title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_E7_AD002_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_E6_AD001_indexed

status: Public on Aug 21 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

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

organism: Mus musculus

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: CP

tag: Sex

value: male

tag: age

tag: strain


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_E6_AD006_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_E6_AD007_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_E9_AD002_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_E6_AD004_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_E5_AD012_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_E6_AD008_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_E5_AD010_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_E5_AD004_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_E5_AD008_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_E5_AD001_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_E5_AD007_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_F10_AD002_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_E5_AD006_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_E5_AD002_indexed


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title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_E4_AD002_indexed


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title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D3_AD006_indexed


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title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D5_AD007_indexed


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title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D2_AD007_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D2_AD002_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D2_AD004_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D1_AD012_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D2_AD006_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D5_AD006_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D1_AD006_indexed


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title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D1_AD007_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D1_AD001_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D2_AD001_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D12_AD012_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D3_AD001_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D12_AD010_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D12_AD007_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D1_AD002_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D12_AD006_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D12_AD004_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C9_AD012_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D11_AD010_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D11_AD008_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C9_AD010_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D11_AD007_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D11_AD002_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D10_AD012_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D10_AD001_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D1_AD008_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D10_AD010_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D11_AD006_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D10_AD007_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D11_AD012_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D10_AD002_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D10_AD004_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C9_AD001_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C9_AD008_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C9_AD007_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D10_AD006_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D12_AD002_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C8_AD007_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C9_AD006_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C8_AD012_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C8_AD010_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C8_AD008_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C9_AD004_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C8_AD001_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C8_AD006_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C8_AD002_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C7_AD012_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C7_AD008_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C9_AD002_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C7_AD006_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C7_AD007_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C8_AD004_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C7_AD002_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C6_AD012_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C6_AD010_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C7_AD001_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D10_AD008_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_D11_AD001_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C6_AD008_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C6_AD007_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C6_AD004_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C6_AD002_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C5_AD012_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C6_AD001_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C5_AD004_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C4_AD006_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C4_AD004_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C5_AD001_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C7_AD004_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C5_AD010_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C4_AD012_indexed


title: Control CN3 [BiSulfite-seq]

city: Columbus

first: Jinsoo

last: Ahn

state: OH

address: 2029 Fyffe Rd

institute: The Ohio State University

data_processing:
Sequenced reads were trimmed for adaptor sequence and low quality reads were eliminated.
The cleaned reads were aligned to the reference genome (Sscrofa11.1) using BSMAP (v2.87) with default parameter settings.
Using methylatio.py script in BSMAP, extraction of the methylation ratio of every single cytosine from the mapping results was conducted.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: Tab-delimited text files include methylation ratios for each sample.
Supplementary_files_format_and_content: Bigwig files contain data that will be diplayed in genome browsers.

organism: Sus scrofa

source_name: embryo

growth_protocol: After electric stimulation of oocytes followed by 2 h of stabilization period, 200 parthenogenetic embryos were placed into oviducts of each of the two LYD surrogate gilts aged 12 months at onset of estrus to produce developed parthenogenetic embryos.

extract_protocol:
From the whole collected embryos of CN and PA (n = 3 for each), genomic DNA was isolated and fragmented.
For optimization of bisulfite conversion of genomic DNA, Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences, Inc. Ann Arbor, MI, USA) was used according to the manufacturer`s instructions.

treatment_protocol: In a fusion chamber with 250 µm diameter wire electrodes, selected oocytes were placed and fusion was achieved by two DC pulses (1 sec interval) of 1.2 kV/cm for 30 µs using an LF101 Electro Cell Fusion Generator.

value: Landrace x Yorkshire x Duroc (LYD)

tag: tissue

value: whole embryo

value: embryonic day 21

tag: treatment

value: untreated


title: Parthenote PA2 [BiSulfite-seq]

value: parthenogenesis


title: Parthenote PA3 [BiSulfite-seq]


title: Control CN1 [BiSulfite-seq]


title: Control CN2 [BiSulfite-seq]


title: Parthenote PA1 [BiSulfite-seq]


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C6_AD006_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C4_AD007_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C4_AD001_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C4_AD002_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C3_AD007_indexed


title: WT_str_2

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

description:
Cells were grown on stretching conditions.
PolyA RNA
processed data file: NormCounts.txt

library_source: transcriptomic

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava pipeline.
Sequencing adaptor contaminations were removed from reads using cutadapt.
Transcript and gene level expression estimates were obtained with RSEM, by aligning preprocessed reads against the Mus musculus transcriptome.
Genome_build: Ensembl genebuild 76 (Mus musculus assembly GRCm38).
Supplementary_files_format_and_content: NormCounts.txt file contains ENSEMBL gene IDs and TMM-normalized counts per million for each gene, in each sample.

molecule: total RNA

source_name: Mouse peritoneal mesothelial cells

growth_protocol: All experiments were conducted with mouse peritoneal mesothelial cells isolated from WT and Cav-1- littermate mice.

extract_protocol:
RNA was extracted with RNeasy micro kit (QIAGEN).
500 ng of total RNA were used to generate barcoded RNA-seq libraries using the NEBNext Ultra RNA Library preparation kit (New England Biolabs). Briefly, poly A+ RNA was purified using poly-T oligo- attached magnetic beads followed by fragmentation and then first and second cDNA strand synthesis. Next, cDNA 3’ ends were adenylated and the adapters were ligated followed by PCR library amplification. Finally, the size of the libraries was checked using the Agilent 2100 Bioanalyzer DNA 1000 chip and their concentration was determined using the Qubit® fluorometer (Life Technologies).
Libraries were sequenced on a HiSeq2500 (Illumina) to generate 61 bases single reads.

treatment_protocol: Cells were grown in static conditions until reaching confluence. Cells were then exposed to mechanical stretching or left in static conditions for 24 hours, before RNA extraction.

tag: genotype/variation

value: WT

tag: cell type

value: Peritoneal mesothelial cells

tag: condition

value: Stretching

tag: animal


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C3_AD010_indexed


title: WT_str_1


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C4_AD010_indexed


title: WT_ctrl_2

description:
Cells were grown on static conditions.
PolyA RNA
processed data file: NormCounts.txt

value: Static


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C2_AD008_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C5_AD006_indexed


title: KO_str_1


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C2_AD012_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C3_AD012_indexed


title: KO_str_2


title: KO_ctrl_1


title: KO_ctrl_2


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C3_AD006_indexed


title: siHIF1A rep3

type: RNA

city: Seoul

first: Jin-Hong

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC).

label: biotin

organism: Homo sapiens

source_name: SW1353 cells transfected with HIF1A siRNA

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: The cells were maintained in 20% O2 at 37°C, and cultured in DMEM (WelGENE Inc., LM001-05) supplemented with 10% FBS (Gibco, 26140079) and 1% antibiotics.

