title: SG11474142_252665246659_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_30 Day 61


title: SG11474142_252665248013_S001_GE1_1105_Oct12_1_1

status: Public on Mar 30 2020

type: RNA

city: Borstel/Suelfeld

first: Maja

last: Reimann

state: Schleswig Holstein

address: Parkallee 35

department: Clinical infectious disease

country: Germany

institute: Research Center Borstel

hyb_protocol: Agilent Low Input Quick Amp Labelling Kit One Color according to manufacturers instructions

data_processing: Data has been log-transformed and normalized (percentile shift) within the Agilent GeneSpring V13 software

molecule: total RNA

organism: Homo sapiens

source_name: Pat_Valid_29 Day 452

extract_protocol: Paxgene blood RNA isolation kit according to manufacturers instructions

treatment_protocol: Whole-blood samples were stored using PAX gene tubes

tag: disease state

value: MDR

tag: tissue

value: whole-blood


title: SG11474142_252665248013_S001_GE1_1105_Oct12_1_2

scan_protocol: Agilent Low Input Quick Amp Labelling Kit One Color according to manufacturers instructions

source_name: Pat_Valid_29 Day 601


title: Mouse2_GFPLiverMet_S08_clean

type: SRA

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

country: USA

institute: Memorial Sloan Kettering Cancer Center

library_source: transcriptomic

data_processing:
library strategy: GTO sequencing
Adapter removal and removing reads shorter than 36bp using Bbduk
Map reads to mm9 genome using STAR aligner
Separate aligned reads into exonic and allnonexonic
Realign exonic reads to reference genome mm9 using Kallisto and obtain read count tables
Realign allnonexonic reads to refenrence genome mm9 using Bowtie 1.0, remove PCR duplicate reads and process for CNV analysis
Genome_build: mm9
Supplementary_files_format_and_content: read count tables for RNAseq section of data, Varbin files with bincounts for DNAseq section

organism: Mus musculus

source_name: Mouse2_Liver Metastasis

growth_protocol: KPC1199-EGFP cells were thawed and passaged in DMEM supplemented with 10% Fetal Bovine Serum, 1% Pencillin/streptomycin

extract_protocol:
Primary tumors were dissociated using collagenase D and trypsin. They were treated with ACK lysis buffer to remove contaminating red blood cells. These dissociated cells were stained with EpCam, CD45 antibodies. Single cells were isolated by flow cytometry for GFP+, EpCAM+, GFP+EpCAM+ and CD45+ from primary tumors. GFP+ cells were isolated from various metastases
Single cells isolated into 10x Lysis Buffer with Rnase inhibitor. Next they were processed for mRNA transcription for first strand synthesis using Oligo-dT primer and cDNA generated is amplified for 15 cycles following SMART-Seq2 PCR primers. Samples were then treated ionically to fragment gDNA and cDNA to 400-700bp fragments. Later gDNA was amplified using SeqXE kit from Sigma Aldirch using manufacturer instructions. resulting cDNA and gDNA fragments are quantified.  Following this, libraries for sequencing were prepared by subjecting the 1ug of gDNA and cDNA fragments to end-repair, 3′ adenylation and ligation of TruSeq barcoded adapters. After ligation, DNA fragments were size selected using Ampure XP beads. A 0.75 ratio of beads to sample was used to select fragments larger than 200bp and avoid adapter dimers. These fragments were further amplified by PCR, cleaned using Qiaquick PCR Purification Kit and then once again size selected using Ampure XP beads with a 0.75 ratio of beads to sample. The final libraries were then quantified on Nanodrop and Bioanalyzer using Agilent's High Sensitivity DNA Analysis Kit. 10nM of each sample was then pooled together and the resulting pool was then sequenced single read 76bp length on the Illumina NextSeq

treatment_protocol: 50000 KPC1199-EGFP cells in matrigel were injected orthotopically into the pancreas of 6-8 week old C57BL/6 male mice. Tumors were allowed to grow for 6-8 weeks before tumors were extracted.

tag: strain

tag: Sex

value: male

tag: tumor type

value: Metastasis

value: Liver

tag: cell type

value: Tumor

tag: marker

value: GFP, Calcien Violet for Live/Dead

tag: molecule type

value: genomic DNA and mRNA


title: Mouse2_GFPLiverMet_S09_clean


title: Mouse2_GFPLiverMet_S10_clean


title: SG11474142_252665248012_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_29 Day 300

label_protocol: Agilent Low Input Quick Amp Labelling Kit One Color according to manufacturers instructions


title: SG11474142_252665246659_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_30 Day 13


title: Mouse2_GFPPeritoneumMet_S43_clean

source_name: Mouse2_Peritoneum Metastasis

value: Peritoneum


title: Mouse2_GFPLiverMet_S05_clean


title: Mouse2_GFPLiverMet_S07_clean


title: Mouse2_GFPLiverMet_S06_clean


title: SG11474142_252665248012_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_29 Day 174


title: SG11474142_252665248012_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_29 Day 97


title: SG11474142_252665248012_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_29 Day 0


title: Mouse2_GFPPeritoneumMet_S37_clean


title: Mouse2_GFPLiverMet_S02_clean


title: SG11474142_252665248011_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_29 Day 13


title: Mouse2_GFPLiverMet_S04_clean


title: Mouse2_GFPLiverMet_S03_clean


title: SG11474142_252665248168_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_29 Day 966


title: Mouse2_GFPLiverMet_S01_clean


title: SG11474142_252665246660_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_30 Day 306


title: Mouse2_GFPLiverMet_S13_clean


title: Mouse2_GFPLiverMet_S12_clean


title: Mouse2_GFPLiverMet_S14_clean


title: Mouse2_GFPLiverMet_S15_clean


title: SG11474142_252665248153_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_28 Day 218

value: Non MDR


title: SG11474142_252665248142_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_28 Day 129


title: Mouse2_GFPLiverMet_S18_clean


title: Mouse2_GFPLiverMet_S16_clean


title: SG11474142_252665248142_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_28 Day 14


title: SG11474142_252665248043_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_29 Day 151


title: SG11474142_252665248142_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_28 Day 0


title: SG11474142_252665248142_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_28 Day 74


title: Mouse2_GFPLiverMet_S17_clean


title: SG11474142_252665248317_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_27 Day 99


title: Mouse2_GFPLiverMet_S21_clean

source_name: Mouse2_Liver Metastasis


title: SG11474142_252665248358_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_27 Day 277


title: Mouse2_GFPLiverMet_S19_clean


title: SG11474142_252665248317_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_27 Day 63


title: SG11474142_252665248317_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_27 Day 176


title: Mouse2_GFPKidneyMet_S50_clean

source_name: Mouse2_Kidney Metastasis

value: Kidney


title: Mouse2_GFPKidneyMet_S51_clean


title: SG11474142_252665248317_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_27 Day 14


title: Mouse2_GFPKidneyMet_S48_clean


title: Mouse2_GFPKidneyMet_S49_clean


title: Mouse2_GFPKidneyMet_S47_clean


title: SG11474142_252665248166_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_26 Day 187


title: SG11474142_252665248166_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_26 Day 175


title: SG11474142_252665248153_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_28 Day 288


title: SG11474142_252665248316_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_27 Day 0


title: SG11474142_252665248166_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_26 Day 63


title: Mouse2_GFPKidneyMet_S46_clean


title: SG11474142_252665248140_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_25 Day 46


title: Mouse2_GFPKidneyMet_S45_clean


title: Mouse2_GFPKidneyMet_S44_clean


title: SG11474142_252665248152_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_26 Day 0


title: Mouse2_GFPLiverMet_S20_clean


title: SG11474142_252665248140_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_25 Day 0


title: SG11474142_252665248140_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_25 Day 12


title: Mouse2_GFPKidneyMet_S42_clean


title: Mouse2_GFPKidneyMet_S43_clean


title: Mouse2_GFPKidneyMet_S41_clean


title: SG11474142_252665248140_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_25 Day 563


title: Mouse2_GFPKidneyMet_S52_clean


title: SG11474142_252665248028_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_25 Day 339


title: SG11474142_252665248168_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_25 Day 649


title: Mouse2_GFPKidneyMet_S40_clean


title: SG11474142_252665248027_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_25 Day 306


title: Mouse2_GFPKidneyMet_S38_clean


title: Mouse2_GFPKidneyMet_S39_clean


title: SG11474142_252665248007_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_24 Day 7


title: Mouse2_GFPKidneyMet_S37_clean


title: SG11474142_252665248152_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_26 Day 13


title: SG11474142_252665248027_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_25 Day 291


title: SG11474142_252665248039_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_24 Day 86


title: SG11474142_252665248006_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_24 Day 43


title: Mouse2_GFPKidneyMet_S32_clean

source_name: Mouse2_Kidney Metastasis


title: Mouse2_GFPKidneyMet_S35_clean


title: Mouse2_GFPKidneyMet_S34_clean


title: SG11474142_252665248006_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_24 Day 13


title: SG11474142_252665246643_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_23 Day 676


title: Mouse2_GFPKidneyMet_S31_clean


title: SG11474142_252665246643_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_23 Day 465


title: SG11474142_252665246643_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_23 Day 590


title: SG11474142_252665246643_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_23 Day 318


title: Mouse2_GFPKidneyMet_S30_clean


title: Mouse2_GFPEpCamPrimary_S48_clean

source_name: Mouse2_Primary Pancreatic Tumor

value: Primary

value: Pancreas

value: GFP, EpCam, Calcien Violet for Live/Dead


title: Mouse2_GFPEpCamPrimary_S47_clean


title: SG11474142_252665246642_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_23 Day 14


title: SG11474142_252665246642_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_23 Day 0


title: Mouse2_GFPEpCamPrimary_S45_clean


title: SG11474142_252665248314_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_22 Day 609


title: Mouse2_GFPEpCamPrimary_S44_clean


title: Mouse2_GFPKidneyMet_S36_clean


title: SG11474142_252665248314_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_22 Day 455


title: Mouse2_GFPKidneyMet_S33_clean


title: SG11474142_252665248313_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_22 Day 300


title: Mouse2_GFPEpCamPrimary_S43_clean


title: SG11474142_252665248314_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_22 Day 216


title: Mouse2_GFPEpCamPrimary_S15_clean


title: Mouse2_GFPEpCamPrimary_S13_clean


title: Mouse2_EpCamPrimary_S41_clean

value: EpCam, Calcien Violet for Live/Dead


title: Mouse2_GFPEpCamPrimary_S14_clean


title: Mouse2_EpCamPrimary_S39_clean


title: SG11474142_252665248313_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_22 Day 13


title: SG11474142_252665248022_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_21 Day 457


title: Mouse2_EpCamPrimary_S40_clean


title: SG11474142_252665246644_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_23 Day 59


title: SG11474142_252665248313_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_22 Day 6


title: SG11474142_252665248023_S001_GE1_1105_Oct12_1_1


title: SG11474142_252665248313_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_22 Day 63


title: SG11474142_252665248022_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_21 Day 182


title: SG11474142_252665248022_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_21 Day 106


title: Mouse2_EpCamPrimary_S38_clean


title: Mouse2_GFPEpCamPrimary_S46_clean


title: Mouse2_EpCamPrimary_S37_clean


title: SG11474142_252665248022_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_21 Day 38


title: Mouse2_GFPEpCamPrimary_S42_clean


title: Mouse2_EpCamPrimary_S35_clean


title: SG11474142_252665248021_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_21 Day 14


title: Mouse2_EpCamPrimary_S36_clean


title: SG11474142_252665248191_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_21 Day 822


title: SG11474142_252665248021_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_21 Day 0


title: SG11474142_252665248306_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_20 Day 457


title: Mouse2_CD45Primary_S34_clean

source_name: Mouse2_Primary Pancreatic Tumor

value: Stromal

value: CD45, Calcien Violet for Live/Dead


title: Mouse2_EpCamPrimary_S34_clean


title: Mouse2_EpCamPrimary_S33_clean


title: SG11474142_252665248306_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_20 Day 304

value: MDR


title: SG11474142_252665248358_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_20 Day 14

value: whole-blood


title: Mouse2_CD45Primary_S33_clean

value: male


title: SG11474142_252665248306_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_20 Day 119


title: SG11474142_252665248133_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_19 Day 389


title: Mouse2_CD45Primary_S31_clean


title: SG11474142_252665248133_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_19 Day 176


