title: RNAseq_N2_larvae_7h

value: 7 h


title: RNAseq_N2_larvae_4h

status: Public on Jul 27 2020

type: SRA

city: Basel

first: Helge

last: Grosshans

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedriche Miescher Institute for Biomedical Research (FMI)

library_source: transcriptomic

data_processing:
3' adapters are trimmed with cutadapt=2.3 (--error-rate = 0.1, --minimum-length = 15, --overlap = 3)
RNA-seq data were mapped to the C. elegans ce10 genome using STAR with default parameters (version 2.7.0f)
reads are counted using htseq-count (version = 0.11.2)
Genome_build: ce10
Supplementary_files_format_and_content: Tab-separated: First column contains gene names (Wormbase identifiers), second column contains summed width of exons per gene, following columns contain raw counts of reads overlapping each gene for each sample.

molecule: total RNA

organism: Caenorhabditis elegans

source_name: synchronized population

growth_protocol: a population of L1 synchronized by egg prep and M9 incubation was grown on OP50 containing agar plates at 25 degrees. Worms were collected hourly by washing of worms with M9 and washing 3 times in M9.

extract_protocol:
RNA was extracted using Trizol and conventional Phenol / Chlorophorm extraction.
Illumina TruSeq mRNA-Seq Sample Prep Kit (Stranded - high input), followed by the Hiseq50 Cycle Single-end reads on HiSeq2500 protocol

tag: strain

tag: developmental stage

value: 4 h


title: RNAseq_N2_larvae_1h

value: 1 h


title: RNAseq N2 48h

data_processing:
RNA-seq data were mapped to the C. elegans genome (ce10) using the qAlign function (splicedAlignment=TRUE) from the QuasR package in R.
Gene expression was quantified using qCount function from the QuasR package in R.
Counts were scaled by total mapped library size for each sample.
A pseudocount of 8 was added and counts were log2-transformed.
lowly expressed genes were excluded (maximum expression – mean-normalized log2-transformed gene width ≤ 6).
Genome_build: ce10
Supplementary_files_format_and_content: Tab-separated: First column contains gene names (WormBase identifiers), second column contains summed width of exons per gene, following columns contain raw counts of reads overlapping each gene for each sample.

growth_protocol: L1 synchronized by egg prep and M9 incubation over night. A population of N2 worms was grown on OP50-containing agar plates at 25 degrees. Worms were collected hourly by washing of worms with M9 and washing 3 times in M9

extract_protocol:
RNA was extracted using Trizol and conventional Phenol/choloform extraction
TruSeq-illumina-mRNA seq followed by Hiseq 50-cycle-single-end-reads on HiSeq2500


title: RNAseq N2 46h


title: PiZZ1 Liver G4

city: Boston

first: Carlos

last: Villacorta-Martin

state: MA

address: 670 Albany St

country: USA

institute: Center for Regenerative Medicine at Boston University

description:
PiZZ1 Liver
G4

data_processing:
Reads were aligned to the ENSEMBL human reference genome GRCh38.91 using STAR
We used the Bioconductor package edgeR to import, filter and normalize the count matrix, followed by the limma package and voom, for linear model fitting and differential expression testing, using empirical Bayes moderation for estimating gene-wise variability prior to significance testing based on the moderated t-statistic.
Genome_build: GRCh38.91
Supplementary_files_format_and_content: EdgeR normalized, counts per million

molecule: polyA RNA

organism: Homo sapiens

source_name: human iPSC

growth_protocol: Undifferentiated iPSCs were maintained on murine embryonic fibroblast feeders with knockout serum replacement supplemented media or in feeder free conditions with mTeSR-1 media.

extract_protocol:
PHH were freshly thawed and RNA was immediately isolated. Total RNA was isolated using miRNeasy kit (Qiagen) per manufacturer’s instruction.
For digital gene expression (DGE) the concentration of all samples was diluted to 5ng/mL in 10mL total volume and sent to the Broad Institute for library construction and sequencing on the Illumina NextSeq500.

treatment_protocol: As previously described we performed iPSC directed differentiation into NKX2-1+ lung progenitors or iHeps using our published protocols (Jacob A et al. Cell Stem Cell 2017, Wilson AA et al STEMCR 2015).

tag: cell line

tag: target differentiation type

value: Liver


title: RNAseq_N2_larvae_8h

value: 8 h


title: PiZZ6 Undiff G9

description:
PiZZ6 Undiff
G9

value: Undiff


title: PiSZ2 Liver G7

description:
PiSZ2 Liver
G7


title: PiZZ3 Liver G5

description:
PiZZ3 Liver
G5


title: RNAseq N2 47h


title: PiZZ1 Undiff G8

description:
PiZZ1 Undiff
G8


title: PiSZ1 Lung G3

description:
PiSZ1 Lung
G3

value: Lung


title: RNAseq N2 44h


title: RNAseq N2 45h


title: MA002 Liver G6

description:
MA002 Liver
G6


title: RNAseq N2 43h


title: PHH G12

description:
PHH
G12

source_name: Primary Hepatocytes

value: PHH


title: PiSZ2 Undiff G11

description:
PiSZ2 Undiff
G11


title: 100-3 Lung G2

description:
100-3 Lung
G2


title: RNAseq N2 40h


title: RNAseq N2 42h


title: PiZZ3 Lung G1

description:
PiZZ3 Lung
G1


title: RNAseq N2 41h


title: RNAseq N2 39h


title: PiZZ6 Undiff F9

description:
PiZZ6 Undiff
F9


title: RNAseq N2 38h


title: MA011 Undiff G10

description:
MA011 Undiff
G10


title: RNAseq N2 37h


title: PiZZ1 Undiff F8

description:
PiZZ1 Undiff
F8


title: EndoPanc51_Sty

type: genomic

city: London

first: Tomohiko

last: Harada

address: Charterhouse Square

department: Centre for Molecular Oncology

country: United Kingdom

institute: Cancer Research UK

description:
BON_cell line_Sty
Hybridised on Affymetrix 250K SNP array

hyb_protocol: Hybridisation was performed at 45°C for 16h in a hybridisation machine (Affymetrix).

scan_protocol: The arrays were washed and stained on the Affymetrix fluidics Station 450 and the signal intensities were measured using the Affymetrix GeneChip® Scanner 3000.

data_processing: The raw images were analysed using the Affymetrix GCOS (Ver1.4) software. For genotyping analysis, we used the Affymetrix GTYPE (Ver4.1) software that implements an accurate genotyping algorithm, BRLMM.

label: biotin

molecule: genomic DNA

source_name: BON cell line

label_protocol: The experiments were performed according to the manufacturer's instructions (GeneChip® Mapping 250K Nsp or Sty Assay Kit). Briefly, 250 ng of tumour/reference DNA was digested by either Nsp or Sty restriction enzyme (New England Biolabs, Boston, MA, USA). After ligation to an appropriate adaptor for each enzyme, PCR reaction was carried out using a generic primer that recognises the adapter sequence. The PCR products from three reactions were pooled, concentrated, fragmented by DNase I and then, labelled with biotin.

extract_protocol: Tumour and reference genomic DNAs were extracted using Qiagen DNA extraction kit (Qiagen Ltd., Sussex, UK).

tag: BON cell line


title: EndoPanc50_Sty

description:
QGP-1_cell line_Sty
Hybridised on Affymetrix 250K SNP array

source_name: QGP-1 cell line

tag: QGP-1 cell line


title: EndoPanc49_Sty

description:
PET10_tumour_Sty
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET10 tissues

tag: Tumour lesion of PET10 tissues


title: RNAseq N2 36h


title: PiSZ1 Liver F7

description:
PiSZ1 Liver
F7


title: EndoPanc40_Sty

description:
PET2_tumour_Sty
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET2 tissues

tag: Tumour lesion of PET2 tissues


title: EndoPanc46_Sty

description:
PET12_tumour_Sty
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET12 tissues

tag: Tumour lesion of PET12 tissues


title: RNAseq N2 35h


title: EndoPanc41_Sty

description:
PET29_tumour_Sty
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET29 tissues

tag: Tumour lesion of PET29 tissues


title: PiZZ3 Liver F5

description:
PiZZ3 Liver
F5


title: EndoPanc44_Sty

description:
PET14_tumour_Sty
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET14 tissues

tag: Tumour lesion of PET14 tissues


title: EndoPanc32_Sty

description:
PET9_tumour_Sty
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET9 tissues

tag: Tumour lesion of PET9 tissues


title: RNAseq N2 34h


title: EndoPanc36_Sty

description:
PET27_tumour_Sty
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET27 tissues

tag: Tumour lesion of PET27 tissues


title: EndoPanc33_Sty

description:
PET19_ref_Sty
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET19 tissues

tag: Non-neoplastic lesion of PET19 tissues


title: EndoPanc39_Sty

description:
PET2_ref_Sty
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET2 tissues

tag: Non-neoplastic lesion of PET2 tissues


title: EndoPanc30_Sty

description:
PET23_tumour_Sty
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET23 tissues

tag: Tumour lesion of PET23 tissues


title: EndoPanc38_Sty

description:
PET20_tumour_Sty
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET20 tissues

tag: Tumour lesion of PET20 tissues


title: MA002 Liver F6

description:
MA002 Liver
F6


title: EndoPanc48_Sty

description:
PET7_tumour_Sty
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET7 tissues

tag: Tumour lesion of PET7 tissues


title: PiSZ3 Lung F4

description:
PiSZ3 Lung
F4


title: RNAseq N2 33h

source_name: synchronized population

tag: strain

tag: developmental stage


title: EndoPanc35_Sty

description:
PET27_ref_Sty
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET27 tissues

tag: Non-neoplastic lesion of PET27 tissues


title: EndoPanc47_Sty

description:
PET18_tumour_Sty
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET18 tissues

tag: Tumour lesion of PET18 tissues


title: PiSZ1 Lung F3

description:
PiSZ1 Lung
F3

source_name: human iPSC

tag: cell line

tag: target differentiation type


title: EndoPanc43_Sty

description:
PET5_tumour_Sty
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET5 tissues

tag: Tumour lesion of PET5 tissues


title: EndoPanc45_Sty

description:
PET11_tumour_Sty
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET11 tissues

tag: Tumour lesion of PET11 tissues


title: EndoPanc29_Sty

description:
PET23_ref_Sty
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET23 tissues

tag: Non-neoplastic lesion of PET23 tissues


title: 100-3 Lung F2

description:
100-3 Lung
F2


title: RNAseq N2 32h


title: EndoPanc34_Sty

description:
PET19_tumour_Sty
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET19 tissues

tag: Tumour lesion of PET19 tissues


title: EndoPanc26_Sty

description:
PET13_tumour_Sty
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET13 tissues

tag: Tumour lesion of PET13 tissues


title: PHH F12

description:
PHH
F12

source_name: Primary Hepatocytes


title: EndoPanc37_Sty

description:
PET20_ref_Sty
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET20 tissues

tag: Non-neoplastic lesion of PET20 tissues


title: RNAseq N2 31h


title: PiSZ2 Undiff F11

description:
PiSZ2 Undiff
F11


title: EndoPanc52_Sty

description:
CM_cell line_Sty
Hybridised on Affymetrix 250K SNP array

source_name: CM cell line

tag: CM cell line


title: RNAseq N2 30h


title: EndoPanc31_Sty

description:
PET9_ref_Sty
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET9 tissues

tag: Non-neoplastic lesion of PET9 tissues


title: EndoPanc42_Sty

description:
PET26_tumour_Sty
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET26 tissues

tag: Tumour lesion of PET26 tissues


title: MA002 Undiff F10

description:
MA002 Undiff
F10


title: RNAseq N2 28h


title: RNAseq N2 27h


title: PIZZ3 Undiff E9

description:
PIZZ3 Undiff
E9


title: PiZZ2 Lung F1

description:
PiZZ2 Lung
F1


title: PiZZ1 Undiff E8

description:
PiZZ1 Undiff
E8


title: EndoPanc28_Sty

description:
PET4_tumour_Sty
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET4 tissues

