title: T cells, DMSO, Day2 c

city: Frankfurt am Main

first: Dominic

middle: Pascal

last: Denk

address: Theodor-Stern-Kai 7

department: Medizinische Klinik 1

institute: Universitätsklinikum Frankfurt

data_processing:
NGS-Integrative Genomics Core Unit Göttingen
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.20.0.422
The sequencing quality was asserted using FastQC
Sequences were aligned to the reference genome mm10 using the STAR aligner (version 2.5.2a) allowing for 2 mismatches within 50 base
Read counts were analyzed in the R/Bioconductor environment (version 3.6.1) using the DESeq2 package version
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

source_name: Spleen

growth_protocol: Isolated murine T cells were maintained in RPMI supplemented with 10% FBS, 10mM Hepes, 1x Non-Essential Amino Acid, 1mM Sodium Pyruvate, 50uM bMercaptoethanol, 100 U/ml penicillin, 100 µg/ml streptomycin and 2mM Glutamax

extract_protocol:
RNeasy mini kit (Qiagen) was used. 200ng of total RNA was used to prepare the library for RNA sequencing.
mRNA-focused RNA libraries were prepared using Illumina’s TruSeq stranded RNA library prep kit.

treatment_protocol: T cell differentiation was induced by stimulation with aCD3/aCD28 stimulation beads and cotreatment with 50um Urolithin A or DMSO for 48h.

value: Spleen

value: T cells

value: WT

value: FVB

value: DMSO


title: T cells, DMSO, Day2 b

status: Public on Oct 18 2022

type: SRA

country: Germany

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: GTML, DMSO, RP, Rep3

city: San Francisco

first: Duygu

last: Kuzuoglu Ozturk

state: California

address: 1450 3rd Street, Helen Diller Cancer Building

country: USA

institute: UCSF

data_processing:
For Riboseq and RNAseq analyses, the sequences were processed as described previously (Ingolia, 2012).
Only-adapter containing reads were used, the first nucleotide of the reads were trimmed.
rRNA-aligned reads were excluded.
Assembly: GRCm38/mm10
Supplementary files format and content: Each dataset contains analysis compared to Control (DMSO) condition. Total RNAseq dataset are labelled as "mrna"; RPFs are labelled as ''ribo" and Translation efficiency calculations are labelled as "trleff"
Supplementary files format and content: Raw read numbers for Riboseq and RNAseq samples were included in 'exprtable-all' file. RNAseq data are labelled as "total", Riboseq as "RP"
Library strategy: Ribo-seq

source_name: Brain

growth_protocol: GTML cells were cultured in complete neurobasal culture media (Gibco) supplemented with B27 (2%), L-Glutamine (1x), EGF (20 µg/L), bFGF (20 µg/L) and Penicillin-streptomycin at 37C. Accutase (Innovate Cell Tech) was used to dissociate the cells.

extract_protocol:
Cells were lysed and a small aliquot was removed for total RNA extraction for RNAseq samples, using Zymo RNA Clean&Concentrator Kit.
The Riboseq and RNAseq libraries were prepared by using ARTseq Ribosome Profiling Kit (Epicentre)

treatment_protocol: 3 hour treatment

value: Brain

value: GTML

value: Human MYCN overexpressed

value: Control


title: T cells, UA, Day2 a

value: Urolithin A


title: T cells, UA, Day2 b


title: GTML, Rapalink, RNA, Rep3

description:
GTML5_M1071-3_total_3_hr_S6
mrna-m1071-all.csv

data_processing:
For Riboseq and RNAseq analyses, the sequences were processed as described previously (Ingolia, 2012).
Only-adapter containing reads were used, the first nucleotide of the reads were trimmed.
rRNA-aligned reads were excluded.
Assembly: GRCm38/mm10
Supplementary files format and content: Each dataset contains analysis compared to Control (DMSO) condition. Total RNAseq dataset are labelled as "mrna"; RPFs are labelled as ''ribo" and Translation efficiency calculations are labelled as "trleff"
Supplementary files format and content: Raw read numbers for Riboseq and RNAseq samples were included in 'exprtable-all' file. RNAseq data are labelled as "total", Riboseq as "RP"

value: Rapalink-1 (50nM)


title: GTML, DMSO, RNA, Rep3


title: GTML, Rapalink, RNA, Rep1

description:
GTML5_M1071-1_total_3_hr_S4
mrna-m1071-all.csv


title: Atg7Hmgb1DKO2-Tum

city: Indianapolis

first: Xiao-Ming

last: Yin

state: IN

address: 975 W Walnut St IB411/406

department: Pathology and Laboratory Medicine

institute: Indiana University

data_processing:
Base calling and quality scoring were performed by Real-Time Analysis (RTA) v2 in Illumina HiSeq4000
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the human genome using STAR (v2.5.3a) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to mm10 genes using featureCounts (from subread v1.5.3) with the following parameters: “-s 2 –p –Q 10”.
The data was filtered by keeping read count per million 10 in more than 3 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using likelihood ratio test method in edgeR (v3.20.8).
Genome_build: mm10
Supplementary_files_format_and_content: raw count

source_name: Liver

extract_protocol: Total RNA was isolated from liver tissues using a GeneTET RNA Purification Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol.

tag: strain

value: Atg7KO; Hmgb1KO

tag: tissue type

value: tumor


title: Atg7Hmgb1DKO3-NT

value: Nontumor


title: Atg7Hmgb1DKO1-Tum


title: Atg7Hmgb1DKO3-Tum


title: Atg7Hmgb1DKO2-NT


title: Atg7Hmgb1DKO1-NT


title: GTML, Rapamycin, RP, Rep1

description:
GTML5_Rapamycin-1_RP_3_hr_S16
ribo-rapa-all.csv
trleff-rapa-all.csv

value: Rapamycin (5 nM)


title: T cells, UA, Day2 c


title: Atg7KO3-NT


title: Atg7KO1-NT


title: Atg7KO2-Tum


title: Atg7KO2-NT


title: Atg7KO3-Tum


title: oDam-Fer1 replicate 3

city: Beijing

first: xi

last: rongwen

address: No. 7 Science Park Road, zhongguancun Life Science Park, Changping District,

country: China

institute: National Institute of Biological Sciences, Beijing

library_source: genomic

data_processing:
Raw sequencing reads were mapped to the D. melanogaster genome (BDGP6) using bowtie2 (version 2.2.4).
R package iDEAR 0.1.0 was subsequently used for establishing highly reliable profiles of Pros-binding sites in Drosophila EEs.
BigWig files were generated for visualization using the deepTools package.
Assembly: D. melanogaster genome (BDGP6)
Supplementary files format and content: bigWig
Library strategy: DamID-seq

