title: Control - Fatty Inadequate Hepatic Function Liver - 0 hours perfusion - replicate 2

tag: liver id

tag: lean or fatty

tag: transplant viability

tag: agent

value: Control

tag: treatment

value: perfusion, 0 hours

tag: condition replicate


title: MB231 PC3 siCTL 3

status: Public on Jul 11 2022

type: SRA

city: Urbana

first: Erik

middle: Russell

last: Nelson

state: IL

address: 407 South Goodwin Ave

department: Molecular and Integrative Physiology

country: USA

institute: University of Illinois at Urbana-Champaign

library_source: transcriptomic

data_processing:
Transcript abundance was quantified using Kallisto (v0.44.0) pseudoalignment, using index built from a transcriptome fasta of Homo sapiens build GRCh38 (Ensembl).
Transcript abundance scaled by the average transcript length and to library size was subsequently summarized to gene-level counts using R package Tximport.
After keeping all the genes that were expressed in at least 1 sample, 27548 genes were left for downstream analysis, and differentially expressed gene analysis was performed using R packages Limma-voom and EdgeR on the logCPM values.
False discovery rate (FDR) method was used to correct for multiple testing.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text file containing LogCPM gene values for all samples
Supplementary_files_format_and_content: tab delimited text file containing the fold change, raw p-value, and FDR values for comparisons between different treatment groups

molecule: total RNA

organism: Homo sapiens

source_name: Triple Negative Breast Cancer Cells

growth_protocol: MDA-MB-231 and MDA-MB-468 cells were grown in DMEM supplemented with 10 % FBS and 1% penicillin-streptomycin antibiotic mixture. MDA-MB-231 control and TLX-overexpressing cells were seeded in 6-well plates at a density of 0.3-0.4 x 106 cells/well for 24 h.

extract_protocol:
RNA extraction was performed using the RNeasy Plus Mini Kit
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). Read 1 aligns to the ANTISENSE strand.

treatment_protocol: Cells were transfected for 48 h with either a universal negative control siRNA or with a TLX-targeting siRNA using DharmaFECT 4 Transfection Reagent.

tag: cell type

value: Breast Adenocarcinoma

tag: cell line

tag: genotype/treatment

value: control siRNA (CTL + siCTL)


title: 68_Batch2_115_2

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
The sequencing data was demultiplexed using Illumina bcl2fastq version 2.20.0.422 BCL to FastQ file converter.
The quality of raw reads was assessed with FastQC version 0.11.8
Reads were mapped to the GRCh38 human genome assembly [https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/] using STAR version 2.5.2b with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the htseq-count algorithm
DESeq2 version 1.22.1 R package was used to produce Raw read counts.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text file containing Raw read counts for each sample (in columns) and each annotated transcript (in rows).

source_name: endocervical cells

growth_protocol: Cervical cytobrush samples collected at the enrolment (n=14) and crossover visit (n=107) were processed for RNA sequencing of cervical cells. The cervical cells were collected using a Digene cervical sampler (Digene Corporation, Gaithersburg, MD, USA). A cervical cytobrush was inserted into the endocervical os, rotated through 360 degrees and placed in a 15ml tube containing 3ml R10 media (10% heat-inactivated fetal calf serum (FCS) in RPMI supplemented with L-glutamine (50 ng/μl), anti-fungin (0.8 ng/μl), penicillin (50 U) and streptomycin (50 ng/μl))  and transported to the laboratory within 4 hours.

extract_protocol:
RNA was extracted from the endocervical cytobrush samples collected at the crossover visit using RNeasy Micro kit (Qiagen, CA) with DNase digest and QIAcube automation stations. The RNA was quantified, and the quality was assessed by Bioanalyzer analysis (Agilent Technologies, Santa Clara, CA)
Libraries were prepared using the Illumina (Illumina Inc. San Diego, CA, USA) TruSeq RNA Exome kit, as per manufacturer’s instructions, with 20 ng of total RNA as input. The amplified libraries were validated by capillary electrophoresis on the Agilent 4200 TapeStation. The libraries were Rawalized, pooled and sequenced on the Illumina HiSeq3000 system employing a single-end 101 cycles run at average read depths of 21 million reads/sample.

treatment_protocol: Upon arrival of the cytobrush at the laboratory, the cytobrush was rotated against the side of the tube to dislodge the cells and the transport medium was used to flush the cytobrush bristles 30 times. The tubes were centrifuged at 1200 rpm for 10 mins to pellet cells. The supernatant was removed from the tube leaving about 50 μl and the pellet gently dislodged by vortexing. 350 μl RLT buffer (QIAGEN) with 1% beta-mercaptoethanol was added to sample. The samples were vortexed for one min to disrupt cells and immediately stored at -80℃.

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: NETEN

tag: hc method

tag: cst

value: CST-I

tag: shannon

tag: bv

value: Neg

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

value: Low

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host

tag: cumulative number of reads

tag: median cv coverage


title: bulk_Nurse_rep2

city: Kunming

first: Liangliang

last: Wang

state: Yunnan

address: South Section, East Outer Ring Road, Chenggong District

country: China

institute: Yunnan University

data_processing:
The 10X samples were each processed by the Cell Ranger v3.1.0 count pipelines to generate single-feature barcode matrices.
The feature barcode matrices of each sample were processed by Seurat version 3.1.5.
For bulk RNA-seq libraries, adapters were trimmed off with the Trimmomatic program v0.39. And  the paired reads were aligned to the honeybee reference genome using STAR softwar v2.7.9. STAR mapping produced reads that were accurately quantified by the RSEM program to obtain count matrices for gene expression. The count matrices were processed with the DEseq2 v1.32.0.
Genome_build: assembly Amel_HAv3.1
Supplementary_files_format_and_content: Single-feature barcode matrices
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Apis mellifera

source_name: Brain cells

extract_protocol:
For single cell libraries, cell suspension was collected after the whole brain was dissected. For bulk  libraries,  Five adult brains were pooled and homogenized in Trizol reagent to extract the total RNA.
For single cell libraries, single-cell 3' gene expression libraries were generated following the manufacturer’s instructions (10X Genomics#1000121, Chromium Next GEM Single Cell 3' Reagent Kits v3.1). For bulk  libraries, the sequencing libraries was  were generated following the manufacturer’s instructions  VAHTS Universal V8 RNA-seq Library Prep Kit (Vazyme#NR605).

tag: tissue

value: brain

tag: developmental stage

value: adult

tag: caste

value: nurse


title: MB231 PC3 siCTL 2

tag: cell type

tag: cell line

tag: genotype/treatment


title: Emricasan - Adequate Hepatic Function Liver - 6 hours perfusion - replicate 4

city: Providence

first: Jennifer

middle: Ann

last: Sanders

state: RI

address: 593 Eddy Street

department: Pediatric Endocrinology

institute: Rhode Island Hospital

data_processing:
The sequencing libraries were clustered on 3 lanes of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions.
The samples were sequenced using a 2x150bp Paired End (PE) configuration.
Image analysis and base calling were conducted by the HiSeq Control Software (HCS).
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted. After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis.
Assembly: hg38
Supplementary files format and content: Raw hit counts table in text file format.

source_name: Liver

extract_protocol:
Tissues samples from livers taken immediately prior to perfusion and after 3 and 6 hours of perfusion were used for bulk transcriptome sequencing. Core needle biopsies from the right liver lobe were collected in RNAlater solution (Sigma-MilleporeMillipore, Waltham, MA, USA) and stored overnight at 4 Celsius. Tissue samples were then removed from solution and stored at -80 Celsius. Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Germantown, MD, USA) according to manufacturer guidelines.
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol: Grafts were perfused for 12 hours on the Liver Assist device (Organ Assist, Groningen, Netherlands) using a previously described protocol (Raigani et al. Clin Transplant. 2020 Nov;34(11):e14069, PMID 32860634). Briefly, perfusate composition consisted of O+ packed red blood cells, human albumin, Lactated Ringer’s solution, and heparin. Bile salts (taurocholate) and lipid-free parenteral nutrition were continuously infused. Perfusate, bile, and tissue biopsies were collected and analyzed at multiple time points. Livers were deemed to be "viable" if they satisfied the following criteria: perfusate lactate < 2.5mmol/L and two or more of the following minor criteria within 4 hours of starting perfusion: a) perfusate pH >7.30, b) arterial flow > 150mL/min and portal flow > 500mL/min, c) evidence of glucose metabolism, d) bile production, and e) visually assessed homogenous perfusion. Livers that failed to meet these criteria were deemed "nonviable".

