title: Retina from C3H rd1 mice, PN21, biological rep 2

description:
Sample name: rd1rd1_d21_2
retina from rd1 C3H mouse aged 21 days

source_name: Retinal RNA from C3H rd1 mice


title: Retina from C3H rd1 mice, PN35, biological rep 1

status: Public on Sep 25 2020

type: RNA

city: Paris

first: Frederic

last: Blond

address: 17 rue Moreau

country: France

institute: Institut de la Vision

description:
Sample name: rd1rd1_d35_1
retina from rd1 C3H mouse aged 35 days

hyb_protocol: Following fragmentation, cRNA was hybridized on the GeneChip Array and the GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2007, Affymetrix).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 7G scanner

data_processing: Normalization: RMA, data analysis: R/Bioconductor

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: The cDNA was transcribed in vitro using RNA Transcript Labeling kit (ENZO Diagnostics, Farmingdale, NY) to form biotin-labeled cRNA

extract_protocol: Neural retinas from wild-type control (C3Hwt/wt) and rd1 (C3Hrd1/rd1) mice were dissected at different post-natal days. Total RNA was purified onto cesium gradient.

tag: strain

tag: genotype/variation

tag: age

tag: tissue

value: retina


title: Retina from C3H rd1 mice, PN28, biological rep 1

description:
Sample name: rd1rd1_d28_1
retina from rd1 C3H mouse aged 28 days


title: Retina from C3H WT mice, PN21, biological rep 1

description:
Sample name: wtwt_d21_1
retina from WT C3H mouse aged 21 days

source_name: Retinal RNA from C3H WT mice

value: WT


title: Retina from C3H WT mice, PN21, biological rep 2

description:
Sample name: wtwt_d21_2
retina from WT C3H mouse aged 21 days


title: Retina from C3H rd1 mice, PN15, biological rep 1

description:
Sample name: rd1rd1_d15_1
retina from rd1 C3H mouse aged 15 days


title: Retina from C3H rd1 mice, PN15, biological rep 2

description:
Sample name: rd1rd1_d15_2
retina from rd1 C3H mouse aged 15 days


title: stage2 rep2

type: SRA

city: Cambridge

first: Ya

last: Min

state: Massachusetts

address: 16 Divinity Ave.

country: USA

institute: Harvard University

description: staminode primordia finish initiating

library_source: transcriptomic

data_processing:
Sequencing was conducted at Novogene (Beijing, China) using the 150 bp paired-end Illumina HiSeq4000 sequencing platform.
The raw sequencing reads were filtered by removing adapters and low-quality reads using Trim Galored v0.6.5 17 (quality Phred score cutoff = 20) and mapped to the Aquilegia coerulea ‘Goldsmith’ v3.1 reference transcriptome (https://phytozome.jgi.doe.gov/) using Kallisto v0.46.118.
Supplementary_files_format_and_content: Tab Separated Value files including estimated counts and tpm for each sample.

organism: Aquilegia coerulea

source_name: floral meristems

growth_protocol: Seeds of Aquilegia coerulea ‘Kiragami’ were purchased from Swallowtail Garden Seeds (Santa Rosa, CA, USA). Seeds were germinated in wet soil and seedlings were grown under conditions of 16h daylight at 18˚C and 8 h dark at 13˚C.

extract_protocol:
Once the plants developed approx. six true leaves, they were transferred into vernalization conditions (16h daylight at 6˚C and 8h dark at 6˚C) for three to four weeks, and subsequently moved back to the regular growth condition. Once the inflorescences started to develop, axillary FMs were quickly dissected on ice using surgical needles and flash frozen in liquid nitrogen. Three sepals were removed from every floral bud collected. The total RNA of all samples was extracted using the RNeasy Micro Kit (Qiagen, Netherlands).
Sequencing libraries were prepared by the Bauer Core facility of Harvard University using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio USA, Inc., CA, USA) for cDNA synthesis and Illumina Nextera XT (Illumina) for library preparation. Libraries were fragmented to an average size of 350 bp.

treatment_protocol: all wild-type

tag: cultivar

value: Kiragami

value: floral meristems

tag: developmental stage

value: developmental stage2

tag: genotype

value: wild-type


title: Retina from C3H rd1 mice, PN13, biological rep 3

description:
Sample name: rd1rd1_d13_3
retina from rd1 C3H mouse aged 13 days


title: Retina from C3H rd1 mice, PN13, biological rep 1

description:
Sample name: rd1rd1_d13_1
retina from rd1 C3H mouse aged 13 days


title: Retina from C3H rd1 mice, PN13, biological rep 2

description:
Sample name: rd1rd1_d13_2
retina from rd1 C3H mouse aged 13 days


title: Retina from C3H rd1 mice, PN21, biological rep 1

description:
Sample name: rd1rd1_d21_1
retina from rd1 C3H mouse aged 21 days


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B12_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: SSs

tag: Sex

value: male


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B12_ad004


title: stage1 rep8

description: stamen primordia initiating

value: developmental stage1


title: stage2 rep1

description: staminode primordia finish initiating


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B12_ad002


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B12_ad001


title: stage1 rep7

description: stamen primordia initiating


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B11_ad012


title: Retina from C3H rd1 mice, PN12, biological rep 1

description:
Sample name: rd1rd1_d12_1
retina from rd1 C3H mouse aged 12 days


title: Retina from C3H WT mice, PN15, biological rep 1

description:
Sample name: wtwt_d15_1
retina from WT C3H mouse aged 15 days


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B11_ad010


title: Retina from C3H WT mice, PN13, biological rep 2

description:
Sample name: wtwt_d13_2
retina from WT C3H mouse aged 13 days


title: stage1 rep5

description: stamen primordia initiating


title: stage1 rep4

description: stamen primordia initiating


title: Retina from C3H rd1 mice, PN11, biological rep 3

description:
Sample name: rd1rd1_d11_3
retina from rd1 C3H mouse aged 11 days


title: Retina from C3H WT mice, PN15, biological rep 2

description:
Sample name: wtwt_d15_2
retina from WT C3H mouse aged 15 days


title: Retina from C3H rd1 mice, PN12, biological rep 2

description:
Sample name: rd1rd1_d12_2
retina from rd1 C3H mouse aged 12 days


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B11_ad008


title: stage1 rep3

description: stamen primordia initiating


title: Retina from C3H WT mice, PN13, biological rep 1

description:
Sample name: wtwt_d13_1
retina from WT C3H mouse aged 13 days


title: Retina from C3H WT mice, PN12, biological rep 2

description:
Sample name: wtwt_d12_2
retina from WT C3H mouse aged 12 days


title: Retina from C3H WT mice, PN13, biological rep 3

description:
Sample name: wtwt_d13_3
retina from WT C3H mouse aged 13 days


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B11_ad007


title: Retina from C3H rd1 mice, PN11, biological rep 1

description:
Sample name: rd1rd1_d11_1
retina from rd1 C3H mouse aged 11 days


title: Retina from C3H rd1 mice, PN11, biological rep 2

description:
Sample name: rd1rd1_d11_2
retina from rd1 C3H mouse aged 11 days


title: stage1 rep6

description: stamen primordia initiating


title: stage1 rep2

description: stamen primordia initiating


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B11_ad006


title: Retina from C3H WT mice, PN12, biological rep 1

description:
Sample name: wtwt_d12_1
retina from WT C3H mouse aged 12 days


title: Retina from C3H WT mice, PN11, biological rep 1

description:
Sample name: wtwt_d11_1
retina from WT C3H mouse aged 11 days


title: Retina from C3H rd1 mice, PN9, biological rep 3

description:
Sample name: rd1rd1_d9_3
retina from rd1 C3H mouse aged 9 days


title: Retina from C3H rd1 mice, PN9, biological rep 2

description:
Sample name: rd1rd1_d9_2
retina from rd1 C3H mouse aged 9 days


title: stage1 rep1

description: stamen primordia initiating


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B11_ad002


title: Retina from C3H rd1 mice, PN9, biological rep 1

description:
Sample name: rd1rd1_d9_1
retina from rd1 C3H mouse aged 9 days


title: Retina from C3H WT mice, PN11, biological rep 2

description:
Sample name: wtwt_d11_2
retina from WT C3H mouse aged 11 days


title: Retina from C3H WT mice, PN9, biological rep 2

description:
Sample name: wtwt_d9_2
retina from WT C3H mouse aged 9 days


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B11_ad001


title: Retina from C3H WT mice, PN11, biological rep 3

description:
Sample name: wtwt_d11_3
retina from WT C3H mouse aged 11 days


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B10_ad012


title: SC011

city: Gent

first: Siebe

last: Loontiens

address: Corneel Heymanslaan 10

department: Center for Medical Genetics

country: Belgium

institute: Ghent University

description:
RNA isolated from sorted T-ALL cells collected from full blown leukemic  shrek  zebrafish
rawCountMatrix_Frazier.txt.gz
Fsample_46

data_processing:
First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide
Counts to GRCz10.91.gtf were generated on the fly by STAR
Genome_build: GRCz10
Supplementary_files_format_and_content: txt file with raw counts

molecule: polyA RNA

organism: Danio rerio

source_name: T-ALL colleted when 90% of zebrafish was taken over by GFP + T-ALL cells.

extract_protocol: Truseq stranded mRNA library prep (illumina, #20020594)

tag: cell type

value: T-ALL

tag: tumor stage

value: Primary T-ALL

tag: lab of sample collection and sequencing

value: Frazer lab


title: SC009

description:
RNA isolated from sorted T-ALL cells collected from full blown leukemic  shrek  zebrafish
rawCountMatrix_Frazier.txt.gz
Fsample_45


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B10_ad010


title: Retina from C3H WT mice, PN9, biological rep 3

description:
Sample name: wtwt_d9_3
retina from WT C3H mouse aged 9 days


title: SC008

description:
RNA isolated from sorted T-ALL cells collected from full blown leukemic  shrek  zebrafish
rawCountMatrix_Frazier.txt.gz
Fsample_44


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B10_ad008


title: Retina from C3H rd1 mice, PN8, biological rep 3

description:
Sample name: rd1rd1_d8_3
retina from rd1 C3H mouse aged 8 days


title: SC007

description:
RNA isolated from sorted T-ALL cells collected from full blown leukemic  shrek  zebrafish
rawCountMatrix_Frazier.txt.gz
Fsample_43


title: SPL001

description:
RNA isolated from sorted GFP positive thymocytes from preleukemic Tg(lck:GFP);shrek mutant fish.
rawCountMatrix_Frazier.txt.gz
Fsample_47

source_name: shrek preleukemic thymocytes

value: thymocytes

value: preleukemic


title: Retina from C3H rd1 mice, PN8, biological rep 2

description:
Sample name: rd1rd1_d8_2
retina from rd1 C3H mouse aged 8 days


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B10_ad007


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B10_ad006


title: Retina from C3H WT mice, PN8, biological rep 2

description:
Sample name: wtwt_d8_2
retina from WT C3H mouse aged 8 days


title: Retina from C3H WT mice, PN8, biological rep 3

description:
Sample name: wtwt_d8_3
retina from WT C3H mouse aged 8 days


title: Retina from C3H rd1 mice, PN8, biological rep 1

description:
Sample name: rd1rd1_d8_1
retina from rd1 C3H mouse aged 8 days


title: Retina from C3H WT mice, PN8, biological rep 1

description:
Sample name: wtwt_d8_1
retina from WT C3H mouse aged 8 days


title: Retina from C3H rd1 mice, PN7, biological rep 3

description:
Sample name: rd1rd1_d7_3
retina from rd1 C3H mouse aged 7 days


title: Retina from C3H WT mice, PN7, biological rep 3

description:
Sample name: wtwt_d7_3
retina from WT C3H mouse aged 7 days


title: Retina from C3H rd1 mice, PN7, biological rep 2

description:
Sample name: rd1rd1_d7_2
retina from rd1 C3H mouse aged 7 days


title: Retina from C3H WT mice, PN9, biological rep 1

description:
Sample name: wtwt_d9_1
retina from WT C3H mouse aged 9 days


title: Retina from C3H rd1 mice, PN7, biological rep 1

description:
Sample name: rd1rd1_d7_1
retina from rd1 C3H mouse aged 7 days


title: Retina from C3H WT mice, PN7, biological rep 2

description:
Sample name: wtwt_d7_2
retina from WT C3H mouse aged 7 days


title: SC005

description:
RNA isolated from sorted T-ALL cells collected from full blown leukemic  shrek  zebrafish
rawCountMatrix_Frazier.txt.gz
Fsample_41


title: SC004

description:
RNA isolated from sorted T-ALL cells collected from full blown leukemic  shrek  zebrafish
rawCountMatrix_Frazier.txt.gz
Fsample_40


