title: MERS-CoV-infected-untreated-sacrifice-3dpi [1C1]

description:
1C1
processed data file: Channappanavar_Raw_Data.txt
processed data file: Processed_files_1C_vs._1T_314genes_2XFC_FDR_0.05.xlsx


title: Breast cancer sample [132_mda_set_ep]

status: Public on May 30 2019

type: RNA

city: Houston

first: Bruno

middle: Valentin

last: Sinn

state: TX

address: 2130 W Holcombe Blvd

department: Translational Molecular Pathology

country: USA

institute: University of Texas - MD Anderson Cancer Center

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized overnight at 46C on Affymetrix U133A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the diagnostic-grade Affymetrix scanner 3000DX.

data_processing: Probe intensities were quantified with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. CEL files were normalized using global scaling with a trimmed mean target intensity of each array arbitrarily set to 600 using the MAS5 algorithm from the simpleaffy package (http://bioconductor.org/packages/2.4/bioc/html/simpleaffy.html).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: breast cancer, hormone receptor-positive

label_protocol: A single-round T7 amplification was used to generate biotin-labeled cRNA for hybridization. At least 1 ug of RNA is required for cRNA synthesis.

extract_protocol: Total RNA was extracted from tissue using Qiagen RNeasy columns.

treatment_protocol: Patients prospectively consented to a research biopsy by fine needle aspiration (FNA), core biopsy or surgical tissue sample.

tag: tissue

value: Breast cancer

tag: immunohistochemistry subtype

tag: ajcc stage

value: IIB

tag: tissue type

value: Surgical tissue


title: Breast cancer sample [128_mda_set_ep]

value: IIA


title: Breast cancer sample [130_mda_set_ep]


title: Breast cancer sample [131_mda_set_ep]


title: Breast cancer sample [069_mda_set_ep]

value: IIIA


title: Breast cancer sample [134_mda_set_ep]


title: Breast cancer sample [066_mda_set_ep]


title: Breast cancer sample [068_mda_set_ep]


title: Breast cancer sample [138_mda_set_ep]


title: Breast cancer sample [065_mda_set_ep]


title: Breast cancer sample [063_mda_set_ep]


title: Breast cancer sample [059_mda_set_ep]


title: Breast cancer sample [060_mda_set_ep]


title: DQ30: Dps_24h

type: SRA

city: Indianapolis

first: Takashi

last: Hato

state: IN

address: 950 W. Walnut St. R2 202

department: Medicine

institute: Indiana University

library_source: transcriptomic

data_processing:
The sequenced data were mapped to the mm10 genome using STAR RNA-seq aligner. Uniquely mapped sequencing reads were assigned to mm10 refGene genes using featureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: text file, featureCounts

organism: Mus musculus

source_name: Kidney

extract_protocol:
Kidneys were snap frozen and RNA was extracted using Qiagen Rneasy Plus Midi Kit with gDNA removal column.
RNA libraries were prepared for sequencing using standard Illumina protocols. Illumina TruSeq Stranded mRNA HT (RS-122-21) was used for library construction. Sequence was performed with 2x75 bp paired-end configuration on HiSeq4000 using HiSeq 3000/4000 PE SBS Kit.

tag: strain

value: Kidney

tag: timepoint

tag: treatment

tag: gender

value: male


title: DQ33: Control

value: Control


title: DQ29: Dps_24h


title: Breast cancer sample [061_mda_set_ep]


title: Breast cancer sample [062_mda_set_ep]


title: DQ32: Control


title: DQ27: Dps_4h


title: DQ26: Dps_4h


title: Breast cancer sample [057_mda_set_ep]

value: IA


title: DQ24: MnDps_24h


title: Breast cancer sample [058_mda_set_ep]


title: DQ23: MnDps_24h


title: DQ21: MnDps_4h


title: DQ20: MnDps_4h


title: DQ28: Dps_24h


title: Breast cancer sample [050_mda_set_ep]


title: DQ19: MnDps_4h


title: Breast cancer sample [055_mda_set_ep]


title: Breast cancer sample [051_mda_set_ep]


title: Breast cancer sample [053_mda_set_ep]


title: Breast cancer sample [052_mda_set_ep]


title: Breast cancer sample [048_mda_set_ep]


title: DQ25: Dps_4h


title: Breast cancer sample [049_mda_set_ep]


title: naive2

city: Oxford

first: Dylan

last: Sheerin

address: Centre for Clinical Vaccinology and Tropical Medicine, Churchill Hospital

department: Paediatrics

country: United Kingdom

institute: University of Oxford

data_processing:
RNA was sequenced (75 bp, paired end) using an Illumina HISeq 4000
Raw fastq files were analysed for sequence quality using fastqc software
Reads were aligned to the Mus musculus reference genome (GRCm38) and genes were quantified using STAR with the --quantMode GeneCounts function
Resultant count matrices were filtered to include only genes with counts per million of greater than 1 million in 5 or more samples (smallest group size)
Count matrices were analysed for differential gene expression using the limma/voom pipeline
Genome_build: GRCm38, release 95
Supplementary_files_format_and_content: Tab-delimited files (.tab) were generated using STAR –quantMode GeneCounts and each value represent the number of reads incident to a gene in a given sample

source_name: Whole blood

extract_protocol:
RNA was extracted from mouse whole blood samples using a Mouse RiboPure(TM)-Blood RNA Isolation Kit (Life Technologies) and depleted for glibin mRNA using a GLOBINclear(TM) mouse/rat Kit (Life Technologies)
Polyadenylated transcripts were oligo (dT) bead-selected, reverse transcribed, amplified and labelled with an Illumina TotalPrep(TM)-96 RNA Amplification Kit (Life Technologies)
Sample fragments were 75 bp size-selected and multiplexed

treatment_protocol: Groups of 5-6 female C57BL/6 mice (6-8 weeks old) were immunised intramuscularly with 1/5 of the human dose of one of the listed vaccines. Mice were given a second dose of vaccine 3 weeks later and cardiac bled to obtain whole blood 24h ours after this second dose.

tag: Sex

value: Female

tag: vaccine/antigen


title: naive5


title: naive6


title: naive4


title: Breast cancer sample [047_mda_set_ep]


title: Breast cancer sample [044_mda_set_ep]


title: Breast cancer sample [045_mda_set_ep]


title: Breast cancer sample [046_mda_set_ep]


title: Breast cancer sample [043_mda_set_ep]


title: mva4

value: MVA virus


title: mva5


title: Breast cancer sample [041_mda_set_ep]


title: Breast cancer sample [042_mda_set_ep]


title: mva2


title: naive1


title: Breast cancer sample [020_mda_set_ep]


title: mva1


title: Breast cancer sample [040_mda_set_ep]


title: lps5

value: E. coli LPS


title: lps4


title: lps3


title: naive3


title: lpxomv6

value: H44/76 lpxL1 OMVs


title: metastasis_140

data_processing:
Probe intensities were quantified with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. CEL files were normalized using global scaling with a trimmed mean target intensity of each array arbitrarily set to 600 using the MAS5 algorithm from the simpleaffy package (http://bioconductor.org/packages/2.4/bioc/html/simpleaffy.html).
MAS5.0 signal intensity for each array was log2 transformed and scaled to a reference distribution of 1322 breast cancer specific genes.

source_name: breast cancer, metastatic sample, hormone receptor-positive

extract_protocol: Total RNA was extracted from tissue using Qiagen Rneasy columns.

treatment_protocol: Patients prospectively consented to a research biopsy by fine needle aspiration (FNA) and to the future assessment of survival endpoints.

value: Breast cancer, metastatic sample

tag: pfs months

tag: oas months

tag: os event

tag: pr status

tag: number of event

tag: prior endocrine sensitivity

tag: visceral disease

tag: protocol treatment

value: H

tag: site biopsied

value: Ovary

tag: stage iv at initial diagnosis

tag: protocol number

value: ER 9

tag: esr1 maf

tag: esr1 mutation

tag: set er_pr rnaseq


title: mva3

tag: strain


title: lpxomv4

tag: Sex


title: metastasis_139

tag: tissue

value: Liver

value: ER 34


title: lpxomv3

tag: vaccine/antigen


title: lps1


title: lpxomv5


title: metastasis_133

tag: pfs months

tag: oas months

value: Bone

value: ER 54


title: metastasis_136

tag: os event

tag: pr status

value: C

value: Soft Tissue

value: ER 63


title: metastasis_134

tag: number of event

tag: prior endocrine sensitivity

value: Lymph node

value: ER 57

value: WT


title: metastasis_137

tag: visceral disease

tag: protocol treatment

value: ER 65


title: lpxomv2

value: Female


title: metastasis_130

tag: site biopsied

tag: stage iv at initial diagnosis

value: ER 37


title: lps6

value: E. coli LPS


title: metastasis_128

value: Breast cancer, metastatic sample

value: H

tag: protocol number

value: ER 48

tag: esr1 maf


title: metastasis_127

value: Skin

value: ER 47

tag: esr1 mutation

tag: set er_pr rnaseq


title: metastasis_138

value: ER 26


title: metastasis_131

value: ER 45


title: metastasis_135

value: Visc. other

value: ER 59


title: metastasis_126

value: ER 44


title: metastasis_129

value: Breast

value: ER 53


title: metastasis_124

value: ER 35

value: WT


title: h44omv3

tag: strain

tag: Sex

value: Female

value: H44/76 OMVs


title: lpxomv1

tag: vaccine/antigen

value: H44/76 lpxL1 OMVs


title: metastasis_132

tag: tissue

value: Breast cancer, metastatic sample

tag: pfs months

value: ER 52


title: lps2

value: E. coli LPS


title: h44omv5


title: h44omv6


title: h44omv4


title: nzomv5

value: NZ98/254 OMVs


title: nzomv3


title: nzomv6


title: nzomv4


title: metastasis_125

tag: oas months

tag: os event

value: H

value: Lymph node

value: ER 39


title: nzomv2


title: nzomv1


title: fhbp6

value: Fhbp


title: fhbp5


title: h44omv2


title: h44omv1


title: metastasis_122

tag: pr status

tag: number of event

value: Bone

value: ER 27


title: fhbp4


title: metastasis_117

tag: prior endocrine sensitivity

tag: visceral disease

value: Soft Tissue

value: ER 14


title: metastasis_123

tag: protocol treatment

tag: site biopsied

value: ER 28


title: metastasis_118

value: Breast

tag: stage iv at initial diagnosis

tag: protocol number

value: ER 16

value: WT


title: metastasis_120

value: ER 21

tag: esr1 maf

tag: esr1 mutation


title: metastasis_119

value: Breast cancer, metastatic sample

value: ER 19

tag: set er_pr rnaseq


title: fhbp3

tag: strain

tag: Sex

value: Female


title: metastasis_116

tag: tissue

value: C

value: ER 11


title: metastasis_121

tag: pfs months

value: H

value: ER 17


title: metastasis_115

tag: oas months

value: ER 8


title: metastasis_114

tag: os event

value: Lymph node

value: ER 7


title: metastasis_112

tag: pr status

value: Soft Tissue

value: ER 1


title: metastasis_113

tag: number of event

value: ER 3


title: fhbp2

tag: vaccine/antigen

value: Fhbp


title: metastasis_108

tag: prior endocrine sensitivity

tag: visceral disease

value: Liver


title: fhbp1


title: metastasis_107

tag: protocol treatment

tag: site biopsied


title: M-MDSCs from non-small lung cancer patient p1

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
RNA-seq data was aligned using bowtie2 against hg19 version of the human genome and RSEM v1.2.31 software was used to estimate raw read counts and FPKM values using transcriptome information from Ensemble v84 set
DESeq2 was used to estimate significance of differential expression between groups
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene as estimated by RSEM

source_name: M-MDSCs

extract_protocol:
Cell pellets containing 500,000 - 1 million cells were lysed in 300 ul of Tri- Reagent (Sigma, St. Louis, MO) and RNA was extracted using the Direct-Zol RNA Mini-Prep Kit (Zymo Research, Irvine, CA), including an on-column DNAseI treatment.
3’ mRNA-seq libraries were generated from DNAseI treated total RNA using the QuantSeq FWD Library Preparation kit (Lexogen, Vienna, Austria), according to manufacturer’s directions.

