title: FGF19ΔKLB-3


title: FGF19WT-1

status: Public on Dec 07 2020

type: SRA

city: Wenzhou

first: Jianlou

last: Niu

state: Zhejiang

address: Chashan Town

country: China

institute: Wenzhou Medical University

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

source_name: liver tissues

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: liver

tag: agent


title: BaF3+BCR-Abl treated with DMSO replicate 1

city: Oslo

first: Jorrit

last: Enserink

address: Ullernchausseen 70

department: Molecular Cell Biology

country: Norway

institute: The Norwegian Radium Hospital

data_processing:
Clean reads (as provided by BGI) were mapped to the GRCm38.85 genome assembly using Tophat2 (v. 2.1.1), then using default options BAM files were indexed using SAMtools.
Differential expression data was produced using cuffquant and cuffdiff with default options, from the cufflinks suite (v 2.2.1 / SVN rev 4237).
Reference genome for the primary assembly and gene annotations used are revision 85 of GRCm38, from ensembl.org.
Genome_build: GRCm38.85 genome assembly
Supplementary_files_format_and_content: xlsx format with raw gene count, average gene count and FPKM values for each sample.
.tdf files were used for visualization in IGV.

source_name: Cell line

growth_protocol: BaF3 cells expressing BCR-Abl were cultured on RPMI-1640 medium supplemented with 10% heat inactivated FBS and 1% Pen/strep.

extract_protocol:
Total RNA was extracted by RNeasy mini kit Qiagen followed by DNase I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BaF3 cells expressing BCR-Abl were treated with 20µM DJ-34 (investigational drug) or DMSO control for 6 hrs.

tag: strain

tag: cell line

value: BaF3 pro B cells

tag: genotype/variation

value: expressing BCR-Abl

value: control


title: BaF3+BCR-Abl treated with DJ34 replicate 2


title: BaF3+BCR-Abl treated with DJ34 replicate 1


title: BaF3+BCR-Abl treated with DJ34 replicate 0


title: BaF3+BCR-Abl treated with DMSO replicate 2


title: Human microglia SC010

city: Montreal

first: Alain

last: Pacis

state: QC

address: 740 Dr Penfield Ave

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

data_processing:
Raw BCL files from the Illumina HiSeq 4000 were demultiplexed into paired-end, gzip-compressed FASTQ files for each channel using Cell Ranger’s mkfastq.
Using Cell Ranger’s count, reads were aligned to the human reference transcriptome (hg38), and transcript counts quantified for each annotated gene within every cell.
Genome_build: hg38
Supplementary_files_format_and_content: HDF5 binary data format

organism: Homo sapiens

source_name: Human microglia SC010

extract_protocol:
Human spinal cord tissue was harvested from organ donors through a collaboration with Transplant Quebec. All procedures are approved by and performed in accordance with the ethical review board at McGill University (IRB#s A04-M53-08B). Familial consent was obtained for each subject. The rapid autopsy spinal cord samples were processed within 2 hours of removal from the spinal column, tissue was kept on ice throughout. The samples were provided from the lumbar region of the cord (L1-L5) of three adults, two females and one male. Tissue was processed as previously described. Briefly, the meninges were carefully removed, and the tissue crosscut into small pieces of 1–2 mm3. A single cell suspension was obtained following mechanical and enzymatic (trypsin) dissociation. Myelin was removed using an isotonic Percoll gradient. Glia cells were located between the myelin and red blood cell layers, this layer was collected, washed and resuspended in ice-cold PBS.
10X Chromium Single Cell 3'

tag: Sex

value: Female

tag: surgery

value: Naive

tag: time point


title: Human microglia SC004

source_name: Human microglia SC004


title: Human microglia SC005B

source_name: Human microglia SC005B

value: Male


title: CVG-1

city: Pittsburgh

first: Bizunesh

last: Abere

state: PENNSYLVANIA

address: 5117 Centre Ave, Research Pav. Suite 1.8

department: Cancer Virology Program

country: USA

institute: Hillman Cancer Center

data_processing:
Raw FastQ files were trimmed with Trim Galore http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ using the following parameters -q 25, -e 0.1, and - length 50, and the quality control was performed with FastQC.
Backspliced splice junctions were identified and mapped using CIRI2 prediction algorithm
Genome_build: MCV (JF813003) and RatPyV2 (KX574453)
Supplementary_files_format_and_content: backsplice junctions identified exported as txt
CVG-1vsMCVoutfile.txt (no circRNA detected)
MS-1vsMCVoutfile.txt (no circRNA detected)
HEK-293-MCV-HFvs MCVoutfile.txt
RatParotidvsRatPyV2outfile.txt

source_name: MCC derived cell line

extract_protocol:
Trizol reagent (Invitrogen) was used to extract total RNA, according to the manufacturer’s instructions and treated with DnaseI (Ambion) to remove geomic DNA.
For RNA qulity control and circRNA library preparation, a total amount of 6 μg RNA per sample was used as input material. Ribosomal RNA was removed by rRNA probe andlinear RNA was removed by Rnase R (Lucigen). The CircRNA was interrupted randomly in adding fragmentation buffer.
Using the fragmented CircRNA as a template, the first strand was synthesized with a random hexamers of six bases, followed by the addition of buffer, dNTPs, RNase H and DNA polymerase I to synthesize the second strand of the cDNA, then the CircRNA was purified by AMPure XP beads. The cohesive ends of the DNA were repaired to blunt ends using T4 DNA polymerase and Klenow DNA polymerase, 3'-end plus A-tail and ligated to the sequencing adapter followed by selection of the size of the fragment with AMPure XP beads, afterwards, the second strand of cDNA containing U was degraded with USER enzyme. CircRNA library was amplified by PCR.

treatment_protocol: Samples 3, HEK-293 cells were transfected with a recircularized MCV-HF genome for 5 days and harvested for RNA extraction.

value: MCC derived cell line

tag: infection status

value: MCV positive

tag: treatment

value: RnaseR+, ribodepleted RNA


title: healthy CD4 lymphocytes_4

city: Toulouse

first: Fabienne

last: MEGGETTO

address: adresse pro

country: France

institute: CTCT INSRM 1037

data_processing:
Read counts of known mRNAs were analyzed using a RSEM-1.2.25 (bowtie2-2.2.6) workflow. Sequence reads were mapped to the human reference genome GRCh38
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: peripheral blood

extract_protocol: libraries were prepared with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina protocol according to the supplier’s recommendations.

tag: cell type

value: Pre-activated (CD3/CD28)


title: healthy CD4 lymphocytes_5


title: healthy CD4 lymphocytes_2


title: BaF3+BCR-Abl treated with DMSO replicate 0


title: HEK-293 MCV-HF

source_name: HEK-293 cell line

value: HEK-293 cell line

value: MCV-HF transfected


title: healthy CD4 lymphocytes_3


title: goat IgG Cut&Run control

status: Public on Dec 08 2020

city: New York

first: Brian

middle: David

last: Dynlacht

state: NY

address: 522 1st Ave, Smilow 1104

department: Dept. of Pathology and Cancer Center

institute: NYU School of Medicine

description: processed data file: eloa_g_peaks.narrowPeak

library_source: genomic

data_processing:
Library strategy: Cut&Run
Peak calling: Bowtie2, MACS2
Mapping: STAR
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: narrowPeak, bigWig

molecule: genomic DNA

source_name: DLD1 colon cancer cell line

growth_protocol: DLD1 cells were cultured in RPMI medium supplemented with 10% fetal bovine serum.

extract_protocol:
RNA was extracted with Trizol Reagent. Cells for ChIP or Cut&Run were fixed with 1% formaldehyde.
RNA-seq libraries were prepared with NEBNext® Small RNA Library Prep Set for Illumina or NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina. ChIP-seq and Cut&Run libraries were made following standard protocol.

treatment_protocol: siRNA targeting Elongin A was purchased from Dharmacon Inc and transfected with RNAiMax at final concentration 50nM. Cells were harvested two days after transfection.

value: Colon cancer cell line

tag: sirna

value: wild type (no siRNA)


title: atacD0-2

first: Mo

last: Ebrahimkhani

state: PA

address: A809B Scaife Hall, 3550 Terrace Street

department: Pathology

institute: University of Pittsburgh

description: diff.peak.annotation.12, diff.peak.annotation.13

data_processing:
.The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS).
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into FASTQ files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification
Raw ATAC-seq reads first went through the pipeline of FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) for quality control. Reads with low sequencing quality and adapter sequences were trimmed out by software Trimmomatic (Bolger et al., 2014).
Then the surviving reads were aligned to reference genome hg19 by Burrows-Wheeler Aligner (Li and Durbin, 2009).
Reads with low mapping quality were filtered out and only primary alignments were kept by SAMtools (Li et al., 2009). Duplicate reads were marked by Picard tool http://broadinstitute.github.io/picard/ .
Once the alignment was done, MACS (Zhang et al., 2008) was applied for peak calling.
Genome_build: hg19
Supplementary_files_format_and_content: For ATACseq, a text with differenctial peak analysis for each comparison of each sample condition

source_name: hiPSC

growth_protocol: Cells were maintained on mTeSR 1 medium until differentiation with regular passaging. For differentiation cells were induced with doxycycline for 5 days with daily medium changes. Cells were then released into single cell suspension with accutase and transduced with lentivirus for further engineering or reseeded as control without transduction and harvested at indicated time points.

extract_protocol: Cultures were acquired in single cell suspension by incubation with accutase for 5 minutes at 37°C, followed by gentle pipetting using a serological pipette to dislodge and dissociate aggregates.  Cells were frozen in mFresR cryopreservation medium. ATAC-Seq library preparation and sequencing reactions were conducted at GENEWIZ, LLC. (South Plainfield, NJ, USA). Live cell samples were thawed, washed, and treated with DNAse I (Life Tech, Cat. #EN0521) to remove genomic DNA contamination. Live cell samples were quantified and assessed for viability using a Countess Automated Cell Counter (ThermoFisher Scientific, Waltham, MA, USA). After cell lysis and cytosol removal, nuclei were treated with Tn5 enzyme (Illumina, Cat. #20034197) for 30 minutes at 37°C and purified with Minelute PCR Purification Kit (QIAGEN, Cat. #28004) to produce tagmented DNA samples. Tagmented DNA was barcoded with Nextera Index Kit v2 (Illumina, Cat. #FC-131-2001) and amplified via PCR prior to a SPRI Bead cleanup to yield purified DNA libraries.

treatment_protocol: No additional treatments aside from lentiviral transduction were performed (if indicated)

value: hiPSC

tag: condition

value: non induced, puripotent

tag: day

value: Day 0

tag: sequenced molecule

value: DNA for ATACseq


title: atacD0-1


title: atacFeLO-1

description: diff.peak.annotation.12, diff.peak.annotation.23

source_name: Fetal liver organoid

extract_protocol: Cultures were acquired in single cell suspension by incubation with trypsin for 10 minutes at 37°C, followed by gentle pipetting using a serological pipette to dislodge and dissociate aggregates.  Cells were frozen in mFresR cryopreservation medium. ATAC-Seq library preparation and sequencing reactions were conducted at GENEWIZ, LLC. (South Plainfield, NJ, USA). Live cell samples were thawed, washed, and treated with DNAse I (Life Tech, Cat. #EN0521) to remove genomic DNA contamination. Live cell samples were quantified and assessed for viability using a Countess Automated Cell Counter (ThermoFisher Scientific, Waltham, MA, USA). After cell lysis and cytosol removal, nuclei were treated with Tn5 enzyme (Illumina, Cat. #20034197) for 30 minutes at 37°C and purified with Minelute PCR Purification Kit (QIAGEN, Cat. #28004) to produce tagmented DNA samples. Tagmented DNA was barcoded with Nextera Index Kit v2 (Illumina, Cat. #FC-131-2001) and amplified via PCR prior to a SPRI Bead cleanup to yield purified DNA libraries.

value: Fetal liver organoid

value: GATA6 induced, no transduction

value: Day 17


title: RNAi of NF-YB RNA-seq Replicate 2

city: Milano

first: Diletta

last: Dolfini

state: MI

address: Via Celoria, 26

department: Bioscience

country: Italy

institute: University of Milan

data_processing:
Alignment performed with bowtie2 within rsem-calculate-expression against hg19 transcriptome.
Gene quantification performed with rsem-calculate-expression.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.genes.results.txt: Tab-delimited text files containing gene expression as counts, TPM and FPKM for each sample.

