title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A6_AD010_indexed


title: genomic DNA from peripheral blood leukocytes 969

status: Public on Aug 31 2020

type: genomic

city: Ann Arbor

first: Minjung

last: Kho

state: Michigan

address: School of Public Health University of Michigan 1415 Washington Heights

country: USA

institute: University of Michigan

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to IIllumina Infinium HumanMethylation450 BeadChip or EPIC BeadChip using standard Illumina protocol

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

data_processing: For each chip, the Minfi R package was used to perform background correction and normalization. The regression on correlated probes (RCP) method was then used to adjust probe-type bias, and ComBat was used to remove confounding effects due to batch or other technical covariates. Data from the two platforms were combined, and ComBat was used to remove the platform effect. Age, gender, and phase effect was preserved when removing platform difference.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral blood leukocytes

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from stored peripheral blood leukocytes using AutoGen FlexStar (AutoGen, Holliston, MA) and DNA was bisulfite converted using the EZ DNA Methylation Kit (Zymo Research, Irvine, CA)

tag: tissue

value: peripheral blood leukocytes

tag: gender

value: M

tag: age(yrs)

tag: systolic blood pressure (mmhg)

tag: diastolic blood pressure (mmhg)


title: genomic DNA from peripheral blood leukocytes 968

value: F


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A7_AD007_indexed

type: SRA

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

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

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

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

tag: brain region

value: SSp

tag: Sex

value: male

tag: age

tag: strain


title: genomic DNA from peripheral blood leukocytes 971


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A6_AD007_indexed


title: genomic DNA from peripheral blood leukocytes 967


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A6_AD012_indexed


title: genomic DNA from peripheral blood leukocytes 965


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A8_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A6_AD008_indexed


title: genomic DNA from peripheral blood leukocytes 964


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A6_AD004_indexed


title: genomic DNA from peripheral blood leukocytes 963


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A6_AD001_indexed


title: genomic DNA from peripheral blood leukocytes 959


title: genomic DNA from peripheral blood leukocytes 961


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A6_AD002_indexed


title: genomic DNA from peripheral blood leukocytes 960


title: genomic DNA from peripheral blood leukocytes 958


title: genomic DNA from peripheral blood leukocytes 955


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A5_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A5_AD010_indexed


title: genomic DNA from peripheral blood leukocytes 947


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A5_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A5_AD006_indexed


title: genomic DNA from peripheral blood leukocytes 950


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A5_AD002_indexed


title: genomic DNA from peripheral blood leukocytes 942


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A4_AD012_indexed


title: genomic DNA from peripheral blood leukocytes 943


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A5_AD001_indexed


title: genomic DNA from peripheral blood leukocytes 954


title: genomic DNA from peripheral blood leukocytes 938


title: genomic DNA from peripheral blood leukocytes 946


title: genomic DNA from peripheral blood leukocytes 937


title: genomic DNA from peripheral blood leukocytes 936


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A3_AD007_indexed


title: genomic DNA from peripheral blood leukocytes 940


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A3_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A4_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A5_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A4_AD007_indexed


title: genomic DNA from peripheral blood leukocytes 935


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A4_AD001_indexed


title: genomic DNA from peripheral blood leukocytes 932


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A3_AD006_indexed


title: genomic DNA from peripheral blood leukocytes 931


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A7_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A3_AD010_indexed


title: genomic DNA from peripheral blood leukocytes 930


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A4_AD010_indexed


title: genomic DNA from peripheral blood leukocytes 928


title: genomic DNA from peripheral blood leukocytes 925


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A4_AD002_indexed


title: genomic DNA from peripheral blood leukocytes 926


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A2_AD012_indexed


title: genomic DNA from peripheral blood leukocytes 924


title: genomic DNA from peripheral blood leukocytes 927


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A3_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A2_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A2_AD008_indexed


title: genomic DNA from peripheral blood leukocytes 923


title: genomic DNA from peripheral blood leukocytes 922


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A3_AD004_indexed


title: genomic DNA from peripheral blood leukocytes 921


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A2_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A2_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A1_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A2_AD001_indexed


title: genomic DNA from peripheral blood leukocytes 920


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A1_AD004_indexed


title: genomic DNA from peripheral blood leukocytes 917


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A2_AD002_indexed


title: genomic DNA from peripheral blood leukocytes 918


title: genomic DNA from peripheral blood leukocytes 916


title: genomic DNA from peripheral blood leukocytes 915


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A1_AD012_indexed


title: genomic DNA from peripheral blood leukocytes 914


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A1_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A1_AD001_indexed


title: genomic DNA from peripheral blood leukocytes 911


title: genomic DNA from peripheral blood leukocytes 910


title: genomic DNA from peripheral blood leukocytes 913


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A12_AD012_indexed


title: genomic DNA from peripheral blood leukocytes 912


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A1_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A4_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A11_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A11_AD004_indexed


title: genomic DNA from peripheral blood leukocytes 905


title: genomic DNA from peripheral blood leukocytes 909


title: genomic DNA from peripheral blood leukocytes 908


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A12_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A12_AD010_indexed


title: genomic DNA from peripheral blood leukocytes 907


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A11_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A11_AD010_indexed


title: genomic DNA from peripheral blood leukocytes 904


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A11_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A11_AD012_indexed


title: genomic DNA from peripheral blood leukocytes 903


title: genomic DNA from peripheral blood leukocytes 901


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A10_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H9_AD007_indexed


title: genomic DNA from peripheral blood leukocytes 898


title: genomic DNA from peripheral blood leukocytes 900


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H9_AD010_indexed


title: genomic DNA from peripheral blood leukocytes 897


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A10_AD012_indexed


title: genomic DNA from peripheral blood leukocytes 892


title: genomic DNA from peripheral blood leukocytes 893


title: genomic DNA from peripheral blood leukocytes 891


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A10_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H9_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A10_AD006_indexed


title: genomic DNA from peripheral blood leukocytes 889


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H9_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A10_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H9_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H8_AD002_indexed


title: genomic DNA from peripheral blood leukocytes 882


title: genomic DNA from peripheral blood leukocytes 881


title: genomic DNA from peripheral blood leukocytes 884


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H8_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A10_AD004_indexed


title: genomic DNA from peripheral blood leukocytes 880


title: genomic DNA from peripheral blood leukocytes 883


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H8_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H8_AD006_indexed


title: genomic DNA from peripheral blood leukocytes 879


title: genomic DNA from peripheral blood leukocytes 878


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H7_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H6_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H7_AD012_indexed


title: genomic DNA from peripheral blood leukocytes 877


title: genomic DNA from peripheral blood leukocytes 890


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H7_AD008_indexed


title: genomic DNA from peripheral blood leukocytes 888


title: genomic DNA from peripheral blood leukocytes 874


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H7_AD002_indexed


title: genomic DNA from peripheral blood leukocytes 873


title: genomic DNA from peripheral blood leukocytes 887


title: genomic DNA from peripheral blood leukocytes 876


title: genomic DNA from peripheral blood leukocytes 872


title: genomic DNA from peripheral blood leukocytes 871


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H6_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H7_AD010_indexed


title: genomic DNA from peripheral blood leukocytes 870


title: genomic DNA from peripheral blood leukocytes 869


title: genomic DNA from peripheral blood leukocytes 867


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H6_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H6_AD001_indexed


title: genomic DNA from peripheral blood leukocytes 866


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H5_AD010_indexed


title: genomic DNA from peripheral blood leukocytes 864


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H5_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H7_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H6_AD007_indexed


title: genomic DNA from peripheral blood leukocytes 865


title: genomic DNA from peripheral blood leukocytes 863


title: normal_pooled

first: Shankar

last: Subramaniam

address: 9500 Gilman Drive

department: Bioengineering

institute: UCSD

library_source: transcriptomic

data_processing:
CASAVA ELAND software was used to map and generate a table of exon, gene, and splice counts in both BA and normal pooled data
DEseq, R package for RNAseq data, was used for differential analysis (Anders and Huber, 2010). The genes among the 40% lower quantile of the total read counts were removed. For variance estimation, the DEseq options of “blind” and “fit-only” were used. The resulting dispersion plot was checked for quality.
Genome_build: hg19
Supplementary_files_format_and_content: tab delimted text file, *.txt.gz. The first nine columns contain information on the Refseq (Refgene) transcripts (such as transcript/gene name). The remaining columns correspond to samples and contain the raw mapped read counts. SetA and SetB correspond to replicates 1 and 2, respectively.

molecule: total RNA

source_name: liver tissue

extract_protocol:
Liver tissue samples were extracted from 6 biliary atresia patients and 6 normal pre-implant liver allografts
The pooled RNA libraries were prepared using Illumina’s mRNA Sequencing Sample Preparation kit (#RS-930-1001) from the explanted liver tissue samples. The pooled RNA libraries for the BA and the normal groups were sequenced on Genome Analyzer II with 36 bp paired-end at the Wistar Institute, Philadelphia. CASAVA software was used to generate a table of exon, gene, and splice counts in both BA and normal groups

value: liver

tag: condition

value: Normal


title: BA_pooled

value: Biliary atresia


title: H3K27Ac_2h_input

city: Boston

first: Li

last: Pan

state: MA

address: 77 Ave Louis Pasteur

department: Pathology

institute: Brigham and Women's Hospital

data_processing:
Reads were trimmed with Trim Galore (v.0.3.7 using cutadapt v.1.8), assessed for quality with FastQC (v.0.11.3), and aligned to GRCh38/hg38 with bowtie (v.2.0.0).
Peaks were identified using MACS2 (v.2.1.1) and annotated using Homer (v3.12, 6-8-2012).
Genome_build: hg38
Supplementary_files_format_and_content: bw files

source_name: Squamous cell carcinoma (SCC) cells

growth_protocol: Cells were grown in keratinocyte medium with 1 μM GSI (compound E).

