title: CEMBA190214_11F_3_CEMBA190214_11F_4_H9_ad010

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

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

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: DG


title: CEMBA190214_11F_3_CEMBA190214_11F_4_H9_ad012

status: Public on Oct 05 2020

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: Sex

value: male

tag: age

tag: strain


title: CEMBA190214_11F_3_CEMBA190214_11F_4_H9_ad008


title: CEMBA190214_11F_3_CEMBA190214_11F_4_H9_ad002


title: CEMBA190214_11F_3_CEMBA190214_11F_4_H9_ad001


title: CEMBA190214_11F_3_CEMBA190214_11F_4_H9_ad004


title: CEMBA190214_11F_3_CEMBA190214_11F_4_H8_ad010


title: CEMBA190214_11F_3_CEMBA190214_11F_4_H7_ad012


title: CEMBA190214_11F_3_CEMBA190214_11F_4_H8_ad006


title: CEMBA190214_11F_3_CEMBA190214_11F_4_H7_ad008


title: CEMBA190214_11F_3_CEMBA190214_11F_4_H9_ad007


title: CEMBA190214_11F_3_CEMBA190214_11F_4_H8_ad004


title: CEMBA190214_11F_3_CEMBA190214_11F_4_H7_ad006


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title: CEMBA190214_11F_1_CEMBA190214_11F_2_H5_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H5_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H5_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H5_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H5_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H5_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H4_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H4_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H4_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H4_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H4_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H4_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H4_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H7_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H4_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H3_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H3_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H3_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H3_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H3_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H3_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H3_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H3_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H2_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H2_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H2_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H2_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H12_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H12_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H2_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H12_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H5_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H12_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H12_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H12_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H11_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H12_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H11_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H11_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H11_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H12_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H2_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H11_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H11_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H2_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H11_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H10_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H10_ad002


title: Ctl.10

type: RNA

city: Galveston

first: Qingjie

last: Li

state: Texas

address: 301 University Blvd

department: Internal Medicine

institute: University of Texas Medical Branch

description: S02 Ctl-10-cy5

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://miRBase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 mL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.  After RNA hybridization, tag-conjugating Alexa Fluor®546 dye was circulated through the microfluidic chip for dye staining.  Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression) (2). (2) Bolstad, B. M., Irizarry, R. A., Astrandand, M., Speed, T. P. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinfo. 19, 185-193.

molecule: total RNA

organism: Rattus norvegicus

label_protocol: Microarray assay was performed using a service provider (LC Sciences).  Total RNA sample (2 µg) were 3’-extended with a poly(A) tail using poly(A) polymerase.  An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining.  Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) (1). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://mirbase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate.  The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry.  (1) (a) Gao, X., Gulari, E., and Zhou, X. (2004) In situ synthesis of oligonucleotide microarrays. Biopolymers 73, 579-596; (b) Zhu, Q., Hong, A., Sheng, N., Zhang, X., Jun, K.-Y., Srivannavit, O., Gulari, E., Gao, X., and Zhou, X. (2007) Microfluidic biochip for nucleic acid and protein analysis. in Methods Mol. Biol. Ed. Rampal, J. B. 382:287-312.

extract_protocol: Qiagen miRNeasy kit was used for total RNA extraction following manufacturer's protocol.

value: Sprague Dawley

value: adult

tag: treatment

value: control

tag: tissue

value: heart


title: DSS.14

description: S05 DSS-14-cy5

value: dextran sodium sulfate (DSS, 3% in drinking water)


title: Ctl.11

description: S03 Ctl-11-cy5


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H10_ad008


title: DSS.13

description: S04 DSS-13-cy5


title: Ctl.9

description: S01 Ctl-9-cy5


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H10_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H10_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H1_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H11_ad007


title: DSS.16

description: S06 DSS-16-cy5


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H1_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H1_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H1_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H1_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H1_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G9_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H10_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_H1_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G9_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G9_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G9_ad006


title: F040_1_CD56_Rep_7

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression from human CD56+ blood cells from a smoking adult

hyb_protocol: Five and one-half micrograms (5.5 μg) of amplified biotin-cDNAs were fragmented and hybridized to each array for 16 hours at 45°C in a rotating hybridization oven.  Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification per the GeneChip Hybridization, Wash and Stain Kit and user manual following protocol FS450-0004.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using TAC Software.

label: biotin

organism: Homo sapiens

source_name: Human CD56+ blood cells from a smoking adult

label_protocol: Fifteen (15) ng of total RNA was amplified as directed in the Nugen WT-Ovation Pico RNA Amplification System protocol and labeling with biotin following the Nugen Encore Biotin Module protocol.

growth_protocol: Human whole blood was collected from smoking and nonsmoking adults

extract_protocol: Total RNA was isolated from purified cell fractions using the AllPrep DNA/RNA/miRNA Universal Kit according to the manufacturer's instructions.

treatment_protocol: Mononuclear layer was isolated directly from whole blood using density gradient centrifuagation with Histopaque-1077 Ficoll.  Using antibody-coated magnetic beads, purified cell fractions were pelleted and frozen at -80C in Qiagen RLT buffer.