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: intestine

growth_protocol: 5-7d old adult female flies with the following genotypes were cultivated in 29°C for 2 days and been used for DamID analysis

extract_protocol:
50-60 midguts were dissected for each sample, and total genome DNA was extracted, followed by DpnII digestion, dephosphorylation (twice the amount of enzymes and treatment time compared to the original protocol), DpnI digestion and T4 ligation of adaptors. Afterwards, fragments were amplified by ligation-mediated PCR, T7 exonuclease treatment and purification, yielding DNA products ranging from 200 to 2000bp. Finally, the products were fragmented and carrying out subsequent library preparation and high-throughput sequencing.
The NEB Next Ultra II DNA library prep kits (New England Biolabs, cat. no. E7645L) was used for library preparation following the protocal provided by the manufacturer

treatment_protocol: cultivated in 29°C for 2 days to induce gene expression

value: intestine

value: enteroendocrine cell

value: expressing oDam-Fer1 in EE cells


title: T cells, DMSO, Day2 a

value: Spleen

value: T cells


title: oDam-Fer1 replicate 1


title: oDam-Pros replicate 2

value: expressing oDam-Pros in EE cells


title: control oDam replicate 3

value: ProsV1-Gal4ts>UAS-GFP; UAS-oDam

value: expressing control Dam in EE cells


title: control oDam replicate 2


title: Pros-depleted EE replicate 3

data_processing:
Raw reads were mapped to D. melanogaster genome (BDGP6)
Counts assigned to protein-coding genes were calculated using featureCounts (v1.6.3)
DESeq2 was then used to identify significantly differently expressed genes using the following parameters: Padj<0.01, and the absolute value of log2 FC>0.5.
GO analysis for differently expressed genes was performed using DAVID
Assembly: D. melanogaster genome (BDGP6)
Supplementary files format and content: tab-delimited text files include raw reads counts values for each Sample

molecule: polyA RNA

growth_protocol: 5-7d old adult female flies with the following genotypes were cultivated in 29°C for 7 days and been used for RNA-sequencing

extract_protocol:
20,000 PI- GFP+ cells were FACS sorted into 300 μl RNA extraction buffer. The following RNA extraction and amplification steps were carried out using Arcturus PicoPure RNA isolation kit (Applied Biosystems, Cat#KIT0204) and Arcturus RiboAmp HS PLUS RNA amplification kit (Applied Biosystems, Cat#KIT0525) respectively, following the manufacturer’s instructions.
The NEB Next Ultra II DNA library prep kits (New England Biolabs, cat. no. E7645L) was used for library preparation following the protocal provided by the manufacturer

treatment_protocol: cultivated in 29°C for 7 days to induce gene expression

value: ProsV1-Gal6ts>UAS-GFP; pros-RNAi

value: pros depletion


title: control oDam replicate 1


title: Pros-depleted EE replicate 2

value: ProsV1-Gal5ts>UAS-GFP; pros-RNAi


title: oDam-Pros replicate 1


title: Control EE replicate 3

value: control


title: Control EE replicate 2


title: Control EE replicate 1


title: Pros-depleted EE replicate 1

value: ProsV1-Gal4ts>UAS-GFP; pros-RNAi


title: V941

type: genomic

city: Madrid

first: Lara

last: Fernández

state: Madrid

address: Carretera Cantoblanco 8

country: Spain

institute: IMDEA Food

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 787

data_processing: Results were analyzed using TaqMan Genotyper software.

label: VIC

organism: Homo sapiens

source_name: Peripheral blood

label_protocol: Genotyping was performed with QuantStudio 12 K Flex Real-Time PCR System (Life Technologies Inc., Carlsbad, CA, USA) using TaqMan OpenArray plates following manufacturer’s instructions.

extract_protocol: Genomic DNA from peripheral blood was extracted using the QIAamp DNA Blood Mini Kit (Qiagen Sciences, Inc, Germantown, MD, USA)