tag: disease state

value: non-small lung cancer

tag: cell type

value: M-MDSC

tag: patientid


title: Monocytes from non-small lung cancer patient p2

source_name: Monocytes

value: Monocytes


title: nhba5

value: NHBA


title: M-MDSCs from non-small lung cancer patient p2


title: M-MDSCs from non-small lung cancer patient p3


title: Monocytes from non-small lung cancer patient p3


title: DQ31: Control

value: Kidney

tag: timepoint

tag: treatment

value: Control

tag: gender

value: male


title: Monocytes from non-small lung cancer patient p1


title: nhba4

tag: strain

tag: Sex

value: Female


title: metastasis_110

tag: tissue

value: Breast cancer, metastatic sample

tag: pfs months

tag: oas months

value: C

tag: stage iv at initial diagnosis

tag: protocol number

tag: esr1 maf

tag: esr1 mutation

tag: set er_pr rnaseq


title: metastasis_109

tag: os event

tag: pr status

tag: number of event

tag: prior endocrine sensitivity

tag: visceral disease

tag: protocol treatment

tag: site biopsied

value: Lymph node


title: nhba6

tag: strain

tag: vaccine/antigen


title: metastasis_101

tag: tissue

value: H

value: Skin


title: metastasis_106

tag: pfs months

value: Bone


title: metastasis_103

tag: oas months


title: metastasis_105

tag: stage iv at initial diagnosis


title: nhba2

tag: Sex


title: nhba3


title: Nascent RNA-seq in THP1 cells 2

first: Thomas

middle: A

last: Milne

address: John Radcliffe Hospital, Headington

department: MRC Weatherall Institute of Molecular Medicine

description: Nascent RNA

data_processing:
RNA-seq reads were aligned to the hg19 genome using STAR
Duplicate reads were removed using samtools rmdup
Read counts were determined using featureCounts (Subread package)
Genome_build: hg19

source_name: Leukemia cell line (THP1)

growth_protocol: Cells were continuously grown in RPMI with 10% FBS, split when they reached a density of 1-2x10e6 cells/ml down to 5x10e5 cells/ml

extract_protocol:
108 4sU-treated cells were lysed in 10ml Trizol. RNA was extracted using chloroform and precipitated with EtOH. 4sU RNA was biotinylated with 1mg/ml Biotin-HPDP and nascent RNA was enriched for using streptavidin-coated beads.
see sample table
DNA libraries were prepared using the NEB Next Ultra Directional RNA library preparation kit for Illumina (E7420).

tag: cell line

value: Leukemia cell line (THP1)

tag: cell type

value: Paediatric monocytic cell line derived from AML M5 with t(9;11)(q21;q23) translocation


title: nada6

value: NadA


title: Nascent RNA-seq in THP1 cells 3

description: Nascent RNA


title: Nascent RNA-seq in THP1 cells 1

description: Nascent RNA


title: metastasis_104

value: Breast

tag: protocol number

tag: esr1 maf

tag: esr1 mutation

tag: set er_pr rnaseq


title: metastasis_100

tag: os event

tag: pr status

tag: number of event

tag: prior endocrine sensitivity


title: nhba1

tag: strain


title: H3K79me2 ChIP seq in THP1 cells

description:
ChIP seq performed using H3K79me2 antibody in THP1 cells
THP1_H3K79me2_peaks.bed.gz

library_source: genomic

data_processing:
Alignment to the genome (Bowtie) maintaining strict read order
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
Removal of PCR duplicates, parsing of informative reads using samtools rmdup
Genome_build: hg19
Peak calling using Homer v4.7

molecule: genomic DNA

growth_protocol: Cells were continuously grown in IMDM (SEM) or RPMI (THP1) with 10% FBS, split when they reached a density of 1-2x10e6 cells/ml down to 5x10e5 cells/ml

extract_protocol:
Cells were washed with PBS and fixed in either 1% FA for 10 minutes (histones) or 2mM DSG for 30 minutes and 1% FA for 30 minutes (transcription factors). Cells were sonicated to give fragments of 100-300bp followed by IP. For ChIP-rx fixed SEM cells were mixed at a 4:1 ratio with fixed Drosophila S2 cells prior to sonication.
DNA libraries were made using the NEBnext ultra DNA library preparation kit for Illumina (Cat no. E7370).

treatment_protocol: Where indicated, cells were treated with EPZ-5676 or DMSO for 7 days

tag: treatment

tag: chip antibody

value: Millipore cat no. 04/835


description:
ChIP seq Input for H3K79me2 in THP1 cells
THP1_H3K79me2_peaks.bed.gz


description:
ChIP seq Input for H3K4me1 in THP1 cells
THP1_H3K4me1_peaks.bed.gz


title: metastasis_96

tag: tissue

tag: pfs months

tag: visceral disease

tag: protocol treatment

tag: site biopsied

value: Soft Tissue


title: metastasis_95

tag: oas months

tag: stage iv at initial diagnosis

value: WT


title: metastasis_93

tag: protocol number

tag: esr1 maf


title: metastasis_98

tag: esr1 mutation

tag: set er_pr rnaseq


title: nada4

tag: Sex

tag: vaccine/antigen


title: metastasis_102

tag: os event

tag: pr status

tag: number of event

tag: prior endocrine sensitivity


title: nada5

tag: strain


title: metastasis_92

tag: tissue

tag: pfs months


title: metastasis_99

tag: visceral disease

tag: protocol treatment


title: metastasis_97

tag: oas months

tag: site biopsied


title: metastasis_91

tag: stage iv at initial diagnosis

tag: protocol number


title: metastasis_89

tag: esr1 maf

tag: esr1 mutation


title: H3K4me1 ChIP seq in THP1 cells

description:
ChIP seq performed using H3K4me1 antibody in THP1 cells
THP1_H3K4me1_peaks.bed.gz

tag: cell line

tag: treatment

tag: cell type

tag: chip antibody

value: Diagenode cat no. pAB-194-050


title: metastasis_94

tag: os event

tag: pr status

tag: number of event

tag: set er_pr rnaseq


title: nada3

tag: strain

tag: Sex

tag: vaccine/antigen


description:
ChIP seq Input for H3K27ac, H3K4me3 in THP1 cells
THP1_H3K27ac_peaks.bed.gz
THP1_H3K4me3_peaks.bed.gz


title: metastasis_88

tag: tissue

tag: pfs months

tag: oas months

tag: prior endocrine sensitivity

tag: visceral disease

tag: protocol treatment


title: metastasis_90

tag: site biopsied

tag: stage iv at initial diagnosis

tag: protocol number

tag: esr1 maf

tag: esr1 mutation


title: nada1


title: H3K4me3 ChIP seq in THP1 cells

description:
ChIP seq performed using H3K4me3 antibody in THP1 cells
THP1_H3K4me3_peaks.bed.gz

tag: cell line

tag: treatment

tag: cell type

tag: chip antibody

value: Diagenode cat no. pAB-003-050


title: bex6

tag: strain

tag: Sex


title: bex5

tag: vaccine/antigen


title: Capture-C_THP1_DOT1Li_replicate_3

description:
Next generation Capture-C products
3C library preparation followed by double oligonucleotide capture

data_processing:
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
In silico restriction enzyme digestion of FASTQ file (custom scripts)
Alignment to the genome (Bowtie -m 2) maintaining strict read order
Removal of PCR duplicates, parsing of informative reads and mapping to restriction enzyme fragments (custom scripts)
Combining data from multiple replicates (custom scripts)
Removal of ploidy regions and off target capture (custom scripts)
Analysis in R to normalise between tracks using the total number of informative interactions
Genome_build: hg19
Supplementary_files_format_and_content: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.)

source_name: Capture-C in DOT1Li treated THP1 cells

growth_protocol: Cells were continuously grown in IMDM with 10% FBS, split when they reached a density of 1-2x10e6 cells/ml down to 5x10e5 cells/ml

extract_protocol:
Cells fixed with 2% formaldehyde and lysed using dounce homogenisation
The Capture-C technologies combine 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments. Detailed description follows. The protocol used for the generation of the 3C libraries was similar to other 3C-based methods. Briefly, cells were crosslinked with 2% formaldehyde, quenched with cold glycine, washed in phosphate buffered saline, resuspended in cold lysis buffer and snap frozen to -80. Cells were thawed on ice, washed in Milli-Q dH2O and Dounce homogenized on ice. Cells were then resuspended with 0.25% SDS and restriction enzyme buffer and incubated at 37 °C for 1h at 1400 rpm on a Thermomixer, followed by a further incubation of 1h after the addition of Triton X-100 (final concentration 1.67%). An overnight digestion was performed using DpnII (final concentration 500U/ml; 37 °C / 1400 rpm). The digested chromatin was ligated overnight using T4 DNA HC ligase (final concentration 10U/ml; 16 °C / 1400 rpm). The samples were de-crosslinked overnight with Proteinase K at 65 °C, followed by a 30 min incubation at 37 °C with RNase. A Phenol/Chloroform extraction was performed, followed by an ethanol precipitation and wash. Digestion efficiencies were assessed by gel electrophoresis and RT-PCR, which showed digestion efficiencies higher than 80%. The DNA contents of the DpnII 3C libraries were quantitated using a Qubit fluorometer. 5 ug DNA was adapter ligated using a strategy based on sonication combined with the NEBNext DNA Library Prep kit. The quality of the libraries was assessed using the Agilent ScreenTape system. Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments. 700 ng of the adapter ligated libraries was hybridized with the biotinylated capture oligonucleotides, using the Nimblegen SeqCap reagents and an adapted protocol. The quality of the resulting captured library was assessed using the Agilent ScreenTape system. The libraries were sequenced using the Illumina NextSeq (150bp paired end reads) platform.

treatment_protocol: Cells were treated with EPZ-5676 or DMSO for 7 days

value: EPZ-5676 at 5uM for 7 days

tag: genes analysed

value: ARID1B, ASH2L, BAZ2B, BCL11A, BCL2, CDK6, ELL2, EP300, EZH2, FLT3, FOS, FUT10, GADD45A, JARID1A, JMJD1C, JUN, LMO4, MBNL1, MED13, MSL3, MYC, OGT, SMYD2, SPI1, SUPT3H, SUZ12, TAPT1, TET2


title: Capture-C_THP1_DOT1Li_replicate_2


title: nada2

value: Female


title: bex3


title: bex4


title: metastasis_84

tag: tissue

value: Breast cancer, metastatic sample

tag: pfs months

tag: oas months

tag: os event

tag: pr status

tag: number of event

tag: set er_pr rnaseq


title: metastasis_86

tag: prior endocrine sensitivity

tag: visceral disease

tag: protocol treatment

tag: site biopsied

tag: stage iv at initial diagnosis

tag: protocol number

tag: esr1 maf


title: metastasis_85

tag: esr1 mutation


title: bex2

tag: strain

tag: Sex

tag: vaccine/antigen


title: Capture-C_THP1_Control_replicate_3

source_name: Capture-C in THP1 cells

tag: cell line

tag: treatment

value: DMSO for 7 days

tag: genes analysed


title: Capture-C_THP1_DOT1Li_replicate_1


title: H3K27ac ChIP seq in THP1 cells

description:
ChIP seq performed using H3K27ac antibody in THP1 cells
THP1_H3K27ac_peaks.bed.gz

tag: cell type

tag: chip antibody

value: Diagenode cat no. C15410196 lot no. A1723-0041D


title: metastasis_83

tag: tissue

tag: pfs months

tag: oas months

tag: os event

tag: pr status

tag: number of event

value: H

value: Lung

tag: set er_pr rnaseq


title: metastasis_80

tag: prior endocrine sensitivity

tag: visceral disease

tag: protocol treatment

value: O

tag: site biopsied

value: Liver

tag: stage iv at initial diagnosis

tag: protocol number

tag: esr1 maf


title: metastasis_78

value: Bone

tag: esr1 mutation


title: metastasis_79

value: Skin


title: metastasis_81


title: metastasis_74

value: C

value: Pleura


title: metastasis_75


title: metastasis_76

value: Soft Tissue


title: Capture-C_THP1_Control_replicate_2

tag: cell line

value: Leukemia cell line (THP1)

tag: treatment

tag: genes analysed


title: metastasis_82

tag: tissue

tag: pfs months


title: metastasis_77

tag: oas months

tag: os event

value: Lymph node


title: metastasis_111

tag: pr status

tag: number of event


title: metastasis_71

tag: prior endocrine sensitivity

value: WT

tag: set er_pr rnaseq


title: metastasis_70

tag: visceral disease

tag: protocol treatment


title: Capture-C_THP1_Control_replicate_1

value: ARID1B, ASH2L, BAZ2B, BCL11A, BCL2, CDK6, ELL2, EP300, EZH2, FLT3, FOS, FUT10, GADD45A, JARID1A, JMJD1C, JUN, LMO4, MBNL1, MED13, MSL3, MYC, OGT, SMYD2, SPI1, SUPT3H, SUZ12, TAPT1, TET2


title: bex1

tag: strain

tag: Sex

value: Female

tag: vaccine/antigen


title: metastasis_73

value: Breast cancer, metastatic sample

tag: site biopsied

tag: stage iv at initial diagnosis

tag: protocol number

tag: esr1 maf

tag: esr1 mutation


title: Capture-C_RS4;11_DOT1Li_replicate_3

source_name: Capture-C in DOT1Li treated RS4;11 cells

tag: cell line

value: Leukemia cell line (RS4;11)