tag: cell type

value: Blood

tag: smoker

value: yes


title: F054_CD56_Rep_1


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G9_ad004


title: F033_1_CD56_Rep_5

description: Gene expression from human CD56+ blood cells from a nonsmoking adult

source_name: Human CD56+ blood cells from a nonsmoking adult

value: no


title: F166_CD56_Rep_14


title: F025_1_CD56_Rep_1


title: F018_CD56_Rep_10


title: F067_CD56_Rep_4


title: F037_1_CD56_Rep_6


title: F031_1_CD56_Rep_4


title: F047_1_CD56_Rep_9


title: F160_CD56_Rep_13


title: F048_1_CD56_Rep_10


title: F026_1_CD56_Rep_2


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G9_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G9_ad001


title: F043_1_CD56_Rep_8


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G9_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G8_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G8_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G8_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G8_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G8_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G8_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G7_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G7_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G7_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G7_ad002


title: F015_CD56_Rep_7


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G7_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G6_ad012


title: F002_CD56_Rep_2


title: F007_CD56_Rep_5


title: F003_CD56_Rep_3


title: F037_1_CD19_Rep_6

description: Gene expression from human CD19+ blood cells from a smoking adult

source_name: Human CD19+ blood cells from a smoking adult


title: F031_1_CD19_Rep_4


title: F001_CD56_Rep_1


title: F014_CD56_Rep_6


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G6_ad008


title: F040_1_CD19_Rep_7


title: F033_1_CD19_Rep_5

description: Gene expression from human CD19+ blood cells from a nonsmoking adult

source_name: Human CD19+ blood cells from a nonsmoking adult


title: F026_1_CD19_Rep_2


title: F017_CD56_Rep_9


title: F016_CD56_Rep_8


title: F043_1_CD19_Rep_8


title: F048_1_CD19_Rep_10


title: F005_CD56_Rep_4


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G7_ad004


title: F025_1_CD19_Rep_1


title: F018_CD19_Rep_10


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G6_ad007


title: F047_1_CD19_Rep_9


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G6_ad006


title: F016_CD19_Rep_8


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G6_ad002


title: F017_CD19_Rep_9


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G5_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G5_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G5_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G6_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G6_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G5_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G4_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G5_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G5_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G4_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G4_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G4_ad007


title: F014_CD19_Rep_6


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G4_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G4_ad004


title: F007_CD19_Rep_5


title: F005_CD19_Rep_4


title: F003_CD19_Rep_3


title: F048_1_CD14_Rep_10

description: Gene expression from human CD14+ blood cells from a smoking adult

source_name: Human CD14+ blood cells from a smoking adult


title: F002_CD19_Rep_2


title: F033_1_CD14_Rep_5

description: Gene expression from human CD14+ blood cells from a nonsmoking adult

source_name: Human CD14+ blood cells from a nonsmoking adult


title: F031_1_CD14_Rep_4


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G4_ad001


title: F043_1_CD14_Rep_8


title: F015_CD19_Rep_7


title: F040_1_CD14_Rep_7


title: F001_CD19_Rep_1


title: F037_1_CD14_Rep_6


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G3_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G3_ad010


title: F047_1_CD14_Rep_9


title: F018_CD14_Rep_10


title: F025_1_CD14_Rep_1


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G3_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G4_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G2_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G3_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G2_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G2_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G2_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G3_ad004


title: F014_CD14_Rep_6


title: F015_CD14_Rep_7


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G2_ad002


title: F005_CD14_Rep_4


title: F016_CD14_Rep_8


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G2_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G12_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G12_ad012


title: F007_CD14_Rep_5


title: F047_1_CD8_Rep_9

description: Gene expression from human CD8+ blood cells from a nonsmoking adult

source_name: Human CD8+ blood cells from a nonsmoking adult


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G12_ad002


title: F002_CD14_Rep_2


title: F003_CD14_Rep_3


title: F048_1_CD8_Rep_10

description: Gene expression from human CD8+ blood cells from a smoking adult

source_name: Human CD8+ blood cells from a smoking adult


title: F001_CD14_Rep_1


title: F043_1_CD8_Rep_8


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G12_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G12_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G2_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G2_ad004


title: F040_1_CD8_Rep_7


title: F037_1_CD8_Rep_6


title: F026_1_CD8_Rep_2


title: F033_1_CD8_Rep_5


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G12_ad004


title: F017_CD14_Rep_9


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G11_ad002


title: F018_CD8_Rep_10


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G11_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G11_ad010


title: F025_1_CD8_Rep_1


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G11_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G11_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G11_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G10_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G10_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G10_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G11_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G10_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G10_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G10_ad004


title: F017_CD8_Rep_9


title: F005_CD8_Rep_4


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G1_ad012


title: F040_1_CD4_Rep_7

description: Gene expression from human CD4+ blood cells from a smoking adult

source_name: Human CD4+ blood cells from a smoking adult


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G1_ad008


title: F015_CD8_Rep_7


title: F001_CD8_Rep_1


title: F014_CD8_Rep_6


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G1_ad010


title: F037_1_CD4_Rep_6


title: F031_1_CD4_Rep_4


title: F007_CD8_Rep_5


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G1_ad007


title: F033_1_CD4_Rep_5

description: Gene expression from human CD4+ blood cells from a nonsmoking adult

source_name: Human CD4+ blood cells from a nonsmoking adult


title: F002_CD8_Rep_2


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G10_ad006


title: F026_1_CD14_Rep_2


title: F048_1_CD4_Rep_10


title: F047_1_CD4_Rep_9


title: F031_1_CD8_Rep_4


title: F016_CD8_Rep_8


title: F043_1_CD4_Rep_8


title: F025_1_CD4_Rep_1


title: F003_CD8_Rep_3


title: F026_1_CD4_Rep_2


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G1_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G1_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G1_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F9_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F9_ad007


