title: Sample262.Pale spear-nosed bat.202894750032_R04C02


title: Sample268.Common vampire bat.202897220006_R04C01

status: Public on Jan 28 2021

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

country: USA

institute: University of California, Los Angeles

description: genomic DNA methylation from tissue=Skin species=Common vampire bat

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the the Beadchip HorvathMammalMethylChip40 using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: SeSaMe normalization as described in W. Zhou et al 2018. PMID: 30085201

label: Cy3 and Cy5

molecule: genomic DNA

organism: Desmodus rotundus

source_name: Skin

label_protocol: Standard Illumina Protocol

growth_protocol: DNA extracted from tissues

extract_protocol: genomic DNA was extracted

treatment_protocol: Standard Illumina Protocol

tag: basename

tag: tissue

value: Skin

tag: canbeusedforagingstudies

value: yes

tag: age (years)

tag: confidenceinageestimate

tag: Sex

value: Male


title: Sample264.Pale spear-nosed bat.202894750032_R06C02

description: genomic DNA methylation from tissue=Skin species=Pale spear-nosed bat

organism: Phyllostomus discolor


title: Sample260.Pale spear-nosed bat.202894750032_R02C02

value: Female


title: Sample261.Common vampire bat.202894750032_R03C02


title: Sample256.Common vampire bat.202894750032_R04C01


title: Sample255.Pale spear-nosed bat.202894750032_R03C01


title: Sample248.Pale spear-nosed bat.202897220061_R02C02


title: Sample249.Pale spear-nosed bat.202897220061_R03C02


title: Sample243.Common vampire bat.202897220061_R03C01


title: Sample246.Pale spear-nosed bat.202897220061_R06C01


title: Sample237.Pale spear-nosed bat.202897220162_R03C02


title: Sample240.Common vampire bat.202897220162_R06C02


title: Sample236.Common vampire bat.202897220162_R02C02


title: Sample251.Pale spear-nosed bat.202897220061_R05C02


title: Sample252.Common vampire bat.202897220061_R06C02


title: Sample244.Pale spear-nosed bat.202897220061_R04C01


title: Sample245.Pale spear-nosed bat.202897220061_R05C01


title: Sample257.Common vampire bat.202894750032_R05C01


title: Sample250.Common vampire bat.202897220061_R04C02


title: Sample241.Common vampire bat.202897220061_R01C01


title: Sample253.Pale spear-nosed bat.202894750032_R01C01


title: Sample238.Common vampire bat.202897220162_R04C02


title: Sample239.Pale spear-nosed bat.202897220162_R05C02


title: Sample247.Common vampire bat.202897220061_R01C02


title: Sample232.Pale spear-nosed bat.202897220162_R04C01


title: Sample258.Pale spear-nosed bat.202894750032_R06C01


title: Sample235.Pale spear-nosed bat.202897220162_R01C02


title: Sample242.Pale spear-nosed bat.202897220061_R02C01


title: Sample233.Pale spear-nosed bat.202897220162_R05C01


title: Sample234.Common vampire bat.202897220162_R06C01


title: Sample259.Common vampire bat.202894750032_R01C02


title: genomic DNA of sample F223_CD8T [201904660013_R06C01]

city: Research Triangle Park

first: Xuting

last: Wang

state: NC

address: 111 TW Alexander Dr

institute: NIEHS/NIH

description: Smoker CD8T genomic DNA

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 and MethylationEPIC Beadchips using standard Illumina protocol

data_processing: Average Beta (processed using minfi preprocessNoob)

label: Cy5 and Cy3

organism: Homo sapiens

label_protocol: 500 ng of DNA was bisulfite converted using the EZ-DNA Methylation kit (Zymo Research)

extract_protocol: Nucleated DNA from blood CD8T cells was collected after sucrose-induced osmotic lysis of cells followed by phenol-chloroform extraction and DNA was stored in Tris-EDTA buffer at -20°C.

tag: cell type

value: CD8 T cells

value: Smoker


title: Sample231.Common vampire bat.202897220162_R03C01


title: genomic DNA of sample F214_CD8T [201904650067_R07C01]

description: Smoker CD8T genomic DNA


title: genomic DNA of sample F213_CD8T [201904650053_R01C01]

description: Smoker CD8T genomic DNA


title: genomic DNA of sample F207_CD8T [201904660189_R05C01]

description: Non-smoker CD8T genomic DNA

value: Non-smoker


title: genomic DNA of sample F209_CD8T [202827620124_R01C01]

description: Smoker CD8T genomic DNA


title: Sample230.Pale spear-nosed bat.202897220162_R02C01


title: Sample229.Common vampire bat.202897220162_R01C01


title: genomic DNA of sample F200_CD8T [200930770035_R03C01]

description: Non-smoker CD8T genomic DNA


title: Sample227.Common vampire bat.202897220094_R05C02


title: Sample226.Pale spear-nosed bat.202897220094_R04C02


title: genomic DNA of sample F199_CD8T [202831040028_R01C01]

description: Non-smoker CD8T genomic DNA


title: genomic DNA of sample F198_CD8T [202827620107_R01C01]

description: Smoker CD8T genomic DNA


title: Sample225.Common vampire bat.202897220094_R03C02


title: genomic DNA of sample F204_CD8T [201959740242_R03C01]

description: Non-smoker CD8T genomic DNA


title: Sample223.Pale spear-nosed bat.202897220094_R01C02


title: Sample222.Pale spear-nosed bat.202897220094_R06C01


title: genomic DNA of sample F192_CD8T [202822930093_R01C01]

description: Non-smoker CD8T genomic DNA


title: Sample224.Common vampire bat.202897220094_R02C02


title: genomic DNA of sample F196_CD8T [202787550009_R01C01]

description: Smoker CD8T genomic DNA


title: Sample220.Common vampire bat.202897220094_R04C01


title: Sample219.Pale spear-nosed bat.202897220094_R03C01


title: 18855_3_D_methylation array

city: Phoenix

first: Nicholas

last: Banovich

state: AZ

address: 445 N. Fifth Street

department: Integrated Cancer genomics division

institute: Translational Genomics Research Institute

hyb_protocol: DNA was bisulphite-converted and hybridised to an Illumina Infinium MethylationEPIC array at the University of Chicago Functional Genomics Facility

scan_protocol: Standard Illumina protocols

data_processing: Standard Illumina protocols

label_protocol: Standard Illumina protocols

growth_protocol: iPSC-derived cardiomyocytes were maintained in Cardiomyocyte Maintenance Media  [500 mL DMEM without glucose (A14430-01, ThermoFisher Scientific), 50 mL FBS (S1200-500, Genemate), 990 mg Galactose (G5388, Sigma-Aldrich), 5 mL 100 mM sodium pyruvate (11360-070, ThermoFisher Scientific), 2.5 mL 1M HEPES (SH3023701, ThermoFisher Scientific), 5 mL Glutamax (35050-061, ThermoFisher Scientific), 5 mL Penicillin/Streptomycin)].

extract_protocol: DNA was extracted from ~1.5 million cells using the ZR-Duet DNA/RNA extraction kit (D7001, Zymo, Irvine, CA, USA).

treatment_protocol: Four conditions were collected per individual: A- normoxia at 10% oxygen, B- hypoxia at 1% oxygen for 6 hours, C- 6 hours hypoxia and re-oxygenation at 10% oxygen for 6 hours and D- 6 hours hypoxia and re-oxygenation at 10% oxygen for 24 hours.

tag: cell line

tag: population

value: Yoruba

value: induced pluripotent stem cell-derived cardiomyocytes

tag: condition


title: LF03

type: SRA

city: BeiJing

first: zhong

last: ann

address: Haidian Yuanmingyuan west road 2

country: China

institute: China Agricurltural University

library_source: transcriptomic

data_processing:
The obtained raw data was filtered to clean data, and then mapped to the Sus. scrofa 11.1 reference genome using the Hisat 2
HTSeq 2 using strict crossover mode and minimum alignment quality of 10 is used to quantify the number of hits per gene, fragments per kilobase million (FPKM)
DESeq2 with outlier replacement and independent filtering was adopted to detect differentially expressed transcripts between high and low lipid deposition groups.
Genome_build: Sus scrofa 11.1

molecule: total RNA

organism: Sus scrofa

source_name: longissimus dorsi

extract_protocol:
LD samples were homogenized and RNAs were extracted in Trizol (Invitrogen, USA) according to the manufacturer’s instructions. Isolated total RNA was quantified (Nanodrop, ND2000) and quality controlled (Agilent, Bioanalyzer 2100).
Only high-quality RNA (RNA integrity number, RIN > 7.0) was used to construct cDNA libraries (TruSeq RNA Sample Preparation Guide, Illumina Inc., San Diego, CA).
All libraries were sequenced on HiSeq 4000 (Illumina Inc., San Diego, CA) with PE 150.

tag: breed

value: Nanyang Black

value: longissimus dorsi

tag: age


title: LF01


title: LF02


title: 18855_3_C_methylation array


title: Sample228.Pale spear-nosed bat.202897220094_R06C02


title: Sample221.Pale spear-nosed bat.202897220094_R05C01


title: Sample217.Pale spear-nosed bat.202897220094_R01C01


title: Sample215.Common vampire bat.202894750007_R05C02


title: Sample214.Pale spear-nosed bat.202894750007_R04C02


title: HF03


title: Sample216.Pale spear-nosed bat.202894750007_R06C02


title: HF02


title: Sample218.Common vampire bat.202897220094_R02C01


title: Sample212.Pale spear-nosed bat.202894750007_R02C02


title: Sample213.Common vampire bat.202894750007_R03C02


title: 18855_3_B_methylation array

source_name: iPSC-derived cardiomyocytes_hypoxia

value: hypoxia


title: HF01


title: Sample210.Pale spear-nosed bat.202894750007_R06C01


title: Sample211.Common vampire bat.202894750007_R01C02


title: Sample209.Common vampire bat.202894750007_R05C01


title: 18852_3_D_methylation array


title: 18852_3_C_methylation array


title: 18852_3_B_methylation array


title: Sample208.Common vampire bat.202894750007_R04C01


title: 18852_3_A_methylation array

source_name: iPSC-derived cardiomyocytes_normoxia

value: normoxia


title: 18855_3_A_methylation array


title: 18511_3_D_methylation array


title: Sample206.Common vampire bat.202894750007_R02C01


title: Sample205.Pale spear-nosed bat.202894750007_R01C01


title: Sample202.Common vampire bat.202897220001_R04C02


title: Sample200.Pale spear-nosed bat.202897220001_R02C02


title: Sample201.Pale spear-nosed bat.202897220001_R03C02


title: Type2 D2

type: RNA

city: Utrecht

first: Balthasar

middle: Adrianus

last: Heesters

state: Utrecht

address: Universiteitsweg 99

department: Pharmaceutical Sciences

country: Netherlands

institute: Utrecht University

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: R/Bioconductor, limma RMA was used for background correction and normalization. Then all probes without a valid or duplicate ENTREZID were removed

label: biotin

source_name: Freshly isolated ILC2 from Blood, stimulated with type 2 cytokines for 6 days

label_protocol: Obtained (depleted) cell suspensions were stained for 30 min at 4°C with fluorochrome-conjugated antibodies (Lin: CD1a, CD3, CD4, CD14, CD34, CD19, FcRεR1a, BDCA2, CD123, TCRαβ, TCRγδ, CRTH2 all in FITC. CD3 in AF700, CD45 in APC-Cy7, CD127 in PECY7, CD161 in BV510, CD94 in PE, CD56 in PETX, NKp44 in APC, CD117 in PEcy5.5). The cells were purified by flow cytometry using a FACSAria IIU (BD Biosciences).

