title: 4-001 (RNA-Seq)


title: 3-007 (RNA-Seq)

status: Public on Mar 10 2021

type: SRA

city: Rochester

first: Daniel

middle: Rothschild

last: OBrien

state: MN

address: 200 First St. SW

country: USA

institute: The Mayo Clinic

library_source: transcriptomic

data_processing:
TopHat for alignment
FeatureCounts to quantify expression
Genome_build: hg38
Supplementary_files_format_and_content: tsv format containg raw gene counts and RPKM normalize expression values

molecule: total RNA

organism: Homo sapiens

source_name: Duodenal mucosa (biopsy)

extract_protocol:
RNA was extracted from freshly frozen biopsy tissue with TRIzol (Ambion, Waltham, Massachusetts) and chloroform.  After centrifugation, the aqueous phase was purified with an RNeasy Mini Kit (Qiagen, Valencia, California). The quality of total RNA samples was assessed by using an Agilent bioanalyzer (Santa Clara, CA).
RNA libraries were prepared according to the manufacturer's instructions for the TruSeq Stranded Total RNA Library preparation kit (Illumina, San Diego, CA). Unique indices, included in the standard TruSeq kits were incorporated at the adaptor ligation step for multiplex sample loading on the flow cells. The flow cells were sequenced as 101×2 paired-end reads on an Illumina HiSeq 4000

tag: tissue

value: Duodenal mucosa (biopsy)

tag: disease state

value: Diabetes Mellitus


title: 2-007 (RNA-Seq)


title: NW1_S1

city: Milan

first: Letizia

last: Messa

address: Piazza Leonardo Da Vinci 32

department: Electronics, Informatics and Bioengineering

country: Italy

institute: Politecnico di Milano

data_processing:
FastQ files were generated via llumina bcl2fastq2 Version 2.17.1.14
Gene and transcript intensities were computed using STAR/RSEM software using Gencode Release m24 (GRCm38) as a reference, using the “-strandness forward” option. Transcript abundance was obtained using the BlueBee® Genomics Platform (Lexogen). Differential expression analysis for mRNA was performed using R package DESeq2
Genome_build: M24
Supplementary_files_format_and_content: BlueBee output:gene_ID, gene_name, locus,  frags_locus, frags_expt, FPKM_THN, comp_frags_locus, comp_frags_expt, FPKM_CHN, status

source_name: Subcutaneous Adipose Tissue

growth_protocol: Biopsies of SAT were collected from a total of 20 subjects: 5 healthy normal weight women (CTRL, age 37 ± 6.7 years, BMI 24.3 ± 0.9 kg/m2), 5 obese women (OBF, age 41 ± 12.5 years, BMI 38.2 ± 4.6 kg/m2), 5 obese women with T2D (OBT2D; age 54.6 ± 14.9 years, BMI 38.1 ± 11.8 kg/m2) and 5 obese men (OBM, age 42.4 ± 6.58 years, BMI 36.9 ± 3.5 kg/m2). Each collected biopsy was weighed and stored in 1 ml of DMEM (Invitrogen Corporation, Jefferson City, MO) supplemented with 2.5% Bovine Serum Albumin (Sigma, St. Louis, MO) per gram of collected tissue.

extract_protocol:
Approximately 500 mg of frozen SAT was homogenized in RLT buffer (Qiagen). RNA from SAT was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer protocol and samples were then treated with the RNase-Free DNase Set (Qiagen). Concentration and quality of the extracted RNA were determined by the NanoDropH ND-1000 spectrophotometer (NanoDrop Technologies, USA) and RNA integrity verified by gel-electrophoresis.
RNA-seq libraries were prepared with the CORALL Total RNA-Seq Library Prep Kit (Lexogen) using 150 ng total RNAs from 5 healthy women, 5 obese women, 5 obese women with T2D and 5 obese men. The RiboCop rRNA Depletion Kit (Lexogen) was used to remove rRNA. Qualities of sequencing libraries were assessed with D1000 ScreenTape Assay using the 4200 TapeStation System (Agilent) and quantified with Qubit™ dsDNA HS Assay Kit (Invitrogen). RNA processing was carried out using Illumina NextSeq 500 Sequencing.

treatment_protocol: The biopsy was immediately transferred to the laboratory and processed. A fragment of the whole adipose tissue biopsy was immediately frozen in liquid nitrogen for RNA extraction.

tag: gender

value: female

tag: age

value: age 37 ± 6.7 years

tag: bmi


title: 3-006 (RNA-Seq)


title: 3-005 (RNA-Seq)


title: 2-005 (RNA-Seq)


title: UT-SCC-14 shANO1_66_2

city: Helsinki

first: Outi

last: Monni

address: Haartmaninkatu 8, Biomedicum 1

country: Finland

institute: University of Helsinki

description: cell line from head and neck squamous cell carcinoma transduced with shPPFIA1 69 shRNA

data_processing:
Base-calling was done with Real-Time Analysis (RTA), RTA v2, (Illumina NextSeq 500). Fastq files were generated by using bcl2fastq.
Read quality was verified by FASTQC v0.11.3. Trimmomatic v0.36 was used for trimming of data and qualimap v2.2 platform was used in analyzing the data.
MultiQC v0.8 tool was used in the data analysis. High quality reads were imported into STAR v2.5 for alignment into BAM files.
Annotation gtf-file used for alignments came from gencode.v28.
Mapped reads were assigned to genomic features using the Subread package and featureCounts.
Genome_build: GRCh38
Supplementary_files_format_and_content: Differential expression analysis was performed by DESeq2 package R v3.2.3 and results underwent logarithmic transformation. Statistical test used was Wald. Processed data files in Excel (.xlsx) format contain log2 fold changes and p-values. Significantly differentially expressed genes were considered those with padj < 0,05 (Benjamin-Hochberg). Comparison of the differentially expressed genes was performed between shANO1 (ANO1 knockdown) and shScramble (control) by using two different constructs and in total three replicates per cell line (UT-SCC-8 and UT-SCC-14).

source_name: head and neck squamous cell carcinoma cell line

growth_protocol: UT-SCC-8 shScramble and shANO1 cell lines were cultured in DMEM media (Lonza), supplemented with fetal bovine serum (10 % FBS, Gibco), penicillin/streptomycin (100 U/ml; Lonza), L-glutamine (2 mM; Lonza) and non-essential amino acids (0,1 mM; NEAA, Lonza). UT-SCC-14 shScramble and shANO1 cell lines were cultured in DMEM:F12 (Lonza) supplemented with FBS (10 %; Lonza), penicillin/ streptomycin (100 U/mL; Lonza), NaBicarbonate (0.1 %, Lonza) and NaPyruvate (0.05 mmol/L/L; Lonza). Cells were incubated at 37 ⁰C at an atmosphere of 5 % CO2.

extract_protocol:
Cell suspension of 500 µl (concentration of 300 000 cells/ml) were suspended in collagen I matrix (500µl) and plated in low adhesion plates (poly-HEMA coated to prevent cell adheresion on the 24-well plates, Corning), and grown as inert in collagen I for five days. To extract the RNA, media was removed from the well, cultures were washed three times with PBS and Trizol (Ambion, Life Technologies) was added on top of the collagen and homogenised by precellys ceramic beads and homogenizator (Precellys). Briefly, RNA was isolated using chloroform/ isopropanol based method and purified with Qiagen RNeasy Mini kit, according to manufacturer's instructions (Qiagen).
1µg of total RNA was subjected to library synthesis. Libraries were prepared according to Illumina's instructions accompanied with RiboZero Complete Gold Human and NEBNext Directional RNA library kit. Library quality was checked by Bioanalyzer analysis (Agilent 2100). Library denaturation and dilution was made according to NextSeq500 system guide.

treatment_protocol: Initially, cells were transduced with technical replicates of two lentiviral constructs (shANO1 65, shANO1 66), in order to silence ANO1 (shANO1 pLKO.1, from Sigma-Aldrich). Cells were incubated with lentiviruses for 72h. Cells were selected with puromycin (1µM/µl). After selection, cells were inserted into three dimensional collagen type I and were grown for five days at +37 ˚C, 5 % CO2. RNA was extracted from collagen type I and purified. For the RNA sequencing and analysis, in total three knockdown samples per each cell line, including at least once construct #65 and #66, were selected for further processing, based on the ANO1-knockdown efficiency of the transductions.

value: tongue primary tumor

tag: cell line

tag: knockdown

value: shANO1 66 (plKO.1)


title: UT-SCC-14 shScramble_2

description: cell line from head and neck squamous cell carcinoma transduced with scramble shRNA

value: ctrl/shScramble (plKO.1)


title: 2-003 (RNA-Seq)


title: UT-SCC-14 shANO1_66_1

description: cell line from head and neck squamous cell carcinoma transduced with shPPFIA1 44 shRNA


title: 1-014 (RNA-Seq)


title: UT-SCC-14 shScramble_3


title: UT-SCC-14 shANO1_65_2

description: cell line from head and neck squamous cell carcinoma transduced with shPPFIA1 14 shRNA

value: shANO1 65 (plKO.1)


title: UT-SCC-14 shScramble_1


title: 1-012 (RNA-Seq)


title: 1-013 (RNA-Seq)


title: UT-SCC-8 shANO1_66_1

value: larynx primary tumor


title: UT-SCC-8 shANO1_65_1


title: UT-SCC-8 shANO1_66_2


title: 2-002 (RNA-Seq)


title: 1-011 (RNA-Seq)


title: 1-010 (RNA-Seq)


title: UT-SCC-8 shScramble_3


title: UT-SCC-8 shScramble_1


title: 1-009 (RNA-Seq)


title: UT-SCC-8 shScramble_2


title: 2-006 (RNA-Seq)


title: 3-004 (RNA-Seq)


title: 1-006 (RNA-Seq)


title: 1-008 (RNA-Seq)


title: 2614_B2_M_36

city: saint-genes-champanelle

first: Pierre-Alexis

last: Billa

address: route de theix

department: UMRH

country: France

institute: INRA

description:
sample name:
CNLX24

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Data were processed using miRDeep2 package (2.0.0.8). The raw reads were firstly trimmed against Illumina adapters, then mapped to the Btau_5.0.1 genome assembly as miRBase v22.1 with the Mapper module.
Precursors and mature miRNAs were identified using the miRDeep2 core module, miRDeep2.pl. Potential miRNAs were annotated accordingly against ortholog miRNAs in goat, sheep and humans (miRBase release 22.1). We used a miRDeep2 score ≥5 as a cut-off threshold.
The normalization and differential expression analysis of the known and predicted miRNAs were conducted with the DESeq2 R package v1.18.1.
Genome_build: Btau_5.0.1
Supplementary_files_format_and_content: tab-delimited text files include raw expression values, normalized values, DESeq2 result for each sample

