title: Blood training 38


title: Blood validation 19

status: Public on Jun 03 2020

type: SRA

city: Changchun

first: Yang

last: Han

address: Xi'an road 5333, Jilin University Heping Campus, Changchun, China

country: China

institute: Jilin University

library_source: genomic

data_processing:
Fastq files were subjected to adaptor trimming by TrimGalore
FastQC were subsequently applied for quality checking of Fastq files.
To estimate DNAm levels for each CpG based on BBA-seq data we used the Bismark tool
Genome_build: hg19
Supplementary_files_format_and_content: Text files list the beta values for all the targeted CpGs

molecule: genomic DNA

organism: Homo sapiens

source_name: Peripheral blood

extract_protocol:
Genomic DNA was isolated from peripheral blood with the QIAamp DNA Mini Kit (Qiagen),or from buccal swab with NucleoSpin Tissue Kit (Macherey-Nagel). Then was bisulfite converted by the EZ DNA Methylation Kit (Zymo)
10 pM DNA library was diluted with 15% PhiX spike-in control and eventually subjected to 250 bp pair-end sequencing on a MiSeq lane (Illunima, CA, USA) using Miseq reagent V2 Nano kit (Illumina).
Library_Strategy: BBA-seq

tag: age

tag: gender

value: F

tag: disease state

value: Healthy

tag: tissue

value: Peripheral blood


title: Blood training 34

value: M


title: Blood validation 7


title: Blood training 33


title: Blood training 29


title: Blood training 30


title: Blood validation 5


title: Blood training 25


title: Blood training 28


title: Blood training 32


title: Round Spermatids-H3K9me3

city: Lucknow

first: Singh

last: Rajender

state: Uttar Pradesh

address: Lucknow

country: India

institute: Central Drug Research Institute

data_processing:
The ChIP-seq reads obtained from the sequencer were demultiplexed using bcl2fastq tool. Quality and adapter trimming was done using FastQC software.
The processed data/reads were then aligned with rat genomic assembly rn6 by using Bowtie 1.2 (parameters -m 1 -best).
Peak calling was done using MACS1.4 with p-value threshold of 0.001 and 10% of FDR cut-off.
Genome_build: Rn6
Supplementary_files_format_and_content: bed files

organism: Rattus norvegicus

source_name: testis

extract_protocol:
Round spermatid cell lysates were prepared from nuclei by sonication and specific Histone modification antibodies were used for histone-DNA chromatin immunoprecipitation (ChIP) assays using the SimpleChIP Enzymatic Chromatin IP kit (9003, CST, USA) according to the protocol provided by the manufacturer.
Immunoprecipitated DNA fragments were subjected to library preparation using TrueSeq DNA Kit (FC-121-2001, Illumina, USA). NEB Next index set 3 was used for barcoding and adapter ligation (E7710S, NEB, USA).  Briefly, 5 – 10 ng of ChIP DNA was subjected to end repair which converts the overhangs resulted from fragmentation into blunt ends using an end repair mix. This end repair mix has 3' to 5' exonuclease activity which removes the 3' overhangs and the polymerase activity fills in the 5' overhangs. After this step, a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments which prevent the end repaired fragments from ligating to each other which is called as A tailing. Following this step, adapter ligation was performed where adapters having indexes were ligated to the ends of the DNA fragments, enabling them for hybridization onto a flow cell. Purification of adapter ligated fragments followed by enrichment of library was done to amplify DNA fragments having adapter sequences. DNA sequencing was performed in Illumina NextSeq 500 platform (Illumina Inc, USA) with a read length of 75 bp and paired end chemistry.

tag: cell type

value: round spermatids

tag: strain

value: Sprague-Dawley

tag: chip antibody

value: rabbit anti-histone H3 (tri methyl K9) antibody (2 μg/IP) (ab8898, Abcam, UK)

tag: treatment

value: no treatment


title: Blood training 22


title: Blood training 31


title: Blood training 21


title: Blood training 27


title: Blood training 24


title: Blood training 26


title: Blood training 19


title: Blood training 20


title: Blood training 17


title: Blood training 16


title: Blood training 15


title: Blood training 14


title: Blood training 13


title: Blood training 23


title: Blood training 12


title: Blood training 10


title: Blood training 11


title: Blood training 8


title: Blood training 7


title: Blood training 9


title: Blood training 18


title: Blood training 6


title: Blood training 4


title: PC_1

city: chengdu

first: ying

last: zhao

state: sichuan

address: huimin

institute: Sichuan Agricultural University

library_source: transcriptomic

data_processing:
After the sample is qualified, the Small RNA Sample Pre Kit is uesd to construct the library. utilizing the special structure of the 3 'and 5' ends of the Small RNA (the 5 'end has a complete phosphate group and the 3' end has a hydroxyl group), total RNA is used as the starting sample, added adapters at both ends of Small RNA directly, and then reversed transcribe to synthesize cDNA. Subsequently, after PCR amplification, PAGE gel electrophoresis is used to separate the target DNA fragments, and the cDNA library is recovered by cutting the gel.
After the library construction is completed, first use Qubit2.0 for preliminary quantification, dilute the library to 1ng / ul, and then use Agilent 2100 to detect the insert size of the library. After the insert size meets the expectations, use the Q-PCR method to carry out the effective concentration of the library Accurate quantification (library effective concentration> 2nM) to ensure library quality.
After passing the library test, the different libraries are pooled according to the requirements of effective concentration and target data volume for HiSeq / MiSeq sequencing.
Genome_build: gga
Supplementary_files_format_and_content: read counts and TPM: xls format as a Microsoft Excel worksheet

molecule: total RNA

organism: Gallus gallus

source_name: Ileum Intestinal mucosa

extract_protocol:
Ileal samples were washed in phosphate buffered saline and then snap-frozen in liquid nitrogen and stored at −80°C until further microRNA analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: group

value: SNE infection group

value: Intestinal mucosa


title: PC_2


title: Blood training 2


title: BL_3

value: Bacillus licheniformis H2 pre-treatment group


title: Blood training 5


title: Blood training 1


title: PC_3


title: BL_2


title: BL_1


title: NC_2

value: control


title: NC_3


title: NC_1


title: Blood training 3


title: T47D cells treated with DMSO, biological rep3

type: RNA

city: Richmond

first: Justin

middle: Michael

last: Craig

state: Virginia

address: 1101 E Marshall St

department: Pathology

country: USA

institute: Virginia Commonwealth University

description: gene expression data from T47D cells serum starved for 24 hours prior to treatment with prolactin and/or NIM811

hyb_protocol: As per the Affymetrix protocol, 10 μg of fragmented cRNA were hybridized on the GeneChip HG U133A 2.0 Arrays (Affymetrix Inc., Santa Clara, CA) for 16 hours at 60 rpm in a 45 °C hybridization oven. The arrays were washed and stained using the GeneChip Hybridization, Wash, and Stain Kit in the Affymetrix fluidics workstation.

scan_protocol: Every chip was scanned at a high resolution, on the Affymetrix GeneChip Scanner 3000 7G according to the GeneChip Expression Analysis Technical Manual procedures (Affymetrix, Santa Barbara, CA). After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the GeneChip Operating Software v1.4 (GCOS) (Affymetrix, Santa Barbara, CA).

data_processing: The 24 resultant .CEL files were analyzed using the R statistical computing language and environment. The data quality of each microarray was assessed by examining the average background, percent of probe sets called present by the MAS5 detection call algorithm, and the 3’:5’ ratio for GAPDH and ACTIN. Additionally, to detect potential spatial artifacts resulting from sub-optimal hybridization conditions, probe level linear models were fit using the R Bioconductor package, “affyPLM”, and plots of the residuals were examined for each microarray. Differential expression was assessed using the “affy” and “limma” Bioconductor packages. Briefly, probesets were quantile normalized and processed by the Robust Multi-Array Average (RMA) algorithm before the manufacturer’s control probesets and probesets considered “absent” in 20 or more arrays by the MAS5 algorithm were filtered from all arrays. Differential expression between treatment conditions was then assessed via moderated t-test adjusted for multiple hypotheses by the Benjamini & Hochberg method.

label: biotin

label_protocol: Each RNA sample was labeled according to the Affymetrix protocol with the following modifications: Starting with 500 ng of total RNA, we performed a single-strand cDNA synthesis primed with a T7-(dT24) oligonucleotide. Second strand cDNA synthesis was performed with E. coli DNA Polymerase I, and biotinylation of the cRNA was achieved by in vitro transcription (IVT) reaction using the GeneChip 3' IVT Express Kit (Affymetrix, Santa Clara, CA). After a 37°C-incubation for 16 hours, the labeled cRNA was purified using the cRNA cleanup reagents from the GeneChip Sample Cleanup Module.

growth_protocol: Prior to RNA isolation, T47D cells were plated in DMEM with 10% FBS at 60% confluency in 10 cm plates and incubated for 24 hours followed by an additional 24 hours of serum starvation in DMEM and 1X ITS Liquid Media Supplement.

extract_protocol: RNA was extracted using the MagMAX-96 for Microarrays Total RNA Isolation Kit (Invitrogen, Life Technologies, Carlsbad, CA) in an automated fashion using the magnetic particle processors MagMAX Express. RNA purity was judged by spectrophotometry at 260, 270, and 280 nm. RNA integrity was assessed by running 1 µL of every sample in RNA 6000 Nano LabChips on the 2100 Bioanalyzer (Agilent Technologies, Foster City, CA).

treatment_protocol: Cells were then treated for 4 hours with either DMSO (0.1%) or NIM811 (10 ug/mL) before stimulation with prolactin (PRL; 250 ng/mL). After 2 hours PRL stimulation, cells were washed with PBS and RNA was extracted.

tag: cell line

value: female

value: breast

value: epithelial

value: ductal carcinoma cell line


title: T47D cells treated with prolactin and NIM811, biological rep2


title: T47D cells treated with NIM811, biological rep3


title: T47D cells treated with prolactin and DMSO, biological rep2


title: T47D cells treated with prolactin and NIM811, biological rep3


title: T47D cells treated with DMSO, biological rep1


title: T47D cells treated with NIM811, biological rep2


title: CxCC_66_HPV16

city: St. Louis

first: Jin

last: Zhang

address: 4511 Forest Park Parkway

department: Radiation Oncology

institute: Washington University School of Medicine

data_processing:
Sequenced reads were aligned to human reference genome GRCh38 (r90) using STAR v2.7.0f.
The aligned reads were sorted and indexed using sambamba v0.6.9.
Gene expression was characterized using featureCounts v1.6.4 to obtain read counts and cufflinks v2.2.1 to obtain normalized FPKM.
Genome_build: GRCh38 (r90)
Supplementary_files_format_and_content: FPKM of all genes for the sample
Supplementary_files_format_and_content: Tab-delimited matrix of FPKM values for all genes of all samples

source_name: Cervix

extract_protocol:
Total RNA was extracted using the TRIzol method, and prepared using Rneasy Mini and Micro Kit following manufacturer's instructions.
Library preparation was performed with 10ug of total RNA. Sample quality was assessed with Agilent bioanalyzer or tapestation. Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies). mRNA was then fragmented in buffer containing 40mM Tris Acetate pH 8.2, 100mM Potassium Acetate and 30mM Magnesium Acetate and heating to 94 degrees for 150 seconds. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12 cycles using primers incorporating unique index tags.