molecule: polyA RNA

source_name: HeLa cell line

growth_protocol: HeLa cells were grown in DMEM high glucose with L-glutamine (EuroClone SpA) supplemented with 10% FBS, 100 U/mL penicillin and 100 µg/mL streptomycin. The day before transfection, 0.15 × 10e6 cells/well were seeded in antibiotic-free medium in a 6-well plate.

extract_protocol:
The RNAs were extracted using TRI-reagent (Merck) and further purified with RNeasy Mini Kit (Qiagen) following the RNA clean-up protocol.
Performed by Novogene. Total RNAs were poly-T purified, randomly fragmented and transformed in cDNA with NEB library preparation protocol.

treatment_protocol: Cells at 25-30% confluence were transfected with 50 nM siRNA using 3.75 µL Lipofectamine 3000 Reagent (ThermoFisher) in 1.5 mL final volume of Optimem (ThermoFischer) per well.

value: HeLa


title: atacDesLO-2

description: diff.peak.annotation.13, diff.peak.annotation.23

source_name: Designer liver organoid

value: Designer liver organoid

value: GATA6 induced, ATF5, PROX1, CYP3A4 gRNA and dCas9 transduced


title: Control RNA-seq Replicate 2

value: scramble oligos


title: atacDesLO-1


title: RNAi of NF-YB RNA-seq Replicate 1


title: RNAi of NF-YB RNA-seq Replicate 3


title: atacFeLO-2


title: Control RNA-seq Replicate 1


title: 936_RocA0.3uM

city: Wakoshi

first: Mingming

last: Chen

state: Saitama

address: Hirisawa 2-2

department: CPR

country: Japan

institute: RIKEN

description: Ribosome Profiling

data_processing:
Library strategy: Ribosome profiling
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
random barcode triming with custom script
rRNA and other non-coding RNA alignment with bowtie2 v2.1.0
Alignment with TopHat v2.0.9
Read quantitation using custom scripts
Genome_build: hg38
Supplementary_files_format_and_content: text files contain three columns: 1. transcript name;2. CDS region (nt) used for read counting;3. read counts

source_name: Rnase I footprinting, ribosome pelleting, RNA extraction

extract_protocol: RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification (for ribosome profiling)

treatment_protocol: DMSO or RocA for 30min

value: RocA 0.3 microM

tag: genetic background

value: WT


title: 520_RocA0.3um

description: Ribosome Profiling


title: 1650_RocA3um

description: Ribosome Profiling

value: RocA 3 microM


title: 375_RocA0.3uM

description: Ribosome Profiling


title: 1650_RocA0.3um

description: Ribosome Profiling


title: Control RNA-seq Replicate 3


title: 936_RocA3uM

description: Ribosome Profiling


title: 375_DMSO2

description: Ribosome Profiling

value: DMSO


title: 375_DMSO1

description: Ribosome Profiling


title: healthy CD4 lymphocytes_1

value: Pre-activated (CD3/CD28)


title: 520_RocA3um

description: Ribosome Profiling


title: 375_RocA3uM

description: Ribosome Profiling


title: 1650_DMSO2

description: Ribosome Profiling


title: 4804-HSC-0006

city: Miami

first: Hitendra

middle: S

last: Chand

state: FL

department: Dept of Immunology & Nano-Medicin

institute: Florida International University Herbert Wertheim College of Medicine

description:
Sample 6
LPS treated

data_processing:
Aligned to reference genome with Hisat2 v2.10 with default parameters.
Cufflinks v2.2.1 was used to assemble reads, using the ENSEMBL v90 reference transcriptome.
All assembled transcripts were merged with CuffMerge.
Differential expression analysis was performed with CuffDiff.
Genome_build: GRCh38
Supplementary_files_format_and_content: FPKM values.xlsx: Cufflinks FPKM sheet which includes each sample, in Excel format.
Supplementary_files_format_and_content: gene_exp.diff: Gene differential analysis output from CuffDiff. “sample_1” corresponds to control samples and “sample_2” corresponds to experiments samples. Conclusions drawn from this file.

source_name: Airway Epithelial Cells

growth_protocol: Primary human airway epithelial cells (HAECs) were differentiated at the air-liquid interface for 14 days in ALI media and ciliary beatings and mucus secretions to assess differentiation.

extract_protocol:
The transwells were cut out of the wells and snap-frozen in RNAlater solutions (RNeasy isolation kit (Qiagen)), stored at -80 freezer till processed for RNA isolation.
Illumina TruSeq Stranded Total RNAseq libraries with ribosomal depletion were prepared per manufacturer’s instructions (Illumina, Inc, San Diego, CA).

treatment_protocol: On day 15, 3 of the ALI transwells were treated with LPS (100 ng/ml) for 2h.

value: Normal Bronchial Epithelial cells

tag: passage

value: LPS


title: 1650_DMSO1

description: Ribosome Profiling


title: skin_equivalent_#3 (mRNA)

type: RNA

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

hyb_protocol: Affymetrix  Human Gene 2.0 ST arrays were washed, stained and scanned according to the protocol described in GeneChip® WT Terminal Labeling and Hybridization User Manual (Fluidics Protocol FS450_0007)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1

data_processing: The data were analyzed withTranscriptome Analysis Console (TAC) 4.0.1 using  default analysis settings. Row data were log2-transformed and normalized by Robust multichip average (RMA) algorithm normalization.

label: biotin

source_name: keratinocytes

label_protocol: 200ng of total RNA were amplified and labeled using the GeneChip® WT PLUS Reagent Kit (Catalog Number 902281, Affymetrix, Santa Clara, CA)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions and subsequent RNA cleanup and concentration was performed using the Rneasy MinElure Cleanup Kit (Qiagen, Venlo, Netherlands)

treatment_protocol: from each conditation (pKC, dKC, SE) one samples from an individual healy participan was analysed

tag: disease state

value: healthy

value: skin equivalent keratinocyte


title: skin_equivalent_#2 (mRNA)


title: PUFA 16 High diet

city: Co. Meath

first: Kate

last: Keogh

address: Dunsany

department: Animal and Bioscience Department

country: Ireland

institute: Teagasc Grange

description:
PUFA-supplemented, high diet post-insemination
JE6-194

data_processing:
Basecalls performed using CASAVA version 1.4
Input reads were then aligned to the bovine reference genome (UMD3.1) using TopHat (v2.0.9).
HTSeq (v0.5.4p5) was employed to calculate the number of sequence reads overlapping all protein-coding genes from the ENSEMBL v74 annotation of the bovine genome.
Genome_build: UMD 3.1
Supplementary_files_format_and_content: Tab delimited txt file of merged gene read counts

organism: Bos taurus

source_name: uterine endometrial tissue

growth_protocol: Estrous cycles in normal nulliparous crossbred beef heifers (n=60) were synchronized in reproductively.  Heifers were offered a concentrate-based diet supplemented (n-3 PUFA; n=32) or not (Control; n=28) with an n-3 PUFA-enriched product for 30 days prior to insemination. Following insemination, animals were allocated, within treatment, to one of two post insemination diets, either remaining on their existing high plane of nutrition (Control + High (n = 14); n-3 PUFA + High (n = 15)), or fed a low plane of nutrition diet (Control + Low (n = 14); n-3 PUFA + Low (n = 17)).

extract_protocol:
Total RNA was extracted from frozen uterine endometrial tissue by homogenisation using the Qiagen Rneasy RNA isolation kit.
Single-end mRNA-seq libraries were constructed using the Illumina Truseq sample prep kit.

value: pufa

tag: diet

value: High diet


title: 4804-HSC-0002

description:
Sample 2
Non-treated controls

value: Untreated


title: PUFA 13 High diet

description:
PUFA-supplemented, high diet post-insemination
JE5-225B

treatment_protocol: Heifers were offered a concentrate-based diet supplemented (n-3 PUFA; n=32) or not (Control; n=28) with an n-3 PUFA-enriched product for 30 days prior to insemination. Following insemination, animals were allocated, within treatment, to one of two post insemination diets, either remaining on their existing high plane of nutrition (Control + High (n = 14); n-3 PUFA + High (n = 15)), or fed a low plane of nutrition diet (Control + Low (n = 14); n-3 PUFA + Low (n = 17)).


title: PUFA 17 High diet

description:
PUFA-supplemented, high diet post-insemination
JE6-8312


title: 4804-HSC-0004

description:
Sample 4
LPS treated


title: 4804-HSC-0003

description:
Sample 3
Non-treated controls


title: 4804-HSC-0005

description:
Sample 5
LPS treated


title: 936_DMSO2

description: Ribosome Profiling


title: 4804-HSC-0001

description:
Sample 1
Non-treated controls


title: proliferating_keratinocyte_#3 (mRNA)

value: proliferating keratinocyte


title: differentiated_keratinocyte_#3 (mRNA)

value: differentiated keratinocyte


title: 936_DMSO1

description: Ribosome Profiling


title: PUFA 12 High diet

description:
PUFA-supplemented, high diet post-insemination
JE5-197


title: differentiated_keratinocyte_#2 (mRNA)


title: differentiated_keratinocyte_#1 (mRNA)


title: proliferating_keratinocyte_#1 (mRNA)


title: 520_DMSO2

description: Ribosome Profiling


title: proliferating_keratinocyte_#2 (mRNA)


title: 520_DMSO1

description: Ribosome Profiling


title: PUFA 11 High diet

description:
PUFA-supplemented, high diet post-insemination
JE4-8345


title: skin_equivalent_#1 (mRNA)


title: PUFA 14 High diet

description:
PUFA-supplemented, high diet post-insemination
JE5-8320


title: PUFA 15 High diet

description:
PUFA-supplemented, high diet post-insemination
JE6-140


title: PUFA 10 High diet

description:
PUFA-supplemented, high diet post-insemination
JE4-147


title: PUFA 7 High diet

description:
PUFA-supplemented, high diet post-insemination
JE3-252


title: PUFA 9 High diet

description:
PUFA-supplemented, high diet post-insemination
JE3-78


title: PUFA 8 High diet

description:
PUFA-supplemented, high diet post-insemination
JE3-271


title: PUFA 5 High diet

description:
PUFA-supplemented, high diet post-insemination
JE2-211


title: PUFA 6 High diet

description:
PUFA-supplemented, high diet post-insemination
JE2-8333


title: PUFA 4 High diet

description:
PUFA-supplemented, high diet post-insemination
JE2-163


title: PUFA 15 Low diet

description:
PUFA-supplemented, low diet post-insemination
JE6-335

value: Low diet


title: PUFA 13 Low diet

description:
PUFA-supplemented, low diet post-insemination
JE5-8302


title: PUFA 1 High diet

description:
PUFA-supplemented, high diet post-insemination
JE1-399


title: PUFA 2 High diet

description:
PUFA-supplemented, high diet post-insemination
JE1-74


title: PUFA 3 High diet

description:
PUFA-supplemented, high diet post-insemination
JE1-8340


title: PUFA 14 Low diet

description:
PUFA-supplemented, low diet post-insemination
JE6-254


title: PUFA 12 Low diet

description:
PUFA-supplemented, low diet post-insemination
JE5-589


title: PUFA 11 Low diet

description:
PUFA-supplemented, low diet post-insemination
JE5-223


title: PUFA 10 Low diet

description:
PUFA-supplemented, low diet post-insemination
JE4-334


title: PUFA 9 Low diet

description:
PUFA-supplemented, low diet post-insemination
JE4-153


title: Unknown Samp 1

city: PLEASANTON

first: Rajiv

last: Dua

state: CA

address: 4300 Hacienda Dr

institute: Roche Molecular Diagnostics

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16-18 hr at 47C on GeneChip HG-U133_Plus_2 Genome Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Raw microarray data was pre-processed by an internal software tool developed at Roche Molecular Systems Inc., Pleasanton, CA, USA.  Specifically, a special DQN signal used the quantities of beta distribution with p = 1.2 and q = 3 for normalization

source_name: Validation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: High Pure formalin-fixed, paraffin-embedded tissue (FFPET) RNA Isolation Kit (Roche Molecular Systems, Pleasanton, California)