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

treatment_protocol: SW1353 cells were transfected with the control, HIF1A, or EPAS1 siRNAs. Transfection was perfomed with METAFECTENE PRO (Biontex, T040).

tag: cell line


title: siEPAS1 rep3

source_name: SW1353 cells transfected with EPAS1 siRNA


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C3_AD001_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C3_AD004_indexed


title: siNC rep2

source_name: SW1353 cells transfected with control siRNA


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C5_AD002_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C2_AD010_indexed


title: siHIF1A rep2


title: siNC rep1


title: siEPAS1 rep1


title: siHIF1A rep1


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C2_AD007_indexed


title: siNC rep3


title: siEPAS1 rep2


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C2_AD004_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C3_AD002_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C2_AD006_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C1_AD002_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C12_AD010_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C1_AD010_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C1_AD012_indexed


title: batch5_AS_F1_3383-P

city: VANCOUVER

first: FENG

last: XU

state: BC

address: Suite 110, 6309 Larkin Dr, 110

department: Department of Pathology and Lab Medicine

country: Canada

institute: UBC

hyb_protocol: GeneChip™ Hybridization, Wash, and Stain Kits were applied in this study.

scan_protocol: GeneChip™ Scanner 3000 System was utilized to scan the arrays in this study.

data_processing:
The analysis tools, including robust multichip array (RMA) algorithm in “affy” (v1.36.1) package and the BrainArray v17 CDF in R (version v3.3.0), were applied to analyze the Microarray expression profile
After the above standard data processing, the normalized expression matrix was log2 transformed to get the final expression matrix

label: Biotin

source_name: lung tissue

label_protocol: The fragmented cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using a proprietary DNA Labeling Reagent that is covalently linked to biotin 5.5μg of single-stranded cDNA is required for fragmentation and labeling.

growth_protocol: Not Applicable.

extract_protocol: “RNeasy Mini” tool kit from Qiagen was applied to extract the total RNA in this study

treatment_protocol: Not Applicable.

tag: patient

tag: disease state

value: Control

value: unused donor control lung


title: batch5_AS_E7_3381-P


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C12_AD006_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C2_AD001_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C1_AD006_indexed


title: batch5_AS_F7_5328-P


title: batch5_AS_F3_5316-P


title: batch5_AS_E1_3365-P


title: batch5_AS_D7_5048-3-P

value: COPD

value: transplanted lung tissue


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C2_AD002_indexed


title: batch5_AS_E3_3372-P


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C1_AD007_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C1_AD008_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C3_AD008_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C12_AD004_indexed


title: batch5_AS_E5_3380-P


title: batch5_AS_F5_3366-2-P


title: batch5_AS_C7_5028-P


title: batch5_AS_C5_5024-P


title: batch5_AS_D3_5036-P


title: batch5_AS_D5_5044-P


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C12_AD007_indexed


title: batch5_AS_D1_5032-P


title: batch5_AS_C3_5016-P


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C1_AD004_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C12_AD008_indexed


title: batch5_AS_C1_5012-P


title: batch5_AS_B5_2425-P


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C1_AD001_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C12_AD001_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C10_AD012_indexed


title: batch5_AS_B3_2675-P


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C11_AD008_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C11_AD012_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C11_AD001_indexed


title: batch5_AS_B7_2776-P


title: batch5_AS_A7_2405-P


title: batch5_AS_B1_2316-P


title: batch4_AS_F1_JHG-41


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C11_AD007_indexed


title: batch4_AS_F3_JHG-43


title: batch4_AS_F5_JHG-45


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C11_AD010_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C11_AD002_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C11_AD006_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C10_AD008_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C10_AD006_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C10_AD007_indexed


title: WT_ctrl_1


title: batch4_AS_E7_JHG-39


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B9_AD010_indexed


title: batch4_AS_E3_JHG-35


title: batch4_AS_E1_JHG-33


title: batch4_AS_D7_JHG-31


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C10_AD001_indexed


title: batch4_AS_E5_JHG-37


title: batch5_AS_A1_2544-P


title: batch4_AS_D3_JHG-27


title: batch4_AS_D5_JHG-29


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C11_AD004_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C10_AD010_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B9_AD008_indexed


title: batch4_AS_D1_JHG-25


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C10_AD004_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B9_AD007_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B9_AD006_indexed


title: batch4_AS_C5_JHG-21


title: batch4_AS_C1_JHG-17


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B9_AD012_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B8_AD006_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B8_AD010_indexed


title: batch4_AS_B5_JHG-13


title: batch4_AS_C7_JHG-23


title: batch4_AS_B3_JHG-11


title: batch4_AS_C3_JHG-19


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B9_AD002_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B9_AD001_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B8_AD004_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B9_AD004_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B8_AD008_indexed


title: batch4_AS_A7_JHG-7


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B8_AD001_indexed


title: batch4_AS_A5_JHG-5


title: batch4_AS_A3_JHG-3


title: batch4_AS_B7_JHG-15


title: batch3_AS_F5_JHG-45


title: batch4_AS_A1_JHG-1


title: batch5_AS_A3_2655-P


title: batch3_AS_F3_JHG-43


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B7_AD012_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B8_AD012_indexed


title: batch3_AS_E5_JHG-37


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B8_AD007_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B7_AD004_indexed


title: batch3_AS_F1_JHG-41


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B7_AD006_indexed


title: batch3_AS_E7_JHG-39


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B8_AD002_indexed


title: batch3_AS_E1_JHG-33


title: batch3_AS_E3_JHG-35


title: batch3_AS_D7_JHG-31


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B7_AD008_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B6_AD010_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B7_AD010_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B5_AD012_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B6_AD007_indexed


title: batch3_AS_D1_JHG-25


title: batch4_AS_B1_JHG-9


title: batch3_AS_C7_JHG-23


title: batch3_AS_C3_JHG-19


title: batch3_AS_C1_JHG-17


title: batch3_AS_D3_JHG-27


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B7_AD002_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B7_AD001_indexed


title: batch3_AS_D5_JHG-29


title: batch3_AS_B7_JHG-15


title: batch3_AS_B5_JHG-13


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B6_AD004_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B6_AD006_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B6_AD008_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B6_AD001_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B6_AD002_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B5_AD010_indexed


title: batch3_AS_B3_JHG-11


title: batch3_AS_C5_JHG-21


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B5_AD007_indexed


title: batch3_AS_A7_JHG-7


title: batch3_AS_A5_JHG-5


title: batch3_AS_A3_JHG-3


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B5_AD002_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B5_AD008_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B5_AD001_indexed


title: batch3_AS_A1_JHG-1


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B6_AD012_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B4_AD010_indexed


title: batch5_AS_A5_2813-P


title: batch2_AS_F5_LCM45


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B5_AD004_indexed


title: batch2_AS_E5_LCM37


title: batch2_AS_E3_LCM35


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B4_AD007_indexed


title: batch2_AS_D7_LCM31


title: batch2_AS_E1_LCM33


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B4_AD006_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B4_AD004_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B4_AD012_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B4_AD002_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B3_AD010_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B4_AD001_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B3_AD007_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B3_AD012_indexed


title: batch2_AS_E7_LCM39


title: batch2_AS_D3_LCM27


title: batch2_AS_C7_LCM23


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_C10_AD002_indexed


title: batch2_AS_D1_LCM25


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B3_AD008_indexed


title: batch2_AS_C1_LCM17


title: batch2_AS_B5_LCM13


title: batch2_AS_B7_LCM15


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B3_AD006_indexed


title: batch2_AS_D5_LCM29


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B7_AD007_indexed


title: batch2_AS_F1_LCM41


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B2_AD007_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B2_AD012_indexed


title: batch2_AS_B3_LCM11


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B3_AD001_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B3_AD004_indexed


title: batch2_AS_C3_LCM19


title: batch2_AS_B1_LCM9


title: batch2_AS_C5_LCM21


title: batch2_AS_A7_LCM7


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B2_AD008_indexed


title: batch2_AS_A5_LCM5


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B2_AD010_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B2_AD006_indexed


title: batch1_JH_F6_47


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B5_AD006_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B3_AD002_indexed


title: batch2_AS_A3_LCM3


title: batch1_JH_F4_45


title: batch1_JH_F2_43


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B1_AD010_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B2_AD002_indexed