extract_protocol: Human blood was obtained from the Sanquin blood bank in Amsterdam. Nasal polyps were obtained from surgeries at Amsterdam UMC

tag: donor id

value: Blood

value: Group 2 innate lymphoid cells (ILC2s)

tag: treatment

value: type 2 cytokines for 6 days


title: Type2 D3


title: Sample207.Pale spear-nosed bat.202894750007_R03C01


title: Type2 D1


title: Sample203.Pale spear-nosed bat.202897220001_R05C02


title: Sample198.Pale spear-nosed bat.202897220001_R06C01


title: Sample199.Common vampire bat.202897220001_R01C02


title: NP D2

source_name: Freshly isolated ILC2 from Nasal polyp

value: Nasal polyp


title: 18511_3_C_methylation array


title: Sample270.Common vampire bat.202897220006_R06C01

value: Skin


title: Sample196.Pale spear-nosed bat.202897220001_R04C01

value: yes


title: Sample204.Common vampire bat.202897220001_R06C02

value: Male


title: Sample197.Common vampire bat.202897220001_R05C01

value: Female


title: Sample195.Common vampire bat.202897220001_R03C01


title: 18511_3_B_methylation array


title: 18511_3_A_methylation array


title: 18855_2_D_methylation array


title: 18855_2_C_methylation array


title: 18855_2_B_methylation array


title: NP D3


title: Baseline D2

source_name: Freshly isolated ILC2 from Blood


title: NP D1


title: Sample193.Common vampire bat.202897220001_R01C01


title: Sample192.Greater spear-nosed bat.202897220140_R06C02

description: genomic DNA methylation from tissue=Skin species=Greater spear-nosed bat

organism: Phyllostomus hastatus


title: Sample254.Common vampire bat.202894750032_R02C01


title: Baseline D3


title: 18855_2_A_methylation array


title: Sample194.Pale spear-nosed bat.202897220001_R02C01


title: 18852_2_D_methylation array


title: Sample188.Greater spear-nosed bat.202897220140_R02C02


title: Baseline D1


title: Sample189.Greater spear-nosed bat.202897220140_R03C02


title: Sample190.Greater spear-nosed bat.202897220140_R04C02


title: Sample187.Greater spear-nosed bat.202897220140_R01C02


title: RMac transferred into clodronate-depleted recipients D35

city: Edinburgh

first: Pieter

middle: Adriaan

last: Louwe

state: Scotland

address: 47 Little France Crescent

department: Centre for Inflammation Research

country: United Kingdom

institute: University of Edinburgh

description: clodronate-depleted recipient

data_processing: Data were imported into nSolver 4.0 software (Nanostring Technologies). Data were annotated by cell-type for analysis (RMac, RMacZ10, IMacZ10).Grouped data were then analysed using the advanced analysis nSolver package according to the manufacturers instructions.   Importantly, donor populations transferred into mirroring (D1-D17) or clodronate-depleted (D20-D37) recipients were obtained on different days and were analysed separately.

organism: Mus musculus

source_name: Peritoneal cavity

extract_protocol: For each of the indicated donor populations 5000 cells  were sorted into 2µl of RLT (QIAGEN). Immediately after cells where: centrifuged at maximum speed 15 seconds, vortexed for 10 seconds and again centrifuged at maximum speed 15 seconds. Cells where stored at -80degrees C until  analysis of the lysate using the nCounter Myeloid innate immunity panel.

tag: donor treatment

value: Naive

tag: host treatment

value: Clodronate-depleted

tag: matrix


title: RMacZ10 transferred into clodronate-depleted recipients D37

description: clodronate-depleted recipient

value: 10ug zymosan


title: RMacZ10 transferred into clodronate-depleted recipients D36

description: clodronate-depleted recipient


title: IMacZ10 transferred into clodronate-depleted recipients D34

description: clodronate-depleted recipient


title: Sample186.Greater spear-nosed bat.202897220140_R06C01

tag: basename


title: Sample183.Greater spear-nosed bat.202897220140_R03C01

tag: tissue


title: Sample191.Greater spear-nosed bat.202897220140_R05C02

tag: canbeusedforagingstudies


title: Sample184.Evening bat.202897220140_R04C01

description: genomic DNA methylation from tissue=Muscle species=Evening bat

organism: Nycticeius humeralis

source_name: Muscle

value: Muscle

tag: age (years)


title: Sample181.Evening bat.202897220140_R01C01

tag: confidenceinageestimate


title: Sample182.Greater spear-nosed bat.202897220140_R02C01

tag: Sex


title: 18852_2_C_methylation array

value: Yoruba

tag: cell type

value: induced pluripotent stem cell-derived cardiomyocytes


title: Sample185.Greater spear-nosed bat.202897220140_R05C01


title: 18852_2_B_methylation array

tag: cell line


title: RMac transferred into clodronate-depleted recipients D32

description: clodronate-depleted recipient


title: Sample179.Greater spear-nosed bat.202897220139_R05C02


title: 18852_2_A_methylation array

tag: population


title: RMac transferred into clodronate-depleted recipients D31

description: clodronate-depleted recipient


title: RMacZ10 transferred into clodronate-depleted recipients D29

description: clodronate-depleted recipient


title: Sample180.Greater spear-nosed bat.202897220139_R06C02


title: 18511_2_D_methylation array

tag: condition


title: RMacZ10 transferred into clodronate-depleted recipients D28

description: clodronate-depleted recipient


title: 18511_2_C_methylation array


title: Sample178.Greater spear-nosed bat.202897220139_R04C02


title: Sample176.Greater spear-nosed bat.202897220139_R02C02


title: Sample177.Evening bat.202897220139_R03C02


title: 18511_2_B_methylation array


title: IMacZ10 transferred into clodronate-depleted recipients D23

description: clodronate-depleted recipient


title: IMacZ10 transferred into clodronate-depleted recipients D21

description: clodronate-depleted recipient


title: Sample174.Greater spear-nosed bat.202897220139_R06C01


title: 19160_D_methylation array


title: Sample173.Greater spear-nosed bat.202897220139_R05C01


title: Sample175.Evening bat.202897220139_R01C02


title: 19160_C_methylation array


title: RMac transferred into clodronate-depleted recipients D20

description: clodronate-depleted recipient


title: Sample172.Evening bat.202897220139_R04C01


title: RMacZ10 transferred into inflamed recipients D17

description: mirroring recipient


title: Sample171.Greater spear-nosed bat.202897220139_R03C01


title: Sample170.Evening bat.202897220139_R02C01


title: Sample169.Greater spear-nosed bat.202897220139_R01C01


title: RMacZ10 transferred into inflamed recipients D14

description: mirroring recipient


title: Sample166.Greater spear-nosed bat.202897220144_R04C02


title: Sample165.Greater spear-nosed bat.202897220144_R03C02


title: 19160_B_methylation array


title: Sample163.Greater spear-nosed bat.202897220144_R01C02


title: 18511_2_A_methylation array


title: IMacZ10 transferred into inflamed recipients D12

description: mirroring recipient


title: Sample161.Evening bat.202897220144_R05C01


title: Sample168.Greater spear-nosed bat.202897220144_R06C02


title: Sample158.Greater spear-nosed bat.202897220144_R02C01


title: Sample162.Greater spear-nosed bat.202897220144_R06C01


title: Sample167.Evening bat.202897220144_R05C02


title: Sample164.Greater spear-nosed bat.202897220144_R02C02


title: Sample160.Greater spear-nosed bat.202897220144_R04C01


title: RMacZ10 transferred into inflamed recipients D10

description: mirroring recipient


title: IMacZ10 transferred into inflamed recipients D9

description: mirroring recipient


title: 19128_B_methylation array


title: 19128_A_methylation array


title: Sample157.Greater spear-nosed bat.202897220144_R01C01


title: RMacZ10 transferred into inflamed recipients D8

description: mirroring recipient


title: Sample156.Evening bat.202897220111_R06C02


title: RMacZ10 transferred into inflamed recipients D11

description: mirroring recipient


title: 19128_D_methylation array


title: RMac transferred into naïve recipients D5

description: mirroring recipient


title: 19108_D_methylation array


title: IMacZ10 transferred into inflamed recipients D7

description: mirroring recipient


title: Sample155.Greater spear-nosed bat.202897220111_R05C02


title: Sample152.Greater spear-nosed bat.202897220111_R02C02


title: Sample154.Greater spear-nosed bat.202897220111_R04C02


title: Sample159.Greater spear-nosed bat.202897220144_R03C01


title: Sample148.Greater spear-nosed bat.202897220111_R04C01


title: Sample150.Evening bat.202897220111_R06C01


title: 19108_C_methylation array


title: Sample149.Greater spear-nosed bat.202897220111_R05C01


title: RMac transferred into naïve recipients D3

description: mirroring recipient


title: Sample151.Greater spear-nosed bat.202897220111_R01C02


title: 19108_B_methylation array


title: 19101_D_methylation array


title: RMac transferred into naïve recipients D2

description: mirroring recipient


title: Sample147.Greater spear-nosed bat.202897220111_R03C01


title: Sample153.Greater spear-nosed bat.202897220111_R03C02


title: Sample146.Evening bat.202897220111_R02C01


title: Sample144.Greater spear-nosed bat.202897220008_R06C02


title: KL rep1

city: Wuhan

first: 鹏

last: 王

email: wangp00678@163.com, wangp94@whu.edu.cn

state: 湖北省

address: 169 Donghu nan road,Wucang District

institute: 武汉大学

description: RNA from single cell using 10x genomics

data_processing:
Illumina Hiseq X Ten platform for sequencing with 151-bp paired-end reads strategy (Novogene)
Quality control of mRNA-seq data was performed by using Fatsqc (v0.11.9) and low-quality bases were trimmed by Trim_galore (0.6.4_dev)
The Cell Ranger software pipeline (version 3.1.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and downsample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
We processed the unique molecular identifier (UMI) count matrix using the R package Seurat (version 3.2.0) with default parameters
Genome_build: Mus_musculus_Ensemble_94
Supplementary_files_format_and_content: matrix.mtx with counts for every gene across two mice

source_name: Tumor sections of Tumor bearing lungs

extract_protocol:
Single-cell suspension were isolated from tumor-bearing KL mice using micro-dissection after 10 weeks of Ad-cre induction. And cells were prepared as described above. Single-cell RNA-seq libraries were prepared with Chromium Single cell 3’Reagent v3.0 Kits according to the manufacturer’s protocol. Single-cell suspensions were loaded on the Chromium Single Cell Controller Instrument (10×Genomics) to generate single cell gel beads in emulsions (GEMs). Briefly, 105 single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. About 15000-20000 cells were added to each channel with a targeted cell recovery estimate of 5000 cells (4400 and 2780 for 2 KL mice, respectively). After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). cDNA was then amplified by PCR with appropriate cycles which depend on the recovery cells. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed, index adaptor ligated and library amplification. Then these libraries were sequenced on the Illumina sequencing platform (HiSeq X Ten), and 151 bp paired-end reads were generated.
single cell RNA libraries were prepared for sequencing using standard Illumina protocols
scRNA-Seq

value: lungs

tag: strain

tag: genotype

value: KrasLSL-G12D/+ Lkb1fl/fl


title: KL rep2

description: RNA from single cell using 10x genomics

value: KrasLSL-G12D/+ Lkb2fl/fl


title: 3981 [abdominal aorta]

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

description: WT mice with 14-day Angiotensin-II (500ng/kg/min) and QDG (1.145g/kg/d) treatment

data_processing:
Data were filtered using the following specifications fastq software，The filtering standards from raw data to clean reads are:：  Check the sample for contamination and, if there is pollution, remove it  If the reads contains a joint sequence, the joint sequence is cut off first  a base having an average base mass of less than 15 on both ends of the readth window is cut with four base lengths as a sliding window;  Remove the number of threads with a high N content. If the N content in a read is more than 5%, the whole read is removed, and the read pair with high low-quality base content is removed. If the low-quality base in one read (the mass value is not higher than the base of 20) exceeds 30%, the whole pair of the reads is removed;  if the truncated read length is less than 50 bp, the entire read is removed  Remove unmatched reads  Q30，Q20 explanation：  Q30 indicates that the sequencing error rate of the base is 0.1%.  Q20 indicates that the sequencing error rate of the base is 1%.
Using String Tie for readcount and FPKM calculation.
Differential expression analyses were performed using the limma package.
Genome_build: GCRmm38/mm10(UCSC)
Supplementary_files_format_and_content: tab_delimited text files include FPKM values for each Sample

organism: Mus

source_name: abdominal aorta

extract_protocol:
The abdominal aorta were dissected and  stored in liquid nitrogen and stored in low temperature.Total RNA was extracted with mirVana miRNA Isolation Kit (Cat. AM1560, Ambion, Austin, USA). RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and RNA concentration was measured by Qubit RNA Assay Kit in a Qubit Fluorometer (Invitrogen, CA, USA).
A total amount of 1 μg RNA per sample was used. In brief, the NEBNext rRNA Depletion Kit was used to remove rRNA from the total RNA. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, Beijing, China) was used to construct the libraries for sequencing following the manufacturer’s instructions.