title: F018_CD4_Rep_10


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F9_ad008


title: 22RV1_SLAM_KB742_1.2uM_8h_3

city: Houston

first: Charles

middle: Yang

last: Lin

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description:
SLAMseq in 22Rv1 castration resistant prostate cancer cells treated with DMSO
SLAM_RAW_EXPRESSION.txt.gz

library_source: transcriptomic

data_processing:
Reads were aligned to hg19 genome and counted using slamdunk.
Genome_build: hg19
Supplementary_files_format_and_content: tab separated text file

source_name: castration resistant prostate cancer

extract_protocol:
22RV1 carcinoma cells were seeded at 60% confluency 18h before being pretreated with 800uM s4U (Sigma, St. Louis, MO) to start the pulse. The cells were incubated in the media with s4U and the 0h samples were collected after 30 minutes by washing the cells with PBS and lysing directly with TRIzol (Invitrogen, Carlsbad, California). The media was replaced with media containing 800uM s4U along with either DMSO, KB742 (1.2uM) or KI-ARv-03 (4uM) and they were collected similarly after 2,4 or 8h post incubation. The RNA from the cells were harvested by total RNA extraction in the presence of 0.1mM DTT to maintain the samples in reducing conditions and the extracted RNA was resuspended with 1mM DTT.  The ERCC RNA Spike-in control mix was added to each sample and thiol modifications were performed by treating 1.5ug of total RNA with freshly prepared Iodoacetamide (IAA) at a final concentration of 10mM. The reactions were quenched, and the thiol modified RNA was ethanol precipitated
The libraries were prepared using the QuantSeq 3′ mRNA-Seq Library Prep Kit (Lexogen, Vienna, Austria) and were sequenced with NextSeq 500/550 High Output Kit v2.5 (75 Cycles) (Illumina, San Diego, CA).

treatment_protocol: DMSO (0.1%) treated for 24 hours

tag: cell line


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F9_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F9_ad002


title: 22RV1_SLAM_KB742_1.2uM_8h_1


title: 22RV1_SLAM_KB742_1.2uM_8h_2


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F8_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_G1_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F9_ad001


title: 22RV1_SLAM_KB742_1.2uM_4h_3


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F8_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F8_ad007


title: F016_CD4_Rep_8


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F8_ad008


title: F015_CD4_Rep_7


title: F017_CD4_Rep_9


title: F014_CD4_Rep_6


title: F007_CD4_Rep_5


title: 22RV1_SLAM_KB742_1.2uM_4h_1


title: 22RV1_SLAM_KB742_1.2uM_2h_3


title: F005_CD4_Rep_4


title: F002_CD4_Rep_2


title: F003_CD4_Rep_3


title: F001_CD4_Rep_1


title: 22RV1_SLAM_KB742_1.2uM_2h_2


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F9_ad006


title: 22RV1_SLAM_KB742_1.2uM_2h_1


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F8_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F8_ad004


title: 22RV1_SLAM_KB742_1.2uM_4h_2


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F8_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F7_ad010


title: 22RV1_SLAM_Karv3_4uM_8h_3


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F8_ad002


title: 22RV1_SLAM_Karv3_4uM_8h_1


title: 22RV1_SLAM_Karv3_4uM_8h_2


title: 22RV1_SLAM_Karv3_4uM_4h_3


title: 22RV1_SLAM_Karv3_4uM_4h_2


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F7_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F7_ad007


title: 22RV1_SLAM_Karv3_4uM_4h_1


title: 22RV1_SLAM_Karv3_4uM_2h_3


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F7_ad006


title: 22RV1_SLAM_Karv3_4uM_2h_2


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F7_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F7_ad002


title: 22RV1_SLAM_Karv3_4uM_2h_1


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F7_ad001


title: 22RV1_SLAM_DMSO_8h_1


title: 22RV1_SLAM_DMSO_8h_2


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F6_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F6_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F7_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F6_ad007


title: 22RV1_SLAM_DMSO_4h_3


title: 22RV1_SLAM_DMSO_4h_2


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F6_ad006


title: 22RV1_SLAM_DMSO_4h_1


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F6_ad004


title: 22RV1_SLAM_DMSO_2h_3


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F6_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F6_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F5_ad006


title: 22RV1_SLAM_0h_3


title: 22RV1_SLAM_DMSO_2h_1


title: 22RV1_SLAM_DMSO_2h_2


title: 22RV1_SLAM_0h_2


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F5_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F5_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F5_ad012


title: 22RV1_SLAM_0h_1


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F5_ad004


title: 22RV1_WCE_DMSO_2

description: WCE input control in 22Rv1 castration resistant prostate cancer cells treated with DMSO

data_processing:
ChIP-seq data processing closely followed AQUAS pipeline (https://github.com/kundajelab/chipseq_pipeline) and phase-3 ENCODE guidelines.
All ChIP-seq datasets were aligned with BWA-ALN to human reference genome hg19/GRCh37.
Low-quality, duplicate, multimapping, and unmapped reads were filtered out. Reads mapping to the mitochondrial genome were also filtered out.
Peaks were called using MACS2 with a p-value threshold of 1e-5.
Genome_build: hg19
Supplementary_files_format_and_content: Read pileups in bedGraph format.

