Discard the supernatant, wash with 0.9 mL 75% ethanol, suspend the precipitation by inverting. 2.6 Centrifuge at 17500×g for 3 min in 4℃ (optional wash with 0.9 mL 75％ ethanol could be used, 17500×g for 3 min in 4℃)。 2.7 Discard the supernatant, centrifuge for a short time and use the tip to remove the residual liquid, air dry for 3-5 min. 2.8 Dissolve the precipitation with 20-200 μL DEPC-H2O or RNase-free water.

value: ovary


title: acRIP_siTDP_IP_3

value: IP


title: NNML12

value: JQ1 replicat 3


title: ISC_GFP-ss_biol rep 01

value: midgut

value: esgts> GFP.NLS,ssHA


title: acRIP_siTDP_Input_3


title: Ovary miRNA, Pregnancy, rep3


title: acRIP_siTDP_Input_2


title: NNML10

value: JQ1 replicat 1


title: acRIP_siTDP_IP_1


title: ISC_GFP_biol rep 02


title: NNML8

value: DMSO replicat 2


title: NNML9

value: DMSO replicat 3


title: NaiveT_rep3

value: not transferred

value: naive


title: NNML7

value: Riva

value: Diffuse Large B-Cell Lymphoma

value: DMSO replicat 1


title: Ovary miRNA, Year 1, rep3


title: acRIP_siTDP_IP_2

value: siTARDBP


title: acRIP_siTDP_Input_1


title: Ovary miRNA, Year 1, rep2


title: acRIP_293T_IgG_1

value: WT

value: IgG


title: Ovary miRNA, Year 1, rep1


title: acRIP_293T_IgG_2


title: NNML5

source_name: Ramos

value: Ramos

value: Burkitt Lymphoma

value: JQ1 replicat 2


title: mock, rep2

city: Yangzhou

first: Mingnan

last: Qu

address: Pazhou Dadao Rd, 17-19

institute: Yangzhou Univerisity

description: Library name: GFP-2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata.
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100.
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9.
Perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: msu7.0
Supplementary files format and content: FPKM values for each Sample.

organism: Oryza sativa

source_name: leaf

growth_protocol: All the plant materials  were grown in pots under fluctuating light and drought stress

extract_protocol:
Total RNA was extracted from rice leaves using a Trelief® RNApre Pure Plant Kit (tsingke, code: TSP411) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The leaves of 3-week-old rice plants were collected.

value: leaf

value: leaf cells


title: mock, rep1

description: Library name: GFP-1


title: ISC_GFP_biol rep 01

value: midgut

value: intestinal stem cell

value: esgts> GFP.NLS

value: female

value: adult


title: acRIP_293T_IP_3

value: IP


title: NNML6

value: JQ1 replicat 3


title: PIF4-OE, rep3

description: Library name: PIF4-GFP-3


title: PIF4-OE, rep2

description: Library name: PIF4-GFP-2


title: NNML3

value: DMSO replicat 3


title: Ovary miRNA, Puberty, rep3

value: ovary


title: acRIP_293T_IP_1


title: NNML4

value: JQ1 replicat 1


title: Ovary miRNA, Puberty, rep2


title: acRIP_293T_IP_2

value: WT


title: Ovary miRNA, Pregnancy, rep1


title: mock, rep3

description: Library name: GFP-3


title: acRIP_293T_Input_2


title: PIF4-OE, rep1

description: Library name: PIF4-GFP-1


title: Ovary miRNA, Day 3, rep1


title: OV81_CTL_1

city: Ann Arbor

first: Karan

last: Bedi

state: MI

address: 1600 Huron Pkwy

department: Biostatistics

institute: University of Michigan

data_processing:
Sequencing for OV81 and OV81-CP40 samples was performed on a Illumina HiSeq 2000 (Illumina, San Diego, CA) with 300 total cycles of paired-end sequencing (150 cycles per read) according to the manufacturer's protocol. Bcl2fastq2 Conversion Software (Illumina, San Diego, CA) was used to generate demultiplexed Fastq files.
Reads were mapped to GRCh38 using STAR v2.5.2a and gene quantifications were calculated using Stringtie v2.1.1 to quantify refGene annotations. Gene read counts were calculated using featureCounts v1.6.1 (subread).
Assembly: hg38
Supplementary files format and content: The columns of the counts.txt files are: (1) gene symbol; (2) sample read count

growth_protocol: Cells were cultured in a humidified atmosphere (5% CO2) at 37°C in DMEM

extract_protocol:
Total RNA was extracted and the Illumina RNAseq kit was used to prepare sequencing libraries
OV81 libraries were sequenced paired-end 100 bp.

value: high grade serous carcinoma

value: control


title: OV81_CTL_3


title: OV81_CTL_2


title: NNML2

value: Ramos

value: Burkitt Lymphoma

value: DMSO replicat 2


title: acRIP_293T_Input_3


title: acRIP_293T_Input_1


title: OV81_CP40_3

value: cisplatin


title: Jurkat cells, unstimulated, replicate 3, RNA-seq

city: Philadelphia

first: Peter

last: Choi

state: PA

address: 3501 Civic Center Blvd, CTRB 4400

department: Pathology and Laboratory Medicine

institute: The Children's Hospital of Philadelphia

data_processing:
Reads were first trimmed with BBDuk using the parameters {ref=adapters ktrim=r k=23 mink=11 hdist=1 tpe tbo qtrim=r trimq=15 qin=auto minlength=30}.
For RNA-seq analysis, we aligned reads to the hg38 genome using STAR with the parameters {-alignSJoverhangMin 8 --alignEndsType Local --outFilterMultimapNmax 1}.
We then ran MAJIQ build across all samples in a given analysis with the parameters {--minreads 2 --min-denovo 2 --minpos 1 --target-lsvs}. We then ran MAJIQ deltapsi or psi with the parameters {--minpos 1 –minreads 2}.
Assembly: hg38
Supplementary files format and content: tab-delimited text files containing merged deltapsi quantifications between pairs of conditions, for both RNA-seq and LSV-seq, for the union of all junctions/events across both.

source_name: Jurkat JSL1

growth_protocol: Jurkat T-cells (JSL1 clone) were cultured in RPMI 1640 media supplemented with 5% fetal bovine serum, 100 U/mL penicillin and 100 ug/mL streptomycin.

extract_protocol:
Total RNA was purified from cells with the Maxwell RSC 48 instrument using the Maxwell RSC simplyRNA Cells Kit (AS1340, Promega).
RNA-seq library preparation was performed by Novogene using standard protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, first-strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, PCR amplification, and purification.