value: abdominal aorta

value: WT

tag: group

value: AngII+QDG


title: 3984 [abdominal aorta]

tag: treatment

value: Angiotensin-II (500ng/kg/min) and QDG (1.145g/kg/d)


title: 3985 [abdominal aorta]


title: 3982 [abdominal aorta]


title: 3983 [abdominal aorta]


title: 4048 [abdominal aorta]

description: WT mice with 14-day Angiotensin-II (504ng/kg/min) treatment

value: Angiotensin-II (500ng/kg/min)

value: AngII


title: 19128_C_methylation array


title: 19108_A_methylation array

value: normoxia


title: 19101_A_methylation array

value: Male


title: KP9 rep_1

description:
KP9A
kp_kp5-1.xlsx;kp_kp9-1.xlsx

data_processing:
Illumina Hiseq X Ten platform for sequencing with 150-bp paired-end reads strategy (Novogene)
Quality control of mRNA-seq data was performed by using Fatsqc (v0.11.9) and low-quality bases were trimmed by Trim_galore (0.6.4_dev)
All RNA-seq data were mapped to the mouse genome (Mus_musculus_Ensemble_94) by Hisat2 (v.2.0.5) and allowed a maximum of two mismatches per read
Gene expression level was calculated by FeatureCounts (v.2.0.0) with default parameters and normalized by FPKM (Fragments Per Kilobase of exon model per Million mapped fragments).
Genome_build: Mus_musculus_Ensemble_94
Supplementary_files_format_and_content: excel with FPKM for every gene and every sample

source_name: Tumor bearing lungs

extract_protocol:
Tumor-burdened lungs from KL/KL5/KL9 mice and KP/KP5/KP9 mice were perfused through alveolar lavage and cardiac lavage with PBS, dry it quickly, and then homogenized in 2 ml of TRIzol (Invitrogen). Total RNAs were prepared and the quality of RNAs was determined by agarose gel electrophoresis and spectrophotometer analysis. Poly(A) mRNA  was subsequently purified from 10μg total RNA using NEBNext Oligo d(T)25 Magnetic Beads Isolation Module. First-strand complementary DNA was synthesized with NEBNext RNA First-Strand Synthesis Module. NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module was used for the synthesis of the complementary strand of first-strand cDNA. The resulting double-stranded DNA was purified and Vazyme TruePrep DNA Library Prep kit V2 was used to prepare libraries followed by sequencing on an Illumina Hiseq X Ten platform with 150-bp paired-end reads strategy (Novogene)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: KrasLSL-G12D/+ Tp53fl/fl Il1f9-/-


title: 3986 [abdominal aorta]

description: WT mice with 14-day Angiotensin-II (502ng/kg/min) treatment


title: 19098_D_methylation array


title: 19101_C_methylation array


title: KP5 rep_3

description:
KP5C
kp_kp5-1.xlsx;kp_kp9-1.xlsx

value: KrasLSL-G12D/+ Tp53fl/fl Il1f5-/-


title: 3989 [abdominal aorta]

description: WT mice with 14-day Angiotensin-II (501ng/kg/min) treatment


title: 19098_C_methylation array


title: KP9 rep_3

description:
KP9C
kp_kp5-1.xlsx;kp_kp9-1.xlsx


title: KP9 rep_2

description:
KP9B
kp_kp5-1.xlsx;kp_kp9-1.xlsx


title: KP5 rep_2

description:
KP5B
kp_kp5-1.xlsx;kp_kp9-1.xlsx


title: 3987 [abdominal aorta]

description: WT mice with 14-day Angiotensin-II (503ng/kg/min) treatment


title: 3994 [abdominal aorta]

description: WT mice with 14-day Saline treatment

value: Saline

value: Control


title: KP5 rep_1

description:
KP5A
kp_kp5-1.xlsx;kp_kp9-1.xlsx


title: 3988 [abdominal aorta]

description: WT mice with 14-day Angiotensin-II (500ng/kg/min) treatment


title: 19101_B_methylation array

value: Yoruba

value: hypoxia


title: KP rep_2

description:
KPC
kp_kp5-1.xlsx;kp_kp9-1.xlsx

value: lungs

value: KrasLSL-G12D/+ Tp53fl/fl


title: 19098_B_methylation array

value: induced pluripotent stem cell-derived cardiomyocytes


title: 19098_A_methylation array


title: Sample143.Greater spear-nosed bat.202897220008_R05C02

value: Skin

value: yes

value: Female


title: RMac transferred into naïve recipients D1

description: mirroring recipient

tag: donor treatment

value: Naive


title: 3971 [abdominal aorta]

description: WT mice with 14-day Saline treatment

value: abdominal aorta

value: WT


title: 18912_D_methylation array


title: 18912_C_methylation array


title: 4086 [abdominal aorta]

description: WT mice with 14-day Saline treatment


title: Sample145.Evening bat.202897220111_R01C01

value: Muscle


title: KP rep_1

description:
KPA
kp_kp5-1.xlsx;kp_kp9-1.xlsx


title: Sample142.Greater spear-nosed bat.202897220008_R04C02


title: KL9 rep_2

description:
A00_9
KL KL9_all_compare.xlsx

value: KrasLSL-G12D/+ Lkb1fl/fl Il1f9-/-


title: 4000 [abdominal aorta]

description: WT mice with 14-day Saline treatment


title: 18912_B_methylation array


title: Sample141.Evening bat.202897220008_R03C02


title: KL9 rep_1

description:
A00_7
KL KL9_all_compare.xlsx


title: 3996 [abdominal aorta]

description: WT mice with 14-day Saline treatment


title: Sample139.Evening bat.202897220008_R01C02


title: 18912_A_methylation array

value: normoxia


title: Sample138.Greater spear-nosed bat.202897220008_R06C01

value: Male


title: Sample140.Greater spear-nosed bat.202897220008_R02C02


title: KL rep_B

description:
A00_2
KL KL9_all_compare.xlsx

value: KrasLSL-G12D/+ Lkb2fl/fl


title: Sample137.Greater spear-nosed bat.202897220008_R05C01


title: Sample134.Greater spear-nosed bat.202897220008_R02C01


title: Sample136.Greater spear-nosed bat.202897220008_R04C01


title: 18858_D_methylation array


title: hESC ZNF91 wt5 H3K4me3 ChIP rep1

city: Amsterdam

first: Frank

last: Jacobs

address: Science Park 904

department: Sammerdam Institute for Life Sciences

institute: University of Amsterdam

description: ZNF91_hESC_H3K4me3-ChIP_wt5_peaks_BED.csv

library_source: genomic

data_processing:
Read quality assessment using FASTQC
Trimmomatic (version 0.38) (Bolger et al. 2014) was used to clip adapter sequences and trim low quality reads
Bowtie2 (version 1.0.1) (Langmead and Salzberg 2012) in –end-to-end –very-sensitive mode was used to map reads to the human genome (Hg19 version). Fragment length for valid paired end fragments was set to a minimum of 80 (-I) and a maximum of 500 (-X).
sam files were converted to bam files sorted by coordinate using Samtools (version 1.7). The rmdup function of Samtools was used to remove potential PCR duplicates
Peak calling was done with MACS2 (version 2.1.1.20160309) (Zhang et al. 2008). All tags at a given location were included (--keep-dup all) and subpeaks were determined (--call-summits)
Hg19
MACS output files (.txt or .csv) and for ZNF91-ChIP a file where a filtering treshold was applied: rep1 MACS score >50 and rep2 MACS score >100. The file shows the peaks present in both replicates.

source_name: hESCs

growth_protocol: H9 human embryonic stem cells were grown on matrigel (Corning) coated dishes. They were cultured in hESC medium that was incubated with mouse embryonic fibroblasts (MEFs) for 24 hours. HESC medium consisted of: DMEM/F12 supplemented with 2mM L-glutamine (Invitrogen), 20% knockout serum replacement (Gibco), penicillin/streptomycin (Invitrogen), non-essential amino acids (Invitrogen), 0.1mM β-mercaptoethanol (Invitrogen). Medium was supplemented with basic fibroblast growth factor (sigma, 8ng/μl) and changed daily to secure pluripotency of hESCs. For maintenance of the culture, cells were grown in colonies and passaged manually by cutting the colonies with a needle

extract_protocol:
hESC colonies were detached from a 60mm dish with a cell scraper and crosslinked immediately after harvest.Cells were lysed and chromatin was shared to fragments ~500bp. Antibody-coated beads were used to extract chromatin
Truseq ChIP sample prep (Illumina, Lot 20194738) was used for library preparation. Provided protocol was followed with the following adjustments: DNA clean & concentrator-5 kit (Zymo research) instead of beads was used for DNA purification. DNA fragment size selection with 2% agarose size selections gels (Invitrogen) using E-Gel sizeSelect II (Invitrogen) was done before and after PCR amplification of indexed ChIP DNA to obtain the 400-500bp fraction.
ChIP seq 75bp paired end reads on a NextSeq 550 device.

treatment_protocol: H9 hESCs were transfected with two gRNAs targeting ZNF91 cloned into pX330-SpCas9-HF1 and clonally expanded

value: H9 Human embryonic stem cells

tag: chip antibody

value: 3.75 μl rabbit anti-H3K4me3 (millipore, 07-473, lot 2930138),

value: ZNF91 wt

tag: crispr clone


title: Sample135.Greater spear-nosed bat.202897220008_R03C01

tag: basename


title: 18858_C_methylation array

value: Yoruba


title: hESC ZNF91 ko13 H3K4me3 ChIP rep1

description: ZNF91_hESC_H3K4me3-ChIP_ko13_peaks_BED.csv

value: ZNF91 ko


title: KL rep_A

description:
A00_1
KL KL9_all_compare.xlsx

tag: tissue

value: lungs

value: KrasLSL-G12D/+ Lkb1fl/fl


title: 18858_B_methylation array

value: induced pluripotent stem cell-derived cardiomyocytes

value: hypoxia


title: KL5 rep_2

description:
A00_5
KL KL5_all_compare.txt

value: KrasLSL-G12D/+ Lkb1fl/fl Il1f5-/-


title: KL5 rep_1

description:
A00_4
KL KL5_all_compare.txt


title: HEK293 ZNF91 ChIP rep 2

description: ZNF91_HEK293_ZNF91-ChIP_peaks_rep1>50_and_rep2>100_BED.csv ZNF91_rep2_peaks.narrowPeak

source_name: HEK293 cells

growth_protocol: HEK293 cells were cultured in DMEM (Invitrogen) supplemented with 10% fetal bovine serum (FBS, Gibco) and 1% penicillin/streptomycin (Invitrogen). 0.25% trypsin/0.01% EDTA (Invitrogen) in PBS was used to passage cells 1:10 every 3-4 days

extract_protocol:
48 hours after transfection a confluent 60mm dish was harvested by mechanical detachment and cross-linked immediately after harvest. Cells were lysed and chromatin was shared to fragments ~500bp. Antibody-coated beads were used to extract chromatin
Truseq ChIP sample prep (Illumina, Lot 20194738) was used for library preparation. Provided protocol was followed with the following adjustments: DNA clean & concentrator-5 kit (Zymo research) instead of beads was used for DNA purification. DNA fragment size selection with 2% agarose size selections gels (Invitrogen) using E-Gel sizeSelect II (Invitrogen) was done before and after PCR amplification of indexed ChIP DNA to obtain the 400-500bp fraction.
ChIP seq 75bp paired end reads on a NextSeq 550 device.

treatment_protocol: HEK293 cells were transfected with pCAG.ZNF91-Glycinelinker-eGFP

value: Human embryonic kidney-293 cells

value: 5 μg rabbit  Anti-GFP (abcam, ab290)

value: wt


title: 18858_A_methylation array

value: Female


title: Sample133.Greater spear-nosed bat.202897220008_R01C01

value: Skin

tag: canbeusedforagingstudies

value: yes


title: Sample132.Greater spear-nosed bat.202897220002_R06C02

tag: age (years)


title: KL rep_2

description:
A00_3
KL KL5_all_compare.txt

value: KrasLSL-G12D/+ Lkb2fl/fl


title: HEK293 ZNF91 ChIP rep 1

description: ZNF91_HEK293_ZNF91-ChIP_peaks_rep1>50_and_rep2>100_BED.csv ZNF91_rep1_peaks.narrowPeak


title: Sample131.Greater spear-nosed bat.202897220002_R05C02

tag: confidenceinageestimate


title: 18855_D_methylation array

tag: Sex


title: OF35Y-iPS

city: Shinjuku

first: Sho

last: Yoshimatsu

state: Tokyo

address: 35 Shinanomachi

department: Physiology

country: Japan

institute: Keio University School of Medicine

data_processing:
Data of RNA-seq (fastq file format) were quality-checked, and low-quality reads (score < 30), adapter sequences, and overrepresented sequences such as poly-A chain were trimmed using the Trim Galore! (ver.0.4.0).
The remaining reads were mapped to the Canis lupus familiaris genome (CamFam3.1) using the STAR (ver.2.5.3a), and the output file (BAM file format) were summarized using the featureCounts (1.5.2).
Genome_build: CanFam3.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Canis lupus familiaris

source_name: Induced pluripotent stem cell

extract_protocol:
RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: iPSC


title: 18855_C_methylation array

tag: cell line


title: 18855_A_methylation array

tag: population

value: normoxia


title: Sample129.Greater spear-nosed bat.202897220002_R03C02

value: Male


title: KL rep_1

description:
A00_2
KL KL5_all_compare.txt


title: 18855_B_methylation array

value: Yoruba

tag: condition


title: 18520_D_methylation array


title: Sample128.Greater spear-nosed bat.202897220002_R02C02


title: lung carcinoma epithelial cells, HU-3

city: 广州

first: HUIXIN

last: GAO

address: 中山二路74号

institute: 中山大学

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (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.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and read counts for each Sample

