title: zf 7dpf wt biol rep 3

value: WT


title: MS patient 18A

status: Public on Oct 26 2022

type: RNA

city: Copenhagen N

first: Atul

last: Anand

address: Ole Maaløes Vej 5, building 2, 3 floor

department: Department of Pathology

country: Denmark

institute: Rigshospitalet

hyb_protocol: 100 ng of total RNA was used for the Agilent miRNA Microarray System with miRNA Complete Labeling and Hyb Kit (Version 3.1.1, Agilent Technologies).  Additionally, the optional microRNA Spike-In kit (#5190-1934, Agilent Technologies) was added.

scan_protocol: scanned on an Agilent DNA Microarray Scanner C with SureScan Technology using the Agilent Microarray Scanner System user Guide

data_processing: Data from the Microarray Scanner C was extracted using Agilent Feature Extraction Software v. 12.03.1 (Agilent Technologies) and a Quality Control report for each microarray slide was provided after the data extraction

molecule: total RNA

organism: Homo sapiens

source_name: PAXgene Blood miRNA

extract_protocol: 210 full blood samples were collected in PAXgene tubes during the TREMEND (Tecfidera in Relapsing-Remitting Multiple Sclerosis: Endothelial Dysfunction) phase IV clinical trial from 52 RRMS patients and 22 controls from March 2014 to August 2016 and kept in 80oC. In 2020, the microRNA was extracted with Blood miRNA Kit from Qiagen. Quality and quantity assessment of extracted RNA on NanoDrop 2000c spectrophotometer (ThermoFischer) and 2100 bioanalyzer (Agilent).

treatment_protocol: Blood samples of patients before and short- and long-term after DMF treatment of the the TREMEND (Tecfidera in Relapsing-Remitting Multiple Sclerosis: Endothelial Dysfunction) phase IV clinical trial

tag: tissue

value: whole blood

tag: timepoint

value: Baseline group

tag: age

tag: Sex

value: female


title: P2-41-31-G2

type: SRA

city: Guangzhou

first: Gong

last: Zhang

state: Guangdong

address: 601,Huangpu Avenue West,Tianhe District

department: College of Life Science and Technology

country: China

institute: Jinan University

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence by cutadapt, low-complexity or low-quality sequence were discard.
mapped to reference using fanse3 with parameters -E5% --indel -S14
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated in . In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19 mRNA from UCSC

source_name: Tumor

extract_protocol:
Tissues were flash frozen on dry ice. RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the library construction for sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: male

value: lung

tag: t stage

tag: n stage

tag: m stage

tag: tumor stage

value: IB

tag: smoking

tag: disease state

value: lung adenocarcinoma


title: CH19101_3

city: Madrid

first: Enrique

last: Vazquez de Luis

state: Madrid

address: Melchor Fernandez Almagro, 3

country: Spain

institute: CNIC

data_processing:
Illumina Casava software used for basecalling and bcl2fastq for demultiplexing.
Sequenced reads quality was evaluated from FastQC.
Reads were trimmed for Illumina adaptors with cutadapt.
Reference Genome was indexed from RSem (Li B et al. 2011) and sequence reads were aligned using RSem.
RNA-Seq data were normalized using Transcripts Per Million (TPM) Trimmed Mean of M values (Robinson MD and A Oshlack 2010).
Assembly: Human sequenced genome GRCh38 v91
Supplementary files format and content: Tab-delimited text files include raw, TPM and RPKM (Reads Per Kilobase Million) values for each sample.

source_name: Blood

extract_protocol:
Total RNA was isolated using RNeasy Micro Kit (Qiagen) and was quantified and purity checked using a NanoDrop ND-1000 (Thermo Scientific, Waltham, MA, USA). RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)
Low Input RNAs were used to amplify the cDNA using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech-Takara). 1 ng of amplified cDNA was used to generate barcoded libraries using the Nextera XT DNA library preparation kit (Illumina). Libraries were quantified using a Qubit™ dsDNA HS assay with the Qubit fluorometer (Life Technologies, Carlsbad, California). Average library size and the size distribution were determined using a DNA 1000 assay in an Agilent 2100 Bioanalyzer. Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20.
Libraries were applied to an Illumina flow cell for cluster generation (SR Cluster Kit cBot) and sequence-by-synthesis single reads of 49 or 60 base length using the SBS Kit (Illumina) were generated on the HiSeq 2500 or the HiSeq 4000 following the standard sequencing protocol. Reads were further processed using the bcl2fastq package (Illumina) to split reads according to adapter indexes and produce fastq files. RNA-Seq was performed at the Genomics Unit of the Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid.

value: Blood

tag: time point

tag: library type

value: Low Input

tag: cell type

value: NK cells


title: zf 7dpf wt biol rep 2

city: Jerusalem

first: Stella

last: Mitrani-Rosenbaum

address: Ein Karem

country: Israel

institute: Hadassah -The Hebrew University Medical Center

data_processing:
NextSeq basecall files were converted to fastq using the bcl2fastq program with default parameters .   Quality-trimming was done using in-house Perl scripts, with a quality threshold of 32. In short, the scripts use a sliding window of 5 bases from the read's end and trim one base at a time until the average quality of the window passes the given threshold. Poly-G, adapter sequences, and poly-T were removed with cutadapt (v1.18), using a minimal overlap of 1 (-O parameter), allowing for read wildcards, and filtering out reads that became shorter than 15 nt (-m parameter). Filtering the remaining reads was done with the fastq_quality_filter (v0.0.14) program, with a quality threshold of 20 at 90 percent or more of the read's positions.
The processed fastq files were aligned to the zebrafish transcriptome and genome using TopHat (v2.1.1). The genome version was GRCz11, with annotations from Ensembl release 95. Alignment allowed up to 6 mismatches per read, a maximum gap of 5 bases, and a total edit distance of 11.
Quantification was done using htseq-count (v0.6.0). Strand information was set to 'reverse', and an annotation file that lacked information for genes of type IG, TR, Artifact, miRNA, Mt_rRNA, Mt_tRNA, ncRNA, piRNA, pre_miRNA, rRNA, ribozyme, sRNA, scRNA, scaRNA, siRNA, snRNA, snoRNA, tRNA and vaultRNA was used.
Normalization and differential expression analysis were done in R with the DESeq2 (v1.22.1) package. Genes with a sum of counts less than 20 over all samples were filtered out. Significance threshold was taken as padj < 0.1 .
Assembly: GRCz11
Supplementary files format and content: An excel file with raw counts, normalized counts and differential expression results. 'raw.' columns are raw counts, 'norm.' columns are the values after DESeq2 normalization. 'baseMean, log2FoldChange, lfcSE, stat, pvalue, padj' are corresponding result of DESeq2 analysis. 'sig' indicates significance according to threshold (padj<0.1).
Supplementary files format and content: Missing values are denoted by '?'.  A value can be missing because it did not appear in the annotation file used for quantification of reads, or because it was filtered by DESeq2.

organism: Danio rerio

source_name: whole embryo

extract_protocol:
Total RNA samples were extracted either from a pool of > 10 embryos/larvae
Library preparation was done using KAPA Stranded mRNA Sequencing Kit

value: whole embryo

tag: genotype


title: MS patient 17D

label_protocol: 100 ng of total RNA was used for the Agilent miRNA Microarray System with miRNA Complete Labeling and Hyb Kit (Version 3.1.1, Agilent Technologies).  Additionally, the optional microRNA Spike-In kit (#5190-1934, Agilent Technologies) was added.

value: 1-year group


title: zf 7dpf wt biol rep 1


title: P2-41-31-F6

source_name: Adjacent normal


title: CH19091_3


title: zf 5dpf gneKO biol rep 3

value: KO


title: zf 7dpf gnehet biol rep 2

value: HT


title: CH19091_2


title: MS patient 17A


title: P2-41-31-F3


title: zf 5dpf gneKO biol rep 2


title: P2-41-31-B10


title: CH19091_1


title: zf 5dpf gneKO biol rep 1


title: CH19088_1


title: P2-41-31-C3


title: zf 5dpf gnehet biol rep 3


title: P2-41-31-A4


title: CH19083_3


title: CH19075_3


title: zf 5dpf gnehet biol rep 2


title: P2-41-31-A1


title: zf 5dpf gnehet biol rep 1


title: CH19075_1


title: zf 5dpf wt biol rep 4


title: P2-41-14-K2


title: P2-41-14-J9

value: IIIa


title: CH16023_2


title: MS patient 17B

value: Early group


title: P2-41-14-A4


title: zf 5dpf wt biol rep 3

value: WT


title: MS patient 14D

value: whole blood


title: P2-41-14-A1


title: zf 5dpf wt biol rep 1


title: siSETX cytoDRIP-seq - S9.6 replicate 2

city: Stanford

first: Karlene

middle: Anne

last: Cimprich

state: CA

address: 318 Campus Drive

country: USA

institute: Stanford University

library_source: genomic

data_processing:
Library strategy: cytoDRIP-seq
Base calling CASAVA v1.8.2
Sequencing adapters were trimmed using cutadapt and then reads were aligned to genome build hg38 with bowtie2 (-- very sensitive).
Reads were seperated into strands with unix processing tools.
Reads processed into bedpe format using bedtools
Reads sorted and duplicate reads were removed using unix text processing tools
Genome_build: hg38
Supplementary_files_format_and_content: Generate bigwig files using bedtools coverageBed and bedGraphToBigWig from UCSC

molecule: other

source_name: HeLa cytoplasmic extract

growth_protocol: HeLa cells were cultured in DMEM (GIBCO) supplemented with 10% FBS, 2 mM L-glutamine and penicillin/streptomycin in 5% CO2 at 37°C.

extract_protocol:
Cells were harvested using trypsin, washed in PBS and pelleted by centrifugation. Cells were fractionated using the Nuclear and Cytoplasmic Extraction kit (Thermo Fisher Scientific) according to manufacturer’s instructions. Cytoplasmic fractions were recovered, and small amounts taken for western blotting and protein quantification, and the rest incubated in 0.4% SDS and 40 μg/ml of proteinase K (Thermo Fisher Scientific) for 90 mins at 37°C, followed by phenol-chloroform extraction and ethanol precipitation. Samples were resuspended in ultrapure distilled water, adjusted to 550 mM NaCl and treated with RNase A (1μg/mL) for 25 min, followed by phenol-chloroform extraction and ethanol precipitation. For immunoprecipitation, 16 μg of S9.6 antibody or mouse IgG were bound to Dynabeads Protein G beads (Thermo Fisher Scientific) in 1× binding buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 1% Triton X-100, 150 mM NaCl, 0.5% sodium deoxycholate) for 4-6h at 4°C. In parallel, samples were resuspended in 1X TE buffer and then pre-cleared with Dynabeads Protein G for 1-2 h in 1× binding buffer. Pre-cleared genomic samples were then added to S9.6 or IgG-bound beads and incubated overnight with rotation at 4°C. Bound beads were washed thrice with TE and then thrice with TSE buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 1% Triton X-100, 0.1% SDS, 150 mM NaCl). Elution was performed in 200μL elution buffer (50 mM Tris pH 8, 10 mM EDTA, 0.5% SDS, 8 μl Proteinase K 20 mg/ml) for 50 min at 50°C. After elution, genomic material was resuspended in 130 μl TE buffer and sonicated in 6 × 16 mm microtubes (Covaris, Woburn, MA, USA) to a peak fragment size of 300 bp, performed on a Covaris machine (E220 evolution) using SonoLab 7.3 software) (10% Duty Factor, 200 cycles/burst, 140 peak incident power, 30s per tube).
DNA libraries were synthesized from ssDNA using the Accel-NGS 1S DNA library kit (Swift Biosciences, Ann Arbor, MI, USA), according to the manufacturer's protocol. Using multiplexing adapters from the 1S Plus Set A Indexing Kit (Swift Biosciences), adapter-ligated DNA was amplified by PCR. Following PCR, DNA fragments 200–600 bp were retained by size selection using a 0.6× volume ratio of AMPure XP beads (Beckman Coulter)/sample followed by 1.0× ratio. Library DNA was analyzed on a Bioanalyzer DNA HS (Agilent, Santa Clara, CA, USA) at the Stanford Protein and Nucleic Acid Facility, quantified by qPCR using NEBNext Library Quant Kit for Illumina (New England Biolabs)

treatment_protocol: HeLa cells were transfected with siRNA against luciferase (Fisher scientific D-001400-01-20) or SETX (GCCAGAUCGUAUACAAUUA)  at 20 nM for 48 hours using Lipofectamine RNAiMAX, according to manufacturer protocols.

