title: sre1-H-hyp: sre1_mutant_high iron_hypoxia

city: Seoul

first: Yong-Joon

last: Cho

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

data_processing:
The sequencing adapter removal and quality-based trimming on raw data was performed by Trimmomatic v. 0.36 with default parameter.
Cleaned reads were mapped to reference genome using tophat2 with '--very-sensitive' option.
For counting reads which mapped to each CDS, featureCounts in Subread package was used.
Finally, retrieved counts were normalized as RPKM (Reads Per Kilobase Million) values.
Genome_build: Cryptococcus neoformans var. grubii H99 (GCA_000149245.3)
Supplementary_files_format_and_content: xlsx file with RPKM value list of each sample and fold changes in low- and high-iron medium under normoxia or hypoxia condition.

organism: Cryptococcus neoformans H99

source_name: Cryptococcus neoformans var. grubii H99

growth_protocol: C. neoformans cells were cultured in YNB + BPS with or without 100 μM of FeCl3 under normoxia or hypoxia condition at 30˚C for 6 hours.

extract_protocol:
Total RNA was extracted using RiboPure-Yeast Kit (Ambion, #AM1926) following manufacturer's instructions.
Library was constructed using Illumina TruSeq RNA Library Prep Kit V2 following manufacturer's instructions.

value: sre1 mutant

tag: culture condition

value: YNB low iron medium + 100 μM of FeCl3 (hypoxia)


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F8_AD002_indexed

status: Public on Sep 01 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

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

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

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

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

tag: brain region

value: MOp

tag: Sex

value: male

tag: age

tag: strain


title: PC3_Res_17

city: Ann Arbor

first: Evan

middle: T

last: Keller

state: MI

address: 2800 Plymouth Rd

institute: University of Michigan

library_source: transcriptomic

data_processing:
Samples were sequenced on Illumina HiSeq 2500 for DU145 cell line and Illumina HiSeq 4000 with single end option for PC3 cell line.
Samples were aligned to Human genome hg38 using bowtie alignment tool.
Poor quality cells were removed as determined using the Fluidigm Singular package.
Genome_build: Human genome hg38
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts

molecule: total RNA

organism: Homo sapiens

growth_protocol: Cells were cultered in RPMI 1640 supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
Cells were trypsinized in 0.05% Trypsin EDTA for 5-10 mins at 37°C and washed with media.  The cell suspension was loaded into the Fluidigm C1TM machine and processed into single cell cDNA libraries according to the manufacturer protocol.
Full length mtotal RNA-seq libraries were generated from single cells captured using the Fluidigm C1TM Single Cell mtotal RNA Seq IFC, 10-17 um and Fluidigm C1TM Single-Cell Reagent Kit for mtotal RNA Seq.  Full length cDNA was converted into sequence ready libraries using SMART-seq v4 Ultra Low Input total RNA kit for Fluidigm C1TM System and SeqAmpTM DNA Polymerase.  Library preparation was completed using Nextera XT DNA library prep kit.

treatment_protocol: Docetaxel resistance was maintained with the addition of 10 nM docetaxel in DMSO in growth media while sensitive cells were maintained with the addition of a final concentration of 0.1% DMSO.

tag: docetaxel

value: Resistant

tag: disease state

value: Prostate cancer

tag: cell line


title: sre1-L-hyp: sre1 mutant_low iron_hypoxia

tag: genotype

value: YNB low iron medium (hypoxia)


title: PC3_Res_16


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F5_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F4_AD006_indexed


title: PC3_Res_15


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F5_AD001_indexed


title: D1_G4_591020 rep1

type: RNA

city: Oxford

first: Julius

last: Muller

state: Oxfordshire

address: ORCRB, Roosevelt Drive

department: Nuffield Department of Medicine

country: United Kingdom

institute: The Jenner Institute, University of Oxford

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Probes were background corrected using negative control probes followed by quantile normalization using the neqc method of Shi et al. (2010) [PMID:20929874].

label: biotin

source_name: Whole Blood

label_protocol: Biotinylated cRNA were prepared with the Ambion Total Prep RNA amplification kit

extract_protocol: Blood samples (2.5mL) were collected from consenting volunteers into PAXgene tubes. Blood samples were incubated at room temperature for 2 hours to precipitate RNA and stored at -80°C until extraction. Total RNA was purified according to the manufacturer’s protocol, including DNAse digestion for 15 minutes at room temperature, and eluted into 100 uL of the supplied elution buffer. Excess globin transcripts were removed from the samples using Human GLOBINclear kits (Life Technologies), prior to amplification.

tag: subject

tag: day

tag: vaccinegroup

tag: efficacy

value: NP


title: sre1-H-nor: sre1_mutant_high iron_normoxia

value: YNB low iron medium + 100 μM of FeCl3 (normoxia)


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F3_AD004_indexed


title: PC3_Res_14


title: PC3_Res_18


title: D0_G1_591030 rep1

value: P


title: D0_G1_592214 rep1


title: sre1-L-nor: sre1 mutant_low iron_normoxia

value: YNB low iron medium (normoxia)


title: D29_G2_591018 rep1


title: C-1_G4_591002 rep1


title: C-1_G3_591025 rep1


title: PC3_Res_13


title: WT-H-hyp: WT_high iron_hypoxia

value: Wild-type


title: WT-H-nor: WT_high iron_normoxia


title: PC3_Res_12


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F3_AD002_indexed


title: WT-L-nor: WT_low iron_normoxia


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F3_AD006_indexed


title: PC3_Res_11


title: WT-L-hyp: WT_low iron_hypoxia


title: Input-Hyp-L: Input_Sre1-L_hypoxia

data_processing:
The sequencing adapter removal and quality-based trimming on raw data was performed by Trimmomatic v. 0.36 with default parameter.
Cleaned reads were mapped to reference genome using tophat2 with '--very-sensitive' option.
callpeak and bdgdiff module from MACS v2 were used to identify differential peaks by comparing control and mutant samples in normoxia and hypoxia condition.
Genome_build: Cryptococcus neoformans var. grubii H99 (GCA_000149245.3)
Supplementary_files_format_and_content: xlsx files with diffential peaks list in normoxia and hypoxia condition.

growth_protocol: C. neoformans cells were cultured in YNB + BPS with or without 100 μM of FeCl3 under normoxia (21% oxygen) or hypoxia (1% oxygen) condition at 30˚C for 6 hours.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Library was constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (#E7645, NEB, UK) following manufacturer's instructions.

tag: chip antibody

value: Anti-FLAG antibody (Abcam, #ab1162)


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F6_AD001_indexed


title: PC3_Res_10


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F3_AD001_indexed


title: D57_G3_591034 rep1


title: Input-Hyp-H: Input_Sre1-H_hypoxia


title: D0_G4_591022 rep1


title: C-1_G2_591021 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F4_AD002_indexed


title: PC3_Res_9


title: Input-Nor-L: Input_Sre1-L_normoxia


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F2_AD012_indexed


title: Input-Nor-H: Input_Sre1-H_normoxia


title: PC3_Res_7


title: PC3_Res_8


title: Hyp-L: Sre1-L_hypoxia


title: PC3_Res_6


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F2_AD006_indexed


title: Hyp-H: Sre1-H_hypoxia


title: Nor-L: Sre1-L_normoxia


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F1_AD010_indexed


title: PC3_Res_4


title: PC3_Res_5


title: D1_G1_593312 rep1


title: Nor-H: Sre1-H_normoxia


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F2_AD001_indexed


title: D0_G2_591006 rep1


title: PC3_Res_3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F2_AD004_indexed


title: C-1_G2_591014 rep1


title: C-1_G3_593307 rep1


title: D0_G3_591025 rep1


title: D29_G1_592214 rep1


title: PC3_Res_2


title: SLAM-seq  ELAVL1-KO THP-1 cell sample 16 h cGAMP stimualtion, 8 hours after uridine chase rep 2

city: Nashville

first: Manuel

last: Ascano

state: TN

address: 2215 Garland Avenue

department: Biochemistry

institute: Vanderbilt University

description:
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina
4579-KR-43_R_S1_L001
SLAM_KO_stimulated_8H_rep2

data_processing:
library strategy: SLAM-seq
RNA-seq and RIP-seq data were aligned to human genome (hg19) using STAR mapper and CPM values for each gene were calculated using DeSeq2
PAR-CLIP data was processed using PARa-lyzer
SLAM-seq data was processed using SLAM-DUNK
Genome_build: Encode hg19
Supplementary_files_format_and_content: counts for RNA-Seq and RIP-seq; PARalyzer output for clusters; SLAM-seq Tcounts outout

source_name: innate immune cell line

growth_protocol: Human THP-1s monocytes (male) were cultured in RPMI (Gibco) with 10% fetal bovin serum (FBS from Peal Serum), 100 μg/ml streptomycin (Gibco), 100 U/ml penicillin (Gibco), 25 μg/ml blasticidin and 100 μg/ml hygromycin (Invivogen).