tag: Sex

value: Female

tag: age

tag: bmi

tag: fat mass

tag: muscle mass

label: FAM


title: V939

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 785

value: Male


title: Atg7KO1-Tum

value: tumor


title: V944

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 790


title: V938

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 784


title: V940

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 786


title: V937

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 783


title: V942

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 788


title: V934

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 782


title: V927

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 777


title: V928

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 778


title: V931

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 779


title: V933

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 781


title: oDam-Fer1 replicate 2


title: V932

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 780


title: V926

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 776


title: V923

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 774


title: V922

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 773


title: V925

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 775


title: V918

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 772


title: V917

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 771


title: V916

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 770


title: V909

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 767


title: V911

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 768


title: V943

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 789


title: V908

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 766


title: V906

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 765


title: V905

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 764


title: V903

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 763


title: V902

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 762


title: V897

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 757


title: V899

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 759


title: V900

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 760


title: V898

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 758


title: V901

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 761


title: V896

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 756


title: V892

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 753


title: V891

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 752


title: V894

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 755


title: V890

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 751


title: V893

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 754


title: V889

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 750


title: V844

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 749


title: V915

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 769


title: V789

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 748


title: V655

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 744


title: V712

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 746


title: V776

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 747


title: V657

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 745


title: V535

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 743


title: V504

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 742


title: V419

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 740


title: V401

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 738


title: V338

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 736


title: V379

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 737


title: V312

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 735


title: V272

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 734


title: V1792

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 730


title: V1850

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 731


title: V248

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 733


title: V1788

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 726


title: V1791

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 729


title: V1790

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 728


title: V1786

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 724


title: V1781

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 719


title: V1789

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 727


title: V1782

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 720


title: V1779

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 717


title: V1785

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 723


title: V481

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 741


title: V410

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 739


title: V1784

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 722


title: V1775

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 713


title: V1778

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 716


title: V1776

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 714


title: V1774

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 712


title: V1772

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 710


title: V1771

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 709


title: V177

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 707


title: V236

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 732


title: V1787

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 725


title: V1768

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 705


title: V1766

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 703


title: V1783

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 721


title: V1780

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 718


title: V1767

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 704


title: V1777

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 715


title: V1763

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 700


title: V1764

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 701


title: V1761

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 698


title: V1760

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 697


title: V1757

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 694


title: V1759

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 696


title: V1758

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 695


title: V1765

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 702


title: V1755

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 692


title: V1756

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 693


title: V1753

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 690


title: V1770

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 708


title: V1754

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 691


title: V1752

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 689


title: V1769

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 706


title: V1749

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 686


title: V1748

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 685


title: V1747

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 684


title: V1746

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 683


title: V1773

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 711


title: V1745

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 682


title: V1762

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 699


title: V1742

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 679


title: V1743

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 680


title: V1744

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 681


title: V1741

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 678


title: V1740

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 677


title: V1739

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 676


title: V1751

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 688


title: V1735

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 673


title: V1750

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 687


title: V1736

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 674


title: V1731

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 670


title: V1728

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 668


title: V1730

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 669


title: V1725

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 665


title: V1726

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 666


title: V1723

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 663


title: V1727

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 667


title: V1722

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 662


title: V1721

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 661


title: V1734

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 672


title: V1719

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 659


title: V1720

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 660


title: V1717

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 657


title: V1718

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 658


title: V1724

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 664


title: V1715

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 655


title: V1713

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 653


title: V1712

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 652


title: V1714

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 654


title: V1710

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 650


title: V1737

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 675


title: V1707

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 647


title: V1704

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 644


title: V1709

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 649


title: V1711

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 651


title: V1708

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 648


title: V1705

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 645


title: V1703

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 643


title: V1699

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 639


title: V1698

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 638


title: V1706

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 646


title: V1695

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 635


title: V1692

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 632


title: V1693

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 633


title: V1690

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 630


title: V1686

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 626


title: V1685

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 625


title: V1716

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 656


title: V1700

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 640


title: V1696

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 636


title: V1678

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 620


title: V1675

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 618


title: V1674

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 617


title: V1679

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 621


title: V1680

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 622


title: V1677

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 619


title: V1684

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 624


title: V1683

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 623


title: V1688

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 628


title: V1694

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 634


title: V1670

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 614


title: V1672

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 615


title: V1673

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 616


title: V1669

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 613


title: V1664

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 609


title: V1668

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 612


title: V1666

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 611


title: V1665

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 610


title: V1732

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 671


title: V1663

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 608


title: V1657

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 602


title: V1660

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 605


title: V1662

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 607


title: V1661

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 606


title: V1659

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 604


title: V1649

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 595


title: V1658

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 603


title: V1656

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 601


title: V1652

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 598


title: V1650

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 596


title: V1653

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 599


title: V1642

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 589


title: V1655

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 600


title: V1640

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 587


title: V1651

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 597


title: V1646

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 592


title: V1648

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 594


title: V1644

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 590


title: V1645

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 591


title: V1641

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 588


title: V1639

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 586


title: V1638

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 585


title: V1635

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 582


title: V1631

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 578


title: V1629

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 577


title: V1632

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 579


title: V1634

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 581


title: V1633

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 580


title: V1636

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 583


title: V1625

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 573


title: V1626

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 574


title: V1622

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 571


title: V1623

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 572


title: V1348

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 570


title: V1637

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 584


title: V1347

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 569


title: V1346

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 568


title: V1345

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 567


title: V1628

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 576


title: V1344

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 566


title: V1340

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 562


title: V1343

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 565


title: V1341

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 563


title: V1697

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 637


title: V1339

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 561


title: V1337

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 559


title: V1338

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 560


title: V1336

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 558


title: V1335

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 557


title: V1333

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 555


title: V1334

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 556


title: V1332

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 554


title: V1331

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 553


title: V1328

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 550


title: V1325

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 547


title: V1324

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 546


title: V1320

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 542


title: V1327

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 549


title: V1326

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 548


title: V1701

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 641


title: V1321

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 543


title: V1318

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 540


title: V1323

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 545


title: V1322

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 544


title: V1317

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 539


title: V1314

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 536


title: V1329

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 551


title: V1315

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 537


title: V1313

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 535


title: V1330

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 552


title: V1312

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 534


title: V1306

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 528


title: V1310

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 532


title: V1308

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 530


title: V1303

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 525


title: V1305

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 527


title: V1319

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 541


title: V1304

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 526


title: V1309

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 531


title: V1691

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 631


title: V1316

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 538


title: V1285

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 522


title: V1296

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 523


title: V1276

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 520


title: V1272

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 517


title: V1278

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 521


title: V1274

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 518


title: V1689

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 629


title: V1270

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 515


title: V1271

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 516


title: V1275

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 519


title: V1311

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 533


title: V1268

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 513


title: V1269

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 514


title: V1265

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 511


title: V1263

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 509


title: V1261

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 507


title: V1260

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 506


title: V1259

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 505


title: V1258

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 504


title: V1254

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 500


title: V1255

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 501


title: V1257

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 503


title: V1250

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 496


title: V1251

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 497


title: V1253

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 499


title: V1256

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 502


title: V1252

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 498


title: V1248

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 494


title: V1267

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 512


title: V1249

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 495


title: V1264

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 510


title: V1244

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 493


title: V1238

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 492


title: V1232

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 491


title: V1228

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 487


title: V1262

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 508


title: V1702

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 642


title: V1230

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 489


title: V1231

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 490


title: V1342

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 564


title: V1227

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 486


title: V1222

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 481


title: V1219

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 478


title: V1229

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 488


title: V1215

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 474


title: V1216

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 475


title: V1226

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 485


title: V1218

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 477


title: V1221

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 480


title: V1225

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 484


title: V1223

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 482


title: V1220

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 479


title: V1212

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 471


title: V1210

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 469


title: V1211

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 470


title: V1209

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 468


title: V1208

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 467


title: V1217

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 476


title: V1213

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 472


title: V1205

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 465


title: V1203

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 463


title: V1201

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 461


title: V1204

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 464


title: V1224

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 483


title: V1202

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 462


title: V1198

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 458


title: V1192

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 452


title: V1194

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 454


title: V1200

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 460


title: V1206

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 466


title: V1199

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 459


title: V1188

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 448


title: V1190

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 450


title: V1187

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 447


title: V1647

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 593


title: V1627

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 575


title: V1196

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 456


title: V1195

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 455


title: V1191

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 451


title: V1193

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 453


title: V1197

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 457


title: V1182

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 442


title: V1185

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 445


title: V1183

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 443


title: V1186

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 446


title: V1181

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 441


title: NCIH1048_non_targeting_gRNA

city: Oxford

first: Yang

last: Shi

address: Old Road Campus Research Building, Roosevelt Drive

country: United Kingdom

institute: Ludwig Institute for Cancer Research, University of Oxford

data_processing:
Read counts for genes were determined by Salmon and normalization was done by DESeq2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized count for each sample

extract_protocol:
Total RNA was extracted by using TRIzol/chloroform extraction method and further treated with DNase by using RNA Clean & Concentrator (Zymo Research #R1014). Poly(A)+ RNA was selected by using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB #E7490S).
RNA-seq libraries were prepared according to the manual for NEBNext® Ultra™ II RNA Library Prep Kit (NEB #E7770L).

value: Small cell lung cancer cell line

value: WT


title: V1179

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 439


title: NCIH1048_COLCA2_gRNA_1

value: COLCA2 knockout


title: NCIH1048_POU2F3_gRNA

value: POU2F3 knockout


title: V1178

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 438


title: V1687

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 627


title: V1189

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 449


title: V1180

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 440


title: NCIH1048_COLCA2_gRNA_2


title: 9_Doxo_150nM_plus_MDL_50uM

city: Huddinge

first: Federico

last: Pietrocola

address: Halsovagen 7C

country: Sweden

institute: Karolinska Institute

data_processing:
Bcl files were converted and demultiplexed to fastq using the bcl2fastq v2.20.0.422 program.
Reads were aligned to Ensembl GRCh38 reference genome using STAR (v2.7.9a).
Mapped reads were then counted in annotated exons using featureCounts v1.5.1
Assembly: hg38/GRCh38
Supplementary files format and content: Tab-delimited text file including matrix of raw counts.

growth_protocol: IMR90 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 200 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA prep ligation library protocol

treatment_protocol: IMR90 cells were treated with 150 nM Doxorubicin (dissolved in deionized water), or 150 nM Doxorubicin + 50 micromolar MDL72527 for 10 days

value: foetal lung fibroblast

value: Doxorubicin + MDL72527


title: 7_Doxo_150nM_plus_MDL_50uM


title: 5_Doxo_150nM

value: Doxorubicin


title: V1174

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 434


title: V1175

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 435


title: 6_Doxo_150nM


title: V1173

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 433


title: V1184

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 444


title: V1177

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 437


title: 4_Doxo_150nM


title: V1168

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 431


title: 3_Ctrl

value: Untreated


title: 8_Doxo_150nM_plus_MDL_50uM


title: V1169

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 432


title: V1166

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 429


title: 1_Ctrl


title: V1165

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 428


title: 2_HepG2 Iso-Seq

city: Bethesda

first: Ashish

last: Lal

state: Maryland

address: 37 Convent Drive, Room 6134

department: NCI

institute: NIH

description: PacBio IsoSeq

data_processing:
PacBio SMRTlink generated raw subreads were converted into HiFi circular consensus sequences (CCS)
PacBio IsoSeq v3 pipeline was used to demultiplex the barcodes and remove primers. Additional refine steps included trimming polyA tails and removing concatemers to generate Full Length Non-Concatemer (FLNC) reads.
Hierarchical clustering,  iterative clustering and merging steps were performed to obtain consensus isoforms and the full-length (FL) consensus sequences
The high-quality FL transcripts were mapped to the reference genome by using the minimap2
Isoform classification and quality control were done using SQANTI3 software
Assembly: hg38
Supplementary files format and content: xlsx: tab-delimited text files include SQUANTI annotated isoforms for each Sample

growth_protocol: SKHEP1 and HepG2 liver cancer cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% PenStrep in a 5% CO2 atmosphere at 37°C.

extract_protocol:
RNA was harvested using RNeasy Plus kit (Qiagen).
RNA libraries for PacBio sequencing  were prepared using PacBio Iso-seq  Library Prep Kit following manufacturer's protocols.

