title: Temporal_Cortex AD (9031356091_E)

value: MALE

value: Subject  71


title: CMT-756-normal

status: Public on Jul 22 2019

type: SRA

city: Seoul

first: Sangwoo

last: Kim

state: State...

address: 50-1 Yonsei-ro, Seodaemun-gu

department: Dept. of Biomedical Systems Informatics

country: South Korea

institute: Yonsei University College of Medicine

description: processed data file: CMT_222S_FPKM.csv

library_source: transcriptomic

data_processing:
Base-calling process was performed using FastQC version 0.10.1.
Alignment was conducted using Tophat version 2.0.9 with Ensembl gene annotation of CanFam3.1 and fr-firststrand library type. Canine reference genome sequence CanFam3.1 (Ensembl, Canis lupus familiaris) was used in alignment process through Bowtie2 Index.
FPKM values are calculated by Cufflinks version 2.1.1 using bam files. Parameters including fr-firststrand, CanFam3.1 GTF, CanFam3.1 Bowtie2 Index are used.
Genome_build: CanFam3.1
Supplementary_files_format_and_content: CMT_222S_FPKM.csv: Comma-separated text file includes FPKM values for each Sample.

molecule: total RNA

organism: Canis lupus familiaris

source_name: canine mammary normal tissue

extract_protocol:
Fresh tissue samples were transferred in to RNAlater (Thermo Fisher Scientific), refrigerated overnight at 4°C and then stored at -80°C. Total RNA was extracted from tissues using RNeasy mini kit (Qiagen).
RNA quality was assessed by analysis of rRNA band integrity on an Agilent RNA 6000 Nano kit. Ahead of cDNA library construction, the 1ug of total RNA and magnetic beads with Oligo (dT) were used to enrich poly (A) mRNA from it. Then, the purified mRNAs were disrupted into short fragments, and the double-stranded cDNAs were immediately synthesized. The cDNAs was subjected to end-repair, poly (A) addition, and connected with sequencing adapters using the TruSeq RNA sample prep Kit (Illumina, CA). The suitable fragments automatically purified by BluePippin 2% agarose gel cassette (Sage Science, MA) were selected as templates for PCR amplification. The final library sizes and qualities were evaluated electrophoretically with an Agilent High Sensitivity DNA kit (Agilent Technologies, CA) and the fragment was found to be between 350–450 bp. Libraries were sequenced on the HiSeq 2500 following the manufacturer's protocols.

tag: dog id

tag: tissue

value: mammary normal tissue

tag: tumor grade

tag: age

tag: diagnosis

value: Carcinoma in benign mixed tumor

tag: Sex

value: Female

tag: neuter status

value: Intact

tag: lymphatic vessel invasion

value: Absent

tag: breed

value: Maltese

tag: er allred score

tag: er status

value: Positive

tag: her2 score (hercep test score)

tag: date of surgery

tag: survival status (until 2018-08-01)

value: loss to follow-up

tag: survival (day)


title: Frontal_Cortex AsymAD (9031356052_J)

type: RNA

city: London

first: Hamel

last: Patel

address: De Crespigny Park

department: Biostatistics and health informatics

country: United Kingdom

institute: King's College London

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data was Maximum Likelihood Estimation (MLE) background corrected using R package “MBCB” (version 1.18.0), log2 transformed, and Robust Spline Normalisation (RSN) using R package “lumi” (version 2.16.0)

label: biotin

organism: Homo sapiens

label_protocol: Total RNA (25ng) was prepared for array expression profiling using the Ovation Pico WTA system (NuGEN Technologies, Inc., San Carlos, CA), as described by the manufacturer

extract_protocol: Total RNA was extracted using RNeasy Lipid Tissue Mini Kit (Qiagen,74804) and according to manufactures protocol.

treatment_protocol: Tissue blocks, approximately 0.5-1cm3, were obtained and stored in RNAlater RNA Stabilization Reagent (Qiagen) before RNA extraction.

tag: gender

value: FEMALE

tag: individual

value: Subject  69

tag: disease state

value: AsymAD


title: Entorhinal_Cortex AD (9371242073_J)

value: Subject  66

tag: tissue

value: AD


title: Temporal_Cortex AD (9345725025_J)


title: Entorhinal_Cortex AD (9371242066_E)

value: Subject  67


title: CMT-743-tumor

description: processed data file: CMT_222S_FPKM.csv

source_name: canine mammary tumor tissue

tag: dog id

value: mammary tumor tissue

tag: tumor grade

value: Simple carcinoma (Solid type)

value: Neutered

value: Present

value: Yorkshire Terrier

value: Y


title: Cerebellum AD (9344744052_G)

source_name: Cerebellum

tag: age

value: Cerebellum


title: CMT-774-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: diagnosis

value: Simple carcinoma (Tubulopapillary type)

tag: Sex

value: Female

value: Intact

value: Absent

value: N

tag: date of death


title: CMT-755-tumor

description: processed data file: CMT_222S_FPKM.csv

value: Benign

value: Simple adenoma

tag: neuter status

tag: lymphatic vessel invasion

tag: breed

value: Schnauzer

value: Positive

value: loss to follow-up


title: CMT-730-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

value: Maltese

tag: er allred score

tag: er status

tag: her2 score (hercep test score)


title: CMT-743-normal

description: processed data file: CMT_222S_FPKM.csv

value: mammary normal tissue

value: Simple carcinoma (Solid type)

value: Neutered

tag: date of surgery

tag: survival status (until 2018-08-01)

tag: survival (day)


title: Frontal_Cortex AD (9345344014_D)

tag: gender

value: FEMALE

tag: individual

value: Subject  66

tag: disease state

value: AD


title: CMT-725-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

tag: tissue

tag: tumor grade

value: Complex carcinoma

value: Female


title: Temporal_Cortex AD (9031356091_H)

tag: age

value: Subject  65


title: CMT-725-normal

description: processed data file: CMT_222S_FPKM.csv

tag: diagnosis

tag: Sex

value: Absent

value: N

tag: date of death


title: Entorhinal_Cortex AsymAD (9031356088_K)

value: MALE

value: Subject  83

value: AsymAD


title: CMT-724-normal

description: processed data file: CMT_222S_FPKM.csv

tag: neuter status

value: Intact

tag: lymphatic vessel invasion

tag: breed

value: Positive

value: Y


title: CMT-719-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

value: Benign

value: Simple adenoma

value: Maltese

tag: er allred score

tag: er status

tag: her2 score (hercep test score)


title: CMT-719-normal

description: processed data file: CMT_222S_FPKM.csv

value: mammary normal tissue

tag: date of surgery

tag: survival status (until 2018-08-01)

tag: survival (day)


title: Entorhinal_Cortex AD (9371242066_D)

tag: gender

tag: individual

value: Subject  64

tag: disease state

value: AD


title: CMT-688-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

tag: tissue

tag: tumor grade

value: Complex carcinoma

value: Female


title: CMT-688-normal

description: processed data file: CMT_222S_FPKM.csv

tag: age

tag: diagnosis

tag: Sex

value: Absent


title: CMT-695-tumor

description: processed data file: CMT_222S_FPKM.csv

value: Benign mixed tumor

tag: neuter status

value: Neutered

tag: lymphatic vessel invasion

value: Poodle

value: loss to follow-up


title: Frontal_Cortex AsymAD (9344744052_F)

value: FEMALE

value: Subject  68

value: AsymAD


title: Cerebellum AD (9344744001_A)

value: MALE

value: Cerebellum


title: Frontal_Cortex AD (9345344002_I)


title: Frontal_Cortex AD (9031356097_H)

value: Subject  65


title: Temporal_Cortex AD (9371242082_J)

value: Subject  63


title: Temporal_Cortex AD (9371242065_C)


title: Frontal_Cortex AD (9345344027_I)


title: Entorhinal_Cortex AD (9371242082_E)


title: Temporal_Cortex AD (9216457028_B)

value: Subject  62


title: Cerebellum AD (9216457020_B)


title: Cerebellum AD (9031356084_H)


title: CMT-685-normal

description: processed data file: CMT_222S_FPKM.csv

value: mammary normal tissue

value: Simple carcinoma (Tubulopapillary type)

value: Intact

tag: breed

value: Maltese

tag: er allred score

value: Positive

value: Y


title: Cerebellum AD (9344744089_E)

value: AD


title: CMT-678-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

value: Complex carcinoma

value: Female

value: Absent

value: Mixed

tag: er status

tag: her2 score (hercep test score)


title: CMT-678-normal

description: processed data file: CMT_222S_FPKM.csv

tag: date of surgery

tag: survival status (until 2018-08-01)

value: loss to follow-up


title: Temporal_Cortex AD (9031356085_G)

tag: gender

value: MALE

value: Subject  61


title: CMT-724-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: survival (day)


title: CMT-667-normal

description: processed data file: CMT_222S_FPKM.csv


title: CMT-685-tumor

description: processed data file: CMT_222S_FPKM.csv


title: CMT-686-tumor

description: processed data file: CMT_222S_FPKM.csv

value: Shih Tzu


title: Frontal_Cortex AD (9216457020_J)

value: FEMALE

tag: individual

value: Subject  62

tag: disease state


title: CMT-660-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

tag: tissue

value: Poodle


title: CMT-659-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: tumor grade

tag: age

value: Simple carcinoma (Tubulopapillary type)

value: Intact


title: CMT-651-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: diagnosis

value: Carcinoma in benign mixed tumor

tag: Sex

value: Neutered

value: Maltese

value: Positive


title: CMT-667-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

value: Complex carcinoma

tag: neuter status

tag: lymphatic vessel invasion

value: Y


title: Temporal_Cortex AD (9345725010_K)

value: Subject  64

value: AD


title: Frontal_Cortex AD (9344744102_A)

value: Subject  60


title: CMT-651-normal

description: processed data file: CMT_222S_FPKM.csv

value: mammary normal tissue

value: Female

value: Absent

tag: breed

tag: er allred score


title: Entorhinal_Cortex control (9216457027_A)

value: MALE

value: Subject  59

value: control


title: Cerebellum control (9031356084_A)

value: Cerebellum


title: Entorhinal_Cortex AD (9371242065_F)