tag: liver id

tag: lean or fatty

value: Lean

tag: transplant viability

value: Adequate Hepatic Function

tag: agent

value: Emricasan

tag: treatment

value: perfusion, 6 hours

tag: condition replicate


title: bulk_Queen_rep1

value: queen


title: 69_Batch2_119_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

value: High

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: avsize


title: Control - Fatty Inadequate Hepatic Function Liver - 3 hours perfusion - replicate 2

tag: liver id

tag: lean or fatty

value: Fatty

tag: transplant viability

value: Inadequate Hepatic Function

tag: agent

value: Control

tag: treatment

value: perfusion, 3 hours

tag: condition replicate


title: 61_Batch1_090_1

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: non-HC

tag: hc method

tag: cst

value: CST-IV

tag: shannon

tag: bv

value: Pos

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: molarity

tag: number of reads uniquely mapped to host

tag: cumulative number of reads

tag: median cv coverage


title: single_cell_Nurse_rep2

tag: tissue

tag: developmental stage

tag: caste


title: MB231 PC3 siCTL 1

tag: cell type

value: Breast Adenocarcinoma

tag: cell line

tag: genotype/treatment

value: control siRNA (CTL + siCTL)


title: Emricasan - Adequate Hepatic Function Liver - 3 hours perfusion - replicate 5

tag: liver id

tag: lean or fatty

tag: transplant viability

tag: agent

tag: treatment

tag: condition replicate


title: 62_Batch1_110_1

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

value: CST-III

tag: shannon

tag: bv

value: Neg

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

value: Low

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: avsize


title: 60_Batch1_069_1

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: molarity

tag: number of reads uniquely mapped to host

tag: cumulative number of reads

tag: median cv coverage


title: Emricasan - Adequate Hepatic Function Liver - 0 hours perfusion - replicate 5

tag: liver id

tag: lean or fatty

value: Lean

tag: transplant viability

value: Adequate Hepatic Function

tag: agent

tag: treatment

value: perfusion, 0 hours

tag: condition replicate


title: MB231 TLX siCTL 3

tag: cell type

tag: cell line

tag: genotype/treatment

value: TLX overexpressing cells treated with control siRNA (TLX+siCTL)


title: single_cell_Forager_rep2

tag: tissue

value: brain

tag: developmental stage

value: adult

tag: caste

value: forager


title: Control_for_CELF6_OE_3rd

city: Wuhan

first: Dong

last: Chen

state: Hubei

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

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Raw reads containing more than 2-N bases were first discarded. Then adaptors and low-quality bases were trimmed from raw sequencing reads using FASTX-Toolkit (Version 0.0.13). The short reads less than 16nt were also dropped.
clean reads were aligned to the GRch38 genome by TopHat2 (Kim, Pertea et al. 2013)  allowing 4 mismatches. Uniquely mapped reads were used for gene reads number counting and FPKM calculation (fragments per kilobase of transcript per million fragments mapped) (Trapnell, Williams et al. 2010) .
The R Bioconductor package edgeR (Robinson, McCarthy et al. 2010) was utilized to screen out the differentially expressed genes (DEGs). A P-value <0.01 and fold change>1.5 or < 2/3 were set as the cut-off criteria for identifying DEGs.
To sort out functional categories of DEGs, Gene Ontology (GO) terms and KEGG pathways were identified using KOBAS 2.0 server (Xie, Mao et al. 2011).Hypergeometric test and Benjamini-Hochberg FDR controlling procedure were used to define the enrichment of each term.
The alternative splicing events (ASEs) and regulated alternative splicing events (RASEs) between the samples were defined and quantified by using the ABLas pipeline as described previously (Xia, Chen et al. 2017) .
Genome_build: GRch38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: A549 cells

growth_protocol: A549 cells line were cultured at 37℃ with 5% CO2 in MEM with 10% fetal bovine serum (FBS), 100 µg/mL streptomycin, 100 U/mL penicillin.

extract_protocol:
Total RNA was extracted by the TRIZOL (Ambion). The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega, Madison, WI, USA) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Nanodrop one (Thermo). The integrity of RNA was further verified by 1.0% agarose gel electrophoresis.
For each sample, 1μg of the total RNA was used for RNA-seq library preparation by VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme). Polyadenylated mRNAs were purified and fragmented, and then converted into double strand cDNA. After the step of end repair and A tailing, the DNAs were ligated to VAHTS RNA Adapters (Vazyme). Purified ligation products corresponding to 200-500 bps were digested with heat-labile UDG, and the single strand cDNA was amplified, purified, quantified, and stored at -80℃ before sequencing.
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina HiSeq 6000 system for 150 nt paired-end sequencing.

treatment_protocol: Plasmid transfection of A549 cells was performed using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol. Transfected cells were harvested after 48h for RT-qPCR and Western blotting analysis.

value: control


title: Control - Fatty Inadequate Hepatic Function Liver - 0 hours perfusion - replicate 1

value: Fatty

value: Inadequate Hepatic Function

value: Control


title: 58_Batch1_071_1

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: non-HC

tag: hc method

tag: cst

value: CST-IV

tag: shannon

tag: bv

value: Pos

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: avsize


title: 66_Batch2_072_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: NETEN

tag: hc method

tag: cst

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: molarity

tag: number of reads uniquely mapped to host

tag: cumulative number of reads

tag: median cv coverage


title: 54_Batch1_042_1

tag: sampleid metadata

tag: subject id

tag: batch

value: High

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: avsize


title: Emricasan - Inadequate Hepatic Function Liver - 0 hours perfusion - replicate 3

tag: liver id

tag: lean or fatty

tag: transplant viability

tag: agent

value: Emricasan

tag: treatment

tag: condition replicate


title: bulk_Forager_rep2

tag: tissue

tag: developmental stage

tag: caste


title: Emricasan - Adequate Hepatic Function Liver - 6 hours perfusion - replicate 1

value: Lean

value: perfusion, 6 hours


title: CELF6_2nd

tag: cell line

value: CELF6 overexpression


title: Emricasan - Adequate Hepatic Function Liver - 0 hours perfusion - replicate 4

value: Adequate Hepatic Function

value: perfusion, 0 hours


title: 53_Batch1_129_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

value: Low

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: molarity

tag: number of reads uniquely mapped to host

tag: cumulative number of reads

tag: median cv coverage


title: Emricasan - Inadequate Hepatic Function Liver - 3 hours perfusion - replicate 3

tag: liver id

tag: lean or fatty

tag: transplant viability

tag: agent

tag: treatment

value: perfusion, 3 hours

tag: condition replicate


title: gE-TK-PRV-DX-3

city: Hangzhou

first: Kailun

last: Zhang

address: Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang

institute: Zhejiang University

description: infected at MOI=5 and harvested at 11 hour post infection

data_processing: RNA-seq was performed using an Illumina HiSeqTM2500 (Illumina, United States) to get the raw data (raw reads). With the reads containing poly-N, adapter and low-quality being removed, clean data (clean reads) were obtained and the paired-end reads were aligned to the pig genome (Ensemble)(Release 76). LncRNAs were identified using TopHat2, and reads that were mapped to the pig genome were assembled using Cufflinks. Cuffdiff was used to calculate the FPKMs (expected number of Fragments Per Kilobase of transcript sequence per Million base pairs sequenced) of both lncRNAs and mRNAs in each sample, and DE transcripts were assigned when the p-value < 0.05. RNA-seq and data analysis was completed by Novogene

organism: Sus scrofa

source_name: porcine kidney epithelial cells

extract_protocol: Total RNA was isolated from infected cells using SuPerfecTRITM Total RNA Isolation Reagent (Pufei) according to the manufacturer.

treatment_protocol: PK-15 cells were infected with PRV-DX, and gE-TK- PRV at a multiplicity of infection (MOI) of 5 and harvested at 11 hour post infection or without, respectively.

tag: cell line

value: infected gE-TK-PRV-DX

tag: genotype/variation

value: attenuated gE/TK gene dual-deficiency


title: gE-TK-PRV-DX-2


title: 51_Batch1_073_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: COC

tag: hc method

tag: cst

value: CST-III

tag: shannon

tag: bv

value: Neg

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: avsize


title: Emricasan - Adequate Hepatic Function Liver - 0 hours perfusion - replicate 1

tag: liver id

tag: lean or fatty

tag: transplant viability

tag: agent

tag: treatment

tag: condition replicate


title: Emricasan - Adequate Hepatic Function Liver - 6 hours perfusion - replicate 5


title: 50_Batch1_073_1

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: non-HC

tag: hc method

tag: cst

value: CST-IV

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: molarity

tag: number of reads uniquely mapped to host

tag: cumulative number of reads

tag: median cv coverage


title: Control - Fatty Inadequate Hepatic Function Liver - 6 hours perfusion - replicate 1

tag: liver id

tag: lean or fatty

value: Fatty

tag: transplant viability

value: Inadequate Hepatic Function

tag: agent

value: Control

tag: treatment

tag: condition replicate


title: single_cell_Queen_rep2

tag: tissue

value: brain

tag: developmental stage

value: adult

tag: caste

value: queen


title: MB231 TLX siCTL 2

tag: cell type

value: Breast Adenocarcinoma

tag: cell line

tag: genotype/treatment

value: TLX overexpressing cells treated with control siRNA (TLX+siCTL)


title: 8T

city: New Orleans

first: Yao-Zhong

last: Liu

state: LA

address: 1440 Canal Street, Suite 1610

department: Biostatistics and Data Science

institute: Tulane University School of Public Health and Tropical Medicine

data_processing:
Raw image data were analyzed using the standard Illumina Pipeline, version 1.8.2.
RNA-seq raw data (fastq data) were passed for overall quality check using FastQC program (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).The transcript quantification analysis of fastq data was performed using the Salmon program (salmon 0.99.0) .
Specifically, an index file was first built using the reference transcriptome for humans (Homo_sapiens.GRCh38.cdna.all.fa). Then fastq data of each sample was aligned to the index file for transcript quantification using “salmon quant” command, which resulted in a quant.sf file containing count information for each transcript. The resultant files, quant.sf files, for all the samples were then grouped and analyzed together using R and Bioconductor’s tximport package, which generated a count matrix, with rows as transcript IDs and columns as specific samples.
The count matrix were then analyzed using DESeq2 package for pairwise differential expression analysis, which produced differentially expressed (DEx) genes (or transcripts) between HCC and non-neoplastic control tissue, based on a model of negative binomial distribution.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file including normalized counts of samples produced using the DESeq2 program

extract_protocol:
Fresh frozen HCC (hepatocellular carcinoma) samples with paired adjacent non-neoplastic tissue samples were used for total RNA extraction, which was performed using the Maxwell 16 LEV simplyRNA Tissue kit (Promega AS1280) following kit instructions and on the Maxwell 16 MDx automated instrument.
RNA libraries were prepared from samples that met the TruSeq® Stranded Total RNA Sample Preparation Guide (15031048 E) input guidelines using the Illumina® TruSeq® Stranded Total (Gold) RNA Sample Preparation kit (Illumina Inc., San Diego, California, USA).