value: hepatocellular carcinoma


title: V1167

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 430


title: V1164

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 427


title: 1_SKHEP1 Iso-Seq

description: PacBio IsoSeq

value: endothelial cells


title: B16F10_5 Doxo 150nM 7days

data_processing:
Basecalling and demultiplexing was performed using Illumina bcl2fastq (v2.20.0.422).
Reads were aligned to Ensembl GRCh38 reference genome using STAR (v2.7.9a).
Gene counts were estimated using featureCounts (v1.5.1).
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text file including matrix of raw counts.

growth_protocol: B16F10 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 200 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: B16F10 cells were treated with 150 nM Doxorubicin (dissolved in deionized water) for 7 days

value: melanoma


title: V1162

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 425


title: V1163

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 426


title: V1159

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 424


title: B16F10_3 Ctrl


title: B16F10_4 Doxo 150nM 7days


title: V1157

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 422


title: V1158

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 423


title: 2_Ctrl


title: V1156

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 421


title: B16F10_1 Ctrl


title: V1176

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 436


title: V1155

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 420


title: V1152

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 418


title: V1153

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 419


title: V1151

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 417


title: RIVA, replicate 1

city: Warsaw

first: Michal

last: Mikula

address: Roentgena 5

department: Experimental Oncology

country: Poland

institute: Maria Skłodowska-Curie National Research Institute of Oncology

data_processing:
The raw reads were processed with Ion Torrent RNASEQAnalysis pipeline (Torrent Suite version 5.0.4) which maps reads to hg19 genome with STAR2 and bowtie2 aligners
Gene counts were generated with htseq-count version 0.6
Assembly: hg19
Supplementary files format and content: htseq normalized count

source_name: RIVA cell line

extract_protocol:
Total RNA was extracted using Gene MATRIX Universal RNA/miRNA Purification Kit (EURx), according to manufacturer instructions.
Poly(A)-containing mRNA was isolated from total RNA with Dynabeads® mRNA DIRECT™ Micro Kit (Thermo). The library libraries were prepared with Ion Total RNA-Seq Kit v2 (Thermo) and sequenced on Ion Porton sequencer as described before (doi: 10.2147/JIR.S307305)

value: wildtype

value: RIVA cell line


title: V1150

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 416


title: LY7, AD-051.4 resistant, replicate 3

source_name: LY7 cell line

value: AD-051.4 resistant

value: LY7 cell line


title: V1149

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 415

value: Female


title: RIVA, AD-051.4 resistant, replicate 3


title: RIVA, AD-051.4 resistant, replicate 1


title: RIVA, replicate 3


title: V1148

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 414


title: V1302

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 524

value: Male


title: RIVA, replicate 2


title: LY7, AD-051.4 resistant, replicate 2


title: V1147

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 413


title: LY7, AD-051.4 resistant, replicate 1


title: LY7, replicate 3

value: wild type


title: RIVA, AD-051.4 resistant, replicate 2


title: V1143

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 410


title: V1141

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 408


title: LY7, replicate 1


title: V1140

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 407


title: V1137

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 405


title: V1138

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 406


title: V1135

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 403


title: V1136

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 404


title: Normoxia sample1 [Norm-Y-1_ATAC-seq]

city: Cologne

first: Peter

last: Tessarz

state: Nordrhein-Westfalen

address: Joseph-Stelzman-Str 9b

institute: Max Planck Institute

data_processing:
fastq reads were mapped to mm10 genome using bowtie2 and duplicates were then removed using MarkDuplicates program of Picard Tools.
The peaks were then called using chromstaR package in differential mode between Normoxia and Hypoxia..
The called peaks were then used in nucleoATAC for nucleosome positioning. The peaks were split into mono, di, tri and nucleosome free regions using standard insert length for each.
The motif scan was performed using motifmatchr R package.
Assembly: mm10
Supplementary files format and content: peaks rpkm table across all 4 samples in tab-delimited text format.

source_name: cell culture

growth_protocol: Bone-marrow MSCs were cultured in T25 flasks under humidified conditions in hypoxia (2% O2, 5% CO2, 37°C) or normoxia (21% O2, 5% CO2, 37°C). Cells were cultured in control α-MEM medium. On day 3 of cell culture the medium was changed,  on day 5 cells  were passaged, using Trypsin-EDTA. On day 12, FACS was used to isolated purified MSCs.

extract_protocol:
ATAc-seq was performed on 50K cells per sample, as described previously (Buenrostro et al., 2013). In brief, cells were harvesred, washed with PBS, resuspended in ice-cold lysis buffer and centrifuged for 10min at 500g at 4C. Nuclei were then incubetaed with the transposition reaction mix, for 30 minutes at 37C, shaking at 250rpm. DNA was purified using the DNA concentrator kit from Zymo Research.
Following DNA purification libraries were prepared using Nextera PCR primers and the NEBNext High-Fidelity PCR Master Mix. Libraries were PCR amplified for 5 cycles. DNA concentration of the libraries was measured with Qubit and library quality was assessed by running samples on the TapeStation.

value: 3-5 months

tag: oxygen level

value: Bone-marrow MSCs


title: Hypoxia sample2 [Hypo-Y-2_ATAC-seq]


title: V1145

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 412


title: V1134

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 402


title: Normoxia sample2 [Norm-Y-2_ATAC-seq]


title: V1133

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 401


title: V1144

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 411


title: V1132

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 400


title: LY7, replicate 2


title: Hypoxia sample1 [Hypo-Y-1_ATAC-seq]


title: V1131

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 399


title: V1307

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 529


title: MEF rep3

city: Barcelona

first: Adria

last: Caballe

address: C/ Baldiri Reixac 10

department: biostatistics

institute: IRB

description: Non-senescent mouse Embryonic Fibroblasts rep3

data_processing:
RNA-Seq: FastQ files were aligned against the mm10 genome with the STAR software v2.3.0e with the following parameter values: outFilterMismatchNoverLmax=0.05; outFilterMatchNmin=25
RNA-Seq: Aligned BAM files were sorted and indexed using sambamba v0.5.9
RNA-Seq: BAM files were merged by combining files of same sampleId using samtools, v1.3
RNA-Seq: RPKM estimations per isoforms were computed with the R package casper v2.16.1 which were then aggregated at the gene level (Ensembl ID)
RNA-Seq: RPKM matrix was log2-transformed and quantile normalized
RNA-Seq: Differential expression between genotype conditions was performed with the R package limma
Assembly: RNA-Seq: mm10 from GENCODE database
Supplementary files format and content: Processed data files contain the RPKM normalized counts per gene in tab delimited format

source_name: MEF

growth_protocol: All cells were maintained in standard DMEM supplemented with 10% FBS and 1% antibiotics (Pen/Strep)

extract_protocol:
Cells were trypsinized and total RNA was extracted using RNeasy® Mini Kit (Qiagen). Immunopeptidome analysis: Cells were trypsinized
RNA libraries were prepared for sequencing using the kits NEBNext® Poly(A) mRNA Magnetic Isolation Module (Cat# E7490) and NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (Cat#E7760), following manufacturer´s instructions and 8 cycles of amplification

treatment_protocol: Non-senescent MEF (MEF rep1, rep2, rep3) were untreated and senescent MEF (SMEF rep1, rep2, rep3) were induced to senescence by doxorubicin treatment (200nM for 48h) and collectec after 8 days from the beggining of the  treatment.