extract_protocol:
15x107 22RV1 carcinoma cells were treated for 24h with DMSO and were crosslinked by adding formaldehyde to a final concentration of 0.8% to the cells in media. The fixation was terminated by adding Glycine to a final concentration of 125mM Glycine on a rocker at RT. The cells were washed in ice cold PBS buffer thrice and the cells were harvested using a cell lifter. The crosslinked cells were then lysed in L1 buffer (50mM Hepes, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% Igepal and 0.25% Triton X 100) with protease inhibitor (PI) at 4C in a rotor. The cells were pelleted and resuspended in L2 buffer (200mM NaCl, 1mM EDTA, 0.5mM EGTA in 10mM Tris) with PI and incubated at RT in a rotor. The nuclei were pelleted by centrifugation at 4°C and were washed twice with the sonication buffer (SE) (10mM Tris, 1mM EDTA, 0.1% SDS). The pellet was resuspended in SE with PI and was sheared using a covaris LE220 sonicator (Covaris, Woburn, MA).
Library preparations for the ChIP samples were performed as described in Buenrostro et al., 2013 with minor changes. In brief to generate multiplexed libraries, A preamplification cycle was performed with the transposed DNA. The DNA was amplified for 5 PCR cycles with Illumina indexed primers (Nextera index kit, Illumina), 25ul of NEBNext High-Fidelity 2x PCR Master Mix (New England Biolabs). 5ul of this amplified DNA was amplified further using a qPCR to determine the appropriate number of cycles of PCR cycles needed to achieve maximum amplification with minimum duplicates. The number of cycles needed was calculated by finding the cycle number that corresponds to 1/4th of the maximum fluorescence intensity. The final amplification was performed in the leftover 45ul from the preamplification reaction using the number of cycles calculated in the qPCR.

tag: antibody epitope

value: DMSO


title: 22RV1_WCE_DMSO_3


title: 22RV1_WCE_DMSO_14MIN_2


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F5_ad007


title: 22RV1_SLAM_DMSO_8h_3


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F4_ad008


title: 22RV1_WCE_DMSO_14MIN_1


title: 22RV1_WCE_DMSO_12MIN_2


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F4_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F4_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F4_ad004


title: 22RV1_WCE_DMSO_1


title: 22RV1_H3K27AC_DMSO_3

description: H3K27AC ChIPmentation in 22Rv1 castration resistant prostate cancer cells treated with DMSO

tag: antibody catalog

value: Cell Signaling Technology 8173


title: 22RV1_WCE_DMSO_12MIN_1


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F4_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F4_ad002


title: 22RV1_H3K27AC_DMSO_2


title: 22RV1_H3K27AC_DMSO_1


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F3_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F4_ad001


title: 22RV1_FOXA1_DMSO_14MIN_1

description: FOXA1 ChIPmentation in 22Rv1 castration resistant prostate cancer cells treated with DMSO

value: Genetex GTX100308

value: DMSO 14MIN


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F3_ad010


title: 22RV1_FOXA1_DMSO_14MIN_2


title: 22RV1_FOXA1_DMSO_12MIN_1

value: DMSO 12MIN


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F3_ad008


title: 22RV1_FOXA1_DMSO_12MIN_2


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F3_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F4_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F3_ad004


title: 22RV1_DMSO_ATAC_2

description: Omni ATAC-seq in 22Rv1 castration resistant prostate cancer cells treated with DMSO

data_processing:
ATAC-seq data processing closely followed Kundaje lab ATAC-seq pipeline (https://github.com/kundajelab/atac_dnase_pipelines) and phase-3 ENCODE guidelines.
All ATAC-seq datasets were aligned with Bowtie2 to human reference genome hg19/GRCh37.
Low-quality, duplicate, multimapping, and unmapped reads were filtered out. Reads mapping to the mitochondrial genome were also filtered out.
Tn5 transposon shifting was performed.
Peaks were called using MACS2 with a p-value threshold of 0.01.
Genome_build: hg19
Supplementary_files_format_and_content: Read pileups in bedGraph format.

extract_protocol:
50,000 live cells in culture medium were treated with DNase at a final concentration of 200 U/ml at 37C for 30 minutes. The cells were washed thrice with PBS to remove DNase followed by lysis with RSB (10mM Tris-HCl, 10mM NaCl, 3 mM MgCl2) containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin and mixed by pipetting up and down 3 times. The cells were lysed on ice for 3 minutes and the reaction was stopped by adding 1ml of ice cold RSB containing 0.1% Tween-20 and mixed by inverting the tubes thrice. The nuclei were pelleted by centrifugation at 4C and the pellet was resuspended in 50ul of transposition mix (25ul 2x TD buffer, 2.5ul transposase, 16.5ul PBS, 0.5ul 1% digitonin, 0.5ul 10% Tween-20, 5ul H2O) and was incubated at 37C for 30 minutes with mixing. The reaction was then cleaned up with a Zymo DNA Clean and Concentrator-5 Kit.
Library preparations for the samples were performed as described in Buenrostro et al., 2013 with minor changes. In brief to generate multiplexed libraries, A preamplification cycle was performed with the transposed DNA. The DNA was amplified for 5 PCR cycles with Illumina indexed primers (Nextera index kit, Illumina), 25ul of NEBNext High-Fidelity 2x PCR Master Mix (New England Biolabs). 5ul of this amplified DNA was amplified further using a qPCR to determine the appropriate number of cycles of PCR cycles needed to achieve maximum amplification with minimum duplicates. The number of cycles needed was calculated by finding the cycle number that corresponds to 1/4th of the maximum fluorescence intensity. The final amplification was performed in the leftover 45ul from the preamplification reaction using the number of cycles calculated in the qPCR.