source_name: lung carcinoma epithelial cells

extract_protocol:
Total RNA of control and HuR-KO cells was extracted with TRIzol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human lung carcinoma epithelial cells

value: HuR-KO


title: lung carcinoma epithelial cells, HU-1


title: lung carcinoma epithelial cells, HU-2


title: lung carcinoma epithelial cells, CON-3

value: control


title: 18520_C_methylation array

value: induced pluripotent stem cell-derived cardiomyocytes


title: lung carcinoma epithelial cells, CON-2


title: 18520_B_methylation array

value: hypoxia


title: lung carcinoma epithelial cells, CON-1


title: 18520_A_methylation array


title: INTACT_RNA_group3_rep5

city: Mainz

first: Susanne

last: Gerber

address: Staudinger Weg 9

department: Institute for Human Genetics

country: Germany

institute: University Medicine Mainz

data_processing:
ATAC-Seq data quality was checked using Fastqc.
ATAC-Seq: Sequence reads were trimmed for adaptor sequence and aligned to mm10 genome. Peaks were called using MACS2 and wig files were generated.
RNA-Seq data quality was checked using Fastqc. STAR aligner was used to align raw reads to reference genome.
RNA-Seq: HTSeq was used to count reads. DESeq was used to perform differential expression analysis.
Genome_build: mm10

molecule: nuclear RNA

source_name: activated neuronal nuclei

extract_protocol:
10,000 INTACT- or FANS- nuclei were collected in 100 μl of RLT buffer followed by flash freezing. RNA was purified using the RNeasy Micro kit (Qiagen 74004) following the manufacturer's instructions.
Libraries were prepared using NuGen Ovation SoLo RNA-Seq System following NuGen's standard protocol. Libraries were prepared with a starting amount of 1.23 ng and amplified in 13 PCR cycles.

value: activated neuronal nuclei

tag: isolation method

value: INTACT


title: INTACT_RNA_group3_rep4


title: 18511_D_methylation array


title: Sample123.Evening bat.202897220002_R03C01

value: Muscle


title: Sample125.Evening bat.202897220002_R05C01


title: Sample130.Evening bat.202897220002_R04C02


title: PAM212 cells, Control

city: Charlestown

first: Jongho

last: Park

state: MA

address: Building 149 13th street

department: Cancer center immunology

institute: MGH

data_processing:
ChIP seq performed using Illumina NovaSeq 6000 system
ChIP-seq reads were aligned to the NCBI:GCA_000001635.8 genome using Novogene seqeuncing system
Mapped the fastq file to the genome
150 bp paired-end reads were generated
Genome_build: NCBI:GCA_000001635.8
Supplementary_files_format_and_content: bigWig file

source_name: Keratinocyte cell line

growth_protocol: PAM212 was cultured with DMEM added 10% FBS, 1X Pen/Strep/Glutamine,  1X NEAA, 1X Hepes and 0.1% Mercaptoethanol

extract_protocol:
Protein-DNA complex were isolated by HA antibody
Libraries were prepared according to Illumina NovaSeq 6000 's protocol

treatment_protocol: PAM212 was transfected with IL-33 construct by lipofectamine 2000 (Thermo Fisher, #11668019)

value: adherent keratinocyte

tag: passage

tag: construct

value: Control

value: HA antibody (Biolegend, #MMS-101P)


title: 18511_C_methylation array

value: Female


title: Sample122.Greater spear-nosed bat.202897220002_R02C01

source_name: Skin

value: Skin

value: yes


title: Sample124.Greater spear-nosed bat.202897220002_R04C01


title: INTACT_RNA_group3_rep3


title: Sample127.Greater spear-nosed bat.202897220002_R01C02


title: Sample121.Evening bat.202897220002_R01C01


title: PAM212 cells, IL-33 full-length

value: IL-33 full-length (1-266 amino acids sequence)


title: Sample126.Greater spear-nosed bat.202897220002_R06C01


title: INTACT_RNA_group3_rep2


title: 18511_B_methylation array

source_name: iPSC-derived cardiomyocytes_hypoxia


title: genomic DNA of sample F190_CD8T [101032570153_R04C02]

description: Smoker CD8T genomic DNA

value: CD8 T cells

value: Smoker


title: 18511_A_methylation array

source_name: iPSC-derived cardiomyocytes_normoxia

value: Yoruba

value: normoxia


title: INTACT_RNA_group3_rep1


title: FANS_RNA_group3_rep7

value: FANS


title: 18505_D_methylation array

value: induced pluripotent stem cell-derived cardiomyocytes


title: PAM212 cells, IL-33 Cytokine

value: IL-33 Cytokine (109-266 amino acids sequence)


title: Sample118.Greater spear-nosed bat.202894750009_R04C02


title: Sample120.Evening bat.202894750009_R06C02

value: Male


title: genomic DNA of sample F187_CD8T [101032570169_R04C02]

description: Non-smoker CD8T genomic DNA

value: Non-smoker


title: 18505_C_methylation array


title: FANS_RNA_group3_rep6

value: activated neuronal nuclei


title: Sample119.Greater spear-nosed bat.202894750009_R05C02


title: genomic DNA of sample F186_CD8T [101032570169_R04C01]

description: Non-smoker CD8T genomic DNA


title: FANS_RNA_group3_rep5


title: Sample116.Evening bat.202894750009_R02C02

value: Muscle


title: genomic DNA of sample F185_CD8T [101032570161_R04C02]

description: Smoker CD8T genomic DNA


title: 18499_D_methylation array


title: 18505_B_methylation array

value: hypoxia


title: FANS_RNA_group3_rep4


title: FANS_RNA_group3_rep3


title: Sample117.Greater spear-nosed bat.202894750009_R03C02


title: FANS_RNA_group3_rep2


title: 18499_C_methylation array


title: genomic DNA of sample F182_CD8T [101032570143_R04C02]

description: Smoker CD8T genomic DNA


title: FANS_RNA_group3_rep1


title: 18505_A_methylation array


title: 18499_B_methylation array


title: INTACT_RNA_group2_rep5

value: INTACT


title: 18499_A_methylation array

value: Female


title: genomic DNA of sample F175_CD8T [100946230056_R04C01]

description: Smoker CD8T genomic DNA


title: genomic DNA of sample F178_CD8T [100946230055_R04C01]

description: Smoker CD8T genomic DNA


title: genomic DNA of sample F176_CD8T [100946230056_R04C02]

description: Smoker CD8T genomic DNA


title: genomic DNA of sample F173_CD8T [101032570152_R04C02]

description: Smoker CD8T genomic DNA


title: INTACT_RNA_group2_rep4


title: MACE-seq_SRSF7_KD_rep2

city: Frankfurt am Main

first: Michaela

last: Müller-McNicoll

address: Max-von-Laue-Str. 13

department: Institute for Cell Biology and Neuroscience

institute: Goethe University Frankfurt

data_processing:
library strategy: MACE (Massive Analysis of cDNA Ends)-seq
The analysis of MACE-seq data was performed as described in Müller et al., 2014 PMID:25052703.
Genome_build: mm10
Supplementary_files_format_and_content: All used PAS in P19 cells in .bed format

molecule: polyA RNA

growth_protocol: Cells were grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum and pennicilin/streptomycin antibiotics at 37˚C with 5% CO2.

extract_protocol:
Total RNA was isolated using the Trizol method.
For MACE-seq, total RNA was subjected to poly(A)+ selection and MACE library preparation according to Müller et al., 2014 PMID:25052703. MACE-seq libraries were sequenced on a Illumina HiSeq2000 platform obtaining 75-bp single-end reads (50 Million per replicate).

treatment_protocol: 5 µg purified esiRNAs were transfected for 36 h using JetPRIME Transfection Reagent (Polyplus) according to the manufacturer’s instructions. EsiRNAs against GFP were used as controls.

tag: treatment

tag: molecule subtype

value: poly(A)+-selected


title: genomic DNA of sample F171_CD8T [3998909053_R06C01]

description: Smoker CD8T genomic DNA


title: MACE-seq_SRSF7_KD_rep1


title: INTACT_RNA_group2_rep2


title: 19160_A_methylation array


title: INTACT_RNA_group2_rep3


title: genomic DNA of sample F172_CD8T [101032570152_R04C01]

description: Smoker CD8T genomic DNA


title: MACE-seq_SRSF3_KD_rep2


title: genomic DNA of sample F170_CD8T [3998909005_R06C02]

description: Smoker CD8T genomic DNA


title: INTACT_RNA_group2_rep1


title: genomic DNA of sample F169_CD8T [3998909005_R06C01]

description: Non-smoker CD8T genomic DNA


title: MACE-seq_SRSF3_KD_rep1


title: genomic DNA of sample F168_CD8T [3998909066_R06C02]

description: Non-smoker CD8T genomic DNA


title: MACE-seq_SRSF3.7_Ctrl_rep2


title: FANS_RNA_group2_rep7


title: Sample115.Greater spear-nosed bat.202894750009_R01C02

value: Skin

value: yes


title: Sample112.Evening bat.202894750009_R04C01


title: MACE-seq_SRSF3.7_Ctrl_rep1


title: Sample114.Greater spear-nosed bat.202894750009_R06C01


title: Sample109.Greater spear-nosed bat.202894750009_R01C01


title: Sample108.Greater spear-nosed bat.202897220145_R06C02


title: genomic DNA of sample F166_CD8T [3998909066_R06C01]

description: Non-smoker CD8T genomic DNA

value: CD8 T cells


title: FANS_RNA_group2_rep6


title: genomic DNA of sample F165_CD8T [3998920151_R06C02]

description: Smoker CD8T genomic DNA

value: Smoker


title: Sample107.Greater spear-nosed bat.202897220145_R05C02


title: Sample110.Greater spear-nosed bat.202894750009_R02C01


title: FANS_RNA_group2_rep5


title: SRSF7_iCLIP_mm9_Rep6 [re-analysis]

data_processing:
library strategy: iCLIP
Basecalls performed using CASAVA version 1.4
For detail on data processing see: König et al. (2010): iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959
Genome_build: mm9
Supplementary_files_format_and_content: BW files containing the genomic coordinates and counts of uniquely mapped X-links for merged replicates.

extract_protocol:
Cells were lysed and treated with RNase I. GFP-tagged proteins were immunoprecipitated with Gamma binding beads coupled to goat anti-EGFP antibody.
After stringent washing, RNA was dephosphorylated and ligated to a 3' linker. Protein-RNA complexes were resolved by denaturing gel electrophoresis and transfered to nitrocellulose membrane. A membrane region above the expected size of the protein was cut and RNA was released by Proteinase K treatment. RNA was reverse transcribed using reverse primer containing a barcode sequence. cDNA was size selected by denaturing gel electrophoresis and circularized by ssDNA circligase. A specific oligonucleotide was annealed to create a restriction site for BamHI and cDNA was linearized by digest with BamHI. Linearized cDNA was PCR amplifiied with Solexa sequencing primers to create the final libraries. For more details see: Huppertz et al., (2014): iCLIP: protein-RNA interactions at nucleotide resolution. Methods. PMID:24184352

treatment_protocol: Cells were washed with PBS and irradiated with 254 nm UV light to crosslink proteins to nucleic acids.

tag: genotype/varaition

tag: antibody

value: anti-EGFP


title: FANS_RNA_group2_rep8


title: SRSF7_iCLIP_mm9_Rep5 [re-analysis]


title: genomic DNA of sample F164_CD8T [3998920151_R06C01]

description: Smoker CD8T genomic DNA


title: Sample111.Greater spear-nosed bat.202894750009_R03C01

extract_protocol: genomic DNA was extracted

tag: basename


title: genomic DNA of sample F163_CD8T [3998909043_R06C02]

description: Smoker CD8T genomic DNA

extract_protocol: Nucleated DNA from blood CD8T cells was collected after sucrose-induced osmotic lysis of cells followed by phenol-chloroform extraction and DNA was stored in Tris-EDTA buffer at -20°C.


