title: AM5

description: YFP positive lung epithelial cells

data_processing:
10X Genomics Cell Ranger 3.0.0 Pipeline was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting.
Genome_build: mm10
Supplementary_files_format_and_content: matrix.mtx.gz, features.tsv.gz, and barcodes.tsv.gz for each library.

source_name: YFP positive lung epithelial cells 7 weeks after Ad5CMV-Cre treatement - Mouse 2

extract_protocol:
Lungs from KRAS-G12D mice 7 weeks after Ad5CMV-Cre treatment were extracted, single cell suspensions generated, and YFP positive and negative cells collected using FACS. Cells were encapsulated and libraries generated using the 10X Genomics Single Cell 3' v2 pipeline. Pooled libraries were sequenced using an Illumina NextSeq500.
10X Genomics 3' Single Cell RNA Sequencing Protocol Version 2

treatment_protocol: Kras LSL-G12D; Rosa26 LSL-YFP mice were given 2.5x10^7 PFU of Ad5CMV-Cre intratracheally to activate oncogenic KRASG12D and YFP expression in the murine lung.

tag: tumor stage

value: 7 weeks

value: Freshly sorted murine lung tissue

value: KRAS-G12D lung epithelial cells

tag: yfp status

value: positive


title: AM4

status: Public on Sep 04 2020

type: SRA

city: Boston

first: Aaron

middle: L.

last: Moye

state: MA

address: 1 Blackfan Circle

department: Stem Cell Program

country: USA

institute: Boston Children's Hospital

description: YFP negative lung epithelial cells

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: YFP negative lung epithelial cells 7 weeks after Ad5CMV-Cre treatement - Mouse 2

tag: genotype

value: Kras LSL-G12D/WT; Rosa26 LSL-YFP/LSL-YFP

tag: tissue

tag: cell type

value: negative


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E2_ad006

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: SSp

tag: Sex

value: male

tag: age

tag: strain


title: AM2

description: YFP positive lung epithelial cells

source_name: YFP positive lung epithelial cells 7 weeks after Ad5CMV-Cre treatement - Mouse 1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E2_ad002


title: AM1

description: YFP negative lung epithelial cells

source_name: YFP negative lung epithelial cells 7 weeks after Ad5CMV-Cre treatement - Mouse 1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E2_ad008


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E12_ad012


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E12_ad006


title: miCLIP replicate 3

city: New York

first: Tom

middle: Samuel

last: Carroll

state: New York

address: 1230 York Avenue

department: Bioinformatics

institute: The Rockefeller University

description: Poly(A)+ RNA

data_processing:
Fastq data was adaptor and quality trimmed using Flexbar with options (—pre-trim-phred 30, -n 20, -s)
Trimmed Fastq was demultiplexed using pyCRAC’s pyBarcodeFilter.py script and deduplicated using the pyFastqDuplicateRemover.py script
Fastq was aligned to the mm10 genome using Novoalign with options (-t 85, -l 16, -s 1, -o Native, -r None, -c 20, -a). Aligned reads were converted to novoalign2bed.pl script in the CIMS CTK toolkit.
m6A sites were called using the CIMS pipeline as part of the CTK toolkit with default parameters
Genome_build: Mm10 (GRCm38 - Dec. 2011) genome build
Supplementary_files_format_and_content: Bigwigs were generated from aligned reads as BED format using the GenomicRanges R package and raw coverage generated by rtracklayer R package.

molecule: polyA RNA

source_name: Skin epithelial cells

extract_protocol:
Back skin dissected from P0 neonates was treated first with 1x dispase to isolate epidermis, which was then digested with 1:1 0.25% Trypsin-EDTA:versene solution to break down tissue. Single cell suspensions were obtained by filtering through 45 µm cell strainers. Epithelial progenitor cells were isolated by FACS. Total RNA was extracted by TRIzol-LS. Poly(A)+ RNA was extracted with the Dynabeads™ mRNA Purification Kit (Thermo-Fisher, 61006) and treated with the RQ1 RNase-free DNase (Promega, M6101) to remove DNA contamination. 7-8 µg Poly(A)+ RNA was used for each biological replicate (pool of 3 litters of pups) to perform miCLIP. After fragmentation, 1/10 of the sample was saved as input to perform parallel library construction without CLIP.
Library construction protocol is as described in Geula et al., 2015, Mapping m6A at Individual-Nucleotide Resolution Using  Crosslinking and Immunoprecipitation (miCLIP)

value: Skin

value: Postnatal day 0

value: wild-type


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E12_ad007


title: miCLIP replicate 2

description: Poly(A)+ RNA


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E12_ad008


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E12_ad004


title: Input replicate 2

description: Poly(A)+ RNA


title: Input replicate 3

description: Poly(A)+ RNA


title: miCLIP replicate 1

description: Poly(A)+ RNA


title: Input replicate 1

description: Poly(A)+ RNA


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E12_ad001


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E11_ad012


title: E17_Skin_Mettl3_Ctrl

data_processing:
The fastq files for each sample were aligned and counted by CellRanger count (version 2.0). All the parameters were follow the default setting described in user nanual (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/2.0/using/count).
Genome_build: mice genome mm10 (refdata-cellranger-mm10-1.2.0), obtained from 10X Genomics website (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/2.0)
Supplementary_files_format_and_content: For each sample, the processed data contained a count matrix file of each gene in each cell, a gene list (all genes detected in the sample), and the cell barcode list (cells detected in the sample)

extract_protocol:
Back skin dissected from E17 embryos was treated first with 0.25% collagenase and then with 1:1 0.25% Trypsin-EDTA:versene solution to break down tissue. Single cell suspensions were obtained by filtering through 45 µm cell strainers. Then YFP+ epithelial cells were isolated by FACS and ratio of living cells is examined by Trypan blue staining.
Chromium™ Single Cell 3’ Library and Gel Bead Kit (V2) (10× Genomics, 120267)

value: Embryonic day 17

value: Mettl3 fl/+, Rosa16-YFP fl/+, K14Cre (Ctrl)


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E12_ad002


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E11_ad010


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E11_ad008


title: E17_Skin_Mettl3_cKO

value: Mettl3 fl/fl, Rosa16-YFP fl/+, K14Cre (cKO)


title: x288_b2_p6_H12_1c_E_S288: Mouse embryonic stomach at E13.5 Batch2

city: Mainz

first: Sergi

last: Sayols

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology, Mainz

data_processing:
Reads were demultiplexed and fastq files were generated with Illumina bcl2fastq-1.8.4
Fastq files were mapped with STAR_2.5.2b onto Ensembl 88 GRCm38 reference
Secondary alignments were filtered with samtools 1.5
Counts for every gene were calculated with Subread’s FeatureCounts (version 1.5.1) using the gene model provided with Ensembl 88 GRCm38 reference
Genome_build: Ensembl 88 GRCm38
Supplementary_files_format_and_content: tab separated file containing counts per gene

source_name: stomach cells

extract_protocol:
Single EpCAM+ and EpCAM- embryonic gastric cells were isolated by FACS directly in 96 well plates supplemented with buffer (Takara, Clontech). ERCC RNA Spike-In Mix (ThermoFisher) were added for quality and normalization controls. Plates were stored at -80°C.
50ng of total RNA was used for cDNA synthesis using Ovation v2.0 kit (NuGEN) according to manufacturer’s instructions. After cDNA fragmentation (Covaris), libraries were prepared using NEBNext v2.0 kit (NEB) according to manufacturer’s instructions.

treatment_protocol: Stomachs were dissected from mouse embryos at indicated stages, cut in pieces of 2 mm and incubated for 10 min with 0.15mg/ml collagenase (Sigma) in PBS at 37°C with shaking at 800 rpm. Single cell suspensions were collected by centrifugation at 200g for 3 min, washed twice and resuspended in PBS supplemented with 2% foetal calf serum. Cells were stained with APC–conjugated anti-EpCAM 1:1000 (eBioscience) for 30 min at room temperature. Living cells were gated by DAPI dye exclusion. Embryonic gastric epithelial cells were isolated as EpCAM+DAPI−, mesenchymal cells were EpCAM-DAPI-. Fluorescence-activated cell sorting was performed using BD FACS Aria III SORP cell sorter (100 μM nozzle)

value: mixed C57BL/6 CD1

value: stomach

value: embryonic day 13.5


title: x288_b1_p3_H12_1c_E_S288: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E11_ad007


title: x287_b2_p6_G12_1c_E_S287: Mouse embryonic stomach at E13.5 Batch2


title: x287_b1_p3_G12_1c_E_S287: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E11_ad006


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E11_ad004


title: x286_b1_p3_F12_1c_E_S286: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E11_ad002


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E11_ad001


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E10_ad012


title: x284_b2_p6_D12_1c_E_S284: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E10_ad008


title: x285_b1_p3_E12_1c_E_S285: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E10_ad007


title: x284_b1_p3_D12_1c_E_S284: Mouse embryonic stomach at E13.5 Batch1


title: x283_b1_p3_C12_1c_E_S283: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E10_ad004


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E1_ad012


title: x282_b1_p3_B12_1c_E_S282: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E10_ad002


title: x281_b2_p6_A12_1c_E_S281: Mouse embryonic stomach at E13.5 Batch2


title: x286_b2_p6_F12_1c_E_S286: Mouse embryonic stomach at E13.5 Batch2


title: x281_b1_p3_A12_1c_E_S281: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E1_ad007


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E1_ad010


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E1_ad006


title: x279_b2_p6_G11_1c_M_S279: Mouse embryonic stomach at E13.5 Batch2


title: x279_b1_p3_G11_1c_M_S279: Mouse embryonic stomach at E13.5 Batch1


title: x280_b1_p3_H11_1c_M_S280: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E1_ad004


title: x285_b2_p6_E12_1c_E_S285: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E10_ad010


title: x283_b2_p6_C12_1c_E_S283: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E1_ad002


title: x278_b2_p6_F11_1c_M_S278: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E1_ad008


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E10_ad006


title: x282_b2_p6_B12_1c_E_S282: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E1_ad001


title: x278_b1_p3_F11_1c_M_S278: Mouse embryonic stomach at E13.5 Batch1


title: x277_b1_p3_E11_1c_M_S277: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D9_ad010


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D9_ad006


title: x277_b2_p6_E11_1c_M_S277: Mouse embryonic stomach at E13.5 Batch2


title: x280_b2_p6_H11_1c_M_S280: Mouse embryonic stomach at E13.5 Batch2


title: x275_b2_p6_C11_1c_M_S275: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D8_ad001


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D9_ad002


title: x275_b1_p3_C11_1c_M_S275: Mouse embryonic stomach at E13.5 Batch1


title: x274_b2_p6_B11_1c_M_S274: Mouse embryonic stomach at E13.5 Batch2


title: x276_b1_p3_D11_1c_M_S276: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D8_ad010


title: x274_b1_p3_B11_1c_M_S274: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D8_ad004


title: x273_b2_p6_A11_1c_M_S273: Mouse embryonic stomach at E13.5 Batch2


title: x273_b1_p3_A11_1c_M_S273: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D8_ad002


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D8_ad006


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D8_ad008


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D9_ad004


title: x272_b2_p6_H10_1c_E_S272: Mouse embryonic stomach at E13.5 Batch2


title: x271_b1_p3_G10_1c_E_S271: Mouse embryonic stomach at E13.5 Batch1


title: x276_b2_p6_D11_1c_M_S276: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D7_ad001


title: x271_b2_p6_G10_1c_E_S271: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D7_ad012


title: x272_b1_p3_H10_1c_E_S272: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D7_ad010