extract_protocol:
RNA-Seq, RIP-Seq, and SLAM-Seq: total RNA was extracted using TriZol.
RNA-Seq and RIP-Seq: ribo-minus and standard Illumina protocol.
PAR-CLIP: small-RNA cloning and TruSeq Small RNA library prep kit
SLAM-Seq: Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina

treatment_protocol: Stimulated cells were treated with EC50 cGAMP for 16 hours to initiate an IRF3 innate immune response

tag: cell type

value: THP-1 monocytic-like cell line

tag: treatment

value: treated for 16 hours with (70 nM cGAMP), 2 x wash with PBS, uridine chase, collected at indicated timepoint


title: D0_G2_591014 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F2_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G2_AD007_indexed


title: SLAM-seq  parental THP-1 cell sample 16 h cGAMP stimualtion, 8 hours after uridine chase rep 2

description:
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina
4579-KR-46_S1_L001
SLAM_CTRL_stimulated_8H_rep2


title: SLAM-seq  parental THP-1 cell sample 16 h cGAMP stimualtion, 1 hour after uridine chase rep 2

description:
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina
4579-KR-44_S1_L001
SLAM_CTRL_stimulated_1H_rep2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F1_AD012_indexed


title: PC3_Sen_90

value: Sensitive


title: D1_G1_591030 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F1_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F1_AD007_indexed


title: PC3_Sen_89


title: SLAM-seq  ELAVL1-KO THP-1 cell sample 16 h cGAMP stimualtion, 1 hour after uridine chase rep 1

description:
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina
4579-KR-43_S1_L001
SLAM_KO_stimulated_1H_rep1

value: ELAVL1-KO THP-1


title: PC3_Res_1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F1_AD008_indexed


title: PC3_Sen_88


title: C-1_G2_593305 rep1


title: PC3_Sen_87


title: D57_G3_593307 rep1


title: D1_G4_591011 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F1_AD002_indexed


title: PC3_Sen_86


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F3_AD012_indexed


title: D57_G1_591016 rep1


title: PC3_Sen_85


title: SLAM-seq  parental THP-1 cell sample 16 h cGAMP stimualtion, 6 hours after uridine chase rep 1

description:
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina
4579-KR-37_S1_L001
SLAM_CTRL_stimulated_6H_rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F4_AD007_indexed


title: SLAM-seq  parental THP-1 cell sample 16 h cGAMP stimualtion, 6 hours after uridine chase rep 2

description:
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina
4579-KR-38_S1_L001
SLAM_CTRL_stimulated_6H_rep2


title: SLAM-seq  parental THP-1 cell sample 16 h cGAMP stimualtion, 8 hours after uridine chase rep 1

description:
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina
4579-KR-41_S1_L001
SLAM_CTRL_stimulated_8H_rep1


title: SLAM-seq  ELAVL1-KO THP-1 cell sample 16 h cGAMP stimualtion, 6 hours after uridine chase rep 2

description:
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina
4579-KR-36_S1_L001
SLAM_KO_stimulated_6H_rep2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F11_AD012_indexed


title: PC3_Sen_84


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F3_AD010_indexed


title: PC3_Sen_83


title: SLAM-seq  ELAVL1-KO THP-1 cell sample 16 h cGAMP stimualtion, 8 hours after uridine chase rep 1

description:
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina
4579-KR-39_S1_L001
SLAM_KO_stimulated_8H_rep1


title: SLAM-seq  ELAVL1-KO THP-1 cell sample 16 h cGAMP stimualtion, 6 hours after uridine chase rep 1

description:
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina
4579-KR-35_S1_L001
SLAM_KO_stimulated_6H_rep1


title: SLAM-seq  parental THP-1 cell sample 16 h cGAMP stimualtion, 3 hours after uridine chase rep 2

description:
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina
4579-KR-34_S1_L001
SLAM_CTRL_stimulated_3H_rep2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F1_AD004_indexed


title: PC3_Sen_82


title: SLAM-seq  parental THP-1 cell sample 16 h cGAMP stimualtion, 3 hours after uridine chase rep 1

description:
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina
4579-KR-33_S1_L001
SLAM_CTRL_stimulated_3H_rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F1_AD001_indexed


title: PC3_Sen_81


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F11_AD006_indexed


title: SLAM-seq  ELAVL1-KO THP-1 cell sample 16 h cGAMP stimualtion, 3 hours after uridine chase rep 1

description:
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina
4579-KR-31_S1_L001
SLAM_KO_stimulated_3H_rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F11_AD010_indexed


title: D1_G1_592214 rep1


title: PC3_Sen_79


title: D1_G2_591012 rep1


title: D1_G1_591016 rep1


title: PC3_Sen_80


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F11_AD007_indexed


title: PC3_Sen_78


title: D57_G4_593303 rep1


title: D29_G2_593305 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F2_AD010_indexed


title: PC3_Sen_77


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F11_AD008_indexed


title: SLAM-seq  ELAVL1-KO THP-1 cell sample 16 h cGAMP stimualtion, 1 hour after uridine chase rep 2

description:
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina
4579-KR-28_S1_L001
SLAM_KO_stimulated_1H_rep2


title: SLAM-seq  ELAVL1-KO THP-1 cell sample 16 h cGAMP stimualtion, 3 hours after uridine chase rep 2

description:
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina
4579-KR-32_S1_L001
SLAM_KO_stimulated_3H_rep2


title: PC3_Sen_76


title: SLAM-seq  parental THP-1 cell sample 16 h cGAMP stimualtion, 1 hour after uridine chase rep 1

description:
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina
4579-KR-29_S1_L001
SLAM_CTRL_stimulated_1H_rep1


title: SLAM-seq  parental THP-1 cell sample 16 h cGAMP stimualtion, 0 hour after uridine chase rep 2

description:
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina
4579-KR-26_S1_L001
SLAM_CTRL_stimulated_0H_rep2


title: D1_G3_593311 rep1


title: D57_G4_591002 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F11_AD004_indexed


title: D29_G3_593302 rep1


title: D1_G4_597403 rep1


title: C-1_G3_591034 rep1


title: D1_G2_591006 rep1


title: D0_G3_591026 rep1


title: PC3_Sen_75


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F11_AD001_indexed


title: C-1_G4_591022 rep1


title: SLAM-seq  ELAVL1-KO THP-1 cell sample 16 h cGAMP stimualtion, 0 hour after uridine chase rep 2

description:
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina
4579-KR-24_S1_L001
SLAM_KO_stimulated_0H_rep2


title: PC3_Sen_74


title: SLAM-seq ELAVL1-KO THP-1 cell sample 16 h cGAMP stimualtion, 0 hour after uridine chase rep 1

description:
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina
4579-KR-23_S1_L001
SLAM_KO_stimulated_0H_rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F11_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F10_AD012_indexed


title: PC3_Sen_73


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F10_AD010_indexed


title: PC3_Sen_72


title: PC3_Sen_71


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F10_AD008_indexed


title: PC3_Sen_70


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F10_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F10_AD001_indexed


title: PC3_Sen_69


title: PC3_Sen_68


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E9_AD006_indexed


title: MCF7_Exp3 Abemaciclib + Fulvestrant

city: Melbourne

first: Shom

last: Goel

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using BWA.
For peak calling MACS2 was used.
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated using MACS2 using the chilin pipeline, peak files generated from MACS2 peak calling

source_name: Breast carcinoma cell line

growth_protocol: Cells were cultured in sterile dishes in media as described. Cells were plated at densities such that final density at time of ChIP-seq was between 60-70%.

extract_protocol:
Cell lines were washed with PBS and crosslinked with 1% paraformaldehyde (Thermo Scientific #28906) for 10 minutes. Cross-linked material was resuspended in 0.1% SDS (50 mM Tris-HCl pH8, 10 mM EDTA) and sonicated for 5 minutes with a Covaris E220 instrument (5% duty cycle, 140 Peak Incident Power, 200 Cycles per burst, 1 mL AFA Fiber milliTUBEs) or a Covaris S2. Soluble chromatin (5 µg) was immunoprecipitated with Protein A/G Dynabeads (Thermo Fisher 10002D, 10004D) and 10 μg of H3K27ac (Diagenode C15410196),
ChIP-seq libraries were constructed using Accel-NGS 2S DNA library kit from Swift Biosciences or NEBNext® UltraTM II kit from New England Biolabs.

treatment_protocol: Abemaciclib (500 nM), palbociclib (500 nM), fulvestrant (100 nM), or DMSO (control) for 7 days for all cell lines.

value: MCF7 breast carcinoma cell line

value: Abemaciclib + Fulvestrant

tag: treatment length

value: 7 days

value: H3K27ac (Diagenode C15410196, polyclonal, lot # A1723-0041D)


title: MCF7_Exp3 DMSO

value: DMSO


title: MDA-MB-453 Abemaciclib

value: MDA-MB-453 breast carcinoma cell line

value: abemaciclib


title: MDA-MB-453 DMSO


title: MCF7_Exp3 Abemaciclib

value: Abemaciclib


title: Neutrophils cells 1

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Reads pairs from each sample were aligned to the human genome and counted into 50 kB bin pairs using the R package diffHic v1.6.0.
Genome_build: hg38
Supplementary_files_format_and_content: The processed data file gives the number of reads supporting each interaction, where an interaction corresponds to a pair of 50 kB bins. The file is a space-delimited text file in Matrix Market Exchange (mtx) format with integer entries. The first two columns give the indices of the two interacting genomic bins and the third column gives the read count. Bin pairs with no reads are omitted. The indices correspond to rows of the BED format file GenomicRegions.bed.gz. The processed data file can be read into R using the readMTX2IntSet function of the diffHic package or the readMM function of the Matrix package.

source_name: Peripheral blood

extract_protocol: In situ Hi-C was performed as described by Rao et al (Cell 2014; PMID: 25497547).

tag: donor

value: Healthy human male

value: CD45+ CD16+ CD66b+ CD11b+ CD49d- human blood neutrophils


title: D0_G4_597403 rep1

value: NP


title: PC3_Sen_67

value: Prostate cancer


title: D29_G1_591015 rep1

value: P


title: PC3_Sen_66


title: C-1_G4_591027 rep1


title: D29_G4_591022 rep1


title: C-1_G3_593302 rep1


title: C-1_G4_591011 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E9_AD004_indexed

tag: brain region

value: MOp

value: male


title: D0_G3_592211 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E9_AD007_indexed

tag: Sex


title: D0_G4_591027 rep1


title: D1_G3_593307 rep1


title: SLAM-seq parental THP-1 cell sample 16 h cGAMP stimualtion, 0 hour after uridine chase rep 1

description:
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina
4579-KR-25_S1_L001
SLAM_CTRL_stimulated_0H_rep1

value: THP-1 monocytic-like cell line

value: treated for 16 hours with (70 nM cGAMP), 2 x wash with PBS, uridine chase, collected at indicated timepoint


title: MCF7 Abemaciclib

value: MCF7 breast carcinoma cell line


title: PC3_Sen_65

value: Sensitive


title: PC3_Sen_64


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F10_AD007_indexed

tag: age


title: MCF7 DMSO

value: 7 days


title: PC3_Sen_63


title: MCF7 Palbociclib

value: palbociclib

value: H3K27ac (Diagenode C15410196, polyclonal, lot # A1723-0041D)