organism: Bos taurus

source_name: Mammary gland biopsy

extract_protocol:
total RNA extraction from 30 to 66 g of mammary glande using miRvana kit
Small RNA-Seq librairies were generated from 2000 ng of total RNA using TruSeq Small RNA Library Prep Kit (Illumina, San Diego, CA), according to manufacturer's instructions. The protocol takes advantage of the natural structure common to most microRNA molecules that have a 3' hydroxyl group resulting from enzymatic cleavage by Dicer or other RNA processing enzymes. Briefly, in the first step, RNA adapters were sequentially ligated to each end of the RNA, first the 3' RNA adapter that is specifically modified to target microRNAs and other small RNAs, then the 5' RNA adapter. Small RNA ligated with 3' and 5' adapters were reverse transcribed and PCR amplified (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 15 sec at 72oC] x 13 cycles; 10 min at 72oC) to create cDNA constructs. Amplified cDNA constructs of 140 to 160 nt were selectively isolated by acrylamide gel purification followed by ethanol precipitation.  The final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: Cow were feed restricted during 6 day at 60% of their net energy of lactation calculated before restriction

tag: feed restriction status

value: After

tag: breed

value: Montbeliarde

value: mammary gland


title: ND16737_ALI

city: Los Angeles

first: Brigitte

last: Gomperts

state: CA

address: 10833 Le Conte Ave, A2-410 MDCC

institute: University of California, Los Angeles

data_processing:
(UCLA) Raw sequencing data were demultiplexed using custom Python scripts.  Read 1 contains both a cell barcode and a molecular barcode (also known as a UMI), read 2 contains the cDNA sequence that is aligned to the reference genome.
(UCLA) Demultiplexed sequencing data were filtered by read quality, adapter- and polyA-trimmed, and reads satisfying a length threshold of 30 nucleotides were aligned to the human genome using Bowtie2 (v2.2.9 with the ‘--very-sensitive’ mode).
(UCLA) Aligned reads were tagged to gene exons using Bedtools Intersect (v2.26.0).
(UCLA) DGE matrices were then generated by counting gene transcripts for all cells within each time point from all Drop-seq experiments using Python.
(UCLA) To correct for any bead synthesis errors/read errors leading to false barcodes, reads with the same corresponding cell barcode were aggregated together, and unique molecular identifiers (UMIs) and cell barcodes were merged within 1 Hamming and 2 Levenshtein distances, respectively.
(UCLA) A digital expression matrix was built by counting the number of unique UMIs per gene within each cell.
(CFF, CSMC) Raw reads were demultiplexed, then aligned to the transcriptome by Cell Ranger pipeline (from 10X Genomics) (STAR aligner, hg38 reference with GENCODE 25 transcriptome annotation). Expression counts for each gene in all samples were collapsed and normalized to unique molecular identifier (UMI) counts. The result is a large digital expression matrix with cell barcodes as rows and gene identities as columns.
Genome_build: hg38
Supplementary_files_format_and_content: Saved Seurat package objects (R, Seurat library) aggregated across all three centers and storing UMI counts per gene in each cell; obe

source_name: Air Liquid Interface Culture Day 28

extract_protocol:
Tissue from the bronchi and carina were dissected, cleaned, and incubated in 16U/mL dispase for 1 hour at room temperature. Tissues were then incubated in 0.5mg/mL DNase for another hour at room temperature. The airway epithelium was then stripped and incubated in Accumax  for 1 hour with shaking at 37°C and then resuspened in PBS/BSA
(UCLA) Single cell suspensions were co-flowed with poly-dT beads, and then cDNA was formed following the standard Dropseq protocol using RT, Kapa polyermase, and Nextera XT transposase. Libraries were size selected against adapters by gel extraction above 200bp. (CFF, CSMC) Standard 10X protocol as recommended by the manufacturer.
(UCLA) Libraries were sequenced at 25bp through the Read1 barcode and 75bp through the Read2 genomic sequence

tag: cell type

value: Cells isolated from cultured hBEs on Day 28 of ALI in Vertex ALI media formulation

tag: genotype

tag: technology

value: 10X Genomics Single Cell RNA Sequencing


title: DD046_ALI

value: WT


title: 1652_B1_M_15

description:
sample name:
CNLX21

value: Before


title: 1652_B2_M_17

description:
sample name:
CNLX22


title: 1-007 (RNA-Seq)


title: ND15656_ALI


title: 2614_B1_M_33

description:
sample name:
CNLX23


title: ND15656

source_name: Airway Epithelium

value: Cells Freshly isolated from dissected human airway material


title: 9615_B2_M_38

description:
sample name:
CNLX16


title: 1640_B2_M_5

description:
sample name:
CNLX20


title: 9615_B1_M_35

description:
sample name:
CNLX15


title: 1640_B1_M_2

description:
sample name:
CNLX19


title: ND16932_ALI


title: 5663_B2_M_29

description:
sample name:
CNLX14


title: ND16737


title: 2187_B2_H_24

description:
sample name:
CNLX12

value: Holstein


title: 2187_B1_H_21

description:
sample name:
CNLX11


title: CF301018


title: 2182_B2_H_23

description:
sample name:
CNLX10


title: ND17494


title: 1155_B2_H_31

description:
sample name:
CNLX8


title: Loucy ABT relapse SPLN

city: Zwijnaarde

first: VIB

last: Single Cell Core

address: Technologiepark-Zwijnaarde 71

department: VIB Single cell core

country: Belgium

institute: VIB

description:
10x Genomics – v3
relapse sample spleen

data_processing:
Raw data bcl files were first demultiplexed using Cell Ranger 3.0.2 mkfastq
Demultiplexed data was then processed using the Cell Ranger 3.0.2 count pipeline
Genome_build: combinaiton of hg19 and mm10
Supplementary_files_format_and_content: h5 files including counts (output CellRanger Count) for each sample

organism:
Homo sapiens
Mus musculus

source_name: Spleen

growth_protocol: Luciferase-positive LOUCY cells were xenografted in 2 female NSG mice. Following engraftment, the mice were treated daily by oral gavage with 50 mg/kg ABT-199 or vehicle (2.5% DMSO, 50% PEG 300, 5% Tween and 42.5% of 0.5% methyl cellulose in water) for 11 days. Bioluminescence was recorded after injection of luciferin, on days 0, 8, and 11 of treatment.

extract_protocol:
On day 11, bone marrow and spleen of vehicle and ABT-199 treated mice were dissociated to obtain a single cell suspension.
Cellular suspensions were loaded on a GemCode Single-Cell Instrument (10x Genomics, Pleasanton) to generate single-cell Gel Bead-in-Emulsion (GEMs). Single-cell RNA-Seq libraries were prepared using GemCode Single-Cell V3 3’Gel Bead and Library kit (10x Genomics) according to the manufacturer’s instructions.

treatment_protocol: The mice were treated for 11 days with either vehicle or ABT-199 (50 mg/kg).

tag: condition

value: Relapse


title: 2182_B1_H_20

description:
sample name:
CNLX9


title: 1155_B1_H_27

description:
sample name:
CNLX7


title: Loucy ABT relapse BM

description:
10x Genomics – v3
relapse sample bone marrow

source_name: Bone marrow


title: ND15989


title: ND15989_ALI


title: 1613_B2_M_32

description:
sample name:
CNLX18


title: 9195_B2_H_6

description:
sample name:
CNLX6


title: cervicitis_3

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

country: China

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 16 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2, Pvalue <= 0.01
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample.

molecule: polyA RNA

source_name: Cervical tissue

extract_protocol:
The 9 patients of Uygur women were hospitalized in First Teaching Hospital of Xinjiang Medical University. Each sample was divided into two parts: one part was put into liquid nitrogen within 10 minutes after separation, and then stored at −80°C, and the other part was used for pathological diagnosis after hematoxylin-eosin (HE) staining. Total RNA was obtained from PBNCs using RNAprep Pure Blood Kit (Tiangen Biotech, Beijing, China) following the manufacturer’s procedure. The RNA concentration and purity werechecked by OD A260/A280 (> 1.8) and A260/A230 (> 1.6), and the yield and quality were accessed using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), RIN number > 7.0.
For each sample, 10μg of the total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo (dT)-conjugated magnetic beads (Invitrogen, Carlsbad, CA, USA) before directional RNA-seq library preparation. The purified mRNAs were then iron fragmented at 95°C followed by end repair and 5' adaptor ligation. Then, reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified, amplified, and stored at -80°C until they were used for sequencing. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions. Illumina NextSeq 500 system was used to collect data from 151-nt pair-end sequences (ABLife Inc., Wuhan, China).

value: Cervical epithelium

value: Cervicitis


title: 8200_B2_H_30

description:
sample name:
CNLX4


title: 1613_B1_M_28

description:
sample name:
CNLX17


title: 8200_B1_H_26

description:
sample name:
CNLX3


title: 1165_B2_H_4

description:
sample name:
CNLX2


title: 5663_B1_M_25

description:
sample name:
CNLX13


title: 1165_B1_H_1

description:
sample name:
CNLX1


title: IIa_3

value: Cervical cancer Iia


title: cervicitis_1


title: IIa_2


title: Hypo_LKO_rep3

city: Daejeon

first: Minho

last: Shong

address: 282, Munhwa-ro

department: School of Medicine

country: South Korea

institute: Chungnam National University

data_processing:
The overall read quality and total bases in Fastq files were checked by FastQC v0.11.5. To perform the trimming, Trimmomatic 0.32 were used for the Illumina paired-end data.
We used the HISAT2 v2.0.5, Bowtie2 v2.2.6, and STAR 2.5.2b program considering the splice alignment for pre-processed reads, mapped the reads to reference genome (UCSC mm10), and then generated the aligned reads.
The aligned reads were assembled into transcripts and the abundance were estimated by StringTie v1.3.3b, which provides FPKM (Fragments Per Kilobase of exon per Million fragments mapped) of transcript as a relative abundance estimates.
After excluding the genes with one more than zero FPKM values, the signal value (FPKM+1) was used to the base 2 logarithm and normalized by quantile normalization methods to reduce the systematic bias. These values were used for comparison analysis of differential expressed genes (DEG) between samples. The false discovery rate (FDR) estimating the rate of type I errors in null hypothesis was determined by adjusting p-value using Benjamini and Hochberg algorithm.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: Hypothalamus

extract_protocol:
Total RNA was extracted from liver, inguinal white adipose tissue, skeletal muscle, and hypothalamus using Trizol reagent. To construct the cDNA libraries, 1 μg of total RNA was used with TruSeq RNA Library Prep Kit v2 (Cat#RS-122-2001, Illumina). RNA fragmentation and random hexamer primed reverse transcription and 100nt paired-end sequencing by Illumina HiSeq4000.
The libraries were prepared according to Illumina’s protocols with TruSeq RNA Sample Preparation v2 Guide (Part # 15026495, Rev. F).

tag: strain

value: Hypothalamus


title: RECTAS_300_2

city: Higashi-Osaka

first: Kei

last: IIDA

state: Osaka

address: Kowakae 3-4-1

country: Japan

institute: Kindai University

data_processing:
RTA (Real Time Analysis) software was used for primary analysis. The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq.
The seuqence data was mapped to the genome sequence with STAR ver. 2.7.1a.
Genome_build: GRCm38 + GRCh38(chr9:108867517-108934135)
Supplementary_files_format_and_content: Expression values of refseq gene models were calculated with RSEM ver. 1.3.0.