title: 22RV1_DMSO_ATAC_1


title: HS034:whole blood

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

data_processing:
Illumina standard primers were trimmed
Paired reads were mapped to the human reference genome (b37) using STAR
Number of reads for each gene was counted using HTSeq
Genome_build: GRCh37
Supplementary_files_format_and_content: raw read count matrix (genes x samples)

source_name: whole blood

extract_protocol:
Whole blood and Skin from punch biopsy were obtained from patients
Libraries were sequencing on the Illumina NextSeq sequencer.

tag: condition

value: HS


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F3_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F3_ad001


title: HS032:whole blood


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F2_ad010


title: HS033:whole blood


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F2_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F2_ad008


title: LXHWT3

city: Wuhan

first: Li

middle: xiao

last: hui

state: Hubei

address: Shizishan Street No. 1, Hongshan District

country: China

institute: Huazhong Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mycobacterium tuberculosis H37Ra whole genome using bowtie2 v2-2.0.5
Fragments per kilobase of exon per million fragments mapped(FPKM). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Mycobacterium tuberculosis H37Ra
Supplementary_files_format_and_content: gene_expression.xls file includes FPKM values for each Sample ...

organism: Mycobacterium tuberculosis H37Ra

source_name: strain

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. RNeasy Mini Kit (Cat#74106, Qiagen) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation


title: HS030:whole blood


title: LXHWT2


title: HS029:whole blood


title: LXHWT1


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F2_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F2_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F2_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F3_ad007


title: HS028:whole blood


title: 22RV1_DMSO_ATAC_3


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F2_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F12_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F12_ad008


title: LXHCMT2


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F12_ad001


title: HS026:whole blood


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F12_ad007


title: LXHCMT1


title: HS021:whole blood


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F12_ad006


title: HS020:whole blood


title: LXHCMT3


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F11_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F11_ad008


title: HS016:whole blood


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F11_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F11_ad002


title: HS013:whole blood


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F12_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F11_ad001


title: HS014:whole blood


title: HS027:whole blood


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F12_ad012


title: HS010:whole blood


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F10_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F11_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F10_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F11_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F11_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F10_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F10_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F10_ad001


title: HS009:whole blood


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F10_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F10_ad006


title: HS008:whole blood


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F10_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F1_ad012


title: HS006:whole blood


title: HS003:whole blood


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F1_ad004


title: HS012:whole blood


title: HS002:whole blood


title: CHS031:whole blood


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E9_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F1_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F1_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F1_ad001


title: cHiC_RIS_2

city: Cambridge

first: Ioana

last: Olan

state: Cambridgeshire

address: Robinson Way

department: Cancer Research UK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

description:
cHi-C
Capture HiC RAS-induced senescence Replicate 2

data_processing:
Fastq files were quality-checked with FastQC, aligned with the HiC-Pro pipeline [Servant et al. 2015, Genome Biology] using default parameters in the configuration file.
Artefacts and duplicates were removed using HiC-Pro and raw matrices as well as ICE-normalised ones were obtained at several resolutions using HiC-Pro.
Hi-C matrices at 40kb resolution (bin size), as well as cHiC matrices at 10kb resolution are provided, as well as the coordinates of the bins they correspond to.
Genome_build: hg19
Supplementary_files_format_and_content: BED: coordinates of the genomic bins
Supplementary_files_format_and_content: TXT: interaction matrix.txt in triplet sparse format

extract_protocol: Hi-C was carried out according to the in-nucleus ligation protocol detailed in (Nagano et al. 2015 Comparison of Hi-C results using in-solution versus in-nucleus ligation, Genome Biol, 16: 175). Capture Hi-C was carried out with SureSelect target enrichment (Agilent Technologies), using a custom-designed biotinylated RNA bait library targetting regions of interest in the human genome and custom paired-end blockers according to the manufacturer’s instructions (Agilent Technologies).

treatment_protocol: IMR90 cells were stably infected with an ER:RAS G12V containing construct. To induce RAS-induced senescence (RIS/Sen), cells were treated with 100nM 4-hydroxytamoxifen (4OHT) for 6 days.