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D7_ad007


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D8_ad007


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D7_ad006


title: x270_b1_p3_F10_1c_E_S270: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D7_ad002


title: x268_b2_p6_D10_1c_E_S268: Mouse embryonic stomach at E13.5 Batch2


title: x269_b2_p6_E10_1c_E_S269: Mouse embryonic stomach at E13.5 Batch2


title: x267_b2_p6_C10_1c_E_S267: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D7_ad008


title: x268_b1_p3_D10_1c_E_S268: Mouse embryonic stomach at E13.5 Batch1


title: x267_b1_p3_C10_1c_E_S267: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D6_ad012


title: x266_b2_p6_B10_1c_E_S266: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D6_ad010


title: x265_b2_p6_A10_1c_E_S265: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D6_ad004


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D6_ad006


title: x266_b1_p3_B10_1c_E_S266: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D7_ad004


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D6_ad002


title: x269_b1_p3_E10_1c_E_S269: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D6_ad008


title: x265_b1_p3_A10_1c_E_S265: Mouse embryonic stomach at E13.5 Batch1


title: x270_b2_p6_F10_1c_E_S270: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D5_ad012


title: x263_b2_p6_G09_1c_M_S263: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D5_ad010


title: x263_b1_p3_G09_1c_M_S263: Mouse embryonic stomach at E13.5 Batch1


title: x262_b2_p6_F09_1c_M_S262: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D5_ad001


title: x262_b1_p3_F09_1c_M_S262: Mouse embryonic stomach at E13.5 Batch1


title: x261_b2_p6_E09_1c_M_S261: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D5_ad004


title: x261_b1_p3_E09_1c_M_S261: Mouse embryonic stomach at E13.5 Batch1


title: x260_b2_p6_D09_1c_M_S260: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D5_ad002


title: x260_b1_p3_D09_1c_M_S260: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D4_ad010


title: x259_b1_p3_C09_1c_M_S259: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D3_ad007


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D3_ad012


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D4_ad012


title: x258_b1_p3_B09_1c_M_S258: Mouse embryonic stomach at E13.5 Batch1


title: x258_b2_p6_B09_1c_M_S258: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D5_ad007


title: x259_b2_p6_C09_1c_M_S259: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D3_ad008


title: x257_b2_p6_A09_1c_M_S257: Mouse embryonic stomach at E13.5 Batch2


title: x257_b1_p3_A09_1c_M_S257: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D5_ad006


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D2_ad007


title: x256_b2_p6_H08_1c_E_S256: Mouse embryonic stomach at E13.5 Batch2


title: x256_b1_p3_H08_1c_E_S256: Mouse embryonic stomach at E13.5 Batch1


title: x255_b2_p6_G08_1c_E_S255: Mouse embryonic stomach at E13.5 Batch2


title: x255_b1_p3_G08_1c_E_S255: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D2_ad006


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D2_ad004


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D3_ad010


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D2_ad002


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D2_ad012


title: x253_b1_p3_E08_10c_E_S253: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D12_ad012


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D12_ad008


title: x252_b2_p6_D08_1c_E_S252: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D12_ad010


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D2_ad001


title: x252_b1_p3_D08_1c_E_S252: Mouse embryonic stomach at E13.5 Batch1


title: x251_b2_p6_C08_1c_E_S251: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D12_ad004


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D12_ad002


title: x251_b1_p3_C08_1c_E_S251: Mouse embryonic stomach at E13.5 Batch1


title: x250_b2_p6_B08_1c_E_S250: Mouse embryonic stomach at E13.5 Batch2


title: x254_b2_p6_F08_0c_E_S254: Mouse embryonic stomach at E13.5 Batch2


title: x250_b1_p3_B08_1c_E_S250: Mouse embryonic stomach at E13.5 Batch1


title: x254_b1_p3_F08_0c_E_S254: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D10_ad012


title: x249_b2_p6_A08_1c_E_S249: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D2_ad008


title: x248_b2_p6_H07_1c_M_S248: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D10_ad010


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D10_ad008


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D10_ad006


title: x247_b2_p6_G07_1c_M_S247: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D10_ad007


title: x248_b1_p3_H07_1c_M_S248: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D10_ad002


title: x245_b2_p6_E07_1c_M_S245: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D1_ad012


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D12_ad001


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D1_ad001


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D1_ad007


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D1_ad010


title: x249_b1_p3_A08_1c_E_S249: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D2_ad010


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D10_ad004


title: x244_b1_p3_D07_1c_M_S244: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D1_ad006


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D10_ad001


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D1_ad004


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D1_ad002


title: x246_b2_p6_F07_1c_M_S246: Mouse embryonic stomach at E13.5 Batch2


title: x242_b1_p3_B07_1c_M_S242: Mouse embryonic stomach at E13.5 Batch1


title: x246_b1_p3_F07_1c_M_S246: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D1_ad008


title: x241_b2_p6_A07_1c_M_S241: Mouse embryonic stomach at E13.5 Batch2


title: x242_b2_p6_B07_1c_M_S242: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C9_ad012


title: x243_b1_p3_C07_1c_M_S243: Mouse embryonic stomach at E13.5 Batch1


title: x244_b2_p6_D07_1c_M_S244: Mouse embryonic stomach at E13.5 Batch2


title: x245_b1_p3_E07_1c_M_S245: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C9_ad007


title: x240_b2_p6_H06_1c_E_S240: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C9_ad010


title: x240_b1_p3_H06_1c_E_S240: Mouse embryonic stomach at E13.5 Batch1


title: x247_b1_p3_G07_1c_M_S247: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C9_ad006


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C9_ad004


title: x243_b2_p6_C07_1c_M_S243: Mouse embryonic stomach at E13.5 Batch2


title: x241_b1_p3_A07_1c_M_S241: Mouse embryonic stomach at E13.5 Batch1


title: x238_b2_p6_F06_1c_E_S238: Mouse embryonic stomach at E13.5 Batch2


title: x239_b1_p3_G06_1c_E_S239: Mouse embryonic stomach at E13.5 Batch1


title: x239_b2_p6_G06_1c_E_S239: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C8_ad002


title: x238_b1_p3_F06_1c_E_S238: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C9_ad008


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C8_ad010


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D12_ad006


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C8_ad007


title: x237_b1_p3_E06_1c_E_S237: Mouse embryonic stomach at E13.5 Batch1


title: x264_b1_p3_H09_1c_M_S264: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C8_ad006


title: x237_b2_p6_E06_1c_E_S237: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C8_ad004


title: x235_b2_p6_C06_1c_E_S235: Mouse embryonic stomach at E13.5 Batch2


title: x236_b1_p3_D06_1c_E_S236: Mouse embryonic stomach at E13.5 Batch1


title: x235_b1_p3_C06_1c_E_S235: Mouse embryonic stomach at E13.5 Batch1


title: x236_b2_p6_D06_1c_E_S236: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C7_ad012


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C8_ad012


title: x234_b2_p6_B06_1c_E_S234: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C7_ad007


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C7_ad010


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C8_ad001


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C7_ad001


title: x233_b1_p3_A06_1c_E_S233: Mouse embryonic stomach at E13.5 Batch1


title: x233_b2_p6_A06_1c_E_S233: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C7_ad004


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C7_ad006


title: x232_b2_p6_H05_1c_M_S232: Mouse embryonic stomach at E13.5 Batch2


title: x231_b1_p3_G05_1c_M_S231: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C7_ad008


title: x230_b2_p6_F05_0c_M_S230: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C7_ad002


title: x232_b1_p3_H05_1c_M_S232: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C6_ad001


title: x231_b2_p6_G05_1c_M_S231: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C6_ad012


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C6_ad007


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C9_ad002


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C6_ad010


title: x229_b2_p6_E05_10c_M_S229: Mouse embryonic stomach at E13.5 Batch2


title: x229_b1_p3_E05_10c_M_S229: Mouse embryonic stomach at E13.5 Batch1


title: x228_b2_p6_D05_1c_M_S228: Mouse embryonic stomach at E13.5 Batch2


title: x230_b1_p3_F05_0c_M_S230: Mouse embryonic stomach at E13.5 Batch1


title: x264_b2_p6_H09_1c_M_S264: Mouse embryonic stomach at E13.5 Batch2


title: x234_b1_p3_B06_1c_E_S234: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D6_ad001


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C6_ad006


title: x253_b2_p6_E08_10c_E_S253: Mouse embryonic stomach at E13.5 Batch2


title: x228_b1_p3_D05_1c_M_S228: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C6_ad004


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C6_ad002


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C6_ad008


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C5_ad007


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C5_ad006


title: x227_b1_p3_C05_1c_M_S227: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C5_ad001


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C5_ad010


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C4_ad012


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C5_ad004


title: x226_b2_p6_B05_1c_M_S226: Mouse embryonic stomach at E13.5 Batch2


title: x225_b2_p6_A05_1c_M_S225: Mouse embryonic stomach at E13.5 Batch2


title: x224_b2_p6_H04_1c_E_S224: Mouse embryonic stomach at E13.5 Batch2


title: x225_b1_p3_A05_1c_M_S225: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C5_ad008


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C4_ad001


title: x223_b2_p6_G04_1c_E_S223: Mouse embryonic stomach at E13.5 Batch2


title: x224_b1_p3_H04_1c_E_S224: Mouse embryonic stomach at E13.5 Batch1


title: x223_b1_p3_G04_1c_E_S223: Mouse embryonic stomach at E13.5 Batch1


title: x222_b2_p6_F04_1c_E_S222: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C4_ad004


title: x222_b1_p3_F04_1c_E_S222: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C4_ad006


title: x227_b2_p6_C05_1c_M_S227: Mouse embryonic stomach at E13.5 Batch2


title: x221_b2_p6_E04_1c_E_S221: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C4_ad007


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C4_ad008


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C4_ad002


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C3_ad012


title: x226_b1_p3_B05_1c_M_S226: Mouse embryonic stomach at E13.5 Batch1


title: x220_b2_p6_D04_1c_E_S220: Mouse embryonic stomach at E13.5 Batch2


title: x221_b1_p3_E04_1c_E_S221: Mouse embryonic stomach at E13.5 Batch1


title: x220_b1_p3_D04_1c_E_S220: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C3_ad007