source_name: HsELP1 (IVS20+6T>C) transgenic mouse

growth_protocol: Mice wer grown in animal facility of cold spring harbor laboratories.

extract_protocol:
DRG was dissected using a dissection microscope. Immediately after dissections, DRG samples were flash-frozen by placing them inside 1.5 mL Eppendorf tubes chilled in dry ice or liquid nitrogen. Trizol was added to the Eppendorf tube and thoroughly homogenized on ice with tissue grinders. Trizol containing the grind up tissue was spun down in 4C centrifuge at 15000 rpm for 10 min. Only the supernatant was used for RNA extraction. Before adding chloroform, the total volume of the Trizol solution containing the DRG RNA was adjusted to 500 uL by adding fresh Trizol. The rest of the steps were conducted by following the manufacturer instructions.
TruSeq stranded mRNA Library kit was used.

treatment_protocol: Mice were p.o. administered for 0.5% carboxy methyl cellulose (CMC) or RECTAS (300 mg/kgBW), followed by second administration of the same dose 4 hours after the administration.

tag: strain/genotype

value: HsELP1 (IVS20+6T>C) transgenic mouse

value: RECTAS (300 mg/kbBW) administration

value: Dorsal Root Ganglia (DRG)


title: RECTAS_300_3


title: RECTAS_300_4


title: IIa_1


title: 30dpt-mDSAC

city: Shanghai

first: Wei

last: Zuo

state: Shanghai

address: No. 500 Zhennan Road, Putuo District, Shanghai

institute: University

data_processing:
We use FastQC to perform basic statistics on the quality of the raw reads. Generally, cellranger count support FASTQ files from raw base call (BCL) files generated by Illumina sequencers as input file.
Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline using default parameters. In brief, for each gene and each cell barcode (filtered by CellRanger), unique molecule identifiers were counted to construct digital expression matrices.
Secondary filtration by Seurat : A gene with expression in more than 3 cells was considered as expressed, and each cell was required to have at least 200 expressed genes. And filter out some of the foreign cells.
Genome_build: mm10-1.2.0
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each single cell

source_name: 30dpt mouse DASC

extract_protocol:
The cell suspension was loaded into Chromium microfluidic chips with 3’ v3 chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed.
Sequencing libraries were constructed with reagents from a Chromium Single Cell 3’ v3 reagent kit (10X Genomics) according to the manufacturer’s instructions.

value: distal airway stem cell

value: C57/B6 mice

tag: time

value: 30 day after transplanted


title: RECTAS_300_1


title: 90dpt-mDSAC

source_name: 90dpt mouse DASC

value: 90 day after transplanted


title: CMC_M3

value: CMC p.o administration


title: Loucy ABT control SPLN

description:
10x Genomics – v3
control sample spleen

value: Control


title: 9195_B1_H_3

description:
sample name:
CNLX5

value: Before

value: mammary gland


title: CINIII_3

value: Cervical intraepithelial neoplasia (stage III)


title: Hypo_LKO_rep1


title: Hypo_Ctrl_rep3


title: CINIII_2


title: Loucy ABT control BM

description:
10x Genomics – v3
control sample bone marrow


title: cervicitis_2


title: CMC_M1


title: CMC_F1


title: HFD MHCII+CD11c+  3#

city: Singapore

first: Christiane

last: Ruedl

state: Singapore

address: 60 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

data_processing:
Illumina bcl2fastq for fastq generation
Sequenced reads were trimmed for adaptor sequence and poor quality reads with Trim_Galore v0.4.5 with parameters -q 20 --stringency 5 --paired
Map trimmed reads to GRCm38 with STAR v2.6.0a using the "multi-sample 2-pass mapping" approach
Gene's read counting with featureCount from the subread package v1.4.6-p5, with parameter -s 0 --primary, on the gene annotation GTF file from GENCODE M19
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include read count per gene for each sample

source_name: Sorted MHCII+CD11c+ macrophages from obese adipose tissue

growth_protocol: Mice were fed with High fat diet or normal diet for 16 weeks

extract_protocol:
Total RNA was extracted from each sorted cell populations by using the PicoPure RNA Isolation Kit
NuGen Ovation® Mouse RNA-Seq System 1-16 protocol

treatment_protocol: Adipose tissue was collected and digested by collagenase to get single cells, which were then sorted into different populations by FACS aria III.

value: Adipose tissue

value: Sorted MHCII+CD11c+ macrophages

tag: treatment

value: HFD 16 weeks

value: Male


title: Hypo_Ctrl_rep2

tag: tissue

value: Hypothalamus


title: HFD MHCII+CD11c+  2#


title: CINIII_1

value: Cervical epithelium

tag: disease state


title: Hypo_Ctrl_rep1


title: Hypo_LKO_rep2


title: HFD MHCII+CD11c+  1#

tag: gender


title: ND MHCII+CD11c-  3#

source_name: Sorted MHCII+CD11c- macrophages from lean adipose tissue

value: Sorted MHCII+CD11c- macrophages

value: ND 16 weeks


title: RNA-seq-A549_SB

city: Wakayama

first: Shogo

last: Ehata

state: Wakayama

address: Kimiidera 811-1

institute: Wakayama Medical University

description:
A549 cells treated with TGF-b and SB431542
q3 in processed data file

data_processing:
RNA-seq reads were trimmed down to 100 bases and processed by Tophat2 (version 2.0.10) and Bowtie2 (version 2.1.0) using hg19 version of index files. Parameters used are as follows: -a 6 --segment-length 25 --no-coverage-search --read-realign-edit-dist 0 -G.
FPKM calculation was performed by using Cuffdiff (cufflinks version 2.1.1, with option -u).
Genome_build: hg19
Supplementary_files_format_and_content: Expression data of the 3 samples were summarized into genes.fpkm_tracking.

growth_protocol: A549 cells were cultured in 6 well plate.

extract_protocol:
Total RNA was isolated with RNeasy (Qiagen).
cDNA libraries were prepared using Dynabeads mRNA DIRECT Purification Kit (Life Technologies) and Ion Total RNA-Seq Kit v.2 (Life Technologies).

treatment_protocol: Cells were seeded into 6-well plates. Cells were treated with or without TGF-b (5 ng/ml) for 3 days.

value: TGF-b (5 ng/ml) and SB431542 (5 µM)

value: lung adenocarcinoma


title: HFD MHCII+CD11c-  3#

source_name: Sorted MHCII+CD11c- macrophages from obese adipose tissue


title: ND MHCII+CD11c-  2#


title: HFD MHCII+CD11c-  2#


title: RNA-seq-A549_TGF-b

description:
A549 cells treated with TGF-b
q2 in processed data file

value: TGF-b (5 ng/ml)


title: ND MHCII+CD11c-  1#


title: HFD MHCII+CD11c-  1#


title: Mus_LKO_rep2

source_name: Gastrocnemius muscle

value: Gastrocnemius muscle


title: Mus_LKO_rep1


title: ND MHCIIlow  3#

source_name: Sorted MHCIIlow macrophages from lean adipose tissue

value: Sorted MHCIIlow macrophages


title: CMC_M2

value: HsELP1 (IVS20+6T>C) transgenic mouse

value: CMC p.o administration

value: Dorsal Root Ganglia (DRG)


title: ND MHCIIlow  2#


title: A549_Smad3mutant_TGF-beta_rep2

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

institute: University of Tokyo

data_processing:
Reference files of the human genome GRCh38 (NCBI build 38, Dec. 2013) and GTF annotation file were obtained from iGenomes (http://support.illumina.com/sequencing/sequencing_software/igenome.html).
RNA-seq reads were aligned and gene abundance in transcripts per million fragments (TPM) were estimated using Hisat2 (version 2.1.0. with default parameters) and Stringtie (version 2.0.4. parameters used: -A -e -G) (Pertea et al, Nat Protocols 2016 11:1650-1667) without de novo transcript assembly.
Genome_build: GRCh38
Supplementary_files_format_and_content: A tab-delimited text file (GTF format) includes coverage, FPKM, and TPM values of genes for each Sample, which was generated by Stringtie.

source_name: A549 cells, Smad3 R104K A105P, TGF-beta treated, replicate 2

growth_protocol: A549 cells were obtained from the American Type Culture Collection. Cells were cloned and used as a parental cell line (A549-P1). Establishment of SMAD3 knockout cells (A549-S3KO) was conducted using Double Nickase Plasmid (sc-4000069-NIC-2, Santa Cruz Biotechnology) as described previously (Nakano N et al, JBC 2020, PMID 32409577; mutations confirmed by sequencing). Cells were cultured at 37°C and 5% CO2 in DMEM medium (Gibco, Thermo Fisher Scientific) supplemented with 10% (v/v) fetal bovine serum (FBS) and 50 units/ml penicillin, and 50 ug/ml streptomycin.

extract_protocol:
RNA was isolated using the RNeasy Plus (Qiagen, Hilden, Germany).
RNA libraries were prepared for sequencing using Dynabeads mRNA DIRECT Purification Kit and the Ion Total RNA-Seq Kit v2 (Thermo Fisher Scientific).

treatment_protocol: A549-S3KO cells were infected with lentivirus carrying wild type Smad3 or Smad3 R104K A105P cDNA. Cells were then stimulated with TGF-beta (1 ng/ml) for 8 h.

value: human lung adenocarcinoma cell line, A549

tag: exogenous gene expression

value: Smad3 R104K A105P


title: Mus_Ctrl_rep2


title: A549_Smad3mutant_noTGF-beta_rep2

source_name: A549 cells, Smad3 R104K A105P, unstimulated control, replicate 2


title: HFD MHCIIlow 2#

source_name: Sorted MHCIIlow macrophages from obese adipose tissue

value: Adipose tissue


title: Mus_Ctrl_rep3


title: HFD MHCIIlow  3#

value: HFD 16 weeks


title: ND MHCIIlow  1#

value: Male


title: HFD MHCIIlow  1#


title: Mus_Ctrl_rep1


title: A549_Smad3_TGF-beta_rep2

source_name: A549 cells, wild type Smad3, TGF-beta treated, replicate 2

value: wild type Smad3


title: A549_Smad3_noTGF-beta_rep2

source_name: A549 cells, wild type Smad3, unstimulated control, replicate 2


title: ND P3  3#

source_name: Sorted monocyte derived cells from lean adipose tissue

value: Sorted monocyte derived cells


title: iWAT_LKO_rep3

source_name: Inguinal white adipose tissue

value: Inguinal white adipose tissue (iWAT)