title: batch1_JH_E8_41


title: batch1_JH_E6_39


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B2_AD001_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B12_AD007_indexed


title: batch3_AS_B1_JHG-9


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B1_AD006_indexed


title: batch1_JH_E3_35


title: batch2_AS_A1_LCM1


title: batch1_JH_E1_33


title: batch1_JH_E4_37


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B1_AD007_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B2_AD004_indexed


title: batch1_JH_D5_29


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B1_AD012_indexed


title: batch1_JH_D3_27


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B12_AD012_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B1_AD001_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B1_AD002_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B12_AD008_indexed


title: batch1_JH_D1_25


title: batch1_JH_C7_23


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B1_AD008_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B1_AD004_indexed


title: batch1_JH_D7_31


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B12_AD004_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B12_AD010_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B12_AD006_indexed


title: batch1_JH_C1_17


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B10_AD012_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B11_AD012_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B11_AD008_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B11_AD007_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B12_AD001_indexed


title: batch1_JH_B5_13


title: batch1_JH_B3_11


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B10_AD010_indexed


title: batch1_JH_B7_15


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B10_AD006_indexed


title: batch1_JH_C5_21


title: batch1_JH_A5_5


title: batch1_JH_A3_3


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B11_AD010_indexed


title: batch1_JH_B1_9


title: batch1_JH_A7_7


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B11_AD006_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B4_AD008_indexed


title: Harmine+PMA-rep3

city: Gainesville

first: Mark

middle: A

last: Wallet

state: Florida

address: 1275 Center Drive

department: Pathology

institute: University of Florida

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Samples were hybridized with GeneChip Human Transcriptome Array 2.0 (Affymetrix) and scanned at the University of Florida Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: CHP files were generated after raw data were analyzed with Expression Console Software (Affymetrix) and normalized by the Robust Multichip Average (RMA) method

source_name: J-Lat 5A8 Cells

label_protocol: Single-stranded cDNA was generated  with the WT Expression Kit (Invitrogen) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: J-Lat 5A8 cells were cultured in RPMI 1640 with 2 mM L-glutamine, 10% heat-inactivated human serum, and 100 IU penicillin/streptomycin at 37 °C with 5% CO2.

extract_protocol: Total RNA was collected and isolated using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Four million cells were treated with harmine (20 µM) or DMSO for 30 minutes. The cells were then treated with cell culture medium or PMA (10 nM) for 2 hours.

tag: agent

value: Harmine+PMA


title: PMA-rep3

value: PMA


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B11_AD004_indexed

value: CP


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B10_AD007_indexed

value: male


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B10_AD008_indexed


title: R2

city: Hong Kong

first: Tongtong

last: Kan

address: 83 Tat Chee Avenue

country: China

institute: City University of Hong Kong

data_processing:
Basecalls performed using Picard IlluminaBasecallsToSam
The reads were tagged using cell barcodes and molecular barcodes, then the 5’ primer sequence and 3’ polyA sequence of the reads were trimmed.
The unmapped reads were aligned to the Genome Reference Consortium Human Build 38 (GRCh38) using STAR aligner.
The uniquely mapped reads were grouped by cell barcode. Within each cell, the total number of distinct UMI sequences was summarized in the DGE matrix.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include the count of unique UMIs for each gene in each cell.

molecule: polyA RNA

source_name: Ovarian cancer

extract_protocol:
Tumors were disaggregated into single cells, and processed according to Drop-seq protocol.
Drop-seq

tag: tumor type

value: relapse

tag: cell number


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B11_AD001_indexed


title: batch1_JH_A1_1


title: R1


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B10_AD004_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B10_AD001_indexed


title: batch1_JH_C3_19


title: DMSO-rep2

value: DMSO


title: M1

value: untreated peritoneal metastasis


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A9_AD012_indexed


title: M2


title: Harmine-rep2

value: Harmine


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A9_AD008_indexed


title: P3

value: primary


title: PMA-rep2


title: Harmine-rep3


title: PMA-rep1


title: Harmine+PMA-rep2


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A9_AD007_indexed


title: DMSO-rep1


title: Harmine+PMA-rep1


title: Harmine-rep1


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B11_AD002_indexed


title: P2


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A9_AD010_indexed


title: P1


title: ex0063_SCC034_504

city: Oxford

first: chao

last: jiang

address: Botnar Research Centre

department: NDORMS

country: United Kingdom

institute: University of Oxford

data_processing:
basecalling with bcl2fastq v2.17.1.14
QC with fastQC v0.11.3
mapping with hisat 2.0.5
quantification with featureCounts 1.5.0
differential gene expression with deseq2 1.16.1
Genome_build: hg38
Supplementary_files_format_and_content: txt file generated from featureCounts

source_name: BM-MSC

growth_protocol: 50,000 cells were seeded in 6-well plates in maintenance medium: MesenPRO-RS™ (Thermo Fisher Scientific, Massachusetts, USA)

extract_protocol:
total RNA was isolated using TRIzol with the Direct-zol RNA kit (ZymoResearch, USA)
RNA-seq library preparation was carried out using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, USA)

treatment_protocol: After 3 days, medium was replaced with osteogenic differentiation medium: DMEM high glucose supplemented with 10% FBS, 1x non-essential amino acids (NEAA), 2mM L-glutamine, 0.28mM ascorbic (Sigma-Aldrich, USA) acid, 10 mM β glycerophosphate, and 10 nM dexamethasone

tag: gender

value: M

tag: hours after osteogenic media added

tag: passage


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A8_AD012_indexed

tag: brain region

tag: Sex

tag: age


title: ex0063_SCC034_168


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A8_AD008_indexed

tag: strain


title: ex0063_SCC034_336


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A8_AD004_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A9_AD002_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A9_AD004_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A9_AD001_indexed


title: ex0063_SCC034_96


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A8_AD007_indexed


title: ex0063_SCC034_120


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A8_AD001_indexed


title: ex0063_SCC034_48


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A9_AD006_indexed


title: ex0063_SCC034_72


title: ex0063_SCC034_24


title: ex0063_SCC034_16


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A8_AD010_indexed


title: ex0063_SCC034_4


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A7_AD012_indexed


title: ex0063_SCC034_8


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A8_AD002_indexed


title: ex0063_SCC034_2


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A7_AD008_indexed


title: ex0063_SCC034_1


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A8_AD006_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A7_AD007_indexed


title: ex0072_0208_168

value: F


title: ex0072_0208_72


title: ex0063_SCC034_0.5


title: ex0063_SCC034_0


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A6_AD012_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A7_AD002_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A6_AD010_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A7_AD001_indexed


title: ex0063_SCC034_12


title: ex0072_0208_2


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A6_AD001_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A7_AD010_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A5_AD007_indexed


title: ex0072_0208_1


title: DMSO-rep3


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A7_AD004_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A5_AD008_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A7_AD006_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A5_AD002_indexed


title: ex0072_1309_168


title: ex0072_0208_24


title: ex0072_1309_72


title: ex0072_0208_6


title: ex0072_1309_6


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A5_AD010_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A6_AD007_indexed


title: batch2_AS_F3_LCM43

tag: tissue


title: ex0072_1309_24


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A5_AD012_indexed


title: ex0072_1309_2


title: ex0072_1309_0


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A5_AD006_indexed


title: 2011020_VMT89618A1

city: Los Angeles

first: Ivette

last: Zelaya

address: 695 Young Drive South, Rm 1524 Gonda

institute: University of California, Los Angeles

data_processing:
Reads were aligned using STAR aligner to the Chlorocebus_sabeus 1.1 genome assembly
Gene counts were generated from uniquely aligned reads using the HTSeq script and default parameters
Genome_build: Chlorocebus_sabeus 1.1 NCBI genome build
Supplementary_files_format_and_content: tab-delimited text file includes raw counts for each sample

organism: Chlorocebus sabaeus

source_name: Hippocampus

extract_protocol:
Total RNA was extracted with PerfectPure (Gentra Systems Inc.) processed with Ribo-Zero Gold kit (Epicentre, WI) to remove ribosomal RNAs.
Sequencing libraries were prepared using Illumina stranded TruSeq RNA sample prep kit following manufacturer's protocol.