tag: Tumour lesion of PET4 tissues


title: RNAseq N2 26h


title: EndoPanc25_Sty

description:
PET13_ref_Sty
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET13 tissues

tag: Non-neoplastic lesion of PET13 tissues


title: EndoPanc21_Sty

description:
PET21_ref_Sty
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET21 tissues

tag: Non-neoplastic lesion of PET21 tissues


title: RNAseq N2 25h

source_name: synchronized population

tag: strain

tag: developmental stage


title: RNAseq N2 29h


title: EndoPanc23_Sty

description:
PET15_ref_Sty
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET15 tissues

tag: Non-neoplastic lesion of PET15 tissues


title: RNAseq N2 24h


title: PiSZ1 Liver E7

description:
PiSZ1 Liver
E7

tag: cell line


title: EndoPanc27_Sty

description:
PET4_ref_Sty
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET4 tissues

tag: Non-neoplastic lesion of PET4 tissues


title: 100-3 Liver E6

description:
100-3 Liver
E6

source_name: human iPSC

tag: target differentiation type


title: 16p2

city: Buffalo

first: Fengwei

last: Yang

address: 955 Main St

institute: University at Buffalo

data_processing:
Illumina Casava1.7 software used for basecalling.
Strand-specific RNA libraries from 1 μg purified RNA using TruSeq stranded total RNA plus Ribo-zero kits (Illumina)
Reads were first trimmed using Cutadapt to remove the 3’ end adapters and trailing sequences, followed by aligning to mouse RefSeq mRNAs using TopHat2 with default.
Transcript counts were estimated using HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw counts for every gene and every sample

organism: Mus musculus

source_name: 16p11.2 duplication_brain prefrontal cortex tissue

extract_protocol:
Trizol extraction method
TruSeq stranded total RNA plus Ribo-zero kits (Illumina)

tag: genotype

value: 16p11.2 duplication (heterozygous)

tag: age

value: post natal week 8

tag: tissue

value: Prefrontal cortex, homogenate


title: PiZZ2 Liver E5

description:
PiZZ2 Liver
E5


title: WT3

source_name: WT_brain prefrontal cortex tissue

value: Wildtype


title: RNAseq N2 22h


title: PiSZ3 Lung E4

description:
PiSZ3 Lung
E4


title: EndoPanc17_Sty

description:
PET1_ref_Sty
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET1 tissues

tag: Non-neoplastic lesion of PET1 tissues


title: EndoPanc22_Sty

description:
PET21_tumour_Sty
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET21 tissues

tag: Tumour lesion of PET21 tissues


title: 16p3


title: WT2


title: WT1


title: SAMPLE 392 PE

type: RNA

city: Turku

first: Michael

last: Gabriel

address: Kiinamyllynkatu 10

country: Finland

institute: University of Turku

description: Patient endometrium

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Endometrium

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

extract_protocol: RNA was extracted with Trizol reagent, further purified with  QIAGEN Rneasy colums and treated with DNase I in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Endometrium

tag: disease stage

tag: cycle phase

value: medication


title: RNAseq N2 21h


title: MA011 Lung E3

description:
MA011 Lung
E3


title: SAMPLE 391 PE

description: Patient endometrium


title: EndoPanc16_Sty

description:
PET22_tumour_Sty
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET22 tissues

tag: Tumour lesion of PET22 tissues


title: EndoPanc19_Sty

description:
PET3_ref_Sty
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET3 tissues

tag: Non-neoplastic lesion of PET3 tissues


title: EndoPanc14_Sty

description:
PET24_tumour_Sty
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET24 tissues

tag: Tumour lesion of PET24 tissues


title: SAMPLE 390 PE

description: Patient endometrium


title: RNAseq N2 20h


title: EndoPanc15_Sty

description:
PET22_ref_Sty
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET22 tissues

tag: Non-neoplastic lesion of PET22 tissues


title: EndoPanc18_Sty

description:
PET1_tumour_Sty
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET1 tissues

tag: Tumour lesion of PET1 tissues


title: SAMPLE 389 PP

description: Patient peritoneum

source_name: Peritoneum

value: Peritoneum

value: secretory


title: EndoPanc12_Sty

description:
PET17_tumour_Sty
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET17 tissues

tag: Tumour lesion of PET17 tissues


title: EndoPanc20_Sty

description:
PET3_tumour_Sty
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET3 tissues

tag: Tumour lesion of PET3 tissues


title: RNAseq N2 19h

source_name: synchronized population

tag: strain

tag: developmental stage


title: SAMPLE 388 PE

description: Patient endometrium


title: SAMPLE 387 DiEIn

description: Deep infiltrating endometriosis lesion intestine

source_name: Intestine

value: Deep infiltrating endometriosis lesion

value: unknown


title: EndoPanc4_Sty

description:
PET16_tumour_Sty
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET16 tissues

tag: Tumour lesion of PET16 tissues


title: SAMPLE 385 SuL

description: Sacrouterine ligament lesion

source_name: Sacrouterine ligament

value: Sacrouterine ligament lesion


title: RNAseq N2 18h


title: EndoPanc13_Sty

description:
PET24_ref_Sty
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET24 tissues

tag: Non-neoplastic lesion of PET24 tissues


title: RNAseq N2 17h


title: PHH E12

description:
PHH
E12

source_name: Primary Hepatocytes

tag: cell line

tag: target differentiation type


title: SAMPLE 384 PE

description: Patient endometrium

tag: tissue

tag: age


title: EndoPanc7_Sty

description:
PET25_ref_Sty
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET25 tissues

tag: Non-neoplastic lesion of PET25 tissues


title: SAMPLE 383 PE

description: Patient endometrium

tag: disease stage

tag: cycle phase


title: EndoPanc24_Sty

description:
PET15_tumour_Sty
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET15 tissues

tag: Tumour lesion of PET15 tissues


title: EndoPanc9_Sty

description:
PET8_ref_Sty
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET8 tissues

tag: Non-neoplastic lesion of PET8 tissues


title: RNAseq N2 16h


title: EndoPanc2_Sty

description:
PET28_tumour_Sty
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET28 tissues

tag: Tumour lesion of PET28 tissues


title: SAMPLE 381 PP Replicate

description: Patient peritoneum

value: Peritoneum Replicate


title: EndoPanc3_Sty

description:
PET16_ref_Sty
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET16 tissues

tag: Non-neoplastic lesion of PET16 tissues


title: EndoPanc8_Sty

description:
PET25_tumour_Sty
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET25 tissues

tag: Tumour lesion of PET25 tissues


title: RNAseq N2 23h


title: EndoPanc5_Sty

description:
PET6_ref_Sty
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET6 tissues

tag: Non-neoplastic lesion of PET6 tissues


title: SAMPLE 381 PP

description: Patient peritoneum


title: SAMPLE 380 PE

description: Patient endometrium

source_name: Endometrium


title: EndoPanc1_Sty

description:
PET28_ref_Sty
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET28 tissues

tag: Non-neoplastic lesion of PET28 tissues


title: PIZZ3 Undiff D9

description:
PIZZ3 Undiff
D9

source_name: human iPSC


title: PiZZ2 Lung E1

description:
PiZZ2 Lung
E1


title: SAMPLE 382 PE

description: Patient endometrium


title: SAMPLE 379 PE

description: Patient endometrium


title: RNAseq N2 13h

tag: strain

tag: developmental stage


title: SAMPLE 377 DiEIn Replicate

value: Deep infiltrating endometriosis lesion Replicate

value: menstruation


title: SAMPLE 378 PE

description: Patient endometrium


title: 100-3 Lung E2

description:
100-3 Lung
E2


title: PiSZ3 Liver D8

description:
PiSZ3 Liver
D8

value: Liver


title: RNAseq N2 15h


title: PiSZ1 Liver D7

description:
PiSZ1 Liver
D7


title: SAMPLE 377 DiEIn


title: EndoPanc11_Sty

description:
PET17_ref_Sty
Hybridised on Affymetrix 250K SNP array

source_name: Non-neoplastic lesion of PET17 tissues

tag: Non-neoplastic lesion of PET17 tissues


title: EndoPanc6_Sty

description:
PET6_tumour_Sty
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET6 tissues

tag: Tumour lesion of PET6 tissues


title: RNAseq N2 14h

source_name: synchronized population


title: EndoPanc10_Sty

description:
PET8_tumour_Sty
Hybridised on Affymetrix 250K SNP array

source_name: tumour lesion of PET8 tissues

tag: Tumour lesion of PET8 tissues


title: SAMPLE 376 PE

description: Patient endometrium

tag: tissue

value: proliferative


title: 100-3 Liver D6

description:
100-3 Liver
D6

tag: cell line

tag: target differentiation type


title: SAMPLE 375 PeLB Replicate

description: Peritoneal endometriosis black lesion

source_name: Peritoneal

value: Peritoneal endometriosis lesion Replicate

tag: age

tag: disease stage


title: SAMPLE 375 PeLB

description: Peritoneal endometriosis black lesion

value: Peritoneal endometriosis lesion

tag: cycle phase


title: RNAseq N2 11h


title: PiZZ3 Liver D5

description:
PiZZ3 Liver
D5


title: SAMPLE 374 PE

description: Patient endometrium


title: RNAseq N2 10h


title: SAMPLE 373 PE

description: Patient endometrium


title: SAMPLE 372 PE

description: Patient endometrium


title: SAMPLE 371 PE Replicate

description: Patient endometrium


title: PiSZ3 Lung D4

description:
PiSZ3 Lung
D4

value: Lung


title: RNAseq N2 12h


title: SAMPLE 371 PE

description: Patient endometrium


title: RNAseq N2 9h


title: SAMPLE 370 PP

description: Patient peritoneum

source_name: Peritoneum


title: RNAseq N2 8h


title: PiZZ6 Lung D2

description:
PiZZ6 Lung
D2


title: PHH D12

description:
PHH
D12

source_name: Primary Hepatocytes

value: PHH


title: SAMPLE 368 PE

description: Patient endometrium


title: SAMPLE 367 PP

description: Patient peritoneum


title: SAMPLE 367 PP Replicate

description: Patient peritoneum


title: SAMPLE 369 DiEIn

source_name: Intestine


title: RNAseq N2 7h


title: SAMPLE 366 DiEIn


title: SAMPLE 365 PE

description: Patient endometrium


title: RNAseq N2 6h


title: MA002 Undiff D10

description:
MA002 Undiff
D10

value: Undiff


title: RNAseq N2 5h


title: PiSZ1 Undiff D11

description:
PiSZ1 Undiff
D11


title: SAMPLE 364 PP

description: Patient peritoneum


title: SAMPLE 363 PeLW

description: Peritoneal endometriosis white lesion


title: SAMPLE 362 PE

description: Patient endometrium

value: Endometrium


title: PiZZ2 Lung D1

description:
PiZZ2 Lung
D1


title: 16p1

source_name: 16p11.2 duplication_brain prefrontal cortex tissue

tag: genotype

value: 16p11.2 duplication (heterozygous)

value: post natal week 8

value: Prefrontal cortex, homogenate


title: SAMPLE 361 PE

description: Patient endometrium

value: medication


title: RNAseq_N2_15h

data_processing:
RNA-seq data were mapped to the C. elegans ce6 genome using the qAlign function (splicedAlignment=TRUE) from the QuasR package in R
Gene expression was quantified using qCount function from the QuasR package in R
Counts were scaled by total mapped library size for each sample
A pseudocount of 8 was added and counts were log2-transformed
Genome_build: ce6
Supplementary_files_format_and_content: Tab-separated: First column contains gene names (Wormbase identifiers), second column contains summed width of exons per gene, following columns contain raw counts of reads overlapping each gene for each sample.