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B10_ad001


title: SC003

description:
RNA isolated from sorted T-ALL cells collected from full blown leukemic  shrek  zebrafish
rawCountMatrix_Frazier.txt.gz
Fsample_39


title: Retina from C3H WT mice, PN7, biological rep 1

description:
Sample name: wtwt_d7_1
retina from WT C3H mouse aged 7 days


title: SC006

description:
RNA isolated from sorted T-ALL cells collected from full blown leukemic  shrek  zebrafish
rawCountMatrix_Frazier.txt.gz
Fsample_42


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B1_ad012


title: SC002

description:
RNA isolated from sorted T-ALL cells collected from full blown leukemic  shrek  zebrafish
rawCountMatrix_Frazier.txt.gz
Fsample_38


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B1_ad001


title: Retina from C3H rd1 mice, PN5, biological rep 2

description:
Sample name: rd1rd1_d5_2
retina from rd1 C3H mouse aged 5 days


title: Retina from C3H rd1 mice, PN6, biological rep 2

description:
Sample name: rd1rd1_d6_2
retina from rd1 C3H mouse aged 6 days


title: SC001

description:
RNA isolated from sorted T-ALL cells collected from full blown leukemic  shrek  zebrafish
rawCountMatrix_Frazier.txt.gz
Fsample_37


title: Retina from C3H rd1 mice, PN6, biological rep 1

description:
Sample name: rd1rd1_d6_1
retina from rd1 C3H mouse aged 6 days


title: OPL4

description:
RNA isolated from sorted GFP positive thymocytes from preleukemic Tg(lck:GFP);otg mutant fish.
rawCountMatrix_Frazier.txt.gz
Fsample_36

source_name: otg preleukemic thymocytes


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B1_ad007


title: Retina from C3H WT mice, PN6, biological rep 2

description:
Sample name: wtwt_d6_2
retina from WT C3H mouse aged 6 days


title: Retina from C3H WT mice, PN6, biological rep 1

description:
Sample name: wtwt_d6_1
retina from WT C3H mouse aged 6 days


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B1_ad010


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B10_ad002


title: OPL3

description:
RNA isolated from sorted GFP positive thymocytes from preleukemic Tg(lck:GFP);otg mutant fish.
rawCountMatrix_Frazier.txt.gz
Fsample_35


title: Retina from C3H WT mice, PN5, biological rep 1

description:
Sample name: wtwt_d5_1
retina from WT C3H mouse aged 5 days


title: Retina from C3H WT mice, PN5, biological rep 2

description:
Sample name: wtwt_d5_2
retina from WT C3H mouse aged 5 days


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B1_ad008


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A9_ad012


title: Retina from C3H rd1 mice, PN5, biological rep 1

description:
Sample name: rd1rd1_d5_1
retina from rd1 C3H mouse aged 5 days


title: ventricle null rep 3 [e17-5_null-3]

city: Chicago

first: Xiaolei

last: Liu

address: 303 e superior street

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to mm10 using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts per gene

source_name: ventricle null

growth_protocol: Prox1 f/f females and VecadCreERT2; Prox1f/f males were set up in breeding cages. Female plugged date was recorded as Embryonic day 0.5

extract_protocol:
Ventricular portions of the embryo hearts were dissected and homogenized. Total RNAs was extracted using Qiagen RNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tamoxifen (5mg/ 40g body weight) was injected into female mice at E13.5 and E14.5 to delete Prox1.

tag: strain background

value: NMRI

value: VecadcreERT2; Prox1f/f

value: Embryonic 17.5

value: heart


title: ventricle null rep 2 [e17-5_null-2]


title: OPL1

description:
RNA isolated from sorted GFP positive thymocytes from preleukemic Tg(lck:GFP);otg mutant fish.
rawCountMatrix_Frazier.txt.gz
Fsample_33


title: OC9

description:
RNA isolated from sorted T-ALL cells collected from full blown leukemic  otg  zebrafish
rawCountMatrix_Frazier.txt.gz
Fsample_32


title: ventricle null rep 1 [e17-5_null-1]


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A9_ad001


title: OC8

description:
RNA isolated from sorted T-ALL cells collected from full blown leukemic  otg  zebrafish
rawCountMatrix_Frazier.txt.gz
Fsample_31


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B1_ad006


title: OPL2

description:
RNA isolated from sorted GFP positive thymocytes from preleukemic Tg(lck:GFP);otg mutant fish.
rawCountMatrix_Frazier.txt.gz
Fsample_34


title: ventricle ctrl rep 3 [e17-5_ctrl-3]

source_name: ventricle ctrl

value: WT


title: OC7

description:
RNA isolated from sorted T-ALL cells collected from full blown leukemic  otg  zebrafish
rawCountMatrix_Frazier.txt.gz
Fsample_30


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A9_ad007


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A9_ad010


title: HFD+Abx-2

city: Osaka

first: Makoto

last: Matsushita

address: 2-2 Yamadaoka, Suita

department: Urology

country: Japan

institute: Osaka University Graduate School of Medicine

description: Mice were fed with antibiotics in the drinking water from 5 to 22 weeks of age. The antibiotics treatment consisted of a mixture of 0.2 g/L ampicillin (Wako), 0.1 g/L vancomycin (Wako), 0.2 g/L metronidazole (Wako), and 0.3 g/L neomycin (Wako).

hyb_protocol: After creating the hybridization cocktail, biotinylated cDNA were hybridized with GeneChip Mouse Gene 2.0 ST Array (Affymetrix) for 16 hours.

scan_protocol: The arrays were scanned using the Affymetrix Gene Chip Scanner 3000.

data_processing: Scanned data were processed using Partek Genomics Suite software.

source_name: Prostate tissue from a mouse model of prostate cancer fed a high-fat diet and treated with antibiotics

label_protocol: Total RNA 1 ug were subjected to cDNA synthesis by Prime Script RT reagent Kit (Takara Bio). Obtained 5.5 μg cDNA were biotinylated and then fragmented by GeneChip WT Terminal Labeling Kit (Affymetrix).

growth_protocol: All mice started to feed high-fat diet (HFD-60, Oriental Yeast) at 5 weeks of age, and the prostates of the mice were collected at 22 weeks of age.

extract_protocol: Frozen prostates were homogenized using gentle MACS tubes (Miltenyi Biotec), and total RNA was extracted using an RNeasy Plus Mini Kit (Qiagen), according to the manufacturer’s standard protocol.

treatment_protocol: Prostates were frozen in RNAlater Tissue Collection: RNA Stabilization Solution (Thermo Fisher Scientific) and stored at -20°C until RNA extraction.

value: Pb-Cre+; Pten(ﬂ/ﬂ)

tag: gender

value: 22 weeks of age

value: prostate

tag: diet

value: high-fat diet

tag: treatment

value: antibiotics


title: HFD+Abx-3

description: Mice were fed with antibiotics in the drinking water from 5 to 22 weeks of age. The antibiotics treatment consisted of a mixture of 0.2 g/L ampicillin (Wako), 0.1 g/L vancomycin (Wako), 0.2 g/L metronidazole (Wako), and 0.4 g/L neomycin (Wako).

value: male


title: HFD-1

source_name: Prostate tissue from a mouse model of prostate cancer fed a high-fat diet


title: OC6

description:
RNA isolated from sorted T-ALL cells collected from full blown leukemic  otg  zebrafish
rawCountMatrix_Frazier.txt.gz
Fsample_29


title: HFD-2


title: SB23: Relapse 7

city: Valencia

first: Antonio

last: Fernandez-Serra

address: Beltraan Baguena, 8-11

department: Molecular Biology Lab

country: Spain

institute: Fundacion Instituto Valenciano de Oncologia

description: miRNA expression data from intestinal GIST from relapsed tumor

hyb_protocol: FlashTag HSR RNA labeling kit (Genisphere)

data_processing: R Bioconductor rma normalization

label: Biotin

organism: Homo sapiens

source_name: Intestinal GIST FFPE tissue

extract_protocol: miRNeasy FFPE Kit according manufacturer’s protocol

value: Gastrointestinal Stromal Tumors (GIST)

tag: state

value: Relapse


title: HFD-3

tag: strain


title: ventricle ctrl rep 2 [e17-5_ctrl-2]

tag: genotype/variation


title: SB339: Relapse 8

scan_protocol: FlashTag HSR RNA labeling kit (Genisphere)


title: HFD+Abx-5

description: Mice were fed with antibiotics in the drinking water from 5 to 22 weeks of age. The antibiotics treatment consisted of a mixture of 0.2 g/L ampicillin (Wako), 0.1 g/L vancomycin (Wako), 0.2 g/L metronidazole (Wako), and 0.6 g/L neomycin (Wako).

tag: age


title: HFD+Abx-1

description: Mice were fed with antibiotics in the drinking water from 5 to 22 weeks of age. The antibiotics treatment consisted of a mixture of 0.2 g/L ampicillin (Wako), 0.1 g/L vancomycin (Wako), 0.2 g/L metronidazole (Wako), and 0.2 g/L neomycin (Wako).

tag: tissue


title: HFD+Abx-4

description: Mice were fed with antibiotics in the drinking water from 5 to 22 weeks of age. The antibiotics treatment consisted of a mixture of 0.2 g/L ampicillin (Wako), 0.1 g/L vancomycin (Wako), 0.2 g/L metronidazole (Wako), and 0.5 g/L neomycin (Wako).


title: ventricle ctrl rep 1 [e17-5_ctrl-1]


title: SC434: Relapse 6

label_protocol: FlashTag HSR RNA labeling kit (Genisphere)


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A9_ad006

value: SSs


title: SC500: Unrelapse 6

description: miRNA expression data from intestinal GIST from unrelapsed tumor

value: Unrelapse


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A9_ad004


title: OC4

description:
RNA isolated from sorted T-ALL cells collected from full blown leukemic  otg  zebrafish
rawCountMatrix_Frazier.txt.gz
Fsample_27

value: T-ALL

value: Primary T-ALL

value: Frazer lab


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A9_ad002


title: OC3

description:
RNA isolated from sorted T-ALL cells collected from full blown leukemic  otg  zebrafish
rawCountMatrix_Frazier.txt.gz
Fsample_26


title: bulkRNA_Adult Naïve CD4 T cells 5

city: San Francisco

first: Daniel

last: Bunis

state: California

address: 35 Medical Center Way, Regeneration Medicine Building 903B

institute: University of California, San Francisco

data_processing:
Sequencing (paired end 2x 100bp) and base calling by Illumina HiSeq 4000.
Low quality reads and ends of reads were trimmed using Trim Galore! (v0.5.0).
Reads were aligned with STAR (v2.6.1b).
Reads for each sample overlapping with exons were quantified with featureCounts (v1.6.2).
Downstream processing and visualization were carried out in R with DESeq2, dittoSeq, clusterProfiler, and other packages.
Genome_build: hg38
Supplementary_files_format_and_content: "bulkCD4_counts.txt" contains a tab separated value table with information about genomic features, and counts for those features for each sample.

source_name: Sort Purified Naïve CD4 T cells

extract_protocol:
Splenic tissue was digested to single cell suspension in media supplemented with collagenase IV and DNAse I for thirty minutes.  All samples were ficolled or percolled to obtain the mononuclear cell layer. Samples were viably cryopreserved until further processing. Mononuclear cell preparations were pre-enriched by immunomagnetic selection with EasySep Human T Cell Isolation Kit (STEMCELL Technologies). Cells were then sorted by FACS into media supplemented with 10% FBS. RNA was extracted from 50,000 sorted cells per sample using RNAqueous Total RNA Isolation columns (Invitrogen AM1912) with addition of QIAshredder homogenization columns (Qiagen 79654) at the cell lysate step.
mRNA was enriched with poly-dT beads (NEB E7490) and turned into libraries with the NEBNext Ultra II Directional RNA Library Prep Kit (NEB E7760) according to the manufacturer’s protocol.