value: primary cervical cancer

tag: figo 2009 stage

tag: hpv genotype


title: CxCC_67_HPV16-66

value: IIIb

value: HPV16, HPV66


title: T47D cells treated with DMSO, biological rep2


title: T47D cells treated with NIM811, biological rep1


title: CxCC_68_HPV16

value: IIb


title: T47D cells treated with prolactin and DMSO, biological rep1


title: CxCC_65_HPV16


title: T47D cells treated with prolactin and DMSO, biological rep3


title: T47D cells treated with prolactin and NIM811, biological rep1


title: Spleen, CB-D10.rep3

city: Chengdu

first: Jing-wen

last: Lin

address: No. 17, Section 3, People's South Road

institute: West China Second Hospital

description:
replicate 3
9440690046_E

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with GeneSpring GX13.1

organism: Mus musculus

source_name: Mouse Spleen

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: Spleens were aseptically removed and were homogenized immediately in TRI reagent (Ambion) by pulsing with a Polytron homogenising unit (Kinematic). RNA was extracted using RiboPure RNA Purification Kit (Ambion)  in accordance with the prescribed protocol provided with the kit. Quality control was performed with Caliper LabChip GX (Caliper Life Sciences)

treatment_protocol: mouse were intraperitoneal injected with 10e5 erythrocytes infected with P. chabaudi CB parasites

value: Female

value: 6-8 weeks

value: Spleen

tag: infection

value: P. c. chabaudi CB

tag: time

value: day 10

tag: mouse selection

value: random


title: Spleen, CB-D9.rep

description:
replicate 3
9440690061_D

value: day 9


title: Spleen, CB-D9.rep1

description:
replicate 1
9440690065_C


title: Spleen, CB-D10.rep1

description:
replicate 1
9440690065_E


title: Spleen, CB-D8.rep3

description:
replicate 3
9440690061_E

value: day 8


title: Spleen, CB-D9.rep2

description:
replicate 2
9440690059_E


title: Spleen, CB-D12.rep3

description:
replicate 3
9440690065_B

value: day 12


title: Spleen, CB-D12.rep2

description:
replicate 2
9440690046_D


title: Spleen, CB-D10.rep4

description:
replicate 4
9440690059_A


title: Spleen, CB-D8.rep2

description:
replicate 2
9440690065_A


title: Spleen, CB-D8.rep4

description:
replicate 4
9440690059_D


title: Spleen, CB-D12.rep1

description:
replicate 1
9440690059_F


title: Spleen, CB-D10.rep2

description:
replicate 2
9440690056_D


title: Spleen, CB-D8.rep1

description:
replicate 1
9440690056_C


title: CxCC_59_HPV18

value: IIa


title: CxCC_61_HPV16


title: CxCC_64_HPV16


title: CxCC_62_none


title: CxCC_63_HPV16


title: CxCC_60_HPV56


title: CxCC_58_none


title: CxCC_57_none


title: CxCC_55_none


title: CxCC_56_HPV16


title: Spleen, CB-D6.rep4

description:
replicate 4
9440690061_B

value: day 6


title: Spleen, CB-D6.rep1

description:
replicate 1
9440690046_C


title: Spleen, CB-D4.rep1

description:
replicate 1
9440690046_B

value: day 4


title: Spleen, CB-D4.rep2

description:
replicate 2
9440690061_C


title: Spleen, CB-D6.rep3

description:
replicate 3
9440690056_A


title: CxCC_52_HPV31


title: CxCC_51_HPV16


title: CxCC_54_HPV16

value: IVb


title: Spleen, CB-D6.rep2

description:
replicate 2
9440690042_F


title: Spleen, CB-D4.rep3

description:
replicate 3
9440690056_E


title: Spleen, CB-D4.rep4

description:
replicate 4
9440690065_F


title: CxCC_53_HPV52

value: primary cervical cancer


title: CxCC_47_HPV18


title: CxCC_48_HPV16

value: IIIb


title: CxCC_46_HPV16


title: EXP2.KIX.CFC.4

city: Iowa City

first: Ethan

last: Bahl

state: IA

address: 25 S Grand Ave

institute: University of Iowa

description:
total RNA (polyA selection)
EXP2.KIX.LEARN.4
processed data file: counts_all.csv

data_processing:
Reads were aligned to the mm10 genome build using STAR version 020201, with default parameters from bcbio-nextgen version 1.0.7.
BAM files were indexed and sorted using SAMtools version 1.6, with default parameters from bcbio-nextgen version 1.0.7.
Gene-level counts were quantified using featureCounts version 1.4.4, with default parameters from bcbio-nextgen version 1.0.7.
Genome_build: mm10 (GRCm38), GENCODE release M14
Supplementary_files_format_and_content: counts_all.csv: Comma-separated text file containing gene-level counts for all samples.

source_name: dorsal hippocampus

extract_protocol:
Dorsal hippocampus were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (poly-A selection or Ribo-zero gold) for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/background

tag: Sex

value: male

value: dorsal hippocampus

tag: experiment

tag: genotype

value: CBP KIX/KIX

tag: exposure

value: learning

tag: paradigm

value: CFC

tag: replicate


title: CxCC_50_HPV33

tag: tissue


title: Spleen, CB-D2.rep4

description:
replicate 4
9440690059_C

tag: strain

tag: gender

value: Female

tag: age

value: 6-8 weeks

value: Spleen

value: P. c. chabaudi CB

value: day 2


title: EXP2.KIX.CFC.3

description:
total RNA (polyA selection)
EXP2.KIX.LEARN.3
processed data file: counts_all.csv

tag: group


title: EXP2.KIX.CFC.2

description:
total RNA (polyA selection)
EXP2.KIX.LEARN.2
processed data file: counts_all.csv


title: Spleen, CB-D2.rep1

description:
replicate 1
9440690056_B

value: random


title: CxCC_43_HPV16

tag: figo 2009 stage


title: EXP2.WT.CFC.4

description:
total RNA (polyA selection)
EXP2.WT.LEARN.4
processed data file: counts_all.csv

value: WT


title: EXP2.WT.CFC.3

description:
total RNA (polyA selection)
EXP2.WT.LEARN.3
processed data file: counts_all.csv


title: Spleen, CB-Naïve-D12.rep1

description:
replicate 1
9440690056_F

value: naïve

value: day 12


title: EXP2.KIX.CFC.1

description:
total RNA (polyA selection)
EXP2.KIX.LEARN.1
processed data file: counts_all.csv


title: Spleen, CB-Naïve-D12.rep2

description:
replicate 2
9440690059_B


title: Spleen, CB-Naïve-D12.rep3

description:
replicate 3
9440690061_A


title: CxCC_42_HPV16

value: IIb

tag: hpv genotype


title: Spleen, CB-D2.rep3

description:
replicate 3
9440690061_F

tag: infection


title: Spleen, CB-D2.rep2

description:
replicate 2
9440690046_A

tag: time


title: CxCC_41_HPV18

value: primary cervical cancer


title: Spleen, CB-Naïve-D0.rep1

description:
replicate 1
9440690042_E

value: day 0

tag: mouse selection


title: CxCC_40_HPV18

value: IIIb


title: EXP2.WT.CFC.2

description:
total RNA (polyA selection)
EXP2.WT.LEARN.2
processed data file: counts_all.csv

tag: strain/background

value: male

value: dorsal hippocampus


title: Spleen, CB-naïve-D0.rep3

description:
replicate 3
9440690046_F


title: EXP2.WT.CFC.1

description:
total RNA (polyA selection)
EXP2.WT.LEARN.1
processed data file: counts_all.csv

tag: Sex

value: learning


title: CxCC_39_HPV16


title: Spleen, CB-Naïve-D0.rep2

description:
replicate 2
9440690065_D


title: CxCC_37_HPV16


title: CxCC_38_HPV16


title: CxCC_45_HPV16


title: EXP2.WT.HOME.1

description:
total RNA (polyA selection)
EXP2.WT.HOME.1
processed data file: counts_all.csv

tag: experiment

value: homecage


title: Mutant Snai1 rep. 3

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

department: Epigenetics and Development Division

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

description:
Snai1_GenewiseCounts.txt
HPC7_MIG_MUT3

data_processing:
Illumina software was used for basecalling.
Sequenced reads were mapped using the align function in the Rsubread package (version 1.22.2, Liao et al. Nucleic Acids Research, 2013) with default parameters.
Gene-level counts were obtained using the featureCounts function (Liao et al. Bioinformatics, 2014) from the Rsubread package (version 1.22.2) using the in-built mm10 annotation.
Data were TMM normalized (Robinson and Oshlack, Genome Biology 2010) in the edgeR package (version 3.15.0, Robinson et al. Bioinformatics 2010) and transformed to log2 counts per million.
Gene-wise linear models (Smyth, SAGMB 2004) with combined observational and sample-level weights (Liu et al. Nucleic Acids Research 2015) were fitted to summarise the values from replicate samples using functionality from the limma package (version 3.29.12, Ritchie et al. Nucleic Acids Research, 2015).
Genome_build: mm10
Supplementary_files_format_and_content: a tab-delimited text file with columns representing Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene for each sample.

source_name: HPC7 cells transduced with mutant Snai1 vector

growth_protocol: HPC7 cells were cultured in vitro in RPMI supplemented with 0.05mM 2-mercaptoethanol, 10% FCS and 100ng/ml mSCF

extract_protocol:
Cells were sorted for GFP expression one week after viral transduction and pelleted for RNA extraction. RNA was extracted using the Qiagen RNeasy midi-prep kit.
RNA libraries were prepared using thre Truseq stranded mRNA kit from Illumina.

treatment_protocol: HCP7 cells were retrovirally transduced with a MSCV-IRES-GFP vector containing either no gene (MIG-0), wild-type Snai1 (MIG-wt) or mutant Snai1 (MIG-MUT) cDNA. The Snai1 mutant cDNA encodes a mutant protein with a F>A amino acid substitution at position 5 of the protein. This mutation impairs Snai1's ability to interact with the Lsd1 protein.

tag: cell line

tag: cell type

value: hematopoietic progenitor cells

tag: genotype

value: Mutant


title: CxCC_44_HPV16

value: IIIa


title: CxCC_36_HPV16


title: CxCC_33_HPV16


title: CxCC_34_HPV16-18

value: HPV16, HPV18


title: CxCC_31_none


title: Wild-type Snai1 rep. 3

description:
Snai1_GenewiseCounts.txt
HPC7_MIG_wt3

source_name: HPC7 cells transduced with wild type Snai1 vector

value: Wild-type


title: Mutant Snai1 rep. 2

description:
Snai1_GenewiseCounts.txt
HPC7_MIG_MUT2


title: Empty Vector Control rep. 3

description:
Snai1_GenewiseCounts.txt
HPC7_MIG_03

source_name: HPC7 cells transduced with empty-vector control

value: Empty Vector control


title: Wild-type Snai1 rep. 2

description:
Snai1_GenewiseCounts.txt
HPC7_MIG_wt2


title: Empty Vector Control rep. 1

description:
Snai1_GenewiseCounts.txt
HPC7_MIG_01


title: EXP2.WT.HOME.3

description:
total RNA (polyA selection)
EXP2.WT.HOME.3
processed data file: counts_all.csv

value: WT

tag: exposure

tag: paradigm

tag: replicate


title: Wild-type Snai1 rep. 1

description:
Snai1_GenewiseCounts.txt
HPC7_MIG_wt1


title: Mutant Snai1 rep. 1

description:
Snai1_GenewiseCounts.txt
HPC7_MIG_MUT1


title: CxCC_32_HPV16

tag: tissue


title: CxCC_27_HPV16


title: CxCC_26_HPV16


title: CxCC_30_none


title: Empty Vector Control rep. 2

description:
Snai1_GenewiseCounts.txt
HPC7_MIG_02


title: EXP2.WT.HOME.2

description:
total RNA (polyA selection)
EXP2.WT.HOME.2
processed data file: counts_all.csv


title: CxCC_25_HPV59


title: CxCC_35_HPV16


title: CxCC_24_HPV16


title: CxCC_23_HPV45


title: CxCC_22_none


title: CxCC_21_HPV16


title: CxCC_20_HPV33


title: CxCC_29_none


title: CxCC_28_HPV16


title: CxCC_18_none


title: CxCC_19_HPV59


title: CxCC_17_HPV16


title: CxCC_15_HPV18


title: CxCC_12_HPV33


title: CxCC_16_HPV16


title: CxCC_13_HPV18


title: CxCC_10_HPV52


title: CxCC_09_HPV16


title: CxCC_07_HPV16


title: Treated_Con5_1

city: Houston

first: Fangrui

last: Wu

state: Texas

address: One Baylor Plaza

institute: Baylor College of Medicine

data_processing:
STAR generated read count for each gene, which was used as the measurement for gene expression.
DEseq2 to normalize and detect DE genes
Genome_build: UCSC hg19
Supplementary_files_format_and_content: normalized abundance measurements

source_name: Leukemia cells Molm-13

growth_protocol: Molm cells were gown in RPMI supplemented with 10% FBS and 1% PenStrep under standard culture conditions. Cells were plated in 1ml at 50,000 cells/ml

extract_protocol:
mRNA was isolated from cells three days after sort using qiagen RNeasy kit.
Sequencing libraries were generated using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

tag: agebt

value: 5 uM inhibitor


title: Treated_Con5_2


title: CxCC_14_HPV16


title: Treated_Con5_3


title: untreated_3

value: Untreated


title: untreated_2


title: untreated_1


title: CxCC_08_HPV58

value: IIb


title: N40-1: wistar rats-rep1

city: Wuhan

first: Ming-zhong

last: Xiao

state: China

address: No. 4, Garden Hill, Wuchang District, Wuhan, China

institute: Hubei Provincial Hospital of TCM

description: liver tissues 1  of  vehicle group

hyb_protocol: The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μL 10 × Blocking Agent and 1 μL of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μL 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μL of hybridization solution was dispensed into the gasket slide and assembled to the expression microarray slide. The slides were incubated for 17 hours at 65 °C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner. (part number G2505C).