value: under 1 yr


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A6_AD006_indexed


title: ex0072_0208_0


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A5_AD004_indexed


title: 2011017_VMT88970A1


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A6_AD004_indexed


title: 2010102_VMT89077A1


title: ex0004_28386_504


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A6_AD002_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A6_AD008_indexed


title: ex0004_28386_336


title: ex0004_28386_168


title: 2010084_VMT51801A1


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A4_AD010_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A4_AD012_indexed


title: 2010072_VMT30440A1


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A4_AD008_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A4_AD002_indexed


title: ex0072_1309_1


title: ex0004_28386_24


title: 2010071_VMT50838A1


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A4_AD006_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A4_AD004_indexed


title: 2010059_VMT12818A1


title: P4


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A3_AD004_indexed


title: ex0004_28386_72


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A5_AD001_indexed


title: ex0004_28386_12


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A3_AD010_indexed


title: 2010053_VMT51373A1


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A3_AD012_indexed


title: 2010055_VMT12390A1


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A3_AD008_indexed


title: 2010052_VMT30868A1


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A3_AD007_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A4_AD007_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A3_AD006_indexed


title: ex0004_28386_6


title: ex0004_28386_8


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A4_AD001_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A3_AD002_indexed


title: 2010051_VMT30226A1


title: ex0004_28386_2


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A2_AD012_indexed


title: ex0004_28386_1


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A3_AD001_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A2_AD008_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A2_AD007_indexed


title: ex0004_28386_0.5


title: 2010045_VMT12925A1


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A2_AD010_indexed


title: 2010040_VMT31082A1


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A2_AD002_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A12_AD010_indexed


title: 2010042_VMT31296A1


title: ex0004_28386_0


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A2_AD006_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A1_AD010_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A2_AD004_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A1_AD007_indexed


title: 2010032_VMT12069A1


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A1_AD008_indexed


title: BM285

city: Taichung

first: Chieh-Lin Jerry

last: Teng

address: 1650 Taiwan Boulevard Sec. 4

department: Division of Hematology/Medical Oncology

country: Taiwan

institute: Taichung Veterans General Hospital

data_processing:
We removed raw sequencing reads with low quality, containing adaptor sequences, or with high contents of unknown bases.  Clean reads were aligned to the Ensembl GRCh37 human reference genome by TopHat2.  We used the HTSeq software to count the mapped reads against Ensembl annotated genes (ENSG IDs).  Gene-level read counts were normalized and tested for differential expression between AML patients with and without CR by an R package DESeq2.
Genome_build: GRCh37
Supplementary_files_format_and_content: HTSeq raw read counts
Supplementary_files_format_and_content: DESeq2-normalized read counts.

source_name: CR_bone marrow

extract_protocol:
We extracted total RNA from pre-treatment bone marrow mononuclear cells using TRIzol (Thermo Fisher Scientific, Inc., Wilmington, Delaware, USA).  RNA samples were purified by using Qiagen RNeasy Mini kit and DNase I (Qiagen, Valencia, CA, USA).  The mRNA contents were enriched by using oligo (dT)-labeled magnetic beads, followed by fragmentation, conversion into cDNA, ligation of sequencing adaptors, and amplification.  All procedures were performed according to manufacturer's instructions.
Library was constructed according to Illumina's instructions. Quality-checked library products were subjected to 75-bp paired-end sequencing by an Illumina NextSeq 500 sequencer (Illumina Inc., San Diego, CA, USA) with a throughput of approximately 20 million reads per sample.

treatment_protocol: All patients received and complete the “7+3” (cytarabine 100–200 mg/M2 for 7 days; idarubicin 12 mg/M2 for 3 days) regimen.  Bone marrow samples were collected before treatment.

tag: subject status

value: acute myeloid leukemia (AML) patient

tag: response to standard induction chemotherapy

value: CR (complete remission)

value: bone marrow


title: BM286

source_name: Non-CR_bone marrow

value: Non-CR (non-complete remission)


title: BM288


title: 2010009_VMT10711A1


title: 2010004_VMT01643A1


title: ex0004_28386_16


title: BM283


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A1_AD006_indexed


title: 2009092_VMT10606A1


title: EXP2.KIX.HOME.2

city: Iowa City

first: Ethan

last: Bahl

state: IA

address: 25 S Grand Ave

institute: University of Iowa

data_processing:
Reads were aligned to the mm10 genome build using STAR version 020201, with default parameters from bcbio-nextgen version 1.0.7
BAM files were indexed and sorted using SAMtools version 1.6, with default parameters from bcbio-nextgen version 1.0.7
Gene-level counts were quantified using featureCounts version 1.4.4, with default parameters from bcbio-nextgen version 1.0.7
Genome_build: mm10, GENCODE release M14
Supplementary_files_format_and_content: CSV text file containing gene-level counts for all samples

source_name: dorsal hippocampus

extract_protocol:
Dorsal hippocampus were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (poly-A selection or Ribo-zero gold) for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain/background

value: dorsal hippocampus

tag: experiment

tag: genotype

value: CBP KIX/KIX

tag: exposure

value: homecage

tag: paradigm

tag: group

tag: replicate


title: 2009091_VMT13567A1


title: EXP2.KIX.HOME.3


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A1_AD004_indexed

value: CP


title: EXP2.KIX.HOME.1

value: male


title: 2010033_VMT12711A1


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A1_AD001_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A1_AD002_indexed


title: KO_4

city: Wuhan

first: Qi

last: shanshan

state: Hubei

address: 1277 Jiefang Avenue

department: Union Hospital

institute: Tongji Medical College, Huazhong University of Science and Technology

data_processing:
Illumina bcl2fastq version 2.19 using for basecalling.
Sequenced reads with 10% low quality bases, adapters and artificial sequences (including UP1, UP2, polyA sequences) introduced during the experimental processes were trimmed by in house scripts.
The trimmed clean reads were aligned to the mm10 whole genome using Tophat2 (v2.1.0) with default settings (Trapnell et al., 2009).
Cufflinks (v2.2.1) with defualt settings was used to quantify transcription levels of annotated genes (Trapnell et al., 2010), and FPKM were calculated
FPKM values were log2-transformed with an offset value of 1.0.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes FPKMs (log2-transformed with an offset value of 1.0) for each sample

extract_protocol:
Colon tissues were harvested and  frozen in liquid nitrongen immediately.Total RNA were isolated by Trizol reagent.3 µg of total RNA per sample was used to generating Sequencing libraries with NEBNext® UltraTM RNA Library Prep Kit.
Libraries were generated following the Illumina's instructions.