tag: passage

tag: vector

tag: tamoxifen

value: Yes, 6 days


title: CHS024:whole blood


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E9_ad006

value: DG


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E9_ad007

value: male


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E9_ad008


title: HiC_RIS_2

description:
Hi-C
HiC RAS-induced senescence Replicate 2


title: CHS023:whole blood


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F9_ad012


title: HiC_Growing_3

description:
Hi-C
HiC Growing Replicate 3

value: ER:HRAS(G12V), MSCV Vector

value: No


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E8_ad008


title: CHS022:whole blood

value: control


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F1_ad007


title: HS007:whole blood


title: CEMBA190214_11F_1_CEMBA190214_11F_2_F1_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E9_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E8_ad006


title: CHS019:whole blood


title: Growing_Input_4

description: Input Growing Replicate 4

data_processing:
Fastq files were quality checked using FastQC [Babraham Institute, Simon Andrews], trimmed using cutadapt 2.0 [https://doi.org/10.14806/ej.17.1.200] with -m 20 --match-read-wildcards -q 28,28 -b GATCGGAAGAGCACACGTCTGAACTCCAGTCAC (paired-end experiments were trimmed simultaneously).
Reads were aligned with bowtie2 [Langmead and Salzberg 2012, Nature Methods] using default parameters and samtools [Li et al. 2009, Bioinformatics] was used for selecting only uniquely mapping reads and removing duplicates.
Alignment files corresponding to multiple lanes were merged using samtools [Li et al. 2009, Bioinformatics].
Peak calling was performed using macs2 [Zhang et al 2008, Genome Biology] in two stages, one with default parameters and one with insert sizes calculated using ChIPQC [Caroll et al. Frontiers in Genetics and R Bioconductor].
BigWig files were obtained by using THOR [Alhoff et al. 2016, Nucleic Acids Research] which performs input subtraction and library normalisation, as well as differential binding analysis.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig (THOR-normalised signal with Input subtracted)

growth_protocol: IMR90 and WI38 cells (ATCC) were cultured in DMEM supplemented with 10% FBS. Cells were maintained in physiological 5% O2.

extract_protocol:
Fixed cells were lysed and sonicated to generate 200-400 bp chromatin fragments before immunoprecipitation.
Libraries were prepared using the NEBnext ultra II DNA-library prep kit for Illumina (E7645) according to manufacturers instructions except that size selection was performed during the final bead purification step using SPRIselect beads (B23319, Beckman Coulter)

treatment_protocol: For RIS samples,IMR90 ER:HRAS(G12V) cells were treated for 6 days with 100nM 4OHT.


title: RIS_Input_4

description: Input RAS-induced senescence Replicate 4


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E8_ad002


title: CHS018:whole blood


title: CHS025:whole blood


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E8_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E9_ad004


title: SMC3_RIS_2

description: SMC3 RAS-induced senescence Replicate 2

tag: chip antibody


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E9_ad001

tag: brain region


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E7_ad012

tag: Sex


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E7_ad010

tag: age


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E8_ad012

tag: strain


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E8_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E7_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E7_ad008


title: CHS015:whole blood


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E7_ad006


title: CHS017:whole blood


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E7_ad004


title: SMC3_Growing_2

description: SMC3 Growing Replicate 2


title: CHS011:whole blood


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E7_ad002


title: HS035:skin

source_name: skin


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E7_ad001


title: SMC3_Growing_1

description: SMC3 Growing Replicate 1


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E8_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E6_ad012


title: RAD21_RIS_4

description: RAD21 RAS-induced senescence Replicate 4

value: Rad21 (gift from Shirahige lab)


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E6_ad010


title: HS034:skin


title: RAD21_RIS_3

description: RAD21 RAS-induced senescence Replicate 3


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E6_ad008


title: RAD21_RIS_2

description: RAD21 RAS-induced senescence Replicate 2


title: HS033:skin


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E6_ad007


title: SMC3_RIS_1

description: SMC3 RAS-induced senescence Replicate 1


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E5_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E6_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E6_ad004


title: HS032:skin


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E6_ad002


title: HS029:skin


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E5_ad012


title: RAD21_RIS_1

description: RAD21 RAS-induced senescence Replicate 1


title: HS028:skin


title: RAD21_Growing_2

description: RAD21 Growing Replicate 2


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E5_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E5_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E5_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E4_ad012


title: RAD21_Growing_1

description: RAD21 Growing Replicate 1


title: HS026:skin


title: RAD21_Growing_3

description: RAD21 Growing Replicate 3


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E5_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E4_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E5_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E4_ad008


title: HS020:skin


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E4_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E4_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E4_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E4_ad007


title: HS013:skin


title: HS016:skin


title: HS014:skin


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E3_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E4_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E3_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E3_ad010


title: HS027:skin


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E3_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E3_ad004


title: HS010:skin


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E2_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E3_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E2_ad008


title: HS009:skin


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E2_ad007


title: HS021:skin


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E2_ad006


title: HS007:skin


title: HS008:skin


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E2_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E2_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E2_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E12_ad010


title: HS003:skin


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E12_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E12_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E12_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E12_ad007


title: HS012:skin


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E12_ad001


title: CHS031:skin


title: HS002:skin


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E12_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E11_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E11_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E11_ad008


title: HS001:skin


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E11_ad001


title: CHS025:skin


title: CHS024:skin


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E11_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E11_ad004


title: CHS023:skin


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E10_ad012


title: CHS022:skin


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E10_ad010


title: HS006:skin


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E10_ad008


title: CHS019:skin


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E10_ad002


title: CHS018:skin


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E12_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E10_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E10_ad001


title: CHS017:skin


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E10_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E10_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E1_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E11_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E1_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E1_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E1_ad006


title: CHS015:skin


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E1_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D9_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E1_ad004