value: PBMCs

value: CD4 T cells

value: adult

tag: subject id

tag: ficoll vs percoll

value: Ficoll


title: bulkRNA_Adult Naïve CD4 T cells 4

tag: developmental stage


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A9_ad008

tag: brain region


title: SC432: Relapse 5


title: OC2

description:
RNA isolated from sorted T-ALL cells collected from full blown leukemic  otg  zebrafish
rawCountMatrix_Frazier.txt.gz
Fsample_25

tag: genotype


title: SC400: Unrelapse 5


title: bulkRNA_Adult Naïve CD4 T cells 3

tag: cell type


title: OC5

description:
RNA isolated from sorted T-ALL cells collected from full blown leukemic  otg  zebrafish
rawCountMatrix_Frazier.txt.gz
Fsample_28

tag: tumor stage


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A8_ad004

tag: Sex


title: bulkRNA_Adult Naïve CD4 T cells 2


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A8_ad010


title: OC10

description:
RNA isolated from sorted T-ALL cells collected from full blown leukemic  otg  zebrafish
rawCountMatrix_Frazier.txt.gz
Fsample_23

tag: lab of sample collection and sequencing


title: SC373: Relapse 3


title: bulkRNA_Adult Naïve CD4 T cells 1


title: bulkRNA_Newborn Naïve CD4 T cells 5

value: umbilical cord blood

value: newborn


title: MPL3

description:
RNA isolated from sorted GFP positive thymocytes from preleukemic Tg(lck:GFP);Tg(rag2:hMYC) mutant fish.
rawCountMatrix_Frazier.txt.gz
Fsample_21

source_name: hMYC preleukemic thymocytes

value: thymocytes

value: Tg(rag2:hMYC), Tg(lck:GFP)

value: preleukemic


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A8_ad008

value: male


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A8_ad006


title: MPL2

description:
RNA isolated from sorted GFP positive thymocytes from preleukemic Tg(lck:GFP);Tg(rag2:hMYC) mutant fish.
rawCountMatrix_Frazier.txt.gz
Fsample_20


title: SC377: Relapse 4

value: Gastrointestinal Stromal Tumors (GIST)


title: bulkRNA_Newborn Naïve CD4 T cells 4


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A8_ad002


title: bulkRNA_Newborn Naïve CD4 T cells 3


title: MPL1

description:
RNA isolated from sorted GFP positive thymocytes from preleukemic Tg(lck:GFP);Tg(rag2:hMYC) mutant fish.
rawCountMatrix_Frazier.txt.gz
Fsample_19


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A8_ad012


title: bulkRNA_Newborn Naïve CD4 T cells 2


title: OC1

description:
RNA isolated from sorted T-ALL cells collected from full blown leukemic  otg  zebrafish
rawCountMatrix_Frazier.txt.gz
Fsample_24


title: HPL3

description:
RNA isolated from sorted GFP positive thymocytes from preleukemic Tg(lck:GFP);hulk mutant fish.
rawCountMatrix_Frazier.txt.gz
Fsample_12

source_name: hulk mutant preleukemic thymocytes


title: bulkRNA_Newborn Naïve CD4 T cells 1


title: SC180: Relapse 2

value: Relapse


title: HPL2

description:
RNA isolated from sorted GFP positive thymocytes from preleukemic Tg(lck:GFP);hulk mutant fish.
rawCountMatrix_Frazier.txt.gz
Fsample_11


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A7_ad012

value: SSs


title: SC149: Unrelapse 3

value: Unrelapse


title: SC244: Unrelapse 4


title: bulkRNA_Fetal Naïve CD4 T cells 5

value: spleen

value: fetal


title: SC141: Unrelapse 1


title: SC143: Relapse 1


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A7_ad010


title: HPL1

description:
RNA isolated from sorted GFP positive thymocytes from preleukemic Tg(lck:GFP);hulk mutant fish.
rawCountMatrix_Frazier.txt.gz
Fsample_10

value: Frazer lab


title: HC9

description:
RNA isolated from sorted T-ALL cells collected from full blown leukemic  hulk  zebrafish
rawCountMatrix_Frazier.txt.gz
Fsample_9

value: T-ALL

value: Primary T-ALL


title: SC144: Unrelapse 2


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A7_ad004


title: bulkRNA_Fetal Naïve CD4 T cells 3

value: CD4 T cells

value: Percoll


title: HC8

description:
RNA isolated from sorted T-ALL cells collected from full blown leukemic  hulk  zebrafish
rawCountMatrix_Frazier.txt.gz
Fsample_8


title: bulkRNA_Fetal Naïve CD4 T cells 2


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A7_ad002


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A7_ad001


title: Osx-Cre;NT3 #25

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 2.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and FPKM values for each gene per sample

source_name: spontaneous trunk tumor

growth_protocol: spontaneous NT3-Tg driven tumor model

extract_protocol:
Tumors were excised to remove any gross overlaying tissue, and either stored at -20C in RNAlater (R0901; Sigma, USA) or flash frozen in liquid nitrogen, and stored at -80C.  Frozen tumors were pulverized in liquid nitrogen using a Mikro Dismembrator (Mikro‐Dismembrator S; B. Braun Biotech International, Melsungen, Germany), resuspended in TRIzol (15596026; Invitrogen, Carlsbad, CA, USA), and stored at –80°C. Total RNA was isolated using a Direct‐zol kit per the manufacturer’s instructions (R2072; Zymo Research, Irvine, CA, USA).
mRNA version 2 library prep kit (Illumina)

value: spontaneous trunk tumor

value: female

tag: tumor latency (days)


title: FSP1-Cre;NT3 #29


title: FSP1-Cre;NT3 #36

source_name: spontaneous perineal tumor

value: spontaneous perineal tumor


title: Osx-Cre;NT3 #13


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A7_ad008


title: bulkRNA_Fetal Naïve CD4 T cells 1


title: HC6

description:
RNA isolated from sorted T-ALL cells collected from full blown leukemic  hulk  zebrafish
rawCountMatrix_Frazier.txt.gz
Fsample_6


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A6_ad012


title: bulkRNA_Fetal Naïve CD4 T cells 4

value: Ficoll


title: HC5

description:
RNA isolated from sorted T-ALL cells collected from full blown leukemic  hulk  zebrafish
rawCountMatrix_Frazier.txt.gz
Fsample_5


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A6_ad001


title: LNJ-ox rep2

city: Frederiksberg C

first: Bin

last: Sun

address: Thorvaldsensvej 40

department: Department of Plant and Environmental Sciences

country: Denmark

institute: Copenhagen Plant Science Centre – University of Copenhagen

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trim-galore 0.6.3 on Galaxy.
Trimmed reads mapped to Arabidopsis thaliana whole genome using HISAT2 2.1.0+galaxy5 on Galaxy.
Reads counted using htseq-count 0.9.1 on Galaxy.
Differentially expressed genes were calculated using limma_voom/3.38.3+galaxy3 on Galaxy.
Genome_build: Arabidopsis thaliana TAIR10. 45
Supplementary_files_format_and_content: tabular include reads count and differentially expressed genes

organism: Arabidopsis thaliana

source_name: 21 days old plants

growth_protocol: Seeds were stratified 48h at 4°C, and grown on soil in a plant growth chamber under long day light conditions (16h light /8h dark) at (22°C day /18°C night).

extract_protocol:
21 days old plant cut root and quick freeze in liquid nitrogen, then grind with mortar. RNA were harvested using Sigma Spectrum™ Plant Total RNA Kit (STRN50).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment

value: LNJ overexpressor

tag: ecotype

value: plants without root

tag: developmental satge

value: 21 days old


title: Osx-Cre;NT3 #18


title: jazD rep2

value: jzaD


title: HC3

description:
RNA isolated from sorted T-ALL cells collected from full blown leukemic  hulk  zebrafish
rawCountMatrix_Frazier.txt.gz
Fsample_3


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A6_ad010

value: SSs

value: male


title: L4815: SVZ_STD_POS4

city: Dresden

first: Gerd

last: Kempermann

state: Saxony

address: Tatzberg 41

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)

data_processing:
Alignment to mm10 mouse genome using STAR
Rsubread used to map reads to ENSEMBL genes
Counts per million (cpm) calculated using EdgeR and low-expressed genes discarded (expression not greater than 1 cpm in at least 75% of samples in at least 1 experimental group)
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text, samples in columns, genes in rows, normalised expression values (cpm)

source_name: Adult neural precursor cells

growth_protocol: Standard housing, ad libitum water and mouse chow, 12:12 light cycle

extract_protocol:
Dentate gyrus or subventricular zone tissue was dissected, enzymatically digested using the Neural Tissue Dissociation Kit (Miltenyi), then washed and resuspended in Hank's balanced salt solution and filtered through a 40 um cell sieve. Cells were then sorted on a FACSAria III cell sorter based on (Nestin-)GFP fluorescence. RNA was extracted using the Qiagen RNeasy micro kit.
Synthesis of cDNA was performed using the SmartScribe reverse transcriptase (Takara Bio) with a universally tailed poly-dT primer and a template switching oligonucleotide, followed by 12 cycles of amplification with Advantage 2 DNA polymerase  (Takara Bio). After ultrasonic shearing of the amplified cDNA (Covaris LE220) samples were subjected to standard Illumina fragment library preparation using the NEBnext Ultra DNA library preparation chemistry (New England Biolabs).

value: Subventricular zone

value: Nestin-positive precursor cells


title: jazD rep1

value: jazD


title: L4823: DG_STD_POS5

value: Hippocampal denate gyrus


title: L4817: DG_STD_POS4


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A6_ad006


title: L4811: DG_STD_POS3


title: LNJ-ox rep1


title: HC2

description:
RNA isolated from sorted T-ALL cells collected from full blown leukemic  hulk  zebrafish
rawCountMatrix_Frazier.txt.gz
Fsample_2

value: T-ALL

value: Primary T-ALL

value: Frazer lab


title: L4809: SVZ_STD_POS3


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A6_ad002


title: Col-0 rep2

value: wild type


title: HC1

description:
RNA isolated from sorted T-ALL cells collected from full blown leukemic  hulk  zebrafish
rawCountMatrix_Frazier.txt.gz
Fsample_1


title: L4805: DG_STD_POS2


title: WT5

description:
RNA of sorted tg(lck-GFP) zebrafish
rawCountMatrix_WT_Frazier.txt.gz
FWTsample_5

source_name: Healthy sorted  thymus

value: thymocytes

value: healthy


title: Col-0 rep1


title: L4803: SVZ_STD_POS2


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A5_ad001

source_name: C57BL/6J Male P56 Mouse Brain


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A5_ad007


title: HC4

description:
RNA isolated from sorted T-ALL cells collected from full blown leukemic  hulk  zebrafish
rawCountMatrix_Frazier.txt.gz
Fsample_4

source_name: T-ALL colleted when 90% of zebrafish was taken over by GFP + T-ALL cells.


title: WT4

description:
RNA of sorted tg(lck-GFP) zebrafish
rawCountMatrix_WT_Frazier.txt.gz
FWTsample_4


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A5_ad010


title: L4801: DG_STD_POS1


title: L4799: SVZ_STD_POS1


title: WT3

description:
RNA of sorted tg(lck-GFP) zebrafish
rawCountMatrix_WT_Frazier.txt.gz
FWTsample_3


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A5_ad006


title: WT2

description:
RNA of sorted tg(lck-GFP) zebrafish
rawCountMatrix_WT_Frazier.txt.gz
FWTsample_2


title: WT1

description:
RNA of sorted tg(lck-GFP) zebrafish
rawCountMatrix_WT_Frazier.txt.gz
FWTsample_1


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A5_ad002


title: L17142: GFP+ROS+++

source_name: Adult hippocampal precursor cells

extract_protocol:
Dentate gyrus was dissected, enzymatically digested using the Neural Tissue Dissociation Kit (Miltenyi), then washed and resuspended in Hank's balanced salt solution and filtered through a 40 um cell sieve. Cells were then sorted on a FACSAria III cell sorter based on (Nestin-)GFP and dihydroethidium fluorescence. RNA was extracted using the SMARTer Ultra Low RNA HV Kit (Clontec).
Synthesis of cDNA was performed using the SmartScribe reverse transcriptase (Takara Bio) with a universally tailed poly-dT primer and a template switching oligonucleotide, followed by 12 cycles of amplification with Advantage 2 DNA polymerase  (Takara Bio). After ultrasonic shearing of the amplified cDNA (Covaris LE220) samples were subjected to standard Illumina fragment library preparation using the NEBnext Ultra DNA library preparation chemistry (New England Biolabs).