value: FEMALE


title: CMT-644-tumor

description: processed data file: CMT_222S_FPKM.csv

value: Simple carcinoma (Solid type)

value: Intact

value: Present

value: Schnauzer

tag: er status

tag: her2 score (hercep test score)

value: N

tag: date of death


title: Temporal_Cortex control (9031356091_A)

tag: gender


title: CMT-644-normal

description: processed data file: CMT_222S_FPKM.csv

value: Positive

tag: date of surgery

tag: survival status (until 2018-08-01)

tag: survival (day)


title: CMT-634-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

value: mammary tumor tissue

value: Carcinoma in benign mixed tumor

value: Neutered

value: Yorkshire Terrier


title: CMT-632-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: tissue

value: Simple carcinoma (Tubulopapillary type)

value: Female

value: King Charles Spaniel

value: Negative

value: Y


title: CMT-613-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: tumor grade

value: Shih Tzu


title: Entorhinal_Cortex AD (9371242066_J)

value: FEMALE

tag: age

tag: individual

value: Subject  58

tag: disease state

value: AD


title: CMT-613-normal

description: processed data file: CMT_222S_FPKM.csv

value: mammary normal tissue

tag: diagnosis

value: Simple carcinoma (Solid type)

tag: Sex

tag: neuter status

value: Intact

value: Present


title: Frontal_Cortex control (9031356097_A)

value: MALE

value: Subject  59

value: control


title: CMT-606-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

value: Neutered

tag: lymphatic vessel invasion

value: Absent

tag: breed

value: Poodle

tag: er allred score

value: Positive


title: CMT-603-tumor

description: processed data file: CMT_222S_FPKM.csv

value: Not applicable

value: Simple carcinoma (Tubulopapillary type)

value: Female

tag: er status

tag: her2 score (hercep test score)

value: loss to follow-up


title: Temporal_Cortex AD (9345725010_H)

tag: gender

value: FEMALE

value: Subject  58

value: AD


title: CMT-606-normal

description: processed data file: CMT_222S_FPKM.csv

value: mammary normal tissue

tag: date of surgery

tag: survival status (until 2018-08-01)

value: Y


title: Cerebellum AD (9344744014_A)

value: Cerebellum


title: CMT-586-normal

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

value: Cocker Spaniel

tag: survival (day)


title: Entorhinal_Cortex AD (9371242065_H)

value: Subject  57

tag: tissue


title: Temporal_Cortex AD (9345344031_B)

tag: age

value: Subject  70


title: Frontal_Cortex AD (9345344009_E)

tag: individual


title: Entorhinal_Cortex AD (9371242066_C)

value: MALE

value: Subject  56

tag: disease state


title: Entorhinal_Cortex control (9216457022_A)

value: Subject  59

value: control


title: Cerebellum AD (9344732094_C)


title: Temporal_Cortex AD (9345344031_I)


title: Frontal_Cortex AD (9344744102_C)


title: CMT-581-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

tag: tumor grade

tag: diagnosis

value: Simple carcinoma (Solid type)

value: Intact

value: Present

value: Chihuahua

value: Positive

value: N

tag: date of death


title: CMT-581-normal

description: processed data file: CMT_222S_FPKM.csv

value: mammary normal tissue

tag: Sex

value: Female

tag: neuter status

tag: lymphatic vessel invasion


title: CMT-538-tumor

description: processed data file: CMT_222S_FPKM.csv

value: Complex carcinoma

value: Absent

tag: breed

value: Yorkshire Terrier

tag: er allred score

tag: er status

value: Y


title: CMT-586-tumor

description: processed data file: CMT_222S_FPKM.csv

value: Simple carcinoma (Tubulopapillary type)

value: Neutered

value: Cocker Spaniel

tag: her2 score (hercep test score)

tag: date of surgery


title: CMT-577-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

value: Carcinosarcoma

value: Schnauzer

tag: survival status (until 2018-08-01)


title: Temporal_Cortex AD (9216457028_C)

tag: gender

value: MALE

value: Subject  55

tag: tissue

value: AD


title: Frontal_Cortex AD (9344744102_I)

tag: age

tag: individual

value: Subject  56


title: CMT-523-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

tag: tumor grade

value: Carcinoma in benign mixed tumor

value: Intact

value: Shih Tzu

value: Positive

value: loss to follow-up

tag: survival (day)


title: CMT-538-normal

description: processed data file: CMT_222S_FPKM.csv

value: mammary normal tissue

tag: diagnosis

value: Complex carcinoma

value: Female

value: Absent

value: Yorkshire Terrier


title: CMT-505-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: Sex

value: Maltese


title: Cerebellum AD (9257302083_C)

value: Cerebellum

tag: disease state


title: Cerebellum AD (9216457020_C)

value: MALE


title: Temporal_Cortex AD (9345725010_I)

value: FEMALE

value: Subject  54


title: Entorhinal_Cortex AD (9371242066_B)

value: AD


title: Frontal_Cortex AD (9345344002_G)


title: Entorhinal_Cortex AsymAD (9216457028_H)

value: Subject  53

value: AsymAD


title: Temporal_Cortex AsymAD (9216457028_D)


title: Cerebellum AsymAD (9216457020_D)


title: CMT-522-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

value: Benign

value: Not applicable

value: complex adenoma

tag: neuter status

value: Intact

tag: lymphatic vessel invasion

value: Dachshund

value: Y


title: CMT-523-normal

description: processed data file: CMT_222S_FPKM.csv

value: mammary normal tissue

value: Carcinoma in benign mixed tumor

value: Female

value: Absent

tag: breed

value: Shih Tzu

tag: er allred score

value: Positive

value: loss to follow-up


title: CMT-496-tumor

description: processed data file: CMT_222S_FPKM.csv

value: Simple carcinoma (Solid type)

value: Yorkshire Terrier

tag: er status

tag: her2 score (hercep test score)


title: Frontal_Cortex AsymAD (9216457028_L)

value: FEMALE

value: Subject  53

value: AsymAD


title: CMT-480-normal

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

value: Benign

value: Simple adenoma

value: Maltese

tag: date of surgery


title: CMT-495-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

value: Intact

value: Present

tag: survival status (until 2018-08-01)


title: CMT-480-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: tissue

value: Y


title: CMT-471-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: age

value: Simple carcinoma (Tubulopapillary type)

value: Female

value: Neutered

value: Cocker Spaniel

value: N

tag: date of death


title: CMT-459-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: tumor grade

value: Complex carcinoma

value: Absent

value: Positive


title: CMT-493-tumor

description: processed data file: CMT_222S_FPKM.csv

value: Simple carcinoma (Solid type)

value: Shih Tzu

tag: survival (day)


title: Temporal_Cortex AsymAD (9345344014_C)

tag: gender

value: FEMALE

tag: individual

value: Subject  52

value: AsymAD


title: Cerebellum AsymAD (9344744014_H)

value: Cerebellum

tag: disease state


title: Frontal_Cortex AsymAD (9216457020_L)

value: Subject  53


title: Frontal_Cortex AsymAD (9344744094_F)


title: CMT-456-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

value: Benign

value: Not applicable

tag: diagnosis

value: Simple adenoma

tag: Sex

tag: neuter status

value: Intact

value: Poodle


title: CMT-776-normal

description: processed data file: CMT_222S_FPKM.csv

value: mammary normal tissue

value: Female

value: Neutered

tag: lymphatic vessel invasion

tag: breed

value: Maltese

tag: er allred score

value: Y


title: Cerebellum AD (9344744089_A)

value: MALE

value: Subject  50

value: AD


title: CMT-476-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

value: Absent

tag: er status

value: Positive

tag: her2 score (hercep test score)


title: Entorhinal_Cortex AD (9371242073_L)

tag: tissue


title: CMT-440-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: age

value: Complex carcinoma

value: Chihuahua

tag: date of surgery

tag: survival status (until 2018-08-01)


title: CMT-442-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

tag: tumor grade

value: Benign

value: Benign mixed tumor

value: Mixed

value: Negative

tag: survival (day)


title: CMT-452-tumor

description: processed data file: CMT_222S_FPKM.csv

value: Complex adenoma

value: Intact


title: CMT-439-tumor

description: processed data file: CMT_222S_FPKM.csv

value: Simple carcinoma (Solid type)

value: Female

value: Neutered

value: Present

value: Miniature Pinscher

value: N

tag: date of death


title: Frontal_Cortex AD (9345344027_E)

tag: gender

value: MALE

tag: individual

value: Subject  50

tag: disease state

value: AD


title: Temporal_Cortex AD (9345725025_L)


title: CMT-439-normal

description: processed data file: CMT_222S_FPKM.csv

value: mammary normal tissue

tag: diagnosis

tag: Sex

tag: neuter status


title: CMT-436-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

value: Complex carcinoma

tag: lymphatic vessel invasion

value: Absent

tag: breed

value: Cocker Spaniel

tag: er allred score

value: Positive

value: loss to follow-up


title: CMT-435-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

value: Intact

value: Mixed

tag: er status

tag: her2 score (hercep test score)

value: Y


title: CMT-458-normal

description: processed data file: CMT_222S_FPKM.csv

tag: tissue

tag: age

value: Female

value: Neutered

value: Pomeranian

tag: date of surgery


title: Frontal_Cortex control (9344744043_K)

value: FEMALE

value: Subject  51

value: control


title: Entorhinal_Cortex AsymAD (9216457022_J)

value: Subject  49

value: AsymAD


title: CMT-435-normal

description: processed data file: CMT_222S_FPKM.csv

value: mammary normal tissue

tag: tumor grade

tag: survival status (until 2018-08-01)

tag: survival (day)


title: CMT-417-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

value: Benign

value: Simple adenoma

value: Shih Tzu


title: Frontal_Cortex AsymAD (9031356097_J)

tag: gender

tag: individual


title: Temporal_Cortex AsymAD (9345344009_L)

value: Subject  48

tag: disease state


title: Temporal_Cortex AsymAD (9031356091_J)


title: Frontal_Cortex AsymAD (9344744094_B)


title: Cerebellum AsymAD (9344744001_L)