extract_protocol:
ChIP assay kit protocol (millipore)
Illumina ChIP DNA library preparation kit

treatment_protocol: GSI washout was performed for 1, 2 and 4 hours.

tag: cell type

value: SCC IC8 cells

tag: cell line

tag: chip antibody

tag: treatment

value: GSI washout for 2h


title: H3K27Ac_4h_input

value: GSI washout for 4h


title: H3K27Ac_0h_input

value: GSI (Compound E 1 microM)


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H7_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H5_AD007_indexed


title: H3K27Ac_1h_input

value: GSI washout for 1h


title: A549

city: Taipei

first: Pinghsing

last: Tsai

state: Taiwan

address: Rm. 825, 7F., No.322, Sec. 2, Shipai Rd., Beitou D

country: Taiwan

institute: Taipei Veterans General Hospital

data_processing:
Quality control of the sequencing: FastQC v0.11.7.
Transcriptomic analysis was performed using Kallisto (alignment (hg19, and defined circRNA from circBase) and quantification) and Sleuth (differential gene expression(DGE)), with transcript abundances calculated as transcripts per kilobase million (TPM).
Expression was defined as TPM≥1.0 and significant DGE as a fold-change (HCC/BEAS) ≥1.0.
Genome_build: hg19
Supplementary_files_format_and_content: excel file includes TPM values for each Sample.

source_name: lung adenocarcinoma cell line with wildtype EGFR

growth_protocol: Human normal lung and lung cancer cell lines were cultured in DMEM with 10 % fetal bovine serum, 100 units/mL penicillin, and 100 μg/mL streptomycin under standard culture conditions (37℃, 95 % humidified air, and 5 % CO2). Subculturing was performed using trypsin-EDTA. Medium was refreshed every two days.

extract_protocol:
Lung cancer cells were washed and collected, and total RNA was harvested using Trizol reagent. After isolation, 1000 ng RNA were quality checked on a 1% agarose gel. rRNA was depleted using the RiboZero kit (Zymo). Libraries were prepared and sequenced on a Illumina HiSeq sequencer with HighOutput.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung adenocarcinoma


title: HCC827

source_name: lung adenocarcinoma cell line with mutated EGFR


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H4_AD008_indexed


title: genomic DNA from peripheral blood leukocytes 862


title: BEAS-2B

source_name: normal lung cell line

value: normal lung


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H4_AD012_indexed


title: genomic DNA from peripheral blood leukocytes 858


title: genomic DNA from peripheral blood leukocytes 860


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H4_AD010_indexed


title: genomic DNA from peripheral blood leukocytes 857


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H3_AD010_indexed


title: genomic DNA from peripheral blood leukocytes 856


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H3_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H4_AD004_indexed


title: genomic DNA from peripheral blood leukocytes 853


title: genomic DNA from peripheral blood leukocytes 852


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H3_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H4_AD002_indexed


title: genomic DNA from peripheral blood leukocytes 848


title: genomic DNA from peripheral blood leukocytes 851


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H3_AD001_indexed


title: genomic DNA from peripheral blood leukocytes 847


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H5_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H3_AD008_indexed


title: genomic DNA from peripheral blood leukocytes 859


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H3_AD002_indexed


title: genomic DNA from peripheral blood leukocytes 844


title: genomic DNA from peripheral blood leukocytes 846


title: Nthy-SEC23B-V594G, DMSO, Day 7, rep3

city: Cleveland

first: Charis

last: Eng

state: OH

address: 9500 Euclid Avenue

department: Genomic Medicine Institute

institute: Cleveland Clinic

description: SEC23B-MUT-treatment_Day 7.diff.txt (Tunica vs DMSO)

data_processing:
Sequencing reads were aligned to the reference human transcriptome (Genome Reference Consortium human genome build 37, hg19) using Tophat/Bowtie and then assembled into RNA transcripts using the Cufflinks package
Following computation of FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values, we calculated differential gene expression using Cuffdiff 2
We compared the treatment response per genotype (Tunicamycin relative to DMSO untreated mock control), at each time point (30 hours and day 7)
Transcripts were considered differentially expressed at q < 0.05 following Benjamini-Hochberg multiple testing correction of the original p-values
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample

source_name: Nthy-SEC23B-V594G, DMSO, Day 7

extract_protocol:
Total RNA was extracted using GeneJET RNA Purification Kit (Thermo, Catalog number:  K0731)
RNA libraries were prepared for sequencing using standard Illumina protocols. TruSeq Stranded Total RNA library prep kit

value: Nthy-ori 3-1 stable cell line

value: Non-malignant thyroid

tag: genotype

value: MUT

value: DMSO

tag: time

value: Day 7

tag: replicate


title: genomic DNA from peripheral blood leukocytes 842

tag: tissue

value: peripheral blood leukocytes

value: M


title: Nthy-SEC23B-V594G, Tunica, Day 7, rep2

source_name: Nthy-SEC23B-V594G, Tunica, Day 7

value: Tunica


title: Nthy-SEC23B-V594G, Tunica, Day 7, rep1


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H12_AD006_indexed

value: SSp

value: male


title: Nthy-SEC23B-V594G, DMSO, Day 7, rep2


title: genomic DNA from peripheral blood leukocytes 840

tag: gender

value: F


title: Nthy-SEC23B-WT, Tunica, Day 7, rep3

description: SEC23B-WT-treatment_Day7.diff.txt (Tunica vs DMSO)

source_name: Nthy-SEC23B-WT, Tunica, Day 7

value: WT


title: genomic DNA from peripheral blood leukocytes 854

tag: age(yrs)


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H3_AD012_indexed


title: Nthy-SEC23B-WT, Tunica, Day 7, rep2


title: Nthy-SEC23B-V594G, Tunica, Day 7, rep3


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H2_AD006_indexed


title: Nthy-SEC23B-WT, Tunica, Day 7, rep1


title: genomic DNA from peripheral blood leukocytes 839

tag: systolic blood pressure (mmhg)


title: Nthy-SEC23B-WT, DMSO, Day 7, rep3

source_name: Nthy-SEC23B-WT, DMSO, Day 7


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H2_AD007_indexed


title: genomic DNA from peripheral blood leukocytes 837

tag: diastolic blood pressure (mmhg)


title: Nthy-SEC23B-WT, DMSO, Day 7, rep2


title: Nthy-SEC23B-WT, DMSO, Day 7, rep1


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H2_AD012_indexed

tag: brain region


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H2_AD008_indexed

tag: Sex


title: genomic DNA from peripheral blood leukocytes 838


title: genomic DNA from peripheral blood leukocytes 836


title: FullTerm patient 8

city: Helsinki

first: Sanna

middle: M

last: Edelman

address: Meilahdentie 2

country: Finland

institute: Helsinki University Central Hospital

data_processing:
Basecalls performed using standard Illumina base-caller
RNA-seq reads were pre-processed using Trimmomatics v0.32 with the following configurations ILLUMINACLIP:TruSeqAdapters-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Pre-processed RNA-seq reads were aligned to the hg38 genome assembly (EnsEMBL v82) using the STAR per-sample 2-pass mapping strategy. STAR v2.3.0e aligner was used with the following configurations --outSAMattributes All --outSAMunmapped Within. The STAR indexes were build from primary assembly sequences and by taking into account transcript annotations.
PCR duplicates were marked with the MarkDuplicates tool of PICARD v1.63 with the following configurations CREATE_INDEX=true VALIDATION_STRINGENCY=SILENT
Counts, Counts per Megabase of library size (CPM), and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using subreadR and edgeR as implemented in the statistical environment R (v.3.3.0)
Genome_build: hg38 genome assembly, EnsEMBL v82
Supplementary_files_format_and_content: Tab-delimited text file (.txt). Columns: 1) element's row number, 2) EnsEMBL gene id, 3) gene model's start coordinate, 4) gene model's stop coordinate, 5) gene model's chromosome, 6) gene name, 7) biotype information, 8) raw count value, 9) CPM value, 10) RPKM value

source_name: cord blood

extract_protocol:
CD4+ T helper cells were isolated with Dynabeads® CD4 Positive Isolation Kit and RNA was harvested by using AllPrep DNA/RNA/miRNA Universal Kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 0.2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
Ribo depletion RNA-Seq

value: CD4+ T helper cell


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H12_AD010_indexed

tag: age


title: FullTerm patient 9


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H2_AD010_indexed

tag: strain


title: Nthy-SEC23B-V594G, DMSO, Day 7, rep1


title: genomic DNA from peripheral blood leukocytes 835


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H2_AD002_indexed


title: PreTerm patient 4


title: genomic DNA from peripheral blood leukocytes 834


title: FullTerm patient 6


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H1_AD012_indexed


title: VeryPreTerm patient 2


title: VeryPreTerm patient 1


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H1_AD006_indexed


title: genomic DNA from peripheral blood leukocytes 831


title: genomic DNA from peripheral blood leukocytes 833


title: FullTerm patient 5


title: FullTerm patient 4


title: genomic DNA from peripheral blood leukocytes 830


title: FullTerm patient 1


title: FullTerm patient 7


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H2_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H12_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_3_CEMBA180529_5B_4_A10_AD001_indexed


title: FullTerm patient 2


title: genomic DNA from peripheral blood leukocytes 825


title: genomic DNA from peripheral blood leukocytes 827


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H1_AD008_indexed


title: PreTerm patient 3


title: genomic DNA from peripheral blood leukocytes 824


title: genomic DNA from peripheral blood leukocytes 823


title: PreTerm patient 2


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H1_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H1_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H11_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H1_AD002_indexed


title: genomic DNA from peripheral blood leukocytes 829


title: genomic DNA from peripheral blood leukocytes 828


title: genomic DNA from peripheral blood leukocytes 821


title: WT_B_T1pos_4

first: Lloyd

last: Bod

address: 60 Fenwood road

institute: Brigham and Women's Hospital and Harvard Medical School

description: Tim-1+ B cell

data_processing:
The paired-end 38bp reads sequenced (26.53M ± 1.62M pairs of reads per sample) for each of the 8 samples (4 Tim-1+ and 4 Tim-1- B cell samples derived from naïve WT mice) were aligned to the mouse mm10 UCSC reference genome using Tophat version 2.0.10 (Kim et al., 2013) with default settings (read alignment rate of 82.81% ± 0.44% properly mapped pairs per sample).
Gene expression levels were quantified for 22,815 genes in the mouse mm10 UCSC reference gene annotations using Cuffquant in the Cufflinks suite version 2.2.1 (Trapnell et al., 2012).
These levels were subsequently normalized across all 8 samples using Cuffnorm with default settings based on “geometric” normalization, which normalizes samples based on the median expression level in each sample, thus reporting normalized expression levels (FPKM: fragments per kilo bases of exons for per million mapped reads).
Genome_build: mm10 UCSC reference genome
Supplementary_files_format_and_content: Tab-delimited text files with gene expression levels (FPKM).