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A5_ad004


title: L17141: GFP+ROS++


title: L17140: GFP+ROS+


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A4_ad002


title: L17139: GFP+ROS+++


title: single-cell_Adult Naïve CD8 T cells 4

description:
processed data metadata file:
CD4-8.best
sample name:
APB4

data_processing:
Sequencing and base calling by Illumina Novaseq (S4 flow cell)
Sequencing reads were quality controlled, matched by cell barcode, aligned to the genome, and overlapping gene features with unique UMIs quantified using cellranger (v2.2.0, 10X genomics)
Sample identities of cellular transcriptomes were identified based on SNPs captured in the mRNA-sequencing using Demuxlet (https://github.com/statgen/demuxlet, commit 85dca0a) in conjunction with BAM alignment files from cellranger output and VCF of genotypes pulled from contemporaneous bulk RNAseq (naive CD4 T cells) of the same samples.
Cells' demuxlet information and transcriptomic counts data were merged using the relevant demuxlet import function of dittoSeq (v0.3).
Downstream processing and visualization were carried out in R with Seurat, dittoSeq, caret, and other packages.
Genome_build: hg38
Supplementary_files_format_and_content: "barcodes.tsv", "genes.tsv", and "matrix.mtx" files contain standard, raw (all barcodes, un-filtered), cellranger aggr output which can be used to build the transcriptomic counts matrix for all samples. ".best" files are the raw output of demuxlet for each 10X well and are tab separated value text files containing sample identity calls for each barcode/cell-droplet.

source_name: Sort Purified Naïve CD8 T cells

extract_protocol:
Splenic tissue was digested to single cell suspension in media supplemented with collagenase IV and DNAse I for thirty minutes.  All samples were ficolled or percolled to obtain the mononuclear cell layer. Samples were viably cryopreserved until further processing. Mononuclear cell preparations were pre-enriched by immunomagnetic selection with EasySep Human T Cell Isolation Kit (STEMCELL Technologies). Cells were then sorted by FACS into media supplemented with 10% FBS.  CD4 or CD8 T cells from distinct samples were then combined into three separate pools for library preparation.
Single cell RNA-seq  library construction was performed with the 10X Chromium Single Cell v2 kit. Each pool of cells was loaded into a separate well, with a target concentration of 50,000cells/well.

value: PBMCs

value: adult

tag: t cell lineage

value: Ficoll


title: single-cell_Adult Naïve CD8 T cells 5

description:
processed data metadata file:
CD8.best
sample name:
APB5


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A4_ad010

tag: strain


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A4_ad008


title: single-cell_Adult Naïve CD8 T cells 3

description:
processed data metadata file:
CD8.best
sample name:
APB3


title: L17137: GFP+ROS+


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A4_ad004


title: single-cell_Adult Naïve CD8 T cells 2

description:
processed data metadata file:
CD8.best
sample name:
APB2


title: SPL002

description:
RNA isolated from sorted GFP positive thymocytes from preleukemic Tg(lck:GFP);shrek mutant fish.
rawCountMatrix_Frazier.txt.gz
Fsample_48

source_name: shrek preleukemic thymocytes

value: preleukemic


title: L17136: GFP+ROS+++


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A4_ad001


title: L17135: GFP+ROS++


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A4_ad012


title: single-cell_Newborn Naïve CD8 T cells 5

description:
processed data metadata file:
CD8.best
sample name:
UCB5

value: umbilical cord blood

value: newborn


title: L17138: GFP+ROS++


title: L17134: GFP+ROS+


title: single-cell_Newborn Naïve CD8 T cells 4

description:
processed data metadata file:
CD8.best
sample name:
UCB4


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A3_ad012

value: SSs

value: male


title: L17133: GFP+ROS+++

value: Nestin-positive precursor cells


title: single-cell_Newborn Naïve CD8 T cells 3

description:
processed data metadata file:
CD8.best
sample name:
UCB3


title: L17132: GFP+ROS++


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A3_ad007


title: FSP1-Cre;NT3 #27

value: spontaneous perineal tumor

value: female


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A3_ad001


title: single-cell_Adult Naïve CD8 T cells 1

description:
processed data metadata file:
CD4-8.best
sample name:
APB1


title: L17131: GFP+ROS+

value: Hippocampal denate gyrus


title: T 30E2 Nail cy3 36Umblical cord blood

type: genomic

city: Tehran

first: Masood

last: Bazrgar

address: Banihashem

country: Iran

institute: Royan Institute

description: Loop Design. Cy5-labeled sample is considered as reference for each array comparison.

hyb_protocol: Samples were hybridized to the Oxford Gene Technology (OGT) 180K array according to the manufacturer's instructions (OGT, Oxford, UK). Samples were mixed by pipetting and quick spin, then transferred to a 95°C water bath for 10 minutes and immediately transferred to 37°C oven for 30 minutes. After quick spin to collect the sample at the bottom of the tube, 100 µl of each hybridization mix loaded to appropriate gasket slide in Agilent chamber. Chamber were closed tightly and placed in Agilent oven at 65°C, with rotation set to 20rpm for 40-hour hybridization.

scan_protocol: After hybridization and washing, the slides were analyzed on an Agilent G2565CA Microarray Scanner with 3 µm resolution.

data_processing: Agilent Feature Extraction Software was used for background subtraction. Agilent feature extraction files are not available for submission to GEO.

source_name: E2 fetus

label_protocol: We analyzed the high quality samples by array comparative genomic hybridization (aCGH) in a simple loop designed separately for samples of each fetus. This dye-swap approach results in dye balance by labeling every sample with Cy3 and Cy5 dyes alternately. 8. 500ng of genomic DNA was diluted in water to a total volume of 10 µl. 5 μl of Random Primers Solution and 5µl of reaction buffer were added to each sample and incubated at 98°C on PCR machine for 20 minutes, then cooled to 4°C on PCR machine for 10 minutes.

extract_protocol: DNA was extracted from dissections of  2 fetuses named  E1and E2, 25 fetal tissues from each fetus, using saltin gout method as previously described by J. Sambrook, D. W. Russell. Rapid isolation of mammalian DNA. Cold Spring Harbor Protocols, 2006 pdb-prot3514..

tag: fetal tissue

value: Nail

value: Umblical cord blood


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A3_ad010

tag: age


title: single-cell_Newborn Naïve CD8 T cells 2

description:
processed data metadata file:
CD8.best
sample name:
UCB2

tag: tissue


title: single-cell_Newborn Naïve CD8 T cells 1

description:
processed data metadata file:
CD4-8.best
sample name:
UCB1

tag: subject id


title: L17129: GFP+ROS++


title: V 21E2 Esophagus cy3 27 cerebrum

value: Esophagus

value: cerebrum


title: U 36E2 Umblical cord blood cy3 21 Esophagus


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A3_ad006


title: R 26E2 cornea cy3 12 Liver

value: cornea

value: Liver


title: P 29 E2 cartilage cy3 24  small intestine

value: cartilage

value: small intestine


title: single-cell_Fetal Naïve CD8 T cells 5

description:
processed data metadata file:
CD8.best
sample name:
FS5

value: spleen

value: fetal

tag: ficoll vs percoll

value: Ficoll


title: single-cell_Fetal Naïve CD8 T cells 3

description:
processed data metadata file:
CD4-8.best
sample name:
FS3

tag: developmental stage

value: Percoll


title: S 12E2 Liver cy3 30Nail


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A3_ad004

tag: brain region

value: SSs

value: male


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A3_ad002


title: Q 24E2 small intestine cy3 26 cornea


title: single-cell_Fetal Naïve CD8 T cells 1

description:
processed data metadata file:
CD8.best
sample name:
FS1


title: HeLa cells, siFBXW7

city: Liège

first: Jean-Claude

last: Twizere

state: Liège

address: CHU - B34 Quartier Hôpital Avenue de l'Hôpital,11

department: Molecular Biology of Diseases

institute: GIGA Institute

data_processing:
Reads were mapped to the human genome (GRCh 37/hg19) using BWA version 0.6 (Li and Durbin, 2009).
We used SWEMBL version 3.3.1 (http://www.ebi.ac.uk/~swilder/SWEMBL/) to identify the peaks. We adjusted parameters for RNA-seq and reference (Input) sequence relative to the number of reads in the samples, with a relative gradient of 0.002 (R parameter)
The peaks were submitted to GREAT version 2.0.2  to annotate nearest genes (minimum distance of 5.0 kb upstream and 1.0 kb downstream of the transcription start sites, up to 1000.0 kb maximum extension).
Genome_build: hg19
Supplementary_files_format_and_content: .xlsx

source_name: HeLa cells

growth_protocol: HeLa cells were cultured in in DMEM supplemented with 10% fetal bovine serum (FBS), 2mM glutamine and penicillin/streptomycin.

extract_protocol:
Total RNA was extracted using GeneJET RNA Purification Kit (Thermo scientific), quantified and tested for RNA quality controlled using Agilent 2100 bioanalyzer using the Eukaryote Total RNA Nano assay.
Total RNA strands were used to generate libraries and sequenced by HiSeq2000 sequencer.

treatment_protocol: HeLa cells were transfected with siCTRL, siEXT1 or siFBXW7, with Calcium Phosphate using ProFection Mammalian Transfection kit from Promega according to manufacturer’s instructions on cells cultured in DMEM at 40-50% confluence. Medium was changed 24 hours later and cells were collected 48h post-transfection.

tag: cell line

value: HeLa

tag: treatment

tag: genotype

value: knockdown of FBXW7


title: HeLa cells, siEXT1-siFBXW7

value: siEXT1 and siFBXW7

value: knockdown of EXT1 and FBXW7


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A3_ad008

tag: Sex


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A2_ad012


title: HeLa cells, siEXT1

value: knockdown of EXT1


title: O 11E2 Pancreas cy3 29 Cartilage

value: Pancreas

value: Cartilage


title: single-cell_Adult Naïve CD4 T cells 4

description:
processed data metadata file:
CD4.best
sample name:
APB4

value: PBMCs

value: adult


title: HeLa cells, siCTRL

value: siCTRL

value: control


title: single-cell_Adult Naïve CD4 T cells 3

description:
processed data metadata file:
CD4-8.best
sample name:
APB3


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A2_ad001


title: single-cell_Adult Naïve CD4 T cells 5

description:
processed data metadata file:
CD4.best
sample name:
APB5


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A2_ad007


title: single-cell_Adult Naïve CD4 T cells 2

description:
processed data metadata file:
CD4.best
sample name:
APB2


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A2_ad010


title: L 32E2 Testis cy3 18 colon

value: Testis

value: colon


title: M 18E2 colon cy3 16  kidney

value: kidney


title: single-cell_Adult Naïve CD4 T cells 1

description:
processed data metadata file:
CD4.best
sample name:
APB1

value: Ficoll


title: HC7

description:
RNA isolated from sorted T-ALL cells collected from full blown leukemic  hulk  zebrafish
rawCountMatrix_Frazier.txt.gz
Fsample_7

tag: cell type

value: T-ALL

tag: tumor stage

value: Primary T-ALL

tag: lab of sample collection and sequencing

value: Frazer lab


title: single-cell_Newborn Naïve CD4 T cells 5

description:
processed data metadata file:
CD4.best
sample name:
UCB5

value: umbilical cord blood

value: newborn


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A2_ad006

value: SSs

value: male


title: single-cell_Newborn Naïve CD4 T cells 4

description:
processed data metadata file:
CD4-8.best
sample name:
UCB4


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A2_ad004


title: C-9 2.1+_Control, In vitro P. falciparum (shield+)

city: Bethesda

first: Surendra

middle: Kumar

last: Prajapati

state: Maryland

address: 4301 Jones Bridge Road

department: Microbiology and Immunology

institute: Uniformed Services University of the Health Sciences

description: Synchronized 10-15 hpi ring stage parasite (shield+)