title: CHS011:skin


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D9_ad010


title: Cremer-2019-HIC011

first: Suhas

last: Rao

data_processing:
The paired end reads were aligned separately using BWA against the hg19 mouse build, PCR duplicates, low mapping quality and unligated reads were removed using Juicer (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016), Contact matrices were constructed at various resolutions and normalized using Juicer (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016)
Genome_build: hg19
Supplementary_files_format_and_content:
*.hic file contains contact matrices at various resolutions in an easy to visualize and access format (Durand, Robinson, et al Cell Systems 2016)
Bedgraph containing deduplicated counts (early and late bedgraphs) or log-2 ratios of early to late binned at 5kb or 50kb resolution (ELratio bedgraph)

source_name: HCT-116 cmvOsTIR1 RAD21-mAC

extract_protocol:
Cells were crosslinked and then lysed with nuclei permeabilized but still intact. DNA was then restricted and the overhangs filled in incorporating a biotinylated base. Free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and then biotinylated ligation junctions were recovered with streptavidin beads.
standard Illumina library construction protocol, Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 8-12 cycles and library fragments of 400-600 bp (insert plus adaptor and PCR primer sequences) were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the NextSeq 500 following the manufacturer's protocols

tag: cell line background

value: cmvOsTIR1, RAD21-mAC

tag: treatment

value: 500uM IAA, 28hrs


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D9_ad008


title: Cremer-2019-HIC010


title: Cremer-2019-HIC009


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D9_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D9_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D9_ad007


title: Cremer-2019-HIC008

value: untreated


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D9_ad001


title: Cremer-2019-HIC007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D8_ad012


title: Cremer-2019-HIC006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D8_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D8_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D8_ad006


title: Cremer-2019-HIC005

value: 500uM IAA, 6hrs


title: CEMBA190214_11F_1_CEMBA190214_11F_2_E1_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D8_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D8_ad001


title: Cremer-2019-HIC004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D8_ad002


title: Cremer-2019-HIC003


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D7_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D7_ad010


title: Cremer-2019-HIC002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D7_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D7_ad004


title: Cremer-2019-HIC001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D6_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D6_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D6_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D8_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D6_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D6_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D5_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D7_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D5_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D5_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D6_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D5_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D7_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D4_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D5_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D4_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D4_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D6_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D7_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D4_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D4_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D4_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D3_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D3_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D3_ad007


title: 7886X17: mG4H_STZ_03

city: Stanford

first: Mark

middle: Emile

last: Pepin

address: 870 Quarry Road

department: Cardiovascular Medicine

institute: Stanford University

hyb_protocol: The hybridizations were performed for 17 hours at 10 rpm and 65°C in a hybridization oven (Agilent) using the Mouse GE 4x44K v2 Microarray Kit (Cat. No. G4846A). Washing and staining of the arrays were performed according to the manufacturer’s recommendation.

scan_protocol: Cy3 intensities were detected by one-color scanning using an Agilent DNA microarray scanner (G2505B) at 5 μm resolution. Scanned image files were inspected for artifacts and then analyzed.

data_processing: Intensity data were extracted using Agilent’s Feature Extraction (FE) software. All chips that passed the QC were analyzed using the Limma package within R.

source_name: heart - left ventricle

label_protocol: Cy3 labeled cRNA was prepared from 0.6 ug RNA using the Low RNA Input linear Amplification Kit Plus, One Color protocol (Agilent 5188-5339) and the Agilent One color RNA Spike-In Kit (Agilent 5188-5252) following the manufacturer's standard protocols

extract_protocol: For each group six individual male mice with at least one sibling pair in another group were harvested between 6 AM and 7 AM, right ventricle was dissected away and left ventricle was immediately placed in RNAlater followed by RNAeasy RNA isolation, purification, cDNA synthesis and labeling.

treatment_protocol: Mice were made diabetic by using the low-dose streptozotocin (STZ) protocol as outlined by the Animal Models of Diabetic Complications Consortium. After 4-6 hr of fasting, mice were injected with a stock solution of STZ (7.5 mg/ml; Axxora LLC, San Diego, CA) at 55 mg/kg of body weight or an equivalent volume of sodium citrate buffer (0.1 M, pH 4.5) for 5 consecutive days.

tag: tissue

value: heart - left ventricle

tag: genotype

value: STZ

tag: blood glucose  (4wks)

tag: bw (4-wks)


title: 7886X24: mG4H_STZ_04


title: 7886X4: mG4H_STZ_05


title: 7886X5: mG4H_STZ_06


title: 7886X10: mG4H_STZ_01


title: 7886X15: mG4H_STZ_02


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D3_ad002

source_name: C57BL/6J Male P56 Mouse Brain


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D3_ad004


title: 7886X7: CON_STZ_06

value: CON


title: 7886X22: CON_STZ_05


title: 7886X13: CON_STZ_02


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D2_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D2_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D2_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D2_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D2_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D2_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D12_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D12_ad010


title: 7886X19: CON_STZ_03


title: 7886X12: CON_STZ_01


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D2_ad001


title: 7886X2: CON_STZ_04


title: 7886X9: mG4H_VEH_06

value: VEH


title: 7886X23: mG4H_VEH_03


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D12_ad008


title: 7886X8: mG4H_VEH_05


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D12_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D12_ad001


title: 7886X20: mG4H_VEH_02


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D12_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D12_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D10_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D12_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D10_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D10_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D10_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D10_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D10_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D10_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D1_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D1_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D1_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D1_ad007


title: iWAT-8am-Shiftwork rep3

city: Duarte

first: Ke

last: Ma

address: 1500 E. Duarte Rd

department: Diabetes Complications & Metabolism

institute: City of Hope-BRI

description:
LFN-45
iWAT-read counts.txt
iWAT-rpkm.txt

data_processing:
RNA-seq sequencing reads were aligned with STAR software to mouse reference genome mm10.
Unique read counts were quantified using HTSeq-count, with GENCODE gene annotations.
Read counts for genes were normalized to FPKM or RPKM and log-transformed using DESeq2, limma and edgeR packages.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: eWAT-read counts.txt, eWAT-log2 fpkm.txt: Raw gene read counts and log2 FPKM for every gene and every sample in eWAT group.
Supplementary_files_format_and_content: iWAT-read counts.txt, iWAT-rpkm.txt: Raw gene read counts and RPKM for every gene and every sample in iWAT group.