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E9_AD001_indexed

tag: strain


title: PC3_Sen_62

tag: docetaxel


title: HNSCC_custom

city: Rehovot

first: Itay

last: Tirosh

address: Herzl 234

country: Israel

institute: WEIZMANN INSTITUTE OF SCIENCE

data_processing:
We used both expression-based and SNP-based methods to assign cells to cell lines. In each of these methods, we compared the single cells to external bulk data of the corresponding cell lines and then either assigned the cells to the most similar cell line or excluded them as potential doublets or low-quality cells. Only cells whose assignments were also consistent between both methods were retained for further analysis. Bulk RNA-seq data was obtained from the DepMap portal (https://depmap.org/; 18q3 data release) 7 for cell lines in the eight CCLE-based pools and was generated as described above for the eight HNSCC cell lines in the custom pool.      For SNP based classification, for each cell we determined the cell line from the pool whose SNP profile (based on bulk RNA-seq data) best matched the observed reference and alternate allele reads across a panel of SNP sites, similar to the Demuxlet method 8. Specifically, we used a logistic regression model for each cell. Models were fit using the R package glmnet 9, and the cell line whose SNP profile produced the highest likelihood under this model was selected. Goodness-of-fit was quantified by the model deviance relative to the null-model deviance. We used a reference panel of 100,000 SNPs that were frequently detected across a panel of 200 cancer cell lines (based on bulk RNA-seq data), and that were detected in the scRNA-seq data from the same cell lines.     For expression-based classification, we used a broadly similar approach. First, we subsetted the gene expression data to genes that were expressed in at least half of all cells or had a maximal expression (measured by the 98th percentile of that gene’s expression across all cells) greater than 3 log2(CPM). Next, we used the Rtsne R package to estimate, for each pool, 3 t-SNE embedding dimensions for each cell, computed based on 50 principle components, using a perplexity parameter of 30, and a theta value of 0.2 (using the first three principle components for initialization). We applied a local ‘smoothing’ to the normalized and centered single-cell expression profiles (ER), using a Gaussian kernel applied to the cell-cell distances in the t-SNE embedding space. The Gaussian kernel bandwidth was set using the method ‘sigest’ from the R package kernlab. Finally, for each cell, we identified the reference cell line from the pool with the most similar bulk RNA-seq gene expression profile (ER, and Pearson correlation similarity).      Detection of putative ‘doublets’, where two or more cells are labeled with the same barcode during droplet-based library preparation, was performed based on the SNP data, using the same generalized linear modeling approach to identify a mixture of two reference cell lines whose combined SNP profiles best explained the SNP data from a given cell. To efficiently estimate the best-fitting reference cell line pair we used a Lasso-regularized generalized linear model. After determining the best-fitting ‘singlet’ and ‘doublet’ models for each putative cell, we then determined whether each putative cell was a singlet, doublet, or a ‘low-quality’ cell based on several statistics. To identify low quality cells we took the maximum of the deviance explained by the singlet model and the deviance explained by the doublet model. We observed that the maximum deviances formed a bimodal distribution. We thus used the local minimum between the two distributions as a threshold and classified all cells with a maximum deviance below this threshold as ‘low quality’. To separate putative doublets from singlets, we then fit a two-component Gaussian mixture model using three variables: (1) the amount of deviance explained by the singlet model; (2) the (log-transformed) deviance-improvement of the doublet model over the singlet model; and (3) the fraction of genes detected in that cell. Cells with a probability greater than 0.75 of belonging to the cluster with higher average doublet improvement were classified as doublets.
Cell barcode filtering, alignment of reads and UMI counting were performed using CellRanger 3.0.1 (10x Genomics). Expression levels were quantified as Ei,j = log2(1 + CPMi,j/10), where CPMi,j refers to 106*UMIi,j/sum[UMI1..n,j], for gene i in sample j, with n being the total number of analyzed genes. The average number of UMIs detected per cell was less than 100,000, thus CPM values were divided by 10, to avoid inflating the differences between detected (Ei,j > 0) and non-detected (Ei,j = 0) genes. For each cell, we quantified the number of detected genes as a proxy for sample quality. We conservatively retained cells with a number of detected genes ranging from 2,000 to 9,000.
Genome_build: hg19
Supplementary_files_format_and_content: Counts-per-million (CPM) data for all human genes with detecetd expression, across all cells included in the study.

molecule: polyA RNA

source_name: pool of cell lines

extract_protocol:
For each pool, we generated a single cell suspension in 0.04% PBS-BSA and loaded approximately 10,500 single cells to the 10X Chromium Controller with a targeted recovery of 6,000 cells.
ScRNA-seq libraries were generated using the 10X Genomics Chromium Single Cell 3’ Kit v2 and the 10x Chromium Controller (10x Genomics) according to the 10X Single Cell 3’ v2 protocol.  Single cells, reagents and single gel beads containing barcoded oligonucleotides were encapsulated into nanoliter-sized droplets and subjected to reverse transcription. Droplets were broken and the barcoded cDNAs were purified with DynaBeads and amplified by 12 cycles of PCR (98°C for 45 s; [98°C for 20 s, 67°C for 30 s, 72°C for 1 min] x 12; 72°C for 1 min). The amplified cDNA was fragmented, end-repaired, ligated with index adaptors, and size-selected with clean-ups between each step using the SPRIselect Reagent Kit (Beckman Coulter). Quality control of the resulting barcoded libraries was performed with the Agilent TapeStation and by PCR with primers specific to the P5 and P7 sequence (NEBNext Library Quant Kit for Illumina, New England Biolabs). Final 3’ scRNA-Seq libraries were diluted to 4 nM, denatured, and further diluted to a concentration of 2.8 pM for sequencing with the following sequencing parameters: Read 1: 26 cycles, i7 index: 8 cycles, i5 index: 0 cycles, Read 2: 58 cycles on the NextSeq 500 (Illumina).

treatment_protocol: Pools were generated consisting of 24-25 cell lines grouped based on growth rate, with the exception of the custom HNSCC pool, which consisted of 8 HNSCC cell lines. Each pool was thawed and cultured in RPMI supplemented with 10% fetal bovine serum for 3 days before scRNA-Seq library generation, with the exception of the HNSCC pool which was generated immediately before library construction.

tag: pool id

value: HNSCC


title: D1_G2_591003 rep1


title: D0_G3_593302 rep1


title: Pool9_9


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E8_AD012_indexed


title: PC3_Sen_61

tag: disease state

tag: cell line


title: PC3_Sen_60


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E9_AD012_indexed


title: D1_G2_591014 rep1

tag: subject


title: PC3_Sen_59


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E8_AD006_indexed


title: Pool7_16


title: C-1_G2_591018 rep1

tag: day


title: PC3_Sen_58


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F10_AD002_indexed


title: Pool5_6


title: PC3_Sen_57


title: D29_G2_591029 rep1

tag: vaccinegroup


title: Pool4_22


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E7_AD012_indexed


title: Pool8_16


title: Pool6_6


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E7_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E9_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E7_AD010_indexed


title: Pool3_22


title: PC3_Sen_55


title: Pool1_19


title: D29_G1_591030 rep1

tag: efficacy


title: PC3_Sen_54


title: D1_G1_591013 rep1


title: PC3_Sen_56


title: PC3_Sen_53


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E8_AD004_indexed


title: C-1_G2_591029 rep1


title: D0_G2_591029 rep1


title: D0_G3_591017 rep1


title: C-1_G3_592211 rep1


title: D57_G3_591028 rep1


title: PC3_Sen_52


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E6_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E8_AD002_indexed


title: Pool1_18


title: Pool17_19


title: Pool2_18


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E6_AD004_indexed


title: Pool16_19


title: PC3_Sen_51


title: Pool15_19


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E9_AD010_indexed


title: D0_G4_591002 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E5_AD012_indexed


title: PC3_Sen_49


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E8_AD010_indexed


title: PC3_Sen_48


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E6_AD010_indexed


title: Pool14_15


title: Pool13_15


title: Pool12_10


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E5_AD007_indexed


title: PC3_Sen_47


title: PC3_Sen_46


title: PC3_Sen_50


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E5_AD010_indexed


title: PC3_Sen_45


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E7_AD001_indexed


title: Pool10_9


title: MCF7_2 Abemaciclib_JunB

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using BWA.
For peak calling MACS2 was used.
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated using MACS2 using the chilin pipeline; peak files generated from MACS2 peak calling

extract_protocol:
For ChIP, cells crosslinked with two agents starting with 2 mM DSG (Pierce) for 45 minutes at room temperature followed by 1 mL of 1% formaldehyde for 10 minutes. Cross-linked cell lines or tissues were quenched with 0.125 M glycine for 5 minutes at room temperature. Cross-linked material was resuspended in 0.1% SDS (50 mM Tris-HCl pH8, 10 mM EDTA) and sonicated for 20 minutes with a Covaris S2.Thirty micrograms of soluble chromatin were immuoprecipiated with Protein A Dynabeads and 3.1 ?g of JunB (CST 3753) antibody.
ChIP-seq libraries were constructed using NEBNextｮ UltraTM II kit from New England Biolabs.

treatment_protocol: Abemaciclib concentration 500 nM or equal volume of DMSO (control) for 7 days for all cell lines.

tag: chip antibody

value: JunB (CST 3753)


title: D1_G3_591017 rep1


title: C-1_G2_593309 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E5_AD004_indexed


title: D0_G1_591015 rep1


title: D29_G3_591028 rep1


title: D57_G2_591029 rep1


title: D57_G4_592204 rep1


title: D29_G4_591011 C rep1


title: D57_G2_593305 rep1


title: MCF7_2 DMSO_JunB

tag: cell type

value: DMSO


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E4_AD006_indexed


title: Pool11_10


title: C-1_G4_592204 rep1


title: D1_G3_591026 rep1


title: PC3_Sen_42


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E4_AD001_indexed


title: MCF7_2 DMSO_Fra2

extract_protocol:
For ChIP, cells crosslinked with two agents starting with 2 mM DSG (Pierce) for 45 minutes at room temperature followed by 1 mL of 1% formaldehyde for 10 minutes. Cross-linked cell lines or tissues were quenched with 0.125 M glycine for 5 minutes at room temperature. Cross-linked material was resuspended in 0.1% SDS (50 mM Tris-HCl pH8, 10 mM EDTA) and sonicated for 20 minutes with a Covaris S2.Thirty micrograms of soluble chromatin were immuoprecipiated with Protein A Dynabeads and 1 ?g of Fra2 (CST 19967) antibody.
ChIP-seq libraries were constructed using NEBNextｮ UltraTM II kit from New England Biolabs.