value: Cerebellum


title: CMT-417-normal

description: processed data file: CMT_222S_FPKM.csv

tag: diagnosis

tag: Sex

value: Intact

value: Absent

value: Positive


title: Entorhinal_Cortex AsymAD (9216457027_J)


title: CMT-458-tumor

description: processed data file: CMT_222S_FPKM.csv

value: Complex carcinoma

value: Female

tag: neuter status

value: Neutered

tag: lymphatic vessel invasion

value: Y


title: Cerebellum AD (9031356069_H)

value: MALE

value: Subject  47

value: AD


title: CMT-407-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: breed

value: Mixed

tag: er allred score


title: CMT-414-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

value: mammary tumor tissue

value: Simple carcinoma

value: Maltese

tag: er status


title: Temporal_Cortex control (9344744052_D)

value: Subject  46

tag: tissue

value: control


title: CMT-402-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: age

value: Simple carcinoma (Tubulopapillary type)

value: Dachshund

tag: her2 score (hercep test score)


title: CMT-392-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: tumor grade

value: Benign

value: Complex adenoma

value: Intact

value: Absent

tag: date of surgery

value: loss to follow-up


title: CMT-381-tumor

description: processed data file: CMT_222S_FPKM.csv

value: Female

value: Neutered

value: Positive

tag: survival status (until 2018-08-01)

value: Y

tag: survival (day)


title: Entorhinal_Cortex AsymAD (9345344031_L)

tag: gender

value: FEMALE

tag: individual

value: Subject  48

value: AsymAD


title: Frontal_Cortex AD (9344744102_G)

value: MALE

value: Subject  45

tag: disease state

value: AD


title: Entorhinal_Cortex AD (9371242066_A)


title: Temporal_Cortex AD (9345344031_G)


title: Temporal_Cortex control (9344744089_K)

value: Subject  51

value: control


title: CMT-374-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

value: Benign

tag: diagnosis

tag: Sex

value: Maltese


title: Entorhinal_Cortex AsymAD (9216457022_L)

value: Subject  43


title: CMT-360-tumor

description: processed data file: CMT_222S_FPKM.csv

value: Simple carcinoma (Tubulopapillary type)

tag: neuter status

tag: lymphatic vessel invasion

value: Present

value: Poodle

value: N

tag: date of death


title: CMT-374-normal

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

value: mammary normal tissue

value: Complex adenoma

value: Female

value: Neutered

value: Absent

tag: breed

tag: er allred score

value: Positive

value: Y


title: Frontal_Cortex control (9344744014_B)

value: MALE

tag: age

value: Subject  42

tag: tissue


title: Frontal_Cortex AsymAD (9031356097_L)

value: FEMALE

value: AsymAD


title: CMT-400-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

tag: tumor grade

value: Not applicable

value: Intact

value: Shih Tzu

tag: er status

tag: her2 score (hercep test score)


title: Entorhinal_Cortex AsymAD (9216457027_L)

value: Subject  43


title: CMT-365-tumor

description: processed data file: CMT_222S_FPKM.csv

value: Complex carcinoma

tag: date of surgery

tag: survival status (until 2018-08-01)

value: N

tag: survival (day)


title: CMT-355-normal

description: processed data file: CMT_222S_FPKM.csv

value: mammary normal tissue

value: Benign

value: Complex adenoma

value: Maltese

value: loss to follow-up


title: CMT-355-tumor

description: processed data file: CMT_222S_FPKM.csv

value: Female

value: Absent

value: Positive


title: Temporal_Cortex control (9344744052_B)

tag: gender

value: MALE

tag: individual

value: Subject  42

tag: disease state

value: control


title: Cerebellum AsymAD (9031356084_J)

value: FEMALE

value: Subject  49

value: Cerebellum

value: AsymAD


title: Entorhinal_Cortex AsymAD (9345725010_L)

value: Subject  44


title: CMT-377-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

tag: diagnosis

value: Complex carcinoma

tag: Sex

tag: neuter status

value: Intact

value: Y


title: Entorhinal_Cortex control (9031356102_B)

value: Subject  41


title: CMT-377-normal

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

value: mammary normal tissue

tag: lymphatic vessel invasion

value: Maltese


title: Frontal_Cortex control (9031356052_B)


title: CMT-354-tumor

description: processed data file: CMT_222S_FPKM.csv

value: Simple carcinoma (Tubulopapillary type)

value: Female

value: Neutered

value: Absent

tag: breed

value: Yorkshire Terrier

tag: er allred score

value: Negative


title: CMT-351-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: tissue

value: Benign

tag: age

value: Complex adenoma

value: Poodle

value: Positive


title: Cerebellum control (9031356069_B)

value: MALE

value: Cerebellum

value: control


title: Temporal_Cortex control (9031356074_B)


title: CMT-348-normal

description: processed data file: CMT_222S_FPKM.csv

tag: tumor grade

value: Complex carcinoma

value: Shih Tzu

tag: er status

value: Y


title: CMT-346-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

value: Sapsaree

tag: her2 score (hercep test score)

tag: date of surgery

value: N

tag: date of death


title: CMT-344-tumor

description: processed data file: CMT_222S_FPKM.csv

value: Simple carcinoma (Solid type)

value: Female

value: Intact

value: Present

tag: survival status (until 2018-08-01)

tag: survival (day)


title: Frontal_Cortex AD (9345344009_D)

tag: gender

value: FEMALE

tag: individual

value: Subject  40

tag: disease state

value: AD


title: Entorhinal_Cortex AD (9371242073_I)


title: CMT-344-normal

description: processed data file: CMT_222S_FPKM.csv

value: mammary normal tissue

tag: diagnosis

tag: Sex

tag: neuter status

value: Yorkshire Terrier

value: Positive


title: CMT-340-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

value: Carcinosarcoma

tag: lymphatic vessel invasion

tag: breed

value: Negative

value: loss to follow-up


title: CMT-340-normal

description: processed data file: CMT_222S_FPKM.csv

tag: tissue

tag: age

tag: er allred score


title: CMT-336-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: tumor grade

value: Complex carcinoma

value: Absent

value: Miniature Schnauzer

tag: er status

tag: her2 score (hercep test score)

value: Y


title: CMT-332-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

value: Osteosarcoma

value: Neutered

value: Maltese

value: Not applicable

tag: date of surgery

tag: survival status (until 2018-08-01)

value: N

tag: date of death


title: CMT-321-tumor

description: processed data file: CMT_222S_FPKM.csv

value: Simple carcinoma (Tubulopapillary type)

value: Female

value: Intact

value: Miniature Pinscher

tag: survival (day)


title: CMT-321-normal

description: processed data file: CMT_222S_FPKM.csv

value: mammary normal tissue

value: Positive


title: Cerebellum control (9216457020_F)

tag: gender

value: MALE

tag: individual

value: Subject  41

value: Cerebellum

tag: disease state

value: control


title: CMT-317-tumor

description: processed data file: CMT_222S_FPKM.csv

value: Benign

tag: diagnosis

value: Complex adenoma

tag: Sex

tag: neuter status

value: Absent

value: Pekingese

value: Y


title: Frontal_Cortex control (9031356076_C)

value: Subject  39


title: CMT-318-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

value: mammary tumor tissue

value: Simple carcinoma (Solid type)

tag: lymphatic vessel invasion

tag: breed

value: Shih Tzu

value: Negative

value: N


title: CMT-308-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: tissue

tag: age

value: Complex carcinoma

value: Female

value: Neutered

value: Pomeranian

tag: er allred score


title: Entorhinal_Cortex control (9031356088_C)

value: MALE


title: Temporal_Cortex AD (9345725025_K)

value: FEMALE

value: Subject  40

value: AD


title: CMT-308-normal

description: processed data file: CMT_222S_FPKM.csv

value: mammary normal tissue

tag: tumor grade

value: Absent

tag: er status

value: Positive

tag: her2 score (hercep test score)


title: Temporal_Cortex AD (9345725010_E)

value: Subject  38


title: CMT-306-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

value: Simple carcinoma (Tubulopapillary type)

value: Intact

value: Mixed

tag: date of surgery

tag: survival status (until 2018-08-01)

value: Y


title: CMT-301-tumor

description: processed data file: CMT_222S_FPKM.csv

value: Complex carcinoma

value: Dachshund

value: Negative

value: loss to follow-up

tag: survival (day)


title: CMT-301-normal

description: processed data file: CMT_222S_FPKM.csv

value: Female

value: Neutered


title: Frontal_Cortex AD (9345344014_E)

tag: gender

value: FEMALE

tag: individual

value: Subject  37


title: Entorhinal_Cortex control (9216457002_C)

value: MALE

value: Subject  39

tag: disease state

value: control


title: Entorhinal_Cortex AD (9371242073_F)

value: Subject  36

value: AD


title: Temporal_Cortex AD (9345725025_F)


title: Entorhinal_Cortex AD (9371242073_K)


title: Frontal_Cortex AD (9345344014_K)


title: Temporal_Cortex AD (9345725010_B)

value: Subject  34


title: Cerebellum AD (9344744052_C)

value: Cerebellum


title: CMT-292-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

tag: diagnosis

value: Simple carcinoma (Tubulopapillary type)

tag: Sex

value: Absent

value: Shih Tzu

value: Positive


title: Frontal_Cortex AD (9345344002_K)


title: Temporal_Cortex control (9031356085_C)


title: Temporal_Cortex control (9031292027_A)

value: Subject  35


title: Cerebellum AsymAD (9344744001_F)

value: Subject  33

value: AsymAD


title: Temporal_Cortex control (9031292027_B)

value: Subject  41


title: CMT-292-normal

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

value: mammary normal tissue

value: Female

tag: neuter status

value: Neutered

value: Y


title: CMT-307-tumor

description: processed data file: CMT_222S_FPKM.csv

value: Intact

tag: lymphatic vessel invasion

tag: breed

value: Poodle


title: CMT-290-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: tissue

tag: age

value: Osteosarcoma

value: Miniature Pinscher

value: Not applicable

value: loss to follow-up


title: Temporal_Cortex AsymAD (9345344009_F)

value: MALE


title: CMT-290-normal

description: processed data file: CMT_222S_FPKM.csv

tag: tumor grade

value: Absent

tag: er allred score


title: CMT-278-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

value: Complex carcinoma

value: Maltese

tag: er status

value: Positive

tag: her2 score (hercep test score)