tag: dataset group

value: Validation

tag: tissue

value: large B-cell lymphoma tissue

tag: subtype (rmsg100)

value: GCB


title: Unknown Samp 3

value: ABC


title: Unknown Samp 6


title: Unknown Samp 4


title: Unknown Samp 5


title: Unknown Samp 2


title: Ref DLBCL No1


title: GCB Samp 19


title: GCB Samp 17


title: Ref DLBCL No2


title: GCB Samp 18


title: GCB Samp 14


title: GCB Samp 21


title: GCB Samp 13


title: GCB Samp 16


title: GCB Samp 11


title: PUFA 8 Low diet

description:
PUFA-supplemented, low diet post-insemination
JE3-8341


title: PUFA 4 Low diet

description:
PUFA-supplemented, low diet post-insemination
JE2-216


title: PUFA 5 Low diet

description:
PUFA-supplemented, low diet post-insemination
JE2-262


title: PUFA 3 Low diet

description:
PUFA-supplemented, low diet post-insemination
JE2-207


title: GCB Samp 12


title: GCB Samp 15


title: GCB Samp 20


title: control 14 High diet

description:
Control, high diet post-insemination
JE6-8342

value: control


title: PUFA 2 Low diet

description:
PUFA-supplemented, low diet post-insemination
JE1-590


title: PUFA 1 Low diet

description:
PUFA-supplemented, low diet post-insemination
JE1-261


title: GCB Samp 9


title: GCB Samp 8


title: control 13 High diet

description:
Control, high diet post-insemination
JE6-326


title: GCB Samp 10


title: GCB Samp 7


title: GCB Samp 6


title: control 12 High diet

description:
Control, high diet post-insemination
JE5-8314


title: MS-1

tag: cell line

value: MCC derived cell line

value: MCV positive

value: RnaseR+, ribodepleted RNA


title: control 9 High diet

description:
Control, high diet post-insemination
JE4-298


title: control 10 High diet

description:
Control, high diet post-insemination
JE4-338


title: control 11 High diet

description:
Control, high diet post-insemination
JE5-138


title: control 8 High diet

description:
Control, high diet post-insemination
JE4-144


title: control 7 High diet

description:
Control, high diet post-insemination
JE3-8343


title: GBC Samp 5


title: GCB Samp 3


title: GCB samp 1


title: EXT DLBCL CNTL 9


title: EXT DLBCL CNTL 7


title: EXT DLBCL CNTL 6


title: GBC Samp 4


title: EXT DLBCL CNTL 8


title: EXT DLBCL CNTL 5


title: control 6 High diet

description:
Control, high diet post-insemination
JE3-322


title: EXT DLBCL CNTL 4


title: control 4 High diet

description:
Control, high diet post-insemination
JE2-161


title: control 2 High diet

description:
Control, high diet post-insemination
JE1-388


title: control 3 High diet

description:
Control, high diet post-insemination
JE1-84


title: control 12 Low diet

description:
Control, low diet post-insemination
JE6-286


title: control 14 Low diet

description:
Control, low diet post-insemination
JE6-8338


title: control 5 High diet

description:
Control, high diet post-insemination
JE2-8309


title: control 11 Low diet

description:
Control, low diet post-insemination
JE5-636


title: control 1 High diet

description:
Control, high diet post-insemination
JE1-119


title: control 13 Low diet

description:
Control, low diet post-insemination
JE6-434


title: EXT DLBCL CNTL 3


title: DLBCL CNTL 7


title: DLBCL CNTL 9


title: EXT DLBCL CNTL 2


title: DLBCL CNTL 8


title: control 9 Low diet

description:
Control, low diet post-insemination
JE4-380


title: control 7 Low diet

description:
Control, low diet post-insemination
JE4-179


title: EXT DLBCL CNTL 1


title: control 8 Low diet

description:
Control, low diet post-insemination
JE4-228


title: control 10 Low diet

description:
Control, low diet post-insemination
JE5-157


title: DLBCL CNTL 6


title: DLBCL CNTL 5


title: control 6 Low diet

description:
Control, low diet post-insemination
JE3-8335


title: control 5 Low diet

description:
Control, low diet post-insemination
JE3-323


title: control 4 Low diet

description:
Control, low diet post-insemination
JE2-8348


title: control 2 Low diet

description:
Control, low diet post-insemination
JE1-588


title: control 1 Low diet

description:
Control, low diet post-insemination
JE1-350


title: PUFA 7 Low diet

description:
PUFA-supplemented, low diet post-insemination
JE3-506


title: DLBCL CNTL 1


title: DLBCL CNTL 2


title: ABC Samp 13


title: ABC Samp 12


title: RZ71_RZ_Day0_RS

city: Perth

first: Wee Loong

last: Chin

address: Level 5, Qq Block, Qeii Medical Centre 6 Verdun St, Nedlands

country: Australia

institute: National Centre For Asbestos Related Diseases

data_processing:
read alignment with Kallisto
count quantification with tximport
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: txt files in compressed gz format

source_name: Renca tumour

growth_protocol: Subcutaneous tumour growth

extract_protocol:
Frozen tumour dissociation with Trizol followed by chloroform extraction and purification using RNeasy MinElute
Illumina 50bp single-end sequencing

treatment_protocol: 100ug anti-CTLA-4 + anti-PDL1 given i.p., follwed by 100ug anti-PDL1 i.p. given 2 and 4 days later *Note some samples were collected before treatment

value: Renca tumour

tag: age

value: 8-10 weeks

tag: gender

value: f

value: aCTLA-4 + aPDL1

tag: group

value: RS

tag: strain

value: balb/c

tag: timepoint


title: ABC Samp 8


title: DLBCL CNTL 3(b)


title: ABC Samp 9


title: DLBCL CNTL 4


title: RZ72_RZ_Day0_NR

tag: treatment

value: NR


title: RZ70_RZ_Day0_NR


title: ABC Samp 11


title: control 3 Low diet

description:
Control, low diet post-insemination
JE2-393


title: ABC Samp 6


title: ABC Samp 5


title: ABC Samp 3


title: ABC Samp 2


title: ABC Samp 7


title: RZ69_RZ_Day0_RS


title: ABC Samp 10


title: ABC Samp 4


title: RZ68_RZ_Day0_NR


title: BV2_OE_C2

first: Alison

last: Goate

address: Icahn (East) Building Floor 10 Room 10-70C, 1425 Madison Ave

department: Department of Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Base-calling was performed with Illumina Casava 1.8.2 software, and demultiplexing was performed using Illumina bcl2fastq Conversion Software v2.18.
Sequence reads were aligned to the mouse reference genome of UCSC mm10 using STAR (v2.5.2a) with default parameters and soft clipping enabled.
Read counts of genes were estimated by featureCounts with default parameters.
Differential gene expression was analyzed in DESeq2 (v1.14) with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files of sample CPM values (counts per million; i.e the raw counts divided by library size in millions).

source_name: BV2 cells

growth_protocol: The BV2 cells were cultured in DMEM (Gibco #11965) supplemented with 5% heat-inactivated fetal bovine serum (FBS, Gibco #16140) and 100 U/ml penicillin-streptomycin (Pen/Strep, Gibco #15140).

extract_protocol:
mRNA was extracted with RNeasy mini kit (QIAgen #74106) including the DNase I treatment step with RNase-Free DNase set (QIAgen #79254) according to manufacturer’s instructions.
Libraries were prepared using TruSeq RNA Sample Prep Kit v2 and sequenced using Illumina HiSeq 2500 with 100-bp single-end reads.

treatment_protocol: No treatment.

value: Empty frame control of mouse PU.1 overexpression


title: BV2_OE_S2

value: Overexpression of mouse PU.1


title: BV2_OE_S3


title: BV2_OE_C3


title: BV2_OE_S1


title: RZ67_RZ_Day0_RS


title: BV2_KD_S3

value: Knock-down of PU.1


title: BV2_OE_C1


title: RZ65_RZ_Day0_RS


title: RZ66_RZ_Day0_NR


title: BV2_KD_S2


title: BV2_KD_S1


title: RZ64_RZ_Day6_NR


title: ABC Samp 1

value: Validation

value: large B-cell lymphoma tissue


title: RZ62_RZ_Day4_NR


title: RZ61_RZ_Day4_RS


title: BV2_KD_C2

value: Scrambled control of PU.1 knock-down


title: BV2_KD_C3


title: RZ59_RZ_Day2_RS


title: RZ58_RZ_Day0_NR


title: RZ57_RZ_Day0_RS


title: RA98-0735

source_name: Training 2

value: Training 2

value: GCB


title: BV2_KD_C1


title: RZ55_RZ_Day6_RS


title: RZ63_RZ_Day6_RS


title: RZ53_RZ_Day4_RS


title: YBT_3

city: Hangzhou

first: Chen

last: Zhiyun

address: No. 9, Street 9, Xiasha economic development zone, Jianggan district

institute: The First Affiliated Hospital of Zhejiang Chinese Medical University

data_processing:
Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 21.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNAcontaining arm were considered to be novel 5p- or 3pderived miRNA candidates.
The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤20). (6) number of nucleotides in one bulge in mature region (≤8) (7) number of biased errors in one bulge in mature region (≤4) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤7) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary_files_format_and_content: miR_seq,a read at 5' or 3' of maximum mapped score in each cluster;len,miR_seq length;genome ID,Reference Genome Information;strand,strand "+" or "-";start
Supplementary_files_format_and_content: pre-miRNA start position;end,Pre-miRNA end position;pre-miRNA_seq,pre-miRNA sequence;#mir/MIR,mapped mir numbers in miRbase, the number in this item eaquals to the sum of mirIDs;
Supplementary_files_format_and_content: mirIDs,all mirID in a cluster, seprated by;rep_mirID,the representative known mirID;rep_mirSeq,is the representative known mir sequence;rep_miRID,the representative known miRID;rep_miRID,the representative known miRID;rep_miRSeq,the representative known miR sequence;type,5' or 3', which means the cluster appears at 5' or 3' end.Sequence in miRbase:New, miRNA identified in this study and not reported in miRBase,mainly for new reported 5p or 3p sequence; Diff, confirming miRNA sequences in miRBase, but different sequences are reported in our study; and  Yes, confirming miRNA sequences in miRBase.SS,Secondary Structure;hairpinLen,pre-miRNA length;CG%,GC Content;dG,Free energy;raw,Raw data; from #reads(all),is the number of reads for isoform at 5' or 3' end;norm,Normalized data.Expression Level:High,The number of reads in the following reported miRNAs is higher than the average copy of the data set.Medium:The number of reads in the following reported miRNAs is higher than 10 and less than average copy of the data set;Low,The number of reads in the following reported miRNAs is less than 10.
Supplementary_files_format_and_content: gp1a:Reads were mapped to miRNAs/pre-miRNAs of specific species in miRbase and the pre-miRNAs were further mapped to genome & EST.
Supplementary_files_format_and_content: gp1b:Reads were mapped to (except for specific species) miRNAs/pre-miRNAs of selected species in miRbase and the pre-miRNAs were further mapped to genome & EST.
Supplementary_files_format_and_content: gp2a:Reads were mapped to miRNAs/pre-miRNAs of selected species in miRbase and the mapped pre-miRNAs were not further mapped to genome, but the reads (and of course the miRNAs of the pre-miRNAs) were mapped to genome. The extended genome sequences from the genome loci may form hairpins.
Supplementary_files_format_and_content: gp2b:Reads were mapped to miRNAs/pre-miRNAs of selected species in miRbase and the mapped pre-miRNAs were not further mapped to genome, but the reads (and of course the miRNAs of the pre-miRNAs) were mapped to genome. The extended genome sequences from the genome loci may not form hairpins.
Supplementary_files_format_and_content: gp3:Reads were mapped to miRNAs/pre-miRNAs of selected species in miRbase and the mapped pre-miRNAs were not further mapped to genome, and the reads were not mapped to genome, either. but the reads were mapped to the miRNAS(Matures)
Supplementary_files_format_and_content: gp4:Reads were not mapped to pre-miRNAs of selected species in miRbase. But the reads were mapped to genome & the extended genome sequences from genome may form hairpins.

source_name: liver

growth_protocol: The mice were exposed to continuous light and 12:12 h light/dark cycle, and provided with food and water ad libitum.