source_name: spleen

growth_protocol: Samples from isolated Tim-1- and Tim-1+ B cells were processed with the SMART-Seq2 protocol (Picelli et al., 2013), and sequenced on Illumina Hi-Seq 2500. The paired-end 38bp reads sequenced (26.53M ± 1.62M pairs of reads per sample) for each of the 8 samples (4 Tim-1+ and 4 Tim-1- B cell samples derived from naïve WT mice) were aligned to the mouse mm10 UCSC reference genome using Tophat version 2.0.10 (Kim et al., 2013) with default settings (read alignment rate of 82.81% ± 0.44% properly mapped pairs per sample). Gene expression levels were quantified for 22,815 genes in the mouse mm10 UCSC reference gene annotations using Cuffquant in the Cufflinks suite version 2.2.1 (Trapnell et al., 2012). These levels were subsequently normalized across all 8 samples using Cuffnorm with default settings based on “geometric” normalization, which normalizes samples based on the median expression level in each sample, thus reporting normalized expression levels (FPKM: fragments per kilo bases of exons for per million mapped reads). Out of the 22,815 quantified reference genes, 15,519 genes were detected in at least one of the 8 samples at a normalized FPKM level > 0. Differential gene expression analysis comparing the 4 Tim-1+ and 4 Tim-1- B cell samples was performed by estimating the asymptotic t-test (Student's t-distribution) p-values, False Discovery Rate (FDR) (Benjamini and Hochberg) values and fold-changes using the ComparativeMarkerSelection module in GenePattern (Reich et al., 2006). Significantly differentially expressed genes were identified using the asymptotic t-test p-value ≤ 0.05 and absolute fold change ≥ 2 selection criteria. Heatmaps visualizing the normalized gene expression levels (zero mean centering and unit standard deviation scaling of the expression levels for each gene, followed by saturating these normalized gene expression levels at +1 and -1) were generated using GENE-E/Morpheus.

extract_protocol:
RNA was isolated using the RNeasy kit (Qiagen) according to manufacturer 's protocol.
Refer to Picelli et al., 2013

value: sorted B cells


title: PreTerm patient 1


title: genomic DNA from peripheral blood leukocytes 826


title: genomic DNA from peripheral blood leukocytes 820


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H11_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H12_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H11_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G9_AD012_indexed


title: Mutyh +/+, HFHC + high-iron diet, without HCC [1001]

type: RNA

city: sapporo

first: hiroki

last: sakamoto

address: west-16, south-1, chuo-ku

department: medical oncology

country: Japan

institute: sapporo medical university

description: wild 1001

hyb_protocol: Biotinylated cDNA is injected into GeneChip Mouse Gene 2.0 ST Array and is hybridized using Hybridization Oven 645 (Affymetrix, Inc.)

scan_protocol: GeneChips were scanned using a GeneChip scanner (Scanner 3000 7G, Affymetrix, Inc.).

data_processing: The data were analyzed with analysis software (Affymetrix Expression Console, Affymetrix, Inc.) as normalization method and data mining software (Affymetrix Transcriptome Analysis Console, Affymetrix, Inc.).

label: biotin

label_protocol: The fragmented cDNA is labeled using Agilent RNA 6000 Nano Kit.

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions included in RNeasy® Lipid Tissue Mini Kit (HB-0144-004_HB _RNY_Lipid_Tissue_0718_WW.pdf).

tag: strain/background

tag: genotype/variation

value: Mutyh +/+

value: Liver

value: HFHC + high-iron diet

tag: diagnosis

value: Without HCC


title: Mutyh +/+, HFHC + high-iron diet, without HCC [1027]

description: wild 1027


title: genomic DNA from peripheral blood leukocytes 817


title: Mutyh -/-, HFHC + high-iron diet, HCC [3003]

description: minor homo 3003

value: Mutyh -/-

value: HCC


title: Mutyh +/+, HFHC + high-iron diet, without HCC [1025]

description: wild 1025


title: Mutyh -/-, HFHC + high-iron diet, HCC [3007]

description: minor homo 3007


title: WT_B_T1neg_3

description: Tim-1- B cell

tag: cell type


title: WT_B_T1pos_3

description: Tim-1+ B cell


title: WT_B_T1neg_4

description: Tim-1- B cell


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H11_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H11_AD004_indexed


title: Mutyh -/-, HFHC + high-iron diet, HCC [3008]

description: minor homo 3008

tag: treatment


title: scRNAseq_Foxj1_Olig2_tdT_4wpi

city: Stockholm

first: Enric

last: Llorens Bobadilla

address: Solnavägen 9

country: Sweden

institute: Karolinska Institutet

description:
mRNA
scRNAseq_Filtered_gene_bc_matrices.csv
scRNAseq_ALL_MGandFibro_filtered_metadata.csv

data_processing:
Alignment with CellRanger ATAC, CellRanger or Bowtie2. Trimming and deduplication with Samtools. BAM coverage to generate cpm bigwig files with deeptools.
Genome_build: mm10
Supplementary_files_format_and_content: tables and bigwig

source_name: spinal cord

extract_protocol:
tissue digestion and flow cytometry
Illumina

tag: strain background

tag: cells

value: ependymal

tag: method


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H11_AD001_indexed


title: WT_B_T1pos_2

description: Tim-1+ B cell


title: WT_B_T1pos_1

description: Tim-1+ B cell


title: scRNAseq_Foxj1_tdT_4wpi


title: genomic DNA from peripheral blood leukocytes 812

tag: tissue


title: scRNAseq_Foxj1_Olig2_tdT_Uninj


title: genomic DNA from peripheral blood leukocytes 813

tag: gender


title: scRNAseq_Foxj1_Olig2_tdT_2wpi


title: WT_B_T1neg_2

description: Tim-1- B cell


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G8_AD012_indexed


title: genomic DNA from peripheral blood leukocytes 818

tag: age(yrs)


title: scRNAseq_Foxj1_tdT_Uninj


title: scRNAseq_Foxj1_tdT_2wpi


title: genomic DNA from peripheral blood leukocytes 811

tag: systolic blood pressure (mmhg)


title: genomic DNA from peripheral blood leukocytes 814

tag: diastolic blood pressure (mmhg)


title: ATACseq_Foxj1_tdT_1dpi_rep2

description:
chromatin
Foxj1_tdT_1dpi_rep2.bigwig


title: genomic DNA from peripheral blood leukocytes 810


title: WT_B_T1neg_1

description: Tim-1- B cell


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H10_AD007_indexed

tag: brain region


title: ATACseq_Foxj1_tdT_Uninj_rep1

description:
chromatin
Foxj1_tdT_Uninj_rep1.bigwig


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H10_AD008_indexed

tag: Sex


title: ATACseq_Foxj1_Olig2_tdT_1dpi_rep2

description:
chromatin
Foxj1_Olig2_tdT_1dpi_rep2.bigwig


title: ATACseq_Foxj1_tdT_Uninj_rep2

description:
chromatin
Foxj1_tdT_Uninj_rep2.bigwig


title: ATACseq_Foxj1_Olig2_tdT_Uninj_rep2

description:
chromatin
Foxj1_Olig2_tdT_Uninj_rep2.bigwig


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H11_AD012_indexed

tag: age


title: genomic DNA from peripheral blood leukocytes 809


title: genomic DNA from peripheral blood leukocytes 808


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G9_AD008_indexed

tag: strain


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H10_AD012_indexed


title: ATACseq_Foxj1_Olig2_tdT_5dpi_rep2

description:
chromatin
Foxj1_Olig2_tdT_5dpi_rep2.bigwig


title: genomic DNA from peripheral blood leukocytes 807


title: ATACseq_Foxj1_Olig2_tdT_Uninj_rep1

description:
chromatin
Foxj1_Olig2_tdT_Uninj_rep1.bigwig


title: ATACseq_Foxj1_tdT_1dpi_rep1

description:
chromatin
Foxj1_tdT_1dpi_rep1.bigwig


title: genomic DNA from peripheral blood leukocytes 805


title: ATACseq_Foxj1_Olig2_tdT_5dpi_rep1

description:
chromatin
Foxj1_Olig2_tdT_5dpi_rep1.bigwig


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G9_AD007_indexed


title: genomic DNA from peripheral blood leukocytes 806


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H10_AD001_indexed


title: ATACseq_Foxj1_tdT_5dpi_rep2

description:
chromatin
Foxj1_tdT_5dpi_rep2.bigwig


title: ATACseq_Foxj1_tdT_5dpi_rep1

description:
chromatin
Foxj1_tdT_5dpi_rep1.bigwig


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G9_AD006_indexed


title: RNAseq_Foxj1_tdT_Uninj_rep2

description:
mRNA
Normalized_counts_Foxj1_tdt_Foxj1_Olig2_tdT_Uninj_1dpi_5dpi_RNAseq


