title: Eimeria maxima APU-2 T36, replicate A

status: Public on Jan 31 2024

type: SRA

city: Bradenton

first: Matthew

middle: S

last: Tucker

state: Florida

address: 5000 Lakewood Ranch Blvd.

country: USA

institute: LECOM

library_source: transcriptomic

data_processing:
Geneious Prime 2023.04
Sequence reads (forward, reverse) from multiple lanes were concatenated to produce single forward and reverse read files
Reads were paired and trimmed with the plugin BBDUK (v. 38.84) with settings: minimum quality 20, Trim Low quality; minimum overlap 20, Trim adapters based on paired rad overhangs; minimum length 30 bp, discard short reads
Trimmed reads were aligned to the NCBI E. maxima Weybridge reference strain sequence using the Geneious RNA mapper. After mapping, expression metrics were calculated per sample, including Transcripts Per Million (TPM). Data were screened for genes meeting specified thresholds throughout the time course.  The DESeq2 package, as implemented in Geneious, calculated pairwise differential expression between time points in grouped biological replicates (within strains or between strains) and global expression (all time points) between strains.  We used thresholds of log2 fold change (FC) >1.5 or <-1.5 with adjusted p-value <0.05 to determine significantly differentially expressed genes. Significantly up-regulated genes meeting specified criteria were identified for further analysis.
Assembly: NCBI assembly EMW001 and ToxoDB v62
Supplementary files format and content: E. maxima mean TPM.xlsx
Supplementary files format and content: E. maxima Mean log2 mapped reads.xlsx

molecule: total RNA

organism: Eimeria maxima

growth_protocol: A group of eight broiler chickens was infected by oral gavage with 3,000 oocysts of E. maxima strain APU-1 and another group of eight broiler chickens was infected by oral gavage with 12,000 oocysts of E. maxima strain APU-2.

extract_protocol:
Total RNA was extracted from frozen oocyst Trizol pellets.  Oocysts were thawed and ground with a Teflon pestle. Homogenates werre mixed with chloroform and centrifuged at 12,000 g for 15 minutes at 4°C. The upper aqueous phase was transferred to new tubes and mixed with 70% ethanol. Total RNA was then isolated using a Qigaen RNeasy kit following manufacturer’s instructions. Total RNA was quantified using a ThermoFisher Scientific Qubit 3.0 fluorometer and quality was assessed using an Agilent Bioanalyzer 2100. RNA samples were frozen at -80°C. Prior to RNA-Seq, DNA was removed from total RNA with an Invitrogen Turbo DNA-free kit.
Libraries were produced from 500 ng of total RNA from biological replicates using an Illumina stranded mRNA Prep Kit (ligation). Bioanalyzer analysis determined the average library size ranged 302-388 bp

treatment_protocol: On day six post-inoculation, feces from each bird infected with a given E. maxima strain (A, B, C, representing biological replicates) were harvested. Unsporulated oocysts were isolated from chicken feces by flotation on saturated salt solution and washed with water.  The final preparation of oocysts was resuspended in 2% v/v potassium dichromate and incubated in a 29°C shaking water bath with aeration. At the beginning of the time course (T0) and other time points (every six hours up to 24 hours [T6, T12, T18, T24] then at an additional 12 hours  [T36, T48] up to 48 hours), a sample was taken from each replicate flask. Oocysts were washed with deionized water and then incubated with sodium hypochlorite. Oocysts were washed again repeatedly and Trizol was added to the pellets before freezing at -80°C.

tag: strain

tag: cell type

value: oocyst

tag: time

value: 36 hr

tag: source

value: oocysts from chicken feces


title: Eimeria maxima APU-2 T24, replicate C

value: 24 hr


title: Eimeria maxima APU-2 T36, replicate B


title: Eimeria maxima APU-2 T48, replicate C

value: 48 hr


title: Eimeria maxima APU-2 T18, replicate B

value: 18 hr


title: Eimeria maxima APU-2 T18, replicate A


title: Eimeria maxima APU-2 T18, replicate C


title: Eimeria maxima APU-2 T48, replicate A


title: Eimeria maxima APU-2 T24, replicate A


title: Eimeria maxima APU-2 T12, replicate C

value: 12 hr


title: Eimeria maxima APU-2 T6, replicate C

value: 6 hr


title: Eimeria maxima APU-2 T12, replicate A


title: Eimeria maxima APU-2 T6, replicate A


title: Eimeria maxima APU-2 T0, replicate B

value: 0 hr


title: Eimeria maxima APU-2 T6, replicate B


title: Eimeria maxima APU-2 T0, replicate A


title: Eimeria maxima APU-1 T48, replicate C


title: Eimeria maxima APU-1 T48, replicate B


title: Eimeria maxima APU-1 T48, replicate A


title: Eimeria maxima APU-2 T24, replicate B


title: Eimeria maxima APU-2 T36, replicate C


title: Eimeria maxima APU-1 T36, replicate B


title: Eimeria maxima APU-1 T36, replicate C


title: Eimeria maxima APU-1 T36, replicate A


title: Eimeria maxima APU-2 T48, replicate B


title: Eimeria maxima APU-2 T12, replicate B


title: Eimeria maxima APU-1 T24, replicate C


title: Eimeria maxima APU-1 T18, replicate B


title: Eimeria maxima APU-1 T18, replicate C


title: Eimeria maxima APU-1 T12, replicate B


title: Eimeria maxima APU-1 T24, replicate A


title: Eimeria maxima APU-1 T0, replicate C


title: Eimeria maxima APU-2 T0, replicate C


title: Eimeria maxima APU-1 T18, replicate A


title: Eimeria maxima APU-1 T6, replicate B


title: Eimeria maxima APU-1 T0, replicate B


title: Eimeria maxima APU-1 T24, replicate B


title: Eimeria maxima APU-1 T6, replicate C


title: Eimeria maxima APU-1 T0, replicate A


title: Eimeria maxima APU-1 T6, replicate A


title: Eimeria maxima APU-1 T12, replicate C


title: Eimeria maxima APU-1 T12, replicate A


title: Barcode-variant plasmid part 2

city: Copenhagen

first: Kristoffer

last: Johansson

address: Ole Maaløes Vej 5

department: Biology

country: Denmark

institute: University of Copenhagen

library_source: other

data_processing:
Barcodes of 18 bases were mapped to variants using exact match. Normalized populations per FACS gate were used to calculate a protein stability index (PSI) and that was finally normalized to an abundance score where 1 is wildtype and 0 the median PSI of nonsence variants
A variant-barcode map was made from long-read sequencing of the plasmid before transfection. Reads were aligned to the synthetic barcode-gfp-parkin construct using BWA software
Assembly: NA
Supplementary files format and content: vamp_parkin.csv: Colon separated file format contaning abundance scores
Supplementary files format and content: barcode_map.csv.gz: Colon separated file format containing the map between barcodes and protein variants
Library strategy: VAMP-seq

molecule: other

organism: synthetic construct

extract_protocol:
Genomic DNA was extracted from cells using the DNeasy blood & tissue Kit (Qiagen) following the manufacturer’s protocol titled “Protocol: Purification of Total DNA from Animal Blood or Cells (Spin-Column Protocol)”
A site-saturation library of codon optimized human parkin were custom synthesized and barcoded. Constructs of PRKN variants fused to GFP and an IRES-mCherry expression control were integrated into a HEK293T landing pad cell line

tag: cell line


title: Barcode-variant plasmid

data_processing:
Barcodes of 18 bases were mapped to variants using exact match.
Normalized populations per FACS gate were used to calculate a protein stability index (PSI) and that was finally normalized to an abundance score where 1 is wildtype and 0 the median PSI of nonsence variants
Toxicity scores were calculated as the slope estimated by a linear regression of the variant frequency at each time point normalized to wildtype
A variant-barcode map was made from long-read sequencing of the plasmid before transfection. Reads were aligned to the synthetic barcode-gfp-ASPA construct using BWA software
Assembly: NA
Supplementary files format and content: abundance_aspa.csv and toxicity_aspa.csv: Colon separated file format contaning abundance and toxicity scores
Supplementary files format and content: barcode_map.csv.gz: Colon separated file format containing the map between barcodes and protein variants
Library strategy: VAMP-seq

extract_protocol:
Genomic DNA extraction was performed using Qiagen DNeasy blood & tissue kit (Cat. No. 69506)
A site-saturation library of codon optimized human ASPA were custom synthesized and barcoded. Constructs of ASPA variants fused to GFP and an IRES-mCherry expression control were integrated into a HEK293T landing pad cell line


title: Barcode-variant plasmid part 1


title: G12

type: genomic

city: Toulouse

first: Joost

last: van Meerwijk

state: HG

address: CHU Purpan – BP 3028

country: France

institute: INSERM

description: Genomic DNA extracted from breast tumors was genotyped using Infinium HumanHap550-v3 Genotyping BeadChips (Illumina).

hyb_protocol: hybridized to Illumina GGP Mouse GIGA-MUGA Arrays according to the supplier’s instructions (Infinium HTS Assay Protocol Guide, 15045738 Rev.A October 2013, Manual Protocol)

scan_protocol: iScan System (Illumina).

data_processing: The thus obtained raw-date were quality controlled and analysed using GenomeStudio Software 2010 with the Genotyping module (Illumina)

label: Cy3, Cy5

molecule: genomic DNA

organism: Mus musculus

label_protocol: DNA was prepared from tail clips of three-day-old NOD, B6 and BC1 (n=94) mice using standard procedures, quality-controlled using a fragment analyser (Agilent), quantified using PicoGreen

growth_protocol: B6, BALB/c, C3H, CBA, DBA/1, and FVB mice were purchased from Janvier-labs, NOD and SJL from Charles River laboratories. Foxp3-Thy1a Rag2-Gfp-mutant B6 and NOD mice were previously described

extract_protocol: DNA was prepared from tail clips of three-day-old NOD, B6, F1, and BC1 mice using standard procedures

treatment_protocol: Thymic lobes from NMRI mice were collected and individually cultured on transwell inserts (0.4μm pores, polycarbonate membrane, Corning) at the air-liquid interface using complete medium (10% FBS) containing 1.35 mM 2-deoxyguanosin (2dGUO, Sigma). Six days later, lobes were intensely washed and cultured for 24h in hanging drops containing 50 000 DN3 (CD4-CD8-TCR−CD25+CD44-) cells FACS-sorted from thymocytes (CD8-depleted using mAb 31M and rabbit complement) from eight-week-old NOD or B6 mice. Lobes were then cultured on transwells for 12 days (cf. Fig. S1d). Lobes were collected and digested in RPMI containing 4μg/ml liberase and 0.1μg/ml DNAse I (Roche) during five minutes at 37°C with vigorous pipetting every two minutes. Cells were then washed, counted and stained for flow cytometry analysis.

value: developing Treg


title: B12

tag: sex,strain


title: H12

source_name: NOD


title: E12


title: G11


title: D11


title: E10


title: A11


title: D10


title: H11


title: C10


title: A12


title: F12


title: B11


title: F10


title: D12


title: F11


title: E11


title: C12


title: G10


title: A10


title: H10


title: B10


title: G9


title: C11


title: H9


title: C9


title: B9


title: F9


title: E8


title: D9


title: F8


title: A9


title: C8


title: G8


title: D8


title: H8


title: B8


title: E7


title: G7


title: A8


title: F7


title: G6


title: B7


title: H7


title: H6


title: A6


title: D7


title: B6


title: E6


title: C7


title: D6


title: C6


title: A7


title: E5


title: F6


title: D5


title: H5


title: G5


title: H4


title: F5


title: C5


title: A5


title: B4


title: G4


title: B5


title: G3


title: C4


title: E4


title: H3


title: E3


title: D4


title: F3


title: H2


title: A4


title: C3


title: B3


title: D2


title: F4


title: A3


title: E2


title: G1


title: F1


title: C2


title: D3


title: B2


title: A1


title: F2


title: H1


title: C1


title: E1


title: B1


title: G2


title: DM178 NL 101719 BF

type: protein

city: North Grafton

first: Jillian

middle: M

last: Richmond

state: Massachusetts

address: 200 Westboro Road

department: Comparative Pathobiology

institute: Tufts Cummings School of Veterinary Medicine

hyb_protocol: Hybridization and RT-PCR was performed per Olink Proteomics manufacturer's protocol

scan_protocol: Plates were read fee-for-service at Olink Proteomics in Watertown, MA

data_processing: Data were analyzed with Olink NPX manager software 2.1.0.224

label: antibody-linked oligonucleotide tag

molecule: protein

organism: Homo sapiens

source_name: blister biopsy

label_protocol: Sample labeling was performed per Olink Proteomics manufacturer's protocol

extract_protocol: Blister biopsies and/or EDTA anticoagulated blood samples were centrifuged at 330xg for 10 minutes. Interstitial skin fluid and/or plasma was frozen in 1mL aliquots and stored at -70C until analysis.