extract_protocol:
Total RNA was extracted using Trizol regent (Invitrogen, CA, USA).
After quality control, the RNA was used to generate small RNA libraries and rRNA-depleted RNA libraries. The small RNA libraries were constructed according to the TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, USA) protocol. rRNA-depleted RNA libraries were made using Epicentre Ribo-Zero Gold Kit (Illumina, San Diego, USA) according to the instruction manual.

treatment_protocol: 24 male C57BL/6 mice, 6-8 weeks old, were purchased from Shanghai Sippr-BK Laboratory Animal Co. Ltd. (production license: SCXK (Hu) 2013-0016).After one week of adaptive feeding, the mice were randomly divided into three groups, namely normal feeding diet (ND) group, Western diet feeding (WD) group and YBT treatment (YBT) group. Eight mice were included in each group. The mice in ND group were fed with normal feed and had water freely. The mice in the other two groups were fed with high-fat diet (10% lard oil, 5% egg yolk powder, 2% cholesterol, 0.5% bile salt and 82.5% basic feed, W/W) and freely drank 20% fructose water for 16 weeks. From the 5th week, the mice in the YBT group were given 22.12g/Kg.d of YBT liquid extract by gavage and mice in the other groups were given an equal volume of physiological saline by gavage for 12 weeks. The feedstuff was purchased from Trophica Animal Feed High-Tech Co. Ltd. China.All the mice of ND, WD and YBT groups were sacrificed at the end of the 16th week. The mice were fasted for 12 hours before experiments (water was not restricted). Blood was taken under anesthesia. The liver specimens were collected and partially fixed in 10% neutral formalin for pathological observation and the remaining liver tissues were stored at -80 °C for further analysis.

tag: Sex

value: male

value: Western diet for 16 weeks combined with YBT treatment for 12 weeks


title: RZ52_RZ_Day2_NR

value: Renca tumour


title: UH1402-38


title: YBT_2


title: RZ51_RZ_Day2_RS

value: 8-10 weeks


title: RA01-1996


title: RZ50_RZ_Day0_NR

value: f


title: RZ60_RZ_Day2_NR

value: aCTLA-4 + aPDL1


title: YBT_1


title: RA01-1606


title: RZ47_RZ_Day6_RS

value: RS


title: RZ48_RZ_Day6_NR

value: balb/c


title: R13-0237


title: RA02-2048


title: R12-0780


title: RZ56_RZ_Day6_NR

value: NR


title: RA02-2130

value: ABC


title: RZ54_RZ_Day4_NR


title: WD_2

value: Western diet for 16 weeks


title: WD_3


title: RZ45_RZ_Day4_RS


title: DLBCL CNTL 10


title: WD_1


title: RZ43_RZ_Day2_RS


title: ND_3

value: Normal diet for 16 weeks


title: RZ42_RZ_Day0_NR


title: R12-0224


title: RZ49_RZ_Day0_RS


title: R10-0432


title: OCI-Ly10


title: RZ40_RZ_Day6_NR


title: RZ41_RZ_Day0_RS


title: RZ39_RZ_Day6_RS


title: OCI-Ly3.3


title: RZ46_RZ_Day4_NR


title: RZ36_RZ_Day2_NR


title: RZ35_RZ_Day2_RS


title: ND_1


title: RZ38_RZ_Day4_NR


title: RZ44_RZ_Day2_NR


title: T18A [RNA-seq]

city: GuangZhou

first: Zhu

last: Hao

address: Shatai Road

institute: Southern Medical University

description: Sample 15

data_processing:
RNA-seq raw data were filtered using the following steps. We removed reads with sequence adaptors and reads with more than 10% ‘N’ bases, and further removed reads with more than 50% bases with QA ≤ 10.
RNA-seq clean data were mapped to hg19 using HISAT2(v.0.1.5)
Gene expression files were obtained using StringTie (1.2.2)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Total RNA was extracted from tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. After DNase I treatment, Ribo-Zero Magnetic Kit is used to remove rRNA before constructing the RNA-seq libraries.By using the fragmentation buffer, the mRNAs and non-coding RNAs are fragmented into short fragments(about 200~500nt), then the first-strand cDNA is synthesized by random hexamer-primer using the fragments as templates, and dTTP is substituted by dUTP during the synthesis of the second strand. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters, then the second strand is degraded using UNG(Uracil-N-Glycosylase) finally. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue type

value: Colorectal tumor tissues

tag: differentiation stage

value: poorly-differentiated

tag: tnm


title: RZ33_RZ_Day0_RS


title: RZ32_RZ_Day6_NR


title: RZ31_RZ_Day6_RS


title: RZ34_RZ_Day0_NR


title: T13A [RNA-seq]

description: Sample 13


title: RZ30_RZ_Day4_NR


title: RZ29_RZ_Day4_RS


title: T2C [RNA-seq]

description: Sample 12


title: ND_2


title: NP14830

value: large B-cell lymphoma tissue


title: RZ37_RZ_Day4_RS


title: NP16371_FP

value: Training 2


title: RZ28_RZ_Day2_NR


title: OCI-Ly19

value: GCB


title: ILS33494PD1_10


title: RZ27_RZ_Day2_RS


title: RZ26_RZ_Day0_NR


title: T160A [RNA-seq]

description: Sample 10

value: moderately-differentiated


title: RZ24_RZ_Day6_NR


title: ILS4453


title: ILS35098PD1_10


title: T132A [RNA-seq]

description: Sample 9


title: RZ23_RZ_Day6_RS


title: RZ22_RZ_Day4_NR


title: T111A [RNA-seq]

description: Sample 8


title: T162A [RNA-seq]

description: Sample 11


title: ILS26049


title: RZ25_RZ_Day0_RS


title: ILS32212


title: ILS30444_FP


title: RZ21_RZ_Day4_RS


title: RZ20_RZ_Day2_NR


title: RZ19_RZ_Day2_RS


title: T85A [RNA-seq]

description: Sample 6

value: well-differentiated


title: RZ16_RZ_Day6_NR

value: Renca tumour


title: T95A [RNA-seq]

description: Sample 7


title: RZ18_RZ_Day0_NR

value: 8-10 weeks


title: T50A [RNA-seq]

description: Sample 5


title: RZ17_RZ_Day0_RS

value: f


title: RZ14_RZ_Day4_NR

value: aCTLA-4 + aPDL1


title: RZ15_RZ_Day6_RS

value: RS


title: RZ13_RZ_Day4_RS

value: balb/c


title: T19A [RNA-seq]

description: Sample 4


title: T14A [RNA-seq]

description: Sample 14


title: EE36


title: ILS26043


title: EE31


title: RZ12_RZ_Day2_NR

value: NR


title: RZ11_RZ_Day2_RS


title: N40A [RNA-seq]

description: Sample 2

source_name: Colorectal tissues_Normal tissue

value: Colorectal tissues

value: Normal tissue

value: Normal


title: RZ10_RZ_Day0_NR


title: N1A [RNA-seq]

description: Sample 3


title: EE28

value: ABC


title: PUFA 6 Low diet

description:
PUFA-supplemented, low diet post-insemination
JE3-269

value: pufa

value: Low diet


title: A-485 + Dox_rep3

city: Lausanne

first: Terytty Yang

last: Li

address: EPFL SV IBI-SV LISP AI 1145

country: Switzerland

institute: EPFL

data_processing:
After sequencing on the BGIseq-500 platform, the raw reads were filtered. Data filtering includes removing adaptor sequences, contamination and low-quality (phred quality < 20) reads from raw reads.
Sequenced reads were mapped to the GRCh38 assembly of the mouse genome using ensembl release 95 gene annotation with STAR aligner version 2.6.0a
Reads were counted using htseq-count version 0.10.0 using these flags: -f bam -r pos -s no -m union -t exon -i gene_id
Genome_build: Homo_sapiens.GRCh38.95
Supplementary_files_format_and_content: xlsx file with counts per gene per sample

source_name: A-485 + Dox_rep3

growth_protocol: Human HepG2 cells were maintained in DMEM medium containing 4.5 g glucose per liter and 10% FBS.

extract_protocol:
On the day of the extraction, 1 ml of TriPure Isolation Reagent (Cat. 11667165001, Roche) was added to each tube. RNA was then extracted by using a column-based kit from Macherey-Nagel (Cat. 740955.250).
RNA libraries were prepared for sequencing using standard BGISeq500 protocols with polyA enrichment

treatment_protocol: HepG2 cells were pretreated with DMSO control or CBP/p300 inhibitor A-485 (5 μM) (Cat. 6387, R&D systems) for 1 hour, and then co-treated with or without 30 μg/ml doxycycline (Cat. D9891, Sigma) for 24 hours and without any other antibiotics.

tag: genotype

value: WT


title: A-485 + Dox_rep2

source_name: A-485 + Dox_rep2


title: EE33

value: Training 2

value: large B-cell lymphoma tissue


title: RZ09_RZ_Day0_RS


title: EE13


title: N4A [RNA-seq]

description: Sample 1


title: T18A [MeDIP-seq]

description: MeDIP-seq

data_processing:
MeDIP-seq raw data  were filtered using the following steps. We removed reads with sequence adaptors and reads with more than 10% ‘N’ bases, and further removed reads with more than 50% bases with QA ≤ 20
MeDIP-seq clean data were mapped to hg19 using Bowtie2 (v2.2.5)
DNA methylation abundance  were calculated by MEDIPS
Genome_build: hg19
Supplementary_files_format_and_content: DNA methylation abundance measurements

extract_protocol:
1.5µg of original genomic DNA was fragmented to DNA smear between 200bp to 500bp using a Bioruptor NGS (Diagenode) sonication system. End repair, <A> base addition and adaptor ligation steps were performed using Illumina’s Paired-End DNA Sample Prep kit following the manufacturer’s instructions. Then, the methylated DNA fractions were immunoprecipitated using the Magnetic Methylated DNA Immunoprecipitation Kit (Diagenode, catalog number: mc-magme-048) with small adjustments. Briefly, 1.5µl of each two control templates (methylated and unmethylated DNA controls) with different sequences were mixed with adapter ligated DNA and heat denatured (95°C, 3min) in a final reaction volume of 90µl within the provided reagents of 24µl MagBuffer A and 6µl MagBuffer B. 7.5µl aliquot of the denatured genomic DNA was saved as input and another 75µl was immunoprecipitated with 5µl of prepared anti-5mC antibody and 20µl of prepared Magbeads. The DNA-antibody-magbeads mixture was incubated overnight at 4°C on a rotating wheel. The DNA-antibody-magbeads mixture was then washed twice using each of 150µl ice-cold MagWash Buffer-1 and washed once with 150µl of ice-cold MagWash Buffer-2. For each buffer, the washing reaction was incubated for 4min at 4°C on a rotating wheel. The input DNA and immunoprecipitated products were then in parallel treated with protease K and purified with ZYMO DNA Clean & Concentrator-5 (ZYMO). The efficiency and sensitivity of immunoprecipitation reaction were detected by qPCR using the enriched DNA and the unbound input DNA. MeDIP-seq library was constructed by PCR amplification with the enriched DNA as template. PCR reaction was performed in 50µl of reaction volume consisting of 20µl MeDIP enriched DNA, 5µl of 2.5mM dNTP, 2µl primers, 5µl of 10X pfx Amplification Buffer, 2µl of 50mM MgSO4, 15.2µl sterilized water and 0.8µl of Platinum pfx DNA polymerase (Invitrogen). The program of amplification was 94°C 2 min, 10 cycles of 94 °C 15s, 62°C 30s and 72°C 30 then prolong with 10min at 72°C. The products could be kept at 12°C. The PCR products were purified using Agencourt Ampure Beads (Beckman Counlter). After analyzing by the Bioanalyzer analysis system (Agilent, Santa Clara, USA) and quantified by the real time PCR, the prepared library was sequenced using Illumina HiSeq2000 with SE50 read length.
DNA libraries were prepared for sequencing using standard Illumina protocols

value: Colorectal tumor tissues

value: poorly-differentiated


title: EE6


title: EE12


title: EE24


title: RZ08_RZ_Day6_NR

value: Renca tumour

value: 8-10 weeks


title: T14A [MeDIP-seq]