tag: treatment

value: EPZ-5676 at 2uM for 7 days

tag: genes analysed


title: metastasis_72

tag: tissue

tag: pfs months

tag: oas months

tag: os event

tag: pr status

value: H

value: ER 78


title: metastasis_68

tag: number of event

tag: prior endocrine sensitivity

tag: visceral disease

tag: protocol treatment

tag: set er_pr rnaseq


title: metastasis_67

tag: site biopsied

value: Lung

tag: stage iv at initial diagnosis


title: metastasis_69

tag: protocol number

tag: esr1 maf


title: Capture-C_RS4;11_DOT1Li_replicate_2

tag: cell line


title: Capture-C_RS4;11_Control_replicate_2

source_name: Capture-C in RS4;11 cells

tag: treatment

value: DMSO for 7 days


title: Capture-C_RS4;11_DOT1Li_replicate_1

tag: genes analysed


title: Capture-C_RS4;11_Control_replicate_3


title: Capture-C_RS4;11_Control_replicate_1


title: ATAC seq in DOT1Li treated RS4;11 cells

description:
Fragmented genomic DNA
ATAC seq performed in RS4;11 cells following 7 day treatment in 2uM EPZ-5676

data_processing:
Alignment to the genome (Bowtie) maintaining strict read order
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
Removal of PCR duplicates, parsing of informative reads using samtools rmdup
Genome_build: hg19
Peak calling using Homer

source_name: MLL-AF4 leukemia cell line (RS4;11)

extract_protocol:
Cells were washed with PBS and lysed with 0.1% IGEPAL CA-630, followed by Tn5 transposase treatment
Libraries were made using the Nextera DNA library prep kit (Illumina)

value: MLL-AF4 leukemia cell line (RS4;11)

tag: cell type

value: Adult precursor pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation


title: ATAC seq in RS4;11 cells

description:
Fragmented genomic DNA
ATAC seq performed in RS4;11 cells following 7 day treatment in DMSO


title: metastasis_66

tag: tissue

tag: pfs months

tag: esr1 mutation


title: metastasis_65

tag: oas months

tag: os event

tag: pr status


title: metastasis_64

tag: number of event

tag: prior endocrine sensitivity

tag: visceral disease


title: metastasis_61

tag: protocol treatment

tag: site biopsied

tag: set er_pr rnaseq


title: metastasis_59

value: Skin

tag: stage iv at initial diagnosis

tag: protocol number

tag: esr1 maf


title: metastasis_63


title: H3K79me3 ChIP seq input in SEM cells treated with 2uM EPZ-5676

description:
Input for ChIP seq performed using H3K79me3 antibody in SEM cells following 7 day treatment with 2uM EPZ-5676
H3K79me3_2uM_EPZ_peaks.bed

data_processing:
Alignment to the genome (Bowtie) maintaining strict read order
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
Removal of PCR duplicates, parsing of informative reads using samtools rmdup
Peak calling using Homer v4.7
Genome_build: hg19
Supplementary_files_format_and_content: bed file reporting called peaks

tag: cell line

value: Leukemia cell line (SEM)

tag: treatment

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation

tag: chip antibody


title: H3K79me3 ChIP seq in SEM cells treated with  DMSO

description:
ChIP seq performed using H3K79me3 antibody in SEM cells following 7 daystreatment with DMSO
H3K79me3_0uM_EPZ_peaks.bed

tag: cell type

value: H3K79me3 (Diagenode pAb-068-050)


title: metastasis_57

tag: tissue

tag: pfs months

value: Soft Tissue

tag: esr1 mutation


title: metastasis_58

tag: oas months

tag: os event

tag: pr status

value: Bone


title: metastasis_60

tag: number of event

tag: prior endocrine sensitivity

tag: visceral disease

value: Lymph node

value: WT


title: metastasis_62

value: Breast cancer, metastatic sample

tag: protocol treatment

tag: site biopsied

tag: set er_pr rnaseq


title: metastasis_55

tag: stage iv at initial diagnosis

tag: protocol number

tag: esr1 maf


title: metastasis_56


title: H3K79me3 ChIP seq input in SEM cells treated with DMSO

description:
Input for ChIP seq performed using H3K79me3 antibody in SEM cells following 7 daystreatment with DMSO
H3K79me3_0uM_EPZ_peaks.bed

tag: cell line

tag: treatment

tag: chip antibody


title: metastasis_54

tag: tissue

tag: pfs months

value: O

value: Breast


title: metastasis_52

tag: oas months

value: H

tag: esr1 mutation


title: H3K79me3 ChIP seq in SEM cells treated with 2uM EPZ-5676

description:
ChIP seq performed using H3K79me3 antibody in SEM cells following 7 day treatment with 2uM EPZ-5676
H3K79me3_2uM_EPZ_peaks.bed

value: EPZ-5676 at 2uM for 7 days

tag: cell type


title: metastasis_51

tag: os event

tag: pr status

tag: number of event


title: metastasis_49

tag: prior endocrine sensitivity

tag: visceral disease

tag: protocol treatment


title: metastasis_48

tag: site biopsied

tag: stage iv at initial diagnosis

tag: set er_pr rnaseq


title: metastasis_45

tag: protocol number

tag: esr1 maf


title: metastasis_46


title: metastasis_44

value: C


title: metastasis_53


title: H3K27ac ChIP seq in SEM cells treated with 2uM EPZ-5676

description:
ChIP seq performed using H3K27ac antibody in SEM cells following 7 day treatment with 2uM EPZ-5676
H3K27ac_2uM_EPZ_peaks.bed

tag: cell line

tag: treatment

tag: chip antibody

value: H3K27ac (Diagenode  C15410196)


title: metastasis_50

tag: tissue

tag: pfs months

tag: oas months


title: H3K27ac ChIP seq input  in SEM cells treated with 2uM EPZ-5676

description:
Input for ChIP seq performed using H3K27ac antibody in SEM cells following 7 day treatment with 2uM EPZ-5676
H3K27ac_2uM_EPZ_peaks.bed

tag: cell type


title: metastasis_42

tag: os event

tag: pr status

tag: esr1 mutation


title: metastasis_43

tag: number of event

tag: prior endocrine sensitivity

tag: visceral disease


title: MYB ChIP seq in SEM cells

description:
ChIP seq performed using MYB antibody in SEM cells
MYB_peaks.bed

source_name: MYB

value: MYB (Abcam ab109127)


title: H3K27ac ChIP seq input in SEM cells treated with DMSO

description:
Input for ChIP seq performed using H3K27ac antibody in SEM cells following 7 day treatment with DMSO
H3K27ac_0uM_EPZ_peaks.bed

value: DMSO for 7 days


title: metastasis_47

tag: protocol treatment

tag: site biopsied

value: Skin

tag: stage iv at initial diagnosis


title: metastasis_41

tag: protocol number

tag: esr1 maf

tag: set er_pr rnaseq


title: MYB ChIP seq input in SEM cells

description:
Input for ChIP seq performed using MYB antibody in SEM cells
MYB_peaks.bed

tag: cell line

value: Leukemia cell line (SEM)

tag: treatment

tag: chip antibody


title: metastasis_37

tag: tissue

tag: pfs months

tag: oas months


title: ERG ChIP seq in SEM cells

description:
ChIP seq performed using ERG antibody in SEM cells
ERG_peaks.bed

source_name: ERG

tag: cell type

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation


title: e10.5_heart_ventriculars

city: Pittsburgh

first: Guang

last: Li

address: 530 45th St. 8116 Rangos Research Center

department: Developmental Biology

institute: University of Pittsburgh

description:
The whole ventricular chambers from mouse embryonic hearts.
oligodT was used to reverse transcribe the single cell derived mRNAs.

data_processing:
The single cell library was sequenced with Illumina hiseq 4000 platform.
Sequencing reads were aligned to mouse MM10 reference genome with Cell Ranger.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: matrix.mtx, barcodes.tsv, genes.tsv

source_name: whole ventricular chambers from embryonic hearts

growth_protocol: Mouse embryonic heart dissected from mouse embryos at E10.5.

extract_protocol:
This step was done by following the 10x Genomics single cell preparation protocol.
This step was done by following the 10x Genomics single cell library preparation protocol.
Only the 3' end of mRNA fragments were used to make library. One end of the fragments were added P5, read1 Illumina sequencing primer, 16 base pairs of 10x barcode, and UMI sequences; The other end ligated with P7, sample index sequences, and Illumina read2 sequencing primer sequences.

tag: strain/background

tag: developmental stage

value: whole ventricular chambers


title: metastasis_38

tag: os event

tag: pr status

tag: number of event

tag: prior endocrine sensitivity

value: Soft Tissue

tag: esr1 mutation


title: ERG ChIP seq input in SEM cells

description:
Input for ChIP seq performed using ERG antibody in SEM cells
ERG_peaks.bed


title: H3K27ac ChIP seq  in SEM cells treated with DMSO

description:
ChIP seq performed using H3K27ac antibody in SEM cells following 7 day treatment with DMSO
H3K27ac_0uM_EPZ_peaks.bed


title: ELF1 ChIP seq in SEM cells

description:
ChIP seq performed using ELF1 antibody in SEM cells
ELF1_peaks.bed

value: ELF1 (Bethyl A301-443A)


title: metastasis_33

tag: visceral disease

tag: protocol treatment

tag: site biopsied

tag: stage iv at initial diagnosis

tag: protocol number


title: metastasis_36

value: Liver

tag: esr1 maf

tag: set er_pr rnaseq


title: ELF1 ChIP seq input in SEM cells

description:
Input for ChIP seq performed using ELF1 antibody in SEM cells
ELF1_peaks.bed

tag: cell line

tag: treatment

tag: chip antibody


title: metastasis_34

tag: tissue

tag: pfs months

tag: oas months

value: WT


title: metastasis_28

value: Breast cancer, metastatic sample

tag: os event

tag: pr status


title: metastasis_39

tag: number of event

tag: prior endocrine sensitivity


title: metastasis_40

tag: visceral disease

tag: esr1 mutation


title: metastasis_31

tag: protocol treatment

value: X

tag: site biopsied

value: Lymph node


title: metastasis_29

value: Bone

tag: stage iv at initial diagnosis

tag: protocol number


title: Sample_86_plus2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized overnight at 46C on Affymetrix U133A or U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

source_name: breast cancer sample profiled on PLUS2 microarray

treatment_protocol: Patients prospectively consented to a surgical tissue sample.

value: Breast cancer

tag: sample number

tag: microarray


title: Sample_88_plus2


title: metastasis_35

value: C

tag: esr1 maf

tag: set er_pr rnaseq


title: CTCF ChIP seq in SEM cells

description:
ChIP seq performed using CTCF antibody in SEM cells
CTCF_peaks.bed

source_name: CTCF

tag: cell line

tag: treatment

tag: cell type

tag: chip antibody

value: CTCF (Millipore 07-729)


title: metastasis_23

tag: tissue

tag: pfs months

tag: oas months

tag: os event

tag: pr status


title: metastasis_26

tag: number of event

tag: prior endocrine sensitivity

tag: visceral disease

tag: protocol treatment

tag: esr1 mutation


title: metastasis_27

tag: site biopsied

tag: stage iv at initial diagnosis

tag: protocol number


title: Sample_85_plus2

tag: sample number

tag: microarray


title: metastasis_24

tag: esr1 maf

tag: set er_pr rnaseq


title: CTCF ChIP seq input in SEM cells

description:
Input for ChIP seq performed using CTCF antibody in SEM cells
CTCF_peaks.bed

tag: cell line

tag: treatment

tag: cell type

tag: chip antibody


title: metastasis_32

tag: tissue

tag: pfs months

tag: oas months

tag: os event

tag: pr status

value: Breast


title: Capture-C in DOT1Li treated SEM cells rep3

description:
Next generation Capture-C products
3C library preparation followed by double oligonucleotide capture
2uM_3

data_processing:
Library strategy: Capture-C
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
In silico restriction enzyme digestion of FASTQ file (custom scripts)
Alignment to the genome (Bowtie -m 2) maintaining strict read order
Removal of PCR duplicates, parsing of informative reads and mapping to restriction enzyme fragments (custom scripts)
Combining data from multiple replicates (custom scripts)
Removal of ploidy regions and off target capture (custom scripts)
Analysis in R to normalise between tracks using the total number of informative interactions
Genome_build: hg19
Supplementary_files_format_and_content: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.)