value: HeLa cells

tag: ip antibody

value: S9.6 (Antibodies Incorporated, Davis, CA, USA)

tag: exogenous treatment

value: siRNA targeting SETX


title: P2-41-13-K4

value: male

tag: tissue

value: lung


title: siSETX cytoDRIP-seq -S9.6 replicate 1


title: siGL3 cytoDRIP-seq - S9.6 replicate 2

value: Control siRNA for luciferase


title: MS patient 16E

tag: timepoint

value: Long term group

value: female


title: MS patient 16A

value: Baseline group

tag: age


title: MS patient 15D

tag: Sex


title: MS patient 16D


title: MS patient 15B


title: MS patient 14B


title: P2-41-13-K1

tag: gender

value: I

value: lung adenocarcinoma


title: zf 3dpf gneKO biol rep 2

value: whole embryo

value: KO


title: MS patient 14A


title: MS patient 15A


title: siGL3 cytoDRIP-seq -S9.6 replicate 1


title: MS patient 12E


title: zf 3dpf gnehet biol rep 3

value: HT


title: siSETX cytoDRIP-seq - IgG replicate 1

value: Mouse IgG (EMD Millipore 12-371)


title: zf 3dpf gneKO biol rep 1


title: zf 3dpf gnehet biol rep 2


title: MS patient 14C

value: Intermediate group


title: siSETX cytoDRIP-seq - IgG replicate 2


title: zf 3dpf gneKO biol rep 3


title: P2-41-13-H3

tag: t stage

value: IVa


title: MS patient 12A

value: whole blood


title: HFD-KO.12

city: Hangzhou

first: Jianing

last: Chen

address: Qingchun Road 79#

institute: Zhejiang university

description:
RELATIVE-genome.xls
reletive abundance in kingdom, class, family, genus and species

data_processing:
library strategy: DNA-seq
Sequencing libraries were prepared and the library quality was evaluated
the library was sequenced and the paired-end reads were generated
The gene sequence data were processed with default parameters
Sequences with ≥97% similarity were assigned to the same operational taxonomic units
The representative sequence for each OTU was screened for further annotation. The output data was further analyzed using Statistical Analysis
Assembly: Not applicatable
Supplementary files format and content: Matrix table with relative abundance for every gene and every sample
Supplementary files format and content: RELATIVE-genome.xls: reletive abundance in kingdom, class, family, genus and species
Supplementary files format and content: otu-FMT.xls: reletive abundance of OTUs
Supplementary files format and content: otu_table.relative for in vivo.xls: reletive abundance of OTUs
Supplementary files format and content: otu_table.relative. in vitro.xls: reletive abundance of OTUs
Supplementary files format and content: otu_table.relative for antibody.xls: reletive abundance of OTUs
Supplementary files format and content: gene.description-TRANS.xls: gene information of transcriptome

molecule: genomic DNA

organism: feces metagenome

source_name: feces

extract_protocol:
Total genome DNA from murine luminal samples from ileocecus was extracted for amplification
Sequencing libraries were prepared and the library quality was evaluated
DNA V3-V4 region or genome

value: feces

value: bacteria

tag: treatment

value: high fat diet


title: MS patient 11D

value: 1-year group


title: siGL3 cytoDRIP-seq - IgG replicate 2

value: HeLa cells

value: Control siRNA for luciferase


title: zf 3dpf gnehet biol rep 1


title: siGL3 cytoDRIP-seq - IgG replicate 1


title: zf 3dpf wt biol rep 3

value: WT


title: MS patient 11A

value: Baseline group

value: female


title: HFD-KO.10


title: HFD-KO.9


title: zf 3dpf wt biol rep 2


title: P2-41-13-H6

value: male

value: lung

value: lung adenocarcinoma


title: zf 3dpf wt biol rep 1

value: whole embryo


title: HFD-KO.8


title: MS patient 10B

value: Early group


title: MS patient 10A


title: mRNA-seq for human iPS cells #2

city: Nagoya

first: Kenji

last: Ichiyanagi

address: Furo-cho, Chikusa-ku

department: Graduate School of Bioagricultural Sciences

country: Japan

institute: Nagoya University

data_processing:
Trim Galore! (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) was used to remove the adapter sequences and 3' nucleotides with low quality scores (Q < 30).
The retained reads were mapped to both the human (hg38) and chimpanzee (panTro5) reference genomes, using TopHat2 (Kim et al. 2013) with default parameters.
The reads were first mapped to panTro5 regardless of the species of mRNA origin, and only the mapped reads were then mapped to hg38.
The mapping data on hg38 was analyzed using the human genome annotation. Gene expression levels were analyzed using Cuffdiff (Trapnell et al. 2013).
Assembly: hg38
Supplementary files format and content: tab-separated files with gene names and FPKM values

molecule: polyA RNA

extract_protocol:
Total cellular RNAs were isolated from ~1×106 cells by using Isogen (TOYOBO) and Direct-ZolTM RNA (ZYMO RESEARCH) according to manufactures’ instructions.
After quality check by Agilent 2100 Bioanalyzer (Agilent Technologies), PolyA-containing mRNAs were purified using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) and used for the preparation of indexed mRNA-seq libraries using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs). oligo(dT)-purified RNA-seq (stranded)

tag: cell line

value: iPS cells

tag: origin of_ipscs

value: dermal fibroblasts


title: mRNA-seq for human iPS cells #1

value: nasal epithelial cells


title: H3K27me3 for human iPS cells #2

data_processing:
Trim Galore! (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) was used to remove the adapter sequences and 3' nucleotides with low quality scores (Q < 30).
The retained reads were mapped to the human (hg38) or chimpanzee (panTro5) reference genomes, using Hisat2 with default parameters.
After de-duplication using samtools, the mapping reasults (in bam format) were used to generate read density files (in tdf format) using igvtools count.
Assembly: hg38 and panTro5
Supplementary files format and content: binary files for read density

extract_protocol:
MNase-digested chromatins were incubated with antibodies against H3K4me3 (Millipore, #07-473) and H3K27me3 (Cell Signaling Technology, #9733),  respectively.  Bound chromatins were collected using anti-IgG antibody-conjugated Dynabeads® M-280 (ThermoFisher).
Sequencing libraries were generated using NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (New England BioLabs).

tag: chip antibody

value: Cell Signaling Technology, #9733


title: HFD-KO.11

value: feces

value: bacteria


title: HFD-KO.5

value: high fat diet


title: Control 9

value: whole blood

value: Control


title: HFD-KO.4


title: HFD-KO.6


title: HFD-KO.3


title: KO_4

city: Natori, Miyagi

first: Keiichi

last: Tamai

address: 1-47, Nodayama, Shiote, Medeshima

institute: Miyagi Cancer Center

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (GE1_107_Sep09) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: HPCM2, CD271 promoter KO

label_protocol: 100 ng of total RNA was labeled using Low Input Quick Amp Labeling Kit

extract_protocol: RNA from cells was purified using RNeasy Mini Kits (Qiagen, Canada)

value: KO


title: H3K27me3 for human iPS cells #1


title: Control 8


title: Control 7


title: KO_2


title: input control of H3K27me3 for human iPS cells #2

value: none (input)


title: Control 6

value: female


title: MS patient 10D

value: 1-year group

value: male


title: KO_1


title: HFD-KO.1


title: KO_3


title: Control 5


title: Control 4


title: EV_4

source_name: HPCM2, control

value: control


title: EV_2


title: H3K4me3 for human iPS cells #2

value: Millipore, #07-473


title: EV_1


title: EV_3


title: HFD-WT.7

value: wild type


title: HFD-KO.2


title: HFD-WT.8


title: input control of H3K4me3 for human iPS cells #2

value: iPS cells


title: d3_b

source_name: HPCM2, CD271-low, day 3

label_protocol: 50 ng of total RNA was labeled using Low Input Quick Amp Labeling Kit

value: CD271-low HPCM2 cells


title: HFD-WT.6


title: input control of H3K27me3 for human iPS cells #1

value: nasal epithelial cells


title: Control 22


title: HFD-WT.5


title: Control 21


title: HFD-WT.4


title: Control 20


title: GLY EV miR 4

city: Pittsburgh

first: Chris

middle: P

last: Kargl

state: Pennsylvania

address: 4200 Fifth Avenue

institute: University of Pittsburgh

data_processing:
Adapter trimming followed by clipping of 4 bases from either ends of the reads and quality trimming was performed through Cutadapt software
After adaptor trimming, reads were trimmed based on quality such that bases above Phred Score 30 and reads with a minimum length of 5 were retained.
3-8 ng of total RNA/sample were sequenced using a NextSeq 500/550 high output v2 kit (Illumina, San Diego, CA, USA)
HO 75 cycle flow cells were utilized and sequencing was performed at 75,000,000 reads per cell.
STAR alignments software version 2.5; NGSUtils, bamutils Mapping software version 0.5.9
Assembly: GRC (GRCm38)
Supplementary files format and content: Raw counts and differential expression data

organism: Mus musculus

source_name: Whole quadriceps muscle

growth_protocol: Male C57BL/6J mice (00664) were purchased from Jackson Laboratory at 10–12 weeks old and housed in the Purdue University Animal facility at a controlled temperature (22 ± 2°C) with 12 h–12 h light–dark cycles. Mice were fed standard rodent chow with free water access.

extract_protocol:
Total RNA was isolated using miRNeasy micro kits from Qiagen according to the manufacturer's instructions.
3-8 ng of RNA was used. Library was constructed using QIAseq miRNA library kit according to manufacturer's protocol.

treatment_protocol: Isolated muscle was gently teased apart to increase surface area and incubated in serum-free DMEM for 24 h. Afterwards, the media was filtered through a 100 μm cell strainer and the EVs were isolated using an ultrafiltration-size exclusion chromatography technique (UF-SEC)

tag: strain

value: skeletal muscle

tag: tissue type

value: Glycolytic muscle

tag: rna source

value: Extracellular vesicles


title: d3_a

tag: time point

tag: cell type


title: d2_b

source_name: HPCM2, CD271-low, day 2


title: H3K4me3 for human iPS cells #1


title: HFD-WT.3

value: feces

value: bacteria

tag: genotype

value: high fat diet


title: Control 3

value: whole blood

value: Control


title: Control 2

value: female


title: Control 19


title: HFD-WT.2


title: d1_b

source_name: HPCM2, CD271-low, day 1


title: Control 18


title: d2_a


title: d1_a


title: input control of H3K4me3 for human iPS cells #1

value: none (input)


title: d0_b

source_name: HPCM2, CD271-low, day 0


title: HFD-WT.1


title: HFD-KO-2

description:
gene.description-TRANS.xls
gene information of transcriptome

data_processing:
Sequencing libraries were prepared and the library quality was evaluated
the library was sequenced and the paired-end reads were generated
The gene sequence data were processed with default parameters
Sequences with ≥97% similarity were assigned to the same operational taxonomic units
The representative sequence for each OTU was screened for further annotation. The output data was further analyzed using Statistical Analysis
Assembly: Not applicatable
Supplementary files format and content: Matrix table with relative abundance for every gene and every sample
Supplementary files format and content: RELATIVE-genome.xls: reletive abundance in kingdom, class, family, genus and species
Supplementary files format and content: otu-FMT.xls: reletive abundance of OTUs
Supplementary files format and content: otu_table.relative for in vivo.xls: reletive abundance of OTUs
Supplementary files format and content: otu_table.relative. in vitro.xls: reletive abundance of OTUs
Supplementary files format and content: otu_table.relative for antibody.xls: reletive abundance of OTUs
Supplementary files format and content: gene.description-TRANS.xls: gene information of transcriptome

source_name: Intestine

value: Intestine

value: epithelium


title: ND-KO.9

value: nornal diet


title: GLY EV miR 3


title: GLY EV miR 1


title: HFD-KO-1


title: ND-KO.8


title: OXI EV miR 3

source_name: Soleus and red gastrocnemius muscle

value: Oxidative muscle


title: ND-KO.7


title: HFD-WT-3

value: wild type


title: Control 16


title: d0_a

value: CD271-low HPCM2 cells


title: Control 14

value: male


title: OXI EV miR 4

value: skeletal muscle


title: GLY EV miR 2

value: Glycolytic muscle


title: Control 13


title: ND-KO.6


title: HFD-WT-2


title: Control 15


title: ND-KO.5


title: HFD-WT-1


title: HFD-KO-3


title: Control 17


title: TAM Pdcd1f/fLysMcre rep2

city: Boston

first: Vassiliki

middle: A.