description: MeDIP-seq


title: RZ07_RZ_Day6_RS

value: f

value: aCTLA-4 + aPDL1


title: DMSO + Dox_rep3

source_name: DMSO + Dox_rep3

value: Dox


title: DMSO + Dox_rep2

source_name: DMSO + Dox_rep2


title: T13A [MeDIP-seq]

description: MeDIP-seq


title: RZ05_RZ_Day4_RS

value: RS

value: balb/c


title: DMSO + Dox_rep1

source_name: DMSO + Dox_rep1


title: RZ06_RZ_Day4_NR

value: NR


title: T2C [MeDIP-seq]

description: MeDIP-seq


title: T162A [MeDIP-seq]

description: MeDIP-seq

value: moderately-differentiated


title: A-485_rep3


title: RZ04_RZ_Day2_NR


title: A-485 + Dox_rep1

source_name: A-485 + Dox_rep1


title: A-485_rep2


title: RZ03_RZ_Day2_RS


title: EE5

value: ABC


title: T160A [MeDIP-seq]

description: MeDIP-seq


title: E1188

value: GCB


title: T132A [MeDIP-seq]

description: MeDIP-seq


title: A-485_rep1


title: EE3


title: E0887


title: T111A [MeDIP-seq]

description: MeDIP-seq


title: RZ01_RZ_Day0_RS


title: DMSO_rep2

value: DMSO


title: RZ02_RZ_Day0_NR


title: AB72_AB1_Day0_NR

source_name: AB1 tumour

value: AB1 tumour


title: T85A [MeDIP-seq]

description: MeDIP-seq

value: well-differentiated


title: DMSO_rep1

value: WT


title: AB71_AB1_Day0_RS


title: HF MɸTSP1 -/- 3

city: lexington

first: Shuxia

last: Wang

state: KY

address: 900 S. Limestone street, Wethington Bldg. Room 583

department: Pharmacology and Nutritional Sciences

institute: University of Kentucky

data_processing:
SOAPnuke software (v 1.5.2, parameters: -1 15-q0.5-n0.1, website: //github.com/BGI-flexlab/SOAPnuke) was used to filter reads.
Sequence reads with adaptors, reads in which unknown nases are more than 10%, or low quality reads, were removed. After filtering, the remaining reads were stored in FASTQ format.
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.

source_name: Liver

extract_protocol:
Livers were removed, flash frozen in liquid nitrogen, and total RNA were extracted using RNAeasy kit from Qiagen. 2 ug total RNA was submitted to BGI company for RNA sequencing analysis.
RNA libraries were prepared for RNA sequencing using standard  BGI protocols.

value: macrophage specific TSP1 knockout

value: HF

value: 10 month old


title: T50A [MeDIP-seq]

description: MeDIP-seq

value: Colorectal tumor tissues


title: T95A [MeDIP-seq]

description: MeDIP-seq


title: AB70_AB1_Day0_NR

value: 8-10 weeks

value: f


title: E0615

value: Training 2

value: large B-cell lymphoma tissue


title: T19A [MeDIP-seq]

description: MeDIP-seq


title: E0626


title: E0612


title: DMSO_rep3


title: HF MɸTSP1 -/- 2


title: E0941


title: E0545


title: AB69_AB1_Day0_RS

value: aCTLA-4 + aPDL1

value: RS

value: balb/c


title: HF MɸTSP1 -/- 1


title: N1A [MeDIP-seq]

description: MeDIP-seq

value: Colorectal tissues

value: Normal tissue

value: Normal


title: E0523

value: GCB


title: E0369

value: ABC


title: AB68_AB1_Day0_NR

value: AB1 tumour

value: NR


title: HF TSP1flox-3

value: WT

value: HF


title: N40A [MeDIP-seq]

description: MeDIP-seq


title: E0355


title: N4A [MeDIP-seq]

description: MeDIP-seq


title: AB67_AB1_Day0_RS


title: E0490


title: AB66_AB1_Day0_NR


title: HF TSP1flox-1

value: 10 month old


title: E0325


title: AB65_AB1_Day0_RS

value: 8-10 weeks


title: LF MɸTSP1 -/- 3

value: macrophage specific TSP1 knockout

value: LF


title: E0321

value: Training 2

value: large B-cell lymphoma tissue


title: Anti-PD-1 treated tumor from Hu-mice [T6]

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
RNA-seq data analysis was performed using RSEM v1.2.12 software and downstream expression analysis was done using DESeq2.
Normalized RNA-seq data was used to enumerate tumor-infiltrating leukocytes using CIBERSORT, an analytical tool from Stanford University.
Supplementary_files_format_and_content: Analyzed data are represented as heat maps or dotplot.

source_name: Melanoma tumor

growth_protocol: Tumor cells grown in humanized mice were obtained at the end of the study.

extract_protocol:
RNA was isolated from tissue blocks using Zymo Direct-Zol RNA MiniPrep kit (Zymo Research).
Total RNA subjected to ribosomal RNA depletion followed by library preparation using ScriptSeq Complete Gold Kit (Illumina).
Libraries were quantified using KAPA Library Quant qPCR kit (Roche) and subjected to 75bp paired-end high output sequencing run on Illumina's NextSeq500.

treatment_protocol: Tumor-bearing humanized mice were treated with anti-PD-1 or control Ig, harvested tumors at the end of the study.

tag: disease

value: Metastatic melanoma

tag: agent


title: Anti-PD-1 treated tumor from Hu-mice [T5]


title: AB63_AB1_Day6_RS

value: f

value: aCTLA-4 + aPDL1

value: RS

value: balb/c


title: AB64_AB1_Day6_NR


title: LF MɸTSP1 -/- 2

tag: diet


title: Anti-PD-1 treated tumor from Hu-mice [T4]


title: LF MɸTSP1 -/- 1


title: Anti-PD-1 treated tumor from Hu-mice [T3]


title: HF TSP1flox-2


title: E0231

tag: dataset group

tag: tissue

value: GCB


title: Anti-PD-1 treated tumor from Hu-mice [T2]


title: AB61_AB1_Day4_RS


title: Anti-PD-1 treated tumor from Hu-mice [T1]


title: LF TSP1flox-2


title: LF TSP1flox-1


title: AB59_AB1_Day2_RS


title: AB60_AB1_Day2_NR


title: E0227

tag: subtype (rmsg100)


title: Control tumor from Hu-mice [Tc2]

value: control Ig


title: CBP/p300 KO + Dox_rep3

data_processing:
After sequencing on the BGIseq-500 platform, the raw reads were filtered. Data filtering includes removing adaptor sequences, contamination and low-quality (phred quality < 20) reads from raw reads.
Sequenced reads were mapped to the GRCm38.p6 assembly of the mouse genome using ensembl release 95 gene annotation with STAR aligner version 2.6.0a
Reads were counted using htseq-count version 0.10.0 using these flags: -f bam -r pos -s no -m union -t exon -i gene_id
Genome_build: Mus_musculus.GRCm38.95
Supplementary_files_format_and_content: xlsx file with counts per gene per sample

source_name: CBP/p300 KO + Dox_rep3

growth_protocol: Mouse embryonic fibroblasts (MEFs) were maintained in DMEM medium containing 4.5 g glucose per liter and 10% FBS. CBP/p300 depletion was achieved by treat the Immortalized Crebbpfl/fl; Ep300fl/fl MEFs stably expressing Cre-ERT2 with  4-OHT as described previously (Weinert, B. T. et al. Cell 174, 231-244, 2018).

treatment_protocol: For doxycycline (Dox) treatment, MEFs were treated with 30 μg/ml doxycycline (Cat. D9891, Sigma) for 24 hours and without any other antibiotics.

tag: cell type

value: MEFs

value: CBP/p300 KO

value: Dox


title: Control tumor from Hu-mice [Tc1]


title: E0212


title: E0235


title: E0211


title: CBP/p300 KO + Dox_rep2

source_name: CBP/p300 KO + Dox_rep2


title: AB62_AB1_Day4_NR

value: AB1 tumour

tag: age

tag: gender

value: NR


title: AB58_AB1_Day0_NR

value: 8-10 weeks

tag: group

tag: strain


title: WPMY-1, RWPE1, 24h, M35

city: Krakow

first: Paweł

last: Wołkow

address: Kopernika 7c

department: Centre for Medical Genomics - OMICRON

country: Poland

institute: Jagiellonian University Medical College

data_processing:
Illumina Casava1.7 software used for basecalling.
Demultiplexed with Bcl2Fastq v.2.20.0.422 software.
The starter/stopper heterodimer sequence from reads removed with Cutadapt v.1.18, accordingly to library manufacturer instructions.
Reads were aligned to GRCh38 (ensembl version 95) with STAR v.2.7.0c, using a two-pass method.
Gene were enumerated using HT-Seq-Count v.0.11.2 (mode=intersection-nonempty) with ensemble version 95 for gene annotation.
Genome_build: GRCh38 (ensembl version 95)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: prostate/stroma fibroblast cells

growth_protocol: WPMY-1 cells were seeded in 6-well plates. RWPE-1 and RWPE-2 cells were seeded on 0.4µm pore size tissue-culture inserts formatted for 6-well plate. After 2 days of incubation, all cells were starved in FBS-free supplemented DMEM/F12 medium for 24h prior coculture.

extract_protocol:
ReliaPrep RNA MiniPrep System (Promega)
Sense mRNA-Seq Library prep Kit v2 (Lexogen)

treatment_protocol: Inserts with RWPE-1 or RWPE-2 cells were added to 6-well plates with WPMY-1 cells, for 6h or 24h. As a control, we used WPMY-1 culture without addition of insert.

value: fibroblasts/myofibroblast

tag: cell line

tag: coculture

tag: time

tag: replicate


title: WPMY-1, RWPE2, 24h, M36


title: E0210


title: CBP/p300 KO + Dox_rep1

source_name: CBP/p300 KO + Dox_rep1

tag: treatment


title: WT + Dox_rep3

source_name: WT + Dox_rep3

tag: genotype

value: WT


title: AB57_AB1_Day0_RS

tag: timepoint


title: WPMY-1, NONE, 24h, M34


title: AB55_AB1_Day6_RS


title: E0196

source_name: Training 2

value: Training 2


title: E0224

value: large B-cell lymphoma tissue


title: AB54_AB1_Day4_NR


title: WT + Dox_rep2

source_name: WT + Dox_rep2


title: WPMY-1, RWPE1, 24h, M32


title: AB53_AB1_Day4_RS


title: WT + Dox_rep1

source_name: WT + Dox_rep1


title: E0144


title: AB56_AB1_Day6_NR


title: WPMY-1, NONE, 24h, M31


title: E0230


title: AB52_AB1_Day2_NR


title: E0194

value: ABC


title: CBP/p300 KO + DMSO_rep2

source_name: CBP/p300 KO + DMSO_rep2

value: DMSO


title: WPMY-1, RWPE2, 24h, M24


title: E0141


title: AB51_AB1_Day2_RS

value: f

value: aCTLA-4 + aPDL1


title: CBP/p300 KO + DMSO_rep1

source_name: CBP/p300 KO + DMSO_rep1


title: WPMY-1, RWPE1, 24h, M23


title: E0142


title: WT + DMSO_rep3

source_name: WT + DMSO_rep3


title: WPMY-1, NONE, 24h, M22


title: CBP/p300 KO + DMSO_rep3

source_name: CBP/p300 KO + DMSO_rep3


title: E0137


title: WPMY-1, RWPE2, 24h, M21


title: E0134


title: WT + DMSO_rep1

source_name: WT + DMSO_rep1


title: WPMY-1, RWPE1, 24h, M20


title: AB47_AB1_Day6_RS

value: RS

value: balb/c


title: E0135

value: GCB


title: WPMY-1, NONE, 24h, M19


title: scSLAM-seq replicate 1

city: Berlin

first: Jan Philipp

last: Junker

address: Hannoversche Str. 28

department: BIMSB

country: Germany

institute: MDC

description: 10x Genomics transcriptome, v2. R2 contains biological information, R1 contains UMI and cell barcode.