extract_protocol:
RNA was extracted using Trizol and conventional Phenol / Chlorophorm extraction.
Illumina TruSeq mRNA-Seq Sample Prep Kit (Strand-sequenced:_any), followed by the Hiseq50 Cycle Single-end reads on HiSeq2500 protocol


title: MA011 Lung D3

description:
MA011 Lung
D3


title: RNAseq_N2_14h


title: SAMPLE 386 PE

description: Patient endometrium


title: SAMPLE 360 PE

description: Patient endometrium


title: SAMPLE 359 PE

description: Patient endometrium


title: SAMPLE 358 PE

description: Patient endometrium

value: secretory


title: PIZZ3 Undiff C9

description:
PIZZ3 Undiff
C9


title: RNAseq_N2_12h


title: SAMPLE 356 PP

description: Patient peritoneum

value: Peritoneum

value: unknown


title: MA011 Liver C7

description:
MA011 Liver
C7


title: SAMPLE 355 PE

description: Patient endometrium


title: SAMPLE 357 DiEIn

value: Deep infiltrating endometriosis lesion


title: SAMPLE 354 PE

description: Patient endometrium


title: 100-3 Liver C6

description:
100-3 Liver
C6


title: RNAseq_N2_10h


title: SAMPLE 352 PE

description: Patient endometrium


title: SAMPLE 353 PE

description: Patient endometrium


title: RNAseq_N2_13h


title: PiZZ2 Liver C5

description:
PiZZ2 Liver
C5


title: SAMPLE 351 PP

description: Patient peritoneum

value: menstruation


title: SAMPLE 350 PE

description: Patient endometrium


title: PiSZ2 Lung C4

description:
PiSZ2 Lung
C4


title: SAMPLE 349 DiEIn Replicate

value: Deep infiltrating endometriosis lesion Replicate


title: SAMPLE 349 DiEIn


title: RNAseq_N2_8h

value: 8 h


title: SAMPLE 348 PE

description: Patient endometrium


title: PiSZ3 Liver C8

description:
PiSZ3 Liver
C8

value: Liver


title: RNAseq_N2_7h

value: 7 h


title: RNAseq_N2_11h


title: SAMPLE 346 PE Replicate

description: Patient endometrium

value: Endometrium Replicate


title: PiZZ6 Lung C2

description:
PiZZ6 Lung
C2

value: Lung


title: SAMPLE 346 PE

description: Patient endometrium


title: PHH C12

description:
PHH
C12

value: PHH


title: RNAseq_N2_6h

value: 6 h


title: PiSZ1 Undiff C11

description:
PiSZ1 Undiff
C11

value: Undiff


title: RNAseq_N2_5h

value: 5 h


title: SAMPLE 343 PE

description: Patient endometrium

value: Endometrium


title: SAMPLE 345 PeLR

description: Peritoneal endometriosis red lesion

value: Peritoneal endometriosis lesion

value: medication


title: 100-3 Undiff C10

description:
100-3 Undiff
C10


title: RNAseq_N2_4h

value: 4 h


title: SAMPLE 344 PE

description: Patient endometrium


title: RNAseq_N2_9h

value: 9 h


title: PiZZ1 Lung C1

description:
PiZZ1 Lung
C1


title: SAMPLE 342 PE

description: Patient endometrium


title: MA011 Lung C3

description:
MA011 Lung
C3


title: SAMPLE 340 PE

description: Endometrium

value: secretory


title: PiZZ2 Undiff B9

description:
PiZZ2 Undiff
B9


title: SAMPLE 339 SuL Replicate

description: Sacrouterine ligament lesion

source_name: Sacrouterine ligament

value: Sacrouterine ligament lesion Replicate


title: SAMPLE 339 SuL

description: Sacrouterine ligament lesion

value: Sacrouterine ligament lesion


title: RNAseq_N2_0h

value: 0 h


title: SAMPLE 345 PeLR Replicate

description: Peritoneal endometriosis red lesion

value: Peritoneal endometriosis lesion Replicate


title: SAMPLE 337 PE

description: Patient endometrium


title: RNAseq_N2_1h

value: 1 h


title: SAMPLE 338 PP

description: Patient peritoneum

value: Peritoneum


title: MA002 Undiff E10

description:
MA002 Undiff
E10


title: PiZZ6 Liver B6

description:
PiZZ6 Liver
B6

value: Liver


title: MA011 Liver B7

description:
MA011 Liver
B7


title: SAMPLE 336 PE

description: Patient endometrium

value: menstruation


title: RNAseq_N2_3hh

value: 3 h


title: SAMPLE 335 PeLB

description: Peritoneal endometriosis black lesion


title: PiSZ3 Liver B8

description:
PiSZ3 Liver
B8


title: rnh201_YPD_TrAEL-seq

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

description: other_yeast_samples_reverse_read_percentage_in_1kb_windows.txt

library_source: genomic

data_processing:
Sequencing data was processed with a custom script (location available from the manuscript) to transfer the first 8bp of a each sequence to the readID of the FastQ file (UMI, unique molecular identifier). In addition, up to and including 3 T bases were removed from the 5'-end following the UMI transfer. The resulting FastQ files were trimmed with Trim Galore (v0.6.5) to remove read-through contamination with the Illumina standard adapter as well as poor base call qualities (cutoff: Phred 20). Trimmed reads were then aligned to the relevant genomes using Bowtie2 (v2.4.1) in --local mode. Following the alignments, reads were de-duplicated taking UMIs as well as mapping position into account, using UmiBam (v0.2.0; https://github.com/FelixKrueger/Umi-Grinder).
Samples were imported into Seqmonk v1.47, truncated to a single base and quantified in windows: for dmc1 total read counts in 20bp windows, for hESC %reverse reads in 250kb windows every 10kb, for SfiI digests total read counts at 13bp cleavage sites, for other samples %reverse reads in 1kb windows
Genome_build: S. cerevisiae R64-1-1 or GRCh38

organism: Saccharomyces cerevisiae

extract_protocol:
For yeast: Cells in ethanol (1-3x107 per plug) were pelleted in round bottom 2 ml tubes by centrifuging 30 s 20,000 g, washed once in 1 ml PFGE wash buffer (10 mM Tris HCl pH 7.5, 50 mM EDTA) and resuspended in 60 µl same with 1 µl lyticase (17 U/ µl in 10 mM KPO4 pH7, 50% glycerol, Merck >2000 U/mg L2524). Samples were heated to 50°C for 1-10 min before addition of 40 µl molten CleanCut agarose (Bio-Rad 1703594), vortexing vigorously for 5 s before pipetting in plug mould (Bio-Rad 1703713) and solidifying 15-30 min at 4°C. Each plug was transferred to a 2 ml tube containing 500 µl PFGE was buffer containing 10 µl 17 U/µl lyticase and incubated 1 hour at 37°. Solution was replaced with 500 µl PK buffer (100 mM EDTA pH 8, 0.2% sodium deoxycholate, 1% sodium N-lauroyl sarcosine, 1 mg/ml Proteinase K) and incubated overnight at 50°. Plugs were rinsed with 1 ml TE, then washed three times with 1 ml TE for 1-2 hours at room temperature with rocking, 10 mM PMSF was added to the second and third washes from 100 mM stock (Merck 93482). Plugs were then digested 1 h at 37°C with 1 µl 1000 U/ml RNase T1 (Thermo EN0541) in 200 µl TE. RNase A was not used as it binds strongly to single stranded DNA [76]. For hESC: 1x106 cells were washed once in 5 ml L buffer (10 mM Tris HCl pH 7.5, 100 mM EDTA, 20 mM NaCl) and resuspended in 60 µl L buffer in a 2 ml tube. Samples were heated to 50°C for 2-3 min before addition of 40 µl molten CleanCut agarose (Bio-Rad 1703594), vortexing vigorously for 5 s before pipetting in plug mould (Bio-Rad 1703713) and solidifying 15-30 min at 4°C. Each plug was transferred to a 2 ml tube containing 500 µl digestion buffer (10 mM Tris HCl pH 7.5, 100 mM EDTA, 20 mM NaCl, 1% sodium N-lauroyl sarcosine, 0.1 mg/ml Proteinase K) and incubated overnight at 50°. Washing as for yeast.
TrAEL-seq: ½ an agarose plug of cells was equilibrated once in 100 µl 1x TdT buffer (NEB) for 30 min at room temperature, then incubated for 2 h at 37°C in 100 µl 1x TdT buffer containing 4 µl 10 mM ATP and 2 µl Terminal Transferase (NEB M0315L). Plugs were rinsed with 1 ml tris buffer (10 mM Tris HCl pH 8.0), equilibrated in 100 µl 1x T4 RNA ligase buffer (NEB) containing 40 µl 50% PEG 8000 for 1 hour at room temperature then incubated overnight at 25°C in 100 µl 1x T4 RNA ligase buffer (NEB) containing 40 µl 50% PEG 8000, 1 µl 10 pM/µl TrAEL-seq adaptor 1 ([App]NNNNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTUGCGCAGGCCATTGGCC[BtndT]GCGCUACACTCTTTCCCTACACGACGCT) and 1 µl T4 RNA ligase 2 truncated KQ (NEB M0373L). Plugs were then rinsed with 1 ml tris buffer, transferred to 15 ml tubes and washed three times in 10 ml tris buffer with rocking at room temperature for 1-2 hours each, then washed again overnight under the same conditions. Plugs were equilibrated for 15 min with 1 ml agarase buffer (10 mM Bis-Tris-HCl, 1 mM EDTA pH 6.5), then the supernatant removed and 50 µl agarase buffer added. Plugs were melted for 20 min at 65°C, transferred for 5 min to a heating block pre-heated to 42°C, 1 µl β-agarase (NEB M0392S) was added and mixed by flicking without allowing sample to cool, and incubation continued at 42°C for 1 h. DNA was ethanol precipitated with 25 µl 10 M NH4OAc, 1 µl GlycoBlue, 330 µl of ethanol and resuspended in 10 µl 0.1xTE. 40 µl reaction mix containing 5µl Isothermal amplification buffer (NEB), 3 µl 100 mM MgSO4, 2µl 10 mM dNTPs and 1µl Bst 2 WarmStart DNA polymerase (NEB M0538S) was added and sample incubated 30 min at 65°C before precipitation with 12.5 µl 10 M NH4OAc, 1 µl GlycoBlue, 160 µl ethanol and re-dissolving pellet in 130 µl 1xTE.  END-seq: ½ an agarose plug of cells was equilibrated for 1 h at room temperature in 100µl NEBuffer 2 with 0.1mM dNTPs, then overnight at 37°C with 100 µl NEBuffer 2 with 0.1 mM dNTPs and 1 µl Klenow (NEB M0210S). Note that this is not the same blunting regimen used in END-seq [11] as Klenow performed best for SfiI-digested yeast genomic DNA in our hands. After rinsing twice with 1 ml tris buffer, plug was transferred to a 15 ml tube and washed three times for 15 min each with 10 ml tris buffer on rocker at room temperature before transfer to a new 2 ml tube. The plug was equilibrated with 100 µl CutSmart buffer containing 5 mM DTT and 1 mM dATP for 1 hour at room temperature before incubation for 2 h at 37°C in another 100 µl of the same buffer containing 1 µl Klenow exo- (NEB M0212S) and 1 µl T4 PNK (NEB M0201S). Plug was rinsed twice with 1 ml tris buffer then washed once with 10 ml of tris buffer for 15 min as above then returned to a 2 ml tube. The plug was equilibrated for 1 h at room temperature in 100 µl 1x Quick Ligation buffer (NEB B6058S) containing 2.7 µl END-seq adaptor 1 ([Phos]GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGUU[BtndT]U[BtndT]UUACACTCTTTCCCTACACGACGCTCTTCCGATC∗T), then overnight at 25°C with another 100 µl of the same buffer containing  2.7 µl END-seq adaptor 1 and 1 µl high concentration T4 DNA Ligase (NEB M0202M). After rinsing twice with 1 ml tris buffer, plug was transferred to a 15 ml tube and washed three times for 1-2 h each with 10 ml tris buffer on rocker at room temperature, then again overnight.  The plug was transferred to a 1.5 ml tube and equilibrated 15 min with 1 ml agarase buffer (10 mM Bis-Tris-HCl, 1 mM EDTA pH 6.5), then the supernatant removed and 50 µl agarase buffer added to the plug. Plug was melted 20 min at 65°C then transferred for 5 min to a heating block pre-heated to 42°C, 1 µl beta-agarase (NEB M0392S) was added and mixed by flicking without allowing sample to cool, and incubation continued at 42°C for 1 h. DNA was ethanol precipitated with 25 µl 10 M NH4OAc, 1 µl GlycoBlue, 330 µl of ethanol and resuspended in 130 µl 1x TE, 15 min at 65°C.
The DNA was transferred to an AFA microTUBE (Covaris 520045) and fragmented in a Covaris E220 using duty factor 10, PIP 175, Cycles 200, Temp 11, then transferred to a 1.5 ml tube containing 8 µl pre-washed Dynabeads MyOne streptavidin C1 beads (Thermo, 65001) re-suspended in 300 µl 2xTN (10 mM Tris pH 8, 2 M NaCl) along with 170 µl water (total volume 600 µl) and incubated 30 min at room temperature on a rotating wheel. Beads were washed once with 500 µl 5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl, 5 min on wheel and once with 500 µl 0.1x TE, 5 min on wheel before re-suspension in 25 µl 0.1x TE. 3.5 μl NEBNext Ultra II End Prep buffer, 1 µl 1 ng/µl sonicated salmon sperm DNA (this is added as a carrier) and 1.5 μl NEBNext Ultra II End Prep enzyme were added and reaction incubated 30 min at room temperature and 30 min at 65°C. After cooling, 1.25 µl 10 pM/µl TrAEL-seq adaptor 2 ([Phos]GATCGGAAGAGCACACGTCTGAACTCCAGTCUUUUGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T ) or END-seq adaptor 2c ([Phos]GATCGGAAGAGCTATTATTTAAATTTTAATTUGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T), 0.5 µl NEBNext ligation enhancer and 15 µl NEBNext Ultra II ligation mix were added and incubated 30 min at room temperature. The reaction mix was removed and discarded and beads were rinsed with 500 µl wash buffer (5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl) then washed twice with 1 ml wash buffer for 10 min on wheel at room temperature and once for 10 min with 1 ml 0.1x TE. Libraries were eluted from beads with 11 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°C, then again with 10.5 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°, and the two eluates combined. An initial test amplification was used to determine the optimal cycle number for each library. For this, 1.25 μl library was amplified in 10 µl total volume with 0.4 µl each of the NEBNext Universal and any NEBNext Index primers with 5 µl NEBNext Ultra II Q5 PCR master mix. Cycling program: 98°C 30s then 18 cycles of [98°C 10 s, 65°C 75 s], 65°C 5 min. Test PCR was cleaned with 8 µl AMPure XP beads (Beckman A63881) and eluted with 2.5 µl 0.1x TE, of which 1 µl was examines on a Bioanalyser high sensitivity DNA