title: CMT-348-tumor

description: processed data file: CMT_222S_FPKM.csv

value: Shih Tzu

tag: date of surgery

tag: survival status (until 2018-08-01)


title: Cerebellum AD (9344744043_C)

tag: gender

value: FEMALE

value: Subject  40

value: Cerebellum

value: AD


title: CMT-278-normal

description: processed data file: CMT_222S_FPKM.csv

value: mammary normal tissue

value: Female

value: Intact

value: Y

tag: survival (day)


title: Frontal_Cortex AsymAD (9344744089_J)

tag: individual

value: Subject  33

tag: disease state

value: AsymAD


title: CMT-272-normal

description: processed data file: CMT_222S_FPKM.csv

value: Benign

tag: diagnosis

value: Complex adenoma

tag: Sex

value: Negative


title: Vc+_GATA2+_ECs_96h_suspended cells [RNA-Seq]

city: Guangzhou

first: Tian

last: Zhang

state: Guangdong

address: 190 Kaiyuan Avenue,Science Park

country: China

institute: GIBH

description: Suspended hematopoietic cells derived from GATA2+_ECs derived in Vc+ condition after replated for 96h

data_processing:
Illumina Casava1.7 software used for basecalling.
Briefly, reads were aligned to human genome (UCSC hg38) using HISAT2 (v2.0.4)
and gene expression was counted using samtools (v1.3.1) and htseq-count (v 0.6.0), filtered by a threshold of at least 20 averaged raw read counts among samples, and then normalized by GC-count and Gene-length using EDASeq (v2.12.0).
Differential expression and PCA plot were performed using DESeq (v 1.18.1) and genes with p-value < 0.05 and fold-change > 2 were considered as significant difference.
Correlation plot was performed using ggplot2 (v2.2.1) and heatmap was performed using pheatmap (v1.0.10).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: count

source_name: Hematopoietic cells

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: cell type

value: hESCs derived hematopoietic cells


title: Vc+_GATA2+_ECs_60h_adhered cells [RNA-Seq]

description: Adhered cell mixture of endothelial and hematopoietic cells derived from GATA2+_ECs derived in Vc+ condition after replated for 60h

value: hESCs derived Endothelial cells and hematopoietic cells


title: Vc+_GATA2+_ECs_60h_suspended cells [RNA-Seq]

description: Suspended hematopoietic cells derived from GATA2+_ECs derived in Vc+ condition after replated for 60h


title: CMT-271-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

value: mammary tumor tissue

value: Simple carcinoma (Tubulopapillary type)

tag: neuter status

value: Neutered

tag: lymphatic vessel invasion

value: Absent

tag: breed

value: Poodle

value: Positive


title: Vc+_GATA2+_ECs_36h [RNA-Seq]

description: Cell mixture of endothelial and hematopoietic cells derived from GATA2+_ECs derived in Vc+condition after replated for 36h

source_name: Endothelial cells and hematopoietic cells


title: Vc+_GATA2+_ECs_0h [RNA-Seq]

description: GATA2+_ECs derived in Vc+ condition

source_name: Endothelial cells

value: hESCs derived Endothelial cells


title: Cerebellum AD (9344744001_G)

value: MALE

tag: age

value: Subject  32

tag: tissue

value: Cerebellum

value: AD


title: Temporal_Cortex AD (9345725010_F)


title: Vc+_GATA2+_ECs_48h [RNA-Seq]

description: Cell mixture of endothelial and hematopoietic cells derived from GATA2+_ECs derived in Vc+condition after replated for 48h


title: Frontal_Cortex AsymAD (9344744052_J)

value: FEMALE

value: Subject  31

value: AsymAD


title: Entorhinal_Cortex AsymAD (9345344027_H)


title: Entorhinal_Cortex control (9031356088_D)

value: Subject  30

value: control


title: Temporal_Cortex AsymAD (9345344002_J)


title: Vc-_GATA2+_ECs_48h [RNA-Seq]

description: Cell mixture of endothelial and hematopoietic cells derived from GATA2+_ECs derived in Vc- condition after replated for 48h

value: hESCs derived Endothelial cells and hematopoietic cells


title: Vc-_GATA2+_ECs_60h [RNA-Seq]

description: Cell mixture of endothelial and hematopoietic cells derived from GATA2+_ECs derived in Vc- condition after replated for 60h


title: CMT-272-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

tag: tumor grade

value: Benign

value: Complex adenoma

value: Female

value: Intact

value: Maltese

tag: er allred score

tag: er status

value: Negative

tag: her2 score (hercep test score)

value: Y


title: CMT-262-tumor

description: processed data file: CMT_222S_FPKM.csv

value: Simple carcinoma (Solid type)

value: Neutered

value: Present

tag: date of surgery

tag: survival status (until 2018-08-01)

value: N

tag: date of death

tag: survival (day)


title: CMT-263-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: diagnosis

value: Simple carcinoma (Tubulopapillary type)

tag: Sex

value: Absent

value: Positive

value: loss to follow-up


title: Vc+_GATA2+_ECs_60h [RNA-Seq]

description: Cell mixture of endothelial and hematopoietic cells derived from GATA2+_ECs derived in Vc+ condition after replated for 60h

tag: cell line

tag: cell type

value: hESCs derived Endothelial cells and hematopoietic cells


title: Vc-_GATA2+_ECs_36h [RNA-Seq]

description: Cell mixture of endothelial and hematopoietic cells derived from GATA2+_ECs derived in Vc- condition after replated for 36h


title: CMT-259-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

value: mammary tumor tissue

value: Not applicable

tag: neuter status


title: Frontal_Cortex control (9031356076_D)

tag: gender

value: FEMALE

tag: individual

value: Subject  30

tag: disease state

value: control


title: Entorhinal_Cortex control (9216457002_D)

tag: age

tag: tissue


title: Vc+_GATA2+_ECs_24h [RNA-Seq]

description: Cell mixture of endothelial and hematopoietic cells derived from GATA2+_ECs derived in Vc+condition after replated for 24h


title: Vc-_GATA2+_ECs_24h [RNA-Seq]

description: Cell mixture of endothelial and hematopoietic cells derived from GATA2+_ECs derived in Vc- condition after replated for 24h


title: Temporal_Cortex control (9031356085_D)


title: CMT-257-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: tumor grade

value: Benign

value: Benign mixed tumor

value: Female

tag: lymphatic vessel invasion

tag: breed

value: Poodle

tag: er allred score

tag: er status


title: Vc-_GATA2+_ECs_0h [RNA-Seq]

description: GATA2+_ECs derived in Vc- condition

value: hESCs derived Endothelial cells


title: Vc+_GATA2+_ECs_rp2 [RNA-Seq]

description: GATA2+_ECs derived in Vc+ condition


title: Entorhinal_Cortex AD (9371242066_L)

value: MALE

value: Subject  29

value: AD


title: Cerebellum control (9031356073_D)

value: Cerebellum


title: CMT-252-tumor

description: processed data file: CMT_222S_FPKM.csv

value: Simple carcinoma (Solid type)

value: Intact

value: Absent

value: Positive

tag: her2 score (hercep test score)

tag: date of surgery

tag: survival status (until 2018-08-01)

value: Y

tag: survival (day)


title: Vc-_GATA2+_ECs_rp1 [RNA-Seq]

description: GATA2+_ECs derived in Vc- condition

tag: cell line

tag: cell type


title: Vc+_GATA2+_ECs_rp1 [RNA-Seq]

description: GATA2+_ECs derived in Vc- condition


title: CMT-250-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

value: mammary tumor tissue

tag: diagnosis

value: Complex carcinoma

tag: Sex

tag: neuter status


title: Vc-_GATA2+_ECs_rp2 [RNA-Seq]

description: GATA2+_ECs derived in Vc+ condition


title: Cerebellum AD (9344744014_C)

tag: gender

tag: age

tag: individual

tag: disease state


title: Vc+_GATA2+ECs_Input

description: GATA2+_ECs derived in Vc+ condition_Input

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were base-called and de-multiplexed using standard Illumina softwares. Bowtie2 was used to align the reads to the human genome hg38. Reads mapped to identical positions with same orientation in the genome were collapsed into one read.
The regions of H3K27me3 enrichment (peaks) were called using the SICER software package, with the input genomic DNA as a background control (parameters: W = 200; G = 600; FDR 0.01 cutoff applied).
Binding profiles and heatmaps were generated using ngsplot  and deeptools.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: bed

molecule: genomic DNA

extract_protocol:
For  ChIP-seq, 1×107 cells of each sample were crosslinked in 1% formaldehyde with rotation for 10 minutes at room temperature. And then these crosslinked reactions were stopped by 0.125 M glycine with rotation for 5 minutes at room temperature. and cell sample were sonicated, and then ChIPed with H3K27me3 antibodies.
DNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line/strain

tag: antibody

tag: genotype


title: CMT-242-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: tissue

tag: tumor grade

value: Simple carcinoma (Tubulopapillary type)

value: Neutered

tag: lymphatic vessel invasion

tag: breed

value: Mixed

tag: er allred score

tag: er status

value: Negative

tag: her2 score (hercep test score)


title: Vc-_GATA2+ECs_H3K27me3

description: GATA2+_ECs derived in Vc- condition_H3K27me3

tag: cell type


title: CMT-245-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

value: Benign

tag: diagnosis

value: Complex adenoma

tag: Sex

value: Female

value: Chihuahua

tag: date of surgery

tag: survival status (until 2018-08-01)

value: loss to follow-up

tag: survival (day)


title: Vc-_GATA2+ECs_H3K4me3

description: GATA2+_ECs derived in Vc- condition_H3K4me3

tag: cell line/strain

value: hESCs derived Endothelial cells


title: Vc-_GATA2+ECs_Input

description: GATA2+_ECs derived in Vc- condition_Input

tag: antibody


title: Vc+_GATA2+ECs_H3K4me3

description: GATA2+_ECs derived in Vc+ condition_H3K4me3

tag: genotype


title: Vc-_GATA2+_ECs_rp2

description: GATA2+_ECs derived in Vc- condition

data_processing:
Illumina Casava1.7 software used for basecalling.
Adaptors were cut from reads using cutadapt (v1.13), and reads were aligned to human genome (UCSC hg38) using bowtie2 (v2.2.5).
Duplicates were removed using samtools (v1.3.1) and Picard Tools (v1.90). Signals were pileupped using MACS2 callpeak and bdgcmp, and differential open peaks were called using MACS2 bdgdiff
Signal density heatmap and profile were plotted using deeptools (v2.4.2), and motifs were found using homer.
Peaks were annotated with gene annotation using ChIPpeakAnno (v3.12.7) and gene ontology analysis was performed using clusterProfiler (v3.6.0).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: bigwig

extract_protocol:
In brief, 5×104 cells of each sample were processed for ATAC-seq.
DNA libraries were prepared for sequencing using standard Illumina protocols.


