title: LM289-v12-Th

status: Public on Jun 22 2020

city: Rotterdam

first: Lucia

last: Campos Carrascosa

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus Medical Center

data_processing:
RNA-Seq reads were processed by alignment to gencode v28 transcriptome using STAR aligner (v2.6.0c)
gene expression was quantified using RSEM (v1.2.14) according to
(Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 2013;29:15–21.) and (Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 2011;12:323.)
Genome_build: hg38
Supplementary_files_format_and_content: TXT file contains log2 transformed TPM counts

source_name: TIL

growth_protocol: TILs were isolated from fresh patient-derived tumor samples. CD25+ cells were positively selected using MACS and stained with CTV. CTV+CD25+ TILs were co-cultured with CTV- TILs for 3 to 5 days in vitro.

extract_protocol:
3 TIL subsets were sorted according to the expression of CD45/CD3/CD4/CD8/CTV(CD25). CD45+CD3+CD8+ TILs, CD45+CD3+CD4+CTV+ TILs and CD45+CD3+CD4+CTV- TILs were sorted directly into RLT+ lysis buffer. RNA was immediately isolated using Rneasy micro kit (Qiagen) according to manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: TILs were cultured in vitro  in the presence of αCD3/CD28 activation beads +/- αOX40_v12 antibody

value: Th

tag: cancer type

value: liver metastasis colorectal cancer

tag: treatment (days in vitro)


title: LM289-v12-Treg

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type

value: Treg


title: LM289-v12-CD8


title: LM289-ctrl-Treg

value: ctrl (5d)


title: LM289-ctrl-CD8


title: LM289-ctrl-Th


title: HCC213-v12-Treg

value: Hepatocellular carcinoma


title: control_1

status: Public on Jun 23 2020

type: RNA

city: Greifswald

first: Anke

last: Schmidt

state: MV

address: Felix-Hausdorff-Str. 2

department: Plasma Life Science

country: Germany

institute: INP Greifswald

description: SAMPLE 1

hyb_protocol: 0.6 µg of Cy3-labeled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent 8x60K custom  design (OaksLab)mouse Microarrays (Design-ID 062646) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 6x8K array slides (Scan resolution 10 µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus musculus

source_name: mouse skin, control, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Bio&Sell, Feucht, Germany). Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer.

extract_protocol: After 24 h, the animals were euthanized by cervical dislocation and the tissue from the skin areas were removed. The tissue samples for RNA and proteins were transferred directly into liquid nitrogen after sampling and stored at - 80 °C until homogenization. fresh tissues from ears were removed, snap-frozen in liquid nitrogen, and stored at -80°C. Homogenization was performed in RNA lysis buffer (Bio&Sell, Feucht, Germany) for gene expression analysis, or in RIPA buffer containing protease and phosphatase inhibitors (cOmplete Mini, phosSTOP, PMSF, Sigma-Aldrich, Traunstein, Germany) for protein validation experiments using a FastPrep-24 5G homogenizator (MP biomedicals, Heidelberg, Germany). The skin samples for histology were placed in 4% paraformaldehyde for further processing.  Paraffin blocks were cut into 5 µm-sections using a microtome to retrieve tissue sections that were stained with hematoxylin and eosin (H&E; Carl-Roth, Karlsruhe, Germany).

treatment_protocol: An atmospheric pressure argon plasma jet (kINPenMed; neoplas tools, Greifswald, Germany) was used, which ionized a flow (5 standard liters per minute) of argon gas (purity 99.9999; Air Liquide, Krefeld, Germany) at 1 MHz. Plasma treatment of wounds was performed using the tip of the plasma effluent at a constant distance of 8 mm using a autoclavable spacer. Mice were exposed to 3 s/mm² or 20 s/mm² of plasma or were left untreated (0s/mm²) and compared to controls (n=9).

tag: tissue

value: skin tissue

tag: gender

value: male

tag: treatment

value: non-treated mouse


title: HCC213-ctrl-CD8


title: LM283-v12-CD8


title: HCC213-v12-CD8


title: HCC213-ctrl-Treg


title: CRC128-v12-Th

value: colorectal cancer


title: HCC213-ctrl-Th


title: HCC213-v12-Th


title: LM283-ctrl-Treg

value: ctrl (4d)


title: CRC128-ctrl-Th

value: ctrl (3d)


title: LM283-ctrl-CD8


title: Human_HEPATOPAC_4106_female_ticlopidine_120µM_48hr [US-1421099]

city: West Point

first: Alexei

middle: A

last: Podtelezhnikov

state: PA

address: 770 Sumneytown Pike

department: Non-clinical Drug Safety

country: USA

institute: Merck & Co., Inc.

description:
Human_Hepatopac_Treatments.tar.gz
US-1421099

data_processing:
Genome alignment and gene quantitation was performed using OmicSoft Array Studio
Cleaned reads were aligned to the Rnor_6.0 and hg38 genome references using the OmicSoft Aligner with a maximum of 2 allowed mismatches
Gene level counts were determined by the RNA-Seq by expectation maximization algorithm as implemented in OmicSoft Array Studio and using Ensembl.R94 gene models
FPKM normalization was applied to RNA-Seq counts followed by log-transformation with smoothing, i.e., log10(FPKM+0.01)
Genome_build: Rnor_6.0 and hg38 genome
Supplementary_files_format_and_content: Count, FPKM

growth_protocol: HEPATOPAC cells were cultured in proprietary Maintenance Medium (containing 10% serum, part number 5032C) in a  37°C humidified incubator with 10% CO2;  other cells were cultured using standard or proprietary hepatocyte procedures.

extract_protocol:
Total RNA was purified from frozen liver or cell culture samples using the MagMAX™ Express Magnetic Particle Processor using the MagMAX™-96 for Microarrays Total RNA Isolation Kit (Thermo Fisher AM1839)
Total RNA samples were converted into cDNA libraries using the KAPA RNA HyperPrep Kit with RiboErase (HMR) Kit (Roche 08098131702) for rat or the TruSeq® Stranded Total RNA Library Prep Human/Mouse/Rat Kit (Illumina 20020596) for human

treatment_protocol: HEPATOPAC cells were treated with compound-containing media on Study Days 2, 5, 7, for a total of 9 days

tag: donor

tag: Sex

value: female

value: ticlopidine

tag: dose

value: 120 microM

tag: time point

value: HEPATOPAC


title: Human_HEPATOPAC_4106_female_ticlopidine_120µM_48hr [US-1421101]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421101


title: Human_HEPATOPAC_4106_female_MK-3207_80µM_120hr [US-1421108]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421108

value: 80 microM


title: Human_HEPATOPAC_4106_female_ticlopidine_120µM_120hr [US-1421110]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421110


title: Human_HEPATOPAC_4106_female_ticlopidine_120µM_120hr [US-1421112]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421112


title: Human_HEPATOPAC_4106_female_ticlopidine_120µM_120hr [US-1421111]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421111


title: Human_HEPATOPAC_4106_female_ticlopidine_120µM_48hr [US-1421102]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421102


title: Human_HEPATOPAC_4106_female_MK-3207_80µM_48hr [US-1421026]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421026


title: Human_HEPATOPAC_4106_female_MK-3207_80µM_48hr [US-1421028]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421028


title: Human_HEPATOPAC_4106_female_MK-3207_80µM_48hr [US-1421027]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421027


title: Human_HEPATOPAC_4106_female_β-Naphthoflavone_25µM_48hr [US-1421020]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421020

value: β-naphthoflavone

value: 25 microM


title: Human_HEPATOPAC_4106_female_β-Naphthoflavone_25µM_48hr [US-1421019]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421019


title: Human_HEPATOPAC_4106_female_MK-3207_80µM_120hr [US-1421106]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421106


title: LM283-v12-Treg

value: liver metastasis colorectal cancer


title: Human_HEPATOPAC_4106_female_vehicle (DMSO)_0.1%_48hr [US-1421015]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421015

value: vehicle (DMSO)


title: Human_HEPATOPAC_4106_female_vehicle (DMSO)_0.1%_48hr [US-1421014]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421014


title: Human_HEPATOPAC_1307_male_warfarin_80µM_120hr [US-1421012]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421012

value: warfarin


title: Human_HEPATOPAC_4106_female_vehicle (DMSO)_0.1%_120hr [US-1421103]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421103


title: Human_HEPATOPAC_4106_female_vehicle (DMSO)_0.1%_120hr [US-1421105]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421105


title: Human_HEPATOPAC_1307_male_warfarin_80µM_120hr [US-1421013]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421013


title: Human_HEPATOPAC_4106_female_MK-3207_80µM_120hr [US-1421107]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421107


title: Human_HEPATOPAC_4106_female_vehicle (DMSO)_0.1%_48hr [US-1421016]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421016


title: Human_HEPATOPAC_1307_male_warfarin_80µM_48hr [US-1421009]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421009


title: Human_HEPATOPAC_1307_male_clarithromycin_30µM_120hr [US-1421004]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421004

value: clarithromycin

value: 30 microM


title: Human_HEPATOPAC_1307_male_warfarin_80µM_48hr [US-1421007]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421007

value: male


title: Human_HEPATOPAC_1307_male_warfarin_80µM_120hr [US-1421011]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421011


title: Human_HEPATOPAC_4106_female_bardoxolone_0.75µM_48hr [US-1421023]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421023

value: bardoxolone

value: 0.75 microM


title: Human_HEPATOPAC_1307_male_warfarin_80µM_48hr [US-1421006]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421006


title: Human_HEPATOPAC_4106_female_β-Naphthoflavone_25µM_48hr [US-1421018]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421018


title: Human_HEPATOPAC_1307_male_clarithromycin_30µM_120hr [US-1421001]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421001


title: Human_HEPATOPAC_1307_male_clarithromycin_30µM_48hr [US-1421096]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421096


title: control_3

description: SAMPLE 3

source_name: mouse skin, control, replicate 3

value: skin tissue

value: non-treated mouse


title: Human_HEPATOPAC_1307_male_clarithromycin_30µM_48hr [US-1421097]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421097


title: Human_HEPATOPAC_1307_male_vehicle (DMSO)_0.1%_120hr [US-1421000]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421000


title: Human_HEPATOPAC_1307_male_vehicle (DMSO)_0.1%_120hr [US-1420999]

description:
Human_Hepatopac_Treatments.tar.gz
US-1420999


title: Human_HEPATOPAC_1307_male_vehicle (DMSO)_0.1%_120hr [US-1421010]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421010


title: Human_HEPATOPAC_1307_male_vehicle (DMSO)_0.1%_48hr [US-1421095]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421095


title: Human_HEPATOPAC_1307_male_clarithromycin_30µM_48hr [US-1421098]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421098


title: Human_HEPATOPAC_4106_female_bardoxolone_0.75µM_48hr [US-1421024]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421024

value: female


title: Human_HEPATOPAC_4106_female_vehicle (DMSO)_0.1%_120hr [US-1421104]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421104


title: Human_HEPATOPAC_4106_female_bardoxolone_0.75µM_48hr [US-1421022]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421022


title: Human_HEPATOPAC_1307_male_clarithromycin_30µM_120hr [US-1421002]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421002


title: Human_HEPATOPAC_1307_male_vehicle (DMSO)_0.1%_48hr [US-1421094]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421094


title: Human_HEPATOPAC_1307_male_vehicle (DMSO)_0.1%_48hr [US-1421005]

description:
Human_Hepatopac_Treatments.tar.gz
US-1421005


title: Human_iPSC derived hepatocytes_donorZ_sex_untreated_0µM_192hr [US-1477746]

description:
Human_Models.tar.gz
US-1477746

value: donorZ

value: untreated

value: 0 microM

value: iPSC derived hepatocytes


title: Human_iPSC derived hepatocytes_donorZ_sex_untreated_0µM_336hr [US-1477838]

description:
Human_Models.tar.gz
US-1477838


title: Human_iPSC derived hepatocytes_donorZ_sex_untreated_0µM_192hr [US-1477761]

description:
Human_Models.tar.gz
US-1477761


title: Human_iPSC derived hepatocytes_donorZ_sex_untreated_0µM_336hr [US-1477758]

description:
Human_Models.tar.gz
US-1477758


title: Human_iPSC derived hepatocytes_donorZ_sex_untreated_0µM_336hr [US-1477744]

description:
Human_Models.tar.gz
US-1477744


title: Human_iPSC derived hepatocytes_donorZ_sex_untreated_0µM_336hr [US-1477823]

description:
Human_Models.tar.gz
US-1477823


title: Human_iPSC derived hepatocytes_donorZ_sex_untreated_0µM_336hr [US-1477708]

description:
Human_Models.tar.gz
US-1477708


title: Human_hepG2_n/a_male_untreated_0µM_0hr [US-1587673]

description:
Human_Models.tar.gz
US-1587673


title: Human_hepG2_n/a_male_untreated_0µM_0hr [US-1587675]

description:
Human_Models.tar.gz
US-1587675


title: Human_iPSC derived hepatocytes_donorZ_sex_untreated_0µM_192hr [US-1477726]

description:
Human_Models.tar.gz
US-1477726


title: Human_iPSC derived hepatocytes_donorZ_sex_untreated_0µM_192hr [US-1477760]