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GEx hybridization buffer was added to the fragmentation mixture and hybridized to Agilent P. falciparum Oligo Microarrays (G2509F, design ID:037237) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.1 (Agilent) using default parameters (protocol GE1_1200_Jun14 and Grid: 037237_D_F_20111117) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Plasmodium falciparum

source_name: In vitro culture (synchronized ring 10-15 hpi)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 40 ng RNA using the One-Color Low RNA Input QuickAmp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Plasmodium falciparum strains were maintained in an atmosphere of N2/CO2/O2: 90/5/5 and complete RPMI medium containing RPMI 1640, 25 mM HEPES, 50 μg ml−1 of hypoxanthine, and 0.3 mgml−1 of glutamine (KD Biomedical, Columbia, MD) supplemented with 25 mM NaHCO3 (pH 7.3), 5 μgml−1 of gentamicin, and 10% human serum (Interstate Blood Bank, Memphis, TN). Transformed lines were maintained in 2.5 nM WR99210 (WR) (Jacobus Pharmaceuticals, Plainsboro, NJ). Sorbitol treatment (5%, 10–30 min at 37 °C) were used for synchronization and parasite stages were quantitated using Giemsa-stained culture smears to determine parasitemia and total RBC.

extract_protocol: RNA from Human blood samples were extracted using Paxgene tube (Paxgene blood RNA kit, PreAnalytiX, Qiagen) while RNA from cultured parasite stored in NucleoZol, was extracetd using RNAEsy microkit (Qiagen). Both extraction protocols included in column DNA digestion. RNA was quantified using nanodrop and integrty was measured using Bioanalyzer.

treatment_protocol: Human blood was withdrawn in paxgene tube and RNA was extracted without any treatment. An aliquot of blood withdrawn separately, was used to determine gametocyte phenotype (Gametocyte conversion rate (GCR)) using an ex vivo gametocyte assay. Gametocyte inducible line (Gdv1.gfp.dd) were grown in presence or absence of shield. Shield protect degradation of GDV1 protein and as a result, parasite complete gametocyte comittment and produces gametocyte comitted ring stage parasite which further differentiate into gametocyte.

value: In vitro culture

tag: gametocyte status

value: High gametocyte (control)


title: K 35E2 chorionic villi cy3 32 Testis

value: chorionic villi


title: N 16E2Kidney cy3 11 Pancreas

value: Kidney

value: Pancreas


title: I 38E2 Amnion cy3 spleen 19E2

value: Amnion

value: spleen


title: C-9 2.1-_Control, In vitro P. falciparum (shield-)

description: Synchronized 10-15 hpi ring stage parasite (shield-)

value: Low gametocyte (control)


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A2_ad002


title: G 14E2 Lung cy3  40 cardiac muscle

value: Lung

value: cardiac muscle


title: RCM47_In vitro P. falciparum

description: Synchronized 10-15 hpi ring stage parasite

value: No gametocyte (control)


title: NG54 1.1+_Control, In vitro P. falciparum (shield+)


title: F 15E2 Thymus cy3  14 Lung

description: Loop Design. Cy5-labeled sample is considered as reference for each array comparison.

value: Thymus


title: single-cell_Newborn Naïve CD4 T cells 3

description:
processed data metadata file:
CD4-8.best
sample name:
UCB3

tag: t cell lineage

value: Ficoll


title: NF54 1.1-_Control, In vitro P. falciparum (shield-)


title: H 40E2cardiac Muscle cy3 38 Amnion

value: cardiac Muscle


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A2_ad008

tag: strain


title: single-cell_Newborn Naïve CD4 T cells 2

description:
processed data metadata file:
CD4.best
sample name:
UCB2

value: umbilical cord blood

value: newborn


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A11_ad007

value: SSs

value: male


title: single-cell_Newborn Naïve CD4 T cells 1

description:
processed data metadata file:
CD4.best
sample name:
UCB1


title: 791_Human blood from malaria patient

description: Gene expression after blood withdrawn in Paxgene tube

organism:
Plasmodium falciparum
Homo sapiens

source_name: Human peripheral blood

value: Whole blood

value: Intermediate GCR


title: single-cell_Fetal Naïve CD4 T cells 5

description:
processed data metadata file:
CD4.best
sample name:
FS5

source_name: Sort Purified Naïve CD4 T cells

value: fetal


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A11_ad008


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A11_ad012


title: single-cell_Fetal Naïve CD4 T cells 4

description:
processed data metadata file:
CD4.best
sample name:
FS4


title: L17128: GFP+ROS+

value: Hippocampal denate gyrus

value: Nestin-positive precursor cells


title: E 39E2 skin cy3 15 Thymus

tag: fetal tissue

value: skin


title: 860_Human blood from malaria patient

value: Low GCR


title: 557_Human blood from malaria patient


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A11_ad006

tag: age


title: C 28E2 cerebellum cy3 13 stomach

value: cerebellum

value: stomach


title: B 33E2 skeletal muscle cy3 28 cerebellum

value: skeletal muscle


title: D 13E2 stomach cy3 39 skin


title: 571_Human blood from malaria patient

tag: tissue


title: 795_Human blood from malaria patient

value: High GCR


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A11_ad004


title: single-cell_Fetal Naïve CD4 T cells 2

description:
processed data metadata file:
CD4-8.best
sample name:
FS2

value: spleen

tag: subject id

value: Percoll


title: 788_Human blood from malaria patient


title: Z 40E1 cardiac muscle cy3 32E1 testis

source_name: E1 fetus

value: cardiac muscle

value: testis


title: single-cell_Fetal Naïve CD4 T cells 1

description:
processed data metadata file:
CD4-8.best
sample name:
FS1

tag: ficoll vs percoll


title: J 19E2 Spleen cy3 35chorionic villi

value: Spleen

value: chorionic villi


title: UY 15E1 Thymus  cy3 cardia muscle-40E1

value: Thymus

value: cardia muscle


title: 786_Human blood from malaria patient

value: Whole blood


title: Adult HSPCs 2

data_processing:
Sequencing and base calling by Illumina Novaseq (S4 flow cell)
Sequencing reads were quality controlled, matched by cell barcode, aligned to the genome, and overlapping gene features with unique UMIs quantified using cellranger (v2.2.0, 10X genomics)
Sample identities of cellular transcriptomes were identified based on SNPs captured in the mRNA-sequencing using Demuxlet (https://github.com/statgen/demuxlet, commit 85dca0a) in conjunction with BAM alignment files from cellranger output and VCF of genotypes pulled from contemporaneous bulk RNAseq (naive CD4 T cells) of the same samples.
Cells' demuxlet information and transcriptomic counts data were merged using the relevant demuxlet import function of dittoSeq (v1.0), then tissue prefixes (which came from the linked T cell samples) were updated to those relevant for these HSPCs samples; "FS" to "FBM" and "APB" to "ABM".
Downstream processing and visualization were carried out in R with Seurat, dittoSeq, caret, and other packages.
Genome_build: hg38
Supplementary_files_format_and_content: "barcodes.tsv", "genes.tsv", and "matrix.mtx" files contain standard, raw (all barcodes, un-filtered), cellranger aggr output which can be used to build the transcriptomic counts matrix for all samples. ".best" file is the raw output of demuxlet and is a tab separated value text file containing sample identity calls for each barcode/cell-droplet.

source_name: Sort Purified HSPCs

extract_protocol:
Fetal bone marrow cells were isolated by dispersion with media from a syringe. All samples were ficolled to obtain the mononuclear cell layer, then viably cryopreserved until further processing. Mononuclear cell preparations were pre-enriched by immunomagnetic selection with EasySep Human CD34 Positive Selection Kit (STEMCELL Technologies). Cells were then sorted by FACS into media supplemented with 10% FBS.  Cells from distinct samples were then combined into a single pool for library preparation.
Single cell RNA-seq  library construction was performed with the 10X Chromium Single Cell v2 kit. Cells were loaded a target concentration of 50,000cells/well.

value: bone marrow

value: HSPCs

tag: developmental stage

value: adult


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A11_ad002

tag: brain region

value: SSs

value: male


title: Adult HSPCs 1


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A10_ad008


title: U 16E1 kidney cy3 15 Thymus

value: kidney


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A10_ad012


title: A 27E2cerebrum cy3 33skeletal muscle

value: cerebrum

value: skeletal muscle


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A10_ad007


title: single-cell_Fetal Naïve CD4 T cells 3

description:
processed data metadata file:
CD4.best
sample name:
FS3

value: spleen

value: fetal


title: 774_Human blood from malaria patient

value: High GCR


title: 767_Human blood from malaria patient

value: Low GCR


title: 589_Human blood from malaria patient


title: T 19E1 Spleen cy3 16E1 kidney

value: Spleen


title: Q 21 E1Esophagus cy3 24E1 small intestine

value: Esophagus

value: small intestine


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A10_ad004


title: Newborn HSPCs 1

value: umbilical cord blood

value: newborn


title: S 33 E1 skeletal muscle cy3 19E1 spleen


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A10_ad002


title: Fetal HSPCs 3

value: bone marrow


title: 550_Human blood from malaria patient

value: Whole blood


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A1_ad012


title: Fetal HSPCs 2

value: HSPCs


title: Newborn HSPCs 2


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A1_ad001

value: SSs


title: 729_Human blood from malaria patient


title: Fetal HSPCs 1


title: 728_Human blood from malaria patient


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A1_ad010

value: male


title: R 24E1 small intestine cy3 33 E1 skletal muscle

value: skletal muscle


title: P 31 E1 genital tuberculum cy3 21E1 Esophagus

value: genital tuberculum


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A1_ad004


title: HSC_mi-6133-5p_TGF rep2

city: Nagoya

first: masaya

last: onishi

address: Kawasumi, Mizuho

department: Virology & Liver unit

institute: Nagoya City University Graduate School of Medical Sciences

data_processing:
NovaSeq Control Software v1.4.0
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh37 whole genome using STAR 2.5.3a (https://github.com/alexdobin/STAR) with parameters    --outSAMtype BAM SortedByCoordinate    --outSAMstrandField intronMotif  --sjdbGTFfile GRCh37.gtf --outFilterMultimapNmax 1 .
Reads mapped onto exons were counted using featureCounts, the Subread package ver1.6.4 (http://subread.sourceforge.net/).
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include counting reads to genomic features used by featureCounts for each Sample
Supplementary_files_format_and_content: Matrix table with mapping information for every sample

growth_protocol: LX-2 cells were cultured in Dulbecco’s modified Eagle’s medium (Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 1% antibiotic antimycotic solution and 2% heat-inactivated fetal bovine serum (Thermo Fisher Scientific). MiRIDIAN MicroRNA miR-6133-5p Mimic or MiRIDIAN MicroRNA Mimic Negative Control #1 (miControl) were purchased from Horizon Discovery Group plc. (Cambridge, UK). Each SMARTpools contains four independent siRNA molecules to ensure efficient gene knockdown. Silencer Select siRNA reagents corresponding to 36 predicted target genes of miR-6133-5p and Silencer Select Negative Control siRNA were purchased from Thermo Fisher Scientific. Two independent Silencer Select siRNA molecules for each gene were mixed equally and used in the following assay to ensure efficient gene knockdown.

extract_protocol:
Total RNA was extracted using ISOGEN (Nippon Gene, Toyama, Japan).
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded mRNA Reference Guide v00)

treatment_protocol: miRNAs  were introduced into LX-2 cells at a final concentration of 20 nmol/L using Lipofectamine RNAiMAX Reagent (Thermo Fisher Scientific), according to the manufacturer’s instructions. Twenty-four hours after transfection, the cells were further cultured with medium containing 5 ng/mL of recombinant human transforming growth factor β1 (rhTGF-β1).

value: hepatic stellate cell

tag: cell line

value: 24 hours after rhTGF-β treatment.