title: Vc+_GATA2+_ECs_rp2

description: GATA2+_ECs derived in Vc+ condition


title: Vc+_GATA2+_ECs_rp1

description: GATA2+_ECs derived in Vc+ condition


title: Vc-_GATA2+_ECs_rp1

description: GATA2+_ECs derived in Vc- condition


title: CMT-242-normal

description: processed data file: CMT_222S_FPKM.csv

tag: tissue

value: mammary normal tissue

tag: age

tag: neuter status


title: Vc+_GATA2+ECs_H3K27me3

description: GATA2+_ECs derived in Vc+ condition_H3K27me3


title: CMT-247-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: tumor grade

value: Simple carcinoma (Solid type)

value: Intact

tag: lymphatic vessel invasion

value: Present

tag: breed

value: Shih Tzu


title: Temporal_Cortex AD (9345725025_B)

tag: gender

value: FEMALE

tag: individual

value: Subject  27

tag: disease state

value: AD


title: Frontal_Cortex AD (9345344002_E)

value: MALE

value: Subject  28


title: 1st and 2nd pharyngeal arches, Kat6a WT replicate 3 (ChIP-seq)

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Base calling and quality scoring was performed by Illumina Real-Time Analysis (v2) software. FASTQ file generation and de-multiplexing was performed by bcl2fastq conversion software (v2.15.0.4).
Technical replicate fastq files were concatenated prior to alignment.
Reads were aligned to the mouse genome by Rsubread version 1.16.1
Read counts were summarized by Entrez Gene ID using the Rsubread's featureCounts function and Rsubread's built-in NCBI annotation.
BAM files were processed using SeqMonk Mapped Sequence Data Analyser Version 0.29.0 (Brabraham Institute). Peaks were identified using MACS peak caller.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files (tsv). Columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene.

organism: Mus musculus

source_name: 1st and 2nd pharyngeal arches

extract_protocol:
ChIP was essentially performed as previously described in detail (Voss et al., 2012 Methods Mol Biol 809:335-52) with the modifications described (Vanyai et al., 2015 Dev Biol 403(1):22-9).
Uniquely indexed libraries were generated per sample with the TruSeq Kit (Illumina), according to manufacturer's instructions.

tag: kat6a genotype

value: WT

tag: strain

tag: developmental stage

value: 1st and 2nd pharyngeal arches

tag: chip antibody

value: anti-V5 antibody (Sigma, A7345)


title: Temporal_Cortex AD (9345725010_G)


title: 1st and 2nd pharyngeal arches, Input Kat6a-V5 fusion (ChIP-seq)

value: Kat6a-V5 fusion


title: Temporal_Cortex AD (9345725010_J)

value: Subject  29


title: Entorhinal_Cortex AD (9371242073_B)


title: Entorhinal_Cortex AD (9371242066_K)


title: 1st and 2nd pharyngeal arches, Kat6a WT replicate 2 (ChIP-seq)


title: Cerebellum AD (9344744043_E)

value: Subject  37

value: Cerebellum


title: 1st and 2nd pharyngeal arches, Kat6a WT replicate 1 (ChIP-seq)


title: CMT-234-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

value: mammary tumor tissue

value: Not applicable

tag: diagnosis

value: Simple carcinoma (Tubulopapillary type)

tag: Sex

value: Female

value: Absent

tag: er allred score

tag: er status

value: Positive

tag: her2 score (hercep test score)

tag: date of surgery

tag: survival status (until 2018-08-01)

value: loss to follow-up

tag: survival (day)


title: 1st and 2nd pharyngeal arches, Kat6a-V5 fusion replicate 1 (ChIP-seq)

tag: tissue


title: CMT-241-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: tumor grade

tag: age

tag: neuter status

value: Neutered

tag: lymphatic vessel invasion

tag: breed

value: Shih Tzu

value: Negative


title: CMT-232-normal

description: processed data file: CMT_222S_FPKM.csv

value: mammary normal tissue

value: Benign

value: Complex adenoma

value: Y


title: 1st and 2nd pharyngeal arches, Kat6a-V5 fusion replicate 3 (ChIP-seq)

tag: kat6a genotype

value: Kat6a-V5 fusion

tag: strain

tag: developmental stage

value: 1st and 2nd pharyngeal arches

value: anti-V5 antibody (Sigma, A7345)


title: CMT-241-normal

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

tag: diagnosis


title: CEL180407JL_SingleCell_RNAseq_arcuate_nucleus_E15_5_S3

city: Buffalo

first: Soo-Kyung

last: Lee

state: NY

address: 109 Cooke Hall

department: Department of Biological Sciences

country: USA

institute: University at Buffalo, The State University of New York

data_processing:
Raw sequencing cell barcodes were filtered to distinguish between valid cell barcodes from empty cell barcodes using an algorithm in Cellranger count v2.1.1.
Filtered reads were aligned to mm10, using STAR v2.4.0 with a default setting.
Gene-barcode count matrix was read using a function Read10X in an R package Seurat v2.0 for downstream analysis.
Gene-barcode matrix was normalized using a global-scaling normalization method LogNormalize in Seurat v2.0, in which gene expression for each cell was normalized by the total expression, multiplied by a scale factor 10,000, and then log-transformed.
For visualization, t-distributed stochastic neighbor embedding (tSNE) technique was used with the perplexity parameter, an expected number of neighbors, set to the default value 30.
Graph-based clustering approach in Seurat was used within a function FindClusters in Seurat v2.0 to group cells together with a resolution parameter 0.6.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited gene-barcode count matrix with genes in rows and barcodes in columns

source_name: E15 hypothalamic arcuate nucleus

extract_protocol:
standard Papain digestion
Single cell RNA-seq data were generated on the 10X emulsion platform (10X Genomics, Pleasanton, CA) according to the manufactures instructions.

tag: genotype

value: Pomc-eGfp

tag: cell type

value: arcuate nucleus neurons


title: CMT-232-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

tag: Sex

tag: er allred score

tag: er status

tag: her2 score (hercep test score)


title: CEL180407JL_SingleCell_RNAseq_arcuate_nucleus_E15_5_S1


title: 1st and 2nd pharyngeal arches, Kat6a-V5 fusion replicate 2 (ChIP-seq)

tag: tissue

tag: chip antibody


title: CEL180407JL_SingleCell_RNAseq_arcuate_nucleus_E15_5_S4

tag: age


title: Cerebellum AD (9344744043_G)

tag: gender

value: FEMALE

tag: individual

value: Subject  27

value: Cerebellum

tag: disease state

value: AD


title: Frontal_Cortex AD (9345344014_G)


title: Entorhinal_Cortex AsymAD (9031356102_I)

value: Subject  26

value: AsymAD


title: Cerebellum AsymAD (9031356069_I)


title: ATAC-sham-7dpi

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

description:
ATAC-non-diff-7dpi-peak.bed
ATAC-sham-7dpi

data_processing:
Reads were mapped to mm9 build of the mouse genome using BWA (Li et al., 2009) using default settings.
The BEDTools suite (Quinlan et al., 2010) was used to distribute the genome wide signal into bins of 500bp. To allow for differential peak calling between datasets, quantile normalization was applied using the deepTools2 suite (Ramirez et al., 2016). Peaks overlapping with TSS (Biomart) were removed.
Genome_build: mm9 (ATAC-seq)
Supplementary_files_format_and_content: ATAC-seq: BED files (peaks called differential or stable between BZ and sham at 4, 7 or 14 days post myocardial infarction).

source_name: Myh6-MerCrMer;nTnG sorted nuclei from sham operated left ventricular tissue

growth_protocol: Animal care and experiments conform to the Directive 2010/63/EU of the European Parliament. All animal work was approved by the Animal Experimental Committee of the Academic Medical Center, Amsterdam, and was carried out in compliance with the Dutch government guidelines. Myh6-MerCreMer (Sohal et al., 2001) , nTnG (JAX stock #023035) and Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/J (JAX stock #021039) mice were bred on the FVB/N background.

extract_protocol: For ATAC-seq, isolated nuclei were GFP sorted on a SH800 flow cytometer (Sony). Samples were gated in such a way that debris, nuclei clumps, and nuclei with no cardiomyocyte origin were excluded. A total of 50.000 nuclei per sample was collected and successively washed with PBS and used as input for ATAC-seq. Prior to sequencing, a quality check was performed to assure cardiomyocyte-specific open chromatin.

treatment_protocol: Tamoxifen (20 mg/kg) was administrated i.p. one week prior to t=0 and repeated the two following days. Myocardial infarction was performed as described previously in Sergeeva et al., 2013.

value: FVB/N

tag: stress

value: sham operation

value: sham operated left ventricular nuclei

tag: time

value: 7 days post-stress

tag: sample type

value: SH800 flow cytometer sorted nuclei


title: ATAC-BZ-7dpi

description:
ATAC-non-diff-7dpi-peak.bed
ATAC-BZ-7dpi

source_name: Myh6-MerCrMer;nTnG sorted nuclei from left ventricular tissue post myocardial infarction

tag: strain

value: myocardial infarction

value: border zone left ventricular nuclei post myocardial infarction


title: ATAC-BZ-14dpi

description:
ATAC-non-diff-14dpi-peak.bed
ATAC-BZ-14dpi

value: 14 days post-stress


title: ATAC-BZ-4dpi

description:
ATAC-non-diff-4dpi-peak.bed
ATAC-BZ-4dpi

data_processing:
Reads were mapped to mm9 build of the mouse genome using bowtie2  using default settings.
The BEDTools suite (Quinlan et al., 2010) was used to distribute the genome wide signal into bins of 500bp. To allow for differential peak calling between datasets, quantile normalization was applied using the deepTools2 suite (Ramirez et al., 2016). Peaks overlapping with TSS (Biomart) were removed.
Genome_build: mm9 (ATAC-seq)
Supplementary_files_format_and_content: ATAC-seq: BED files (peaks called differential or stable between BZ and sham at 4, 7 or 14 days post myocardial infarction).