title: RNAseq_Foxj1_Olig2_tdT_5dpi_rep2


title: genomic DNA from peripheral blood leukocytes 803


title: ATACseq_Foxj1_Olig2_tdT_1dpi_rep1

description:
chromatin
Foxj1_Olig2_tdT_1dpi_rep1.bigwig


title: genomic DNA from peripheral blood leukocytes 801


title: genomic DNA from peripheral blood leukocytes 800


title: RNAseq_Foxj1_Olig2_tdT_5dpi_rep1


title: RNAseq_Foxj1_Olig2_tdT_Uninj_rep2


title: RNAseq_Foxj1_tdT_5dpi_rep2


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H10_AD010_indexed


title: RNAseq_Foxj1_tdT_1dpi_rep2


title: RNAseq_Foxj1_tdT_5dpi_rep1


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G8_AD006_indexed


title: RNAseq_Foxj1_tdT_Uninj_rep1


title: genomic DNA from peripheral blood leukocytes 797


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G9_AD002_indexed


title: RNAseq_Foxj1_Olig2_tdT_1dpi_rep1


title: genomic DNA from peripheral blood leukocytes 796


title: RNAseq_Foxj1_tdT_1dpi_rep1


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G9_AD004_indexed


title: RNAseq_Foxj1_Olig2_tdT_Uninj_rep1


title: sg-kiaa1522 rep3

city: Shanghai

first: Boshi

last: Wang

address: No.800 Dongchuan Road

country: China

institute: Shanghai Cancer Institute

data_processing:
Clean data was generated by trimming the adaptor and filtering rRNAs using Seqtk (https://github.com/lh3/seqtk)
Clean reads were mapped to mouse genome (GRCm38) with Hisat2(version:2.0.4)
The uniquely mapped fragments of genes were counted by Stringtie(version:1.3.0).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include counts for each gene in each sample

source_name: Mouse lung

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina

value: Lung

tag: cell line


title: genomic DNA from peripheral blood leukocytes 795

value: peripheral blood leukocytes


title: genomic DNA from peripheral blood leukocytes 793

value: M


title: sg-kiaa1522 rep2


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G8_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G8_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G7_AD012_indexed


title: sg-con rep3

value: control


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_H10_AD002_indexed

value: SSp


title: RNAseq_Foxj1_Olig2_tdT_1dpi_rep2


title: scATACseq_non_neuronal_Uninjured_spinal cord

description:
chromatin
sc_atac_barcodes.tsv
sc_atac_filtered_metadata.csv
sc_atac_matrix.mtx
sc_atac_peaks.tsv


title: sg-con rep1


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G7_AD008_indexed

value: male


title: genomic DNA from peripheral blood leukocytes 799


title: Tbx4_Tsc2WT_mesenchyme_2

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

data_processing:
Fastq files were align to the mm9 reference genome using STAR and default parameters
Ensmebl v67 gene annotations were used for gene counts, gene counts were obtain using STAR
Raw gene counts were transformed using 'LIMMA-Voom' method
Genome_build: mm9
Supplementary_files_format_and_content: Voom transformed abundance measurements

source_name: CD45-EpCAM-CD31- PDPN- bead sorted Tbx4CreTsc2WT mouse lung total mesenchymal cells

extract_protocol: Total RNA was isolated from all cell subpopulations and subjected to the bulk mRNA sequencing using Illumina HiSeq2500.

tag: age (weeks)

tag: genotype

value: WildType

value: Female


title: genomic DNA from peripheral blood leukocytes 791


title: sg-con rep2


title: Tbx4_Tsc2WT_mesenchyme_3


title: genomic DNA from peripheral blood leukocytes 789

value: F


title: genomic DNA from peripheral blood leukocytes 788


title: Tbx4_Tsc2WT_mesenchyme_1


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G7_AD010_indexed


title: Tbx4_Tsc2KO_mesenchyme_3

source_name: CD45-EpCAM-CD31- PDPN- bead sorted Tbx4CreTsc2KO mouse lung total mesenchymal cells


title: genomic DNA from peripheral blood leukocytes 787

source_name: peripheral blood leukocytes


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G8_AD007_indexed

source_name: C57BL/6J Male P56 Mouse Brain


title: Tbx4_Tsc2KO_mesenchyme_1


title: genomic DNA from peripheral blood leukocytes 786


title: Tbx4_Tsc2WT_PDPN_3

source_name: CD45-EpCAM-CD31- PDPN+ bead sorted Tbx4CreTsc2WTmouse lung lymphatic endothelial cells


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G7_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G7_AD001_indexed


title: sg-kiaa1522 rep1


title: genomic DNA from peripheral blood leukocytes 785


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G7_AD007_indexed


title: Tbx4_Tsc2WT_PDPN_2


title: Tbx4_Tsc2KO_PDPN_3

source_name: CD45-EpCAM-CD31- PDPN+ bead sorted Tbx4CreTsc2KO mouse lung lymphatic endothelial cells


title: Tbx4_Tsc2WT_PDPN_1


title: genomic DNA from peripheral blood leukocytes 784


title: Tbx4_Tsc2KO_PDPN_1


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G6_AD006_indexed


title: Tbx4_Tsc2KO_PDPN_2


title: Tbx4_Tsc2WT_Cd31_3

source_name: CD45-EpCAM-CD31+ bead sorted Tbx4CreTsc2WT mouse lung vascular endothelial cells


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G5_AD008_indexed


title: genomic DNA from peripheral blood leukocytes 781


title: Tbx4_Tsc2WT_Cd31_1


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G7_AD002_indexed


title: Tbx4_Tsc2WT_Cd31_2


title: genomic DNA from peripheral blood leukocytes 780


title: Tbx4_Tsc2KO_Cd31_2

source_name: CD45-EpCAM-CD31+ bead sorted Tbx4CreTsc2KO mouse lung vascular endothelial cells


title: Tbx4_Tsc2KO_Cd31_3


title: Tbx4_Tsc2KO_Cd31_1


title: genomic DNA from peripheral blood leukocytes 779


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G5_AD012_indexed


title: Tbx4_Tsc2WT_Epcam_2

source_name: CD45-EpCAM+ bead sorted Tbx4CreTsc2WT mouse lung total epitheilal cells


title: Tbx4_Tsc2WT_Epcam_3


title: Tbx4_Tsc2WT_Epcam_1


title: genomic DNA from peripheral blood leukocytes 778


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G5_AD007_indexed


title: Tbx4_Tsc2KO_Epcam_3

source_name: CD45-EpCAM+ bead sorted Tbx4CreTsc2KO mouse lung total epitheilal cells


title: genomic DNA from peripheral blood leukocytes 783


title: genomic DNA from peripheral blood leukocytes 775


title: Tbx4_Tsc2KO_Epcam_1


title: genomic DNA from peripheral blood leukocytes 774


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G6_AD002_indexed


title: Tbx4_Tsc2WT_Cd45_3

source_name: CD45+ bead sorted Tbx4CreTsc2WT mouse lung total immune cells


title: Tbx4_Tsc2KO_Epcam_2


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G6_AD010_indexed


title: Tbx4_Tsc2WT_Cd45_2


title: genomic DNA from peripheral blood leukocytes 773


title: Tbx4_Tsc2KO_Cd45_3

source_name: CD45+ bead sorted Tbx4CreTsc2KO mouse lung total immune cells


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G6_AD008_indexed


title: genomic DNA from peripheral blood leukocytes 772


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G6_AD012_indexed


title: Tbx4_Tsc2WT_Cd45_1


title: Tbx4_Tsc2KO_Cd45_2


title: Tbx4_Tsc2KO_Cd45_1


title: genomic DNA from peripheral blood leukocytes 769


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G5_AD004_indexed


title: BTLT3_S2Hoxb1Mu

city: MARSEILLE

first: Sonia

last: Stefanovic

address: 27 BD JEAN MOULIN

country: France

institute: INSERM U1251

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
RNA-Seq reads were aligned using the STAR aligner version 2.5.2
Transcripts abundance was computed using HTSEQ-count 0.9.12 and the background was estimated through read counts from intergenic regions using windows of 5 kb length
Normalisation and differential gene expression analysis between conditions were performed using R (R version 3.3.4) and DESEQ2
Genome_build: mm10
Supplementary_files_format_and_content: The final processed data files is the output of the DESEQ2 package. This file contains the gene name, the base mean , the log2foldchange, the test value, the p-value, the adjusted p-value and the normalized count foreach sample.