tag: disease status

value: DM

tag: location

value: nonlesional


title: DM193 NL 081720 BF


title: VB067 L BF

value: CLE

value: lesional


title: VB194 L BF

value: UV


title: CL190 NL 031020 BF


title: CB 049 020620 BF

value: Healthy

value: healthy


title: VB127 VL BF

value: Vitiligo


title: A2


title: VB175 NL BF

value: Morphea


title: DM145 NL 011419 BF


title: D1


title: CB 036 BF


title: CL067 NL BF


title: CL067 L1 BF


title: DM 178 L 101719 BF


title: CB 035 BF


title: VB127 NL BF

value: CLE/Vitiligo


title: CL179 NL BF_1


title: DM158 L BF


title: CL179 L BF_1


title: CL067 L2 BF


title: DM 178 L 031020 BF


title: VB127 LL BF


title: VB194 NL BF


title: CL143 L BF


title: BCSCs-Exosome-1

type: RNA

city: xuzhou

first: Tingting

last: Tang

address: huaihai road 84

country: China

institute: xuzhou medical university

description:
Gene expression of lncRNAs in exosomes derived from BCSCs and non-BCSCs.
LC Human ceRNA array V1.0

hyb_protocol: For hybridization,  RNase H was added to the 2nd-Cycle cDNA from above and Incubated for 45 min at 37 °C, then 5 min at 95 °C, then for at least 2 min at 4 °C. After hybridization, microarrays were washed by using GeneChip® Hybridization, Wash, and Stain Kit.

scan_protocol: After hybridization, slides were scanned on the Agilent Microarray Scanner G5761A (Agilent technologies, Santa Clara, CA, US).

data_processing:
Data were extracted with Feature Extraction software 12.0.3.1 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm. The microarray experiments were performed by following the protocol of Agilent technologies at LC Sciences Corporation (Hangzhou, China).
Genes with pvalue<0.05 and a fold change of at least 2 were selected for further analysis. Hierarchical Clustering was performed to show the distinguishable lncRNAs’ expression patterns among samples with Cluster 3.0 and TreeView software.

label: biotinylated

source_name: non-CD44+CD24- MDA-MB-231 cells

label_protocol: Total RNA was checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilenttechnologies, Santa Clara, CA, US). RNA samples of each group were then used to generate biotinylated cRNA targets for the LC Human ceRNA array V1.0 (4*180K, Design ID:085202).

extract_protocol: Total RNA of BCSC-Exos and non-BCSC-Exos were isolated using RNA Isolation Kit #58000 (Norgen, Canada) according to the manufacturer’s instructions, and purified by using a RNeasy Mini Kit (Qiagen, Germany).

treatment_protocol: We used flow cytometry sorting to obtain CD44+CD24- MDA-MB-231 cells and non-CD44+CD24- MDA-MB-231 cells. The exosomes the culture supernatant were purified by sequential centrifugation

value: Human breast cancer cells

tag: sample type

value: BCSCs-Exosome


title: DM145 L 011419 BF


title: BCSCs-Exosome-2


title: DM 154 NL BF


title: CONTROL_SAMPLE_US_CS_AS_2 2

source_name: Olink control

value: Control


title: CL179 NL BF_2


title: VB175 L BF


title: VB067 NL BF


title: CL143 NL Hem BF

value: nonlesional hemorrhagic


title: Non-BCSCs-Exosome-2

source_name: CD44+CD24- MDA-MB-231 cells

value: Non-BCSCs-Exosome


title: CONTROL_SAMPLE_US_CS_AS_2 1


title: DM 158 NL BF


title: DM 193 L 081720 BF


title: CL179 L BF_2


title: Non-BCSCs-Exosome-1


title: E88_28d

city: Jinan

first: yuwei

last: Zhang

state: Shandong

address: No.16992 Jingshi Road

department: Pathogenobiology

institute: SDCDC

description: tpm of 18 samples at 28 days.txt

data_processing:
CLC Genomics Workbench v 21.0.1
RNA-seq data were processed quality control (QC), trimming and mapping to the human reference genome hg38 using CLC Genomics Workbench.
Gene expression level was measured based on the transcripts per million (TPM).
Assembly: hg38
Supplementary files format and content: tab-delimited text files includeTPM values for each Sample

source_name: PBMC

extract_protocol:
Total RNA was extracted from PBMCs by using the RNeasy Mini Kit.
A total amount of 100 ng total RNA per sample was used to prepare for the rRNA-depleted cDNA library by Stranded Total RNA Prep Ligation with Ribo-Zero Plus Kit (Illumina, USA)

value: PBMC

tag: treatment

value: Protein Subunit Vaccine

value: Day 28

tag: developmental stage

value: elderly adult


title: DM 154 L BF

value: DM


title: CL143 NL BF

value: CLE

value: nonlesional


title: E67_28d

description: tpm of 18 samples at 28 days.txt


title: Steatotic Hep G2 cells treated with negative control, sample 3

city: Jerusalem

first: Yonat

last: Tzur

address: Givat Ram Campus

country: Israel

institute: Hebrew University of Jerusalem

data_processing:
FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used for quality control and reads were further trimmed and filtered using Flexbar (version 0.11.9).  Exclusion of potential rRNA sequences was achieved by filtering out the reads derived from rRNA sequences using bowtie2 and performing the alignment to the reference genome (GRCh38.p14, release 109) using STAR aligner with gtf file excluding rRNA coordinates. The transcripts were subsequently quantified using HTSeq.
Assembly: GRCh38.p14, realease 109
Supplementary files format and content: raw counts

source_name: Hep G2

extract_protocol:
RNA was extracted using the miRNeasy Mini Kit (Qiagen, 217004) according to the manufacturer's protocol, followed by RNA concentration determination (NanoDrop 2000, Thermo Scientific), standard gel electrophoresis for quality assesement, and RIN determination (Bioanalyzer 6000, Agilent). RIN was determined to be above 9.5 for all samples.
Libraries were constructed from 500ng total RNA using KAPA Stranded mRNA-Seq Kit (KAPA Biosystems Wilmington, USA) and the RNA fraction was sequenced on the NextSeq 500 System (Illumina) at the Center for Genomic Technologies Facility, the Hebrew University of Jerusalem
polyA-selection

value: Hep G2


title: Steatotic Hep G2 cells treated with negative control, sample 4


title: CL 190 L 031020 BF

value: lesional


title: E9

value: developing Treg


title: E57_28d

description: tpm of 18 samples at 28 days.txt


title: E40_28d

description: tpm of 18 samples at 28 days.txt


title: Steatotic Hep G2 cells treated with LysTTT-5'tRF mimic, sample 1


title: Steatotic Hep G2 cells treated with LysTTT-5'tRF mimic, sample 2


title: B38_28d

description: tpm of 18 samples at 28 days.txt

value: Inactivated Vaccine


title: E39_28d

description: tpm of 18 samples at 28 days.txt


title: B18_28d

description: tpm of 18 samples at 28 days.txt


title: E82_28d

description: tpm of 18 samples at 28 days.txt


title: E74_28d

description: tpm of 18 samples at 28 days.txt


title: B05_28d

description: tpm of 18 samples at 28 days.txt


title: B16_28d

description: tpm of 18 samples at 28 days.txt


title: B40_28d

description: tpm of 18 samples at 28 days.txt


title: DM178 NL 031020 BF

tag: description

value: did not amplify


title: B39_28d

description: tpm of 18 samples at 28 days.txt


title: B37_28d

description: tpm of 18 samples at 28 days.txt


title: B32_28d

description: tpm of 18 samples at 28 days.txt


title: E57_7d

value: Day 7


title: E74_7d


title: E52_7d


title: E67_7d


title: E97_28d

description: tpm of 18 samples at 28 days.txt


title: E39_7d


title: B40_7d


title: B17_28d

description: tpm of 18 samples at 28 days.txt


title: B30_28d

description: tpm of 18 samples at 28 days.txt


title: E88_7d


title: miRNA-seq_6B3

city: New Orleans

first: Mona

last: Elgazzaz

state: LA

address: 533 Bolivar Street

department: Cardiovascular Center

institute: LSUHSC

description: QIAseq_miRNA_NGS_Data_Analysis_6B_vs_3B_5B

data_processing:
Fastqs were converted from bcl using Illumina Basespace FASTQ Generation version 1.0.0
Primary and secondary data analyses were done using Qiagen data analysis protal
Assembly: mm10

source_name: RD-RD Female

extract_protocol:
At 3 month age, mice were euthanized and hypothalamus was flash frozen on dry ice for RNA extraction.
The library was constructed using QIAseq miRNA library kit following manufacturor's instruction

treatment_protocol: For Dams, C57BL/6J mice were maintained on either 52% fat high sucrose diet TD.04059.PWD hypercaloric diet (HCD) or regular chow diet (RD) for 1 month prior to mating and were kept on this diet for the duration of pregnancy and lactation. For offspring, mice were placed on either HCD or RD at weaning time and maintained until they reached 3 months old.

tag: tissue

value: Hypothalamus

tag: Sex

value: female

tag: genotype

value: WT

value: RD (no treatment)


title: E81_7d

value: PBMC


title: E97_7d

value: Protein Subunit Vaccine


title: B30_7d


title: B18_7d


title: B17_7d


title: E91_7d


title: B05_7d


title: miRNA-seq_6A4

description: QIAseq_miRNA_NGS_Data_Analysis_6A_vs_4A_5A_3A

source_name: RD-RD Male

value: male


title: miRNA-seq_6B2


title: miRNA-seq_6B1


title: miRNA-seq_6A3


title: E40_7d

value: elderly adult


title: B32_7d


title: B38_7d


title: miRNA-seq_5B3

source_name: RD-HCD Female

value: Perinatal RD and postnatal HCD


title: miRNA-seq_5B2


title: miRNA-seq_6A1


title: miRNA-seq_5B1


title: miRNA-seq_5A7

description:
QIAseq_miRNA_NGS_Data_Analysis_6A_vs_4A_5A_3A
QIASeq_miRNA_Volcano_Plot_Dataset_5A_vs_3A

source_name: RD-HCD Male


title: miRNA-seq_5A6


title: B16_7d


title: miRNA-seq_5A5


title: miRNA-seq_4B3

source_name: HCD-RD Female

value: Perinatal HCD and postnatal RD


title: Liver_NASH_2w_rep2

city: Hirosaki

first: Mitsuru

last: Chiba

state: Aomori

address: 66-1 Hon-cho

department: Graduate School of Health Sciences

country: Japan

institute: Hirosaki University

description: gene expression in liver of 8-week-old mouse

hyb_protocol: SurePrint G3 mouse miRNA microarray slides (8 × 60 K, Ver.21.0) were hybridized with the Cy3-labeled miRNA in a hybridization solution prepared with a Gene Expression Hybridization Kit (Agilent Technologies) for 20 hours at 55°C in a rotating hybridization oven (Agilent Technologies), according to the manufacturer’s instructions. After hybridization, microarray slides were washed for 5 min at room temperature with GE Wash Buffer 1 (Agilent Technologies) and for 5 min at 37°C with GE Wash buffer 2 (Agilent Technologies), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the SureScan Microarray Scanner (G4900DA) (Agilent Technologies) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 2 μm high sensitivity, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5 (Agilent Technologies) using default parameters (Protocol name: miRNA_1105_Oct12 and Grid name: 070155_D_F_20141006) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Liver

label_protocol: The miRNA Complete Labeling and Hyb kit (Agilent Technologies) were used to label miRNAs in 2.5 ng of serum total RNA or 100 ng of liver total RNA with cyanine 3 (Cy3) fluorescent dye following the manufacturer’s instructions.

extract_protocol: Total RNA was extracted from livers and 200 μL of serum using ISOGEN II (Nippon Gene) following the manufacturer’s instructions. Total RNA concentration from livers was measured by NanoDrop spectrophotometer (NanoDrop Technologies). All total RNA from livers had 260/280 nm absorbance ratios of 1.8–2.0. Ethachinmate (Nippon Gene) was used to precipitate total RNA from serum. A Quant-iT RiboGreen RNA Reagent and Kit (Thermo Fisher Scientific, Inc.) was used to measure total RNA concentration from serum.