treatment_protocol: Cells were either left unstimulated or stimulated with 20 ng/mL of the phorbol ester PMA (524400, Millipore Sigma) for 48 hrs.

value: Jurkat JSL1

value: T lymphocyte

value: unstimulated


title: Ovary miRNA, Day 3, rep3


title: Ovary mRNA, Pregnancy, rep2

data_processing:
mRNAseq data processing step Data filtering  The sequencing data was filtered with SOAPnuke [1] by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com). RNA identification  Bowtie2[2] was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included. Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1) [3]. The heatmap was drawn by pheatmap (v1.0.8) [4] according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) [5].  Gene Annotation To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) . [1]SOAPnuke (v1.5.6) -l 15 -q 0.2 -n 0.05 [2]Bowtie2 (2.3.4.3) -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 1 -k 200 [3]RSEM (v1.3.1) --forward-prob 0 [4]Pheatmap (1.0.8) [5]DESeq2 Q value ≤ 0.05 (or FDR ≤ 0.001)
Assembly: GCF_000003025.6_Sscrofa11.1
Supplementary files format and content: Microsoft Excel 97-2003 (.xls) core_table.xls:gene_id mirbase_id mature_seq mature_chr mature_seq_length exp read_count average_exp average_read_count diffexp_deseq2_qvalue diffexp_deseq2_pvalue diffexp_log2fc
Supplementary files format and content: Microsoft Excel 97-2003 (.xls) core_table_gene.xls:st_gene_id  gene_id  gene_symbol  fpkm tpm read_coun  norm_read_count average average_tpm average_read_count  norm_average_read_count  diffexp_deseq2_qvalue diffexp_deseq2_pvalue diffexp_log2fc gene_symbol  gene_other_symbol gene_type gene_tran_num  gene_tran_list gene_coding_capacity  gene_known_novel  gene_chr  gene_start  gene_end  gene_strand  gene_map_loc  url_ncbi_gene_id  url_hgnc_gene_id  url_ensembl_gene_id  url_genecard_gene_id  url_mirbase_gene_id  gene_kegg_k_id  cog  eggnog  genebank  go_c  go_f go_p  interpro  kegg_disease  kegg_module  kegg_pathway  kegg_reaction  pfam  reactome  tf  tf_cofactors  uniprot primary_seq

extract_protocol:
mRNA Library Construction Protocol 1 Sample QC Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. 3 mRNA Fragmentation The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented. 4 cDNA Synthesis Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. 5 End Repair, Add A and Adaptor Ligation After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs. 6 PCR The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC The corresponding library quality control protocol will be selected depending upon product requirements. 8 Circularization Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. 9 Sequencing Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).
1 Tissue Sample Fragmentation and Lysis 1.1 Grinding Machine 1.1.1 Transfer appropriate sample to corresponding grinding tube, 1.1.2 Add 1.5 mL TRIzol lysis buffer, transfer to the grinding machine, grind 30 s, stay at 5 min 1.2 Liquid Nitrogen Grinding and Crushing 1.2.1 Dispense 1.5 mL of TRIzol lysis buffer to a 2 mL tube. 1.2.2 Take appropriate amount of tissue samples, grind the tissue samples into powder with liquid nitrogen and transfer into the lysis buffer. Stand flat for 5 min for the fully lysis of tissue cells. 1.3 Cell Sample Lysis Add appropriate TRIzol lysis buffer into the cell sample tube (1 mL TRIzol for 1×106 cells) 2 Sample Purification 2.1 Centrifuge the tissue samples after grinding and crushing at 12000×g for 5 min in 4℃. 2.2 Transfer the supernatant to the centrifuge tube with 300 µL Chloroform/isoamyl alcohol (24:1) mix thoroughly by upside down violent shaking； 2.3 Centrifuge at 12000×g for 8 min in 4℃ (optional extraction with equal supernatant volume of chloroform/isoamyl alcohol (24:1) could be used if the middle layer is thick and the water phase turbidity). 2.4 Transfer the supernatant to the 1.5 mL centrifuge tube, add 2/3 volume of Isopropyl alcohol, (optional 2µL 5 mg/mL glycogen for low-input tissue and cell sample to help precipitation). Gently invert and mix, place in -20℃ refrigerator for more than 2 h. 2.5 Centrifuge at 17500×g for 25 min in 4℃. Discard the supernatant, wash with 0.9 mL 75% ethanol, suspend the precipitation by inverting. 2.6 Centrifuge at 17500×g for 3 min in 4℃ (optional wash with 0.9 mL 75％ ethanol could be used, 17500×g for 3 min in 4℃)。 2.7 Discard the supernatant, centrifuge for a short time and use the tip to remove the residual liquid, air dry for 3-5 min. 2.8 Dissolve the precipitation with 20-200 μL DEPC-H2O or RNase-free water.


title: Ovary miRNA, Puberty, rep1


title: OV81_CP40_2


title: NNML1

data_processing:
Reads were quality-checked using FastQC. (Dobin 226 et al., 2013).
Reads were then aligned to H. sapiens genome build hg38 using STAR 2.7.1a
Raw read counts for each gene were calculated using HTSeqCount 0.11.2.
Read counts were normalized using log2 of RPM normalization
Assembly: hg38
Supplementary files format and content: Normalized counts (log2 RPM) for each sample

extract_protocol:
RNA was extracted from 3 million cells with NucleoSpin 210 RNA extraction kit (Macherey-Nagel) according to manufacturer's instructions.
(Samples 1-36) RNA-Seq libraries were generated according to manufacturer's instructions from 500 ng of total RNA using the Illumina Stranded mRNA Prep, Ligation kit and IDT for Illumina RNA UD Indexes Ligation (Illumina, San Diego, USA). Briefly, Oligo(dT) magnetic beads were used to purify and capture the mRNA molecules containing polyA tails.The purified mRNA were then fragmented at 94oC for 8 min and copied into first strand complementary DNA (cDNA) using reverse transcriptase and random primers. Second strand cDNA synthesis further generated blunt-ended double-stranded cDNA and incorporated dUTP in place of dTTP to achieve strand specificity by quenching the second strand during amplification. Following A-tailing of DNA fragments and ligation of pre-index anchors, PCR amplification was used to add indexes and primer sequences and to enrich DNA libraries (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x12cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using SPRIselect beads (Beckman-Coulter, Villepinte, France) and the final libraries were checked for quality and quantified using capillary electrophoresis. (Samples 37-60) Librairies were prepared according to BGI procedures.