tag: sampleID

tag: replicate id

value: MEF

tag: condition


title: MEF rep1

description: Non-senescent mouse Embryonic Fibroblasts rep1


title: SMEF rep1

description: Senescent mouse Embryonic Fibroblasts rep2

source_name: SMEF

value: SMEF


title: SMEF rep3

description: Senescent mouse Embryonic Fibroblasts rep3


title: SMEF rep2


title: V1142

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 409


title: Normoxia sample 4 [N4_RNA-seq]

data_processing:
fastq reads were processed with the zUMIs pipeline. Reads were mapped on mm10 genome with Ensembl annotation GRCm38.91
Assembly: mm10
Supplementary files format and content: sample (columns) and genes (rows) -wise read count table

extract_protocol:
RNA was isolated using Direct-zol and RNA MiniPrep kit from Zymoresearch, according to manufacturer's instructions.
RNA-seq libraries were prepared for sequencing using standard Illumina protocols


title: Normoxia sample 3 [N3_RNA-seq]


title: B16F10_2 Ctrl

value: WT


title: Normoxia sample 1 [N1_RNA-seq]


title: V1130

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 398


title: MEF rep2

description: Non-senescent mouse Embryonic Fibroblasts rep2


title: B16F10_6 Doxo 150nM 7days

value: Doxorubicin


title: Normoxia sample 2 [N2_RNA-seq]


title: V1126

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 394


title: V1128

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 396


title: V1127

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 395


title: V1125

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 393


title: Hypoxia sample 4 [H4_RNA-seq]


title: Hypoxia sample 3 [H3_RNA-seq]


title: V1124

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 392


title: V1123

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 391


title: Hypoxia sample 1 [H1_RNA-seq]


title: V1120

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 390


title: 124153_mRNA-Seq Plasmablast cell Bhlha15(CreER/CreER)

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

data_processing:
RNA-Seq Sequence Alignment: Sequence reads that passed the Illumina quality filtering were considered for alignment. Reads have been adapter trimmed with cutadapt and aligned with STAR version 2.4.2. to the mouse genome assembly version of July 2007 (NCBI37/mm9).
RNA-Seq Read Counting: Counting has been done with FeatureCounts version 1.5 and converted to TPMs using R 3.6 and custom scripts.
TPM calculation: In case of Bhlha15 comparison (plasma cells), genes annotated with “IGTRC” and “ENSMUSG” were excluded from the TPM calculation.
Genome_build: mm9
Supplementary_files_format_and_content: txt = normalized count values, such as TPMs, in ASCII text format tab delimited.

source_name: spleen

extract_protocol:
NebNext UltraII RNA Library Prep Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: iGB, day 8

value: Plasmablast cell


title: Hypoxia sample 2 [H2_RNA-seq]


title: V1129

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 397


title: V1115

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 388


title: 124152_mRNA-Seq Plasmablast cell Bhlha15(CreER/CreER)


title: V1116

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 389


title: 124155_mRNA-Seq Plasmablast cell Cd23-Cre Xbp1(fl/fl)

value: Cd23-Cre Xbp1(fl/fl)


title: 124151_mRNA-Seq Plasmablast cell Xbp1(fl/fl)

description: mRNA-Seq Plasmablast cell Xbp1(fl/fl)


title: 124154_mRNA-Seq Plasmablast cell Cd23-Cre Xbp1(fl/fl)


title: V1111

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 385


title: V1112

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 386


title: 124150_mRNA-Seq Plasmablast cell Xbp1(fl/fl)

description: mRNA-Seq Plasmablast cell Xbp1(fl/fl)


title: 137951_mRNA-Seq Plasmacell Cd23-Cre Bhlha15(fl/fl)

treatment_protocol: NP-KLH immunization day 7

tag: chip antibody

value: Plasmacell

value: Cd23-Cre Bhlha15(fl/fl)


title: V1110

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 384


title: V1109

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 383


title: V1108

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 382


title: 137949_mRNA-Seq Plasmacell wildtype

description: mRNA-Seq Plasmacell wildtype

value: wildtype


title: V1107

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 381


title: 137948_mRNA-Seq Plasmacell wildtype

description: mRNA-Seq Plasmacell wildtype


title: V1106

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 380


title: V1105

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 379


title: 29435_Xbp1 Bio-ChIP-Seq pre-Plasmablast and Plasmablast cell Xbp1s(bio/bio) R26(BirA/+)

data_processing:
ChIP-Seq Sequence Alignment: Sequence reads that passed the Illumina quality filtering were considered for alignment. For ChIP-seq, the reads were aligned to the mouse genome assembly version of July 2007 (NCBI37/mm9), using the Bowtie version 1.0.0 for experimental and 0.12.5. for the input sample.
ChIP-Seq read coverage: Read coverage tracks were calculated with the BEDTool program version 2.27.1, were normalized to reads per millions (RPM) using the SAMTools version 1.9 as well as the KentTools version 20190507.
ChIP-Seq peak calling: Where necessary (e.g. for the comparisons of peak regions), reads were down-sampled to the lowest read number in the samples to be compared, using the Picard tool version 2.18.27. Peaks were called with the MACS program version 2.2.5, and a mature B-cell input sample (GSE77744) as a control. We filtered all peaks for significance (P value < 10-10).
Genome_build: mm9
Supplementary_files_format_and_content: bed = MACS peak coordinates in BED format; bw = read coverage (reads per million) in bigWIG format

extract_protocol:
ChIP DNA Clean and Concentrator kit (Zymo Research)
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: LPS, 4 days

value: Streptavidin

value: pre-Plasmablast and Plasmablast cell

value: Xbp1s(bio/bio) R26(BirA/+)


title: Heart, TAC-HF-4

city: Boston

first: Haobo

last: Li

state: MA

address: MEDR410 / Lunder Bldg Dock, 255 Charles St

department: Department of Anesthesia, Critical Care, and Pain Medicine

institute: Massachusetts General Hospital and Harvard Medical School

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw sequence image files from the sequencer were converted to the fastq format and checked for quality: per base sequence quality, the per base sequence content, per base N content, sequence length distribution, adapter and k-mer content and sequence duplication levels are collected for each sequencing run using fastqc.
fastqs are then aligned to the mouse reference genome (mm9) using STAR46 aligner.
Alignment statistics such as average red length, percentage of uniquely mapped reads, percentage of multi-mapped reads and number of splice junctions are collated. Only reads that are uniquely mapped will be considered for read annotation to gene features. Reads are annotated with the ENSEMBL 75 gene transfer format (gtf) file using Salmon.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Heart, TAC-HF

extract_protocol:
Hearts were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries. Libraries were made with the RiboZero kit followed by the NEB RNA lib kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: TAC for 8 weeks

tag: tissue

value: Heart


title: V1103

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 378

value: Female


title: 124832_Bhlha15 Bio-ChIP-Seq Plasmablast cell Bhlha15(fl/fl) R26(BirA/BirA)

value: Bhlha15(fl/fl) R26(BirA/BirA)


title: Heart, TAC-HF-3


title: V1102

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 377


title: Heart, TAC-HF-2


title: V1113

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 387


title: Heart, TAC-HF-1


title: V1100

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 375

value: Male


title: V1099

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 374


title: Heart, Sham-HF-4

source_name: Heart, Sham-HF

value: Sham surgical operation


title: Heart, Sham-HF-3


title: V1098

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 373


title: V1096

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 372


title: V1095

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 371


title: Heart, Sham-HF-2


title: V1094

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 370


title: Heart, Sham-HF-1


title: V1214

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 473


title: 137950_mRNA-Seq Plasmacell Cd23-Cre Bhlha15(fl/fl)


title: Heart, TAC-LVH-4

source_name: Heart, TAC-LVH

value: TAC for 2 weeks


title: 124833_Bhlha15 Bio-ChIP-Seq Plasmablast cell Bhlha15(fl/fl) R26(BirA/BirA)