title: Mouse2_CD45Primary_S30_clean


title: Mouse2_CD45Primary_S29_clean


title: Mouse2_CD45Primary_S27_clean


title: Mouse2_CD45Primary_S25_clean


title: SG11474142_252665248133_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_19 Day 134


title: SG11474142_252665248003_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_19 Day 0


title: SG11474142_252665248357_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_18 Day 180


title: SG11474142_252665248133_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_19 Day 14


title: SG11474142_252665248358_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_20 Day 0


title: Mouse2_CD45Primary_S24_clean


title: SG11474142_252665248357_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_18 Day 60


title: Mouse2_CD45Primary_S23_clean


title: SG11474142_252665248357_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_18 Day 14


title: Mouse2_CD45Primary_S26_clean


title: Mouse2_CD45Primary_S22_clean


title: SG11474142_252665248147_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_17 Day 195


title: SG11474142_252665248146_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_17 Day 56


title: Mouse2_CD45Primary_S20_clean


title: Mouse2_CD45Primary_S32_clean


title: Mouse2_CD45Primary_S19_clean


title: SG11474142_252665248146_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_17 Day 14


title: Mouse2_CD45Primary_S18_clean


title: Mouse2_CD45Primary_S28_clean


title: SG11474142_252665248146_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_17 Day 0


title: SG11474142_252665248003_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_16 Day 13


title: Mouse2_CD45Primary_S35_clean

source_name: Mouse2_Primary Pancreatic Tumor


title: SG11474142_252665248003_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_16 Day 0


title: Mouse2_CD45Primary_S16_clean


title: Mouse2_CD45Primary_S17_clean


title: Mouse1_GFPPrimary_S56_clean

source_name: Mouse1_Primary Pancreatic Tumor


title: SG11474142_252665248357_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_18 Day 20


title: Mouse1_GFPNegativePrimaryBulk_S44_clean


title: SG11474142_252665248134_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_15 Day 25


title: SG11474142_252665248134_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_15 Day 13


title: SG11474142_252665248134_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_15 Day 81


title: Mouse1_GFPPrimary_S55_clean


title: SG11474142_252665248135_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_15 Day 349


title: Mouse1_GFPPrimary_S52_clean


title: Mouse1_GFPPrimary_S54_clean


title: Mouse2_CD45Primary_S21_clean


title: Mouse1_GFPPrimary_S51_clean


title: Mouse1_GFPPrimary_S53_clean


title: Mouse1_GFPPrimary_S49_clean


title: Mouse1_GFPPrimary_S50_clean


title: SG11474142_252665248148_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_14 Day 13


title: SG11474142_252665248148_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_14 Day 0


title: SG11474142_252665248038_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_13 Day 286


title: Mouse1_GFPPrimary_S48_clean


title: SG11474142_252665248040_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_13 Day 91


title: Mouse1_GFPPrimary_S47_clean


title: Mouse1_GFPPrimary_S46_clean


title: SG11474142_252665248037_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_13 Day 1


title: SG11474142_252665248038_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_13 Day 13


title: Mouse1_GFPPrimary_S45_clean


title: SG11474142_252665248038_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_13 Day 287


title: Mouse1_GFPPrimary_S44_clean


title: SG11474142_252665248134_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_15 Day 0


title: SG11474142_252665248191_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_13 Day 124


title: SG11474142_252665248153_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_14 Day 176


title: Mouse1_GFPPrimary_S43_clean


title: SG11474142_252665248018_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_12 Day 182


title: Mouse1_GFPPrimary_S41_clean

source_name: Mouse1_Primary Pancreatic Tumor


title: SG11474142_252665248018_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_12 Day 320


title: Mouse1_GFPPrimary_S40_clean


title: SG11474142_252665248017_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_12 Day 13


title: Mouse1_GFPPrimary_S39_clean


title: Mouse1_GFPPrimary_S42_clean


title: SG11474142_252665248018_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_12 Day 55


title: Mouse1_GFPPrimary_S37_clean


title: SG11474142_252665248148_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_14 Day 71


title: Mouse1_GFPPrimary_S38_clean


title: SG11474142_252665248017_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_12 Day 0


title: SG11474142_252665247081_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_11 Day 613


title: Mouse1_GFPPrimary_S35_clean


title: SG11474142_252665247081_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_11 Day 465


title: SG11474142_252665247080_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_11 Day 17


title: Mouse1_GFPPrimary_S34_clean


title: SG11474142_252665247080_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_11 Day 3


title: Mouse1_GFPPrimary_S33_clean


title: SG11474142_252665248168_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_11 Day 992


title: SG11474142_252665248040_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_11 Day 305


title: Mouse1_GFPPrimary_S31_clean


title: SG11474142_252665247080_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_11 Day 62


title: Mouse1_GFPPrimary_S32_clean


title: Mouse1_GFPPrimary_S30_clean


title: SG11474142_252665248316_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_10 Day 182


title: SG11474142_252665248316_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_10 Day 154


title: Mouse1_GFPPrimary_S28_clean


title: Mouse1_GFPPrimary_S29_clean


title: SG11474142_252665248037_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_9 Day 460


title: Mouse1_GFPPrimary_S27_clean


title: Mouse1_GFPPrimary_S24_clean


title: SG11474142_252665248316_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_10 Day 48


title: SG11474142_252665248036_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_9 Day 190


title: Mouse1_GFPPrimary_S26_clean

source_name: Mouse1_Primary Pancreatic Tumor


title: SG11474142_252665248314_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_10 Day 13


title: Mouse1_GFPPrimary_S25_clean


title: Mouse1_GFPPrimary_S22_clean


title: Mouse1_GFPPrimary_S21_clean


title: SG11474142_252665248036_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_9 Day 8


title: SG11474142_252665248036_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_9 Day 63


title: Mouse1_GFPPrimary_S23_clean


title: SG11474142_252665248037_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_9 Day 351


title: SG11474142_252665248036_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_9 Day 13


title: Mouse1_GFPPrimary_S36_clean


title: SG11474142_252665248008_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_9 Day 0


title: Mouse1_GFPPeritoneumMet_S53_clean

source_name: Mouse1_Peritoneum Metastasis

value: Metastasis


title: Mouse1_GFPPeritoneumMet_S52_clean


title: SG11474142_252665248017_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_8 Day 610


title: Mouse1_GFPPeritoneumMet_S50_clean


title: SG11474142_252665248017_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_8 Day 463


title: Mouse1_GFPPeritoneumMet_S51_clean


title: SG11474142_252665248037_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_9 Day 618


title: SG11474142_252665248016_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_8 Day 265


title: Mouse1_GFPPeritoneumMet_S49_clean


title: Mouse1_GFPPeritoneumMet_S47_clean


title: SG11474142_252665248016_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_8 Day 181


title: SG11474142_252665248016_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_8 Day 229


title: Mouse1_GFPPeritoneumMet_S46_clean


title: SG11474142_252665248137_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_7 Day 506


title: SG11474142_252665248137_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_7 Day 344


title: Mouse1_GFPPeritoneumMet_S45_clean


title: SG11474142_252665248136_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_7 Day 2


title: Mouse1_GFPPeritoneumMet_S42_clean


title: SG11474142_252665248136_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_7 Day 14


title: Mouse1_GFPPeritoneumMet_S41_clean


title: Mouse1_GFPPeritoneumMet_S54_clean


title: Mouse1_GFPPeritoneumMet_S44_clean


title: SG11474142_252665248042_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_6 Day 5


title: Mouse1_GFPPeritoneumMet_S40_clean


title: SG11474142_252665248136_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_5 Day 211


title: SG11474142_252665248016_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_8 Day 306


title: Mouse1_GFPPeritoneumMet_S39_clean


title: SG11474142_252665248136_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_5 Day 59


title: Mouse1_GFPPeritoneumMet_S38_clean


title: SG11474142_252665248043_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_6 Day 22


title: Mouse1_GFPPeritoneumMet_S37_clean


title: Mouse1_GFPPeritoneumMet_S35_clean


title: SG11474142_252665248135_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_5 Day 23


title: Mouse1_GFPPeritoneumMet_S48_clean

source_name: Mouse1_Peritoneum Metastasis


title: SG11474142_252665248135_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_5 Day 14


title: Mouse1_GFPPeritoneumMet_S36_clean


title: SG11474142_252665248135_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_5 Day 1


title: Mouse1_GFPPeritoneumMet_S34_clean


title: SG11474142_252665248015_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_8 Day 0


title: Mouse1_GFPPeritoneumMet_S33_clean


title: SG11474142_252665247081_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_4 Day 3


title: SG11474142_252665248040_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_4 Day 607


title: Mouse1_GFPPeritoneumMet_S32_clean


title: Mouse1_GFPPeritoneumMet_S30_clean


title: siZBP1_rep2

city: chengdu

first: Peng

last: Deng

state: Sichuan

address: No.14 Renmin South Rd 3rd Section

department: West China School of Stomotology

country: China

institute: Sichuan University

data_processing:
The reads were aligned to the mm10 build of the mouse genome using Tophat.
Expression of the transcript was determined using Cufflinks with Refseq mRNAs to guide assembly.
Genome_build: mm10

source_name: bone marrow–derived mesenchymal stem/progenitor cells

growth_protocol: Cells were cultuled in DMEM, containing  heat-inactivated FBS, plus 100 U/ml of K-Penicillin G and 100 mg/ml of Streptomycin sulfate at 37°C with a humidified atmosphere of 5% CO2.

extract_protocol:
Total RNA was harvested using Trizol reagent, and mRNA was purified using Dynabeads mRNA purification kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Transfection with siRNAs was performed using Lipofectamine RNAiMAX reagent according to the manufacturer's instructions.

tag: age

tag: sirna


title: ch12_Med14Nsmash_chipseq_Irf4_APR48h

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

library_source: genomic

data_processing:
base calling: illumina CASAVA 1.8.2
ChIP-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm)

molecule: genomic DNA

source_name: CH12 B cell line

growth_protocol: CH12 B lymphoma cells were cultured in RPMI-1640 media supplemented with 10% FBS (Gemini), 1% Penicillin-Streptomycin and 50 µM of -mercaptoethanol (Thermo Fisher Scientific). A 3xFlag and small molecule–assisted shutoff (SMASh) tag was introduced to the N-terminus of Med14 using CRISPR-Cas9 based knock-in via homologous recombination. Single cell clones were established and degradation of Med14 was assessed by western blotting for Med14 (Abcam) after treatment of cells with 3 M Asunaprevir (MCE).

extract_protocol:
ChIP-Seq: Cultured cells were fixed with 1% formaldehyde (Sigma) for 10’ at 37°C. Fixation was quenched by addition of glycine (Sigma) at a final concentration of 125 mM. Twenty million fixed cells were washed with PBS and resuspended in 1 ml of RIPA buffer (10 mM Tris [pH 7.6], 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 1× Complete Mini EDTA free proteinase inhibitor (Roche)) or stored at −80°C until further processing. Sonication was performed using Covaris S2 sonicator at duty cycle 20%, intensity 5, cycle/burst 200 for 30 min or Branson sonifier at amplitude 35%, 12 cycles of 20” sonication and 30” of pause. For native chip, chromatin was digested with Mnase (Sigma) in digestion buffer (50 mM Tris-HCl, pH7.6, 1 mM CaCl2, 0.2% Triton X-100, butyrate 5 mM) for 5’ at  37°C and dialyzed against RIPA buffer for 2hrs at 4°C. Five micrograms of antibody were incubated with 40 μl of Dynabeads Protein A (or G) for 40 min at room temperature. Antibody-bound beads were added to 500 μl of sonicated or Mnase-digested chromatin, incubated at 4°C overnight, and washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (pH 8.0) plus 0.2% Triton X-100, and once with TE (pH 8.0). Crosslinking was reversed by incubating the beads at 65°C for 4 hr in the presence of 0.3% SDS and 1 mg/ml Proteinase K. ChIP DNA was purified by phenol-chloroform extraction followed by ethanol precipitation.
ChIP-Seq :  Library was prepared in Ovation SP Ultralow library system (Nugen). 50 cycles of sequencing data were acquired on the HiSeq 3000 or Novaseq 6000 (Illumina).