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C3_ad001


title: x219_b2_p6_C04_1c_E_S219: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C3_ad010


title: x219_b1_p3_C04_1c_E_S219: Mouse embryonic stomach at E13.5 Batch1


title: x218_b2_p6_B04_1c_E_S218: Mouse embryonic stomach at E13.5 Batch2


title: x218_b1_p3_B04_1c_E_S218: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C3_ad006


title: x216_b2_p6_H03_1c_M_S216: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C3_ad004


title: x217_b1_p3_A04_1c_E_S217: Mouse embryonic stomach at E13.5 Batch1


title: eWAT macrophages that are mtD2+ rep4

city: St. Louis

first: Brian

last: DeBosch

state: Missouri

address: 660 South Euclid Avenue

department: Pediatrics and Cell Biology & Physiology

institute: Washington University School of Medicine

description: 8.GGAGTCC.run_2805_s_2_withindex_sequence.txt_GGAGTCC

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4b
Gene counts quantitated with Subread:featureCount 1.45 with CPM and RPKM transformations added with custom Rscripting.
Genome_build: Ensembl GRCm38.76
Supplementary_files_format_and_content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: eWAT macrophages that are mtD2+

growth_protocol: 0.1% collagenase type II was used to isolate the stromal vascular fraction (SVF) of epididiymal white adipose tissue from adipocyte-specific mitochondria reporter (MitoFat) mice

extract_protocol:
RNeasy Micro Kit (Qiagen)
Clontech SMARTer Ultra-Low RNA kit

treatment_protocol: SVF cells were stained with a viability dye, CD45, F4/80, and CD64 for cell sorting on a BD Aria

value: MitoFat

tag: mouse id

value: Mouse 4

value: Epididymal white adipose tissue

value: live CD45+ F4/80+ CD64+ mtD2+ cells


title: eWAT macrophages that are mtD2+ rep3

description: 7.CCATCAT.run_2805_s_2_withindex_sequence.txt_CCATCAT

value: Mouse 3


title: x217_b2_p6_A04_1c_E_S217: Mouse embryonic stomach at E13.5 Batch2


title: x215_b2_p6_G03_1c_M_S215: Mouse embryonic stomach at E13.5 Batch2


title: eWAT macrophages that are mtD2+ rep1

description: 5.GATGGCC.run_2805_s_2_withindex_sequence.txt_GATGGCC

value: Mouse 1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C3_ad002

value: SSp


title: x215_b1_p3_G03_1c_M_S215: Mouse embryonic stomach at E13.5 Batch1


title: x214_b2_p6_F03_1c_M_S214: Mouse embryonic stomach at E13.5 Batch2


title: eWAT macrophages that are mtD2+ rep2

description: 6.TGACTCT.run_2805_s_2_withindex_sequence.txt_TGACTCT

value: Mouse 2

value: male


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C2_ad012


title: CEMBA180426_8B_1_CEMBA180426_8B_2_D6_ad007


title: x214_b1_p3_F03_1c_M_S214: Mouse embryonic stomach at E13.5 Batch1


title: x213_b1_p3_E03_1c_M_S213: Mouse embryonic stomach at E13.5 Batch1


title: x213_b2_p6_E03_1c_M_S213: Mouse embryonic stomach at E13.5 Batch2


title: eWAT macrophages that are mtD2- rep3

description: 3.AGTTATG.run_2805_s_2_withindex_sequence.txt_AGTTATG

source_name: eWAT macrophages that are mtD2-

value: live CD45+ F4/80+ CD64+ mtD2- cells


title: eWAT macrophages that are mtD2- rep4

description: 4.CCGGCAG.run_2805_s_2_withindex_sequence.txt_CCGGCAG


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C2_ad001


title: eWAT macrophages that are mtD2- rep1

description: 1.CGCTACA.run_2805_s_2_withindex_sequence.txt_CGCTACA


title: x211_b2_p6_C03_1c_M_S211: Mouse embryonic stomach at E13.5 Batch2


title: eWAT macrophages that are mtD2- rep2

description: 2.ATGTTCT.run_2805_s_2_withindex_sequence.txt_ATGTTCT


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C2_ad006


title: x210_b2_p6_B03_1c_M_S210: Mouse embryonic stomach at E13.5 Batch2


title: x212_b1_p3_D03_1c_M_S212: Mouse embryonic stomach at E13.5 Batch1


title: x210_b1_p3_B03_1c_M_S210: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C2_ad004


title: x216_b1_p3_H03_1c_M_S216: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C2_ad010


title: x209_b2_p6_A03_1c_M_S209: Mouse embryonic stomach at E13.5 Batch2


title: x209_b1_p3_A03_1c_M_S209: Mouse embryonic stomach at E13.5 Batch1


title: x207_b2_p6_G02_1c_E_S207: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C2_ad002


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C2_ad008


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C2_ad007


title: x208_b2_p6_H02_1c_E_S208: Mouse embryonic stomach at E13.5 Batch2


title: x207_b1_p3_G02_1c_E_S207: Mouse embryonic stomach at E13.5 Batch1


title: x206_b2_p6_F02_1c_E_S206: Mouse embryonic stomach at E13.5 Batch2


title: x208_b1_p3_H02_1c_E_S208: Mouse embryonic stomach at E13.5 Batch1


title: x205_b2_p6_E02_1c_E_S205: Mouse embryonic stomach at E13.5 Batch2


title: x212_b2_p6_D03_1c_M_S212: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C12_ad012


title: x206_b1_p3_F02_1c_E_S206: Mouse embryonic stomach at E13.5 Batch1


title: x211_b1_p3_C03_1c_M_S211: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C12_ad010


title: x205_b1_p3_E02_1c_E_S205: Mouse embryonic stomach at E13.5 Batch1


title: x204_b2_p6_D02_1c_E_S204: Mouse embryonic stomach at E13.5 Batch2


title: x204_b1_p3_D02_1c_E_S204: Mouse embryonic stomach at E13.5 Batch1


title: AD_HI, biological rep8

type: RNA

city: Fukuoka

first: Yusaku

last: Nakabeppu

state: Fukuoka

address: 3-1-1 Maidashi Higashi-ku

department: Department of Immunobiology and Neuroscience

country: Japan

institute: Medical Institute of Bioregulation, Kyushu University

description: 2020/09/03 newly added

hyb_protocol: Following fragmentation, 5.5 µg of cDNA were hybridized for 17 hr at 45℃ on Affymetrix Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000 7G.

data_processing: CEL files were imported into Affymetrix Expression Console Software, and CHP files were generated.

label: biotin

organism: Homo sapiens

source_name: Hippocampus of of AD brain

label_protocol: The Ambion WT Expression Kit and the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix) were used to generate amplified and biotinylated sense-strand DNA targets from expressed transcripts (100 ng of total RNA).

growth_protocol: We examined postmortem human brains donated for the Hisayama study.

extract_protocol: Total RNA was isolated using a combination of Isogen (Nippon Gene) and the RNeasy Mini Kit (Qiagen), according to the manufacturers’ instructions.

treatment_protocol: During autopsy dissection, parts of the frontal cortex, temporal cortex and hippocampus were cut out from each brain, and preserved at –80°C until RNA preparation.

value: Hippocampus

value: F


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C12_ad007


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C12_ad006


title: x203_b2_p6_C02_1c_E_S203: Mouse embryonic stomach at E13.5 Batch2


title: Donor 2, Timepoint 22, Replicate C

city: Saarbrücken

first: Tim

last: Kehl

address: Campus E2.1, P.O. box 151150

department: Center for Bioinformatics

institute: Saarland University

description: Gene expression after T cell activation (Timepoint 22)

hyb_protocol: Hybridization was performed using the Gene Expression Hybridization Kit and Human SurePrint G3 Gene Expression Microarrays (V3, G4851C; Agilent Technologies, Santa Clara, California, United States) following the manufacturer’s protocol.

scan_protocol: Arrays were scanned with a resolution of 3 µm. Raw data was extracted using Feature Extraction software (Agilent Technologies, Santa Clara, California, United States).

data_processing: Raw expression values were background corrected, quantile normalized and log2 transformed using the limma R-package (method = normexp, offset = 16).

label_protocol: The synthesis of labeled cRNA was performed using Low Input Quick Amp Labeling Kit (One-Color) (Agilent Technologies, Santa Clara, California, United States). The cRNA samples were purified by RNeasy Mini Kit (Qiagen, Hilden, Germany) and concentrations of the purified samples were determined by NanoDrop™ 2000c Spectrophotometer (Thermo Fisher Scientific Inc., Waltham, Massachusetts, United States) following the instructions of the labeling kit.

growth_protocol: Venous blood samples were obtained from two age and gender matched volunteers (female; Donor 1: Age 26 years; Donor 2: Age 23 years). Samples were collected using lithium heparin containing vacutainer collection tubes (S-Monovette®, Sarstedt AG& Co. KG, Numbrecht, Germany). PBMCs were isolated by Ficoll density gradient centrifugation. CD4+ T cells were isolated by negative selection (Human CD4+ T cell Isolation Kit, Miltenyi Biotech, Bergisch Gladbach, Germany). Cells were resolved and cultured in RPMI 1640 medium (Life Technologies GmbH, Darmstadt, Germany), supplemented with 10 % heat inactivated fetal bovine serum (Biochrom GmbH, Berlin, Germany), penicillin (100 U/mL) and streptomycin (100 μg/mL)

extract_protocol: Total RNA was extracted in a semi-automated procedure, using QIAcube robot systems and following the manufacturers` instructions for miRNeasy Micro Kit (Qiagen, Hilden, Germany). The RNA was quantified by Qubit® Fluorometer using Qubit® RNA HS Assay Kit (Thermo Fisher Scientific Inc., Waltham, Massachusetts, United States). RNA integrity was verified using Agilent 2100 Bioanalyzer instrument and RNA Pico Kit (Agilent Technologies, Santa Clara, California, United States). To determine mRNA expression profiles, 25 ng total RNA of each sample was utilized within mRNA One-Color Microarray-Based Gene Expression analysis.

treatment_protocol: 3.5x105 cells/well of the freshly isolated CD4+ cells were seeded into 100 µl of medium within a 96-well plate by using a multichannel pipette. Cells were subsequently activated in separate wells by αCD2/αCD3/αCD28 MACSiBead™ particles (T cell activation/expansion kit, human, Miltenyi Biotec GmbH, Bergisch Gladbach, Germany). Sampling during a total time period of 24 h was conducted, collecting cells of each donor from three separate wells at intervals of 2 h. Cells were pelleted and lysed immediately by QIAzol® Lysis Reagent from miRNeasy Micro Kit (Qiagen, Hilden, Germany). Samples were frozen (-70 °C) for less than 2 months before RNA extraction.

tag: gender

value: female


title: Donor 2, Timepoint 20, Replicate C

description: Gene expression after T cell activation (Timepoint 20)


title: Donor 2, Timepoint 24, Replicate C

description: Gene expression after T cell activation (Timepoint 24)


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C12_ad004


title: x202_b2_p6_B02_1c_E_S202: Mouse embryonic stomach at E13.5 Batch2


title: x202_b1_p3_B02_1c_E_S202: Mouse embryonic stomach at E13.5 Batch1


title: x201_b2_p6_A02_1c_E_S201: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C12_ad001


title: x201_b1_p3_A02_1c_E_S201: Mouse embryonic stomach at E13.5 Batch1


title: Donor 2, Timepoint 18, Replicate C

description: Gene expression after T cell activation (Timepoint 18)


title: x200_b2_p6_H01_1c_M_S200: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C11_ad012


title: Donor 2, Timepoint 12, Replicate C

description: Gene expression after T cell activation (Timepoint 12)


title: x199_b2_p6_G01_1c_M_S199: Mouse embryonic stomach at E13.5 Batch2


title: x203_b1_p3_C02_1c_E_S203: Mouse embryonic stomach at E13.5 Batch1


title: x198_b1_p3_F01_1c_M_S198: Mouse embryonic stomach at E13.5 Batch1


title: x199_b1_p3_G01_1c_M_S199: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C11_ad008


title: x198_b2_p6_F01_1c_M_S198: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C11_ad007


title: x197_b2_p6_E01_1c_M_S197: Mouse embryonic stomach at E13.5 Batch2


title: Donor 2, Timepoint 10, Replicate C

description: Gene expression after T cell activation (Timepoint 10)


title: Donor 2, Timepoint 8, Replicate C

description: Gene expression after T cell activation (Timepoint 8)


title: Donor 2, Timepoint 16, Replicate C

description: Gene expression after T cell activation (Timepoint 16)


title: Donor 2, Timepoint 6, Replicate C

description: Gene expression after T cell activation (Timepoint 6)