source_name: PCM1 sorted nuclei from BZ left ventricular tissue post myocardial infarction

growth_protocol: Animal care and experiments conform to the Directive 2010/63/EU of the European Parliament. All animal work was approved by the Animal Experimental Committee of the Academic Medical Center, Amsterdam, and was carried out in compliance with the Dutch government guidelines. Cdh5-Cre; Sun1-sfGFP/- background mice were bred on the FVB/N background.

extract_protocol: For ATAC-seq, isolated nuclei were GFP sorted on a SH800 flow cytometer (Sony). a PCM1 pulldown was performed to enrich for cardiomyocytes. Samples were paired end sequenced at 76x76 bp on a nextseq 500.

treatment_protocol: Myocardial infarction was performed as described previously in Sergeeva et al., 2013.

value: 4 days post-stress

value: PCM-1 sorted nuclei


title: ATAC-sham-14dpi

description:
ATAC-non-diff-14dpi-peak.bed
ATAC-sham-14dpi


title: CMT-231-normal

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

value: mammary normal tissue

tag: tumor grade

tag: diagnosis

value: Carcinosarcoma

value: Female

tag: neuter status

value: Intact

tag: lymphatic vessel invasion

value: Absent

tag: breed

value: Pomeranian

value: Negative

tag: date of surgery

tag: survival status (until 2018-08-01)

value: N

tag: date of death

tag: survival (day)


title: CMT-227-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: tissue

value: mammary tumor tissue

tag: age

value: Complex carcinoma

tag: Sex

value: Maltese

tag: er allred score

tag: er status

value: Positive

tag: her2 score (hercep test score)

value: loss to follow-up


title: CMT-233-tumor

description: processed data file: CMT_222S_FPKM.csv

value: Simple carcinoma (Tubulopapillary type)

value: Shih Tzu


title: CEL180407JL_SingleCell_RNAseq_arcuate_nucleus_E15_5_S2

tag: strain

tag: genotype

value: Pomc-eGfp

tag: cell type

value: arcuate nucleus neurons


title: ATAC-sham-4dpi

description:
ATAC-non-diff-4dpi-peak.bed
ATAC-sham-4dpi

source_name: PCM1 sorted nuclei from sham operated left ventricular tissue

growth_protocol: Animal care and experiments conform to the Directive 2010/63/EU of the European Parliament. All animal work was approved by the Animal Experimental Committee of the Academic Medical Center, Amsterdam, and was carried out in compliance with the Dutch government guidelines. Cdh5-Cre; Sun1-sfGFP/- background) mice were bred on the FVB/N background.

value: FVB/N

tag: stress

value: sham operation

value: sham operated left ventricular nuclei

tag: time

value: 4 days post-stress

tag: sample type

value: PCM1-sorted nuclei


title: CMT-217-normal

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

value: mammary normal tissue

tag: tumor grade

tag: diagnosis

value: Female

tag: neuter status

value: Intact

tag: lymphatic vessel invasion

value: Absent

tag: breed

value: Y


title: CMT-217-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: tissue

value: mammary tumor tissue

tag: age

value: Complex carcinoma

value: Maltese

tag: date of surgery

tag: survival status (until 2018-08-01)

tag: survival (day)


title: Frontal_Cortex AsymAD (9344744043_J)

tag: gender

value: FEMALE

tag: individual

value: Subject  24

tag: disease state

value: AsymAD


title: CMT-231-tumor

description: processed data file: CMT_222S_FPKM.csv

value: Carcinosarcoma

tag: Sex

value: Pomeranian

tag: er allred score

tag: er status

value: Negative

tag: her2 score (hercep test score)

value: N

tag: date of death


title: Frontal_Cortex AsymAD (9031356052_I)

value: Subject  26


title: CMT-215-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

tag: tumor grade

value: Benign

tag: diagnosis

value: Benign mixed tumor

value: Poodle

value: Positive


title: Frontal_Cortex control (9344744001_K)

value: MALE

value: Subject  25

value: control


title: Cerebellum AsymAD (9344732094_F)

value: Cerebellum


title: Temporal_Cortex AsymAD (9345344002_A)


title: Cerebellum AsymAD (9257302083_F)


title: Cerebellum AsymAD (9344744001_J)

value: Subject  23


title: Ets1/2 null EC, biological rep3

city: Columbus

first: Michael

last: Ostrowski

state: Ohio

address: 460 W. 12th Avenue, Room - 598

department: Department of Molecular & Cellular Biochemistry

institute: The Ohio State University

description: Gene expression data from EC with Ets1/2 deletion

hyb_protocol: Following fragmentation, labeled cRNA was hybridized to the mouse chip 430A.2. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)

data_processing: RMA method was applied to the primary data to correct the technical bias and summarize gene expression values over probe-sets

source_name: Aortic EC isolated from mouse infected with lentivirus-egfp-Cre

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2007, Affymetrix).

growth_protocol: EC were isolated from mouse aorta

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: EC were grown in complete EC media (DMEM-F12+20% FBS+heparin+ECGS+PS) in a 37º incubator with 5% CO2.

value: 4 Weeks

value: Aorta

tag: cell type

value: Endothelial Cells

tag: genotype

value: Ets1-/-; Ets2fl/fl + lentiviral-egfp-Cre


title: CMT-210-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: tissue

value: mammary tumor tissue

tag: age

value: Simple carcinoma (Tubulopapillary type)

value: Female

tag: neuter status

value: Intact

tag: lymphatic vessel invasion

value: Absent

tag: breed


title: Ets2 null EC, biological rep3

description: Gene expression data from EC with wild type Ets2

value: Ets1+/+; Ets2fl/fl + lentiviral-egfp-Cre


title: CMT-210-normal

description: processed data file: CMT_222S_FPKM.csv

value: mammary normal tissue

value: Poodle

tag: date of surgery

tag: survival status (until 2018-08-01)

value: N

tag: survival (day)


title: Ets2 null EC, biological rep2


title: Ets1/2 null EC, biological rep1


title: CMT-206-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: Sex

value: Neutered

value: Miniature Pinscher

tag: er allred score

value: Positive

value: Y


title: Ets1/2 null EC, biological rep2

value: 4 Weeks


title: Ets2 null EC, biological rep1

value: Aorta


title: CMT-206-normal

description: processed data file: CMT_222S_FPKM.csv

tag: er status

tag: her2 score (hercep test score)


title: CMT-203-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

value: Benign

value: Complex adenoma

value: Pomeranian


title: Entorhinal_Cortex AsymAD (9345344014_L)

tag: gender

value: FEMALE

tag: individual

value: Subject  24

tag: disease state

value: AsymAD


title: Temporal_Cortex AsymAD (9345344009_J)

value: Subject  23


title: Ets1 null EC, biological rep3

description: Gene expression data from EC with wild type Ets1

source_name: Aortic EC isolated from mouse infected with lentivirus-egfp

tag: cell type

value: Endothelial Cells

tag: genotype

value: Ets1-/-; Ets2fl/fl + lentiviral-egfp


title: RNA_seq_MV411_M2_50_rep2

city: Beirut

first: Pierre

last: Khoueiry

address: Bliss street

department: Biochemistry and Molecular Genetics

country: Lebanon

institute: American University of Beirut

data_processing:
Quality check for raw sequencing reads was performed using FastQC
ChIP-seq and Chem-seq reads were aligned to the hg19 genome assembly using bwa with default parameters
Data were filtered for duplicated reads using samtools
Peaks were called using a MACS2 derived pipeline on two replicates for each sample using a combination of lenient and strick p-value largely inspired by the IDR workflow.
Bigwig profiles were created using deeptools normalized using the RPGC method with input subtracted
Genome_build: hg19
Supplementary_files_format_and_content: processed data files include signal files (biwig) and peak files (bed)

source_name: AML cells

growth_protocol:
MV4;11 and K562 cells were grown in RPMI-1640 supplemented with 10% FBS, in a humidified incubator (37 °C, 5% CO2).
MV4;11 and K562 cells were grown in RPMI-1640 supplemented with 10% FBS, in a humidified incubator (37 °C, 5% CO2).