data_processing:
zebrafish tomo-seq
demultiplexing with bcl2fastq v2.18.0.12
mapping with STAR v2.5.3a
split counts by section barcode
Genome_build: GRCz10 - release 90
Supplementary_files_format_and_content: csv file containing gene counts per section
xenopus tomo-seq
demultiplexing with bcl2fastq v2.18.0.12
mapping with STAR v2.5.3a
split counts by section barcode and translate gene identifier to gene names
Genome_build: X. tropicalis v9.1 genome assembly, X.laevis v9.2 genome assembly
Supplementary_files_format_and_content: csv file containing gene counts per section
scSLAM-seq zebrafish
demultiplexing using cellranger mkfastq v3.0.2
mapping and whitelisting of cells with cellranger v3.0.2
splitting labeled reads (>1 T-C mutation) from unlabeled into separate fastq files (submitted to this GEO entry)
mapping with STARsolo v2.7.0f_0328
single cell analysis in seurat v3.1.2
Genome_build: GRCz11
Supplementary_files_format_and_content: _barcodes.tsv list of barcodes, _genes.tsv list of genes, and _matrix.tsv count matrix

organism: Danio rerio

source_name: shield stage embryos (6 hpf)

extract_protocol: none provided by the submitter

value: AB wildtype

value: 4sUTP injected

tag: extraction protocol

value: Methanol fixed single-cell suspension, 10x Genomics transcriptome.


title: AB48_AB1_Day6_NR

source_name: AB1 tumour

value: AB1 tumour


title: E0132


title: AB46_AB1_Day4_NR

value: NR


title: E0133


title: AB50_AB1_Day0_NR

value: 8-10 weeks


title: WPMY-1, RWPE2, 6h, M15

value: fibroblasts/myofibroblast


title: AB44_AB1_Day2_NR


title: AB49_AB1_Day0_RS


title: WPMY-1, RWPE1, 6h, M14


title: WPMY-1, NONE, 6h, M13


title: WT + DMSO_rep2

source_name: WT + DMSO_rep2

value: MEFs

value: WT


title: WPMY-1, RWPE2, 6h, M09


title: E0128

value: Training 2

value: large B-cell lymphoma tissue


title: AB43_AB1_Day2_RS


title: AB42_AB1_Day0_NR


title: LF TSP1flox-3

source_name: Liver

tag: diet

value: LF

value: 10 month old


title: WPMY-1, NONE, 6h, M07


title: WPMY-1, RWPE1, 6h, M08


title: AB45_AB1_Day4_RS

value: f

value: aCTLA-4 + aPDL1


title: AB39_AB1_Day6_RS

value: RS

value: balb/c


title: AB38_AB1_Day4_NR


title: AB40_AB1_Day6_NR


title: AB41_AB1_Day0_RS


title: E0130

tag: dataset group

value: GCB


title: E0111

tag: tissue


title: AB37_AB1_Day4_RS


title: WPMY-1, RWPE1, 6h, M05


title: WPMY-1, RWPE2, 6h, M03


title: E0124

tag: subtype (rmsg100)


title: WPMY-1, NONE, 6h, M04

tag: cell type


title: AB36_AB1_Day2_NR

tag: age


title: AB35_AB1_Day2_RS

tag: gender


title: WPMY-1, RWPE1, 6h, M02


title: E0061


title: WPMY-1, RWPE2, 6h, M06


title: WPMY-1, NONE, 6h, M01


title: E0110

value: ABC


title: DEV21


title: AB34_AB1_Day0_NR

tag: group


title: DEV22


title: AB33_AB1_Day0_RS

tag: strain


title: DEV9


title: E0071


title: AB32_AB1_Day6_NR


title: DEV12


title: DEV8


title: ATF5+PROX1-1

city: Pittsburgh

description: Ind TF

data_processing:
Sequencing was performed on Illumina NextSeq500 for a single read 75bp run. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program. A raw FASTQ quality check was performed using FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Reads were then mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 (Langmead and Salzberg, 2012) and the gene expression level was estimated using RSEM v1.2.15 (Li and Dewey, 2011).
EdgeR’s (Robinson et al., 2010) TMM (trimmed mean of M-values) algorithm was used to normalize the gene expression data.
Reads were then mapped to the hg19 genome set using Bowtie2 and Tophat (Trapnell et al., 2009).
The resulting BAM file allowed for collection of information on the alignment via PicardTools (http://broadinstitute.github.io/picard/) CollectRNASeqMetrics program. A Genebody analysis was performed using the ngsplot (Shen et al., 2014) toolkit.
Genome_build: hg19
Supplementary_files_format_and_content: For bulk RNAseq, a comma separated file with abundance measurement matirx in CPM. For ATACseq, a comma separated file with peak calling for each sample and differential peak analysis for each sample comparison.

source_name: ATF5+PROX1 liver organoid

extract_protocol: Tissues were harvested and lysed by adding 500μL Trizol (Life Technologies) directly to the tissue culture well and storing at -80°C.  For extraction, lysate was thawed on ice, 100μL chloroform was added, vortexed for 30 seconds, and centrifuged at 12,000g for 15 minutes at 4°C.  After centrifugation the aqueous phase was transferred to a QIAGEN gDNA eliminator column and centrifuged at 10,000g for 1 minute at room temperature. The flow-through was mixed with an equal volume of 70% EtOH and transferred to an RNEasy mini spin column.  The manufacturer protocol for the RNEasy Plus Mini Kit (QIAGEN) was followed for the rest of the extraction procedure. Libraries for RNA-Seq were prepared with KAPA Hyper Stranded RNA-Seq Kit. The workflow consists of mRNA enrichment, cDNA generation, and end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane.

value: ATF5+PROX1 liver organoid

tag: condition

value: GATA6 induced, PROX1 and ATF5 transduced

tag: day

value: Day 17

tag: sequenced molecule

value: bulk RNA


title: DEV15


title: PROX1-2

description: Ind TF

source_name: PROX1 liver organoid

value: PROX1 liver organoid

value: GATA6 induced, PROX1 transduced


title: DEV17


title: AB31_AB1_Day6_RS

value: AB1 tumour

value: 8-10 weeks


title: DesLO-2

description: Ind TF

source_name: Designer liver organoid

value: Designer liver organoid

value: GATA6 induced, ATF5, PROX1, CYP3A4 gRNA and dCas9 transduced


title: AB30_AB1_Day4_NR

value: NR


title: DesLO-1

description: Ind TF


title: ATF5+PROX1-2

description: Ind TF


title: AB28_AB1_Day2_NR

value: f


title: 3735_R7

city: TOULOUSE

first: gilles

last: FOUCRAS

state: State/Province/Region

address: 23 Chemin des Capelles

institute: ENVT INRA

data_processing:
Read quality was assessed with FastQC software. Reads were aligned in comparison to the bovine reference genome (UMD3.1.87) with STAR software
Count table was generated with Cufflinks/RSEM
Identification of differentially expressed genes (DEGs) was performed with DESeq2 package within the R environment
Genome_build: Bos_taurus.UMD3.1.87
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Blood

extract_protocol:
Whole blood samples were lysed using the buffer provided in the kit and stored at -80°C. Total RNA was extracted on silica columns with Nucleospin RNA blood kit (Macherey-Nagel).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Holstein

value: Blood

value: 15 month

tag: immunization protocol

value: Intramuscular immunization with heat-killed E.coli P4 and boost with E.coli P4 supernate by intrammamary route

tag: time

value: 7 days after boost

tag: immunization routes

value: Intramuscular / Intramammary


title: DEV2

value: Training 2

value: large B-cell lymphoma tissue

value: ABC


title: AB27_AB1_Day2_RS

tag: treatment

value: aCTLA-4 + aPDL1

value: RS

value: balb/c

tag: timepoint


title: DEV1

tag: dataset group

value: GCB


title: RA98-0727

source_name: Training 1

value: Training 1

tag: tissue


title: RA99-1655

tag: subtype (rmsg100)


title: RA98-0715


title: R09-0660


title: No tdxn ctl-1

first: Mo

last: Ebrahimkhani

institute: University of Pittsburgh

description: Ind TF

source_name: Fetal liver organoid

value: Fetal liver organoid

value: GATA6 induced, no transduction

value: Day 17

value: bulk RNA


title: AB26_AB1_Day0_NR

value: AB1 tumour

value: 8-10 weeks

value: f

value: NR


title: No tdxn ctl-2

description: Ind TF


title: AB29_AB1_Day4_RS


title: R07-1114


title: mmB DesLO D17-1

description: mmB Timelapse

value: Designer liver organoid

value: GATA6 induced, ATF5, PROX1, CYP3A4 gRNA and dCas9 transduced


title: 3729_C12

value: Holstein

value: Blood

value: 15 month

value: Adjuvant

value: 12 hours post infection

value: Intramuscular (x2)


title: AB24_AB1_Day6_NR

value: aCTLA-4 + aPDL1

value: balb/c


title: NP16980

value: Training 1

value: large B-cell lymphoma tissue

value: GCB


title: NP16960


title: 3732_I0

value: Intramuscular immunization with heat-killed E.coli P4 and boost with same vaccine

value: 0 days after first immunization


title: 3732_C40

value: 40 hours post infection


title: mmB FeLO D17-2

description: mmB Timelapse

value: Fetal liver organoid

value: GATA6 induced, no transduction

value: Day 17

value: bulk RNA


title: AB25_AB1_Day0_RS

value: AB1 tumour

value: 8-10 weeks

value: f

value: RS


title: AB23_AB1_Day6_RS


title: 3725_I0

value: Holstein

value: Blood

value: 15 month

value: Intramuscular immunization with heat-killed E.coli P4 and boost with E.coli P4 supernate by intrammamary route

value: Intramuscular / Intramammary


title: mmB DesLO D17-2

description: mmB Timelapse

value: Designer liver organoid

value: GATA6 induced, ATF5, PROX1, CYP3A4 gRNA and dCas9 transduced


title: mmB FeLO D17-1

description: mmB Timelapse


title: AB22_AB1_Day4_NR

value: aCTLA-4 + aPDL1

value: NR

value: balb/c


title: AB21_AB1_Day4_RS


title: 0297_C12

value: Adjuvant

value: 12 hours post infection

value: Intramuscular (x2)


title: NP14766

value: Training 1

value: large B-cell lymphoma tissue

value: ABC


title: NP15272


title: mmB D10-2

description: mmB Timelapse

value: Fetal liver organoid

value: GATA6 induced, no transduction

value: Day 10

value: bulk RNA


title: 3734_I7

value: Holstein

value: Blood

value: 15 month

value: Intramuscular immunization with heat-killed E.coli P4 and boost with E.coli P4 supernate by intrammamary route

value: 7 days after first immunization


title: 0293_C4

value: 0 hours post infection


title: mmB D10-1

description: mmB Timelapse


title: AB19_AB1_Day2_RS

value: AB1 tumour

value: 8-10 weeks

value: f

value: aCTLA-4 + aPDL1

value: RS

value: balb/c


title: NP16361

value: Training 1

value: large B-cell lymphoma tissue

value: ABC


title: mmB D5-2

description: mmB Timelapse

source_name: mesendoderm

value: mesendoderm

value: GATA6 induced, no transduction

value: Day 5


title: AB17_AB1_Day0_RS


title: AB20_AB1_Day2_NR

value: NR


title: WPMY-1, RWPE2, 24h, M33

source_name: prostate/stroma fibroblast cells

tag: cell type

value: fibroblasts/myofibroblast

tag: cell line

tag: coculture

tag: replicate


title: ILS32144

value: GCB


title: 0289_I0

value: Holstein

value: Blood

tag: age

value: 15 month

value: Intramuscular immunization with heat-killed E.coli P4 and boost with same vaccine

value: 0 days after first immunization

value: Intramuscular (x2)


title: mmB D5-1

description: mmB Timelapse

tag: condition

value: bulk RNA


title: 0289_C40

value: 40 hours post infection


title: mmB D0-1

description: mmB Timelapse

source_name: hiPSC

value: hiPSC

value: non induced, puripotent

tag: day

value: Day 0


title: E0356

value: Training 1

value: large B-cell lymphoma tissue

value: ABC


title: 0293_C40

value: Adjuvant


title: 267

city: Adelaide

first: Simon

last: Conn

state: South Australia

address: Sturt Road, Bedford Park

department: College of Medicine and Public Health

institute: Flinders University

description: rRNA depleted, RNase R treated, total RNA

data_processing:
High-throughput sequencing was performed using Illumina NextSeq
Raw reads were trimmed off adapter and low quality reads in the sequencer and generated FASTQ files
The FASTQ files were mapped aganist the human refrence genome (hg19) using STAR spliced alignment algorith (versions 2.7.0)
Aligned with parameters and –chimericSegmentMin 20, --quantMode GeneCounts
The resulting STAR produced chemiric junction file for each sample processed by CIRCexplorer2 (version 2.3.3) to estimate circRNA abundance
Genome_build: hg19
Supplementary_files_format_and_content: circRNA abundance

source_name: brain tumour

growth_protocol: Tumour and healthy brain were harvested by neurosurgeon during excision of tumour from consenting patient

extract_protocol:
RNA was extracted using TriZOL and Direct-zol RNA extration columns (Zymo Research). RNA (ug) was digested with Rnase R (2U/ug RNA; Epicentre) for 30mins at 37oC, then purified by Rneasy MinElute Cleanup kit (Qiagen).
Libraries were constructed with RNase R-treated RNA using the TruSeq Stranded Total RNA library preparation kit (with Ribo-zero rRNA depletion module).