description:
Human_Models.tar.gz
US-1477760


title: Human_hepG2_n/a_male_untreated_0µM_0hr [US-1587672]

description:
Human_Models.tar.gz
US-1587672


title: BloodSample10Chemo: 1Radiation: 1

type: genomic

city: Los Angeles

first: Mary

middle: Elizabeth

last: Sehl

state: CA

address: 100 UCLA Medical Plaza, Suite 550

department: Medicine / Hematology-Oncology

institute: UCLA

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing: Noob normalization using preprocessNoob in the minfi R package

label: Cy3, Cy5

molecule: genomic DNA

source_name: BloodSample10Chemo: 1Radiation: 1

label_protocol: Bisulfite conversion was performed on 500 ng of DNA using the llumina Infinium Methylation Assay protocol in the EZ DNA Methylation kit (Zymo Research). Next the samples were loaded onto the Infinium Human MethylationEPIC BeadChip

extract_protocol: Genomic DNA of whole blood samples

tag: age

tag: chemotherapy any

tag: radiationtherapy any

tag: female

tag: batch number


title: Human_iPSC derived hepatocytes_donorZ_sex_untreated_0µM_168hr [US-1587640]

description:
Human_Models.tar.gz
US-1587640


title: Human_iPSC derived hepatocytes_donorZ_sex_untreated_0µM_168hr [US-1587647]

description:
Human_Models.tar.gz
US-1587647


title: Human_iPSC derived hepatocytes_donorZ_sex_untreated_0µM_168hr [US-1587643]

description:
Human_Models.tar.gz
US-1587643


title: Human_iPSC derived hepatocytes_donorZ_sex_untreated_0µM_0hr [US-1587616]

description:
Human_Models.tar.gz
US-1587616


title: Human_primary hepatocytes_CDP_male_untreated_0µM_336hr [US-1589956]

description:
Human_Models.tar.gz
US-1589956

value: CDP

value: primary hepatocytes


title: Human_iPSC derived hepatocytes_donorZ_sex_untreated_0µM_72hr [US-1587615]

description:
Human_Models.tar.gz
US-1587615


title: Human_iPSC derived hepatocytes_donorZ_sex_untreated_0µM_72hr [US-1587617]

description:
Human_Models.tar.gz
US-1587617


title: Human_iPSC derived hepatocytes_donorZ_sex_untreated_0µM_192hr [US-1477740]

description:
Human_Models.tar.gz
US-1477740


title: Human_iPSC derived hepatocytes_donorZ_sex_untreated_0µM_0hr [US-1587604]

description:
Human_Models.tar.gz
US-1587604


title: Human_iPSC derived hepatocytes_donorZ_sex_untreated_0µM_192hr [US-1477748]

description:
Human_Models.tar.gz
US-1477748


title: Human_primary hepatocytes_CDP_male_untreated_0µM_336hr [US-1589929]

description:
Human_Models.tar.gz
US-1589929


title: Human_iPSC derived hepatocytes_donorZ_sex_untreated_0µM_72hr [US-1587632]

description:
Human_Models.tar.gz
US-1587632


title: Human_iPSC derived hepatocytes_donorZ_sex_untreated_0µM_0hr [US-1587612]

description:
Human_Models.tar.gz
US-1587612


title: Human_primary hepatocytes_CDP_male_untreated_0µM_168hr [US-1589926]

description:
Human_Models.tar.gz
US-1589926


title: Human_primary hepatocytes_CDP_male_untreated_0µM_336hr [US-1589925]

description:
Human_Models.tar.gz
US-1589925


title: Human_primary hepatocytes_CDP_male_untreated_0µM_168hr [US-1589923]

description:
Human_Models.tar.gz
US-1589923


title: Human_primary hepatocytes_CDP_male_untreated_0µM_72hr [US-1589958]

description:
Human_Models.tar.gz
US-1589958


title: Human_primary hepatocytes_CDP_male_untreated_0µM_0hr [US-1589953]

description:
Human_Models.tar.gz
US-1589953


title: Human_liver model A_donorY_male_untreated_0µM_336hr [US-1589916]

description:
Human_Models.tar.gz
US-1589916

value: donorY

value: liver model A


title: Human_iPSC derived hepatocytes_donorZ_sex_untreated_0µM_336hr [US-1477743]

description:
Human_Models.tar.gz
US-1477743


title: Human_primary hepatocytes_CDP_male_untreated_0µM_0hr [US-1589942]

description:
Human_Models.tar.gz
US-1589942


title: Human_liver model A_donorY_male_untreated_0µM_336hr [US-1589915]

description:
Human_Models.tar.gz
US-1589915


title: Human_primary hepatocytes_CDP_male_untreated_0µM_72hr [US-1589921]

description:
Human_Models.tar.gz
US-1589921


title: Human_primary hepatocytes_CDP_male_untreated_0µM_72hr [US-1589914]

description:
Human_Models.tar.gz
US-1589914


title: Human_primary hepatocytes_CDP_male_untreated_0µM_168hr [US-1589917]

description:
Human_Models.tar.gz
US-1589917


title: Human_primary hepatocytes_CDP_male_untreated_0µM_0hr [US-1589902]

description:
Human_Models.tar.gz
US-1589902


title: Human_liver model A_donorY_male_untreated_0µM_168hr [US-1589931]

description:
Human_Models.tar.gz
US-1589931


title: Human_liver model A_donorY_male_untreated_0µM_336hr [US-1589900]

description:
Human_Models.tar.gz
US-1589900


title: Human_liver model A_donorY_male_untreated_0µM_168hr [US-1589903]

description:
Human_Models.tar.gz
US-1589903


title: Human_liver model A_donorY_male_untreated_0µM_0hr [US-1589973]

description:
Human_Models.tar.gz
US-1589973


title: Human_liver model A_donorY_male_untreated_0µM_0hr [US-1589938]

description:
Human_Models.tar.gz
US-1589938


title: Human_liver model A_donorY_male_untreated_0µM_0hr [US-1589911]

description:
Human_Models.tar.gz
US-1589911


title: Liver_F1_CastxBL6

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

library_source: genomic

data_processing:
Standard Illumina base-calling pipeline.
As first step in the processing, the first 8 bp of Read 2 were removed and written into the readID of both reads as an in-line barcode, or UMI (Unique Molecular Identifier). This UMI was then later used during the de-duplication step with "deduplicate bismark --barcode mapped_file.bam".
Raw sequence reads were then trimmed to remove both poor quality calls and adapters using Trim Galore (v0.6.2 for hybrid mouse tissues, v0.4.4 for human and inbred mouse tissues, www.bioinformatics.babraham.ac.uk/projects/trim_galore/, Cutadapt version 2.3 for hybrid mouse tissues, v1.9.1 for human and inbred mouse tissues), parameters: --paired). Trimmed reads were aligned to the mouse or human reference genome in paired-end mode. Alignments were carried out with Bismark v0.14.4 for hybrid mouse tissues and v0.18.2 for human and inbred mouse tissues (Krueger and Andrews, 2011)  CpG methylation calls were extracted from the mapping output using the Bismark methylation extractor (v0.22.1 for hybrid mouse tissues, v0.18.2 for human and inbred mouse tissues). Deduplication was then carried out with deduplicate_bismark, using the --bacode option to take UMIs into account (see above)). For hybrid mouse strain experiments, the data was aligned to a hybrid genome of Black6/CAST (the genome was prepared with the SNPsplit package (v0.3.4, https://github.com/FelixKrueger/SNPsplit)). Following alignment and deduplication, reads were split allele-specifically with SNPsplit.
Genome_build: GRCm38
Genome_build: GRCh38
Supplementary_files_format_and_content:  [Bismark coverage file]  The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

source_name: liver

extract_protocol:
[Sample collection protocol]  Genomic DNA was isolated using the DNeasy Blood and Tissue Kit (Qiagen) or the AllPrep DNA/RNA Micro Kit (Qiagen) according to manufacturer’s instructions and eluted into TE buffer or H2O.
The IMPLICON protocol consists of 2 PCR reactions. In the first reaction each sample is amplified with each primer pair in individual reactions: 30ng (2μl of 66μl eluted bisulfite treated DNA) of bisulfite treated DNA is amplified with 1.2μl of 10μM primer pool (final 1.5μM) containing both forward and reverse primers in 4μl of 2x KAPA HiFi Uracil+ ReadyMix in a final volume of 8μl. DNA was amplified using the following conditions: initial denaturation at 95°C for 5min, 30 cycles of 98°C denaturation for 20 seconds, variable annealing temperature for 15 seconds and extension at 72°C for 60 seconds; followed by a final extension at 72°C for 10 minutes. All PCR reactions for each individual sample were pooled together and samples cleaned-up using 1.5x AMPure XP beads and eluted in 20μl H2O. In the second PCR reaction, barcoded Illumina adapters are attached to the pooled PCR samples ensuring that each sample pool receives a unique reverse barcoded adapter. The 20μl PCR pool was amplified using 1μl of 10μM Illlumina PE1.0 primer (same for all samples) and 1μl of 10μM Illumina iTAG primer (distinct for each sample) and 25μl 2x KAPA HiFi Uracil+ ReadyMix in a 50μl volume reaction using the following conditions: initial denaturation at 98°C for 45 seconds, 5 cycles of 98°C denaturation for 15 seconds, 65°C annealing for 30 seconds and extension at 72°C for 30 seconds; followed by a final extension at 72°C for 5 minutes. Reactions were cleaned-up with 1x AMPure XP beads and eluted in 20μl. Libraries were verified by running 1:30 dilutions on Agilent bioanalyzer.

treatment_protocol: 1μg of genomic DNA was bisulfite converted using the EZ DNA methylation Gold kit (Zymo Research) according to manufacturer’s instructions with either magnetic bead or column clean-up and eluted/resuspended in 66μl elution buffer to obtain a final concentration of ~15ng/μl bisulfite converted DNA.

tag: strain

value: liver

tag: protocol

value: isolated from CASTxBl6 hybrid mouse


title: Heart_F1_BL6xCast

source_name: heart

value: heart

value: isolated from Bl6xCAST hybrid mouse


title: Liver_F1_BL6xCast


title: Human_liver model A_donorY_male_untreated_0µM_Xhr [US-1589933]

description:
Human_Models.tar.gz
US-1589933

value: Xhr


title: Human_HEPATOPAC_3121A_female_untreated_0µM_216hr [US-1587596]

description:
Human_Models.tar.gz
US-1587596

value: HEPATOPAC


title: Human_HEPATOPAC_3121A_female_untreated_0µM_216hr [US-1587598]

description:
Human_Models.tar.gz
US-1587598


title: Human_liver model A_donorY_male_untreated_0µM_Xhr [US-1589948]

description:
Human_Models.tar.gz
US-1589948


title: Heart_F1_CastxBL6


title: Human_HEPATOPAC_3121A_female_untreated_0µM_216hr [US-1587594]

description:
Human_Models.tar.gz
US-1587594


title: Ear_F1_BL6xCast

source_name: ear

value: ear


title: Human_HEPATOPAC_3121A_female_untreated_0µM_120hr [US-1587588]

description:
Human_Models.tar.gz
US-1587588


title: Human_liver model A_donorY_male_untreated_0µM_168hr [US-1589959]

description:
Human_Models.tar.gz
US-1589959


title: Ear_F1_CastxBL6


title: Brain_F1_CastxBL6

source_name: brain

value: brain


title: 6month_lung

source_name: lung

value: lung

value: isolated from 6 month old male mouse


title: Brain_F1_BL6xCast


title: 6month_liver


title: Human_HEPATOPAC_3121A_female_untreated_0µM_120hr [US-1587583]

description:
Human_Models.tar.gz
US-1587583

value: female

value: untreated


title: Human_liver_donorX3_sex_untreated_0µM_0hr [US-1587610]

description:
Human_Models.tar.gz
US-1587610

value: male

value: 0 microM


title: Human_liver_donorX4_sex_untreated_0µM_0hr [US-1587611]

description:
Human_Models.tar.gz
US-1587611


title: Human_HEPATOPAC_3121A_female_untreated_0µM_120hr [US-1587582]

description:
Human_Models.tar.gz
US-1587582


title: Human_liver_donorX2_sex_untreated_0µM_0hr [US-1587609]

description:
Human_Models.tar.gz
US-1587609


title: 6month_heart


title: 3month_lung

value: isolated from 3 month old male mouse


title: BloodSample6Chemo: 1Radiation: 1

source_name: BloodSample6Chemo: 1Radiation: 1


title: Human_liver model A_donorY_male_untreated_0µM_Xhr [US-1589934]

description:
Human_Models.tar.gz
US-1589934

value: donorY


title: 3month_liver


title: Human_liver_donorX1_sex_untreated_0µM_0hr [US-1587602]

description:
Human_Models.tar.gz
US-1587602


title: siB/siM-3

city: Cleveland

first: Darcie

middle: D

last: Seachrist

state: OH

address: 2109 Adelbert Rd,, Pharmacology Department SOM RT300

institute: Case Western Reserve University

description:
RNA isolated 48h post transfection
146_Double_KD_sensitive_exons

data_processing:
fastq files were aligned to version hg19 using Olego (Wu et al., 2013)
The Quantas pipeline was used to infer transcript structure and quantify alternative splicing and gene expression (Yan et al., 2015)
Genes expressed at RPKM>=2 in one group and had a fold change expression of 2 or greater and adjusted p-value < 0.01 were considered signficantly differentially expressed.
Signficant splicing changes were determined using a FDR<0.05, adjusted p value < 0.05 and average RPKM across biological replicates >=1 in both conditions.
Genome_build: hg19
Supplementary_files_format_and_content: RPKM

source_name: epithelial breast cancer cell line; derived from metasatic pleural effusion

growth_protocol: MDA-MB-231 cells were cultured in RPMI-1640 supplmented with 10% fetal bovine serum and 1% penicillin/streptomycin

extract_protocol:
RNA was isolated using the Rneasy Plus Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold for rRNA removal was used. Illumina TruSeq libraries were tagged with unique adapter-indexes. Final libraries were validated on the Agilent 2100 Bioanalyzer, quantified via qPCR (KAPA Biosystems Illumina Library Quantification Kit) and pooled at equimolar ratios

treatment_protocol: cells were tranfected with either 100nM non-targeting siRNA (siNS), or 100nM SMARTpool siRNAs targeting either BCL11A, MBNL1 or the combination of both BCL11A and MBNL1 at 50nM each.