value: DMSO replicat 1


title: Ovary mRNA, Pregnancy, rep3


title: Ovary mRNA, Pregnancy, rep1


title: OV81_CP40_1


title: GF tissue, 6M after graft, 4

city: Gwangjin-gu

first: Min-Gi

last: Han

state: Seoul

address: Neungdong-ro 120

department: 1Department of Stem Cells and Regenerative Technology

country: South Korea

institute: Konkuk University

description: Library name: sample10

data_processing:
the construction of library was performed using QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen, Austria) according to the manufacturer’s instructions.
The read count data were processed based on Trimmed Mean of M-values + Counts per million (TMM+CPM) normalization using DEseq2 (v1.42.0).
Assembly: Sscrofa11.1
Supplementary files format and content: normalized expression table in text file format

source_name: testis

growth_protocol: cells injected into dorsal skin of SKID mouse with high concentrate Matrigel, and cultured for 6 months.

extract_protocol:
RNA was isolated using Trizol reagent (Invitrogen). RNA quality was assessed by Agilent 4200 TapeStation System (Agilent Technologies), and RNA quantification was performed using Qubit (Thermo Fisher).
the construction of library was performed using QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen, Austria) according to the manufacturer’s instructions.

value: testis

value: primary cell

value: germ cell and teticular fibroblast


title: GF tissue, 6M after graft, 3

description: Library name: sample9


title: Liver, replicate 3, LSV-seq

data_processing:
Reads were first trimmed with BBDuk using the parameters {ref=adapters ktrim=r k=23 mink=11 hdist=1 tpe tbo qtrim=r trimq=15 qin=auto minlength=30}.
For LSV-seq analysis, the umi-tools extract command was used to first extract the 10-nucleotide UMI from each read using the parameters {--bc-pattern=NNNNNNNNNN}, followed by STAR alignment with the parameters {-alignSJoverhangMin 8 --alignEndsType Local --outFilterMultimapNmax 1}. Then, umicollapse with parameter {--two-pass} was used to mark UMI read duplicate groups. Because the initial 5’ end primer sequence is also expected to be shared between identical reads, we appended the first 13 nucleotides beyond the UMI to the marked UMI sequences. Final deduplicated reads were selected using custom scripts which first filtered for reads which were at least 30 nucleotides in length, then selected one of the maximal length reads at random for each marked UMI group (consisting of both the marked UMI group itself and the downstream primer barcode).
To quantify splicing, we ran the MAJIQ build command with the parameters {--minreads 2 --mindenovo 2 --minpos 1} and calculated splice ratios with psi-coverage using parameters {--target-lsvs --stack-pvalue-threshold 0 --minbins 1 --minreads 2}.
Assembly: hg38
Supplementary files format and content: tab-delimited text files containing merged deltapsi quantifications between pairs of conditions, for both RNA-seq and LSV-seq, for the union of all junctions/events across both.
Library strategy: LSV-seq

source_name: Liver

extract_protocol:
Total RNA from human adult normal tissues was obtained from a commercial vendor (BioChain Institute Inc.).
For LSV-seq library preparation, the targeted primer pool was gradually annealed to input RNA using a touchdown step and first-strand cDNA synthesis was carried out at an elevated temperature of 60°C to maximize the specificity of the RT reaction. Next, second-strand synthesis was performed and the double-stranded DNA then served as a template for linear amplification by in vitro transcription (IVT). The IVT amplified RNA (aRNA) was then fragmented and subjected to an additional RT step to append a second adapter sequence. The resulting cDNA was then amplified by PCR to generate the final sequencing library.

value: Liver


title: Ovary miRNA, Day 3, rep2

value: ovary


title: FO tissue, 6M after graft, 4

description: Library name: sample6

value: testicular fibroblast


title: Jurkat cells, unstimulated, replicate 2, RNA-seq


title: Jurkat cells, stimulated, replicate 3, RNA-seq

value: PMA stimulation


title: FO tissue, 6M after graft, 3

description: Library name: sample5


title: Ovary mRNA, Year 1, rep3


title: Ovary mRNA, Year 1, rep2


title: GF tissue, 6M after graft, 2

description: Library name: sample8


title: Liver, replicate 2, LSV-seq


title: FO tissue, 6M after graft, 2

description: Library name: sample4


title: Jurkat cells, stimulated, replicate 2, RNA-seq


title: Jurkat cells, stimulated, replicate 1, RNA-seq


title: Ovary mRNA, Year 1, rep1


title: Ovary mRNA, Puberty, rep3


title: FO tissue, 6M after graft, 1

description: Library name: sample3


title: 5D testis tissue, control, 2

description: Library name: sample2


title: Heart right atrium, replicate 3, LSV-seq

source_name: Heart right atrium

value: Heart right atrium


title: Ovary mRNA, Puberty, rep2


title: Liver, replicate 1, LSV-seq


title: GF tissue, 6M after graft, 1

description: Library name: sample7


title: MR-3

city: Beijing

first: mengxia

last: fu

address: xicheng road

institute: fuwai hospital

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
For 10x data, Cell Ranger 6.1.2 was used to quantify gene expression leve with human reference version GRCh38.
The output of Cell Ranger filtered gene expression matrix were analyzed by R software (Version 3.6.1) with the Seurat package (Version 3.2.0).
Before the downstream analysis, low-quality cells were excluded and retained the high-quality single-cell data that met the following criterial: Briefly, cells with high likelihood of being doublets were filtered out by employing DoubletFinder (2.0.3). Then, we merged all samples and removing all cells with >3 median absolute deviations difference in read numbers and mitochondrial reads3 as the reviewer suggested. Finally, we excluded HBB or MYL2 positive cells to remove the red blood cells and cardiomyocytes.
After removal of low-quality cells, the gene expression matrices were normalized by the NormalizeData function in Seurat.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: mitral valve