molecule: polyA RNA

source_name: Amplified ds cDNA with Ovation V2 Nugen kit

extract_protocol:
SHF was microdissected, flash frozen on dry ice, and RNA was harvested using the NucleoSpin® RNA XS kit
Amplified cDNA was prepared from 2 ng of total RNA using the Ovation RNA-seq system V2 (NuGEN Technologies, Inc.) following manufacturer's instructions. Briefly, first-strand cDNA was prepared from total RNA using a combination of random and poly-T DNA/RNA chimeric SPIA primers and reverse transcriptase, resulting in a cDNA/mRNA hybrid molecule. Priming sites created by a heating fragmentation of the mRNA within the cDNA/mRNA complex were used to synthesize the second strand cDNA using a DNA polymerase. The resulting double-stranded cDNA with a unique RNA/DNA heteroduplex at one end was purified using Agencourt RNAClean XP beads (Beckman Coulter Inc.). The purified product was then used as the substrate of a linear amplification process, SPIA (single primer isothermal amplification). During the amplification step, RNase H degrades RNA in DNA/RNA heteroduplex at the 5'end of the first cDNA strand, creating a binding site for the DNA/RNA SPIA chimeric primer, then DNA polymerase starts replication at the 3'end of the primer displacing the existing forward strand. The process including SPIA DNA/RNA primer binding, DNA replication, strand displacement and RNA degradation is repeated and results in rapid generation of microgram quantities of amplified cDNA. Amplified cDNA was purified using AMPure XP beads (Beckman Coulter Inc.) and 500 ng was fragmented by sonication using a Covaris E210 instrument (with duty cycle: 10X, intensity: 5 and cycle/burst: 200 for 180 seconds).    The next steps of RNA-Seq Library preparation were performed using Ovation Ultralow Library System kit (NuGEN Technologies, Inc.) according to manufacturer's instructions. Briefly, in this system 100 ng of amplified cDNA were blunted, phosphorylated and ligated to indexed adapter dimers. The libraries were then enriched by PCR amplification (2 min at 72 degrees Celsius; [30 sec at 94 degrees Celsius, 30 sec at 60 degrees Celsius, 1 min at 72 degrees Celsius] x 6 cycles; 5 min at 72 degrees Celsius) and surplus PCR primers were removed by purification using AMPure XP beads. DNA libraries were checked for quality using 2100 Bioanalyzer (Agilent) and quantified using Kapa Sybr Fast Light Cycler 480 qPCR Kit  (Kapa Biosystems) following manufacturer's instructions.

value: second heart field region

tag: Stage


title: Tbx4_Tsc2KO_mesenchyme_2


title: BTLT4_S2Hoxb1Mu


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G5_AD002_indexed


title: BTLT2_S1WT

value: WT


title: genomic DNA from peripheral blood leukocytes 768


title: S-30-A rep1

city: Nanjing

first: Xiannan

last: Meng

address: Hankou Road 22

institute: Nanjing University

description: miRNA.txt, piRNA.txt

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data)
The reference genomes and the annotation file were downloaded from MM10. Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
Mapping reads to mature miRNA and hairping which recorded in miRBase (release 21) to identiy known-miRNA. After excluded the reads mapped to known miRNA/ncRNA/repeat region/mRNA region, the remaining reads were used to predict novel miRNA, the keys of prediction is hairping structure and stability. The software for identification and prediction is miRDeep2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: testis

extract_protocol:
testes were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.NEBNext® Ultra™ RNA Library Prep Kit for Illumina®（ #E7530L， NEB） was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina

value: Balb/c

value: post natal six month

tag: treatment

value: 30 ug/L MC-LR exposure)


title: genomic DNA from peripheral blood leukocytes 767


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G5_AD001_indexed


title: S-30-B rep2

description: miRNA.txt, piRNA.txt


title: S-con-B rep2

description: miRNA.txt, piRNA.txt


title: genomic DNA from peripheral blood leukocytes 764


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G7_AD006_indexed


title: S-con-A rep1

description: miRNA.txt, piRNA.txt


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G4_AD006_indexed


title: genomic DNA from peripheral blood leukocytes 762


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G4_AD010_indexed


title: PEC2_46

city: SAO PAULO

first: Robson

middle: José de

last: Almeida

state: SAO PAULO

address: RUA VERGUEIRO 235 249

department: Pós Graduação Stricto Sensu em Medicina

country: Brazil

institute: Universidade Nove de Julho

data_processing:
The alignment was made by ION S5 default protocol.
We made a conversion from .bam to fastq through 'samtools fastq'.
The compression to bz2 was made through bzip2.
Genome_build: hg18 (NCBI36)
Supplementary_files_format_and_content: Matrix_Pregnant_CTL_versus_Pregnant_Pre_Eclampsia.xlsx: Excel file containing the reads of each sample.

source_name: whole blood

extract_protocol:
The venous blood was collected in PAXgene Blood RNA tube and extracted with the PAXgene Blood RNA Kit.
Ion AmpliSeq Transcriptome Human Gene Expression Kit Catalog Number A26325, A26326, and A26327.

tag: diagnosis

value: Preeclamptic

value: Whole blood

tag: gestational age

tag: tsh

tag: sbp

tag: dbp


title: CTL_44

description: Matrix_Pregnant_CTL_versus_Pregnant_Pre_Eclampsia.xlsx

value: Healthy pregnancy

tag: tissue


title: PEC3_47


title: CTL_43


title: PEC4_48


title: genomic DNA from peripheral blood leukocytes 759

tag: gender

tag: age(yrs)

tag: systolic blood pressure (mmhg)


title: BTLT1_S1WT


title: genomic DNA from peripheral blood leukocytes 758

tag: diastolic blood pressure (mmhg)


title: genomic DNA from peripheral blood leukocytes 765


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G4_AD004_indexed

tag: brain region

tag: Sex

tag: age


title: OXY-KLH_1B11_11_S10

city: MINNEAPOLIS

first: Marco

last: Pravetoni

state: Minnesota

address: NILS HASSELMO HALL, 312 CHURCH ST SE, NILS HASSELMO HALL

department: Pharmacology

institute: University of Minnesota

data_processing:
Raw sequence that passed CASAV 1.8P/F filter were assessed by fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Read mapping was performed via hisat2 (2.1.0) using the mouse genome (mm10) as a reference.
Counts were quantified via Feature counts (Subread Package).
Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen, Redwood city, CA) using raw read counts.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

source_name: Vaccine with IL-4 depletion_Activated T cells from spleen/LN

extract_protocol:
RNA was extracted using the RNAeasy Kit from Qiagen
RNA libraries were prepared for sequencing using Takara Pico Mammalian (ribo-depletion) protocols

treatment_protocol: Mice were injected with 0.5 mg of an IL-4 depleting antibody or saline i.p on days -2 and 1. Mice were immunized with sKLH or OXY-sKLH on day 0. Spleen and lymph nodes were harvested on day 7 and immediately processed for cell sorting.

tag: strain

value: Vaccine with IL-4 depletion (OXY-sKLH +αIL-4 mAb, clone 11b11)

tag: cell type

value: Activated T cells from spleen/lymph nodes


title: OXY-KLH_11B11_12


title: genomic DNA from peripheral blood leukocytes 757

value: peripheral blood leukocytes

value: M


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G4_AD008_indexed

value: SSp


title: OXY-KLH_11B11_9_S8

value: male


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G3_AD010_indexed


title: genomic DNA from peripheral blood leukocytes 756


title: genomic DNA from peripheral blood leukocytes 763


title: OXY-KLH8_S7

source_name: Vaccine_Activated T cells from spleen/LN

value: Vaccine (OXY-sKLH)


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G4_AD002_indexed


title: CTL_41


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G5_AD010_indexed


title: OXY-KLH6_S5


title: OXY-KLH5_S4


title: OXY-KLH_11B11_10_S9


title: KLH4_S3

source_name: control_Activated T cells from spleen/LN

value: control (sKLH carrier protein)


title: PEC1_45


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G3_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G3_AD012_indexed


title: KLH2_S1


title: genomic DNA from peripheral blood leukocytes 752

value: F


title: KLH3_S2


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G3_AD006_indexed


title: genomic DNA from peripheral blood leukocytes 754


title: genomic DNA from peripheral blood leukocytes 746


title: genomic DNA from peripheral blood leukocytes 745


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G2_AD001_indexed


title: genomic DNA from peripheral blood leukocytes 749


title: genomic DNA from peripheral blood leukocytes 743


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G2_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G3_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G2_AD008_indexed


title: genomic DNA from peripheral blood leukocytes 741


title: genomic DNA from peripheral blood leukocytes 742


title: genomic DNA from peripheral blood leukocytes 739


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G2_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G2_AD006_indexed


title: genomic DNA from peripheral blood leukocytes 737


title: genomic DNA from peripheral blood leukocytes 736


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G2_AD004_indexed


title: rag_bulk_3

city: Hamburg

first: Krystian

middle: Daniel

last: Fita

address: Martinistrasse 52

department: Department of Neurosurgery

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description:
replicate 3
mm_15

data_processing:
Sequencing reads were aligned to the mouse reference assembly (GRCm38.87) using STAR version 2.5.2b (https://github.com/alexdobin/STAR/releases)
Differential expression analysis was carried out using DESeq2 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html)
Genome_build: GRCm38.87

source_name: ex vivo GL261 tumor

growth_protocol: GL261 cells were propagated in DMEM containing 4.5 g/L glucose, 4 mM L-Glutamine, and 1 mM pyruvate (31966-021, Gibco), supplemented with 10% fetal bovine serum, 25 mM HEPES, 100 U/mL, penicillin, and 100 mg/mL streptomycin.

extract_protocol:
RNA was extracted using Nucelospin columns and quantified by the Agilent Bioanalyser RNA 6000 kit.
All samples were sequenced in the genomic core facility of Münster University on a NextSeq 500 v2 sequencer, using the NEBNext mRNA isolation module and NEBNext RNA Ultra directional library prep kit.

treatment_protocol: Tumors were excised from symptomatic mice (C57BL/6 WT or Pfp/Rag2-/-, 6 mice each) previously injected with GL261 GFP+ cells. Single cell suspensions were obtained by collagenase digestion (1.5 mg/mL, Biochrom). After filtration and washing, the cells were sorted using a BD FACSAria IIIu cell sorter into GFP+ tumor cells and GFP- non-tumor cells. These samples were compared to bulk unsorted cells that contained both populations and to GL261 in vitro cultured cells used for mice injection (all in triplicate).

tag: genotype

value: Pfp/Rag2 -/-

tag: cells sorted by facs before rna extraction

value: no

tag: sorted cell population

tag: cell line

value: GL261 GFP


title: rag_bulk_2

description:
replicate 2
mm_14


title: in_vitro_GFP_1

description:
replicate 1
mm_34

source_name: in vitro cell culture

value: yes

value: GFP positive


title: genomic DNA from peripheral blood leukocytes 734

first: Minjung

last: Kho

address: School of Public Health University of Michigan 1415 Washington Heights

institute: University of Michigan

data_processing: For each chip, the Minfi R package was used to perform background correction and normalization. The regression on correlated probes (RCP) method was then used to adjust probe-type bias, and ComBat was used to remove confounding effects due to batch or other technical covariates. Data from the two platforms were combined, and ComBat was used to remove the platform effect. Age, gender, and phase effect was preserved when removing platform difference.