value: brain

tag: disease state

value: glioma


title: 0281_R7

tag: breed

value: Holstein

value: 7 days after boost


title: AB15_AB1_Day6_RS

value: AB1 tumour

value: 8-10 weeks

tag: gender

value: f

value: aCTLA-4 + aPDL1

tag: group

value: RS

tag: strain

value: balb/c


title: E0278

value: GCB


title: E0345


title: 0289_C4

value: Blood

value: 15 month

tag: immunization protocol

value: Intramuscular immunization with heat-killed E.coli P4 and boost with same vaccine

tag: time

value: 0 hours post infection

tag: immunization routes

value: Intramuscular (x2)


title: E0349

tag: dataset group

value: Training 1

tag: tissue

value: large B-cell lymphoma tissue


title: E0324

tag: subtype (rmsg100)

value: ABC


title: AB18_AB1_Day0_NR

tag: treatment

value: NR

tag: timepoint


title: E0229


title: mmB D0-2

address: A809B Scaife Hall, 3550 Terrace Street

description: mmB Timelapse

value: hiPSC

value: non induced, puripotent

value: Day 0

tag: sequenced molecule

value: bulk RNA


title: AB14_AB1_Day4_NR

value: AB1 tumour

tag: age

value: 8-10 weeks

value: f

value: aCTLA-4 + aPDL1


title: 0281_C40

value: Holstein

value: Blood

value: 40 hours post infection


title: AB13_AB1_Day4_RS

value: RS

value: balb/c


title: E0326

value: Training 1

value: GCB


title: 61

value: brain

value: glioma


title: 169


title: 0275_R7

value: 15 month

value: Adjuvant

value: 7 days after boost

value: Intramuscular (x2)


title: 0286_C40

value: Intramuscular immunization with heat-killed E.coli P4 and boost with same vaccine


title: AB16_AB1_Day6_NR

value: AB1 tumour

value: 8-10 weeks

value: NR


title: AB12_AB1_Day2_NR

value: f

value: aCTLA-4 + aPDL1


title: AB10_AB1_Day0_NR


title: 0275_C40

value: Holstein

value: Blood

value: 40 hours post infection


title: 203


title: AB11_AB1_Day2_RS

value: RS

value: balb/c


title: 0274_C12

value: 12 hours post infection


title: AB08_AB1_Day6_NR


title: 172

value: brain

value: glioma


title: E0228

value: Training 1

value: large B-cell lymphoma tissue

value: ABC


title: E0222

value: GCB


title: 214


title: 154


title: 0279_I0

value: 15 month

value: Intramuscular immunization with heat-killed E.coli P4 and boost with same vaccine

value: 0 days after first immunization

value: Intramuscular (x2)


title: 170


title: AB07_AB1_Day6_RS

value: AB1 tumour

value: 8-10 weeks

value: f

value: aCTLA-4 + aPDL1


title: AB09_AB1_Day0_RS

value: RS


title: 213


title: 3732_I7

value: Holstein

value: Blood

value: 7 days after first immunization


title: 3727_R7

value: 7 days after boost


title: AB06_AB1_Day4_NR

value: NR

value: balb/c


title: 3727_I7


title: E0223

value: Training 1

value: large B-cell lymphoma tissue


title: 150

value: brain

value: glioma


title: E0146

value: GCB


title: 3727_C40

value: 15 month

value: Intramuscular immunization with heat-killed E.coli P4 and boost with same vaccine

value: 40 hours post infection

value: Intramuscular (x2)


title: E0145

value: ABC


title: E0221


title: E0220


title: 217


title: AB05_AB1_Day4_RS

value: AB1 tumour

value: 8-10 weeks

value: f

value: aCTLA-4 + aPDL1

value: RS


title: 190


title: 207


title: E0129


title: 3725_I7

value: Holstein

value: Blood

value: Intramuscular immunization with heat-killed E.coli P4 and boost with E.coli P4 supernate by intrammamary route

value: 7 days after first immunization

value: Intramuscular / Intramammary


title: 3727_C12

value: 12 hours post infection


title: AB03_AB1_Day2_RS

value: balb/c


title: AB04_AB1_Day2_NR

value: NR


title: 160

value: brain

value: glioma


title: AB02_AB1_Day0_NR


title: 158


title: E0126

value: Training 1

value: large B-cell lymphoma tissue


title: AB01_AB1_Day0_RS

value: AB1 tumour


title: E0044

value: GCB


title: 0292_C4

value: 15 month

value: 0 hours post infection


title: AS-267279-LR-39248

first: Anna

last: Dolnik

address: Augustenburger Platz 1

department: Campus Virchow-Klinikum (CVK)

institute: Charité Universitätsmedizin Berlin

description: mRNA single end RNAseq of Myc-transgenic lymphoma cells transduced with empty vector MSCV-GFP

data_processing:
base-calling was performed according Illumina recommendations bcl2fastq-1.8.4.
50 bp single-end reads  (Illumina) were aligned to reference genome mm10 and gtf.-transcriptome annotation release M7 (GENCODE) using STAR two-pass mode ( star 2.4.2a).
GENCODE M7 gtf.-file was used for quantification, performed by STAR (star 2.4.2a) , followed by normalisation, transformation and differential gene expression analysis in DEseq2 -1.12.4.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

source_name: B220 sorted Myc-transgenic suv39h1-/ lymphoma cells transduced with empty vector MSCV-GFP

extract_protocol:
RNA extraction was performed using Qiagen RNeasy+ kit (Qiagen)  according manufacturer instructions.
Library was generated using SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara) followed by Nextera XT Kit (Illumina).

value: Myc-transgenic suv39h1-/- lymphoma cells transduced with empty vector MSCV-GFP

tag: overexpression

tag: transduced with

value: control (empty vector MSCV-GFP)


title: E0023


title: 3725_C4

value: Holstein

value: Blood


title: 0293_R7

value: Adjuvant

value: 7 days after boost

value: Intramuscular (x2)


title: 0297_C4


title: 179

source_name: Healthy brain tissue

tag: disease state

value: healthy


title: 0292_C40

tag: breed

value: Intramuscular immunization with heat-killed E.coli P4 and boost with E.coli P4 supernate by intrammamary route

value: 40 hours post infection

value: Intramuscular / Intramammary


title: AS-267277-LR-39248

description: mRNA single end RNAseq of Myc-transgenic lymphoma cells transduced with Caspase Recruitment Domain Family Member 11 with mutation in L244P (CARD11-L244P) in MSCV-GFP

source_name: B220 sorted Myc-transgenic suv39h1-/ lymphoma cells transduced with CARD11-L244P in MSCV-GFP

value: overexpression of mutated CARD11


title: AS-267278-LR-39248


title: 170_MC_NOR

value: brain


title: AS-267268-LR-39248


title: 0289_I7

value: Intramuscular immunization with heat-killed E.coli P4 and boost with same vaccine

value: 7 days after first immunization


title: 0289_R7

value: 15 month


title: 158_MC_NOR


title: AS-229637-LR-34597


title: 0286_R7


title: DEV5

value: Training 1

value: large B-cell lymphoma tissue

value: ABC


title: DEV7

value: GCB


title: DEV3


title: DEV4


title: DEV19


title: 267_MC_NOR


title: PROX1-1

description: Ind TF

value: PROX1 liver organoid

tag: condition

value: GATA6 induced, PROX1 transduced

tag: day

value: Day 17

value: bulk RNA


title: AS-229636-LR-34597

value: Myc-transgenic suv39h1-/- lymphoma cells transduced with empty vector MSCV-GFP


title: 0286_I0

value: Holstein

value: Blood

value: 0 days after first immunization

value: Intramuscular (x2)


title: nonALI2

city: Utrecht

first: Jelte

last: van der Vaart

address: Universiteitsweg 100

department: Center for Molecular Medicine

country: Netherlands

institute: University Medical Center Utrecht

description:
demultiplexed.48.CS2C8U6
Bulk RNA sequencing of untreated human non-air-liquid interface culture from lung bud tip organoids

data_processing:
Paired end reads were aligned to the transcriptome using bwa. Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the human genome release hg38. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus.
Genome_build: hg38
Supplementary_files_format_and_content: raw counts; UMI deduplicated, annotation pooled, normalized abundance counts

growth_protocol: Airway organoids were passaged by mechanical disruption at 1:2 to 1:4 ratios after 10–14 days of culture. Airway organoid medium (Sachs et al., 2019)  was changed every 4 days. To obtain differentiated organoid-derived cultures, organoids were dissociated into single cells using TrypLE express (Gibco; #12604013). Cells were seeded on Transwell membranes (Corning) coated with rat tail collagen type I (Fisher Scientific). Single cells were seeded in AO growth medium : complete base medium (CBM; Stemcell Pneumacult-ALI; #05001) at a 1:1 ratio. After 2-4 days, confluent monolayers were cultured at air‐liquid interphase in CBM. Medium was changed every 5 days. After 8 weeks of differentiation, cultures were used for infection experiments.  Fetal lung bud tip organoids were passaged by mechanical disruption at 1:2 to 1:4 ratios after 10–14 days of culture. Fetal lung (FL) medium (Nikolic et al., 2017)  was changed every 4 days. To obtain differentiated organoid-derived cultures, 105 donor-specific fetal lung mesenchymal cells were seeded in 12-well plates in AdDF+++ containing 10% FCS. The next day, organoids were dissociated into small clumps using TrypLE express. Cells were seeded on Transwell membranes (Corning‐3460). Clumps were seeded in FL : BEpiCM (bronchial epithelial cell growth medium; Sciencell; Cat. No. 3211) at a 1:1 ratio. BEpiCM was made by mixing basal medium (Sciencell; Cat. No. 3211-b) and DMEM at a 1:1 ratio and adding bronchial epithelial cell growth supplement (BEpiCGS, Sciencell; Cat. No. 3262), penicillin (100 IU/mL), streptomycin (100 IU/mL) and 0.001 μM retinoic acid. ROCK inhibitor was added for the first 5 days to prevent apoptosis (Y-27632; Sigma; Y0503; 10µM). After 4-7 days, confluent monolayers were cultured at air‐liquid interphase in BEpiCM. Eighty percent of the medium was changed every 4-5 days. After 14 days of differentiation, cultures were used for infection experiments.

extract_protocol:
Total RNA was extracted using the standard TRIzol (Invitrogen) protocol and used for library preparation and sequencing.
mRNA was processed as described previously, following an adapted version of the single-cell mRNA seq protocol of CEL-Seq (Hashimshony et al., 2016; Simmini et al., 2014). In brief, samples were barcoded with CEL-seq primers during a reverse transcription and pooled after second strand synthesis. The resulting cDNA was amplified with an overnight In vitro transcription reaction. From this amplified RNA, sequencing libraries were prepared with Illumina Truseq small RNA primers.

treatment_protocol: 2D differentiated cultures were washed twice with 200 ul AdDF+++ before inoculation from the apical side at a MOI of 0.01 or 0.1 (as indicated) in 200 μL AdDF+++ per well. Next, cultures were incubated at 37°C 5% CO2 for 2 hours before washing 3 times in 200 μL AdDF+++.