tag: tumor status

value: carcinoma

tag: patient id


title: single_cell_Queen_rep1


title: 63_Batch2_009_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: NETEN

tag: hc method

tag: cst

value: CST-I

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

value: Low

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host


title: bulk_Forager_rep1

tag: tissue

tag: developmental stage

tag: caste

value: forager


title: 59_Batch1_071_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

value: CST-III

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

value: Pos

tag: ph

tag: inflammation category kmeans

value: High

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: cumulative number of reads

tag: median cv coverage


title: PRV-DX-3

tag: cell line

tag: treatment

value: infected with PRV-DX

tag: genotype/variation

value: wild type


title: Emricasan - Adequate Hepatic Function Liver - 6 hours perfusion - replicate 2

tag: liver id

tag: lean or fatty

value: Lean

tag: transplant viability

value: Adequate Hepatic Function

tag: agent

value: Emricasan

value: perfusion, 6 hours

tag: condition replicate


title: 8N

tag: tumor status

value: non-neoplastic

tag: patient id


title: 48_Batch1_029_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

value: CST-IV

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host


title: Control_for_CELF6_OE_2nd

tag: cell line

tag: treatment

value: control


title: PRV-DX-2

tag: genotype/variation


title: MOCK-3

description: control

value: uninfected


title: Emricasan - Adequate Hepatic Function Liver - 3 hours perfusion - replicate 2

tag: liver id

tag: lean or fatty

tag: transplant viability

tag: agent

value: perfusion, 3 hours

tag: condition replicate


title: single_cell_Nurse_rep1

tag: tissue

value: brain

tag: developmental stage

value: adult

tag: caste

value: nurse


title: CELF6_3rd

value: CELF6 overexpression


title: MOCK-1

description: control


title: Control_for_CELF6_OE_1st


title: 6T

tag: tumor status

value: carcinoma

tag: patient id


title: MOCK-2

description: control


title: Emricasan - Adequate Hepatic Function Liver - 3 hours perfusion - replicate 1


title: 44_Batch1_109_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: CCVR

tag: hc method

value: NETEN

tag: cst

tag: shannon

tag: bv

value: Pos

tag: nugent score

tag: bv prior

value: Neg

tag: ph

tag: inflammation category kmeans

value: High

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: cumulative number of reads

tag: median cv coverage


title: 9N

tag: tumor status

tag: patient id


title: single_cell_Forager_rep1

tag: tissue

tag: developmental stage

tag: caste

value: forager


title: CELF6_1st

tag: cell line

tag: treatment


title: OE2

city: Lyon

first: Fabrice

last: Lavial

address: 28 rue Laennec

country: France

institute: CRCL

data_processing:
Sequenced reads were mapped to mm8 (release M19) whole genome and reads per gene were counted using STAR (ver. 2.5b).
Read counts were analyzed with R DeSeq2 package.
Supplementary files format and content:  raw counts, normalized counts, csv file including FC, p-value and adjusted p-value

organism: Mus musculus

source_name: mouse embryonic fibroblasts

growth_protocol: MEF were generated from E13.5 reprogrammable mice embryos and cultivated in DMEM medium supplemented with 10% foetal bovine serum (FBS), 100U/ml penicillin / streptomycin (PS), 1mM sodium pyruvate, 2mM L-glutamine, 0.1mM Non Essential Amino Acids (NEAA) and 0.1mM b-mercaptoethanol.

extract_protocol:
RNAs were extracted with Nucleospin RNA kit from Macherey Nagel.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MEF are infected with Bcl11b shRNA targetting particles or overexpressing plasmids and RNA were collected after 3 days

tag: cell type

value: embryonic fibroblasts

tag: condition

value: mouse embryonic fibroblasts induced to overexpress Bcl11b

tag: strain


title: 43_Batch1_094_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

value: CST-III

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host


title: gE-TK-PRV-DX-1

tag: cell line

tag: treatment

value: infected gE-TK-PRV-DX

tag: genotype/variation

value: attenuated gE/TK gene dual-deficiency


title: KD2

tag: cell type

tag: condition

value: mouse embryonic fibroblasts induced to downregulate Bcl11b

tag: strain


title: Emricasan - Adequate Hepatic Function Liver - 0 hours perfusion - replicate 2

tag: liver id

tag: lean or fatty

value: Lean

tag: transplant viability

value: Adequate Hepatic Function

tag: agent

value: Emricasan

value: perfusion, 0 hours

tag: condition replicate


title: 45_Batch1_113_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

value: CST-IV

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

value: Low

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: cumulative number of reads

tag: median cv coverage


title: 52_Batch1_129_1

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: non-HC

tag: hc method

tag: cst

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: ifny

tag: tnfa

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host


title: scRNA-KO2

city: London

first: Alex

last: Leung

state: London

address: 11-43 Bath Street

country: United Kingdom

institute: UCL Institute Of Ophthalmology

library_source: transcriptomic single cell

data_processing:
Demultiplexing NextSeq sequencer base call files were used to generate FASTQ files of the sequencing reads using the 10X Genomics Cell Ranger command mkfastq (version 3.0.2). Feature count matrices were then generated using the Cell Ranger command count, which performs read alignment to the GRCm38 mouse genome and unique molecular identifier counting.
The R toolkit package Seurat (v3.1.4; https://github.com/satijalab/seurat) was used for further downstream analysis. Cell barcodes, genes, and expression count matrices of each sample were separately loaded into Seurat with a pre-filter of a minimum of 200 genes detected per sample. Log-Normalization, which normalizes the feature expression for each cell within the sample, and Feature Selection, which extracts genes that exhibit high cell-cell variation within the dataset, were performed for each sample dataset.
Following normalization, all sample datasets were then integrated using FindIntegrationAnchors and IntegrateData, which use an anchoring method to coordinate cell types among different samples69 and integrate them into one Seurat object dataset. The integrated dataset was then scaled, and Principal Component Analysis was performed. The top 20 principal components were then used for a graph-based clustering approach.
The resulting 32 clusters were then projected to a two-dimensional plane and visualized as a Uniform Manifold Approximation and Projection. The FindAllMarkers function was then applied to extract the differentially expressed genes per cluster by comparing each cluster with the remaining dataset using the Wilcoxon Rank Sum test.
Assembly: GRCm38
Supplementary files format and content: zipped folder containing CellRanger mkfastq output, which includes barcodes, features and count matrix .tsv
Supplementary files format and content: tab-delimited text file from DESeq2 contain log2 fold change of each read between pooled control and treated samples per gene with p and q-values

source_name: Retinal Tissue

extract_protocol:
After obtaining the retinal tissue from mouse eye dissection, the Papain Dissociation System (Worthington, Columbus, OH, USA) was used to dissociate the tissues into a single-cell suspension. ). Briefly, the retinal tissue was placed in a mixture of 100 µl papain solution and 5 µl of DNase solution. The mixture was incubated at 37 °C for 15 min after gentle titration. The dissociated cell solution was then diluted with 900 µl of PBS and passed through a 35 µm cell filter.
Dissociated samples were loaded onto the 10X Chromium system, and single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3’ reagent kit v3. Following the manufacturer’s protocol, single cells were captured in nanolitre-scale Gel Beads-in-emulsion (10X Genomics), where cells were lysed and cDNA was synthesized by reverse transcription of RNA, and all cells were tagged with the same 10X barcode. Following PCR amplification, enzymatic fragmentation, adaptor attachment, and sample indexing, the constructed library was then sequenced using the NextSeq 500 system (Illumina).