title: FANS_RNA_group2_rep4

tag: tissue


title: SRSF7_iCLIP_mm9_Rep4 [re-analysis]


title: Sample113.Greater spear-nosed bat.202894750009_R05C01

tag: canbeusedforagingstudies


title: FANS_RNA_group2_rep3


title: Sample105.Evening bat.202897220145_R03C02

tag: age (years)


title: SRSF7_iCLIP_mm9_Rep3 [re-analysis]


title: Sample106.Evening bat.202897220145_R04C02

tag: confidenceinageestimate


title: Sample103.Greater spear-nosed bat.202897220145_R01C02

tag: Sex


title: Sample102.Greater spear-nosed bat.202897220145_R06C01


title: Sample104.Greater spear-nosed bat.202897220145_R02C02


title: Sample101.Greater spear-nosed bat.202897220145_R05C01


title: FANS_RNA_group2_rep2


title: SRSF7_iCLIP_mm9_Rep2 [re-analysis]


title: genomic DNA of sample F160_CD8T [3998909055_R06C01]

description: Smoker CD8T genomic DNA

tag: cell type


title: Sample100.Greater spear-nosed bat.202897220145_R04C01


title: FANS_RNA_group2_rep1


title: INTACT_RNA_group1_rep4


title: genomic DNA of sample F158_CD8T [3998909159_R06C01]

description: Smoker CD8T genomic DNA


title: SRSF7_iCLIP_mm9_Rep1 [re-analysis]

tag: cell line


title: genomic DNA of sample F155_CD8T [3998909045_R06C01]

description: Non-smoker CD8T genomic DNA


title: SRSF3_iCLIP_mm9_Rep3 [re-analysis]


title: SRSF3_iCLIP_mm9_Rep2 [re-analysis]


title: genomic DNA of sample F154_CD8T [3998909142_R06C02]

description: Non-smoker CD8T genomic DNA


title: INTACT_RNA_group1_rep2


title: genomic DNA of sample F153_CD8T [3998909142_R06C01]

description: Non-smoker CD8T genomic DNA


title: SRSF3_iCLIP_mm9_Rep1 [re-analysis]


title: INTACT_RNA_group1_rep1


title: Sample99.Greater spear-nosed bat.202897220145_R03C01


title: iCLIP_FIP1_P19_sample_CGGA_Rep6

tag: barcode sequence

value: CGGA


title: genomic DNA of sample F152_CD8T [3998909206_R06C02]

description: Smoker CD8T genomic DNA


title: FANS_RNA_group1_rep4

value: FANS


title: Sample98.Evening bat.202897220145_R02C01


title: genomic DNA of sample F151_CD8T [3998909206_R01C02]

description: Smoker CD8T genomic DNA


title: FANS_RNA_group1_rep3


title: INTACT_RNA_group1_rep3


title: Sample96.Large flying fox.202897220010_R06C02

description: genomic DNA methylation from tissue=Skin species=Large flying fox

organism: Pteropus vampyrus


title: FANS_RNA_group1_rep2


title: Sample97.Greater spear-nosed bat.202897220145_R01C01


title: iCLIP_FIP1_P19_sample_TATT_Rep5

value: TATT


title: Sample94.Variable flying fox.202897220010_R04C02

description: genomic DNA methylation from tissue=Skin species=Variable flying fox

organism: Pteropus hypomelanus


title: Sample95.Large flying fox.202897220010_R05C02


title: Sample93.Large flying fox.202897220010_R03C02


title: Sample91.Large flying fox.202897220010_R01C02


title: FANS_RNA_group1_rep1


title: iCLIP_FIP1_P19_sample_TTGT_Rep4

value: TTGT


title: genomic DNA of sample F148_CD8T [3998920168_R01C01]

description: Smoker CD8T genomic DNA


title: INTACT_ATAC_rep3

extract_protocol:
50,000 INTACT or FANS nuclei were collected in 50 μL cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) and centrifuged at 750 xg for 15 min using a cold centrifuge (4 oC). Immediately after centrifugation, the pellet was resuspended in the transposase reaction mix (25 μL 2× TD buffer, 2.5 μL transposase (Illumina FC-121–1030) and 22.5 μL nuclease-free water). The transposition reaction was carried out for 30 min at 37 °C.  Following transposition, the sample was purified using a Qiagen MinElute kit (Qiagen, 28006) following the manufacturer's instructions.
Libraries were amplified using 1× NEBnext PCR master mix (NEB M0541) and 1.25 μM of custom Nextera PCR primers 1 and 2 (See Buenrostro et al. 2013). An optimization qPCR quantification was performed as described in Buenrostro et al. 2013.  After 11–12 cycles of PCR amplification, samples were further purified using Qiagen MinElute kit. Samples were further purified using AMPure beads XP (Beckman Coulter) with a ratio of x0.9 of beads to samples. The purified samples were then analyzed in bioanalyzer (Agilent) prior to sequencing


title: Sample92.Variable flying fox.202897220010_R02C02


title: genomic DNA of sample F189_CD8T [101032570153_R04C01]

description: Smoker CD8T genomic DNA


title: genomic DNA of sample F145_CD8T [3998909134_R01C01]

description: Non-smoker CD8T genomic DNA


title: INTACT_ATAC_rep2


title: iCLIP_FIP1_P19_sample_GGTT_Rep1

value: GGTT


title: iCLIP_FIP1_P19_sample_CGGA_Rep7


title: Sample90.Variable flying fox.202897220010_R06C01


title: genomic DNA of sample F144_CD8T [3998909165_R01C02]

description: Non-smoker CD8T genomic DNA

value: Non-smoker


title: genomic DNA of sample F142_CD8T [3998909160_R01C02]

description: Non-smoker CD8T genomic DNA


title: genomic DNA of sample F149_CD8T [3998920168_R01C02]

description: Non-smoker CD8T genomic DNA


title: INTACT_ATAC_rep1

value: activated neuronal nuclei


title: genomic DNA of sample F147_CD8T [3998909134_R01C02]

description: Non-smoker CD8T genomic DNA


title: FANS_ATAC_rep3


title: iCLIP_FIP1_P19_noUV_CCGG_Rep1

value: no UV control

value: CCGG


title: iCLIP_CPSF5_P19_sample_CGGA_Rep6


title: iCLIP_FIP1_P19_sample_GGTT_Rep2


title: Sample89.Large flying fox.202897220010_R05C01


title: iCLIP_FIP1_P19_sample_TTGT_Rep3


title: genomic DNA of sample F141_CD8T [3998909160_R01C01]

description: Non-smoker CD8T genomic DNA


title: Sample87.Variable flying fox.202897220010_R03C01


title: iCLIP_CPSF5_P19_sample_CGGA_Rep5


title: Sample88.Large flying fox.202897220010_R04C01


title: FANS_ATAC_rep1


title: genomic DNA of sample F138_CD8T [3998909153_R01C02]

description: Non-smoker CD8T genomic DNA


title: iCLIP_CPSF5_P19_sample_GGCA_Rep4

value: GGCA


title: iCLIP_CPSF5_P19_sample_GGCA_Rep3


title: genomic DNA of sample F136_CD8T [3998909152_R03C02]

description: Smoker CD8T genomic DNA


title: Sample85.Variable flying fox.202897220010_R01C01

value: Male


title: Cas+CO

city: Da’an Dist

first: Tse-en

state: Taipei City

address: No. 1, Sec. 4, Roosevelt Rd., Da’an Dist., Taipei City 106, Taiwan (R.O.C.)

department: Veterinary medicine

country: Taiwan

institute: National Taiwan University

data_processing:
Total 1-2 µg RNA was purified using poly-T oligo-attached magnetic beads following the reference guide of TruSeq® Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, US).
RNA was fragmented using divalent cations at 94℃, the cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H.
cDNA fragments went through an end repair process including the addition of a single “A” base, and the ligation of the adapters.
The products were then purified and enriched with PCR to create the final cDNA library.
Genome_build: Paired-end 75 nucleotide reads from each mRNA library were obtained using NextSeq500 (Illumina Inc., CIC bioGUNE, Bilbao, Spain).
Supplementary_files_format_and_content: Matrix table with expression in log2(TPM+1) for every gene and every sample

source_name: Epididymis

growth_protocol: Male ICR mice were purchased from National Laboratory Animal Center (NAR Labs, Taiwan)

extract_protocol:
Tissue RNA from each experimental group was extracted with the RNeasy Mini Kit (QIAGEN, NL), following the recommendations of the manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: castration surgery was performed by bilateral removal of testes and left intact epididymes in the animals. Control animals underwent the same surgical procedures except for removing their testes (sham). Fourteen days post-surgery, five castrated mice were subcutaneously given testosterone propionate (5 mg/kg body weight, dissolved in corn oil) for 10 consecutive days (Cas+T); the other five castrated animals received corn oil served as vehicle controls (Cas+CO).

tag: strain

value: ICR

value: castration with corn oil supplementation


title: genomic DNA of sample F135_CD8T [3998909152_R03C01]

description: Non-smoker CD8T genomic DNA


title: Sham

value: surgical control


title: LN_C57g

city: Woolloongabba

first: Chenhao

last: Zhou

state: QLD

address: 37 Kent Street

country: Australia

institute: The University of Queensland Frazer Institute

data_processing:
Single cell RNA-seq data was processed using the 10x Genomics Cell Ranger Software (v3.0.2). The command “cellranger mkfastq” was used to demultiplex raw BCL files and generate FASTQ files for individual samples. The command “cellranger count” was used to align RNA-Seq reads to the pre-built mouse reference genome GRCm38 (mm10) and to filter out low quality cell barcodes and unique molecular identiﬁers (UMI). The resulting single-cell gene count matrices were further processed using the Seurat R package (v3.0.5)
Single cell TCR V(D)J-seq data for each sample was processed using Cell Ranger software with the command “cellranger vdj” to perform sequence assembly and paired clonotype calling. For each sample, Cell Ranger generated an output file containing V(D)J information and complementarity-determining region 3 (CDR3) sequences of TCR α- and β-chain for individual cells.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: tsv, csv.gz

source_name: TCRβ+ T cells

extract_protocol:
skin grafts and axillary draining lymph nodes (DLNs) were collected from each recipient. Samples from 7 recipient mice were pooled for each genotype and tissue and were digested enzymatically and mechanically. Live CD45+ cells of skin grafts and Live CD45+ TCRβ+ cells of DLNs were sorted from single cell suspensions via flow cytometric activated cell sorting.
The 10x Genomics Chromium instrument was used to partition each single cell with barcoded beads. This was followed by generation of single cell barcoded 5’ cDNA library using the chromium Single Cell 5’ Library & Gel Bead Kit (PN-1000014; 10X Genomics) per the manufacturer’s instructions. cDNAs were used for both RNA-seq library generation and TCR V(D)J targeted enrichment followed by V(D)J library generation using the Chromium Single Cell V(D)J Enrichment Kit, Mouse T Cells (PN-1000071; 10X Genomics) per the manufacturer’s instructions. Libraries for RNA-seq and V(D)J libraries were sequenced on Illumina NextSeq500 platform using a 150 cycle and 300 cycle High-Output Kit (Illumina), respectively.

tag: genotype

value: Wildtype

tag: age

value: 8-12 weeks

value: female

value: axillary lymph node

value: CD45+ TCRBeta+ T cells


title: FANS_ATAC_rep2

tag: isolation method

value: FANS


title: Sample86.Large flying fox.202897220010_R02C01

data_processing: SeSaMe normalization as described in W. Zhou et al 2018. PMID: 30085201

value: Skin

value: yes


title: Sample84.Large flying fox.202897220011_R06C02


title: iCLIP_CPSF5_P19_sample_GGTC_Rep1

value: anti-EGFP

value: GGTC


title: iCLIP_CPSF5_P19_noUV_CCGG_Rep1

value: no UV control


title: genomic DNA of sample F140_CD8T [3998909178_R01C02]

description: Non-smoker CD8T genomic DNA

data_processing: Average Beta (processed using minfi preprocessNoob)

value: CD8 T cells

value: Non-smoker


title: back skin, WT_3

data_processing:
Filtering was done using SOAPnuke
Mapping to mm10 using STAR
Gene/Transcript expression was done with RSEM
Differentially expressed gene screening was done with DESeq2R Seq package
Genome_build: mm10
Supplementary_files_format_and_content: readcount, FPKMs

source_name: Mouse back skin

growth_protocol: IL-33KO and WT mice were treated DNFB (allergen) on their back skin three times a week for 22days and then total RNA from back skin were collected.