data_processing: Gene expression ratios were determined. If a gene had a P value and expression fold-change value of less than 0.05 and 2.0 respectively, it was deemed differentially expressed.

source_name: liver tissues

label_protocol: RNA labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar).

growth_protocol: Specific-pathogen-free (SPF) male Wistar rats (180 ± 10 g) were purchased from Hubei Province Experimental Animal Research Center. All the rats were kept under controlled environmental conditions at 21 ± 2 °C and with a 12-h light/dark cycle and fed drinking water and pellet food ad libitum.

extract_protocol: Total RNA was isolated from hepatic tissues using RNA isolation kit (Tiangen, Chnia) following the manufacturer’s protocol. Reagents were treated with diethylpyrocarbonate (DEPC) (Sigma-Aldrich, St. Louis, MO). RNA degradation and contamination were monitored on 1% agarose gel electrophoresis. RNA purity was assessed using a Nano Photometer spectrophotometer (Implen, CA, USA). RNA integrity was assessed by standard denaturing. A portion of the total RNA was used for DNA microarray, and the rest was used for the first cDNA strand synthesis.

tag: strain

value: Wistar

tag: gender

value: liver


title: N40-3: wistar rats-rep3

description: liver tissues 3  of  vehicle group


title: CxCC_06_HPV16

value: primary cervical cancer

tag: figo 2009 stage

tag: hpv genotype


title: N40-2: wistar rats-rep2

description: liver tissues 2  of  vehicle group

value: male


title: CxCC_05_none

value: IIIb


title: siGDF11 rep1

first: Weiqing

last: Liu

address: No.14, Third section, Renmin Nan Road

institute: West China Hospital of Stomatology, Sichuan University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was builtusing Hisat2 v2.0.5 andpaired-endcleanreadswerealignedtothereferencegenomeusingHisat2v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: Homo_sapiens_Ensemble_94.fa
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

source_name: dental pulp

extract_protocol:
total RNA was extracted using the RNeasy mini kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.
Libraries were prepared according to Illumina's instructions of RNA sample. Paired-end method was adopted for further processes.

value: human dental pulp stem cells (hDPSCs)

tag: treatment

value: GDF11 siRNA

value: GDF11 Knockdown


title: siGDF11 rep2


title: siGDF11 rep3


title: CxCC_03_HPV16

value: IVa


title: siCTRL rep2

value: control siRNA

value: control


title: CxCC_02_HPV18


title: CxCC_04_HPV16


title: CxCC_11_HPV16


title: siCTRL rep3


title: CxCC_01_HPV16


title: siCTRL rep1


title: PIM7

city: Hong Kong

first: Chi Ho

address: 6th Floor, The Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam

department: Centre for PanorOmic Sciences

country: Hong Kong

institute: The University of Hong Kong

data_processing:
Sequencing reads were assigned to each sample using Illumina bcl2fastq software. In terms of sequence quality, an average of 94% of the bases achieved a quality score of Q30, where Q30 denotes the accuracy of a base call to be 99.9%.
Sequencing reads were first filtered for adapter sequence and low quality sequence followed by retaining only reads with read length ≥ 40bp. Low Quality is defined as: Reads with more than 5% unknown bases (“N”) or reads having more than 50% of bases with quality value <= 11. Subsequently, sequencing reads were filtered for rRNA sequence and remaining reads were used for downstream analysis.
Reads were mapped to the reference genome using STAR Version 2.5.2 (default parameters) with the following exception: twopassMode: Basic. Human Genome GRCh38 (downloaded from GENCODE) was used as reference genome.
Expression of genes/transcripts was quantified using RSEM Version 1.2.31. Differentially expression analysis was done using EBSeq Version 1.18.0.
Genome_build: Human genome (GRCh38)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include TPM values for each Sample.

source_name: Hepatocellular carcinoma

extract_protocol:
Total RNA from mouse tumor tissues were extracted using Trizol reagent (Invitrogen) according to manufacturer's protocol.
Quality and quantity of total RNA samples were assessed using the RNA 6000 Nano total RNA assay (Agilent) by Agilent 2100 Bioanalyzer and Qubit 2.0 Fluorometer, respectively. The mean RIN score of the RNA samples submitted to library preparation was 8.75. One microgram of total RNA was used for library preparation using KAPA Stranded mRNA-Seq Kit (KR0960-v3.15). Purified mRNA was fragmented to 200-300bp by incubation at 94oC for 6 min in the presence of magnesium ions. The amplified double-stranded cDNA underwent 3' adenylation and indexed adaptor ligation using xGen® Dual Index UMI Adapters. The denatured libraries were subjected to sequencing (2 x 151bp) using NovaSeq 6000 system (Illumina).

treatment_protocol: Mice were treated with vehicle or PIM447 (60mg/kg) by oral gavage three times a week for two weeks. PIM447 was formulated in 5% dextrose with 15% DMSO.

value: MHCC-97L xenograft

tag: formulation

value: 5% dextrose with 15% DMSO


title: normoxia_VC_3

city: Los Angeles

first: Michel

middle: M

last: Sun

state: CA

address: 675 Charles E Young Dr S

department: Ophthalmology

institute: UCLA

data_processing:
RNA sequencing and library preparation - KAPA RNA HyperPrep Kit with RiboErase (Roche Sequencing, cat#KK8561, Pleasanton, CA, USA)
Sequencing - Illumina HiSeq3000 System for a single-read 50 run (Illumina, San Diego, CA)
Data quality check - Illumina SAV
Demultiplexing - Illumina Bcl2fastq2 v 2.17 program
Bioinformatics - edgeR, Partek flow, and Ingenuity Pathway Analysis (IPA)
Count normalization - TMM
Differential Gene expression analysis  - DEseq2 (version 1.26.0)
Genome_build: The reads were mapped to the latest UCSC transcript set using STAR - 2.27a and GRCh38
Supplementary_files_format_and_content: gene counts and normalized gene counts, tab delimited, per-sample

source_name: ARPE-19 cell line

growth_protocol: Spontaneously arising retinal pigment epithelium (ARPE-19) cells were cultured using Dulbecco’s modified Eagle’s media F-12 supplemented with 10% fetal bovine serum, 1% 100X HEPES, 1% L-glutamine, and 1% Penicillin/Streptomycin at 37°C in a 5% CO2 humidified incubator. EMP2 overexpression (ARPE-19/EMP2) and vector control ARPE-19 cell line (ARPE-19/VC) were achieved by a stable transfection of ARPE-19 cells with an EMP2-overexpressing or a control construct via retroviral transduction, as previously described (Fu et al., 2014).

extract_protocol:
Total RNA was extracted from cells using RNeasy Mini Kit (Qiagen) and RNA concentration was measured using a Nanodrop spectrophotometer (ThermoFisher Scientific). Three replicates of each sample at 2 µg of RNA were submitted for sequencing and analysis (Technology Center for Genomics and Bioinformatics, UCLA). RNA sequencing and library preparation was using the KAPA RNA HyperPrep Kit with RiboErase (Roche Sequencing, cat#KK8561, Pleasanton, CA, USA), according to the manufacturer’s instructions.
The work flow consisted of rRNA depletion, cDNA generation, end repair to generate blunt ends, A-tailing, adaptor ligation, and PCR amplification. Different adaptors were used for multiplexing samples in one lane. Sequencing was performed on the Illumina HiSeq3000 System for a single-read 50 run (Illumina, San Diego, CA). Data quality check was done on Illumina SAV. Demultiplexing was performed with the Illumina Bcl2fastq2 v 2.17 program.

treatment_protocol: ARPE-19 cell panels were cultured for two weeks in previously stated normoxic conditions prior to exposure to hypoxic conditions. ARPE-19 cell cultures were placed in a hypoxia chamber (BioSpherix, Parish, NY) for 4 hours at 37°C with 0.5% O2, 5% CO2, and balance N2 (UCLA Cylinder Management, Los Angeles, CA).

value: retinal epithelial cells

tag: oxygen status

value: normoxia

tag: emp2 expression

value: vector control


title: normoxia_WT_3

value: wild type


title: Ctrl5

value: Vehicle


title: PIM8


title: Ctrl1


title: hypoxia_WT_3

value: hypoxia


title: Cardiomyocytes, Treated, High, 24 h (ms-90)

city: Frederick

first: Patric

last: Schyman

state: Maryland

address: 2405 Whittier Drive, Suite 200

institute: Biotechnology HPC Software Applications Institute (BHSAI)

data_processing:
RNA-seq data were analyzed using the Kallisto tool (version 0.42.4) for read alignment and quantification.
We calculate uncertainties of transcript abundance estimates by repeating the analyses 100 times after resampling with replacement. We pseudo-aligned the reads to the human transcriptome (GRCh38.p12) downloaded from the Ensembl website
Kallisto input: kallisto quant -i $REF_KAL2 -b 100 -o human/"$sample"  $DATA_DIR/3744-"$sample"_R1_001.fastq.gz $DATA_DIR/3744-"$sample"_R2_001.fastq.gz -t 10
Genome_build: Human transcriptome (GRCh38.p12)
Supplementary_files_format_and_content: tab-delimited text files, including abundance measurements

source_name: Heart

growth_protocol: We cultured human hepatocytes, renal cells, and cardiomyocytes for an additional 18 hours before adding thioacetamide-S-oxide or vehicle (maintenance medium; MM250 for hepatocytes and EpiCM for renal cells).

extract_protocol:
Total RNA was isolated from culture cells using TRIzol Reagent (Thermo Fisher Scientific, Waltham, MA) and the direct-zol RNA MiniPrep kit (Zymo Research, Irvine, CA). The isolated RNA samples were then submitted to the Vanderbilt University Medical Center VANTAGE Core (Nashville, TN) for RNA quality determination and sequencing. Total RNA quality was assessed using a 2100 Bioanalyzer (Agilent, Santa Clara, CA).
At least 200 ng of DNase-treated total RNA with high RNA integrity was used to generate poly-A-enriched mRNA libraries, using KAPA Stranded mRNA sample kits with indexed adaptors (New England BioLabs). Library quality was assessed using the 2100 Bioanalyzer (Agilent), and libraries were quantitated using KAPA library Quantification kits (KAPA Biosystems). Pooled libraries were subjected to 150-bp double-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq6000). Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.

value: Heart

value: Cardiomyocytes

value: thioacetamide-S-oxide

tag: duration

tag: dose

value: High (0.75 mM)


title: Cardiomyocytes, Treated, High, 24 h (ms-89)

tag: cell type


title: hypoxia_VC_3

tag: cell line


title: Cardiomyocytes, Treated, High, 24 h (ms-88)


title: normoxia_OE_3

value: overexpressing


title: hypoxia_OE_3


title: Cardiomyocytes, Treated, High, 24 h (ms-87)


title: Cardiomyocytes, Treated, High, 24 h (ms-86)


title: normoxia_WT_2


title: hypoxia_KD_3

value: knock down


title: Cardiomyocytes, Treated, Low, 24 h (ms-85)


title: Cardiomyocytes, Treated, Low, 24 h (ms-83)


title: normoxia_OE_2


title: Cardiomyocytes, Treated, Low, 24 h (ms-84)


title: normoxia_KD_2


title: hypoxia_WT_2


title: Cardiomyocytes, Treated, Low, 24 h (ms-81)


title: Cardiomyocytes, Treated, Low, 24 h (ms-82)


title: normoxia_KD_3


title: hypoxia_VC_2


title: Cardiomyocytes, Vehicle, 24 h (ms-80)

value: Control


title: normoxia_WT_1


title: normoxia_VC_1


title: normoxia_KD_1


title: Cardiomyocytes, Vehicle, 24 h (ms-77)


title: Cardiomyocytes, Treated, High, 9 h (ms-74)

value: 9 h


title: Cardiomyocytes, Vehicle, 24 h (ms-79)


title: Cardiomyocytes, Treated, High, 9 h (ms-75)


title: Cardiomyocytes, Vehicle, 24 h (ms-78)


title: hypoxia_WT_1


title: Cardiomyocytes, Treated, High, 9 h (ms-72)


title: Cardiomyocytes, Treated, High, 9 h (ms-73)


title: normoxia_VC_2


title: hypoxia_OE_1


title: Cardiomyocytes, Treated, High, 9 h (ms-71)


title: hypoxia_VC_1


title: hypoxia_KD_1


title: Cardiomyocytes, Treated, Low, 9 h (ms-70)


title: hypoxia_OE_2


title: Cardiomyocytes, Treated, Low, 9 h (ms-68)


title: hypoxia_KD_2


title: DMSO control for AFB1, yeast cells expressing CYP1A2 and NAT2, 3

city: Albany

first: Michael

middle: Thomas

last: Fasullo

state: New York

address: 257 Fuller Road

department: Nanobioscience

institute: SUNY Polytechnic Institute

description:
C8B0CANXX_Results__CYP1A2nat214_uptag_only__DMSO_AFB1.xls
PCR amplified barcode tagged DNA

data_processing:
Quality assessment to generate fastq file
Demultiplex
Trim Reads
Count barcodes
Analyze barcode count data
Supplementary_files_format_and_content: Samples were generated by the TCC package in R using TMM normalization with the edger test method and iteration value of 3.