treatment_protocol: Blood obtained from the heart was collected in BD Microtainer tubes with serum separator additive BD Microgard closure (Becton Dickinson Biosciences). Blood was then centrifuged at 6000 × G at room temperature for 3 min, and serum was collected. Livers were stored at -80°C immediately after removal.

tag: gender

tag: age

value: 8 weeks

value: Liver


title: miRNA-seq_6A2

tag: strain


title: Liver_Control_6w_rep2

description: gene expression in liver of 12-week-old mouse

value: 12 weeks


title: miRNA-seq_4A2

source_name: HCD-RD Male


title: Liver_NASH_6w_rep2


title: Liver_Control_2w_rep1


title: miRNA-seq_4B1


title: miRNA-seq_3B3

source_name: HCD-HCD Female

value: Perinatal and postnatal HCD


title: Liver_Control_6w_rep1


title: miRNA-seq_4B2


title: Liver_Control_1w_rep2

description: gene expression in liver of 7-week-old mouse

value: 7 weeks


title: Liver_Control_2w_rep2


title: Liver_NASH_1w_rep2


title: miRNA-seq_4A3


title: miRNA-seq_3A3

source_name: HCD-HCD Male


title: Liver_NASH_6w_rep1


title: miRNA-seq_4A1


title: Liver_Control_1w_rep1


title: miRNA-seq_3B1


title: miRNA-seq_3A2


title: Serum_NASH_2w_rep2

description: gene expression in serum of 8-week-old mouse

source_name: Serum

value: Serum


title: Serum_Control_6w_rep2

description: gene expression in serum of 12-week-old mouse


title: Serum_NASH_6w_rep2


title: Liver_NASH_1w_rep1


title: Serum_NASH_2w_rep1


title: Serum_NASH_6w_rep


title: miRNA-seq_3B2


title: miRNA-seq_3A1


title: RNA-seq_6B2

description:
TrtGrp6B_vs_TrtGrp4B.deseq.counts
TrtGrp6B_vs_TrtGrp4B.deseq.res
TrtGrp6B_vs_TrtGrp4B.deseq.rlog

data_processing:
Raw reads were trimmed and mapped on Banana Slug Analytics Platform
Differentially expressed genes were analyzed using Deseq
Pathway analyses were performed using Advaita iPathwayGuide platform
Assembly: mm10
Supplementary files format and content: excels containing gene fkpm value

extract_protocol:
At 3 month age, mice were euthanized and hypothalamus was flash frozen on dry ice for RNA extraction.
The library was constructed using TruSeq Stranded mRNA kit following manufacturor's instruction


title: Liver_NASH_2w_rep1


title: RNA-seq_6B1


title: Trail.mye.DDC.038.Parenchymal.IBA1Posi

city: Rochester

first: Alexander

middle: Quinn

last: Wixom

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

description:
Trail.mye | DDC | 038 | IBA1 Posi
Image file: Trail.mye_038.tiff

data_processing:
Base calling was performed with the Illumina bcl2fastq
FASTQ files were converted into digital count conversion (DCC) and STATS files using GeoMx NGS Pipeline
DCC files were uploaded to the GeoMx DSP to generate the initial, spatially resolved, dataset
Gene counts were mapped to specific ROIs and normalized using Q3 normalization strategy in keeping with NanoString GeoMx recommendations. (https://nanostring.com/resources/introduction-to-geomx-normalization-cta-whitepaper/)
Assembly: mm10
Supplementary files format and content: comma-delimited files with normalized transcriptome gene expression
Library strategy: GeoMx Seq

source_name: Parenchymal

growth_protocol: Animals were reared on a 12-hour light-dark cycle and had ad-libitum access to food and water.

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with fluorescence labeled antibodies for visualization of morphological structures. Regions of interest (ROI) are selected on the visualized tissue. Using fluorescent morphology markers and auto-segmentation algorithm, individual segments was divided. The photocleaved oligos were aspirated via a microcapillary tube and stored in microplate wells by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (https://doi.org/10.1038/s41587-020-0472-9)
Each collection of oligo tags from one well (representing an AOI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR. After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

treatment_protocol: Animals were raised on an intermittent feeding schedule for a total of 21 days (5 days Control/DDC diet-3 days Chow- 5 days Control/DDC diet- 3 days Chow-5 days Control/DDC diet).  Experiment was terminated on day 22.

value: Parenchymal

tag: cell type

tag: diet

value: DDC


title: RNA-seq_6B3

value: Hypothalamus

value: female


title: RNA-seq_6A3

description:
TrtGrp6A_vs_TrtGr4A.deseq.counts
TrtGrp6A_vs_TrtGr4A.deseq.res
TrtGrp6A_vs_TrtGr4A.deseq.rlog

value: WT

value: RD (no treatment)


title: Serum_Control_6w_rep1


title: Serum_NASH_1w_rep2

description: gene expression in serum of 7-week-old mouse


title: Trail.mye.DDC.037.Parenchymal.IBA1Posi

description:
Trail.mye | DDC | 037 | IBA1 Posi
Image file: Trail.mye_037.tiff


title: Serum_Control_2w_rep2


title: Trail.mye.DDC.036.Periportal.PanCKPosi

description:
Trail.mye | DDC | 036 | PanCK Posi
Image file: Trail.mye_036.tiff

source_name: Periportal

value: Periportal

value: PanCKPosi


title: RNA-seq_6A1

value: male


title: RNA-seq_6A2


title: Serum_Control_2w_rep1


title: Trail.mye.DDC.035.Periportal.PanCKPosi

description:
Trail.mye | DDC | 035 | PanCK Posi
Image file: Trail.mye_035.tiff


title: Serum_NASH_1w_rep1


title: RNA-seq_5B3

description:
control5B_vs_comparison3B.deseq.counts
control5B_vs_comparison3B.deseq.res
control5B_vs_comparison3B.deseq.rlog

value: Perinatal RD and postnatal HCD


title: Serum_Control_1w_rep2


title: Trail.mye.DDC.034.Periportal.IBA1Posi

description:
Trail.mye | DDC | 034 | IBA1 Posi
Image file: Trail.mye_034.tiff


title: RNA-seq_5B1


title: Trail.mye.DDC.033.Periportal.IBA1Posi

description:
Trail.mye | DDC | 033 | IBA1 Posi
Image file: Trail.mye_033.tiff


title: RNA-seq_5A5

description:
5A_vs_3A control_vs_comparison.deseq.counts
5A_vs_3A control_vs_comparison.deseq.res
5A_vs_3A control_vs_comparison.deseq.rlog


title: Trail.mye.DDC.034.Periportal.PanCKPosi

description:
Trail.mye | DDC | 034 | PanCK Posi
Image file: Trail.mye_034.tiff


title: RNA-seq_5A7


title: Trail.mye.DDC.032.Periportal.IBA1Posi

description:
Trail.mye | DDC | 032 | IBA1 Posi
Image file: Trail.mye_032.tiff


title: Trail.mye.DDC.036.Periportal.IBA1Posi

description:
Trail.mye | DDC | 036 | IBA1 Posi
Image file: Trail.mye_036.tiff


title: RNA-seq_5A6


title: Trail.mye.DDC.033.Periportal.PanCKPosi

description:
Trail.mye | DDC | 033 | PanCK Posi
Image file: Trail.mye_033.tiff


title: RNA-seq_4B1

value: Perinatal HCD and postnatal RD


title: RNA-seq_4B3


title: Trail.mye.CON.031.Parenchymal.IBA1Posi

description:
Trail.mye | CON | 031 | IBA1 Posi
Image file: Trail.mye_031.tiff

value: CON


title: Trail.mye.DDC.032.Periportal.PanCKPosi

description:
Trail.mye | DDC | 032 | PanCK Posi
Image file: Trail.mye_032.tiff


title: RNA-seq_4B2

description:
TrtGrp6B_vs_TrtGrp4B.deseq.counts
TrtGrp6B_vs_TrtGrp4B.deseq.res
TrtGrp6B_vs_TrtGrp4B.deseq.rlog


title: Trail.mye.CON.030.Parenchymal.IBA1Posi

description:
Trail.mye | CON | 030 | IBA1 Posi
Image file: Trail.mye_030.tiff


title: RNA-seq_4A3

description:
TrtGrp6A_vs_TrtGr4A.deseq.counts
TrtGrp6A_vs_TrtGr4A.deseq.res
TrtGrp6A_vs_TrtGr4A.deseq.rlog


title: RNA-seq_4A2


title: Trail.mye.CON.029.Periportal.IBA1Posi

description:
Trail.mye | CON | 029 | IBA1 Posi
Image file: Trail.mye_029.tiff


title: Trail.mye.CON.029.Periportal.PanCKPosi

description:
Trail.mye | CON | 029 | PanCK Posi
Image file: Trail.mye_029.tiff


title: Trail.mye.DDC.035.Periportal.IBA1Posi

description:
Trail.mye | DDC | 035 | IBA1 Posi
Image file: Trail.mye_035.tiff


title: RNA-seq_4A1


title: Trail.mye.CON.028.Periportal.IBA1Posi

description:
Trail.mye | CON | 028 | IBA1 Posi
Image file: Trail.mye_028.tiff


title: RNA-seq_3B3

description:
control5B_vs_comparison3B.deseq.counts
control5B_vs_comparison3B.deseq.res
control5B_vs_comparison3B.deseq.rlog


title: Trail.mye.CON.028.Periportal.PanCKPosi

description:
Trail.mye | CON | 028 | PanCK Posi
Image file: Trail.mye_028.tiff


title: RNA-seq_5B2


title: Trail.mye.CON.027.Periportal.IBA1Posi

description:
Trail.mye | CON | 027 | IBA1 Posi
Image file: Trail.mye_027.tiff


title: Trail.mye.CON.027.Periportal.PanCKPosi

description:
Trail.mye | CON | 027 | PanCK Posi
Image file: Trail.mye_027.tiff


title: RNA-seq_3B1


title: RNA-seq_3A3

description:
5A_vs_3A control_vs_comparison.deseq.counts
5A_vs_3A control_vs_comparison.deseq.res
5A_vs_3A control_vs_comparison.deseq.rlog


title: RNA-seq_3A2


title: Trail.mye.CON.026.Periportal.PanCKPosi

description:
Trail.mye | CON | 026 | PanCK Posi
Image file: Trail.mye_026.tiff


title: RNA-seq_3A1


title: WT.DDC.013.Periportal.PanCKPosi

description:
WT | DDC | 013 | PanCK Posi
Image file: WT_013.tiff


title: WT.DDC.013.Periportal.IBA1Posi

description:
WT | DDC | 013 | IBA1 Posi
Image file: WT_013.tiff


title: WT.DDC.012.Parenchymal.IBA1Posi

description:
WT | DDC | 012 | IBA1 Posi
Image file: WT_012.tiff


title: WT.DDC.011.Periportal.IBA1Posi

description:
WT | DDC | 011 | IBA1 Posi
Image file: WT_011.tiff


title: WT.DDC.010.Parenchymal.IBA1Posi

description:
WT | DDC | 010 | IBA1 Posi
Image file: WT_010.tiff


title: WT.DDC.007.Periportal.IBA1Posi

description:
WT | DDC | 007 | IBA1 Posi
Image file: WT_007.tiff


title: WT.DDC.009.Periportal.IBA1Posi

description:
WT | DDC | 009 | IBA1 Posi
Image file: WT_009.tiff


title: WT.DDC.009.Periportal.PanCKPosi

description:
WT | DDC | 009 | PanCK Posi
Image file: WT_009.tiff


title: WT.DDC.011.Periportal.PanCKPosi

description:
WT | DDC | 011 | PanCK Posi
Image file: WT_011.tiff


title: WT.CON.005.Periportal.PanCKPosi

description:
WT | CON | 005 | PanCK Posi
Image file: WT_005.tiff


title: WT.CON.004.Parenchymal.IBA1Posi

description:
WT | CON | 004 | IBA1 Posi
Image file: WT_004.tiff


title: WT.DDC.007.Periportal.PanCKPosi

description:
WT | DDC | 007 | PanCK Posi
Image file: WT_007.tiff


title: WT.CON.005.Periportal.IBA1Posi

description:
WT | CON | 005 | IBA1 Posi
Image file: WT_005.tiff


title: WT.CON.003.Periportal.IBA1Posi

description:
WT | CON | 003 | IBA1 Posi
Image file: WT_003.tiff


title: WT.CON.003.Periportal.PanCKPosi

description:
WT | CON | 003 | PanCK Posi
Image file: WT_003.tiff


title: RNA-seq_3B2

description:
control5B_vs_comparison3B.deseq.counts
control5B_vs_comparison3B.deseq.res
control5B_vs_comparison3B.deseq.rlog