title: Mus_LKO_rep3


title: ND P3  2#

value: ND 16 weeks


title: A549_Smad3mutant_TGF-beta_rep1

source_name: A549 cells, Smad3 R104K A105P, TGF-beta treated, replicate 1


title: HFD P3  3#

source_name: Sorted monocyte derived cells from obese adipose tissue


title: iWAT_LKO_rep2


title: RNA-seq-A549_no_treatment

description:
untreated A549 cells
q1 in processed data file

value: no treatment


title: HFD P3  2#

source_name: Sorted monocyted derived cells from obese adipose tissue

value: Sorted monocyted derived cells


title: iWAT_LKO_rep1


title: A549_Smad3_TGF-beta_rep1

source_name: A549 cells, wild type Smad3, TGF-beta treated, replicate 1


title: ND P3  1#


title: HFD P3  1#


title: Bbs8 Knockout P29 #4

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

institute: Tigem

description: Transcriptome profile of BBs8 knockout, biological rep4

data_processing:
Sequence reads were trimmed using bbduk software(https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/usage-guide/) (bbmap suite 37.31) to remove adapter sequences, poly-A tails and low-quality end bases (regions with average quality below 6) and then aligned on mm10 reference sequence using STAR
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: Retinal Pigment Epithelial Cells (Isolated)

growth_protocol: The morning after mating was considered as embryonic day (E) 0.5 and up to 24 h after birth was considered as postnatal day (P) 0. Animals were sacrificed by cervical dislocation. Generation of Bbs8-/- mice and genotyping was previously described. Tadenev et al., PNAS 2011

extract_protocol:
RNA was quantified and mixed at 10ng/µl
Total RNA (30 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit  (Lexogen, Vienna, Austria) according to manufacturer's instructions
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the NovaSeq500 (Illumina) with a read length of 100 bp

treatment_protocol: No treatment was performed

tag: developmental stage

value: Post natal day 29 - Isolated RPE cells

value: BBs8 knockout

value: not determined


title: A549_Smad3mutant_noTGF-beta_rep1

source_name: A549 cells, Smad3 R104K A105P, unstimulated control, replicate 1

tag: cell line


title: iWAT_Ctrl_rep3


title: Bbs8 Knockout P29 #1

description: Transcriptome profile of BBs8 knockout, biological rep1


title: Control P29 #4

description: Transcriptome profile of wild type , biological rep4

value: wild type


title: A549_Smad3_noTGF-beta_rep1

source_name: A549 cells, wild type Smad3, unstimulated control, replicate 1


title: Control P29 #3

description: Transcriptome profile of wild type , biological rep3


title: Bbs8 Knockout P29 #3

description: Transcriptome profile of BBs8 knockout, biological rep3


title: iWAT_Ctrl_rep2


title: Sample_cko_pp24

city: Bunkyo-ku

first: Takashi

last: Shimizu

description: Gene expression data of heart

data_processing:
Illumina CASAVA1.8.2 software used for basecalling and demultiplexing.
Reads were trimmed with Trimmomatic.
The trimmed reads were aligned to the mouse reference genome mm10 with HISAT2.
Sequencing tracks normalized by the mapped read counts were generated with deepTools.
Genome_build: Genome Reference Consortium Mouse Build 38 (mm10)
Supplementary_files_format_and_content: bigwig

source_name: mouse heart

extract_protocol:
Total RNA was isolated from hears by using a miRNeasy micro Kit (Qiagen) with the DNase digestion step, according to the manufacturer’s instructions.
Libraries were prepared according to Illumina's instructions.

value: heart

value: PERK mutant

tag: developmental sgtage

value: postpartum


title: Sample_cko_pp23

description: Gene expression data of heart


title: Liver_LKO_rep3

source_name: Liver

value: Liver


title: Control P29 #1

description: Transcriptome profile of wild type , biological rep1


title: Control P29 #2

description: Transcriptome profile of wild type , biological rep2


title: Bbs8 Knockout P11 #4

source_name: Retinal Pigment Epithelial  (Eye Cups)

value: Post natal day 11 - RPE Eye Cups


title: Bbs8 Knockout P11 #3


title: Liver_LKO_rep1


title: Sample_cko_np21

description: Gene expression data of heart

value: nulliparous


title: Sample_cko_np20

description: Gene expression data of heart


title: Bbs8 Knockout P29 #2

description: Transcriptome profile of BBs8 knockout, biological rep2


title: iWAT_Ctrl_rep1


title: Liver_Ctrl_rep3


title: Liver_Ctrl_rep2


title: Control P11 #3


title: Control P11 #2


title: Liver_Ctrl_rep1


title: Sample_cko_pp22

description: Gene expression data of heart


title: F4/80+ liver macrophages WT

city: Toulouse

first: Armelle

last: YART

address: 4bis avenue H. Curien

department: RESTORE

institute: INSERM U1301

data_processing:
Raw sequencing reads were demultiplexed, mapped to the mouse reference genome (build mm10) and gene-expression matrices were generated using CellRanger (version 2.1.0).
This gene-expression matrix was further filtered in Seurat 2.0 and cells with less than 100 genes or 1000 unique molecular identifiers (UMIs) were discarded as well as cells with more than 8000 expressed (multiplets) genes and more than 20% of mtRNA. In total 284,897,143 reads were mapped and 1856 cells were detected with a sequencing saturation of 92.8%
Genome_build: mm10
Supplementary_files_format_and_content: h5

source_name: liver

extract_protocol:
Liver were flushed with PBS, scissor-minced, then digested with collagenase D for 20 min at 37°C. After centrifugation at 600 g for 10 min, stromal cells were separated in 30% percoll and pellets containing stromal cells were incubated with erythrocyte lysis buffer, then CD45+/F4/80+ cells (pool of 6 animals per genotype) were sorted by flow cytometry.
Single cell libraries were prepared with the Chromium Single Cell 3’ Library & Gel Bead Kit v2 & i7 Multiplex Kit and A Chip Kit from 10X Genomics. The barcoded library was sequenced on an Illumina HiSeq3000 in 150-8-150 paired-end configuration

value: F4/80 positive cells sorted by flow cytometry

tag: genetic background

value: C57B6x129Sv mixed background

value: wildtype


title: F4/80+ liver macrophages NS


title: Control P11 #1


title: Sample_flx_pp16

description: Gene expression data of heart

value: wild-type


title: Bbs8 Knockout P11 #2


title: HgCl2 rep1

city: Seoul

first: Jung-Woong

last: Kim

address: 84 Heuksuk-ro Dongjak-ku

department: Life Science

institute: Chung-Ang University

data_processing:
Illumina Casava software used for basecalling
Sequenced read were trimmed for adaptor sequence, and masked for low-quality sequence using TrimGalore
Alignment to GRCh38.98 whole genome with STAR 2.5.4b and read feature counting with Rsubread 2.0.1
Normalized by voom function from limma and edgeR 3.28.1
FPKM were calculated using a fpkm function from DESeq2 1.26.0 and differential gene expression by edgeR 3.28.1
Genome_build: GRCh38.98
Supplementary_files_format_and_content: txt files include raw counts, normalized counts(FPKM)

extract_protocol:
Total RNA was extracted using Trizol reagent and mRNA was extracted by mRNA pull-down using poly-A tagged bead.
RNA libraries were prepared for sequencing using standard Truseq RNA Illumina protocols.

treatment_protocol: 5 μM of mercury chloride (HgCl2) was treated in H1299 cells for 48 hours.

value: HgCl2 treatment


title: ZYE_T_IP

city: Beijing

first: Zhenyuan

last: Han

address: No.22, Zhongguancun South Avenue Haidian District

institute: Peking University School of Stomatology

data_processing:
Fastp software  were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter.
Then sequence quality of IP and Input samples were also verified using fastp. We used HISAT2 to map reads to the reference genomeHomo sapiens (Version: v96).
Mapped reads of IP and input libraries were provided for R package exomePeak, which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software.
MEME and HOMER were used for de novo and known motif finding followed by localization of the motif with respect to peak summit.
Called peaks were annotated by intersection with gene architecture using R package ChIPseeker.
Then StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)).
The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR.
Genome_build: hg38
Supplementary_files_format_and_content: peak text files

source_name: invasive malignant pleomorphic adenoma tissue

extract_protocol:
Briefly, fragmented RNA was incubated with anti-m6A polyclonal antibody (Synaptic Systems, 202003) in IP buffer for 2 hours at 4°C. The mixture was then immunoprecipitated by incubation with protein-A beads (Thermo Fisher) at 4°C for an additional 2 hours.Then, bound RNA was eluted from the beads with N6-methyladenosine (BERRY & ASSOCIATES, PR3732) in IPP buffer and then extracted with Trizol reagent (Invitrogen, CA, USA) by following the manufacturer’s instruction. Purified RNA was used for RNA-seq library generation with NEBNext® Ultra™ RNA Library Prep Kit (NEB). Both the input sample without immunoprecipitation and the m6A IP samples were subjected to 150 bp paired-end sequencing on illumina Novaseq™ 6000.
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. Then the cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). Then the IP RNA was reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 following the vendor's recommended protocol.

tag: treatment type

value: Surgery

tag: vital status

value: Alive


title: Sample_flx_pp17

description: Gene expression data of heart

tag: genotype


title: ZYE_T_input

value: invasive malignant pleomorphic adenoma tissue


title: ZYE_G_IP

source_name: normal salivary gland

value: normal salivary gland


title: EtOH rep2


title: Unconditioned In-vitro culture media, biological rep3

type: RNA

city: Brampton

first: Paul

middle: Nico

last: Del Rio

state: ON

address: 195 Kingswood Drive

department: Reproductive and Biotechnology Laboratory

country: Canada

institute: University of Guelph

hyb_protocol: Following fragmentation, ~50ng of cRNA were heated to 99˚C for 5 minutes, then heated at 45˚C for 5 minutes, prior to hybridization via constant agitation at 60rpm for 16 hours at 48˚C on an Affymetrix 450 Fluidics Station.

scan_protocol: Genechips were scanned using the Affymetrix GCS 3,000 Scanner

data_processing: RMA algorithm. Data was processed with Affymetrix Genechip command console software and analyzed using Affymetric Transcriptome Analysis Concole whereby probesets were differentially expressed at a fold-change of ≤ -2 or  ≥ 2, ≥ 50% of samples have a detectable ablove background value of < 0.05 and a false discovery rate of < 0.05.

label: Biotin

source_name: Unconditioned Media

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from ~50ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: Bovine embryos were in-vitro produced following standard laboratory procedures. Briefly, ovaries were obtained from the local abbotoir and oocytes were retrieved and matured for 24 hours prior to co-culture with bovine sperm for in-vitro fertilization. After 18 hours, presumptive zygotes were transferred to in-vitro culture media and grown in groups of 20 to the desired time stage of development. 2-cell, 8-cell, and blastocyst embryos were cultured for 18-30 hours, 60-80 hours, and 168-192 hours post fertilization. At each time point, embryos were remove from the in-vitro culture media and approximetely 25 µL of spent in-vitro culture media was extracted from each in-vitro culture drops. Spent media samples from each developmental stage was pooled together, flash frozen in liquid nitrogen, and stored at -80 ˚C until total RNA extraction.