extract_protocol:
Rneasy mini kit
TruSeq RNA Sample Preparation Kit
K562 and MV4;11 cells were treated with either DMSO or increasing concentration of I-BET151 for 6 hours at 37C.  After treatment, cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and cross-linking was stopped by the addition of 0.125 M glycine.  Cells were then lysed using the SimpleChIP® Enzymatic Chromatin IP Kit (CST #9004) and DNA was digested to mostly mononucleosomes as recommended by the manufacturer
Library preparation of immunoprecipitated DNA was done using the NEBNext® ChIPSeq Library Prep Master Mix Set for Illumina® (NEB) and samples were sequenced in a 50bp single end run on the Illumina HiSeq-2000

treatment_protocol:
Cells treated with 50nM I-BET151
Cells were seeded at 5000 cells/well in 96well plates, 1ul of I-BET151 was added per well from 100x DMSO stocks (final DMSO concentration: 1%) and cells were incubated for 72hrs.  Cell viability was measured using Cell TiterGlo assay kit (Promega) following manufacturer instructions

value: Biphenotypic B Myelomonocytic Leukemia

tag: chip antibody


title: RNA_seq_MV411_M2_DMSO_rep1

treatment_protocol:
Cells treated with DMSO as control
Cells were seeded at 5000 cells/well in 96well plates, 1ul of I-BET151 was added per well from 100x DMSO stocks (final DMSO concentration: 1%) and cells were incubated for 72hrs.  Cell viability was measured using Cell TiterGlo assay kit (Promega) following manufacturer instructions


title: Temporal_Cortex AD (9371242082_L)

value: MALE

tag: age

value: Subject  22

tag: tissue

value: AD


title: RNA_seq_MV411_M3_500_rep2

treatment_protocol:
Cells treated with 500nM I-BET151
Cells were seeded at 5000 cells/well in 96well plates, 1ul of I-BET151 was added per well from 100x DMSO stocks (final DMSO concentration: 1%) and cells were incubated for 72hrs.  Cell viability was measured using Cell TiterGlo assay kit (Promega) following manufacturer instructions


title: Frontal_Cortex AsymAD (9344744094_K)


title: CMT-207-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

tag: tumor grade

tag: diagnosis

value: Female

tag: neuter status

value: Intact

tag: lymphatic vessel invasion

value: Absent

tag: breed

value: Maltese

value: Positive

value: N

tag: date of death


title: Ets1 null EC, biological rep1

value: 4 Weeks

value: Aorta

value: Ets1-/-; Ets2fl/fl+ lentiviral-egfp


title: RNA_seq_MV411_M3_DMSO_rep2


title: U20S_hCINAP KO

city: Beijing

first: Ruidan

last: Xu

address: Haidian district

institute: Peking University

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq reads were aligned to the hg19 genome assembly using Tophat(version 2.0.12)
The expression level were calculated and normalized by cufflinks(version 2.2.1)
Bisulfite sequencing reads were mapping to the converted hg19 genome using bismark(version 0.7.6)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include fpkm values for each Sample

source_name: U20S_hCINAP KO

extract_protocol:
RNA purity was checked using the kaiaoK5500®Spectrophotometer (Kaiao, Beijing, China).RNA integrity and concentration was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA concentration of library was measured using Qubit® RNA Assay Kit in Qubit® 3.0 to preliminary quantify and then dilute to 1ng/μl. Insert size was assessed using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA), and qualified insert size was accurate quantification using StepOnePlus™ Real-Time PCR System (Library valid concentration＞10 nM).

tag: cell line

tag: genotype/variation

value: hCINAP knockout (-/-)

tag: passage


title: CMT-201-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

value: Complex carcinoma

tag: Sex

tag: er allred score

tag: er status

tag: her2 score (hercep test score)

tag: date of surgery

tag: survival status (until 2018-08-01)

value: loss to follow-up

tag: survival (day)


title: RNA_seq_MV411_M2_5000_rep2

treatment_protocol:
Cells treated with 5000nM I-BET151
Cells were seeded at 5000 cells/well in 96well plates, 1ul of I-BET151 was added per well from 100x DMSO stocks (final DMSO concentration: 1%) and cells were incubated for 72hrs.  Cell viability was measured using Cell TiterGlo assay kit (Promega) following manufacturer instructions

tag: cell type

value: Biphenotypic B Myelomonocytic Leukemia

tag: chip antibody


title: Ets1/2 Wild type EC, biological rep2

description: Gene expression data from EC with wild type Ets1/2

tag: age

tag: tissue

value: Endothelial Cells

tag: genotype

value: Ets1+/+; Ets2+/+ + lentiviral-egfp


title: Ets1 null EC, biological rep2


title: Ets1/2 Wild type EC, biological rep3


title: U20S_hCINAP WT

source_name: U20S_hCINAP WT

value: hCINAP wild-type (WT)


title: Entorhinal_Cortex AD (9371242082_G)

tag: gender

value: MALE

tag: individual

value: Subject  22

tag: disease state

value: AD


title: Ets1/2 Wild type EC, biological rep1


title: Cerebellum AD (9344744089_G)

value: Cerebellum


title: RNA_seq_MV411_M1_50_rep1


title: Temporal_Cortex AD (9371242065_E)


title: CMT-201-normal

description: processed data file: CMT_222S_FPKM.csv

source_name: canine mammary normal tissue

value: mammary normal tissue

tag: tumor grade

tag: diagnosis

value: Female

tag: neuter status

value: Intact

tag: lymphatic vessel invasion

value: Absent

tag: breed

value: Maltese


title: Frontal_Cortex AD (9345344027_K)


title: RNA_seq_MV411_M1_5000_rep1


title: RNA_seq_K562_K3_DMSO_rep3

source_name: CML cells

value: Chronic Myelogenous Leukemia


title: CMT-193-normal

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

value: Simple carcinoma (Anaplastic type)

tag: Sex

value: Present

value: Schnauzer

tag: er allred score

tag: er status

value: Negative

tag: her2 score (hercep test score)

value: N

tag: date of death


title: CMT-193-tumor

description: processed data file: CMT_222S_FPKM.csv

source_name: canine mammary tumor tissue

value: mammary tumor tissue

tag: age

tag: date of surgery

tag: survival status (until 2018-08-01)

tag: survival (day)


title: RNA_seq_K562_K3_500nM_rep3

tag: cell type

tag: chip antibody


title: RNA_seq_K562_K2_50nM_rep2


title: RNA_seq_K562_K2_DMSO_rep2


title: CMT-190-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: tissue

tag: tumor grade

value: Complex carcinoma

value: Neutered

value: Positive


title: RNA_seq_K562_K2_5000nM_rep2


title: CMT-197-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: diagnosis

value: Simple carcinoma (Tubulopapillary type)

tag: neuter status


title: RNA_seq_K562_K1_500nM_rep2


title: RNA_seq_K562_K2_500nM_rep2


title: RNA_seq_K562_K1_50nM_rep1


title: RNA_seq_K562_K1_DMSO_rep1


title: RNA_seq_K562_K1_500nM_rep1


title: CMT-188-tumor

description: processed data file: CMT_222S_FPKM.csv

value: Carcinoma in benign mixed tumor

tag: lymphatic vessel invasion

tag: breed

value: Y


title: Input3_MV411_Control_Input_N_N_NA_rep1

growth_protocol:
Lysates from untreated cells were incubated either with DMSO or with 10uM I-BET121 for 2.5 hours at at 4°C
MV4;11 and K562 cells were grown in RPMI-1640 supplemented with 10% FBS, in a humidified incubator (37 °C, 5% CO2).

extract_protocol:
Dynabeads MyOne Streptavidin T1 (Thermo Scientific #65602) coupled to biotinylated I-BET121 were added to the lysate and incubated for 1 hr at 4°C
Library preparation for Chem-seq was done using the NEBNext® ChIPSeq Library Prep Master Mix Set for Illumina® (NEB) and samples were sequenced in a 50bp single end run on the Illumina HiSeq-2000
K562 and MV4;11 cells were treated with either DMSO or increasing concentration of I-BET151 for 6 hours at 37C.  After treatment, cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and cross-linking was stopped by the addition of 0.125 M glycine.  Cells were then lysed using the SimpleChIP® Enzymatic Chromatin IP Kit (CST #9004) and DNA was digested to mostly mononucleosomes as recommended by the manufacturer
Library preparation of immunoprecipitated DNA was done using the NEBNext® ChIPSeq Library Prep Master Mix Set for Illumina® (NEB) and samples were sequenced in a 50bp single end run on the Illumina HiSeq-2000

treatment_protocol:
NA
Cells were seeded at 5000 cells/well in 96well plates, 1ul of I-BET151 was added per well from 100x DMSO stocks (final DMSO concentration: 1%) and cells were incubated for 72hrs.  Cell viability was measured using Cell TiterGlo assay kit (Promega) following manufacturer instructions

value: Biphenotypic B Myelomonocytic Leukemia


title: BET4_MV411_Chem_BET_151_L_10uM_rep1

description:
BETChem_MV411_Chem_BET_151_L_10uM_RPGC_inputSub.bw
MV411_Chem_BET_151_C_10uM.bed

treatment_protocol:
10uM I-BET121 for 2.5 hours at at 4°C
Cells were seeded at 5000 cells/well in 96well plates, 1ul of I-BET151 was added per well from 100x DMSO stocks (final DMSO concentration: 1%) and cells were incubated for 72hrs.  Cell viability was measured using Cell TiterGlo assay kit (Promega) following manufacturer instructions

value: biotinylated I-BET121


title: CMT-187-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

tag: Sex

value: Female

value: Absent

value: Bichon Frise


title: CMT-184-normal

description: processed data file: CMT_222S_FPKM.csv

value: mammary normal tissue

value: Intact

value: Shih Tzu

tag: er allred score

tag: er status


title: CMT-197-normal

description: processed data file: CMT_222S_FPKM.csv

value: Maltese

tag: her2 score (hercep test score)

tag: date of death


title: Entorhinal_Cortex AsymAD (9031356094_K)

tag: gender

value: FEMALE

tag: age

tag: individual

value: Subject  21

tag: disease state

value: AsymAD


title: Temporal_Cortex control (9031292027_C)

value: MALE

value: Subject  20

value: control


title: Temporal_Cortex AsymAD (9031292037_K)


title: Temporal_Cortex AsymAD (9031356081_K)


title: CMT-188-normal

description: processed data file: CMT_222S_FPKM.csv

value: Carcinoma in benign mixed tumor

value: Neutered

value: Positive

tag: date of surgery

tag: survival status (until 2018-08-01)

tag: survival (day)


title: BET6_MV411_Chem_BET_151_L_10uM_rep2

tag: cell type

value: Biphenotypic B Myelomonocytic Leukemia

tag: chip antibody

value: biotinylated I-BET121


title: BET7_MV411_Chem_BET_DMSO_L_NA_rep2

description:
BETChem_MV411_Chem_BET_DMSO_L_NA_RPGC_inputSub.bw
MV411_Chem_BET_DMSO_C_NA.bed

treatment_protocol:
DMSO for 2.5 hours at at 4°C
Cells were seeded at 5000 cells/well in 96well plates, 1ul of I-BET151 was added per well from 100x DMSO stocks (final DMSO concentration: 1%) and cells were incubated for 72hrs.  Cell viability was measured using Cell TiterGlo assay kit (Promega) following manufacturer instructions


title: Frontal_Cortex control (9031356052_C)

tag: tissue


title: CMT-183-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

tag: tumor grade

value: Not applicable

tag: diagnosis

value: Simple carcinoma (Solid type)