tag: genotype

value: lymphoma cell line

tag: chip antibody

value: Santa Cruz, M-17, SC6059

tag: experimental type

value: ChIPseq

tag: treatment


title: ch12_Med14Nsmash_chipseq_Pu1_APR0h

value: Santa Cruz, T-21, SC352


title: ch12_Med14Nsmash_chipseq_Pu1_APR48h


title: SG11474142_252665247082_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_4 Day 362


title: ch12_Med14Nsmash_chipseq_Irf4_APR0h


title: ch12_Med14Nsmash_chipseq_Brd4_DMSO

value: DMSO


title: SG11474142_252665247082_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_4 Day 180


title: scramble_control_rep2

value: bone marrow–derived mesenchymal stem/progenitor cells

value: scramble control


title: Mouse1_GFPPeritoneumMet_S29_clean

value: Peritoneum

value: Tumor

value: GFP, Calcien Violet for Live/Dead

value: genomic DNA and mRNA


title: siZBP1_rep1


title: scramble_control_rep1


title: SG11474142_252665248168_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_4 Day 971


title: Mouse1_GFPPeritoneumMet_S28_clean


title: Mouse1_GFPPeritoneumMet_S27_clean


title: SG11474142_252665248154_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_3 Day 273

value: Non MDR


title: Mouse1_GFPPeritoneumMet_S31_clean


title: ch12_Med14Nsmash_chipseq_Brd4_APR48h


title: SG11474142_252665248141_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_3 Day 182


title: Mouse1_GFPPeritoneumMet_S26_clean


title: Mouse1_GFPPeritoneumMet_S25_clean


title: SG11474142_252665247081_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_4 Day 89


title: Mouse1_GFPPeritoneumMet_S24_clean


title: Mouse1_GFPPeritoneumMet_S23_clean


title: SG11474142_252665248141_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_3 Day 27


title: SG11474142_252665248141_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_3 Day 15


title: Mouse1_GFPPeritoneumMet_S22_clean


title: Mouse1_GFPPeritoneumMet_S21_clean


title: ZD-mir31KO LF38

city: Parma

first: Guidantonio

last: Malagoli Tagliazucchi

address: Via Gramsci 14

department: Division of Research and Innovation

country: Italy

institute: Hospital of Parma

description:
ZD-mir31KO
gene expression data from esophageal epithelia  of rats ZD-mir31KO

scan_protocol: Chips were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.

data_processing: We determined the transcriptional profiles, using Affymetrix Rat 230 2.0 Genome GeneChip. The processing of raw files was performed using Expression Console (Affymetrix, 1.4.46). The normalization was performed using Robust Multiarray Normalization (RMA) implemented in Expression Console and the (Rat_230.CDF).

label: biotin

organism: Rattus norvegicus

source_name: esophageal epithelia

label_protocol: biotin

extract_protocol: Esophageal epithelial samples frozen in liquid nitrogen were pulverized to a fine powder using a chilled hammer.  Total RNA was extracted from the pulverized samples using an animal tissue RNA extraction Kit (#25700, Norgen Biotek, Ontario, Canada).  The integrity of RNA was analyzed by Agilent 2100 Bioanalyzer and RNA integrity number was ≥ 8 for all samples.

treatment_protocol: WT Rats: Four-week-old male Sprague-Dawley rats were divided into four Zn-deficient (ZD) groups and a Zn-sufficient (ZS) group. ZD rats were fed ad libitum and ZS rats were pair-fed to deficient animals to match their decreased food consumption. The animals received PBS-formulated LNA-antimiR oligonucleotides or were untreated, forming four cohorts -  ZD:antimiR/5-wk (n=12), ZD:antimiR/20-wk (n=11), ZD:CTRL (untreated, n = 20), and ZS:CTRL (untreated, n=8). Over a period of the first five weeks, ZD:antimiR/5-wk and ZD:antimiR/20-wk cohorts received via tail vein a loading dose of antimiR (20 mg kg-1), followed by 9 maintenance doses (6 mg kg-1,  twice weekly). Starting at week 5, the animals were given four intragastric doses of N-nitrosomethylbenzylamine (NMBA) (2 mg kg-1, once/week for four weeks). During and following NMBA administration (15 weeks), ZD:antimiR/20-wk rats received 20 additional antimiR doses (6 mg kg-1, twice/week for 5 weeks and then once/week for the remaining 10 weeks). The animals were weighed weekly and sacrificed 48 h after the final dose of antimiR or 15 weeks after the 1st NMBA dose.  miR-31 KO Rats (generated by CRISPR/Cas9 technology in Sprague-Dawley rat strain): Four-week old male miR-31-/- and miR-31+/+ littermates were randomly divided into a ZD or ZS dietary group . The rats were treated with NMBA, using the same NMBA-induced tumor assay as described for WT rats.


title: ZD-mir31KO LF34

hyb_protocol: We determined the transcriptional profiles, using Affymetrix Rat 230 2.0 Genome GeneChip.


title: SG11474142_252665248042_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_2 Day 17


title: SG11474142_252665248004_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_2 Day 203


title: Mouse1_GFPPeritoneumMet_S20_clean

source_name: Mouse1_Peritoneum Metastasis


title: SG11474142_252665248141_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_3 Day 83


title: ZD-mir31KO LF39


title: ZD-mir31KO LF35


title: ZD-mir31KO LF36


title: ZS-mir31KO LF32

description:
ZS-mir31KO
gene expression data from esophageal epithelia  of rats ZS-mir31KO


title: ZD-mir31KO LF37


title: SG11474142_252665247087_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_2 Day 27


title: SG11474142_252665248191_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_3 Day 1


title: ZS-mir31KO LF30


title: ZS_untreated_CTRL LF17

description:
ZS_untreated_CTRL
gene expression data from esophageal epithelia  of rats ZS untreated CTRL

value: ZS untreated


title: ZS_untreated_CTRL LF19


title: ZS_untreated_CTRL LF18


title: ZS-mir31KO LF31


title: SG11474142_252665248041_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_1 Day 181


title: ZD_untreated_CTRL LF15

description:
ZD_untreated_CTRL
gene expression data from esophageal epithelia  of rats ZD untreated CTRL

value: ZD untreated


title: ZS_untreated_CTRL LF20


title: SG11474142_252665248041_S001_GE1_1105_Oct12_1_2

source_name: Pat_Valid_1 Day 133

value: whole-blood


title: ZD_untreated_CTRL LF14


title: SG11474142_252665248041_S001_GE1_1105_Oct12_1_1

source_name: Pat_Valid_1 Day 71


title: ZD_untreated_CTRL LF11


title: ZD_untreated_CTRL LF12


title: ZD_untreated_CTRL LF13


title: ZD-Anti-miR31_5weeks LF10

description:
ZD-Anti-miR31_5weeks
gene expression data from esophageal epithelia  of rats ZD-Anti-miR31 5weeks


title: CEM WNT7A_Rep3

city: Guadalajara

first: Christian

middle: David

last: Barreto Vargas

state: Jalisco

address: Sierra Mojada 800

department: División de Inmunología

country: Mexico

institute: Centro de Investigación Biomédica de Occidente

description:
CEM cell line transduced with the WNT7A ORF into the pLVX vector. It is the third replicated used in this study.
560610A06_13_2015-02-13_modificada_paco_2015-02-17T175913_532.pair

hyb_protocol: Hybridization was performed for 20 hours using the Human Expression 12x135K arrays (Roche Diagnostics, Basel, Switzerland)

scan_protocol: Scanning was performed with the Nimblegene MS200 microarray scanner.

data_processing: All images were normalized with DEVA ver. 12 software (Roche Diagnostic, Basel, Switzerland) for grid alignment and analysis. Normalized data were analyzed using the CLC Main Workbench ver. 7.0.3 software.

source_name: T-cell acute lymphoblastic leukemia transduced with pLVX+WNT7A

label_protocol: Labeling was performed using the Nimblegene One-Color DNA labeling kit (Roche Diagnostics, Basel, Switzerland=

growth_protocol: All cell lines were grown at 37ºC and 5%CO2 atmosphere in RPMI-1640 medium supplemented with 10% Fetal Bovine Serum, 100 U/ml penicilln, 1 mg/ml streptomycin. All produced mentioned before were acquired from Gibco, Thermofisher, MA, USA.

extract_protocol: Total RNA was extracted with the GeneJet RNA Purification Kit (Thermo Scientific, Waltham, MA, USA). RNA integrity was analyzed using the 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA) and the Agilent RNA 6000 Nano Kit (Agilent, Santa Clara, CA, USA). cDNA was generated with the cDNA synthesis system (Agilent, Santa Clara, CA, USA).

tag: cell line

value: CEM-CCRF (CRL8436)

value: T-cell acute lymphoblastic leukemia

value: Transduced with WNT7A ORF into pLVX vector


title: CEM WNT7A_Rep2

description:
CEM cell line transduced with the WNT7A ORF into the pLVX vector. It is the second replicated used in this study.
560610A06_13_2015-02-13_modificada_paco_2015-02-17T175913_532.pair


title: ZD-Anti-miR31_5weeks LF7


title: SG11474142_252665248013_S001_GE1_1105_Oct12_1_3

source_name: Pat_Valid_1 Day 1


title: ZD-Anti-miR31_20weeks LF5

description:
ZD-Anti-miR31_20weeks
gene expression data from esophageal epithelia  of rats ZD-Anti-miR31 20weeks


title: CEM pLVX_Rep3

description:
CEM cell line transduced with the empty vector. It is the third replicated used in this study.
560610A05_13_2015-02-13_modificada_paco_2015-02-17T175904_532.pair

source_name: T-cell acute lymphoblastic leukemia transduced with empty vector (pLVX)

value: Transduced with empty vector (pLVX)


title: ZS_untreated_CTRL LF16


title: SG11474142_252665248013_S001_GE1_1105_Oct12_1_4

source_name: Pat_Valid_1 Day 14


title: ZD-Anti-miR31_5weeks LF6


title: ZD-Anti-miR31_5weeks LF9


title: Reg3: regressed tumor (D13_reg_L4.D710)

city: San Francisco

first: Andrei

last: Goga

state: CA

address: 513 Parnassus Ave

department: Cell & Tissue Biology

institute: UCSF

data_processing:
Sequencines passed the Illumina Purity Filer (PF reads), a per base quality score was assigned as defined by Illumina-scaled Phred metric (base calling).
Reads were aligned to the reference genome using STAR
Differential expression analysis between two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package
Genome_build: GRCm38
Supplementary_files_format_and_content: excel file containing log2FC and p values for differential expression analysis

source_name: mouse mammary tumor

extract_protocol:
Cells were flash frozen using liquid nitrogen. RNA was isolated using the RNAeasy kit according to the instructions (Qiagen), amount and quality of specimenswas confirmed using Agilent BioAnalyzer and NanoDrop analysis
Library preparation and Illumina RNAseq was performed by Q2 Solutions (www.q2labsolutions.com) using TruSeq Stranded mRNA library preparation. DNA fragments were generated and amplified using Clonal Single Molecule Array technology (Cluster Building). Sequences were determined using the Clonal Single Molecule Array and performing Sequencing-by-Synthesis using Reversible Terminator Chemistry.

treatment_protocol: 10 tumors were harvested from mice that were fed doxycycline (MYC ON), three mammary glands from mice that were never fed doxycycline (CTL) and five regressed tumors from mice that were taken off doxycycline for 72 hours (MYC OFF, Reg)

value: off doxycycline chow for 3 days

value: FVB/N

value: mouse mammary tumor


title: Reg4: regressed tumor (F13_reg_L4.D711)


title: Reg5: regressed tumor (H12_reg_L4.D712)


title: ZD-Anti-miR31_20weeks LF1


title: ZD-Anti-miR31_20weeks LF4


title: ZD-Anti-miR31_20weeks LF3


title: CEM pLVX_Rep1

description:
CEM cell line transduced with the empty vector. It is the first replicated used in this study.
560610A05_13_2015-02-13_modificada_paco_2015-02-17T175904_532.pair


title: dorsal back skin at P50, collected at ZT09, treated with 1% IMQ for 24 hr [Wt_24h_ZT09]

city: irvine

first: Elyse

middle: Noelani

last: Greenberg

state: California

address: 839 medical sciences court, sprague hall rm. 250

institute: UC Irvine

description:
Wt_24h_ZT09
RNA from 2-5 pooled mouse back skin samples

hyb_protocol: Affeymetrix SOP was followed.