organism: Saccharomyces cerevisiae

source_name: yeast cells expressing CYP1A2 and NAT2

extract_protocol: Equal amounts of PCR amplified barcodes were pooled for DNA sequencing using the illumina platform

tag: agent

value: DMSO control for AFB1


title: AFB1, yeast cells expressing CYP1A2 and NAT2, 1


title: Cardiomyocytes, Treated, Low, 9 h (ms-67)


title: normoxia_OE_1


title: Cardiomyocytes, Treated, Low, 9 h (ms-66)


title: AFB1, yeast cells expressing CYP1A2 and NAT2, 2


title: Cardiomyocytes, Vehicle, 24 h (ms-76)


title: AFB1, yeast cells expressing CYP1A2, 2

description:
C8B0CANXX_Results__CYP1A2_uptag_only__DMSO_AFB1.xls
PCR amplified barcode tagged DNA

source_name: yeast cells expressing CYP1A2


title: AFB1, yeast cells expressing CYP1A2, 3


title: DMSO control for AFB1, yeast cells expressing CYP1A2, 2


title: Cardiomyocytes, Vehicle, 9 h (ms-64)


title: AFB1, yeast cells expressing CYP1A2 and NAT2, 3


title: DMSO control for AFB1, yeast cells expressing CYP1A2 and NAT2, 2


title: AFB1, yeast cells expressing CYP1A2, 1


title: CxCC_49_HPV33

value: primary cervical cancer

value: IIIa


title: Renal tube epithelial cells, Treated, High, 24 h (ms-59)

source_name: Kidney

value: Kidney

value: Renal tube epithelial cells

value: High (1.00 mM)


title: Renal tube epithelial cells, Treated, High, 24 h (ms-58)


title: AFB1, yeast cells (BY4743 library), 3

description:
C8B0CANXX_Results__No_CYP_uptag_only__DMSO_AFB1.xls
PCR amplified barcode tagged DNA

source_name: yeast cells (BY4743 library)


title: Cardiomyocytes, Vehicle, 9 h (ms-62)


title: Renal tube epithelial cells, Treated, High, 24 h (ms-60)


title: AFB1, yeast cells (BY4743 library), 2


title: Renal tube epithelial cells, Treated, High, 24 h (ms-56)


title: AFB1, yeast cells (BY4743 library), 1


title: Cardiomyocytes, Vehicle, 9 h (ms-65)


title: Renal tube epithelial cells, Treated, Low, 24 h (ms-55)


title: DMSO control for AFB1, yeast cells (BY4743 library), 3


title: DMSO control for AFB1, yeast cells expressing CYP1A2 and NAT2, 1


title: Renal tube epithelial cells, Treated, High, 24 h (ms-57)


title: DMSO control for AFB1, yeast cells (BY4743 library), 2


title: Renal tube epithelial cells, Treated, Low, 24 h (ms-53)


title: Renal tube epithelial cells, Treated, Low, 24 h (ms-54)


title: DMSO control for AFB1, yeast cells (BY4743 library), 1


title: Cardiomyocytes, Vehicle, 9 h (ms-63)


title: DMSO control for AFB1, yeast cells expressing CYP1A2, 3

source_name: yeast  cells expressing CYP1A2


title: Renal tube epithelial cells, Treated, Low, 24 h (ms-52)


title: Renal tube epithelial cells, Treated, Low, 24 h (ms-51)


title: DMSO control for AFB1, yeast cells expressing CYP1A2, 1


title: Renal tube epithelial cells, Vehicle, 24 h (ms-50)


title: Renal tube epithelial cells, Vehicle, 24 h (ms-49)


title: Renal tube epithelial cells, Vehicle, 24 h (ms-48)


title: DW46: Diwu Yanggan capsule treatment group-rep3

description: liver tissues 3  of Diwu Yanggan capsule treatment group

treatment_protocol: For the model and DWYG groups, the rats received partial hepatectomy and then orally administered 20 mg/kg 2-AAF once a day for one week. Meanwhile, the rats of the DWYG group were orally administrated 10 mL/kg once a day until sacrificed.

value: Wistar

value: male

value: liver


title: Renal tube epithelial cells, Vehicle, 24 h (ms-46)

value: Vehicle


title: Model43: 2-AAF/PHmodel-rep3

description: liver tissues 2  of   2-AAF/PH model


title: s8_E10_M

city: Clayton

first: Craig

middle: Allen

last: Smith

address: Wellington Road

department: Anatomy and Developmental Biology

institute: Monash University

data_processing:
Alignment - Reads aligned to chicken genome (protein-coding and lincRNA from ensembl v92 annotation) with cellRanger (v2.0.1, –force-cells) using STAR (v2.5.1b). The gene annotation was extended to include reads aligned just downstream, adding an extra 1000bp downstream of the last exon of each transcript. Samples aggregated without normalisation.
Gene quantification with featureCounts (subread v1.6.1, parameters: -s 1 -R BAM -O), and UMI-tools (v0.5.4)
Filtered to cells with at least 500 reads across 100 diffferent genes with no more than 30% of counts belonging to the 5 most abundant genes. Filtered to genes in at least 20 cells (in any sample). Using scran(v1.8.4) and Scater (v1.6.3).
Genome_build: galgal5
Supplementary_files_format_and_content: counts file

molecule: polyA RNA

source_name: embryonic left gonad cells

growth_protocol: Fertile chicken eggs were incubated at 37.5°C such that different developmental stages were reached on the same day.

extract_protocol: Chromium Single Cell 3' Library & Gel Bead Kit V2

tag: num individuals

tag: Sex

value: Male

tag: developmental stage

value: embryonic gonad (left)


title: s6_E8_M

tag: tissue


title: DW21: Diwu Yanggan capsule treatment group-rep2

description: liver tissues 2  of Diwu Yanggan capsule treatment group

tag: strain


title: Renal tube epithelial cells, Treated, High, 9 h (ms-45)

value: thioacetamide-S-oxide


title: Renal tube epithelial cells, Treated, High, 9 h (ms-44)


title: s7_E10_F

value: Female


title: s5_E8_F


title: s3_E6_F


title: Model1: 2-AAF/PHmodel-rep1

description: liver tissues 1  of   2-AAF/PH model

tag: gender


title: Renal tube epithelial cells, Treated, High, 9 h (ms-42)


title: Renal tube epithelial cells, Treated, High, 9 h (ms-43)


title: s2_E4_M


title: s1_E4_F


title: Renal tube epithelial cells, Treated, Low, 9 h (ms-39)


title: Renal tube epithelial cells, Treated, High, 9 h (ms-41)


title: Renal tube epithelial cells, Treated, Low, 9 h (ms-40)


title: Renal tube epithelial cells, Treated, Low, 9 h (ms-37)


title: Renal tube epithelial cells, Vehicle, 24 h (ms-47)


title: Renal tube epithelial cells, Treated, Low, 9 h (ms-36)


title: Renal tube epithelial cells, Vehicle, 9 h (ms-35)


title: Renal tube epithelial cells, Vehicle, 9 h (ms-34)


title: DW9: Diwu Yanggan capsule treatment group-rep1

description: liver tissues 1  of Diwu Yanggan capsule treatment group


title: Renal tube epithelial cells, Vehicle, 9 h (ms-33)


title: Renal tube epithelial cells, Vehicle, 9 h (ms-32)


title: s4_E6_M


title: Renal tube epithelial cells, Vehicle, 9 h (ms-31)


title: Model28: 2-AAF/PHmodel-rep2

description: liver tissues 2  of   2-AAF/PH model


title: Gata2 -77 enhancer mutant sample 2

city: Madison

first: Emery

last: Bresnick

state: WI

address: 8457 WIMR 1111 Highland Ave.

department: Cell and Regenerative Biology

institute: University of Wisconsin-Madison

data_processing:
CellRanger v2.0.2 was used to align the raw sequencer to output to mm10 transcriptome and quantify UMI counts
Scater v1.10.1 and scran v1.10.2 were used for further quality control and normalization, respectively.
Seurat v2.3.4 and cluster v2.0.1 were used dimension reduction and kmeans clustering.
SPRING was also used for dimension reduction.  The files count_sce_subsamp.csv, gene_list.csv, and spring_grouping.csv were used for these analyses.
MAST v1.8.2 was used for differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: An .rda file containing the processed data in the form of SingleCellExperiment object.

source_name: E14.5 fetal liver

extract_protocol:
Fetal livers were harvested and stained for cell sorting in PBS containing 2% FBS, 5 mM Glucose and 2.5 mM EDTA. Cells were sorted into PBS containing 10% FBS.
Libraries were prepared using 10x Genomics Chromium Platform.

value: fetal liver

tag: genotype


title: Gata2 WT Sample 1

value: wild type


title: Primary hepatocytes, Treated, High, 24 h (ms-30)

source_name: Liver

value: Liver

value: Primary hepatocytes

value: High (0.25 mM)


title: Primary hepatocytes, Treated, High, 24 h (ms-29)


title: Gata2 WT Sample 2


title: Primary hepatocytes, Treated, High, 24 h (ms-28)


title: Gata2 -77 enhancer mutant sample 1


title: duizhao48-xin-2

city: Yangzhou

first: Shaohua

last: Shi

state: Jiangsu

address: 48 East Wenhui Road

department: College of Veterinary Medicine

institute: Yangzhou University

data_processing:
Use Seqtk [1] to filter the data obtained by sequencing to remove the linker sequence contained in the reads; remove the bases with a quality Q less than 20 at the 3 'end, that is, the base error rate is less than 0.01, where Q = -10logerror_ratio Remove reads with a length of less than 25; remove ribosome RNA reads of the species.
The Hisat2 (version: 2.0.4) spliced mapping algorithm is used to perform Genome mapping on the pre-processed reads. This algorithm allows the readings that cannot be matched with full length to be mapped. Intersub-region) Transcriptome sequencing data; default parameters are used. The comparison result generated by Mapping is a BAM file
We first applied Stringtie (version: 1.3.0) [4, 5] to count the number of Fragments of each gene after Hisat2 comparison, then normalized by TMM (trimmed mean of M values) [6] method, and finally Use the perl script to calculate the FPKM value of each gene.
Genome_build: Galgal5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Hearts was harvested using RNAiso Plus Total RNA extraction  reagent. Illumina TruSeq RNA Sample Prep Kit (Vazyme-NR602-02) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Hearts were removed, Liquid nitrogen frozen storage, dry ice transport.