tag: tissue

value: Retinal Tissue

tag: genotype


title: 5N

tag: tumor status

value: non-neoplastic

tag: patient id


title: 9T

value: carcinoma


title: Emricasan - Inadequate Hepatic Function Liver - 6 hours perfusion - replicate 3

tag: liver id

tag: lean or fatty

tag: transplant viability

value: Inadequate Hepatic Function

tag: agent

tag: treatment

value: perfusion, 6 hours

tag: condition replicate


title: 7T


title: 4T


title: 49_Batch1_106_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: COC

tag: hc method

value: NETEN

tag: cst

value: CST-I

tag: shannon

tag: bv

value: Pos

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

value: High

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: cumulative number of reads

tag: median cv coverage


title: Emricasan - Adequate Hepatic Function Liver - 3 hours perfusion - replicate 4

tag: liver id

tag: lean or fatty

value: Lean

tag: transplant viability

tag: agent

tag: treatment

value: perfusion, 3 hours

tag: condition replicate


title: 4N

tag: tumor status

tag: patient id


title: 7N


title: scRNA-WT2

tag: tissue

tag: genotype

value: Control


title: 47_Batch1_171_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: CCVR

tag: hc method

tag: cst

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host


title: 6N

tag: tumor status

tag: patient id


title: scRNA-KO5

tag: tissue

tag: genotype


title: 38_Batch1_058_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

value: CST-IV

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: cumulative number of reads

tag: median cv coverage


title: 57_Batch1_063_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

value: Neg

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host


title: 41_Batch1_076_2

tag: sampleid metadata

tag: subject id

tag: batch

value: CST-III

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: cumulative number of reads

tag: median cv coverage


title: PRV-DX-1

tag: cell line

tag: treatment

value: infected with PRV-DX

tag: genotype/variation

value: wild type


title: OE1

tag: cell type

value: embryonic fibroblasts

tag: condition

value: mouse embryonic fibroblasts induced to overexpress Bcl11b

tag: strain


title: 5T

tag: tumor status

value: carcinoma

tag: patient id


title: 3N

value: non-neoplastic


title: scRNA-WT1

tag: tissue

value: Retinal Tissue

tag: genotype


title: scRNA-KO4


title: intestinal eosinophils of propionate-fed mice 1

city: Yokohama

first: Hiroshi

last: Ohno

state: Kanagawa

address: 1-7-22 Suehiro-cho

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

data_processing:
bcl2fast1 v1.8.4 software used for base-calling
Default parameters of Hisat2 v2.2.1 use for alignment
featureCounts v2.0.1 used for TPM normalization
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM fille
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Mus

source_name: Small intestine

extract_protocol:
Total RNA was extracted from isolated intestinal eosinophils of propionate-fed mice and control mice by using the RNeasy Mini kit (QIAGEN)
Library preparation was performed with a TruSeq RNA Library Prep Kit v2(illumina). RNA sequencing was performed on an illumina Nextseq 2000 in a 50-base single-end mode.

value: Small intestine

value: Eoshinophil

value: WT

value: Propionate


title: scRNA-KO3


title: 40_Batch1_067_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

tag: shannon

tag: bv

value: Int

tag: nugent score

tag: bv prior

value: Pos

tag: ph

tag: inflammation category kmeans

value: Low

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host


title: 37_Batch1_048_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: CCVR

tag: hc method

tag: cst

value: CST-I

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: cumulative number of reads

tag: median cv coverage


title: 42_Batch1_082_2

tag: sampleid metadata

tag: subject id

tag: batch

value: CST-III

value: Neg

value: High

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host


title: 2T

tag: tumor status

tag: patient id


title: scRNA-KO1

tag: tissue

tag: genotype


title: KD1

tag: cell type

value: embryonic fibroblasts

tag: condition

value: mouse embryonic fibroblasts induced to downregulate Bcl11b

tag: strain


title: scRNA-WT3

value: Control


title: 3T

value: carcinoma


title: ctrl1

value: control mouse embryonic fibroblasts


title: 39_Batch1_062_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

value: CST-IV

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: cumulative number of reads

tag: median cv coverage


title: ctrl2

tag: cell type

tag: condition

tag: strain


title: 36_Batch1_022_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host


title: 35_Batch1_019_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: cumulative number of reads

tag: median cv coverage


title: FAK KO

city: Chicago

first: Md Zahid

last: Akhter

address: 835 S Wolcott Ave

department: Pharmacology & Regenerative Medicine

institute: University of Illinois at Chicago

description: Flow sorted lung endothelial cells (CD31+CD45-) pooled from 5 mice.

library_source: genomic

data_processing:
Adapter trimming
Gene Annotation
Peak calling
Feature counts
Differential analysis
Assembly: mm10

molecule: genomic DNA

source_name: Lung

growth_protocol: FAK floxe and EC-FAK knockout mice were maintained following Institute Animal Care and Use guidelines.

extract_protocol: Lungs harvested from FAK flox and EC-FAK knockout mice  were subjected to single cell suspension and stained with anti-CD31 and CD45 antibodies. Endothelial cells (GFP+CD31+CD45-) were flow sorted and chromatin was extracted and processed for Tn5-mediated tagmentation and adapter incorporation, according to the manufacturer’s protocol (Nextera DNA sample preparation kit, Illumina®) at 37 °C for 30 min.

tag: tissue

value: Lung

tag: cell type

value: Endothelial cells

tag: genotype

value: EC-FAK knockout


title: intestinal eosinophils of control mice 2

value: Small intestine

value: Eoshinophil

value: WT

tag: treatment


title: intestinal eosinophils of propionate-fed mice 2

value: Propionate


title: 2N

tag: tumor status

value: non-neoplastic

tag: patient id


title: intestinal eosinophils of control mice 1


title: 21T


title: Control

value: FAK Flox


title: CLP+Marein1, scRNAseq

city: wuhan

first: Fuquan

address: Institute of Anesthesia and Critical Care, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277, Jiefang Avenue, Wuhan 430022, China

institute: wuhan union hospital

description: 10x Genomics

data_processing:
Cell Ranger (version 5.0.0) was used to process the raw data and generate the raw unique molecular identifier(UMI) count matrix. The merged matrix was transferred into the R statistical environment for further analysis using the Seurat package (v. 4.1.2)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung

extract_protocol:
After the lung tissue was washed twice with pre-cooled RPMI 1640+0.04% BSA medium under sterile conditions, the samples was sufficiently cut into small pieces of about 0.5 mm3.Then the samples were incubated with a mixture of 2 ml of trypsin (Gibco, Cat: R001100), 1 ml of collagenase II (Biofrox, Cat:2275MG100) and 100 µl of DNase (Servicebio, Cat: 1121MG010) for 1 h on a 37 °C shaker. The digested cell suspension was filtered 1-2 times with a BD 40 μm cell sieve, and centrifuged at 300 g for 5 min at 4°C. After the pellet was resuspended with an appropriate amount of medium, an equal volume of red blood cell lysate (MACS, Cat. No. 130-094-183) was added. After mixing, let stand at 4°C for 10 min, the cell suspension was centrifuged at 300g for 5 min, and the supernatant was discarded. The pellet was washed once with medium, centrifuged at 300 g for 5 min, the supernatant was discarded, the cell pellet was resuspended with 100 μl of medium, and the cell concentration and viability were calculated by Luna cell counter.For CD45 sorting, the prepared single cell suspensions was subjected to Magnetic-activated cell sorting (MACS) using Miltenyi mouse CD45 magnetic beads according to the manufacturer's recommendations. The CD45- and CD45+ cell suspensions were mixed 1:1 for single-cell sequencing.
The single-cell library was prepared following the protocol of the 10×Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1

tag: agent

value: lung

tag: age

value: 6-8 weeks old


title: 21N


title: CLP, scRNAseq

description: 10x Genomics

value: CLP


title: patient 4_PV > MF-3

type: RNA

city: Cambridge

first: David

last: Mooney

state: MA

address: 58 Oxford Street

institute: Harvard University

description: Codeset NS_INFL_HS_V2_C2534

hyb_protocol: Multiplexed mRNA quantification was performed using Nanostring nCounter GX Human Inflammation Kit (Seattle, WA) and analyzed by nSolver and nCounter Advanced Analysis.

scan_protocol: Hybridized samples were loaded on nanoString cartridges for analysis.

data_processing: Data were analyzed using nSolver and nCounter Advanced Analysis.

source_name: bone marrow biopsy

label_protocol: not provided

extract_protocol: BWH specimens were fixed in Bouin’s fixative and decalcified in RapidCal Immuno (BBC Biochemical) for 15 minutes, followed by routine processing. Specimens from MGH were fixed in B-plus fixative for a minimum of 4 hours and decalcified in RapidCal Immuno (BBC Biochemical) for 30 minutes, followed by routine processing. RNA was isolated from 50 μm sections prepared from fixed, decalcified and paraffin-embedded bone marrow biopsies using Qiagen RNeasy Kit (Germantown, MD)

tag: diagnosis

value: PV progressing to MF

tag: grading

tag: date


title: 32_Batch1_038_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: COC

tag: hc method

tag: cst

value: CST-I

tag: shannon

tag: bv

value: Neg

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

value: Low

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host


title: patient 4_PV > MF-2

description: Codeset NS_INFL_HS_V2_C2534

label: Nanostring nCounter GX Human Inflammation Kit

tag: diagnosis

tag: grading

tag: date


title: 34_Batch1_008_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: CCVR

tag: hc method

tag: cst

value: CST-III

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

value: High

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: cumulative number of reads

tag: median cv coverage


title: Sham, scRNAseq

description: 10x Genomics

tag: agent

value: Sham

tag: tissue

tag: age


title: Sample 29_PMF-3

description: Codeset NS_INFL_HS_V2_C2534

label: Nanostring nCounter GX Human Inflammation V2 Kit

tag: diagnosis

value: primary myelofibrosis (PMF)

tag: grading


title: 18T

tag: tumor status

value: carcinoma

tag: patient id


title: 30_Batch1_023_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

value: Int

tag: ph

tag: inflammation category kmeans

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host


title: 1N

tag: tumor status

value: non-neoplastic

tag: patient id


title: 18N


title: 29_Batch1_141_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: cumulative number of reads

tag: median cv coverage


title: 31_Batch1_021_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: Pos

tag: inflammation category kmeans

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host


title: 16T

tag: tumor status

tag: patient id


title: Sample 27_PMF-3

description: Codeset NS_INFL_HS_V2_C2534

tag: diagnosis

tag: grading


title: Sample 28_PMF-3

description: Codeset NS_INFL_HS_V2_C2534


title: 28_Batch1_161_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: cumulative number of reads