scan_protocol: GeneChip 3000 Scanner 7G

data_processing:
Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
Plier normalized microarray values were log2 normalized and mean centered across samples being compared to. For genes with multiple reads, the read with the highest average expression across groups was used and the others were excluded from further analysis.

source_name: Wild-type, dorsal back skin

label_protocol: RNA was processed using the affymetrix Mouse Exon 1.0 ST (Affymetrix) manufacturer protocol

extract_protocol: RNAlater preserved samples were processed using the Qiagen RNAeasy kit. RNA integrity numbers and concentrations were checked via agilent bioanalyzer and nanodrop, respectively. Only samples with RINs over 7.5 were used. Samples were pooled for 5-7 mice for certain samples, and 2-5 for other samples.

treatment_protocol: mouse whole back skin was shaved 2 days prior to treatment, and then treated with 1% IMQ or left untreated and mice were sacraficed . Whole dorsal back skin was excised and stored at 4C in RNAlater.

tag: strain background

value: wild-type

value: 1% IMQ for 24 hr

value: full thickness dorsal back skin


title: CEM WNT7A_Rep1

description:
CEM cell line transduced with the WNT7A ORF into the pLVX vector. It is the first replicated used in this study.
560610A06_13_2015-02-13_modificada_paco_2015-02-17T175913_532.pair


title: CEM pLVX_Rep2

description:
CEM cell line transduced with the empty vector. It is the second replicated used in this study.
560610A05_13_2015-02-13_modificada_paco_2015-02-17T175904_532.pair


title: ZD-Anti-miR31_5weeks LF8


title: ZD-Anti-miR31_20weeks LF2


title: dorsal back skin at P50, collected at ZT15, treated with 1% IMQ for 6 hr [Wt_6h_ZT15]

description:
Wt_6h_ZT15
RNA from 2-5 pooled mouse back skin samples

value: 1% IMQ for 6 hr


title: dorsal back skin at P50, collected at ZT13, treated with 1% IMQ for 4 hr [Wt_4h_ZT13]

description:
Wt_4h_ZT13
RNA from 2-5 pooled mouse back skin samples

value: 1% IMQ for 4 hr


title: dorsal back skin at P50, collected at ZT11, treated with 1% IMQ for 2 hr [Wt_2h_ZT11]

description:
Wt_2h_ZT11
RNA from 2-5 pooled mouse back skin samples

value: 1% IMQ for 2 hr


title: dorsal back skin at P50, collected at ZT10, treated with 1% IMQ for 1 hr [Wt_1h_ZT10]

description:
Wt_1h_ZT10
RNA from 2-5 pooled mouse back skin samples

value: 1% IMQ for 1 hr


title: dorsal back skin at P50, collected at ZT09, untreated [Wt_0h_ZT09]

description:
Wt_0h_ZT09
RNA from 2-5 pooled mouse back skin samples

value: untreated


title: BJAB WNT7A_Rep2

description:
BJAB cell line transduced with the WNT7A ORF into the pLVX vector. It is the second replicated used in this study.
560610A09_13_2015-02-13_modificada_paco_2015-02-17T175936_532.pair

source_name: B-cell leukemia transduced with pLVX+WNT7A

value: BJAB ACC757

value: B-cell leukemia derived from Burkitt lymphoma


title: Reg1: regressed tumor (A-2-44_reg_L9)


title: BJAB WNT7A_Rep3

description:
BJAB cell line transduced with the WNT7A ORF into the pLVX vector. It is the third replicated used in this study.
560610A09_13_2015-02-13_modificada_paco_2015-02-17T175936_532.pair


title: dorsal back skin at P50, collected at ZT19, treated with 1% IMQ for 24 hrs [Wt_MD.ZT19.1 day IMQ]

description:
Wt_MD.ZT19.1 day IMQ
RNA from 5-7 pooled mouse back skin samples

value: 1% IMQ for 24 hours


title: BJAB WNT7A_Rep1

description:
BJAB cell line transduced with the WNT7A ORF into the pLVX vector. It is the first replicated used in this study.
560610A09_13_2015-02-13_modificada_paco_2015-02-17T175936_532.pair


title: BJAB pLVX_Rep3

description:
BJAB cell line transduced with the empty vector. It is the third replicated used in this study.
560610A08_13_2015-02-13_modificada_paco_2015-02-17T175928_532.pair

source_name: B-cell leukemia transduced with empty vector (pLVX)


title: MYC10: tumor (H7_L4.D708)

value: doxycycline chow


title: Mouse1_GFPPeritoneumMet_S19_clean

value: male

value: Metastasis

value: Peritoneum

value: Tumor

value: GFP, Calcien Violet for Live/Dead

value: genomic DNA and mRNA


title: MYC9: tumor (F7_L4.D707)

value: FVB/N

value: mouse mammary tumor


title: Mouse1_GFPPeritoneumMet_S18_clean


title: Reg2: regressed tumor (B-1-6_reg_L8.D703)

value: off doxycycline chow for 3 days


title: dorsal back skin at P50, collected at ZT19, untreated [Wt_MD.ZT19.CONTROL]

description:
Wt_MD.ZT19.CONTROL
RNA from 5-7 pooled mouse back skin samples

value: wild-type

value: full thickness dorsal back skin


title: Mouse1_GFPPeritoneumMet_S17_clean


title: MYC8: tumor (D8_L1.D706)


title: BJAB pLVX_Rep2

description:
BJAB cell line transduced with the empty vector. It is the second replicated used in this study.
560610A08_13_2015-02-13_modificada_paco_2015-02-17T175928_532.pair

value: Transduced with empty vector (pLVX)


title: Mouse1_GFPPeritoneumMet_S16_clean


title: MYC6: tumor (D6_L4.D706)


title: MYC7: tumor (D7_L1.D705)


title: dorsal back skin at P50, collected at ZT07, treated with 1% IMQ for 24 hrs [Wt_MD.ZT07.1 day IMQ]

description:
Wt_MD.ZT07.1 day IMQ
RNA from 5-7 pooled mouse back skin samples


title: MYC5: tumor (B-1-9_L3.D705)


title: dorsal back skin at P50, collected at ZT19, treated with 1% IMQ for 24 hrs [Wt_EN.ZT19.1 day IMQ]

description:
Wt_EN.ZT19.1 day IMQ
RNA from 5-7 pooled mouse back skin samples


title: ZS-mir31KO LF33

description:
ZS-mir31KO
gene expression data from esophageal epithelia  of rats ZS-mir31KO

source_name: esophageal epithelia


title: Mouse1_GFPPeritoneumMet_S15_clean


title: dorsal back skin at P50, collected at ZT19, untreated [Wt_EN.ZT19.CONTROL]

description:
Wt_EN.ZT19.CONTROL
RNA from 5-7 pooled mouse back skin samples

value: untreated


title: dorsal back skin at P50, collected at ZT07, treated with 1% IMQ for 24 hrs [Wt_EN.ZT07.1 day IMQ]

description:
Wt_EN.ZT07.1 day IMQ
RNA from 5-7 pooled mouse back skin samples


title: dorsal back skin at P50, collected at ZT07, untreated [Wt_EN.ZT07.CONTROL]

description:
Wt_EN.ZT07.CONTROL
RNA from 5-7 pooled mouse back skin samples


title: dorsal back skin at P50, collected at ZT19, treated with 1% IMQ for 24 hrs [Wt_AD.ZT19.1 day IMQ]

description:
Wt_AD.ZT19.1 day IMQ
RNA from 5-7 pooled mouse back skin samples


title: BJAB pLVX_Rep1

description:
BJAB cell line transduced with the empty vector. It is the first replicated used in this study.
560610A08_13_2015-02-13_modificada_paco_2015-02-17T175928_532.pair

value: BJAB ACC757


title: dorsal back skin at P50, collected at ZT07, treated with 1% IMQ for 24 hrs [Wt_AD.ZT07.1 day IMQ]

description:
Wt_AD.ZT07.1 day IMQ
RNA from 5-7 pooled mouse back skin samples


title: Mouse1_GFPPeritoneumMet_S14_clean


title: dorsal back skin at P50, collected at ZT07, untreated [Wt_MD.ZT07.CONTROL]

description:
Wt_MD.ZT07.CONTROL
RNA from 5-7 pooled mouse back skin samples


title: dorsal back skin at P50, collected at ZT19, untreated [Wt_AD.ZT19.CONTROL]

description:
Wt_AD.ZT19.CONTROL
RNA from 5-7 pooled mouse back skin samples


title: dorsal back skin at P50, collected at ZT09, untreated [Wt.control.ZT09]

description:
Wt.control.ZT09
RNA from 5-7 pooled mouse back skin samples

source_name: Wildtype, dorsal back skin


title: dorsal back skin at P50, collected at ZT07, untreated [Wt_AD.ZT07.CONTROL]

description:
Wt_AD.ZT07.CONTROL
RNA from 5-7 pooled mouse back skin samples


title: dorsal back skin at P50, collected at ZT09, treated with 1% IMQ for 24 hrs [Bmal1.KO.24.hr.IMQ..ZT09]

description:
Bmal1.KO.24.hr.IMQ..ZT09
RNA from 5-7 pooled mouse back skin samples

source_name: Bmal1 KO, dorsal back skin

value: Bmal1 KO


title: dorsal back skin at P50, collected at ZT09, untreated [Bmal1.KO.control.ZT09]

description:
Bmal1.KO.control.ZT09
RNA from 5-7 pooled mouse back skin samples


title: MYC4: tumor (B-1-5_L1)


title: dorsal back skin at P50, collected at ZT09, treated with 1% IMQ for 24 hrs [Wt.24.hr.IMQ..ZT09]

description:
Wt.24.hr.IMQ..ZT09
RNA from 5-7 pooled mouse back skin samples

source_name: wildtype, dorsal back skin

value: 1% IMQ for 24 hours


title: Mouse1_GFPPeritoneumMetBulk_S43_clean

source_name: Mouse1_Peritoneum Metastasis


title: MYC3: tumor (B-1-4_L3.D703)

value: doxycycline chow


title: Mouse1_GFPPeritoneumMet_S13_clean

value: male


title: dorsal back skin at P50, collected at ZT19, treated with 1% IMQ for 5 consecutive days [Wt_ZT19_5 day IMQ]

description:
Wt_ZT19_5 day IMQ
RNA from 5-7 pooled mouse back skin samples

value: 1% IMQ for 5 consecutive days


title: MYC2: tumor (A-2-2_L3)


title: Mouse1_GFPNegativePeritoneumMetBulk_S55_clean

value: Metastasis

value: Peritoneum


title: dorsal back skin at P50, collected at ZT01, treated with 1% IMQ for 5 consecutive days [wt_ZT01.5 day IMQ]

description:
wt_ZT01.5 day IMQ
RNA from 5-7 pooled mouse back skin samples


title: dorsal back skin at P50, collected at ZT07, treated with 1% IMQ for 5 consecutive days [Wt_ZT07.5 day IMQ]

description:
Wt_ZT07.5 day IMQ
RNA from 5-7 pooled mouse back skin samples


title: MYC1: tumor (A-2-1_L1.D702)


title: CTL3: control tissue (Ctl5_L4)

source_name: mouse mammary gland

value: no treatment

value: mouse mammary gland


title: Mouse1_EpCamPrimary_S60_clean

source_name: Mouse1_Primary Pancreatic Tumor

value: Primary

value: Pancreas

value: Tumor

value: EpCam, Calcien Violet for Live/Dead

value: genomic DNA and mRNA


title: CTL2: control tissue (Ctl2_L2)

value: FVB/N


title: Mouse1_EpCamPrimary_S59_clean


title: DOX3: sample MYC expression off (3 days)

data_processing:
Sequencines passed the Illumina Purity Filer (PF reads), a per base quality score was assigned as defined by Illumina-scaled Phred metric (base calling).
Reads were aligned to the reference genome using STAR
Differential expression analysis between two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package
Genome_build: mm9
Supplementary_files_format_and_content: excel file containing log2FC and p values for differential expression analysis

source_name: lymphoma cell line

treatment_protocol: Cells were grown in presence of solvent (CTL) or doxycycline to switch off MYC expression (DOX)

value: B-cell lymphoma

value: doxycycline


title: dorsal back skin at P50, collected at ZT07, treated with 1% IMQ for 24 hrs [wt._ZT07.IMQ.24.hr]