tag: sirna

tag: cell line


title: siB/siM-2


title: Mouse_liver_C57Bl6_female_untreated_0µM_0hr [TT19-2507_19-0004_L]

description:
Rat_Models.tar.gz
TT19-2507_19-0004_L


title: 15month_heart

tag: cell type

value: isolated from 15 month old male mouse


title: siMBNL1-3

description:
RNA isolated 48h post transfection
110_MBNL1_sensitive_exons


title: siMBNL1-2


title: 15month_liver

value: liver


title: Mouse_liver_C57Bl6_female_untreated_0µM_0hr [TT19-2507_19-0003_L]

description:
Rat_Models.tar.gz
TT19-2507_19-0003_L

tag: tissue


title: siMBNL1-1


title: siBCL11A-1

description:
RNA isolated 48h post transfection
MB231_siBCL11A_DE_genes
107_BCL11A_sensitive_exons


title: siBCL11A-2


title: siNS-2

description:
RNA isolated 48h post transfection
MB231_siBCL11A_DE_genes


title: Mouse_liver_C57Bl6_female_untreated_0µM_0hr [TT19-2507_19-0002_L]

description:
Rat_Models.tar.gz
TT19-2507_19-0002_L


title: 3month_heart


title: H11FoveaS1

first: Wenjun

last: Yan

state: MA

address: 52 Oxford Street

department: Department of Molecular  and Cellular Biology

institute: Harvard University

description:
Fovea retina of right eye from donor 11
count_mat_donor_H11.csv

data_processing:
Sample demultiplexing with the mkfastq function from Cell Ranger software( version 2.1.0 and version 3.0.2, 10X Genomics)
Sample alignment with the count function from Cell Ranger software (version 2.1.0 and version 3.0.2,10X Genomics)
Genome_build: GRCh38
Supplementary_files_format_and_content: Csv files including gene count matrix from each donor

source_name: Fovea retina

extract_protocol:
Single cell libraries were generated by minor modifications of methods developed for macaque retina. Briefly, a ~1.5 mm diameter circular region centered on the foveal pit was dissected from the retina, and peripheral retinal pieces were pooled from all retinal quadrants. Dissected tissues were digested with papain (Worthington, LS003126) for 30min at 37oC. Following digestion, samples were dissociated and triturated into single cell suspensions with 0.04% bovine serum albumin (BSA) in Ames. Dissociated cells from digested peripheral retinas were incubated with CD90 microbeads (Miltenyi Biotec, 130-096-253; 1 ml per 107 cells) to enrich RGCs or with anti-CD73 (BD Biosciences, clone AD2; 5 ml per 107 cells) followed by anti-mouse IgG1 microbeads (Miltenyi Biotec, 130-047-102; 10 ml per 107 cells) to deplete rods. Incubations were at room temperature for 10 min. CD90 positive cells or CD73 negative cells were selected via large cell columns through a MiniMACS Separator (Miltenyi Biotec). Foveal samples were used without further processing.
Single cell libraries were made with Chromium 3’ v2 or V3 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500.
Chromium 3’ v2/v3 platform (10X Genomics, Pleasanton, CA)

treatment_protocol: All human eyes used for sequencing and histological studies were collected 3-14 hours post mortem through the Rapid Autopsy Program, Massachusetts General Hospital, with all but one collected ≤6.5 hours post mortem. The globe was immediately transported back to the lab in a humid chamber. Hemisection was performed to remove the anterior chamber, and the posterior pole was immersed in Ames equilibrated with 95% O2/5% CO2 before further dissection and dissociation. All donors were confirmed to have no history or clinical evidence of ocular disease or intraocular surgery.

value: Fovea retina cells


title: H5FoveaS5

description:
Fovea retina of left eye from donor 5
count_mat_donor_H5.csv


title: H9FoveaS1

description:
Fovea retina of left eye from donor 9
count_mat_donor_H9.csv


title: siBCL11A-3


title: 8366_Brain_WTPBS

city: Salzburg

first: Rodolphe

last: Poupardin

address: Strubergasse 22

country: Austria

data_processing:
Quality control of raw sequencing data was conducted using FastQC tool (Andrews, S. (2010). FastQC:  A Quality Control Tool for High Throughput Sequence Data [Online]. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were then mapped to the genome (Mus musculus genome GRCm38) using bowtie2 (version 2.2.2, (Langmead and Salzberg, 2012)). Reads that overlap with genes were then counted using HTSEQ tool (version 0.11.2, (Anders et al., 2015), -m intersection-nonempty -s no -i gene_id -t exon).
Expression values of protein coding genes were first normalized and differential expression analysis between the different groups was conducted using Deseq2 (Love et al., 2014)
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimited txt files with HT-seq count output for all samples

source_name: Brain

growth_protocol: Female and male APP Swedish PS1 dE9 mice expressing a chimeric mouse/human mutant amyloid precursor protein (Mo/HuAPP695swe) and a mutant human presenilin 1 (PS1-dE9) both directed to CNS neurons under the prion protein promoter (available by Jackson Laboratory, http://www.jax.org/strain/005864) were used. Mice were housed at the Paracelsus Medical University Salzburg in groups under standard conditions at a temperature of 22°C and a 12 h light/dark cycle with ad libitum access to standard food and water. Animal care, handling, genotyping and experiment were approved by local ethical committees (BMBWF-66.019/0005-V/3b/2018).

extract_protocol:
After manual perfusion, animals were decapitated and the brain region of interest was dissected from one brain hemisphere. Brain regions were immediately transferred to RNA later (Sigma) and stored at -80°C. Tissue was homogenized in 1 ml Trizol (TRI®Reagent; Sigma). For phase separation, 150 µl of 1 bromo 3 chloropropane (Sigma) were added, vortexed and centrifuged (15 min. at 12.000 × g at 4°C). After transferring the aqueous phase into a new tube 1 µl GlycoBlue™ (Invitrogen) and 500 µl 2-Propanol p.A. (Millipore) were added and vortexed. To obtain RNA, samples were centrifuged (10 min. at 12000 x g at 4°C). The pellet was washed with 1 ml 75% ethanol, dried and re suspended in 30 µl RNase-free water (pre warmed to 55°C). RNA was stored at -80°C for further analysis.
The library preparation was done using TruSeq® Stranded mRNA Sample preparation kit (Illumina inc). The starting material (500 ng) of total RNA was mRNA enriched using the oligo(dT) bead system. The isolated mRNA was subsequently fragmented using enzymatic fragmentation. Then first strand synthesis and second strand synthesis were performed and the double stranded cDNA was purified (AMPure XP, Beckman Coulter). The cDNA was end repaired, 3’ adenylated and Illumina sequencing adaptors ligated onto the fragments ends, and the library was purified (AMPure XP). The mRNA stranded libraries were pre-amplified with PCR and purified (AMPure XP). The libraries size distribution was validated and quality inspected on a Bioanalyzer 2100 or BioAnalyzer 4200 tapeStation (Agilent Technologies). High quality libraries are pooled based in equimolar concentrations based on the Bioanalyzer Smear Analysis tool (Agilent Technologies). The library pool(s) were quantified using qPCR and optimal concentration of the library pool used to generate the clusters on the surface of a flowcell before sequencing on a NextSeq500) instrument (75 cycles) according to the manufacturer instructions (Illumina Inc.).

treatment_protocol: For the in vivo experiment, 12-months old APP-PS1 and WT mice were used. Animals were treated for a total of 4 weeks with an anti-CD8a antibody (clone 2.43 #BE0061, BioXCell), a respective isotype control antibody (rat IgG2b clone LTF-2 #BE0090, BioXCell) or PBS. Mice were injected i.p. for 3 consecutive days and additionally on the 5th day, followed by 2 injections per week for a total of 10 injections á 0.8 mg of respective antibody. PBS treated mice received 100 µL of PBS

value: WT

value: Female

value: PBS


title: 8541_Brain_APPPS1PBS


title: siNS-1


title: 8528_Brain_APPPS1antiCD8

value: Male


title: 8357_Brain_APPPS1PBS


title: 8538_Brain_APPPS1antiCD8


title: H5FoveaS4


title: siB/siM-1


title: 15month_lung


title: 8503_Brain_WTPBS


title: 8355_Brain_APPPS1antiCD8


title: 8502_Brain_APPPS1PBS


title: H5FoveaS1


title: 8361_Brain_APPPS1antiCD8


title: H5FoveaS2


title: 8359_Brain_APPPS1PBS


title: 8363_Brain_WTPBS


title: 8505_Brain_WTPBS


title: H3FoveaS3

description:
Fovea retina of right eye from donor 3
count_mat_donor_H3.csv


title: H4FoveaS1

description:
Fovea retina of left eye from donor 4
count_mat_donor_H4.csv


title: H3FoveaS2


title: 8356_Brain_WTPBS


title: Mouse_liver_C57Bl6_female_untreated_0µM_0hr [TT19-2507_19-0001_L]

description:
Rat_Models.tar.gz
TT19-2507_19-0001_L


title: H3FoveaS1


title: 8364_Brain_APPPS1PBS


title: H3CD90S1

description:
Peripheral retina of right eye from donor 3
count_mat_donor_H3.csv

source_name: Peripheral retina

value: Peripheral retina cells enriched with CD90 microbeads


title: 8383_Brain_APPPS1antiCD8

value: brain


title: H3CD90S2


title: H5FoveaS3


title: H2Fovea2S1

description:
Fovea retina of left eye from donor 2
count_mat_donor_H2.csv


title: H2Fovea1S1

description:
Fovea retina of right eye from donor 2
count_mat_donor_H2.csv


title: H3CD73dpS2

value: Peripheral retina cells depleted by anti-CD73  followed by anti-mouse IgG1 microbeads


title: H3CD73dpS1


title: H1CD73dpS1

description:
Peripheral retina of left eye from donor 1
count_mat_donor_H1.csv


title: H1CD90S1


title: NEG_056

city: Seattle

first: Nicole

middle: A P

last: Lieberman

state: WA

address: 850 Republican St S130

department: Laboratory Medicine

institute: University of Washington

data_processing:
Illumina Casava1.7 software used for basecalling.
Single end reads were adapter and quality trimmed by Trimmomatic v0.39, aligned to Ensembl v96 human transcriptome by Kallisto v0.46, and collapsed to gene level annotations by Biomart. Only samples with >500000 human reads were included for further analysis
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Nasopharyngeal Swab

extract_protocol:
RNA was isolated from NP swabs in viral transport media using the Roche MagNAPure or Qiagen BioRobot
First strand cDNA was synthesized by SuperScriptIV/Random hexamers, second strand by Sequenase v2.0, and libraries constructed by Nextera XT Kit

tag: sars-cov-2 positivity

value: neg

tag: gender

value: F

value: S


title: NEG_063

value: U


title: NEG_058

value: M


title: NEG_057


title: NEG_059


title: NEG_062


title: NEG_060


title: NEG_065

value: R


title: L3F_M1BP-RNAi_ZKSCAN3_male_noGonads_rep2

city: Marseille

first: Andrew

middle: J

last: Saurin

address: Campus de Luminy

country: France

institute: IBDM / CNRS

description:
RNA-Seq of L3F WT male M1BP RNAi+ZKSCAN3 fat bodies Rep2
WT_M1BPi_ZKSCAN3_dmel6_exon_counts.txt
DGE_M1BPiZKSCAN3_vs_M1BPi_dmel6_FDR01_logFC_ordered.txt
M1BPi_ZKSCAN3_2

data_processing:
Basecalls performed using RTA (Illumina)
RNA-seq reads were aligned to the dm6 genome assembly using subread-align
Gene exon counts were made using featureCounts
RNA-Seq differentially expressed genes were called using DESeq2 using a false discovery rate (FDR;padj) cut-off of 0.001
ChIP-Seq peak calling was performed using MACS2 using low stringency on individual replicates. Final peaks were called using an Irreproducible Discovery Rate (IDR) of 0.1% according to guidelines set out by the ENCODE consortium.
Genome_build: dm6
Supplementary_files_format_and_content: DGE files show the DESeq output of differentially expressed genes of L3W versus L3F or L3F M1BP RNAi versus L3F at FDR 0.1% (padj <0.001)
Supplementary_files_format_and_content: Bed files were prepared using MACS2 and represent peaks called in both replicates having an IDR of 0.1%.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Drosophila 3rd instar larval fat body