tag: transfection

value: transfected with miR-6133-5p


title: 704_Human blood from malaria patient


title: HSC_mi-6133-5p_TGF rep1

tag: treatment


title: HSC_miControl_TGF rep2

value: miControl


title: 634_Human blood from malaria patient

value: High GCR


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A1_ad002

tag: Sex


title: 640_Human blood from malaria patient


title: K 18E1 Colon cy3 38E1 amnion

value: Colon

value: amnion


title: CEMBA181210_5C_1_CEMBA181210_5C_2_A1_ad008


title: 633_Human blood from malaria patient

value: Low GCR


title: I 14E1 lung cy3 23E1 Aorta

value: lung

value: Aorta


title: LN 25E1 Bone cy3 Skin 39E1

value: Bone

value: Skin


title: HSC_miControl_TGF rep1

tag: cell type


title: J 23E1 Aorta cy3 18E1 Colon


title: L  38E1 amnion cy3 25E1 Bone


title: RNA-seq from UC Davis FAANG chicken skeletal muscle rep B

status: Public on Sep 24 2020

first: Colin

last: Kern

address: 9500 Gilman Dr

institute: UC San Diego

data_processing:
Reads were trimmed with Trim Galore! 0.4.5 with the default arguments
Reads were aligned with STAR 2.5.4a to the galGal6, Sscrofa11.2, and ARS-UCD1.2 genomes with the arguments --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20
Alignments were filtered with Samtools 1.10 using argument -q 30
Gene counts were obtained with htseq-count 0.11.1 using the Ensembl 99 annotations with arguments -r pos --stranded=reverse
Genome_build: galGal6,susScr11,bosTau9
Supplementary_files_format_and_content: bam file, aligned reads generated by data processing steps
Supplementary_files_format_and_content: 2-column tsv, Ensembl gene ID and raw read count

organism: Gallus gallus

source_name: Muscle

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen, Carlsbad, CA) according to the manufacturer’s protocol. DNase I (Ambion, Austin, TX) digestion was carried out after RNA isolation and the RNA concentration and purity were determined by measuring absorbance at 260 nm and A260/A280 ratio using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). RNA samples were stored at − 80 °C until further use. Total RNA (1 μg) was subjected to two rounds of hybridization to oligo (dT) beads (Invitrogen, Carlsbad, CA) to enrich poly-adenylated transcripts.
Stranded RNA-seq libraries were prepared using the TruSeq RNA Illumina protocol, and libraries were sequenced on an Illumina HiSeq-3000 using 100 bp PE

value: skeletal muscle


title: RNA-seq from UC Davis FAANG chicken spleen rep A

source_name: Spleen

value: spleen


title: RNA-seq from UC Davis FAANG chicken spleen rep B


title: O 39 E1 Skin surface cy3 31 E1 genital tuberculum

value: Skin surface


title: RNA-seq from UC Davis FAANG chicken liver rep B

source_name: Liver

value: liver


title: RNA-seq from UC Davis FAANG chicken liver rep A


title: RNA-seq from UC Davis FAANG chicken hypothalamus rep A

source_name: Hypothalamus

value: hypothalamus


title: RNA-seq from UC Davis FAANG chicken cerebral cortex rep B

source_name: Cortex

value: cerebral cortex


title: RNA-seq from UC Davis FAANG chicken hypothalamus rep B


title: H 13E1  stomach cy3 14E1 lung

value: stomach


title: RNA-seq from UC Davis FAANG chicken lung rep B

source_name: Lung


title: F 28E1-cerebellum cy3 27E1-cerebrum

value: cerebellum

value: cerebrum


title: RNA-seq from UC Davis FAANG chicken lung rep A


title: RNA-seq from UC Davis FAANG chicken cerebellum rep B

source_name: Cerebellum


title: RNA-seq from UC Davis FAANG chicken cerebellum rep A


title: RNA-seq from UC Davis FAANG chicken adipose rep B

source_name: Adipose

value: adipose


title: RNA-seq from UC Davis FAANG chicken skeletal muscle rep A


title: H3K4me3 from UC Davis FAANG pig spleen rep P350

data_processing:
Reads were trimmed with Trim Galore! 0.4.5 with the default arguments
Reads were aligned with BWA mem 0.7.17 to the galGal6, Sscrofa11.2, and ARS-UCD1.2 genomes
Alignments were filtered with Samtools 1.10 using arguments -F 1804 -q 30
Duplicates were removed with Picard toolkit 2.18.17
Genome_build: galGal6,susScr11,bosTau9
Supplementary_files_format_and_content: bam file, aligned reads generated by data processing steps
Supplementary_files_format_and_content: bed file, peak calls using Macs 2.1.1 -q 0.01

organism: Sus scrofa

extract_protocol:
ChIP-seq experiments were performed on frozen tissue using the iDeal ChIP-seq kit for Histones (Diagenode Cat.#C01010059, Denville, NJ) according to the manufacturer’s protocol except for the following changes. 20-30 mg of frozen tissue was powdered using liquid nitrogen in pre-chilled mortar. Cross-linking was performed with 1% formaldehyde which was diluted from 16% methanol-free formaldehyde (Thermo Scientific, Cat.#28906, Waltham, MA) for 8 minutes and quenched with glycine for 10 minutes. Nuclei were harvested by centrifugation at 2000g for 5 minutes and resuspended in iS1 buffer for incubation on ice for 30 minutes. Chromatin was sheared using the Covaris E220 between 6-12 minutes depending on the tissue. For immunoprecipitation experiments, about 1000 ng of sheared chromatin (estimated from DNA extraction) was used as input after which the kit protocol was followed with 1 μg (histone modifications) or 1.5 μg (CTCF) of antibody. The following antibodies used were from Diagenode: H3K4me3 (in kit), H3K27me3 (#C15410069), H3K27ac (#C15410174), H3K4me1 (#C15410037), and CTCF (#15410210). An input (no antibody) was performed for each sample.
NEBNext Ultra DNA library prep kit for Illumina libraries (New England Biolabs #E7645L, Ipswich, MA) was used for library construction, selecting for 150-200 bp (H3K4me3, H3K27ac, CTCF) or 200-400 bp (H3K27me3, H3K4me1) insert fragment sizes using Ampure beads (Beckman Coulter #A63881). Libraries were sequenced on Illumina’s HiSeq 4000 with single-end 50 bp reads.

tag: chip antibody


title: H3K4me3 from UC Davis FAANG pig spleen rep P348


title: E 12E1 Liver cy3 28 E1 Cerebellum

value: Liver

value: Cerebellum


title: D 11E1 Pancreas cy3 12E1 Liver

value: Pancreas


title: G 27E1 cerebrum cy3 13E1  stomach


title: C 14E1 Lung cy3 11E1 Pancreas

value: Lung


title: RNA-seq from UC Davis FAANG chicken cerebral cortex rep A


title: H3K4me3 from UC Davis FAANG pig skeletal muscle rep P350


title: H3K4me3 from UC Davis FAANG pig liver rep P348


title: H3K4me3 from UC Davis FAANG pig lung rep P350

value: lung


title: H3K4me3 from UC Davis FAANG pig liver rep P350


title: H3K4me3 from UC Davis FAANG pig lung rep P348


title: RNA-seq from UC Davis FAANG chicken adipose rep A


title: H3K4me3 from UC Davis FAANG pig hypothalamus rep P348


title: H3K4me3 from UC Davis FAANG pig hypothalamus rep P350


title: H3K4me3 from UC Davis FAANG pig cerebral cortex rep P348


title: H3K4me3 from UC Davis FAANG pig cerebral cortex rep P350


title: H3K4me3 from UC Davis FAANG pig cerebellum rep P350


title: A 32 E1 Testis cy329E1 Cartilage

value: Testis

value: Cartilage


title: H3K4me3 from UC Davis FAANG pig cerebellum rep P348


title: H3K4me3 from UC Davis FAANG pig adipose rep P350


title: 590_Human blood from malaria patient

value: Whole blood

value: High GCR


title: H3K4me3 from UC Davis FAANG pig skeletal muscle rep P348

value: skeletal muscle


title: H3K4me3 from UC Davis FAANG pig adipose rep P348


title: B 29E1 Cartilage cy3 14E1 Lung


title: H3K4me1 from UC Davis FAANG pig spleen rep P350

value: spleen


title: H3K4me1 from UC Davis FAANG pig spleen rep P348


title: H3K4me1 from UC Davis FAANG pig skeletal muscle rep P350


title: H3K4me1 from UC Davis FAANG pig skeletal muscle rep P348


title: H3K4me1 from UC Davis FAANG pig lung rep P348


title: H3K4me1 from UC Davis FAANG pig hypothalamus rep P350

value: hypothalamus


title: H3K4me1 from UC Davis FAANG pig liver rep P350

value: liver


title: H3K4me1 from UC Davis FAANG pig hypothalamus rep P348


title: H3K4me1 from UC Davis FAANG pig cerebral cortex rep P350

value: cerebral cortex


title: H3K4me1 from UC Davis FAANG pig cerebellum rep P350

value: cerebellum


title: H3K27me3 from UC Davis FAANG pig skeletal muscle rep P350

data_processing:
Reads were trimmed with Trim Galore! 0.4.5 with the default arguments
Reads were aligned with BWA mem 0.7.17 to the galGal6, Sscrofa11.2, and ARS-UCD1.2 genomes
Alignments were filtered with Samtools 1.10 using arguments -F 1804 -q 30
Duplicates were removed with Picard toolkit 2.18.17
Genome_build: galGal6,susScr11,bosTau9
Supplementary_files_format_and_content: bam file, aligned reads generated by data processing steps
Supplementary_files_format_and_content: bed file, peak calls using Macs 2.1.1 -q 0.05 --broad