source_name: Capture-C in DOT1Li treated SEM cells

extract_protocol:
SEM cells fixed with 2% formaldehyde and lysed using dounce homogenisation
The Capture-C technologies combine 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments. Detailed description follows. The protocol used for the generation of the 3C libraries was similar to other 3C-based methods. Briefly, cells were crosslinked with 2% formaldehyde (this was varied for the reduced crosslinking experiments), quenched with cold glycine, washed in phosphate buffered saline, resuspended in cold lysis buffer and snap frozen to -80. Cells were thawed on ice, washed in Milli-Q dH2O and Dounce homogenized on ice. Cells were then resuspended with 0.25% SDS and restriction enzyme buffer and incubated at 37 °C for 1h at 1400 rpm on a Thermomixer, followed by a further incubation of 1h after the addition of Triton X-100 (final concentration 1.67%). An overnight digestion was performed using DpnII (final concentration 500U/ml; 37 °C / 1400 rpm). The digested chromatin was ligated overnight using T4 DNA HC ligase (final concentration 10U/ml; 16 °C / 1400 rpm). The samples were de-crosslinked overnight with Proteinase K at 65 °C, followed by a 30 min incubation at 37 °C with RNAse. A Phenol/Chloroform extraction was performed, followed by an ethanol precipitation and wash. Digestion efficiencies were assessed by gel electrophoresis and RT-PCR, which showed digestion efficiencies higher than 80%. The DNA contents of the DpnII 3C libraries were quantitated using a Qubit fluorometer. Different strategies were used for the sequencing library preparation. For the low-input experiments, the LI Capture-C or Tag-Capture-C protocol was used, for which 50-200 ng of DNA was adapter ligated using a strategy based on sonication combined with the NEBNext Ultra DNA Library Prep kit, or the Illumina Nextera DNA Library Prep kit, respectively. For the reduced cross-linking experiments, the NG Capture-C protocol was used, for which 5 ug of DNA was adapter ligated using a strategy based on sonication combined with the NEBNext DNA Library Prep kit. The quality of the libraries was assessed using the Agilent ScreenTape system. Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments. 700 ng-2 ug of the adapter ligated libraries was hybridized with the biotinylated capture oligonucleotides, using the Nimblegen SeqCap reagents and an adapted protocol. The quality of the resulting captured library was assessed using the Agilent ScreenTape system. The libraries were sequenced using the Illumina NextSeq (150bp paired end reads) platform.

value: EPZ-5676 at 2uM for 7 days

tag: genes analyzed

value: ARID1B, ASH2L, BAZ2B, BCL11A, BCL2, CDK6, ELL2, EP300, EZH2, FLT3, FOS, FUT10, GADD45A, JARID1A, JMJD1C, JUN, LMO4, MBNL1, MED13, MSL3, MYC, OGT, SMYD2, SPI1, SUPT3H, SUZ12, TAPT1, TET2


title: metastasis_25

tag: number of event

tag: prior endocrine sensitivity

tag: visceral disease

tag: protocol treatment

tag: site biopsied

tag: esr1 mutation


title: metastasis_22

value: O

tag: stage iv at initial diagnosis

tag: protocol number

tag: esr1 maf

tag: set er_pr rnaseq


title: Sample_84_plus2

tag: sample number

tag: microarray


title: metastasis_20

tag: tissue

tag: pfs months


title: metastasis_21

tag: oas months

tag: os event


title: Capture-C in DOT1Li treated SEM cells rep2

description:
Next generation Capture-C products
3C library preparation followed by double oligonucleotide capture
2uM_2

tag: cell line

value: Leukemia cell line (SEM)

tag: cell type

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation

tag: treatment

tag: genes analyzed


title: Capture-C in DOT1Li treated SEM cells rep1

description:
Next generation Capture-C products
3C library preparation followed by double oligonucleotide capture
2uM_1


title: Capture-C in SEM cells rep3

description:
Next generation Capture-C products
3C library preparation followed by double oligonucleotide capture
0uM_3

source_name: Capture-C in SEM cells

value: DMSO for 7 days


title: Sample_83_plus2


title: metastasis_19

tag: pr status

tag: number of event

tag: prior endocrine sensitivity

tag: visceral disease

tag: protocol treatment

value: H


title: metastasis_87

tag: site biopsied

tag: stage iv at initial diagnosis

tag: protocol number

tag: esr1 maf

tag: esr1 mutation


title: ATAC seq in DOT1Li treated SEM cells rep5

description:
Fragmented genomic DNA
ATAC seq performed in SEM cells following 7 day treatment with EPZ-5676

data_processing:
Alignment to the genome (Bowtie) maintaining strict read order
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
Removal of PCR duplicates, parsing of informative reads using samtools rmdup
Genome_build: hg19
Peak calling using Homer
Statistical analysis using Diffbind (edgeR)
Supplementary_files_format_and_content: called peaks

source_name: ATAC seq in DOT1Li treated SEM cells

extract_protocol:
SEM cells were washed with PBS and lysed with 0.1% IGEPAL CA-630, followed by Tn5 transposase treatment
Libraries were made using the Nextera DNA library prep kit (Illumina)


title: metastasis_17

source_name: breast cancer, metastatic sample, hormone receptor-positive

tag: tissue

tag: pfs months

tag: set er_pr rnaseq


title: Capture-C in SEM cells rep2

description:
Next generation Capture-C products
3C library preparation followed by double oligonucleotide capture
0uM_2

tag: cell line


title: Sample_74_plus2

tag: sample number

tag: microarray


title: metastasis_16

tag: oas months

tag: os event

value: Liver


title: metastasis_14

tag: pr status

tag: number of event

value: ER 97

value: WT


title: Sample_80_plus2


title: Capture-C in SEM cells rep1

description:
Next generation Capture-C products
3C library preparation followed by double oligonucleotide capture
0uM_1

tag: cell type

tag: treatment

tag: genes analyzed


title: Sample_79_plus2


title: metastasis_13

value: Breast cancer, metastatic sample

tag: prior endocrine sensitivity

tag: visceral disease

tag: protocol treatment

tag: site biopsied

value: Soft Tissue

tag: stage iv at initial diagnosis

value: ER 96


title: metastasis_11

tag: tissue

tag: pfs months

tag: protocol number

value: ER 94

tag: esr1 maf

tag: esr1 mutation


title: Sample_75_plus2

value: Breast cancer

tag: sample number

tag: microarray


title: metastasis_12

tag: oas months

tag: os event

tag: pr status

value: Lymph node

value: ER 95

tag: set er_pr rnaseq


title: metastasis_10

tag: number of event

value: C

value: Breast

value: ER 93


title: metastasis_8

tag: prior endocrine sensitivity

value: ER 88


title: ATAC seq in DOT1Li treated SEM cells rep4

tag: cell line

value: Leukemia cell line (SEM)

tag: cell type

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation

tag: treatment

value: EPZ-5676 at 2uM for 7 days


title: metastasis_18

tag: visceral disease

tag: protocol treatment

value: H

tag: site biopsied

tag: stage iv at initial diagnosis


title: metastasis_7

tag: tissue

tag: pfs months

tag: protocol number

value: ER 87

tag: esr1 maf


title: metastasis_6

tag: oas months

value: ER 86

tag: esr1 mutation


title: ATAC seq in DOT1Li treated SEM cells rep3


title: metastasis_5

value: Breast cancer, metastatic sample

tag: os event

tag: pr status

value: ER 85


title: metastasis_9

tag: number of event

value: ER 91

tag: set er_pr rnaseq


title: Sample_66_plus2

tag: sample number

tag: microarray


title: Sample_67_plus2


title: Sample_65_plus2


title: ATAC seq in DOT1Li treated SEM cells rep1

tag: cell line

tag: cell type

tag: treatment


title: metastasis_3

tag: prior endocrine sensitivity

tag: visceral disease

tag: protocol treatment

tag: site biopsied

value: Liver

value: ER 82


title: metastasis_2

tag: tissue

tag: pfs months

value: Lymph node

tag: stage iv at initial diagnosis

tag: protocol number

value: ER 75

value: WT


title: metastasis_1

tag: oas months

tag: os event

value: Soft Tissue

value: ER 72

tag: esr1 maf

tag: esr1 mutation


title: ATAC seq in SEM cells rep5

description:
Fragmented genomic DNA
ATAC seq performed in SEM cells following 7 day treatment in DMSO

source_name: ATAC seq in SEM cells

value: DMSO for 7 days


title: 10_0_percent_cancer

description: SAMPLE 100

source_name: 0 % breast cancer, 100 % normal breast

treatment_protocol: Patients prospectively consented to a research biopsy by fine needle aspiration (FNA).

tag: breast cancer sample id

tag: normal breast tissue sample id


title: Sample_58_plus2

value: Breast cancer

tag: sample number

tag: microarray


title: ATAC seq in SEM cells rep4

tag: cell line

value: Leukemia cell line (SEM)

tag: cell type

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation

tag: treatment


title: metastasis_4

tag: pr status

tag: number of event

tag: prior endocrine sensitivity

tag: visceral disease

tag: protocol treatment

value: H

value: ER 84

tag: set er_pr rnaseq


title: 10_10_percent_cancer

description: SAMPLE 99

source_name: 10 % breast cancer, 90 % normal breast


title: Sample_46_plus2

tag: tissue


title: ATAC seq in SEM cells rep3


title: Sample_73_plus2


title: metastasis_15

tag: pfs months

tag: oas months

tag: os event

tag: site biopsied

value: Bone

tag: stage iv at initial diagnosis

tag: protocol number


title: 10_50_percent_cancer

description: SAMPLE 97

source_name: 50 % breast cancer, 50 % normal breast

tag: breast cancer sample id

tag: normal breast tissue sample id


title: 10_85_percent_cancer

description: SAMPLE 94

source_name: 85 % breast cancer, 15 % normal breast


title: 10_90_percent_cancer

description: SAMPLE 93

source_name: 90 % breast cancer, 10 % normal breast


title: 10_100_percent_cancer

description: SAMPLE 91

source_name: 100 % breast cancer, 0 % normal breast


title: 10_75_percent_cancer

description: SAMPLE 96

source_name: 75 % breast cancer, 25 % normal breast


title: 10_95_percent_cancer

description: SAMPLE 92

source_name: 95 % breast cancer, 5 % normal breast


title: 10_25_percent_cancer

description: SAMPLE 98

source_name: 25 % breast cancer, 75 % normal breast


title: Sample_32_plus2

tag: sample number

tag: microarray


title: Sample_22_plus2


title: Sample_41_plus2


title: Sample_50_plus2


title: ATAC seq in SEM cells rep2

tag: cell line

tag: cell type

tag: treatment


title: 10_80_percent_cancer

description: SAMPLE 95

source_name: 80 % breast cancer, 20 % normal breast


title: ATAC seq in SEM cells rep1


title: 9_0_percent_cancer

description: SAMPLE 90


title: 9_25_percent_cancer

description: SAMPLE 88


title: Sample_19_plus2

source_name: breast cancer sample profiled on PLUS2 microarray


title: 9_10_percent_cancer

description: SAMPLE 89


title: Sample_15_plus2


title: Sample_16_plus2


title: H3K27me3 ChIPseq 12M NP IKO

city: New York

first: Taiyi

middle: Diana

last: Kuo

state: NY

address: 1150 St Nicholas Ave., Ste. 237

institute: Columbia University

data_processing:
Reads were aligned to mouse genome mm10 using the Burrows-Wheeler Aligner (BWA) algorithm with default settings
These reads passed Illumina’s purity filter, and aligned with no more than 2 mismatches. Duplicate reads were removed, and only uniquely mapped reads with mapping quality greater or equal to 25 were subjected for further analysis.
Reads were extended to 200bp at their 3’ ends, and bigwig files were created for visualization using Active Motif software (Active Motif Inc., CA).
For H3K4me3, peak locations were determined using the MACS algorithm (v1.4.2) with a cutoff of p value = 1 x 10-7
H3K27me3 enriched regions were identified using the SICER algorithm with FDR of 1 x 10-10, gap size of 200-bp
Genome_build: mm10
Supplementary_files_format_and_content: bw

source_name: FAC-sorted pancreatic beta cells

growth_protocol: Mice were fed a standard chow diet or 60% high fat diet, and maintained on a 12h light cycle (lights on at 7am).

extract_protocol:
We purified the pancreatic islets (Kuo et al, JBC 2016) and FAC-sorted the beta cells. ChIP was performed using appropriate antibody against modified histone.
ChIP DNA libraries were prepared from ChIP DNA with the following steps: end-repair, dA-addition, adaptor ligation and PCR amplification.
The resulting ChIPseq DNA libraries were quantified with Bioanalyzer (Agilent), and sequenced on Illumina NextSeq 500 with 75-nt reads and single-end.

treatment_protocol: We generated mice lacking FoxO1 in pancreatic β cells using RIP-Cre transgenics to excise the floxed FoxO1 gene. For Gc studies, we purchased the sperms from UC Davis KOMP repository (Gctm1.1(KOMP)Vlcg) to generate Gc total knockout mice.