last: Boussiotis

state: MA

address: 330 Brookline Ave

institute: Beth Israel Medical Center

data_processing:
Raw sequencing reads were quality-checked using FastQC (v0.11.5) and data were pre-processed with Cutadapt (v2.5) for adapter removal following best practices. Gene expression quantification was performed by aligning against the GRCm38 genome using STAR (v2.7.3a) and quantifying reads against Ensembl v984 annotated transcript loci with featureCounts (Subread 1.6.2). Differential gene expression analysis was performed using DESeq2 (v1.24.0), while ClusterProfiler (v3.12.0) was utilized for downstream functional investigations.
Assembly: mm10
Supplementary files format and content: Gene count matrix, raw counts, featureCounts output
Supplementary files format and content: Normalized abundance matrix, DESeq2 output

source_name: Tumor-associated Macrophages (TAM)

growth_protocol: Mice were implanted with tumors as described in the overall design section.

extract_protocol:
Total RNA was isolated from the cells using the Qiagen RNeasy Mini Kit (Qiagen, cat# 74104).
400ng of total RNA was then used in Illumina’s TruSeq Stranded mRNA Library kit (Cat# 20020594) for polyA mRNA isolation and library construction.
Libraries were sequenced on Illumina NextSeq 500 as paired-end 42-nt reads. Sequence reads were analyzed with the STAR alignment – DESeq2 software pipeline

treatment_protocol: MDSC were collected from spleens and TAMs were collected from the tumor site from tumor-bearing mice

value: CD11b+F4/80+ TAMs

tag: inplanted tumor cells


title: Control 12

source_name: PAXgene Blood miRNA

tag: tissue


title: TAM Pdcd1f/fLysMcre rep3


title: Control 11

tag: timepoint


title: OXI EV miR 2

value: Extracellular vesicles


title: ND-KO.4

value: feces

value: bacteria


title: TAM Pdcd1f/fLysMcre rep1


title: TAM Pdcd1f/f rep3


title: T. maritima, 80, stationary, biol rep 4

city: 't Horntje (Texel)

first: Diana

middle: X.

last: Sahonero-Canavesi

address: Landsdiep 4

country: Netherlands

institute: NIOZ

data_processing:
Adapter sequences and poor quality reads were removed with Trimmomatic v0.36 (parameter settings: Illuminaclip: TruSeq3-SE.fa:2:30:10, leading: 20, trailing: 20, sliding window: 5: 20 min length: 40);
Poly-G tails were removed using cutadapt v1.16 with the --nextseq-trim parameter set to 20
Gene counts were calculated using Salmon v1.1.0 with the mapping-based mode against the reference genome of T. maritima MSB8 (NCBI Reference Sequence: NC_021214.1)
Quantification estimates were imported into R/Bioconductor with tximport and differential gene expression between growth phases and temperatures was assessed with DESeq2 v1.26.0 using the default values
Assembly: NCBI Reference Sequence: NC_021214.1
Supplementary files format and content: tab-delimited text files include raw counts and TPM values for each sample

organism: Thermotoga maritima

source_name: bacterial cell

growth_protocol: Thermotoga maritima (strain MSB8, DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, DSM 3109) was cultivated in basal media under anaerobic conditions in 120-ml batch cultures in 250 ml serum bottles. Cultures were incubated either at optimal (80°C) or lower (55°C) growth temperatures. Growth was monitored by measuring the optical density (OD) at 600 nm and by fluorescent microscopy

extract_protocol:
Cell pellets were defrosted on ice and washed with 500 µL of DNase/RNase free water (New England Biolabs). Cells were resuspended in 700 µL of RLT buffer, and 50 mg of acid-washed glass beads (0.1 µm diameter) were added to a safe-lock tube containing the cell suspension. Cell disruption was performed with the OMNI bead mill Homogenizer (6.3 m/s) 2x. RNA was extracted with the RNeasy® Mini Kit (QIAGEN). The cells were harvested at early exponential, exponential, and stationary phases by centrifugation at 3500 rpm for 10 min at 4°C. The supernatant was discarded, and the remaining pellet was immediately frozen at -20°C for RNA extraction. 18 µl (2 µg) of total RNA was hybridized with the Pan-Prokaryote riboPOOL 3’-biotinylated probe (siTOOLs Biotech). The rRNA was subsequently depleted with Hydrophilic streptavidin magnetic beads (New England Biolabs). The depleted rRNA sample was purified before library preparation with RNA clean and concentration (Zymo research) and eluted in 15 µl of DNase-/RNase- Free Water. Samples were QC analyzed with the Agilent RNA 6000 Nano Chips and the Agilent 2100 Bioanalyzer system and stored at -80oC until library preparation
RNA libraries for RNA-seq were prepared using TruSeq RNA stranded kit following manufacturer's protocols and sequenced at the Utrecht Sequencing facility (USeq, The Netherlands)

value: bacterial cell

tag: growth phase

value: stationary

tag: growth temperature

value: 80° C


title: T. maritima, 80, stationary, biol rep 5


title: ND-KO.3


title: OXI EV miR 1


title: T. maritima, 80, stationary, biol rep 3


title: ND-KO.2


title: Control 1

value: whole blood

value: Control

tag: age

tag: Sex

value: female


title: Drosophila csRNAinput r1

city: La Jolla

first: Nathaniel

last: Delos Santos

address: 9500 Gilman Drive MC 0640

institute: University of California San Diego

description: CsRNA-seq input on Drosophila melanogaster embryonic cells, 0-12h

data_processing:
Binary base calls retrieved from NextSeq 500
Conversion to fastq performed with bcl2fastq 2.17
Reads preprocessed for adapter removal with (HOMER v4.11) homerTools trim -3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20
Preprocessed reads aligned using STAR 2.7.9a against the dm6 genome with annotation file dm6.ensGene.gtf
conversion to HOMER (v4.11) tag directories with makeTagDirectory dm6.fa -checkGC -fragLength 50 -single
Nascent TSS called with getTSSfromReads.pl -min 3
Nascent TSS peaks file converted to BED file using awk
Sxpanded to +/-200 bp around TSS using bedtools (v2.30.0) slop
Sorted using bedtools sort
Cluster deduplicated using bedtools cluster -s and awk
Scores converted with log(x+1)/log(2) using awk
Converted to scored FASTA file using python -m mepp.get_scored_fasta (v0.1.0)
Assembly: dm6
Supplementary files format and content: BED files

organism: Drosophila melanogaster

source_name: embryo

growth_protocol: Canton S wild-type Drosophila melanogaster flies were grown at 25˚C at 70-80% humidity in population cages.

extract_protocol:
Small RNAs of ~20-60 nt were size selected form 2-5 µg of total RNA by denaturing gel electrophoresis. A 10% input sample was taken aside and the remainder enriched for 5’Caped RNAs with 3’-OH. Monophosphorylated RNAs were selectively degraded by Terminator 5´-Phosphate-Dependent Exonuclease (Lucigen). Subsequent 5’dephosporylation by CIP (NEB) followed by decapping with RppH (NEB) augments Cap-specific 5’adapter ligation by T4 RNA ligase 1 (NEB). The 3’ adapter was ligated using truncated T4 RNA ligase 2 (NEB) without prior 3’ repair to select against degraded RNA fragments.
Following cDNA synthesis, libraries were amplified for 12-14 cycles and sequenced SE75 on the Illumina NextSeq500.

treatment_protocol: The embryos were collected on molasses-agar plates covered with yeast.

value: Canton S wild type

value: embryonic cells

tag: developmental stage

value: embryo 0-12h


title: Control 10


title: TAM Pdcd1f/f rep2


title: TAM Pdcd1f/f rep1


title: Drosophila csRNA-seq r3

description: CsRNA-seq on Drosophila melanogaster embryonic cells, 0-12h


title: ND-KO.1

tag: treatment

value: nornal diet


title: ND-WT.10

value: wild type


title: T. maritima, 80, stationary, biol rep 2


title: Drosophila csRNA-seq r2


title: T. maritima, 80, stationary, biol rep 1


title: plasma small extracellular, MI, 12h rep2

city: Birmingham

first: Chaoshan

last: Han

state: Alabama

address: VH G100H 1670 University Blvd

department: Biomedical Engineering

institute: University of Alabama at Birmingham

data_processing:
5' adaptor trimmed
GeneGlobe Data Analysis Center
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: miRbase
Supplementary files format and content: files include RPKM values for each Sample

source_name: plasma

growth_protocol: normal diet

extract_protocol:
small extracellular vesicle harvested from the blood by differential centrifuge, and then extract RNA by Trizol- chloroform-isoproponal method
QIAseq miRNA Library Kit

treatment_protocol: mice sham surgery and myocardial infarction surgery

value: plasma

value: MI surgery


title: Drosophila csRNA-seq r1


title: T. maritima, 80, exp, biol rep 5

value: exponential


title: ND-WT.9


title: T. maritima, 80, exp, biol rep 4


title: plasma small extracellular, MI, 12h rep1


title: ND-WT.8


title: plasma small extracellular, sham, 12h rep2

value: sham surgery


title: ND-WT.7

value: feces


title: T. maritima, 80, exp, biol rep 3


title: Sh5103

city: Beijing

first: Yabing Nan

last: Yabing Nan

address: 17 Panjiayuan Nanli, Chaoyang Diistrict

institute: Cancer Hospital Chinese Academy of Medical Sciences

data_processing:
Raw data were filtered using Trimmomatic (version 0.36) and deduplicated with FastUniq (version 1.1).
Clean reads were mapped to the reference genome by using bowtie2 software (version 2.2.6) with default parameters. RSeQC software (version 2.6) was used for read distribution analysis, and the insert length was counted using Collect Insert Size Metrics tools from Picard software (version 2.8.2).
Peak calling was conducted using MACS2 software (Version 2.1.1), and peak annotation and distribution analysis were performed using BEDTools (Version 2.25.0).
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: peak text files

source_name: ESCC cells

extract_protocol:
10 000–50 000 cells were treated with cell lysis buffer, and nuclei were collected by centrifugation for 5 min at 500 g.
Transposition was performed and high-throughput DNA sequencing library was obtained using TruePrep DNA Library Prep Kit V2 for Illumina kit (TD501; Vazyme Biotech). The library products were then enriched, quantified, and sequenced on a Novaseq 6000 sequencer (Illumina) by using the PE150 model.

tag: cell line

value: Human ESCC cell line

value: HCP5 silence


title: Sh5102


title: plasma small extracellular, sham, 12h rep1


title: ND-WT.5

value: bacteria


title: ND-WT.6


title: Sol8 KO D biol rep 3

data_processing:
The reads were quality-trimmed with cutadapt (v1.18), with a quality threshold of 28 at both ends, with --nextseq-trim option. After that, the remaining poly-G sequences were removed from the 3' end, then adapter sequences were removed from the 3' end, then poly-T stretches were removed from the 5' end. All the sequences were removed using a minimal overlap of 1 (-O parameter), allowing for read wildcards, and filtering out reads that became shorter than 15 nt (-m parameter). Finally low quality reads were filtered out using fastq_quality_filter, with a quality threshold of 20 at 90 percent or more of the read's positions.
The processed fastq files were aligned to the mouse transcriptome and genome using TopHat (v2.1.1), with the genome version GRCm38, and annotations from Ensembl release 95. The parameters were -N 6 --read-gap-length 5 --read-edit-dist 11 --segment-length 20 --no-coverage-search --library-type fr-firststrand, allowing up to 6 mismatches per read, a maximum gap of 5 bases, and a total edit distance of 11.
Quantification was done using htseq-count (v0.6.1) with annotations from Ensembl release 95. Strand information was set to 'reverse', and an annotation file that lacked information for genes of type IG, TR, Artifact, miRNA, Mt_rRNA, Mt_tRNA, ncRNA, piRNA, pre_miRNA, rRNA, ribozyme, sRNA, scRNA, scaRNA, siRNA, snRNA, snoRNA, tRNA and vaultRNA was used.
Normalization and differential expression analysis were done with the DESeq2 package (v1.22.1). Genes with a sum of counts less than 10 over all samples were filtered out. Significance threshold was taken as padj<0.05.
Significant genes were further filtered to include only genes with a large enough effect. This was achieved by requiring a baseMean of at least 5 and an absolute log2FoldChange bigger than 7.5/sqrt(baseMean) + 0.9
Assembly: GRCm38
Supplementary files format and content: Excel file of the processed results
Supplementary files format and content: 'Rawc.' columns are raw counts, 'Normc.' columns are the values after DESeq2 normalization. 'baseMean, Log2FoldChange, lfcSE, stat, pvalue, padj' are corresponding result of DESeq2 analysis. 'sig' indicates significance according to our threshold (padj<0.05). 'best' column gives the information on further filtering described above (False for non-significant genes, True for significant genes that did not pass further filtering, and 'THR' for significant genes that passed further filtering threshold)

source_name: muscle

extract_protocol: Library preparation was done using KAPA stranded mRNA kit (Cat# KK8421, Roche, Israel).