tag: treatment


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E4_AD010_indexed


title: PC3_Sen_44


title: PC3_Sen_41


title: PC3_Sen_40


title: PC3_Sen_43


title: MCF7-2 DMSO

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using BWA.
For peak calling MACS2 was used.
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated using MACS2 using the chilin pipeline

extract_protocol:
Cells were washed in phosphate-buffered saline (PBS), cross-linked with 1% formaldehyde (methanol-free) for 10 minutes at room temperature, quenched with 0.125 M glycine for 5 min at room temperature and washed with PBS complete. Cells were resuspended in lysis buffer (1%SDS, 50 mM Tris-HCl pH8, 10 mM EDTA) containing protease and deacetylase inhibitors, and incubated on ice for 15 min. Lysed cells were sonicated for 5 minutes with a Covaris E220 sonicator (PIP140, DF5%, 200cpb), in 1ml AFA Fiber milliTUBEs. 10 µg of soluble chromatin were immunoprecipitated overnight with ER antibody [10 ?g of Santa Cruz (HC20- SC543)] on protein A and G magnetic beads; and finally washed, eluted and DNA purified.
ChIP-seq libraries were constructed using Accel-NGS 2S DNA library kit from Swift Biosciences.

treatment_protocol: Abemaciclib concentration 500 nM or DMSO for 7 days for all cell lines.

tag: treatment length

value: ER (Santacruz, Cat# sc-543, clone HC-20, Lot # A1F0316)


title: PC3_Sen_39


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E6_AD002_indexed


title: PC3_Sen_38


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E4_AD007_indexed


title: serum miRNAs, Study ID 9086997

city: Miami

first: Alberto

last: Pugliese

state: FL

address: 1450 NW 10th Ave.

department: Diabetes Research Institute

institute: University of Miami

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
797-A008965_1_1

data_processing:
Illumina CASAVA  version 10196100F) is used for base calling and generation of FASQ files
HTG EdgeSeq Parser software (version 10196100G) is used for alignment to a priori defined target sequences.  Requirements include %Q30 >= 85%, %PF >= 75%, and 180 < CD < 290
Post-sequencing quality control using three quality control metrics: 1) Percent of reads allocated to the Positive control probe must not exceed 14%, 2) Total aligned reads must exceed 500,000, and 3) Relative Standard Deviaion (CV) of counts within a sample must exceed 0.08 (CV is calculated after removal of counts from ANT and POS control probes and log2 transformation after addition of 2 to avoid taking the log of 0).
Supplementary_files_format_and_content: VLP00150 NewOnset_miRNA Median Normalized.csv, VLP00150 NewOnset_miRNA_raw CPM.csv

source_name: serum

extract_protocol:
HTG EdgeSeq WT-miRNA Assay (Tucson, Arizona)
Serum samples were processed by adding HTG Lysis Buffer to lyse and/or permeabilize the RNA available to subsequently bind to corresponding target-specific Nuclease Protection Probes (NPPs). The lysed samples was transferred to a 96-well micro-titer plate. Target capture was done by adding NPPs to the lysed samples to hybridize to the target mRNA. Then S1 nuclease was added to digest non-hybridized miRNA and excess NPPs, leaving target mRNA/NPP duplexes. S1 digestion was terminated by heat denaturation of S1 enzyme. The processed samples were used as template to set up PCR reactions with primer tags. These tags share common sequences that are complementary to 5’-end and 3’-end “wing” sequences of the probes and common adaptors required for cluster generation for deep sequencing. The library was prepared using HTG EdgeSeq PCR processing. Following library preparation, it was quantified using HTG EdgeSeq KAPA Library Quantification for Illumina Sequencing. All samples and controls were quantified in triplicate.
HTG EdgeSeq KAPA Library Quantification/Calculator

tag: tissue

value: serum

value: Type 1 Diabetes

tag: age at diagnosis (years)

value: M

tag: age at draw (years)


title: serum miRNAs, Study ID 9012279

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
797-A008947_1_1

tag: Sex


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E5_AD006_indexed

tag: brain region

tag: age

tag: strain


title: D0_G4_593303 rep1

value: P


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E4_AD012_indexed

value: MOp


title: MCF7_2 Abemaciclib_Fra2

value: Abemaciclib


title: C-1_G1_591030 rep1


title: D29_G2_591012 rep1


title: PC3_Sen_37

tag: docetaxel

tag: disease state

value: Prostate cancer


title: D29_G4_597403 rep1

tag: subject

value: NP


title: PC3_Sen_35

tag: cell line


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E3_AD004_indexed

value: male


title: serum miRNAs, Study ID 9028704

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
797-A008944_1_1


title: D1_G3_593302 rep1

tag: day

tag: vaccinegroup


title: serum miRNAs, Study ID 9053717

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
797-A008928_1_1


title: serum miRNAs, Study ID 9043362

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
797-A008934_1_1

value: F


title: D0_G4_591020 rep1

tag: efficacy


title: PC3_Sen_36

value: Sensitive


title: PC3_Sen_34


title: D1_G2_593305 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E4_AD004_indexed


title: serum miRNAs, Study ID 9066472

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
797-A008921_1_1


title: MCF7-2 Abemaciclib

tag: cell type

value: MCF7 breast carcinoma cell line

value: abemaciclib

value: 7 days

tag: chip antibody


title: PC3_Sen_33


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E3_AD007_indexed


title: PC3_Sen_32


title: D0_G1_591016 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E2_AD012_indexed


title: serum miRNAs, Study ID 9070958

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
797-A008912_1_1


title: PC3_Sen_31


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E5_AD001_indexed


title: serum miRNAs, Study ID 9078920

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
796-A008977_1_1


title: serum miRNAs, Study ID 9052887

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
797-A008926_1_1


title: D29_G4_593310 C rep1


title: PC3_Sen_30


title: D0_G2_591003 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E7_AD006_indexed


title: D57_G2_591003 rep1


title: C-1_G2_591003 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E3_AD010_indexed


title: serum miRNAs, Study ID 9075725

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
796-A008971_1_1


title: PC3_Sen_28


title: PC3_Sen_29


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E3_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E2_AD002_indexed


title: serum miRNAs, Study ID 9099623

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
796-A008970_1_1


title: PC3_Sen_27


title: serum miRNAs, Study ID 9011645

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
796-A008959_1_1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E1_AD010_indexed


title: PC3_Sen_26


title: D29_G4_591002 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E1_AD006_indexed


title: serum miRNAs, Study ID 9076795

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
796-A008973_1_1


title: C-1_G1_591016 rep1


title: serum miRNAs, Study ID 9001582

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
796-A008954_1_1


title: PC3_Sen_25


title: serum miRNAs, Study ID 9025248

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
796-A008952_1_1


title: serum miRNAs, Study ID 9022044

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
796-A008950_1_1


title: D1_G1_591024 rep1


title: PC3_Sen_24


title: D57_G3_593302 rep1


title: PC3_Sen_23


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E2_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E2_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E1_AD008_indexed


title: D57_G1_591013 rep1


title: D0_G1_593312 rep1


title: serum miRNAs, Study ID 9032640

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
796-A008946_1_1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E2_AD006_indexed


title: PC3_Sen_22


title: serum miRNAs, Study ID 9043972

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
796-A008935_1_1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E1_AD002_indexed


title: serum miRNAs, Study ID 9055515

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
796-A008931_1_1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E11_AD012_indexed


title: PC3_Sen_20


title: PC3_Sen_19


title: serum miRNAs, Study ID 9054527

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
796-A008930_1_1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E11_AD007_indexed


title: serum miRNAs, Study ID 9051955

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
796-A008925_1_1


title: PC3_Sen_18


title: PC3_Sen_17


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E11_AD006_indexed


title: C-1_G1_591013 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E1_AD004_indexed


title: serum miRNAs, Study ID 9066421

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
796-A008923_1_1


title: PC3_Sen_21


title: serum miRNAs, Study ID 9059631

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
796-A008917_1_1


title: C-1_G4_593303 rep1


title: PC3_Sen_15


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E2_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E1_AD001_indexed


title: serum miRNAs, Study ID 9066062

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
796-A008920_1_1


title: D29_G3_593311 rep1


title: D1_G4_593310 rep1


title: PC3_Sen_14


title: D29_G4_591027 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E11_AD004_indexed


title: D29_G3_591026 rep1


title: serum miRNAs, Study ID 9077483

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
795-A008975_1_1


title: PC3_Sen_16


title: PC3_Sen_13


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E11_AD008_indexed


title: D1_G3_591025 rep1


title: serum miRNAs, Study ID 9069703

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
796-A008910_1_1


title: D57_G3_592212 rep1


title: PC3_Sen_12


title: D1_G4_593303 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E11_AD001_indexed


title: serum miRNAs, Study ID 9090413

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
795-A008968_1_1


title: serum miRNAs, Study ID 9089814

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
795-A008966_1_1


title: serum miRNAs, Study ID 9087246

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
795-A008964_1_1


title: PC3_Sen_11


title: D1_G3_591034 rep1


title: D1_G3_592212 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E10_AD012_indexed


title: PC3_Sen_10


title: serum miRNAs, Study ID 9009811

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
795-A008958_1_1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E10_AD010_indexed


title: D29_G3_591034 rep1


title: PC3_Sen_9


title: serum miRNAs, Study ID 9005361

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
795-A008956_1_1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E11_AD002_indexed


title: PC3_Sen_8


title: PC3_Sen_7


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D9_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D9_AD010_indexed


title: serum miRNAs, Study ID 9028086

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
795-A008942_1_1


title: serum miRNAs, Study ID 9045312

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
795-A008936_1_1


title: serum miRNAs, Study ID 9022910

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
795-A008951_1_1


title: PC3_Sen_6


title: PC3_Sen_5


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E10_AD002_indexed


title: serum miRNAs, Study ID 9053881

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
795-A008929_1_1


title: D57_G2_591006 rep1


title: PC3_Sen_4


title: C-1_G3_591017 rep1


title: PC3_Sen_3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E10_AD004_indexed