growth_protocol:
WT or cgGal4 crossed to WT or M1BP RNAi larvae were reared at 25oC and fed only normal Drosophila media
Cells were grown in T-flasks to a density of not more than 7x10^6 cells/ml in Schneider Medium supplemented with 10% FBS

extract_protocol:
RNA was extracted with Qiagen Rneasy kit; Chromatin was prepared according to the modENCODE procedure
DNA and mRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
cgGal4 crossed to WT or M1BP RNAi larvae were reared at 25oC and fed only normal Drosophila media
Cells were treated with 10 microMolar Copper Sulphate for 24 h prior to chromatin preparation

tag: developmental stage

value: 3rd instar feeding

value: fat body

tag: genotype


title: L3F_ZKSCAN3_male_noGonads_rep1

description:
RNA-Seq of L3F WT male ZKSCAN3 fat bodies Rep1
WT_M1BPi_ZKSCAN3_dmel6_exon_counts.txt
DGE_ZKSCAN3_vs_WT_dmel6_FDR01_logFC_ordered.txt
ZKSCAN3_1


title: NEG_054


title: NEG_051


title: NEG_052


title: L3F_ZKSCAN3_male_noGonads_rep2

description:
RNA-Seq of L3F WT male ZKSCAN3  fat bodies Rep2
WT_M1BPi_ZKSCAN3_dmel6_exon_counts.txt
DGE_ZKSCAN3_vs_WT_dmel6_FDR01_logFC_ordered.txt
ZKSCAN3_2


title: L3F_M1BP-RNAi_male_noGonads_rep1

description:
RNA-Seq of L3F WT male M1BP RNAi fat bodies Rep1
WT_M1BPi_ZKSCAN3_dmel6_exon_counts.txt
DGE_M1BPi_vs_WT_dmel6_FDR01_logFC_ordered.txt
M1BPi_1


title: L3F_M1BP-RNAi_male_noGonads_rep2

description:
RNA-Seq of L3F WT male M1BP RNAi fat bodies Rep2
WT_M1BPi_ZKSCAN3_dmel6_exon_counts.txt
DGE_M1BPi_vs_WT_dmel6_FDR01_logFC_ordered.txt
M1BPi_2


title: NEG_050


title: NEG_049


title: L3F_WT_male_noGonads_rep1

description:
RNA-Seq of L3F WT male fat bodies Rep1
WT_M1BPi_ZKSCAN3_dmel6_exon_counts.txt
DGE_M1BPi_vs_WT_dmel6_FDR01_logFC_ordered.txt
DGE_ZKSCAN3_vs_WT_dmel6_FDR01_logFC_ordered.txt
DGE_M1BPiZKSCAN3_vs_M1BPi_dmel6_FDR01_logFC_ordered.txt
WT_1


title: NEG_048


title: L3F_WT_male_noGonads_rep2

description:
RNA-Seq of L3F WT male fat bodies Rep2
WT_M1BPi_ZKSCAN3_dmel6_exon_counts.txt
DGE_M1BPi_vs_WT_dmel6_FDR01_logFC_ordered.txt
DGE_ZKSCAN3_vs_WT_dmel6_FDR01_logFC_ordered.txt
DGE_M1BPiZKSCAN3_vs_M1BPi_dmel6_FDR01_logFC_ordered.txt
WT_2


title: L3W WT_female_rep2

description:
RNA-Seq of L3W WT female fat bodies Rep2
WT_female_F_W_dmel6_exon_counts.txt
DGE_L3W_vs_L3F_dmel6_FDR01_logFC1.xlsx
L3W_2

value: 3rd instar wandering

value: wild type


title: NEG_047


title: NEG_046


title: L3F_M1BP-RNAi_ZKSCAN3_male_noGonads_rep1

description:
RNA-Seq of L3F WT male M1BP RNAi+ZKSCAN3 fat bodies Rep1
WT_M1BPi_ZKSCAN3_dmel6_exon_counts.txt
DGE_M1BPiZKSCAN3_vs_M1BPi_dmel6_FDR01_logFC_ordered.txt
M1BPi_ZKSCAN3_1


title: NEG_055


title: L3F WT_female_rep1

description:
RNA-Seq of L3F WT female fat bodies Rep1
WT_female_F_W_dmel6_exon_counts.txt
DGE_L3W_vs_L3F_dmel6_FDR01_logFC1.xlsx
L3F_1


title: NEG_040


title: NEG_037


title: NEG_043


title: NEG_038


title: NEG_042


title: Rat_liver_strain_sex_untreated_dose_duration [US-1466953]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1466953

organism: Rattus norvegicus

tag: treatment

value: untreated

tag: dose

value: dose

value: duration

value: liver


title: NEG_039

tag: age


title: tph-1_mg280_1_S6_R1

city: Piscataway

first: Christopher

last: Rongo

state: NJ

address: 190 Frelinghuysen Rd

department: Genetics

institute: Waksman Institute / Rutgers University

data_processing:
Libraries were sequenced on an Illumina HiSeq 2500 in Rapid Run Mode, resulting in high quality sequence reads (FAST QC Phred score average of 40 out to the full 75 bp length). Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the C. elegans whole genome (WS245) using STAR 2.5.1a.
Normalization and statistical analysis on gene counts were performed with EdgeR using generalized linear model functionality and tagwise dispersion estimates.
Genome_build: WS245
Supplementary_files_format_and_content: Excel spreadsheet (.xlsx files) of hits counts, one column per sample

organism: Caenorhabditis elegans

source_name: tph-1_mg280_whole body

growth_protocol: Developmentally synchronized animals were obtained by hypochlorite treatment of gravid adults to release embryos.  Synchronized embryos were hatched on NGM plates and grown at 20°C until 48h after the L4 stage of development.  Fluorodeoxyuridine was used to prevent the development of second-generation embryos once animals reached fertile adulthood (Gandhi, Santelli et al., 1980).

extract_protocol:
Total RNA was isolated from animals using trizol (Invitrogen) combined with Bead Beater lysis in  biological replicates for each genotype
An mRNA library (single-end, 75-bp reads) was prepared for each sample/replicate using Illumina Truseq with PolyA selection

tag: genotype/variation

value: odIs77 transgene in tph-1 mutant background

value: L4 stage plus 48 hours

value: whole body


title: NEG_036

value: neg


title: tdc-1_n3419_1_S5_R1

source_name: tdc-1_n3419_whole body

treatment_protocol: Fluorodeoxyuridine was used to prevent the development of second-generation embryos once animals reached fertile adulthood (Gandhi, Santelli et al., 1980).

value: odIs77 transgene in tdc-1 mutant background


title: tph-1_mg280_3_S6_R1


title: tdc-1_n3419_3_S5_R1


title: NEG_035

value: F


title: tdc-1_n3419_2_S11_R1


title: tbh-1_ok1196_3_S4_R1

source_name: tbh-1_ok1196_whole body

value: odIs77 transgene in tbh-1 mutant background


title: NEG_032

value: U


title: NEG_030

value: T


title: NEG_028

value: M


title: NEG_031


title: tbh-1_ok1196_2_S10_R1


title: L3W WT_female_rep1

description:
RNA-Seq of L3W WT female fat bodies Rep1
WT_female_F_W_dmel6_exon_counts.txt
DGE_L3W_vs_L3F_dmel6_FDR01_logFC1.xlsx
L3W_1

value: fat body


title: tbh-1_ok1196_1_S4_R1


title: NEG_027


title: L3F WT_female_rep2

description:
RNA-Seq of L3F WT female fat bodies Rep2
WT_female_F_W_dmel6_exon_counts.txt
DGE_L3W_vs_L3F_dmel6_FDR01_logFC1.xlsx
L3F_2

value: 3rd instar feeding


title: cat-2_e1112_3_S2_R1

source_name: cat-2_e1112_whole body

value: odIs77 transgene in cat-2 mutant background


title: NEG_026

value: S


title: cat-2_e1112_2_S8_R1


title: tph-1_mg280_2_S12_R1


title: NEG_025


title: NEG_024


title: cat-2_e1112_1_S2_R1


title: odIs77_2_S7_R1_001

source_name: odIs77_whole body

value: odIs77 transgene in wild type background


title: odIs77_3_S1_R1_001


title: NEG_023


title: NEG_022


title: odIs77_1_S1_R1_001


title: NEG_021


title: NEG_020


title: Rat_liver_strain_sex_untreated_dose_duration [US-1470477]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1470477

value: untreated

value: dose

tag: time point

value: duration


title: NEG_019


title: NEG_014

value: C


title: NEG_013

value: R


title: NEG_012

value: neg


title: NEG_011


title: NEG_010


title: NEG_008


title: NEG_009


title: NEG_007


title: NEG_005


title: NEG_018


title: NEG_003


title: NEG_016


title: NEG_001


title: Hyperplastic Mammary gland Rep 3

city: New York

first: Aitziber

last: Buque Martinez

state: New York

address: 1300 York Avenue

department: Radiation Oncology

institute: Weill Cornell Medical College

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® MTA1.0 (Affymetrix) at 45°C for 17 hours

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls. The observations of some of these metrics and the study of the distribution of raw data show no outlier experiment.  RMA normalization is performed using Partek software with Affymetrix CDF file.

label: biotin

source_name: Hyperplastic Mammary gland Rep 3

label_protocol: 200 ng of total RNA is reverse transcribed following the GeneChip® WT Plus Reagent Kit (Affymetrix) .  Briefly, the resulting double strand cDNA is used for in vitro transcription with T7 RNA polymerase (all these steps are included in the WT cDNA synthesis and amplification kit of Affymetrix). After purification according to Affymetrix protocol, 5.5 ug of Sens Target DNA are fragmented and biotin labelled.

growth_protocol: Fifty mg slow-release (90 days) medroxyprogesterone acetate (MPA) pellets (Innovative Research of America) were implanted subcutaneously by surgery into 6-9 week-old female (day 0). Mice were administered 200 µL of a 5 mg mL-1 7,12-dimethylbenz[a]anthracene (DMBA; from Sigma-Aldrich) solution in corn oil (Sigma-Aldrich), by oral gavage once a week on weeks 1, 2, 3, 5, 6 and 7 after implantation of the MPA pellet.

extract_protocol: Mammary gland tissue was removed from the mice and RNA freshly extracted using Qiagen RNeasy kits.

treatment_protocol: Normal mammary gland was recovered from female mices that were not exposed to either MPA nor DMBA. Hyperplastic mammary glands were recovered from female mice that underwent MPA/DMBA protocol but did not develop any tumor. Mammary gland tumors were recovered from female mice once the tumor reach the size of 0.7-1 cm^2

value: Female


title: NEG_006


title: Hyperplastic Mammary gland Rep 2

source_name: Hyperplastic Mammary gland Rep 2


title: POS_436

value: pos

value: Unknown

value: not collected


title: POS_437


title: POS_438


title: Normal Mammary gland Rep 5

source_name: Normal Mammary gland Rep 5


title: Hyperplastic Mammary gland Rep 6

source_name: Hyperplastic Mammary gland Rep 6


title: Normal Mammary gland Rep 1

source_name: Normal Mammary gland Rep 1


title: Hyperplastic Mammary gland Rep 5

source_name: Hyperplastic Mammary gland Rep 5


title: Hyperplastic Mammary gland Rep 1

source_name: Hyperplastic Mammary gland Rep 1


title: Normal Mammary gland Rep 2

source_name: Normal Mammary gland Rep 2


title: POS_433


title: Mammary gland tumor Rep 1

source_name: Mammary gland tumor Rep 1


title: Mammary gland tumor Rep 5

source_name: Mammary gland tumor Rep 5


title: Normal Mammary gland Rep 4

source_name: Normal Mammary gland Rep 4


title: Mammary gland tumor Rep 3

source_name: Mammary gland tumor Rep 3


title: POS_435

source_name: Nasopharyngeal Swab


title: POS_431


title: POS_432


title: NEG_002

value: F


title: Normal Mammary gland Rep 3

source_name: Normal Mammary gland Rep 3


title: Hyperplastic Mammary gland Rep 4

source_name: Hyperplastic Mammary gland Rep 4


title: Mammary gland tumor Rep 4

source_name: Mammary gland tumor Rep 4


title: Mammary gland tumor Rep 2

source_name: Mammary gland tumor Rep 2


title: Normal Mammary gland Rep 6

source_name: Normal Mammary gland Rep 6


title: Mammary gland tumor Rep 6

source_name: Mammary gland tumor Rep 6


title: NEG_004

value: M


title: POS_424

value: T


title: POS_430


title: POS_429


title: POS_426


title: POS_434


title: POS_427


title: POS_428


title: POS_421

value: Q


title: POS_423


title: POS_422


title: POS_420


title: POS_419


title: POS_416


title: POS_417


title: POS_415


title: POS_418


title: POS_412

value: L


title: POS_414


title: POS_408


title: POS_413

value: N


title: POS_411

value: G


title: Ezh1+/- ; Six2TGCEzh2-/-

city: New Orleans

first: Samir

middle: S

last: El-Dahr

state: Louisiana

address: 1430 Tulane Avenue

department: Pediatric Nephrology

institute: Tulane University

description: Ezh1+/- Six2TGCEzh2-/- NPCs

data_processing:
10x Cellranger V.2.1.0 was used to generate Fastq files, perform alignment,filtering,barcode counting,UMI counting and aggregation.
Seurat V.3.1.2 for scRNA QC and Monocle 2.14 for pseudotime analysis
mm10
H5 file filtered-gene-barcode-matrix can be deconvoluted to tsv and mtx files