tag: genotype/variation

value: colon


title: EXP2.KIX.HOME.4


title: 2009086_VMT09766A1


title: 2009088_VMT00971A1


title: KO_3


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A12_AD012_indexed


title: BM274


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A12_AD007_indexed


title: 2009084_VMT12497A1


title: BM271


title: BM270


title: BM277


title: ctr_3

value: wild type


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_B10_AD002_indexed


title: BM267


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A12_AD008_indexed


title: 2009078_VMT01067A1


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A12_AD006_indexed


title: 2009075_VMT08830A1


title: BM265


title: BM263


title: BM273


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A12_AD004_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A12_AD002_indexed


title: BM262


title: KO_1


title: 2009085_VMT09976A1


title: 2009060_VMT10396A1


title: 2009077_VMT08533A1


title: ctr_2


title: ctr_4


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A11_AD012_indexed


title: BM261


title: 2009064_VMT10501A1


title: BM276


title: ctr_1


title: 2009050_VMT09662A1


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A11_AD010_indexed


title: BM259


title: Human xenograft tumor isolated from mouse treated with control + cisplatin [G4_157]

city: Mexico

first: Sandra

middle: Lorena

last: Romero-Cordoba

state: Mexico

address: Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan. México, D.F.

department: Cancer Genomics

country: Mexico

institute: National Instute of Genomic Medicine

description:
8-week-old female immunodeficient Fox Chase SCID mice.
Mouse treated with cel-miR-67 negative control + intraperitoneal injection of 2 mg/kg cisplatin.
Replicate 6

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing:
Raw expression data were processed using the lumi package on Bioconductor. Gene raw data were normalized with quantile algorithm and log2 transformed. Probes with a detection p < 0.01 were maintained for the analysis. Quality control was performed on raw and processed data, all samples fulfilling quality control procedures were included (N=23). Probes were annotated using the illuminaHumanv4.db package and biomart R dependency. Genes evaluated by multiple probes were collapsed by the highest detection value.
Differentially expressed genes among the biological conditions (treated with: miR-302b (N=5), miR-302b+cisplatin (N=6), cel-miR-67 control (N=6) and cel-miR-67 control+cisplatin (N=6)) were identified by linear modeling implemented in limma package of Bioconductor on R environment. Genes with a log fold change of ≥0.5 or ≤-0.5 and p value < 0.05 were considered as significantly differentially expressed.

label_protocol: Biotin label protocol.

growth_protocol: In vivo experiments were performed with 8-week-old female immunodeficient Fox Chase SCID mice (CB17/Icr-Prkdcscid/IcrIcoCrl) purchased from Charles Rivers. Mice were housed at the animal facility of Fondazione IRCCS Istituto Nazionale dei Tumori of Milan. All animal experiments were approved by the Ethics Committee for Animal Experimentation of Fondazione IRCSS Istituto Nazionale dei Tumori of Milan.

extract_protocol: 23 collected mice tumors were homogenized and total RNA was isolated with Trizol reagent (Thermo Fischer Scientific) by the Functional Genomics and Bioinformatics Core facility of Fondazione IRCCS Istituto Nazionale dei Tumori of Milan. RNA quality was assessed with the Agilent Bioanalyzer (Agilent Technologies) using the RNA 6000 Nano Kit (Agilent). RNA concentrations were measured with the NanoDrop ND-100 spectrophotometer (NanoDrop Technologies).

treatment_protocol:
For treatments, we used miR-302b mimic or cel- miR-67 negative control (Tema Ricerca). Dried miRNA oligonucleotides were resuspended in sterile water to obtain a 10 mg/ml stock. MiRNAs were then formulated within lipid nanoparticles using MaxSuppressor In Vivo RNA-LANCEr II (Bioo Scientific). Cisplatin was obtained from Fondazione IRCCS Istituto Nazionale dei Tumori pharmacy and diluted in physiological saline at 1 mg/ml concentration.
Orthotopic triple negative breast tumors were generated in mice (N=28) by injecting 5x10e6 cells/each of MDA-MB-231 cells, resuspended in 200 µl of a 1:1 mixture with PBS and Matrigel (Corning), in the mammary fat pad. When tumors were palpable (50 mm3), mice were divided into 4 groups of 7 mice each, maintaining the same mean tumor volume in all groups. Two groups of mice were treated with 50 µl of lipid nanoparticles containing 20 µg miR-302b mimic, and the other 2 groups with 50 µl of lipid nanoparticles containing 20 µg cel-miR- 67 negative control, administered every 3 days by peritumoral injection. After 24 h of each nanoparticle treatment, both the group of mice treated with miR-302b mimic and the one treated with cel-miR- 67 negative control, received an intraperitoneal injection of 2 mg/kg cisplatin, while the others were treated with an equal volume of physiological saline solution. Tumor growth was measured every 3 days using a caliper, and at the end of the five treatment cycles, mice were euthanized. Finally, tumors were collected and frozen at -80°C.

tag: mouse strain

value: Immunodeficient Fox Chase SCID mouse

value: Human xenograft breast triple negative tumor

tag: treatment

value: cel-miR-67 negative control + cisplatin


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A11_AD008_indexed

tag: brain region


title: BM258


title: Human xenograft tumor isolated from mouse treated with control + cisplatin [G4_156]

description:
8-week-old female immunodeficient Fox Chase SCID mice.
Mouse treated with cel-miR-67 negative control + intraperitoneal injection of 2 mg/kg cisplatin.
Replicate 5


title: 2009048_VMT09246A1


title: Human xenograft tumor isolated from mouse treated with control + cisplatin [G4_155]

description:
8-week-old female immunodeficient Fox Chase SCID mice.
Mouse treated with cel-miR-67 negative control + intraperitoneal injection of 2 mg/kg cisplatin.
Replicate 4


title: 2009007_VMT00329A1


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A11_AD007_indexed

tag: Sex


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A11_AD002_indexed

tag: age


title: BM247


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A11_AD004_indexed

tag: strain


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A11_AD001_indexed


title: BM251

tag: tissue


title: cDNA_UMT-derived CD8+ T cells

city: Kyoto

first: Kenji

last: Chamoto

state: Kyoto

address: Yoshida Konoe-cho, Sakyo-ku

department: Department of Immunology and Genomic Medicine

country: Japan

institute: Graduate School of Medicine, Kyoto University

description: single strand RNA-Seq (3' GEX)

data_processing:
demultiplexed reads were processed (filtering low quality reads, mapping, counting) by Cell Ranger ver. 3.0.2
Gene expression matrices in CSV were generated by the cellranger mat2csv command
Genome_build: Ensembl mouse mm10
Supplementary_files_format_and_content: Gene expression matrix (N (cells)×M (genes))

source_name: B cell defective (BCD) - µ membrane tail deletion (µMT)

extract_protocol:
CD8+ T cells were purified by autoMACS (Miltenyi Biotec; 130-096-543) and/or Mojosort system (MojoSort; 480008, 480044) according to the manufacturer’s instructions.
Peripheral CD8+ T cell populations derived from WT and B cell defective (µMT) strains each were labeled with oligoDNA-tagged antibodies against CD44 and CD62L (TotalSeq-A provided from BioLegend) and used for the single cell transcriptome analysis using 10x Genomics Chromium Controller. Sequencing libraries for gene expression were established by 3′ Library Construction Kit v3 (10X Genomics) and oligoDNA-antibody-tagged libraries were established by a procedure provided from BioLegend with custom primer sets. Expected target cell numbers and read depth are 3,000 cells each and 100,000 paired-end reads/cell. Gene expression-derived and antibody-derived libraries were pooled at the ratio of 9:1 for sequencing.