tag: median cv coverage


title: WT_MI_II-3

city: Birmingham

first: Abolfazl

last: Zarjou

state: AL

address: 618 Zeigler Research Building, 703 South 19th Street

department: Medicine

institute: University of Alabama at Birmingham

data_processing:
Basecalls performed using Illumina bcl2fastq version 2.18.0.12
FASTQ files were aligned with STAR version 2.7.5b using parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated using HTSeq-count version 0.11.3 using parameters -m union -r pos -t exon -i gene_id -a 10 -s no -f bam
Normalization and differential expression was done by DESeq2 following their default parameters in their vignette
Assembly: Gencode GRCm38 p6 Release M24
Supplementary files format and content: tab-delimited text file containing Ensembl IDs and raw count values for each sample

source_name: myocardium

extract_protocol:
RNA was harvested from tissues by TRIzol (Invitrogen, CA). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: mice were subjected to 3 hours of reperfusion after 45 minutes of ischemia with the released suture around the LAD left inside. Then the mice were sacrificed. The aorta was cannulated, and the heart was washed with PBS. Subsequently, the suture around the LAD was ligated. The heart was perfused with a 5% solution of phthalo blue dye (Sigma) in normal saline (1ml per heart). The ischemic zone and the non-ischemic zone were separated using scissors to cut along the margin of the blue dye (unstained area is the ischemic zone and the blue dye-stained area is the non-ischemic zone).

tag: tissue

value: myocardium

tag: genotype

value: WT

tag: treatment

value: MI


title: WT_MK_II-2


title: CLP_48H, scRNAseq

description: 10x Genomics

tag: agent

value: lung

tag: age

value: 6-8 weeks old


title: WT_Baseline_II-7

value: Baseline


title: Sample 25_PMF-3

description: Codeset NS_INFL_HS_V2_C2534

tag: diagnosis

tag: grading


title: 16N

tag: tumor status

tag: patient id


title: 27_Batch1_156_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: COC

tag: hc method

tag: cst

tag: shannon

tag: bv

value: Neg

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host


title: Sample 26_PMF-3

description: Codeset NS_INFL_HS_V2_C2534

tag: diagnosis

tag: grading


title: 26_Batch1_138_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

value: CST-IV

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

value: Low

tag: sti bacterial any

tag: ct

tag: ng

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: cumulative number of reads

tag: median cv coverage


title: Sample 24_PMF-3

description: Codeset NS_INFL_HS_V2_C2534

tag: diagnosis

tag: grading


title: 1T

tag: tumor status

tag: patient id


title: WT_Baseline_I-6

tag: tissue

tag: genotype

tag: treatment


title: WT_Baseline_I-4


title: 25_Batch1_091_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

value: NETEN

tag: cst

value: CST-III

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: any sti no tv

tag: sti prior visit

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host


title: Sample 23_PMF-3

description: Codeset NS_INFL_HS_V2_C2534

tag: diagnosis

value: primary myelofibrosis (PMF)

tag: grading


title: Sample 22_PMF-3

description: Codeset NS_INFL_HS_V2_C2534


title: WT_MI_II-1

tag: tissue

tag: genotype

tag: treatment


title: KO_MI_II-6

value: FtH KO


title: 14T

tag: tumor status

value: carcinoma

tag: patient id


title: 14N

value: non-neoplastic


title: 15T


title: KO_MI_II-5


title: 13T


title: 24_Batch1_084_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

value: CST-I

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

value: High

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: cumulative number of reads

tag: median cv coverage


title: Sample 21_PMF-3

description: Codeset NS_INFL_HS_V2_C2534

tag: diagnosis

tag: grading


title: 23_Batch1_075_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

tag: shannon

tag: bv

value: Pos

tag: nugent score

tag: bv prior

tag: ph

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host


title: KO_Baseline_I-3

tag: tissue

value: myocardium

tag: genotype

tag: treatment


title: 22_Batch1_070_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

tag: shannon

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: cumulative number of reads

tag: median cv coverage


title: Sample 19_PMF-3

description: Codeset NS_INFL_HS_V2_C2534

tag: diagnosis

tag: grading


title: KO_Baseline_I-2

tag: tissue

tag: genotype

tag: treatment


title: 21_Batch1_053_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host


title: 19_Batch1_045_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

tag: shannon

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: cumulative number of reads

tag: median cv coverage


title: 20_Batch1_047_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: bv

tag: nugent score

tag: bv prior

value: Int

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host


title: 15N

tag: tumor status

tag: patient id


title: KO_Baseline_I-1

tag: tissue

tag: genotype

tag: treatment


title: KO_MI_II-4

value: MI


title: 12N


title: Sample 17_PMF-3

description: Codeset NS_INFL_HS_V2_C2534

tag: diagnosis

tag: grading


title: Sample 18_PMF-3

description: Codeset NS_INFL_HS_V2_C2534


title: 17_Batch1_024_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: cumulative number of reads

tag: median cv coverage


title: Sample 16_PMF-3

description: Codeset NS_INFL_HS_V2_C2534

tag: diagnosis

tag: grading


title: Sham4

city: Tel Aviv

first: Lior

last: Mayo

state: Israel

address: Britannia Bldg. Room 204, Tel Aviv univeristy

country: Israel

institute: Tel Aviv Unoversity

data_processing:
RNA-seq reads were aligned using Kallisto to mouse genome version mm10, and expression levels were calculated using RSEM
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: astrocytes

extract_protocol:
Ribotag ip
RNA extracted from immunoprecipitated polyribosomes was used to prepare libraries by NebNext rRNA depletion kit (#E6310), NEBNext® Ultra™ II RNA Library Prep Kit for Illumina (#E7770G), and NEBNext® Multiplex Oligos for Illumina® (#E7335G) kit, according to manufacturers’ instructions. Libraries were normalized, pooled, and sequenced on the Illumina NextSEQ 500 with the NextSeq 500/550 Mid Output Kit v2.5 (150 Cycles) (#20024904), according to manufacturers’ instructions

treatment_protocol: GfapCRE:Rpl22HA mice were intracranially implanted with GL261 glioma cells (GBM) or injected with PBS (sham)

tag: treatment

value: Sham (PBS)

tag: cell type

value: astrocytes

tag: tissue

value: Brain


title: 14_Batch1_157_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

tag: shannon

tag: bv

value: Neg

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host


title: 11T

tag: tumor status

tag: patient id


title: 13N


title: 16_Batch1_083_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: CCVR

tag: hc method

tag: cst

tag: shannon

tag: bv

tag: nugent score

value: Low

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: cumulative number of reads

tag: median cv coverage


title: Sample 20_PMF-3

description: Codeset NS_INFL_HS_V2_C2534

tag: diagnosis

tag: grading


title: 12T

tag: tumor status

tag: patient id


title: Sham2

tag: treatment

tag: cell type

tag: tissue


title: Sham1


title: Sham3


title: Sample 15_PMF-3

description: Codeset NS_INFL_HS_V2_C2534


title: HCC1806_2D_MYC-OE-Rep2

city: Farmington

first: Olga

last: Anczukow

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory for Genomic Medicine

data_processing:
Read filtering and cropping of reads to same length using Trimmomatic (v0.39)
Mapping of reads to Gencode GRCh38 v.32 reference transcript annotation using STAR in 2-pass mode (v2.7.3a)
Transcript assembly and quantification with Stringtie (v2.1.3b)
Differential splicing using rMATS (v4.1.0)
Genome_build: GRCh38.p13 v32
Supplementary_files_format_and_content: gene_count_matrix

source_name: human triple negative breast cancer cells

growth_protocol: 2D-grown HCC1806 cells were maintained in DMEM (Gibco) supplemented with 15% FBS and 1% penicillin streptomycin (Sigma) and were harvested by scraping adherent cells in PBS once ~90% confluence was reached.

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen) including DNase I treatment per manufacturer instructions.
Barcoded RNA libraries were prepared starting with 500ng of total RNA using the TrueSeq stranded mRNA kit with polyA selection (Illumina), and quantified using a Bioanalyzer DNA 1000 chip (Agilent).
Libraries were sequenced as 150bp paired-end reads at 100-200 million reads per library on an Illumina NovaSeq, equal amounts of 18 libraries were pooled per lane.