title: H3K27me3 from UC Davis FAANG pig lung rep P350


title: H3K27me3 from UC Davis FAANG pig spleen rep P350


title: H3K27me3 from UC Davis FAANG pig spleen rep P348


title: H3K27me3 from UC Davis FAANG pig skeletal muscle rep P348


title: H3K4me1 from UC Davis FAANG pig adipose rep P348


title: H3K4me1 from UC Davis FAANG pig adipose rep P350


title: H3K27me3 from UC Davis FAANG pig lung rep P348


title: H3K27me3 from UC Davis FAANG pig cerebral cortex rep P350


title: H3K27me3 from UC Davis FAANG pig hypothalamus rep P350


title: H3K27me3 from UC Davis FAANG pig cerebellum rep P350


title: H3K27me3 from UC Davis FAANG pig liver rep P348


title: H3K4me1 from UC Davis FAANG pig lung rep P350


title: H3K27me3 from UC Davis FAANG pig adipose rep P350


title: H3K27me3 from UC Davis FAANG pig liver rep P350


title: H3K27me3 from UC Davis FAANG pig cerebellum rep P348


title: H3K27me3 from UC Davis FAANG pig cerebral cortex rep P348


title: H3K4me1 from UC Davis FAANG pig liver rep P348


title: H3K27me3 from UC Davis FAANG pig hypothalamus rep P348


title: H3K27ac from UC Davis FAANG pig skeletal muscle rep P348


title: H3K27ac from UC Davis FAANG pig skeletal muscle rep P350


title: H3K27ac from UC Davis FAANG pig lung rep P350


title: H3K27ac from UC Davis FAANG pig spleen rep P350


title: H3K27ac from UC Davis FAANG pig lung rep P348


title: H3K4me1 from UC Davis FAANG pig cerebellum rep P348


title: H3K27ac from UC Davis FAANG pig liver rep P350


title: H3K27ac from UC Davis FAANG pig cerebral cortex rep P348


title: H3K27ac from UC Davis FAANG pig hypothalamus rep P348


title: H3K27ac from UC Davis FAANG pig hypothalamus rep P350


title: H3K27ac from UC Davis FAANG pig liver rep P348


title: H3K27me3 from UC Davis FAANG pig adipose rep P348


title: H3K27ac from UC Davis FAANG pig cerebellum rep P348


title: CTCF from UC Davis FAANG pig spleen rep P350


title: H3K27ac from UC Davis FAANG pig cerebellum rep P350


title: H3K4me1 from UC Davis FAANG pig cerebral cortex rep P348


title: CTCF from UC Davis FAANG pig spleen rep P348


title: CTCF from UC Davis FAANG pig lung rep P350


title: CTCF from UC Davis FAANG pig liver rep P350


title: H3K27ac from UC Davis FAANG pig adipose rep P348


title: CTCF from UC Davis FAANG pig skeletal muscle rep P350


title: CTCF from UC Davis FAANG pig liver rep P348


title: CTCF from UC Davis FAANG pig hypothalamus rep P350


title: H3K27ac from UC Davis FAANG pig adipose rep P350


title: H3K27ac from UC Davis FAANG pig spleen rep P348


title: CTCF from UC Davis FAANG pig skeletal muscle rep P348


title: CTCF from UC Davis FAANG pig lung rep P348


title: CTCF from UC Davis FAANG pig cerebral cortex rep P348


title: CTCF from UC Davis FAANG pig cerebral cortex rep P350


title: CTCF from UC Davis FAANG pig hypothalamus rep P348


title: CTCF from UC Davis FAANG pig adipose rep P350


title: CTCF from UC Davis FAANG pig cerebellum rep P348


title: CTCF from UC Davis FAANG pig adipose rep P348


title: CTCF from UC Davis FAANG pig cerebellum rep P350


title: H3K27ac from UC Davis FAANG pig cerebral cortex rep P350


title: H3K4me3 from UC Davis FAANG cattle spleen rep M08

organism: Bos taurus


title: H3K4me3 from UC Davis FAANG cattle lung rep M22


title: H3K4me3 from UC Davis FAANG cattle skeletal muscle rep M22


title: H3K4me3 from UC Davis FAANG cattle lung rep M08


title: H3K4me3 from UC Davis FAANG cattle skeletal muscle rep M08


title: H3K4me3 from UC Davis FAANG cattle liver rep M22


title: H3K4me3 from UC Davis FAANG cattle hypothalamus rep M08


title: H3K4me3 from UC Davis FAANG cattle liver rep M08


title: H3K4me3 from UC Davis FAANG cattle cerebral cortex rep M08


title: H3K4me3 from UC Davis FAANG cattle cerebellum rep M08


title: H3K4me3 from UC Davis FAANG cattle adipose rep M22


title: H3K4me3 from UC Davis FAANG cattle adipose rep M08


title: H3K4me1 from UC Davis FAANG cattle spleen rep M08


title: H3K4me3 from UC Davis FAANG cattle cerebral cortex rep M22


title: H3K4me1 from UC Davis FAANG cattle skeletal muscle rep M08


title: H3K4me1 from UC Davis FAANG cattle skeletal muscle rep M22


title: H3K4me1 from UC Davis FAANG cattle spleen rep M22


title: H3K4me1 from UC Davis FAANG cattle lung rep M08


title: H3K4me3 from UC Davis FAANG cattle cerebellum rep M22


title: H3K4me1 from UC Davis FAANG cattle hypothalamus rep M08


title: H3K4me1 from UC Davis FAANG cattle liver rep M08


title: H3K4me1 from UC Davis FAANG cattle hypothalamus rep M22


title: H3K4me1 from UC Davis FAANG cattle lung rep M22


title: H3K4me1 from UC Davis FAANG cattle liver rep M22


title: H3K4me1 from UC Davis FAANG cattle cerebellum rep M22


title: H3K4me1 from UC Davis FAANG cattle cerebral cortex rep M22


title: H3K4me3 from UC Davis FAANG cattle spleen rep M22


title: H3K4me1 from UC Davis FAANG cattle cerebellum rep M08


title: H3K4me3 from UC Davis FAANG cattle hypothalamus rep M22


title: H3K4me1 from UC Davis FAANG cattle adipose rep M22


title: H3K4me1 from UC Davis FAANG cattle adipose rep M08


title: H3K27me3 from UC Davis FAANG cattle spleen rep M22


title: 747_Human blood from malaria patient

value: Low GCR


title: H3K27me3 from UC Davis FAANG cattle spleen rep M08


title: H3K27ac from UC Davis FAANG cattle skeletal muscle rep M08


title: H3K27me3 from UC Davis FAANG cattle cerebellum rep M08


title: H3K27me3 from UC Davis FAANG cattle cerebellum rep M22


title: H3K27me3 from UC Davis FAANG cattle hypothalamus rep M22


title: H3K27me3 from UC Davis FAANG cattle lung rep M22


title: H3K27me3 from UC Davis FAANG cattle liver rep M22


title: H3K27ac from UC Davis FAANG cattle spleen rep M22


title: H3K27me3 from UC Davis FAANG cattle hypothalamus rep M08


title: H3K27ac from UC Davis FAANG cattle lung rep M08


title: H3K27ac from UC Davis FAANG cattle liver rep M08


title: H3K27me3 from UC Davis FAANG cattle adipose rep M22

value: adipose


title: H3K27me3 from UC Davis FAANG cattle cerebral cortex rep M22


title: H3K27me3 from UC Davis FAANG cattle skeletal muscle rep M08


title: H3K27me3 from UC Davis FAANG cattle cerebral cortex rep M08


title: H3K27me3 from UC Davis FAANG cattle skeletal muscle rep M22


title: H3K27ac from UC Davis FAANG cattle hypothalamus rep M08


title: H3K27me3 from UC Davis FAANG cattle lung rep M08


title: H3K27ac from UC Davis FAANG cattle cerebral cortex rep M08


title: H3K27ac from UC Davis FAANG cattle cerebral cortex rep M22


title: H3K4me1 from UC Davis FAANG cattle cerebral cortex rep M08


title: H3K27ac from UC Davis FAANG cattle liver rep M22


title: H3K27me3 from UC Davis FAANG cattle liver rep M08


title: H3K27ac from UC Davis FAANG cattle skeletal muscle rep M22


title: H3K27ac from UC Davis FAANG cattle cerebellum rep M22


title: H3K27ac from UC Davis FAANG cattle lung rep M22


title: H3K27ac from UC Davis FAANG cattle spleen rep M08


title: H3K27me3 from UC Davis FAANG cattle adipose rep M08


title: H3K27ac from UC Davis FAANG cattle cerebellum rep M08


title: CTCF from UC Davis FAANG cattle spleen rep M22


title: CTCF from UC Davis FAANG cattle spleen rep M08


title: H3K27ac from UC Davis FAANG cattle hypothalamus rep M22


title: CTCF from UC Davis FAANG cattle lung rep M08


title: CTCF from UC Davis FAANG cattle skeletal muscle rep M22


title: CTCF from UC Davis FAANG cattle skeletal muscle rep M08


title: CTCF from UC Davis FAANG cattle hypothalamus rep M22


title: CTCF from UC Davis FAANG cattle cerebellum rep M22


title: CTCF from UC Davis FAANG cattle cerebral cortex rep M22


title: CTCF from UC Davis FAANG cattle adipose rep M22


title: CTCF from UC Davis FAANG cattle lung rep M22


title: W1D5I

city: Beijing

first: Jiaxing

last: Wang

address: No. 49 Huanyuan Nortk Road

country: China

institute: Peking University Third Hospital

data_processing:
cDNA library construction and sequencing were performed by BGISEQ platform
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to Mus_musculus genome sequence (GCF_000001635.26_GRCm38.p6) using HIAST (v2.0.4)
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set then expression level of gene was calculated by RSEM (v1.2.12)
differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05.
Genome_build: GCF_000001635.26_GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files includetab-delimited text files include expression value for each Sample

source_name: heart

extract_protocol:
after perfusion of phosphate buffer solution, hearts were removed from mice, flash frozen on dry ice, and the apex cordis was seperated for RNA extraction with Trizol reagent.
At least 1 µg DNase-treated total RNA, with at least 30% of the RNA fragments with a size >200 nt, was used to generate RNA Access libraries (Illumina) following the manufacturer’s recommendations. Library quality was assessed using the 2100 Bioanalyzer (Agilent). The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI, Shenzhen, China).

value: DCA, 10mg/kg/d


title: H3K27ac from UC Davis FAANG cattle adipose rep M08


title: W1D1I


title: W1C6I

value: Vehicle


title: W1D4I


title: W1D6I


title: CTCF from UC Davis FAANG cattle cerebellum rep M08


title: W1D2I


title: CTCF from UC Davis FAANG cattle cerebral cortex rep M08


title: CTCF from UC Davis FAANG cattle adipose rep M08


title: W1D3I


title: CTCF from UC Davis FAANG cattle liver rep M08


title: H3K27ac from UC Davis FAANG cattle adipose rep M22


title: W1C5I


title: W1C4I


title: W1C3I


title: W1C2I


title: CTCF from UC Davis FAANG cattle liver rep M22


title: CTCF from UC Davis FAANG cattle hypothalamus rep M08


title: W1C1I


title: W1C6A


title: W1C5A


title: W1C2A


title: W1C3A


title: W1C4A


title: W1C1A


title: MTB_control_rep3

city: Moscow

first: Artem

last: Grigorov

address: Ulitsa Miklukho-Maklaya, 16/10

department: Genomics and Postgenomic Technologies

country: Russia

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

data_processing:
Sequenced reads were mapped to M. tuberculosis H37Rv genome (GenBank accession code AL123456.3) using bowtie2 v2.3.4.3 with parameters -p 4 --local --dovetail
Fragments counting was performed using FeatureCounts (Annotation of the genome was retrieved from Mycobrowser). For every annotated gene, the number of fragments overlapping the gene at least by one nucleotide was calculated. Only unambiguously mapped, non-chimeric fragments were used. The files "Counts_XXX.txt" represent these counts (File "Counts_all.csv" contains values for all samples).
Search for differentially expressed genes was done with DESeq2 package (using only CDS transcripts). The results are represented in file "DifferentialExpression.csv".
Genome_build: AL123456.3
Supplementary_files_format_and_content: *txt: Tab-delimited text files include abundance measurements for each Sample.
Supplementary_files_format_and_content: Counts_all.csv: Comma-separated text file includes abundance measurements for all Samples.
Supplementary_files_format_and_content: DifferentialExpression.csv: Comma-separated text file includes differential expression values.

organism: Mycobacterium tuberculosis H37Rv

source_name: bacterial culture

growth_protocol: To obtain the log-phase bacteria for challenge, 50 µl from a thawed aliquot was added to 30 ml of Dubos broth base (BD) supplemented with 0.5% fatty acid-poor BSA (Calbiochem) and incubated for 2 weeks at 37°C. The resulting suspension was washed two times at 3000 g, 20 min, 4°C with Ca2+- and Mg2+-free PBS containing 0.2 mM EDTA and 0.025% Tween 80, re-suspended in PBS with 0.025% Tween 80 and ﬁltered through a 5 µm-pore-size ﬁlter (Millipore) to remove clumps.

extract_protocol:
Total RNA was isolated by phenol-chloroform extraction after cell disruption with Bead Beater (BioSpec Products).
After isolation, RNA was treated with Turbo DNase (Life Technologies) to remove traces of genomic DNA. RNA samples were depleted of both prokaryotic and eukaryotic rRNA with Ribo-Zero Gold rRNA Removal Kit (Illumina) (Samples MF_MTB_rep 1-3) or RiboMinus Transcriptome Isolation Kit, Bacteria (ThermoFisher) (Samples MTB_control_rep 1-3). Sequencing libraries were generated using the resulting ribosomal transcript-depleted RNA and NEBNext Ultra II Directional RNA Library Prep Kit (NEB) according to the manufacturers’ protocol.