tag: cell type

value: Differentiating lung bud tip

value: Mock

tag: genotype

value: Wildtype


title: 0282_C4

value: 15 month

tag: immunization protocol

value: Adjuvant

tag: time

value: 0 hours post infection


title: AS-229635-LR-34597

value: overexpression of mutated CARD11


title: AS-229634-LR-34598

value: control (empty vector MSCV-GFP)


title: DEV16

data_processing: Raw microarray data was pre-processed by an internal software tool developed at Roche Molecular Systems Inc., Pleasanton, CA, USA.  Specifically, a special DQN signal used the quantities of beta distribution with p = 1.2 and q = 3 for normalization

tag: dataset group

value: Training 1

value: large B-cell lymphoma tissue

value: GCB


title: DEV18

tag: tissue


title: fetal3D2

description:
demultiplexed.44.CS2C8U6
Bulk RNA sequencing of untreated human fetal lung bud tip organoid culture

value: Lung bud tip


title: nonALI1

description:
demultiplexed.46.CS2C8U6
Bulk RNA sequencing of untreated human non-air-liquid interface culture from lung bud tip organoids


title: 0281_C4

value: Intramuscular immunization with heat-killed E.coli P4 and boost with same vaccine

tag: immunization routes


title: DEV14

tag: subtype (rmsg100)


title: AS-229633-LR-34597

value: Myc-transgenic suv39h1-/- lymphoma cells transduced with empty vector MSCV-GFP


title: AS-154069-LR-22668


title: 0279_R7

value: Holstein

value: Blood

value: 7 days after boost


title: AS-153974-LR-23137

description: mRNA single end RNAseq of Myc-transgenic lymphoma cells transduced with CD79BY196H molecule (CD79B) in MSCV-GFP

source_name: B220 sorted Myc-transgenic lymphoma cells transduced with CD79BY196H in MSCV-GFP

value: Myc upregulated lymphoma

value: overexpression of CD79BY196H


title: SmallAirway_2_SARS-CoV-2

description:
demultiplexed.40.CS2C8U6
Bulk RNA sequencing of human small airway 2D culture infected with SARS-CoV-2 for 72 hours

value: Small airway

tag: treatment

value: Wildtype


title: 0275_I7

value: 15 month

value: Adjuvant

value: 7 days after first immunization

value: Intramuscular (x2)


title: SmallAirway_2_mock

description:
demultiplexed.36.CS2C8U6
Bulk RNA sequencing of untreated human small airway 2D culture

source_name: untreated human small airway 2D culture

value: Mock


title: 0275_C12

value: 12 hours post infection


title: SmallAirway_1_SARS-CoV-2

description:
demultiplexed.38.CS2C8U6
Bulk RNA sequencing of human small airway 2D culture infected with SARS-CoV-2 for 72 hours


title: AS-153972-LR-23136


title: DEV11

value: Training 1

value: large B-cell lymphoma tissue

value: ABC


title: 6UN4FA93

value: GCB


title: AS-153970-LR-23136

description: mRNA single end RNAseq of Myc-transgenic lymphoma cells transduced with Programmed Cell Death 1 Ligand 1 (PD-L1) in MSCV-GFP

source_name: B220 sorted Myc-transgenic lymphoma cells transduced with  PD-L1 in MSCV-GFP

value: overexpression of PD-L1


title: DEV13


title: Bronchioalveo_2_SARS-CoV-2_2

description:
demultiplexed.24.CS2C8U6
Bulk RNA sequencing of human bronchioalveolar 2D culture infected with SARS-CoV-2 for 72 hours

value: Bronchioalveolar


title: 3735_I7

value: Holstein

value: Blood

value: Intramuscular immunization with heat-killed E.coli P4 and boost with E.coli P4 supernate by intrammamary route

value: Intramuscular / Intramammary


title: AS-153969-LR-23136

value: Myc upregulated lymphoma


title: 0274_C4

value: 15 month

value: 0 hours post infection


title: Bronchioalveo_2_SARS-CoV-2_1

description:
demultiplexed.22.CS2C8U6
Bulk RNA sequencing of human bronchioalveolar 2D culture infected with SARS-CoV-2 for 72 hours

value: Wildtype


title: 3734_R7

value: 7 days after boost


title: 0281_C12

value: Intramuscular immunization with heat-killed E.coli P4 and boost with same vaccine

value: Intramuscular (x2)


title: fetal3D1

description:
demultiplexed.42.CS2C8U6
Bulk RNA sequencing of untreated human fetal lung bud tip organoid culture

value: Lung bud tip

value: Mock


title: AS-153968-LR-23135


title: SmallAirway_1_mock

description:
demultiplexed.34.CS2C8U6
Bulk RNA sequencing of untreated human small airway 2D culture

value: Small airway


title: AS-153973-LR-23137

value: overexpression of CD79BY196H


title: Bronchioalveo_2_mock_1

description:
demultiplexed.18.CS2C8U6
Bulk RNA sequencing of untreated human bronchioalveolar 2D culture


title: 3734_I0

value: 0 days after first immunization


title: Bronchioalveo_2_mock_2

description:
demultiplexed.20.CS2C8U6
Bulk RNA sequencing of untreated human bronchioalveolar 2D culture

value: Bronchioalveolar


title: AS-153967-LR-23135

description: mRNA single end RNAseq of Myc-transgenic lymphoma cells transduced with  MYD88-L265P in MSCV-GFP

source_name: B220 sorted Myc-transgenic lymphoma cells transduced with  MYD88-L265P in MSCV-GFP

value: overexpression of mutated MYD88


title: Bronchioalveo_1_SARS-CoV-2_2

description:
demultiplexed.8.CS2C8U6
Bulk RNA sequencing of human bronchioalveolar 2D culture infected with SARS-CoV-2 for 72 hours


title: 3729_R7

value: Holstein

value: Blood

value: Adjuvant


title: AS-153966-LR-23135

value: Myc upregulated lymphoma


title: HeLa:MondoA-KO_DMSO rep2

city: Salt Lake City

first: Donald

middle: E

last: Ayer

state: UT

address: 2000 Circle of Hope

institute: University of Utah

data_processing:
STAR 2.6 was used to align the reads to GRCh38/hg38
featureCounts was used to obtain read counts for each gene
FastQC and MultiQC were used to assess sequencing and alignment quality
Genome_build: hg38
Supplementary_files_format_and_content: counts

growth_protocol: Cells were grown in standard 6-well dishes in DMEM with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was extracted from cells using a Zymo Research Quick-RNA MiniPrep kit (cat #11-330T) according to the manufacturer's guidelines.
1 µg total RNA was used to generate libraries using a Kapa Stranded mRNA-Seq kit with mRNA capture beads (cat # KK8421) according to the manufacturer's guidelines.

treatment_protocol: Cells were treated with DMSO or 100nM RocA for four hours prior to harvesting.

tag: cell line

value: HeLa

value: MondoA-KO

value: DMSO


title: HeLa:MondoA-KO_RocA rep1

value: RocA


title: HeLa:MondoA-KO_RocA rep2


title: 3729_I0

tag: age

value: 15 month


title: HeLa:MondoA-KO_DMSO rep1


title: AS-153965-LR-23135

tag: overexpression


title: Bronchioalveo_1_mock_2

description:
demultiplexed.4.CS2C8U6
Bulk RNA sequencing of untreated human bronchioalveolar 2D culture

value: Wildtype


title: 3725_R7

value: Intramuscular immunization with heat-killed E.coli P4 and boost with E.coli P4 supernate by intrammamary route

value: 7 days after boost

value: Intramuscular / Intramammary


title: HeLa_RocA rep1

source_name: HeLa

value: WT


title: 0297_I0

value: 0 days after first immunization

value: Intramuscular (x2)


title: DEV10

extract_protocol: High Pure formalin-fixed, paraffin-embedded tissue (FFPET) RNA Isolation Kit (Roche Molecular Systems, Pleasanton, California)

value: Training 1

value: large B-cell lymphoma tissue

value: ABC


title: AS-153964-LR-23134

value: overexpression of mutated MYD88

tag: transduced with


title: 0297_C40

value: Holstein

value: Blood

value: Adjuvant

value: 40 hours post infection


title: Bronchioalveo_1_mock_1

description:
demultiplexed.2.CS2C8U6
Bulk RNA sequencing of untreated human bronchioalveolar 2D culture

value: Bronchioalveolar

value: Mock


title: AS-153963-LR-23134

value: Myc upregulated lymphoma


title: SRRM4-3

description: rRNA depleted, RNase R treated, total RNA

data_processing:
High-throughput sequencing was performed using Illumina NextSeq
Raw reads were trimmed off adapter and low quality reads in the sequencer and generated FASTQ files
The FASTQ files were mapped aganist the human refrence genome (hg19) using STAR spliced alignment algorith (versions 2.7.0)
Aligned with parameters and –chimericSegmentMin 20, --quantMode GeneCounts
The resulting STAR prduced chemiric junction file for each sample processed by CIRCexplorer2 (version 2.3.3) to estimate circRNA abundance
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include gene counts for each sample
Supplementary_files_format_and_content: Tab-delimited text files include CIRCexplorer2 produced number of Junction reads for each sample

source_name: Cell culture

growth_protocol: Human embryonic kidney cells (HEK293) were grown in DMEM with 10% FBS at 37oC

treatment_protocol: Cells were transfected with emtpy vector (pcDNA3.1::FLAG, Conn et al., 2015, Cell) or SRRM4 cloned into the same vector. SRRM4 was PCR amplified from sequence verified clone (DNASU, HsCD00295084) using EcoRI/EcoRV sites. Transfection was achieved using Lipofectamine 2000, with RNA harvested 48 hrs posot-transfection.

value: HEK293, human embryonic kidney

tag: passages


title: HeLa_DMSO rep2

value: HeLa

value: DMSO


title: AS-153962-LR-23134


title: HeLa_DMSO rep1

value: WT


title: Bronchioalveo_1_SARS-CoV-2_1

description:
demultiplexed.6.CS2C8U6
Bulk RNA sequencing of human bronchioalveolar 2D culture infected with SARS-CoV-2 for 72 hours

value: Wildtype


title: 0293_I7

tag: breed

value: 15 month

value: 7 days after first immunization

value: Intramuscular (x2)


title: SRRM4-2


title: 0293_I0

value: 0 days after first immunization


title: SRRM4-1


title: EV3


title: AS-153959-LR-22999

description: mRNA single end RNAseq of Myc-transgenic lymphoma cells transduced with NF-kappa-B Inhibitor Zeta (NFKBIZ) in MSCV-GFP

source_name: B220 sorted Myc-transgenic lymphoma cells transduced with  NFKBIZ in MSCV-GFP

value: overexpression of NFKBIZ

value: NFKBIZ


title: 4797-010

city: Boston

first: Adam

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

description: Gene expression from single bronchial epithelial cells from subject in imaging cluster 1.

data_processing:
FASTQ files were aligned to the human genome (GRCh37.75) using STAR v2.5.2b in a two-pass manner.
Quality control was performed using FastQC v0.11.3 and RSeQC v2.6.4 and summarized using MultiQC v0.9.
Posterior mean counts were generated using RSEM v1.3.0.
BAM files were processed using Picard v2.8.0 to add read group information.
Genome_build: GRCh37.75

source_name: Bronchial epithelial cells

extract_protocol:
Total RNA was isolated using the QIAGEN miRNeasy Mini kit following the manufacturer's instructions.
Sequencing libraries were prepared from total RNA samples using Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold following the manufacturer's instructions.

tag: Sex

value: Male

tag: pack years

tag: imaging cluster


title: 0292_C12

source_name: Blood

value: Holstein

value: Blood

value: Intramuscular immunization with heat-killed E.coli P4 and boost with E.coli P4 supernate by intrammamary route

value: 12 hours post infection

value: Intramuscular / Intramammary


title: 4797-011

description: Gene expression from single bronchial epithelial cells from subject in imaging cluster 3.

value: Female


title: 0289_C12

value: Intramuscular immunization with heat-killed E.coli P4 and boost with same vaccine


title: 4797-009


title: AS-153958-LR-22999

value: Myc upregulated lymphoma


title: EV2

value: HEK293, human embryonic kidney


title: 4797-008


title: 0286_C4

value: 0 hours post infection


title: EV1


title: 4797-007