source_name: peripheral blood leukocytes

extract_protocol: genomic DNA was extracted from stored peripheral blood leukocytes using AutoGen FlexStar (AutoGen, Holliston, MA) and DNA was bisulfite converted using the EZ DNA Methylation Kit (Zymo Research, Irvine, CA)


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G3_AD008_indexed

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

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

source_name: C57BL/6J Male P56 Mouse Brain

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


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G2_AD002_indexed


title: genomic DNA from peripheral blood leukocytes 733


title: wt_bulk_3

description:
replicate 3
mm_12

value: WT


title: rag_bulk_1

description:
replicate 1
mm_13


title: wt_bulk_2

description:
replicate 2
mm_11


title: genomic DNA from peripheral blood leukocytes 738


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G4_AD012_indexed


title: rag_GFP_p3

description:
replicate 3
mm_9


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G1_AD008_indexed


title: rag_GFP_p1

description:
replicate 1
mm_7


title: genomic DNA from peripheral blood leukocytes 731


title: in_vitro_GFP_2

description:
replicate 2
mm_35


title: in_vitro_GFP_3

description:
replicate 3
mm_36


title: rag_GFP_p2

description:
replicate 2
mm_8


title: genomic DNA from peripheral blood leukocytes 732


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G2_AD012_indexed


title: wt_GFP_p3

description:
replicate 3
mm_6


title: genomic DNA from peripheral blood leukocytes 728


title: genomic DNA from peripheral blood leukocytes 727


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G1_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G1_AD012_indexed


title: wt_non_p3

description:
replicate 3
mm_3

value: GFP negative


title: wt_GFP_p2

description:
replicate 2
mm_5


title: wt_non_p2

description:
replicate 2
mm_2


title: genomic DNA from peripheral blood leukocytes 726


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G1_AD002_indexed


title: wt_bulk_1

description:
replicate 1
mm_10


title: wt_non_p1

description:
replicate 1
mm_1


title: genomic DNA from peripheral blood leukocytes 724


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G1_AD001_indexed


title: Batf3 stimulated 3

city: Würzburg

first: Wolfgang

last: Kastenmüller

address: Versbacher Str. 9

institute: University of Wuerzburg

data_processing:
Demultiplexed FASTQ files were generated and reads were quality filtered with the local run manager software from Illumina version 2.2.0.
Sequenced reads were trimmed for adaptor sequence, then mapped to GRCm38.98 whole genome using STAR aligner version 2.7 with default parameters.
Raw counts were generated using featureCounts from the Rsubread R package.
Genome_build: GRCm38.98
Supplementary_files_format_and_content: tab-delimited text files include non-normalized counts values for each sample, including gene_id, Ensembl ID and biotype for each gene.

source_name: Batf3 stimulated

extract_protocol:
RNeasy Mini Kit (Qiagen) following manufactures instruction.
DNA libraries suitable for sequencing were prepared from 100 ng of total RNA with oligo-dT capture beads for poly-A-mRNA enrichment using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) according to manufacturer’s instructions. After 15 cycles of PCR amplification, the size distribution of the barcoded DNA libraries was estimated ~320 bp by electrophoresis on Agilent High Sensitivity Bioanalyzer microfluidic chips

treatment_protocol: Cells were transduced with control or Batf3 containing vector, sorted for succesfully transduced cells and either left non-stimulated for 6h or coincubated with 1 μg/ml plate-bound anti-CD3e (clone 2C11) plus 1 μg/ml anti-CD28 Abs (clone 37.51, both BioXCell)

tag: strain background

value: TCR transgenic OT-I mouse

value: spleen

value: CD8 T cells

tag: vector

value: Batf3 expressing vector

tag: treatment

value: plus anti-CD3/CD28 (1ug/ml) (stimulated)


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G11_AD007_indexed

value: SSp


title: genomic DNA from peripheral blood leukocytes 723

tag: tissue

value: peripheral blood leukocytes


title: genomic DNA from peripheral blood leukocytes 721

tag: gender

value: M


title: Batf3 non-stimulated 2

source_name: Batf3 non-stimulated

value: IL-15 (100ng/ml) (non-stimulated)


title: Batf3 non-stimulated 3


title: OXY-KLH7_S6

value: Balb/c

value: male

value: Vaccine (OXY-sKLH)

value: Activated T cells from spleen/lymph nodes


title: Batf3 stimulated 1


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G1_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G12_AD008_indexed


title: Batf3 non-stimulated 1


title: genomic DNA from peripheral blood leukocytes 719

value: F

tag: age(yrs)


title: ctrl. stimulated 3

source_name: ctrl. stimulated

value: control


title: genomic DNA from peripheral blood leukocytes 718

tag: systolic blood pressure (mmhg)


title: ctrl. non-stimulated 3

source_name: ctrl. non-stimulated


title: ctrl. stimulated 1


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G12_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G12_AD004_indexed


title: genomic DNA from peripheral blood leukocytes 717

tag: diastolic blood pressure (mmhg)


title: ctrl. non-stimulated 2


title: Batf3 stimulated 2


title: genomic DNA from peripheral blood leukocytes 715


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G12_AD001_indexed

tag: brain region


title: genomic DNA from peripheral blood leukocytes 711


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G11_AD010_indexed

tag: Sex


title: genomic DNA from peripheral blood leukocytes 709


title: wt_GFP_p1

description:
replicate 1
mm_4

value: WT

value: yes

value: GFP positive

value: GL261 GFP


title: genomic DNA from peripheral blood leukocytes 707


title: genomic DNA from peripheral blood leukocytes 705


title: CTL_42

tag: diagnosis

value: Healthy pregnancy

value: Whole blood

tag: age

tag: gestational age

tag: tsh

tag: sbp

tag: dbp


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G11_AD006_indexed

tag: strain


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G12_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G12_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G10_AD007_indexed


title: ctrl. stimulated 2

tag: strain background

value: TCR transgenic OT-I mouse

value: spleen

tag: cell type

value: CD8 T cells

value: plus anti-CD3/CD28 (1ug/ml) (stimulated)


title: genomic DNA from peripheral blood leukocytes 704

value: peripheral blood leukocytes

value: M


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G11_AD008_indexed

value: SSp

value: male


title: genomic DNA from peripheral blood leukocytes 701


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G10_AD010_indexed


title: genomic DNA from peripheral blood leukocytes 700


title: ctrl. non-stimulated 1

tag: vector

tag: treatment

value: IL-15 (100ng/ml) (non-stimulated)


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G10_AD012_indexed


title: genomic DNA from peripheral blood leukocytes 697

tag: tissue

tag: gender

value: F


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G10_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G11_AD001_indexed


title: genomic DNA from peripheral blood leukocytes 694

tag: age(yrs)

tag: systolic blood pressure (mmhg)


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F9_AD012_indexed

tag: brain region


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G1_AD010_indexed

tag: Sex


title: genomic DNA from peripheral blood leukocytes 693

tag: diastolic blood pressure (mmhg)


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G11_AD004_indexed

tag: age


title: genomic DNA from peripheral blood leukocytes 692


title: genomic DNA from peripheral blood leukocytes 691


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F9_AD010_indexed


title: genomic DNA from peripheral blood leukocytes 688


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F9_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G3_AD004_indexed


title: genomic DNA from peripheral blood leukocytes 702


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F9_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F9_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G10_AD001_indexed


title: genomic DNA from peripheral blood leukocytes 695


title: genomic DNA from peripheral blood leukocytes 684


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F9_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F8_AD012_indexed


title: genomic DNA from peripheral blood leukocytes 682


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F8_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F9_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F8_AD008_indexed


title: genomic DNA from peripheral blood leukocytes 690


title: genomic DNA from peripheral blood leukocytes 678


title: genomic DNA from peripheral blood leukocytes 687


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F8_AD006_indexed


title: I5IER5-72h rep1

first: Li

last: Pan

address: 77 Ave Louis Pasteur

institute: Brigham and Women's Hospital

description:
I5/IER5 (I5 cells with IER5 added back)
two runs for all 36 RNA-seq library samples

data_processing:
Reads were trimmed with Trim Galore (v.0.3.7 using cutadapt v.1.8), assessed for quality with FastQC (v.0.11.3), and aligned to GRCh38/hg38 using gencode release 27 annotations and STAR (v.2.5.3a)
Raw counts from two sequencing runs were loaded into R, summed, and filtered to exclude transcripts with <0.5 reads per million mapped before performing differential expression (DE) analysis with edgeR (v.3.16.5) and RUVSeq (v.1.8.0)
Genome_build: hg38
Supplementary_files_format_and_content: Excel file with raw counts of every gene and every sample

source_name: Squamous cell carcinoma (SCC) cells

extract_protocol:
Total RNA was prepared with Trizol (Life Technology) and RNeasyMini columns (Qiagen).
RNA libraries were constructed using the NEBNext Ultra II RNALibrary Prep kit (New England BioLab).

treatment_protocol: GSI washout was performed for 4h, 24h and 72 hours.