description:
wt._ZT07.IMQ.24.hr
RNA from 5-7 pooled mouse back skin samples

value: wild-type

value: full thickness dorsal back skin


title: Mouse1_EpCamPrimary_S58_clean


title: Mouse1_GFPPrimaryBulk_S57_clean


title: dorsal back skin at P50, collected at ZT19, treated with 1% IMQ for 24 hrs [wt_ZT19.IMQ.24.hr]

description:
wt_ZT19.IMQ.24.hr
RNA from 5-7 pooled mouse back skin samples

value: 1% IMQ for 24 hours


title: dorsal back skin at P50, collected at ZT19, treated with 1% IMQ for 6 hrs [wt_ZT19_6h_IMQ]

description:
wt_ZT19_6h_IMQ
RNA from 5-7 pooled mouse back skin samples

value: 1% IMQ for 6 hours


title: dorsal back skin at P50, collected at ZT01, treated with 1% IMQ for 24 hrs [wt_ZT01.IMQ.24.hr]

description:
wt_ZT01.IMQ.24.hr
RNA from 5-7 pooled mouse back skin samples


title: CTL1: control tissue (Ctl1_L1.D701)


title: DOX2: sample MYC expression off (3 days)


title: dorsal back skin at P50, collected at ZT13, untreated [wt.ZT13.control]

description:
wt.ZT13.control
RNA from 5-7 pooled mouse back skin samples

value: untreated


title: dorsal back skin at P50, collected at ZT19, untreated [wt.ZT19.control]

description:
wt.ZT19.control
RNA from 5-7 pooled mouse back skin samples


title: dorsal back skin at P50, collected at ZT13, treated with 1% IMQ for 5 consecutive days [Wt_ZT13 5 day IMQ]

description:
Wt_ZT13 5 day IMQ
RNA from 5-7 pooled mouse back skin samples

value: 1% IMQ for 5 consecutive days


title: Mouse1_EpCamPrimary_S08_clean

value: male


title: dorsal back skin at P50, collected at ZT07, untreated [wtZT07.control]

description:
wtZT07.control
RNA from 5-7 pooled mouse back skin samples


title: Mouse1_EpCamPrimary_S06_clean


title: dorsal back skin at P50, collected at ZT13, treated with 1% IMQ for 24 hrs [wt_ZT13.IMQ.24.hr]

description:
wt_ZT13.IMQ.24.hr
RNA from 5-7 pooled mouse back skin samples


title: DOX1: sample MYC expression off (3 days)


title: CTL3: control sample MYC expression on

value: solvent (EtOH)


title: RNA-seq GFAP+_KO4

city: Cambridge

first: Li-Huei

last: Tsai

state: Massachusetts

department: Picower Institute for Learning and Memory

institute: MIT

data_processing:
RNA-seq data analysis: The generated fastq files were aligned to the UCSC mouse reference genome assembly mm9 using TopHat. The TopHat program used high-throughput short read aligner Bowtie to align the reads to the reference genome. The aligned reads were processed by Cufflinks 2.0.0. Relative abundance of transcript was measured by Fragments Per Kilobase of exon per Million mapped fragments (FPKM). The GTF annotation files for UCSC mm9 was used for gene annotation.
ChIP-Seq data analysis: Sequencing reads were mapped to mouse genome assembly (mm9) using BWA aligner (samse option). Duplicate reads were removed by samtools. Bed alignment files were generated using bedtools. Peak calling was also performed using MACS2.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph format for ChIP-Seq signal intensity across the genome, FPKM table format for individual RNA-Seq data

source_name: cortex, Nuclei RNA

extract_protocol:
RNA-Seq: cDNA libraries were prepared using High-Throughput 3’Digital Gene Expression (HT-3’DGE) method for 13M mouse brain. RNA of GFAP+ nuclei was extracted using RNeasy Plus Mini Kit (QIAGEN, 74134) according to the manufacturer’s protocol. SMART-Seq v4 Ultra Low Input RNA Kit (Clontech, 634890).
ChIP-Seq: Libraries were prepared from ~1-5 ng ChIP (or input) DNA as described previously (Gjoneska et al., 2015)

value: cortex

value: Hdac1f/f, Nestin-Cre


title: RNA-seq GFAP+_WT4


title: RNA-seq GFAP+_KO3


title: RNA-seq GFAP+_KO1


title: RNA-seq GFAP+_WT3


title: RNA-seq GFAP+_WT2


title: RNA-seq GFAP+_WT1


title: RNA-seq GFAP+_KO2


title: dorsal back skin at P50, collected at ZT07, treated with 1% IMQ for 6 hrs [wt_ZT07_6h_IMQ]

description:
wt_ZT07_6h_IMQ
RNA from 5-7 pooled mouse back skin samples


title: CTL2: control sample MYC expression on


title: RNA-Seq Hdac1 cKO; 5XFAD4

source_name: hippocampus, total RNA

value: hippocampus

value: Hdac1f/f, Nestin-Cre, 5XFAD


title: RNA-Seq Hdac1 cKO; 5XFAD5


title: Mouse1_EpCamPrimary_S05_clean

value: Primary

value: Pancreas

value: Tumor

value: EpCam, Calcien Violet for Live/Dead


title: dorsal back skin at P50, collected at ZT01, untreated [wt.ZT01.control]

description:
wt.ZT01.control
RNA from 5-7 pooled mouse back skin samples


title: Mouse1_EpCamPrimary_S04_clean

value: genomic DNA and mRNA


title: RNA-Seq Hdac1 cKO; 5XFAD3


title: CTL1: control sample MYC expression on

value: B-cell lymphoma

value: FVB/N


title: RNA-Seq Hdac1 cKO; 5XFAD2


title: HepG2 KO3 (G5)

city: Boston

first: Yu-Xin

last: Xu

state: United States

address: 185 Cambridge Street Simches Research Building, CPZN 5.500

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

data_processing:
Base calling:  RTA-1.18.64.0
FASTQ generation:  bcl2fastq-1.8.4
Read trimming:  trimmomatic-0.35
Read QC:  fastQC-0.10.1
Alignment:  STAR-2.4.2
Mapping statistics:  bamtools-2.3.0
Differential expression:  cufflinks-2.2.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited gene-level differential expression output from Cuffdiff

source_name: EDEM3 KO HepG2 cell clone transfected with lentivirus containing CRISPR/cas9 and EDEM3 sgRNA

growth_protocol: Standard culture with DMEM medium suppplemented with 10% fetal bovine serum

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to the manufacturer’s procedures
Ilumina TruSeq Stranded Total RNA with Ribo-Zero Globin

treatment_protocol: The cells were infected with lentiviruses containing CRISPR/cas9 with control and EDEM3 sgRNAs

tag: cell tissue

value: HepG2 hepatoma cells

value: KO HepG2


title: Mouse1_EpCamPrimary_S02_clean


title: Mouse1_EpCamPrimary_S03_clean


title: RNA-Seq Hdac1 cKO; 5XFAD1


title: RNA-Seq 5XFAD6

value: Hdac1f/f, 5XFAD


title: HepG2 KO2 (GL-5)


title: RNA-Seq 5XFAD5


title: RNA-Seq 5XFAD4


title: RNA-Seq 5XFAD3


title: Mouse1_EpCamPrimary_S01_clean


title: HepG2 KO1 (GX-A)


title: RNA-Seq 5XFAD2


title: Mouse1_GFPEpCamPrimary_S20_clean

value: GFP, EpCam, Calcien Violet for Live/Dead


title: Mouse1_GFPEpCamPrimary_S19_clean

value: male


title: RNA-Seq 5XFAD1


title: Mouse1_EpCamPrimary_S07_clean


title: Mouse1_GFPEpCamPrimary_S18_clean


title: RNA-Seq 3mo WT2

description: RNA-Seq 3mo WT

data_processing:
RNA-seq data analysis: The generated fastq files were aligned to the UCSC mouse reference genome assembly mm9 using TopHat. The TopHat program used high-throughput short read aligner Bowtie to align the reads to the reference genome. The aligned reads were processed by Cufflinks 2.0.0. Relative abundance of transcript was measured by Fragments Per Kilobase of exon per Million mapped fragments (FPKM). The GTF annotation files for UCSC mm9 was used for gene annotation.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph format for ChIP-Seq signal intensity across the genome, FPKM table format for individual RNA-Seq data

source_name: hippocampus

extract_protocol: RNA-Seq: cDNA libraries were prepared using Illumina TruSeq Total RNA Sample Prep Kits (Illumina)


title: HepG2 WT2

source_name: EDEM3 WT HepG2 cell clone transfected with lentivirus containing CRISPR/cas9 and control sgRNA

value: WT HepG2


title: RNA-Seq 3mo HDAC1_KO3

description: RNA-Seq 3mo HDAC1_KO


title: RNA-Seq 3mo HDAC1_KO2

description: RNA-Seq 3mo HDAC1_KO


title: RNA-Seq 3mo HDAC1_KO1

description: RNA-Seq 3mo HDAC1_KO


title: RNA-Seq 3mo WT1

description: RNA-Seq 3mo WT


title: HepG2 WT1


title: WT_M_10729

city: Ann Arbor

first: William

middle: R

last: Swindell

state: MI

address: 1500 E. Medical Center Drive

department: Dermatology

institute: University of Michigan

description: RNA extracted from brown adipose tissue

data_processing:
Sequence data were converted to FASTQ Sanger format using Illumina's bcl2fastq version 1.8.4 and aligned to the University of California, Santa Cruz mouse mm10 genome using TopHat version 2.0.11 and the short read aligner Bowtie was used to assemble transcripts and estimate abundances.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Processed data includes FPKM values for all mouse genes (GRCm38/mm10) and each sample (.txt files).

source_name: Brown adipose tissue

growth_protocol: GHRH-KO mice and their littermate controls (on a mixed C57BL6 and 129SV background) were bred in the colony derived from Roberto Salvatori laboratory and housed under standard conditions (12-hr light/12-hr dark cycle at 20–23°C).

extract_protocol:
Brown adipose tissue (BAT) was immediately harvested, snap-frozen in liquid nitrogen and then stored at −80°C. The tissues was homogenized with RNA extraction buffer (TRIZOL reagent; Life Technologies, CA) to yield total RNA following manufacturer instructions.
RNA sequencing was performed on Illumina HiSeq2000 platform with 2×50bp paired-end sequencing configuration. Briefly, the quality of the total RNA was assessed using the Agilent 2100 Bioanalyzer followed by 2 rounds of poly A+ selection and conversion to cDNA. The TruSeq library generation kit was used to construct the cDNA library as per the manufacturer’s instructions (Illumina, San Diego, CA). The cDNA library was quantitated using qPCR in a Roche LightCycler 480 with the Kapa Biosystems kit for library quantitation (Kapa Biosystems, Woburn, MA) prior to sequencing. Paired end 2 × 50 bp sequencing runs were performed in the Illumina HiSeq2500.

treatment_protocol: Animals had access to ad libitum water and Lab Diet Formula 5001 mouse chow (23% protein, 4.5% fat, 6% fiber, Nestle Purina, St. Louis, MO).

value: WT

value: Male


title: KO_M_10723

description: RNA extracted from brown adipose tissue

value: KO


title: Mouse1_GFPEpCamPrimary_S16_clean


title: WT_M_10727

description: RNA extracted from brown adipose tissue


title: KO_M_10722

description: RNA extracted from brown adipose tissue


title: Mouse1_GFPEpCamPrimary_S15_clean


title: 3_U_PreMt_miRNA-seq

city: Helsinki

first: Maija

middle: L

last: Castrén

state: Helsinki

address: P.O.BOX 63

department: Faculty of Medicine/Physiology

country: Finland

institute: University of Helsinki

description:
3_U_FXS13_premutation
Sample Collection: Urine was collected in preservation tubes (Norgen Biotek Corp) and stored at 4oC until miRNA extraction.

data_processing:
Raw sequence data were imported in CLC Genomics Workbench (version 7.0.3;  https://www.qiagenbioinformatics.com/) for read quality inspection, adapter trimming and miRNA annotation based on miRBase (http://www.mirbase.org/). The count data was grouped on mature miRNAs.
The count data was  imported to R/Bioconductor (v. 3.1.0) (R Core Team, 2015) where the normalization and statistical testing were carried out with the DESeq2 package.