value: muscle

value: myotube

value: Gne KO

value: differentiated


title: Sh5101


title: T. maritima, 80, exp, biol rep 1

value: bacterial cell

value: 80° C


title: T. maritima, 80, exp, biol rep 2


title: C5103

value: control


title: Sol8 KO D biol rep 2


title: C5102


title: ND-WT.4

source_name: feces

value: nornal diet


title: T. maritima, 80, early exp, biol rep 5

value: early exponential


title: Sol8 KO D biol rep 1


title: ND-WT.3

value: wild type


title: Sol8 KO P biol rep 3

value: myoblast

value: proliferation


title: C5101


title: T. maritima, 80, early exp, biol rep 4


title: Sol8 KO P biol rep 2


title: Sh1503


title: ND-WT.1


title: Sh1502


title: Sol8 KO P biol rep 1


title: T. maritima, 80, early exp, biol rep 2


title: T. maritima, 80, early exp, biol rep 1


title: Sh1501


title: T. maritima, 55, stationary, biol rep 5

value: stationary

value: 55° C


title: BY UBR1 -469A>T 5

city: Minneapolis

first: Mahlon

last: Collins

state: MN

address: 6-160 Jackson Hall, 321 Church St SE

department: Genetics, Cell Biology, and Development

institute: University of Minnesota

data_processing:
We used fastp (command ‘fastp –cut_mean_quality 15 –length_required 36 --dedup –detect_adapter_for_pe’) to remove reads with a length less than 36 bp and any reads where the mean quality dropped below a mean quality score of 15 in a 4 bp window. We also used fastp to trim adapter sequences from the ends of all reads.
We used Kallisto (command: ‘kallisto quant’) to pseudoalign processed reads to the S. cerevisiae transcriptome, which was obtained from Ensembl (version 96)
We used RSeQC to compute transcript integrity numbers (TINs; script ‘tin.py’) and filtered out genes with a TIN < 1.
Differentially expressed genes were called using DeSeq2 using a false discovery rate of 0.1.
Assembly: S. cerevisiae transcriptome (Ensembl, version 96)
Supplementary files format and content: Processed .tsv files contain estimated counts for all genes computed by Kallisto

organism: Saccharomyces cerevisiae

growth_protocol: We isolated total RNA from 5 independent biological replicates each of BY4741 UBR1 wild-type and BY UBR1 -469A>T. All 10 samples were grown and harvested at the same time. Strains were grown overnight in 5 mL of SC medium. The following day, the cultures were diluted to an OD of 0.05 in 100 mL of fresh SC medium and grown for approximately 7 hours. When the optical density (OD) of each culture was approximately 0.40, the cells were pelleted by centrifugation at 3, 000 rpm for 10 minutes. Pellets were then washed by resuspending them in 1 mL of sterile ultrapure water, followed by centrifugation at 3, 000 rpm for 3 minutes to again pellet the cells. Following this step, cell pellets were resuspended in 1 mL of ultrapure water and split into 4 aliquots, each containing 250 µL. After re-centrifuging and discarding the supernatant, the pellets were snap frozen by immersion in liquid nitrogen, followed by storage at −80 °C. Pellets were subsequently used for RNA isolation.

extract_protocol:
Total RNA was extracted from frozen cell pellets using the ZR Fungal/Bacterial miniprep kit (Zymo), according to the manufacturer’s instructions. Briefly, total RNA was isolated from cell pellets in two batches, each containing equal numbers of BY UBR1 wild-type and BY UBR1 -469A>T samples. After thawing, pellets were resuspended in lysis buffer and transferred to screwcap lysis tubes containing glass beads. Tubes were secured in a Mini-BeadBeater (BioSpec Products, Bartlesville, OK, USA) and cells were processed in 5 cycles of 2 minutes of agitation followed by 2 minutes at −80 °C. The cell lysate/bead mixture was centrifuged for 1 minute at 16, 000 x g and 400 µL of 95% ethanol was added to the cleared supernatant followed by mixing. Samples were then spun through a binding column and on-column DNA digest was performed with DNase I (Zymo) according to the manufacturer’s instructions. Total RNA was eluted from columns using 50 µL of RNase-free ultrapure water. The concentration of each sample was quantified using RiboGreen; all samples had a concentration greater than 300 ng/µL. The integrity of each sample was assessed at UMGC using the Tapestation (Agilent) and an RNA ScreenTape. RNA integrity numbers ranged from 9.7 to 10.0 (where 10.0 is the maximum possible score), with a median value of 9.9. All RNA samples were stored at −80 °C.
We isolated mRNA from each total RNA sample using the 550 ng of total RNA input and the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB). All samples were processed in a single batch and the isolated mRNA from each sample was used to prepare RNA sequencing libraries using the NEBNext Ultra II Directional RNA Library Prep kit (NEB) according to the manufacturer’s instructions. Libraries were amplified using NEBNext Ultra II Q5 polymerase and unique combinations of primers from the NEBNext Multiplex Oligos for Illumina (NEB). The following amplification protocol was used: initial denaturation at 98 °C for 30 seconds, followed by 10 cycles of 98 °C (10 seconds; denaturation), 65 °C (75 seconds; annealing and extension), and a 65 °C final extension for 5 minutes. PCR reactions were pooled using equal amounts of DNA and submitted to UMGC for three quality control assays, which measured the library concentration by PicoGreen, library functionality by KAPA qPCR, and library size using the Tapestation electrophoresis system (Agilent). The resulting library contained a small amount of adapter dimer (approximately 9%), which was subsequently removed via a bead-based cleanup. The final, cleaned library passed all three QC assays and was sequenced on a Next-Seq 2000 instrument (Illumina) in paired-end mode with 150 bp reads. The sequencing run generated 1,367,252,076 reads with an average of 136,725,207 (range: 112,285,619 to 152,571,763) reads per sample.

value: yeast


title: Sol8 WT D biol rep 2

value: WT


title: BY UBR1 -469A>T 4


title: C1502

value: Human ESCC cell line


title: BY UBR1 -469A>T 3


title: T. maritima, 55, stationary, biol rep 4


title: Sol8 WT D biol rep 1

value: muscle


title: ND-WT.2

value: feces

value: bacteria


title: C1501


title: T. maritima, 55, stationary, biol rep 3


title: T. maritima, 55, stationary, biol rep 2


title: sh45103

data_processing:
Clean reads were obtained after the removal of reads containing adapter and ploy-N and having low quality.
HISAT2 was used to align the clean reads to the reference genome.
Differential expression was assessed using DESeq by using read counts as input.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: Text file for counts and RPKM values of each gene

extract_protocol:
TRIzol extraction
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ESCC

value: Human ESCC cell

value: HCP5 silence


title: Sol8 WT P biol rep 3


title: BY UBR1 -469A>T 1


title: T. maritima, 80, early exp, biol rep 3

value: bacterial cell

value: 80° C


title: T. maritima, 55, stationary, biol rep 1


title: BY UBR1 -469A>T 2


title: sh45102


title: Sol8 WT P biol rep 1


title: BY UBR1 wild-type 5

value: UBR1 wild-type


title: Sol8 WT D biol rep 3

value: myotube

value: differentiated


title: sh45101


title: T. maritima, 55, exp, biol rep 5

value: exponential


title: C1503

value: control


title: BY UBR1 wild-type 4


title: T. maritima, 55, exp, biol rep 4

value: 55° C


title: BY UBR1 wild-type 3

value: yeast


title: TAM_Shp2f/fLysMcre_2

description: TAM Shp2f/fLysMcre rep2

data_processing:
Raw sequencing reads were quality-checked using FastQC (v0.11.5) and data were pre-processed with Cutadapt (v2.5) for adapter removal following best practices. Gene expression quantification was performed by aligning against the GRCm38 genome using STAR (v2.7.3a) and quantifying reads against Ensembl v984 annotated transcript loci with featureCounts (Subread 1.6.2). Differential gene expression analysis was performed using DESeq2 (v1.24.0), while ClusterProfiler (v3.12.0) was utilized for downstream functional investigations.
Genome_build: mm10
Supplementary_files_format_and_content: Gene count matrix, raw counts, featureCounts output
Supplementary_files_format_and_content: Normalized abundance matrix, DESeq2 output

growth_protocol: Mice were implanted with tumors as descrived in the overall design section.

value: Tumor-associated Macrophages (TAM)


title: T. maritima, 55, exp, biol rep 3


title: T. maritima, 55, exp, biol rep 2


title: TAM_Shp2f/fLysMcre_3

description: TAM Shp2f/fLysMcre rep3


title: TAM_Shp2f/fLysMcre_1

description: TAM Shp2f/fLysMcre rep1


title: Sol8 WT P biol rep 2

value: myoblast

value: WT

value: proliferation


title: BY UBR1 wild-type 2


title: BY UBR1 wild-type 1


title: shc5102


title: TAM_Shp2f/f_2

description: TAM Shp2f/f rep2


title: T. maritima, 55, early exp, biol rep 5

value: early exponential


title: TAM_Shp2f/f_1

description: TAM Shp2f/f rep1


title: Schizont parasites nuclear fraction

city: Khlong Nung

first: Pavita

last: Kaewprommal

state: Pathum Thani

department: NBT

country: Thailand

institute: NSTDA

description: nuclear RNA

data_processing:
Library strategy: Iso-Seq
PacBio® Sequel™ subreads.bam raw data were processed using the SMRTLink v5.0.1 program suite (PacBio®) with the Iso-Seq method
Full-length non-chimeric (FLNC) circular consensus sequences (CCS) were extracted by SMRTlink v5.0.1 for iterative clustering and polishing. After polishing, low quality (quiver accuracy < 0.99) or high quality (quiver accuracy > 0.99) sequences in fastq format were outputted.
For each iso-seq library, the high-quality (hq) and low-quality (lq) full-length non-chimeric consensus sequences in .fastq format were aligned separately to the P. falciparum 3D7 v3 reference genome using the minimap2 tool (Li, 2018) in the spliced alignment mode guided by PlasmoDB-53 reference genome annotation with maximum intron 5 kb, settings: -ax splice:hq -uf -G 5k --secondary=no --junc-bed.
Candidate non-redundant isoform annotations were generated from the aligned reads using the Transcriptome Annotation by Modular Algorithms (TAMA) program package (https://github.com/GenomeRIK/tama.git). Aligned read .sam files were used as input for the TAMA collapse tool with “low” settings: -x capped -rm low_mem -sj sj_priority -log log_off -lde 5 -sjt 20 -a 100 -z100 -m 20. The isoform annotations from TAMA collapse in .bed12 format were converted to .gtf format with the tama_convert_bed_gtf_ensembl_no_cds.py program.
Genome_build: Plasmodium falciparum 3D7 GCA_000002765.3
Supplementary_files_format_and_content: Candidate non-redundant isoform annotations  in .gtf format

organism: Plasmodium falciparum 3D7

source_name: Intraerythrocytic parasites

growth_protocol: Plasmodium falciparum was cultured in vitro in human O+ erythrocytes and medium containing 8% pooled, heat inactivated human serum and buffered RPMI as described previously (Shaw et al., 2007).