tag: growth and treatment

value: YPD

tag: fix and post-processing

value: 70% ethanol


title: SAMPLE 341 PP

description: Patient peritoneum

value: unknown


title: SAMPLE 333 DiEIn

value: Deep infiltrating endometriosis lesion


title: dnl4_rad51_RAF_TrAEL-seq

source_name: BY4741 dnl4 rad51

value: BY4741 dnl4 rad51

value: Ypraf


title: PiSZ2 Lung B4

description:
PiSZ2 Lung
B4

value: Lung


title: RNAseq_N2_2h

value: 2 h


title: SAMPLE 332 PE

description: Patient endometrium

value: Endometrium

value: proliferative


title: PiSZ2 Undiff E11

description:
PiSZ2 Undiff
E11

value: Undiff


title: MA002 Lung B3

description:
MA002 Lung
B3


title: mut_rep2

city: Milan

first: Matteo

last: Chiara

address: via celoria 26

department: Biosciences

country: Italy

institute: University of Milan

data_processing:
Reads were mapped on the Zm00001d.2 gene models annotation of the B73 reference assembly (ZmB73_RefGen_v4) of the maize genome, as obtained from http://plants.ensembl.org/info/website/ftp/index.html, using the bowtie2 program
Estimation of gene expression levels was performed using RSEM
Only genes with a median read count of 10 or more were considered (10 reads in at least 3 samples).
Differential expression analysis was performed applying the latest versions of DESeq2 (Love et al., 2014) and Limma (Ritchie et al., 2015)
Genome_build: ZmB73_RefGen_v4
Supplementary_files_format_and_content: Estimation of gene expression levels according to RSEM

organism: Zea mays

source_name: seedlings

extract_protocol:
Pure Link RNA Mini Kit (Invitrogen)
TruSeq Stranded mRNA, Illumina

value: seedlings

value: coleoptile


title: mut_rep3


title: rnh202_YPD_TrAEL-seq


title: wt_rep3

value: wild type


title: clb5_YPD_TrAEL-seq

source_name: BY4741 clb5

value: BY4741 clb5


title: mut_rep1


title: SAMPLE 335 PeLB Replicate

description: Peritoneal endometriosis black lesion

value: Peritoneal endometriosis lesion Replicate

value: secretory


title: SAMPLE 334 PE

description: Patient endometrium


title: wt_rep2


title: PiSZ1 Undiff B11

description:
PiSZ1 Undiff
B11


title: wt_rep1


title: PiZZ6 Lung B2

description:
PiZZ6 Lung
B2


title: Sem_Fluid_SP79_FB

city: Davis

first: Laura

middle: M

last: Brutscher

state: CA

address: One Shields Avenue

department: Entomology and Nematology

institute: University of California, Davis

data_processing:
Reads were filtered for quality using the cutadapt software package version 1.8.385. Adapter contamination was removed and a minimum average quality score of 25 was required.
Filtered reads were then aligned to the most recent build (4.5) of the Apis mellifera genome using Hisat2 version 2.1.089 under default parameters.
Using reads from samples that aligned to the Apis mellifera genome, gene read counts were generated using the HTSeq software version 0.9.190 with the -i Dbxref and -t gene options.
Differential gene expression was assessed using the limma software package91 using default parameters (FDR < 0.05). Briefly, genes that had fewer than 20 aligned reads in each sample were filtered from analysis (min.count = 20). Read counts were then normalized via the default trimmed mean of M-values (TMM) method.
Genome_build: Apis mellifera genome 4.5
Supplementary_files_format_and_content: The processed data file "HTSeq_counts_Brain_FB.txt" is a tab-delimited file containing the number of raw reads for each sample aligning to the Apis Mellifera genome (4.5) as determined by the HTSeq step.

organism: Apis mellifera carnica

source_name: fat body

growth_protocol: queens were reared into adults from larvae in queenless colonies and placed in mininuclei as adults

extract_protocol:
Brains and fat bodies were dissected from queens and RNA from these tissues was extracted and Dnased using QIAGEN RNeasy RNA Extraction kit.
Libraries were constructed using the standard protocols and kit contents of the NEBNext Ultra RNA Library Prep Kit for Illumina.

treatment_protocol: queens were injected in the abdomen with Hayes solution, semen, or seminal fluid or remained untreated

value: fat body

tag: caste

value: virgin queen

tag: treatment

value: injected with seminal fluid


title: BY4741_RAF_to_GAL_TrAEL-seq

value: Ypraf + 2% Gal for 5 hours

value: 70% ethanol


title: Sem_Fluid_SP35_FB


title: 3xCUP1_TrAEL-seq

source_name: BY4742 3xCUP1

value: BY4742 3xCUP1

value: SD


title: PiZZ1 Lung B1

description:
PiZZ1 Lung
B1

value: Lung


title: Sem_Fluid_SP1_FB


title: Semen_S83_FB

value: injected with semen


title: BY4741_YPD_TrAEL-seq

value: YPD


title: PiZZ2 Undiff A9

description:
PiZZ2 Undiff
A9

value: Undiff


title: PiZZ2 Liver B5

description:
PiZZ2 Liver
B5

value: Liver


title: Semen_S29_FB


title: Semen_S38_FB


title: PiSZ3 Undiff B12

description:
PiSZ3 Undiff
B12


title: 3xCUP1_Cu_TrAEL-seq

value: SD, 6 hours with 1mM CuSO4


title: Semen_S27_FB


title: BY4741_RAF_TrAEL-seq

value: Ypraf


title: PiSZ2 Liver A8

description:
PiSZ2 Liver
A8


title: 3xCUP1_END-seq


title: dnl4_rad51_RAF_to_GAL_TrAEL-seq

value: BY4741 dnl4 rad51


title: 3xCUP1_Cu_END-seq


title: Semen_S24_FB


title: Hayes_H74_FB

value: injected with Hayes solution


title: Hayes_H75_FB


title: fob1_SfiI_END-seq

source_name: MEP diploid fob1

value: MEP diploid fob1

value: 70% ethanol, SfiI digested


title: 100-3 Undiff B10

description:
100-3 Undiff
B10

source_name: human iPSC


title: MA011 Liver A7

description:
MA011 Liver
A7


title: Hayes_H73_FB

value: fat body

value: virgin queen


title: Sem_Fluid_SP76_FB

value: injected with seminal fluid


title: Sem_Fluid_SP16_FB


title: PiZZ6 Liver A6

description:
PiZZ6 Liver
A6


title: SAMPLE 344 PE Replicate

description: Patient endometrium

source_name: Endometrium

value: Endometrium Replicate

value: menstruation


title: shCtCl2

city: Shanghai

first: Minyi

last: Ou

address: 393 Middle Huaxia Road, Pudong, Shanghai, 201210

country: China

institute: ShanghaiTech University

data_processing:
Raw reads were mapped to the hg19 reference using Hisat2 software
Transcripts were measured with StringTie/prepDE.py
Differentially expressed genes were identified using R  package Ballgown.
Genome_build: hg19
Supplementary_files_format_and_content: Raw counts in CSV format

source_name: organoid

growth_protocol: Stable cell line generated by virus transfection was processed as previous reported protocal from our lab.

extract_protocol:
Following the standard procedure for Qiagen HiPure Total RNA Mini Kit
Finished by Novogene company

treatment_protocol: ES cell line for shCTCL was transfected by Lentivirus containing RNAi sequence

tag: cell type

value: H9 ES-derived cells

value: cells transfected by shCTCLl lentivirus

value: shCTCL


title: Hayes_H53_FB


title: Hayes_H51_FB


title: PiSZ2 Lung A4

description:
PiSZ2 Lung
A4

value: Lung


title: Con2

value: cells transfected by control lentivirus

value: shCtrl


title: Control_C77_FB

value: control


title: shCtCl1


title: MA002 Lung A3

description:
MA002 Lung
A3


title: Con1


title: PiZZ3 Lung A2

description:
PiZZ3 Lung
A2


title: TP53 BOB ENDO MMS 72h Rep 3

first: Alastair

last: Crisp

address: Francis Crick Avenue

institute: MRC Laboratory of Molecular Biology

data_processing:
Adaptors were removed and reads quality trimmed using TrimGalore v0.4.4 (https://github.com/FelixKrueger/TrimGalore) with default settings
Read were aligned to the Human genome version GRCh38.87 using TopHat v2.1.0 (https://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-4-r36)
Reads were quantified per genomic region and differential expression was calculated using Cufflinks v2.2.1 (https://www.nature.com/articles/nbt.2450)
Genome_build: human GRCh38.87
Supplementary_files_format_and_content: Cufflinks tab-delimited expression values

source_name: BOBSC hiSPCs

growth_protocol: Essential 8 Flex Medium or Endoderm differentiation medium was used for Undifferentiated (UD) samples and Endoderm differentiated (ENDO) samples respectively. Cells were treated to differentiate as described in Yiangou et al Stem Cell Reports 2019.

extract_protocol:
RNA was extracted using the Rneasy Qiagen Extraction Mini Kit
NEBnext Ultra II

treatment_protocol: MMS treated cells were treated with 5ppm MMS at 24 hours.