tag: strain background

value: mixed 129J-C57BL/6

tag: genotype/variation

value: RIP-Cre/FoxO1 floxed (IKO)

tag: age

tag: parity

value: nulliparous

value: FAC-sorted pancreatic beta cells

tag: chip antibody

value: anti-H3K27me3, Millipore 07-449 (RRID:AB_310624)


title: H3K27me3 ChIPseq DM

value: multiparous, i.e. 3 pregnancies


title: H3K27me3 ChIPseq 12M NP WT

value: wild type


title: 9_50_percent_cancer

description: SAMPLE 87


title: H3K27me3 ChIPseq 3M IKO


title: 9_75_percent_cancer

description: SAMPLE 86


title: metastasis_30

tag: tissue

value: Breast cancer, metastatic sample

tag: pfs months

tag: oas months

tag: pr status

tag: number of event

tag: prior endocrine sensitivity

tag: visceral disease

tag: protocol treatment

value: O

value: Liver

tag: esr1 maf

tag: esr1 mutation

tag: set er_pr rnaseq


title: H3K27me3 ChIPseq NGT

value: WT

tag: cell type


title: H3K27me3 ChIPseq 3M WT

tag: strain background


title: Sample_13_plus2

value: Breast cancer

tag: sample number

tag: microarray


title: 9_95_percent_cancer

description: SAMPLE 82

tag: breast cancer sample id

tag: normal breast tissue sample id


title: Sample_17_plus2

tag: tissue


title: 9_100_percent_cancer

description: SAMPLE 81


title: 8_10_percent_cancer

description: SAMPLE 79


title: H3K4me3 ChIPseq DM

tag: genotype/variation

tag: age

tag: parity

tag: chip antibody

value: anti-H3K4me3, Active Motif 39159 (RRID:AB_2615077)


title: 8_0_percent_cancer

description: SAMPLE 80


title: 8_25_percent_cancer

description: SAMPLE 78


title: H3K4me3 ChIPseq NGT


title: 9_90_percent_cancer

description: SAMPLE 83


title: 9_85_percent_cancer

description: SAMPLE 84


title: Sample_14_plus2


title: 8_50_percent_cancer

description: SAMPLE 77


title: 8_75_percent_cancer

description: SAMPLE 76


title: 8_80_percent_cancer

description: SAMPLE 75


title: H3K4me3 ChIPseq 12M NP IKO


title: 8_85_percent_cancer

description: SAMPLE 74


title: ATAC seq in DOT1Li treated SEM cells rep2

tag: cell line

value: Leukemia cell line (SEM)

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation

tag: treatment

value: EPZ-5676 at 2uM for 7 days


title: Sample_12_plus2


title: H3K4me3 ChIPseq 12M NP WT


title: 8_90_percent_cancer

description: SAMPLE 73


title: Sample_8_plus2


title: 8_95_percent_cancer

description: SAMPLE 72


title: 9_80_percent_cancer

description: SAMPLE 85


title: Sample_6_plus2


title: H3K4me3 ChIPseq 3M IKO


title: 8_100_percent_cancer

description: SAMPLE 71


title: 7_10_percent_cancer

description: SAMPLE 69


title: Sample_3_plus2


title: 7_50_percent_cancer

description: SAMPLE 67


title: 7_0_percent_cancer

description: SAMPLE 70


title: H3K4me3 ChIPseq 3M WT


title: MS_MUT1

city: Farmington

first: William

middle: F

last: Flynn

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

description:
Plzf lu/lu cells (plate 3)
read 1 is used for cell/transcript labeling and read 2 contains the transcript sequence
Cell barcodes are bases 1-12 (12bp) and UMIs are 13-20 (8bp) of read 1.
MS17_MUT_counts_merged.csv

data_processing:
Each plate was loaded with the same set of cell barcodes.  I.e., well A1 in all plates had the same barcode.  So each cell can be identified by a barcode-plate. A mapping file with the barcode sequence for each well is available on the series record as WellBarcodes.csv.
Paired-end fastqs were generated using BCL2Fastq v2.18.0.12 (Illumina)
Digital expression matrices were constructed for each pair of fastqs using Drop-seq_tools v1.13 (http://mccarrolllab.com/dropseq/) in the following manner: bam creation with Picard (v2.9.3) FastqToSam;
cell and umi tagging, filtering, trimming with Drop-seq_tools TagBamWithReadSequenceExtended, FilterBAM, TrimStartingSequence, PolyATrimmer;
alignment with STAR (v2.5.4a) to GRCm38_74 genome and picard (v2.9.3) SortSam; merging and tagging with picard (v2.9.3) MergeBamAlignment and Drop-seq_tools (v1.13) TagReadWithGeneExon;
expression matrix creation with Drop-seq_tools (v1.13) DigitalExpression; expression matrices from the 3 Plfz +/+ samples were concatenated together, same for those from the 2 Plfz lu/lu samples.
Genome_build: GRCm38_74
Supplementary_files_format_and_content: CSV, gene-cell expression matrix of raw 3' end counts for Plfz +/+ and Plfz lu/lu cells respectively. Column headers include the barcode_plate information:
*_wt1 = MS_WT1
*_wt2 = MS_WT2
*_wt3 = MS_MUT2-WT3
*_mut1 = MS_MUT1
*_mut2 = MS_MUT2-WT3

source_name: Mus musculus testes

extract_protocol:
Single cell suspensions from Plzf +/+ and Plzf lu/lu testes carrying the Eomes-tdTomato knockin allele were prepared using a two-step collagenase and trypsin enzymatic digestion procedure. Cells were filtered first with an 40um nylon membrane followed by a 25um filter. DNase I was added to the cell suspension to prevent clumping. Cells were washed once in PBS and finally suspended at a concentration of 1-2x106 cells/ml, analyzed and sorted on Becton Dickinson FACSVantage cell sorter. Cells from littermate mice that were negative for Eomes-tdTomato were used to gate the positive staining cell population and DAPI was used to gate out the dead cells. Single cells were flow sorted into individual wells of a Bio-Rad hard shell 384 well plate. The plate was immediately transferred and stored in a -80C freezer.
Custom designed Drop-Seq barcodes from Integrated DNA Technologies (IDT) were delivered into each well of each 384 well plate. All primers in one well shared the same unique cell barcode and billions of different unique molecular identifiers (UMIs). An Echo 525 liquid handler was used to dispense 1ul of primers and reaction reagents into each well in the plate for the cell lysis and cDNA synthesis. Following cDNA synthesis, the contents of each well were collected and pooled into one tube using a Caliper SciClone Liquid Handler. After treatment with exonuclease I to remove unextended primers, the cDNA was PCR amplified for 13 cycles. The 10 cDNA was fragmented and amplified for sequencing with the Nextera XT DNA sample prep kit (Illumina) using custom primers (see below) that enabled the specific amplification of only the 3′ ends.

tag: strain

tag: genotype

value: Plfz lu/lu

value: testes

value: germ cell


title: MS_MUT2-WT3

description:
Plzf lu/lu (A1-C14) and Plzf +/+ (C16-P24) cells (plate 4)
read 1 is used for cell/transcript labeling and read 2 contains the transcript sequence
Cell barcodes are bases 1-12 (12bp) and UMIs are 13-20 (8bp) of read 1.
MS17_WT_counts_merged.csv
MS17_MUT_counts_merged.csv

value: mixed sample (not demultiplexed): Plfz lu/lu or Plfz +/+


title: MS_WT2

description:
Plzf +/+ cells (plate 2)
read 1 is used for cell/transcript labeling and read 2 contains the transcript sequence
Cell barcodes are bases 1-12 (12bp) and UMIs are 13-20 (8bp) of read 1.
MS17_WT_counts_merged.csv

value: Plfz +/+


title: 7_90_percent_cancer

description: SAMPLE 63


title: 7_85_percent_cancer

description: SAMPLE 64


title: 7_80_percent_cancer

description: SAMPLE 65


title: 7_75_percent_cancer

description: SAMPLE 66


title: Sample_4_plus2


title: MS_WT1

description:
Plzf +/+ cells (plate 1)
read 1 is used for cell/transcript labeling and read 2 contains the transcript sequence
Cell barcodes are bases 1-12 (12bp) and UMIs are 13-20 (8bp) of read 1.
MS17_WT_counts_merged.csv


title: Sample_70_plus2


title: 7_25_percent_cancer

description: SAMPLE 68


title: 7_95_percent_cancer

description: SAMPLE 62


title: Sample_69_plus2


title: 6_10_percent_cancer

description: SAMPLE 59


title: 6_25_percent_cancer

description: SAMPLE 58


title: Sample_71_plus2


title: Sample_10_plus2


title: 6_50_percent_cancer

description: SAMPLE 57


title: Sample_72_plus2


title: Sample_18_plus2


title: 7_100_percent_cancer

description: SAMPLE 61


title: Sample_9_plus2


title: 6_75_percent_cancer

description: SAMPLE 56


title: Sample_11_plus2


title: Disomic, siAPP treated, 2 years, replicate 3

city: Orangeburg

first: Sandipkumar

last: Darji

address: 140 Old Orangeburg Rd, Bldg 39

department: Center for Dementia Research

institute: Nathan Kline Institute for Psychiatric Research

description:
TMM_normalized_CountsPerMillion_siRNA_treatment.txt
TMM_normalized_TPMCounts_siRNA_treatment.txt
TMM_normalized_CountsPerMillion.txt
TMM_normalized_TPMCounts.txt
wt.siapp6

data_processing:
For base-calling CASAVA version 1.8 was used to generate FASTQ files
STAR aligner (version 2.3.1z9) was used to align sequencing files with reference genome
HTSeq (version 0.6.1p2) was used for quantifying aligned reads.
For samples ds7-10 and wt7-11, the raw reads counts were obtained from public repository ARCHS4 (Lachmann A, Torre D, Keenan AB, Jagodnik KM, Lee HJ, Wang L, Silverstein MC, Ma’ayan A. Massive mining of publicly available RNA-seq data from human and mouse. Nature Communications 9. Article number: 1366 (2018)).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: TMM_normalized_CountsPerMillion_siRNA_treatment.txt is a tab-delimited text file containing read counts converted into CPM (counts per million) from trisomic and disomic samples with and without siRNA treatment (against human APP or -ve control DsiRNA) after filtering at CPM of 0.3 and TMM-normalization offered by R/Biocnductor's EdgeR package. CPM accounts for library size differences between samples  and TMM normalization accounts for composition bias and is ideal for comparison of "between" libraries on a relative scale for count based DGE analysis.
Supplementary_files_format_and_content: TMM_normalized_TPMCounts_siRNA_treatment.txt is a tab-delimited text file containing Transcripts per Million (TPM) counts from trisomic and disomic samples with and without siRNA treatment (against human APP or -ve control DsiRNA) after TMM-normalization.TPM counts accounts for individual gene length differences and is the most suited for "within" library comparison (i.e gene A vs gene B in the same library)
Supplementary_files_format_and_content: TMM_normalized_CountsPerMillion.txt is a tab-delimited text file containing read counts converted into CPM (counts per million) from trisomic and disomic samples of 5 months and 2 years old unrelated individuals. The raw read counts were filtered at threshold of cpm = 0.3 before TMM-normalization.
Supplementary_files_format_and_content: TMM_normalized_TPMCounts.txt is a tab-delimited text file containing Transcripts per Millionn (TPM) counts from Trisomic and disomic samples of 5 months and 2 years old unrelated individuals. The raw read counts were converted to TPM counts before TMM-normalization.

source_name: Skin Fibroblast

growth_protocol: Samples were purchased from the Coriell Cell Repositories (AG07096, AG04823, GM04617, GM08680, AG07095, AG06922, GM08429, GM5381) and maintained according to the distributor’s protocols (http://ccr.coriell.org/).  Throughout the study, fibroblasts were used below passage number 15 to keep the original character and morphology.

extract_protocol:
RNA was extracted 3 days after transfection using RNeasy Micro Kit (Qiagen) according to the manufacturer’s specifications
500 ng of total RNA were prepared using TruSeq RNA Sample prep kit V2 (Ilumina Inc., San Diego, CA, USA) following manufacturers’ instructions for the samples DS-1-6 and 2N-1-6.  Quality of libraries was assessed using Agilent 2200 TapeStation system.

treatment_protocol: For transfection, siRNA against human APP and negative control DsiRNA were purchased from Integrated DNA Technologies (IDT), and cells were cultured with antibiotic-free media 24 hours before transfection. siPortAmine (siPORTTM Amine, Thermo Fisher # AM4503),  was used as the transfection agent.