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C11_ad006


title: Donor 2, Timepoint 4, Replicate C

description: Gene expression after T cell activation (Timepoint 4)


title: x196_b2_p6_D01_1c_M_S196: Mouse embryonic stomach at E13.5 Batch2


title: x197_b1_p3_E01_1c_M_S197: Mouse embryonic stomach at E13.5 Batch1


title: x196_b1_p3_D01_1c_M_S196: Mouse embryonic stomach at E13.5 Batch1


title: x195_b2_p6_C01_1c_M_S195: Mouse embryonic stomach at E13.5 Batch2


title: x194_b2_p6_B01_1c_M_S194: Mouse embryonic stomach at E13.5 Batch2


title: Donor 2, Timepoint 2, Replicate C

description: Gene expression after T cell activation (Timepoint 2)


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C11_ad002


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C11_ad001


title: x194_b1_p3_B01_1c_M_S194: Mouse embryonic stomach at E13.5 Batch1


title: x193_b1_p3_A01_1c_M_S193: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C10_ad012


title: Donor 2, Timepoint 14, Replicate C

description: Gene expression after T cell activation (Timepoint 14)


title: x192_b2_p5_H12_1c_E_S192: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C11_ad004


title: Donor 2, Timepoint 24, Replicate B


title: Donor 2, Timepoint 0, Replicate C

description: Gene expression after T cell activation (Timepoint 0)


title: Donor 2, Timepoint 22, Replicate B


title: Donor 2, Timepoint 20, Replicate B


title: x195_b1_p3_C01_1c_M_S195: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C10_ad010


title: x192_b1_p2_H12_1c_E_S192: Mouse embryonic stomach at E13.5 Batch1


title: x191_b1_p2_G12_1c_E_S191: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C10_ad008


title: x191_b2_p5_G12_1c_E_S191: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C10_ad007


title: x189_b2_p5_E12_1c_E_S189: Mouse embryonic stomach at E13.5 Batch2


title: x190_b2_p5_F12_1c_E_S190: Mouse embryonic stomach at E13.5 Batch2


title: x193_b2_p6_A01_1c_M_S193: Mouse embryonic stomach at E13.5 Batch2


title: x190_b1_p2_F12_1c_E_S190: Mouse embryonic stomach at E13.5 Batch1


title: x189_b1_p2_E12_1c_E_S189: Mouse embryonic stomach at E13.5 Batch1


title: x188_b2_p5_D12_1c_E_S188: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C10_ad006


title: x188_b1_p2_D12_1c_E_S188: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C10_ad004


title: x187_b2_p5_C12_1c_E_S187: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C10_ad002


title: Donor 2, Timepoint 12, Replicate B


title: Donor 2, Timepoint 16, Replicate B


title: Donor 2, Timepoint 14, Replicate B


title: LZ018 (iNOA_2)

city: Zhuhai

first: Liangyu

last: Zhao

state: Guangdong

address: 52th Meihua Road, Zhuhai, China

country: China

institute: Shanghai Jiao Tong University School of Medicinethe Fifth Affiliated Hospital of Sun Yat-sen University

data_processing:
Cell Ranger software (version 2.2.0), provided by 10× Genomics, was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and downsample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells.
Cells were further filtered according to the following threshold parameters: the total number of expressed genes, 500 to 9000; total UMI count, less than 35,000; and proportion of mitochondrial genes expressed, <40%.
Genome_build: hg18
Supplementary_files_format_and_content: UMI values for each cell

source_name: testis tissue

extract_protocol:
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit (P/N 120237, 10× Genomics) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols (Illumina Novaseq 6000)

tag: disease state

value: Non -obstructive azoospermia (NOA)

value: testis

tag: condition

value: pathologic

tag: group


title: LZ019 (iNOA_3)


title: Donor 2, Timepoint 10, Replicate B


title: Donor 2, Timepoint 8, Replicate B


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C10_ad001


title: x187_b1_p2_C12_1c_E_S187: Mouse embryonic stomach at E13.5 Batch1

value: mixed C57BL/6 CD1

value: stomach

value: embryonic day 13.5


title: Donor 2, Timepoint 18, Replicate B


title: x186_b2_p5_B12_1c_E_S186: Mouse embryonic stomach at E13.5 Batch2


title: LZ017 (iNOA_1)


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C1_ad012


title: LZ016 (17 yo)

value: normal spermatogenesis

value: physiologic

value: 17 yo


title: x185_b2_p5_A12_1c_E_S185: Mouse embryonic stomach at E13.5 Batch2


title: LZ015 (Adult_5)


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C1_ad001


title: x186_b1_p2_B12_1c_E_S186: Mouse embryonic stomach at E13.5 Batch1


title: Donor 2, Timepoint 6, Replicate B


title: Donor 2, Timepoint 4, Replicate B


title: Donor 2, Timepoint 2, Replicate B


title: LZ012 (KS_3)


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C1_ad006


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C11_ad010


title: LZ013 (Adult_3)


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C1_ad010


title: x184_b1_p2_H11_1c_M_S184: Mouse embryonic stomach at E13.5 Batch1


title: LZ011 (2 yo)

value: 2 yo


title: x184_b2_p5_H11_1c_M_S184: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C1_ad004

value: SSp


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C1_ad002


title: x183_b1_p2_G11_1c_M_S183: Mouse embryonic stomach at E13.5 Batch1


title: LZ009 (5 yo)

value: 5 yo


title: Donor 2, Timepoint 0, Replicate B


title: Donor 2, Timepoint 24, Replicate A


title: x182_b2_p5_F11_1c_M_S182: Mouse embryonic stomach at E13.5 Batch2


title: Donor 2, Timepoint 22, Replicate A


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B9_ad012

value: male


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C1_ad007


title: LZ010 (KS_2)


title: LZ014 (Adult_4)


title: x185_b1_p2_A12_1c_E_S185: Mouse embryonic stomach at E13.5 Batch1


title: Donor 2, Timepoint 20, Replicate A


title: LZ008 (11 yo)

value: 11 yo


title: Donor 2, Timepoint 14, Replicate A


title: Donor 2, Timepoint 12, Replicate A


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B9_ad001


title: Donor 2, Timepoint 16, Replicate A


title: x182_b1_p2_F11_1c_M_S182: Mouse embryonic stomach at E13.5 Batch1


title: LZ007 (Adult_2)


title: Donor 2, Timepoint 18, Replicate A


title: x183_b2_p5_G11_1c_M_S183: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_C1_ad008


title: LZ005 (8 yo)

value: 8 yo


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B9_ad010


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B9_ad007


title: x181_b1_p2_E11_1c_M_S181: Mouse embryonic stomach at E13.5 Batch1


title: LZ004 (KS_1)


title: x180_b1_p2_D11_1c_M_S180: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B9_ad006


title: HORSE5 (HORSE5)

city: Bologna

first: Luca

last: Morandi

address: via Altura 3

department: DIBINEM

country: Italy

institute: University of Bologna

data_processing:
Reads were mapped by BWAmeth generating the .bam file which was processed by MethylDackel using hg38 for human samples, Felis_catus_9.0 for feline samples as a reference;
EPIC-TABSAT web-tool
Methylation Plotter Webtool
ClustVis webtool
EasyROC
Genome_build: hg38
Supplementary_files_format_and_content: Table 1: Clinical details of mammalian species other than human included in this study:
Supplementary_files_format_and_content: Table 2: genomic regions investigated in this study (reference genome: hg38; gene annotations were retrieved from UCNE database[2] and from Bajerano database[1]):
Supplementary_files_format_and_content: Table 3: Best and worst AUC values for all the seven UCNEs; the number indicates the position on the genome taking into account hg38 as a reference:
Supplementary_files_format_and_content: Table S1: Summary Table with the mean, the standard deviation, the minimum, the maximum and p value of the Kruskal-Wallis test for each position and group of samples comparing all SCC from all the species together vs normal samples and feline stomatitis
Supplementary_files_format_and_content: Table S2: Summary Table comparing human normal donors vs SCC
Supplementary_files_format_and_content: Table S3: Summary Table with the mean, the standard deviation, the minimum, the maximum and p value of the Kruskal-Wallis test for feline SCC vs feline normal samples and feline stomatitis
Supplementary_files_format_and_content: TUCRDataFinalJuly2020: methylation level of each CpG for all cases

organism: Equus caballus

source_name: oral mucosa

extract_protocol:
MasterPure DNA purification kit or QuickExtract FFPE DNA Extraction kit
Locus-specific amplicon libraries were generated with tagged primers in two steps: a first PCR amplification for target enrichment, and a second shorter amplification session (8 cycles) to allow the barcoding of the template-specific amplicons obtained from the first amplification step using the Nextera™ Index Kit (Illumina, San Diego, CA, USA)

treatment_protocol: Formali Fixed Paraffin Embedded Tissue or oral brushing specimens

value: Normal

value: oral brush

tag: tnm

value: Normal oral mucosa


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B9_ad004


title: HORSE4 (HORSE4)


title: HORSE3 (HORSE3)


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B9_ad002


title: x181_b2_p5_E11_1c_M_S181: Mouse embryonic stomach at E13.5 Batch2


title: x179_b2_p5_C11_1c_M_S179: Mouse embryonic stomach at E13.5 Batch2


title: x179_b1_p2_C11_1c_M_S179: Mouse embryonic stomach at E13.5 Batch1


title: Donor 2, Timepoint 8, Replicate A

value: female


title: HORSE2 (HORSE2)


title: Donor 2, Timepoint 10, Replicate A


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B8_ad001


title: Donor 2, Timepoint 4, Replicate A


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B9_ad008


title: x178_b2_p5_B11_1c_M_S178: Mouse embryonic stomach at E13.5 Batch2


title: x178_b1_p2_B11_1c_M_S178: Mouse embryonic stomach at E13.5 Batch1


title: x180_b2_p5_D11_1c_M_S180: Mouse embryonic stomach at E13.5 Batch2


title: HORSE1 (HORSE1)