value: hiPSC

tag: passage

value: TP53 KO


title: Control_C64_FB


title: PiSZ3 Undiff A12

description:
PiSZ3 Undiff
A12

value: Undiff


title: Control_C68_FB


title: TP53 BOB ENDO MMS 72h Rep 2


title: MA011 Undiff A11

description:
MA011 Undiff
A11


title: Sem_Fluid_SP76_Brain

source_name: brain

value: brain


title: Control_C49_FB


title: TP53 BOB ENDO MMS 72h Rep 1


title: 100-3 Undiff A10

description:
100-3 Undiff
A10


title: Control_C20_FB


title: PiZZ1 Liver A5

description:
PiZZ1 Liver
A5

value: Liver


title: PiZZ1 Lung A1

description:
PiZZ1 Lung
A1


title: Sem_Fluid_SP16_Brain


title: TP53 BOB ENDO UT 72h Rep 2


title: TP53 BOB ENDO UT 72h Rep 1


title: Sem_Fluid_SP1_Brain


title: IP-LR1E: 8-oxoG RIP Air pollution

city: Austin

first: Lydia

last: Contreras

state: TX

address: 200 E. Dean Keeton St Stop C0400

department: McKetta Department of Chemical Engineering

institute: University of Texas at Austin

data_processing:
Illumina NextSeq 500
Sequence reads were trimmed for adaptor sequence using Cutadapt 1.14, followed by quality check using FastQC
Reads were aligned to Ensembl comprehensive human genome annotation (GENCODE 26, GRCh38.p12) using STAR 2.6.0c, allowing novel splice junctions and using a two-pass mapping approach. Alignment was performed using parameters recommended in the STAR manual for ENCODE standards
RSEM was used to estimate transcript abundances and then differential expression and 8-oxoG enrichment  were performed using DESeq2 in R version 3.6.1.
Transcripts were annotated using biomaRt in R.
Genome_build: GRCh38.p12

source_name: BEAS-2B cells

growth_protocol: Cell cultures for exposures (passage 3 from parent stock) were initiated from T75 cultures incubated for 4 days in complete Bronchial Epithelial Cell Growth medium (BEGM, Lonza, Walkersville, MD) with a 70-80% confluency. Cells were passaged to collagen-coated inserts (30 mm diameter, hydrophilic PTFE with pore size of 0.4 µm, EMD Millipore, Burlington, MA) housed in 6-well plates (Corning Costar Clear Multiple Well Plates, Corning, NY) with a seeding density of 200,000 cells and incubated for 24 hours with 0.8 ml and 1.1 ml of medium in the apical and basolateral side, respectively. Cell culture inserts were coated with 1 ml of 57 µg/ml of Bovine Collagen Type I (Advanced BioMatrix, Carlsbad, CA) in BEGM at least 24 h before seeding. Two hours before exposure, the medium from the apical cell surface was completely removed, and the medium from the basolateral cell surface was renewed with fresh complete medium.

extract_protocol:
Following exposure, each insert membrane was treated with 1 ml of TRIzol in the apical side and gently mixed to ensure thorough lysis. The whole lysate was collected and frozen until the day of the extraction. TRIzol RNA extraction was conducted following TRIzol’s manufacturer instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells adhered to membrane inserts housed in 6-well plates (with lid off) were exposed in a modular cell exposure chamber (MIC-101 Billups-Rothenberg, San Diego, CA) to an air pollution mixture for 1.5 hours. Before the cell exposure chamber, 1.52 LPM (litters per minute) of the air pollution mixture was mixed with 0.08 LPM CO2 (5% final concentration).

value: BEAS-2B cells (ATCC CRL-9609)

value: Lung, bronchus

tag: disease

value: Normal

tag: rip antibody

value: Anti-8-oxo-dG Monoclonal Antibody (clone 15A3)

tag: passages


title: IP-LR2E: 8-oxoG RIP Air pollution


title: TP53 BOB UD MMS 72h Rep 3


title: IP-LR2C: 8-oxoG RIP Clean air control


title: TP53 BOB ENDO UT 72h Rep 3


title: Semen_S83_Brain

value: virgin queen

value: injected with semen


title: Semen_S38_Brain


title: TP53 BOB UD MMS 72h Rep 1


title: Lung cancer LU1170

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChips using the standard Illumina protocol.

scan_protocol: Arrays were imaged using High Scan SQ using the standard recommended Illumina scanner setting.

data_processing: Signal intensities were obtained from GenomeStudio (Illumina), converted to beta-values, filtered, and normalized to remove biases between Infinium I and II probes. Non-autosomal beta-values were filtered from the final data matrix.

label: Cy3, Cy5

source_name: Lung tumor

label_protocol: Standard Illumina labelling protocol.

extract_protocol: Genomic DNA from fresh frozen lung tumor/normal tissue was extracted using Allprep (Qiagen).

tag: gender

value: Male

tag: histology

value: LCC


title: Lung cancer LU1113


title: IP-LR1C: 8-oxoG RIP Clean air control

tag: tissue


title: Semen_S29_Brain


title: Lung cancer LU800

value: Female


title: in-LR2E: Input RNA Air pollution


title: TP53 BOB UD MMS 72h Rep 2


title: TP53 BOB UD UT 72h Rep 3


title: Lung cancer LU812


title: Lung cancer LU1080

value: LCNEC


title: Semen_S27_Brain


title: Semen_S24_Brain


title: in-LR2C: Input RNA Clean air control


title: TP53 BOB UD UT 72h Rep 2


title: TP53 BOB UD UT 72h Rep 1


title: in-LR1C: Input RNA Clean air control


title: SAMPLE 347 PE

description: Patient endometrium

value: Endometrium

value: unknown


title: Hayes_H74_Brain

value: injected with Hayes solution


title: Hayes_H75_Brain


title: Lung cancer LU818


title: GFP_OCA_R3

city: Innsbruck

first: Jose Miguel

last: Ramos Pittol

address: Innrain 80-82

department: Institute of Biochemistry

country: Austria

institute: University of Innsbruck

description:
Replicate 3
GFP_OCA.bw
genes.count_table

data_processing:
Sequencing reads were aligned to the reference genome (hg19 assembly, NCBI37) using Tophat2.18 (--b2-sensitive --microexon-search -p 2 -G Homo_sapiens.GRCh37.87.gtf)
Duplicated reads were removed with Samtools rmdup (v1.9 , using htslib 1.9)
The normalized read numbers per gene were calculated using the cuffnorm feature of Cufflinks (v2.2.1  linked against Boost version 105500) against the Homo_sapiens.GRCh37.87 gene annotation
For visualization, a single file was generated per condition with Samtools merge on the sequenced replicates
Genomic coverage files were generated with deepTools2 bamCoverage (--binSize 1 --normalizeUsing RPGC --effectiveGenomeSize 2736124973)  per condition
Genome_build: hg19
Supplementary_files_format_and_content: *.bw BigWig format containing genomic coverage per condition.
Supplementary_files_format_and_content: *.count_table Normalized count values per gene

source_name: Cultured cell line

growth_protocol: HepG2 cells were cultured in DMEM 1g/l glucose + 10% FCS in 10cm petri dishes. FXR isoforms or GFP was lentivirally transduced on a pLV(EF1a) IRES-PuroR vector. 2ug/ml puromycin was used for selection of positive clones.

extract_protocol:
Total RNA was purified from treated HepG2 using TRIzoL (Invitrogen) reagent according to manufacturer’s instructions. RNA was stored at -80C until further processing
mRNA was isolated using the Poly(A) Beads (NEXTflex). Sequencing libraries were prepared using the Rapid Directional RNA-Seq Kit (NEXTflex)

treatment_protocol: Cells were seeded in 6 well plates and treated for 8 hours with 5 µM Obeticholic acid in DMSO, or DMSO alone (0.1% vol/vol)

tag: transgene

value: GFP

tag: selection

value: Puromycin

value: OCA 5 uM

tag: treatment duration


title: WT BOB ENDO MMS 72h Rep 2

value: hiPSC

value: Wild-type


title: Hayes_H73_Brain

value: brain


title: WT BOB ENDO MMS 72h Rep 3


title: GFP_OCA_R2

description:
Replicate 2
GFP_OCA.bw
genes.count_table


title: Hayes_H53_Brain


title: WT BOB ENDO MMS 72h Rep 1


title: Lung cancer LU835


title: WT BOB ENDO UT 72h Rep 3


title: WT BOB ENDO UT 72h Rep 2


title: GFP_DMSO_R3

description:
Replicate 3
GFP_DMSO.bw
genes.count_table

value: DMSO


title: GFP_DMSO_R2

description:
Replicate 2
GFP_DMSO.bw
genes.count_table


title: GFP_OCA_R1

description:
Replicate 1
GFP_OCA.bw
genes.count_table


title: Control_C64_Brain

value: control


title: Control_C77_Brain

value: virgin queen


title: GFP_DMSO_R1

description:
Replicate 1
GFP_DMSO.bw
genes.count_table


title: Hayes_H51_Brain


title: Lung cancer LU714


title: Lung cancer LU716


title: Lung cancer LU735


title: Lung cancer LU641


title: FXRa2_OCA_R3

description:
Replicate 3
FXRa2_OCA.bw
genes.count_table


title: Lung cancer LU737


title: Control_C49_Brain


title: Control_C20_Brain


title: WT BOB UD MMS 72h Rep 2


title: FXRa2_OCA_R2

description:
Replicate 2
FXRa2_OCA.bw
genes.count_table


title: WT BOB UD MMS 72h Rep 3


title: WT BOB UD MMS 72h Rep 1


title: WT BOB ENDO UT 72h Rep 1


title: Lung cancer LU631


title: FXRa2_OCA_R1

description:
Replicate 1
FXRa2_OCA.bw
genes.count_table


title: Lung cancer LU616


title: in vivo 12w-2 [24]

city: Matsumoto

first: Shin

last: Kadota

address: 3-1-1 Asahi

department: Regenerative Science and Medicine

country: Japan

institute: Shinshu University

data_processing:
Sequenced reads were trimmed by Trimmomatic (v0.39) with parameters of SLIDINGWINDOW:10:30. All samples were separated human and rat reads using Xenome (v1.0.0). Reads classified as human were mapped to the hg38 reference with STAR (v2.7.2a) and gene count matrix was generated with featureCounts (v1.6.4).
Differential expression analysis was performed using the edgeR package, with trimmed mean of M values (TMM) normalization.  PCA plots were performed using PCAtools package, with transcripts per million (TPM) normalization.
Genome_build: hg38
Supplementary_files_format_and_content: featurecounts_3-12-23-28Enid2 contains raw counts and tpm-normalized_counts.csv contains TPM normalized data.

organism:
Homo sapiens
Rattus norvegicus

source_name: human embryonic cell-derived cardiomyocyte in rat heart

growth_protocol: Undifferentiated human embryonic stem cells reached 90% confluency, E8 medium was supplied with 1 uM of Wnt activator CHIR99201 (Sigma-Aldrich). The next day (day 0), E8 medium was changed to the cardiac differentiation medium (RPMI 1640 with B27 supplement minus insulin (Gibco) plus L-glutamine adding activin A (100 ng/mL, R&D) and Matrigel. On day1, bone morphologic protein 4 (BMP4; 10 ng/mL, R&D) and CHIR99201, followed by addition of Wnt inhibitor XAV939 (1 uM Sigma-Aldrich) on day 3-4. After day 7, medium was changed to RPMI 1640 with B27 supplement (Gibco) every other day. The cells were heat-shocked at 43ºC for 30 minutes and cryopreserved on day 20.