title: Heart, TAC-LVH-2


title: V1093

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 369


title: V1092

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 368


title: V1101

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 376


title: Heart, Sham-LVH-3

source_name: Heart, Sham-LVH


title: Heart, TAC-LVH-1


title: V1088

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 364


title: Heart, Sham-LVH-2


title: V1090

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 366


title: V1087

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 363


title: Heart, Sham-LVH-1


title: V1086

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 362


title: Heart, Running-4

source_name: Heart, Running

value: Wheel running


title: Heart, Sham-LVH-4


title: Heart, Running-3


title: Heart, TAC-LVH-3


title: V1082

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 359


title: Heart, Running-1


title: Heart, Running-2


title: V1081

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 358


title: Heart, Sedentary-3

source_name: Heart, Sedentary

value: Sedentary


title: Heart, Sedentary-2


title: V1091

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 367


title: V1078

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 355


title: V1075

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 354


title: V1080

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 357


title: V1079

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 356


title: Heart, Sedentary-1


title: V1089

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 365


title: V1074

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 353


title: V1073

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 352


title: V1085

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 361


title: CVS_72175_Male_Spontaneous

city: Los Angeles

first: Margareta

middle: D

last: Pisarska

state: CA

address: 8635 West Third Street Suite 160

department: Obstetrics and Gynecology

institute: Cedars-Sinai Medical Center

description:
Spontaneous Male; sample batch=ART Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

data_processing:
After quality check with FastQC, transcript abundances were quantified against the human reference genome (Ensembl build GRCh38) using Kallisto. Transcript counts were combined per gene to generate gene counts.
DESeq2 differential expression analysis was performed using Kallisto raw counts rounted and converted to integers. Four DESeq2 models were run to compare different modes of conception, adjusted for fetal sex and RNA-seq dataset. The dataset adjustment corrected for batch effects from RNA isolation and/or sequencing runs and is recommended as a covariate in any models using this data.
DESeq2 results were annotated with R package annotables using Ensembl release 91.
Log2FPKM expression values were corrected for batch effects using the limma R package function removeBatchEffect() and the RNAseq dataset for each sample. Log2FPKM values were converted to FPKM and then to transcripts per million (TPM) values.
Assembly: GRCh38, Ensembl release 91
Supplementary files format and content: Counts matrix: raw Kallisto counts for each sample and each gene, not corrected for batch effects.
Supplementary files format and content: Counts matrix: batch-corrected log2FPKM and TPM expression values.
Supplementary files format and content: Datasets: DESeq2 differential expression analysis results. Columns: gene = Ensembl Gene ID, symbol = gene symbol, chr = chromosome, start and end are GRCh38 chromosome locations, biotype from Ensembl release 91, description from Ensembl, baseMean = counts normalized for sequencing depth (all samples), log2FoldChange = ratio of group1/group2 expression from DESeq2 (group1 vs group2 as in file name order), lfcSE = log2FoldChange standard error,. pvalue = Wald test, padj = Benjamini-Hochberg False Discovery Rate adjusted pvalue.

source_name: Placenta - chorionic villi

growth_protocol: Continuing human pregnancies undergoing chorionic villus sampling (a prenatal test) in late first trimester.

extract_protocol:
Chorionic villi tissue was homogenized in RLT Plus lysis buffer (QIAGEN) containing 1% beta-mercaptoethanol, physically dissociated with single use needles attached to a 1 mL syringe. Total RNA was isolated from the homogenate using the AllPrep DNA/RNA Mini Kit (QIAGEN) following the manufacturer protocol.
RNA-seq libraries of >200 nt RNA were constructed from 200 ng total RNA per sample using Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold sample prep kits (Illumina). Libraries were depleted of cytoplasmic and mitochondrial ribosomal RNAs.

treatment_protocol: Pregnancies are spontaneous (unassisted, not medically assisted) or conceived with fertility treatments (NIFT: non-IVF fertility treatments, IVF: in vitro fertilization). Chorionic villi tissue discarded after CVS was stored in RNAlater RNA Stabilization Reagent (QIAGEN) and stored at -80C until further processing.

value: Placenta - chorionic villi

value: WT

value: Spontaneous

tag: rnaseq dataset

value: ART Set2

tag: fetal sex

tag: fetal race

value: Caucasian

tag: fetal ethnicity

value: NonHispanic

tag: gestational age_at_cvs_(days)


title: V1070

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 350


title: V1071

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 351


title: V1068

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 348


title: V1084

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 360


title: CVS_72066_Female_NIFT

description:
NIFT Female; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

tag: genotype

tag: treatment

value: NIFT

value: ART Set1


title: V1069

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 349

tag: Sex

tag: age


title: CVS_72160_Male_Spontaneous


title: CVS_72064_Female_IVF

description:
IVF Female; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: IVF


title: CVS_72094_Female_NIFT

description:
NIFT Female; sample batch=ART Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: CaucasianAsianBiracial


title: Heart, Sedentary-4

tag: strain

value: Heart


title: V1067

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 347

value: Female

tag: bmi

tag: fat mass

tag: muscle mass


title: CVS_72057_Male_NIFT

description:
NIFT Male; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: Male


title: CVS_72034_Female_Spontaneous

description:
Spontaneous Female; sample batch=Sex Diff Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: Sex Diff Set2


title: CVS_72056_Male_IVF

description:
IVF Male; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv


title: V1064

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 344


title: V1066

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 346


title: V1065

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 345


title: CVS_71997_Male_Spontaneous

description:
Spontaneous Male; sample batch=ART Supplemental
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: ART Supplemental


title: V1063

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 343


title: V1062

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 342


title: V1061

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 341


title: V1060

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 340


title: CVS_71990_Female_Spontaneous


title: CVS_71991_Male_IVF


title: CVS_71961_Female_IVF

description:
IVF Female; sample batch=ART Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv


title: V1059

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 339


title: V1057

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 338


title: CVS_71959_Female_IVF


title: V1056

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 337


title: V1053

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 334


title: V1055

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 336


title: CVS_71922_Male_Spontaneous

description:
Spontaneous Male; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv


title: CVS_71998_Female_Spontaneous

description:
Spontaneous Female; sample batch=ART Supplemental
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv


title: CVS_71890_Male_IVF

description:
IVF Male; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv


title: CVS_71889_Female_Spontaneous

description:
Spontaneous Female; sample batch=ART Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: Hispanic


title: CVS_71887_Female_Spontaneous


title: CVS_71910_Male_Spontaneous

description:
Spontaneous Male; sample batch=ART Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv


title: V1052

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 333


title: CVS_71853_Female_NIFT

description:
NIFT Female; sample batch=ART Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv


title: CVS_72020_Female_Spontaneous

description:
Spontaneous Female; sample batch=Sex Diff Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv


title: V1051

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 332


title: CVS_71766_Male_NIFT

description:
NIFT Male; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv


title: V1047

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 329


title: V1049

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 331


title: V1048

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 330


title: CVS_71696_Female_IVF

description:
IVF Female; sample batch=ART Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv


title: CVS_71642_Female_IVF


title: CVS_71752_Male_NIFT


title: V1046

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 328


title: CVS_71625_Female_Spontaneous


title: V1045

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 327


title: CVS_71602_Female_Spontaneous


title: CVS_71623_Male_Spontaneous


title: V1054

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 335


title: V1043

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 325


title: V1044

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 326


title: V1042

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 324


title: CVS_71825_Female_IVF

description:
IVF Female; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv


title: CVS_71523_Male_Spontaneous

description:
Spontaneous Male; sample batch=Sex Diff Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv


title: V1037

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 319


title: CVS_71595_Male_IVF

description:
IVF Male; sample batch=ART Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv


title: V1041

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 323


title: CVS_71587_Female_IVF


title: CVS_71529_Male_NIFT

description:
NIFT Male; sample batch=ART Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv


title: CVS_71526_Female_NIFT

description:
NIFT Female; sample batch=ART Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv


title: CVS_71532_Male_Spontaneous


title: V1040

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 322


title: V1039

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 321


title: V1038

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 320


title: V1034

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 317


title: V1033

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 316


title: CVS_71477_Female_Spontaneous

description:
Spontaneous Female; sample batch=ART Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv


title: V1032

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 315


title: CVS_71483_Female_IVF


title: CVS_71466_Male_Spontaneous

description:
Spontaneous Male; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv


title: CVS_71465_Male_IVF

description:
IVF Male; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv


title: V1030

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 313


title: CVS_71468_Female_NIFT

description:
NIFT Female; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv


title: V1031

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 314


title: CVS_71536_Male_Spontaneous

description:
Spontaneous Male; sample batch=Sex Diff Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv


title: CVS_71462_Male_NIFT

description:
NIFT Male; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv


title: V1036

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 318


title: V1029

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 312


title: CVS_71452_Female_IVF

description:
IVF Female; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv


title: V1027

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 310


title: CVS_71457_Male_NIFT

description:
NIFT Male; sample batch=ART Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv


title: CVS_71432_Female_NIFT


title: V1028

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 311


title: V0967

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 309


title: CVS_71417_Female_IVF


title: V0955

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 308


title: CVS_71379_Female_Spontaneous

description:
Spontaneous Female; sample batch=ART Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv


title: V0954

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 307


title: 49-56-map2

city: Novosibirsk

first: Alexey

last: Pindyurin

address: Acad. Lavrentiev Ave. 8/2

country: Russia

institute: IMCB SB RAS

description:
49-56.xlsx
49-56-mapping replicate 2

data_processing:
MPRA_decoder script https://github.com/Code-master2020/MPRAdecoder
Supplementary files format and content: excel tables include unique association of Barcodes and ROIs, read counts for all normalization and expression replicates, expression mean values, RPM expression values, expression values normalized to the wild-type reference construct
Library strategy: MPRA

growth_protocol: Dulbecco’s modification of Eagle’s medium (DMEM; Gibco) supplemented with 10% fetal bovine serum (FBS; Gibco), 7.5% NaHCO3, 100 IU/ml of penicillin and 100 μg/ml of streptomycin

extract_protocol:
The harvested cells were lysed in 1 ml of TRI Reagent™ Solution (Ambion) and total RNA was isolated according to manufacturer’s instructions. Ten μg of purified RNA was incubated with 3 U of DNase I (Thermo Fisher Scientific) and 40 U of DpnI restriction enzyme (New England Biolabs) at 37 °C for 30 min to remove traces of genomic and plasmid DNA. The RNA was purified using CleanRNA Standard kit (Evrogen) according to the manufacturer’s instructions. Two μg of purified total RNA were reverse-transcribed into cDNA using anchored oligo(dT)20 primer and 100 U of RevertAid Reverse Transcriptase (Thermo Fisher Scientific) according to manufacturer’s instructions.
The mapping samples were prepared according to a two-round conventional PCR using primers specific to the ends of fixed sequences mCP1 and mCP3. The expression samples were prepared by PCR amplification of the BC sequences using 1/20 of cDNA as a template and primers specific to the ends of fixed sequences neCP1 and neCP2. The normalization samples were prepared by PCR amplification of the using plasmid DNA as a template and primers specific to the ends of fixed sequences neCP1 and neCP2.

treatment_protocol: One day before transfection, 5 × 10^5 HEK239T cells were seeded in a well of a 6-well plate. The cells were transfected with 400 ng of each MPRA plasmid library mixed with equimolar pool of two wild-type and deltaC reference constructs in a 99:1 molar ratio using Effectene Transfection Reagent (QIAGEN) according to the manufacturer’s instructions. After 48 h, the cells were harvested for total RNA isolation

tag: cell line

tag: cell type

value: Human embryonic kidney


title: 49-56-norm2

description:
49-56.xlsx
49-56-normalization replicate 2


title: 49-56-norm1

description:
49-56.xlsx
49-56-normalization replicate 1


title: 49-56-exp2

description:
49-56.xlsx
49-56-expression replicate 2


title: 49-56-map1

description:
49-56.xlsx
49-56-mapping replicate 1


title: CVS_71352_Male_IVF

description:
IVF Male; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: Placenta - chorionic villi


title: CVS_71347_Female_NIFT

description:
NIFT Female; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: WT


title: 49-56-exp1

description:
49-56.xlsx
49-56-expression replicate 1


title: CVS_71354_Female_IVF

description:
IVF Female; sample batch=ART Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv


title: V0936

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 304


title: V0948

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 306


title: V0945

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 305


title: 45-52-norm2

description:
45-52.xlsx
45-52-normalization replicate 2


title: 45-52-norm1

description:
45-52.xlsx
45-52-normalization replicate 1


title: 45-52-map2

description:
45-52.xlsx
45-52-mapping replicate 2


title: V0935

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 303


title: CVS_71320_Female_NIFT


title: CVS_71319_Female_IVF


title: 45-52-exp1

description:
45-52.xlsx
45-52-expression replicate 1


title: 45-52-exp2

description:
45-52.xlsx
45-52-expression replicate 2


title: V0930

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 302


title: 41-48-norm2

description:
41-48.xlsx
41-48-normalization replicate 2


title: V0929

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 301


title: 41-48-map2

description:
41-48.xlsx
41-48-mapping replicate 2


title: 41-48-exp2

description:
41-48.xlsx
41-48-expression replicate 2


title: 41-48-map1

description:
41-48.xlsx
41-48-mapping replicate 1


title: CVS_71304_Female_NIFT

description:
NIFT Female; sample batch=ART Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv


title: V0921

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 299


title: 41-48-norm1

description:
41-48.xlsx
41-48-normalization replicate 1


title: CVS_71313_Male_Spontaneous

description:
Spontaneous Male; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: Spontaneous


title: 45-52-map1

description:
45-52.xlsx
45-52-mapping replicate 1


title: CVS_71309_Female_NIFT

value: ART Set2


title: 41-48-exp1

description:
41-48.xlsx
41-48-expression replicate 1


title: V0924

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 300


title: CVS_71266_Male_Spontaneous

value: Caucasian


title: V0920

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 298


title: 37-44-map2

description:
37-44.xlsx
37-44-mapping replicate 2


title: 37-44-norm1

description:
37-44.xlsx
37-44-normalization replicate 1


title: 37-44-map1

description:
37-44.xlsx
37-44-mapping replicate 1


title: 37-44-exp1

description:
37-44.xlsx
37-44-expression replicate 1


title: 37-44-exp2

description:
37-44.xlsx
37-44-expression replicate 2


title: CVS_71253_Male_Spontaneous

description:
Spontaneous Male; sample batch=ART Supplemental
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: NonHispanic


title: CVS_71246_Female_IVF

description:
IVF Female; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv


title: 33-40-map2

description:
33-40.xlsx
33-40-mapping replicate 2


title: V0919

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 297


title: 33-40-norm2

description:
33-40.xlsx
33-40-normalization replicate 2


title: CVS_71265_Male_Spontaneous


title: 37-44-norm2

description:
37-44.xlsx
37-44-normalization replicate 2


title: 33-40-norm1

description:
33-40.xlsx
33-40-normalization replicate 1


title: V0914

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 296


title: 33-40-map1

description:
33-40.xlsx
33-40-mapping replicate 1


title: CVS_71240_Male_NIFT

description:
NIFT Male; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: NIFT


title: 33-40-exp2

description:
33-40.xlsx
33-40-expression replicate 2


title: CVS_71238_Male_IVF

description:
IVF Male; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: ART Set1