source_name: Embryonic Kidneys

extract_protocol:
Libraries were prepared from individual cells  (for the respective genotypes) using the droplet-based method as was outlined by10X Genomics. Indexed libraries were sequenced on a NextSeq500 (Illumina) sequencer to obtain 75 bp paired-end reads using the v2 chemistry.
v2.chemistry 10X Genomics
H5 file filtered-gene-barcode-matrix can be deconvoluted to tsv and mtx files

value: Ezh1+/- ; Six2TGCEzh2-/-


title: POS_406


title: P2 Six2TGC (Six2-GFP::CreTg)

description: P2 Six2TGC NPCs

source_name: Postnatal Kidneys

value: Six2TGC (Six2-GFP::CreTg)


title: Ezh1-/- ; Six2TGCEzh2-/-

description: Ezh1-/- ; Six2TGCEzh2-/- NPCs

value: Ezh1-/- ; Six2TGCEzh2-/-


title: Six2TGCEzh2-/-

description: Six2TGCEzh2-/- NPCs


title: POS_407


title: E16 Six2TGC (Six2-GFP::CreTg)

description: E16.5 Six2TGC NPCs


title: POS_405


title: P02_EzhQUAD

description: Ezh1-/- ; Six2TGCEzh2-/- NPCs

data_processing:
Concatenate paired-end reads run across multiple lanes for each sample such that there exist one forward (_1.fastq.gz) and one reverse (_2.fastq.gz) reads file for each sample.
Assess quality of reads using FASTQC(v0.11.7)
Aligned paired-end Fastq files to mm10 using Bowtie2
Samtools to remove Mitochondrial reads
Picard tools v1.77 to remove Duplicates
Call narrow peaks using MACS2
Bedtools to generate sorted bdg and bigwig files for viewing in IGV
mm10
Bigwig files

source_name: Neonatal Kidneys

extract_protocol:
Corces et al., 2017
Buenrostro et al., 2013
Omni-ATAC


title: POS_403


title: POS_402


title: POS_404


title: P0EZH12KO

description: Ezh1-/- ; Six2TGCEzh2-/- NPCs


title: P0EZH12KOA

description: Ezh1-/- ; Six2TGCEzh2-/- NPCs


title: POS_401


title: POS_409


title: POS_410


title: P0EZH1hetEZH2KO

description: Ezh1+/- Six2TGCEzh2-/- NPCs


title: POS_399

value: K


title: POS_398


title: P0EZH12Tri6

description: Ezh1+/- Six2TGCEzh2-/- NPCs


title: POS_396

value: J


title: P0H2

description: P0 Six2TGC NPCs


title: POS_400


title: P0EZH12Tri7

description: Ezh1+/- Six2TGCEzh2-/- NPCs


title: P0H3

description: P0 Six2TGC NPCs


title: POS_397


title: POS_395


title: POS_394


title: P0H1

description: P0 Six2TGC NPCs


title: EZH12KO

description: Ezh1-/- ; Six2TGCEzh2-/- NPCs


title: P0EZH2KOb

description: Six2TGCEzh2-/- NPCs


title: E16EZH12ko

description: Ezh1-/- ; Six2TGCEzh2-/- NPCs


title: POS_392


title: A7_E16EzhQUAD

description: Ezh1-/- ; Six2TGCEzh2-/- NPCs


title: POS_391


title: A6_E16EzhQUAD

description: Ezh1-/- Six2TGCEzh2-/- NPCs


title: E16Ezh1hetEzh2null-1

description: Ezh1+/- Six2TGCEzh2-/- NPCs


title: E16Ezh1hetEzh2null-2

description: Ezh1+/- Six2TGCEzh2-/- NPCs


title: POS_390


title: POS_389


title: POS_386


title: POS_387


title: A8_EzhTriple

description: Ezh1+/- Six2TGCEzh2-/- NPCs


title: POS_388


title: E16EZH1hetEZH2KO

description: Ezh1+/- Six2TGCEzh2-/- NPCs


title: P0EZH2KOa

description: Six2TGCEzh2-/- NPCs


title: POS_385


title: POS_384


title: E16EZH2KO

description: Six2TGCEzh2-/- NPCs


title: E16EZH1KO

description: Ezh1-/- Six2TGC NPCs

value: Ezh1-/- ; Six2TGC


title: POS_382


title: POS_393


title: POS_383


title: E16EZH1KOa

description: Ezh1-/- Six2TGC NPCs


title: E16WTb

description: E16.5 Six2TGC NPCs


title: E16WTc

description: E16.5 Six2TGC NPCs


title: E16WTa

description: E16.5 Six2TGC NPCs


title: POS_380

value: H


title: POS_377

value: pos


title: POS_378


title: POS_379


title: POS_376


title: POS_381


title: POS_375


title: POS_374


title: POS_373


title: POS_371

value: A


title: POS_372


title: POS_369


title: POS_370

value: not collected


title: POS_367

value: F


title: POS_366


title: POS_365


title: POS_364


title: MK-4256 07-4183

hyb_protocol: Hybridization to custom rat Affymetrix arrays (containing 43,686 probesets, GEO platform GPL28473)

scan_protocol: labeling and scanning were completed following the manufacturer's recommendations

data_processing: profiles were normalized using robust multi-array average followed by ratio’ing to corresponding vehicle control samples within each study.

source_name: liver after q.d. dosing

label_protocol: 50 ng of each purified RNA sample was amplified and labeled using a custom automated version of the NuGEN Ovation WB protocol

extract_protocol: Approximately 24hrs after dosing, animals were sacrificed, livers removed, a section (~50-100mg) frozen on dry ice and stored at ~-80C until total RNA was isolated. Frozen liver was pulverized in Trizol reagent, extracted with Chloroform, and further purified using the RNEasy column RNA isolation procedure (Qiagen, Chatsworth, CA).

treatment_protocol: Male Sprague Dawley, strain Crl:CD(SD), or Wistar, strain Crl:WI(HAN), rats were obtained from Charles River Laboratories (Raleigh, NC) for studies conducted in United States, or from Charles River Laboratories France Saint Germain sur l'Arbresle FRANCE, for studies conducted in Mirabel.  Animals were 6–10 weeks of age, weighing 120–425 grams. The rats were housed individually in wire mesh cages (at 18°C–26°C, relative humidity of 50 ± 20% on a 12-h light/12-h dark cycle), fed PMI Certified Rodent Diet (SD-restricted [fed 16–22g shortly after dosing 1× per day]; Wistar ad libitum). Animals were acclimated for at least 4 days prior to randomization into treatment groups. All animal husbandry and experimental procedures were in accordance with the Guide for the Care and Use of Laboratory Animals (Institute of Laboratory Animal Resources, Commission on Life Sciences, National Research Council, 1996) and were approved by the Institutional Animal Care and Use Committee of the facility in which the studies were conducted. Animals were dosed daily via oral gavage with vehicle or with compounds for indicated dose and durations and sacrificed 24h later.

value: liver

tag: pid

tag: Sex

tag: vehicle

value: 10% Polysorbate 80

tag: dose (mkd)

tag: days of administration

tag: covalent binding (pmol-eq/mg protein)