value: control

value: heart


title: duizhao48-xin-1


title: duizhao48-xin-3


title: Primary hepatocytes, Treated, Low, 24 h (ms-23)


title: X234-48-xin-3

source_name: Fowl adenovirus-4 at 48 hpi _Heart

value: Fowl adenovirus-4 at 48 hpi


title: Primary hepatocytes, Treated, Low, 24 h (ms-24)


title: Primary hepatocytes, Treated, Low, 24 h (ms-25)


title: Renal tube epithelial cells, Treated, Low, 9 h (ms-38)

value: Kidney

value: Renal tube epithelial cells

value: 9 h


title: X234-48-xin-2


title: Primary hepatocytes, Treated, High, 24 h (ms-26)


title: X234-48-xin-1


title: Primary hepatocytes, Treated, Low, 24 h (ms-21)


title: X234-48-pi-3

data_processing:
Use Seqtk [1] to filter the data obtained by sequencing to remove the linker sequence contained in the reads; remove the bases with a quality Q less than 20 at the 3 'end, that is, the base error rate is less than 0.01, where Q = -10logerror_ratio Remove reads with a length of less than 25; remove ribosome RNA reads of the species.
The Hisat2 (version: 2.0.4) spliced mapping algorithm is used to perform Genome mapping on the pre-processed reads. This algorithm allows the readings that cannot be matched with full length to be mapped. Intersub-region) Transcriptome sequencing data; default parameters are used. The comparison result generated by Mapping is a BAM file
We first applied Stringtie (version: 1.3.0) [4, 5] to count the number of Fragments of each gene after Hisat2 comparison, then normalized by TMM (trimmed mean of M values) [6] method, and finally Use the perl script to calculate the FPKM value of each gene.
Genome_build: Galgal5
Supplementary_files_format_and_content: FPKM and raw counts values for each Sample

source_name: Fowl adenovirus-4 at 48 hpi _spleen

extract_protocol:
spleens was harvested using RNAiso Plus Total RNA extraction  reagent. Illumina TruSeq RNA Sample Prep Kit (Vazyme-NR602-02) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: spleens were removed, Liquid nitrogen frozen storage, dry ice transport.

value: spleen


title: Primary hepatocytes, Treated, Low, 24 h (ms-22)


title: X234-48-pi-2


title: Primary hepatocytes, Vehicle, 24 h (ms-20)

value: Control

value: Vehicle


title: Primary hepatocytes, Vehicle, 24 h (ms-19)


title: X234-48-pi-1


title: Primary hepatocytes, Vehicle, 24 h (ms-18)


title: Primary hepatocytes, Treated, High, 24 h (ms-27)


title: X221pi-3


title: Primary hepatocytes, Vehicle, 24 h (ms-17)


title: X221pi-2


title: Primary hepatocytes, Vehicle, 24 h (ms-16)


title: duizhao-pi-3

source_name: duck-origin H7N9 AIV at 24 hpi _spleen

value: duck-origin H7N9 AIV at 24 hpi


title: Primary hepatocytes, Treated, High, 9 h (ms-15)

value: thioacetamide-S-oxide


title: X221pi-1


title: Primary hepatocytes, Treated, High, 9 h (ms-14)


title: duizhao-pi-2


title: duizhao-pi-1


title: X221fei-3

source_name: duck-origin H7N9 AIV_lung

extract_protocol:
lungs was harvested using RNAiso Plus Total RNA extraction  reagent. Illumina TruSeq RNA Sample Prep Kit (Vazyme-NR602-02) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: lungs were removed, Liquid nitrogen frozen storage, dry ice transport.

value: duck-origin H7N9 AIV

value: lung


title: Primary hepatocytes, Treated, High, 9 h (ms-11)


title: Primary hepatocytes, Treated, High, 9 h (ms-12)


title: X221fei-2


title: Primary hepatocytes, Treated, High, 9 h (ms-13)


title: X221fei-1


title: Primary hepatocytes, Treated, Low, 9 h (ms-9)


title: Primary hepatocytes, Treated, Low, 9 h (ms-10)


title: duizhao-fei-3


title: Primary hepatocytes, Treated, Low, 9 h (ms-8)


title: Primary hepatocytes, Treated, Low, 9 h (ms-7)


title: duizhaofei-2


title: Primary hepatocytes, Treated, Low, 9 h (ms-6)


title: Primary hepatocytes, Vehicle, 9 h (ms-5)


title: Primary hepatocytes, Vehicle, 9 h (ms-4)


title: Primary hepatocytes, Vehicle, 9 h (ms-2)


title: Primary hepatocytes, Vehicle, 9 h (ms-1)


title: Primary hepatocytes, Vehicle, 9 h (ms-3)


title: AML446

city: Nottingham

first: Sergio

last: Rutella

address: Clifton Campus

department: John van Geest Cancer Research Centre

country: United Kingdom

institute: Nottingham Trent University

description:
Pan Cancer Immune panel
GPL25714-446

hyb_protocol: Hybridisation was performed in a PCR for 20 hours at 65°C.

scan_protocol: Scanned with NanoString Digital analyser with 555 FOV

data_processing: Data was normalised using the nSolver software, version 4.0.

label: Nanostring bar coding

source_name: Bone Marrow

label_protocol: RNA ispecies were identified and counted using the NanoString PanCancer Immune Profiling Panel.

growth_protocol: Human Samples

extract_protocol: RNA extraction was carried out using Qiagen RNeasy RNA isolation kits. Quantitation of RNA was performed using Nanodrop and Qubit RNA high sensitivity assay.

treatment_protocol: At time of initial diagnosis, achievement of complete remission and relapse.

tag: subject status

value: patient with acute myeloid leukaemia

tag: age (years)

tag: disease stage at sampling

value: Relapse

value: Bone Marrow


title: AML445

description:
Pan Cancer Immune panel
GPL25714-445


title: AML444

description:
Pan Cancer Immune panel
GPL25714-444


title: AML438

description:
Pan Cancer Immune panel
GPL25714-438

value: Complete remission


title: AML443

description:
Pan Cancer Immune panel
GPL25714-443


title: AML436

description:
Pan Cancer Immune panel
GPL25714-436

value: Diagnosis


title: AML439

description:
Pan Cancer Immune panel
GPL25714-439


title: AML437

description:
Pan Cancer Immune panel
GPL25714-437


title: AML441

description:
Pan Cancer Immune panel
GPL25714-441


title: AML442

description:
Pan Cancer Immune panel
GPL25714-442


title: AML440

description:
Pan Cancer Immune panel
GPL25714-440


title: AML447

description:
Pan Cancer Immune panel
GPL25714-447


title: AML435

description:
Pan Cancer Immune panel
GPL25714-435


title: AML434

description:
Pan Cancer Immune panel
GPL25714-434


title: duizhao-fei-1

tag: treatment

value: control


title: AML428

description:
Pan Cancer Immune panel
GPL25714-428


title: AML429

description:
Pan Cancer Immune panel
GPL25714-429


title: AML430

description:
Pan Cancer Immune panel
GPL25714-430


title: AML433

description:
Pan Cancer Immune panel
GPL25714-433


title: AML431

description:
Pan Cancer Immune panel
GPL25714-431


title: AML432

description:
Pan Cancer Immune panel
GPL25714-432


title: AML426

description:
Pan Cancer Immune panel
GPL25714-426


title: AML425

description:
Pan Cancer Immune panel
GPL25714-425


title: AML424

description:
Pan Cancer Immune panel
GPL25714-424


title: AML423

description:
Pan Cancer Immune panel
GPL25714-423


title: AML422

description:
Pan Cancer Immune panel
GPL25714-422


title: AML420

description:
Pan Cancer Immune panel
GPL25714-420


title: AML419

description:
Pan Cancer Immune panel
GPL25714-419


title: AML427

description:
Pan Cancer Immune panel
GPL25714-427


title: AML416

description:
Pan Cancer Immune panel
GPL25714-416


title: AML418

description:
Pan Cancer Immune panel
GPL25714-418


title: AML414

description:
Pan Cancer Immune panel
GPL25714-414


title: AML413

description:
Pan Cancer Immune panel
GPL25714-413


title: AML410

description:
Pan Cancer Immune panel
GPL25714-410


title: AML417

description:
Pan Cancer Immune panel
GPL25714-417


title: AML412

description:
Pan Cancer Immune panel
GPL25714-412


title: AML411

description:
Pan Cancer Immune panel
GPL25714-411


title: AML415

description:
Pan Cancer Immune panel
GPL25714-415


title: Cardiomyocytes, Treated, Low, 9 h (ms-69)

value: Heart

value: Cardiomyocytes


title: AML409

description:
Pan Cancer Immune panel
GPL25714-409


title: AML402

description:
Pan Cancer Immune panel
GPL25714-402


title: AML406

description:
Pan Cancer Immune panel
GPL25714-406


title: AML405

description:
Pan Cancer Immune panel
GPL25714-405


title: AML403

description:
Pan Cancer Immune panel
GPL25714-403


title: AML404

description:
Pan Cancer Immune panel
GPL25714-404


title: AML401

description:
Pan Cancer Immune panel
GPL25714-401


title: AML400

description:
Pan Cancer Immune panel
GPL25714-400


title: AML408

description:
Pan Cancer Immune panel
GPL25714-408


title: AML397

description:
Pan Cancer Immune panel
GPL25714-397


title: AML398

description:
Pan Cancer Immune panel
GPL25714-398


title: AML399

description:
Pan Cancer Immune panel
GPL25714-399


title: AML396

description:
Pan Cancer Immune panel
GPL25714-396


title: AML421

description:
Pan Cancer Immune panel
GPL25714-421


title: AML407

description:
Pan Cancer Immune panel
GPL25714-407


title: AML395

description:
Pan Cancer Immune panel
GPL25714-395


title: Cardiomyocytes, Vehicle, 9 h (ms-61)