source_name: subcutaneous white adipose tissue

extract_protocol:
Total RNA was extracted using Trizol followed by DNase digestion and Qiagen RNeasy column purification.
Sequencing libraries were prepared with Kapa RNA mRNA HyperPrep kit according to the manufacturer's protocol, and sequenced on Illumina HiSeq 2500 with SR V4 Kit with the single read mode of 51 cycles of read1 and 7 cycles of index read.

treatment_protocol: Normal control groups were maintained in a regular lighting condition of 12-h light, 12-h dark cycle (lights on 5AM; lights off 5PM). Shiftwork groups were subjected to a weekly rotating light schedule, with normal L/D cycle of lights on 5AM and lights off 5PM for first 4 days of the week from Monday to Thursday and reversed L/D cycle for rest 3 days from Friday to Sunday with lights on at 5PM and lights off at 5AM. This schedule was maintained for 24 weeks.

value: inguinal subcutaneous adipose tissue

value: shiftwork group

tag: time point

value: 8am (ZT3)


title: iWAT-8am-Shiftwork rep2

description:
LFN-39
iWAT-read counts.txt
iWAT-rpkm.txt


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D1_ad006

value: DG


title: 7886X14: mG4H_VEH_01


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D1_ad004

value: male


title: iWAT-8am-Shiftwork rep1

description:
LFN-38
iWAT-read counts.txt
iWAT-rpkm.txt


title: 7886X3: mG4H_VEH_04


title: 7886X21: CON_VEH_05


title: 7886X1: CON_VEH_01


title: 7886X6: CON_VEH_06


title: 7886X18: CON_VEH_04


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C9_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C9_ad010


title: 7886X16: CON_VEH_03


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C9_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C9_ad008


title: iWAT-8am-Normal control rep1

description:
LFN-14
iWAT-read counts.txt
iWAT-rpkm.txt

value: normal control group


title: 7886X11: CON_VEH_02


title: iWAT-8am-Normal control rep2

description:
LFN-15
iWAT-read counts.txt
iWAT-rpkm.txt


title: eWAT-5pm-Shiftwork rep2

description:
5pmS-46
eWAT-read counts.txt
eWAT-log2 fpkm.txt

source_name: visceral white adipose tissue

value: epididymal white adipose tissue


title: iWAT-8am-Normal control rep3

description:
LFN-16
iWAT-read counts.txt
iWAT-rpkm.txt


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C9_ad006


title: eWAT-5pm-Shiftwork rep3

description:
5pmS-47
eWAT-read counts.txt
eWAT-log2 fpkm.txt


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C8_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C9_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C8_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C8_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C8_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C9_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C8_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_D1_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C8_ad002


title: eWAT-5pm-Normal control rep2

description:
5pmN-15
eWAT-read counts.txt
eWAT-log2 fpkm.txt


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C7_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C7_ad008


title: eWAT-5pm-Normal control rep1

description:
5pmN-14
eWAT-read counts.txt
eWAT-log2 fpkm.txt


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C7_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C7_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C7_ad004


title: eWAT-8am-Shiftwork rep3

description:
8amS-44
eWAT-read counts.txt
eWAT-log2 fpkm.txt


title: eWAT-8am-Shiftwork rep2

description:
8amS-42
eWAT-read counts.txt
eWAT-log2 fpkm.txt


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C6_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C6_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C6_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C7_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C6_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C7_ad001


title: eWAT-8am-Normal control rep3

description:
8amN-23
eWAT-read counts.txt
eWAT-log2 fpkm.txt


title: eWAT-8am-Shiftwork rep1

description:
8amS-41
eWAT-read counts.txt
eWAT-log2 fpkm.txt


title: eWAT-5pm-Shiftwork rep1

description:
5pmS-45
eWAT-read counts.txt
eWAT-log2 fpkm.txt


title: eWAT-8am-Normal control rep1

description:
8amN-21
eWAT-read counts.txt
eWAT-log2 fpkm.txt


title: eWAT-8am-Normal control rep2

description:
8amN-22
eWAT-read counts.txt
eWAT-log2 fpkm.txt


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C5_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C5_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C5_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C6_ad001


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C6_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C5_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C7_ad012


title: eWAT-5pm-Normal control rep3

description:
5pmN-16
eWAT-read counts.txt
eWAT-log2 fpkm.txt


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C5_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C4_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C4_ad008


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C5_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C4_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C4_ad010


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C4_ad002


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C4_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C4_ad004


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C3_ad012


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C6_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C3_ad007


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C3_ad006


title: CEMBA190214_11F_1_CEMBA190214_11F_2_C3_ad010