value: SCC IC8 cells

tag: cell line

tag: genotype

value: I5 cells with IER5 added back

value: GSI washout for 72h


title: I5-72h rep3

description:
I5 (SC2 cells with IER5 deleted by Crispr)
two runs for all 36 RNA-seq library samples

value: SC2 cells with IER5 deleted by Crispr


title: genomic DNA from peripheral blood leukocytes 677


title: genomic DNA from peripheral blood leukocytes 676


title: I5IER5-72h rep2


title: genomic DNA from peripheral blood leukocytes 683


title: I5-72h rep2


title: genomic DNA from peripheral blood leukocytes 755


title: SC2-72h rep3

description:
SC2/cV (wild-type cells with control vector)
two runs for all 36 RNA-seq library samples

value: wild-type cells with control vector


title: I5IER5-72h rep3


title: genomic DNA from peripheral blood leukocytes 674


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F8_AD001_indexed


title: SC2-72h rep1


title: genomic DNA from peripheral blood leukocytes 673


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F7_AD012_indexed


title: I5IER5-24h rep3

value: GSI washout for 24h


title: SC2-72h rep2


title: genomic DNA from peripheral blood leukocytes 672


title: I5IER5-24h rep2


title: I5IER5-24h rep1


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F7_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F7_AD007_indexed


title: I5-24h rep2


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F8_AD004_indexed


title: I5-72h rep1


title: genomic DNA from peripheral blood leukocytes 669


title: I5-24h rep1


title: SC2-24h rep3


title: SC2-24h rep2


title: genomic DNA from peripheral blood leukocytes 667


title: SC2-24h rep1


title: genomic DNA from peripheral blood leukocytes 665


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_G10_AD006_indexed


title: I5IER5-4h rep1

value: GSI washout for 4h


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F6_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F7_AD002_indexed


title: I5IER5-4h rep3


title: I5IER5-4h rep2


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F6_AD010_indexed


title: I5-4h rep3


title: genomic DNA from peripheral blood leukocytes 663


title: I5-24h rep3


title: I5-4h rep2


title: genomic DNA from peripheral blood leukocytes 664


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F6_AD008_indexed


title: I5-4h rep1


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F6_AD007_indexed


title: SC2-4h rep3


title: genomic DNA from peripheral blood leukocytes 670


title: genomic DNA from peripheral blood leukocytes 661


title: I5IER5-0h rep3

value: GSI (Compound E 1 microM)


title: SC2-4h rep1


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F6_AD006_indexed


title: genomic DNA from peripheral blood leukocytes 660


title: I5IER5-0h rep2


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F6_AD004_indexed


title: I5IER5-0h rep1


title: genomic DNA from peripheral blood leukocytes 659


title: I5-0h rep3


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F6_AD001_indexed


title: genomic DNA from peripheral blood leukocytes 656


title: genomic DNA from peripheral blood leukocytes 655


title: I5-0h rep1


title: SC2-0h rep2


title: SC2-0h rep3


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F5_AD012_indexed


title: genomic DNA from peripheral blood leukocytes 652


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F5_AD008_indexed


title: I5-0h rep2


title: genomic DNA from peripheral blood leukocytes 654


title: MCF10A siNT  RNAPII ChIP-seq

city: New Haven

first: Susan

middle: J

last: Baserga

state: CT

address: 333 Cedar St., SHM C114

institute: Yale University

data_processing:
Data analysis was completed by Active Motif.
Reads were aligned to the hg38 reference genome. Tags were normalized by random sampling to the sample with the smallest number of unique alignments without duplicate reads.
Peak calling was performed using SICER 1.1 with a FDR of 1x10-10 and a gap size of 600 base pairs.
Genes were considered differentially occupied if the fold change was ≥ 2 or ≤ -2, and the max tags (5’ ends of aligned reads) value was ≥ 150.
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text file including RNAPII differential occupancy information (log2 fold change), max tags, and Sicer peak calling analysis for all genes for both the siPAX9 and siNT samples

source_name: MCF10A cells

growth_protocol: MCF10A cells (ATCC CRL-10317) were grown in Dulbecco’s modified Eagle’s medium/Nutrient mixture F-12 (DMEM-F12, Gibco 1130-032) supplemented with 5% horse serum (Gibco 16050), 20 ng/mL epidermal growth factor (Sigma E4127), 0.5 μg/mL hydrocortisone (Sigma H0135), 100 ng/mL Cholera toxin (Sigma C8052), and 10 μg/mL insulin (Sigma I1882) at 37 °C in a humidified incubator with 5% CO2.

extract_protocol:
MCF10A cells were fixed in 10% fixing solution (11% formaldehyde, 0.1 M NaCl, 1 mM EDTA (pH 8.0), and 50 mM HEPES (pH 7.9)) for 15 minutes at room temperature. Cross-linking was stopped with 5% v/v 2.5 M glycine at room temperature for 5 minutes. Cells were washed once in PBS-Igepal (0.5%). Cells were washed again in PBS-Igepal (0.5%) with 1 mM PMSF. The cells were centrifuged at 800 x g, the supernatant removed, and the cell pellet was flash frozen on dry ice.
Further steps of the TranscriptionPath RNAPII ChIP-seq protocol were performed by Active Motif. Chromatin immunoprecipitation was completed using an RNAPII antibody (Active Motif, Clone H4B, Cat. No. 39097). Sequencing was performed using the Illumina NextSeq 500 sequencing system with 75 nt sequence reads.

treatment_protocol: siRNA knockdown was performed in 6-well plates with 1x105 cells per well. After 24 hours, siRNAs (30 nM final) were reverse transfected for 72 hours using Lipofectamine® RNAimax as per the manufacturer’s instructions.

value: breast epithelial cells

value: non-targeting siRNAs for 72 hours


title: MCF10A pooled input

value: To control for local copy number changes, equal amounts of unprecipitated genomic DNA from each sample were pooled and used to generate a Next-Generation sequencing library which was sequenced in parallel with the ChIP-Seq samples.


title: MCF10A siPAX9  RNAPII ChIP-seq

value: siRNAs targeting PAX9 for 72 hours


title: genomic DNA from peripheral blood leukocytes 651

city: Ann Arbor

value: peripheral blood leukocytes

value: M


title: SC2-4h rep2


title: PDX1-2_CFSE_High

city: Seoul

first: Ho-Young

last: Lee

address: Gwanak-ro 1

department: College of Pharmacy

country: South Korea

institute: Seoul National University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: NSCLC PDX

growth_protocol: Stained cells were maintained in a humidified atmosphere of 37°C with 5% CO2

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: Cells were stained with 25μM CFSE dye (BioLegend #423801) at 37°C, 20min. Stained cells were quanched with cell culture media, seeded in culture plates and then incubated for 7 days.

tag: cfse dye retain

value: High (upper,>90%)

tag: nsclc cell line or primary cultured cancer cells from nsclc pdx models

value: primary cultured cancer cells from NSCLC PDX


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F5_AD002_indexed

city: La Jolla

value: SSp

value: male

tag: strain


title: genomic DNA from peripheral blood leukocytes 650

value: F


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F5_AD004_indexed


title: PDX1-1_CFSE_High


title: SK-MES-1_CFSE_Low_2

source_name: NSCLC

value: Low (lower, <10%)

value: NSCLC cell line


title: genomic DNA from peripheral blood leukocytes 649


title: SC2-0h rep1

city: Boston

value: SCC IC8 cells

value: wild-type cells with control vector


title: SK-MES-1_CFSE_High_2


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F4_AD008_indexed


title: SK-MES-1_CFSE_High_1


title: genomic DNA from peripheral blood leukocytes 644


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F5_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F4_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F4_AD007_indexed


title: H1299_CFSE_Low_2


title: PDX1-1_CFSE_Low


title: H1299_CFSE_Low_1


title: genomic DNA from peripheral blood leukocytes 643


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F4_AD012_indexed


title: SK-MES-1_CFSE_Low_1


title: genomic DNA from peripheral blood leukocytes 642


title: H460_CFSE_Low_2


title: H1299_CFSE_High_2


title: H460_CFSE_Low_1


title: H1299_CFSE_High_1


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F4_AD006_indexed


title: genomic DNA from peripheral blood leukocytes 641


title: H460_CFSE_High_2


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F7_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F4_AD001_indexed


title: genomic DNA from peripheral blood leukocytes 640


title: H460_CFSE_High_1


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F3_AD012_indexed


title: genomic DNA from peripheral blood leukocytes 638


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F4_AD002_indexed


title: genomic DNA from peripheral blood leukocytes 637


title: genomic DNA from peripheral blood leukocytes 636


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F3_AD007_indexed


title: genomic DNA from peripheral blood leukocytes 634


title: genomic DNA from peripheral blood leukocytes 633


title: H40-cancer

city: Wuhan

first: Chunjiang

last: He

state: Hubei

address: Donghu Road 185

institute: Wuhan University

data_processing:
Sequenced reads were mapped to hg38 whole genome using STAR v2.7.1a.
Counts were calculated by FeatureCounts v1.6.4.
Genome_build: hg38
Supplementary_files_format_and_content: counts.txt

source_name: cancer tissue

extract_protocol:
Total RNA was extracted from  adjacent normal tissues and cancer tissues samples of breast cancer patients, following by rRNA depletion from the total RNA. Then, the RNA was reverse transcribed to cDNA and constructed into a strand-specific library. Illumina hiseq XTen was performed for the sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: source

value: cancer tissue


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F3_AD010_indexed


title: H42-cancer


title: H39-cancer


title: H40-adj

source_name: adjacent normal tissue

value: adjacent normal tissue


title: genomic DNA from peripheral blood leukocytes 631


title: H39-adj


title: H38-cancer


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F2_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F3_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F2_AD010_indexed


title: genomic DNA from peripheral blood leukocytes 632


title: H37-cancer


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F2_AD007_indexed


title: genomic DNA from peripheral blood leukocytes 630


title: genomic DNA from peripheral blood leukocytes 708


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F2_AD006_indexed


title: H36-cancer


title: genomic DNA from peripheral blood leukocytes 627


title: H36-adj


title: H42-adj


title: H40-blood, breast cancer

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Reads were mapped to hg38  whole genome using STAR_2.6.0c.
Using featureCounts v1.6.4 to count the  each exon counts
Genome_build: hg38
Supplementary_files_format_and_content: breast_cancer_blood_counts.txt