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B8_ad010


title: x177_b2_p5_A11_1c_M_S177: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B8_ad007


title: Donor 2, Timepoint 0, Replicate A


title: x177_b1_p2_A11_1c_M_S177: Mouse embryonic stomach at E13.5 Batch1


title: Donor 2, Timepoint 6, Replicate A


title: Donor 1, Timepoint 24, Replicate C


title: x176_b2_p5_H10_1c_E_S176: Mouse embryonic stomach at E13.5 Batch2


title: Donor 2, Timepoint 2, Replicate A


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B8_ad006


title: Pten -/- scRNA

first: Neel

last: Shah

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

data_processing:
De-multiplexing and analyzed: CellRanger pipeline (10x Genomics)
Doublets and high mitochondrial reads removed using CellRanger pipeline (10x Genomics)
Data visualization: Loupe Browser (10x Genomics)
Genome_build: mm9
Supplementary_files_format_and_content: cloupe

source_name: Murine prostate organoid line

growth_protocol: Standard organoid growth media/conditions in 3D matrigel conditions

extract_protocol:
17,000 cells loaded onto the ChromiumTM Controller (10× Genomics)
Chromium Single Cell 5' Library & Gel Bead Kit (10× Genomics)
10x Genomics platform scRNA-Seq

value: Prostate

value: Pten -/-


title: AP7483TUCR (AP7483)

value: SCC

value: FFPE

value: Squamous Cell Carcinoma


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B8_ad008


title: Wildtype scRNA

value: Wildtype


title: x176_b1_p2_H10_1c_E_S176: Mouse embryonic stomach at E13.5 Batch1

value: mixed C57BL/6 CD1

value: stomach

value: embryonic day 13.5


title: x175_b2_p5_G10_1c_E_S175: Mouse embryonic stomach at E13.5 Batch2


title: Donor 1, Timepoint 20, Replicate C


title: Treat2

city: Nanchang

first: su

last: tie

address: XueFu road 999,HongGuTang newly-developed area,NanChang City,JiangXi province

department: Jiangxi Medical College

institute: Nanchang university

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using HISAT. Ana then the transcripts were assembled using Cufflinks.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Assembly transcripts were compared with annotated lncRNA in NONCODE database (http://www.noncode.org/) using Cuffcompare. The novel transcripts were predicted with CPC, txCdsPredict, CNCI and pfam algorithm.
Genome_build: mm9
NONMMUGnnnn IDs and sequences can be found in http://www.noncode.org/
Supplementary_files_format_and_content: txt files include gene_id, transcript_id(s), length expected_count, FPKM values for each Sample

source_name: ovary

extract_protocol:
The ovaries were homogenized and ovarian total RNA was extracted in accordance with manufacturer’s instructions from TRIzol (Invitrogen company, USA). the concentration and purity of the total RNA samples were evaluated using a NanoPhotometer (IMPLEN, Munich, Germany) with optical density measurements at 1.8 < A260/A280 < 2.0. The integrity of RNA was always checked by electrophoresis in 1.5% agarose gels.
Strand-specific LncRNA library was generated with the TruSeq® Stranded kit. The sequencing was conducted using Illumina HiSeqTM 4000 with PE100 according to the manufacturer’s instructions developed by BGI (Wuhan, China). About 10 G clean data were used to bioinformatic analysis.

value: follicle after the initiation

value: ovary


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B7_ad012

value: SSp

value: male


title: x175_b1_p2_G10_1c_E_S175: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B7_ad001


title: Treat1


title: Donor 1, Timepoint 14, Replicate C


title: Pten -/- R26-ERG scRNA

value: Pten -/- R26-ERG


title: Donor 1, Timepoint 18, Replicate C


title: Donor 1, Timepoint 22, Replicate C


title: Donor 1, Timepoint 10, Replicate C


title: Donor 1, Timepoint 12, Replicate C


title: x174_b2_p5_F10_1c_E_S174: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B8_ad002


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B7_ad007


title: x174_b1_p2_F10_1c_E_S174: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B7_ad006


title: CK1

value: ovarian follicle before the initiation


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B7_ad010


title: x173_b2_p5_E10_1c_E_S173: Mouse embryonic stomach at E13.5 Batch2


title: Donor 1, Timepoint 6, Replicate C


title: YueLab-RNA-seq-Blood-rep2

city: CHICAGO

first: Yu

last: Luan

state: Illinois

address: 303 E. Superior Simpson Querrey 7-518

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

data_processing:
RNA-seq reads were aligned to zv10 genome assembly using STAR; The TPM value of gene expression was caculated using RSEM
ChIP-seq and ATAC-seq reads were aligned to zv10 genome assembly using Bowtie2;H3K27ac, H3K4me3 ChIP-seq were called using MACS2 with the following  setting: ChIP-seq q-value <10e-2, p-value<10e-5, Change>1,FC>2. ATAC-seq: q-value<10e-2 and p-value<10e-5.For the ATAC-seq, the peak length were fixed to 500 bp. We only selected the peak with the most significant signal if several peaks overlap with each other in each tissue.Since the H3K9me3 and H3K9me2 makers are broad domain, we called the peak using Homer with the parameter “-region -size 1000”, and peaks within 5 kb were merged together.
HiC matrix was generated using HiC-Pro
WGBS data were mapped to in silico bisulfite-converted zebrafish genome reference by using Bismark
For the scATAC-seq, the BCL files generated from sequencing were used as inputs to the 10X Genomics Cell Ranger ATAC-seq pipeline; then the FASTQ files were aligned to the GRCz10 genome using BWA and the fragments with MAPQ>30 were kept for further analysis and each fragment is associated with a single cell barcode.
Genome_build: zv10(GRCz10)
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi-C for each Sample.**All replicates were merged

organism: Danio rerio

source_name: YueLab-RNA-seq-Blood

growth_protocol:
RNA-seq: Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions
ChIP-seq, ATAC-seq, Hi-C and WGBS: Ault Tuebingen zebrafish were raised under standard laboratory conditions

extract_protocol:
RNA-seq: For each RNA-seq experiment, the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk, ten 1-dpf fish were dechorionated with pronase and trunk were cut off for RNA-seq. For embryonic neuron, green cells from Tg(Huc:Kaede) cells were sorted by FACS and approxinately 20,000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol (Invitrogen).
RNA-seq: The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit (Agilent) according to the manufacturer’s protocol. Briefly, polyA RNA was purified from 1000 ng of total RNA using oligo (dT) beads (Invitrogen). Extracted RNA was first fragmented, then followed by reverse transcription, end repair, adenylation, adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent) and Kapa Library Quantification Kit (Kapa Biosystems) and then followed by pair-end 2X 50 bp high-throughput sequencing using HiSeq 2500 (Illumina).
ChIP-seq: All the tissues were ground in the liquid nitrogen and fixed by 1% formaldehyde at room temperature for 15 min. 0.2 M glycine was added and incubated at room temperature for 5 min to quench the fixation. Fixed tissues were then washed once by cold 1X PBS. Tissue pellet was resuspended and incubated on ice for 10 min in 100 µL of ChIP-seq lysis buffer (20 mM Tris-HCl, pH 8.0, 1% SDS, 50 mM EDTA, 1X proteinase inhibitor cocktail). Next, 900 µL cold 1X TE buffer was added to dilute SDS concentration and the nuclei suspension was sonicated using Covaris E220 with the following parameters: 140 W, duty factor 5, 200 per burst. Sonication time is variable, depending on tissue types. To check the chromatin fragmentation size, 20 µL of input chromatin was reverse crosslinked in elution buffer (20 mM Tris-HCl, pH 8.0, 1% SDS, 1 mM EDTA) at 65 °C overnight, treated with Rnase A and proteinase K and purified by phenol-chloroform extraction. Input DNA was then loaded on a Lonza flash gel to make sure that the majority of DNA size distributes between 100-300 bp. To prepare antibody-beads complex, 3 µg of histone H3K27ac antibody (Active Motif, 39133) or H3K4me3 antibody (EMD Millipore, 07-473) was mix with 12 µL M-280 sheep anti-rabbit IgG Dynabeads (ThermoFisher, 11203D) in 150 µL of 5 mg/mL BSA/1X PBS buffer, with rotation at 4 °C for 3 h. After incubation, antibody-beads complex was washed once with BSA/1X PBS buffer. About 200 µg chromatin was used per IP. Equal volume of master mix (1X TE, 2% Triton X-100, 0.2% sodium deoxycholate, 2X proteinase inhibitor cocktail) was mixed with 200 µg chromatin and then incubated with antibody-beads complex overnight with rotation. The next morning, the beads were washed 5 times with cold RIPA wash buffer (20 mM Tris-HCl, pH 8.0, 1% NP-40, 0.7% sodium deoxycholate, 500 mM LiCl, 1 mM EDTA, 1X proteinase inhibitor cocktail). Then the chromatin bound on the beads was eluted by 150 µL of elution buffer at 65 °C for 30 min.
ChIP-seq: To prepare the library, eluted chromatin was reverse crosslinked and purified by phenol-chloroform extraction. Then DNA was end-repaired by END-IT DNA end-repair kit (Epicentre, ER81050) according to kit’s protocol, added A using Klenow  fragment (3’->5’ exo-) (NEB, M0212S), ligated with Illumina TruSeq adaptor (Illumina, FC-121-3001) and subsequently amplified by PCR (Roche, kk2601). The quality and quantity of all the libraries were checked using BioAnalyzer High Sensitivity DNA Kit (Agilent). The libraries were sequenced on Illumina HiSeq 2500 with reads length of 2X 50 bp or 2X 100 bp.
ATAC-seq: Tuebingen adult tissues were ground in liquid nitrogen,resuspended in 1 mL of lysis buffer (1X PBS, 0.2% NP-40, 5% BSA, 1 mM DTT, protease inhibitors), followed by incubation at  4 °C for 10 min on an overhead shaker. After that, lysate was filtered through 40 m cell strainer and nuclei were collected at 1000X g for 5 min.
ATAC-seq: Tagmentation was performed immediately according to ATAC-seq protocol reported previously(Buenrostro et al., 2013)
Hi-C: For brain tissue, two adult Tuebingen brains were slightly ground into small granules in liquid nitrogen and resuspended in 1 mL of cold hypotonic buffer (20 mM Tris-HCl, pH 8.0, 10 mM NaCl, 20 mM EDTA). Granular brains were then dounce homogenized with loose pestle for 20 times. The top of the homogenate was carefully transferred into a new tube and fixed with 2% formaldehyde at room temperature for 10 min. 0.2 M of glycine was added to stop fixation. For muscle tissue, 60 mg of Tuebingen muscle was first chopped into small pieces and digested by 0.25% trypsin at room temperature for 30 min. After neutralization with FBS, muscle cells were resuspended in cold 1X PBS and fixed with 2% of formaldehyde at room temperature for 10 min. 0.2 M glycine was then added to stop fixation.
Hi-C: Hi-C experiments on adult zebrafish brain and muscle tissues were performed according to previously published protocol(Rao et al., 2014). The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent) and Kapa Library Quantification Kit (Kapa Biosystems) and then followed by pair-end 2X 100 bp high-throughput sequencing using HiSeq 2500  or HiSeq 4000(Illumina).
WGBS: Tübingen adult tissues were dissected, and the genomic DNA was extracted using DNeasy Blood & Tissue Kit (Qiagen, 69504). Then 1 µg of genomic DNA of each adult tissue was subjected to bisulfite conversion using EZ DNA Methylation-Gold Kits
WGBS: The final libraries were prepared using the Accel-NGS® Methyl-Seq DNA Library Kit.
scATAC-seq: Single-cell ATAC-seq (scATAC-seq) was performed in one female brain and one male brain, respectively, on the 10X Genomics platform. To isolate nuclei, freshly dissected single brain was transferred to 1 mL NbActiv1 medium (BrainBits, NbActiv1 500) with a wide-bore pipette tip to break the tissue into small pieces. Then the tissue was broken up completely using regular-bore pipette tips followed by filtering through a 30 µm cell strainer. The isolated cells were spun down at 500 g for 5 min at 4 °C and then lysed in 100 µL chilled 0.1X Lysis Buffer (10 mM Tris HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 1% BSA,0.01% Tween-20, 0.01% NP40 and 0.001% digitonin) on ice for 5 min. Then 1 mL chilled Wash Buffer (10 mM Tris HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.1% Tween-20) was added to the lysed cells and cells were spun down at 500 g for 5 min at 4 °C. At last, 300 µL chilled Diluted Nuclei Buffer (10x Genomics, PN 2000153/2000207) was added to resuspend the nuclei. The nuclei were filtered again using a 30 µm cell strainer before cell counting
scATAC-seq: Around 12,000 nuclei were used for one Tn5 tagmentation reaction, and the scATAC-seq library was prepared and sequenced exactly according to the company’s user guide.