value: BCD

tag: cell type

value: CD8+ T cells


title: ADT_WT-derived CD8+ T cells

description: CITE-Seq (Cell Surface Protein detection using oligoDNA-tagged antibodies)

source_name: wild-type (WT)

value: WT


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A11_AD006_indexed


title: ADT_UMT-derived CD8+ T cells


title: cDNA_WT-derived CD8+ T cells

description: single strand RNA-Seq (3' GEX)


title: BM250

tag: subject status

value: acute myeloid leukemia (AML) patient

tag: response to standard induction chemotherapy


title: BM232

value: CR (complete remission)


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A10_AD012_indexed


title: Human xenograft tumor isolated from mouse treated with control + cisplatin [G4_133]

description:
8-week-old female immunodeficient Fox Chase SCID mice.
Mouse treated with cel-miR-67 negative control + intraperitoneal injection of 2 mg/kg cisplatin.
Replicate 2


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A10_AD010_indexed


title: Human xenograft tumor isolated from mouse treated with control + cisplatin [G4_130]

description:
8-week-old female immunodeficient Fox Chase SCID mice.
Mouse treated with cel-miR-67 negative control + intraperitoneal injection of 2 mg/kg cisplatin.
Replicate 1


title: Human xenograft tumor isolated from mouse treated with control + cisplatin [G4_134]

description:
8-week-old female immunodeficient Fox Chase SCID mice.
Mouse treated with cel-miR-67 negative control + intraperitoneal injection of 2 mg/kg cisplatin.
Replicate 3


title: BM226

value: bone marrow


title: Human xenograft tumor isolated from mouse treated with control [G3_138]

description:
8-week-old female immunodeficient Fox Chase SCID mice.
Mouse treated with cel-miR-67 negative control.
Replicate 3

value: cel-miR-67 negative control


title: Human xenograft tumor isolated from mouse treated with control [G3_153]

description:
8-week-old female immunodeficient Fox Chase SCID mice.
Mouse treated with cel-miR-67 negative control.
Replicate 5


title: Human xenograft tumor isolated from mouse treated with control [G3_143]

description:
8-week-old female immunodeficient Fox Chase SCID mice.
Mouse treated with cel-miR-67 negative control.
Replicate 4


title: Human xenograft tumor isolated from mouse treated with control [G3_nonumG3]

description:
8-week-old female immunodeficient Fox Chase SCID mice.
Mouse treated with cel-miR-67 negative control.
Replicate 6


title: BM246

value: Non-CR (non-complete remission)


title: RNA-Seq Piezo_KO

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

description:
antibodies for negative enrichment: anti mouse CD3 (17A2; BioLegend #100205), anti mouse CD19 (1D3/CD19; BioLegend #152403), anti mouse Ter119 (TER-119; BioLegend #116223)
negatively enriched by FACS-sorting
mouse bone marrow cells

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Cell Ranger software.
ChIP-Seq data mapped with Bowtie2
BAM to bedgraph performed using bedtools and bedgraph to bigwig performed using bedGraphToBigWig v4
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files, BAM files, gene names and genes-barcodes (tsv files) matrices (matrix file)

source_name: Knockout

extract_protocol: Total RNA was extracted using an RNeasy mini kit (Qiagen, Valencia, CA) and cDNA was synthesized using the iScript cDNA Synthesis Kit (BioRad, Hercules, CA). For ChIP-Seq preparation, the EMD Millipore Acetyl-Histone H3 Immunoprecipitation (ChIP) Assay Kit was used according to the manufacturer's protocols.

value: murine bone marrow cells

tag: antibody


title: ChIP-Seq_ChIP WT1

source_name: WT control 1

tag: genotype

value: Anti-Histone H4 Antibody, pan, clone 62-141-13, rabbit monoclonal from EMD Millipore (cat# 05-858)


title: RNA-Seq Piezo_WT

source_name: WT


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A10_AD008_indexed

source_name: C57BL/6J Male P56 Mouse Brain

value: CP


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A10_AD007_indexed

value: male


title: BM222


title: BM225


title: ChIP-Seq_Input WT2

source_name: WT input 2

value: input


title: ChIP-Seq_Input WT1

source_name: WT input 1


title: BM219


title: ChIP-Seq_ChIP WT2

source_name: WT control 2


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A10_AD006_indexed


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A10_AD004_indexed


title: Human xenograft tumor isolated from mouse treated with control [G3_117]

description:
8-week-old female immunodeficient Fox Chase SCID mice.
Mouse treated with cel-miR-67 negative control.
Replicate 1


title: BM213


title: ChIP-Seq_Input LyzM1

source_name: Knockout Input 1


title: BM203


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A10_AD002_indexed


title: Human xenograft tumor isolated from mouse treated with miR302b + cisplatin [G2_144]

description:
8-week-old female immunodeficient Fox Chase SCID mice.
Mouse treated with 50 µl of lipid nanoparticles containing 20 µg miR-302b + intraperitoneal injection of 2 mg/kg cisplatin.
Replicate 4

value: miR-302b + cisplatin


title: ChIP-Seq_Input LyzM2

source_name: Knockout Input 2


title: BM152


title: Human xenograft tumor isolated from mouse treated with miR302b + cisplatin [G2_146]

description:
8-week-old female immunodeficient Fox Chase SCID mice.
Mouse treated with 50 µl of lipid nanoparticles containing 20 µg miR-302b + intraperitoneal injection of 2 mg/kg cisplatin.
Replicate 5

value: Immunodeficient Fox Chase SCID mouse


title: BM146


title: Human xenograft tumor isolated from mouse treated with miR302b + cisplatin [G2_151]

description:
8-week-old female immunodeficient Fox Chase SCID mice.
Mouse treated with 50 µl of lipid nanoparticles containing 20 µg miR-302b + intraperitoneal injection of 2 mg/kg cisplatin.
Replicate 6

value: Human xenograft breast triple negative tumor


title: ChIP-Seq_ChIP LyzMCre

source_name: Cre Control 1


title: BM137


title: CD4+CD44+T single cell RNA-seq

city: Beijing

first: Huiping

last: Lu

address: Tsinghua university

institute: Tsinghua university

data_processing:
For RNA-seq, Illumina Casava1.7 software used for basecalling.
For RNA-seq, sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9
For RNA-seq, the reads were  normalized to fragments by using the TopHat and Cufflinks software pipeline.
For single cell RNA-seq, alignment, filtering, barcode counting and unique molecular identifier counting were performed using Cell Ranger v.2.1.0. Data were further analyzed using Seurat v.2. Marker genes were identified by the Seurat function FindAllMarkers.Trajectory analysis was performed with Monocle v.2.
For ATAC-seq, paired-end reads were mapped to the mm10 reference genome using Bowtie2. Peak calling was performed using MACS2 to identify areas of sequence tag enrichment. BedTools was used to find common intersections between identified peaks (1 base pair minimum overlap) and to create a merged peak list. DNA transcription factor motif analysis across the merged peak list was computed using hypergeometric optimization of motif enrichment (HOMER; homer.ucsd.edu/homer/).
Genome_build: mm9 (for RNA-seq), mm10 (for ATAC-seq)
Supplementary_files_format_and_content: excel files include RPKM values for each Sample

source_name: draining lymph nodes

extract_protocol:
Sostdc1-EGFP-Tfh,Sostdc1-EGFP+Tfh,non-Tfh,Tfr and non-Tfr Treg cells were sorted,and RNA was harvested using Trizol reagent. RNA library preparation was conducted using an NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer’s protocols.CD4+CD44+ T cells were sorted and then analyzed by single cell RNA-seq.The scRNA-seq libraries were generated using Chromium single cell 3′ library and bead kit v.2 (10xgenomics) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols. Single cell RNA-seq libraries were generated using Chromium single cell 3′ library and bead kit v.2 (10xgenomics) according to the manufacturer’s protocol.ATAC-seq DNA library was constructed using TruePrep DNA Library Prep Kit V2 for Illumina and TruePrep Index Kit V2 for Illumina.