extract_protocol: Qiazol extraction for total RNA extract was performed as per manufacturer's instructions

tag: source

value: in-vitro culture media that did not contact any embryos (negative control)


title: Sample_flx_np14

description: Gene expression data of heart


title: Control P11 #4

value: wild type


title: Sample_flx_pp18

description: Gene expression data of heart

value: heart


title: ZYE_G_input


title: Unconditioned In-vitro culture media, biological rep2


title: EtOH rep1


title: Unconditioned In-vitro culture media, biological rep1


title: YLR_T_input


title: Blastocyst spent media, biological rep3

source_name: Blastocyst embryo spent media (168-192 hours post fertilization)

value: spent media conditioned with group-cultured blastocyst bovine embryos


title: CD73 Positive Replicate2

city: philadelphia

first: suraj

last: peri

state: PA

address: 333 cottman ave

department: biostatistics and bioinformatics

institute: Fox chase cancer center

data_processing:
Reads were aligned using STAR and analyzed using HOMER.
Genome_build: Mm10
Supplementary_files_format_and_content: genes.fpkm_table.xlsx

source_name: Fetal liver derived CD73+ gdTCR+

growth_protocol: Immature Rag2-deficient fetal liver progenitors were differentiated into DN3 thymocytes and isolated by flow cytometry. In addition the DN3 thymocytes were transduced with the KN6 gamma-delta T cell receptor and exposed to ligand-expressing OP9 monolayers to enable differentiation. After 3 days, progeniotrs that had not yet lost alpha-beta fate potential (CD73-) and those that had lost alpha-beta fate potential and committed to the gamma-delta fate (CD73+) were isolated by flow cytometry.

extract_protocol: Samples were lysed in Trizol folowing which otal RNA was isolated and processed as previously described(Miyazaki et al., 2017).

tag: cell type

value: Fetal liver derived CD73+ gdTCR+

value: Culture on OP9-DL1 monolayer


title: YLR_G_IP


title: YLR_G_input


title: RPMI-8226_Alone

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 2.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each gene per sample

source_name: Myeloma Cell Line

growth_protocol: MSCs were isolated by surface adherence, and seeded into 6-well plates at a density of 150,000 cells/well and grown until 80-90% confluent. To generate bone marrow adipocytes (BMAs), MSCs were differentiated for 21 days in hMSC adipogenic media consisting of DMEM/F12 supplemented with FBS, antibiotic/antimycotic, 500 µM IBMX, 50 µM indomethacin, 1 µM dexamethasone, and 1 µM insulin.

extract_protocol:
Total RNA was harvested in QIAZOL and prepared via Qiagen miRNEASY Kit with DNase On-column digestion (Qiagen; Hildnen, Germany)
TruSeq RNA Library Prep Kit v2 (Illumina)

treatment_protocol: After 21 days, differentiated adipocytes were washed and myeloma cells (OPM-2, MM.1S, and RPMI-8226) were added via transwell co-culture (0.4 µm pores) at a density of 500,000 cells/well in RPMI-1640 media containing FBS and antibiotic/antimycotic for 72 hours. Following co-culture the individual cell types were then pooled (n=2 wells) prior to RNA extraction.

tag: growth protocol

value: Myeloma Cell Line RPMI-8226


title: CD73 Positive Replicate1


title: DN3 Replicate2

source_name: Fetal liver derived DN3

value: Fetal liver derived DN3


title: Blastocyst spent media, biological rep2


title: Sample_flx_np13

description: Gene expression data of heart

value: nulliparous


title: YLR_T_IP


title: SYL_T_IP


title: RPMI-8226+R18-0186


title: 8-cell embryo spent media, biological rep2

source_name: 8-cell embryo spent media (60-80 hours post fertilization)

value: spent media conditioned with group-cultured 8-cell bovine embryos


title: Blastocyst spent media, biological rep1


title: SYL_T_input


title: CD73 Negative Replicate 2

source_name: Fetal liver derived CD73- gdTCR+

value: Fetal liver derived CD73- gdTCR+


title: R18-0186_MAT+RPMI-8226

source_name: Bone Marrow Adipocyte

value: Bone Marrow Adipocyte


title: DN3 Replicate1


title: SYL_G_IP


title: SYL_G_input


title: 8-cell embryo spent media, biological rep1


title: MM.1S_Alone

value: Myeloma Cell Line MM.1S


title: CD73+ E2A IP

library_source: genomic

data_processing:
Bowtie short read aligner was used to align ChIPSeq data.
Aligned reads were subsequently analyzed using HOMER.
Genome_build: mm10
Supplementary_files_format_and_content: Bed_peak files were obtained using MACS 1.4.2. command line tool. Data were analyzed using E2A and HEB ChIP-Seq samples as treatment samples and input samples as controls.

molecule: genomic DNA

growth_protocol: Immature Rag2-deficient fetal liver progenitors were differentiated into DN3 thymocytes and isolated by flow cytometry. In addition the DN3 thymocytes were transduced with the KN6 gamma-delta T cell receptor and exposed to ligand-expressing OP9 monolayers to enable differentiation. After 3 days, progeniotrs that had not yet lost alpha-beta fate potential (CD73-) and those that had lost alpha-beta fate potential and committed to the gamma-delta fate (CD73+) were isolated by flow cytometry. These samples where then subjected to ChIP-Seq analysis with antibodies reactive with E2A and HEB proteins. Isolated genomic DNA was then sequenced. Duplicate samples were prepared, sequenced and concatenated into a single file.

extract_protocol:
Chromatin immunoprecipitation was performed as previously described(In et al., 2017; Miyazaki et al., 2011).  Cells were lysed and sonicated, and sonicated chromatin was immunoprecipitated with 10 mg anti-E2A (affinity-purified rabbit polyclonal sera raised against the last 12 amino acids of the C-terminus of E2A) or 10 mg anti-HEB (affinity-purified rabbit polyclonal sera raised against the last 12 amino acids of the C-terminus of HEB).  Samples were washed and bound chromatin was eluted.  Crosslinking was reversed overnight at 65°C.  Samples were treated with RNase A and proteinase K, and DNA was purified using the ChIP DNA Clean and Concentrator Kit (Zymo).
For ChIP-Seq, purified DNA was ligated to an adaptor, amplified by PCR (Illumina) and sequenced.

treatment_protocol: At day 7 of culture, Rag2-/- DN3 cells were harvested and cultured overnight on MIY-KN6 gdTCR-producing GP+E cells in the presence of 5 ng/ml IL7, 5 ng/ml Flt3L, and 8 mg/ml polybrene (Sigma Aldrich).  YFP+ DN3 (Thy1.2+ CD4- CD8- CD25+ CD44-) cells were electronically sorted and cultured for 3 days on OP9-DL1 monolayers.  At day 3 of culture, cells were harvested and fixed for 10 minutes at 20°C with 1% (wt/vol) formaldehyde, following which the Thy1+ YFP+ CD4- CD8- CD24+ CD73- and Thy1+ YFP+ CD4- CD8- CD24+ CD73+ subsets were purified by flow cytometry.

tag: strain

value: BALB/c

tag: chip antibody

value: anti-mouse E2A

value: Fetal liver progenitor derived


title: R18-0186_MAT


title: CD73+ HEB IP

value: anti-mouse HEB

tag: treatment


title: GLF_T_IP

tag: tissue

value: invasive malignant pleomorphic adenoma tissue

value: Surgery

value: Alive


title: 2-cell embryo spent media, biological rep3

source_name: 2-cell embryo spent media (18-30 hours post fertilization)

value: spent media conditioned with group-cultured 2-cell bovine embryos


title: MM.1S_+_R17-0107_MAT


title: 8-cell embryo spent media, biological rep3


title: 2-cell embryo spent media, biological rep2


title: 2-cell embryo spent media, biological rep1


title: CD73 Negative Replicate 1


title: GLF_T_input


title: R17-0107_MAT


title: GLF_G_IP

value: normal salivary gland


title: CD73+ Input

value: Fetal liver derived CD73+ gdTCR+

value: Culture on OP9-DL1 monolayer


title: CD73- HEB IP


title: CD73- E2A IP


title: R17-0107_MAT_+_MM.1S


title: OTHERS12: Other liver disease_rep12

first: Xunjiang

last: Wang

address: 1200 Cai Lun Road,Zhangjiang Hi-TechPark,Pudong New Area

department: Shanghai R & D Center for Standardization of Traditional Chinese Medicines

institute: Shanghai University of Traditional Chinese Medicine

description: Gene expression of non-Gynura japonica-induced liver injury

hyb_protocol: Each slide was hybridized with 1.65 μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent technologies, Santa Clara, USA) according to the manufacturer’s instructions.

scan_protocol: Place the chip right in slide holder, place the sample point and face down, and then put it in the scanner. Open the Agilent Scan Control software for 8 x 60 k chips, select AgilentG3_miRNA mode (resolution 3 microns). Set to automatically file access, confirm the scanner status to ready, click Scan Slot m - n, confirm the placement of the chip position. The above steps, when confirmed start scanning chip

data_processing: Scanning image Feature Extraction are analyzed with Agilent Feature Extraction (AFE) software version 10.7.1.1 or higher outliers were excluded. Get background subtract and space to trend signal strength for processing. Uneven function markers in the feature extraction function of outliers are excluded.

source_name: Peripheral Blood

label_protocol: Sample tag and reagents are included in the hybrid need Agilent’s miRNA Complete Labeling and Hyb Kit (p/n 5190-0456), Agilent’s miRNA Spike-In Kit (p/n 5190-1934), used for the quality control of marking and hybridization reaction in the experimental process.

extract_protocol: A total of 2.5 ml fasting venous blood was collected from each PA-HSOS patient or healthy volunteer and stabilized in PAXgene Blood RNA Tubes (PreAnalytiX, Hombrechtikon, Switzerland). The whole blood was left 2 h at room temperature and stored at -80℃ until subsequent analysis. Total RNA >18 nucleotides (including miRNA) was extracted and purified using PAXgene Blood miRNA Kit (PreAnalytiX, Hombrechtikon, Switzerland) in accordance with the manufacture’s instruction. The extracted RNA was checked for an RNA Integrity Number (RIN) to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). RNA purity and concentration were determined using a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE).