value: Tuebingen

value: Blood


title: Pten -/- R26-ERG ERG CRISPR scRNA

value: Prostate

value: Pten -/- R26-ERG ERG CRISPR


title: Donor 1, Timepoint 8, Replicate C

value: female


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B7_ad004


title: x200_b1_p3_H01_1c_M_S200: Mouse embryonic stomach at E13.5 Batch1


title: x172_b2_p5_D10_1c_E_S172: Mouse embryonic stomach at E13.5 Batch2


title: YueLab-muscle-HiC-rep2

description: Hi-C(DpnII)

source_name: YueLab-muscle-HiC

value: Muscle


title: x173_b1_p2_E10_1c_E_S173: Mouse embryonic stomach at E13.5 Batch1


title: YueLab-RNA-seq-Blood-rep1


title: CK2


title: Donor 1, Timepoint 4, Replicate C


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B7_ad002


title: x172_b1_p2_D10_1c_E_S172: Mouse embryonic stomach at E13.5 Batch1


title: YueLab-muscle-HiC-rep1

description: Hi-C(DpnII)


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B7_ad008


title: Donor 1, Timepoint 0, Replicate C


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B6_ad012


title: x171_b2_p5_C10_1c_E_S171: Mouse embryonic stomach at E13.5 Batch2


title: Donor 1, Timepoint 2, Replicate C


title: Donor 1, Timepoint 22, Replicate B


title: x171_b1_p2_C10_1c_E_S171: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B6_ad001


title: Donor 1, Timepoint 24, Replicate B


title: YueLab-Input-Blood-rep2

description:
processed data file:
YueLab-ChIP-seq-blood_H3K9me2.peak.gz
YueLab-ChIP-seq-blood_H3K9me3.peak.gz
YueLab-ChIP-seq-Blood_H3K27ac_merged.narrowPeak.gz

source_name: YueLab-Input-Blood


title: Donor 1, Timepoint 20, Replicate B


title: YueLab-Input-Blood-rep1


title: x170_b2_p5_B10_1c_E_S170: Mouse embryonic stomach at E13.5 Batch2


title: x170_b1_p2_B10_1c_E_S170: Mouse embryonic stomach at E13.5 Batch1


title: YueLab-H3K9me3-Blood-rep2

tag: chip-seq antibody

value: Abcam, ab8898


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B6_ad010


title: x169_b2_p5_A10_1c_E_S169: Mouse embryonic stomach at E13.5 Batch2


title: YueLab-H3K9me3-Blood-rep1


title: x169_b1_p2_A10_1c_E_S169: Mouse embryonic stomach at E13.5 Batch1


title: Donor 1, Timepoint 18, Replicate B


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B6_ad004


title: Donor 1, Timepoint 16, Replicate B


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B6_ad002


title: Donor 1, Timepoint 14, Replicate B


title: YueLab-H3K9me2-Blood-rep1

value: Cell Signaling, 4658


title: YueLab-H3K9me2-Blood-rep2


title: x168_b2_p5_H09_1c_M_S168: Mouse embryonic stomach at E13.5 Batch2

value: mixed C57BL/6 CD1


title: Donor 1, Timepoint 12, Replicate B


title: Donor 1, Timepoint 16, Replicate C


title: Donor 1, Timepoint 10, Replicate B


title: Donor 1, Timepoint 8, Replicate B


title: YueLab-H3K4me3-Blood-rep2

value: EMD Millipore, 07-473


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B6_ad008


title: YueLab-H3K4me3-Blood-rep1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B6_ad007


title: x168_b1_p2_H09_1c_M_S168: Mouse embryonic stomach at E13.5 Batch1

value: stomach

value: embryonic day 13.5


title: x167_b1_p2_G09_1c_M_S167: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B5_ad001


title: x167_b2_p5_G09_1c_M_S167: Mouse embryonic stomach at E13.5 Batch2


title: Donor 1, Timepoint 6, Replicate B


title: YueLab-H3K27ac-Blood-rep2

value: Active Motif, 39133


title: YueLab-H3K27ac-Blood-rep1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B5_ad007

value: SSp


title: x166_b2_p5_F09_1c_M_S166: Mouse embryonic stomach at E13.5 Batch2


title: x166_b1_p2_F09_1c_M_S166: Mouse embryonic stomach at E13.5 Batch1


title: Donor 1, Timepoint 4, Replicate B


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B5_ad010

value: male


title: YueLab-ATACseq-Testis-rep2

source_name: YueLab-ATACseq-Testis

value: Testis


title: x165_b2_p5_E09_1c_M_S165: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B5_ad012


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B6_ad006


title: Donor 1, Timepoint 2, Replicate B


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B5_ad006


title: YueLab-ATACseq-Spleen-rep2

source_name: YueLab-ATACseq-Spleen

value: Spleen


title: Donor 1, Timepoint 0, Replicate B


title: x165_b1_p2_E09_1c_M_S165: Mouse embryonic stomach at E13.5 Batch1


title: Donor 1, Timepoint 24, Replicate A


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B5_ad004

source_name: C57BL/6J Male P56 Mouse Brain


title: YueLab-ATACseq-Muscle-rep2

source_name: YueLab-ATACseq-Muscle

value: Tuebingen


title: Donor 1, Timepoint 22, Replicate A


title: x164_b2_p5_D09_1c_M_S164: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B5_ad002


title: YueLab-ATACseq-Muscle-rep1


title: x163_b2_p5_C09_1c_M_S163: Mouse embryonic stomach at E13.5 Batch2


title: YueLab-brain-HiC-rep2

description: Hi-C(DpnII)

source_name: YueLab-brain-HiC

value: Brain


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B4_ad012


title: YueLab-ATACseq-Liver-rep2

source_name: YueLab-ATACseq-Liver

value: Liver


title: x164_b1_p2_D09_1c_M_S164: Mouse embryonic stomach at E13.5 Batch1

source_name: stomach cells


title: x163_b1_p2_C09_1c_M_S163: Mouse embryonic stomach at E13.5 Batch1


title: YueLab-ATACseq-Kidney-rep2

source_name: YueLab-ATACseq-Kidney

value: Kidney


title: x162_b2_p5_B09_1c_M_S162: Mouse embryonic stomach at E13.5 Batch2


title: YueLab-ATACseq-Intestine-rep2

source_name: YueLab-ATACseq-Intestine

value: Intestine


title: x162_b1_p2_B09_1c_M_S162: Mouse embryonic stomach at E13.5 Batch1


title: YueLab-ATACseq-Skin-rep2

source_name: YueLab-ATACseq-Skin

value: Skin


title: Donor 1, Timepoint 20, Replicate A

value: female


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B4_ad001


title: YueLab-ATACseq-Heart-rep2

source_name: YueLab-ATACseq-Heart

value: Heart


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B4_ad010


title: Donor 1, Timepoint 16, Replicate A


title: Donor 1, Timepoint 14, Replicate A


title: YueLab-ATACseq-Colon-rep2

source_name: YueLab-ATACseq-Colon

value: Colon


title: Donor 1, Timepoint 18, Replicate A


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B4_ad006


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B5_ad008


title: Donor 1, Timepoint 10, Replicate A


title: x161_b1_p2_A09_1c_M_S161: Mouse embryonic stomach at E13.5 Batch1

value: mixed C57BL/6 CD1


title: x161_b2_p5_A09_1c_M_S161: Mouse embryonic stomach at E13.5 Batch2

value: stomach


title: Donor 1, Timepoint 8, Replicate A


title: Donor 1, Timepoint 12, Replicate A


title: Donor 1, Timepoint 6, Replicate A


title: Donor 1, Timepoint 4, Replicate A


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B4_ad004


title: x160_b2_p5_H08_1c_E_S160: Mouse embryonic stomach at E13.5 Batch2

value: embryonic day 13.5


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B4_ad007


title: YueLab-ATACseq-Blood-rep2

source_name: YueLab-ATACseq-Blood

value: Blood


title: x160_b1_p2_H08_1c_E_S160: Mouse embryonic stomach at E13.5 Batch1


title: x159_b2_p5_G08_1c_E_S159: Mouse embryonic stomach at E13.5 Batch2


title: WT_Mock3

city: Shanghai

first: Yang

state: Shanghai

address: 300 Fenglin RD

institute: Shanghai Center for Plant Stress Biology, and CAS Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences

description: 1/2 MS for 12 hours

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo sapiens whole genome using hisat v2.1.0 with default parameter
The expression level of each transcript was calculated according to the (TPM/PFKM) method. RSEM v1.3.1 was used to quantify gene abundances
Differential gene expression analysis was done using R package DESeq2 v1.24.0
Genome_build: tair10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Seedlings were grown vertically for 9 days before treatment.

extract_protocol:
Total RNA was extracted with Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: These seedlings (0.05 ~ 0.1 g) were treated on 1/2 MS medium.

value: wildtype

tag: ecotype

value: 9-day-old seedlings

tag: treatment

value: 1/2 MS for 12 hours


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B4_ad002

value: SSp

value: male


title: WT_Mock2

description: 1/2 MS for 12 hours


title: x159_b1_p2_G08_1c_E_S159: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B3_ad012


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B4_ad008


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B3_ad001


title: YueLab-ATACseq-Blood-rep1

value: Tuebingen


title: x158_b2_p5_F08_0c_E_S158: Mouse embryonic stomach at E13.5 Batch2


title: x158_b1_p2_F08_0c_E_S158: Mouse embryonic stomach at E13.5 Batch1


title: WT_Man3

description: 300 mM mannitol for 12 hours

value: 300 mM mannitol for 12 hours


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B3_ad007


title: Donor 1, Timepoint 2, Replicate A


title: CJ23_23_A_117: CD105pos (CD105KO) PaF TGFB1 1

city: MANCHESTER

first: Alexander

last: Kononov

address: Oglesby Building, 555 Wilmslow Rd,

country: United Kingdom

institute: Cancer Research UK Manchester Institute

data_processing:
Sequencing reads (single-end) were aligned to the mouse reference genome GRCm38.mm10 using STAR aligner version 2.5.1b
Gene annotation was taken from Ensembl build 92
Read counts were determined by using the featureCounts function from Bioconductor package Rsubread version 1.28.1
Analysis of differential gene expression was performed with the DESeq2 library [3] (version 1.26.0) using raw count data for each sample and controlling for batch effects. Genes displaying an FDR-adjusted p-value ≤ 0.05 were defined as differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with DEseq2 normalised gene expression for every gene for every sample

source_name: Fibroblasts from B6 mouse pancreas

growth_protocol: Cells isolated and expanded as described in Hutton et al

extract_protocol:
Cells lysed in plates with RLT buffer. Lysis and subsequent RNA isolation was conudcted as per instructions ffor the Qiagen RNeasy micro kits
RNA libraries were prepared for sequencing using standard Illumina protocols (note: single end reads)
RNA-seq (HiSeq HT 2x101bp, Quantseq 3' RNAseq libraries)

treatment_protocol: In vitro plated cells were stimlated with recombinant proteins for 6h as described in Hutton et al

value: Pancreas - in vitro expanded

value: Fibroblast


title: WT_Man2

description: 300 mM mannitol for 12 hours


title: CJ23_44_A_118: CD105pos (CD105KO) PaF TGFB1 2


title: Donor 1, Timepoint 0, Replicate A2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B3_ad010