value: draining lymph nodes

value: Sostdc1-EGFP heterozygous


title: non-Tfh rep2 RNA-seq

description: non-Tfh Sostdc1-EGFP-Tfh Sostdc1-EGFP+Tfh rep2 RNA-seq.xls


title: ChIP-Seq_ChIP LY2M2_ChIP-Seq

source_name: Cre Control 2


title: BM135


title: non-Tfh rep1 RNA-seq

description: non-Tfh Sostdc1-EGFP-Tfh Sostdc1-EGFP+Tfh rep1 RNA-seq.xls


title: BM118


title: Model_2 [ncRNA]

city: JiNan

first: Xue

last: Liu

state: ShangDong

address: Wenhua West Road

institute: The Affiliated Hospital of Shandong University of TCM

data_processing:
Illumina Casava1.8 software used for basecalling.
Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
We aligned reads of samples to the reference genome using HISAT2 package.
The mapped reads of each sample were assembled using StringTie, all transcriptomes were merged to reconstruct a comprehensive transcriptome.
Unmapped reads were still mapped to genome using tophat-fusion. CIRCExplorer2 was used to denovo assemble the mapped reads to circular RNAs at first; Then, back splicing reads were identified in unmapped reads by tophat-fusion and CIRCExplorer2. All samples were generated unique circular RNAs.
Genome_build: Rattus_norvegicus Ensembl relaese-94
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each isoforms

organism: Rattus norvegicus

source_name: lung

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure. The total RNA quantity and purity were analysis of Aglient 2100 Bioanalyzer and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 10 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero™ rRNA removal kit (Illumina, San Diego, USA).Then the left RNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, USA).

tag: sample type

value: bleomycin-induced pulmonary fibrosis model


title: Liver_beta_conglutin_7day_treatment

city: Guadalajara

first: Carmen

middle: Magdalena

last: Gurrola-Díaz

state: Jalisco

address: Sierra Mojada 950

department: Departamento de Biología Molecular y Genómica

institute: Universidad de Guadalajara

hyb_protocol: Equivalent amounts of labelled cDNA were hybridized on printed arrays using UniHyb solution (TeleChem International Inc., USA) for 14 h, 42 °C.

scan_protocol: Array images were acquired and quantified in a GenePix 4100-A reader using GenePix software (Molecular Devices, USA).

data_processing: The genArise free software package was used to analyze the microarray data (Computing Unit of Cellular Physiology Institute of UNAM, http://www.ifc.unam.mx/genarise/). This software is a tool for dual-color microarray data implemented in the R language. It contains specific functions to perform an analysis of DNA microarrays data to detect genes that are significantly differentially expressed under different conditions by calculating an intensity-dependent Z-score.

source_name: liver, vehicle-treated (control), seven day treatment

label_protocol: High-quality total RNA was retrotranscribed using dUTP-Alexa555 or dUTP-Alexa647 fluorophores with the First-Strand cDNA Synthesis kit (ThermoFisher Scientific, USA). Incorporated fluorophores were analyzed by measuring the absorbance at 555 nm and 650 nm for Alexa555 and Alexa647, respectively.

growth_protocol: Male Wistar rats were caged, fed a standard rodent chow diet and water ad libitum, and maintained under a 24 ± 2 °C temperature, 55 ± 5% humidity, and 12 h-dark/light cycles.

extract_protocol: The liver was removed, washed in sterile saline, excised, and homogenized in RLT buffer. Later, total RNA was extracted using RNeasy Mini Kit (QIAGEN, USA) following manufacturer instructions.

treatment_protocol: Adult animals were fasted overnight (12 h) and chemically-induced to diabetes by a single intraperitoneal injection of STZ (65 mg/kg BW). Diabetes (glycaemia levels > 200 mg/dl) was confirmed 72 h after tue induction, and the animals were randomly allocated into one of two groups as follows: 1) STZ-Ctrl, diabetic rats receiving only vehicle (0.9% w/v NaCl) or 2) STZ-βC120, rats induced to diabetes and treated with beta-conglutin (120 mg/kg BW) dissolved in 0.9% NaCl. The treatment was administered for seven consecutive days.

value: Wistar

value: Male

value: Liver

tag: developmental stage

value: Adult

source_name: liver, beta-conglutin-treated, seven day treatment


title: Human xenograft tumor isolated from mouse treated with miR302b + cisplatin [G2_129]

description:
8-week-old female immunodeficient Fox Chase SCID mice.
Mouse treated with 50 µl of lipid nanoparticles containing 20 µg miR-302b + intraperitoneal injection of 2 mg/kg cisplatin.
Replicate 1


title: Model_3 [ncRNA]


title: 171222_CEMBA_mm_P56_P63_4D_CEMBA171219_4D_1_CEMBA171219_4D_2_A10_AD001_indexed

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

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

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.


title: Model_1 [ncRNA]


title: Sostdc1-EGFP+Tfh rep2 RNA-seq


title: BM101

source_name: Non-CR_bone marrow

value: acute myeloid leukemia (AML) patient

value: bone marrow


title: Human xenograft tumor isolated from mouse treated with miR302b [G1_128]

description:
8-week-old female immunodeficient Fox Chase SCID mice.
Mouse treated with 50 µl of lipid nanoparticles containing 20 µg miR-302b.
Replicate 3


title: Control_3 [ncRNA]

value: control


title: Human xenograft tumor isolated from mouse treated with miR302b + cisplatin [G2_141]

description:
8-week-old female immunodeficient Fox Chase SCID mice.
Mouse treated with 50 µl of lipid nanoparticles containing 20 µg miR-302b + intraperitoneal injection of 2 mg/kg cisplatin.
Replicate 3


title: Human xenograft tumor isolated from mouse treated with miR302b [G1_136]

description:
8-week-old female immunodeficient Fox Chase SCID mice.
Mouse treated with 50 µl of lipid nanoparticles containing 20 µg miR-302b.
Replicate 4


title: Human xenograft tumor isolated from mouse treated with miR302b [G1_152]

description:
8-week-old female immunodeficient Fox Chase SCID mice.
Mouse treated with 50 µl of lipid nanoparticles containing 20 µg miR-302b.
Replicate 5


title: Model_3 [miRNA]

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Genome_build: Rattus_norvegicus Ensembl relaese-94
Supplementary_files_format_and_content: excel, expression profiles

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure. The total RNA quantity and purity were analysis of Aglient 2100 Bioanalyzer and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.