tag: disease state

value: whole blood

value: male


title: GLF_G_input


title: OTHERS11: Other liver disease_rep11

value: non-Gynura japonica-induced liver injury

tag: gender

value: female


title: CD73- Input

value: Fetal liver derived CD73- gdTCR+


title: Opm2_Alone

value: Myeloma Cell Line OPM-2


title: OTHERS10: Other liver disease_rep10


title: CWG_T_IP


title: DN3 E2A IP

value: Fetal liver derived DN3

value: BALB/c


title: CWG_T_input


title: R18-0075 MAT+Opm2

value: Bone Marrow Adipocyte


title: OTHERS09: Other liver disease_rep9


title: Sample_flx_np15

description: Gene expression data of heart

value: heart

value: wild-type

value: nulliparous


title: DN3 HEB IP

value: anti-mouse HEB

value: Fetal liver progenitor derived


title: OTHERS08: Other liver disease_rep8


title: R18-0075 MAT


title: CWG_G_IP

value: normal salivary gland

value: Surgery

value: Alive


title: DN3 Input

value: Culture on OP9-DL1 monolayer


title: OxLDL_3

city: jiangsu

first: li

last: Gao

address: 639 longmian avenue

institute: China pharmaceutical university

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100). And After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam).
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam). Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64).
After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam).
The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html) or DESeq2(http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html),and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs.
Genome_build: GRCh38
Supplementary_files_format_and_content: 4_genes_fpkm_expression.txt

source_name: HK-2 cells

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: HK-2 cells

value: human kidney tubular epithelial cell

value: 25 µg/mL OX-LDL for 48 h


title: Opm2+R18-0075_MAT


title: CWG_G_input


title: OTHERS07: Other liver disease_rep7

value: non-Gynura japonica-induced liver injury

value: whole blood

value: male


title: OxLDL_2


title: OxLDL_1


title: Control_3

value: untreated


title: OTHERS06: Other liver disease_rep6


title: Control_2


title: PC2

city: Essen

first: Manuela

last: Wuelling

address: Universitätsstrasse 2

department: Developmental Biology

country: Germany

institute: University Duisburg-Essen

data_processing:
FascQC, version v0.11.9
Trimmomatic, version 0.36 was used to remove adatars and reads with a quality score below 20
Kallisto (version 0.43.1), Bray et al. 2016 was used to calculate TPM values
Genome_build: mm10
Supplementary_files_format_and_content: tab-separated text files witht TPM values for all transcripts of each sample

source_name: cartilage from E14.5 forelimbs

extract_protocol:
Cryosections of E14.5 and E15.5 mouse forelimbs were used for laser-microdissection of primary chondrocyes, RNA was extracted with the RNAeasy micro kit (Qiagen)
10 ng RNA were used with the NuGen Ovation FFPE library system kit and mouse lnDA-C primers

value: primary proliferating chondrocytes

value: cartilage from E14.5 forelimbs

tag: age


title: HC4

source_name: cartilage from E15.5 forelimbs

value: primary hypertrophic chondrocytes

value: cartilage from E15.5 forelimbs


title: OTHERS02: Other liver disease_rep2


title: OTHERS01: Other liver disease_rep1


title: OTHERS05: Other liver disease_rep5

value: female


title: OTHERS03: Other liver disease_rep3


title: OTHERS04: Other liver disease_rep4


title: Control_1


title: HC3


title: Doxyclyline-treated cells at 48h, biological rep. 3

city: Izmir

first: Mehmet

last: Ozturk

address: Dokuz Eylul University Health Campus

department: Izmir Biomedicine and Genome Center

country: Turkey

institute: Izmir Biomedicine and Genome Center

description: Gene expression data from doxycyline-treated p73 expressing HEP3B cells at 48h, biological replicate 3

hyb_protocol: Following fragmentation, 15ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Gene Array Scanner. GeneChip Opreating Software (GCOS, Affymetrix) was used to collect and store the data.

data_processing: The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The signal intensity was converted to log2 values using Bioconductor package in R 3.5.1.

source_name: Hep3B cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were grown in DMEM medium containing 10% FBS and 1% Penicillin/Streptomycin, and stored in incubator at 37C, 5% CO2.

extract_protocol: The total RNA were extracted using Nucleospin RNA II kit (MN) according to the manufecturer's protocol.

treatment_protocol: Cells were treated and/or un-treated with doxycycline (1ug/ml) for 12h, 24h (in duplicates) and 48h (in triplicates)

value: Liver cancer cell line

value: Doxyclyline

tag: time point


title: Doxyclyline-treated cells at 48h, biological rep. 2

description: Gene expression data from doxycyline-treated p73 expressing HEP3B cells at 48h, biological replicate 2


title: Untreated cells at 48h, biological rep. 3

description: Gene expression data from untreated HEP3B cells at 48h, biological replicate 3


title: Mock-infected HK-2-rep3

city: Hong Kong

first: Philip

last: Yeung

address: Queen Mary Hospital Compound, Pokfulam

country: Hong Kong

institute: The University of Hong Kong

data_processing:
High-throughput sequencing raw reads were processed with Cutadapt removing constant lentivirus vector and hair-pin loop nucleotide sequences.
The  sequences were then aligned to human reference genome (GENCODE GRCh38) using Bowtie2
the number of reads mapping to shRNA probes and shRNA target genes were counted using HTSeq
The shRNA probes and shRNA target genes were generated by retrieving unique and properly paired alignments to non-overlapping genomic locations with a mapping quality over 15, following by target gene annotation (GENCODE GRCh38 annotation v24).
shRNA counts were median-normalized and analysed with DESeq2
the gene counts of raw reads within each treatment group by median normalization
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNAs were extracted by TRIzol (ThermoFisher).
Fifty nanograms of each library was then first purified by AMPure XP (Beckman Coulter) before end-repairing. Next, the 3’ end of the libraries were ligated to adaptors using xGen Dual Index UMI Adapters (IDT) according to the manufacturer’s protocol. The adaptor-ligated libraries were then validated by Agilent Bioanalzyer, Qubit and qPCR for quality control analysis. After, the adaptor-ligated libraries were pair-end sequenced using NovaSeq 6000 (Illumina).
KAPA Hyper Prep Kit (KAPA Biosystems)

tag: cell line

value: Mock-infected


title: S7_HC_Igg

data_processing:
fastqc (version v0.11.9) > 20
prinseqlite trimming to 60 bp
mapping to mm10 (UCSC, Dec. 2011)
samtool, mapping quality >30
Picard tools, filtering of duplicates
hiddenDomains for peak calling, bin size 200 bp, max. read count 30, p> 0.6, 20 bp for narrow, 800 bp for braod peaks
intersection of conservative peaks  biological replicates
Genome_build: mm10
Supplementary_files_format_and_content: bed files, peak calling with Hidden domain
Supplementary_files_format_and_content: bed files of the intersection

source_name: cartilage from E15.5 mouse embryo

extract_protocol:
proliferating chondrocyte were isolated from E13.5, hypertrophic chondrocytes from E15.5 mouse embryos
cell sorting was perfomred on a FACSAria II cell sorter with a 70 µm nozzle. Chip was isoaled with True MicroChip Kit (Diagenode).
MicroPlex Library preparation Kit V2 (Diagenode)

value: cartilage from E15.5 mouse embryo

value: IgG (Diagenode C15410206)


title: S5_HC_Igg


title: HSOS08: Blood_hepatic sinusoidal obstruction syndrome_rep8

description: Gene expression of Gynura japonica-induced hepatic sinusoidal obstruction syndrome (HSOS)


title: PC1


title: Untreated cells at 48h, biological rep. 2

description: Gene expression data from untreated HEP3B cells at 48h, biological replicate 2


title: Doxyclyline-treated cells at 48h, biological rep. 1

description: Gene expression data from doxycyline-treated p73 expressing HEP3B cells at 48h, biological replicate 1


title: HSOS09: Blood_hepatic sinusoidal obstruction syndrome_rep9

value: Gynura japonica-induced hepatic sinusoidal obstruction syndrome (HSOS)


title: S2_HC_Igg


title: Mock-infected HK-2-rep2


title: Mock-infected HK-2-rep1


title: S8_PC_IgG

source_name: cartilage from E13.5 mouse embryo

value: cartilage from E13.5 mouse embryo


title: HSOS07: Blood_hepatic sinusoidal obstruction syndrome_rep7


title: S6_PC_IgG


title: Doxyclyline-treated cells at 24h, biological rep. 2

description: Gene expression data from doxycyline-treated p73 expressing HEP3B cells at 24h, biological replicate 2


title: SARS-CoV-2-infected HK-2-rep3


title: S3_HC_Igg


title: Liver_LKO_rep2

city: Daejeon

first: Minho

last: Shong

address: 282, Munhwa-ro

institute: Chungnam National University

data_processing:
The overall read quality and total bases in Fastq files were checked by FastQC v0.11.5. To perform the trimming, Trimmomatic 0.32 were used for the Illumina paired-end data.
We used the HISAT2 v2.0.5, Bowtie2 v2.2.6, and STAR 2.5.2b program considering the splice alignment for pre-processed reads, mapped the reads to reference genome (UCSC mm10), and then generated the aligned reads.
The aligned reads were assembled into transcripts and the abundance were estimated by StringTie v1.3.3b, which provides FPKM (Fragments Per Kilobase of exon per Million fragments mapped) of transcript as a relative abundance estimates.
After excluding the genes with one more than zero FPKM values, the signal value (FPKM+1) was used to the base 2 logarithm and normalized by quantile normalization methods to reduce the systematic bias. These values were used for comparison analysis of differential expressed genes (DEG) between samples. The false discovery rate (FDR) estimating the rate of type I errors in null hypothesis was determined by adjusting p-value using Benjamini and Hochberg algorithm.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Liver

extract_protocol:
Total RNA was extracted from liver, inguinal white adipose tissue, skeletal muscle, and hypothalamus using Trizol reagent. To construct the cDNA libraries, 1 μg of total RNA was used with TruSeq RNA Library Prep Kit v2 (Cat#RS-122-2001, Illumina). RNA fragmentation and random hexamer primed reverse transcription and 100nt paired-end sequencing by Illumina HiSeq4000.
The libraries were prepared according to Illumina’s protocols with TruSeq RNA Sample Preparation v2 Guide (Part # 15026495, Rev. F).

value: Liver


title: HSOS06: Blood_hepatic sinusoidal obstruction syndrome_rep6

city: Shanghai


title: Doxyclyline-treated cells at 24h, biological rep. 1

description: Gene expression data from doxycyline-treated p73 expressing HEP3B cells at 24h, biological replicate 1


title: SARS-CoV-2-infected HK-2-rep2


title: S5_PC_IgG


title: Untreated cells at 24h, biological rep. 2

description: Gene expression data from untreated HEP3B cells at 24h, biological replicate 2


title: SARS-CoV-2-infected HK-2-rep1


title: S4_PC_IgG


title: HSOS04: Blood_hepatic sinusoidal obstruction syndrome_rep4


title: Doxyclyline-treated cells at 12h, biological rep. 2

description: Gene expression data from doxycyline-treated p73 expressing HEP3B cells at 12h, biological replicate 2


title: S3_PC_IgG


title: HSOS03: Blood_hepatic sinusoidal obstruction syndrome_rep3


title: S2_PC_IgG


title: PC3 Pladienolide B 0.5 µM treated for 24 h rep1

city: Ariake, Koto-ku, Tokyo

first: Kyoko

last: Matsumoto

department: Cancer Chemotherapy Center

institute: Japanese Foundation for Cancer Research

data_processing:
Illumina Real Time Analysis software was used for base calling.
Raw sequence reads were trimmed to remove adaptor sequences, contaminant DNA and PCR duplicates, and those with a quality lower than Q20 were removed using Trimmomatic 0.38.
The sequence reads were aligned to the GRCh38 reference genome using HISAT2 version 2.10, Bowtie2 2.3.5.1.
All reads were assembled with String Tie software version 2.1.3b, using annotated genes from the NCBI database. Low quality transcripts are filtered.
Afterwards, TMM normalization are performed. Statistical analysis is performed using fold change, exactTest using edgeR per comparison pair. The significant results are selected on conditions of |fc| >= 2 and exactTest raw p-value < 0.05.
Genome_build: GRCh38

source_name: Human prostate cancer

growth_protocol: PC-3 cells were cultured in vitro in 24-well EZ-BindShut plates in 1 mL DMEM containing 3% heat-inactivated FBS and incubated for 72 h.