title: WT.CON.001.Periportal.PanCKPosi

description:
WT | CON | 001 | PanCK Posi
Image file: WT_001.tiff


title: HFCF3

city: Hangzhou

first: zhaowei

last: cai

state: Zhejiang

address: Binwen road 548

department: Laboratory Animal Research Center

institute: zhejiang chinese medical university

data_processing:
Cutadapt 1.9 software was used to remove the reads that contained adaptor contamination
Raw sequencing data were evaluated by FAST-QC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc), an online bioinformatics program used to characterize quality distributions of nucleotides, position-specific sequencing qualities, GC contents, the proportions of PCR duplication, and k-mer frequencies
Raw reads after quality control testing were then mapped to the reference pig enome version 11.1 (Sscrofa 11.1) using Hisat2 software
The normalized expression level of each gene was measured by Fragments Per Kilobase of exon per Million Reads (FPKM).
Assembly: Sscrofa 11.1
Supplementary files format and content: table-delimited text file includes raw counts for each sample
Supplementary files format and content: table-delimited text file includes FPKM values for each sample

organism: Sus scrofa

source_name: abdominal aorta

extract_protocol:
Abdominal aorta tissue were subjected to total RNA extraction using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). Sequencing libraries were prepared using a mRNA-Seq Sample Prep Kit (Illumina, San Diego, CA, USA) following the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Male Wuzhishan pigs fed either normal chow diet or a high fat, high cholesterol, and high fructose diet for six months

value: abdominal aorta

value: Wuzhishan pigs

value: 3-4 months old

value: High fat high cholesterol and high fructose diet


title: BEC_rep2_H3K27me3

city: Philadelphia

first: Takeshi

last: Katsuda

state: PA

address: 421 Curie Blvd, BRB II/III Rm531

department: Perelman School of Medicine

institute: University of Pennsylvania

library_source: genomic

data_processing:
library strategy: CUT&Tag
Reads were aligned to the mouse genome (mm10) using Bowtie2 with options ‘--very-sensitive -X 1000 --dovetail -1’
Duplicates were removed using Picard (http://broadinstitute.github.io/picard/).
Assembly: mm10
Supplementary files format and content: The bigwig files (.bw) are generated by converting the bam files to bigwig using bamCoverage with CPM normalization.
Supplementary files format and content: Peak calling was performed using MACS2 without Isotype controls as input files. Called peaks were filtered using the mm10-blacklist.v2 file.

extract_protocol:
The cells were lightly crosslinked by in 1 ml DMEM containing 0.1-0.15% formalin at RT for 1 min. Crosslinking was quenched by adding 50 ul 2.5 M glycine and rotated at RT for 10 minutes.
The cells were resuspended in nuclear extraction buffer (NE buffer) (20 mM HEPES, pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% glycerol, 0.5 mM spermidine and EDTA-free protease inhibitors) (approximately 100 ul per 100,000 cells), and incubated on ice for 10 minutes.
The extracted nuclei were washed once in NE buffer by centrifugation at 1,300 ×g at 4 °C for 3 minutes. The supernatant was removed, and the nuclei were resuspended in NE buffer, and aliquoted into an 8-well strip tube (100 ul per reaction).
Then, 10 ul Concanavalin A-coated magnetic beads (EpiCypher) were added, and incubated at RT for 10 minutes. The nuclei/bead conjugate was bound to a magnet, the supernatant was removed, and were resuspended in 50 ul antibody reaction buffer (Wash150-T buffer with 5% digitonin and 0.5 M EDTA; the composition of Wash150-T buffer is 20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM spermidine, EDTA-free protease inhibitors and 0.05% Triton X-100), 0.5 ul antibody was added and incubated at 4°C overnight.
After removal of the supernatant, the beads were resuspended in 50 ul Wash150-T buffer containing 0.5 ul secondary antibody, and incubated at RT for 30 minutes. Following two washes in 200 ul cold Wash150-T buffer, beads were resuspended in 50 ul Wash300-T buffer (20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM spermidine, EDTA-free protease inhibitors and 0.05% Triton X-100).
Then, 2.5 ul pAG-Tn5 (EpiCypher) was added, and the samples were incubated at RT for 1 hour. While on the magnet, the supernatant was removed, and the samples were washed twice in 200 ul cold Wash300-T buffer. Following resuspension in 50 ul Tagmentation buffer (Wash300-T buffer with 10 mM MgCl2 (Sigma)), Tn5 digestion was performed at 37 °C for 1 hour.
The supernatant was discarded, and the beads were washed once in in 50 ul TAPS buffer (10 mM TAPS (Boston BioProducts), pH 8.5, 0.2 mM EDTA). Tagmentation was quenched by adding 5 ul SDS release buffer (10 mM TAPS, pH 8.5, 0.1%SDS), mixed thoroughly by vortex and incubated at 58 °C for 1 hour. Then, 15 ul SDS quench buffer (0.67% Triton X-100) was added and mixed thoroughly by vortex.
Then, 2 ul universal i5 primer (10 uM), 2 ul barcode i7 primer (10 uM), and 25 ul CUTANA® High Fidelity 2X PCR Master Mix for CUT&Tag (EpiCypher) was added, and PCR was performed (1 cycle of 20 °C for 5 min; 1 cycle of 72 °C for 5 min; 1 cycle of 98 °C for 45 seconds, 14-21 cycles of 98°C for 15 seconds and 60°C for 10 seconds; 72°C for 1 minute). The DNA was cleaned up with 1.3× AMPure XP beads (Beckman) following the standard procedure.

treatment_protocol: Rosa26-LSL-Cas9-EGFP mice were injected with AAV8-TBG-Cre retro-orbitally at 5e11 gc/mouse. One week after injection, DDC challenge was started and continued for 8-9 weeks. Control mice were maintained on normal diet throughout the experiment.

value: Liver

value: Biliary epithelial cells

value: Wild type

value: AAV8-TBG-Cre injected; treated with DDC for 8-9 weeks


title: Trail.mye.CON.026.Periportal.IBA1Posi

description:
Trail.mye | CON | 026 | IBA1 Posi
Image file: Trail.mye_026.tiff


title: BEC_rep1_H3K27me3


title: HFCF2


title: HFCF1


title: NC2

value: Normal chow diet


title: NC1


title: NC3


title: Rep_late_rep2_H3K27me3

value: Late reprogrammed cells


title: IUGR-male, replicate 2, scRNAseq

first: yusen

last: wei

institute: Zhejiang University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: the Ensembl Sus scrofa 11.1 reference genome (release 105)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

molecule: polyA RNA

extract_protocol:
Freshly collected DC and Si8 from RedMUC298trTg mice were flushed with ice-cold HBSSwo (Mg2+/Ca2+ free supplemented with 10mM HEPES, pH 7.2) to remove luminal content. The tissue was inverted and inflated by injection of HBSSwo. Epithelial isolation was performed by incubation of tissue with pre-digestion buffer (HBSSwo, 5 mM EDTA, 5% v/v FCS, 1 mM DTT) in a shaking incubator. The isolated epithelial cells were resuspended in digestion buffer (HBSS with Mg2+/Ca2+ supplemented with 2 mg/ml collagenase type I and 40 U/ml DNase I) and incubated at 37 °C for 30 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSSwo, 2% v/v FCS, 5mM EDTA). Alive GCs were sorted using a FACS Jazz (Becton Dickinson) according to the presence or absence of mCherry signal using a C57Bl6 mouse as negative control. Goblet cells were washed in HBSS-/- and resuspended in HBSS-/- supplemented with 0.04% w/v BSA.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: one-week old


title: IUGR-female, replicate 1, scRNAseq

description: 10x Genomics


title: Rep_intermed_rep2_H3K27me3

value: Intermediately reprogrammed cells


title: NBW-female, replicate 1, scRNAseq

description: 10x Genomics


title: Rep_late_rep1_H3K27me3


title: Rep_intermed_rep1_H3K27me3


title: Rep_early_rep2_H3K27me3

value: Early reprogrammed cells


title: BEC_rep2_H3K27ac


title: IUGR-male, replicate 3, scRNAseq

description: 10x Genomics


title: Rep_early_rep1_H3K27me3


title: NBW-male, replicate 3, scRNAseq

description: 10x Genomics


title: Hep_rep2_H3K27me3

value: Hepatocyte

value: AAV8-TBG-Cre injected; harvested without DDC treatement


title: IUGR-male, replicate 1, scRNAseq

description: 10x Genomics


title: NBW-male, replicate 2, scRNAseq

description: 10x Genomics


title: BEC_rep1_H3K27ac


title: Hep_rep1_H3K27me3


title: Rep_late_rep3_H3K27ac


title: NBW-male, replicate 1, scRNAseq

description: 10x Genomics


title: Rep_late_rep2_H3K27ac


title: Rep_late_rep3_H3K27me3


title: Rep_intermed_rep2_H3K27ac


title: ecd1, nub>Dam-RNase H1 replicate 1

city: Cologne

first: Mirka

last: Uhlirova

state: NRW

address: Joseph-Stelzmann Str. 26

department: Institute for Genetics

country: Germany

institute: CECAD Research Center  Cologne

description:
Dam-RNase H1 ecd1
Supplementary Dataset 6a unique_gene_results_RNH_ctrl_peaks.txt
Supplementary Dataset 6b unique_gene_results_for_ecd1_peaks.txt

data_processing:
Sequencing data were processed using the damidseq_pipeline (Marshall and Brand, 2015) to generate normalized gff files.
Dam-RNase H1 binding peaks were identified using a peak finding program based on one described by Wolfram et al. (2012).
Scripts are available on request from Tony D. Southall.
Assembly: BDGP6.27
Supplementary files format and content: .txt files: contain genes associated to each Dam-RNase H1 peak in control and ecd1 samples, with additional peak information

organism: Drosophila melanogaster

source_name: Wing disc, L3

growth_protocol: Dosophila crosses were kept on a diet consisting of 0.8% agar, 8% cornmeal, 1% soymeal, 1.8% dry yeast, 8% malt extract and 2.2% sugar-beet syrup, supplemented with 0.625% propionic acid and 0.15% Nipagin, and maintained at 25 °C. Wing discs were collected from third-instar larvae 7 days after egg-laying

extract_protocol:
DNA extraction from dissected third instar Drosophila larvae and sequencing of methylation-specific PCR amplicons was performed according to the Nature protocols on DamID-Seq published by Vogel et al. (2007) and Marshall et al. (2016).
Sequencing libraries were generated according to the Illumina protocol for ChIP-Seq library preparation. Samples were pair-end sequenced on an Illumina HiSeq 2000 instrument at 50 bp read length.

treatment_protocol: Larvae were transferred from 25 °C to 29 °C for 24 hours on day 6 after egg laying, leading to inactivation of mutant ecd1 and expression of Dam- constructs.

value: Wing disc, L3

value: nub>Dam-RNase H1; ecd1

value: 29 °C for 24h


title: Rep_late_rep1_H3K27ac


title: ecd1, nub>Dam-RNase H1 replicate 2


title: ecd1, nub>Dam-RNase H1 replicate 3


title: Rep_intermed_rep1_H3K27ac


title: ecd1, nub>Dam control

value: nub>Dam; ecd1


title: Rep_early_rep2_H3K27ac


title: Hep_rep2_H3K27ac


title: nub>Dam-RNase H1 replicate 2

description:
Dam-RNase H1 control
Supplementary Dataset 6a unique_gene_results_RNH_ctrl_peaks.txt
Supplementary Dataset 6b unique_gene_results_for_ecd1_peaks.txt

value: nub>Dam-RNase H1


title: Rep_early_rep1_H3K27ac


title: P7 NSCs, Control3 [MC3]

city: Beijing

first: Yufei

last: Wei

address: 5 Dong Dan San Tiao

institute: Peking Union Medical College

data_processing:
Trim Smart-seq2 public primer sequence from the Reads.
Remove the contaminated reads for adapters, the low quality reads and the reads whose N base more than 5% for total bases.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Assembly: mm10
Supplementary files format and content: Document in xlsx format includes counts and statistical analysis for each gene symbol, along with GO analysis and KEGG information.