title: AML371

description: Pan Cancer Immune panel

source_name: AML_bone marrow_Diagnosis


title: AML372

description: Pan Cancer Immune panel


title: AML373

description: Pan Cancer Immune panel


title: AML392

description: Pan Cancer Immune panel


title: AML393

description: Pan Cancer Immune panel


title: AML394

description: Pan Cancer Immune panel


title: AML389

description: Pan Cancer Immune panel


title: AML388

description: Pan Cancer Immune panel


title: AML391

description: Pan Cancer Immune panel


title: AML390

description: Pan Cancer Immune panel


title: AML387

description: Pan Cancer Immune panel


title: AML370

description: Pan Cancer Immune panel


title: AML365

description: Pan Cancer Immune panel


title: AML366

description: Pan Cancer Immune panel


title: AML367

description: Pan Cancer Immune panel


title: AML369

description: Pan Cancer Immune panel


title: AML368

description: Pan Cancer Immune panel


title: AML375

description: Pan Cancer Immune panel


title: AML374

description: Pan Cancer Immune panel


title: AML376

description: Pan Cancer Immune panel


title: AML381

description: Pan Cancer Immune panel


title: AML377

description: Pan Cancer Immune panel


title: AML378

description: Pan Cancer Immune panel


title: AML385

description: Pan Cancer Immune panel


title: AML380

description: Pan Cancer Immune panel


title: AML386

description: Pan Cancer Immune panel


title: AML382

description: Pan Cancer Immune panel


title: AML379

description: Pan Cancer Immune panel


title: AML384

description: Pan Cancer Immune panel


title: AML360

description: Pan Cancer Immune panel


title: AML362

description: Pan Cancer Immune panel


title: AML361

description: Pan Cancer Immune panel


title: AML363

description: Pan Cancer Immune panel


title: AML364

description: Pan Cancer Immune panel


title: AML356

description: Pan Cancer Immune panel


title: AML354

description: Pan Cancer Immune panel


title: AML355

description: Pan Cancer Immune panel


title: AML349

description: Pan Cancer Immune panel


title: AML347

description: Pan Cancer Immune panel


title: AML348

description: Pan Cancer Immune panel


title: AML352

description: Pan Cancer Immune panel


title: AML350

description: Pan Cancer Immune panel


title: AML353

description: Pan Cancer Immune panel


title: AML344

description: Pan Cancer Immune panel


title: AML351

description: Pan Cancer Immune panel


title: AML343

description: Pan Cancer Immune panel


title: AML342

description: Pan Cancer Immune panel


title: AML335

description: Pan Cancer Immune panel


title: AML337

description: Pan Cancer Immune panel


title: AML346

description: Pan Cancer Immune panel


title: AML341

description: Pan Cancer Immune panel


title: AML338

description: Pan Cancer Immune panel


title: AML357

description: Pan Cancer Immune panel


title: AML345

description: Pan Cancer Immune panel


title: AML359

description: Pan Cancer Immune panel


title: AML336

description: Pan Cancer Immune panel


title: AML340

description: Pan Cancer Immune panel


title: AML332

description: Pan Cancer Immune panel


title: AML330

description: Pan Cancer Immune panel


title: AML334

description: Pan Cancer Immune panel


title: AML331

description: Pan Cancer Immune panel


title: AML333

description: Pan Cancer Immune panel


title: AML339

description: Pan Cancer Immune panel


title: AML358

description: Pan Cancer Immune panel


title: AML327

description: Pan Cancer Immune panel


title: AML329

description: Pan Cancer Immune panel


title: AML328

description: Pan Cancer Immune panel


title: AML326

description: Pan Cancer Immune panel


title: AML325

description: Pan Cancer Immune panel


title: AML319

description: Pan Cancer Immune panel


title: AML321

description: Pan Cancer Immune panel


title: AML324

description: Pan Cancer Immune panel


title: AML309

description: Pan Cancer Immune panel


title: AML320

description: Pan Cancer Immune panel


title: AML316

description: Pan Cancer Immune panel


title: AML318

description: Pan Cancer Immune panel


title: AML311

description: Pan Cancer Immune panel


title: AML313

description: Pan Cancer Immune panel


title: AML314

description: Pan Cancer Immune panel


title: AML317

description: Pan Cancer Immune panel


title: AML308

description: Pan Cancer Immune panel


title: AML315

description: Pan Cancer Immune panel


title: AML307

description: Pan Cancer Immune panel


title: AML310

description: Pan Cancer Immune panel


title: AML306

description: Pan Cancer Immune panel


title: AML305

description: Pan Cancer Immune panel


title: AML304

description: Pan Cancer Immune panel


title: AML303

description: Pan Cancer Immune panel


title: AML302

description: Pan Cancer Immune panel


title: AML312

description: Pan Cancer Immune panel


title: AML301

description: Pan Cancer Immune panel


title: AML299

description: Pan Cancer Immune panel


title: AML300

description: Pan Cancer Immune panel


title: AML298

description: Pan Cancer Immune panel


title: AML297

description: Pan Cancer Immune panel


title: AML296

description: Pan Cancer Immune panel


title: AML295

description: Pan Cancer Immune panel


title: AML294

description: Pan Cancer Immune panel


title: AML292

description: Pan Cancer Immune panel


title: AML287

description: Pan Cancer Immune panel


title: AML289

description: Pan Cancer Immune panel


title: AML290

description: Pan Cancer Immune panel


title: AML291

description: Pan Cancer Immune panel


title: AML286

description: Pan Cancer Immune panel


title: AML284

description: Pan Cancer Immune panel


title: AML285

description: Pan Cancer Immune panel


title: AML283

description: Pan Cancer Immune panel


title: AML280

description: Pan Cancer Immune panel


title: AML281

description: Pan Cancer Immune panel


title: AML282

description: Pan Cancer Immune panel


title: AML274

description: Pan Cancer Immune panel


title: AML276

description: Pan Cancer Immune panel


title: AML277

description: Pan Cancer Immune panel


title: AML275

description: Pan Cancer Immune panel


title: AML278

description: Pan Cancer Immune panel


title: AML273

description: Pan Cancer Immune panel


title: AML272

description: Pan Cancer Immune panel


title: AML293

description: Pan Cancer Immune panel


title: AML271

description: Pan Cancer Immune panel


title: AML270

description: Pan Cancer Immune panel


title: AML268

description: Pan Cancer Immune panel


title: AML269

description: Pan Cancer Immune panel


title: AML288

description: Pan Cancer Immune panel


title: AML279

description: Pan Cancer Immune panel


title: AML265

description: Pan Cancer Immune panel


title: AML266

description: Pan Cancer Immune panel


title: AML261

description: Pan Cancer Immune panel


title: AML260

description: Pan Cancer Immune panel


title: AML264

description: Pan Cancer Immune panel


title: AML257

description: Pan Cancer Immune panel


title: AML258

description: Pan Cancer Immune panel


title: AML259

description: Pan Cancer Immune panel


title: AML256

description: Pan Cancer Immune panel


title: AML255

description: Pan Cancer Immune panel


title: AML267

description: Pan Cancer Immune panel


title: AML253

description: Pan Cancer Immune panel


title: AML252

description: Pan Cancer Immune panel


title: AML249

description: Pan Cancer Immune panel


title: AML248

description: Pan Cancer Immune panel


title: AML251

description: Pan Cancer Immune panel


title: AML263

description: Pan Cancer Immune panel


title: AML262

description: Pan Cancer Immune panel


title: AML245

description: Pan Cancer Immune panel


title: AML240

description: Pan Cancer Immune panel


title: AML243

description: Pan Cancer Immune panel


title: AML241

description: Pan Cancer Immune panel


title: AML242

description: Pan Cancer Immune panel


title: AML246

description: Pan Cancer Immune panel


title: AML254

description: Pan Cancer Immune panel


title: AML247

description: Pan Cancer Immune panel


title: AML250

description: Pan Cancer Immune panel


title: AML322

description: Pan Cancer Immune panel


title: AML238

description: Pan Cancer Immune panel


title: AML244

description: Pan Cancer Immune panel


title: AML239

description: Pan Cancer Immune panel


title: AML235

description: Pan Cancer Immune panel


title: AML233

description: Pan Cancer Immune panel


title: AML231

description: Pan Cancer Immune panel


title: AML232

description: Pan Cancer Immune panel


title: AML237

description: Pan Cancer Immune panel


title: AML230

description: Pan Cancer Immune panel


title: AML236

description: Pan Cancer Immune panel


title: AML229

description: Pan Cancer Immune panel


title: AML228

description: Pan Cancer Immune panel


title: AML225

description: Pan Cancer Immune panel


title: AML219

description: Pan Cancer Immune panel


title: AML224

description: Pan Cancer Immune panel


title: AML220

description: Pan Cancer Immune panel


title: AML223

description: Pan Cancer Immune panel


title: AML234

description: Pan Cancer Immune panel


title: AML222

description: Pan Cancer Immune panel


title: AML221

description: Pan Cancer Immune panel


title: AML218

description: Pan Cancer Immune panel


title: AML217

description: Pan Cancer Immune panel


title: AML215

description: Pan Cancer Immune panel


title: AML216

description: Pan Cancer Immune panel


title: AML214

description: Pan Cancer Immune panel


title: AML213

description: Pan Cancer Immune panel


title: AML212

description: Pan Cancer Immune panel


title: AML226

description: Pan Cancer Immune panel


title: AML227

description: Pan Cancer Immune panel


title: AML206

description: Pan Cancer Immune panel


title: AML323

description: Pan Cancer Immune panel


title: AML207

description: Pan Cancer Immune panel


title: AML208

description: Pan Cancer Immune panel


title: AML210

description: Pan Cancer Immune panel


title: AML204

description: Pan Cancer Immune panel


title: AML202

description: Pan Cancer Immune panel


title: AML201

description: Pan Cancer Immune panel


title: AML200

description: Pan Cancer Immune panel


title: AML203

description: Pan Cancer Immune panel


title: AML199

description: Pan Cancer Immune panel


title: AML198

description: Pan Cancer Immune panel


title: AML195

description: Pan Cancer Immune panel


title: AML196

description: Pan Cancer Immune panel


title: AML193

description: Pan Cancer Immune panel


title: AML194

description: Pan Cancer Immune panel


title: AML209

description: Pan Cancer Immune panel


title: AML191

description: Pan Cancer Immune panel


title: AML192

description: Pan Cancer Immune panel


title: AML189

description: Pan Cancer Immune panel


title: AML197

description: Pan Cancer Immune panel


title: AML205

description: Pan Cancer Immune panel


title: AML211

description: Pan Cancer Immune panel


title: AML188

description: Pan Cancer Immune panel


title: AML190

description: Pan Cancer Immune panel


title: AML187

description: Pan Cancer Immune panel


title: Keratoconus patient 18

city: New York

first: Shukti

last: Chakravarti

address: 430 E 29th St

department: Department of Ophthalmology and Pathology

institute: NYU Langone Medical Center

description: King Khalid Eye hospital, Riyadh, Saudi Arabia

data_processing:
Raw images were generated using the HiSeq Control software v2.2.38, base calling using an integrated primary analysis software, Real time Analysisv1.18.61.0, and converted into FASTQ files using the Illumina package bcl2fastq v1.8.4.
The alignment of reads against the human reference genome hg19 was performed using the STAR 2.6.0a software.
Reads Per Kilobase of exon per Megabase of library size (RPKM) 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.
Gene expression quantification using Cufflinks 2.2.1.
The differential expression analysis was conducted by Cuffdiff and DESeq2 (version: 1.24.0).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw reads count for every gene and every sample

source_name: Cornea

extract_protocol:
Total RNA was isolated from individual corneas by homogenization in 1 ml  TRIzol Reagent (Life Technologies -15596–026) at room temperature and  chloroform-extracted. The RNA in the aqueous phase was precipitated using  0.5 ml of 100% isopropanol and collected by centrifugation at 12,000 g,  washed with 75% ethanol and resuspended in RNAse-free water.
TruSeq stranded RNA library kit construction protocol

tag: disease

value: Keratoconus

tag: age

value: M

tag: ancestry

value: Middle Eastern

tag: atopy/allergy

value: Absent

tag: disease severity

value: Severe


title: Keratoconus patient 19

value: F


title: Keratoconus patient 17


title: AML186

description: Pan Cancer Immune panel


title: Keratoconus patient 15


title: Keratoconus patient 14

value: Vernal keratoconjuctivitis


title: Keratoconus patient 12


title: Keratoconus patient 13


title: Keratoconus patient 11

value: Seasonal allergic conjunctivitis


title: AML184

description: Pan Cancer Immune panel


title: AML182

description: Pan Cancer Immune panel


title: AML183

description: Pan Cancer Immune panel


title: Keratoconus patient 7

description: Wilmer Eye Institute, Johns Hopkins School of medicine, Baltimore

value: African American


title: AML181

description: Pan Cancer Immune panel

value: patient with acute myeloid leukaemia


title: Keratoconus patient 1

value: Unknown


title: AML179

description: Pan Cancer Immune panel

value: Bone Marrow


title: Keratoconus patient 2


title: Keratoconus patient 4

value: Eczema, hay fever, allergies


title: Keratoconus patient 6

value: Asthma


title: Keratoconus patient 8


title: AML178

description: Pan Cancer Immune panel

value: Diagnosis


title: AML180

description: Pan Cancer Immune panel


title: Keratoconus patient 3


title: Keratoconus patient 5


title: Keratoconus patient 10


title: Keratoconus patient 9


title: Control 7

description: Lions Eye Institute for Transplant and Research, Florida

value: healthy control


title: AML177

description: Pan Cancer Immune panel


title: Keratoconus patient 16


title: Control 6


title: Control 5


title: AML185

description: Pan Cancer Immune panel


title: AML176

description: Pan Cancer Immune panel


title: Control 4


title: Control 2

value: European American


title: Control 3


title: Control 1


title: AML174

description: Pan Cancer Immune panel


title: MOLT4 RNA-seq

city: West Haven

first: Sarah

middle: A

last: Slavoff

state: Connecticut

address: Yale University West Campus-Building 600

department: Chemistry

institute: Yale University- West Campus

data_processing:
Basecalls were performed with CASAVA version 1.8.2
75bp paired end reads were aligned to the GRCh38.p13 genome and transcriptome annotations using tophat version 2.1.1 with default parameters
Gene expression was quantified using cufflinks version 2.2.2 with the cuffdiff command using the GRCh38.p13 transcriptome as reference and default parameters.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited file which contains FPKM values and statistical comparison between K562 and Molt4 gene expression

source_name: MOLT4 cell line

growth_protocol: the cells were grown at 37 C/5% CO2 in DMEM supplemented with 10% FBS/1% Pen-strep

extract_protocol:
whole RNA was extracted from 1 T-25 flask using the Qiagen Rneasy Kit, according to the manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: cell type

value: T lymphoblast


title: AML175

description: Pan Cancer Immune panel


title: K562 RNA-seq

source_name: K562 cell line

value: erythrocyte


title: AML173

description: Pan Cancer Immune panel


title: MDA-MB-231_TEAD1_DMSO_1

city: South San Francisco

first: Rohit

last: Reja

address: 1 DNA Way

institute: Genentech

data_processing:
Illumina v1.8 software used for basecalling
Raw reads were aligned to the human reference GRCh38) using GSNAP (with parameters -M 2 -n 10 -B 2 -i 1 --pairmax-dna=1000 --terminal-threshold=1000 --gmap-mode=none --clip-overlap). Reads were filtered to include only uniquely mapped reads.
MultiGPS (v.0.7.4) was used to call peaks per sample relative to input. Statistically significant binding events were determined using the following criteria: fold enrichment values ≥1.5 and q < 0.001
Genome_build: GRCh38
Supplementary_files_format_and_content: Peak files are in XLS format