extract_protocol:
For extraction of total RNA, the washed pellet of saponin-liberated parasites was suspended in Trizol™ reagent and RNA extracted according to the manufacturer’s instructions (Invitrogen). For subcellular fractionation, saponin-liberated parasites were disrupted by trituration in 0.3 mL of parasite lysis buffer (20 mM Hepes, pH 7.8, 10 mM KCl, 15 mM MgCl2 1 mM DTT, 1x Complete protease inhibitor cocktail no EDTA (Roche), 0.65% Nonidet P-40, Superasin™ RNase inhibitor (Thermo Fisher) 40 U/mL). Nuclei were pelleted by centrifugation at 2500 g for 5 min and supernatant was removed by aspiration. Supernatants from schizont and trophozoite parasite lysates were combined. Cytoplasmic RNA was extracted from the supernatant using 6 M urea as a denaturant described in (Hoppe-Seyler et al., 1991). Nuclei were washed thrice with 1 mL parasite lysis buffer prior to extraction of nuclear RNA with Trizol™ reagent as described for total RNA.
5' capped mRNA was enriched using recombinant eIF4E-eIF4G fusion protein. 100-300 ng samples of purified 5′ cap-enriched mRNA were converted to cDNA using a SMARTer™ PCR cDNA Synthesis Kit (Clontech) as recommended by the manufacturer. Double-stranded cDNA was PCR-amplified following the recommendations for PacBio® Iso-Seq Template Preparation for Sequel™ Systems. The amplified DNA was initially purified using 0.4x AMPure beads, and a portion of each was gel-purified to enrich for fragments >4 kb using a Gel extraction kit (Qiagen). The gel-purified fraction was combined with the remainder of non-size selected DNA. The pooled DNA was purified using 0.4x AMPure beads. Purified DNA samples were sent on dry ice to Novogene AIT (Singapore) for PacBio® Sequel™ sequencing service in which PacBio® Sequel™ sequencing libraries were constructed using the standard PacBio® protocol.

treatment_protocol: Cultured parasites were synchronized by 60% percoll gradient separation to enrich late stages followed by enrichment of ring stages by sorbitol treatment (Lambros & Vanderberg, 1979). Parasites were harvested immediately (ring stage), 12 h (trophozoite stage) and 24 h (schizont stage) after synchronization. Parasites were liberated from the host cell by treatment with 0.1% (w/v) saponin. Parasite pellets were washed thrice with phosphate buffered saline (1x PBS; 137 mM NaCl, 2.7 mM KCl, 8 mM Na2HPO4, and 2 mM KH2PO4)  prior to extraction.

value: Schizont


title: TAM_Shp2f/f_3

description: TAM Shp2f/f rep3


title: sh41502

value: ESCC

value: Human ESCC cell


title: T. maritima, 55, early exp, biol rep 4

value: bacterial cell


title: Combined Schizont and Trophozoite cytoplasmic fraction

description: cytoplasmic RNA

value: Schizont/Trophozoite


title: shc5101


title: Trophozoite parasites nuclear fraction

description: nuclear RNA

value: Trophozoite


title: sh41501

value: HCP5 silence


title: shc5103


title: Ring parasites nuclear fraction

description: nuclear RNA

value: Ring


title: sh41503


title: T. maritima, 55, early exp, biol rep 3


title: shc1503


title: MDSC_Shp2f/fLysMcre_2

description: MDSC Shp2f/fLysMcre rep2

source_name: Myeloid-derived Suppressor Cells (MDSC)

value: Myeloid-derived Suppressor Cells (MDSC)


title: T. maritima, 55, early exp, biol rep 2


title: MDSC_Shp2f/fLysMcre_1

description: MDSC Shp2f/fLysMcre rep1


title: Trophozoite parasites  total fraction


title: shc1501

value: control


title: T. maritima, 55, early exp, biol rep 1

value: 55° C


title: MDSC_Shp2f/f_2

description: MDSC Shp2f/f rep2


title: T. maritima, 55, exp, biol rep 1

value: exponential


title: Schizont parasites total fraction


title: shc1502


title: GR-Hpd scgRNA_Hpd miR, NTBC withdrawal, rep2

status: Public on Oct 25 2022

city: Portland

first: Amita

last: Tiyaboonchai

state: OR

address: 3181 SW Sam Jackson Park Rd.

department: Pediatrics

institute: Oregon Health & Science University

data_processing:
Conversion to FASTQ using bcl2fastq 2.17
For TPM: Paired-end fastq sequences trimmed suing trim-galore (ver0.6.3)
Pseudoalignment with kallisto (ver 0.44.0) and gencode (ver24) annotation.
Bioconda package bioconductor-tximport (ver 1.12.1) was used to create abundances (TPMs).
For custom alignments: Bowtie (v1) used to create custom indexes and alignment by using a 50 base wide windown.
Assembly: mm10
Supplementary files format and content: csv file includes matrix of TPM for each sample
Supplementary files format and content: text file includes matrix of unqiue counts using the custom index alignment for integrated sequences

source_name: Liver

extract_protocol:
RNAzol
Libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina

value: Liver

value: Received rAAV GR-Hpd_miR  as neonates

tag: selection

value: Selection by NTBC withdrawal


title: GR-Hpd scgRNA_Hpd miR, NTBC withdrawal, rep3


title: Ring parasites  total fraction


title: MDSC_Shp2f/f_1

description: MDSC Shp2f/f rep1


title: GR-Cypor scgRNA+ spCas9, APAP selection, rep3

value: Received rAAV GR-Cypor scgRNA as neonates

value: APAP selection


title: No treatment


title: GR-Cypor scgRNA+ spCas9, APAP selection, rep2


title: GR-Cypor scgRNA+ spCas9, APAP selection, rep1


title: GR-Hpd scgRNA_Hpd miR, NTBC withdrawal, rep1


title: GR-Cypor scgRNA+ spCas9, no selection, rep2

value: No APAP selection


title: GR-Cypor scgRNA+ spCas9, no selection, rep3


title: GR-Cypor scgRNA+ spCas9, no selection, rep1


title: HOMO-AngII

city: Singapore

first: Gabriel

last: Chew

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

description: HOMO-AngII (S37)

data_processing:
For scRNA-seq analysis (at 7 days after Ang II infusion), pre-processing involved removing genes which are not detected in at least 10 cells. Cell filtering criteria include filtering of cells with number of features and/or number of counts outside the 10th and 90th percentiles. For each library, we employed Seurat (v4.0.1) for normalization using “LogNormalize” method and a scale factor of 10000. FindVariablesFeatures() was used to obtain the top 5000 feature genes. Mitochondrial genes were removed. ScaleData() was used for scaling, while dimension reduction was accomplished using RunPCA() and RunUMAP() with number of dimensions set at 50. Scds (1.6.0) was used to calculate doublet hybrid score. After which, cells with greater than hybrid score of 0.5 were removed as doublets. Cell cycle scoring was done using CellCycleScoring() with markers from Tirosh et al, 2015. Finally, the 4 libraries (WT, WT Ang-II, WWP2Mut/Mut, and WWP2Mut/Mut Ang-II) are subsequently merged that yielded an expression matrix of 16,273 genes and 13,014 cells
Genome_build: GRCm38 (mm10-3.0.0 provided by 10x Genomics)
Supplementary_files_format_and_content: Rdata

source_name: CD45+ sorted cardiac cells

growth_protocol: . Mice were bred and maintained in animal facility at Duke-NUS medical school prior to use. All mice were housed in a specific pathogen–free (SPF) environment and complied with all relevant ethical regulations according to guidelines issued by the National Advisory Committee on Laboratory Animal Research. Protocol with IACUC number 2016/SHS/1170 was approved by Institutional Animal Care and Use Committee of National University of Singapore, Duke-NUS Medical School.

extract_protocol:
Isolated single cell suspensions were converted to barcoded scRNA-seq libraries by using the Chromium Single Cell 3′Library, Gel Bead & Multiplex Kit, and Chip Kit V3, loading an estimated 7,000–12,000 cells per library/well and following the manufacturer's instructions. Indexed libraries were sequenced using Illumina HiSeq 4000, where 150bp pair-end sequences were obtained.
Sequencing reads were aligned and quantified to the mouse genome GRCm38 (mm10-3.0.0 provided by 10x Genomics) using Cellranger count (v3.1.0).

value: cardiac

value: Miniosmotic pumps loaded with Ang-II and sacrificed at 7 days post infusion

tag: strain


title: HOMO

description: HOMO (S38)

value: Miniosmotic pumps loaded with saline and sacrificed at 7 days post infusion


title: WT

description: WT (S36)

value: WT


title: r63: Rds, LV-IG treated as control, biol rep 2

city: CULVER CITY US

first: XIAN-JIE

last: YANG

address: 4037 Coogan Circle, Culver City, Culver City, Culver City

department: Ophthalmology

institute: Stein Eye Institute, UCLA School of Medicine

description: Influence of CNTF on mouse retinal transcriptome

data_processing:
Quality of individual sequences were evaluated using the FastQC software (www.bioinformatics.babraham.ac.uk/projects/fastqc/) after adapter trimming with the cutadapt software (cutadapt.readthedocs.io/en/stable/).
The reads were filtered to exclude those with more than 5% unknown bases, reads which contained more than 20% bases with quality score below 15, and reads with only adapters.  After filtering, the median size was 5.65 Gb per library (range 3.66–7.26 Gb).
Sequenced reads were then aligned to the Mouse reference mm10 from UCSC (genome-euro.ucsc.edu) using Hisat2 (v2.0.4).
The expression levels were normalized by calculating the fragments per kilobase million reads (FPKM) values.
For processed data, the differential expression of transcripts was calculated using DESeq2, with statistical significance p<0.01.
Assembly: mm10
Supplementary files format and content: The table contains the gene expression profiles (fpkm>1 in >=1 sample) of 9 samples, with statistic analysis from DESeq2

source_name: retina

extract_protocol:
The RNeasy RNA extraction kit was used to isolate total RNA from dissected neural retinas without the retinal pigment epithelium and other ocular tissues.  On-column DNaseI digestion was performed and RNA was collected in RNase-free water, following manufacturer’s instructions (Qiagen, Hilden, Germany).  The RNA quality was determined on an Agilent 2100 Bioanalyzer.   All samples passed the quality filters.
Sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold Library Prep kit.  Libraries were loaded onto the HiSeq 4000 Sequencer for paired-end sequencing with read length of 69 bp.

value: retina

value: Rds

value: Subretinal injection of LV-IG


title: DKOIP

city: New York

first: Dan

last: Littman

state: NY

address: 430 East 29th St Room 403

institute: New York University School of Medicine

data_processing:
ChIP-seq(2): ChIP-seq fastq files were aligned to the mm10 reference genome using star v 2.7.3a.  Bam files were converted to bigwig files via deeptools v 3.3.0 bamCoverage and normalized by RPGC using --ignoreDuplicates and --centerReads.  Deeptools computeMatrix and plotHeatmap were used to make heat maps.  Macs2 was used to call peaks using a significance cutoff of 0.05. Every treatment file had a corresponding control file during peak calling.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig for ATAC and ChIP, normalized count file for bulk RNAseq

source_name: lymphoid organ

growth_protocol: Naïve T cells were purified from lymph nodes and spleens of six to eight week old WT or RORaKO mice, by sorting live (DAPI-), CD4+CD25-CD62L+CD44low naïve T cells using a FACSAria (BD). Cells were cultured in IMDM (Sigma) supplemented with 10% heat-inactivated FBS (Hyclone), 10U/ml penicillin-streptomycin (Invitrogen), 10g/ml gentamicin (Gibco), 4mM L-glutamine, and 50μM β-mercaptoethanol.

extract_protocol:
Lysates were clarified from sonicated PFA-fixed nuclei, and Twin-strep-tagged RORa-DNA complexes were isolated with Strep-Tactin.
ChIP-Seq libraries were prepared with the KAPA HyperPlus Kit (Roche) following the manufacturer's protocols.

treatment_protocol: For T cell polarization, 1 x 10^5 cells were seeded in 200μl/well in 96-well plates that were pre-coated with a 1:20 dilution of goat anti-hamster IgG in PBS (STOCK = 1mg/ml, MP Biomedicals Catalog # 55398).  Naïve T cells were primed with anti-CD3ε (0.25μg/mL) and anti-CD28 (1μg/mL) for 24 hours prior to polarization. Cells were further cultured for 48h under Th17 polarizing conditions; Th17 (0.3 ng/mL TGF-β, 20 ng/mL IL-6, 20 ng/mL IL-23, 2.5μg/mL anti-IL-4, 2.5μg/mL anti-IFNg).