extract_protocol:
For collection of in vitro samples, total RNA was extracted by ISOGEN (Nippon Gene), phenol and chloroform. For in vivo samples, rat hearts of each time points were collected and immediately embedded in an OCT-embedding compound and kept in -80℃. Tissues were sectioned at a thickness of 10 µm using a cryostat (Leica). The graft areas were captured using laser microdissection system (Leica) from unstained unfixed specimens attached on the membrane coated slides (Leica 11600289). Total RNA was extracted by Arcturus PicoPure RNA Isolation Kit (Thermo).
cDNA was synthesized by SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (TaKaRa). Library preparations were conducted using Nextera DNA Library Prep Kit

treatment_protocol: 2 x 10^7 human embryonic stem cell-derived cardiomyocytes were directly injected to rat hearts (in vivo samples)

tag: cell line

tag: host rat strain

tag: tissue/cell type

value: Cardiomyocytes

tag: developmental/differentiation stage

value: differentiation day 104


title: FXRa2_DMSO_R3

description:
Replicate 3
FXRa2_DMSO.bw
genes.count_table


title: WT BOB UD UT 72h Rep 3

tag: genotype


title: WT BOB UD UT 72h Rep 2


title: in vivo 12w-1 [23]


title: FXRa2_DMSO_R2

description:
Replicate 2
FXRa2_DMSO.bw
genes.count_table

tag: treatment


title: in-LR1E: Input RNA Air pollution

tag: cell type

value: BEAS-2B cells (ATCC CRL-9609)

value: Lung, bronchus

value: Normal


title: FXRa2_DMSO_R1

description:
Replicate 1
FXRa2_DMSO.bw
genes.count_table


title: in vivo 4w-2 [26]

value: differentiation day 48


title: WT BOB UD UT 72h Rep 1

tag: passage


title: Lung cancer LU591

value: Female

value: LCC


title: TP53 BOB ENDO MMS 48h Rep 3

value: TP53 KO


title: in vivo 4w-1 [25]


title: FXRa1_OCA_R3

description:
Replicate 3
FXRa1_OCA.bw
genes.count_table

value: Puromycin


title: in vivo 2w-2 [28]

value: differentiation day 34


title: FXRa1_OCA_R2

description:
Replicate 2
FXRa1_OCA.bw
genes.count_table

value: OCA 5 uM


title: Lung cancer LU605


title: TP53 BOB ENDO MMS 48h Rep 1

value: hiPSC


title: Lung cancer LU580

value: Male

value: LCNEC


title: Lung cancer LU565


title: TP53 BOB ENDO UT 48h Rep 3


title: Lung cancer LU558


title: TP53 BOB ENDO MMS 48h Rep 2


title: Lung cancer LU401


title: Lung cancer LU546


title: FXRa1_DMSO_R3

description:
Replicate 3
FXRa1_DMSO.bw
genes.count_table

value: DMSO


title: FXRa1_OCA_R1

description:
Replicate 1
FXRa1_OCA.bw
genes.count_table


title: Lung cancer LU492


title: FXRa1_DMSO_R2

description:
Replicate 2
FXRa1_DMSO.bw
genes.count_table


title: in vivo 2w-1 [27]


title: Lung cancer LU438


title: cord blood CD34+, OP9-DLL1_HES1_3

city: Ghent

first: Matthias

last: De Decker

address: Corneel Heymanslaan 10

department: Diagnostic Sciences

country: Belgium

institute: Ghent University

data_processing:
Fastq files were mapped against GRCh38p5 using STAR 2.4.2a.
Counts were called by specifying the quantMode flag during mapping and by providing an approriate gtf file obtained from gencode (v20).
Raw counts were normalized using the DESeq2 package in R.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file include DESeq2-normalized values for each sample.

source_name: cord blood CD34+

growth_protocol: CD34+ were isolated from cord blood and cultured for two days in complete IMDM containing 10% heat-inactivated FCS, 100 U/ml penicillin, 100 µg/ml streptomycin and 2 mM L-glutamine, supplemented with 20 ng/ml TPO, 100 ng/ml SCF and 100 ng/ml FLT3L.

extract_protocol:
RNA from sorted cells was harvested using Trizol reagent and the miRNeasy Micro Kit (Qiagen)
RNA sequencing libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep FWD kit (Lexogen)

treatment_protocol: Precultured CD34+ cells were transduced with HES1-or HES4-encoding retrovirus and cultured for one day on OP9-GFP or OP9-DLL1. Subsequently eGFP+CD45+CD34+Lin- were sorted.

value: cord blood-derived HPC

tag: feeder

value: OP9-DLL1 (Notch-ON)

tag: construct


title: TP53 BOB ENDO UT 48h Rep 2


title: DRGO-CTRL-3

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

institute: Ospedale San Raffaele

data_processing:
Fastq files were mapped to the mm10 mouse reference genome with the STAR aligner v2.7 (Dobin et al., 2013).
Differential gene expression and Functional enrichment analyses were performed with DESeq2 (Love et al., 2014) and GSEA (Huang et al., 2009), respectively.
Statistical and downstream bioinformatics analyses were performed within the R environment.
Gene expression heatmaps were produced with GENE-E (Broad Institute).
Genome_build: hg38

source_name: iPSC-derived

extract_protocol:
RNA was isolated with Trizol (Thermo Fisher), and treated with DNase I (NEB) according to manufacturer's instructions.
Library preparation was done with TruSeq RNA Library Prep Kit v2 (Illumina) according to manufacturer's instructions.

value: Dorsal Root Ganglia Organoid


title: TP53 BOB ENDO UT 48h Rep 1


title: TP53 BOB UD UT 48h Rep 3


title: DRGO-CTRL-2


title: TP53 BOB UD MMS 48h Rep 1


title: cord blood CD34+, OP9-DLL1_HES1_2


title: TP53 BOB UD MMS 48h Rep 3


title: TP53 BOB UD MMS 48h Rep 2


title: cord blood CD34+, OP9-DLL1_HES1_1


title: cord blood CD34+, OP9-DLL1_HES4_3


title: DRGO-CTRL-1


title: Lung cancer LU505


title: Lung cancer LU294


title: Lung cancer LU181


title: TP53 BOB UD UT 48h Rep 2


title: FXRa1_DMSO_R1

description:
Replicate 1
FXRa1_DMSO.bw
genes.count_table


title: Lung cancer LU321


title: Lung cancer LU387


title: Lung cancer LU328


title: cord blood CD34+, OP9-DLL1_Ctrl_3

value: LIE-Ctrl


title: Lung cancer LU195


title: Atg7∆/∆ LP7

city: New Brunswick

first: SAURABH

middle: V

last: LADDHA

state: NEW JERSEY

address: 195 Little Albany Street

department: Center for Systems and Computational Biology

institute: Rutgers Cancer Institute of New Jersey

data_processing:
Sequenced reads were processed, aligned and counts summarised using Cellranger 2.1 pipeline
Seurat (V3.0) R package was used to process raw UMI matrices and procude UMI counts per 10,000 unique molecules identified per cell
Individual samples dataset underwent quality control for removing any cells with fewer than 200 genes/cell or > 5000 genes/cell and greater than 20% reads mapped to mitochondrial genes.
We used default parameter for Seurat pipeline, unless stated. Individual samples dataset underwent quality control for removing any cells with fewer than 200 genes/cell or > 5000 genes/cell and greater than 20% reads mapped to mitochondrial genes. Using this criteria, we recovered ~90% of the cells (Supplementary Table 12). Filtered gene expression matrix for each cell then normalized (logNormalize) by total expression with an arbitrary scaling factor of 10,000 and log-transformed the gene expression matrix.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited UMI counts per 10,000 unique molecules detected and log transformed

source_name: mouse tumors

growth_protocol: To assess the consequence of acute Atg7 deletion on tumorigenesis of C57Bl/6J isogenic male tumor cells, one week post TAM treatment, MB49 (0.25 x 106 cells) cells were resuspended in 100 ul PBS and injected subcutaneously into the dorsal flanks of mice (2 tumors per mouse). Three weeks post cell injection, mice were sacrificed and tumors were collected.

extract_protocol:
Resected mouse tumors from Atg7+/+ and Atg7∆/∆ hosts were placed in complete media supplemented with 10% FBS and kept on ice.  Dissociation of the tumor tissue was carried out using a commercially-available mouse tumor dissociation kit and the Miltenyi GentleMACS dissocation system (Miltenyi Biotec, Cologne, Germany).  Isolated cells were filtered through a 40mm mesh strainer and PBMC’s were isolated by density-dependent centrifugation.  Cells were washed complete media (10% FBS), then counted and assessed for viability using a Countess II cell counter (Invitrogen). Cells were then suspended to 1x10^6 per ml in complete media (10% FBS) for single cell emulsion preparation.
scRNA-seq libraries were prepared according to 10X Genomics specifications (10X Genomics, Pleasanton, CA).  Independent cell suspensions were loaded for droplet-encapsulation by the Chromium Controller (10X Genomics). Single-cell cDNA synthesis, amplification, and sequencing libraries were generated using the Single cell 5’ Reagent Kit following the manufacturer’s instructions.  The libraries were shipped on dry ice to Novogene (Sacramento, CA), and sequenced in a single lane of an Illumina NovaSeq 6000 (Settings: Read1: 26, i7: 8, Read2: 91, for 200M bp paired-end reads per sample).

treatment_protocol: Mice were treated with TAM everyday for 4 days to induce Atg7 deletion.

tag: atg7 genotype

value: KO

tag: strain

value: C57BL/6 UbcreERT2/+;Atg7f/f

tag: genome build

value: MB49 Mouse Urothelial Cancer Cell Line


title: Lung cancer LU209

tag: gender

value: Female

tag: histology


title: Atg7+/+ LP6

value: Wild Type

value: C57BL/6 UbcreERT2/+;Atg7+/+


title: Lung cancer LU154

value: LCC


title: Lung cancer LU114


title: WT BOB ENDO MMS 48h Rep 1

value: Wild-type


title: Lung cancer LU370


title: WT BOB ENDO MMS 48h Rep 3


title: cord blood CD34+, OP9-DLL1_Ctrl_1


title: cord blood CD34+, OP9-DLL1_HES4_1


title: WT BOB ENDO MMS 48h Rep 2


title: Lung cancer LU101


title: cord blood CD34+, OP9-DLL1_Ctrl_2


title: Control_C68_Brain

tag: tissue

value: brain

tag: caste

value: virgin queen

value: control


title: Atg7+/+ LP5

tag: cell line


title: Atg7∆/∆  LP3


title: Atg7∆/∆ LP4


title: WT BOB ENDO UT 48h Rep 2

value: hiPSC


title: cord blood CD34+, OP9-GFP_HES1_2

value: OP9-GFP (Notch-OFF)


title: cord blood CD34+, OP9-GFP_HES1_3

value: cord blood-derived HPC


title: WT BOB ENDO UT 48h Rep 3


title: Atg7∆/∆ LP8


title: Atg7+/+ LP2


title: Lung cancer LU10

value: Male

value: LCNEC


title: WT BOB ENDO UT 48h Rep 1


title: cord blood CD34+, OP9-GFP_HES1_1


title: Atg7+/+ LP1


title: WT BOB UD MMS 48h Rep 2


title: WT BOB UD MMS 48h Rep 3


title: Organoids_AA3

city: Beijing

first: Qingyu

last: Wang

address: Qinghua East Road No.17

department: College of Food Science and Nutritional Engineering

institute: China Agricultural University

data_processing:
Raw data of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: Fa: ftp://ftp.ensembl.org/pub/release-91/fasta/mus_musculus/dna/
Genome_build: Gtf: ftp://ftp.ensembl.org/pub/release-91/gtf/mus_musculus/
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample.

source_name: small intestinal organoids

growth_protocol: After isolated from mouse proximal small intestine, crypts were resuspended in the mixture of Matrigel (Corning, 356237). The basic culture medium is growth media (Stemcell Technologies, 06005) with penicillin/streptomycin/gentamicin (Solarbio Life Science, P1410). Organoids were passaged every three days.

extract_protocol:
Total RNA extraction of the treated small intestinal epithelial organoids was collected at Day 3 after passaging using RNAprep pure Micro Kit (Tiangen Biotech (Beijing) Co., LTD., DP420).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Arachidonic acid (Sigma, A3611) was dissolved in cold 0.1% EtOH, and 0.1% EtOH were treated as control group.