source_name: neural stem cells

growth_protocol: NSCs were cultured in DMEM/F12 proliferation medium supplemented with 2% B27 supplement, 20 ng/ml EGF, 20 ng/ml bFGF and 0.2% BSA for proliferation.

extract_protocol:
RNA was isolated from the 7th day culturing NSCs with TRIzol reagent (Invitrogen).A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: neural stem cells

value: WT

value: NSCs proliferation medium


title: P7 NSCs, Control2 [MC2]


title: nub>Dam-RNase H1 replicate 3


title: nub>mRFP; ecd-RNAi, Xrp1-RNAi rep 2

data_processing:
Initial quality control of the raw data was performed using FastQC (RRID:SCR_014583).
Illumina sequencing adapters were removed from the sequencing reads with the cutadapt tool version 3.5 (Martin, 2011; RRID:SCR_011841)
For differential gene expression analysis, kallisto v0.46.1 (Bray et al., 2016; RRID:SCR_016582) was used for pseudoalignment of obtained reads to the complete Drosophila melanogaster transcriptome (BDGP6.28, Ensembl release 102) and transcript-level abundance quantification using 100 bootstrap samples.
Summarization of the obtained estimated counts to gene-level was performed using tximport v1.22.0 (Bray et al., 2015; RRID:SCR_016752).
Differential gene expression was determined using DESeq2 v1.34.0 (Love et al., 2014; RRID:SCR_015687).
Intron retention was analyzed using NxtIRFcore v1.2.1 (Wang and Ritchie 2022) and IRFinder v2.0.1 (Middleton et al., 2017)
Assembly: BDGP6.28, Ensembl release 104
Supplementary files format and content: csv: comma-separated table with DEseq2 normalized count
Supplementary files format and content: txt: tab-delimited table of DESeq2 results
Supplementary files format and content: tsv: per intron DESeq2 differential retention results

extract_protocol:
For RNA isolation, 150 WDs were dissected from third instar larvae in 1xPBS and snap-frozen in liquid nitrogen, and processed according to standard TRI Reagent protocol (Sigma Aldrich, #T9424) with DNase I treatment (Invitrogen, #AM2238).
For RNA sequencing, 2 μg of total RNA was used for library preparation (Illumina TruSeq Stranded total RNA Ribo-Zero). Pair-end sequencing (four biological replicates of each experimental group) at a read length of 100 bp was performed on an Illumina HiSeq 2000 machine.

treatment_protocol: RNAi against ecd was driven in the nubbin domain of D. melanogaster larvae continuously until sample collection

value: nub>mRFP; ecd-RNAi, Xrp1-RNAi

value: ecd RNAi + Xrp1 RNAi


title: nub>Dam-RNase H1 replicate 1


title: Rep_late_rep3_H3K4me3

value: Liver

value: Wild type

value: AAV8-TBG-Cre injected; treated with DDC for 8-9 weeks


title: BEC_rep2_H3K4me3

value: Biliary epithelial cells


title: nub>mRFP; ecd-RNAi, Xrp1-RNAi rep 4


title: P7 NSCs, Mutant1 [MT1]

value: Sirt6 knockout


title: nub>Dam control

description:
Dam-only control
Supplementary Dataset 6a unique_gene_results_RNH_ctrl_peaks.txt
Supplementary Dataset 6b unique_gene_results_for_ecd1_peaks.txt

value: nub>Dam


title: P7 NSCs, Mutant2 [MT2]


title: nub>mRFP; ecd-RNAi, Xrp1-RNAi rep 3


title: nub>mRFP; ecd-RNAi, Xrp1-RNAi rep 1


title: s12 HP-AKI

first: Jessica

last: Hohenstein

data_processing:
TopHat v2.1.0 for alignment
FeatureCounts to quantify expression
edgeR for defining differentially expressed genes
Assembly: GRCm38
Supplementary files format and content: tsv format containg raw gene counts and RPKM normalize expression values

source_name: kidney

extract_protocol:
trizol and Qiagen total RNA kit
TruSeq RNA Sample Prep Kit v2

treatment_protocol: Sham and HP-AKI treatment

value: kidney

value: harvested 1 day after HP-AKI


title: s13 HP-AKI


title: nub>mRFP; ecd-RNAi rep 4

value: Wing disc, L3

value: nub>mRFP; ecd-RNAi

value: ecd RNAi


title: Rep_late_rep2_H3K4me3

value: Late reprogrammed cells


title: s11 HP-AKI


title: s9 HP-AKI


title: Hep_rep1_H3K27ac

value: Hepatocyte

value: AAV8-TBG-Cre injected; harvested without DDC treatement


title: Rep_intermed_rep2_H3K4me3

value: Intermediately reprogrammed cells


title: s8 HP-AKI


title: s7 HP-AKI


title: nub>mRFP; ecd-RNAi rep 3


title: BEC_rep1_H3K4me3


title: s5 Sham

value: sham


title: nub>mRFP; ecd-RNAi rep 2


title: s4 Sham


title: Rep_early_rep2_H3K4me3

value: Early reprogrammed cells


title: s6 Sham


title: P7 NSCs, Control1 [MC1]

value: neural stem cells

value: WT

value: NSCs proliferation medium


title: nub>mRFP; ecd-RNAi rep 1


title: s3 Sham


title: Rep_intermed_rep1_H3K4me3

value: Liver

value: Wild type

value: AAV8-TBG-Cre injected; treated with DDC for 8-9 weeks


title: Rep_late_rep1_H3K4me3


title: s1 Sham

value: kidney


title: s2 Sham


title: nub>mRFP rep 4

value: nub>mRFP

value: no treatment


title: P7 NSCs, Mutant3 [MT3]

value: Sirt6 knockout


title: Rep_early_rep1_H3K4me3


title: Hep_rep2_H3K4me3


title: RNA-seq_6A4

description:
TrtGrp6A_vs_TrtGr4A.deseq.counts
TrtGrp6A_vs_TrtGr4A.deseq.res
TrtGrp6A_vs_TrtGr4A.deseq.rlog

value: Hypothalamus

value: male

value: RD (no treatment)


title: nub>mRFP rep 3

value: Wing disc, L3


title: nub>mRFP rep 2


title: Hep_rep1_H3K4me3

value: Hepatocyte

value: AAV8-TBG-Cre injected; harvested without DDC treatement


title: BEC_rep2_H3K4me1

value: Biliary epithelial cells


title: nub>mRFP rep 1


title: BEC_rep1_H3K4me1


title: nub>mRFP; ecd-RNAi replicate 4

data_processing:
Initial quality control of the raw data was performed using FastQC (RRID:SCR_014583).
Illumina sequencing adapters were removed from the sequencing reads with the cutadapt tool version 3.5 (Martin, 2011; RRID:SCR_011841)
For differential gene expression analysis, kallisto v0.46.1 (Bray et al., 2016; RRID:SCR_016582) was used for pseudoalignment of obtained reads to the complete Drosophila melanogaster transcriptome (BDGP6.28, Ensembl release 102) and transcript-level abundance quantification using 100 bootstrap samples.
Summarization of the obtained estimated counts to gene-level was performed using tximport v1.22.0 (Bray et al., 2015; RRID:SCR_016752).
Differential gene expression was determined using DESeq2 v1.34.0 (Love et al., 2014; RRID:SCR_015687).
Assembly: BDGP6.28, Ensembl release 102
Supplementary files format and content: csv: comma-separated table with DEseq2 normalized count
Supplementary files format and content: txt: tab-delimited table of DESeq2 results

value: nub>mRFP; ecd-RNAi

value: ecd RNAi


title: Parental cells under normoxia

city: New Taipei City

first: Shaochen

last: Lee

address: 510 Zhongzheng Rd., Xinzhuang Dist.

department: School of Medicine

country: Taiwan

institute: FuJen Catholic University

description: NN

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

label: Biotin

source_name: culture cells

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

growth_protocol: The cells were maintained in DMEM medium supplemented with 10% (v/v) FBS, 100 units/ml penicillin, and 100 ug/ml streptomycin under 5% CO2 with 100% humidity at 37 degree

extract_protocol: RNA was extracted with Trizol reagent

treatment_protocol: The cancer stem-like cells were derived from parental A2058 cells by continuing selection using 100 uM carmustine for 6 months

tag: phenotype

value: parental

value: normoxia


title: Rep_late_rep3_H3K4me1

value: Liver

value: Late reprogrammed cells

value: Wild type


title: nub>mRFP; ecd-RNAi replicate 2


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 60

city: Hamburg

first: Swenja

last: Gödicke

address: Martinistrasse 52

institute: Research Institute Children‘s Cancer Center Hamburg

description:
205689130036_R07C01
60_high

hyb_protocol: 100-500 ng DNA were used for bisulfite conversion with the EZ DNA Methylation Kit (Zymo Research). Afterwards, the DNA Clean & Concentrator-5 (Zymo Research) and the Infinium HD FFPE DNA Restore Kit (Illumina) were used to clean and restore the converted DNA.

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

label: Cy5 and Cy3

source_name: Posterior fossa

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was isolated from FFPE tissue using the ReliaPrep™ FFPE gDNA Miniprep System (Promega) according to manufacturer’s instructions.

value: Posterior fossa ependymoma


title: genomic DNA from routine diagnostics of posterior fossa type A ependymoma case 60

description:
201959750082_R08C01
60_overall


title: genomic DNA from low cell density areas of posterior fossa type A ependymoma case 61

description:
205689130014_R04C01
61_low


title: genomic DNA from low cell density areas of posterior fossa type A ependymoma case 55

description:
205134980017_R01C01
55_low1


title: genomic DNA from routine diagnostics of posterior fossa type A ependymoma case 61

description:
204788480074_R04C01
61_overall


title: genomic DNA from low cell density areas of posterior fossa type A ependymoma case 60

description:
205689130036_R06C01
60_low


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 61

description:
205689130014_R05C01
61_high


title: Serum_Control_1w_rep1

description: gene expression in serum of 7-week-old mouse

value: 7 weeks

value: Serum


title: Cancer stem-like under hypoxia

description: BRX

tag: cell line

value: Cancer stem-like

value: hypoxia


title: nub>mRFP; ecd-RNAi replicate 3


title: Rep_intermed_rep2_H3K4me1

value: Intermediately reprogrammed cells

value: AAV8-TBG-Cre injected; treated with DDC for 8-9 weeks


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 55, fourth sample

description:
205134980017_R02C01
55_high1


title: Cancer stem-like under normoxia

description: BRN


title: Rep_late_rep2_H3K4me1


title: Parental cells under hypoxia

description: NX


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 55, second sample

description:
206238130100_R07C01
55_high2


title: nub>mRFP; ecd-RNAi replicate 1

value: Wing disc, L3


title: genomic DNA from low cell density areas of posterior fossa type A ependymoma case 54, third sample

description:
206238130100_R01C01
54_low3


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 55, third sample

description:
206238130100_R08C01
55_high3


title: genomic DNA from low cell density areas of posterior fossa type A ependymoma case 54, second sample

description:
206238130091_R08C01
54_low2


title: nub>mRFP replicate 4

value: nub>mRFP

value: no treatment


title: genomic DNA from low cell density areas of posterior fossa type A ependymoma case 54

description:
205134980017_R03C01
54_low1


title: Rep_late_rep1_H3K4me1


title: Rep_intermed_rep1_H3K4me1


title: genomic DNA from low cell density areas of posterior fossa type A ependymoma case 54, fourth sample

description:
206238130100_R02C01
54_low4


title: nub>mRFP replicate 2


title: genomic DNA from low cell density areas of posterior fossa type A ependymoma case 55, second sample

description:
206238130100_R06C01
55_low2


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 54, fourth sample

description:
206238130100_R05C01
54_high4


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 54, second sample

description:
206238130100_R03C01
54_high2


title: Rep_early_rep2_H3K4me1

value: Early reprogrammed cells


title: Hep_rep2_H3K4me1

value: Hepatocyte

value: AAV8-TBG-Cre injected; harvested without DDC treatement


title: genomic DNA from low cell density areas of posterior fossa type A ependymoma case 51

description:
205118950108_R03C01
51_low


title: genomic DNA from routine diagnostics of posterior fossa type A ependymoma case 51