value: lymphoid organ

tag: isolate

tag: disease

tag: disease stage

tag: chip antibody

value: polyclonal rabbit anti-RORgt antibodies (homemade)


title: c71: Rds, LV-CNTF treated, biol rep 3

tag: genotype

value: Subretinal injection of LV-CNTF


title: r48: Rds, LV-IG treated as control, biol rep 1


title: w74: wild type, biol rep 3

value: Wild type


title: w64: wild type, biol rep 1


title: c49: Rds, LV-CNTF treated, biol rep1


title: WT-AngII

description: WT-AngII (S48)


title: DKOinput


title: r69: Rds, LV-IG treated as control, biol rep 3


title: WTIP


title: WTinput


title: AKOinput


title: w70: wild type, biol rep 2


title: c55: Rds, LV-CNTF treated, biol rep 2


title: DG-input 1

data_processing:
ChIP-seq: ChIP-seq fastq files were aligned to the mm10 reference genome using star v 2.7.3a.  Bam files were converted to bigwig files via deeptools v 3.3.0 bamCoverage and normalized by RPGC using --ignoreDuplicates and --centerReads.  Deeptools computeMatrix and plotHeatmap were used to make heat maps.  Macs2 was used to call peaks using a significance cutoff of 0.5. Every treatment file had a corresponding control file during peak calling.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig for ATAC and ChIP, normalized count file for bulk RNAseq

extract_protocol:
Lysates were clarified from sonicated PFA-fixed nuclei, and Twin-strep-tagged RORa-DNA complexes were isolated with Strep-Tactin.
ChIP-Seq libraries were prepared with the SMARTer® ThruPLEX® DNA-Seq Kit (Takara, R400674) following the manufacturer's protocols.

treatment_protocol: For T cell polarization, 1 x 10^5 cells were seeded in 200μl/well in 96-well plates that were pre-coated with a 1:20 dilution of goat anti-hamster IgG in PBS (STOCK = 1mg/ml, MP Biomedicals Catalog # 55398).  Naïve T cells were primed with anti-CD3ε (0.25μg/mL) and anti-CD28 (1μg/mL) for 24 hours prior to polarization. Cells were further cultured for 48h under Th-lineage polarizing conditions; Th0 (Con. : 100U/mL IL-2, 2.5μg/mL anti-IL-4, 2.5μg/mL anti-IFNg), Th17 (0.3 ng/mL TGF-β, 20 ng/mL IL-6, 20 ng/mL IL-23, 2.5μg/mL anti-IL-4, 2.5μg/mL anti-IFNg).

value: RORa-TwinStrep(TS)

value: Strep-Tactin®XT (IBA Lifesciences)


title: DG-IP-1


title: AKOIP


title: DG-IP-2


title: AKO-DLN-4

data_processing:
RNAseq: Bulk RNAseq fastq files were aligned to the mm10 reference genome using star v 2.7.3a. Bam files were converted to bigwig files via deeptools v 3.3.0 bamCoverage for visualization.  DEseq2 was used for differential gene analysis.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig for ATAC and ChIP, normalized count file for bulk RNAseq

source_name: Spinal cord

extract_protocol:
RNAs were purified from the ex vivo isolated IL17eGFP+ wild type (WT) or Rora knock-out Th17 cells from the draining lymph nodes or spinal cords of immunized 1:1 (WT:KO) mixed bone marrow  chimeras at peak of Experimental autoimmune encephalomyelitis (EAE)
RNA-Seq libraries were prepared with the SMART-Seq® v4 PLUS Kit (Takara, R400752) following the manufacturer's protocols.

value: Spinal cord

value: EAE

value: Peak

value: BM chimera


title: AKO-DLN-14


title: AKO-DLN-6


title: aTS-Input_1st

value: RORA-TS


title: WT-DLN-13


title: WT-Th17-DLN-1


title: WT-Th17-DLN-3


title: scRNA-seq_mBCC

first: Anthony

last: Oro

address: 269 Campus Drvie

department: Dermatology

description: single cell RNA-seq

data_processing:
scRNA data was processed using the 10x Genomics CellRanger pipeline
Seurat was used to call cluster and generate UMAPs
Monocle was used to perform pseudotime analysis
Genome_build: mm10
Supplementary_files_format_and_content: count matrix

source_name: mouse BCC

growth_protocol: Ptch1+/-;p53f/f;K14CreER mice were induced to form tumors (Whitson et al., 2018; PMID: 29400712)

extract_protocol:
Tumors were dissociated by first mincing into pieces smaller than 1 mm in diameter and then incubated in 40 mL of a 0.5% collagenase solution (Gibco; 25200056) for 1hrs with rotation at 37°C . 5 mL of 0.25% Trypsin was then added and incubated for an additional 15min with rotation at 37°C . Cells were then FACS sorted for live cells, and then processed using the 10X Genomics Next GEM scRNA-Seq solution.
Library construction followed the 10X Genomics Next GEM scRNA-Seq pipeline.

treatment_protocol: No additional treatment for Sample 1/mBCC sample. For Sample 2/mBCC_DMSO and Sample 3/mBCC_VISMO, primary Ptch1+/-;p53f/f;K14CreER tumor cells were transplanted into NodScid host, which then formed tumors. Once tumors were formed, mice were either treated with Vismodegib (100 mg/kg) or DMSO control for 2 weeks and then harvested.

value: Mouse tumor from Ptch1+/-;p53f/f;K14CreER model


title: AKO-CNS-12


title: WT-CNS-7


title: WT-CNS-15


title: WT-CNS-9


title: AKO-CNS-10


title: aTS-IP_1st


title: DG-input 2


title: NoMtzDDex_Replicate 1

city: Baltimore

first: Kevin

last: Emmerich

state: MD

address: 400 N Broadway

department: Human Genetics

institute: Johns Hopkins University

data_processing:
Rstudio
Raw sequencing data (in the form of fasta.gz files) was downloaded and unzipped and then terminal function cutadapt was used to remove Nextera sequencing adapters
Samples were then read into fastqc for quality control to ensure proper and similarly sized libraries, complete removal of adapters and high sequence quality scores throughout. Sequencing for each sample occurred over two lanes and thus read files were combined using the “cat” terminal function
Read files were then mapped to the most recent Ensembl reference genome for Danio rerio GRCz11/danRer11 using kallisto
To identify differential expressed genes (DEGs) between conditions, a matrix file containing all Ensembl transcript ID’s and 12 columns, one for each sample, were read into the edgeR Bioconductor package (version 3.34.1) in R/R Studio (versions 4.0.3 and 1.4.1103, respectively)
Assembly: GRCz11/danRer11
Supplementary files format and content: one matrix text file with gene names in ENSDART IDs and then a column for each sample

source_name: eye

extract_protocol:
RNA was extracted using the RNeasy Micro Kit (Qiagen, 74004)
Libraries were produced using the ClonTech SMARTer Ultra Low Input RNA-v4  (Takara 634440) kit

value: eye

value: Tg(rho:YFP Eco. NfsB)gmc500

value: No Mtz to ablate rods but then injection with D-Dex and 24h till recovery


title: Mtz_Replicate1

value: 24h Mtz to ablate rods, 24h recovery before collection


title: NoMtz_Replicate 1

value: Untreated controls


title: NoMtzDDex_Replicate 2


title: Mtz_Replicate2


title: MtzDDex_Replicate 3

value: 24h Mtz to ablate rods, then injection with dendrimer conugated Dexamethasone and 24h recovery before collection


title: NoMtzDDex_Replicate 3


title: NoMtz_Replicate 3


title: NoMtz_Replicate 2


title: miRNA-seq_s1275C

city: Columbus

first: Ayse

middle: Selen

last: Yilmaz

state: OH

address: 1800 Cannon Drive

department: Biomedical Informatics

institute: OSU

data_processing:
Adaptor seqeunces were removed using Cutadapt
Trimmed reads aligned to MIRBASE stemloop seqeunces
Read counts per miRNA was genereated using custom scripts
Assembly: MIRBASE v21
Supplementary files format and content: Total read counts per miRNA

source_name: CLL,1275 A, Control

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq small RNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: CLL cells were resuspended in RPMI with 10% FBS and 400mM abexinostat was added for 24 h beofre being harvested along with the time matched control.

value: Blood, PBMC

tag: cell type

value: Human peripheral blood mononuclear cells

tag: disease state

value: CLL

value: control


title: miRNA-seq_s1275A

source_name: CLL,1275 Abexinostat 400mM 24h

growth_protocol: CLL cells were resuspended in RPMI with 10% FBS

tag: tissue

value: HDAC inhibitor, Abexinostat 400mM, 24h


title: miRNA-seq_s1119C

source_name: CLL,1119, Control


title: miRNA-seq_s1124C

source_name: CLL,1124, Control


title: miRNA-seq_s1228A

source_name: CLL,1228 Abexinostat 400mM 24h


title: miRNA-seq_s1766C

source_name: CLL,1766 , Control


title: miRNA-seq_s1124A

source_name: CLL,1124 Abexinostat 400mM 24h


title: miRNA-seq_s1228C

source_name: CLL,1228 , Control


title: miRNA-seq_s1766A

source_name: CLL,1766 Abexinostat 400mM 24h


title: miRNA-seq_s0813A

source_name: CLL,0813 Abexinostat 400mM 24h


title: MtzDDex_Replicate1


title: miRNA-seq_s0813C

source_name: CLL,0813, Control


title: miRNA-seq_s0798C

source_name: CLL,0798, Control


title: miRNA-seq_s0798A

source_name: CLL,0798 Abexinostat 400mM 24h


title: miRNA-seq_s0572C

source_name: CLL,0572, Control


title: miRNA-seq_s0621A

source_name: CLL,0621 Abexinostat 400mM 24h


title: miRNA-seq_s0621C

source_name: CLL,0621, Control


title: miRNA-seq_s0572A

source_name: CLL,0572 ,Abexinostat 400mM 24h


title: miRNA-seq_s0109C

source_name: CLL,0109, Control


title: miRNA-seq_s0109A

source_name: CLL,0109 Abexinostat 400mM 24h


title: RNA-seq_s1124C

data_processing:
Libraries were sequenced on a HiSeq4000 at the Genomic Shared Resource at the Ohio State University through Nationwide Children's Hospital Biomedical Genomics Core generating 100 bp reads.
Reads were aligned with HISAT2 aligner and then transcript counts were generated with the featureCounts function from the Rsubread package.
Assembly: GRCh37, Ensembl annotation build 75
Supplementary files format and content: Reads counts per million (cpm) were calculated using R limma voom package.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: del 13 q