title: Donor 1, Timepoint 0, Replicate A


title: CJ23_17_A_91: CD105pos (CD105KO) PaF baseline (no stim) 3

value: No stim


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B3_ad006


title: WT_Man1

description: 300 mM mannitol for 12 hours


title: CJ23_36_A_119: CD105pos (CD105KO) PaF TGFB1 3


title: WT_ABA3

description: 100 µM ABA for 12 hours

value: 100 microM ABA for 12 hours


title: x157_b1_p2_E08_10c_E_S157: Mouse embryonic stomach at E13.5 Batch1


title: WT_ABA2

description: 100 µM ABA for 12 hours


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B3_ad002


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B3_ad004


title: x156_b1_p2_D08_1c_E_S156: Mouse embryonic stomach at E13.5 Batch1


title: WT_Mock1

description: 1/2 MS for 12 hours


title: x156_b2_p5_D08_1c_E_S156: Mouse embryonic stomach at E13.5 Batch2


title: WT_ABA1

description: 100 µM ABA for 12 hours


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B3_ad008


title: x157_b2_p5_E08_10c_E_S157: Mouse embryonic stomach at E13.5 Batch2


title: CJ23_06_A_62: CD105neg PaF IFNg 2

value: IFNg


title: x155_b2_p5_C08_1c_E_S155: Mouse embryonic stomach at E13.5 Batch2


title: CJ23_42_A_89: CD105pos (CD105KO) PaF baseline (no stim) 1


title: b123Mock3

description: 1/2 MS for 12 hours


title: CJ23_29_A_61: CD105neg PaF IFNg 1


title: b123Mock2

description: 1/2 MS for 12 hours


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B2_ad002


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B2_ad008


title: x154_b2_p5_B08_1c_E_S154: Mouse embryonic stomach at E13.5 Batch2


title: CJ23_47_A_19: CD105pos PaF IFNg 3


title: x155_b1_p2_C08_1c_E_S155: Mouse embryonic stomach at E13.5 Batch1


title: CJ23_19_A_18: CD105pos PaF IFNg 2


title: CJ23_20_A_90: CD105pos (CD105KO) PaF baseline (no stim) 2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B12_ad012


title: CJ23_21_A_63: CD105neg PaF IFNg 3


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B12_ad010


title: b123Mock1

description: 1/2 MS for 12 hours


title: x154_b1_p2_B08_1c_E_S154: Mouse embryonic stomach at E13.5 Batch1


title: CJ23_16_A_17: CD105pos PaF IFNg 1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B12_ad008


title: b123Man3

description: 300 mM mannitol for 12 hours


title: x153_b1_p2_A08_1c_E_S153: Mouse embryonic stomach at E13.5 Batch1


title: x153_b2_p5_A08_1c_E_S153: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B12_ad007


title: b123Man1

description: 300 mM mannitol for 12 hours


title: b123Man2

description: 300 mM mannitol for 12 hours


title: CJ23_43_A_71: CD105neg PaF IL1a 3


title: CJ23_39_A_70: CD105neg PaF IL1a 2


title: b123ABA3

description: 100 µM ABA for 12 hours


title: CJ23_18_A_69: CD105neg PaF IL1a 1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B12_ad004


title: x152_b1_p2_H07_1c_M_S152: Mouse embryonic stomach at E13.5 Batch1


title: x152_b2_p5_H07_1c_M_S152: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B12_ad001


title: b123ABA2

description: 100 µM ABA for 12 hours


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B11_ad012


title: x151_b1_p2_G07_1c_M_S151: Mouse embryonic stomach at E13.5 Batch1


title: CJ23_45_A_26: CD105pos PaF IL1a 2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B11_ad010


title: x151_b2_p5_G07_1c_M_S151: Mouse embryonic stomach at E13.5 Batch2


title: CJ23_14_A_27: CD105pos PaF IL1a 3


title: CJ23_09_A_25: CD105pos PaF IL1a 1


title: x150_b2_p5_F07_1c_M_S150: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B11_ad008


title: x150_b1_p2_F07_1c_M_S150: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B11_ad007


title: CJ23_13_A_50: CD105neg PaF TGFB1 2


title: CJ23_03_A_49: CD105neg PaF TGFB1 1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B11_ad004


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B11_ad006


title: x149_b2_p5_E07_1c_M_S149: Mouse embryonic stomach at E13.5 Batch2


title: HuT 78 shPRKCQ TPA_3

city: Santander

first: Jose

middle: P.

last: Vaque

state: Cantabria

address: Avenida Cardenal Herrera Oria s/n Facultad de Medicina

department: Molecular Biology

country: Spain

institute: University of Cantabria

description: HUT78MYLA_NTC_TPA_vs_shPRKCQ_TPA_Processed data

data_processing:
Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 2.7.7)
RNA-seq paired-end reads were mapped against the human reference genome (GRCh38) using STAR version 2.5.3a (Dobin A. et al 2013) with ENCODE parameters for long RNA
Annotated genes (GENCODE version 29) were quantified using RSEM version 1.3.0 with default parameters (Li B. et al 2014)
Differential expression analysis was performed with DESeq2 version 1.18.1 (Love M. et al 2014).
Genome_build: GRCh38
Supplementary_files_format_and_content: Text files include Gene ID, log2FoldChange, pvalue and adjusted pvalue

source_name: CTCL cell line

growth_protocol: MyLa/HuT 78 NTC and MyLa HutT 78 shPRKCQ cells were growth in RPMI-1640 supplemented with 10% fetal bovine serum and 1% streptomycin sulphate and potassium penicillin. For PRKCQ knock down cells were cultured in the presence of 1ug/ml doxycycline during at least 72h before treatment

extract_protocol:
High-quality total RNA (RNA integrity number (RIN) >8) was isolated using TRIzol reagent (Invitrogen) following the manufacturer’s instructions
The RNA-Seq libraries were prepared following the TruSeq®Stranded mRNA LT Sample Prep Kit protocol (Illumina). Total RNA (500ng) was enriched for the polyA mRNA fraction and fragmented by divalent metal cations at high temperature. In order to achieve the directionality, the second strand cDNA synthesis was performed in the presence of dUTP. The blunt-ended double stranded cDNA was 3´adenylated and Illumina platform compatible adaptors with Unique Dual Indexes and Unique Molecular Identifiers (Integrated DNA Technologies) were ligated. The ligation product was enriched with 15 PCR cycles and the final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay (Agilent).

treatment_protocol: Cells were treated with control vehicle (DMSO) or TPA (10ng/ml) during 24h)

value: Lymphoblast

tag: disease

value: Sézary syndrome

value: shRNA PRKCQ

value: TPA


title: HuT 78 shPRKCQ TPA_1


title: HuT 78 shPRKCQ TPA_2


title: HuT 78 NTC TPA_3

value: Non-targeting control


title: HuT 78 NTC TPA_2


title: b123ABA1

description: 100 µM ABA for 12 hours

tag: genotype


title: CJ23_11_A_7: CD105pos PaF TGFB1 3

tag: tissue


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B11_ad002


title: CJ23_28_A_6: CD105pos PaF TGFB1 2

tag: cell type


title: HuT 78 NTC TPA_1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B11_ad001

tag: brain region


title: HuT 78 shPRKCQ DMSO_2

description: HUT78MYLA_NTC_DMSO_vs_shPRKCQ_DMSO_Processed data

value: vehicle


title: HuT 78 shPRKCQ DMSO_3


title: x148_b1_p2_D07_1c_M_S148: Mouse embryonic stomach at E13.5 Batch1

value: mixed C57BL/6 CD1

value: stomach

value: embryonic day 13.5


title: CJ23_25_A_51: CD105neg PaF TGFB1 3


title: x147_b2_p5_C07_1c_M_S147: Mouse embryonic stomach at E13.5 Batch2


title: x149_b1_p2_E07_1c_M_S149: Mouse embryonic stomach at E13.5 Batch1


title: CJ23_04_A_47: CD105neg PaF baseline (no stim) 3


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B10_ad010

value: SSp

tag: Sex

value: male


title: x147_b1_p2_C07_1c_M_S147: Mouse embryonic stomach at E13.5 Batch1

tag: age


title: HuT 78 shPRKCQ DMSO_1


title: CJ23_32_A_46: CD105neg PaF baseline (no stim) 2

tag: strain


title: HuT 78 NTC DMSO_3


title: x146_b1_p2_B07_1c_M_S146: Mouse embryonic stomach at E13.5 Batch1


title: CJ23_30_A_3: CD105pos PaF baseline (no stim) 3


title: CJ23_38_A_45: CD105neg PaF baseline (no stim) 1


title: HuT 78 NTC DMSO_2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B10_ad007


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B10_ad008


title: x148_b2_p5_D07_1c_M_S148: Mouse embryonic stomach at E13.5 Batch2


title: x145_b2_p5_A07_1c_M_S145: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B10_ad004


title: CJ23_48_A_5: CD105pos PaF TGFB1 1


title: x145_b1_p2_A07_1c_M_S145: Mouse embryonic stomach at E13.5 Batch1


title: HuT 78 NTC DMSO_1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B10_ad006


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B1_ad012


title: MyLa shPRKCQ TPA_2

value: Mycosis fungoides


title: MyLa shPRKCQ TPA_3


title: x144_b1_p2_H06_1c_E_S144: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B10_ad002


title: x143_b2_p5_G06_1c_E_S143: Mouse embryonic stomach at E13.5 Batch2


title: MyLa shPRKCQ TPA_1


title: CJ23_15_A_1: CD105pos PaF baseline (no stim) 1

value: Pancreas - in vitro expanded


title: x146_b2_p5_B07_1c_M_S146: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B1_ad007


title: MyLa NTC TPA_3


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B1_ad010


title: x142_b2_p5_F06_1c_E_S142: Mouse embryonic stomach at E13.5 Batch2


title: CJ23_22_A_2: CD105pos PaF baseline (no stim) 2

value: Fibroblast


title: x142_b1_p2_F06_1c_E_S142: Mouse embryonic stomach at E13.5 Batch1


title: MyLa NTC TPA_1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B1_ad006


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B1_ad004


title: MyLa shPRKCQ DMSO_3


title: x141_b2_p5_E06_1c_E_S141: Mouse embryonic stomach at E13.5 Batch2


title: MyLa shPRKCQ DMSO_2


title: x141_b1_p2_E06_1c_E_S141: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B1_ad001


title: x144_b2_p5_H06_1c_E_S144: Mouse embryonic stomach at E13.5 Batch2


title: MyLa shPRKCQ DMSO_1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B1_ad008


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A9_ad012


title: MyLa NTC DMSO_3


title: x140_b2_p5_D06_1c_E_S140: Mouse embryonic stomach at E13.5 Batch2


title: x140_b1_p2_D06_1c_E_S140: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A9_ad001


title: MyLa NTC TPA_2


title: x143_b1_p2_G06_1c_E_S143: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A9_ad007


title: X207

city: Cincinnati

first: Shailendra

last: Patel

state: OH

address: 231 Albet Sabin Way

department: Endorcrinology

institute: University of Cincinnati

data_processing:
Fastq files were trimmed to remove adapter and low quality sequences using Trimmomatic V 0.33
Trimmed reads were mapped to the reference (mm10) using hisat2 V 2.0.5
After trimming the reads were quantified using Kallisto V 0.43.1, this gives us TPM and Counts
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM and COUNTS for all samples

source_name: Macrophage

growth_protocol: All animals were group housed with 4 animals per cage in climate controlled facility with 12hr light/dark cycle, and allowed to feed ad libitum on standard rodent chow.