description:
201959750082_R05C01
51_overall


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 54, third sample

description:
206238130100_R04C01
54_high3


title: nub>mRFP replicate 1


title: nub>mRFP replicate 3


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 54

description:
205134980017_R04C01
54_high1


title: MRC0010 Adeno_6

city: Cambridge

first: Marc

last: Sze

state: MA

address: 320 Bent Street

institute: Merck

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using Cell Ranger Software (v3.0.0)
Single-Cell RNA-seq reads were mapped to the human genome (GRCh38) using CellRanger and then processed through Seurat v3.0. Cells with mitochondria percentage over 10% or extreme unique gene totals (less than 500 or over 5,000 per cell) were removed from the analysis. The data after QC inspection was then normalized using sctransform, and all libraries were merged after batch effect removal through Harmony. Following the standard protocol provided by Seurat authors, principal components were computed and used for the UMAP dimensionality reduction. Cell clusters were identified at resolution 0.3 and annotated based on prior knowledge. One cluster was labeled as proliferating cells due to high expression of cell-cycle regulation genes such as STMN1. Two clusters with low cell count were expressing markers of more than one primary cell type and were removed from downstream analysis.
Assembly: GRCh38
Supplementary files format and content: .rds files

source_name: lung

extract_protocol:
All tissue samples from 9 patients for the scRNA sequencing (cohort A) were obtained from Brigham and Women’s Hospital, with patient consent approved by the Institutional Review Board protocol DFCI #98-063. LADC samples from a cohort B of 7 patients for IMC were purchased from commercial suppliers with patient informed consents. Tumors (T) or Adjacent Non-Tumor (ANT) tissues from cohort A were minced with scissors and digested with a human tumor dissociation kit (Miltenyi Biotec, 130-095-929) as per the manufacturer’s protocol with some modifications. For digesting lung samples for MRC001-005, the digestion cocktail from the kit was used, whereas the digestion cocktail with the addition of 0.8 mg/mL dispase II (Sigma, 4942078001) was used to digest the rest of samples.
Sorted viable cells were processed by Chromium Single cell 3′ Reagent v3 kits (10XGenomics, 120234) to synthesis single cell cDNAs and prepare barcoded libraries per as the manufacturer’s protocol. Sorted live cells were suspended into a cell density at around 1 million cells/mL in 0.1% BSA of PBS. To minimize doublet percentages, 4000 cells for donor MRC001-003 or 6000 cells for the remaining donors were loaded into each lane of a 10X chip. Cells were then partitioned into single-cell gel beads in emulsions (GEMs) inside the Chromium instrument, where full-length cDNA synthesis occurred. Cleaned-up cDNAs were then amplified, fragmented, and attached with 5′-adaptor and sample index. Libraries were sequenced using a 150 bp paired-end configuration.

tag: group

value: Tumor

value: lung


title: MRC0010 Adeno_7

description: 10x Genomics


title: MRC0010 Adeno_4

description: 10x Genomics


title: Hep_rep1_H3K4me1

value: Liver


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 51

description:
205118950108_R04C01
51_high


title: genomic DNA from low cell density areas of posterior fossa type A ependymoma case 49, second sample

description:
206359150141_R02C01
49_low2


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 49, second sample

description:
206359150141_R04C01
49_high2


title: MRC0010 Adeno_5

description: 10x Genomics


title: genomic DNA from routine diagnostics of posterior fossa type A ependymoma case 49

description:
205724780156_R03C01
49_overall


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 49

description:
206359150141_R03C01
49_high1


title: MRC0010 Adeno_3

description: 10x Genomics


title: genomic DNA from low cell density areas of posterior fossa type A ependymoma case 48

description:
205689130014_R06C01
48_low


title: Rep_early_rep1_H3K4me1

value: Wild type


title: genomic DNA from routine diagnostics of posterior fossa type A ependymoma case 48

description:
204860510018_R01C01
48_overall

value: Posterior fossa ependymoma


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 48

description:
205689130014_R07C01
48_high


title: genomic DNA from low cell density areas of posterior fossa type A ependymoma case 47

description:
206359150140_R04C01
47_low


title: MRC0010 Adeno_2

description: 10x Genomics


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 47

description:
206359150140_R05C01
47_high1


title: MRC0010 Adeno ANT_8

description: 10x Genomics

value: Adjacent Non-Tumor


title: genomic DNA from low cell density areas of posterior fossa type A ependymoma case 49

description:
206359150141_R01C01
49_low1


title: MRC0010 Adeno_1

description: 10x Genomics


title: MRC0010 Adeno ANT_7

description: 10x Genomics


title: genomic DNA from routine diagnostics of posterior fossa type A ependymoma case 46

description:
201959750153_R08C01
46_overall


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 47, second sample

description:
206359150140_R06C01
47_high2


title: genomic DNA from low cell density areas of posterior fossa type A ependymoma case 46

description:
205689130036_R08C01
46_low


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 46

description:
205689130061_R01C01
46_high


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 42

description:
205118950092_R07C01
42_high


title: genomic DNA from low cell density areas of posterior fossa type A ependymoma case 42

description:
205118950092_R06C01
42_low


title: MRC0010 Adeno ANT_6

description: 10x Genomics


title: MRC0010 Adeno ANT_5

description: 10x Genomics


title: MRC0010 Adeno ANT_4

description: 10x Genomics


title: MRC0010 Adeno ANT_3

description: 10x Genomics


title: MRC009 Adeno_8

description: 10x Genomics


title: genomic DNA from routine diagnostics of posterior fossa type A ependymoma case 42

description:
201959740229_R03C01
42_overall


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 41, third sample

description:
206359150141_R08C01
41_high3


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 41, fourth sample

description:
206359150141_R07C01
41_high4


title: genomic DNA from low cell density areas of posterior fossa type A ependymoma case 41, third sample

description:
206359150141_R05C01
41_low3


title: MRC0010 Adeno ANT_2

description: 10x Genomics


title: genomic DNA from low cell density areas of posterior fossa type A ependymoma case 41

description:
205134980017_R07C01
41_low1


title: genomic DNA from routine diagnostics of posterior fossa type A ependymoma case 41

description:
205310760090_R04C01
41_overall


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 41

description:
205134980017_R08C01
41_high1


title: genomic DNA from low cell density areas of posterior fossa type A ependymoma case 41, second sample

description:
206359150141_R06C01
41_low2


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 41, second sample

description:
205689130014_R03C01
41_high2


title: MRC0010 Adeno ANT_1

description: 10x Genomics


title: genomic DNA from low cell density areas of posterior fossa type A ependymoma case 38, second sample

description:
206238130091_R03C01
38_low2


title: genomic DNA from low cell density areas of posterior fossa type A ependymoma case 38

description:
206238130091_R02C01
38_low1


title: MRC009 Adeno_7

description: 10x Genomics


title: HI.3615.002.RPI8.29_hab

city: Montreal

first: Gustavo

last: Turecki

state: Quebec

address: 6875 Boulevard LaSalle

department: Psychiatry

country: Canada

institute: McGill University

data_processing:
Adapters and low-quality bases (Phred score < 15) were trimmed with cutadapt v2.10
The exceRpt pipeline v4.6.3 with the options STAR_alignEndsType=EndToEnd, STAR_outFilterMismatchNmax=0, and STAR_outFilterMatchNmin=16 was used to align trimmed reads to the genome (GRCh38) and quantify the snoRNAs into counts
Only snoRNAs with greater than or equal to 10 counts in 70% of the samples within either the control or MDD group were retained for later steps
DESeq2 v1.38.1 was used to normalize the counts with the median of ratios method and to perform differential expression analysis on our dataset
Assembly: GRCh38

source_name: Habenula

extract_protocol:
RNA was extracted from all brain samples using a combination of the miRNeasy Mini kit and the RNeasy MinElute Cleanup kit (Qiagen), with DNase treatment, and divided into small (<200 nt) and large (>200 nt) fractions. RNA quality was assessed using the Agilent 2200 Tapestation.
Small RNA libraries were prepared from the small RNA fraction, using the Illumina TruSeq Small RNA protocol following the manufacturer’s instructions.
RNA-seq. All samples were sequenced at the McGill University and Genome Quebec Innovation Centre (Montreal, Canada) using Illumina HiSeq2000 with 50nt single-end reads

value: Habenula

value: Control


title: HI.3615.002.RPI6.27_hab


title: HI.3615.002.RPI5.26_hab


title: HI.3615.002.RPI9.30_hab


title: HI.3615.002.RPI7.28_hab


title: MRC009 Adeno_5

description: 10x Genomics


title: genomic DNA from low cell density areas of posterior fossa type A ependymoma case 37

description:
206486310150_R06C01
37_low1


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 37, second sample

description:
206486310018_R01C01
37_high2


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 37, third sample

description:
206486310018_R02C01
37_high3


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 38

description:
206238130091_R04C01
38_high


title: genomic DNA from low cell density areas of posterior fossa type A ependymoma case 27, second sample

description:
206350360172_R08C01
27_low2


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 37

description:
206486310150_R08C01
37_high1


title: genomic DNA from routine diagnostics of posterior fossa type A ependymoma case 38

description:
204316900155_R03C01
38_overall


title: MRC009 Adeno_6

description: 10x Genomics


title: MRC009 Adeno_4

description: 10x Genomics


title: genomic DNA from low cell density areas of posterior fossa type A ependymoma case 37, second sample

description:
206486310150_R07C01
37_low2


title: genomic DNA from low cell density areas of posterior fossa type A ependymoma case 27

description:
205134980017_R05C01
27_low1


title: HI.3615.002.RPI4.25_hab


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 27, second sample

description:
206350360188_R01C01
27_high2


title: MRC009 Adeno_3

description: 10x Genomics


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 27

description:
205134980017_R06C01
27_high1


title: HI.3615.002.RPI39.24_hab


title: genomic DNA from low cell density areas of posterior fossa type A ependymoma case 26

description:
206238130091_R05C01
26_low


title: HI.3615.002.RPI3.23_hab


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 26, second sample

description:
206238130091_R07C01
26_high2


title: MRC009 Adeno_2

description: 10x Genomics


title: HI.3615.002.RPI2.22_hab


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 26

description:
206238130091_R06C01
26_high1


title: Male_placenta_SED_Con_1

city: Little Rock

first: Meghan

middle: Lynne

last: Ruebel

state: AR

address: 15 Children's Way

institute: USDA-ARS/Arkansas Childrens Hospital

description: Gene expression data from dpc 18.5 placenta from dams provide with a volunatary running well 10 weeks prior to concenption and through pregnancy (EX) or without a running wheel (SED)

hyb_protocol: Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Mouse Genome 230 2.0 for 16 h at 45ºC in the hybridization oven set at 60 rpm.

scan_protocol: The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000

data_processing: .CEL files generated using GeneChip Command Console (Affymetrix). Data analysis was performed using functions in the affy, limma and sva packages in R.  CEL files were processed using RMA algorithm for background adjustment, normalization, and log2-transformation of perfect-match values. Genes were filtered based on ±1.4-fold change and p-value < 0.05

label: biotin

source_name: dpc 18.5  placenta Sedentary group

label_protocol: First- and second- strand cDNA synthesis (from 5 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions

extract_protocol: Total RNA from individual placentas from SED and EX dams were isolated using TRI Reagent and purified using RNeasy columns (Qiagen) including on-column deoxyribonuclease digestion

treatment_protocol: Dams were provided with a volunatary running well 10 weeks prior to concenption and through pregnancy (EX) or without a running wheel (SED)  and placentas were collected at late pregnancy (dpc 18.5)

tag: tissuse

value: Placenta

value: Male

tag: treatment group

value: Sedentary


title: Female_placenta_EX_Con_1

source_name: dpc 18.5 placenta Exercise group

value: Female

value: Exercise


title: MRC009 Adeno_1

description: 10x Genomics


title: Male_placenta_EX_Con_1


title: genomic DNA from routine diagnostics of posterior fossa type A ependymoma case 26

description:
204792170076_R08C01
26_overall


title: Female_placenta_SED_Con_1


title: HI.3615.002.RPI11.21_hab

value: Case


title: MRC009 Adeno ANT_8

description: 10x Genomics


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 22

description:
205689130090_R03C01
22_high


title: HI.3615.002.RPI10.20_hab


title: genomic DNA from low cell density areas of posterior fossa type A ependymoma case 21

description:
205118950108_R01C01
21_low


title: Male_placenta_SED_Con_3


title: Male_placenta_SED_Con_2


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 21

description:
205118950108_R02C01
21_high


title: MRC009 Adeno ANT_7

description: 10x Genomics


title: HI.3615.001.RPI9.19_hab


title: Female_placenta_SED_Con_3


title: Female_placenta_EX_Con_3


title: MRC009 Adeno ANT_6

description: 10x Genomics


title: genomic DNA from low cell density areas of posterior fossa type A ependymoma case 18