source_name: human breast cancer cells

extract_protocol:
Cells were plated and dosed with either DMSO or small molecular (Compound 2) at 10 mM for 24 hrs. For dual cross-linking, cells were first incubated with 2 mM disuccinimidyl glutarate (ThermoFisher, 20593) for 20 min and then with formaldehyde at 1% (v/v) for an additional 10 min. Nuclei were extracted and sheared to an average length of 300-600 bp using truChIP Chromatin Shearing Kit (Covaris, 520154) following the manufacturer’s guidelines. All chromatin immunoprecipitation samples were supplemented with 20 ng of Drosophila chromatin (Active Motif, 53083) and 2 µg of a Drosophila-specific antibody (Active Motif, 61686) for normalization of ChIP-seq samples. For immunoprecipitations, 20 µg of sheared chromatin was incubated with 3-5 µg of antibody at 4 °C overnight. Complexes were captured by incubating with 40 mL Protein A Dynabeads (ThermoFisher, 10002D) for 2 hr at 4 °C. ChIP’d DNA was purified using ChIP DNA Clean & Concentrator (Zymo Research, D5205) following elution from magnetic beads, digestion with RNase and proteinase K, and reversal of crosslink by heating at 65 °C. 10 ng of purified DNA was used to generate libraries with the Ovation Ultra Low Library Prep Kit (NuGEN, 0344NB-32). Sequencing was performed on an Illumina HiSeq 2500 platform.
Libraries were prepared using standard protocols for the Ovation Ultralow System. Briefly, samples were PCR-amplified and sized using the Agilent 2100Bioanalyzer. Barcoded libraries were sequenced 50 bp single end on HiSeq 2500 (Illumina).

value: 51 years

tag: chip antibody

value: anti TEF1/TEAD-1 (Abcam, ab133533)

value: DMSO


title: MDA-MB-231_TEAD1_treat_1

value: small molecular (Compound 2) at 10 mM


title: MDA-MB-231_TEAD1_DMSO_2


title: MDA-MB-231_TEAD1_treat_2


title: 15089

city: Burnaby

first: Amy

middle: H.

last: Lee

state: BC

address: 8888 University Drive

department: Molecular Biology and Biochemistry

country: Canada

institute: Simon Fraser University

data_processing:
Samples were pooled and sequenced on a HiSeq 2500 sequencer (Illumina), using the High Output 100-bp single-end run, at the University of British Columbia Sequencing Centre.
FASTQ reads were aligned to the GRCh37(hg19) human reference genome using the STAR(v2.5) aligner
Count generation was done using htseq-count(v0.6.1p1).
Genome_build: GRCh37(hg19) human reference
Supplementary_files_format_and_content: tab deliminted files containing uniquely mapped reads per gene for each sample

source_name: Whole blood

extract_protocol:
RNA was extracted from stabilised blood using an amended version of the PAXgene™ Blood RNA System Kit (PreAnalytix; Qiagen/Becton Dickson). Briefly, samples were thawed at room temperature for up to 2 hours.
cDNA library synthesis were prepared using the KAPA Stranded RNA-seq Library Preparation Kit as per the manufacturer’s instructions

tag: gestational age (days)

tag: birth weight (grams)

tag: Sex

value: female

tag: clinical group

value: Confirmed late-onset sepsis


title: Detroit_X1_562_TEAD1_treat_2

source_name: human pharynx cancer cells

value: Adult


title: Detroit_X1_562_TEAD1_DMSO_1


title: 15106

value: male


title: MDA-MB-231_input


title: Detroit_X1_562_input


title: 15080

value: No late-onset sepsis


title: Detroit_X1_562_TEAD1_treat_1


title: Detroit_X1_562_TEAD1_DMSO_2


title: 15102


title: AML171

description: Pan Cancer Immune panel

value: patient with acute myeloid leukaemia

tag: tissue

value: Bone Marrow


title: AML170

description: Pan Cancer Immune panel

tag: subject status


title: AML168

description: Pan Cancer Immune panel

tag: age (years)


title: AML169

description: Pan Cancer Immune panel

tag: disease stage at sampling


title: AML172

description: Pan Cancer Immune panel


title: AML167

description: Pan Cancer Immune panel


title: AML166

description: Pan Cancer Immune panel


title: 15055

value: Possible late-onset sepsis


title: 15062


title: 15076


title: 15070


title: 15054


title: 15053


title: AML165

description: Pan Cancer Immune panel

value: Diagnosis


title: AML164

description: Pan Cancer Immune panel


title: 15045


title: 15018


title: 15017


title: 15024


title: 15022


title: 15011


title: AML162

description: Pan Cancer Immune panel


title: 15004


title: AML161

description: Pan Cancer Immune panel


title: At_Feeding4

city: Cambridge

first: Archana

last: Singh

state: England

address: Downing Street

department: Plant Science

institute: Cambridge University

data_processing:
Raw fastq files were converted to fasta format.
Adapter sequences and reads less than 20 nt were trimmed using Trim Galore
Trimmed reads were aligned to the human genome (v.38) using HISAT2
Count matrix for genes was created using Kallisto
Differential expression analysis was done using the DESeq2 package available in R
Genome_build: Arabidopsis thaliana

organism: Arabidopsis thaliana

source_name: Leaf

growth_protocol: A.thaliana plants were grown on 20°C .

extract_protocol:
Total RNA was extracted  using RNeasy Mini Kit (250) from QIAGEN
Strand-specific libraries constructed using the Illumina TruSeq RNA Library Preparation kit following manufacturer’s instructions

treatment_protocol: Aphids were caged on rosette leaves on 4-week-old A. thaliana plants for 24 hrs.

tag: line

value: Caged with Myzus persicae

value: Leaf


title: 15003


title: AML160

description: Pan Cancer Immune panel


title: At_Feeding2


title: At_Feeding3


title: AML159

description: Pan Cancer Immune panel


title: EXP1.KIX.MWM.3

city: Iowa City

first: Ethan

last: Bahl

address: 25 S Grand Ave

institute: University of Iowa

description:
total RNA (Ribo-Zero gold)
EXP1.KIX.LEARN.3
processed data file: counts_all.csv

data_processing:
Reads were aligned to the mm10 genome build using STAR version 020201, with default parameters from bcbio-nextgen version 1.0.7.
BAM files were indexed and sorted using SAMtools version 1.6, with default parameters from bcbio-nextgen version 1.0.7.
Gene-level counts were quantified using featureCounts version 1.4.4, with default parameters from bcbio-nextgen version 1.0.7.
Genome_build: mm10 (GRCm38), GENCODE release M14
Supplementary_files_format_and_content: counts_all.csv: Comma-separated text file containing gene-level counts for all samples.

source_name: dorsal hippocampus

extract_protocol:
Dorsal hippocampus were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (poly-A selection or Ribo-zero gold) for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/background

value: dorsal hippocampus

tag: experiment

tag: genotype

value: CBP KIX/KIX

tag: exposure

value: learning

tag: paradigm

value: MWM

tag: group

tag: replicate


title: At_Control3

value: Control


title: At_Control4


title: AML158

description: Pan Cancer Immune panel


title: AML156

description: Pan Cancer Immune panel


title: At_Control2


title: At_Control1


title: EXP1.KIX.MWM.1

description:
total RNA (Ribo-Zero gold)
EXP1.KIX.LEARN.1
processed data file: counts_all.csv


title: EXP1.KIX.MWM.2

description:
total RNA (Ribo-Zero gold)
EXP1.KIX.LEARN.2
processed data file: counts_all.csv


title: AML163

description: Pan Cancer Immune panel


title: AML155

description: Pan Cancer Immune panel


title: AML154

description: Pan Cancer Immune panel


title: EXP1.WT.MWM.3

description:
total RNA (Ribo-Zero gold)
EXP1.WT.LEARN.3
processed data file: counts_all.csv

value: WT


title: At_Feeding1


title: AML153

description: Pan Cancer Immune panel


title: EXP1.WT.HOME.3

description:
total RNA (Ribo-Zero gold)
EXP1.WT.HOME.3
processed data file: counts_all.csv

value: homecage


title: EXP1.WT.HOME.2

description:
total RNA (Ribo-Zero gold)
EXP1.WT.HOME.2
processed data file: counts_all.csv


title: EXP1.WT.MWM.1

description:
total RNA (Ribo-Zero gold)
EXP1.WT.LEARN.1
processed data file: counts_all.csv


title: EXP1.WT.MWM.2

description:
total RNA (Ribo-Zero gold)
EXP1.WT.LEARN.2
processed data file: counts_all.csv


title: AML157

description: Pan Cancer Immune panel


title: AML151

description: Pan Cancer Immune panel


title: S-15: Skin

city: Shanghai

first: Hailiang

address: NO 1239, siping road

institute: Tongji university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to GRCm38.84 whole genome using tophat2
Genes expression level is quantified by cuffquant.
Reads aligned to genes were calculated using cufflinks.
Genome_build: GRCm38.84
Supplementary_files_format_and_content: Read count and FPKM ( Fragments Per Kilobase Million) for each Sample

source_name: Skin

extract_protocol:
Back skin was unhaired and digested with elastase(0.2mg/ml) in DMEM medium for 20min at 37°C, then the tissue was minced and digested with type Ⅳ collagenase (4 mg/ml) in DMEM medium for 1.5h at 37°C. Digested tissue was successively filtered through 70-μm and 40-μm cell strainers (BD Biosciences) and then centrifuged with 500g for 5min. The cell pellet was resuspended with PBS. Tomato+ cells were sorted by Bio-Rad S3e and then single cells were picked with fluorescence microscope.
Libraries were prepared according to Nextera® XT DNA Library Prep Kit for Illumina  (Cat# FC-131-1096)
RNA-seq (SMART-Seq v4 3’ DE Kit)

tag: strain

value: Skin

tag: developmental stage

value: adult

tag: treatment

value: Injection of Tamoxifen 2mg/30g a mouse once a day for 3 days


title: EXP1.WT.HOME.1

description:
total RNA (Ribo-Zero gold)
EXP1.WT.HOME.1
processed data file: counts_all.csv

tag: Sex

value: male


title: AML152

description: Pan Cancer Immune panel

value: patient with acute myeloid leukaemia


title: S-17: Skin


title: S-16: Skin


title: AML150

description: Pan Cancer Immune panel

value: Bone Marrow


title: S-14: Skin


title: S-12: Skin


title: S-13: Skin


title: S-11: Skin


title: S-10: Skin


title: AML148

description: Pan Cancer Immune panel


title: AML147

description: Pan Cancer Immune panel


title: S-9: Skin


title: S-8: Skin


title: S-7: Skin


title: AML146

description: Pan Cancer Immune panel


title: S-6: Skin


title: S-5: Skin


title: S-2: Skin


title: S-3: Skin


title: S-4: Skin


title: AML149

description: Pan Cancer Immune panel


title: F_15: Inguinal adipose tissue

source_name: Inguinal adipose tissue

extract_protocol:
Adipose tissues were washed with PBS, minced, and digested with type II collagenase (2 mg/ml) in KRBB containing 10 mM HEPES (pH 7.4), and 3% BSA for 1 hr at 37°C.Digested tissue was successively filtered through 70-μm and 40-μm cell strainers (BD Biosciences) and then centrifuged with 500g for 5min. The cell pellet was resuspended with PBS. Tomato+ cells were sorted by Bio-Rad S3e and then single cells were picked with fluorescence microscope.
Libraries were prepared according to Nextera® XT DNA Library Prep Kit for Illumina  (Cat# FC-131-1096)
RNA-seq (SMART-Seq v4 3’ DE Kit)