title: V0913

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 295


title: 33-40-exp1

description:
33-40.xlsx
33-40-expression replicate 1


title: V0910

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 293


title: 29-36-map2

description:
29-36.xlsx
29-36-mapping replicate 2


title: 29-36-norm2

description:
29-36.xlsx
29-36-normalization replicate 2


title: 29-36-exp1

description:
29-36.xlsx
29-36-expression replicate 1


title: 29-36-norm1

description:
29-36.xlsx
29-36-normalization replicate 1


title: CVS_71235_Female_IVF

value: IVF


title: V0907

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 292


title: 25-32-map2

description:
25-32.xlsx
25-32-mapping replicate 2


title: 25-32-map1

description:
25-32.xlsx
25-32-mapping replicate 1


title: V0895

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 290


title: 25-32-norm2

description:
25-32.xlsx
25-32-normalization replicate 2


title: CVS_71138_Female_Spontaneous

description:
Spontaneous Female; sample batch=Sex Diff Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: CaucasianAsianBiracial


title: CVS_71117_Female_NIFT

description:
NIFT Female; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv


title: 29-36-exp2

description:
29-36.xlsx
29-36-expression replicate 2


title: 25-32-exp1

description:
25-32.xlsx
25-32-expression replicate 1


title: 21-28-norm1

description:
21-28.xlsx
21-28-normalization replicate 1


title: V0904

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 291


title: 29-36-map1

description:
29-36.xlsx
29-36-mapping replicate 1


title: CVS_71098_Female_Spontaneous

description:
Spontaneous Female; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv


title: 21-28-map2

description:
21-28.xlsx
21-28-mapping replicate 2


title: U87 cell,ART,Day9 [U87-ART-1]

city: beijing

first: xiangying

last: yan

address: Dongzhimen Jiedao

institute: Institute of Chinese Medicine

hyb_protocol: The purity and concentration of DNA was estimated using Nanodrop 2000 (Thermo) / Quibt3.0. Then 500 ng DNA of each sample was used to bisulfite converted using EZ DNA Methylation Kits(Zymo Research, USA),then converted products were put into 850K BeadChips in accordance with manufacturer guide and protocol(Illumina).

scan_protocol: scan：AutoLoader 2.x, Dual-Scanner Configuration (110/220 V)

data_processing: The data were mainly analyzed using ChAMP package in R. And we used β value to represent DNA methylation level / the proportion of methylated each CpG site . First , we filtered probes with detection p-value β value matrix were normalized using BMIQ for adjusting type I and type II probe bias . Next, we used SVA (Singular Value Decomposition Analysis) to analysis the batch effect caused by BeadChip Slide and Array , then applied Combat  to correct this batch effect. We annotated all CpG sites using EPICanno.ilm10b4.hg19. Differential Methylated CpGs Position(probes) were calculated by champ.DMP() function , the adj.p values were computed using the Benjamini-Hochberg method. CpGs having |Δβ|≥0.20 / 0.10 / 0.06 and adjusted p-value≤0.05 / p-value≤0.01 were considered as DMPs. Differential Methylated Region were calculated using ProbeLasso, all CpGs were for DMR calling and minSigProbesLasso、lassoRadius、boundary were the default value . In order to evaluate the DMP and DMR biologic processes ,cellular components ,molecular and pathway , we conducted Gene Ontology(GO) and KEGG enrichment analysis respectively using R package. Finally, we use Functional Epigenetic Modules to infer differential methylated gene modules in protein to protein iinteraction network(PPI) using FEM package. Additionally , we use Conumee [11] package to analysis copy number variation.

label: ddTTPDNP, ddGTPBiotin, ddCTPBiotin, ddATPDNP, ddGTPBioT

source_name: Glioma

label_protocol: Standard Illumina Protocol

growth_protocol: DMEM medium with 10%FBS and 1%PS was added

extract_protocol: DNA was isolated from whole blood / peripheral blood / tissue by using DNeasy Blood and Tissue   Kit (Qiagen).

treatment_protocol: DMEM medium with 10%FBS,1%PS or different doses of artesunate were added

value: brain,grade IV

value: artesunate treated


title: U251 cell,ART,Day9 [U251-ART-1]


title: V0874

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 288

value: Male


title: V0872

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 287


title: U87 cell,Control,Day9 [U87-3]

value: control


title: U251 cell,Control,Day9 [U251-3]


title: U87 cell,Control,Day9 [U87-2]


title: 21-28-norm2

description:
21-28.xlsx
21-28-normalization replicate 2


title: U251 cell,ART,Day9 [U251-ART-3]


title: CVS_71092_Female_Spontaneous

description:
Spontaneous Female; sample batch=ART Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: Female


title: U87 cell,Control,Day9 [U87-1]


title: 21-28-map1

description:
21-28.xlsx
21-28-mapping replicate 1


title: V0870

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 286


title: V0868

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 285


title: 25-32-exp2

description:
25-32.xlsx
25-32-expression replicate 2


title: U251 cell,ART,Day9 [U251-ART-2]


title: U251 cell,Control,Day9 [U251-2]


title: CVS_71197_Female_Spontaneous

value: Hispanic


title: U251 cell,Control,Day9 [U251-1]


title: CVS_71141_Female_Spontaneous

value: Sex Diff Set2


title: V0864

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 284


title: 17-24-norm2

description:
17-24.xlsx
17-24-normalization replicate 2

value: Human embryonic kidney


title: CVS_71075_Male_IVF

description:
IVF Male; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: Placenta - chorionic villi

value: WT


title: 21-28-exp1

description:
21-28.xlsx
21-28-expression replicate 1


title: CVS_71074_Male_NIFT

description:
NIFT Male; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv


title: CVS_71060_Male_Spontaneous

description:
Spontaneous Male; sample batch=ART Supplemental
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: Spontaneous

value: ART Supplemental


title: 17-24-map1

description:
17-24.xlsx
17-24-mapping replicate 1


title: 17-24-exp2

description:
17-24.xlsx
17-24-expression replicate 2


title: 21-28-exp2

description:
21-28.xlsx
21-28-expression replicate 2


title: 17-24-map2

description:
17-24.xlsx
17-24-mapping replicate 2


title: V0862

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 283


title: 17-24-exp1

description:
17-24.xlsx
17-24-expression replicate 1


title: CVS_71057_Female_NIFT

description:
NIFT Female; sample batch=ART Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: ART Set2

value: Caucasian


title: V0861

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 282


title: V0860

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 281


title: CVS_71059_Male_NIFT

description:
NIFT Male; sample batch=ART Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: NIFT

value: NonHispanic


title: CVS_71050_Male_NIFT

value: ART Set1


title: V0859

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 280


title: V0857

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 279


title: CVS_71049_Male_Spontaneous


title: V0888

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 289


title: 17-24-norm1

description:
17-24.xlsx
17-24-normalization replicate 1


title: V0912

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 294


title: 25-32-norm1

description:
25-32.xlsx
25-32-normalization replicate 1


title: CVS_71055_Male_Spontaneous


title: V0856

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 278


title: CVS_71045_Male_Spontaneous

description:
Spontaneous Male; sample batch=ART Set1
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv


title: V0831

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 277


title: CVS_71032_Male_IVF

description:
IVF Male; sample batch=ART Set2
counts_kallisto_N141_gene-level_not-dataset-corrected.csv
gene-expression_log2FPKM_dataset-corrected_N141.csv
gene-expression_TPM_dataset-corrected_N141.csv

value: IVF

value: CaucasianAsianBiracial


title: U87 cell,ART,Day9 [U87-ART-3]

value: brain,grade IV

value: artesunate treated


title: V0830

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 276

value: Male


title: V0828

description:
TaqMan® SNP Genotyping Assays; Human; MED
SAMPLE 274

value: Female