tag: cell line

tag: genotype

value: MYC-OE


title: 12_Batch1_125_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: NETEN

tag: hc method

tag: cst

value: CST-IV

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host


title: 13_Batch1_145_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: mg

tag: multiple stis

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: cumulative number of reads

tag: median cv coverage


title: GBM4

tag: treatment

value: GBM (GL261)

tag: cell type

tag: tissue


title: Sample 13_PMF

description: Codeset NS_INFL_HS_V2_C2534

tag: diagnosis

value: primary myelofibrosis (PMF)

tag: grading


title: Sample 14_PMF-3

description: Codeset NS_INFL_HS_V2_C2534


title: Sample 12_PMF

description: Codeset NS_INFL_HS_V2_C2534


title: HCC1806_2D_MYC-OE-Rep1

tag: cell line

tag: genotype


title: GBM3


title: 11_Batch1_122_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

value: CST-III

tag: shannon

tag: bv

tag: nugent score

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host


title: GBM2

tag: treatment

tag: cell type

tag: tissue


title: 11N

tag: tumor status

value: non-neoplastic

tag: patient id


title: HCC1806_2D_MYC-OE-Rep3

tag: cell line

tag: genotype


title: 10_Batch1_120_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

tag: shannon

tag: bv

value: Pos

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

value: High

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: cumulative number of reads

tag: median cv coverage


title: Sample 11_PMF

description: Codeset NS_INFL_HS_V2_C2534

tag: diagnosis

tag: grading


title: 9_Batch1_107_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host


title: GBM1

tag: treatment

tag: cell type

tag: tissue


title: Sample 10_PMF

description: Codeset NS_INFL_HS_V2_C2534

tag: diagnosis

tag: grading


title: HCC1806_2D_3XSR-Rep2

tag: cell line

tag: genotype


title: 8_Batch1_104_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: cumulative number of reads

tag: median cv coverage


title: HCC1806_2D_3XSR-Rep1

tag: cell line

tag: genotype


title: Lingo3_rep3

city: Philadelphia

first: De'Broski

last: Herbert

state: PA

address: 3900 Spruce Street

department: Pathobiology

institute: University of Pennsylvania

data_processing:
Fastq files were trimmed with trimmomatic version 0.39, to remove Truseq universal and indexed adapter sequences, and low quality reads
trimmed fastq files were aligned to version 81 of mouse reference genome GRCm38 using the STAR aligner
Sorted BAM files resulting from the alignments were quantified to genes using htseq-count, using the union mode for read overlap resolution
Genes with group average counts of less than 5 were removed from the dataset in R, and expression count data was normalized using DESeq2 in R
Genome_build: GRCm38 version 81
Supplementary_files_format_and_content: tab deliniated text files include read counts from htseq-count, and normalized expression values, and statistical output from DESeq2

source_name: Colon epithelial cell fraction

growth_protocol: Colon tissue was harvested, and epithelial cells were washed off in a EDTA DTT wash, and RNA was isolated within 1 hour of tissue harvesting

extract_protocol:
total RNA was isolated with the Qiagen RNAeasy plus kit, RNA yield was determined by Qubit fluorometer, and RNA quality was determined with TapeStation
libraries were prepared using the TruSeq Stranded Total RNA LT Kit with Ribo-Zero Gold, according to the manufacturer’s instructions.

treatment_protocol: Mice were grown under niave conditions

tag: tissue

value: Colon

tag: cell type

value: Epithelial cells obtained by EDTA wash

tag: age

value: 2 months


title: HCC1806_2D_3XCTL-Rep3

value: control


title: Sample 8_PMF

description: Codeset NS_INFL_HS_V2_C2534

tag: diagnosis

tag: grading


title: 7_Batch1_101_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

value: CST-I

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host


title: Sample 9_PMF

description: Codeset NS_INFL_HS_V2_C2534

tag: diagnosis

tag: grading


title: HCC1806_2D_3XCTL-Rep2

tag: cell line

tag: genotype


title: HCC1806_2D_3XSR-Rep3


title: HCC1806_2D_3XCTL-Rep1


title: Sample 7_PMF

description: Codeset NS_INFL_HS_V2_C2534


title: 6_Batch1_092_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

tag: shannon

tag: bv

value: Int

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: cumulative number of reads

tag: median cv coverage


title: Lingo3_rep1

tag: tissue

tag: cell type

tag: age

tag: genotype


title: 5_Batch1_065_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

tag: shannon

tag: bv

value: Neg

tag: nugent score

tag: bv prior

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host


title: 4_Batch1_046_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: cumulative number of reads

tag: median cv coverage


title: OCI-AML5-Cas9 EKO cells overexpressing YFP control vector, day 7

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20.
Reads were trimmed using Trim Galore and aligned to the sgRNA sequences using Bowtie aligner v2.3.3. Synthetic rescue/positive selection and synthetic lethality/negative selection beta scores, as well as statistical significance, were determined using MAGeCK-MLE method.
Supplementary_files_format_and_content: Tab-delimited file with columns being a. sgRNA identifier, b. Gene, c-f, counts for the specified sample identifier.

source_name: OCI-AML5-Cas9 EKO

growth_protocol: OCI-AML5-Cas9 EKO library cells were infected for 3 days with HMGA2-YFP or YFP expressing vectors, then treated with Doxycyclin (2 ug/mL) for 7 days for Cas9 activation to induce gene KO. Cells were then expanded for 7 days (splited with fresh media every 2 days).

extract_protocol:
Proteinase-K/ammonium acetate/ethanol extraction - in-house protocol
Illumina index sequencies were added to each sample by PCR (PCR2)

treatment_protocol: Media: DMEM, 10% FBS, 10ng/ml GM-CSF. No chemical treatment was applied.

tag: cell type

value: AML cell line

tag: time

value: day 7

tag: cell line

value: OCI-AML5-Cas9 EKO

tag: vector

value: overexpressing YFP control vector


title: WT_rep3

tag: tissue

tag: age

tag: genotype

value: wild type


title: WT_rep2


title: Sample 5_PMF

description: Codeset NS_INFL_HS_V2_C2534

tag: diagnosis

value: primary myelofibrosis (PMF)

tag: grading


title: OCI-AML5-Cas9 EKO cells overexpressing HMGA2-YFP vector, day 7

value: overexpressing HMGA2-YFP vector


title: 3_Batch1_018_2

city: Atlanta

first: Gregory

address: 954 Gatewood Dr

institute: Yerkes National Primate Research Center

data_processing:
The sequencing data was demultiplexed using Illumina bcl2fastq version 2.20.0.422 BCL to FastQ file converter.
The quality of raw reads was assessed with FastQC version 0.11.8
Reads were mapped to the GRCh38 human genome assembly [https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/] using STAR version 2.5.2b with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the htseq-count algorithm
DESeq2 version 1.22.1 R package was used to produce Raw read counts.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text file containing Raw read counts for each sample (in columns) and each annotated transcript (in rows).

extract_protocol:
RNA was extracted from the endocervical cytobrush samples collected at the crossover visit using RNeasy Micro kit (Qiagen, CA) with DNase digest and QIAcube automation stations. The RNA was quantified, and the quality was assessed by Bioanalyzer analysis (Agilent Technologies, Santa Clara, CA)
Libraries were prepared using the Illumina (Illumina Inc. San Diego, CA, USA) TruSeq RNA Exome kit, as per manufacturer’s instructions, with 20 ng of total RNA as input. The amplified libraries were validated by capillary electrophoresis on the Agilent 4200 TapeStation. The libraries were Rawalized, pooled and sequenced on the Illumina HiSeq3000 system employing a single-end 101 cycles run at average read depths of 21 million reads/sample.

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: NETEN

tag: hc method

tag: cst

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

value: Low

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host


title: Sample 4_PMF

description: Codeset NS_INFL_HS_V2_C2534

tag: diagnosis

tag: grading


title: Lingo3_rep2

tag: tissue

tag: cell type

tag: age

tag: genotype


title: OCI-AML5-Cas9 EKO cells overexpressing YFP control vector, day 0

tag: time

value: day 0

tag: cell line

tag: vector


title: OCI-AML5-Cas9 EKO cells overexpressing HMGA2-YFP vector, day 0


title: Sample 3_PMF

description: Codeset NS_INFL_HS_V2_C2534


title: 2_Batch1_013_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: cumulative number of reads

tag: median cv coverage


title: npas4l_mut

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

description: Mattonet_adata_obs.csv, Mattonet_udata_obs.csv

data_processing:
Reads were aligned against the zebrafish genome (DanRer11) and counted by StarSolo  followed by secondary analysis in Annotated Data Format. Preprocessed counts were further analysed using Scanpy.
Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed only 16 cells in total that did not express between 1000 and 7000 genes or had an mitochondrial content less than 6%. Further, we filtered genes if they were detected in less than 30 cells (<0.3%).
Raw counts per cell were normalised to the median count over all cells and transformed into log space to stabilise variance. We initially reduced dimensionality of the dataset using PCA, retaining 50 principal components. Subsequent steps, like low-dimensional UMAP embedding and cell clustering via community detection, were based on the initial PCA.
Final data visualization was done by scVelo and cellxgene packages.
Genome_build: DanRer11
Supplementary_files_format_and_content: Mattonet_adata_obs.csv: basic anndata observations (Sample, n_genes_by_counts, log1p_total_counts, pct_counts_is_mito, n_genes_detected, leiden_clustering)
Supplementary_files_format_and_content: Mattonet_udata_obs.csv: velocity anmdata observations (initial_size_unspliced, initial_size_spliced, initial_size, n_counts, velocity_self_transition, root_cells, end_points, velocity_pseudotime)

organism: Danio rerio

source_name: npas4l reporter positive cells

extract_protocol:
Tails from ~150 npas4l heterozygous (npas4lbns423/+) and trans-heterozygous (npas4lbns423/bns297) mutant embryos were cut at the anterior end of the yolk extension at 20 hpf in DMEM/F10+5%FBS+0.01% tricaine on agarose-coated plates. The cells were dissociated using the Pierce Cardiomyocyte dissociation kit according to manufacturer instructions and FACS sorted for GFP-fluorescence using an AriaIII-sorter and DAPI as indicator for dead cells.
The cell suspensions were counted with Moxi cell counter and diluted according to manufacturer’s protocol to obtain 5000 single cell data points per sample. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10xGenomics). Single cell RNAseq library preparation was done using standard protocol.