source_name: blood

extract_protocol:
Total RNA was extracted from blood samples of breast cancer patients, following by rRNA depletion from the total RNA. Then, the RNA was reverse transcribed to cDNA and constructed into a strand-specific library. Illumina hiseq XTen was performed for the sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: individual

value: patient H40

tag: disease state

value: breast cancer

value: blood


title: H42-blood, breast cancer

value: patient H42


title: H39-blood, breast cancer

value: patient H39


title: genomic DNA from peripheral blood leukocytes 625

value: peripheral blood leukocytes


title: H38-adj


title: H38-blood, breast cancer

value: patient H38


title: genomic DNA from peripheral blood leukocytes 623


title: genomic DNA from peripheral blood leukocytes 622

value: M


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F2_AD002_indexed

value: SSp


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F1_AD012_indexed

value: male


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F1_AD010_indexed


title: H37-blood, breast cancer

value: patient H37


title: H36-blood, breast cancer

value: patient H36


title: H37-adj


title: genomic DNA from peripheral blood leukocytes 620

value: F


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F2_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F1_AD008_indexed


title: genomic DNA from peripheral blood leukocytes 618


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F2_AD004_indexed


title: genomic DNA from peripheral blood leukocytes 626


title: lncRNA profile of case96N

city: GZ

first: Rui-qi

last: WANG

state: Guangdong

address: 651 DONGFENG EAST ROAD, GUANGZHOU 510060, P. R. CH

department: state key lab

institute: SUN YAN-SEN UNIVERSITY CANCER CENTER

description: The microarray was used to acquire lncRNA expression profiles of 2412 lncRNAs.

hyb_protocol: The labeled RNAs were hybridized to the array with a 1×hybridization solution (5× Denhart’s solution, 0.5% SDS, 5× SSC) in a Hybridization Chamber (Corning Inc, Corning, NY, USA) at 46°C for 12 to 16 hours.

scan_protocol: Scanned in a LuxScanTM -10K Scanner (capitalBio Inc.,Beijing, China).

data_processing: Quantile normalization across multiple arrays,GPR normailization software, log 2 transformation of expression levels was used.

source_name: non-small-cell lung cancer

label_protocol: 2.5 μg of total RNA of intrahepatic cholangiocarcinoma/normal intrahepatic bile duct tissue was employed with 100 nmol/L of pCp-DY647 (Dharmacon, Lafayette, CO, USA) and 15 Units of T4 RNA ligase (USB, Cleveland, Oh, USA) in a total reaction volume of 20 µL at 16°C overnight

extract_protocol: Total RNA was extracted using an acid phenol/chloroform extraction method followed by ethanol precipitation.

tag: status after 3 years

value: Alive


title: lncRNA profile of case96T


title: lncRNA profile of case82T

value: Dead


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F11_AD006_indexed


title: lncRNA profile of case82N


title: lncRNA profile of case80N


title: lncRNA profile of case80T


title: genomic DNA from peripheral blood leukocytes 616

tag: tissue


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F1_AD004_indexed


title: genomic DNA from peripheral blood leukocytes 615

tag: gender


title: lncRNA profile of case79T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F1_AD002_indexed


title: genomic DNA from peripheral blood leukocytes 612

tag: age(yrs)


title: genomic DNA from peripheral blood leukocytes 611

tag: systolic blood pressure (mmhg)


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F12_AD002_indexed

tag: brain region


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F1_AD001_indexed

tag: Sex


title: lncRNA profile of case791T


title: lncRNA profile of case793T


title: lncRNA profile of case79N


title: genomic DNA from peripheral blood leukocytes 610

tag: diastolic blood pressure (mmhg)


title: lncRNA profile of case786T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F2_AD012_indexed

tag: age


title: lncRNA profile of case78T


title: lncRNA profile of case786N


title: lncRNA profile of case789T


title: lncRNA profile of case784T


title: genomic DNA from peripheral blood leukocytes 607


title: lncRNA profile of case782T


title: genomic DNA from peripheral blood leukocytes 608


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F11_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F12_AD006_indexed


title: genomic DNA from peripheral blood leukocytes 605


title: PDX1-2_CFSE_Low

value: Low (lower, <10%)

value: primary cultured cancer cells from NSCLC PDX


title: lncRNA profile of case781T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F12_AD012_indexed


title: lncRNA profile of case778T


title: lncRNA profile of case776T


title: lncRNA profile of case779T


title: lncRNA profile of case780T


title: genomic DNA from peripheral blood leukocytes 604


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F1_AD006_indexed


title: genomic DNA from peripheral blood leukocytes 603


title: lncRNA profile of case771T


title: lncRNA profile of case776N


title: lncRNA profile of case767N


title: lncRNA profile of case766T


title: lncRNA profile of case765T


title: genomic DNA from peripheral blood leukocytes 600


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F12_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F11_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F11_AD004_indexed


title: lncRNA profile of case764N


title: lncRNA profile of case763T


title: genomic DNA from peripheral blood leukocytes 599


title: lncRNA profile of case75T


title: lncRNA profile of case760T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F11_AD012_indexed


title: lncRNA profile of case768T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F11_AD002_indexed


title: genomic DNA from peripheral blood leukocytes 596


title: lncRNA profile of case759T


title: lncRNA profile of case758T


title: genomic DNA from peripheral blood leukocytes 602


title: lncRNA profile of case757T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F11_AD007_indexed


title: genomic DNA from peripheral blood leukocytes 595


title: lncRNA profile of case757N


title: genomic DNA from peripheral blood leukocytes 601


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F10_AD012_indexed


title: genomic DNA from peripheral blood leukocytes 591


title: lncRNA profile of case753T


title: genomic DNA from peripheral blood leukocytes 597


title: lncRNA profile of case753N


title: genomic DNA from peripheral blood leukocytes 590


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F10_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F10_AD007_indexed


title: genomic DNA from peripheral blood leukocytes 589


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E9_AD008_indexed


title: lncRNA profile of case758N


title: genomic DNA from peripheral blood leukocytes 587


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F10_AD010_indexed


title: lncRNA profile of case756T


title: lncRNA profile of case74N


title: lncRNA profile of case74T


title: lncRNA profile of case752N


title: lncRNA profile of case749T


title: genomic DNA from peripheral blood leukocytes 586


title: genomic DNA from peripheral blood leukocytes 645


title: lncRNA profile of case749N


title: lncRNA profile of case739T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E9_AD012_indexed


title: lncRNA profile of case739N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E9_AD010_indexed


title: genomic DNA from peripheral blood leukocytes 585


title: lncRNA profile of case738T


title: genomic DNA from peripheral blood leukocytes 584


title: lncRNA profile of case728T


title: lncRNA profile of case729T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F10_AD006_indexed


title: genomic DNA from peripheral blood leukocytes 583


title: lncRNA profile of case728N


title: lncRNA profile of case725T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E9_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E9_AD002_indexed


title: lncRNA profile of case724T


title: genomic DNA from peripheral blood leukocytes 580


title: lncRNA profile of case724N


title: lncRNA profile of case734T


title: genomic DNA from peripheral blood leukocytes 582


title: lncRNA profile of case721T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E9_AD001_indexed


title: genomic DNA from peripheral blood leukocytes 578


title: lncRNA profile of case721N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E8_AD012_indexed


title: lncRNA profile of case722N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E8_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E9_AD007_indexed


title: genomic DNA from peripheral blood leukocytes 576


title: lncRNA profile of case719T


title: lncRNA profile of case718N


title: lncRNA profile of case719N


title: lncRNA profile of case725N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E8_AD008_indexed


title: genomic DNA from peripheral blood leukocytes 581


title: lncRNA profile of case717T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E8_AD001_indexed


title: lncRNA profile of case722T


title: genomic DNA from peripheral blood leukocytes 569


title: lncRNA profile of case714N


title: lncRNA profile of case714T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_F10_AD002_indexed


title: genomic DNA from peripheral blood leukocytes 568


title: lncRNA profile of case711T


title: lncRNA profile of case718T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E8_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E8_AD004_indexed


title: lncRNA profile of case709T


title: genomic DNA from peripheral blood leukocytes 563


title: lncRNA profile of case717N


title: genomic DNA from peripheral blood leukocytes 571


title: genomic DNA from peripheral blood leukocytes 558


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E7_AD012_indexed


title: lncRNA profile of case705T


title: lncRNA profile of case706N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E7_AD010_indexed


title: genomic DNA from peripheral blood leukocytes 570


title: lncRNA profile of case706T


title: genomic DNA from peripheral blood leukocytes 557


title: lncRNA profile of case703N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E7_AD008_indexed


title: lncRNA profile of case711N


title: lncRNA profile of case701T


title: genomic DNA from peripheral blood leukocytes 555


title: lncRNA profile of case705N


title: lncRNA profile of case703T


title: lncRNA profile of case709N


title: lncRNA profile of case701N


title: lncRNA profile of case700T


title: genomic DNA from peripheral blood leukocytes 554


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E7_AD006_indexed


title: lncRNA profile of case699T


title: lncRNA profile of case699N


title: genomic DNA from peripheral blood leukocytes 553


title: lncRNA profile of case698T


title: genomic DNA from peripheral blood leukocytes 552


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E7_AD002_indexed


title: genomic DNA from peripheral blood leukocytes 551


title: lncRNA profile of case697T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E8_AD007_indexed


title: lncRNA profile of case697N


title: lncRNA profile of case696T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E7_AD007_indexed


title: genomic DNA from peripheral blood leukocytes 547


title: genomic DNA from peripheral blood leukocytes 546


title: genomic DNA from peripheral blood leukocytes 543


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E6_AD010_indexed