title: D29_G2_591003 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E10_AD006_indexed


title: serum miRNAs, Study ID 9057958

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
795-A008915_1_1


title: serum miRNAs, Study ID 9032746

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
795-A008927_1_1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E10_AD001_indexed


title: D29_G1_593312 rep1


title: C-1_G1_591024 rep1


title: C-1_G4_597403 rep1


title: serum miRNAs, Study ID 9072093

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
795-A008913_1_1


title: D57_G3_592211 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_E10_AD007_indexed


title: PC3_Sen_2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D9_AD008_indexed


title: DU145_Res_72

value: Resistant


title: C-1_G3_593311 rep1


title: D1_G2_591029 rep1


title: serum miRNAs, Study ID 9095723

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
794-A008969_1_1


title: serum miRNAs, Study ID 9075939

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
794-A008972_1_1


title: D29_G1_591013 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D9_AD002_indexed


title: serum miRNAs, Study ID 9084703

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
794-A008962_1_1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D9_AD001_indexed


title: DU145_Res_70


title: DU145_Res_69


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D8_AD012_indexed


title: D0_G3_592212 rep1


title: serum miRNAs, Study ID 9007576

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
794-A008957_1_1


title: C-1_G1_592214 rep1


title: serum miRNAs, Study ID 9029174

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
794-A008945_1_1


title: DU145_Res_68


title: DU145_Res_67


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D8_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D7_AD006_indexed


title: DU145_Res_66


title: serum miRNAs, Study ID 9039395

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
794-A008941_1_1


title: DU145_Res_71


title: D29_G2_591014 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D9_AD007_indexed


title: DU145_Res_65


title: D57_G1_591024 rep1


title: serum miRNAs, Study ID 9022175

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
794-A008961_1_1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D6_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D8_AD004_indexed


title: serum miRNAs, Study ID 9047707

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
794-A008939_1_1


title: C-1_G3_591026 rep1


title: D29_G3_593307 rep1


title: D57_G1_592214 rep1


title: DU145_Res_64


title: C-1_G1_591015 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D8_AD002_indexed


title: D1_G4_591002 rep1


title: D0_G2_593309 rep1


title: serum miRNAs, Study ID 9056377

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
794-A008932_1_1


title: C-1_G3_591028 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D5_AD010_indexed


title: DU145_Res_62


title: serum miRNAs, Study ID 9064486

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
794-A008922_1_1


title: DU145_Res_61


title: serum miRNAs, Study ID 9074059

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
794-A008916_1_1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D6_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D7_AD010_indexed


title: DU145_Res_63


title: serum miRNAs, Study ID 9051781

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
794-A008924_1_1


title: D29_G3_592211 rep1


title: D29_G2_591006 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D8_AD007_indexed


title: D0_G3_593307 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D6_AD012_indexed


title: DU145_Res_58


title: DU145_Res_59


title: serum miRNAs, Study ID 9067527

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
794-A008908_1_1


title: PAR-CLIP THP1 stimulated sample rep 2

description:
TruSeq Small RNA Library Preparation Kits
stimulated_clusters
untrimmed4
PC_THP1_stimulated_rep2

data_processing:
library strategy: PAR-CLIP
RNA-seq and RIP-seq data were aligned to human genome (hg19) using STAR mapper and CPM values for each gene were calculated using DeSeq2
PAR-CLIP data was processed using PARa-lyzer
SLAM-seq data was processed using SLAM-DUNK
Genome_build: Encode hg19
Supplementary_files_format_and_content: counts for RNA-Seq and RIP-seq; PARalyzer output for clusters; SLAM-seq Tcounts outout

value: THP-1 monocytic-like cell line

tag: treatment

value: treated for 16 hours with (70 nM cGAMP)

tag: antibody

value: monoclonal anti-FLAG M2 antibody (sigma F1804-5MG)


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D8_AD010_indexed


title: PAR-CLIP THP1 stimulated sample rep 1

description:
TruSeq Small RNA Library Preparation Kits
stimulated_clusters
untrimmed2
PC_THP1_stimulated_rep1


title: DU145_Res_57


title: DU145_Res_56


title: D1_G3_592211 rep1


title: D0_G3_591028 rep1


title: D0_G2_591021 rep1


title: serum miRNAs, Study ID 9074703

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
794-A008914_1_1

tag: tissue

value: serum

value: Type 1 Diabetes

tag: age at diagnosis (years)


title: D1_G2_593309 rep1


title: DU145_Res_60


title: PAR-CLIP THP1 naïve sample rep 2

description:
TruSeq Small RNA Library Preparation Kits
naïve_clusters
untrimmed3
PC_THP1_naive_rep2

value: untreated


title: serum miRNAs, Study ID 9049861

description:
VLP00150 NewOnset_miRNA Median Normalized.csv
VLP00150 NewOnset_miRNA_raw CPM.csv
794-A008940_1_1

tag: Sex

tag: age at draw (years)


title: D1_G4_591027 rep1

value: P


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D7_AD001_indexed

tag: brain region

value: MOp

tag: age


title: DU145_Res_55

tag: docetaxel

value: Prostate cancer


title: DU145_Res_54

tag: disease state


title: PAR-CLIP THP1 naïve sample rep 1

description:
TruSeq Small RNA Library Preparation Kits
naïve_clusters
untrimmed1
PC_THP1_naive_rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D5_AD006_indexed

tag: strain


title: DU145_Res_52

tag: cell line


title: DU145_Res_53


title: D0_G1_591024 rep1

tag: subject

tag: day


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D6_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D7_AD004_indexed


title: DU145_Res_51


title: D1_G4_591022 rep1

tag: vaccinegroup

tag: efficacy


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D4_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D5_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D4_AD012_indexed


title: DU145_Res_50


title: D57_G4_591020 rep1

value: NP


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D3_AD010_indexed

value: male


title: DU145_Res_49


title: D0_G4_591011 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D4_AD006_indexed


title: D57_G4_591011 rep1


title: D29_G3_591017 K rep1


title: C-1_G2_591012 rep1


title: DU145_Res_47


title: D57_G4_597403 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D5_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D4_AD002_indexed


title: DU145_Res_46


title: DU145_Res_44


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D5_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D5_AD007_indexed


title: DU145_Res_43


title: D57_G1_591015 rep1


title: DU145_Res_45


title: DU145_Res_42


title: DU145_Res_48


title: D1_G3_591028 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D3_AD007_indexed


title: DU145_Res_41


title: DU145_Res_40


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D3_AD002_indexed


title: D29_G4_592204 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D3_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D4_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D2_AD006_indexed


title: D57_G2_593309 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D2_AD001_indexed


title: DU145_Res_38


title: DU145_Res_39


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D4_AD007_indexed


title: DU145_Res_37


title: C-1_G2_591006 rep1


title: DU145_Res_36


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D3_AD006_indexed


title: DU145_Res_35


title: C-1_G3_592212 rep1


title: D1_G2_591018 rep1


title: D0_G4_593310 rep1


title: D1_G4_592204 rep1


title: D29_G2_591021 rep1


title: D57_G3_591026 rep1


title: PC3_Sen_1


title: D1_G2_591021 rep1


title: C-1_G4_591020 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D3_AD004_indexed


title: DU145_Res_34


title: DU145_Res_33


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D2_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D1_AD004_indexed


title: DU145_Res_31


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D2_AD007_indexed


title: DU145_Res_30


title: DU145_Res_32


title: DU145_Res_29


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D1_AD007_indexed


title: DU145_Res_28


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D1_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D1_AD010_indexed


title: DU145_Res_26


title: DU145_Res_27


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D2_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D1_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D10_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D10_AD010_indexed


title: D0_G2_593305 rep1


title: DU145_Res_24


title: DU145_Res_23


title: D29_G2_593309 rep1


title: D57_G4_591027 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D10_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D1_AD001_indexed


title: D57_RTSS_5026 rep2

value: RTSS

tag: efficacy [sterile protected, delayed, not protected]


title: D0_G3_591034 rep1


title: D57_RTSSplus_5025 rep2

value: RTSSplus

value: SP


title: D0_G2_591018 rep1


title: D1_RTSSplus_5024 rep1


title: D57_RTSS_5103 rep1


title: D29_RTSSplus_5107 rep1


title: DU145_Res_25


title: D1_RTSS_5046 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D10_AD006_indexed


title: DU145_Res_21


title: D57_RTSS_5045 rep1


title: D29_RTSSplus_5111 rep1


title: D57_RTSSplus_5111 rep1


title: DU145_Res_20


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D10_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D10_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C9_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D10_AD004_indexed


title: DU145_Res_17


title: DU145_Res_22


title: DU145_Res_18


title: D29_RTSS_5106 rep1


title: D1_RTSS_5109 rep1

value: D


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C9_AD007_indexed


title: D0_RTSS_5105 rep1


title: D0_RTSS_5112 rep1


title: DU145_Res_19


title: D29_RTSS_5112 rep1


title: DU145_Res_16


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C9_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C9_AD006_indexed


title: DU145_Res_15


title: DU145_Res_12


title: DU145_Res_14


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C8_AD012_indexed


title: DU145_Res_13


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_D4_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C8_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C8_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C9_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C8_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C9_AD004_indexed


title: DU145_Res_9


title: DU145_Res_10


title: DU145_Res_8


title: DU145_Res_7


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C8_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C9_AD002_indexed


title: D0_RTSS_5106 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C8_AD001_indexed


title: DU145_Res_11


title: DU145_Res_6


title: DU145_Res_5


title: D1_RTSSplus_5111 rep1


title: DU145_Res_4


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C7_AD002_indexed


title: DU145_Res_3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C6_AD010_indexed


title: DU145_Res_2


title: D0_RTSS_5109 rep1


title: DU145_Res_1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C8_AD002_indexed


title: 99_S31_L004_R1_001_W16_NL

city: New York

first: Ana

last: Pavel

state: NY

address: One Gustave L. Levy Place

department: Dermatology

institute: Icahn School of Medicine at Mount Sinai

description: exp.csv

data_processing:
RNA-seq sample quality was assessed using FastQC and MultiQC.
Samples were aligned to human reference genome based on STAR RNA-sequencing aligner and sequencing reads were assigned to genomic features by featureCounts.
Genomic features with 0 counts in more than 20% of the samples were filtered out.
Data was then transfromed to log2-counts per million by voom-transform.
Fold changes (FCHs) vs. baseline were estimated and hypothesis testing was conducted with contrasts under the general framework for linear models in limma package. P-values were adjusted using the Benjamini-Hochberg procedure, which controls False Discovery Rate (FDR).
Genome_build: GRCh38

source_name: Skin biopsy

extract_protocol:
Total RNA was extracted from skin biopsy samples using Qiagen miRNeasy Mini kit.
The libraries were generated using TruSeq Stranded mRNA Library Prep kit following manufactory protocol. Briefly, mRNA was first extracted from 240ng of total RNA using oligo-dT magnetic beads and fragmented at high temperature. A cDNA library was then prepared from the fragemented mRNA by revervse transcription, second strand synthesis and ligation of specific adapters.
Next generation sequencing was performed on Illumina Hiseq 4000 with single-ended 100 red cycles. Image analysis and bases calling was conducted in real-time by the Illumina analysis pipeline.