value: C57BL/6 wt

value: proximal small intestine

value: small intestinal organoids


title: cord blood CD34+, OP9-GFP_HES4_3


title: cord blood CD34+, OP9-GFP_HES4_2


title: Organoids_AA2


title: cord blood CD34+, OP9-GFP_HES4_1


title: Organoids_AA1


title: cord blood CD34+, OP9-DLL1_HES4_2

value: OP9-DLL1 (Notch-ON)


title: WT BOB UD UT 48h Rep 3


title: WT BOB UD MMS 48h Rep 1


title: Organoids_Ctrl2


title: Organoids_Ctrl3


title: cord blood CD34+, OP9-GFP_Ctrl_2

value: LIE-Ctrl


title: WT BOB UD UT 48h Rep 2


title: cord blood CD34+, OP9-GFP_Ctrl_3


title: WT BOB UD UT 48h Rep 1


title: cord blood CD34+, OP9-GFP_Ctrl_1


title: TP53 BOB ENDO UT 24h Rep 2

value: TP53 KO


title: TL naa10Δ glycerol rep1

city: Heidelberg

first: Ulrike

middle: Anne

last: Friedrich

address: Im Neuenheimer Feld 282

department: ZMBH

country: Germany

institute: Heidelberg University

description: OTHER (ribosome footprints)

data_processing:
Trimming (barcode and adapter removal, filtering for low quality) by Cutadapt v.1.9.1 with the following parameters: -a CTGTAGGCACCATCAATTCGTATGCCGTCTTCTGCTTG -m 20 -O 1 --quality-base=33
Alignment to S. cerevisiae rRNA by Bowtie2 v.2.1.0.0 (rRNA aligned reads were excluded)
Alignment to S. cerevisiae genome by Tophat2 v.2.0.8b with the following parameters: --bowtie-n -a4 -i40 -I2000 -g1 --max-insertion-length 0 --max-deletion-length 0 --no-novel-juncs --no-convert-bam
Read distribution (RNA-Seq) or Center weighting (Ribosome Profiling) to determine the read/ribosome position using scripts provided in Döring et al. 2017 and Shiber et al. 2018
Genome_build: Saccharomyces cerevisiae S288C R64
Supplementary_files_format_and_content: Pickled File of a Python 3 dictionary: key = each chromosomal position (e.g. 01[tab]0060354 means chromosome 1, position 60,354); value = list of raw read on plus strand, [tab], raw read on minus strand, [tab], nucleotide (G/A/T/C), [tab], norm read on plus strand, [tab], norm read on minus strand (norm reads are raw reads normalized to total read number of the sample *1,000,000 = RPM)

source_name: Yeast

growth_protocol: Yeast cells were grown in the indicated growth medium and at the indicated temperature (see COLUMN: characteristics: growth conditions), at 130rpm to mid-log phase.

extract_protocol:
RNA was extracted using the hot acid phenol method as described in Döring et al. 2017.
Libraries from total mRNA or ribosome footprints were prepared following the previously published protocol (Döring et al. 2017, Shiber et al. 2018).
RNA-Seq and OTHER (Ribosome Profiling)

treatment_protocol: 100 OD600nm of mid-log culture was filtered (All-Glass Filter 90mm, Millipore), flash frozen in liquid nitrogen and lysed by mixer milling (2 min, 30 Hz, MM400, Retsch) with 600 µl lysis buffer (20 mM Tris-HCl pH 8.0, 140 mM KCl, 6 mM MgCl2, 0.1% NP-40, 0.1 mg/ml cycloheximide, 1 mM PMSF, 2x protease inhibitor cocktail (Complete EDTA-free, Roche), 0.02 U/ml DNaseI (recombinant DNaseI, Roche), 20 mg/ml leupeptin, 20 mg/ml aprotinin, 10 mg/ml E-64, 40 mg/ml bestatin). Thawed cell lysates were cleared from cell debris by centrifugation (20,000xg, 5 min, 4°C). From this sample, 200 µl total RNA were taken for RNA-Seq (see COLUMN: characteristic: sample type -  total mRNA) and 1000 µl total RNA were used for further nuclease digestion and ribosome profiling (see COLUMN: characteristic: sample type -  ribosome footprints). Ribosome footprints were generated by a digest with RNase I (Ambion, 1 hr, 25°C, 650 rpm) which was stopped by 10 µl SUPERase-In (Ambion). Monosome fractions were generated by polysome profiling (as described in Döring et al. 2017) and pooled for each sample.

tag: growth condition

value: SC+glycerol (2%), 30 C

tag: sample type

value: ribosome footprints

value: BY4741 naa10-delta


title: TL naa10Δ glycerol rep2

description: OTHER (ribosome footprints)


title: Organoids_Ctrl1


title: TP53 BOB ENDO UT 24h Rep 1


title: TP53 BOB ENDO UT 24h Rep 3


title: TL WT glycerol rep2

description: OTHER (ribosome footprints)

value: BY4741 WT


title: TP53 BOB UD UT 24h Rep 2


title: TL WT glycerol rep1

description: OTHER (ribosome footprints)


title: TP53 BOB UD UT 24h Rep 1


title: WT BOB ENDO UT 24h Rep 3

value: Wild-type


title: TL naa20Δ heat rep2

description: OTHER (ribosome footprints)

value: SCD, 37 C

value: BY4741 naa20-delta


title: ExVivo_BMDM_KO_rep2

city: Wuhu

first: Xueqin

last: Li

address: 2 Western Zheshan Road

institute: wannan medical college

description: miRNA expression in the BMDM of lncRNA AK085865 knock-out C57BL/6J mice

hyb_protocol: Each Agilent Mouse miRNA (8*60K, Design ID:070155) array slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: The slides were scanned using an Agilent Microarray Scanner G2505C (Agilent Technologies) with default settings with the following settings: Dye channel: Green, Scan resolution = 3 μm, PMT: 100%, and 20-bit.

data_processing: The Agilent Feature Extraction software (version10.7.1.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed using GeneSpring software (version 13.1, Agilent Technologies).

source_name: Bone marrow-derived macrophages, lncRNA AK085865 knock-out mice, replicate 2

label_protocol: Total RNA from each sample was amplified and labeled by using a Low Input Quick Amp WT Labeling Kit (Agilent Technologies), following the manufacturer’s instructions. Labeled cRNA were purified using an RNeasy mini kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured using a NanoDrop ND-2000.

growth_protocol: Bone marrow-derived macrophages (BMDMs) were isolated from C57BL/6J wild type or lncRNA AK085865 knock-out mice by flushing the femurs with Dulbecco’s modified Eagle’s medium (DMEM) medium. Macrophages plated on 6-well plates (1 × 106 cells/well) were maintained in DMEM supplemented with 20% fetal bovine serum and 20% L929 supernatant at 37°C and 5% CO2 for 7 days.

extract_protocol: Total RNA was extracted using TRIzol (Life Technologies), following the manufacturer’s instructions. RNA quantity and quality were measured by using a NanoDrop ND-2000, and RNA integrity was assessed using an Agilent Bioanalyzer 2100 (Agilent Technologies) and denaturing agarose gel electrophoresis. Total RNA was further purified using an RNeasy mini kit (Qiagen) and RNase-Free DNase Set (Qiagen).

treatment_protocol: After 7 d of culture, the medium was removed, and the cells were cultured in RPMI 1640 supplemented with 10% FBS for an additional 24 h.

value: Bone marrow-derived macrophages

value: lncRNA AK085865 knock-out


title: ExVivo_BMDM_KO_rep1

source_name: Bone marrow-derived macrophages, lncRNA AK085865 knock-out mice, replicate 1


title: ExVivo_BMDM_WT_rep2

description: miRNA expression in the BMDM of wildtype C57BL/6J mice

source_name: Bone marrow-derived macrophages, wildtype mice, replicate 2

value: wild type


title: TL naa10Δ heat rep2

description: OTHER (ribosome footprints)


title: Stalled products, t = 2 min, replicate 2

city: Cambridge UK

first: Julian

middle: E

last: Sale

address: Cambridge Biomedical Campus, Francis Crick Ave

department: PNAC

description: DNA amplicons

data_processing:
Reads associated to the stall products were pre-processed with cutadapt to trim the dC-tails using a quality cut-off of 20 and identifying tails with a minimum of 10 consecutive Cs (or Gs on the reverse reads). Reads were mapped to an artificial library chromosome using Bowtie 2 using the local and end-to-end functions for the stalled and extended products respectively.
The number of mapped reads associated to each sequence from the library was obtained using the idxstats command of Samtools.
Genome_build: The artificial library chromosome is reported in the STR_genome.fasta file
Supplementary_files_format_and_content: Processed data files (in TSV format) are the outputs from the idxstats Samtools command and report the number of reads mapped to each sequence from the artificial library chromosome

organism: synthetic construct

source_name: Synthetic library

extract_protocol:
The replication products were separated on a 6 % urea-PAGE gels and the bands corresponding to the fully extended and stalled products were excised, the gel matrix crushed and replication products were recovered by ethanol precipitation. Stalled products were then prepared for PCR amplification by adding poly-dC homopolymer tails to their 3' ends using a terminal transferase (TdT). PCR amplifications of the extended products and the parental library were performed using the exact same conditions in order not to introduce PCR biases due to the presence of structures within the templates.
DNA sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer’s instructions. Each library was purified on 8% TBE gels, quantified using the KAPA library quantification kit (Roche) and sequenced on an Illumina HiSeq 4000 with 2 × 150 bp paired-end runs.

tag: condition

value: Stalled products, t = 2 min


title: ExVivo_BMDM_WT_rep1

source_name: Bone marrow-derived macrophages, wildtype mice, replicate 1

tag: genotype


title: WT BOB ENDO UT 24h Rep 2

value: hiPSC


title: Stalled products, t = 4 min, replicate 2

description: DNA amplicons

value: Stalled products, t = 4 min


title: Stalled products, t = 30 min, replicate 2

description: DNA amplicons

value: Stalled products, t = 30 min


title: Stalled products, t = 1 min, replicate 2

description: DNA amplicons

value: Stalled products, t = 1 min


title: WT BOB ENDO UT 24h Rep 1


title: TL naa10Δ heat rep1

description: OTHER (ribosome footprints)


title: TL WT heat rep2

description: OTHER (ribosome footprints)


title: Stalled products, t = 0.5 min, replicate 2

description: DNA amplicons

value: Stalled products, t = 0.5 min


title: Stalled products, t = 4 min, replicate 1

description: DNA amplicons


title: TL WT heat rep1

description: OTHER (ribosome footprints)


title: WT BOB UD UT 24h Rep 2


title: WT BOB UD UT 24h Rep 3


title: Stalled products, t = 30 min, replicate 1

description: DNA amplicons


title: TL naa20Δ SILAC-BG SCD rep2

description: OTHER (ribosome footprints)

value: SCD, 30 C

value: BY4741 arg4-delta lys1-delta naa20-delta


title: TP53 BOB UD UT 24h Rep 3

value: TP53 KO


title: CD4+ cells from healthy human PBMC

first: Adrian

last: Liston

address: Babraham Research Campus

institute: The Babraham Institute

data_processing:
Step1: cellranger mkfastq (Cell Ranger V.3.1, 10x Genomics)
Step2: cellranger count (Cell Ranger V.3.1, 10x Genomics)
Step3: Quality control (Genes expressed in >= 5 cells, cells with gene count more than 200 and less than 4000, cells with less than 20% mitochondrial genes), Seurat V3
Genome_build: GRCh38-3.0.0
Supplementary_files_format_and_content: A matrix of raw UMI counts for CD4 Tcells for each feature (i.e. gene; row) that are detected in each cell (column)  in each sample

source_name: PBMC

extract_protocol:
Human CD4+ cells were extracted from PBMCs and brain tissueas described in the methods of the manuscript
GemCode Single-Cell Instrument and Single Cell 3′ Library & Gel Bead Kit v2 and Chip Kit (10x Genomics)

value: PBMC


title: TL naa20Δ SILAC-BG SCD rep1

description: OTHER (ribosome footprints)

value: ribosome footprints


title: TL naa20Δ heat rep1

description: OTHER (ribosome footprints)


title: Stalled products, t =2 min, replicate 1

description: DNA amplicons

value: Stalled products, t =2 min


title: CD4+ cells from healthy human brain

source_name: Brain

value: Brain


title: shATR4_diff72_rep2

city: Chicago

first: Yan

state: IL

address: 900 East 57th St.