extract_protocol:
Samples were washed by PBS to remove the remaining blood cells and then cut into small pieces. These small pieces were washed by PBS again and digested in DPBS (Gibco, 14040133) containing 0.28 U/mL Liberase TM (Roche, 05401119001) at 37 °C for 45 minutes, followed by gently shaking. The single-cell suspension was filtered with a 40 μm cell strainer and collected by centrifugation at 400g, 4 °C for 5 minutes. The supernatant was discarded, and the cell pellets were resuspended in 1 mL ACK lysing buffer (Gibco, A1049201) and incubated for 5 minutes at room temperature. The resulting suspension was further diluted to 10x the initial volume with cold PBS, and centrifuged at 400g, 4 °C for 5 minutes. The cell precipitate was resuspended in 500 μl cold DMEM containing 10% fetal bovine serum and use immediately.
Single-cell suspensions were processed through the 10x Genomics Chromium System (10x Genomics, Pleasanton, CA, USA), followed by the construction of 3’ gene expression v3.1 libraries and sequencing on an Illumina Noveseq6000 sequencer. Briefly, cells (>90% viability), reagents, gel beads, and partitioning oil are loaded onto 10x Chromium Chip B. Ideally, each individual cell is wrapped with an oil drop that contains gel beads and reagents. This creates an independent reaction space for each cell called gel bead in emulsion (GEM). The primers provided by the gel bead contain a sequencing primer, barcode, UMI, and poly (dT) sequence. The cell in the GEM is lysed, and incubation of the GEM produces barcoded, full-length cDNA from poly-adenylated mRNA. Next, all cDNAs are pooled together, and the steps of general library construction are performed including amplification, fragmentation, end repair, adapter ligation, and sample index PCR (98 °C for 45 seconds; [98 °C for 20 seconds, 67 °C for 30 seconds, and 72 °C for 1 minute] x 14 cycles; 72 °C for 1 minute). The libraries were then sequenced using Illumina Noveseq6000 by CapitalBio Technology (Beijing, China).

value: mitral valve


title: Heart right atrium, replicate 2, LSV-seq


title: Heart right atrium, replicate 1, LSV-seq


title: NC-3

description: 10x Genomics


title: Ovary mRNA, Day 3, rep3


title: MR-1

description: 10x Genomics


title: 5D testis tissue, control, 1

description: Library name: sample1


title: Ovary mRNA, Puberty, rep1


title: Ovary mRNA, Day 3, rep2


title: Brain cerebellum tissue, replicate 3, LSV-seq

source_name: Brain cerebellum

value: Brain cerebellum


title: rpoC-G1122D-rpoB-H482Q-R-2

city: Ithaca

first: John

middle: D

last: Helmann

state: NY

address: 123 Wing drive

department: Microbiology

institute: Cornell University

description:
Library name: Sample 10
Column name in 4023D_rawCounts_rpoC-G1122D-rpoB-H482Q-R-2

data_processing:
Reads were trimmed for low quality and adaptor sequences with TrimGalore v0.6.0, a wrapper for cutadapt and fastQC
Unwanted reads were removed with STAR v 2.7.0e.
Assembly: Reads were mapped to the reference genome (ensemble database, Bacillus subtilis subsp. subtilis str. 168 (GCA_000009045)) using STAR v2.7.0e. SARTools and DESeq2 v1.26.0 were used to generate normalized counts and statistical analysis of differential gene expression.
Supplementary files format and content: tab-delimited txt file contains raw counts for each sample
Supplementary files format and content: xlsx file contains the data of the mutants normalized by WT counts that was used in analysis

organism: Bacillus subtilis

source_name: Whole cell lysate

growth_protocol: WT (HB26336), rpoB H482Y (HB26341), rpoB H482Q (HB28141), rpoC G1122D (HB26291) and rpoB H482Q-rpoC G1122D (HB26332) mutants were grown in LB medium till ~0.4 OD600nm

extract_protocol:
RNA was isolated from 1.5 mL of cells grown till ~0.4 OD600nm using QIAGEN RNeasy Kit (Cat. No. 74106). Genomic DNA contamination was removed by treating RNA with TURBO DNA-free kit from Invitrogen (Cat. No. AM1907)
UDI-barcoded RNAseq libraries were generated with the NEBNext Ultra II RNA Library Prep Kit. Each library was quantified with Qubit (dsDNA HS kit; Thermo Fisher) and the size distribution was determined with Fragment Analyzer prior to pooling

treatment_protocol: Cells were NOT treated with any antibiotics

value: Whole cell lysate


title: rpoB-H482Q-R-2

description:
Library name: Sample 9
Column name in 4023D_rawCounts_rpoB-H482Q-R-2


title: NC-2

description: 10x Genomics


title: Brain cerebellum tissue, replicate 2, LSV-seq


title: rpoB-H482Y-R-2

description:
Library name: Sample 8
Column name in 4023D_rawCounts_rpoB-H482Y-R-2


title: Ovary mRNA, Day 3, rep1


title: Brain cerebellum tissue, replicate 1, LSV-seq


title: rpoC-G1122D-R-2

description:
Library name: Sample 7
Column name in 4023D_rawCounts_rpoC-G1122D-R-2


title: MR-2

description: 10x Genomics


title: wild-type-R-2

description:
Library name: Sample 6
Column name in 4023D_rawCounts_wild-type-R-2


title: Jurkat cells, unstimulated, replicate 3, LSV-seq

extract_protocol:
Total RNA was purified from cells with the Maxwell RSC 48 instrument using the Maxwell RSC simplyRNA Cells Kit (AS1340, Promega).
For LSV-seq library preparation, the targeted primer pool was gradually annealed to input RNA using a touchdown step and first-strand cDNA synthesis was carried out at an elevated temperature of 60°C to maximize the specificity of the RT reaction. Next, second-strand synthesis was performed and the double-stranded DNA then served as a template for linear amplification by in vitro transcription (IVT). The IVT amplified RNA (aRNA) was then fragmented and subjected to an additional RT step to append a second adapter sequence. The resulting cDNA was then amplified by PCR to generate the final sequencing library.


title: Jurkat cells, unstimulated, replicate 2, LSV-seq


title: RNA-seq, HeLa, USP39, KD, rep3

description: RNA-seq

data_processing:
RNA-seq: Reads were mapped to the human genome hg38 using STAR (v2.6.1d) with default parameters. Mapped reads were counted with htSeq-count.
Mapped reads were analysed with DESeq2 for differential expression.  Alternative splicing was analyzed with the MAJIQ framework (version 2.3). BAM files of Ctrl and KD experiments together with the GENCODE gene annotation (version 38) served as input. majiq build and majiq deltapsi were executed with default parameters while for voila modulize the following parameters were adjusted: --changing-between-group-dpsi 0.05, --non-changing-between-group-dpsi 0.02, --changing-between-group-dpsi-secondary 0.025, --probability-changing-threshold 0.9, --probability-non-changing-threshold 0.5 and --show-all.
Assembly: hg38
Supplementary files format and content: Count tables in .txt format.