extract_protocol:
Epithelial region of back skin was isolated and homogenized in RLT buffer with addition of 1% 2-mercaptoethanol. Homogenized samples were stored in TriZol reagent and total RNA extracted using the  Rneasy Mini kit (QIAGEN, #74104)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were treated 0.25% DNFB in acetone:olive oil (3:1) solution on back skin

value: WT

tag: treatment

value: DNFB (allergen) on back skin

value: back skin


title: genomic DNA of sample F133_CD8T [3998909186_R03C01]

description: Smoker CD8T genomic DNA

value: Smoker


title: Sample82.Large flying fox.202897220011_R04C02

value: Female


title: Cas+T

value: ICR

value: castration with testosterone supplementation


title: LN_E7g

value: 8-12 weeks

value: female

value: axillary lymph node


title: genomic DNA of sample F130_CD8T [3998909095_R03C01]

description: Non-smoker CD8T genomic DNA


title: Sample83.Variable flying fox.202897220011_R05C02

value: Skin


title: genomic DNA of sample F129_CD8T [3998909109_R03C02]

description: Smoker CD8T genomic DNA


title: back skin, WT_2


title: iCLIP_CPSF5_P19_sample_GGTC_Rep2


title: Sample79.Large flying fox.202897220011_R01C02

value: yes

value: Male


title: back skin, WT_1


title: skin_E7g

source_name: CD45+ cells

value: skin graft

value: CD45+ cells


title: Sample81.Variable flying fox.202897220011_R03C02


title: genomic DNA of sample F134_CD8T [3998909186_R03C02]

description: Non-smoker CD8T genomic DNA

value: CD8 T cells


title: Sample78.Variable flying fox.202897220011_R06C01


title: Sample80.Large flying fox.202897220011_R02C02


title: Sample76.Variable flying fox.202897220011_R04C01


title: genomic DNA of sample F125_CD8T [3998909195_R03C02]

description: Smoker CD8T genomic DNA


title: skin_C57g

value: Wildtype


title: Sample77.Large flying fox.202897220011_R05C01


title: RNA-seq_Diff_rep3

description: processed data file: countTable_Diff_vs_UD.csv

data_processing:
RNA-seq: Reads were trimmed with Cutadapt and mapped to the mouse genome mm10 using STAR (v2.6.1d) with default parameters.
Mapped reads were counted with the summarizeOverlaps function of the GenomicAlignments (version v1.18.1) R package using the “Union” mode and the exons of all genes in the GENCODE annotation (vM18) as features.
Genome_build: mm10
Supplementary_files_format_and_content: Count tables in .csv format.

extract_protocol:
Total RNA was isolated using the Trizol method.
For RNA-seq, total RNA was subjected to poly(A)+ selection and Illumina library preparation following standard procedures. RNA-seq libraries were sequenced on an Illumina NextSeq 500 instrument (single-end 75-nt reads; 50 million reads per replicate).
RNA-seq; UD vs Diff is strand-specific, KD Srsf3, Srsf7 and Cpsf6 is not strand-specific

treatment_protocol: 5 µg purified esiRNAs were transfected for 36 h (SRSF3&SRSF7) and 48 h (CPSF6) using JetPRIME Transfection Reagent (Polyplus) according to the manufacturer’s instructions. EsiRNAs against GFP (SRSF3&SRSF7) or Luciferase (CPSF6) were used as controls. P19 wild type cells were differentiated into neuronal cells using retinoic acid according to Nakayama et al. 2014. PMID:24583076

value: Diff

tag: molecule subtype

value: poly(A)+-selected


title: genomic DNA of sample F121_CD8T [3998909169_R03C02]

description: Non-smoker CD8T genomic DNA

value: Non-smoker


title: back skin, IL-33KO_3

value: IL-33 KO

value: DNFB (allergen) on back skin

value: back skin


title: genomic DNA of sample F120_CD8T [3998909169_R03C01]

description: Non-smoker CD8T genomic DNA


title: back skin, IL-33KO_2


title: genomic DNA of sample F119_CD8T [3998909096_R04C02]

description: Non-smoker CD8T genomic DNA


title: back skin, IL-33KO_1


title: RNA-seq_Diff_rep1


title: genomic DNA of sample F118_CD8T [3998909096_R04C01]

description: Non-smoker CD8T genomic DNA


title: RNA-seq_Undiff_rep2

value: Undiff


title: Sample75.Large flying fox.202897220011_R03C01


title: RNA-seq_Undiff_rep1


title: Sample74.Variable flying fox.202897220011_R02C01

value: Female


title: Sample73.Large flying fox.202897220011_R01C01


title: RNA-seq_Diff_rep2


title: Ec55989 Stationary 3 (Sta3)

city: Paris

first: Marta

last: Lourenço

state: Please Select

address: 25-28 Rue du Dr Roux

country: France

institute: Institut Pasteur

data_processing:
quality check using fastQC
cleanup of the reads using cutadapt.
read alignment with bowtie
files were transformed in BAM and SAM with samtools
read counts with featureCounts
statistical analysis was performed using the R software, packages including DESeq2 and the SARTools package
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Escherichia coli 55989

source_name: bacterial cells grown in stationary culture

growth_protocol: Strain 55989 was grown overnight at 37C with shaking in 4 different replicates. Cultures were refreshed until OD of approximately 0.5, when half of the volumes were collected for RNA extraction while the second half were kept at 37°C with shaking until OD of approximately 5, to collect the second half corresponding to stationary phase cultures. For intestinal samples, axenic mice received by oral gavage 200µL of strain 55989 (107 CFU prepared from an overnight culture in LB at 37°C) in sterile sucrose sodium bicarbonate solution (20% sucrose and 2.6% sodium bicarbonate, pH 8). Three days after gavage mice are sacrificed and the intestinal sections are collected and immediately frozen in liquid nitrogen (ileum, cecum and colon).

extract_protocol:
The RNA extraction process of invitro cells started with the centrifugation of cells and the subsequent addition of TRIzol (sigma T-9424) for lysis. For invivo samples TRIzol (sigma T-9424) was subsequently added to the frozen samples which were homogenized (Oligo-Macs, Mylteny). The total RNA of both in vitro and in vivo samples was purified through a standard organic extraction (phenol/chloroform) followed by ethanol precipitation. Afterwards RNA was submitted to RNeasy mini kit (Qiagen) for better purification and remaining genomic DNA was removed using on-column RNAse-free DNAse set protocol (Qiagen).
RNA integrity was assessed with bioanalyser system (Agilent) and RNA Integrity Number (RIN) and the ribosomal ratio (23S/16S) was considered. The rRNA-depleted RNA were obtained by using the RiboZerorRNA depletion kit, for eucaryote and procaryote called ’epidemiology’ (Illumina). Libraries preparation was performed with TruSeq Stranded RNA LT prep kit (Illumina) with final validation on a DNA Agilent Chip (bioanalyser system) and final DNA quantifications were performed with sensitive fluorescent-based quantitation assays ("Quant-It" assays kit and QuBitfluorometer, Invitrogen). Samples were then normalized to 2nM concentrations and multiplexed. Afterwards samples were denatured at a concentration of 1nM using 0.1N NaOH, at room temperature and was finally diluted at 9,5 pM
Single-read sequencing was performed using HiSeq 2500 Illumina sequencing machine (65 cycles, with 7 index base read).

value: bacterial cells


title: genomic DNA of sample F115_CD8T [3998909138_R04C01]

description: Non-smoker CD8T genomic DNA


title: RNA-seq_CPSF6_KD_rep2

description: processed data file: ccountTable_KD.CPSF6_vs_Ctrl.csv


title: Sample71.Variable flying fox.202897220023_R05C02

city: Los Angeles

first: Steve

address: 695 Charles E. Young Drive South, Box 708822

institute: University of California, Los Angeles


title: Ec55989 Stationary 2 (Sta2)


title: Ec55989 Stationary 1 (Sta1)


title: genomic DNA of sample F113_CD8T [3998888077_R05C02]

city: Research Triangle Park

first: Xuting

address: 111 TW Alexander Dr

institute: NIEHS/NIH

description: Non-smoker CD8T genomic DNA


title: Ec55989 Exponential 4 (Exp4)

source_name: bacterial cells grown in exponential culture


title: RNA-seq_CPSF6_KD_rep1


title: Sample72.Large flying fox.202897220023_R06C02


title: Sample70.Large flying fox.202897220023_R04C02


title: RNA-seq_CPSF6_Ctrl_rep2


title: genomic DNA of sample F112_CD8T [3998888077_R05C01]

description: Non-smoker CD8T genomic DNA


title: genomic DNA of sample F111_CD8T [3998888028_R05C02]

description: Non-smoker CD8T genomic DNA


title: RNA-seq_Undiff_rep3


title: Ec55989 Stationary 4 (Sta4)


title: Ec55989 Exponential 3 (Exp3)


title: genomic DNA of sample F117_CD8T [3998909138_R04C02]

description: Non-smoker CD8T genomic DNA


title: Ec55989 Exponential 2 (Exp2)


title: Sample69.Variable flying fox.202897220023_R03C02


title: Sample68.Large flying fox.202897220023_R02C02


title: RNA-seq_SRSF7_KD_rep2

description: processed data file: countTable_KD.SRSF7_vs_Ctrl.csv


title: genomic DNA of sample F108_CD8T [3998888028_R05C01]

description: Non-smoker CD8T genomic DNA


title: genomic DNA of sample F106_CD8T [3998888001_R05C01]

description: Non-smoker CD8T genomic DNA


title: Ec55989 Exponential 1 (Exp1)


title: Sample66.Large flying fox.202897220023_R06C01


title: RNA-seq_SRSF7_KD_rep1


title: genomic DNA of sample F105_CD8T [3998888078_R05C02]

description: Non-smoker CD8T genomic DNA


title: RNA-seq_SRSF3_KD_rep2

description: processed data file: countTable_KD.SRSF3_vs_Ctrl.csv


title: Sample67.Variable flying fox.202897220023_R01C02


title: RNA-seq_SRSF3_KD_rep1


title: RNA-seq_CPSF6_Ctrl_rep1


title: Ec55989 Colon 2 (Col2)

source_name: bacterial cells grown in vivo (colon samples from monocolonized C3H mice)

value: bacterial cells/intestinal cells


title: genomic DNA of sample F102_CD8T [3998888014_R05C01]

description: Non-smoker CD8T genomic DNA


title: Ec55989 Colon 1 (Col1)


title: RNA-seq_SRSF3.7_Ctrl_rep1


title: genomic DNA of sample F101_CD8T [3998888029_R05C01]

description: Non-smoker CD8T genomic DNA


title: Sample65.Variable flying fox.202897220023_R05C01

value: Skin


title: Sample64.Large flying fox.202897220023_R04C01

value: yes


title: Ec55989 Colon 4 (Col4)


title: w1118/Rpb3 CUT&Tag_Rep 2

city: CANBERRA

first: Jiayu

last: Wen

state: ACT

address: 133 Garran Rd

department: Department of Genome Science

institute: John Curtin School of Medical Research, The Australian National University

description: w1118/Rpb3 Rep 2

data_processing:
Library strategy: CUT&Tag
The ATAC-seq samples of wild-type H3wt and mutant H3K14R stage 15 embryos in three biological replicates were mapped to the Drosophila melanogaster (dm6) genome assembly using Bowtie2 with default parameters after adaptor trimming by Trimmomatic. The high quality and uniquely mapped reads (MAPQ > 20) were used for further analysis.
The CUT&Tag samples of PolII with a Rpb3 antibody in wild-type and H3K14R stage 15 embryos in three replicates were mapped to dm6 using Bowtie2 (bowtie2 --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700). We mapped the reads to the human (hg38) genome assembly as the spike-in reads.
Genome_build: dm6
Supplementary_files_format_and_content: bigwig for coverage; xlsx file for RNA-seq count table

organism: Drosophila melanogaster

source_name: whole embryo

growth_protocol: Embryos, larvae and adult flies were always kept at 25°C.

extract_protocol:
[ATAC-seq]  Crude nuclear extract was prepared in ATAC lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2 0.1% IGEPAL), followed by tagmentation using Tn5 Transposase (Illumina, 15027865). Tagmented DNA was purified using Agencourt AMPure XP beads (Beckman coutler, A63880).
[ATAC-seq]  Following tagmentation DNA was amplified using primers from Nextera Index Kit.
[CUT&Tag]  Crude nuclear extract was prepared in Nuclear Extraction buffer (20 mM HEPES pH 7.9, 10 mM KCl, 0.5 mM spermidine, 0,1% Triton X-100, 20% glycerol) followed by binding to Concanavalin A-coated beads (Polysciences, Inc. 86057-3) and incubation with primary antibody. Tagmentation was performed using Protein A-Tn5 fusion protein.
[CUT&Tag]  Following tagmentation DNA was amplified using primers from Nextera Index Kit.