department: Center for Research Informatics

institute: The University of Chicago

data_processing:
Raw sequencing QC assessement: FastQC v0.115
Alignment: STAR v2.5.2b
Post alignement QC assessment: RSeQC and Picard tools v2.9.0
Gene transcripts assembly: featureCounts
Differentially expressed genes analysis: edgeR
Genome_build: GENCODE human genome model: GRCh38 v24
Supplementary_files_format_and_content: tab-delimited text files include gene features raw counts values summarized by featureCouts for each Sample.

source_name: CIN612 cells transduced with shATR#4 vectors

growth_protocol: CIN612 Keratinoctyes were incubated in E-media and differentiated in high calcium media

extract_protocol:
Qiagen Reasy kit
RNA libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

value: CIN612 Keratinoctye cell line

tag: shRNA

value: shATR#4 vector

value: ATR knockdown

tag: treatment

value: Differentiation 72 hours


title: TL WT SILAC-BG SCD rep1

description: OTHER (ribosome footprints)

value: BY4741 arg4-delta lys1-delta


title: TL WT SILAC-BG SCD rep2

description: OTHER (ribosome footprints)


title: TL naa10Δ SCD rep2

description: OTHER (ribosome footprints)

value: BY4741 naa10-delta


title: replenish 12 h rep3

city: Shenzhen

first: Xuemei

last: Mao

address: Baishi Road

department: IAS

institute: Shenzhen University

data_processing:
Zebra process software (version 0.5.0.13875) was used for basecalling.
Data was filtered by software SOAPnuke (version v1.5.2, parameters -l 15 -q 0.5 -n 0.1) to remove reads with adaptors, unknown bases (more than 10%), and low quality reads.
HISAT (version v2.0.4) was used to do the genome mapping, and clean reads were mapped to reference genes using Bowtie2 (version v2.2.5).
Gene expression level (FPKM) was calculated with RSEM software (version v1.2.12)
Genome_build: Chromochloris zofingiensis v5.2.3.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Chromochloris zofingiensis

source_name: microalgae

growth_protocol: Chromochloris zofingiensis  were grown in 250 ml columns of photoreactor with 80 μE m-2 s-1 continuous illumination and 1.5% CO2 enriched air.

extract_protocol:
Total RNA was extracted  using the plant RNA extraction kit (TaKaRa, Japan) and poly-A  mRNA was purified using poly-T oligo-attached magnetic beads.
The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers, which was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then had the addition of a single 'A' base and subsequent ligation of the adapter. The products were purified and enriched with PCR amplification. The PCR yield was quantified by Qubit, and samples were pooled together to make a single strand DNA circle (ssDNA circle), which gave the final library.

tag: time point


title: shATR4_diff0_rep2

value: Differentiation 0 hours


title: TL naa10Δ SCD rep1

description: OTHER (ribosome footprints)


title: WT BOB UD UT 24h Rep 1

city: Cambridge

source_name: BOBSC hiSPCs

tag: cell type

value: hiPSC

tag: passage

value: Wild-type


title: shATR2_diff72_rep2

source_name: CIN612 cells transduced with shATR#2 vectors

value: shATR#2 vector


title: Parental library, replicate 2-2

description: DNA amplicons

value: Parental library


title: Parental library, replicate 1-2

description: DNA amplicons


title: TL WT SCD rep2

description: OTHER (ribosome footprints)

value: SCD, 30 C

value: BY4741 WT


title: shATR2_diff0_rep2


title: Parental library, replicate 1-1

description: DNA amplicons


title: replenish 12 h rep2


title: TRC_diff72_rep2

source_name: CIN612 cells transduced with scramble control vectors

value: scramble control vector

value: control


title: TL WT SCD rep1

description: OTHER (ribosome footprints)

value: ribosome footprints


title: SS 48 h rep3


title: Extended products, t = 4 min, replicate 2

description: DNA amplicons

value: Extended products, t = 4 min


title: replenish 12 h rep1


title: TL hmlΔ naa10Δ rep2

description: OTHER (ribosome footprints)

value: YPD, 30 C

value: BY4741 naa10-delta hml-delta


title: TRC_diff0_rep2

value: CIN612 Keratinoctye cell line


title: Stalled products, t = 0.5 min, replicate 1

description: DNA amplicons

value: Stalled products, t = 0.5 min


title: SS 48 h rep2


title: Parental library, replicate 2-1

description: DNA amplicons


title: Stalled products, t = 1 min, replicate 1

description: DNA amplicons

value: Stalled products, t = 1 min


title: Extended products, t = 2 min, replicate 2

description: DNA amplicons

value: Extended products, t = 2 min


title: SS 48 h rep1


title: TL hmlΔ rep2

description: OTHER (ribosome footprints)

value: BY4741 hml-delta


title: shATR4_diff0_rep1

value: shATR#4 vector

value: ATR knockdown

value: Differentiation 0 hours


title: SS 24 h rep3


title: Extended products, t = 30 min, replicate 2

description: DNA amplicons

value: Extended products, t = 30 min


title: shATR2_diff72_rep1

value: shATR#2 vector

value: Differentiation 72 hours


title: TL hmlΔ rep1

description: OTHER (ribosome footprints)


title: SS 24 h rep2


title: Extended products, t = 0.5 min, replicate 2

description: DNA amplicons

value: Extended products, t = 0.5 min


title: shATR2_diff0_rep1


title: Extended products, t = 4 min, replicate 1

description: DNA amplicons


title: TL naa20Δ rep2

description: OTHER (ribosome footprints)

value: BY4741 naa20-delta


title: TRC_diff72_rep1

value: scramble control vector

value: control


title: SS 24 h rep1


title: Extended products, t = 30 min, replicate 1

description: DNA amplicons


title: TL naa20Δ rep1

description: OTHER (ribosome footprints)

value: YPD, 30 C

value: ribosome footprints


title: TL hmlΔ naa10Δ rep1

description: OTHER (ribosome footprints)

value: BY4741 naa10-delta hml-delta


title: TRC_diff0_rep1

value: CIN612 Keratinoctye cell line


title: TL naa10Δ rep2

description: OTHER (ribosome footprints)

value: BY4741 naa10-delta


title: Extended products, t = 2 min, replicate 1

description: DNA amplicons

value: Extended products, t = 2 min


title: SS 12 h rep2


title: shATR4_diff72_rep1


title: Extended products, t = 1 min, replicate 1

description: DNA amplicons

value: Extended products, t = 1 min


title: SS 12 h rep1


title: TL naa10Δ rep1

description: OTHER (ribosome footprints)


title: Extended products, t = 1 min, replicate 2

description: DNA amplicons


title: TL WT rep2

description: OTHER (ribosome footprints)

value: BY4741 WT


title: TL WT rep1

description: OTHER (ribosome footprints)


title: Extended products, t = 0.5 min, replicate 1

description: DNA amplicons


title: IP_R4c: 8-oxoG RIP Clean air control

data_processing:
Illumina HiSeq 4000 Real-Time Analysis (RTA v2) basecalling
Sequence reads were trimmed for adaptor sequence using Trimmomatic 0.36, followed by quality check using FastQC
Reads were aligned to Ensembl comprehensive human genome annotation (GENCODE 26, GRCh38.p10) using STAR 2.5.3a, allowing novel splice junctions and using a two-pass mapping approach. Alignment was performed using parameters recommended in the STAR manual for ENCODE standards
RSEM was used to estimate transcript abundances and then differential expression and 8-oxoG enrichment  were performed using DESeq2 in R version 3.4.0.
Transcripts were annotated using biomaRt in R.
Genome_build: GRCh38.p10

source_name: BEAS-2B cells

extract_protocol:
Following exposure, each insert membrane was treated with 1 ml of TRIzol in the apical side and gently mixed to ensure thorough lysis. The whole lysate was collected and frozen until the day of the extraction. TRIzol RNA extraction was conducted following TRIzol’s manufacturer instructions. To prevent artificial oxidation of RNA by dissolved oxygen in solutions, ethanol (200 Proof, OmniPur, EMD Millipore, Burlington, MA), isopropanol (molecular biology grade, IBI Scientific, Dubuque, IA) and nuclease-free water (Ambion, Austin, TX) used in the downstream steps after TRIzol were purged with ultra-high purity N2 for 30 min.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells adhered to membrane inserts housed in 6-well plates (with lid off) were exposed in a modular cell exposure chamber (MIC-101 Billups-Rothenberg, San Diego, CA) to an air pollution mixture (generated from the reaction of 790 ppb acrolein, 670 ppb methacrolein, and 4 ppm ozone) for 1.5 hours. Before the cell exposure chamber, 1.52 LPM (litters per minute) of the air pollution mixture was mixed with 0.08 LPM CO2 (5% final concentration).

value: BEAS-2B cells (ATCC CRL-9609)

value: Lung, bronchus

tag: disease

value: Normal

tag: rip antibody

value: Anti-8-oxo-dG Monoclonal Antibody (clone 15A3)

tag: passages


title: SS 6 h rep2

tag: strain


title: SS 6 h rep3


title: IP_R3x: 8-oxoG RIP Air pollution


title: SS 12 h rep3


title: TS naa20Δ rep2

value: total mRNA


title: TS naa20Δ rep1


title: IP_R3c: 8-oxoG RIP Clean air control


title: IP_R4x: 8-oxoG RIP Air pollution


title: SS 0 h rep3


title: TS naa10Δ rep2


title: TS naa10Δ rep1


title: in_R4x: Input RNA Air pollution


title: SS 0 h rep1


title: in_R3x: Input RNA Air pollution


title: in_R5x: Input RNA Air pollution


title: SeViPS(HU)-derived vascular endothelial cells lot #2

city: Shinjuku-ku

first: Kumiko

last: Saeki

state: Tokyo

address: 1-21-1 Toyama

department: Department of disease control

institute: National Center for Global Health and Medicine

hyb_protocol: Cy3-labelled RNA was fragmented at 100oC for 5 minutes in a reaction volume of 45 ul containing Hyb Spike In and Agilent blocking agent following the manufacturers instructions. 28 ul of Agilent hybridization buffer was added to 17 uL of total RNA solution and hybridized to Agilent Human miRNA Microarray (8x60K) Rel21.0 (G4872A) for 17 hours at 55oC in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 070156_D_F_20141006) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: lot 2 of vascular endothelial cells generated from human iPS line that was produced from HUVEC by using a Sendai virus vector

label_protocol: Cyanine-3 (Cy3) labeled total RNA was prepared from 0.1 ug RNA using the One-Color MicroArray-Based miRNA Analysis(miRNA Complete Labeling Reagent and Hyb Kit). 0.1 ng of total RNA samples was dephosphorylated, labeled with Cy3-pCp, purified on Micro Bio-Spin columns, dried.

growth_protocol: Primary cultured human vascular endothelial cells (VECs) were cultured on 0.1% gelatin-coated plates using EGM®-2 BulletKit (Lonza Group Ltd. Basel, Switzerland) and human embryonic stem (ES)/iPS-derived VECs were cultured on 0.1% gelatin-coated plates using VEC-differentiation medium (Nakahara M et al., Cloning Stem Cells 11: 509-522, 2009). Cells were subcultured at split ratios of 1:2 ~ 1:3 twice a week.

extract_protocol: Total RNAs were isolated by using miRNeasy Mini Kit (Cat# 217004, Qiagen, Hilden, Germany) following the manufacturer's protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: sample group

value: Type-II VECs


title: SeViPS(BJ)-derived vascular endothelial cells lot #2

source_name: lot 2 of vascular endothelial cells generated from human iPS line that was produced from BJ fibroblast by using a Sendai virus vector


title: KhES3-derived vascular endothelial cells at early passages

description: young ES(KhES3)dEC

source_name: human ES cell (KhES-3)-derived vascular endothelial cells (at passage 1)


title: TS WT rep2

source_name: Yeast


title: TS WT rep1