treatment_protocol: Mice were injected with 2 ml 3% peptone (Sigma) in saline in peritoneal cavities (i. p.). Five days later, mice were injected i. p. with 200 × 10e6 M. tuberculosis H37Rv in 1 ml of Ca2+- and Mg2+-free PBS-0,025% Tween 80. Two hours later, peritoneal exudate cells (PEC) were aspirated from peritoneal cavities with Ca2+- and Mg2+-free PBS supplemented with 2% FCS and 10 U of heparin/ml. The macrophage content among PEC was always >80%, as estimated by Giemsa staining and non-specific esterase stain. To remove extracellular mycobacteria we employed differential buoyant density: for free mycobacteria = 1.1-1.2 g/ml, for macrophages associated with mycobacteria <1.09 g/ml. Isolated PEC were washed at 300 g, 8 min, 4°C with PBS containing 2% FCS, re-suspended in isotonic Percoll Plus solution (GE Healthcare) to ρ = 1.1 g/ml, over-layered with isotonic Percoll Plus of ρ=1.09 g/ml and pure PBS and centrifuged at 800 g, 20 min, 4°C. The interphase between Percoll 1.09 g/ml and PBS layers was collected, washed once with PBS at 300 g, 8 min, 4°C, re-suspended in 4 ml of deionized water with 1mM EDTA with 0.05% Tween 80 at pH = 6.5, and put into a Dounce homogenizer. After disruption of macrophages by 10 frictions, the isotonicity of lysate was restored with 4 ml of 2x PBS. Lysates were filtered through a 5 µm-pore-size filter, centrifuged at 3000 g, 20 min, 4°C, and mycobacterial pellet was suspended in 1 ml of Trizol. For controls pure M. tuberculosis H37Rv cultured in Dubos broth was centrifuged at 3000 g, 20 min, 4°C, and mycobacterial pellet was suspended in 1 ml of Trizol.

tag: condition

value: Dubos broth


title: MTB_control_rep1


title: MTB_control_rep2


title: MF_MTB_rep2

source_name: in vivo infected macrophages

value: in vivo macrophage infection


title: MF_MTB_rep3


title: Thymocytes CD34+ 2 EPICseq

city: South San Francisco

first: Juliette

last: Roels

address: 1 DNA Way

institute: Genentech

data_processing:
Library strategy: EPICseq
Reads were trimmed using TrimGalore (v0.4.5) and aligned with Bismark (v0.20.0) on the human genome version hg38.
Normalized β values were extracted using the methylkit package in R
Genome_build: hg38

source_name: Human postnatal thymus

extract_protocol:
genomic DNA was extracted and purified using the Qiagen DNeasy Kit according to standard instructions
500ng of DNA was used for TruSeq Methyl Capture EPIC sequencing (Illumina).

value: Human postnatal thymus

tag: disease state

value: Normal thymoocytes CD34+ 4- 1-


title: T-ALL 7

source_name: T-ALL blasts

value: T-ALL blasts

value: NKX2-1 T-ALL


title: T-ALL 2

value: ETP-ALL


title: T-ALL 3

value: HOXA T-ALL


title: T-ALL 5

value: TLX T-ALL


title: T-ALL 12

value: TAL/LMO T-ALL


title: Thymocytes CD34+ 1 EPICseq


title: T-ALL 4


title: T-ALL 11


title: T-ALL 6


title: T-ALL 10


title: T-ALL 14


title: T-ALL 13


title: T-ALL 9


title: T-ALL 1


title: Thymocytes DP 2 EPICseq

value: Normal thymoocytes DP CD4+CD8+ (Double Positive) CD3-


title: MF_MTB_rep1


title: Thymocytes DP 1 EPICseq


title: T-ALL 8


title: Dolinoy_RNA_Liver_Pb_3week_Male_biorep3

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

description: UUID:5c71f35db0e3512dc90467e8,QC_score:3,QC_stats:Pass

data_processing:
RNA-seq and ATAC-seq were sequenced by data production centers and processed by the TaRGET II DCC with standardized data processing pipelines. Library QC was assayed based on key QC parameters. Please refer to the TaRGET II data portal for detailed pipeline description and QC standard (https://data.targetepigenomics.org).
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak output for ATAC-seq and gene count table for RNA-seq

extract_protocol:
Sample collection was performed by Dana Dolinoy lab at University of Michigan. 3 week mice were CO2 euthanized. Liver and blood cells from individual mouse were isolated for subsequent DNA and RNA extractions according to the standard operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.
ATAC-seq and mRNA-seq experiments were performed by Dana Dolinoy lab at University of Michigan. mRNA and nuclei from 3 weekmice liver and blood were isolated for subsequent ATAC-seq and mRNA-seq library preparations according to the operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.

value: Avy

value: 3 week

tag: gender

value: Male

value: Liver

value: Pb 16ppm lead acetate


title: Dolinoy_RNA_Liver_Pb_3week_Male_biorep2

description: UUID:5c71ebdeb0e35146ec046796,QC_score:3,QC_stats:Pass

tag: strain


title: Dolinoy_RNA_Liver_Pb_3week_Female_biorep4

description: UUID:5c71fcbdb0e351509104684b,QC_score:3,QC_stats:Pass

value: Female


title: Dolinoy_RNA_Liver_Pb_3week_Female_biorep5

description: UUID:5c72007eb0e3513823046859,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_Pb_3week_Female_biorep3

description: UUID:5c71edbe1bf47405c5c74848,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_Pb_3week_Female_biorep7

description: UUID:5c720c731bf4746ff4c749d0,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_Pb_3week_Male_biorep7

description: UUID:5c720ddab0e351cbec04693c,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_Pb_3week_Male_biorep4

description: UUID:5c71ff8e1bf474f50ec748ea,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_Pb_3week_Male_biorep6

description: UUID:5c72092a1bf474140dc7497d,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_Pb_3week_Female_biorep6

description: UUID:5c7208761bf47430a6c7496b,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_Pb_3week_Male_biorep5

description: UUID:5c720221b0e351d508046876,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_Pb_3week_Male_biorep1

description: UUID:5c71eba2b0e3512ad6046794,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_Pb_3week_Female_biorep1

description: UUID:5c71eb66b0e351116b046791,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_Ctrl_3week_Male_biorep4

description: UUID:5c720a55b0e35153d904690f,QC_score:3,QC_stats:Pass

value: Control Diet Control


title: Dolinoy_RNA_Liver_DEHP_3week_Female_biorep1

description: UUID:5c71ec56b0e351a06e046797,QC_score:3,QC_stats:Pass

value: DEHP (bis (2-ethylhexyl) phthalate) 25mg DEHP/kg


title: Dolinoy_RNA_Liver_DEHP_3week_Female_biorep6

description: UUID:5c72124eb0e351e5ea04696c,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_DEHP_3week_Female_biorep2

description: UUID:5c72061eb0e3511d100468c9,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_DEHP_3week_Male_biorep3

description: UUID:5c7207feb0e3511c710468f7,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_DEHP_3week_Female_biorep3

description: UUID:5c72074ab0e3510ccf0468e6,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_DEHP_3week_Female_biorep5

description: UUID:5c720b451bf474d9e1c749b6,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_Pb_3week_Female_biorep2

description: UUID:5c71ebdeb0e3515d36046795,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_Ctrl_3week_Male_biorep6

description: UUID:5c7226ee1bf4742458c74a5e,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_DEHP_3week_Male_biorep4

description: UUID:5c720b091bf4748f06c749ab,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_DEHP_3week_Male_biorep6

description: UUID:5c721bad1bf474e03fc74a59,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_DEHP_3week_Male_biorep5

description: UUID:5c720bbdb0e3515d15046935,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_DEHP_3week_Male_biorep1

description: UUID:5c71ec911bf474da8ac74842,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_Ctrl_3week_Male_biorep7

description: UUID:5c7227de512a5d23428f0a51,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_DEHP_3week_Male_biorep2

description: UUID:5c7206951bf47424e5c74945,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_DEHP_3week_Female_biorep4

description: UUID:5c720aceb0e3513c9d04691b,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_Ctrl_3week_Male_biorep5

description: UUID:5c7226751bf4747b64c74a5d,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_Ctrl_3week_Female_biorep6

description: UUID:5c7227651bf474f601c74a61,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_Ctrl_3week_Female_biorep7

description: UUID:5c72281a512a5db3ad8f0a52,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_Ctrl_3week_Male_biorep3

description: UUID:5c72052d1bf474b1e6c74933,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_Ctrl_3week_Female_biorep3

description: UUID:5c7204791bf474a5f0c74928,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_Ctrl_3week_Female_biorep4

description: UUID:5c7209dd1bf474e1a2c7498f,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_Ctrl_3week_Male_biorep1

description: UUID:5c71eb291bf47423e6c74833,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_Ctrl_3week_Male_biorep2

description: UUID:5c720402b0e351d10f0468a3,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_Ctrl_3week_Female_biorep2

description: UUID:5c720311b0e35151ca046885,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_Pb_3week_Male_biorep1

description: UUID:5c71da85b0e35114a9046759,QC_score:3,QC_stats:Pass

value: Blood


title: Dolinoy_RNA_Liver_Ctrl_3week_Female_biorep5

description: UUID:5c7224591bf47406b9c74a5c,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Liver_Ctrl_3week_Female_biorep1

description: UUID:5c71eaed1bf474d7ecc74830,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_Pb_3week_Female_biorep7

description: UUID:5c71e90eb0e3515a75046780,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_Pb_3week_Male_biorep4

description: UUID:5c71e54d1bf474d677c7480e,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_Pb_3week_Male_biorep6

description: UUID:5c71e7e1b0e351a391046778,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_Pb_3week_Female_biorep5

description: UUID:5c71e58ab0e351643f046763,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_Pb_3week_Male_biorep5

description: UUID:5c71e5891bf474cd65c74810,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_Pb_3week_Male_biorep3

description: UUID:5c71e4991bf474048fc7480a,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_Pb_3week_Female_biorep4

description: UUID:5c71e4d6b0e351cef5046760,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_Pb_3week_Female_biorep6

description: UUID:5c71e7a6b0e3517b92046775,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_DEHP_3week_Male_biorep4

description: UUID:5c71e896b0e3512ddd04677d,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_DEHP_3week_Male_biorep2

description: UUID:5c71e6f1b0e3514b2e04676e,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_DEHP_3week_Male_biorep6

description: UUID:5c71e985b0e35141a5046786,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_DEHP_3week_Male_biorep5

description: UUID:5c71e8d21bf4747024c7481e,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_DEHP_3week_Male_biorep3

description: UUID:5c71e76ab0e351fdf9046772,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_Pb_3week_Female_biorep3

description: UUID:5c71e45eb0e3518ba804675f,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_DEHP_3week_Male_biorep1

description: UUID:5c71e4211bf4741b20c74807,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_Pb_3week_Male_biorep2

description: UUID:5c71e2f71bf4742de9c74805,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_Pb_3week_Female_biorep2

description: UUID:5c71dbb1ccede3747f884a8f,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_Pb_3week_Male_biorep7

description: UUID:5c71e94ab0e35171e2046783,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_DEHP_3week_Female_biorep5

description: UUID:5c71e8d11bf474e366c7481d,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_DEHP_3week_Female_biorep3

description: UUID:5c71e72d1bf4744d59c74814,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_DEHP_3week_Female_biorep4

description: UUID:5c71e859b0e351855604677b,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_Pb_3week_Female_biorep1

description: UUID:5c71d9d2ccede311a0884a8d,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_DEHP_3week_Female_biorep6

description: UUID:5c71e949b0e35141d2046782,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_Ctrl_3week_Male_biorep6

description: UUID:5c71ea3ab0e35101de04678d,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_Ctrl_3week_Male_biorep4

description: UUID:5c71e81d1bf47426bdc74817,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_Ctrl_3week_Male_biorep3

description: UUID:5c71e67a1bf474823ec74813,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_DEHP_3week_Female_biorep2

description: UUID:5c71e6b5b0e351d79104676c,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_Ctrl_3week_Female_biorep6

description: UUID:5c71ea391bf4745580c74829,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_Ctrl_3week_Male_biorep5

description: UUID:5c71e9fd1bf4740d4cc74825,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_Ctrl_3week_Male_biorep7

description: UUID:5c71ea761bf4747ea8c7482a,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_DEHP_3week_Female_biorep1

description: UUID:5c71e3e6b0e351c67304675e,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_Ctrl_3week_Female_biorep5

description: UUID:5c71e9c2b0e3511b2104678b,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_Ctrl_3week_Female_biorep2

description: UUID:5c71e5c6b0e3512432046764,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_Ctrl_3week_Female_biorep4

description: UUID:5c71e81e1bf4745336c74819,QC_score:3,QC_stats:Pass


title: Dolinoy_RNA_Blood_Ctrl_3week_Male_biorep2

description: UUID:5c71e6021bf474c468c74811,QC_score:3,QC_stats:Pass