tag: ba-lra score


title: POS_363

value: M


title: MK-7246 08-0037

tag: tissue

value: 0.5% Methylcellulose


title: MK-7246 08-0007

value: Vehicle


title: POS_361

tag: sars-cov-2 positivity


title: POS_362

tag: gender


title: POS_368


title: MK-7246 08-0035


title: MK-7246 08-0003


title: MK-7246 08-0005


title: MK-7246 08-0031


title: MK-4256 07-4153


title: MK-4256 07-4155


title: MK-4256 07-4179


title: MK-7246 08-0039


title: MK-4256 07-4185


title: filorexant 07-2127

value: filorexant

value: 20% vit E TPGS


title: MK-7246 08-0001


title: MK-4256 07-4149


title: MK-4256 07-4151


title: MK-4256 07-4181


title: filorexant 07-2123


title: POS_359


title: POS_358


title: POS_357


title: POS_356


title: POS_355


title: POS_360


title: POS_352

value: O


title: POS_351


title: POS_354


title: filorexant 07-2105


title: filorexant 07-2121


title: filorexant 07-2119


title: filorexant 07-2103


title: filorexant 07-2099


title: POS_349


title: POS_348


title: POS_350


title: POS_353


title: POS_347


title: POS_425

value: Unknown

value: T


title: POS_346

value: P


title: filorexant 07-2101


title: POS_344


title: CMPD P 08-1117

value: CMPD P


title: CMPD P 08-1085


title: CMPD P 08-1115


title: POS_343


title: CMPD P 08-1111


title: CMPD P 08-1113


title: CMPD P 08-1083


title: CMPD P 08-1087


title: CMPD P 08-1081


title: POS_342


title: POS_341


title: POS_338


title: POS_340


title: CMPD N 07-1575

value: CMPD N


title: CMPD N 07-1543


title: CMPD N 07-1571


title: CMPD N 07-1541


title: POS_345

value: pos


title: CMPD N 07-1567


title: MK-5932 07-1635


title: CMPD N 07-1537


title: MK-5932 07-1637


title: POS_335


title: POS_334


title: MK-5932 07-1631


title: POS_332


title: POS_333


title: POS_339


title: POS_337


title: MK-5932 07-1633


title: POS_330


title: POS_336


title: POS_329


title: POS_328


title: POS_331


title: MK-5932 07-1607


title: MK-5932 07-1605


title: MK-5932 07-1601


title: POS_327


title: POS_324


title: POS_326


title: POS_325


title: CMPD M 05-0075

value: CMPD M


title: CMPD M 05-0071


title: CMPD M 05-0073


title: POS_321


title: CMPD M 05-0047


title: CMPD M 05-0045


title: POS_320

value: E


title: CMPD M 05-0077

value: F


title: CMPD M 05-0041

value: liver


title: MK-5932 07-1603


title: POS_318

value: not collected


title: CMPD M 05-0043


title: POS_317

value: M


title: POS_316


title: CMPD L 05-2219

value: CMPD L

value: 0.5% Methylcellulose


title: CMPD L 05-2217


title: POS_322


title: POS_323


title: POS_315


title: CMPD L 05-2215


title: CMPD L 05-2213


title: CMPD L 05-2179

value: Vehicle


title: POS_314


title: CMPD L 05-2177


title: CMPD L 05-2175


title: POS_319


title: POS_310


title: POS_313


title: POS_311


title: POS_312


title: POS_308


title: POS_307


title: CMPD K 08-0037

value: CMPD K

value: 0.5% Methylcellulose w/ 0.02% (w/v) SLS


title: CMPD K 08-0031


title: CMPD K 08-0007


title: POS_306


title: CMPD K 08-0033


title: CMPD K 08-0035


title: CMPD L 05-2173


title: CMPD K 08-0001


title: POS_304


title: POS_303


title: CMPD K 08-0005


title: POS_309


title: POS_302


title: CMPD K 08-0003


title: POS_300


title: POS_301


title: CMPD J 10-0076

value: CMPD J


title: CMPD J 10-0074


title: CMPD J 10-0078


title: CMPD J 10-0046


title: POS_299


title: CMPD J 10-0048


title: POS_305


title: POS_298


title: POS_297

value: D


title: POS_296


title: CMPD J 10-0080


title: CMPD J 10-0042


title: POS_295


title: CMPD I 07-3697

value: CMPD I


title: POS_293


title: POS_292


title: POS_291


title: CMPD J 10-0044


title: POS_289

value: O


title: POS_290


title: CMPD I 07-3691


title: POS_288

value: P


title: CMPD I 07-3671


title: CMPD I 07-3675


title: POS_287

value: pos


title: CMPD I 07-3673


title: CMPD I 07-3677


title: POS_286


title: CMPD I 07-3693


title: CMPD I 07-3695


title: CMPD N 07-1573

value: CMPD N

value: 10% Polysorbate 80


title: POS_285

value: F


title: POS_284


title: POS_282


title: POS_283


title: CMPD H 07-0839

value: liver

value: CMPD H

value: 20% vit E TPGS


title: CMPD H 07-0837


title: POS_281

value: M


title: CMPD H 07-0835


title: CMPD H 07-0833


title: CMPD H 07-0809


title: CMPD H 07-0807


title: CMPD N 07-1539


title: CMPD H 07-0805


title: POS_279


title: POS_278


title: POS_277


title: POS_280


title: POS_275


title: POS_276

value: N


title: POS_273


title: POS_272

value: not collected


title: POS_274


title: POS_271


title: MK-5046 06-0127

value: Vehicle

value: 0.5% Methylcellulose


title: MK-5046 09-0068


title: MK-5046 09-0066


title: CMPD H 07-0803


title: MK-5046 06-0157


title: POS_268


title: POS_270


title: MK-5046 06-0159


title: POS_266


title: POS_269


title: POS_265


title: MK-5046 09-0070


title: POS_264


title: POS_263


title: MK-5046 09-0072


title: MK-5046 06-0125


title: POS_267


title: CMPD G 06-2135


title: MK-5046 06-0129


title: CMPD G 06-2167

value: CMPD G


title: CMPD G 06-2129


title: CMPD G 06-2165


title: CMPD G 06-2131


title: CMPD G 06-2161


title: CMPD F 09-0040

value: CMPD F


title: POS_262

value: L


title: CMPD G 06-2133


title: POS_261


title: CMPD F 09-0038


title: CMPD F 09-0036


title: POS_257


title: POS_259


title: CMPD F 09-0034


title: POS_258


title: POS_256

value: E


title: POS_255


title: POS_254


title: POS_253

value: D


title: POS_252

value: pos

value: C


title: CMPD F 09-0006


title: CMPD F 09-0002


title: POS_251


title: CMPD E 10-0038

value: CMPD E

value: 10% Polysorbate 80


title: CMPD F 09-0004

value: liver


title: POS_260

value: F


title: POS_250


title: CMPD E 10-0036


title: CMPD E 10-0034


title: CMPD E 10-0004


title: CMPD E 10-0008


title: POS_249


title: POS_247


title: POS_246


title: CMPD E 10-0006


title: POS_245


title: MK-0288 10-0040


title: CMPD E 10-0040


title: POS_244


title: MK-0288 10-0038


title: POS_243


title: POS_242


title: MK-0288 10-0034


title: POS_240


title: POS_239


title: POS_238


title: MK-0288 10-0004


title: POS_241


title: MK-0288 10-0006


title: CMPD E 10-0002


title: CMPD D 10-0040

value: CMPD D


title: MK-0288 10-0036

value: M


title: POS_237


title: POS_236


title: MK-0288 10-0002


title: POS_234


title: CMPD D 10-0008


title: CMPD D 10-0034


title: CMPD D 10-0038


title: POS_233


title: POS_232


title: POS_230

value: B


title: POS_231

value: not collected


title: POS_229


title: POS_228


title: MK-8825 07-2215


title: CMPD D 10-0002

value: Vehicle


title: CMPD D 10-0004


title: CMPD D 10-0006


title: CMPD D 10-0036


title: MK-8825 07-2209

value: 0.5% Methylcellulose


title: MK-8825 07-2211


title: MK-8825 07-2213


title: POS_224

value: H


title: MK-8825 07-2183


title: MK-8825 07-2185


title: POS_226


title: POS_225


title: POS_221


title: MK-8825 07-2179


title: POS_223

value: K


title: MK-3207 06-1687


title: POS_220


title: MK-3207 06-1685


title: POS_222


title: POS_219


title: MK-3207 06-1689


title: MK-3207 06-1657


title: MK-3207 06-1683


title: POS_227


title: MK-3207 06-1655


title: CMPD F 09-0008


title: POS_218

value: J


title: POS_217

value: G


title: MK-8825 07-2181


title: POS_213

value: Q


title: POS_215

value: pos


title: POS_216


title: POS_214


title: POS_211


title: POS_212


title: POS_209


title: POS_208


title: POS_210


title: POS_207


title: MK-2918 05-1577


title: POS_206


title: MK-2918 05-1547


title: MK-2918 05-1549


title: MK-3207 06-1653


title: MK-3207 06-1659


title: MK-2918 05-1545


title: MK-2918 05-1543


title: MK-3984 09-0096

value: 0.9% (w/v) Sodium Chloride for Injection


title: POS_202


title: MK-3984 09-0094


title: POS_203


title: MK-3984 09-0090


title: MK-3984 09-0082


title: MK-3984 09-0080


title: POS_204


title: MK-2918 05-1573


title: POS_199


title: POS_200


title: POS_201


title: MK-3984 09-0068


title: MK-3984 09-0084


title: POS_205


title: POS_197


title: POS_198


title: MK-3984 09-0092


title: MK-3984 09-0070


title: MK-3984 09-0064


title: MK-3984 09-0066


title: POS_196


title: MK-3984 09-0072


title: POS_195


title: MK-3984 09-0062


title: MK-3984 09-0060


title: MK-3984 09-0058


title: MK-3984 09-0048


title: POS_189


title: POS_191


title: MK-3984 09-0046


title: MK-3984 09-0078


title: POS_190


title: POS_194


title: POS_192


title: POS_188


title: MK-3984 09-0044


title: POS_187


title: POS_186


title: MK-3984 09-0040


title: POS_185


title: POS_182


title: POS_183


title: POS_184


title: POS_193


title: MK-3984 09-0042


title: POS_181


title: MK-3984 09-0032


title: MK-3984 09-0030


title: MK-3984 09-0028


title: MK-3984 09-0034


title: POS_180


title: POS_178

value: L


title: POS_179


title: APAP 09-0038

value: acetaminophen


title: POS_177


title: APAP 09-0040

value: liver


title: APAP 09-0039

value: F


title: MK-3984 09-0036


title: POS_175


title: POS_174


title: POS_176


title: APAP 09-0037


title: APAP 09-0035


title: APAP 09-0006


title: MK-3984 09-0038


title: POS_172


title: POS_170


title: POS_173


title: APAP 09-0033


title: MK-3984 09-0026


title: APAP 09-0032


title: APAP 09-0002


title: POS_168


title: APAP 09-0034


title: POS_167


title: APAP 09-0004


title: POS_166


title: POS_171


title: APAP 09-0001


title: POS_165


title: POS_163


title: POS_169


title: APAP 09-0003


title: CMPD C 06-2121

value: CMPD C


title: CMPD C 06-2125

value: M


title: CMPD C 06-2127


title: CMPD B 07-2563

value: CMPD B

value: Imwitor 742/Polysorbate 80 (1:1, w/w)


title: CMPD C 06-2093

value: Vehicle


title: POS_162


title: CMPD C 06-2091

value: 0.5% Methylcellulose


title: POS_161


title: POS_160

value: H


title: POS_159


title: POS_158


title: POS_164


title: POS_157


title: POS_155

value: K


title: POS_156


title: POS_154

value: not collected

value: P


title: POS_153


title: POS_152

value: N


title: CMPD B 07-2543


title: CMPD B 07-2559


title: CMPD C 06-2089


title: CMPD B 07-2561


title: CMPD B 07-2545


title: POS_151

value: pos


title: CMPD B 07-2557


title: CMPD A 00-0050

value: CMPD A


title: POS_150


title: CMPD B 07-2541


title: POS_149


title: CMPD A 00-0049


title: POS_148


title: APAP 09-0005


title: POS_145


title: POS_146


title: CMPD A 00-0048


title: POS_144


title: CMPD A 00-0045


title: CMPD B 07-2547


title: CMPD A 00-0011


title: CMPD A 00-0012


title: CMPD A 00-0047


title: CMPD A 00-0052


title: POS_143

value: L


title: CMPD A 00-0002


title: CMPD A 00-0046


title: CMPD A 00-0044


title: POS_142


title: POS_141


title: POS_138


title: POS_147


title: POS_137


title: POS_136


title: POS_135


title: CMPD A 00-0008


title: CMPD A 00-0005


title: CMPD A 00-0006


title: CMPD A 00-0009


title: CMPD A 00-0003


title: CMPD A 00-0004


title: CMPD A 00-0010


title: CMPD A 00-0001


title: POS_134


title: POS_139


title: POS_133


title: POS_130


title: POS_131


title: POS_126


title: POS_127


title: POS_128


title: POS_132


title: POS_129


title: POS_125


title: POS_124


title: POS_122


title: CMPD A 00-0007


title: POS_123


title: Hif1a△SMC-PBS, 3

city: beijing

first: Dan

last: Qi

state: Please Select

address: No.10 Xitoutiao Road, YouAnmen

country: China

institute: Capital Medical University

description: Gene expression data from Hif1a△SMC mice VSMCs treated with PBS for 24 hours

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Hif1aDSMC mice VSMCs treated with PBS for 24 hours

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The VSMCs were cultured in smooth muscle cells medium (SMCM) supplemented with 10% fetal bovine serum(FBS), 1% smooth muscle growth supplement (SMGS) and 1% penicillin streptomycin (PS). The VSMCs were cultured at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Hif1afl/fl mice and Hif1a△SMC mice VSMCs treated with 150μM CoCl2 or an equal volume of  PBS for 24 hours.

value: VSMCs

tag: agent

value: PBS

value: male


title: Hif1a△SMC-CoCl2, 1

description: Gene expression data from Hif1a△SMC mice VSMCs treated with CoCl2 for 24 hours

source_name: Hif1aDSMC mice VSMCs treated with CoCl2 for 24 hours


title: Hif1a△SMC-CoCl2, 2


title: Biopsy_end.of.cold.ischemia_patient_46

city: Toronto

first: Ricardo

last: Zamel

state: Ontario

address: 101 College St.

country: Canada

institute: University Health Network

hyb_protocol: According to manufacturer guidelines

scan_protocol: According to manufacturer guidelines

data_processing: Affymetrix CEL files were imported and processed using RMA in R version 3.5.1 with the affy package. We used an alternative CDF probset description file from Brainarray (version 20) at the University of Michigan (Nucleic Acid Research 33 (20), e175; http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp): hgu133plus2hsentrezgcdf_20.0.0.zip

label_protocol: According to manufacturer guidelines

extract_protocol: RNA was extracted from snap frozen samples using the RNeasy Mini Kit (Qiagen; Hilden, Germany). RNA quality was assessed using Nanodrop spectrophotometer (VWR; Radnor, PA) and Bioanalyzer (Agilent; Santa Clara, CA)

tag: paired samples

tag: timepoint

value: CIT

value: peripheral lung biopsy


title: Biopsy_2hrs.reperfusion_patient_45


title: POS_120

value: M


title: Hif1a△SMC-CoCl2, 3


title: POS_119

value: F


title: Hif1afl/fl-PBS,3

description: Gene expression data from Hif1afl/fl mice VSMCs treated with PBS for 24 hours


title: Hif1afl/fl-CoCl2, 3

description: Gene expression data from Hif1afl/fl mice VSMCs treated with CoCl2 for 24 hours