source_name: HeLa

extract_protocol:
Total RNA was isolated using the Trizol method.
For RNA-seq, total RNA was subjected to polyA selection and Illumina library preparation following standard procedures. RNA-seq libraries were sequenced on an Illumina NovaSeq6000 instrument (paired-end 150-nt reads; 50 million reads per replicate).
strand-specific

value: HeLa

value: USP39 KD


title: CGH: U06-607094_v_Wm82

type: genomic

city: Saint Paul

first: Robert

middle: M

last: Stupar

state: MN

address: 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

institute: University of Minnesota

description: Sample 7

hyb_protocol: Genomic DNA were hybridized to the microarray according to the manufacturer instructions (NimbleGen CGH User Guide Ver 9.1)

scan_protocol: Slides were scanned on the NimbleGen MS 200 Scanner (Roche/NimbleGen, Madison,WI) according to the array manufacturer instructions (NimbleGen CGH User Guild Ver 9.1)

data_processing:
Data was analyzed using the Roche NimbleGen DEVA software.
log2 ratio following normalization of the test genotype compared to the Williams 82 reference genome

molecule: genomic DNA

organism: Glycine max

source_name: DNA from soybean line U06-607094

label_protocol: 500 ng of genomic DNA was labeled and amplified using the NimbleGen Dual-Color Labeling Kit according to the NimbleGen CGH User Guide Ver 9.1.

growth_protocol: single plant leaf tissue

extract_protocol: Genomic DNA samples were isolated using the Qiagen Plant DNeasy protocol

value: single plant leaf tissue

tag: strain

source_name: DNA from soybean line Wm82-ISU-01


title: CGH: UX2569-122-3_v_Wm82

description: Sample 5

source_name: DNA from soybean line UX2569-122-3


title: rpoC-G1122D-rpoB-H482Q-R-1

description:
Library name: Sample 5
Column name in 4023D_rawCounts_rpoC-G1122D-rpoB-H482Q-R-1


title: NC-1

description: 10x Genomics


title: Jurkat cells, unstimulated, replicate 1, RNA-seq

value: Jurkat JSL1

value: T lymphocyte


title: Jurkat cells, unstimulated, replicate 1, LSV-seq

value: unstimulated


title: RNA-seq, HeLa, USP39, KD, rep2

description: RNA-seq


title: rpoB-H482Q-B2-1

description:
Library name: Sample 4
Column name in 4023D_rawCounts_rpoB-H482Q-B2-1


title: rpoB-H482Y-B-1

description:
Library name: Sample 3
Column name in 4023D_rawCounts_rpoB-H482Y-B-1


title: Jurkat cells, stimulated, replicate 2, LSV-seq


title: CGH: UX2569-176-5_v_Wm82

description: Sample 4

source_name: DNA from soybean line UX2569-176-5


title: CGH: PI243540_v_Wm82

description: Sample 2

source_name: DNA from soybean line PI243540


title: RNA-seq, HeLa, USP39, KD, rep1

description: RNA-seq


title: RNA-seq, HeLa, USP39, Ctrl, rep1

description: RNA-seq

value: Ctrl


title: Jurkat cells, stimulated, replicate 3, LSV-seq


title: wild-type-R-1

description:
Library name: Sample 1
Column name in 4023D_rawCounts_wild-type-R-1


title: rpoC-G1122D-R-1

description:
Library name: Sample 2
Column name in 4023D_rawCounts_rpoC-G1122D-R-1


title: Jurkat cells, stimulated, replicate 1, LSV-seq


title: CGH: UX2569-159-2_v_Wm82

description: Sample 3

source_name: DNA from soybean line UX2569-159-2


title: RNA-seq, HeLa, USP39, Ctrl, rep2

description: RNA-seq


title: Guts mid-aged

status: Public on Dec 26 2024

city: Gif-sur-Yvette

first: Katarzyna

last: Siudeja

address: 1, Avenue de la Terrasse

institute: Institute for Integrative Biology of the Cell (I2BC), INSERM U1280, CEA, CNRS, Université Paris-Saclay

description: Library name: ONT_cDNA_Guts_25d

data_processing:
Illumina RNA-seq libraries were aligned to the masked reference genome plus chrTE, which contained consensus transposable element sequences for D. melanogaster, using STAR 2.7.10a with the following parameters: --sjdbOverhang 100 --outFilterMultimapNmax 1 --winAnchorMultimapNmax 10 --outMultimapperOrder Random --outFilterMismatchNoverLmax 0.3 --quantMode GeneCounts quantification mode. The expression count tables were grouped for all samples, and the counts were normalized using TMM normalization method from the edgeR R package.
Raw ONT cDNA reads were basecalled with guppy v6.0.1 using the following parameters for the flowcell and sequencing kit: --flowcell FLO-MIN106 --kit SQK-DCS109. Basecalled reads were trimmed and oriented with pychopper v2, developed by ONT. Basecalled reads were aligned to the masked reference genome plus chrTE, which contained consensus transposable element sequences for D. melanogaster, using minimap2 with the -x splice preset and the --secondary=no parameter. Read counts were quantified using featureCounts v2.0.1 from the Subread package with the following parameters: -Q 5 -L.
Assembly: dm6.48 and consensus transposable element sequences for D. melanogaster
Supplementary files format and content: tabulated text files with raw and normalized counts

source_name: gut

growth_protocol: Flies were maintained on a standard medium at 25°C with a day/night light cycle. Adult progeny was collected over 2–4 days after eclosion and kept at a density of 25-30 flies/tube (mixed sexes). Flies were flipped to fresh tubes every 2-3 days until needed. For aging experiments 3 time-points were analyzed: young 5-7-day-old, mid-age 20-25-days-old and aged 50-60-days-old.