description:
205689130029_R05C01
18_low


title: Male_placenta_EX_Con_3


title: genomic DNA from low cell density areas of posterior fossa type A ependymoma case 22

description:
205689130090_R02C01
22_low


title: Female_placenta_SED_Con_2


title: Female_placenta_EX_Con_2


title: Male_placenta_EX_Con_2


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 18

description:
205689130029_R06C01
18_high


title: MRC009 Adeno ANT_5

description: 10x Genomics


title: genomic DNA from routine diagnostics of posterior fossa type A ependymoma case 18

description:
201959740230_R08C01
18_overall


title: HI.3615.001.RPI6.17_hab


title: genomic DNA from low cell density areas of posterior fossa type A ependymoma case 11

description:
205735130056_R03C01
11_low


title: MRC009 Adeno ANT_4

description: 10x Genomics


title: genomic DNA from routine diagnostics of posterior fossa type A ependymoma case 21

description:
201959750061_R06C01
21_overall


title: genomic DNA from low cell density areas of posterior fossa type A ependymoma case 10

description:
205118950066_R06C01
10_low


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 11

description:
205735130056_R04C01
11_high


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 10

description:
205118950066_R07C01
10_high


title: HI.3615.001.RPI5.16_hab


title: MRC009 Adeno ANT_3

description: 10x Genomics


title: genomic DNA from low cell density areas of posterior fossa type A ependymoma case 4

description:
206359150140_R07C01
04_low


title: HI.3615.001.RPI48.15_hab


title: HI.3615.001.RPI8.18_hab


title: genomic DNA from posterior fossa type A epenymoma R12 relapse

description:
R12_relapse
206644430084_R04C01

tag: who-grade

tag: age (years)

value: m

tag: extent of resectoin

value: STR

tag: material

value: FFPE

tag: time to first relapse (years)


title: genomic DNA from high cell density areas of posterior fossa type A ependymoma case 4

description:
206359150140_R08C01
04_high

tag: tissue


title: MRC009 Adeno ANT_2

description: 10x Genomics


title: genomic DNA from posterior fossa type A epenymoma R12 primary

description:
R12_primary
204792170076_R08C01

tag: Sex


title: MRC009 Adeno ANT_1

description: 10x Genomics


title: HI.3615.001.RPI46.13_hab

tag: treatment


title: genomic DNA from posterior fossa type A epenymoma R11 relapse

description:
R11_relapse
206238130101_R01C01


title: MRC008 Adeno_7

description: 10x Genomics

value: Tumor


title: genomic DNA from posterior fossa type A epenymoma R10 relapse

description:
R10_relapse
206648960060_R04C01

value: f

value: GTR


title: genomic DNA from posterior fossa type A epenymoma R9 relapse

description:
R9_relapse
206144080139_R06C01


title: genomic DNA from posterior fossa type A epenymoma R11 primary

description:
R11_primary
206359150140_R04C01


title: HI.3615.001.RPI43.11_hab


title: MRC008 Adeno_6

description: 10x Genomics

value: lung


title: MRC008 Adeno_5

description: 10x Genomics


title: genomic DNA from posterior fossa type A epenymoma R10 primary

description:
R10_primary
205134980017_R05C01


title: genomic DNA from posterior fossa type A epenymoma R9 primary

description:
R9_primary
204894630046_R07C01


title: HI.3615.001.RPI41.10_hab


title: genomic DNA from posterior fossa type A epenymoma R8 primary

description:
R8_primary
201465900042_R07C01


title: MRC008 Adeno_4

description: 10x Genomics


title: genomic DNA from posterior fossa type A epenymoma R7 relapse

description:
R7_relapse
205756370079_R05C01


title: HI.3615.001.RPI40.9_hab


title: MRC008 Adeno_3

description: 10x Genomics


title: MRC008 Adeno_2

description: 10x Genomics


title: genomic DNA from posterior fossa type A epenymoma R7 primary

description:
R7_primary
203020780099_R06C01


title: HI.3615.001.RPI47.14_hab


title: HI.3615.001.RPI37.8_hab


title: HI.3615.001.RPI44.12_hab


title: HI.3615.001.RPI12.7_hab


title: Genomic DNA from ependymoma 2022

first: Michael

last: Bockmayr

address: Martinistr. 52

department: Pediatric Hematology and Oncology

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip or the Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using the iScan System and the standard recommended Illumina scanner setting.

data_processing:
Statistical analysis was performed using the minfi package version 1.46.0 with the statistical programming language R version 4.3.0.
Average beta-values after combining arrays and normalization using the Noob method.

source_name: ependymoma 2022

label_protocol: Standard Illumina protocol

extract_protocol: DNA was isolated using the ReliaPrep™ FFPE gDNA Miniprep System (Promega) according to manufacturer’s instructions. About 100-500 ng DNA was used for bisulfite conversion by the EZ DNA Methylation Kit (Zymo Research). The DNA Clean & Concentrator-5 (Zymo Research) and the Infinium HD FFPE DNA Restore Kit (Illumina) were employed to clean and restore the converted DNA.

value: M

tag: age

tag: localization

value: spinal

tag: patho diagnosis

value: Ependymoma II

tag: classification result v12

tag: classification score


title: Genomic DNA from ependymoma 2023

source_name: ependymoma 2023

value: Anaplastic ependymoma III


title: MRC008 Adeno_1

description: 10x Genomics


title: Genomic DNA from ependymoma 2020

source_name: ependymoma 2020


title: HI.3615.001.RPI11.6_hab

value: Habenula

value: Control


title: genomic DNA from posterior fossa type A epenymoma R8 relapse

description:
R8_relapse
203985930014_R08C01


title: Genomic DNA from ependymoma 2018

source_name: ependymoma 2018

value: F


title: Genomic DNA from ependymoma 2019

source_name: ependymoma 2019


title: MRC008 Adeno ANT CD45+_4

description: 10x Genomics

value: Adjacent Non-Tumor


title: Genomic DNA from ependymoma 2017

source_name: ependymoma 2017


title: Genomic DNA from ependymoma 2014

source_name: ependymoma 2014


title: MRC008 Adeno ANT CD45+_3

description: 10x Genomics


title: Genomic DNA from ependymoma 2013

source_name: ependymoma 2013


title: HI.3607.008.RPI44.3_hab


title: MRC008 Adeno ANT CD45+_2

description: 10x Genomics


title: Genomic DNA from ependymoma 2016

source_name: ependymoma 2016


title: HI.3607.008.RPI45.4_hab


title: Genomic DNA from ependymoma 2015

source_name: ependymoma 2015


title: HI.3615.001.RPI1.5_hab


title: Genomic DNA from ependymoma 2011

source_name: ependymoma 2011


title: HI.3607.008.RPI43.2_hab


title: MRC007 Adeno_8

description: 10x Genomics


title: Genomic DNA from ependymoma 2010

source_name: ependymoma 2010


title: MRC008 Adeno ANT CD45+_1

description: 10x Genomics


title: Genomic DNA from ependymoma 2012

source_name: ependymoma 2012


title: Genomic DNA from ependymoma 2009

source_name: ependymoma 2009


title: HI.3590.008.RPI37.1_hab

source_name: Habenula


title: MRC007 Adeno_7

description: 10x Genomics

source_name: lung


title: Genomic DNA from ependymoma 2008

source_name: ependymoma 2008


title: MRC007 Adeno_6

description: 10x Genomics


title: Genomic DNA from ependymoma 2006

source_name: ependymoma 2006


title: Genomic DNA from ependymoma 2007

source_name: ependymoma 2007


title: MRC007 Adeno_5

description: 10x Genomics


title: AGS-Input

first: Peng

last: Gao

address: Wen Hua Xi Road 44

institute: Shandong University

data_processing:
The library was denatured with 0.1M NaOH to generate single-stranded DNA molecules, and loaded onto channels of the flow cell at 8pM concentration, amplified in situ using TruSeq Rapid SR cluster kit (#GD-402-4001, Illumina). Sequencing was carried out by running 100 cycles on Illumina HiSeq 2000 according to the manufacturer’s instructions.
After the sequencing platform generated the sequencing images, the stages of image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8). After passing Solexa CHASTITY quality filter, the clean reads were aligned to human reference genome UCSC build hg19 using BOWTIE (V2.1.0). Aligned reads were used for peak calling of the ChIP regions using MACS V1.4.0. Statistically significant ChIP-enriched regions (peaks) were identified by comparison two samples, using a p-value threshold of 10-5. Then the peaks in each sample were annotated by the nearest gene using the newest UCSC RefSeq database.
Assembly: hg19

source_name: AGS

growth_protocol: RPMI-1640, 10% fetal bovine serum. Cells were cultured at 37℃ at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated.
10 ng DNA of each sample was converted to phosphorylated blunt-ended with T4 DNA polymerase, Klenow polymerase and T4 polymerase (NEB); An ‘A’ base was added to the 3' end of the blunt phosphorylated DNA fragments using the polymerase activity of Klenow (exo minus) polymerase (NEB); Illumina's genomic adapters were ligated to the A tailed DNA fragments; PCR amplification was performed to enrich ligated fragments using Phusion High Fidelity PCR Master Mix with HF Buffer (Finnzymes Oy). The enriched product of ~200-500 bp was cut out from gel and purified.

tag: cell line

value: AGS

tag: antibody


title: Genomic DNA from ependymoma 2004

source_name: ependymoma 2004


title: AGS-IP

value: anti-CREB1 antibody (Cell Signaling, MA, USA, Cat# 9197, rabbit monoclonal)


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1945]

city: Berlin

first: Anna

last: Dolnik

address: Augustenburger Platz 1

department: Campus Virchow-Klinikum (CVK)

institute: Charité Universitätsmedizin Berlin

data_processing:
base-calling was performed according Illumina recommendations bcl2fastq-1.8.4.
50 bp single-end reads (Illumina) were aligned to reference genome hg38 (ENSEMBL) and Homo_sapiens.GRCh38.98.gtf.-transcriptome annotation release (ENSEMBL) using STAR two-pass mode ( star 2.7).
GRCh38.98.gtf.-transcriptome annotation release (ENSEMBL, release 98) was used for quantification, performed by RSEM 1.3.0, followed by TPM normalisation in RSEM-1.3.0.
Assembly: hg38
Supplementary files format and content: output of rsem package: txt table with normalized counts

source_name: CD138+  cells or bone marrow with CD138+ over 75%

extract_protocol:
RNA extraction was performed using AllPrep Kit (Qiagen) according manufacturer instructions.
Library was generated using TruSeq RNA Exome Kit (Illumina) followed by sequencing on NextSeq (Illumina).

tag: cell type

tag: subject status

value: multiple myeloma relapse


title: Genomic DNA from ependymoma 2002

source_name: ependymoma 2002


title: MRC007 Adeno_4

description: 10x Genomics

tag: group


title: MRC007 Adeno_3

description: 10x Genomics


title: Genomic DNA from ependymoma 2000

source_name: ependymoma 2000


title: Genomic DNA from ependymoma 1999

source_name: ependymoma 1999


title: Genomic DNA from ependymoma 1998

source_name: ependymoma 1998

value: Low grade glioma


title: MRC007 Adeno_2

description: 10x Genomics


title: Input_HCT116_PANDAR282W

city: Shanghai

first: yangfei

last: Xing

state: Shanghai

address: 197 Rui Jin Er Road

department: Shanghai Institute of Hematology

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
ChIP-seq reads were aligned to the hg38 genome using bowtie 2.2.9
Enriched p53 peaks relative to a background input were called using MACS2
The read counts within 500 bases of each peak summit were extracted using the HOMER suite and used for motif analysis of p53 binding
The makeUCSCfile package from the HOMER suite was used to generate bigWig and bedGraph files
Genome_build: hg38
Supplementary_files_format_and_content: bigwig format for visualization in IGV or washU Genome Browser

source_name: p53-null HCT116 cells

growth_protocol: p53-null HCT116 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM; Gibco) supplemented with 10% (v/v) fetal bovine serum (FBS; Gibco), L-glutamine, and appropriate antibiotics. Cell cultures were maintained in a 5% CO2 humidified incubator at 37℃.