title: POS_117


title: POS_116


title: Hif1a△SMC-PBS, 1


title: Hif1afl/fl-PBS,2

source_name: Hif1afl/fl mice VSMCs treated with PBS for 24 hours


title: POS_115


title: POS_121


title: Biopsy_end.of.cold.ischemia_patient_45


title: Hif1afl/fl-CoCl2, 1

source_name: Hif1afl/fl mice VSMCs treated with CoCl2 for 24 hours


title: POS_114


title: Hif1a△SMC-PBS, 2


title: Hif1afl/fl-CoCl2, 2


title: Hif1afl/fl-PBS,1


title: POS_118


title: Biopsy_2hrs.reperfusion_patient_43


title: POS_113


title: POS_109

value: C


title: POS_112


title: Biopsy_2hrs.reperfusion_patient_46


title: POS_108

value: B


title: POS_107


title: POS_111


title: POS_106


title: Biopsy_2hrs.reperfusion_patient_41


title: Biopsy_end.of.cold.ischemia_patient_42


title: Biopsy_end.of.cold.ischemia_patient_44


title: Biopsy_2hrs.reperfusion_patient_44


title: Biopsy_2hrs.reperfusion_patient_40


title: POS_104


title: Biopsy_end.of.cold.ischemia_patient_41


title: POS_103


title: Biopsy_end.of.cold.ischemia_patient_43


title: Biopsy_2hrs.reperfusion_patient_39


title: Biopsy_end.of.cold.ischemia_patient_40


title: Biopsy_end.of.cold.ischemia_patient_39


title: POS_100


title: POS_099


title: POS_098

value: Q


title: POS_097


title: POS_105


title: Biopsy_2hrs.reperfusion_patient_38


title: Biopsy_2hrs.reperfusion_patient_37


title: Biopsy_end.of.cold.ischemia_patient_37


title: Biopsy_2hrs.reperfusion_patient_36


title: Biopsy_end.of.cold.ischemia_patient_38


title: Biopsy_end.of.cold.ischemia_patient_36


title: POS_101


title: POS_102


title: Biopsy_2hrs.reperfusion_patient_35


title: Biopsy_end.of.cold.ischemia_patient_35


title: Biopsy_2hrs.reperfusion_patient_34


title: POS_095

value: O


title: POS_093


title: POS_094


title: POS_096


title: POS_089


title: Biopsy_end.of.cold.ischemia_patient_34


title: POS_090


title: POS_092


title: Biopsy_2hrs.reperfusion_patient_33


title: Biopsy_end.of.cold.ischemia_patient_33


title: POS_088


title: Biopsy_2hrs.reperfusion_patient_31


title: Biopsy_end.of.cold.ischemia_patient_32


title: POS_087


title: Biopsy_end.of.cold.ischemia_patient_31


title: Biopsy_2hrs.reperfusion_patient_32


title: Biopsy_2hrs.reperfusion_patient_30


title: POS_086


title: POS_085


title: POS_084

value: I


title: POS_083


title: POS_082

value: not collected


title: POS_080


title: POS_081


title: Biopsy_2hrs.reperfusion_patient_29


title: Biopsy_end.of.cold.ischemia_patient_29


title: POS_078


title: Biopsy_end.of.cold.ischemia_patient_27


title: Biopsy_2hrs.reperfusion_patient_28


title: Biopsy_2hrs.reperfusion_patient_26


title: POS_079


title: Biopsy_end.of.cold.ischemia_patient_28


title: Biopsy_2hrs.reperfusion_patient_27


title: POS_073


title: POS_072


title: Biopsy_end.of.cold.ischemia_patient_25


title: Biopsy_end.of.cold.ischemia_patient_30


title: Biopsy_end.of.cold.ischemia_patient_26


title: POS_075


title: Biopsy_end.of.cold.ischemia_patient_24


title: Biopsy_2hrs.reperfusion_patient_24


title: POS_077


title: Biopsy_2hrs.reperfusion_patient_23


title: Biopsy_2hrs.reperfusion_patient_25


title: POS_071


title: POS_070


title: Biopsy_end.of.cold.ischemia_patient_23


title: POS_076


title: POS_069


title: POS_067


title: POS_066


title: POS_074


title: Biopsy_end.of.cold.ischemia_patient_22


title: Biopsy_2hrs.reperfusion_patient_21


title: POS_065


title: Biopsy_end.of.cold.ischemia_patient_21


title: POS_064


title: Biopsy_2hrs.reperfusion_patient_20


title: Biopsy_end.of.cold.ischemia_patient_19


title: Biopsy_end.of.cold.ischemia_patient_20


title: Biopsy_2hrs.reperfusion_patient_19


title: POS_063

value: E


title: POS_060

value: pos


title: POS_059


title: POS_058


title: POS_062


title: Biopsy_end.of.cold.ischemia_patient_18


title: POS_061


title: POS_057


title: POS_068


title: Biopsy_2hrs.reperfusion_patient_18


title: POS_056


title: POS_055


title: Biopsy_end.of.cold.ischemia_patient_15


title: Biopsy_end.of.cold.ischemia_patient_16


title: Biopsy_2hrs.reperfusion_patient_16


title: Biopsy_2hrs.reperfusion_patient_17


title: Biopsy_2hrs.reperfusion_patient_15


title: POS_052


title: POS_053


title: Biopsy_end.of.cold.ischemia_patient_17


title: POS_051


title: Biopsy_2hrs.reperfusion_patient_13


title: POS_050


title: Biopsy_end.of.cold.ischemia_patient_14


title: POS_049


title: POS_047


title: Biopsy_end.of.cold.ischemia_patient_13


title: Biopsy_2hrs.reperfusion_patient_14


title: POS_045


title: POS_046


title: Biopsy_2hrs.reperfusion_patient_11


title: POS_044


title: Biopsy_end.of.cold.ischemia_patient_12


title: Biopsy_2hrs.reperfusion_patient_42


title: Biopsy_end.of.cold.ischemia_patient_11


title: POS_042


title: Biopsy_2hrs.reperfusion_patient_12


title: POS_043


title: Biopsy_2hrs.reperfusion_patient_9


title: Biopsy_2hrs.reperfusion_patient_10


title: POS_040


title: Biopsy_end.of.cold.ischemia_patient_10


title: POS_048


title: DF2_RIP_WT_rep1

city: Chicago

first: Chuan

last: He

state: IL

address: 929 E 57th Street

department: Chemistry

institute: University of Chicago

description: Sample: 17

data_processing:
Base-calling was performed using CASAVA.
sequencing data were sent to trim-galore to remove low quality reads and adaptor sequence contaminants under default parameters except for “–length 50,”
Remaining reads were then aligned to the mouse transcriptome annotation based on mm10 assembly using hisat2 aligner (v2.1.0), default parameters were used.
Reads count for each gene is calculated by featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: csv; reeads count

extract_protocol:
Total RNA for RNA-seq was extracted with Trizol and the Direct-zol RNA Kit. For m6A seq, polyA RNAs were enriched with the Dynabeads mRNA Purification Kit and fragmented to 150 nt with Bioruptor Pico sonicator. Fragments containing m6A were enriched with the EpiMark N6-methyladenosine Enrichment Kit. To perform RIP-seq, YTHDF2 antibodies were incubated with Protein A Dynabeads. Cells were lysed with lysis buffer (50 mM HEPES, 150 mM KCl, 2 mM EDTA, 0.5% NP40, 0.5 mM DTT, protease and RNase inhibitors). Debris was removed and the lysate was incubated with the protein-bound-beads at 4C for 4 hours. The beads were washed with wash buffer (50 mM HEPES, 200 mM NaCl, 2 mM EDTA, 0.05% NP40, 0.5 mM DTT, protease and RNase inhibitors). YTHDF2 bound RNAs were eluted with Trizol.
All libraries were constructed with the SMARTer Stranded Total RNA-Seq Kit v2 (Takara)

treatment_protocol: For RNA-seq analysis, sorted pro-B cells were cultured with 15ng/mL IL-7 for 0h (IL7_0H group) or 6h(IL7_6H group) before being subject to analysis. For YTHDF2 RIP-seq and m6A-seq, sorted cells were directly used for analysis without any further treatment.

tag: cell type

value: proB cell

tag: genotype

value: wild type

tag: rip antibody

tag: treatment


title: Biopsy_2hrs.reperfusion_patient_8


title: DF2_RIP_WT_rep2

description: Sample: 18


title: Biopsy_end.of.cold.ischemia_patient_9


title: POS_039

tag: age


title: Biopsy_2hrs.reperfusion_patient_7


title: Biopsy_end.of.cold.ischemia_patient_8


title: Biopsy_end.of.cold.ischemia_patient_7


title: DF2_Input_WT_rep2

description: Sample: 16


title: DF2_Input_WT_rep1

description: Sample: 15


title: POS_037


title: Biopsy_2hrs.reperfusion_patient_6


title: POS_036


title: m6A_Input_WT_rep1

description: Sample: 11


title: m6A_IP_WT_rep2

description: Sample: 14

value: anti-m6A from EpiMark® N6-Methyladenosine Enrichment Kit


title: Biopsy_end.of.cold.ischemia_patient_6


title: POS_041


title: m6A_IP_WT_rep1

description: Sample: 13


title: POS_034


title: POS_035


title: m6A_Input_WT_rep2

description: Sample: 12


title: IL7H6_M14ko_rep2

description: Sample: 10

value: Mettl14 Knockout


title: IL7H6_M14ko_rep1

description: Sample: 9


title: POS_033


title: Biopsy_2hrs.reperfusion_patient_4


title: Biopsy_2hrs.reperfusion_patient_5


title: IL7H6_WT_rep2

description: Sample: 7


title: POS_032

value: H


title: proB_M14ko_rep1

description: Sample: 4


title: Biopsy_end.of.cold.ischemia_patient_5

value: CIT


title: IL7H6_WT_rep3

description: Sample: 8


title: proB_WT_rep2

description: Sample: 2


title: POS_030


title: proB_WT_rep1

description: Sample: 1


title: proB_WT_rep3

description: Sample: 3


title: Biopsy_end.of.cold.ischemia_patient_4

value: peripheral lung biopsy


title: Biopsy_2hrs.reperfusion_patient_22


title: Biopsy_2hrs.reperfusion_patient_2


title: Biopsy_end.of.cold.ischemia_patient_3


title: Biopsy_2hrs.reperfusion_patient_3


title: POS_029

value: M


title: Mouse_liver_strain_sex_untreated_dose_duration [US-1457228]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1457228

value: untreated

tag: dose

value: dose

tag: time point

value: duration

value: liver


title: Mouse_liver_strain_sex_untreated_dose_duration [US-1457227]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1457227


title: POS_028

value: J


title: SpreB3_WT

first: Xiaolong

last: Cui

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

data_processing:
Sequencing reads were trimmed of low quality nucleotides by trim_galore.
Trimmed reads were mapped to mouse genome mm9 by bowtie2.
Reads mapped to mitochondrial genome were removed.
Samtools was used to remove PCR duplication.
Deeptools was further used to generate normalized bigwig files.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig normalized signal.

source_name: B cell

extract_protocol:
Chromatin accessibility was assayed using an adaptation of the assay for transposase accessible-chromatin (ATAC)-seq (Buenrostro et al. 2013) as previously described (King and Klose 2017), using 5x10^5 nuclei.
ATAC-seq libraries were prepared by PCR amplification using custom-made Illumina barcodes (Buenrostro et al. 2013) and the NEBNext High-Fidelity 2X PCR Master Mix (NEB). Libraries were purified with two rounds of Agencourt AMPure XP bead cleanup (Agencourt, 1.5X bead:sample ratio), and were sequenced using the Illumina HiSeq 2000 platform using 50 bp single-end reads.

tag: strain

value: PreB cell


title: SpreB3_KO

value: Mettl14 knock out


title: SpreB2_WT


title: proB_M14ko_rep2

description: Sample: 5


title: POS_027

value: F


title: SpreB2_KO


title: Biopsy_end.of.cold.ischemia_patient_2


title: POS_031

value: pos


title: ProB3_WT

value: ProB cell


title: ProB3_KO


title: Biopsy_end.of.cold.ischemia_patient_1


title: POS_025


title: ProB2_KO


title: ProB2_WT

value: wild type


title: POS_023

value: I


title: POS_022


title: P032

data_processing:
Sequencing reads were trimmed of low quality nucleotides by trim_galore.
Trimmed reads were mapped to human genome mm9 by HISAT.
Only uniquely mapped reads were kept for down-stream analyses.
Gene expression profiles were calculated by Cuffdiff.
Genome_build: mm9
Supplementary_files_format_and_content: For each RNA-Seq group, fpkm_tracking files from Cuffdiff are provided.

source_name: in vitro cultured B cell

extract_protocol:
Total RNA was isolated from transfected cells with TRIZOL reagent. Poly-adenylated RNA was enriched by using FastTrack MAG Maxi mRNA isolation kit (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mettl14 KO

value: on day 7 after induced differentiation


title: P024

value: on day 5 after induced differentiation


title: P031


title: adr1 triple_4h_avrRpt2_Rep1.1

city: Chapel Hill

first: Isai

last: Salas Gonzalez

address: 250 Bell Tower Drive, Room 4244

institute: The University of North Carolina at Chapel Hill

data_processing:
Initial quality assessment of the Illumina RNA-Seq reads was performed using FastQC version 0.11.7.
Trimmomatic version 0.36 was used to identify and discard reads containing the Illumina adaptor sequence.
The resulting high-quality reads were then mapped against the TAIR10 Arabidopsis reference genome using HISAT2 version 2.1.0 with default parameters.
The featureCounts function from the Subread package was then used to count reads that mapped to each one of the 27,206 nuclear protein-coding genes, we used these counts to construct a raw count table of expression.
Genome_build: TAIR 10
Supplementary_files_format_and_content: Tab delimited file containing the count matrix

organism: Arabidopsis thaliana

source_name: leaf disc

growth_protocol: Arabidopsis plants were grown at short day conditions (8-hour light/16-hour dark cycle at 21°C/18°C and 45% humidity. Arabidopsis sequence data for helper NLRs is available under the following AGI accession numbers: ADR1/At1g33560, ADR1-L1/At4g33300, ADR1-L2/At5g04720, NRG1.1/NRG1A/At5g66900, NRG1.2/NRG1B/At5g66910.

extract_protocol:
RNA was purified from plant tissue using the RNeasy 96 Kit (Qiagen). The plant “user developed protocol” was followed except for the addition of a 96% ethanol wash step after the second RPE wash to ensure removal of residual salts. Purified RNAs were kept at -80C.
Illumina-based mRNA-Seq libraries were prepared from 1 μg RNA following [61]. Briefly, mRNAs were selected using Sera-mag oligo(dT) magnetic beads (GE Healthcare Life Sciences). RNAs were washed and fragmented at 94°C for 6 minutes. First-strand cDNA synthesis was performed using random hexamers and reverse transcriptase (Superscript III reverse transcriptase, Invitrogen). Second-strand cDNA synthesis was done using DNA Polymerase I and RNAseH. Double-stranded cDNAs were end-repaired using T4 DNA polymerase, T4 polynucleotide kinase, and Klenow polymerase. The DNA fragments were then adenylated using Klenow exo-polymerase to allow the ligation of Illumina adapters (Kapa Dual-indexed adapter kit, Roche). Unless specified, reagents were purchased from Enzymatics.
Library quality control and quantification were performed using the 5200 Fragment Analyser and the NGS fragment kit (Agilent). Libraries were sequenced using Illumina HiSeq4000 sequencers to generate 50-bp single-end reads.