tag: ptid

tag: timepoint

tag: treatment

value: Placebo

tag: tissuetype

value: NL


title: 98_S30_L004_R1_001_W4_LS

description: exp.csv

value: LS


title: 97_S29_L004_R1_001_BL_LS

description: exp.csv

value: BL


title: 96_S28_L004_R1_001_BL_NL

description: exp.csv


title: 95_S27_L004_R1_001_W16_LS

description: exp.csv

value: Secukinumab


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C7_AD004_indexed

tag: Sex


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C5_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C7_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C7_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C6_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C7_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C6_AD002_indexed


title: 94_S9_L002_R1_001_W16_NL

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C5_AD004_indexed


title: D1_RTSS_5112 rep1


title: D1_RTSS_5105 rep1


title: D29_RTSS_5105 rep1


title: D1_RTSS_5106 rep1


title: D57_RTSS_5105 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C5_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C5_AD001_indexed


title: D29_RTSS_5109 rep1


title: D71_RTSSplus_5107 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C5_AD006_indexed


title: D0_RTSSplus_5111 rep1


title: D15_RTSSplus_5005 rep1


title: D0_RTSS_5045 rep1


title: D15_RTSSplus_5107 rep1


title: D0_RTSS_5046 rep1


title: 92_S25_L002_R1_001_BL_LS

description: exp.csv


title: D29_RTSSplus_5104 rep1


title: 91_S24_L002_R1_001_BL_NL

description: exp.csv


title: 90_S23_L002_R1_001_W16_LS

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C6_AD001_indexed


title: D1_RTSSplus_5116 rep1


title: 93_S26_L002_R1_001_W4_LS

description: exp.csv


title: 9_S9_L002_R1_001_W16_NL

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C4_AD010_indexed


title: D0_RTSS_5103 rep1


title: D0_RTSSplus_5107 rep1


title: D57_RTSSplus_5107 rep1


title: D29_RTSS_5046 rep1


title: D1_RTSSplus_5107 rep1


title: D57_RTSSplus_5031 rep1


title: D1_RTSS_5039 rep2


title: D1_RTSSplus_5005 rep1


title: D0_RTSS_5006 rep1


title: 89_S22_L002_R1_001_W16_NL

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C4_AD012_indexed


title: D29_RTSS_5006 rep1


title: 87_S20_L002_R1_001_BL_LS

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C4_AD006_indexed


title: 88_S21_L002_R1_001_W4_LS

description: exp.csv


title: 86_S8_L002_R1_001_BL_NL

description: exp.csv


title: 85_S19_L002_R1_001_W16_LS

description: exp.csv


title: 84_S18_L002_R1_001_W16_NL

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C4_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C3_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C3_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C6_AD004_indexed


title: 81_S15_L002_R1_001_BL_NL

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C4_AD007_indexed


title: 82_S16_L002_R1_001_BL_LS

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C3_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C7_AD006_indexed


title: 80_S14_L002_R1_001_W16_LS

description: exp.csv


title: 8_S8_L002_R1_001_W4_LS

description: exp.csv


title: D29_RTSSplus_5005 rep1


title: D29_RTSS_5007 rep1


title: 79_S13_L002_R1_001_W16_NL

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C3_AD010_indexed


title: D57_RTSS_5006 rep1


title: 83_S17_L002_R1_001_W4_LS

description: exp.csv


title: D0_RTSSplus_5005 rep1


title: D15_RTSSplus_5004 rep1


title: D57_RTSSplus_5004 rep1


title: 78_S12_L002_R1_001_W4_LS

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C3_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C3_AD001_indexed


title: 77_S11_L002_R1_001_BL_LS

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C4_AD002_indexed


title: D0_RTSSplus_5015 rep1


title: 76_S66_L008_R1_001_BL_NL

description: exp.csv


title: D29_RTSSplus_5017 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C2_AD004_indexed


title: 75_S65_L008_R1_001_W16_LS

description: exp.csv


title: D1_RTSSplus_5002 rep1


title: D0_RTSSplus_5017 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C2_AD002_indexed


title: D29_RTSSplus_5011 rep1


title: 74_S64_L008_R1_001_W16_NL

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C2_AD001_indexed


title: 73_S63_L008_R1_001_W4_LS

description: exp.csv


title: D57_RTSSplus_5005 rep1


title: D1_RTSS_5006 rep1


title: 71_S61_L008_R1_001_BL_NL

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C2_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C2_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C11_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C1_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C2_AD010_indexed


title: 70_S6_L001_R1_001_W16_LS

description: exp.csv


title: 7_S7_L002_R1_001_BL_LS

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C11_AD006_indexed


title: D0_RTSSplus_5011 rep1


title: 68_S60_L008_R1_001_BL_LS

description: exp.csv


title: D29_RTSSplus_5015 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C11_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C11_AD010_indexed


title: 72_S62_L008_R1_001_BL_LS

description: exp.csv


title: 66_S5_L001_R1_001_W16_NL

description: exp.csv


title: 67_S59_L008_R1_001_W16_LS

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C1_AD007_indexed


title: D29_RTSS_5001 rep1


title: D1_RTSSplus_5018 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C11_AD007_indexed


title: D57_RTSSplus_5018 rep1


title: D1_RTSSplus_5017 rep1


title: D1_RTSSplus_5015 rep1


title: D15_RTSSplus_5018 rep1


title: D71_RTSSplus_5015 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C1_AD001_indexed


title: D57_RTSSplus_5011 rep1


title: 63_S62_L008_R1_001_BL_NL

description: exp.csv


title: 61_S60_L008_R1_001_W16_NL

description: exp.csv


title: 62_S61_L008_R1_001_W16_LS

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C11_AD008_indexed


title: 60_S59_L008_R1_001_W4_LS

description: exp.csv


title: 64_S63_L008_R1_001_BL_LS

description: exp.csv


title: 6_S6_L002_R1_001_BL_NL

description: exp.csv


title: D71_RTSSplus_5018 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C1_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C10_AD010_indexed


title: 59_S58_L008_R1_001_BL_LS

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C10_AD012_indexed


title: 58_S57_L008_R1_001_BL_NL

description: exp.csv


title: 57_S56_L008_R1_001_W16_LS

description: exp.csv


title: 55_S54_L007_R1_001_W4_LS

description: exp.csv


title: 56_S55_L008_R1_001_W16_NL

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C10_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C10_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C11_AD001_indexed


title: D71_RTSSplus_5011 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C10_AD002_indexed


title: D29_RTSSplus_5018 rep1


title: 54_S53_L007_R1_001_BL_LS

description: exp.csv


title: D1_RTSS_5007 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B9_AD004_indexed


title: D1_RTSSplus_5011 rep1


title: D15_RTSSplus_5002 rep1


title: 53_S52_L007_R1_001_BL_NL

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B9_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C11_AD002_indexed


title: 52_S51_L007_R1_001_BL_LS

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B9_AD010_indexed


title: D0_RTSSplus_5018 rep1


title: 51_S4_L001_R1_001_BL_NL

description: exp.csv


title: D71_RTSSplus_5002 rep1


title: D15_RTSSplus_5015 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C10_AD008_indexed


title: D29_RTSSplus_5004 rep1


title: D57_RTSSplus_5017 rep1


title: 50_S50_L007_R1_001_W16_LS

description: exp.csv


title: D71_RTSSplus_5111 rep1


title: D57_RTSSplus_5015 rep1


title: D71_RTSSplus_5104 rep1


title: D0_RTSSplus_5002 rep1


title: Input_Batch_L

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: Input DNA

data_processing:
Basecalls were performed using  bcl2fastq v2.17 for NextSeq output.
ChIP-seq reads were trimmed from the 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

growth_protocol: HCT116 cells (ATCC CCL-247) were grown at 37 °C in DMEM supplemented with 10% FBS (Fisher Scientific, 35-015-CV).