source_name: urine

extract_protocol:
Urine miRNAs were extracted with Urine microRNA Puriﬁcation Kit (Norgen Biotek Corp., Ontario, Canada) according to the manufacturer’s instructions.
Fragment libraries were prepared for each sample with TruSeq Small RNA Library Prep Kit (Illumina) as instructed by the manufacturer.
Fragment libraries sequenced using the HiSeq 2500 system (Illumina) as instructed by the manufacturer.

value: urine

value: 175 repeats in the FMR1 gene

tag: gender

tag: age (years)


title: KO_F_10720

description: RNA extracted from brown adipose tissue

value: Female


title: WT_F_10715

description: RNA extracted from brown adipose tissue


title: WT_F_10714

description: RNA extracted from brown adipose tissue


title: 2_U_FXS_miRNA-seq

description:
2_U_FXS12
Sample Collection: Urine was collected in preservation tubes (Norgen Biotek Corp) and stored at 4oC until miRNA extraction.

tag: tissue

value: 300 repeats in the FMR1 gene


title: 1_U_CNTRL_miRNA-seq

description:
1_U_CONTROL
Sample Collection: Urine was collected in preservation tubes (Norgen Biotek Corp) and stored at 4oC until miRNA extraction.

value: normal


title: SubSample

city: Seattle

first: Martin

last: Prlic

state: WA

address: 1100 Fairview Ave, Mail stop E5-110

institute: Fred Hutch

description:
Sample 2
Flow sorted Live CD45+ PBMCs from one healthy donor
Samples labeled as ‘AbSeq’ also have RNA sequencing data

data_processing:
Library strategy: AbSeq + RNAseq
Sample 1 aligned RNA reads using PBMC_Rhapsody_amplicons.fasta and aligned protein reasd using AbSeq_41plex.fasta
Sample 2 aligned RNA reads using PBMC_Rhapsody_amplicons.fasta and aligned protein reasd using AbSeq_38plex.fasta
Sample 3 aligned RNA reads using BD_Rhapsody_T_Cell_Expression_Panel_Hs.fasta and aligned protein reasd using AbSeq_Stim.fasta
FASTQ files were processed with BD Rhapsody Analysis Pipeline hosted by SevenBridges Genomics
FASTQ files were processed with CellRanger software v2.1.1 and Donor 3 sample sheet
Genome_build: GRCh38
Supplementary_files_format_and_content: comma separated values with abundance measurements for each target.

source_name: Frozen PBMC

extract_protocol:
RNA was extracted using BD Rhapsody or 10x genomics protocols
single-cell RNAseq

treatment_protocol: T and NK cells were stimulated for 1 hour with PMA/ Ionomycin

value: PBMC

tag: phenotype

value: CD45+ Live Cells

tag: individual(s)

value: Donor 4


title: KO_F_10717

description: RNA extracted from brown adipose tissue

tag: Sex


title: HepG2 WT3

value: HepG2 hepatoma cells


title: 10x_Donor3_2

description:
Sample 4
Flow sorted Live CD45+ PBMCs from one healthy donor (technical replicate of 10x_Donor3_1)

data_processing:
Sample 1 aligned RNA reads using PBMC_Rhapsody_amplicons.fasta and aligned protein reasd using AbSeq_41plex.fasta
Sample 2 aligned RNA reads using PBMC_Rhapsody_amplicons.fasta and aligned protein reasd using AbSeq_38plex.fasta
Sample 3 aligned RNA reads using BD_Rhapsody_T_Cell_Expression_Panel_Hs.fasta and aligned protein reasd using AbSeq_Stim.fasta
FASTQ files were processed with BD Rhapsody Analysis Pipeline hosted by SevenBridges Genomics
FASTQ files were processed with CellRanger software v2.1.1 and Donor 3 sample sheet
Genome_build: GRCh38
Supplementary_files_format_and_content: comma separated values with abundance measurements for each target.

tag: cell type

value: Donor 3


title: CTBA50-2

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

description: The group information is prefixed with CTBA50_2 in the column of processed data file

data_processing:
First, the raw data were filtered to get clean reads. HISAT was used to map the clean reads to genome. Bowtie2 was used to map to the reference genes sequence.  RSEM was used to quantify the expression level.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: FPKM for all samples and genes (csv format)

growth_protocol: 3 weeks of age of ICR mice were treated with 40 microgram/g bodywieght for once. After 2 weeks, the testes were collected for culture. At the same time the testes from non-busulfan treated mice were collected for culture also as control.

extract_protocol:
Testis samples were isolated for RNA. Then RNA samples were sequenced.
cDNA libaray was constructed for the sequencing.

treatment_protocol: The collected testes were culture in DMEM/F12 medium with 10% FBS, with or without AOS (10 microgram/mL, or 50microgram/mL) at 37 ℃ and 5% CO2 for 48 h (two days).

tag: strain

value: ICR

value: Testis

value: B+A50 (Busulfan treated mouse testes in 50 microgram/mL AOS in medium)


title: CTBA10-3

description: The group information is prefixed with CTBA10_3 in the column of processed data file

value: B+A10 (Busulfan treated mouse testes in 10 microgram/mL AOS in medium)


title: CTBA50-3

description: The group information is prefixed with CTBA50_3 in the column of processed data file


title: WT_F_10713

description: RNA extracted from brown adipose tissue

value: WT


title: Mouse1_GFPEpCamPrimary_S13_clean

value: male

tag: tumor type

value: Primary

value: Pancreas

value: Tumor

tag: marker

value: GFP, EpCam, Calcien Violet for Live/Dead

tag: molecule type

value: genomic DNA and mRNA


title: Mouse1_GFPEpCamPrimary_S11_clean


title: Mouse1_GFPEpCamPrimary_S12_clean


title: Mouse1_GFPEpCamPrimary_S10_clean


title: CTBA50-1

description: The group information is prefixed with CTBA50_1 in the column of processed data file


title: CTBA10-1

description: The group information is prefixed with CTBA10_1 in the column of processed data file


title: CTBA0-1

description: The group information is prefixed with CTBA0_1 in the column of processed data file

value: B+A0 (Busulfan treated mouse testes in medium)


title: CTBA10-2

description: The group information is prefixed with CTBA10_2 in the column of processed data file


title: PBMC AbSeq_2

description:
Sample 1
Flow sorted Live CD45+ PBMCs from three different healthy donors
Samples labeled as ‘AbSeq’ also have RNA sequencing data

value: PBMC

value: Donor 1, Donor 2, Donor 3


title: 10x_Donor3_1

description:
Sample 4
Flow sorted Live CD45+ PBMCs from one healthy donor

value: CD45+ Live Cells


title: PBMC AbSeq_1


title: Mouse1_CD45Primary_S43_clean

value: Stromal

value: CD45, Calcien Violet for Live/Dead


title: Mouse1_GFPEpCamPrimary_S09_clean


title: 4_U_CNTRL_miRNA-seq

description:
4_U_CONTROL
Sample Collection: Urine was collected in preservation tubes (Norgen Biotek Corp) and stored at 4oC until miRNA extraction.

value: urine

tag: genotype

value: normal


title: Mouse1_GFPEpCamPrimary_S17_clean


title: Mouse1_CD45Primary_S42_clean


title: CTBA0-3

description: The group information is prefixed with CTBA0_3 in the column of processed data file

value: ICR

value: Testis


title: CTA10-2

description: The group information is prefixed with CTA10_2 in the column of processed data file

value: AOS10 (Non-busulfan treated mouse testes in 10 microgram/mL AOS in medium)


title: T18

city: Jongno-gu

first: Sun-Wha

last: Im

state: Seoul

address: 103, Daehak-ro

department: Genomic Medicine Institute, Medical Research Center

country: South Korea

institute: Seoul National University

data_processing:
For expression analysis, we used RSEM (v1.2.31) to calculate the read counting and Fragments Per Kilobase Million (FPKM) values for the Ensemble gene set.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for all Samples

source_name: bladder cancer tumor

extract_protocol:
RNA was extracted from tumor FFPE tissue using the Trizol method.
By using the Illumina TruSeq RNA Access Library Preparation Kit, RNA sequencing library was constructed for RNA samples with DV200 values of >30%.

tag: tumor (pt) stage

value: Ta

tag: tumor grade

value: Low

tag: sex of patient

value: Male

tag: age of patient at diagnosis


title: CTA50-2

description: The group information is prefixed with CTA50_2 in the column of processed data file

tag: treatment

value: AOS50 (Non-busulfan treated mouse testes in 50 microgram/mL AOS in medium)


title: CTA50-3

description: The group information is prefixed with CTA50_3 in the column of processed data file


title: Mouse1_CD45Primary_S41_clean

data_processing:
library strategy: GTO sequencing
Adapter removal and removing reads shorter than 36bp using Bbduk
Map reads to mm9 genome using STAR aligner
Separate aligned reads into exonic and allnonexonic
Realign exonic reads to reference genome mm9 using Kallisto and obtain read count tables
Realign allnonexonic reads to refenrence genome mm9 using Bowtie 1.0, remove PCR duplicate reads and process for CNV analysis
Genome_build: mm9
Supplementary_files_format_and_content: read count tables for RNAseq section of data, Varbin files with bincounts for DNAseq section

value: male

value: Primary

value: Pancreas


title: CTA10-1

description: The group information is prefixed with CTA10_1 in the column of processed data file


title: CTA0-3

description: The group information is prefixed with CTA0_3 in the column of processed data file

value: AOS0 (Non-busulfan treated mouse testes in medium)


title: CTA50-1

description: The group information is prefixed with CTA50_1 in the column of processed data file


title: T17

value: PUNLMP


title: CTBA0-2

description: The group information is prefixed with CTBA0_2 in the column of processed data file

value: B+A0 (Busulfan treated mouse testes in medium)


title: T8


title: Mouse1_CD45Primary_S40_clean

value: Stromal

value: genomic DNA and mRNA


title: scRNA_seq_AOS10

description: The group information is prefixed with TA10 in the column of processed data file

data_processing:
We used CellRanger count pipeline 2.2.0 to analyze the sequencing data and generated the single cell information. To generate same number of total cells for downstream analysis, we used augments ‘--force-cells=5000 \’.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files stores normalized and log-transformed single cell expression value

extract_protocol:
Testis were isolated and washed with PBS solution supplemented with 0.04% bovine serum albumin. Then, the testis were digested with 1X TrypLE™ Express (Cat# 12605010) for 3 min to obtain single cell pellets. The single-cell Gel-Bead in Emulsions (GEMs) were then generated with Chromium 10x Genomics single-cell system by using single-cell 3’ Library and Gel Bead Kit V2 (10x Genomics, Cat#120237). Captured cells were then lysed and the released RNA were barcoded through reverse transcription in individual GEMs.
Single-cell RNA-seq libraries were prepared using Single Cell 3’ Library Gel Bead Kit V2 (10x Genomics, 120237) following the manufacture’s introduction.