extract_protocol:
Total RNA was extracted using FastGene RNA Basic Kit (Nippon Genetics, Tokyo, Japan) and potential DNA contamination was eliminated by using TURBO DNA-free Kit (Thermo Fisher Scientific).
Libraries are prepared using the TruSeq Stranded mRNA LT sample Prep Kit (Illumina) following manufacturer's instruction.

treatment_protocol: Cells were transfected with SF3B2 or control siRNAs by using Lipofectamine RNAiMAX with reverse transfection method and incubated for 72 h under the 3D culture conditions. On the other hands, cells were treated with 0.5 micromolar of Pladienolide B for 24 h under the 3D culture conditions.

value: Pladienolide B 0.5 µM for 24 h


title: Untreated cells at 24h, biological rep. 1

description: Gene expression data from untreated HEP3B cells at 24h, biological replicate 1


title: PC3 DMSO treated rep2

value: DMSO


title: Untreated cells at 12h, biological rep. 2

description: Gene expression data from untreated HEP3B cells at 12h, biological replicate 2


title: HSOS02: Blood_hepatic sinusoidal obstruction syndrome_rep2

value: whole blood

value: male


title: HSOS01: Blood_hepatic sinusoidal obstruction syndrome_rep1


title: PC3 Pladienolide B 0.5 µM treated for 24 h rep2


title: S1_PC_IgG

value: primary proliferating chondrocytes


title: Bbs8 Knockout P11 #1

description: Transcriptome profile of BBs8 knockout, biological rep1

data_processing:
Sequence reads were trimmed using bbduk software(https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/usage-guide/) (bbmap suite 37.31) to remove adapter sequences, poly-A tails and low-quality end bases (regions with average quality below 6) and then aligned on mm10 reference sequence using STAR
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: Retinal Pigment Epithelial  (Eye Cups)

extract_protocol:
RNA was quantified and mixed at 10ng/µl
Total RNA (30 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit  (Lexogen, Vienna, Austria) according to manufacturer's instructions
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the NovaSeq500 (Illumina) with a read length of 100 bp

tag: developmental stage

value: Post natal day 11 - RPE Eye Cups

value: BBs8 knockout


title: Doxyclyline-treated cells at 12h, biological rep. 1

description: Gene expression data from doxycyline-treated p73 expressing HEP3B cells at 12h, biological replicate 1


title: Sample_cko_np19

description: Gene expression data of heart

data_processing:
Illumina CASAVA1.8.2 software used for basecalling and demultiplexing.
Reads were trimmed with Trimmomatic.
The trimmed reads were aligned to the mouse reference genome mm10 with HISAT2.
Sequencing tracks normalized by the mapped read counts were generated with deepTools.
Genome_build: Genome Reference Consortium Mouse Build 38 (mm10)
Supplementary_files_format_and_content: bigwig

source_name: mouse heart

extract_protocol:
Total RNA was isolated from hears by using a miRNeasy micro Kit (Qiagen) with the DNase digestion step, according to the manufacturer’s instructions.
Libraries were prepared according to Illumina's instructions.

value: heart

value: PERK mutant

tag: developmental sgtage

value: nulliparous


title: HgCl2 rep2

value: HgCl2 treatment


title: Untreated cells at 12h, biological rep. 1

description: Gene expression data from untreated HEP3B cells at 12h, biological replicate 1

value: Liver cancer cell line

value: untreated


title: Untreated cells at 48h, biological rep. 1

description: Gene expression data from untreated HEP3B cells at 48h, biological replicate 1


title: CTRL09: Blood_healthy donors_rep9

description: Gene expression of healthy donors

value: healthy

value: female


title: S5_HC_H3K36me3

value: primary hypertrophic chondrocytes

value: cartilage from E15.5 mouse embryo

value: H3K36me3 (Diagenode C15410058)


title: PC3 DMSO treated rep1

value: DMSO


title: S7_HC_H3K36me3


title: PC3 siSF3B2 treated rep2

value: si SF3B2


title: CTRL08: Blood_healthy donors_rep8

description: Gene expression of healthy donors

value: whole blood


title: adipose tissue, patient  32

city: Milano

first: Stefano

last: Percio

state: Milano

address: Via Amadeo 42

department: DRAST

institute: Fondazione IRCCS - Istituto Nazionale dei Tumori

description: gene expression data from retroperitoneal liposarcoma patient

hyb_protocol: Hybridization was performed according to manufacturer's standard protocols.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Arrays were RMA normalized (Irizarry et al. 2003) and differential expression determined using the following R packages from the Bioconductor project: oligo (Carvalho et al. 2010), limma (Smyth 2004).

source_name: adipose tissue

label_protocol: RNA was labeled and processed according to manufacturer's recommended protocols.

extract_protocol: RNA was extracted from snap-frozen tissues using Qiagen RNeasy kit purification performed according to the manufacturer's instructions.

value: adipose tissue


title: HSOS05: Blood_hepatic sinusoidal obstruction syndrome_rep5

value: Gynura japonica-induced hepatic sinusoidal obstruction syndrome (HSOS)


title: S3_HC_H3K27me3R

value: H3K27me3 (Diagenode C15410069)


title: well differentiated liposarcoma, patient  32

source_name: well differentiated liposarcoma

value: well differentiated liposarcoma


title: CTRL07: Blood_healthy donors_rep7

description: Gene expression of healthy donors

value: male


title: CTRL06: Blood_healthy donors_rep6

description: Gene expression of healthy donors


title: adipose tissue, patient  31


title: dedifferentiated liposarcoma, patient  32

source_name: dedifferentiated liposarcoma

value: dedifferentiated liposarcoma


title: PC3 sictrl treated rep2

value: si ctrl


title: KKD024N

city: Los Angeles

first: Brigitte

last: Gomperts

address: 10833 Le Conte Ave, A2-410 MDCC

institute: University of California, Los Angeles

data_processing:
(UCLA) Raw sequencing data were demultiplexed using custom Python scripts.  Read 1 contains both a cell barcode and a molecular barcode (also known as a UMI), read 2 contains the cDNA sequence that is aligned to the reference genome.
(UCLA) Demultiplexed sequencing data were filtered by read quality, adapter- and polyA-trimmed, and reads satisfying a length threshold of 30 nucleotides were aligned to the human genome using Bowtie2 (v2.2.9 with the ‘--very-sensitive’ mode).
(UCLA) Aligned reads were tagged to gene exons using Bedtools Intersect (v2.26.0).
(UCLA) DGE matrices were then generated by counting gene transcripts for all cells within each time point from all Drop-seq experiments using Python.
(UCLA) To correct for any bead synthesis errors/read errors leading to false barcodes, reads with the same corresponding cell barcode were aggregated together, and unique molecular identifiers (UMIs) and cell barcodes were merged within 1 Hamming and 2 Levenshtein distances, respectively.
(UCLA) A digital expression matrix was built by counting the number of unique UMIs per gene within each cell.
(CFF, CSMC) Raw reads were demultiplexed, then aligned to the transcriptome by Cell Ranger pipeline (from 10X Genomics) (STAR aligner, hg38 reference with GENCODE 25 transcriptome annotation). Expression counts for each gene in all samples were collapsed and normalized to unique molecular identifier (UMI) counts. The result is a large digital expression matrix with cell barcodes as rows and gene identities as columns.
Genome_build: hg38
Supplementary_files_format_and_content: Saved Seurat package objects (R, Seurat library) aggregated across all three centers and storing UMI counts per gene in each cell; obe

source_name: Airway Epithelium

extract_protocol:
Tissue from the bronchi and carina were dissected, cleaned, and incubated in 16U/mL dispase for 1 hour at room temperature. Tissues were then incubated in 0.5mg/mL DNase for another hour at room temperature. The airway epithelium was then stripped and incubated in Accumax  for 1 hour with shaking at 37°C and then resuspened in PBS/BSA
(UCLA) Single cell suspensions were co-flowed with poly-dT beads, and then cDNA was formed following the standard Dropseq protocol using RT, Kapa polyermase, and Nextera XT transposase. Libraries were size selected against adapters by gel extraction above 200bp. (CFF, CSMC) Standard 10X protocol as recommended by the manufacturer.
(UCLA) Libraries were sequenced at 25bp through the Read1 barcode and 75bp through the Read2 genomic sequence

value: Cells isolated from dissected and FACS sorted human airway material

tag: technology

value: 10X Genomics Single Cell RNA Sequencing


title: well differentiated liposarcoma, patient  31


title: S7_HC_H3K27ac

value: H3K27ac (Abcam ab4729)


title: S5_HC_H3K27acR


title: S2_HC_H3K27me3


title: CTRL05: Blood_healthy donors_rep5

description: Gene expression of healthy donors

value: healthy

value: female


title: KKD023N


title: CTRL04: Blood_healthy donors_rep4

description: Gene expression of healthy donors


title: CTRL03: Blood_healthy donors_rep3

description: Gene expression of healthy donors


title: CTRL02: Blood_healthy donors_rep2

description: Gene expression of healthy donors


title: dedifferentiated liposarcoma, patient  31


title: S2_HC_H3K9me3

value: primary hypertrophic chondrocytes

value: cartilage from E15.5 mouse embryo

value: H3K9me3 (Diagenode C1541093)


title: PC3 siSF3B2 treated rep1

value: si SF3B2


title: CTRL01: Blood_healthy donors_rep1

description: Gene expression of healthy donors

value: whole blood


title: KKD020N


title: S2_HC_H3K9ac

value: H3K9ac (Abcam ab61231)


title: S3_HC_H3K9ac


title: KKD019N


title: well differentiated liposarcoma, patient  30


title: S5_HC_H3K4me3

value: H3K4me3 (Diagenode K0292100)


title: S2_HC_H3K4me3


title: dedifferentiated liposarcoma, patient  30


title: KKCFFT32N


title: cf019


title: adipose tissue, patient  30

value: adipose tissue


title: SRM_05

city: Heidelberg

first: Ahmed

last: Sadik

address: Im Neunheimer Feld 280

department: Metabolic Crosstalk in Cancer

institute: DKFZ

description: Cultured for 72h under 19.5% O2

hyb_protocol: According to Affymetrix WT PLUS Reagent Kit user manual, 5.5 ug of fragmented and labeled ss-cDNA were hybridized for 17 hr at 45°C on Affymetrix Mouse Gene 2.0 ST Arrays.

scan_protocol: Gene Expression Microarrays were scanned using the Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays (P/N 702731)

data_processing: The Affymetrix microarray chips “mouse gene 2.0 ST” were analyzed using the oligo package and annotated using NetAffx. CEL files were imported from disk followed by RMA normalization and summary to the transcript level.

label_protocol: The Affymetrix WT PLUS Reagent Kit is used to generate labeled ss-cDNA from input amounts of 100ng total RNA

growth_protocol: Primary liver hepatocytes post harvest and attachment on collagen coated plates and prestartvation, hepatocytes were maintained in culture with phenol red-free Williams E medium supplemented with 2 mM L-glutamine, and 1 % (v/v) penicillin/streptomycin 100 x.