extract_protocol:
Gut and head tissues were dissected in cold, RNase‐free PBS, transferred to 100 μl of TRIzol Reagent (Thermo Fisher Scientific), homogenized with a plastic pestle and snap‐frozen in liquid nitrogen for storage at −80°C. Upon thawing, samples were further processed according to the TRIzol Reagent manufacturer’s protocol. Purified RNA was treated with DNase (Ambion) for 1 h at 37°C, further purified with phenol‐chloroform extraction and isopropanol precipitation, and resuspended in RNase‐free water. All samples had A260/280 ratios above 1.9 and A260/230 ratios above 2.0. RNA integrity was checked on Bioanalyzer (Agilent) using the Agilent RNA 6000 Nano Kit and concentrations were assayed with the Qubit RNA Broad Range Assay Kit (Thermo Fisher Scientific).
For the short-read transcriptome analysis, 700ng of total RNA was used to prepare libraries according to the TruSeq Stranded mRNA protocol (Illumina). Samples were processed in biological triplicates. 2X100 bp paired‐end sequencing was performed on Novaseq (Illumina). For long-read Oxford Nanopore (ONT) cDNA sequencing, we first prepared mRNA with Dynabeads mRNA Purification Kit (Invitrogen #61006) starting from 100 mg of DN-ase digested total RNA, according to the manufacturer’s protocol. mRNA concentration was quantified with the Qubit RNA Broad Range Assay Kit (Thermo Fisher Scientific) and sample quality was checked on Bioanalyzer (Agilent). Samples were then prepared according to the protocol for ONT Direct cDNA sequencing (SQK-DCS109, Oxford Nanopre), using 150 ng of purified mRNA as input. Samples were run on MinION using R9.4.1 flow cells (Oxford Nanopore Technologies) and 48 h‐long sequencing runs.

value: gut

value: whole tissue

value: w1118; rover2R:14M /UAS-2xGFP/+ ; ProsGAL4/+

value: no treatment

tag: batch

value: mid-aged flies (20-25 days)


title: CGH: Suweon97_v_Wm82

description: Sample 1

source_name: DNA from soybean line Suweon97


title: RNA-seq, HeLa, USP39, Ctrl, rep3

description: RNA-seq

data_processing:
RNA-seq: Reads were mapped to the human genome hg38 using STAR (v2.6.1d) with default parameters. Mapped reads were counted with htSeq-count.
Mapped reads were analysed with DESeq2 for differential expression.
Alternative splicing was analyzed with the MAJIQ framework (version 2.3). BAM files of Ctrl and KD experiments together with the GENCODE gene annotation (version 38) served as input. majiq build and majiq deltapsi were executed with default parameters while for voila modulize the following parameters were adjusted: --changing-between-group-dpsi 0.05, --non-changing-between-group-dpsi 0.02, --changing-between-group-dpsi-secondary 0.025, --probability-changing-threshold 0.9, --probability-non-changing-threshold 0.5 and --show-all.
Assembly: hg38
Supplementary files format and content: Count tables in .txt format.

extract_protocol:
Total RNA was isolated using the Trizol method.
For RNA-seq, total RNA was subjected to polyA selection and Illumina library preparation following standard procedures. RNA-seq libraries were sequenced on an Illumina NovaSeq6000 instrument (paired-end 150-nt reads; 50 million reads per replicate).


title: gastric cancer-Chemotherapy [G78T]

city: Fukuoka

first: Chikanori

last: Tsutsumi

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Surgery and Oncology, Graduate School of Medical Sciences

country: Japan

institute: Kyushu University

data_processing:
Raw sequencing reads were aligned to the human reference genome GRCh38 and processed to a matrix representing the UMI’s per cell barcode per gene using Cell Ranger v7.1.0 (10x Genomics)
Output files were analyzed with the R v4.2.1 package "Seurat v4.3.0".
To merge the data of all samples, we used the "SCTransform" package for the normalization and variance stabilization of molecular count data.
Assembly: GRCh38 human reference genome
Supplementary files format and content: rds file

source_name: gastric cancer

extract_protocol:
Single-cell library preparation was performed according to the manual of the Chromium Next GEM Single-cell 3' Reagent Kits v3.1. The cell suspensions were loaded on the Single-cell G Chip for gel bead-in-emulsion (GEM) generation and barcoding. cDNA library thus was generated with a droplet-based sequencing platform (10X Genomics). Next, reverse transcription, RT cleanup cDNA amplification, and quantification was performed to construct a 3’ gene library.
The libraries were sequenced on NovaSeq6000 (Illumina) or DNBSEQ-G400 (MGI Tech).

value: gastric cancer

tag: age

tag: gender

value: Male

value: Chemo


title: gastric cancer [G75T]

value: no


title: KO_CA_Fluid_1

city: Santa Cruz

first: Upasna

last: Sharma

state: CA

address: 1156 High Street

department: Molecular, Cell & Developmental Biology

institute: UC Santa Cruz

data_processing:
Libraries were processed using the tRAX pipeline modiified to include and map to the sequences of rRNAs and rRNA genomic repeats
for epididymis sequences were trimmed using cutadapt -m 15  --adapter=AGATCGGAAGAGCACACGTC using trax trimadapters.py
for epididymal fluid sequences were trimmed using  Seqprep  -L 22 -A GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -B AGATCGGAAGAGCGTCGTGTAGG  followed by umi_tools extract  --bc-pattern=NNNNNNN   using trax trimadapters.py to generate unpaired input into trax
for sperm  sequences were trimmed using  cutadapt -m 22 --adapter=NGATCGGAAGAGCACACGTCTGAACTCCAGTCAC  followed by umi_tools extract  --bc-pattern=NNNNNNN  using trax trimadapters.py to generate unpaired input into trax
Assembly: mm10
Supplementary files format and content: tab-delimited table including read counts

source_name: epididymal fluid

growth_protocol: Tissue samples were collected from wild type and Rnase9-12 knockout FVB mice at age 8-12 weeks old.

extract_protocol:
Total RNA was extracted from the tissues using trizol method
Libraries were treated with PNK and then constructed using  ARM-seq or OTTR-seq protocols

value: epididymal fluid

tag: section

value: Cauda

tag: library prep

value: OTTR-seq


title: gastric cancer-Chemotherapy [G76T]

tag: tissue

value: Chemo+Tz


title: WT_CA_Fluid_3

value: WT


title: WT_CA_Fluid_1


title: SAMP8 mice_TFQA treatment_rep1

type: RNA

city: Tsukuba City

first: Hongyu

last: Lin

state: Ibaraki

address: Tennodai 1-1-1

department: Life and Earth Sciences

institute: University of Tsukuba

description:
Gene expression data from neural stem cells of adult mice
SAMP8 TFQA_1 Avg (log2)

hyb_protocol: Following fragmentation, 100 ng of cRNA were hybridized for 16 h at 45 ºC on GeneChip Mouse Genome Array. Gene Chips were washed and stained in the Gene Atlas Fluidics Station 400.

scan_protocol: Gene Chips were scanned using the GeneChip Scanner 3000 (thermo Fisher Science, Japan).