value: AOS 10 (AOS 10 mg/kg body weight (BW))


title: Mouse1_CD45Primary_S39_clean

value: CD45, Calcien Violet for Live/Dead


title: CTA10-3

description: The group information is prefixed with CTA10_3 in the column of processed data file

value: ICR


title: T9


title: CTA0-2

description: The group information is prefixed with CTA0_2 in the column of processed data file

value: Testis


title: Mouse1_CD45Primary_S37_clean


title: scRNA_seq_AOS0

description: The group information is prefixed with TA0 in the column of processed data file

value: AOS 0 (control)


title: scRNA_seq_B+A10

description: The group information is prefixed with TBA10 in the column of processed data file

value: B+A 10 (busulfan plus AOS 10 mg/kg BW)


title: Mouse1_CD45Primary_S38_clean


title: Mouse1_CD45Primary_S36_clean


title: CTA0-1

description: The group information is prefixed with CTA0_1 in the column of processed data file


title: ChIP-Seq HDAC1_rep3

extract_protocol:
RNA-Seq: Hippocampi were isolated from the brains of mice at 13 to 14 months. Total RNA was extracted using TRIzol reagent followed by DNase treatment to eliminate genomic DNA contamination. ChIP-Seq: Hippocampi from wild-type C57BL/6J mice were isolated for HDAC1 ChIP-Seq.
RNA-Seq: cDNA library was constructed using High throughput 3' digital gene expression (HT-3'DEG) method (Soumillon et al., 2014).
ChIP-Seq: Libraries were prepared from ~1-5 ng ChIP (or input) DNA as described previously (Gjoneska et al., 2015)

value: hippocampus

tag: antibody

value: HDAC1 CST #5356


title: T15

value: Ta

value: Male


title: ChIP-Seq HDAC1_rep2


title: T5

value: Low


title: Mouse1_CD45Primary_S35_clean

extract_protocol:
Primary tumors were dissociated using collagenase D and trypsin. They were treated with ACK lysis buffer to remove contaminating red blood cells. These dissociated cells were stained with EpCam, CD45 antibodies. Single cells were isolated by flow cytometry for GFP+, EpCAM+, GFP+EpCAM+ and CD45+ from primary tumors. GFP+ cells were isolated from various metastases
Single cells isolated into 10x Lysis Buffer with Rnase inhibitor. Next they were processed for mRNA transcription for first strand synthesis using Oligo-dT primer and cDNA generated is amplified for 15 cycles following SMART-Seq2 PCR primers. Samples were then treated ionically to fragment gDNA and cDNA to 400-700bp fragments. Later gDNA was amplified using SeqXE kit from Sigma Aldirch using manufacturer instructions. resulting cDNA and gDNA fragments are quantified.  Following this, libraries for sequencing were prepared by subjecting the 1ug of gDNA and cDNA fragments to end-repair, 3′ adenylation and ligation of TruSeq barcoded adapters. After ligation, DNA fragments were size selected using Ampure XP beads. A 0.75 ratio of beads to sample was used to select fragments larger than 200bp and avoid adapter dimers. These fragments were further amplified by PCR, cleaned using Qiaquick PCR Purification Kit and then once again size selected using Ampure XP beads with a 0.75 ratio of beads to sample. The final libraries were then quantified on Nanodrop and Bioanalyzer using Agilent's High Sensitivity DNA Analysis Kit. 10nM of each sample was then pooled together and the resulting pool was then sequenced single read 76bp length on the Illumina NextSeq

value: male

value: Primary

value: Pancreas


title: T3

value: PUNLMP


title: RNA-Seq HDAC1_KO5

tag: genotype/variation

value: Hdac1f/f, Nestin-Cre


title: ChIP-Seq WCE_rep 2

tag: tissue

value: WCE


title: T10


title: T2


title: Mouse1_CD45Primary_S32_clean

value: Stromal

value: genomic DNA and mRNA


title: RNA-Seq HDAC1_KO3


title: ChIP-Seq WCE_rep 1


title: RNA-Seq WT 4


title: RNA-Seq HDAC1_KO2


title: Mouse1_CD45Primary_S34_clean

value: CD45, Calcien Violet for Live/Dead


title: ChIP-Seq_MCF7_CARM1_CTL

city: Xiamen

first: Jiancheng

last: Ding

state: Fujian

address: School of Pharmaceutical Sciences, Xiamen University Xiang`an South Road

institute: Xiamen University

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg19 genome assembly using Bowtie version 2.2.1 with the default options.
The bigwig files were generated by using HOMER, in which the total tags are normalized to 1.00e+07.
Peaks are called by using Homer findPeaks script
Genome_build: hg19

source_name: breast cancer

growth_protocol: MCF7 cells were cultured in DMEM medium supplemented with 10% FBS.

extract_protocol:
For ChIP assays, cells were maintained in stripping medium (phenol red free) for three days before treating with or without estrogen (E2, 10-7 M) for 1 hr. Cells were then fixed with 1% formaldehyde (Sigma) for 10 mins at room temperature (RT) (for MED12 ChIP), or fixed with disuccinimidyl glutarate (DSG) (2 mM) (Proteochem) for 45 mins at RT, washed twice with PBS and then double-fixed with 1% formaldehyde for another 10 mins at RT (for CARM1 ChIP). Fixation was stopped by adding glycine (0.125 M) and incubated for 5 mins at RT, followed by washing with PBS twice. Chromatin DNA was sheared to 300~500 bp average in size through sonication. Resultant was immunoprecipitated with anti-MED12, anti-Pol II or anti-CARM1 antibody overnight at 4 ℃, followed by incubation with protein G magnetic beads (Bio-Rad, 161-4023) for an additional 2 hrs. After washing and elution, the protein-DNA complex was reversed by heating at 65 ℃ overnight. Immunoprecipitated DNA was purified by using QIAquick spin columns (Qiagen) and subjected to high throughput sequencing.
The libraries were constructed following NEB’s Chip-Seq Sample prep kit. Briefly, Chip DNA was end-blunted and added with an ‘A’ base so the adaptors from Illumina with a ‘T’ can ligate on the ends. Then 200–400 bp fragments are gel-isolated and purified. The library was amplified by 18 cycles of PCR.

treatment_protocol: MCF7 cells were maintained in stripping medium (phenol red free) for three days before treating with or without estrogen (E2, 10-7 M) for 1h.

tag: cell line

tag: chip antibody

value: cell signaling,3H2

value: ethanol


title: RNA-Seq HDAC1_KO1


title: ChIP-Seq WCE_rep 3


title: Mouse1_CD45Primary_S31_clean

tag: Sex


title: Mouse1_CD45Primary_S30_clean

tag: cell type


title: ChIP-Seq_MCF7_CARM1_E2

value: estrogen


title: RNA-Seq WT 2

value: hippocampus


title: RNA-Seq WT 3


title: Mouse1_CD45Primary_S29_clean

tag: strain


title: RNA-Seq WT 1


title: PCBP2 silencing NUTLIN polysomal replicate 4

city: Trento

first: Erik

last: Dassi

state: TN

address: Via Sommarive, 9

department: CIBIO

institute: University of Trento

data_processing:
Illumina Casava 1.8 software was used for basecalling and demultiplexing.
Sequenced reads were trimmed for adaptor sequence and low-quality nucleotides, then quantified against the Gencode v25 transcriptome using Salmon 0.7.2 with default parameters
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: tab-delimited text file includes raw read counts for each Sample

source_name: PCBP2 silencing NUTLIN polysomal

growth_protocol: HCT116 cells were maintained in RPMI (Gibco) supplemented with 10% FBS, antibiotics (100 units/mL penicillin plus 100 mg/mL streptomycin) and 2mM L-glutamine. Cultures were maintained at 37°C in a 5% CO2 incubator.

extract_protocol:
Polysomal separation was performed as follows: samples were loaded in 15-50% linear sucrose gradients, ultra-centrifuged and fractionated with an automated fraction collector. All the fractions containing subpolysomal or polysomal RNA were identified and pooled in two separate tubes. RNA was purified by extraction with 1 volume of phenol-chloroform and, after isopropanol precipitation, a washing step in 70% v/v ethanol was performed in order to remove phenol contaminations.
RNA libraries were prepared for sequencing using standard Illumina protocols: Illumina TruSeq RNA Sample Prep Kit was used with 1.5 ug of total or polysomal RNA as input.

treatment_protocol: HCT116 cells were transduced with lentiviral vectors containing a pLK0.1 plasmid expressing shRNA sequences against DHX30 or PCBP2. A scramble sequence SHC206 was also used. Cells were allowed to reach 60-70% confluence before treatment with 10 mM Nutlin-3a (Nutlin) or only  DMSO at 0.1% (v/v).

value: PCBP2 silencing

tag: agent

value: nutlin

tag: fraction

value: polysomal RNA


title: T4

value: Ta

value: Male


title: ChIP-Seq HDAC1_rep1

value: HDAC1 CST #5356


title: Mouse1_CD45Primary_S28_clean

value: male

tag: tumor type

value: Primary

value: Pancreas

tag: marker

tag: molecule type


title: RNA-Seq HDAC1_KO4

value: Hdac1f/f, Nestin-Cre


title: PCBP2 silencing NUTLIN polysomal replicate 3

tag: genotype


title: Mouse1_CD45Primary_S27_clean

value: Stromal


title: Mouse1_CD45Primary_S26_clean

value: genomic DNA and mRNA


title: methylation_63_Vehicle

type: genomic

city: Chicago

first: Emma

last: Thompson

state: IL

address: 920 E 58th St, CLSC Rm 501

department: Human Genetics

institute: The University of Chicago

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using standard Illumina scanner settings

data_processing:
Probes located on the sex chromosomes and those with detection P values > 0.01 in 75% of samples were removed. Probes mapping to more than one genomic location or overlapping with known SNPs (MAF>5% in either African Americans or European Americans) were also excluded. Data were processed using Minfi; Infinium type I and type II probe bias were corrected using SWAN. Raw probe values were corrected for color imbalance and background by control normalization.
normalized data file includes normalized (SWAN and background normalization) Average Beta
The raw data file "Unprocessed_Methylation_FinalGEO.csv" includes unmethylated and methylated signal intensities

source_name: primary cultured airway smooth muscle cell

label_protocol: Standard Illumina protocol.

growth_protocol: ASMCs were cultured in 96-well Nusil coated plates in serum free media for 48 hours prior to cytokine exposure.

extract_protocol: Genomic DNA from IL-13, IL-17, IL-13+IL-17, or vehicle-exposed airway smooth muscle cells was extracted and purified using the AllPrep Kit from QIAgen according to standard instructions

treatment_protocol: ASMCs were exposed to IL-13 (10ng/mL), IL-17 (3ng/mL), IL-13+IL-17, or vehicle (10% FBS in PBS) for 24 hours prior to RNA and DNA extraction.

tag: donor

value: Vehicle

tag: asthma

value: No

tag: age

value: Female

tag: imputedsmoking

tag: race

value: EuropeanAmerican


title: methylation_63_IL-13

value: primary cultured airway smooth muscle cell

tag: treatment


title: methylation_63_IL-17


title: PCBP2 silencing NUTLIN polysomal replicate 2

tag: cell line

value: PCBP2 silencing


title: methylation_26_IL-13

value: Yes

value: AfricanAmerican


title: methylation_26_Combined

value: Combined


title: methylation_26_IL-17

value: Male


title: methylation_26_Vehicle


title: PCBP2 silencing NUTLIN polysomal replicate 1

value: nutlin

value: polysomal RNA


title: methylation_61_IL-13


title: Mouse1_CD45Primary_S25_clean

city: New York

first: Yu-Jui

last: Ho

institute: Memorial Sloan Kettering Cancer Center

value: male

value: Primary

tag: tissue

value: CD45, Calcien Violet for Live/Dead


title: PCBP2 silencing DMSO polysomal replicate 4

source_name: PCBP2 silencing DMSO polysomal

value: DMSO


title: Mouse1_CD45Primary_S24_clean

tag: Sex

value: Pancreas

value: Stromal

value: genomic DNA and mRNA


title: methylation_61_Vehicle

tag: cell type

value: Vehicle

value: No


title: PCBP2 silencing DMSO polysomal replicate 3


title: methylation_61_Combined

value: primary cultured airway smooth muscle cell

value: EuropeanAmerican


title: Mouse1_CD45Primary_S23_clean

tag: strain


title: PCBP2 silencing DMSO polysomal replicate 2

value: PCBP2 silencing

tag: agent


title: methylation_61_IL-17


title: PCBP2 silencing DMSO polysomal replicate 1

tag: fraction


title: methylation_10_Combined

value: Yes


title: methylation_10_IL-17


title: Mouse1_CD45Primary_S22_clean

tag: tumor type


title: methylation_63_Combined

value: Combined

value: Female


title: Mouse1_CD45Primary_S21_clean

tag: marker


title: methylation_10_IL-13

value: Male


title: methylation_10_Vehicle


title: methylation_33_Combined


title: Mouse1_CD45PrimaryBulk_S33_clean

tag: molecule type


title: DNA_4N_9_S93

data_processing:
library strategy: scWGS for CNV analysis
Adapter removal and removing reads shorter than 36bp using Bbduk
Reads aligned to refenrence genome mm9 using Bowtie 1.0, remove PCR duplicate reads and process for CNV analysis
The duplicate removed aligned reads were then assigned to variable length bins across the genome based on where they align in the genome
The average bin counts were calculated and used as the diploid 2N average. Bins with higher number are considered as amplified and those with lower are considered deleted. CNV profiles were generated using R.
Genome_build: mm9
Supplementary_files_format_and_content: Varbin files with bincounts for CNV analysis

source_name: KPC1199EGFP Adherent cells at passage 9

extract_protocol:
Adherent cells were trypsinzed, counted and resuspended in NST-DAPI buffer. Cells were sorted on flow cytometer based on the DNA content to obtain single nuclei for scWGS
Single cells isolated into 10x Lysis and Fragmentation Buffer were processed for genomic DNA amplification using SeqXE kit from Sigma Aldrich. Manufacturer's instructions very followed for gDNA amplification. Library preparation was done by end repair, adenylation, adapter ligation and PCR steps.