title: Human xenograft tumor isolated from mouse treated with miR302b [G1_127]

description:
8-week-old female immunodeficient Fox Chase SCID mice.
Mouse treated with 50 µl of lipid nanoparticles containing 20 µg miR-302b.
Replicate 2


title: BM040

value: Non-CR (non-complete remission)


title: Human xenograft tumor isolated from mouse treated with miR302b + cisplatin [G2_140]

description:
8-week-old female immunodeficient Fox Chase SCID mice.
Mouse treated with 50 µl of lipid nanoparticles containing 20 µg miR-302b + intraperitoneal injection of 2 mg/kg cisplatin.
Replicate 2


title: Control_1 [ncRNA]


title: Sostdc1-EGFP-Tfh rep1 RNA-seq


title: Model_2 [miRNA]


title: Sostdc1 ko Tfr ATAC-seq

data_processing:
For RNA-seq, Illumina Casava1.7 software used for basecalling.
For RNA-seq, sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9
For RNA-seq, the reads were  normalized to fragments by using the TopHat and Cufflinks software pipeline.
For single cell RNA-seq, alignment, filtering, barcode counting and unique molecular identifier counting were performed using Cell Ranger v.2.1.0. Data were further analyzed using Seurat v.2. Marker genes were identified by the Seurat function FindAllMarkers.Trajectory analysis was performed with Monocle v.2.
For ATAC-seq, paired-end reads were mapped to the mm10 reference genome using Bowtie2. Peak calling was performed using MACS2 to identify areas of sequence tag enrichment. BedTools was used to find common intersections between identified peaks (1 base pair minimum overlap) and to create a merged peak list. DNA transcription factor motif analysis across the merged peak list was computed using hypergeometric optimization of motif enrichment (HOMER; homer.ucsd.edu/homer/).
Genome_build: mm9 (for RNA-seq), mm10 (for ATAC-seq)
Supplementary_files_format_and_content: bw

value: Tfr

value: Sostdc1 homo


title: Parthenote PA3 RNA-seq

city: Columbus

first: Jinsoo

last: Ahn

address: 2029 Fyffe Rd

institute: The Ohio State University

data_processing:
Sequenced reads were trimmed for adaptor sequence and low quality reads were eliminated.
Then, the cleaned reads were aligned to the reference genome (Sscrofa11.1) using HISAT2 (v2.1.0) with default parameter settings, except for the parameter --dta regarding tailored transcriptome assembly.
BAM format containing RNA-seq alignments were produced and sorted by SAMtools (v1.9).
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: Tab-delimited text files include normalized read counts for each sample.
Supplementary_files_format_and_content: Matrix table displays raw or processed gene counts for every sample.

source_name: embryo

extract_protocol:
Total RNA from whole CN embryos (n = 3) and whole PA embryos (n = 3) samples was isolated with TRIzol reagent. DNase I was treated to the RNA samples to avoid genomic DNA contamination. One ug of total RNA was used to construct cDNA libraries with the TruSeq RNA Sample Prep Kit v.2.
RNA libraries were prepared for sequencing according to Illumina's instructions accompanying the TruSeq RNA Sample Prep Kit v.2.

value: Landrace x Yorkshire x Duroc (LYD)

value: whole embryo

value: embryonic day 21

value: parthenogenesis


title: Sostdc1-EGFP-Tfh rep2 RNA-seq

value: draining lymph nodes


title: Model_1 [miRNA]


title: Parthenote PA2 RNA-seq


title: Parthenote PA1 RNA-seq


title: Control_2 [ncRNA]


title: Sostdc1-EGFP+Tfh rep1 RNA-seq

value: Sostdc1-EGFP heterozygous


title: WT Tfr ATAC-seq

value: WT


title: Control_2 [miRNA]


title: Control_3 [miRNA]


title: Human xenograft tumor isolated from mouse treated with miR302b [G1_126]

description:
8-week-old female immunodeficient Fox Chase SCID mice.
Mouse treated with 50 µl of lipid nanoparticles containing 20 µg miR-302b.
Replicate 1

value: Immunodeficient Fox Chase SCID mouse

value: Human xenograft breast triple negative tumor


title: Sostdc1 ko Tfr RNA-seq

description: RNA-seq KO-Tfr_WT-Tfr.txt


title: Control CN3 RNA-seq

value: untreated


title: U87IL33 DNLS c4-3

city: Calgary

first: Stephen

middle: M

last: Robbins

state: Alberta

address: 3330 Hospital Drive N.W.

department: Oncology

institute: University of Calgary

hyb_protocol: Probes and target transcripts were hybridized overnight at 65°C for 16 hours per the manufacturer’s protocol. Hybridized samples were purified on the NanoString nCounter Prep Station using the high-sensitivity protocol, in which excess capture and reporter probes were removed and transcript-specific ternary complexes were immobilized on a streptavidin-coated cartridge.

scan_protocol: The samples were scanned at maximum scan resolution on the nCounter Digital Analyzer.

data_processing:
Data analysis with nSolver software (NanoString Technologies). Samples that passed QC were further analyzed for fold change and normalized expression levels.
The expression levels of each gene were normalized, to both positive control probes and housekeeping genes built-in each probe set, by the nSolver Analysis Software.

source_name: Mutant

label_protocol: 100 ng of total RNA in a final volume of 5 μl was mixed with a 3′ biotinylated capture probe and a 5′ reporter probe tagged with a fluorescent barcode from the nCounter Inflammation Panel (Mouse v2) gene expression code set.

growth_protocol: Six- to 8-week-old female SCID mice were housed in groups of three to five and maintained on a 12-hr light/dark schedule with a temperature of 22 °C±1 °C and a relative humidity of 50 ± 5%. Food and water were available ad libitum. All procedures were reviewed and approved by the University of Calgary Animal Care Committee. table transfectants of U87 or U251 cells were maintained in complete medium [Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum (FBS), 1% penicillin/streptomycin, 2 mM L-glutamine and 1 mM sodium pyruvate at 37ºC in a humidified 5% CO2 incubator. Cells were passaged by harvesting with Puck’s EDTA when they reached 80%–90% confluence.

extract_protocol: Total RNA was isolated from intracranial xenografts derived from U87pcDNA, IL-33 and DNLS cells. RNA was isolated using mirVana miRNA isolation kit (Ambion) according to the manufacturer's protocol. Total RNA purification to remove genomic DNA was carried out with Qiagen kit of RNeasy® Plus Micro following the manufacturer’s protocols. RNA Integrity Number (RIN) was assessed with RNA 6000 NanoChip on Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: U87pcDNA or U87 IL-33 or U87 IL-33 DNLS human glioma cells (5×10^4 cells/mouse) were implanted into the brain of mice by intracranial injection. Mice were monitored weekly. Animals bearing U87 tumors were sacrificed at 1 week after tumor implantation.

value: SCID

value: 6-8 weeks

value: Brain

tag: implanted cells

value: Human Glioma U87 expressing IL-33 DNLS


title: U87IL33 DNLS c4-4


title: Control CN2 RNA-seq


title: Control_1 [miRNA]

value: control


title: BM255

value: acute myeloid leukemia (AML) patient

value: Non-CR (non-complete remission)

value: bone marrow


title: Arabidopsis_WT_L2_G11 (WGBS)

city: Athens

first: Robert

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

data_processing:
MethylC-seq: analysis was performed by Methylpy 1.3
Genome_build: Arabidopsis thaliana TAIR10 reference genome
Supplementary_files_format_and_content: methylome tab delimited text file, see "allc_column_header_descriptions.txt" for column headers

organism: Arabidopsis thaliana

source_name: Arabidopsis_WT_L2_G11 (WGBS)

growth_protocol: Seeds were planted and grown in 16-hour  day lengths and samples were harvested from young  above ground tissue. Tissue was flash frozen in liquid  nitrogen and DNA was isolated using a Qiagen  Plant DNeasy kit (Qiagen, Valencia, CA, USA) according  to the manufacturer’s instructions.

extract_protocol: MethylC-seq: prepared as previously described in (Urich et al. 2015).

tag: lineage

value: lineage 2 generation 11

value: leaf

tag: ecotype


title: WT Tfr RNA-seq

description: RNA-seq KO-Tfr_WT-Tfr.txt

value: Tfr