data_processing:
The raw CEL data were normalized using the transcriptome analysis cosole (TAC) software ver.4.0.1 following the robust multichip average (RMA) algorithm (Thermo Fisher Scientific, Japan)
#%result_name=Analysis_69
#%array_type=Clariom_S_Mouse
#%annotation=Clariom_S_Mouse.r1.na36.mm10.a1.transcript.csv

label: biotin

source_name: Brain of 6 months old adult male SAMP8 mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 9.1 ug total RNA.

growth_protocol: 6 months old adult male SAMP8 and SMAR1 mice (Japan SLC company, Japan) were used for the experiment. Brains were isolated and collected after 37 days TFQA treatment,

extract_protocol: Total RNA was extracted from neural stem cells using the ISOGEN kit (Nippon Gene Co. Ltd., Tokyo, Japan), following the manufacturer's instructions. Total RNA concentration was determined using the NanoDrop 2000 spectro photometer (Thermo Fisher Scientific, USA).

treatment_protocol: SAMP8 and SAMR1 mice were randomly assigned to three groups: SAMR1 water treatment, SAMP8 water treatment and 1 mg/Kg TFQA SAMP8 mice treatment. SAMP8 mice were treated with 1 mg/Kg  TFQA for 37 days.

value: Brain

tag: cell type

value: neural stem cells

value: SAMRP 8 mice

value: 6 months old adult

value: male

value: TFQA treatment


title: gastric cancer [G74T]


title: WT_CA_Fluid_2


title: SAMP8 mice_TFQA treatment_rep3

description:
Gene expression data from neural stem cells of adult mice
SAMP8 TFQA_3 Avg (log2)


title: SAMR1 mice_water treatment_rep3

description:
Gene expression data from neural stem cells of adult mice
SAMR1 Water_3 Avg (log2)

source_name: Brain of 6 months old adult male SAMR1 mice

value: SAMR1 mice

value: water


title: gastric cancer [G71T]

value: gastric cancer


title: gastric cancer [G70T]

value: Male


title: SAMP8 mice_water treatment_rep3

description:
Gene expression data from neural stem cells of adult mice
SAMP8 Water_3 Avg (log2)


title: SAMP8 mice_water treatment_rep1

description:
Gene expression data from neural stem cells of adult mice
SAMP8 Water_1 Avg (log2)


title: KO_CO_Fluid_2

value: Corpus


title: KO_CO_Fluid_3


title: SAMR1 mice_water treatment_rep1

description:
Gene expression data from neural stem cells of adult mice
SAMR1 Water_1 Avg (log2)


title: SAMP8 mice_TFQA treatment_rep2

description:
Gene expression data from neural stem cells of adult mice
SAMP8 TFQA_2 Avg (log2)


title: SAMP8 mice_water treatment_rep2

description:
Gene expression data from neural stem cells of adult mice
SAMP8 Water_2 Avg (log2)


title: gastric cancer [G67T]

value: no


title: gastric cancer [G69T]

value: Female


title: SAMR1 mice_water treatment_rep2

description:
Gene expression data from neural stem cells of adult mice
SAMR1 Water_2 Avg (log2)


title: WT_CO_Fluid_3

value: epididymal fluid


title: CGH: U00-429037_v_Wm82

description: Sample 6

source_name: DNA from soybean line U00-429037

value: single plant leaf tissue


title: KO_CO_Fluid_1

value: OTTR-seq


title: KO_CA_Fluid_2

value: Cauda


title: gastric cancer [G66T]


title: KO_CA_Fluid_3


title: gastric cancer-Chemotherapy [G72T]

value: Chemo+Tz


title: WT_CO_Fluid_1

value: WT


title: WT_CO_Fluid_2


title: KO_CP_Fluid_3


title: KO_CP_Fluid_2


title: WT_CP_Fluid_3


title: KO_CP_Fluid_1


title: WT_CP_Fluid_1


title: WT_CP_Fluid_2


title: KO_CA_Sperm_2

source_name: sperm

value: sperm


title: KO_CA_Sperm_3


title: KO_CA_Sperm_4


title: day10_KO

city: Tianjin

first: Zhen

last: Yang

address: Weijin Street

institute: Nankai University

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: breast tumor

extract_protocol:
Mice were euthanized and dissected at different days after tumor implantation to collect tumor tissues. Tumor tissues were cut into pieces and enzymatically digested with 1 mg/mL collagenase I, 1 mg/mL collagenase IV, and 300 μg/mL DNase I at 37 °C for 45 min. The suspension was then filtered through a 70 μm Nylon Cell Strainer (Corning Life Sciences) and centrifuged at 500 g for 5 min. Erythrocytes were removed by hypotonic lysis for 5 min at room temperature.  The single cells were then incubated for 30 min with FcR blocking anti-mouse CD16/32 antibody followed by incubation with PE anti-mouse CD45 antibody for another 30 min on ice. The CD45+ immune cells were sorted by SONY MA900 Multi-Application Cell Sorter.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, sorted immune cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: breast tumor

value: immune cells

tag: host strain

value: BALB/c

value: Cd28 KO


title: KO_CA_Sperm_1

tag: genotype


title: gastric cancer-Chemotherapy [G64T]

tag: treatment

value: Chemo


title: WT_CA_Sperm_3


title: WT1

city: Warsaw

first: Bartosz

last: Wojtas

address: Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology

description:
Library name: SAR_F09_0001_P01_V11
SAR_F09_0001_P01_V11

data_processing:
mapping by STAR
MarkDuplicates
Counts features by Featurecounts
Assembly: hg38
Supplementary files format and content: text file, feturecounts program output

source_name: glioma

extract_protocol:
homogenization of frozen glioma samples in TRI Reagent® (Thermo Fisher Scientific, Waltham, MA, USA)
polyA+ KAPA Library kit

value: glioma

tag: cell line

value: cell line LN18

value: cell line from ATCC derived from glioma tumor


title: KO3

description:
Library name: SAR_F17_0006_P01_V21
SAR_F17_0006_P01_V21

value: cell line LN229

value: KO

value: CRISPR/Cas9 RECQL4 deletion


title: WT2

description:
Library name: SAR_F09_0003_P01_V11
SAR_F09_0003_P01_V11


title: SW480

city: Nanjing

first: Gu

last: Yuanyuan

address: 163 Xianlin Road

department: School of Life Sciences

institute: Nanjing University

description: oxaliplatin untreated

hyb_protocol: After stopping the labeling procedure, the Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual. a, The total 25 μL mixture from Hy3™-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min. b, Then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA) c, Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon)

scan_protocol: the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs between two groups were identified through Fold change and P-value. Differentially expressed miRNAs between two samples were filtered through Fold change. Finally, hierarchical clustering was performed to show distinguishable miRNA expression profiling among samples.