tag: condition

value: Disomic

value: 2 years

tag: gender

value: Male

value: siRNA against human APP

tag: batch

value: B


title: 6_85_percent_cancer

description: SAMPLE 54


title: Disomic, siAPP treated, 2 years, replicate 2

description:
TMM_normalized_CountsPerMillion_siRNA_treatment.txt
TMM_normalized_TPMCounts_siRNA_treatment.txt
TMM_normalized_CountsPerMillion.txt
TMM_normalized_TPMCounts.txt
wt.siapp5


title: Disomic, siAPP treated, 2 years, replicate 1

description:
TMM_normalized_CountsPerMillion_siRNA_treatment.txt
TMM_normalized_TPMCounts_siRNA_treatment.txt
TMM_normalized_CountsPerMillion.txt
TMM_normalized_TPMCounts.txt
wt.siapp4


title: Disomic, siAPP treated, 5 months, replicate 2

description:
TMM_normalized_CountsPerMillion_siRNA_treatment.txt
TMM_normalized_TPMCounts_siRNA_treatment.txt
TMM_normalized_CountsPerMillion.txt
TMM_normalized_TPMCounts.txt
wt.siapp2

value: 5 months


title: Disomic, siAPP treated, 5 months, replicate 3

description:
TMM_normalized_CountsPerMillion_siRNA_treatment.txt
TMM_normalized_TPMCounts_siRNA_treatment.txt
TMM_normalized_CountsPerMillion.txt
TMM_normalized_TPMCounts.txt
wt.siapp3


title: 6_0_percent_cancer

description: SAMPLE 60


title: 6_100_percent_cancer

description: SAMPLE 51


title: Disomic, siAPP treated, 5 months, replicate 1

description:
TMM_normalized_CountsPerMillion_siRNA_treatment.txt
TMM_normalized_TPMCounts_siRNA_treatment.txt
TMM_normalized_CountsPerMillion.txt
TMM_normalized_TPMCounts.txt
wt.siapp1


title: 6_80_percent_cancer

description: SAMPLE 55


title: Sample_2_plus2


title: 6_90_percent_cancer

description: SAMPLE 53


title: Trisomic, siAPP treated, 2 years, replicate 3

description:
TMM_normalized_CountsPerMillion_siRNA_treatment.txt
TMM_normalized_TPMCounts_siRNA_treatment.txt
TMM_normalized_CountsPerMillion.txt
TMM_normalized_TPMCounts.txt
ds.siapp6

value: Trisomic


title: 6_95_percent_cancer

description: SAMPLE 52


title: 5_80_percent_cancer

description: SAMPLE 45


title: Sample_5_plus2

value: Breast cancer


title: Trisomic, siAPP treated, 2 years, replicate 2

description:
TMM_normalized_CountsPerMillion_siRNA_treatment.txt
TMM_normalized_TPMCounts_siRNA_treatment.txt
TMM_normalized_CountsPerMillion.txt
TMM_normalized_TPMCounts.txt
ds.siapp5


title: 5_10_percent_cancer

description: SAMPLE 49


title: 5_75_percent_cancer

description: SAMPLE 46


title: Sample_87_plus2


title: 5_50_percent_cancer

description: SAMPLE 47


title: 5_95_percent_cancer

description: SAMPLE 42


title: 5_25_percent_cancer

description: SAMPLE 48


title: 5_100_percent_cancer

description: SAMPLE 41


title: Sample_1_plus2


title: 4_0_percent_cancer

description: SAMPLE 40


title: 5_85_percent_cancer

description: SAMPLE 44


title: 5_90_percent_cancer

description: SAMPLE 43


title: Sample_81_plus2


title: Sample_82_plus2


title: Sample_78_plus2


title: Trisomic, siAPP treated, 2 years, replicate 1

description:
TMM_normalized_CountsPerMillion_siRNA_treatment.txt
TMM_normalized_TPMCounts_siRNA_treatment.txt
TMM_normalized_CountsPerMillion.txt
TMM_normalized_TPMCounts.txt
ds.siapp4


title: Trisomic, siAPP treated, 5 months, replicate 3

description:
TMM_normalized_CountsPerMillion_siRNA_treatment.txt
TMM_normalized_TPMCounts_siRNA_treatment.txt
TMM_normalized_CountsPerMillion.txt
TMM_normalized_TPMCounts.txt
ds.siapp3


title: Sample_7_plus2


title: 5_0_percent_cancer

description: SAMPLE 50


title: Trisomic, siAPP treated, 5 months, replicate 1

description:
TMM_normalized_CountsPerMillion_siRNA_treatment.txt
TMM_normalized_TPMCounts_siRNA_treatment.txt
TMM_normalized_CountsPerMillion.txt
TMM_normalized_TPMCounts.txt
ds.siapp1


title: 4_25_percent_cancer

description: SAMPLE 38


title: Disomic, -ve control DsiRNA treated, 2 years, replicate 3

description:
For DS vs 2N DGE, this sample is wt6
TMM_normalized_CountsPerMillion_siRNA_treatment.txt
TMM_normalized_TPMCounts_siRNA_treatment.txt
TMM_normalized_CountsPerMillion.txt
TMM_normalized_TPMCounts.txt
wt.ctr6

value: negative control DsiRNA


title: Disomic, -ve control DsiRNA treated, 2 years, replicate 2

description:
For DS vs 2N DGE, this sample is wt5
TMM_normalized_CountsPerMillion_siRNA_treatment.txt
TMM_normalized_TPMCounts_siRNA_treatment.txt
TMM_normalized_CountsPerMillion.txt
TMM_normalized_TPMCounts.txt
wt.ctr5


title: 4_10_percent_cancer

description: SAMPLE 39


title: 4_50_percent_cancer

description: SAMPLE 37


title: 4_95_percent_cancer

description: SAMPLE 32


title: Disomic, -ve control DsiRNA treated, 2 years, replicate 1

description:
For DS vs 2N DGE, this sample is wt4
TMM_normalized_CountsPerMillion_siRNA_treatment.txt
TMM_normalized_TPMCounts_siRNA_treatment.txt
TMM_normalized_CountsPerMillion.txt
TMM_normalized_TPMCounts.txt
wt.ctr4

value: A


title: Sample_68_plus2


title: Sample_21_plus2


title: Sample_76_plus2


title: Trisomic, siAPP treated, 5 months, replicate 2

description:
TMM_normalized_CountsPerMillion_siRNA_treatment.txt
TMM_normalized_TPMCounts_siRNA_treatment.txt
TMM_normalized_CountsPerMillion.txt
TMM_normalized_TPMCounts.txt
ds.siapp2


title: 4_75_percent_cancer

description: SAMPLE 36


title: Sample_77_plus2


title: 4_80_percent_cancer

description: SAMPLE 35


title: 4_85_percent_cancer

description: SAMPLE 34


title: 3_80_percent_cancer

description: SAMPLE 25


title: 3_0_percent_cancer

description: SAMPLE 30


title: 4_100_percent_cancer

description: SAMPLE 31


title: Disomic, -ve control DsiRNA treated, 5 months, replicate 3

description:
For DS vs 2N DGE, this sample is wt3
TMM_normalized_CountsPerMillion_siRNA_treatment.txt
TMM_normalized_TPMCounts_siRNA_treatment.txt
TMM_normalized_CountsPerMillion.txt
TMM_normalized_TPMCounts.txt
wt.ctr3


title: Sample_20_plus2


title: Sample_30_plus2


title: 3_75_percent_cancer

description: SAMPLE 26


title: 3_10_percent_cancer

description: SAMPLE 29


title: 3_50_percent_cancer

description: SAMPLE 27


title: 3_25_percent_cancer

description: SAMPLE 28


title: 3_90_percent_cancer

description: SAMPLE 23


title: 4_90_percent_cancer

description: SAMPLE 33


title: Disomic, -ve control DsiRNA treated, 5 months, replicate 1

description:
For DS vs 2N DGE, this sample is wt1
TMM_normalized_CountsPerMillion_siRNA_treatment.txt
TMM_normalized_TPMCounts_siRNA_treatment.txt
TMM_normalized_CountsPerMillion.txt
TMM_normalized_TPMCounts.txt
wt.ctr1


title: Sample_29_plus2


title: 3_85_percent_cancer

description: SAMPLE 24


title: 3_95_percent_cancer

description: SAMPLE 22


title: Sample_28_plus2


title: Trisomic, -ve control DsiRNA treated, 2 years, replicate 2

description:
For DS vs 2N DGE, this sample is ds5
TMM_normalized_CountsPerMillion_siRNA_treatment.txt
TMM_normalized_TPMCounts_siRNA_treatment.txt
TMM_normalized_CountsPerMillion.txt
TMM_normalized_TPMCounts.txt
ds.ctr5


title: 3_100_percent_cancer

description: SAMPLE 21


title: 2_0_percent_cancer

description: SAMPLE 20


title: Trisomic, -ve control DsiRNA treated, 2 years, replicate 1

description:
For DS vs 2N DGE, this sample is ds4
TMM_normalized_CountsPerMillion_siRNA_treatment.txt
TMM_normalized_TPMCounts_siRNA_treatment.txt
TMM_normalized_CountsPerMillion.txt
TMM_normalized_TPMCounts.txt
ds.ctr4


title: 2_75_percent_cancer

description: SAMPLE 16


title: Trisomic, -ve control DsiRNA treated, 5 months, replicate 3

description:
For DS vs 2N DGE, this sample is ds3
TMM_normalized_CountsPerMillion_siRNA_treatment.txt
TMM_normalized_TPMCounts_siRNA_treatment.txt
TMM_normalized_CountsPerMillion.txt
TMM_normalized_TPMCounts.txt
ds.ctr3


title: 2_50_percent_cancer

description: SAMPLE 17


title: Disomic, -ve control DsiRNA treated, 5 months, replicate 2

description:
For DS vs 2N DGE, this sample is wt2
TMM_normalized_CountsPerMillion_siRNA_treatment.txt
TMM_normalized_TPMCounts_siRNA_treatment.txt
TMM_normalized_CountsPerMillion.txt
TMM_normalized_TPMCounts.txt
wt.ctr2


title: Sample_26_plus2


title: Sample_27_plus2


title: 2_80_percent_cancer

description: SAMPLE 15


title: 2_25_percent_cancer

description: SAMPLE 18


title: Trisomic, -ve control DsiRNA treated, 5 months, replicate 2

description:
For DS vs 2N DGE, this sample is ds2
TMM_normalized_CountsPerMillion_siRNA_treatment.txt
TMM_normalized_TPMCounts_siRNA_treatment.txt
TMM_normalized_CountsPerMillion.txt
TMM_normalized_TPMCounts.txt
ds.ctr2


title: 2_85_percent_cancer

description: SAMPLE 14


title: Trisomic, -ve control DsiRNA treated, 5 months, replicate 1

description:
For DS vs 2N DGE, this sample is ds1
TMM_normalized_CountsPerMillion_siRNA_treatment.txt
TMM_normalized_TPMCounts_siRNA_treatment.txt
TMM_normalized_CountsPerMillion.txt
TMM_normalized_TPMCounts.txt
ds.ctr1


title: Trisomic, -ve control DsiRNA treated, 2 years, replicate 3

description:
For DS vs 2N DGE, this sample is ds6
TMM_normalized_CountsPerMillion_siRNA_treatment.txt
TMM_normalized_TPMCounts_siRNA_treatment.txt
TMM_normalized_CountsPerMillion.txt
TMM_normalized_TPMCounts.txt
ds.ctr6


title: Sample_24_plus2


title: 2_95_percent_cancer

description: SAMPLE 12


title: 2_90_percent_cancer

description: SAMPLE 13


title: 2_10_percent_cancer

description: SAMPLE 19


title: Sample_25_plus2


title: 1_10_percent_cancer

description: SAMPLE 9


title: Sample_64_plus2


title: 2_100_percent_cancer

description: SAMPLE 11


title: 1_25_percent_cancer

description: SAMPLE 8


title: Sample_31_plus2


title: Sample_63_plus2


title: Sample_23_plus2


title: 1_0_percent_cancer

description: SAMPLE 10


title: 1_85_percent_cancer

description: SAMPLE 4


title: Sample_62_plus2


title: 1_75_percent_cancer

description: SAMPLE 6


title: Sample_59_plus2


title: 1_90_percent_cancer

description: SAMPLE 3


title: 1_50_percent_cancer

description: SAMPLE 7


title: 1_100_percent_cancer

description: SAMPLE 1


title: Sample_57_plus2


title: 1_95_percent_cancer

description: SAMPLE 2


title: Sample_52_plus2


title: Sample_56_plus2


title: D2.OR 3D tumor_2

city: Cleveland

last: Schiemann

state: Ohio

address: 2103 Cornell Road

institute: Case Western Reserve University

hyb_protocol: Probe hybridization was performed according to the manufacturer’s recommendations, and the resulting probe signals were normalized using the Affymetrix Expression Console Software package

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
RMA expression value derived from Expression Console software
Data analysis was performed using the Affymetrix Transcriptome Analysis Console, Ingenuity Pathway Analysis, and KEGG analysis software.

source_name: lung

label_protocol: Affymetrix Sensation Plus labeling protocol was used to prepare the RNA samples for interrogation on Affymetrix GeneChip Mouse 2.0 ST microarrays

growth_protocol: Tumor cells were injected into the lateral tail vein of BALB/c mice and tumors were allowed to form in the lungs.

extract_protocol: Tumors were harvested from mice and were promptly formalin fixed and paraffin embedded. These tissues were sectioned and stained with crystal violet to visualize tumor sections. Tumors were extracted using laser capture microdissection. Total RNA extraction was accomplished using the RNeasy FFPE Kit (Qiagen, 73504)

treatment_protocol: Prior to injection into mice, primed- 3D D2.OR and D2.A1 cells were grown on Cultrex reconstituted basement membrane extracts (Trevigen, 3533-001-02) for 3-5 days. Unprimed-2D cells were grown using tissue culture plates

tag: Sex

value: Female

tag: histology

value: Spindle

value: Primed- 3D

value: lung


title: D2.OR 2D tumor_3

value: Unprimed- 2D


title: D2.OR 3D tumor_3


title: D2.OR 3D tumor_1


title: D2.OR 2D tumor_2


title: Sample_45_plus2

data_processing: Probe intensities were quantified with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. CEL files were normalized using global scaling with a trimmed mean target intensity of each array arbitrarily set to 600 using the MAS5 algorithm from the simpleaffy package (http://bioconductor.org/packages/2.4/bioc/html/simpleaffy.html).