treatment_protocol: Plants for bacterial infiltration assays were grown for 6 weeks under short day conditions (8h light/16h dark at 21°C/18°C and 45% humidity). For bacterial growth curves, Pst DC3000 ∆hrcC and Pst DC3000 expressing either AvrRps4, AvrRpt2, EV, AvrRpm1, grown on KB plates containing appropriate antibiotics, were re-suspended in 10 mM MgCl2 to a final concentration of 5x105 (OD600 0.001).  Plants were hand-infiltrated with the bacterial suspension.

value: adr1 triple

tag: time

tag: rep


title: P029

value: Mettl14 WT


title: P030


title: adr1 triple_4h_avrRps4_Rep3.1


title: P023


title: POS_026

source_name: Nasopharyngeal Swab

value: M


title: P022


title: Biopsy_2hrs.reperfusion_patient_1

value: peripheral lung biopsy


title: P021


title: POS_021


title: adr1 triple_4h_avrRpm1_Rep2.1


title: primed_H9KN2_replicate2

data_processing:
Standard Illumina base-calling pipeline.
As first step in the processing, the first 8 bp of Read 2 were removed and written into the readID of both reads as an in-line barcode, or UMI (Unique Molecular Identifier). This UMI was then later used during the de-duplication step with "deduplicate bismark --barcode mapped_file.bam".
Raw sequence reads were then trimmed to remove both poor quality calls and adapters using Trim Galore (v0.6.2 for hybrid mouse tissues, v0.4.4 for human and inbred mouse tissues, www.bioinformatics.babraham.ac.uk/projects/trim_galore/, Cutadapt version 2.3 for hybrid mouse tissues, v1.9.1 for human and inbred mouse tissues), parameters: --paired). Trimmed reads were aligned to the mouse or human reference genome in paired-end mode. Alignments were carried out with Bismark v0.14.4 for hybrid mouse tissues and v0.18.2 for human and inbred mouse tissues (Krueger and Andrews, 2011)  CpG methylation calls were extracted from the mapping output using the Bismark methylation extractor (v0.22.1 for hybrid mouse tissues, v0.18.2 for human and inbred mouse tissues). Deduplication was then carried out with deduplicate_bismark, using the --bacode option to take UMIs into account (see above)). For hybrid mouse strain experiments, the data was aligned to a hybrid genome of Black6/CAST (the genome was prepared with the SNPsplit package (v0.3.4, https://github.com/FelixKrueger/SNPsplit)). Following alignment and deduplication, reads were split allele-specifically with SNPsplit.
Genome_build: GRCm38
Genome_build: GRCh38
Supplementary_files_format_and_content:  [Bismark coverage file]  The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

source_name: H9-KN2 human embryonic stem cell line

extract_protocol:
[Sample collection protocol]  Genomic DNA was isolated using the DNeasy Blood and Tissue Kit (Qiagen) or the AllPrep DNA/RNA Micro Kit (Qiagen) according to manufacturer’s instructions and eluted into TE buffer or H2O.
The IMPLICON protocol consists of 2 PCR reactions. In the first reaction each sample is amplified with each primer pair in individual reactions: 30ng (2μl of 66μl eluted bisulfite treated DNA) of bisulfite treated DNA is amplified with 1.2μl of 10μM primer pool (final 1.5μM) containing both forward and reverse primers in 4μl of 2x KAPA HiFi Uracil+ ReadyMix in a final volume of 8μl. DNA was amplified using the following conditions: initial denaturation at 95°C for 5min, 30 cycles of 98°C denaturation for 20 seconds, variable annealing temperature for 15 seconds and extension at 72°C for 60 seconds; followed by a final extension at 72°C for 10 minutes. All PCR reactions for each individual sample were pooled together and samples cleaned-up using 1.5x AMPure XP beads and eluted in 20μl H2O. In the second PCR reaction, barcoded Illumina adapters are attached to the pooled PCR samples ensuring that each sample pool receives a unique reverse barcoded adapter. The 20μl PCR pool was amplified using 1μl of 10μM Illlumina PE1.0 primer (same for all samples) and 1μl of 10μM Illumina iTAG primer (distinct for each sample) and 25μl 2x KAPA HiFi Uracil+ ReadyMix in a 50μl volume reaction using the following conditions: initial denaturation at 98°C for 45 seconds, 5 cycles of 98°C denaturation for 15 seconds, 65°C annealing for 30 seconds and extension at 72°C for 30 seconds; followed by a final extension at 72°C for 5 minutes. Reactions were cleaned-up with 1x AMPure XP beads and eluted in 20μl. Libraries were verified by running 1:30 dilutions on Agilent bioanalyzer.

value: embryonic stem cells

tag: cell line

value: H9-KN2 human embryonic stem cell line

tag: protocol

value: cultured in primed conditions


title: adr1 triple_T0_T0_Rep3


title: POS_020

tag: sars-cov-2 positivity

value: J


title: primed_H9KN2_replicate1


title: adr1 triple_4h_avrRps4_Rep2.1


title: adr1 triple_4h_avrRps4_Rep1.1


title: IL7H6_WT_rep1

description: Sample: 6

value: proB cell


title: POS_019

tag: gender


title: POS_024

value: F


title: adr1 triple_4h_avrRpm1_Rep1.1


title: Human_blood_F2

source_name: peripheral blood

value: peripheral blood

value: isolated from healthy human volunteer


title: adr1 triple_4h_EV_Rep2.1

value: EV


title: Human_blood_F1


title: adr1 triple_4h_EV_Rep3.1


title: POS_018

value: pos


title: Ctrl_E_iPSC

source_name: induced pluripotent stem cells

value: induced pluripotent stem cells

value: derived from control patient fibroblasts


title: Ctrl_Fib

source_name: fibroblasts

value: fibroblasts

value: control patient fibroblast


title: adr1 triple_T0_T0_Rep2.1

value: adr1 triple


title: POS_017

value: H


title: Ctrl_D_iPSC


title: POS_016

value: I


title: adr1 triple_4h_EV_Rep1.1


title: AS_E_iPSC

value: derived from Angelman Syndrome (AS) patient fibroblast


title: POS_015

value: G


title: adr1 triple_0.5h_avrRpt2_Rep3.1


title: POS_014

value: M


title: POS_013

value: not collected


title: AS_A_iPSC


title: AS_B_iPSC


title: naive_H9KN2

value: embryonic stem cells

value: H9-KN2 human embryonic stem cell line

value: cultured in naive conditions


title: AS_D_iPSC


title: adr1 triple_8h_EV_Rep2.1


title: adr1 triple_T0_T0_Rep1.1


title: adr1 triple_0.5h_avrRpt2_Rep2.1


title: POS_012

value: F


title: POS_011


title: adr1 triple_0.5h_avrRpm1_Rep3.1


title: adr1 triple_4h_avrRpt2_Rep2.1


title: POS_009


title: adr1 triple_0.5h_avrRpt2_Rep1.1


title: POS_010


title: POS_008


title: adr1 triple_0.5h_avrRps4_Rep3.1


title: adr1 triple_0.5h_avrRpm1_Rep2.1


title: AS_Fib

value: Angelman syndrome patient fibroblast


title: adr1 triple_8h_avrRpt2_Rep3.1


title: POS_006

value: pos


title: adr1 triple_0.5h_avrRps4_Rep2.1


title: POS_007


title: adr1 triple_0.5h_avrRpm1_Rep1.1


title: adr1 triple_0.5h_EV_Rep3.1

value: EV


title: POS_003


title: POS_005


title: adr1 triple_8h_avrRpm1_Rep3.1


title: Human_HEPATOPAC_4202_female_untreated_0µM_216hr [human_D9_3]

description:
Human_Models.tar.gz
human_D9_3

data_processing:
Genome alignment and gene quantitation was performed using OmicSoft Array Studio
Cleaned reads were aligned to the Rnor_6.0 and hg38 genome references using the OmicSoft Aligner with a maximum of 2 allowed mismatches
Gene level counts were determined by the RNA-Seq by expectation maximization algorithm as implemented in OmicSoft Array Studio and using Ensembl.R94 gene models
FPKM normalization was applied to RNA-Seq counts followed by log-transformation with smoothing, i.e., log10(FPKM+0.01)
Genome_build: Rnor_6.0 and hg38 genome
Supplementary_files_format_and_content: Count, FPKM

extract_protocol:
Total RNA was purified from frozen liver or cell culture samples using the MagMAX™ Express Magnetic Particle Processor using the MagMAX™-96 for Microarrays Total RNA Isolation Kit (Thermo Fisher AM1839)
Total RNA samples were converted into cDNA libraries using the KAPA RNA HyperPrep Kit with RiboErase (HMR) Kit (Roche 08098131702) for rat or the TruSeq® Stranded Total RNA Library Prep Human/Mouse/Rat Kit (Illumina 20020596) for human

tag: donor

tag: Sex

value: female

value: untreated

value: 0 microM

tag: tissue

value: HEPATOPAC


title: adr1 triple_0.5h_avrRps4_Rep1.1

value: adr1 triple


title: adr1 triple_8h_avrRps4_Rep3.1


title: adr1 triple_0.5h_EV_Rep2.1


title: adr1 triple_8h_avrRpt2_Rep1.1


title: adr1 triple_8h_avrRpm1_Rep2.1


title: adr1 triple_0.5h_EV_Rep1.1


title: Human_HEPATOPAC_4202_female_untreated_0µM_216hr [human_D9_2]

description:
Human_Models.tar.gz
human_D9_2


title: adr1 triple_8h_avrRps4_Rep2


title: Human_HEPATOPAC_4202_female_untreated_0µM_216hr [human_D9_1]

description:
Human_Models.tar.gz
human_D9_1


title: adr1 triple_8h_avrRpm1_Rep1.1


title: POS_002

value: I


title: adr1 triple_8h_EV_Rep3.1


title: Human_HEPATOPAC_4202_female_untreated_0µM_168hr [human_D7_3]

description:
Human_Models.tar.gz
human_D7_3


title: Human_HEPATOPAC_4202_female_untreated_0µM_168hr [human_D7_2]

description:
Human_Models.tar.gz
human_D7_2


title: adr1 triple_8h_avrRps4_Rep1.1


title: POS_004


title: adr1 triple_4h_avrRpt2_Rep3.1


title: adr1 triple_8h_EV_Rep1.1


title: Human_HEPATOPAC_4202_female_untreated_0µM_168hr [human_D7_1]

description:
Human_Models.tar.gz
human_D7_1


title: Rat_HEPATOPAC_SD_male_flutamide_80µM_48hr [US-1465636]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465636

value: Sprague Dawley

value: male

value: flutamide

value: 80 microM


title: Human_HEPATOPAC_4202_female_untreated_0µM_120hr [human_D5-3]

description:
Human_Models.tar.gz
human_D5-3


title: Rat_HEPATOPAC_SD_male_flutamide_80µM_48hr [US-1465635]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465635


title: Rat_HEPATOPAC_SD_male_flutamide_80µM_48hr [US-1465634]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465634


title: Rat_HEPATOPAC_SD_male_flutamide_30µM_48hr [US-1465633]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465633

value: 30 microM


title: POS_001

value: M


title: adr1 triple_8h_avrRpt2_Rep2.1


title: Human_HEPATOPAC_4202_female_untreated_0µM_120hr [human_D5_2]

description:
Human_Models.tar.gz
human_D5_2


title: Rat_HEPATOPAC_SD_male_flutamide_30µM_48hr [US-1465632]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465632


title: adr1 triple_4h_avrRpm1_Rep3.1


title: adr1 triple_4h_avrRpt2_Rep1


title: Rat_HEPATOPAC_SD_male_flutamide_80µM_24hr [US-1465630]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465630


title: Human_HEPATOPAC_4202_female_untreated_0µM_120hr [human_D5_1]

description:
Human_Models.tar.gz
human_D5_1


title: Rat_HEPATOPAC_SD_male_flutamide_80µM_24hr [US-1465629]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465629


title: Human_HEPATOPAC_4202_female_untreated_0µM_48hr [human_D2_3]

description:
Human_Models.tar.gz
human_D2_3


title: Rat_HEPATOPAC_SD_male_flutamide_80µM_24hr [US-1465628]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465628


title: Rat_HEPATOPAC_SD_male_flutamide_30µM_24hr [US-1465627]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465627


title: Human_HEPATOPAC_4202_female_untreated_0µM_48hr [human_D2_2]

description:
Human_Models.tar.gz
human_D2_2


title: Rat_HEPATOPAC_SD_male_flutamide_30µM_24hr [US-1465626]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465626


title: Rat_HEPATOPAC_SD_male_flutamide_80µM_6hr [US-1465624]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465624


title: adr1 triple_4h_avrRps4_Rep2


title: Human_HEPATOPAC_4202_female_untreated_0µM_48hr [human_D2_1]

description:
Human_Models.tar.gz
human_D2_1


title: Rat_HEPATOPAC_SD_male_flutamide_80µM_6hr [US-1465623]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465623


title: adr1 triple_4h_avrRpm1_Rep1


title: adr1 triple_4h_EV_Rep3


title: Rat_HEPATOPAC_SD_male_MK-3207_80µM_48hr [US-1465590]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465590


title: adr1 triple_4h_avrRps4_Rep1


title: Rat_HEPATOPAC_SD_male_MK-3207_80µM_48hr [US-1465589]

description:
Rat_Hepatopac_Treatments.tar.gz
US-1465589