extract_protocol: Cells were cross-linked with 1% formaldehyde for 8 min at room temperature, and quenched in 125 mM glycine for 5 min. Cells were scrapped and lysed with ChIP buffer A (Cell Signal Technology, 7006) supplemented with protease inhibitors cocktail (Target Mol, C0001). The nuclear pellet was spin down and fragmented to 100–300 bp using Micrococcal Nuclease (Cell Signal Technology, 10011) for 20 min at 37°C in ChIP Buffer B (Cell Signal Technology, 7007), followed by sonication using Bioruptor Pico SOP (30 s on, 30 s off, 3 cycles). After centrifugation at 16000 g for 10 min, the supernatant is collected and incubated with 3 μg p53 antibody DO1 (Abcam, ab1101) or mouse immunoglobulin G (Santa Cruz Biotechnology, sc-2025) overnight at 4°C. The immunoprecipitation reactions were transferred to protein G agarose (Invitrogen, 15920-010) at 4°C for 1 h. The immunocomplexes were then washed with high salt buffer (50 mM HEPES pH 7.5, 500 mM NaCl, 1 mM EDTA, 0.1% Na-Deoxycholate, 1% TritonX-100) for 3 times and TE buffer (10 mM Tris-HCl pH 8.0, 2 mM EDTA) for twice, followed by elution with 50 μl elution buffer (10 mM Tris-HCl pH 8.0). Cross-linking was reversed at 65°C for 4 h, followed incubation with proteinase K and RNAase A. DNA was purified using QIAquick® PCR Purification Kit (QIAGEN, 28106).   ChIP-seq libraries were prepared using MicroPlex Library Preparation Kit v2 (Diagenode C05010014) and the Agencourt AMPure XP system (Beckman Coulter A63880) was used to select 350–550 bp libraries. Sequencing was carried out on the Illumina MiSeq and HiSeq platforms.

treatment_protocol: p53-null HCT116 cells were stably expressed wild-type p53 or mutant p53 followed by 24 h ATO treatment (PANDAs).

value: p53-null HCT116 cells

tag: chip antibody

value: treated with ATO for 24 hours

tag: genotype

value: stably expressing mutant p53(R282W)


title: Genomic DNA from ependymoma 1995

source_name: ependymoma 1995

value: Subependymoma


title: MRC007 Adeno ANT_6

description: 10x Genomics

value: lung


title: Input_HCT116_PANDAM133T

value: stably expressing mutant p53(M133T)


title: MRC007 Adeno_1

description: 10x Genomics

value: Tumor


title: HCT116_PANDAR282W


title: Genomic DNA from ependymoma 1993

source_name: ependymoma 1993

value: M

value: spinal


title: Input_HCT116_p53WT

value: untreated

value: stably expressing WT p53


title: HCT116_PANDAM133T


title: MRC007 Adeno ANT_5

description: 10x Genomics


title: HCT116_p53WT


title: Genomic DNA from ependymoma 2005

source_name: ependymoma 2005

value: Ependymoma II


title: Genomic DNA from ependymoma 2003

source_name: ependymoma 2003


title: Genomic DNA from ependymoma 1989

source_name: ependymoma 1989


title: Genomic DNA from ependymoma 1990

source_name: ependymoma 1990


title: MRC007 Adeno ANT_4

description: 10x Genomics

source_name: lung

value: Adjacent Non-Tumor


title: Genomic DNA from ependymoma 1988

source_name: ependymoma 1988


title: MRC007 Adeno ANT_3

description: 10x Genomics


title: 163_OE

city: Barcelona

first: Xavier

last: Santamaria

state: Barcelona

address: Av. Diagonal 463 Bis Pl. 4

country: Spain

institute: Bioliquid Inovative Genetics SLU

description:
Sample ID:
163

data_processing:
Quality of reads was checked with FastQC software23. Preprocessing of reads was performed with fastx-toolkit24 and specific aScidea perl scripts property of aScidea S.L. (Ascidea Computational Biology Solutions, S.L., Sant Cugat, Spain) to filter regions of low quality. Raw reads with good quality  were mapped using Tophat_2.1.125 and Bowtie2_2.2.826.
The Homo sapiens genome version GRCh38 was used as reference. Genomic annotations were obtained from Illumina iGenomes27.
The transcript isoform level and gene level counts were calculated and fragments per kilobase per million reads mapped (FPKM) were normalized using Cufflinks_2.2.1 software28.
Resulting p-values were adjusted using Benjamini and Hochberg method29 to obtain false discovery rate (FDR). Lists of differentially expressed genes (DEGs) were filtered by ln(fold change)(FC) > 1 and q-value < 0.05. Main statistical analyses were performed using the Bioconductor Project30.
Different comparisons were done using CLC_Genomics Workbench 8.0.2 software31. The comparisons made were as follows: DIE (n = 4) versus control (n = 19); OE (n = 8) versus control (n = 19); Adeno (n = 6) versus control (n = 19); DOA (DIE + OE + Adeno; n = 18) versus control (n = 19).
Genome_build: GRCh38
Supplementary_files_format_and_content: txt files containing the read distribution in each sample and the bamstats per sample
Supplementary_files_format_and_content: xlsx. File contains the fragments per kilobase million (fpkm) per sample and per each transcript

source_name: OE

growth_protocol: endometrial biopsies were obtained by a Cornier Pipelle

extract_protocol:
High Pure FFPET-RNA Isolation Kit (Roche) following manufacturer’s instructions.
Library preparation was obtained using TruSeq_Stranded Total_RNA_LT, w/ Ribo-Zero Gold, Set_A kit. According to standard protocols, purified amplicons were pooled in equimolar amounts and paired-end sequenced via flow cell at 2x50nt on an Illumina Hi-Seq-2000 platform

treatment_protocol: Samples were fixed with paraformaldehyd 4% ON and embedded in paraffin

value: endometrium

tag: disease state

value: OE

tag: mesntrual cycle phase

value: SE

tag: history of endometriosis

value: no

tag: hypermenorrhea

value: yes

tag: dysmenorrhea

tag: fertility

tag: polyps

tag: myomas

tag: laparoscopy

tag: hormones

tag: smoker


title: 133_OE

description:
Sample ID:
133

tag: tissue

tag: age


title: Genomic DNA from ependymoma 1997

source_name: ependymoma 1997

tag: Sex

tag: localization

tag: patho diagnosis

tag: classification result v12

tag: classification score


title: Genomic DNA from ependymoma 1987

source_name: ependymoma 1987


title: MRC007 Adeno ANT_2

description: 10x Genomics

tag: group


title: Genomic DNA from ependymoma 1985

source_name: ependymoma 1985


title: Genomic DNA from ependymoma 1986

source_name: ependymoma 1986

value: F

value: Ependymaler Tumor


title: Genomic DNA from ependymoma 1992

source_name: ependymoma 1992


title: Genomic DNA from ependymoma 1984

source_name: ependymoma 1984


title: Genomic DNA from ependymoma 1983

source_name: ependymoma 1983

value: V. a. niedriggradigen ependymalen Tumor


title: MRC007 Adeno ANT_1

description: 10x Genomics

value: lung


title: 135_OE

description:
Sample ID:
135

tag: disease state

tag: mesntrual cycle phase

tag: history of endometriosis


title: MRC006 Adeno_8

description: 10x Genomics


title: 142_OE

description:
Sample ID:
142

value: ME

tag: hypermenorrhea

tag: dysmenorrhea

tag: fertility


title: Genomic DNA from ependymoma 1981

source_name: ependymoma 1981


title: Genomic DNA from ependymoma 1980

source_name: ependymoma 1980


title: Genomic DNA from ependymoma 1982

source_name: ependymoma 1982


title: Genomic DNA from ependymoma 1979

source_name: ependymoma 1979

value: Papillary ependymoma


title: 137_OE

description:
Sample ID:
137

value: PE

tag: polyps

tag: myomas

tag: laparoscopy


title: MRC006 Adeno_6

description: 10x Genomics

value: Tumor

tag: tissue


title: Genomic DNA from ependymoma 1991

source_name: ependymoma 1991

value: M

tag: age

value: spinal

value: Anaplastic ependymoma III


title: MRC006 Adeno_7

description: 10x Genomics


title: Genomic DNA from ependymoma 1978

source_name: ependymoma 1978

tag: Sex

value: Tanycytic ependymoma II


title: 149_OE

description:
Sample ID:
149

value: endometrium

tag: hormones

tag: smoker


title: Genomic DNA from ependymoma 1976

source_name: ependymoma 1976

tag: localization

value: posterior fossa

tag: patho diagnosis

value: Ependymoma II

tag: classification result v12


title: MRC006 Adeno_5

description: 10x Genomics

source_name: lung

tag: group


title: 151_OE

description:
Sample ID:
151

tag: disease state

value: OE

tag: mesntrual cycle phase

value: SE

value: no


title: Genomic DNA from ependymoma 1977

source_name: ependymoma 1977

tag: classification score


title: MRC006 Adeno_4

description: 10x Genomics


title: Genomic DNA from ependymoma 1974

source_name: ependymoma 1974

value: F

value: Zelluläres Ependymoma II


title: 148_OE

description:
Sample ID:
148

source_name: OE

tag: history of endometriosis

value: yes

tag: hypermenorrhea

tag: dysmenorrhea


title: 143_DIE

description:
Sample ID:
143

source_name: DIE

value: DIE

tag: fertility

tag: polyps

tag: myomas


title: Genomic DNA from ependymoma 1973

source_name: ependymoma 1973

tag: age

value: Subependymoma


title: Genomic DNA from ependymoma 1972

source_name: ependymoma 1972


title: MRC006 Adeno_3

description: 10x Genomics

tag: tissue

value: lung


title: Genomic DNA from ependymoma 1970

source_name: ependymoma 1970


title: 130_DIE

description:
Sample ID:
130

value: PE

tag: laparoscopy

tag: hormones


title: Genomic DNA from ependymoma 1971

source_name: ependymoma 1971

tag: localization


title: Genomic DNA from ependymoma 1969

source_name: ependymoma 1969

tag: patho diagnosis


title: 234_DIE

description:
Sample ID:
234

tag: smoker


title: Genomic DNA from ependymoma 1934

source_name: ependymoma 1934

tag: Sex

value: M

tag: OS status

tag: os [months]

tag: classification result v12


title: MRC004 Adeno_7

description: 10x Genomics

tag: group

value: Tumor


title: Genomic DNA from ependymoma 1936

source_name: ependymoma 1936

value: spinal

tag: classification score


title: Genomic DNA from ependymoma 1937

source_name: ependymoma 1937

value: Anaplastic ependymoma III


title: Genomic DNA from ependymoma 1935

source_name: ependymoma 1935


title: 182_Adeno

description:
Sample ID:
182

source_name: Adeno

value: endometrium

tag: disease state

value: Adeno

tag: mesntrual cycle phase

tag: history of endometriosis

tag: hypermenorrhea

tag: dysmenorrhea


title: Genomic DNA from ependymoma 1975

source_name: ependymoma 1975

tag: age

value: Tanycytic ependymoma II


title: MRC004 Adeno_6

description: 10x Genomics

tag: tissue


title: 195_Adeno

description:
Sample ID:
195

value: ME

tag: fertility

tag: polyps

tag: myomas

tag: laparoscopy

tag: hormones


title: Genomic DNA from ependymoma 1933

source_name: ependymoma 1933

tag: Sex

tag: localization

tag: patho diagnosis

tag: OS status


title: Genomic DNA from ependymoma 1932

source_name: ependymoma 1932

tag: os [months]

tag: classification result v12

tag: classification score


title: Genomic DNA from ependymoma 1931

source_name: ependymoma 1931


title: MRC004 Adeno_4

description: 10x Genomics

source_name: lung

tag: group


title: Genomic DNA from ependymoma 1929

source_name: ependymoma 1929


title: MRC006 Adeno_2

description: 10x Genomics


title: MRC004 Adeno_3

description: 10x Genomics


title: Genomic DNA from ependymoma 1644

source_name: ependymoma 1644

value: posterior fossa

tag: resection

value: STR

value: Ependymoma III

tag: pfs status

tag: pfs [months]


title: Genomic DNA from ependymoma 1938

source_name: ependymoma 1938

value: F

tag: age

value: Ependymoma II


title: 131_DIE

description:
Sample ID:
131

source_name: DIE

tag: tissue

tag: disease state

value: DIE

tag: mesntrual cycle phase

tag: history of endometriosis

value: no

tag: hypermenorrhea

value: yes

tag: dysmenorrhea

tag: fertility

tag: smoker


title: 183_Adeno

description:
Sample ID:
183

value: PE

tag: polyps

tag: myomas

tag: laparoscopy

tag: hormones


title: MRC006 Adeno_1

description: 10x Genomics

tag: group

value: lung