tag: developmental stage

value: rabbit anti-Rpb3

tag: spike-in

value: Human HeLa cells


title: w1118/Rpb3 CUT&Tag_Rep 3

description: w1118/Rpb3 Rep 3

tag: antibody


title: Sample63.Large flying fox.202897220023_R03C01

last: Horvath

tag: basename

tag: tissue


title: Sample62.Variable flying fox.202897220023_R02C01

tag: canbeusedforagingstudies

tag: age (years)


title: genomic DNA of sample F098_CD8T [3998888030_R05C02]

last: Wang

description: Non-smoker CD8T genomic DNA


title: Sample61.Large flying fox.202897220023_R01C01

tag: confidenceinageestimate

tag: Sex

value: Male


title: Sample60.Variable flying fox.202894750028_R06C02


title: H3K14R/Rpb3 CUT&Tag_Rep 3

description: H3K14R/Rpb3 Rep 3

value: Df(2L)HisCFRT40A; 12xHisGUH3K14R


title: w1118/Rpb3 CUT&Tag_Rep 1

description: w1118/Rpb3 Rep 1


title: genomic DNA of sample F097_CD8T [3998888030_R05C01]

description: Smoker CD8T genomic DNA

tag: cell type

value: CD8 T cells

value: Smoker


title: Ec55989 Colon 3 (Col3)


title: H3K14R/Rpb3 CUT&Tag_Rep 2

description: H3K14R/Rpb3 Rep 2


title: genomic DNA of sample F096_CD8T [3998888039_R05C02]

description: Smoker CD8T genomic DNA


title: RNA-seq_SRSF3.7_Ctrl_rep2

tag: cell line

value: poly(A)+-selected


title: genomic DNA of sample F093_CD8T [3998888039_R05C01]

description: Non-smoker CD8T genomic DNA

value: Non-smoker


title: Sample56.Large flying fox.202894750028_R02C02


title: Sample58.Variable flying fox.202894750028_R04C02

value: no


title: H3K14R/Rpb3 CUT&Tag_Rep 1

description: H3K14R/Rpb3 Rep 1

tag: strain


title: Sample57.Large flying fox.202894750028_R03C02


title: genomic DNA of sample F100_CD8T [3998888029_R05C02]

description: Non-smoker CD8T genomic DNA


title: genomic DNA of sample F103_CD8T [3998888014_R05C02]

description: Non-smoker CD8T genomic DNA


title: genomic DNA of sample F092_CD8T [3998888007_R05C02]

description: Smoker CD8T genomic DNA


title: genomic DNA of sample F091_CD8T [3998888007_R05C01]

description: Non-smoker CD8T genomic DNA


title: Sample54.Large flying fox.202894750028_R06C01


title: H3wt_ATAC-seq_Rep2

data_processing:
The ATAC-seq samples of wild-type H3wt and mutant H3K14R stage 15 embryos in three biological replicates were mapped to the Drosophila melanogaster (dm6) genome assembly using Bowtie2 with default parameters after adaptor trimming by Trimmomatic. The high quality and uniquely mapped reads (MAPQ > 20) were used for further analysis.
The CUT&Tag samples of PolII with a Rpb3 antibody in wild-type and H3K14R stage 15 embryos in three replicates were mapped to dm6 using Bowtie2 (bowtie2 --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700). We mapped the reads to the human (hg38) genome assembly as the spike-in reads.
Genome_build: dm6
Supplementary_files_format_and_content: bigwig for coverage; xlsx file for RNA-seq count table


title: H3wt_ATAC-seq_Rep3


title: Sample59.Large flying fox.202894750028_R05C02


title: Sample55.Variable flying fox.202894750028_R01C02


title: H3wt_ATAC-seq_Rep1


title: H3K14R_ATAC-seq_Rep3


title: genomic DNA of sample F089_CD8T [3998888089_R05C01]

description: Smoker CD8T genomic DNA


title: genomic DNA of sample F090_CD8T [3998888089_R05C02]

description: Smoker CD8T genomic DNA


title: H3K14R_ATAC-seq_Rep2


title: genomic DNA of sample F087_CD8T [3998888085_R05C01]

description: Non-smoker CD8T genomic DNA


title: H3K14R_ATAC-seq_Rep1


title: genomic DNA of sample F084_CD8T [3998888082_R06C02]

description: Non-smoker CD8T genomic DNA


title: genomic DNA of sample F085_CD8T [3998888090_R06C01]

description: Non-smoker CD8T genomic DNA


title: genomic DNA of sample F086_CD8T [3998888090_R05C02]

description: Non-smoker CD8T genomic DNA


title: Wing_disc_Input_DNA_Rep2

data_processing:
RNA-Seq: After trimming the adaptor sequences using Trimmomatic, the RNA-seq reads were mapped to the Drosophila melanogaster (dm6) genome assembly using HISAT2 with default parameters. One of the four replicates of ΔHisC/+;H3K14R sample was an outlier detected by the PCA analysis and was removed from the subsequent analysis. We performed RNA-seq differential expression analysis (DE) of H3K14R vs. H3wt and H3K14R vs. ΔHisC/+;H3K14R  using DEseq2 Bioconductor package.
ChIP-Seq: We mapped ChIP-seq reads to the Drosophila melanogaster (dm6) genome assembly using Bowtie2 with default parameters after adaptor trimming by Trimmomatic. The uniquely mapped reads with a mapping quality MAPQ > 20 were used for further analysis. We generated the coverage tracks for ChIP samples, which were normalized to the library sizes and Input samples. We performed peak calling of the ChIP-seq reads against the Input reads with the HOMER2 peak caller.
Genome_build: dm6
Supplementary_files_format_and_content: bigwig for coverage; xlsx file for RNA-seq count table

source_name: wing disc

extract_protocol:
After sonication, the soluble chromatin was cleared by centrifugation and histone-DNA complexes were isolated with antibody.
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (NEB).

value: wing disc

tag: strain/genotype

value: third instar larva

tag: chip antibody


title: Wing_disc_Input_DNA_Rep3


title: genomic DNA of sample F083_CD8T [3998888082_R05C01]

description: Smoker CD8T genomic DNA


title: Wing_disc_ChIP-seq_Rep3


title: genomic DNA of sample F082_CD8T [3998888084_R06C02]

description: Non-smoker CD8T genomic DNA


title: Wing_disc_ChIP-seq_Rep2


title: Sample51.Variable flying fox.202894750028_R03C01


title: Wing_disc_Input_DNA_Rep1


title: genomic DNA of sample F081_CD8T [3998888084_R06C01]

description: Non-smoker CD8T genomic DNA


title: Wing_disc_ChIP-seq_Rep1


title: genomic DNA of sample F079_CD8T [3998888038_R06C01]

description: Non-smoker CD8T genomic DNA


title: Sample52.Large flying fox.202894750028_R04C01


title: Sample50.Large flying fox.202894750028_R02C01


title: Sample53.Variable flying fox.202894750028_R05C01


title: genomic DNA of sample F078_CD8T [3998579162_R02C02]

description: Non-smoker CD8T genomic DNA


title: genomic DNA of sample F077_CD8T [3998579162_R02C01]

description: Non-smoker CD8T genomic DNA


title: Sample48.Large flying fox.202897220053_R06C02


title: Sample49.Variable flying fox.202894750028_R01C01


title: Sample43.Large flying fox.202897220053_R01C02


title: genomic DNA of sample F076_CD8T [3999119153_R02C02]

description: Non-smoker CD8T genomic DNA


title: Sample42.Variable flying fox.202897220053_R06C01


title: Sample45.Large flying fox.202897220053_R03C02


title: Sample46.Variable flying fox.202897220053_R04C02


title: Sample47.Large flying fox.202897220053_R05C02


title: Embryo_ChIP-seq_Millipore

value: whole embryo

value: 12-13h AEL (After Egg Laying)


title: Sample44.Variable flying fox.202897220053_R02C02


title: ΔHisC/+;H3K14R_RNA-seq_Rep3

extract_protocol:
Twenty embryos per replicate were homogenized in 300 µL TRIzol LS Reagent followed by total RNA purification using the Direct-zol RNA MicroPrep kit (R2060, ZymoResearch).
RNA libraries were prepared using the TruSeq Stranded Total RNA kit (Illumina).


title: Embryo_Input_DNA


title: Embryo_ChIP-seq_Abcam


title: THP1_5Gy_Bioreplicate_2

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

description:
human monocytic leukemia cell line (THP1) under ionizing radiation exposure (5Gy)
processed data file: Raw_TEcount_Expression_Matrix.txt
processed data file: Normalized_TEcount_Expression_Matrix.txt

data_processing:
The raw sequencing data were demuxed using bcl2fastq2 conversion software 2.20 (Illumina).
Raw sequence reads were quality inspected by sample via FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) then adaptor clipped (TruSeq3-PE-2.fa:2:30:10) and quality trimmed (HEADCROP:13 SLIDINGWINDOW:4:20 MINLEN:15) using Trimmomatic (http://www.usadellab.org/cms/?page=trimmomatic). Reference mapping was performed using surviving read pairs against GRCh38.98 (--sjdbOverhang 74 --winAnchorMultimapNmax 100 --outFilterMultimapNmax 100 --outSAMtype BAM SortedByCoordinate) using STAR (https://github.com/alexdobin/STAR). After, mapping files were indexed using samtools (http://samtools.sourceforge.net/) and the number of counts per known annotated gene (ftp://ftp.ensembl.org/pub/release-99/gtf/homo_sapiens/Homo_sapiens.GRCh38.99.gtf.gz) and annotated transposable element (http://labshare.cshl.edu/shares/mhammelllab/www-data/TEtranscripts/TE_GTF/GRCh38_rmsk_TE.gtf.gz) were enumerated (--sortByPos --format BAM --stranded reverse --mode multi) using the TEcount tool (https://pypi.org/project/TEtranscripts/).
Enumerated counts for known annotated genes and known annotated transposable elements were organized across samples in matrix form then import into R (https://cran.r-project.org/). In R, counts were corrected using the counts per million procedure (cpm), pedestalled by 2, Log2 transformed, then quantile normalized. Quality of the normalized data was challenged with no outliers detected via Tukey box plot, Pearson correlation heat map, and covariance-based Principal Component Analysis (PCA) scatterplot. Lowess modeling of the normalized data by sample type (Coefficient of Variation ~ Mean) was then performed and the fits over plotted for inspection. The lowest mean expression value across the fits at which the linear relationship with Coefficient of Variation was grossly lost was defined as the noise threshold for the data. Annotated genes and elements not having a value greater than this threshold for at least one sample were discarded as noise-biased. Surviving genes and/or elements having a value less than the threshold were floored to equal the threshold and tested for differences across sample types using the one factor Analysis of Variance (ANOVA) test under Benjamini Hochberg (BH) False Discovery Rate (FDR) Multiple Comparison Correction (MCC) condition. Annotated genes and/or elements having a corrected p-value < 0.05 by this test were further post hoc tested using Tukey’s Honest Significant Difference (TukeyHSD) method. Genes and/or elements having a p-value < 0.05 by this test for a specific comparison of sample types that also have a linear fold difference of means >= 1.5X were deemed to be those having differential expression between the two sample types respectively. Final summarization of sample type relationships using the union set of differentially expressed genes and/or elements was accomplished via clustered heatmap using the heatmap.2 function.
Genome_build: GRCh38
Supplementary_files_format_and_content: Two data files are provided in tab-delimited text format. One file (Raw_TEcount_Expression_Matrix.txt) describes the raw TEcount enumerated expression for each known gene and transposable element in rows with samples organized in columns. The other file (Normalized_TEcount_Expression_Matrix.txt)  describes the normalized TEcount expression in Quantile(Log2(CPM(Counts)+2)) units for each known gene and transposable element in rows with samples organized in columns.

source_name: Primary THP1 cells

growth_protocol: The acute monocytic leukemia cell line THP1 (from S. Tsuchiya; provided by the NIH AIDS Research & Reference Reagent Program) was maintained at 37°C and 5% CO2 in RPMI-1640 culture media supplemented with 10% FBS, penicillin/streptomycin, and L-Glutamine. MDMs were prepared from PBMCs of normal donors using adherence to plastic, and differentiated in the presence of M-CSF as described earlier (NCBI PMID 9191852). The cells were allowed to differentiate for 7 days in Dutch modified RPMI-1640 culture medium (Gibco) supplemented with 10% human serum (Corning), penicillin/streptomycin, sodium pyruvate and L-Glutamine in the presence of 10 nM M-CSF (PeproTech). Half of the medium was replaced every third day and after day 8, cultivation was performed for 14-21 days without additional growth factors. Where indicated, PMA was added at a 20 nM final concentration and poly(I:C) was added at a 2 µg/ml final concentration.

extract_protocol:
Total RNA was extracted from non-irradiated or 5 Gy irradiated THP1 cells (three biological replicates of each sample) or primary human MDM (from four healthy donors) as described above. After DNase I treatment, RNA was re-purified using RNeasy Plus Mini Kit (Qiagen) following manufacturer instruction. The total RNA integrity was assessed using automated capillary electrophoresis with a Fragment Analyzer (Agilent).
For all samples with an RQI > 8.0, a total of >75 ng RNA was used as input for library preparation using the TruSeq Stranded Total RNA Library Preparation Kit (Illumina, San Diego, CA). The sequencing libraries were quantified by quantitative PCR using a KAPA Library Quantification Kit for NGS (Kapa Biosystems) on a Roche Light Cycler 480 Instrument II and the size distribution was assessed with a Fragment Analyzer.
The sequencing libraries were pooled and sequenced on a NextSeq 500 Desktop Sequencer (Illumina) using a NextSeq 500 High Output Kit v2 with paired-end reads of 75 bp in length.