extract_protocol:
1x10^8 cells were fixed in 1% formaldehyde (Sigma, 252549) in PBS for 15- 20 min at room temperature and quenched with 1/10th volume of 1.25 M glycine for 5 minutes at room temperature. Cells were collected at 1,000xg for 5 minutes, washed in PBS, pelleted at 1,000xg for 5 min and pellets were flash frozen in liquid nitrogen and stored at -80°C until use. Pellets were thawed on ice and resuspended in 10 ml lysis buffer 1 (50 mM HEPES, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% IGEPAL CA-630, 0.25% Triton X-100 with 5μl/ml Sigma 8340 protease inhibitor cocktail incubated on ice 10 minutes, pelleted 1,500xg and subsequently washed in lysis buffer 2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and 5ul/ml protease inhibitor) as with lysis buffer 1 before resuspending in 1 ml lysis buffer 3 (10 mM tris-HCl pH 8.0, 1 mM EDTA, 0.1% SDS and 5 ul/ml protease inhibitors) for sonication. Chromatin was sheared in a 1 ml milliTUBE with AFA fiber on a Covaris E220 using 10% duty factor for 2 min. The sheared chromatin concentration was estimated with Nanodrop at OD 260 and diluted to 1 mg/ml in ChIP Dilution Buffer (10% Triton X-100, 1M NaCl and 1% Sodium deoxycholate). 1 mg chromatin was combined with 4 μg hybridoma tissue culture supernatant and rotated overnight at 4°C. 40 μl protein A/G Dynabeads was added and incubated for 2-4 hr rotating at 4°C. Samples were washed 5 times with 1 ml RIPA buffer, 2 times with TE with 50 mM NaCl. Chromatin was eluted with 800 μl elution buffer (50 mM Tris pH 8.0, 1 mM EDTA, 0.1% SDS) for 30 min at 65°C shaking at 1,500 rpm in a ThermoMixer (Eppendorf). Supernatants were collected, digested with 20 μl of 20 mg/ml Proteinase K and incubated overnight at 65°C. DNA was purified with phenol chloroform extraction. 500 μl of the aqueous phase was precipitated with 20 μl 5M NaCl, 1.5 μg glycogen and 1 ml EtOH on ice for 1 hr or at -20°C overnight.
Sequencing libraries were prepared with the KAPA HTP library prep kit (Roche) using 1-10 ng DNA and libraries were size selected with AMPure XP beads (Beckman Coulter).

treatment_protocol:
Heat shock and non-heat shock HCT116 cells were washed with PBS before fixing with 1% formaldehyde (Sigma, 252549) in PBS for 15 minutes and processing for ChIP-seq.
For RNAi, Lentiviruses were mixed with an equal volume of fresh media supplemented with 10% FBS and polybrene was added at a final concentration of 5 µg/mL to increase infection efficiency. The medium was changed 6 hours after infection. Cells were selected with 2 µg/ml puromycin for three days before processing for ChIP-seq.

tag: cell type

value: colorectal carcinoma


title: Input_Batch_M

description: Input DNA


title: 5_S5_L002_R1_001_W16_LS

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B8_AD010_indexed

tag: brain region


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B8_AD012_indexed

tag: age


title: 49_S49_L007_R1_001_W16_NL

description: exp.csv


title: Input_NRF1_3H3

description: Input DNA


title: 48_S48_L007_R1_001_W4_LS

description: exp.csv


title: Input_Batch_K

description: Input DNA


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B9_AD002_indexed


title: D1_RTSS_5045 rep1


title: D15_RTSSplus_5111 rep1


title: Input_NRF1_3D4_sh1

description: Input DNA


title: Input_NRF1_3D4_sh2

description: Input DNA


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_C10_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B9_AD007_indexed


title: D1_RTSSplus_5104 rep1


title: 47_S47_L007_R1_001_BL_LS

description: exp.csv


title: Input_NRF1_3D4_NonT

description: Input DNA


title: D1_RTSSplus_5004 rep1


title: 46_S46_L007_R1_001_BL_NL

description: exp.csv


title: D29_RTSS_5045 rep1


title: 44_S44_L006_R1_001_W4_LS

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B8_AD006_indexed


title: Input_HSF1_1A6_HSF1_1C1_43

description: Input DNA


title: 43_S43_L006_R1_001_BL_LS

description: exp.csv


title: D57_RTSS_5046 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B8_AD004_indexed


title: D29_RTSS_5103 rep1


title: Input_HSF1_1A10_HSF1_1A8_HSF1_1A9_HSF1_1D11_HSF2_2C1_43

description: Input DNA


title: Input_HSF1_1A6_HSF1_1C1_37

description: Input DNA


title: D1_RTSS_5103 rep1


title: D29_RTSS_5039 rep1


title: 42_S42_L006_R1_001_BL_NL

description: exp.csv


title: Input_HSF1_1A10_HSF1_1A8_HSF1_1A9_HSF1_1D11_HSF2_2C1_37

description: Input DNA


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B8_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B9_AD001_indexed


title: 45_S45_L006_R1_001_W16_LS

description: exp.csv


title: D0_RTSS_5039 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B7_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B9_AD006_indexed


title: D0_RTSSplus_5027 rep1


title: 40_S40_L006_R1_001_W16_NL

description: exp.csv


title: Input_Batch_I

description: Input DNA


title: Input_Batch_H

description: Input DNA


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B6_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B7_AD001_indexed


title: 4_S4_L002_R1_001_W16_NL

description: exp.csv


title: D29_RTSSplus_5025 rep1


title: D1_RTSSplus_5025 rep1


title: 39_S39_L006_R1_001_W4_LS

description: exp.csv


title: Input_Batch_F

description: Input DNA


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B7_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B6_AD010_indexed


title: 41_S41_L006_R1_001_W16_LS

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B7_AD002_indexed


title: Input_Batch_D

description: Input DNA


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B6_AD004_indexed


title: D29_RTSS_5038 rep1


title: Input_Batch_E

description: Input DNA


title: D71_RTSSplus_5024 rep1


title: 36_S36_L005_R1_001_W4_LS

description: exp.csv


title: 35_S35_L005_R1_001_BL_LS

description: exp.csv


title: Input_Batch_G

description: Input DNA


title: D1_RTSS_5039 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B8_AD007_indexed


title: Input_Batch_C

description: Input DNA


title: Input_Batch_B

description: Input DNA


title: 34_S34_L005_R1_001_BL_NL

description: exp.csv


title: D57_RTSSplus_5025 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B7_AD012_indexed


title: Input_Batch_A

description: Input DNA


title: D57_RTSS_5026 rep1


title: D1_RTSS_5038 rep1


title: 37_S37_L006_R1_001_BL_NL

description: exp.csv


title: D15_RTSSplus_5031 rep1


title: 33_S33_L005_R1_001_W16_LS

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B6_AD001_indexed


title: YEATS4_1D2

description: ChIP-seq

tag: antibody

tag: associated input


title: 32_S32_L005_R1_001_W16_NL

description: exp.csv


title: D29_RTSS_5020 rep1


title: 31_S31_L005_R1_001_W4_LS

description: exp.csv


title: YEATS2_1B3

description: ChIP-seq


title: WHSC1_2A11

description: ChIP-seq


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B5_AD007_indexed

tag: strain


title: 38_S38_L006_R1_001_BL_LS

description: exp.csv


title: WHSC1_2A1

description: ChIP-seq

tag: cell line


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B5_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B6_AD007_indexed


title: 30_S30_L005_R1_001_BL_LS

description: exp.csv


title: USP7_1B6

description: ChIP-seq


title: 3_S3_L002_R1_001_W4_LS

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B7_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B5_AD006_indexed


title: D29_RTSSplus_5024 rep1

tag: subject


title: D57_RTSS_5029 rep1

tag: day


title: 29_S29_L005_R1_001_BL_NL

description: exp.csv


title: D57_RTSS_5039 rep1

tag: vaccinegroup


title: TRIM24_1B12

description: ChIP-seq


title: D0_RTSS_5026 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B5_AD004_indexed


title: D29_RTSSplus_5027 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B5_AD001_indexed


title: D29_RTSS_5029 rep1


title: TCEAL8_1C4

description: ChIP-seq


title: 27_S27_L004_R1_001_W16_NL

description: exp.csv


title: D1_RTSS_5026 rep1


title: 28_S28_L005_R1_001_W16_LS

description: exp.csv


title: SNAPC4_3A7

description: ChIP-seq


title: 25_S25_L004_R1_001_BL_LS

description: exp.csv


title: 26_S26_L004_R1_001_W4_LS

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B4_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B5_AD010_indexed


title: SNAPC4_1G11

description: ChIP-seq


title: SMARCE1_2F1

description: ChIP-seq


title: 24_S24_L004_R1_001_BL_NL

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B4_AD007_indexed


title: D0_RTSS_5007 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B6_AD002_indexed


title: 23_S23_L004_R1_001_W16_LS

description: exp.csv


title: SMARCE1_1G7

description: ChIP-seq


title: SMARCE1_2E9

description: ChIP-seq


title: 22_S22_L004_R1_001_W16_NL

description: exp.csv


title: D71_RTSSplus_5017 rep1


title: 21_S21_L004_R1_001_W4_LS

description: exp.csv


title: SMARCD1_2B5

description: ChIP-seq


title: 20_S20_L004_R1_001_BL_LS

description: exp.csv


title: SMARCD1_2B3

description: ChIP-seq


title: D29_RTSSplus_5002 rep1


title: D57_RTSSplus_5002 rep1


title: D71_RTSSplus_5005 rep1


title: D15_RTSSplus_5017 rep1


title: D0_RTSSplus_5004 rep1


title: SMARCC2_7B6

description: ChIP-seq


title: SMARCC2_1A3

description: ChIP-seq


title: 2_S2_L002_R1_001_BL_LS

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B4_AD004_indexed


title: D15_RTSSplus_5011 rep1


title: D71_RTSSplus_5004 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B4_AD002_indexed


title: 19_S19_L004_R1_001_BL_NL

description: exp.csv


title: 18_S18_L003_R1_001_W16_LS

description: exp.csv


title: SMARCC1_1F1

description: ChIP-seq


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B4_AD001_indexed


title: SMARCB1_2C4

description: ChIP-seq


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B4_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B3_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B3_AD007_indexed


title: D1_RTSS_5029 rep1


title: 170_S40_L005_R1_001_W16_NL

description: exp.csv


title: SMARCAL1_1G7

description: ChIP-seq


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B3_AD012_indexed


title: D0_RTSS_5019 rep1


title: D15_RTSSplus_5025 rep1


title: 17_S17_L003_R1_001_W16_NL

description: exp.csv


title: SMARCAL1_1G2

description: ChIP-seq


title: 169_S39_L005_R1_001_W16_LS

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B3_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B2_AD012_indexed