value: Inguinal adipose tissue


title: S-1: Skin


title: F_12: Inguinal adipose tissue


title: F_14: Inguinal adipose tissue


title: F_11: Inguinal adipose tissue


title: F_10: Inguinal adipose tissue


title: AML143

description: Pan Cancer Immune panel

value: Diagnosis


title: AML140

description: Pan Cancer Immune panel


title: F_9: Inguinal adipose tissue


title: F_8: Inguinal adipose tissue


title: AML141

description: Pan Cancer Immune panel


title: F_13: Inguinal adipose tissue


title: AML142

description: Pan Cancer Immune panel


title: F_6: Inguinal adipose tissue


title: AML137

description: Pan Cancer Immune panel


title: AML139

description: Pan Cancer Immune panel


title: F_7: Inguinal adipose tissue


title: AML138

description: Pan Cancer Immune panel


title: F_5: Inguinal adipose tissue


title: AML136

description: Pan Cancer Immune panel


title: F_4: Inguinal adipose tissue


title: AML145

description: Pan Cancer Immune panel


title: AML144

description: Pan Cancer Immune panel


title: F_1: Inguinal adipose tissue


title: AML135

description: Pan Cancer Immune panel


title: B_14: Bone

source_name: Bone

extract_protocol:
Tibiae, radii and ulnae were flushed with a needle to remove the marrow. The bones were washed thoroughly with PBS for at least 5 times. Then the bones were minced and digested with type II collagenase at 37°C. Digested tissue was successively filtered through 70-μm and 40-μm cell strainers (BD Biosciences) and then centrifuged with 500g for 5min. The cell pellet was resuspended with PBS. Tomato+ cells were sorted by Bio-Rad S3e and then single cells were picked with fluorescence microscope.
Libraries were prepared according to Nextera® XT DNA Library Prep Kit for Illumina  (Cat# FC-131-1096)
RNA-seq (SMART-Seq v4 3’ DE Kit)

value: bone


title: AML134

description: Pan Cancer Immune panel


title: B_12: Bone


title: B_9: Bone


title: B_8: Bone


title: B_7: Bone


title: B_5: Bone


title: F_3: Inguinal adipose tissue


title: B_6: Bone


title: B_10: Bone


title: B_13: Bone


title: B_4: Bone


title: B_3: Bone


title: 75_GLPV

city: Gödöllő

first: Éva

last: Várallyay

address: 4 Szent-Györgyi Albert Street

department: Agricultural Biotechnology Institute

country: Hungary

institute: National Agricultural Research and Innovation Centre

description: pooled RNA from different organs originated from forced twigs

data_processing:
The quality check of the sequenced small RNA libraries was done by FastQC Program and CLC Genomic Workbench 11
Trimming of raw reads was performed using the CLC Genomic Workbench 11
Removing redundant reads using the CLC Genomic Workbench 11
Supplementary_files_format_and_content: count

organism: Vitis vinifera

source_name: leaf, flower, tendril, shoot tip sample

extract_protocol:
CTAB method (Gambino, 2008: https://doi.org/10.1002/pca.1078 )
modified Illumina Trueseq small RNA kit protocol: https://doi.org/10.1007/978-1-4939-7683-6_9

tag: cultivar

tag: plant source

value: different organs from forced twigs of Baco22 plant

tag: agent

value: Grapevine line pattern virus


title: F_2: Inguinal adipose tissue

tag: tissue


title: B_2: Bone


title: AML132

description: Pan Cancer Immune panel

tag: subject status

tag: age (years)

tag: disease stage at sampling


title: AML133

description: Pan Cancer Immune panel


title: AML129

description: Pan Cancer Immune panel


title: B_1: Bone


title: Zeb2 cKO 3

city: Utrecht

first: Eva

last: van Rooij

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
strand-specific single-end 75bp reads were generated on an Illumina NextSeq 500
Reads were mapped to mouse reference genome GRCm38/mm10 and quantified using the ensembl database for gene annotations
Differential expression was calculated using DESeq v1.2 with pooled dispersion estimates
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: .txt file containing the count matric of all samples for each gene

source_name: Zeb2 cKO Border region 14p/MI

growth_protocol: Mouse were maintained under standard conditions

extract_protocol:
Border region of the infarcted region was isolated. RNA was isolated from tissue using Trizol according to manufacturer's protocol
libraries were prepared from non-ribosomal RNA using the TruSeq Stranded Total RNA Library Prep Kit (Illumina) with Ribo-Zero according to the manufacturer’s protocol.

treatment_protocol: Mice received a permanent occlusion of the LAD artery

value: C57BL/6J (backcrossed)

value: heart

tag: tissue site

value: Border region of infarct

tag: time after infarct

value: 14 days

value: Zeb2 cKO


title: AML128

description: Pan Cancer Immune panel


title: AML130

description: Pan Cancer Immune panel


title: Zeb2 cKO 2

tag: genotype


title: B_11: Bone


title: Zeb2 cKO 1


title: Nb-RdR1-ToLCV-2

description: small RNA

data_processing:
Raw FASTQ files were converted to FASTA format. Reads containing unassigned nucleotides were excluded.
The 3’ adapter was trimmed by using first 8 nt of the 3’ HiSeq 2500 adapter (TGGAATTC).
The HD reads were mapped (no mismatch allowed) to the N. benthamiana genome and ToLCV genome (DNA-A: AY190290; DNA-B: AY190291) using PatMaN.
The HD signatures (four assigned degenerate nucleotides at the ligating ends) of the reads were also trimmed.
The latest set of plant miRNAs were downloaded from miRBase (v21).
Differential expression analysis was performed by DESeq2  package of R.

organism: Nicotiana benthamiana

source_name: Leaf sample

growth_protocol: Wild-type and NtRDR1 N benthamiana plants were grown at 22°C .

extract_protocol:
Total RNA from the leaf samples were isolated by TRIzol reagent (Invitrogen)
sRNA cDNA-libraries were prepared  using HD adapters. sRNA libraries were generated from the total RNA isolated from wild-type N. benthamiana and NtRDR1 N. benthamiana.

treatment_protocol: Infectious Agrobacterium tumefaciens (A. tumefaciens) strain EHA105 harbouring ToLCV was inoculated in wild-type N. benthamiana and NtRDR1 N. benthamiana.

value: NtRDR1 overexpression line

value: ToLCV-infected

value: Leaf sample


title: Nb-RdR1-ToLCV-3

description: small RNA


title: AML126

description: Pan Cancer Immune panel


title: AML131

description: Pan Cancer Immune panel


title: AML124

description: Pan Cancer Immune panel


title: Nb-RdR1-ToLCV-1

description: small RNA


title: WT 2

source_name: WT Border region 14p/MI

value: WT


title: Nb-ToLCV-2

description: small RNA

value: Wild type


title: Nb-ToLCV-3

description: small RNA


title: WT 1


title: WT 3


title: AML123

description: Pan Cancer Immune panel

value: patient with acute myeloid leukaemia


title: AML127

description: Pan Cancer Immune panel

value: Bone Marrow


title: Nb-ToLCV-1

description: small RNA


title: AML122

description: Pan Cancer Immune panel


title: AML121

description: Pan Cancer Immune panel


title: Hand2-M13

city: Oklahoma City

first: Jonathan

middle: D

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes and Human Disease

institute: Oklahoma Medical Research Foundation

data_processing:
none provided by the submitter
Genome_build: mm10
Supplementary_files_format_and_content: coujnts

source_name: EDL muscle

extract_protocol: Illumina TruSeq v2

value: EDL muscle

value: Male

tag: age in months


title: Nb-RdR1-3

description: small RNA

value: mock-treated


title: Hand2-M12


title: Nb-RdR1-2

description: small RNA


title: Hand2-4


title: Hand2-F12

value: Female


title: Nb-RdR1-1

description: small RNA


title: AML125

description: Pan Cancer Immune panel

source_name: AML_bone marrow_Diagnosis

value: Diagnosis


title: Nb-WT-3

description: small RNA


title: Hand2-12


title: AML120

description: Pan Cancer Immune panel


title: AML118

description: Pan Cancer Immune panel


title: AML119

description: Pan Cancer Immune panel


title: Hand2-11


title: Nb-WT-2

description: small RNA


title: AML117

description: Pan Cancer Immune panel


title: Hand2-10


title: AML116

description: Pan Cancer Immune panel


title: Nb-WT-1

description: small RNA


title: EV-M9

description: Empty Vector


title: AML115

description: Pan Cancer Immune panel


title: EV-M8

description: Empty Vector


title: AML114

description: Pan Cancer Immune panel


title: EV-M7

description: Empty Vector


title: AML112

description: Pan Cancer Immune panel


title: EV-M11

description: Empty Vector


title: SPT6_DMSO_R2

city: Leicester

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

institute: University of Leicester

description: Corresponding Input is ChIP-seq Input LEO1 DMSO R2

data_processing:
Adapters were trimmed with Cutadapt v1.9.1
Mapping to the hg38 genome was performed with Tophat2 v2.1.0 (mNET-seq) or with Bowtie2 v2.2.5 (ChIP-seq)
Extraction of properly paired and properly mapped reads and Bam files sorting and indexing were done with SAMtools v. 1.6
Mapped reads were de-duplicated with Picard (ChIP-seq)
Bigwig files were generated with the Deeptools2 bamCoverage tool
Genome_build: hg38 (except HEK293 CDK12as Pol II, Ser2P, and Ser5P ChIP-seq which are mapped on the hg19)
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples

source_name: HEK293 CDK12as

growth_protocol: HEK293 CDK12as cells were maintained in DMEM with 10% fetal bovine serum

extract_protocol:
DNA were purified from chromatin IP products. Total RNA were purified from immunoprecipitated RNA polymerase II.
For ChIP-seq, libraries were prepared using Illumina's TruSeq ChIP library Preparation Kit according to Illumina's instructions. For mNET-seq, libraries were prepared using NEBNext® Small RNA Library Prep Set for Illumina, according to NEB's instructions.

treatment_protocol: Cells were treated with 1-NM-PP1 for 15 minutes.

tag: cell line

value: HEK293 CDK12as

tag: antibody

value: 15616S, Cell Signalling Technology

value: DMSO


title: SPT6_NM_15min_R1

value: NM 15 minutes


title: SPT6_NM_15min_R2

description: Corresponding Input is ChIP-seq Input LEO1 NM 15 minutes R2


title: Ser5_NM_15min_R2

value: ab5131:Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) antibody - ChIP Grade. Abcam


title: EV-M10

description: Empty Vector


title: EV-F9

description: Empty Vector


title: Ser5_NM_15min_R1


title: AML110

description: Pan Cancer Immune panel


title: AML109

description: Pan Cancer Immune panel


title: EV-F8

description: Empty Vector


title: Ser5_DMSO_R2


title: Ser5_DMSO_R1


title: EV-F7

description: Empty Vector


title: AML107

description: Pan Cancer Immune panel


title: EV-F11

description: Empty Vector


title: AML105

description: Pan Cancer Immune panel


title: AML113

description: Pan Cancer Immune panel


title: Ser2_NM_15min_R1

value: ab5095:Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) antibody - ChIP Grade. Abcam


title: AML104

description: Pan Cancer Immune panel


title: Ser2_DMSO_R2


title: PACs_SMK_Pool_de_4_ech

city: montreal

first: michel

last: desjarlais

state: quebec

address: 5415 Blvd L’Assomption

department: Department of Ophthalmology,

institute: Maisonneuve-Rosemont Hospital Research Center, University of Montréal, Montréal, Québec, Canada.

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 0 mismatch in the index.
Sequenced fragments were trimmed in for sequencing adapters and candidates longer than 17bp where mapped to the reference genome mm10 using Tophat version 2.0.10.
Known miRNA extracted from miRBase mm10 version 21 were then quantified by counting the number of reads that fall into each of their location on the genome using HTSeq count version 0.5.4, keeping the contribution of ambiguously matched reads.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited files include columns: A. miRNA identifier, B. readcount and C. readcount per million reads sequenced (RPM).

source_name: bone marrow-derived PAC

growth_protocol: PACs extraction from bone marrow and cultured in fibronectine coated dish with EGM for 4 days.

extract_protocol:
Ambion mirVana™ miR isolation kit (Life Technologies)
NGS

treatment_protocol: ischemia induced surgically by feroral artery removal

tag: cell type

value: proangiogenic cells (PACs)

tag: genotype/variation

tag: condition

value: mice subjected to smoking

tag: age of mice

value: 2 months

tag: pathological aspect

value: hindlimg ischemia

tag: other phenotype

value: NV trigger by ischemia


title: AML103

description: Pan Cancer Immune panel

value: patient with acute myeloid leukaemia

value: Bone Marrow


title: SPT6_DMSO_R1

tag: treatment


title: AML102

description: Pan Cancer Immune panel

tag: tissue


title: PACs_CTL_Pool_de_6_ech

value: healty young control mice


title: AML108

description: Pan Cancer Immune panel

tag: subject status