extract_protocol: Post anasthesia, liver of the mice were perfused with EGTA buffer containing collagenase enzyme. Post perfusion, hepatocytes were carefully released from the hepatic bag into suspension medium and platted on collagenase coated plates for attachment.

treatment_protocol: Cells were exposed for 72 hours to either normal oxygen concentration of 19.5% or to reduced hypoxic oxygen concentration of 1%

value: Primary Hepatocytes

tag: mouse

value: Mouse 3

tag: condition

value: Normoxia

value: wildtype C57BL/6


title: S6_PC_H3K36me3

value: primary proliferating chondrocytes

value: cartilage from E13.5 mouse embryo

value: H3K36me3 (Diagenode C15410058)


title: adipose tissue, patient  28


title: SRM_06

description: Cultured for 72h under 1% O2

value: Hypoxia


title: h18

value: Cells isolated from dissected and FACS sorted human airway material

tag: genotype

value: WT

value: 10X Genomics Single Cell RNA Sequencing


title: adipose tissue, patient  24


title: SRM_03

description: Cultured for 72h under 19.5% O2

tag: cell type

value: Mouse 2


title: S5_PC_H3K36me3


title: S4_PC_H3K36me3


title: SRM_02

description: Cultured for 72h under 1% O2

value: Mouse 1


title: SRM_04

description: Cultured for 72h under 1% O2


title: dedifferentiated liposarcoma, patient  28

value: dedifferentiated liposarcoma


title: well differentiated liposarcoma, patient  28

value: well differentiated liposarcoma


title: dd39p


title: dedifferentiated liposarcoma, patient  24


title: SRM_01

description: Cultured for 72h under 19.5% O2


title: dd10p


title: S8_PC_H3K27me3

value: H3K27me3 (Diagenode C15410069)


title: well differentiated liposarcoma, patient  24


title: S6_PC_H3K27me3


title: dd49p


title: dd09p


title: S2_PC_H3K27me3


title: cc05p


title: cc04p


title: cc02p


title: S8_PC_H3K27ac

value: H3K27ac (Abcam ab4729)


title: adipose tissue, patient  15

value: adipose tissue


title: cc01p


title: well differentiated liposarcoma, patient  15


title: dedifferentiated liposarcoma, patient  15


title: S3_PC_H3K27ac


title: well differentiated liposarcoma, patient  12


title: adipose tissue, patient  12


title: S6_PC_H3K9me3

value: H3K9me3 (Diagenode C1541093)


title: adipose tissue, patient  11


title: well differentiated liposarcoma, patient  11


title: MM1-O2-WT

city: Busan

first: LEE

middle: SEONG

last: HYUK

address: Haeyang-ro

department: Department of Marine Biotechnology

institute: Korea Institute of Ocean Science and Technology

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using Trimmomatic 0.32 as default parameter, then mapped to mm8 whole genome using bowtie v 2.2.4 with parameters -t --very-sensitive
Differential expression profiles were calculated by edgeR and DESeq
Genome_build: PRJNA59043 (2013-06-10)
Supplementary_files_format_and_content: Excel file includes differential expression profiles and locus tags for genes of T. onnurineus NA1

organism: Thermococcus onnurineus NA1

source_name: RNA from Archaeal cells

extract_protocol:
After cell harvest, RNA samples were prepared using TRIzol reagent. Genomic DNA was eliminated by DNaseI treatment.
To remove rRNA in total RNA, Ribo-Zero rRNA Removal Kits (Human/Mouse/Rat) (MRZH-11124, Epicentre, USA) was used. Illumina Stranded TruSeq Total RNA Sample Prep Kit (Cat#FC-122-2201) was used with 1 ug of rRNA depleted RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.

value: RNA from Archaeal cells

tag: media

value: MM1-O2 (O2-supplied media)

tag: growth phase

value: exponential phase


title: Spleen Mock 003

city: Pittsburgh

first: SHIVKUMAR

middle: of

last: BIRADAR

address: 130 De Soto St

department: Infectious Diseases and Microbiology

institute: University of Pittsburgh

hyb_protocol: Total RNA (50ng) was hybridized to reporter and capture probe sets at 65°C for 24 h. Hybridized samples were loaded on the nCounter Human Immunology v2 Panel.

scan_protocol: Post-hybridization steps and scanning was performed on the nCounter Profiler

data_processing: RCC files were analyzed using nSolver analysis software (Version 4.0) as per the manufacturer's protocols.

label: biotin

source_name: Spleen

label_protocol: Total RNA (50ng) isolated from spleen tissue of BLTS mice was labelled with probes of nCounter Human Immunology v2 Panel

extract_protocol: HIV infected, and PBS-inoculated humanized mice were sacrificed at 5-7 weeks post HIV infection. Fully developed spleen tissue of humanized mice were collected, and single cells were isolated following mechanical dissociation and total RNA was isolated using Qiagen RNA isolation kit Cat# 74104.

treatment_protocol: BLTS humanized mice were divided into four groups of three mice per group and infected with 10ng HIV-p24 or PBS. Three different HIV strains were used. (HIV-WT/ HIV dNef/ HIV-Y115D).

tag: infection

value: PBS


title: S5_PC_H3K27ac

value: primary proliferating chondrocytes

tag: strain

value: cartilage from E13.5 mouse embryo

tag: chip antibody


title: dedifferentiated liposarcoma, patient  11

tag: tissue


title: Spleen Mock 002


title: KO-2

city: Philadelphia

first: Anuradha

middle: A

last: Shastri

state: Pennsylvania

address: 233 S 10th Street

institute: Thomas Jefferson University

description: Gene expression value derived from Expression Console Software

hyb_protocol: Affymetrix gene chips Mouse array was hybridized with fragmented and biotin-labeled target (5 µg) in 220 ul of hybridization cocktail. Target denaturation was performed at 99°C for 5 min. and then 45°C for 5 min, followed by hybridization for 18 h.

scan_protocol: Chips (Mouse Gene 2.0-ST) were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.

data_processing: CHP files were generated by Exon Level-SST-RMA normalization from Affymetrix cel file by using Expression Console Software 1.4. TC group was compare with C group by using Transcriptome Analysis Console software 3.1.

source_name: miR-21-/-;MMTV-PyMT mice

label_protocol: Fragmented biotin labeled cDNA (from 100 ng of RNA) was synthesized using the Affymetrix GeneChip WT PLUS reagent kit.

growth_protocol: Male MMTV-PyMT mice were crossed with female miR-21+/+ and miR-21-/- mice to generate homozygous male/female miR-21+/+;MMTV-PyMT and miR-21-/-;MMTV-PyMT  mice. Only female miR-21+/+ and miR-21-/-;MMTV-PyMT mice were used for experiments due to their mature mammary tissue. miR-21+/+ and miR-21-/-;MMTV-PyMT mice were monitored for 18 weeks or until they reached humane end points for both primary and metastatic tumor formation. Tumor-bearing miR-21+/+;MMTV-PyMT and miR-21-/-;MMTV-PyMT mice were irradiated (8 Gy) when their tumors reached 1000mm3 and were permitted to grow until the total tumor volume reached 2000mm3

extract_protocol: Total RNA from tumor tissues was isolated using RNeasy Mini Kit (Qiagen, USA) according to the manufacturer’s protocol.

treatment_protocol: Half the Tumor-bearing miR-21+/+;MMTV-PyMT and miR-21-/-;MMTV-PyMT mice were irradiated (8 Gy)

value: Mammary fat pad primary tumor

tag: background strain

value: MMTV-PyMT

value: miR-21 KO

tag: treatment

value: untreated


title: KO-RT-1

value: irradiated


title: dedifferentiated liposarcoma, patient  12

value: dedifferentiated liposarcoma


title: S2_PC_H3K9me3


title: MM1-WT


title: S3_PC_H3K9me3


title: KO-1


title: Spleen Mock 001


title: adipose tissue, patient  10


title: OA4

city: Bethesda

first: Haiming

last: Cao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

data_processing:
Sequenced reads were trimmed using trimgalore
The trimmed reads were aligned tomouse (hg38) genome using HISAT2 align with parameters --no-mixed --no-discordant.
Aligned reads were transformed into .bam files and sorted by coordinate using sambamba view and sambamba sort.
Read counts were generated using the featureCounts program from the subread package.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file includes reads counts  for each sample

source_name: Primary Hepatocyte

growth_protocol: The cryopreserved primary human hepatocytes were obtained from Thermo Fisher Scientific. Manufacture’s recommendations were followed when culturing of primary human hepatocytes. Specifically, hepatocytes were thawed, pelleted, resuspended with plating medium (William’s medium E supplemented with Hepatocyte Plating Supplement Pack) (Thermo Scientific) and seeded in 24 well plate pre-coated with type I collage at a density of 5x105 cells/ well.

extract_protocol:
Total RNA was isolated from primary human hepatocytes using KingFisher PURE RNA tissue Kit.
RNA libraries were prepared for sequencing using standard Illumina kit and protocols; strand-specific

treatment_protocol: For omega-3 fatty acid treatment, EPA, DHA and OA from Cayman chemical were dissolved in ethanol and further dilute 1:1000 in incubation medium (serum free) containing 1% fatty acid free BSA (Sigma). Overnight plated primary human hepatocytes were cultured in serum free incubation medium, washed and then refed with incubation medium containing 1% fatty acid free BSA and different treatments (ethanol as vehicle or 200M DHA/EPA/OA) for 16 hours before cells were harvested for RNA extraction.

value: hepatocyte

value: OA


title: OA5


title: Spleen Nef mutant Y115D 003


title: well differentiated liposarcoma, patient  10

value: well differentiated liposarcoma


title: OA3


title: S3_PC_H3K9ac

value: H3K9ac (Abcam ab61231)


title: Spleen Nef mutant Y115D 002


title: S1_PC_H3K9ac


title: WT-RT-2

source_name: miR-21+/+;MMTV-PyMT mice

value: WT


title: adipose tissue, patient  3

value: adipose tissue


title: WT-2


title: WT-1


title: dedifferentiated liposarcoma, patient  10


title: KO-RT-2


title: WT+ RT-1


title: S2_PC_H3K9ac


title: OA2


title: Spleen Nef mutant Y115D 001


title: S2_PC_H3K4me3

value: H3K4me3 (Diagenode K0292100)


title: EPA5

value: EPA


title: OA1


title: well differentiated liposarcoma, patient  3


title: dedifferentiated liposarcoma, patient  3


title: Spleen delta Nef 002

value: HIV dNef


title: S1_PC_H3K4me3

value: primary proliferating chondrocytes


title: KKD022N

value: Cells isolated from dissected and FACS sorted human airway material

value: 10X Genomics Single Cell RNA Sequencing


title: EPA4


title: S7_PC_H3K4me3

value: cartilage from E13.5 mouse embryo


title: PC3 sictrl treated rep1

value: si ctrl


title: Spleen delta Nef 001


title: EPA3


title: Spleen Wild type 003

value: HIV-WT


title: EPA2


title: EPA1


title: DHA5

value: DHA


title: Spleen Wild type 001


title: DHA4


title: Spleen Wild type 002