title: RNA-seq_s1119C

source_name: CLL,1119, Control


title: RNA-seq_s1124A

source_name: CLL,1124, Abexinostat 400mM 24h


title: RNA-seq_s0813A

source_name: CLL,0813, Abexinostat 400mM 24h


title: RNA-seq_s0813C


title: RNA-seq_s0621C


title: RNA-seq_s1119A

source_name: CLL,1119, Abexinostat 400mM 24h


title: miRNA-seq_s1119A

source_name: CLL,1119 Abexinostat 400mM 24h


title: MtzDDex_Replicate 2

source_name: eye


title: RNA-seq_s1766A

source_name: CLL,1766, Abexinostat 400mM 24h

value: del 11q


title: RNA-seq_s1228C

source_name: CLL,1228, Control


title: RNA-seq_s1766C

source_name: CLL,1766, Control


title: RNA-seq_s0798A

source_name: CLL,0798, Abexinostat 400mM 24h


title: RNA-seq_s1228A

source_name: CLL,1228, Abexinostat 400mM 24h


title: RNA-seq_s0798C

source_name: CLL,0798, Control


title: RNA-seq_s0109C


title: RNA-seq_s0572C

source_name: CLL,0572, Control


title: RNA-seq_s0572A

source_name: CLL,0572, Abexinostat 400mM 24h

value: HDAC inhibitor, Abexinostat 400uM, 24h


title: Co-culture DFSCs 2

first: Xiaoyu

middle: yu

last: Lin

state: Beijing

address: You an men

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Primary culture

growth_protocol: DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

treatment_protocol: Co-culture

value: Primary culture

value: stem cell

value: WT

value: Co-culture


title: Co-culture DFSCs 3


title: Co-culture DFSCs 1


title: Control DFSCs 1

value: No


title: Control DFSCs 2


title: Control DFSCs 3


title: DF 3

source_name: Dental

value: Dental

value: Dental follicle tissue


title: RNA-seq_s1275A

source_name: CLL,1275, Abexinostat 400mM 24h


title: RNA-seq_s0621A

source_name: CLL,0621, Abexinostat 400mM 24h


title: DF 2


title: DF 1


title: RNA-seq_s0109A

source_name: CLL,0109, Abexinostat 400mM 24h


title: RNA-seq_s1275C

source_name: CLL,1275, Control


title: SR4-6

city: Montreal

first: Naglaa

last: Shoukry

state: QC

address: Tour Viger, Local 09.414, 900 rue St-Denis

country: Canada

institute: CRCHUM

data_processing:
FASTQs were generated from the raw sequencing BCL files using bcl2fastq2 v2.20.0.422.
The BAM files were generated by aligning the R1 FASTQ (without any further processing) using STAR (v2.5.1b) on a hg19 index with an overhang of 99bp.
The STAR default parameters were used. Unmapped reads were kept in the BAM. The BAMs were directly written sorted by coordinates.
Assembly: hg19 Human Genome (GenBank:GCA_000001405.1 RefSeq:GCF_000001405.13)
Supplementary files format and content: space-delimited text files include counts for each sample

source_name: PBMC

extract_protocol:
Total RNA was extracted from thawed cryopreserved PBMC samples using the RNEasy Mini kit (Qiagen) according to manufacturer’s instructions.
The RNA quality was assessed using the  Agilent Bioanalyzer 2100 system (Agilent Technologies). All RNA samples displayed an RNA  integrity numbers (RIN) score superior to 8. RNA samples were sent to the Genome Quebec  Innovation Center for RNA-seq libraries preparation using the NEB mRNA stranded library  preparation.

value: PBMC

value: Late Acute II


title: SR4-4

value: Pre-reinfection


title: SR4-5

value: Early Acute II


title: SR4-7


title: SR2-4


title: SR2-3


title: SR2-2


title: SR1-6


title: SR7.2


title: SR7.3


title: SR1-4


title: SR1-5


title: SR7.1


title: SR6.4

value: Follow-up


title: SR6.3


title: SR6.1


title: SR5.4


title: SR5.3


title: SR5.1


title: SR5.2


title: SR2-5


title: SR3.4


title: SR3.2


title: SR3.3


title: SR1-7


title: THP-1-ONC-500 nM

city: changchun

first: yongwei

last: su

address: 2699 qianjin street

institute: Jilin university

description: THP-1-ONC-500 nM

data_processing:
Basecalls performed using CASAVA version 1.8
RNA-seq reads were mapped to human genome by hisat2 software.
Cuffdiff2 software was used to perform differentially expressed gene analysis.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM, count

source_name: AML cell line

extract_protocol: Total RNA was extracted using TRIzol. RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina) according to the manufacturers instructions.

tag: agent

value: ONC-500 nM


title: MV4-11-ONC-500 nM

description: MV4-11-ONC-500 nM


title: U937-ONC-500 nM

description: U937-ONC-500 nM


title: CTS-ONC-500 nM

description: CTS-ONC-500 nM

value: CTS


title: SR6.2


title: input

city: Shanghai

first: Haoyan

last: Chen

state: Shanghai

address: 145 Shandong Road

institute: Renji Hospital

data_processing:
Sequence reads were mapped to the human genome (hg19) using Bowtie with the default options .
bed file was generated by MACS2 with the default options
Genome_build: hg19
Supplementary_files_format_and_content: peak summits in bed format

source_name: HCT116 cells

growth_protocol: The human HCT116 colorectal cancer cell were cultured in RPMI-1640 medium (Gibco, USA) supplemented with 10 % fetal bovine serum at 37 °C in an atmosphere of 5 % CO2.

extract_protocol:
Genomic DNA fragments of HCT116 cells with different treatment was harvested using Phenolic chloroform reagent
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The HCT116 colorectal cells were transfected with ENO1-IT1 siRNA or control siRNA for 48 hours. Then cells were collected and chromatin  was sonicated and immunoprecipitated with different primary antibodies.

value: human colorectal cancer cells

tag: passage

value: none (input)


title: ENO1-IT1 siRNA-H3K27ace

value: anti-Acetyl-Histone H3 (Lys27) (D5E4) XP antibody (CST, Lot NO. 8173)


title: control siRNA-KAT7

value: anti-KAT7 antibody (abcam Lot NO. ab70183)


title: ENO1-IT1 siRNA-KAT7


title: MOLM-13-ONC-500 nM

description: MOLM-13-ONC-500 nM


title: U937-Ctrl

value: control


title: CTS-Ctrl

description: CTS-Ctrl


title: THP-1-Ctrl


title: MV4-11-Ctrl


title: SR3.1


title: control siRNA-H3K27ace


title: 1140, SCZ, H3K9me2_ChIP-seq

city: Chicago

first: Rajiv

middle: P.

last: Sharma

state: Illinois (IL)

address: 1601 West Taylor St room 285

institute: Univ Illinois Chicago

data_processing:
Ends trimmed with Trimmomatic v2.0
ChIP-seq reads were aligned to the hg19 genome assembly using BowTie2
Differential occupation sites determined using diffReps
Assembly: hg19
Supplementary files format and content: Ends trimmed with Trimmomatic v2.0, ChIP-seq reads were aligned to the hg19 genome assembly using BowTie2
Supplementary files format and content: Differential occupation sites determined using diffReps

source_name: Brodmann Area 9/10 - prefrontal cortex

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were constructed off-site at University of Illinois - Urbana Champaign sequencing facility

value: Brodmann Area 9/10 - prefrontal cortex

value: brain cell

value: H3K9me2 antibody (Abcam, ab1220)

value: SCZ


title: 1100, SCZ, H3K9me2_ChIP-seq


title: 1097, SCZ, H3K9me2_ChIP-seq


title: 1102, SCZ, H3K9me2_ChIP-seq


title: 1096, SCZ, H3K9me2_ChIP-seq


title: 1126, SCZ, H3K9me2_ChIP-seq


title: 1106, SCZ, H3K9me2_ChIP-seq


title: 1095, SCZ, H3K9me2_ChIP-seq


title: 1120, SCZ, H3K9me2_ChIP-seq


title: MOLM-13-Ctrl


title: 1082, SCZ, H3K9me2_ChIP-seq


title: 1081, SCZ, H3K9me2_ChIP-seq


title: 1139, NPC, H3K9me2_ChIP-seq

value: NPC


title: 1115, SCZ, H3K9me2_ChIP-seq


title: 1137, NPC, H3K9me2_ChIP-seq


title: 1141, NPC, H3K9me2_ChIP-seq


title: 1104, SCZ, H3K9me2_ChIP-seq


title: 1135, NPC, H3K9me2_ChIP-seq


title: 1110, NPC, H3K9me2_ChIP-seq


title: 1132, NPC, H3K9me2_ChIP-seq


title: 1099, NPC, H3K9me2_ChIP-seq


title: 1113, SCZ, H3K9me2_ChIP-seq


title: 1124, NPC, H3K9me2_ChIP-seq


title: 1086, NPC, H3K9me2_ChIP-seq


title: 1088, NPC, H3K9me2_ChIP-seq


title: 1080, NPC, H3K9me2_ChIP-seq


title: 1074, NPC, H3K9me2_ChIP-seq


title: 1070, NPC, H3K9me2_ChIP-seq


title: 4797-006-54

city: Boston

first: Adam

middle: C

last: Gower

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

description: Gene expression data from nasal brushing 4797-006-54.

data_processing:
Demultiplexing and creation of FASTQ files were performed using BaseSpace.
Samples were aligned using hg19 and 2-pass STAR alignment (v2.5.2b). Gene-level posterior mean counts were calculated using RSEM (v1.3.0) and Ensembl Gene annotation build 75.
Posterior mean counts were filtered to exclude those that did not have more than one count per million (cpm) in at least 10% of the samples, and then corrected for sequencing batch using ComBat-seq.
Assembly: hg19
Supplementary files format and content: DECAMP_nasal_COVID19_posterior_mean_counts.tsv: a tab-separated value (TSV) file containing the posterior mean counts as computed by RSEM
Supplementary files format and content: DECAMP_nasal_COVID19_normalized_counts.tsv: a tab-separated value (TSV) file containing the ComBat-corrected counts for a subset of features that passed expression filtering.

source_name: Brushing of nasal epithelium

extract_protocol:
Total RNA was isolated from nasal and bronchial brushings using the miRNeasy Mini Kit [QIAGEN].
Libraries were generated using the Illumina TruSeq Stranded Total RNA kit.

value: Brushing of nasal epithelium

tag: subject

value: Female

tag: age

tag: smoking status

value: Current smoker

tag: fev1 %_predicted


title: 4797-012-55

description: Gene expression data from nasal brushing 4797-012-55.

tag: Sex

value: Male

value: Former smoker


title: 4797-007-55

description: Gene expression data from nasal brushing 4797-007-55.


title: 1087, NPC, H3K9me2_ChIP-seq


title: 4797-011-55

description: Gene expression data from nasal brushing 4797-011-55.


title: 1098, SCZ, H3K9me2_ChIP-seq


title: 1093, NPC, H3K9me2_ChIP-seq


title: 4797-004-55

description: Gene expression data from nasal brushing 4797-004-55.


title: 4796-060-54

description: Gene expression data from nasal brushing 4796-060-54.


title: 4796-065-54

description: Gene expression data from nasal brushing 4796-065-54.


title: 4796-047-54

description: Gene expression data from nasal brushing 4796-047-54.


title: 4797-001-55

description: Gene expression data from nasal brushing 4797-001-55.


title: 4796-066-54

description: Gene expression data from nasal brushing 4796-066-54.


title: 4796-050-55

description: Gene expression data from nasal brushing 4796-050-55.


title: 4796-063-54

description: Gene expression data from nasal brushing 4796-063-54.


title: 4796-046-54

description: Gene expression data from nasal brushing 4796-046-54.


title: 4797-005-55

description: Gene expression data from nasal brushing 4797-005-55.


title: 4796-039-55

description: Gene expression data from nasal brushing 4796-039-55.


title: 4796-043-54

description: Gene expression data from nasal brushing 4796-043-54.


title: 4796-035-54

description: Gene expression data from nasal brushing 4796-035-54.


title: 4796-045-54

description: Gene expression data from nasal brushing 4796-045-54.


title: 4796-064-54

description: Gene expression data from nasal brushing 4796-064-54.


title: 4797-008-54

description: Gene expression data from nasal brushing 4797-008-54.


title: 4796-034-54

description: Gene expression data from nasal brushing 4796-034-54.


title: 4796-037-55

description: Gene expression data from nasal brushing 4796-037-55.


title: 4796-033-54

description: Gene expression data from nasal brushing 4796-033-54.


title: 4797-003-55

description: Gene expression data from nasal brushing 4797-003-55.


title: 4796-072-54

description: Gene expression data from nasal brushing 4796-072-54.


title: 4796-032-55

description: Gene expression data from nasal brushing 4796-032-55.


title: 4796-044-54

description: Gene expression data from nasal brushing 4796-044-54.


title: 4796-030-55

description: Gene expression data from nasal brushing 4796-030-55.


title: 4796-023-54

description: Gene expression data from nasal brushing 4796-023-54.


title: 4796-029-55

description: Gene expression data from nasal brushing 4796-029-55.


title: 4796-031-54

description: Gene expression data from nasal brushing 4796-031-54.


title: 4796-017-55

description: Gene expression data from nasal brushing 4796-017-55.


title: 4796-022-54

description: Gene expression data from nasal brushing 4796-022-54.


title: 4796-020-55

description: Gene expression data from nasal brushing 4796-020-55.


title: 4796-005-54

description: Gene expression data from nasal brushing 4796-005-54.


title: 4796-009-55

description: Gene expression data from nasal brushing 4796-009-55.


title: 4796-003-54

description: Gene expression data from nasal brushing 4796-003-54.