tag: sample number

tag: microarray


title: D2.A1 3D epithelial_2

value: Epithelial


title: D2.A1 3D epithelial_1


title: clpex mouse mutant 3

city: Columbus

first: Rolf

last: Stottmann

state: OHIO

address: 575 Children's Crossroads

department: Pediatrics

institute: Nationwide Children's Hospital

data_processing:
Alignment and variant detection was performed using the Broad Institute‘s web-based Genome Analysis Tookit (GATK)
Genome_build: mm9

source_name: DNA from mouse tissue

extract_protocol:
flash frozen, genomic DNA extracted
NimbleGen EZ Exome (mouse)

value: embryo


title: Monocyte-like precursors of granulocytes, replicate 3

hyb_protocol: Hybridized on Illumina Illumina Mouse WG6v2 BeadChip

scan_protocol: Illumina Setting with PMTFactor=2

data_processing: Illumina GenomeStudio software was used to export expression levels and detection p-values for each probe of each sample

source_name: Bone marrow Ly6C high cells

label_protocol: RNA quality was validated using the Agilent Bioanalyzer and the RNA Nano chip (Agilent, Santa Clara, CA) and quantity was determined using the NanoDrop 2000 Spectrophotometer (ThermoFischer, Waltham, MA). Biotin Labeling of RNA at 100ng with Illumina approved RNA amplification kit (Epicentre, Madison, WI).

extract_protocol: 1-2 million cells were lysed in 1 ml of Tri- Reagent and RNA was extracted using phase separation and isopropanol precipitation as recommended by the vendor.

value: Bone marrow

tag: cell type

value: Monocyte-like precursors of granulocytes (MLPG)

tag: cell population

value: Ly6C high cells

tag: replicate


title: Monocyte-like precursors of granulocytes, replicate 1

tag: tissue


title: Sample_44_plus2

extract_protocol: Total RNA was extracted from tissue using Qiagen RNeasy columns.


title: clpex mouse mutant 2


title: clpex mouse mutant 1


title: Granulocytic progenitors, replicate 2

source_name: Bone marrow Ly6C low cells

value: Granulocytic progenitors (GP)

value: Ly6C low cells


title: Granulocytic progenitors, replicate 3


title: Clpex mutant E9.5 (5 pooled embryos)

data_processing:
CSBB [Computational Suite for Bioinformaticians and Biologists: https://github.com/csbbcompbio/CSBB-v3.0]. CSBB   has multiple modules, RNA-Seq module is focused on carrying out analysis steps on sequencing data, which comprises of quality check, alignment, quantification and generating mapped read visualization files.
Quality check of the sequencing reads was performed using FASTQC  (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc).
Reads were mapped (to mm10 version of Mouse genome) and quantified using RSEM-v1.3.0
Genome_build: mm10
Supplementary_files_format_and_content: excel file with log FC, P-value average mut and wt TPM values

source_name: whole embryo

extract_protocol:
Embryos were harvested accroding to plug date, dissected in PBS, and flash frozen on dry ice. RNA was isolated by BGI.
BGISEQ-500 Transcriptome

tag: sequencing

value: Transcriptome

tag: background

value: Mixed background


title: Granulocytic progenitors, replicate 1


title: WT E9.5 (5 pooled embryos)


title: MT-CHC01R1.5_rep1

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

hyb_protocol: Six hundred ng of labeled RNA were hybridized on Human Gene Expression 4x44K glass arrays.

scan_protocol: Arrays were scanned and images analyzed by the Feature Extraction Software from Agilent Technologies (version 10.7)

data_processing: Raw data were then processed using the Bioconductor package Limma (Linear models for microarray analysis). Background correction was performed with the normexp method with an offset of 50, and quantile was used for the between-array normalization. The empirical Bayes method was used to compute a moderated t-statistics

source_name: cell line derived fron PDX

label_protocol: For GEP analysis, 100 ng of total RNA was amplified and labeled using Low Input Quick Amp Labeling Kit, one-color kit (Agilent Technologies).

growth_protocol: cell lines were cultured in KODMEM/F12 +10% FBS + P/S. The MT-CHC01R1.5 were cultured in the same conditions with the addition of 1.5 uM of Gemcitabine

extract_protocol: Briefly, cells at 70% of confluence were lyzed using TRIZOL and scraped in ice. RNA extraction and purification was performed using the Absolutely RNA miRNA kit (Agilent Technologies), following the manufacturer’s instructions

value: intrahepatic cholangiocarcinoma cell line resistant to gemcitabine

tag: cell line


title: D2.A1 3D spindle_2

tag: treatment


title: MT-CHC01R1.5_rep2


title: D2.A1 3D spindle_1


title: Sample_40_plus2

value: Breast cancer


title: Sample_39_plus2


title: MT-CHC01_rep1

value: intrahepatic cholangiocarcinoma cell line


title: D2.A1 2D epithelial_3

value: Female


title: MT-CHC01_rep2


title: W3A-3

city: Madrid

first: Maria Jesus

last: Larriba

state: Madrid

address: Arturo Duperier 4

department: Cancer Biology

country: Spain

institute: Instituto de Investigaciones Biomedicas "Alberto Sols"

data_processing:
Image analysis and per-cycle base calling were performed with Illumina Real-Time Analysis (RTA1.13) software
Conversion to fastq read format and sequence alignment to the GRCh37/hg19 assembly of the human genome with ELAND v2e alignment algorithm were achieved using Illumina CASAVA 1.8 software
Genome_build: GRCh37/hg19 assembly of the human genome
Supplementary_files_format_and_content: xlsx file containing the raw number of reads per gene for all samples

growth_protocol: CCD-18Co (ATCC CRL-1459) human normal colon myofibroblasts were cultured in Minimum Essential Medium plus 10% foetal bovine serum (both from Life Technologies)

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen)
1 µg of total RNA was used. RNA Integrity Numbers were 9.2-9.6 (Agilent 2100 Bioanalyzer). PolyA+ fractions were purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by 9 cycles of PCR with Illumina PE primers. The resulting purified cDNA library of template molecules of known strand origin was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on an Illumina Genome Analyzer IIx using Illumina TruSeq SBS Kit v5 following manufacturer's protocols.

treatment_protocol: CCD-18Co human normal colon myofibroblasts were treated with 100 nM 1a,25-dihydroxyvitamin D3 (Sigma-Aldrich), 100 ng/ml recombinant human Wnt3A (R&D Systems), both, or the corresponding vehicles (ethanol for 1a,25-dihydroxyvitamin D3; 0.1% BSA in PBS for Wnt3A) for 24 hours

value: normal colon

value: myofibroblast


title: W3A-2

source_name: CCD-18Co human normal colon myofibroblasts


title: W3A-1


title: W3AVD-2

value: Wnt3A + 1a,25-dihydroxyvitamin D3


title: W3AVD-1


title: D2.A1 2D epithelial_2

value: Unprimed- 2D

value: lung


title: Sample_37_plus2


title: D2.A1 2D epithelial_1

value: Epithelial


title: Sample_36_plus2


title: Sample_38_plus2


title: Sample_35_plus2


title: W3AVD-3


title: VD-2

value: 1a,25-dihydroxyvitamin D3


title: VD-1


title: D2.A1 2D spindle_3

value: Spindle


title: Ctrl3

value: vehicle


title: Ctrl-2


title: D2.A1 2D spindle_2


title: Sample_34_plus2


title: D2.A1 2D spindle_1


title: VD-3


title: Sample_33_plus2


title: Sample_60_plus2


title: Sample_61_plus2


title: Ctrl-1


title: Adipose_control diet_32week_rep1

city: Beijing

first: Qian

last: Zhang

address: No. 1 Shuaifuyuan, Dongcheng District

country: China

institute: Peking Union Medical College Hospital

description: gene expression data from adipose from control

hyb_protocol: The sample preparation and hybridation of each cDNAs on Affymetrix GeneChip® Mouse Gene 2.0 ST arrays based on manufacturer's instruction.

scan_protocol: Arrays were scanned using the GeneChip® Scanner 3000 Affymetrix)

data_processing: All arrays were uploaded into Genespring v12.5 (Agilent Tchnologies, USA) for data normalization, quality control and first-pass analysis. Differentially expressed genes were then identified through fold change as well as P value calculated with t-test. The threshold set for differentially regulated genes was a fold change>1.5 and a P value<0.05.

source_name: control diet, 32 week

label_protocol: biotin

extract_protocol: Total tissue RNA was extracted using total RNA Isolation Kit (mirVanaTM, ABI).

value: adipose

tag: age

value: 32 week


title: Adipose_maternal chromium restriction diet_32week_rep3

description: gene expression data from adipose from maternal chromium restriction

source_name: maternal chromium restriction diet, 32week


title: B6-520Nf2Cdkn2aBap1

first: yinfei

last: tan

address: 333 cottman ave

department: Genomic Core

institute: Fox Chase Cancer Center

description:
SN930
520
mRNA enriched

data_processing:
Alignment to mm10.
Count with HTseq.
DE analysis with DEseq2.
Pathway analysis with ConcensusPathDb.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *tsv: Tab-separated text files include HTseq results.
Supplementary_files_format_and_content: Double-vs-Triple-tumors.xlsx: Excel file includes DEseq2 results.

source_name: Mouse MM

growth_protocol: Cells were maintained in RPMI 1640 supplemented with 10% FBS, 1x Penicillin/Streptomycin, 2mM L-Glutamine, and 5 ug/mL Insulin in a 37C incubator with 5% CO2.

extract_protocol:
Total RNA was isolated using a Trizol and RNA min-prep Purification Kit (Zymo Research) according to manufacturer's instructions.
NEBNext® Ultra™ II RNA Library Prep (Cat#E7775L).

value: MM

tag: genotype

value: Triple knockout


title: B5-487Nf2Cdkn2aBap1

description:
SN930
487
mRNA enriched


title: SET2_usv101_nutrient-starved_R1

city: Seoul

first: Kyung-Tae

last: Lee

address: Yonsei-ro 50, Seodaemun-gu

department: Biotechnology

country: South Korea

institute: Yonsei University

data_processing:
Illumina Casava1.7 software used for basecalling.
and the sequenced reads were trimmed to remove the adaptor sequence, and masked for low-complexity or low-quality sequence by using Trimmomatic v0.32 with ‘adapter seq’ of TruSeq3-PE.fa and MINLEN:36.
The reads were aligned to the Cryptococcus neoformans var. grubii H99 (from Broad Institute) using Tophat v2.0.13 with the Bowtie v2.2.3 algorithm.
Tophat was performed with “-G” option and other parameters were default. Transcript assembly and abundance estimation was performed by Cufflinks v2.2.1. To correct the sequence expression count bias, we used ‘--max-bundle-frags 50000000’ option. The isoform transcripts were also calculated, and the relative transcript abundances were displayed via FPKM (Fragments Per Kilobase of exon per Million fragments mapped).
Genome_build: Cryptococcus neoformans var. grubii H99 (from Broad Institute)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM and expected counts for each Sample.

molecule: polyA RNA

organism: Cryptococcus neoformans H99

source_name: H99_total RNA

growth_protocol: Cryptococcus neoformans WT and deletion mutant strains were inoculated into 50 ml of YPD medium liquid medium and cultured overnight at 30°C in a shaking incubator. Cells were subinnoculated in fresh YPD medium until OD600 indicated 0.6 to 0.8.

extract_protocol:
Incubated cells were spun down, frozen in liquid nitrogen and lyophilized overnight. Total RNA was isolated by trizol extraction method using Easy-blue (iNtRON). The prepared total RNAs were purified with RNeasy Mini Kit (QIAGEN). The concentration was measured by Quant-IT RiboGreen (Invitrogen).
The quality of the RNA was verified by the TapeStation RNA screentape (Agilent) and the RNA Integrity Number (RIN) greater than 7.0 was used to construct the cDNA library (TruSeq mRNA Sample Prep kit, Illumina).

treatment_protocol: For the nutrient-starvation, the subinoculated cells were washed three times with phosphate-buffered saline, and resuspended in liquid YNB medium containing ammonium sulfate without glucose. After resuspension, cells were further incubated at 30°C in shaking incubator for 2 h.