tag: cell type

value: sorted npas4l reporter positive cells

tag: Stage

value: 20 hpf


title: Sample 6_PMF

description: Codeset NS_INFL_HS_V2_C2534

tag: diagnosis

tag: grading


title: Sample 2_PMF

description: Codeset NS_INFL_HS_V2_C2534


title: npas4l_het


title: Sample 1_PMF

description: Codeset NS_INFL_HS_V2_C2534


title: 1_Batch1_007_2

last: Tharp

source_name: endocervical cells

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

value: CST-IV

tag: shannon

tag: bv

value: Pos

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

value: High

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host


title: WT_rep1

tag: tissue

value: Colon

tag: cell type

value: Epithelial cells obtained by 5 mM EDTA + 2.5 mM DTT wash

tag: age

value: 2 months

tag: genotype


title: Medulloblastoma cell line F02_67896

status: Public on Jul 10 2022

type: genomic

city: San Diego

first: Jill

middle: P

last: Mesirov

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

hyb_protocol: Genomic DNA was digested, adaptor ligated, and amplified by polymerase chain reaction to achieve fragments ranging from 200 base pairs to 1,100 base pairs. These fragments were pooled, concentrated, and additionally fragmented with DNaseI, which was followed by labeling, denaturing, and hybridization to arrays in batches of 96 samples

scan_protocol: Arrays were then scanned by using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Signal intensities were normalized against a reference set of normal genomic DNA data, as previously described.
The processed data was generated using archived module (SNPFileCreator_SNP6) on the GenePattern Server. That module is currently archived in GitHub: https://github.com/genepattern/SNPFileCreator_SNP6.
column header informaton:
1. Sample (sample name)
2. Chromosome (chromosome number)
3. Start Position (segment start position, in bases)
4. End Position (segment end position, in bases)
5. Num markers (number of markers in segment)
6. Seg.CN (log2() -1 of copy number)]

label: Biotin

source_name: Medulloblastoma cell line F02_67896

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: DNA was prepared by using the Puregene DNA Extraction Kit (Gentra Systems, Minneapolis, MN), and total RNA was extracted by using Trizol (Invitrogen, Carlsbad, CA), both per manufacturers' instructions.

treatment_protocol: Snap-frozen tumors were obtained from Children's Oncology Group (ACNS02B3; n = 89) and from Children's Hospital Boston (n = 55), University of Washington Medical Center (n = 27), Texas Children's Hospital (n = 24), and Johns Hopkins Medical Center (n = 10). Normal cerebellum (n = 11) was obtained from University of Washington Medical Center and NICHD Brain and Tissue Bank for Developmental Disorders, University of Maryland, Baltimore, MD. All samples were collected with approval from respective institutional review boards, and proper informed consent and/or assent was obtained from all patients or their parents.    Tumors were processed at Children's Hospital Boston except for samples from Texas Children's, where similar protocols were used

value: medulloblastoma

tag: cell line


title: Medulloblastoma cell line D07_67976

source_name: Medulloblastoma cell line D07_67976


title: Medulloblastoma cell line F01_46638

source_name: Medulloblastoma cell line F01_46638


title: Medulloblastoma cell line A03_46660

source_name: Medulloblastoma cell line A03_46660


title: Medulloblastoma cell line F11_89096

source_name: Medulloblastoma cell line F11_89096


title: Medulloblastoma cell line H07_89036

source_name: Medulloblastoma cell line H07_89036


title: Medulloblastoma cell line D09_89060

source_name: Medulloblastoma cell line D09_89060


title: Medulloblastoma cell line E08_89046

source_name: Medulloblastoma cell line E08_89046


title: Medulloblastoma cell line E09_89062

source_name: Medulloblastoma cell line E09_89062


title: Medulloblastoma cell line D08_89044

source_name: Medulloblastoma cell line D08_89044


title: Medulloblastoma cell line D01_88932

source_name: Medulloblastoma cell line D01_88932


title: Medulloblastoma cell line B12_89104

source_name: Medulloblastoma cell line B12_89104


title: Medulloblastoma cell line D04_88980

source_name: Medulloblastoma cell line D04_88980


title: Medulloblastoma cell line B06_89008

source_name: Medulloblastoma cell line B06_89008


title: Medulloblastoma cell line B01_88928

source_name: Medulloblastoma cell line B01_88928


title: Medulloblastoma cell line D06_110206

source_name: Medulloblastoma cell line D06_110206


title: Medulloblastoma cell line B11_67652

source_name: Medulloblastoma cell line B11_67652


title: Medulloblastoma cell line F08_47154

source_name: Medulloblastoma cell line F08_47154


title: Medulloblastoma cell line B01_95100

source_name: Medulloblastoma cell line B01_95100


title: Medulloblastoma cell line E11_47200

source_name: Medulloblastoma cell line E11_47200


title: Medulloblastoma cell line H03_88588

source_name: Medulloblastoma cell line H03_88588


title: Medulloblastoma cell line D12_95280

source_name: Medulloblastoma cell line D12_95280


title: Medulloblastoma cell line H05_88620

source_name: Medulloblastoma cell line H05_88620


title: Medulloblastoma cell line H06_88636

source_name: Medulloblastoma cell line H06_88636


title: Medulloblastoma cell line F06_95188

source_name: Medulloblastoma cell line F06_95188


title: Medulloblastoma cell line H02_88572

source_name: Medulloblastoma cell line H02_88572


title: Medulloblastoma cell line G04_88986

source_name: Medulloblastoma cell line G04_88986


title: Medulloblastoma cell line G12_88730

source_name: Medulloblastoma cell line G12_88730


title: Medulloblastoma cell line G10_88698

source_name: Medulloblastoma cell line G10_88698


title: Medulloblastoma cell line G11_88714

source_name: Medulloblastoma cell line G11_88714


title: Medulloblastoma cell line G08_88666

source_name: Medulloblastoma cell line G08_88666


title: Medulloblastoma cell line G09_88682

source_name: Medulloblastoma cell line G09_88682


title: Medulloblastoma cell line H03_147728

source_name: Medulloblastoma cell line H03_147728


title: Medulloblastoma cell line G06_67002

source_name: Medulloblastoma cell line G06_67002


title: Medulloblastoma cell line E07_147786

source_name: Medulloblastoma cell line E07_147786


title: Medulloblastoma cell line G07_88650

source_name: Medulloblastoma cell line G07_88650


title: Medulloblastoma cell line E12_151146

source_name: Medulloblastoma cell line E12_151146


title: Medulloblastoma cell line D02_150984

source_name: Medulloblastoma cell line D02_150984


title: Medulloblastoma cell line A06_66990

source_name: Medulloblastoma cell line A06_66990


title: Medulloblastoma cell line A06_88238

source_name: Medulloblastoma cell line A06_88238


title: Medulloblastoma cell line A03_88190

source_name: Medulloblastoma cell line A03_88190


title: Medulloblastoma cell line A01_88158

source_name: Medulloblastoma cell line A01_88158


title: Medulloblastoma cell line G08_70118

source_name: Medulloblastoma cell line G08_70118


title: Medulloblastoma cell line E03_70034

source_name: Medulloblastoma cell line E03_70034


title: Medulloblastoma cell line B12_48862

source_name: Medulloblastoma cell line B12_48862


title: Medulloblastoma cell line D05_70064

source_name: Medulloblastoma cell line D05_70064


title: HCHF_2years_SAMPLE 108

city: Winston-Salem

first: Laura

middle: A

last: Cox

state: NC

address: Medical Center Boulevard

department: Internal medicine-Section of Molecular Medicine

institute: Wake Forest School of Medicine

description: IL_BPP2yc_324_16101_HFHC_2yr_liv.AVG_Signal

hyb_protocol: Standard Illumina hybridization protocol

data_processing:
data for all samples were pre-processed identically for background correction and normalization with Illumina
Data filtering: Only those transcripts whose detection levels equaled or exceeded 0.2 (of the detection p-value 0.95) in greater or equal to 50% of the total sample were filtered. The filtered transcript data were quantile normalized and log2 transformed.
normalized data file includes quantile normalized and log2 transformed with GUI R

label: biotin

organism: Papio hamadryas

source_name: Baboon Frozen Liver

label_protocol: cRNA was synthesized and biotin labeled using Illumina TotalPrep RNA Amplification Kit.