source_name: exosomes isolated from cell culture

label_protocol: After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling by following steps: a, 1μLRNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture  was incubated for 30 min at 37°C. b, The Reaction was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C。 c, Terminated by incubation for 15 min at 65°C

extract_protocol: After 48h, the medium was harvested and centrifuged at 2500g for 20 min to remove cells, debris and apoptosis bodies, then centrifuged at 10000g for 1 h and filtered with 0.22μm filter to remove MV. The supernatant was subjected to 70 min ultracentrifugation at 110,000g at 4℃. Finally, PBS was used to re-suspend the pellet.

treatment_protocol: After cells were seeded in the same density and cultured overnight, cell culture medium was replaced to 2% FBS containing 20μM oxaliplatin or not.

value: colorectal cancer cell

tag: agent


title: KO4

description:
Library name: SAR_F17_0008_P01_V21
SAR_F17_0008_P01_V21


title: day10_NC

value: NC


title: L-OHPT

description: oxaliplatin treated

value: oxaliplatin


title: KO2

description:
Library name: SAR_F09_0004_P01_V21
SAR_F09_0004_P01_V21


title: WT_CA_Sperm_4

value: Cauda

value: OTTR-seq


title: KO1

description:
Library name: SAR_F09_0002_P01_V21
SAR_F09_0002_P01_V21


title: day6_KO


title: day6_NC


title: WT_CA_Sperm_1

value: sperm

value: WT


title: WT4

description:
Library name: SAR_F17_0007_P01_V11
SAR_F17_0007_P01_V11


title: Epi_KO_CA _3

source_name: epididymis

value: epididymis

value: ARM-seq


title: Epi_WT_CA_2


title: WT_CA_Sperm_2


title: Epi_WT_CA_1


title: Epi_KO_CO _2

value: Corpus


title: WT3

description:
Library name: SAR_F17_0005_P01_V11
SAR_F17_0005_P01_V11


title: Epi_WT_CO _3


title: OFT_23

city: Richmond

first: Grayson

middle: Welch

last: Way

email: waygw@vcu.edu, waygw@outlook.com

state: Virginia

address: 1217 E Marshall Street Room 534

department: Microbiology and Immunology

institute: VCU

hyb_protocol: Samples were prepared for nCounter gene expression profiling with a custom version of the commercially available human metabolic panel following the manufacterer's recommendations (NanoString Technologies).

scan_protocol: Scanning was performed by the nCounter Digital Analyzer.

data_processing: The data were analyzed using ROSALIND® (https://rosalind.bio/), which features a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Differentially expressed genes (DEGs) were identified based on statistical significance between two groups using a cutoff criterion of P < 0.05 and |fold change (FC)| > 1.5.

label: NanoString reporter

source_name: Intestinal pinch biopsy

label_protocol: Oligonucleotide probe hybridization following the manufacturer's (NanoString Technologies) protocol.

extract_protocol: Total RNA was isolated using TRIzol reagent (Thermo Fisher Scientific, Inc, Waltham, MA, USA) following the instructions.

tag: group

value: After FMT

tag: status

value: Decompensated

tag: patientid

value: Duodenum


title: OFT_28


title: OFT_29


title: Epi_KO_CA _2


title: Epi_WT_CA_3


title: Epi_KO_CA _1


title: OFT_21


title: OFT_19

value: Baseline


title: Epi_WT_CO _2


title: OFT_24


title: OFT_18


title: Epi_WT_CO _1


title: OFT_26


title: OFT_16


title: OFT_22


title: Epi_KO_CP_2

value: Caput


title: OFT_20


title: Epi_KO_CP_3


title: Epi_KO_CP_1


title: OFT_17


title: OFT_25


title: OFT_27


title: Epi_WT_CP_3


title: Epi_WT_CP_2


title: Epi_KO_CO _1


title: OFT_15


title: OFT_14


title: Epi_WT_CP_1


title: OFT_13


title: OFT_12


title: VR-0850

city: New York

first: Zeguo

last: Sun

address: 1468 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

data_processing:
The raw RNA sequencing data was aligned to human genome hg38 using STAR 2.5.3a with default parameters and the expression of each gene was quantified with HTseq count with default parameters.
Assembly: hg38
Supplementary files format and content: Raw count expression matrix.

source_name: Whole blood

extract_protocol: Total RNA was isolated from the whole blood stored in PAXgene tubes and then subjected to standard RNA sequencing libraries generation by following manufacturer protocol.

value: Whole blood

tag: ethnicity

value: Not Hispanic or Latino

tag: race

value: African American

value: Pre-transplant


title: VR-0786


title: VR-0811

value: European


title: VR-0784

value: Hispanic or Latino

value: Latin American


title: OFT_11


title: OFT_9


title: OFT_10


title: VR-0783


title: OFT_8


title: OFT_6


title: OFT_5


title: VR-0778


title: VR-0782


title: VR-0777


title: OFT_3


title: OFT_4


title: VR-0776


title: VR-0842


title: VR-0775


title: VR-0774


title: OFT_2


title: OFT_1


title: Ascending_12

value: Rifaximin

value: Ascending Colon


title: VR-0773


title: VR-0771


title: Ascending_11

value: Compensated


title: VR-0769


title: Ascending_10

value: Lactulose Rifaximin


title: OFT_7


title: Ascending_09


title: VR-0779


title: VR-0765

value: Asian


title: Ascending_08


title: Ascending_07


title: VR-0705


title: Ascending_06

value: Control


title: Ascending_05


title: VR-0688


title: VR-0685


title: VR-0686


title: VR-0684


title: Ascending_04


title: Ascending_03


title: Duodenum_12


title: Ascending_02


title: VR-0683


title: VR-0682


title: VR-0681

value: Unknown


title: Duodenum_11

value: Duodenum


title: VR-0724


title: VR-0679


title: VR-0767


title: VR-0678


title: VR-0677


title: VR-0671


title: Duodenum_10


title: Duodenum_08


title: Duodenum_07

value: Lactulose Only Rifaximin only

value: Decompensated


title: Duodenum_09


title: VR-0666

value: Whole blood


title: VR-0645

value: Not Hispanic or Latino


title: VR-0644

value: African American


title: VR-0643

value: Pre-transplant


title: Ascending_01


title: VR-0642


title: Duodenum_06


title: Duodenum_03


title: Duodenum_04

value: Rifaximin only


title: Duodenum_05


title: VR-0640


title: VR-0641


title: Duodenum_01