treatment_protocol: No treatment

tag: strain background

value: Pancreatic cancer tumor cell line

tag: labelling for flow

value: EGFP expression

tag: molecule subtype

value: genomic DNA in nuclei


title: methylation_33_Vehicle

tag: donor

tag: asthma

tag: age


title: methylation_24_IL-13

tag: treatment

tag: imputedsmoking

tag: race


title: DNA_4N_8_S92

tag: cell line


title: DHX30 silencing NUTLIN polysomal replicate 4

source_name: DHX30 silencing NUTLIN polysomal

tag: genotype

value: DHX30 silencing

value: nutlin

value: polysomal RNA


title: DNA_4N_7_S91

tag: cell type


title: methylation_24_Combined

tag: Sex


title: methylation_24_Vehicle


title: DHX30 silencing NUTLIN polysomal replicate 1

tag: agent

tag: fraction


title: methylation_33_IL-17


title: methylation_42_IL-17


title: DHX30 silencing DMSO polysomal replicate 4

source_name: DHX30 silencing DMSO polysomal

value: DMSO


title: DNA_4N_6_S90


title: DHX30 silencing DMSO polysomal replicate 3


title: methylation_42_IL-13


title: DNA_4N_5_S89


title: methylation_42_Combined


title: methylation_42_Vehicle


title: Mouse1_GFPEpCamPrimary_S14_clean

source_name: Mouse1_Primary Pancreatic Tumor

tag: strain

value: male

tag: tumor type

value: Primary

tag: tissue

value: Pancreas

value: Tumor

tag: marker

value: GFP, EpCam, Calcien Violet for Live/Dead

value: genomic DNA and mRNA


title: DHX30 silencing DMSO polysomal replicate 2


title: DNA_4N_4_S88

tag: strain background

tag: labelling for flow

tag: molecule subtype


title: methylation_9_Combined

value: primary cultured airway smooth muscle cell

tag: donor

tag: asthma

value: No

tag: age

value: Yes

value: EuropeanAmerican


title: DHX30 silencing NUTLIN polysomal replicate 3


title: methylation_24_IL-17

tag: treatment

value: Female

tag: imputedsmoking

tag: race


title: methylation_33_IL-13

tag: cell type


title: DHX30 silencing NUTLIN polysomal replicate 2

tag: cell line

tag: genotype


title: DHX30 silencing DMSO polysomal replicate 1

tag: agent

tag: fraction


title: DNA_4N_3_S87

value: Pancreatic cancer tumor cell line

value: EGFP expression


title: methylation_9_IL-17

tag: Sex


title: DNA_4N_2_S86

value: genomic DNA in nuclei


title: ShC-S

city: BREST

first: Delphine

last: Bernard

address: 22 avenue Camille Desmoulins

department: Faculté de Médecine

country: France

institute: UMR1078 - Université de Bretagne Occidentale

data_processing:
Sequencing was performed on an Illumina HiSeq 3000.
Quality control of sequencing reads was performed using FastQC.
Adapter removal was perfomed using Trim Galore 0.4.1
Reads were aligned using Bismark v0.16.1 and followed by methylation calling using the corresponding bismark functionality
The methylKit package ( (Altuna Akalin, (2012). " Genome Biology , 13:R87)  was used for data processing and analysis
Genome_build: hg19
Supplementary_files_format_and_content: csv file including tthe output of methylKit (DMR, CpGs minimum per tile, q-value < 0.01 and  ≥25% average differences)

source_name: Ovarian cancer

growth_protocol: Cells were passed in RPMI culture media supplemented with 10% fetal bovine serum

extract_protocol:
Genomic DNA was extracted from SKOV3 (M) and (E) clones with Blood & Cell Culture DNA Mini Kit (Qiagen)
100ng genomic DNA was then digested using the methylation-insensitive enzyme MspI, fragment ends were filled in and adapters were ligated. After size selection by AMPure XP beads, fragments were subjected for bisulfite conversion. Samples were sequenced on an Illumina platform, Single-Read, read length 50 bp (SR50). The adapter sequences and low-quality base calls (< 30) were trimmed from the 3’ end using Trimmomatic programm. The bisulfite converted sequencing reads were then aligned to the human reference genome using Bismark program. Differentially methylated regions (DMRs) were determined.

value: ShRNA control


title: scramble NUTLIN polysomal replicate 4

source_name: scramble NUTLIN polysomal

value: wild type

value: nutlin

value: polysomal RNA


title: Ly75-OV-S

value: LY75 overexpression in LY75 suppression shRNA


title: Ly75-KO-S

value: LY75 suppression wich CRISPR


title: DNA_4N_12_S96

address: 417 E 68th St


title: methylation_9_Vehicle

value: Vehicle


title: methylation_1_Combined

value: Combined

value: Male


title: scramble NUTLIN polysomal replicate 2


title: scramble NUTLIN polysomal replicate 3


title: DNA_4N_11_S95


title: scramble NUTLIN polysomal replicate 1


title: ShLy75-S

value: LY75 suppression shRNA


title: ChIP-Seq_MCF7_Med12_siCARM1_E2

tag: chip antibody

value: estrogen+siRNA


title: DNA_4N_10_S94


title: methylation_1_IL-17

value: primary cultured airway smooth muscle cell

value: No


title: DNA_4N_1_S85


title: methylation_1_IL-13

value: EuropeanAmerican


title: scramble DMSO polysomal replicate 4

source_name: scramble DMSO polysomal

value: DMSO


title: ChIP-Seq_MCF7_Med12_siCARM1

value: ethanol+siRNA


title: methylation_9_IL-13

value: Female

value: Yes


title: ChIP-Seq_MCF7_Med12_siCTL_E2

value: estrogen+siCTL


title: DNA_2N+_Bulk_S84

value: Pancreatic cancer tumor cell line

value: EGFP expression

value: genomic DNA in nuclei


title: scramble DMSO polysomal replicate 2

value: wild type

value: polysomal RNA


title: methylation_1_Vehicle

value: Vehicle


title: ChIP-Seq_MCF7_Med12_siCTL

value: ethanol+siCTL


title: DNA_2N+_9_S57


title: methylation_39_Vehicle

value: Male

value: AfricanAmerican


title: H3K27ac_Rep1

city: Ithaca

first: Marcos

last: Simoes-Costa

address: 526 Campus Rd

department: Molecular Biology and Genetics

institute: Cornell University

data_processing:
Base calling was performed using CASAVA 1.8
Sequenced reads were trimmed for adaptor sequence using cutadapt v1.18, and mapped to the galGal5 genome using Bowtie 2 v2.3.4.3 with parameters --local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 1000
Duplicate reads were marked using MarkDuplicates function of Picard tools v 2.0.4 and reads were filtered using samtools  v1.9 -F 1804 -f 2
Bigwig plots were generated using deeptools v3.1.2 bamCoverage function with the following parameters: --binSize 5 --normalizeUsing RPGC --effectiveGenomeSize 1218492533 --extendReads
Genome_build: Galgal5
Supplementary_files_format_and_content: BigWig files (normalized to 1X genome size.

organism: Gallus gallus

source_name: Chick neural crest

extract_protocol:
Dorsal neural tubes were dissected from HH9+ (8ss) embryos, and a total of 20 neural folds were used/sample for CUT&RUN experiment. Cells were dissociated in Accumax (Accutase, SCR006) cell dissociation solution for 20 minutes at RT under mild agitation. CUT&RUN was perfromed as described by Skene and Henikoff, 2017.
CUT&RUN libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, E7645) using manufactures protocol. The libraries were sequenced with paired-end 37bp reads on an Illumina NextSeq500 instrument.
CUT&RUN

tag: Stage

tag: antibody

value: rabbit anti-Histone 3(K27ac) (abcam, ab177178)


title: H3K27ac_Rep2


title: DNA_2N+_8_S56

tag: strain background

tag: labelling for flow


title: methylation_39_IL-17

value: primary cultured airway smooth muscle cell

tag: donor

value: No


title: methylation_39_Combined

value: Combined

tag: asthma


title: DNA_2N+_6_S54

tag: molecule subtype


title: Yap1_Rep3

value: rabbit anti-ActiveYap1(abcam, ab205270)


title: methylation_20_IL-17

tag: treatment

tag: age

value: Female

value: EuropeanAmerican


title: DNA_2N+_5_S53


title: Yap1_Rep1


title: DNA_2N+_4_S52


title: methylation_20_IL-13

value: Yes

tag: imputedsmoking

tag: race


title: DNA_2N+_35_S83

tag: cell line

tag: cell type

value: Pancreatic cancer tumor cell line


title: DNA_2N+_34_S82

value: EGFP expression


title: scramble DMSO polysomal replicate 1

tag: genotype

tag: agent

value: DMSO


title: methylation_20_Vehicle

tag: Sex


title: DNA_2N+_32_S80

value: genomic DNA in nuclei


title: methylation_15_IL-13


title: DNA_2N+_33_S81


title: methylation_39_IL-13


title: DNA_2N+_31_S79


title: methylation_15_Combined


title: methylation_15_Vehicle


title: scramble DMSO polysomal replicate 3

value: wild type

tag: fraction

value: polysomal RNA


title: DNA_2N+_7_S55


title: DNA_2N+_30_S78


title: methylation_15_IL-17


title: Yap1_Rep2

tag: Stage


title: methylation_19_IL-17


title: DNA_2N+_3_S51


title: methylation_19_IL-13


title: DNA_2N+_28_S76


title: DNA_2N+_29_S77


title: methylation_19_Vehicle

value: Vehicle


title: methylation_20_Combined


title: DNA_2N+_27_S75


title: ch12_Med14Nsmash_chipseq_SP1_DMSO_rep2

city: bethesda

first: Seolkyoung

last: Jung

address: 10 Center Dr

institute: NIH

data_processing:
base calling: illumina CASAVA 1.8.2
ChIP-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm)

source_name: CH12 B cell line

extract_protocol:
ChIP-Seq: Cultured cells were fixed with 1% formaldehyde (Sigma) for 10’ at 37°C. Fixation was quenched by addition of glycine (Sigma) at a final concentration of 125 mM. Twenty million fixed cells were washed with PBS and resuspended in 1 ml of RIPA buffer (10 mM Tris [pH 7.6], 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 1× Complete Mini EDTA free proteinase inhibitor (Roche)) or stored at −80°C until further processing. Sonication was performed using Covaris S2 sonicator at duty cycle 20%, intensity 5, cycle/burst 200 for 30 min or Branson sonifier at amplitude 35%, 12 cycles of 20” sonication and 30” of pause. For native chip, chromatin was digested with Mnase (Sigma) in digestion buffer (50 mM Tris-HCl, pH7.6, 1 mM CaCl2, 0.2% Triton X-100, butyrate 5 mM) for 5’ at  37°C and dialyzed against RIPA buffer for 2hrs at 4°C. Five micrograms of antibody were incubated with 40 μl of Dynabeads Protein A (or G) for 40 min at room temperature. Antibody-bound beads were added to 500 μl of sonicated or Mnase-digested chromatin, incubated at 4°C overnight, and washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (pH 8.0) plus 0.2% Triton X-100, and once with TE (pH 8.0). Crosslinking was reversed by incubating the beads at 65°C for 4 hr in the presence of 0.3% SDS and 1 mg/ml Proteinase K. ChIP DNA was purified by phenol-chloroform extraction followed by ethanol precipitation.
ChIP-Seq :  Library was prepared in Ovation SP Ultralow library system (Nugen). 50 cycles of sequencing data were acquired on the HiSeq 3000 or Novaseq 6000 (Illumina).

tag: tissue

value: lymphoma cell line

tag: chip antibody

value: Abcam, ab13370

tag: experimental type

value: ChIPseq


title: methylation_19_Combined

value: primary cultured airway smooth muscle cell

tag: donor

value: Male


title: methylation_55_Vehicle

tag: asthma

value: No


title: DNA_2N+_26_S74

tag: strain background

tag: labelling for flow

tag: molecule subtype


title: ch12_Med14Nsmash_chipseq_SP1_APR60h_rep2

tag: treatment


title: ch12_Med14Nsmash_chipseq_SP1_DMSO_rep1