treatment_protocol: The irradiation experiments were performed in a 137Cs irradiator (JL Shepherd Associates, San Fernando, CA, USA) at ambient temperature (22-25°C) and atmosphere. The dose rate during all experiments was approximately 34 Gy/h; however, the exact irradiation time was calculated on the day of each experiment.

value: Monocytic leukemia cell line

tag: irradiation

tag: sample group

value: THP1 5Gy


title: Sample41.Large flying fox.202897220053_R05C01

value: Skin

value: Female


title: genomic DNA of sample F075_CD8T [9994014135_R05C01]

description: Non-smoker CD8T genomic DNA


title: ΔHisC/+;H3K14R_RNA-seq_Rep2


title: genomic DNA of sample F074_CD8T [3999119153_R02C01]

description: Non-smoker CD8T genomic DNA


title: Sample38.Large flying fox.202897220053_R02C01

value: yes


title: ΔHisC/+;H3K14R_RNA-seq_Rep1


title: THP1_5Gy_Bioreplicate_1


title: Sample39.Variable flying fox.202897220053_R03C01


title: THP1_5Gy_Bioreplicate_3


title: genomic DNA of sample F073_CD8T [3999120036_R02C02]

description: Non-smoker CD8T genomic DNA


title: THP1_0Gy_Bioreplicate_3

description:
human monocytic leukemia cell line (THP1) under no ionizing radiation exposure (0Gy)
processed data file: Raw_TEcount_Expression_Matrix.txt
processed data file: Normalized_TEcount_Expression_Matrix.txt

value: THP1 0Gy


title: Sample40.Large flying fox.202897220053_R04C01


title: THP1_0Gy_Bioreplicate_2


title: genomic DNA of sample F069_CD8T [3999120035_R03C01]

description: Smoker CD8T genomic DNA


title: THP1_0Gy_Bioreplicate_1


title: MDM_5Gy_Bioreplicate_4

description:
primary human monocyte-derived macrophages (MDM) under ionizing radiation exposure (5Gy)
processed data file: Raw_TEcount_Expression_Matrix.txt
processed data file: Normalized_TEcount_Expression_Matrix.txt

source_name: Primary human MDM cells

value: Primary monocyte-derived macrophages (MDM)


title: H3wt_RNA-seq_Rep3


title: genomic DNA of sample F068_CD8T [3999120109_R03C02]

description: Smoker CD8T genomic DNA


title: genomic DNA of sample F067_CD8T [3999120109_R03C01]

description: Smoker CD8T genomic DNA


title: genomic DNA of sample F072_CD8T [3999120036_R02C01]

description: Smoker CD8T genomic DNA


title: Sample37.Variable flying fox.202897220053_R01C01


title: MDM_5Gy_Bioreplicate_2


title: genomic DNA of sample F066_CD8T [3999120111_R03C02]

description: Smoker CD8T genomic DNA


title: H3wt_RNA-seq_Rep1


title: H3K14R_RNA-seq_Rep3

value: Df(2L)HisCFRT40A; 12xHisGUH3K14R


title: H3wt_RNA-seq_Rep4


title: MDM_5Gy_Bioreplicate_1


title: genomic DNA of sample F065_CD8T [3999120111_R03C01]

description: Non-smoker CD8T genomic DNA

value: CD8 T cells


title: H3K14R_RNA-seq_Rep2


title: H3K14R_RNA-seq_Rep1


title: genomic DNA of sample F064_CD8T [3999119156_R03C02]

description: Smoker CD8T genomic DNA

value: Smoker


title: genomic DNA of sample F062_CD8T [3999120013_R03C02]

description: Smoker CD8T genomic DNA


title: MDM_5Gy_Bioreplicate_3


title: H3K14R_RNA-seq_Rep4


title: genomic DNA of sample F104_CD8T [3998888078_R05C01]

description: Smoker CD8T genomic DNA


title: Sample2 of Group3

city: Seoul

first: Joung-Ho

last: Moon

address: Daehak-ro

department: Department of Conservative Dentistry and Dental Research Institute, School of Dentistry

country: South Korea

institute: Seoul National University

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to hg19 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -C -e
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: stem cells from dental pulp

growth_protocol: Dental pulp stem cells were obtained from third-molars and cultured with MEM Alpha (Gibco) at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Tissue RNA extraction performed by QIAGEN RNeasy mini kit with QIAZOL reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Samples of Group1 and 2 were cultured with 15% FBS, samples of Group3 were cultured with 60% FBS.

value: hDPSCs

tag: age

tag: culture

value: 60% serum

tag: sample name


title: Sample34.Large flying fox.202897220129_R04C02

value: Male


title: genomic DNA of sample F061_CD8T [9994014173_R05C02]

description: Smoker CD8T genomic DNA


title: Sample36.Large flying fox.202897220129_R06C02


title: Sample1 of Group3


title: genomic DNA of sample F060_CD8T [3999120013_R03C01]

description: Smoker CD8T genomic DNA


title: MDM_0Gy_Bioreplicate_2

description:
primary human monocyte-derived macrophages (MDM) under no ionizing radiation exposure (0Gy)
processed data file: Raw_TEcount_Expression_Matrix.txt
processed data file: Normalized_TEcount_Expression_Matrix.txt


title: Sample2 of Group2

value: 15% serum


title: genomic DNA of sample F057_CD8T [9994014173_R05C01]

description: Smoker CD8T genomic DNA


title: MDM_0Gy_Bioreplicate_1


title: MDM_0Gy_Bioreplicate_4


title: Sample35.Variable flying fox.202897220129_R05C02


title: Sample32.Large flying fox.202897220129_R02C02


title: Sample1 of Group2


title: Sample33.Variable flying fox.202897220129_R03C02


title: MDM_0Gy_Bioreplicate_3


title: genomic DNA of sample F056_CD8T [3999119110_R04C01]

description: Smoker CD8T genomic DNA


title: Sample31.Large flying fox.202897220129_R01C02


title: Sample28.Variable flying fox.202897220129_R04C01


title: bulkRNA_F239

first: Douglas

middle: A.

last: Bell

address: PO Box 12233

department: Immunity Inflammation and Disease Lab

institute: National Institute of Environmental Health Sciences

data_processing:
Aligned with STAR version 2.6.0c
Gene read counts obtained using featureCounts from the Subread package version 1.5.1 using release 27 of the GENCODE annotation
Gene read counts normalized using size factors from DESeq2 version 1.14.1
Genome_build: hg19
Supplementary_files_format_and_content: counts: 1st column = Gene symbol, 2nd column = Gene read counts normalized by DESeq2 size factor

source_name: Human CD8+ blood cells from a smoking adult

growth_protocol: Human whole blood was collected from smoking and nonsmoking adults

extract_protocol:
Total RNA was isolated from purified cell fractions using the AllPrep DNA/RNA/miRNA Universal Kit according to the manufacturer's instructions.
RNA from isolated CD8+ purified cell fractions were prepared using the TruSeq Stranded Total RNA Library Prep Gold (Illumina)

treatment_protocol: Mononuclear layer was isolated directly from whole blood using density gradient centrifuagation with Histopaque-1077 Ficoll.  Using antibody-coated magnetic beads, purified cell fractions were pelleted and frozen at -80C in Qiagen RLT buffer.

value: Blood

tag: smoker


title: bulkRNA_F209


title: Sample27.Large flying fox.202897220129_R03C01

tag: basename


title: Sample29.Large flying fox.202897220129_R05C01

tag: tissue


title: Sample2 of Group1


title: genomic DNA of sample F055_CD8T [3999120014_R04C02]

description: Non-smoker CD8T genomic DNA

value: Non-smoker


title: Sample1 of Group1


title: bulkRNA_F120

source_name: Human CD8+ blood cells from a nonsmoking adult

value: no


title: Sample24.Large flying fox.202897220071_R06C02

source_name: Skin

tag: canbeusedforagingstudies


title: KB_H_48

last: Pajonk

address: 10833 Le Conte Ave

institute: UC Los Angeles

data_processing:
Novogene Standard RNA-Seq pipeline
Genome_build: Homo_sapiens_hg19
Supplementary_files_format_and_content: read counts

growth_protocol: HK-374 cells were grown in DMEM containing 10% FBS, 1% pen/strep media at 37°C in a 5% CO2 incubator. Cells were grown as monolayers, sorted for zsGreen-negative cells by purging all ZsGreen-positive cells. The sorted cells were grown overnight at 50,00 cells/well density in a 6-well plate with complete media.

extract_protocol:
Total RNA was isolated using Trizol reagent. The treated cells were lysed in 1 ml of Trizol reagent, rocked for 5 min to obtain a homogenous mixture and then transferred to RNAeasy mini kit (Qiagen) colimns for RNA isolation by following manufacturer's protocol.
The RNA sequencing library was generated using NEBNext® Ultra RNA Library Prep Kit (New England Biolabs) according to manufacturer’s protocols. The library concentration was quantified using a Qubit 3.0 fluorometer (Life Technologies), and then diluted to 1 ng/uL before checking insert size on an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany) and quantifying to greater accuracy by quantitative Q-PCR (library molarity >2 nM). The library was sequenced on Illumina NovaSeq6000 with an average of 20M reads per RNA sample.

treatment_protocol: The following day the sorted cells were treated with either saline or QTP (10 uM) 1 hour before irradiation. After 1 hour, the cells were treated again with saline or QTP and then irradiated at 4 Gy (using an experiemntal X-ray irradiator at a dose rate of 5.519 Gy/min. The X-ray beam was operated st 300 kV and hardened using a 4 mm Be, a 3 mm Al, and a 1.5 mm cu filter and calibrated using NIST-traceable dosimetry). Corresponding control cells were sham irradiated. The cells were then incubated and the RNA samples extracted at 1 and 48 hours post irradiation.

value: Glioblastoma

tag: source

value: patient-derived


title: bulkRNA_F093


title: KB_H_47


title: genomic DNA of sample F053_CD8T [9994014167_R05C02]

description: Smoker CD8T genomic DNA


title: Sample26.Variable flying fox.202897220129_R02C01

value: Skin

tag: age (years)

tag: confidenceinageestimate


title: genomic DNA of sample F054_CD8T [3999120014_R04C01]

description: Smoker CD8T genomic DNA

tag: cell type


title: Sample25.Large flying fox.202897220129_R01C01

tag: Sex

value: Female


title: genomic DNA of sample F049_CD8T [3999119085_R04C01]

description: Non-smoker CD8T genomic DNA


title: KB_H_46

tag: cell line


title: bulkRNA_F061

value: yes


title: genomic DNA of sample F052_CD8T [3999120049_R04C02]

description: Smoker CD8T genomic DNA


title: bulkRNA_F075


title: KB_H_44


title: Sample30.Variable flying fox.202897220129_R06C01


title: genomic DNA of sample F047_CD8T [9994014061_R05C02]

description: Non-smoker CD8T genomic DNA


title: bulkRNA_F043


title: genomic DNA of sample F045_CD8T [3999119108_R04C02]

description: Non-smoker CD8T genomic DNA


title: bulkRNA_F040


title: KB_H_42


title: Sample21.Variable flying fox.202897220071_R03C02


title: bulkRNA_F198


title: KB_H_45


title: genomic DNA of sample F048_CD8T [9994014167_R05C01]

description: Smoker CD8T genomic DNA


title: genomic DNA of sample F043_CD8T [9994014061_R05C01]

description: Non-smoker CD8T genomic DNA


title: bulkRNA_F047


title: Sample22.Large flying fox.202897220071_R04C02


title: Sample23.Variable flying fox.202897220071_R05C02


title: KB_H_43


title: Sample19.Variable flying fox.202897220071_R01C02


title: Sample18.Large flying fox.202897220071_R06C01


title: Sample16.Large flying fox.202897220071_R04C01


title: Sample15.Large flying fox.202897220071_R03C01


title: bulkRNA_F037


title: Sample20.Large flying fox.202897220071_R02C02


title: genomic DNA of sample F044_CD8T [3999119108_R05C01]

description: Non-smoker CD8T genomic DNA


title: Sample17.Variable flying fox.202897220071_R05C01


title: KB_H_41


title: KB_H_40


title: bulkRNA_F033


title: KB_H_37


title: genomic DNA of sample F040_CD8T [9994014159_R05C02]

description: Smoker CD8T genomic DNA


title: KB_H_39


title: bulkRNA_F031


title: genomic DNA of sample F030_CD8T [3999119100_R05C01]

description: Smoker CD8T genomic DNA


title: Sample13.Large flying fox.202897220071_R01C01


title: Sample14.Variable flying fox.202897220071_R02C01


title: genomic DNA of sample F026_CD8T [9994014166_R05C02]

description: Non-smoker CD8T genomic DNA