extract_protocol:
Livers were stored in RNA later at -80 degrees until RNA extraction according to manufacturer protocol with Qiagen RNeasy RNA extraction kit.
RNA libraries were prepared for sequencing using TruSeq RNA Library Prep Kit v2  and NEBNext Ultra Directional RNA Library Prep kit

treatment_protocol: No other treatment, only difference between groups is the genetics

value: Dhcr24flx/flx, Alb-Cre-

value: Male

tag: library prep kit

value: TruSeq RNA Library Prep Kit v2


title: X205

value: Dhcr24flx/flx, Alb-Cre+


title: X208

value: Female


title: X206


title: CEMBA180426_8B_1_CEMBA180426_8B_2_B1_ad002


title: x139_b1_p2_C06_1c_E_S139: Mouse embryonic stomach at E13.5 Batch1


title: x138_b2_p5_B06_1c_E_S138: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A9_ad010


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A9_ad006


title: BT549-PTEN-PolII-Rep1 (control)

city: Cleveland

first: Ata

last: Abbas

address: 10900 Euclid Ave

department: Division of Hematology & Oncology

institute: Case Western Reserve University

data_processing:
Base calling and generation of FASTQ files performed using standard CASAVA pipeline
Reads were aligned against hg38 by using Bowtie2.
BAM files were normalized by depth after removal of PCR duplicates and blacklisted regions.
For generating heatmap and metagene plots, ngs.plot program was used.
Genome_build: hg38
Supplementary_files_format_and_content: Library normalized bigWig files were provided.

source_name: Breast cancer cell line

growth_protocol: Cells were cultured in DMEM/F-12 medium (Life Technologies, Grand Island, NY) supplemented with 10% FBS (Thermo Scientific Gibco, Waltham, MA) at 37°C with 5% CO2.

extract_protocol:
Chromatin was immunoprecipitated using RNA Pol II antibody, washed, reverse-crosslinked, and DNA isolated using the phenol-chloroform method. Input DNA isolated using the phenol-chloroform method
10ng precipitated DNA was used to prepare library using Illumina TruSeq ChIP library preparation kit.

treatment_protocol: Three hours of glucose deprivation

tag: cell line

value: PTEN over-expressed

value: control

tag: chip antibody

value: Rpb1 (D8L4Y) (Cell Signaling cat# 14958)


title: G8KO-Stig-Liver

source_name: Liver

growth_protocol: Global ABCG8 KO male mice fed with low sterol diet having 0.005 % ezetimibe (LS+Ez) along with water at libitum  till weaning phase.

extract_protocol:
Livers were stored in RNA later at -80 degrees until RNA extraction according to manufacturer protocol with Qiagen RNeasy RNA extraction kit.
RNA libraries were prepared for sequencing using TruSeq RNA Library Prep Kit v2

treatment_protocol: Post-weaned global ABCG8 KO male mice were fed with different diets such as low sitosterol, high sitosterol, ergosterol and stigmasterol for 12 weeks and then euthainized to collect the livers

tag: diet

value: Stigmasterol


title: G8KO-HS-Adrenal

source_name: Adrenal

value: High Sitosterol


title: BT549-PTEN-PolII-Rep2 (control)


title: x138_b1_p2_B06_1c_E_S138: Mouse embryonic stomach at E13.5 Batch1

value: mixed C57BL/6 CD1

value: stomach


title: G8KO-Ergo-Liver

value: Ergosterol


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A9_ad004

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

source_name: C57BL/6J Male P56 Mouse Brain

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

value: SSp

value: male


title: x137_b2_p5_A06_1c_E_S137: Mouse embryonic stomach at E13.5 Batch2

value: embryonic day 13.5


title: BT549-PTEN-Input-Rep1 (control)


title: BT549-PTEN-Input-Rep2 (control)


title: MyLa NTC DMSO_2

value: Lymphoblast

value: Mycosis fungoides

tag: condition

value: Non-targeting control

value: vehicle


title: x139_b2_p5_C06_1c_E_S139: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A9_ad002


title: G8KO-LS-Liver

value: Low Sitosterol

value: Male


title: BT549-Vector-PolII-Rep2 (control)

value: WT


title: MyLa NTC DMSO_1


title: G8KO-LS-Adrenal


title: BT549-Vector-PolII-Rep1 (control)

value: control


title: x136_b2_p5_H05_1c_M_S136: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A8_ad012


title: x136_b1_p2_H05_1c_M_S136: Mouse embryonic stomach at E13.5 Batch1


title: x135_b2_p5_G05_1c_M_S135: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A8_ad001


title: BT549-Vector-Input-Rep2 (control)


title: ID38_VisitC_Input_Control

city: Toronto

first: Bharati

last: Bapat

state: Ontario

address: 60 Murray Street, Rm L6-304B

department: Lunenfeld-Tanenbaum Research Institute

country: Canada

institute: Sinai Health System

data_processing:
Fastq files were generated using Illumina bcl2fastq version 1.8.4.
Alignment to hg19 genome was performed using BWA mem version 0.7.6a
After read mapping quality filtering(QA>5),  duplicates were marked and collaped using Picard tools (version 1.52 ), and reads were directionally extended to 175bp.
Bigwig files were generated using the UCSC wigToBigwig tool (version 4).
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig

source_name: cfDNA

extract_protocol:
Plasma was separated from whole blood and cfDNA was extracted using the Qiagen circulating nucleic acids kit.
Libraries were prepared using a published protocol (PMID: 30429608). Briefly, end-repair, A-tailing and Illumina adapter ligation was performed using the KAPA hyper prep kit. Methylated cfDNA was immunoprecipated and purified using the Diagenode MagMeDIP and IPure kits. Prior to MeDIP, 10% of the adapter-ligated cfDNA sample was set aside as an input control. Both MeDIP and input control samples were then amplified using KAPA hyper prep kit protocols, followed by size selection.

tag: individual

value: patient ID38

tag: treatment visit

value: C

tag: sample type

value: Input Control

value: Plasma

tag: medip antibody


title: G8KO-HS-Liver

value: High Sitosterol


title: BT549-Vector-Input-Rep1 (control)

tag: treatment


title: x135_b1_p2_G05_1c_M_S135: Mouse embryonic stomach at E13.5 Batch1

extract_protocol:
Single EpCAM+ and EpCAM- embryonic gastric cells were isolated by FACS directly in 96 well plates supplemented with buffer (Takara, Clontech). ERCC RNA Spike-In Mix (ThermoFisher) were added for quality and normalization controls. Plates were stored at -80°C.
50ng of total RNA was used for cDNA synthesis using Ovation v2.0 kit (NuGEN) according to manufacturer’s instructions. After cDNA fragmentation (Covaris), libraries were prepared using NEBNext v2.0 kit (NEB) according to manufacturer’s instructions.

value: mixed C57BL/6 CD1

value: stomach


title: x134_b2_p5_F05_0c_M_S134: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A8_ad010

first: Joseph

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

value: SSp

value: male


title: x137_b1_p2_A06_1c_E_S137: Mouse embryonic stomach at E13.5 Batch1

value: embryonic day 13.5


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A9_ad008


title: x134_b1_p2_F05_0c_M_S134: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A8_ad006


title: V26T

type: genomic

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

institute: Josep Carreras Research Institute (IJC)

hyb_protocol: BS-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (Illumina HiSeq2000) using standard recommended Illumina scanner setting

data_processing:
Data were processed using R studio
Average Beta

label: Cy5 and Cy3

source_name: CD4+ T cells isolated from PBMCs of healthy donor

label_protocol: Standard Illumina Protocol

growth_protocol: 15 ml of peripheral blood was collected from 16 healthy donors and 48 SSc patients in Lithium Heparin tubes

extract_protocol: DNA was extracted utilizing the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen, Hilden, Germany) according to manufacturers’ instructions.

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were separated by laying on Lymphocytes Isolation Solution (Rafer, Zaragoza, Spain) and centrifuged without braking. PBMCs were stained with fluorochrom-conjugated antibody against CD4-APC (BD Pharmingen, New Jersey, USA) in staining buffer (PBS with 2 mM of EDTA and 4 % FBS) for 20 mins. Gating strategies were employed to eliminate doublets, cell debris and DAPI+ cells. Lymphocytes were separated by forward and side scatter, in which CD4+ cells were separated by positive selection.

tag: donor

value: Healthy donor

tag: gender

value: M

tag: skin disease

value: HD

tag: lung disease


title: ID38_VisitB_Input_Control

value: B

tag: tissue


title: V25T

value: F


title: ID38_VisitC_MeDIP-seq

value: MeDIP


title: x133_b2_p5_E05_10c_M_S133: Mouse embryonic stomach at E13.5 Batch2

first: Sergi

address: Ackermannweg 4

institute: Institute of Molecular Biology, Mainz

data_processing:
Reads were demultiplexed and fastq files were generated with Illumina bcl2fastq-1.8.4
Fastq files were mapped with STAR_2.5.2b onto Ensembl 88 GRCm38 reference
Secondary alignments were filtered with samtools 1.5
Counts for every gene were calculated with Subread’s FeatureCounts (version 1.5.1) using the gene model provided with Ensembl 88 GRCm38 reference
Genome_build: Ensembl 88 GRCm38
Supplementary_files_format_and_content: tab separated file containing counts per gene

source_name: stomach cells

tag: age


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A8_ad008

city: La Jolla

last: Ecker

tag: brain region

tag: Sex

tag: strain


title: Cyp3a-KO

tag: genotype

value: Cyp3a4 global KO

value: Male


title: Cyp27-KO

value: Cyp27a1 global KO


title: Cyp3a-27dKO

value: Cyp27a1-Cyp3a4 global double KO


title: WT

value: WT


title: ID38_VisitB_MeDIP-seq

value: patient ID38

value: Plasma


title: H20T


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A8_ad007


title: x133_b1_p2_E05_10c_M_S133: Mouse embryonic stomach at E13.5 Batch1

value: mixed C57BL/6 CD1

value: stomach


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A7_ad007

value: SSp

value: male


title: ID38_VisitA_Input_Control

value: A

value: Input Control


title: H19T

value: Healthy donor

value: HD


title: x132_b2_p5_D05_1c_M_S132: Mouse embryonic stomach at E13.5 Batch2

value: embryonic day 13.5


title: x132_b1_p2_D05_1c_M_S132: Mouse embryonic stomach at E13.5 Batch1


title: ID38_VisitA_MeDIP-seq

value: MeDIP


title: H18T

value: F


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A7_ad002


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A6_ad001


title: ID37_VisitC_Input_Control

value: patient ID37

value: C


title: x131_b2_p5_C05_1c_M_S131: Mouse embryonic stomach at E13.5 Batch2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A6_ad007


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A8_ad004


title: ID37_VisitC_MeDIP-seq


title: S47T

source_name: CD4+ T cells isolated from PBMCs of SSc patient

value: Systemic sclerosis

value: lcSSc

value: PAH


title: x131_b1_p2_C05_1c_M_S131: Mouse embryonic stomach at E13.5 Batch1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A6_ad010


title: ID37_VisitB_Input_Control

value: B

value: Plasma


title: x130_b2_p5_B05_1c_M_S130: Mouse embryonic stomach at E13.5 Batch2

value: mixed C57BL/6 CD1

value: stomach


title: S48T


title: S46T

value: ssSSc


title: S45T

value: Initial


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A6_ad004

value: SSp

value: male


title: x129_b2_p5_A05_1c_M_S129: Mouse embryonic stomach at E13.5 Batch2


title: x130_b1_p2_B05_1c_M_S130: Mouse embryonic stomach at E13.5 Batch1


title: ID37_VisitB_MeDIP-seq


title: ID37_VisitA_Input_Control

value: A

value: Input Control


title: CEMBA180426_8B_1_CEMBA180426_8B_2_A6_ad002