extract_protocol: RNA was extracted from the homogenate and impurities removed using the RNeasy MinElute Kit

treatment_protocol: Biotinylated cRNA were prepared with the Amp kit for Illumina arrays

tag: gender

value: Male

tag: timepoint

value: 2 years

tag: diet

value: HCHF diet

value: liver

tag: sample number


title: HCHF_2years_SAMPLE 109

description: IL_BPP2yc_327_16289_HFHC_2yr_liv.AVG_Signal

scan_protocol: Standard Illumina hybridization protocol

value: Female


title: Medulloblastoma cell line B09_95036

source_name: Medulloblastoma cell line B09_95036


title: Medulloblastoma cell line G06_48776

source_name: Medulloblastoma cell line G06_48776


title: Medulloblastoma cell line A11_95066

source_name: Medulloblastoma cell line A11_95066


title: Medulloblastoma cell line C05_70062

source_name: Medulloblastoma cell line C05_70062


title: Medulloblastoma cell line A08_95018

source_name: Medulloblastoma cell line A08_95018


title: HCHF_2years_SAMPLE 111

description: IL_BPP2yc_333_17268_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 104

description: IL_BPP2yc_312_17233_HFHC_2yr_liv.AVG_Signal


title: Medulloblastoma cell line B10_95052

source_name: Medulloblastoma cell line B10_95052


title: HCHF_2years_SAMPLE 107

description: IL_BPP2yc_321_16000_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 106

description: IL_BPP2yc_318_15820_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 105

description: IL_BPP2yc_315_19165_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 101

description: IL_BPP2yc_303_16329_HFHC_2yr_liv.AVG_Signal


title: Medulloblastoma cell line D05_151032

source_name: Medulloblastoma cell line D05_151032


title: HCHF_2years_SAMPLE 98

description: IL_BPP2yc_294_16408_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 100

description: IL_BPP2yc_300_15279_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 96

description: IL_BPP2yc_288_16017_HFHC_2yr_liv.AVG_Signal


title: Medulloblastoma cell line A04_151010

source_name: Medulloblastoma cell line A04_151010


title: HCHF_2years_SAMPLE 95

description: IL_BPP2yc_285_15175_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 110

description: IL_BPP2yc_330_16517_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 99

description: IL_BPP2yc_297_17776_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 97

description: IL_BPP2yc_291_18141_HFHC_2yr_liv.AVG_Signal


title: Medulloblastoma cell line B08_48798

source_name: Medulloblastoma cell line B08_48798


title: HCHF_2years_SAMPLE 93

description: IL_BPP2yc_279_17971_HFHC_2yr_liv.AVG_Signal


title: Medulloblastoma cell line B04_94956

source_name: Medulloblastoma cell line B04_94956


title: HCHF_2years_SAMPLE 103

description: IL_BPP2yc_309_16761_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 91

description: IL_BPP2yc_273_17190_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 86

description: IL_BPP2yc_258_14172_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 92

description: IL_BPP2yc_276_14924_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 90

description: IL_BPP2yc_270_16787_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 89

description: IL_BPP2yc_267_15545_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 83

description: IL_BPP2yc_249_17981_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 81

description: IL_BPP2yc_243_14154_HFHC_2yr_liv.AVG_Signal


title: Tamoxifen_NCD-2

city: Daejeon

first: Jung Tae

last: Kim

address: 282 Munhwaro

department: School of Medicine

country: South Korea

institute: Chungnam National University

data_processing:
Trimmed reasds is mapped into reference genome using HISAT2
After read mapping, transcript assembly was performed by StringTie to get expression profile
Differential expression genes were compared through DESeq2 using the obtained read count data.
Assembly: mm10
Supplementary files format and content: Excel file include FPKM values and read counts for each sample

source_name: Thyroid

extract_protocol:
Total RNA was isolated from the thyroid glands using TRIzol reagent (Life Technologies, Eugene, OR, USA) and transcribed into complementary DNA (cDNA).
TruSeq Stranded Total RNA Sample Prep Guide (Part # 15031048 Rev. E) using TruSeq Stranded Total RNA LT Sample Prep Kit (Human Mouse Rat) was performed

treatment_protocol: Tamoxifen is injceted for 1wk to induce BRAFV600E mutation at mice age 8 wk. And high fat diet feeding was performed from mice age 10wk to 22wk for 12wk

value: Thyroid

value: BRAFV600E mutated

tag: treatment

value: Chow diet


title: Tamoxifen_HFD-10

value: High fat diet


title: Tamoxifen_HFD-2


title: HCHF_2years_SAMPLE 102

description: IL_BPP2yc_306_16363_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 94

description: IL_BPP2yc_282_14944_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 87

description: IL_BPP2yc_261_14355_HFHC_2yr_liv.AVG_Signal


title: Tamoxifen_NCD-8


title: HCHF_2years_SAMPLE 85

description: IL_BPP2yc_255_17898_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 84

description: IL_BPP2yc_252_17165_HFHC_2yr_liv.AVG_Signal


title: Tamoxifen_HFD-9


title: single-nucleus sample 4

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

description:
SN4
sn_count_table.csv

data_processing:
Raw sequencing data were demultiplexed, aligned to the human genome (GRCh38) and UMI-collapsed using CellRanger.
Assembly: GRCh38
Supplementary files format and content: CSV gene counts

molecule: polyA RNA

source_name: Pancreatic islets

extract_protocol:
Nuclei or cells were  lysed in droplets using the 10X Chromium instrument.
Reverse transcription was performed in droplet and library construction was performed according to the 10X Chromium Single Cell 3' Reagent Kit.

value: Pancreatic islets


title: HCHF_2years_SAMPLE 88

description: IL_BPP2yc_264_14852_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 77

description: IL_BPP2yc_231_17871_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 82

description: IL_BPP2yc_246_17141_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 79

description: IL_BPP2yc_237_18015_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 76

description: IL_BPP2yc_228_17340_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 74

description: IL_BPP2yc_222_16827_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 75

description: IL_BPP2yc_225_17873_HFHC_2yr_liv.AVG_Signal


title: single-nucleus sample 3

description:
SN3
sn_count_table.csv


title: HCHF_2years_SAMPLE 80

description: IL_BPP2yc_240_14058_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 78

description: IL_BPP2yc_234_17903_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 73

description: IL_BPP2yc_219_17325_HFHC_2yr_liv.AVG_Signal


title: single-cell sample 4

description:
SC4
sc_count_table.csv


title: single-cell sample 1

description:
SC1
sc_count_table.csv


title: single-nucleus sample 2

description:
SN2
sn_count_table.csv


title: HCHF_2years_SAMPLE 72

description: IL_BPP2yc_216_13694_HFHC_2yr_liv.AVG_Signal


title: single-nucleus sample 1

description:
SN1
sn_count_table.csv


title: single-cell sample 3

description:
SC3
sc_count_table.csv


title: single-cell sample 2

description:
SC2
sc_count_table.csv


title: HCHF_2years_SAMPLE 71

description: IL_BPP2yc_213_17826_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 70

description: IL_BPP2yc_210_17199_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 66

description: IL_BPP2yc_198_12218_HFHC_2yr_liv.AVG_Signal


title: ZNF597_WT_K09_OE015_x6_S4

city: Seattle

first: Alice

last: Berger

state: Washington

address: 1100 Fairview Ave N, Mailstop C2-023

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

data_processing:
Illumina HiSeq 4000 reads were aligned by STAR v2.5.3a to BAM files.
Picard tools v.1.114 used mark duplicate reads, add read group info, and reorder BAMs.
BAMs are indexed using samtools v.0.1.19
FeatureCounts from Subread v.1.5.3 was used to quantify gene transcripts
EdgeR v.3.22.3 was used to normalize read counts and obtain CPM and RPKM values.
CPM values were used to filter the gene list  down to the 12,887 genes with average log2CPM >0.1 across all samples. RPKM values were converted into TPM values.
Assembly: hg19/GRCh37
Supplementary files format and content: transcript_quants_log2TPM.csv is a comma-separated values file of the log2 of TPM values of all samples. Each row is a gene transcript and each column is a sample.

growth_protocol: Cells were cultured for one day before and 96 hours after treatment.

extract_protocol:
Cells were lysed and RNA extracted with TRIzol (Invitrogen)
Nextera XT Index Kit v2, 75bp paired-end pre-pooled libraries

treatment_protocol: Cells were transduced with the ORF construct (if applicable) one day after plating. Infection efficiency is assessed at 24 hours post-infection with antibody selection.

value: lung adenocarcinoma

tag: ectopic exression

value: ZNF597 WT


title: ZNF597_WT_K09_OE015_x5_S4


title: ZNF597_WT_V5_L01_OE015_x6_S4


title: HCHF_2years_SAMPLE 68

description: IL_BPP2yc_204_14908_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 67

description: IL_BPP2yc_201_18395_HFHC_2yr_liv.AVG_Signal


title: ZNF597_WT_V5_L01_OE015_x5_S4


title: ZNF597_WT_V5_L01_0E015_x3_G10


title: ZNF597_WT_K09_0E015_x3_E10


title: HCHF_2years_SAMPLE 64

description: IL_BPP2yc_192_16371_HFHC_2yr_liv.AVG_Signal


title: ZNF597_WT_V5_L01_0E015_x2_G4


title: HCHF_2years_SAMPLE 69

description: IL_BPP2yc_207_16708_HFHC_2yr_liv.AVG_Signal


title: ZNF597_WT_K09_0E015_x2_E4


title: HCHF_2years_SAMPLE 63

description: IL_BPP2yc_189_17139_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 62

description: IL_BPP2yc_186_16338_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 61

description: IL_BPP2yc_183_16400_HFHC_2yr_liv.AVG_Signal


title: ZNF597_p.V21L_J13_OE015_x5_S4

value: ZNF597 p.V21L


title: ZNF597_p.V21L_J13_0E015_x3_C10


title: HCHF_2years_SAMPLE 60

description: IL_BPP2yc_180_16321_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 59

description: IL_BPP2yc_177_17916_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 58

description: IL_BPP2yc_174_17829_HFHC_2yr_liv.AVG_Signal


title: ZNF597_p.L283V_N03_OE015_x6_S4


title: ZNF597_p.L283V_N03_0E015_x3_D11


title: ZNF597_p.L283V_N03_OE015_x5_S4


title: HCHF_2years_SAMPLE 57

description: IL_BPP2yc_171_16880_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 65

description: IL_BPP2yc_195_16413_HFHC_2yr_liv.AVG_Signal