title: 168_S38_L005_R1_001_W4_LS

description: exp.csv


title: 167_S37_L005_R1_001_BL_NL

description: exp.csv


title: SMARCAL1_1C4

description: ChIP-seq


title: SMAD4_2D1

description: ChIP-seq


title: 166_S36_L005_R1_001_BL_LS

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B3_AD006_indexed


title: SMAD4_2B3

description: ChIP-seq


title: SMAD4_2A5

description: ChIP-seq


title: 165_S35_L005_R1_001_W16_NL

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B1_AD010_indexed


title: Input_Batch_J

description: Input DNA


title: SMAD4_1H2

description: ChIP-seq


title: D0_RTSSplus_5024 rep1


title: SMAD4_1G12

description: ChIP-seq


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B2_AD007_indexed


title: 164_S34_L005_R1_001_W16_LS

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B3_AD001_indexed


title: D57_RTSSplus_5027 rep1


title: D71_RTSSplus_5031 rep1


title: D1_RTSSplus_5031 rep1


title: D29_RTSS_5026 rep1


title: D15_RTSSplus_5027 rep1


title: D15_RTSSplus_5024 rep1


title: D0_RTSSplus_5025 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B1_AD007_indexed


title: SMAD4_1G11

description: ChIP-seq


title: 162_S32_L004_R1_001_BL_NL

description: exp.csv


title: 163_S33_L005_R1_001_W4_LS

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B2_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B3_AD004_indexed


title: SMAD4_1D3

description: ChIP-seq


title: 161_S31_L004_R1_001_BL_LS

description: exp.csv


title: D1_RTSSplus_5027 rep1


title: SMAD4_1C10

description: ChIP-seq


title: SMAD4_1D12

description: ChIP-seq


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B4_AD006_indexed


title: 16_S16_L003_R1_001_W4_LS

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B2_AD001_indexed


title: D71_RTSSplus_5025 rep1


title: 159_S29_L004_R1_001_BL_NL

description: exp.csv


title: D71_RTSSplus_5027 rep1


title: SMAD2_1C12

description: ChIP-seq


title: D0_RTSS_5020 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B1_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B2_AD010_indexed


title: 157_S27_L004_R1_001_W4_LS

description: exp.csv


title: SKIL_1D1

description: ChIP-seq


title: SIRT1_1F6

description: ChIP-seq


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B1_AD001_indexed


title: 158_S28_L004_R1_001_BL_LS

description: exp.csv


title: SMAD2_1B10

description: ChIP-seq


title: SIRT1_1E11

description: ChIP-seq


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B2_AD006_indexed


title: SCML4_1F9

description: ChIP-seq


title: 160_S30_L004_R1_001_W4_LS

description: exp.csv


title: 155_S25_L004_R1_001_BL_LS

description: exp.csv


title: D0_RTSSplus_5031 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B11_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B1_AD006_indexed


title: 154_S24_L003_R1_001_W16_NL

description: exp.csv


title: 153_S36_L005_R1_001_W16_LS

description: exp.csv


title: SCML4_1D6

description: ChIP-seq


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B2_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B11_AD007_indexed


title: D1_RTSSplus_5042 rep1


title: D29_RTSSplus_5031 rep1


title: D57_RTSS_5020 rep1


title: RNF20_1D7

description: ChIP-seq


title: 151_S35_L005_R1_001_BL_NL

description: exp.csv


title: D0_RTSS_5029 rep1


title: D57_RTSS_5019 rep1


title: D1_RTSS_5019 rep1


title: D1_RTSS_5020 rep1


title: RCOR3_1B6

description: ChIP-seq


title: 156_S26_L004_R1_001_BL_NL

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B11_AD012_indexed


title: 150_S23_L003_R1_001_BL_LS

description: exp.csv


title: RCOR3_1B2

description: ChIP-seq


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B11_AD006_indexed


title: 15_S15_L003_R1_001_BL_LS

description: exp.csv


title: 149_S22_L003_R1_001_W16_LS

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B11_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B11_AD001_indexed


title: RCOR2_3F4

description: ChIP-seq


title: RCOR2_1E10

description: ChIP-seq


title: 146_S21_L003_R1_001_BL_NL

description: exp.csv


title: 145_S20_L003_R1_001_W4_LS

description: exp.csv


title: PRDM4_2D1

description: ChIP-seq


title: hepatocyte_CLIP-seq_acf_tg_10

city: Iowa City

first: Jesse

last: Riordan

state: IA

address: 375 Newton Road

institute: University of Iowa

description: Primary hepatocytes isolated from 12 week-old A1cf +/Tg mice were seeded on 10 mm collagen-coated plates, washed and exposed to 400mJ/cm2 of 254 nm UV light in a Stratalinker 2400 (Stratagene). Hepatocytes were scraped in 1ml Lysis buffer containing 50 mM HEPES pH 7.5, 150 mM KCL, 2 mM EDTA, 1 mM NaF, 0.5% (v/v) NP40, 1 mM DTT, 1x protease inhibitors, 2 mM Na3VO4, 5 mM Sodium Pyrophosphate and RNAsin (Promega), incubated 5 min on ice and frozen at -80 °C. Cell lysis was completed by homogenization and the lysate cleared by centrifugation at 13,000g 15 min at 4 °C. RNAsin-treated lysates were treated with RQ1 DNAse (Promega) 5 min at 37 °C followed by 15 min incubation at room temperature with RNAse T1 (Fermentas). A1CF-RNA complexes were immunoprecipitated, washed and treated on-beads with RNAse-T1, ligated with RNA adapters (RL5a-TYE705 and RL3-biotin), resolved on SDS-PAGE and transferred to nitrocellulose. The RNP complexes were excised and treated with Proteinase K (Thermo Scientific). Phenol/chloroform-purified RNA was subjected to cDNA synthesis using DP3 primer, followed by PCR amplification using DP5a and DP3 primers and Platinum Pfx DNA polymerase (Invitrogen). PCR conditions were as followed: 94 °C 2 min, 40 cycles at 94 °C 30 sec, 58 °C 30 sec, 68 °C 30 sec, 68 °C 10 min. PCR products were gel-purified and subjected to a second round of amplification using DSFP5a and indexed DSFP3 primer (RPIX-D3) (one per template) with the following conditions: 94 °C 2 min, 35 cycles at 94 °C 30 sec, 62 °C 45 sec, 68 °C 45 sec, 68 °C 10 min.  Final PCR products were gel purified and submit for High throughput sequencing using sequencing primer SSP1. Primer sequences are as follows: RL5a-TYE705: 5’-AGGGAGGACGAUGCGG-3’; RL3-biotin: 5’-GGCGACCUUCACUGACUGUG-3’; DP5a: 5’-AGGGAGGACGATGCGG-3’; DP3: 5’-CCGCTGGAAGTGACTGACAC-3’; DSFP5a: 5’-AATGATACGGCGACCACCGACTATGGATACTTAGTCAGGGAGGACGATGCGG-3’; RPIX1-DP3: 5’-CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCACCGCTGGAAGTGACTGACAC-3’.

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4b
Gene counts derived with Subread:featureCount 1.45.  RPKM and CPM calculated from gene counts with custom R scripting.
Genome_build: Ensembl Release 76 GRCm38.76
Supplementary_files_format_and_content: Gene counts in tab-delimitted text format

source_name: Isolated hepatocytes

growth_protocol: Studies in primary hepatocytes: Livers were perfused and digested with 0.05% collagenase (Type IV, C5138, Sigma) and hepatocytes plated on collagen-coated dishes overnight.

extract_protocol:
Total RNA was extracted using TRIzol and treated with DNAse. For each genotype and condition, 3 pools were prepared, each containing RNAs from 3-4 separate mice, for a total of 10 mg RNA per final pool.
RNA pools were subjected to oligo(dT) selection and cDNA library preparation and whole transcriptome sequencing on an Illumina HiSeq2000.

value: 12 weeks

tag: tissue

value: Isolated hepatocytes


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B10_AD010_indexed


title: PRDM4_2B4

description: ChIP-seq


title: D29_RTSS_5019 rep1

tag: efficacy [sterile protected, delayed, not protected]


title: 144_S19_L003_R1_001_BL_LS

description: exp.csv

tag: ptid


title: D57_RTSS_5038 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B10_AD012_indexed


title: hepatocyte_CLIP-seq_acf_tg_9


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B10_AD007_indexed


title: hepatocyte_CLIP-seq_acf_tg_8


title: D57_RTSS_5001 rep1


title: D0_RTSS_5001 rep1


title: D57_RTSS_5007 rep1


title: PRDM2_2A4

description: ChIP-seq


title: hepatocyte_CLIP-seq_acf_tg_7


title: PRDM4_2B3

description: ChIP-seq


title: 143_S18_L003_R1_001_BL_NL

description: exp.csv

tag: timepoint


title: 142_S17_L003_R1_001_W4_LS

description: exp.csv

tag: treatment


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B10_AD006_indexed


title: 141_S16_L002_R1_001_BL_LS

description: exp.csv

tag: tissuetype


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B11_AD002_indexed

tag: Sex


title: hepatocyte_CLIP-seq_acf_tg_6


title: 140_S15_L002_R1_001_BL_NL

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B10_AD001_indexed


title: PRDM1_2C5

description: ChIP-seq

tag: cell type


title: hepatocyte_CLIP-seq_acf_tg_5


title: PRDM1_2B9

description: ChIP-seq


title: PRDM2_2A1

description: ChIP-seq


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A9_AD012_indexed

tag: brain region


title: 14_S14_L003_R1_001_BL_NL

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A9_AD010_indexed

tag: age


title: PCGF6_1A2

description: ChIP-seq

tag: antibody


title: 139_S14_L002_R1_001_W4_LS

description: exp.csv


title: 138_S13_L002_R1_001_BL_LS

description: exp.csv


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A9_AD001_indexed


title: 137_S12_L002_R1_001_BL_NL

description: exp.csv


title: PCGF3_1D5

description: ChIP-seq

tag: associated input


title: PCGF6_1A11

description: ChIP-seq


title: hepatocyte_CLIP-seq_acf_tg_2

tag: strain


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_B10_AD002_indexed


title: hepatocyte_CLIP-seq_acf_tg_1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_A9_AD006_indexed


title: PCGF3_1B4

description: ChIP-seq

tag: cell line


title: liver_12mo_wt_NJ_3

source_name: Liver

value: 12 months

value: Liver


title: hepatocyte_CLIP-seq_acf_tg_4


title: 135_S10_L002_R1_001_BL_NL

description: exp.csv