title: 4795-094-55

description: Gene expression data from nasal brushing 4795-094-55.


title: 4795-098-54

description: Gene expression data from nasal brushing 4795-098-54.


title: 4795-074-54

description: Gene expression data from nasal brushing 4795-074-54.


title: 4795-069-55

description: Gene expression data from nasal brushing 4795-069-55.


title: 4795-086-54

description: Gene expression data from nasal brushing 4795-086-54.


title: 4796-015-55

description: Gene expression data from nasal brushing 4796-015-55.


title: 4795-058-54

description: Gene expression data from nasal brushing 4795-058-54.


title: 4795-091-55

description: Gene expression data from nasal brushing 4795-091-55.


title: 4795-096-55

description: Gene expression data from nasal brushing 4795-096-55.


title: 4795-095-54

description: Gene expression data from nasal brushing 4795-095-54.


title: 4795-075-55

description: Gene expression data from nasal brushing 4795-075-55.


title: 4796-004-54

description: Gene expression data from nasal brushing 4796-004-54.


title: 4795-099-54

description: Gene expression data from nasal brushing 4795-099-54.


title: 4795-068-54

description: Gene expression data from nasal brushing 4795-068-54.


title: 4795-054-55

description: Gene expression data from nasal brushing 4795-054-55.


title: 4795-087-55

description: Gene expression data from nasal brushing 4795-087-55.


title: 4795-065-54

description: Gene expression data from nasal brushing 4795-065-54.


title: 4795-062-54

description: Gene expression data from nasal brushing 4795-062-54.


title: 4795-067-55

description: Gene expression data from nasal brushing 4795-067-55.


title: 4795-051-55

description: Gene expression data from nasal brushing 4795-051-55.


title: 4795-046-55

description: Gene expression data from nasal brushing 4795-046-55.


title: 4795-047-55

description: Gene expression data from nasal brushing 4795-047-55.


title: 4795-045-55

description: Gene expression data from nasal brushing 4795-045-55.


title: 4795-042-54

description: Gene expression data from nasal brushing 4795-042-54.


title: 4795-041-55

description: Gene expression data from nasal brushing 4795-041-55.


title: 4795-040-55

description: Gene expression data from nasal brushing 4795-040-55.


title: 4795-035-54

description: Gene expression data from nasal brushing 4795-035-54.


title: 4795-032-55

description: Gene expression data from nasal brushing 4795-032-55.


title: 4795-031-55

description: Gene expression data from nasal brushing 4795-031-55.


title: 4795-028-54

description: Gene expression data from nasal brushing 4795-028-54.


title: 4795-018-54

description: Gene expression data from nasal brushing 4795-018-54.


title: 4795-026-54

description: Gene expression data from nasal brushing 4795-026-54.


title: 4795-027-54

description: Gene expression data from nasal brushing 4795-027-54.


title: 4795-017-55

description: Gene expression data from nasal brushing 4795-017-55.


title: 4795-039-54

description: Gene expression data from nasal brushing 4795-039-54.


title: 4795-036-55

description: Gene expression data from nasal brushing 4795-036-55.


title: 4795-004-54

description: Gene expression data from nasal brushing 4795-004-54.


title: 4795-005-55

description: Gene expression data from nasal brushing 4795-005-55.


title: 4795-008-55

description: Gene expression data from nasal brushing 4795-008-55.


title: 4795-013-55

description: Gene expression data from nasal brushing 4795-013-55.


title: 4795-014-55

description: Gene expression data from nasal brushing 4795-014-55.


title: 4793-024-54

description: Gene expression data from nasal brushing 4793-024-54.


title: 4795-030-55

description: Gene expression data from nasal brushing 4795-030-55.


title: 4793-011-54

description: Gene expression data from nasal brushing 4793-011-54.


title: 4795-007-54

description: Gene expression data from nasal brushing 4795-007-54.


title: 4795-024-2-55

description: Gene expression data from nasal brushing 4795-024-2-55.


title: 4793-009-55

description: Gene expression data from nasal brushing 4793-009-55.


title: 4793-008-54

description: Gene expression data from nasal brushing 4793-008-54.


title: 4795-022-55

description: Gene expression data from nasal brushing 4795-022-55.


title: 4795-016-54

description: Gene expression data from nasal brushing 4795-016-54.


title: 4793-002-54

description: Gene expression data from nasal brushing 4793-002-54.


title: 4793-005-54

description: Gene expression data from nasal brushing 4793-005-54.


title: 4795-002-55

description: Gene expression data from nasal brushing 4795-002-55.


title: 4795-009-55

description: Gene expression data from nasal brushing 4795-009-55.


title: 4793-001-54

description: Gene expression data from nasal brushing 4793-001-54.


title: 4792-001-54

description: Gene expression data from nasal brushing 4792-001-54.


title: 4791-003-55

description: Gene expression data from nasal brushing 4791-003-55.


title: 4791-002-55

description: Gene expression data from nasal brushing 4791-002-55.


title: 4791-001-55

description: Gene expression data from nasal brushing 4791-001-55.


title: 4790-041-55

description: Gene expression data from nasal brushing 4790-041-55.


title: 4790-057-55

description: Gene expression data from nasal brushing 4790-057-55.


title: 4790-033-55

description: Gene expression data from nasal brushing 4790-033-55.


title: 4790-026-55

description: Gene expression data from nasal brushing 4790-026-55.


title: 4790-031-54

description: Gene expression data from nasal brushing 4790-031-54.


title: 4790-027-54

description: Gene expression data from nasal brushing 4790-027-54.


title: 4790-032-55

description: Gene expression data from nasal brushing 4790-032-55.


title: 4790-039-55

description: Gene expression data from nasal brushing 4790-039-55.


title: 4790-025-55

description: Gene expression data from nasal brushing 4790-025-55.


title: 4790-021-55

description: Gene expression data from nasal brushing 4790-021-55.


title: 4790-022-55

description: Gene expression data from nasal brushing 4790-022-55.


title: 4790-019-54

description: Gene expression data from nasal brushing 4790-019-54.


title: 4790-018-55

description: Gene expression data from nasal brushing 4790-018-55.


title: 4790-017-55

description: Gene expression data from nasal brushing 4790-017-55.


title: 4790-016-55

description: Gene expression data from nasal brushing 4790-016-55.


title: 4790-020-55

description: Gene expression data from nasal brushing 4790-020-55.


title: 4793-007-55

description: Gene expression data from nasal brushing 4793-007-55.


title: 4790-012-54

description: Gene expression data from nasal brushing 4790-012-54.


title: 4790-014-54

description: Gene expression data from nasal brushing 4790-014-54.


title: 4790-009-54

description: Gene expression data from nasal brushing 4790-009-54.


title: 4792-010-55

description: Gene expression data from nasal brushing 4792-010-55.


title: 4790-013-55

description: Gene expression data from nasal brushing 4790-013-55.


title: 4790-053-54

description: Gene expression data from nasal brushing 4790-053-54.


title: 4790-006-55

description: Gene expression data from nasal brushing 4790-006-55.


title: 4790-007-55

description: Gene expression data from nasal brushing 4790-007-55.


title: 4790-024-55

description: Gene expression data from nasal brushing 4790-024-55.


title: 4790-008-54

description: Gene expression data from nasal brushing 4790-008-54.


title: 4790-004-54

description: Gene expression data from nasal brushing 4790-004-54.


title: 4790-003-55

description: Gene expression data from nasal brushing 4790-003-55.


title: 4438-029-55

description: Gene expression data from nasal brushing 4438-029-55.


title: 4438-035-54

description: Gene expression data from nasal brushing 4438-035-54.


title: 4790-011-55

description: Gene expression data from nasal brushing 4790-011-55.


title: 4438-034-55

description: Gene expression data from nasal brushing 4438-034-55.


title: 4714-002-55

description: Gene expression data from nasal brushing 4714-002-55.


title: 4438-021-54

description: Gene expression data from nasal brushing 4438-021-54.


title: 4438-007-55

description: Gene expression data from nasal brushing 4438-007-55.


title: 4438-025-55

description: Gene expression data from nasal brushing 4438-025-55.


title: 4438-017-54

description: Gene expression data from nasal brushing 4438-017-54.


title: 4438-020-55

description: Gene expression data from nasal brushing 4438-020-55.


title: 4438-011-54

description: Gene expression data from nasal brushing 4438-011-54.


title: 4438-022-55

description: Gene expression data from nasal brushing 4438-022-55.


title: 4438-006-55

description: Gene expression data from nasal brushing 4438-006-55.


title: 4438-028-55

description: Gene expression data from nasal brushing 4438-028-55.


title: 4438-005-55

description: Gene expression data from nasal brushing 4438-005-55.


title: 4438-016-54

description: Gene expression data from nasal brushing 4438-016-54.


title: 4438-008-55

description: Gene expression data from nasal brushing 4438-008-55.


title: 4438-026-54

description: Gene expression data from nasal brushing 4438-026-54.


title: 4438-030-54

description: Gene expression data from nasal brushing 4438-030-54.


title: 4438-004-55

description: Gene expression data from nasal brushing 4438-004-55.


title: 4790-002-55

description: Gene expression data from nasal brushing 4790-002-55.


title: 4790-001-55

description: Gene expression data from nasal brushing 4790-001-55.


title: 4790-005-55

description: Gene expression data from nasal brushing 4790-005-55.


title: 4438-003-54

description: Gene expression data from nasal brushing 4438-003-54.


title: 4438-001-54

description: Gene expression data from nasal brushing 4438-001-54.


title: 4238-020-55

description: Gene expression data from nasal brushing 4238-020-55.


title: 4438-002-55

description: Gene expression data from nasal brushing 4438-002-55.


title: 4790-015-55

description: Gene expression data from nasal brushing 4790-015-55.


title: 4438-018-55

description: Gene expression data from nasal brushing 4438-018-55.


title: 4202-027-54

description: Gene expression data from nasal brushing 4202-027-54.


title: 4238-017-55

description: Gene expression data from nasal brushing 4238-017-55.


title: 4202-011-54

description: Gene expression data from nasal brushing 4202-011-54.


title: 4202-025-54

description: Gene expression data from nasal brushing 4202-025-54.


title: 4202-010-55

description: Gene expression data from nasal brushing 4202-010-55.


title: 4797-041-60

description: Gene expression data from bronchial brushing 4797-041-60.

data_processing:
Demultiplexing and creation of FASTQ files were performed using BaseSpace.
Samples were aligned using hg19 and 2-pass STAR alignment (v2.5.2b). Gene-level posterior mean counts were calculated using RSEM (v1.3.0) and Ensembl Gene annotation build 75.
Posterior mean counts were filtered to exclude those that did not have more than one count per million (cpm) in at least 10% of the samples, and then corrected for sequencing batch using ComBat-seq.
Assembly: hg19
Supplementary files format and content: DECAMP_bronchial_COVID19_posterior_mean_counts.tsv: a tab-separated value (TSV) file containing the posterior mean counts as computed by RSEM
Supplementary files format and content: DECAMP_bronchial_COVID19_normalized_counts.tsv: a tab-separated value (TSV) file containing the ComBat-corrected counts for a subset of features that passed expression filtering.

source_name: Brushing of bronchial epithelium

value: Brushing of bronchial epithelium


title: 4238-005-55

description: Gene expression data from nasal brushing 4238-005-55.


title: 4202-006-55

description: Gene expression data from nasal brushing 4202-006-55.


title: 4202-017-55

description: Gene expression data from nasal brushing 4202-017-55.


title: 4202-002-55

description: Gene expression data from nasal brushing 4202-002-55.


title: 4797-051-60

description: Gene expression data from bronchial brushing 4797-051-60.


title: 4202-024-55

description: Gene expression data from nasal brushing 4202-024-55.


title: 4202-012-54

description: Gene expression data from nasal brushing 4202-012-54.


title: 4797-033-60

description: Gene expression data from bronchial brushing 4797-033-60.


title: 4797-031-60

description: Gene expression data from bronchial brushing 4797-031-60.


title: 4202-009-55

description: Gene expression data from nasal brushing 4202-009-55.


title: 4797-046-60

description: Gene expression data from bronchial brushing 4797-046-60.


title: 4797-052-60

description: Gene expression data from bronchial brushing 4797-052-60.


title: 4797-025-60

description: Gene expression data from bronchial brushing 4797-025-60.