tag: strain

value: H99 total RNA

tag: genotype/variation

value: usv101 mutant

tag: growth medium

value: YNB medium containing AS without glucose


title: SET2_usv101_nutrient-starved_R2


title: SET2_usv101_nutrient-rich_R2

value: YPD medium


title: SET2_usv101_nutrient-rich_R3


title: Adipose_control diet_32week_rep3


title: SET2_usv101_nutrient-rich_R1


title: SET2_mbs1_nutrient-starved_R3

value: mbs1 mutant


title: Adipose_control diet_32week_rep2


title: Adipose_maternal chromium restriction diet_32week_rep2


title: SET2_usv101_nutrient-starved_R3


title: Sample_54_plus2

value: Breast cancer


title: Sample_51_plus2


title: Sample_55_plus2


title: Sample_48_plus2


title: Sample_53_plus2


title: Sample_49_plus2


title: Liver_control diet_32week_rep1

type: genomic

description: control diet, 32 week

hyb_protocol: Labeled DNA was hybridized to the Arraystar Mouse ReqSeq Promoter Array.

scan_protocol: Array was scanned with Agilent Scanner G2505C.

data_processing: After normalization, raw data was input into SignalMap Software to observe and evaluate the methylation peaks.

label: Cy 5

source_name: MeDIP DNA from control diet, 32 week

label_protocol: Immunoprecipitated methylated DNA was labeled with Cy5 fluorophere and the input genomic DNA was labeled with Cy3 fluorophere.

extract_protocol: Genomic DNA was extracted from fat samples using Dneasy Blood & Tissue Kit.

value: liver

label: Cy 3

source_name: input DNA from control diet, 32week


title: Liver_maternal chromium restriction diet_32week_rep2

source_name: MeDIP DNA from maternal chromium restriction diet, 32week

source_name: input DNA from maternal chromium restriction diet, 32week


title: Liver_control diet_32week_rep2

description: control diet, 32 week


title: Liver_control diet_32week_rep3

description: control diet, 32 week


title: SET2_mbs1_nutrient-starved_R2


title: SET2_mbs1_nutrient-starved_R1


title: SET2_mbs1_nutrient-rich_R3


title: B1-3Nf2Cdkn2aBap1

description:
SN933
3
mRNA enriched


title: Total RNA-seq in ML-2 cells

description: RNA

data_processing:
RNA-seq reads were aligned to the hg19 genome using STAR
Duplicate reads were removed using samtools rmdup
Read counts were determined using featureCounts (Subread package)
Genome_build: hg19

source_name: Leukemia cell line (ML-2)

extract_protocol:
RNA was extracted from 1 million cells using the RNeasy Mini kit (Qiagen), with on-column DNase-digestion.
see sample table
DNA libraries were prepared using the NEB Next Ultra Directional RNA library preparation kit for Illumina (E7420).

value: Leukemia cell line (ML-2)

value: Monocytic cell line derived from AML M4 with t(6;11)(q27;q23) translocation


title: B2-390Nf2Cdkn2aBap1

description:
SN934
390
mRNA enriched


title: SET2_mbs1_nutrient-rich_R2


title: Adipose_maternal chromium restriction diet_32week_rep1


title: A5-411Nf2Cdkn2a

description:
SN931
411
mRNA enriched

value: Double knockout


title: Liver_maternal chromium restriction diet_32week_rep3

description: maternal chromium restriction diet, 32week


title: Liver_control diet_16week_rep3

description: miRNA expression data from liver from control

hyb_protocol: Labeled miRNA was hybridized to the array.

scan_protocol: After hybridization, the chips were scanned by using a Genechip Array Scanner 3000 (Affymetrix).

data_processing: The data were generated by Affymetrix Expression Console software v1.1.

source_name: control diet, 16 week

label_protocol: RNA was labeled by Biontin.

extract_protocol: Total RNA was extracted by mirVanaTM RNA Isolation Kit (ABI)

value: 16 week


title: Liver_maternal chromium restriction diet_32week_rep1


title: SET2_mbs1_nutrient-rich_R1


title: SPI1  ChIP seq in SEM cells

description:
ChIP seq performed using SPI1 antibody in SEM cells
SPI1_peaks.bed

data_processing:
Alignment to the genome (Bowtie) maintaining strict read order
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
Removal of PCR duplicates, parsing of informative reads using samtools rmdup
Peak calling using Homer v4.7
Genome_build: hg19
Supplementary_files_format_and_content: bed file reporting called peaks

extract_protocol:
Cells were washed with PBS and fixed in either 1% FA for 10 minutes (histones) or 2mM DSG for 30 minutes and 1% FA for 30 minutes (transcription factors). Cells were sonicated to give fragments of 100-300bp followed by IP. For ChIP-rx fixed SEM cells were mixed at a 4:1 ratio with fixed Drosophila S2 cells prior to sonication.
DNA libraries were made using the NEBnext ultra DNA library preparation kit for Illumina (Cat no. E7370).

value: Leukemia cell line (SEM)

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation

tag: chip antibody


title: B4-466Nf2Cdkn2aBap1

description:
SN930
466
mRNA enriched


title: Liver_control diet_16week_rep2


title: Liver_control diet_16week_rep1


title: Liver_maternal chromium restriction diet_16week_rep3

description: miRNA expression data from liver from maternal chromium restriction

source_name: maternal chromium restriction diet, 16week


title: Sample_43_plus2

source_name: breast cancer sample profiled on PLUS2 microarray


title: Liver_maternal chromium restriction diet_16week_rep2


title: 1_80_percent_cancer

description: SAMPLE 5

data_processing:
Probe intensities were quantified with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. CEL files were normalized using global scaling with a trimmed mean target intensity of each array arbitrarily set to 600 using the MAS5 algorithm from the simpleaffy package (http://bioconductor.org/packages/2.4/bioc/html/simpleaffy.html).
MAS5.0 signal intensity for each array was log2 transformed and scaled to a reference distribution of 1322 breast cancer specific genes.

source_name: 80 % breast cancer, 20 % normal breast

extract_protocol: Total RNA was extracted from tissue using Qiagen Rneasy columns.

tag: breast cancer sample id

tag: normal breast tissue sample id


title: Sample_42_plus2

tag: sample number

tag: microarray


title: Sample_47_plus2


title: Monocyte-like precursors of granulocytes, replicate 2

source_name: Bone marrow Ly6C high cells

value: Bone marrow

tag: cell type

value: Monocyte-like precursors of granulocytes (MLPG)

tag: cell population

value: Ly6C high cells


title: Liver_maternal chromium restriction diet_16week_rep1

tag: tissue


title: SET2_hob1_nutrient-starved_R3

value: hob1 mutant


title: SPI1  ChIP seq input in SEM cells

description:
Input for ChIP seq performed using SPI1 antibody in SEM cells
SPI1_peaks.bed


title: RNAseq DM

data_processing:
For the analysis, 60 to 73 million read-pairs were used, and TopHat algorithm was utilized to align reads to mouse genome mm10.
The alignments in the BAM files were further analyzed using the Cufflinks suite of programs (running consecutively with Cufflinks, Cuffcompare, Cuffdiff).
The output shows the known genes with their RNAseq metrics in FPKM.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: FAC-sorted pancreatic beta cells

growth_protocol: Mice were fed a standard chow diet, and maintained on a 12h light cycle (lights on at 7am).

extract_protocol:
We purified the pancreatic islets (Kuo et al, JBC 2016) and FAC-sorted the beta cells.
RNA was isolated with Nucleospin RNA kit (Macherey-Nagel) with DNase I treatment.
Directional poly-A RNAseq libraries were prepared and sequenced as PE100 (100bp paired-end reads) on Illumina Hiseq 2500 in high output mode.

treatment_protocol: We generated mice lacking FoxO1 in pancreatic β cells using RIP-Cre transgenics to excise the floxed FoxO1 gene.

tag: strain background

value: mixed 129J-C57BL/6

value: RIP-Cre/FoxO1 floxed (IKO)

tag: parity

value: multiparous, i.e. 3 pregnancies

value: FAC-sorted pancreatic beta cells


title: SET2_hob1_nutrient-starved_R2

value: H99 total RNA

value: YNB medium containing AS without glucose


title: SET2_hob1_nutrient-starved_R1


title: RUNX2 ChIP seq input in SEM cells

description:
Input for ChIP seq performed using RUNX2 antibody in SEM cells
RUNX2_peaks.bed

tag: cell line


title: RNAseq NGT

value: WT


title: RNAseq 12M NP IKO

value: nulliparous


title: FLI1  ChIP seq in SEM cells

description:
ChIP seq performed using FLI1 antibody in SEM cells
FLI1_peaks.bed

tag: treatment

value: FLI1 (Abcam ab15289)


title: SET2_hob1_nutrient-rich_R2

value: YPD medium


title: Adipose_control diet_16week_rep3

description: miRNA expression data from adipose from control

value: adipose

tag: age

value: 16 week


title: FLI1  ChIP seq input in SEM cells

description:
Input for ChIP seq performed using FLI1 antibody in SEM cells
FLI1_peaks.bed

value: Leukemia cell line (SEM)

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation


title: RNAseq 12M NP WT

value: wild type


title: RNAseq 3M IKO


title: A3-375Nf2Cdkn2a

description:
SN930
375
mRNA enriched

value: MM

tag: genotype

value: Double knockout


title: Adipose_control diet_16week_rep2


title: Adipose_control diet_16week_rep1


title: RNAseq 3M WT

value: mixed 129J-C57BL/6


title: SET2_WT_nutrient-starved_R3

tag: strain


title: Six2c

city: Parkville

first: Belinda

last: Phipson

state: VIC

address: 1G Royal Parade

country: Australia

institute: WEHI

data_processing:
The 10x Genomics Cell Ranger pipeline (v1.3.1) was used to align, filter and de-duplicate reads before counting those overlapping genes to produce count matrices for each sample.
Count matrics for Six2a, Six2b, and Six2c were combined using cellranger aggr with no normalisation. The resulting dataset consisst of a matrix file (matrix.mtx) containing the UMI count values, barcode file (matrix.tsv) containing the detected cell barcodes and gene file (genes.tsv) containing the ENSEMBL ids of the detected genes. The dense matrix of the full dataset is provided in CSV format (counts.csv).
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger output files and CSV file containing count matrix.

source_name: mouse kidney

growth_protocol: Kidneys from multiple litters of Six2GFP+ mouse embryos at E14.5 were pooled into three replicate tubes.

extract_protocol:
Chromium Single Cell Library kit V2
Illumina HiSeq HT chemistry- 100bp paired end sequencing

treatment_protocol: Six2GFP+ cells were isolated using gates for Six2GFP fluorescence, propidium iodide to exclude dead cells, and size to exclude cell debris and doublets. Isolated Six2GFP+ cells were collected and stored on ice in 50% PBS, 50% DMEM with 5% FCS, then run in parallel on a 10x chip.

value: nephron progenitor


title: RUNX2 ChIP seq in SEM cells

description:
ChIP seq performed using RUNX2 antibody in SEM cells
RUNX2_peaks.bed


title: SET2_WT_nutrient-starved_R2

tag: genotype/variation


title: Adipose_maternal chromium restriction diet_16week_rep2

description: miRNA expression data from adipose from maternal chromium restriction


title: SET2_hob1_nutrient-rich_R3

value: hob1 mutant

tag: growth medium


title: SET2_WT_nutrient-starved_R1


title: Adipose_maternal chromium restriction diet_16week_rep1


title: Adipose_maternal chromium restriction diet_16week_rep3


title: Intestine and colon, normal, pool#3 (n=5 donors)_total RNA

city: Québec

first: Chantal

last: Guillemette

state: Québec

address: 2705 blvd Laurier

department: Faculty of Pharmacy

country: Canada

institute: Laval University

description: Tissue biopsy

data_processing:
Illumina CASAVA software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and then mapped to Hg19 whole genome and UGT reference transcriptome (Tourancheau, The Pharmacogenomics Journal, 2016; 16:60-70)  using tophat v2.0.13 (parameters: --no-novel-juncs) and bowtie v1.0.0-1 (Trapnell, Nat Biotechnol. 2013;31:46-53)
The aligned reads were assembled by Cufflinks program to produce transcripts annotated to the same reference genome.
Genome_build: hg19
Supplementary_files_format_and_content: cufflinks output

extract_protocol:
RNA was extracted from 1 ug of each tissue using TriReagent followed by RNA cleanup using QIAGEN RNeasy Mini Kit with DNAse I. Equal amount of RNA from 3 tissue samples (or 5 tissue samples for normal intestine/colon) were pooled and External RNA Controls Consortium (ERCC) standards RNA Spike-In Mix 1 (ThermoFisher Scientific) were spiked into pooled RNA samples. 1 ug total RNA from each pool was used to prepare sequencing librairies with Illumina TruSeq RNA Sample Prep Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Sex

value: pooled male and female

value: Intestine and colon


title: Intestine and colon, tumor, pool#1 (n=3 donors)_total RNA

description: Tissue biopsy


title: Intestine and colon, tumor pool#3 (n=3 donors)_total RNA

description: Tissue biopsy


title: Intestine and colon, tumor, pool#2 (n=3 donors)_total RNA

description: Tissue biopsy


title: SET2_WT_nutrient-rich_R3

value: H99 total RNA


title: SET2_hob1_nutrient-rich_R1


title: Intestine and colon, normal, pool#2 (n=5 donors)_total RNA

description: Tissue biopsy


title: Six2a