value: Female

tag: neuter status

tag: lymphatic vessel invasion

value: Absent

tag: breed

value: Negative

value: Y


title: Cerebellum control (9031356069_C)

source_name: Cerebellum

value: Cerebellum


title: CMT-184-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

value: Complex carcinoma

tag: Sex

value: Intact

value: Shih Tzu

tag: er allred score

tag: er status

tag: her2 score (hercep test score)


title: BET5_MV411_Chem_BET_DMSO_L_NA_rep1


title: input_DNA_ChIP_MV4;11_IBET_5000_nM_rep2

extract_protocol:
K562 and MV4;11 cells were treated with either DMSO or increasing concentration of I-BET151 for 6 hours at 37C.  After treatment, cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and cross-linking was stopped by the addition of 0.125 M glycine.  Cells were then lysed using the SimpleChIP® Enzymatic Chromatin IP Kit (CST #9004) and DNA was digested to mostly mononucleosomes as recommended by the manufacturer
Library preparation of immunoprecipitated DNA was done using the NEBNext® ChIPSeq Library Prep Master Mix Set for Illumina® (NEB) and samples were sequenced in a 50bp single end run on the Illumina HiSeq-2000
K562 and MV4;11 cells were treated with either DMSO or increasing concentration of I-BET151 for 6 hours at 37C.  After treatment, cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and cross-linking was stopped by the addition of 0.125 M glycine.  Cells were then lysed using the SimpleChIP® Enzymatic Chromatin IP Kit (CST #9004) and DNA was digested to mostly mononucleosomes as recommended by the manufacturer
Library preparation of immunoprecipitated DNA was done using the NEBNext® ChIPSeq Library Prep Master Mix Set for Illumina® (NEB) and samples were sequenced in a 50bp single end run on the Illumina HiSeq-2000

treatment_protocol:
Cells were seeded at 5000 cells/well in 96well plates, 1ul of I-BET151 was added per well from 100x DMSO stocks (final DMSO concentration: 1%) and cells were incubated for 72hrs.  Cell viability was measured using Cell TiterGlo assay kit (Promega) following manufacturer instructions
Cells were seeded at 5000 cells/well in 96well plates, 1ul of I-BET151 was added per well from 100x DMSO stocks (final DMSO concentration: 1%) and cells were incubated for 72hrs.  Cell viability was measured using Cell TiterGlo assay kit (Promega) following manufacturer instructions


title: Entorhinal_Cortex control (9031356102_C)

tag: gender

value: MALE

tag: age

tag: individual

value: Subject  20

tag: disease state

value: control


title: input_DNA_ChIP_MV4;11_IBET_500_nM_rep2

tag: cell type


title: input_DNA_ChIP_MV4;11_DMSO_rep2

tag: chip antibody


title: input_DNA_ChIP_MV4;11_IBET_500_nM_rep1


title: input_DNA_ChIP_MV4;11_IBET_5000_nM_rep1


title: Input4_MV411_Control_Input_N_N_NA_rep2


title: input_DNA_ChIP_K562_IBET_5000_nM_rep2

value: Chronic Myelogenous Leukemia


title: input_DNA_ChIP_K562_IBET_500_nM_rep2


title: input_DNA_ChIP_K562_IBET_5000_nM_rep1


title: CMT-173-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: tissue

value: Benign

value: Simple adenoma

value: Maltese

value: Positive

tag: date of surgery

tag: survival status (until 2018-08-01)

value: loss to follow-up

tag: survival (day)


title: input_DNA_ChIP_K562_IBET_50_nM_rep2


title: Cerebellum control (9031356084_B)

value: Subject  19


title: Entorhinal_Cortex control (9216457022_B)


title: Temporal_Cortex control (9031356074_C)


title: CMT-162-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

tag: tumor grade

tag: diagnosis

value: Benign mixed tumor

value: Female

tag: neuter status

tag: lymphatic vessel invasion

value: Absent


title: input_DNA_ChIP_MV4;11_DMSO_rep1

value: Biphenotypic B Myelomonocytic Leukemia


title: input_DNA_ChIP_K562_IBET_500_nM_rep1


title: CMT-162-normal

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

value: mammary normal tissue

tag: Sex

value: Intact

tag: breed

tag: er allred score


title: Temporal_Cortex control (9031356091_B)

tag: gender

value: MALE

tag: age


title: Frontal_Cortex control (9031356097_B)

tag: individual

tag: disease state


title: Cerebellum AsymAD (9031356072_K)

value: FEMALE

value: Subject  21

value: Cerebellum

value: AsymAD


title: input_DNA_ChIP_MV4;11_IBET_50_nM_rep2

tag: cell type

tag: chip antibody


title: input_DNA_ChIP_K562_IBET_50_nM_rep1

value: Chronic Myelogenous Leukemia


title: CMT-159-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: tissue

value: Simple carcinoma (Tubulopapillary type)

value: Neutered

value: Mixed

tag: er status

tag: her2 score (hercep test score)

tag: date of surgery

value: Y


title: CMT-169-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

tag: tumor grade

tag: diagnosis

value: Complex carcinoma

value: Positive

tag: survival status (until 2018-08-01)

tag: survival (day)


title: BRD4_ChIPSeq_IBET151_5000nM_MV4;11_rep1

description:
BRD4_MV411_ChIP_BRD4_151_C_5000nM_RPGC_inputSub.bw
MV411_ChIP_BRD4_151_C_5000nM.bed

value: BRD4 (Bethyl labs #A301-985A)


title: input_DNA_ChIP_K562_DMSO_rep1


title: BRD4_ChIPSeq_IBET151_5000nM_MV4;11_rep2

value: Biphenotypic B Myelomonocytic Leukemia


title: Entorhinal_Cortex control (9216457027_B)

value: Subject  19

value: control


title: BRD4_ChIPSeq_IBET151_500nM_MV4;11_rep1

description:
BRD4_MV411_ChIP_BRD4_151_C_500nM_RPGC_inputSub.bw
MV411_ChIP_BRD4_151_C_500nM.bed


title: CMT-158-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

value: Benign

value: Benign mixed tumor

tag: Sex

value: Female

tag: neuter status

value: Intact

tag: lymphatic vessel invasion

value: Absent

value: Dachshund


title: BRD4_ChIPSeq_IBET151_50nM_MV4;11_rep1

description:
BRD4_MV411_ChIP_BRD4_151_C_50nM_RPGC_inputSub.bw
MV411_ChIP_BRD4_151_C_50nM.bed


title: BRD4_ChIPSeq_IBET151_50nM_MV4;11_rep2


title: CMT-156-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: age

value: Complex adenoma

tag: breed

value: Shih Tzu

tag: er allred score

value: Negative


title: input_DNA_ChIP_K562_DMSO_rep2

tag: cell type

value: Chronic Myelogenous Leukemia


title: Temporal_Cortex AsymAD (9031356085_I)

tag: gender

value: FEMALE

tag: individual

value: Subject  17

tag: disease state

value: AsymAD


title: Temporal_Cortex control (9344744052_I)

value: Subject  18

tag: tissue


title: BRD4_ChIPSeq_IBET151_500nM_MV4;11_rep2

value: Biphenotypic B Myelomonocytic Leukemia

tag: chip antibody

value: BRD4 (Bethyl labs #A301-985A)


title: Entorhinal_Cortex AsymAD (9216457002_I)


title: Frontal_Cortex AsymAD (9031356077_K)

value: Subject  21


title: Entorhinal_Cortex AsymAD (9031356088_I)


title: BRD4_ChIPSeq_DMSO_MV4;11_rep2

description:
BRD4_MV411_ChIP_BRD4_DMSO_C_NA_RPGC_inputSub.bw
MV411_ChIP_BRD4_DMSO_C_NA.bed


title: Cerebellum AsymAD (9031356073_I)

value: Cerebellum


title: RNA_seq_MV411_M1_500_rep1


title: BRD4_ChIPSeq_IBET151_5000nM_K562_rep1

description:
BRD4_K562_ChIP_BRD4_151_C_5000nM_RPGC_inputSub.bw
K562_ChIP_BRD4_151_C_5000nM.bed


title: CMT-153-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

tag: tumor grade

value: Complex carcinoma

value: Yorkshire Terrier

tag: er status

value: Positive

tag: her2 score (hercep test score)

tag: date of surgery

value: N

tag: date of death


title: BRD4_ChIPSeq_IBET151_5000nM_K562_rep2


title: CMT-157-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

value: Benign

tag: diagnosis

value: Simple adenoma

tag: Sex

value: Female

value: Intact

value: Absent

value: Mixed

tag: survival status (until 2018-08-01)

value: Y

tag: survival (day)


title: BRD4_ChIPSeq_DMSO_MV4;11_rep1


title: BRD4_ChIPSeq_IBET151_50nM_K562_rep2

description:
BRD4_K562_ChIP_BRD4_151_C_50nM_RPGC_inputSub.bw
K562_ChIP_BRD4_151_C_50nM.bed

value: Chronic Myelogenous Leukemia


title: BRD4_ChIPSeq_IBET151_500nM_K562_rep2

description:
BRD4_K562_ChIP_BRD4_151_C_500nM_RPGC_inputSub.bw
K562_ChIP_BRD4_151_C_500nM.bed


title: CMT-149-normal

description: processed data file: CMT_222S_FPKM.csv

value: mammary normal tissue

tag: age

tag: neuter status

tag: lymphatic vessel invasion

tag: breed

value: Maltese

tag: er allred score

value: loss to follow-up


title: CMT-149-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: tissue


title: Frontal_Cortex AsymAD (9031356076_I)

tag: gender

value: FEMALE

tag: individual

value: Subject  17

tag: disease state

value: AsymAD


title: BRD4_ChIPSeq_IBET151_50nM_K562_rep1

tag: cell type

tag: chip antibody

value: BRD4 (Bethyl labs #A301-985A)


title: BRD4_ChIPSeq_DMSO_K562_rep2

description:
BRD4_K562_ChIP_BRD4_DMSO_C_NA_RPGC_inputSub.bw
K562_ChIP_BRD4_DMSO_C_NA.bed


title: CMT-148-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

tag: tumor grade

value: Simple carcinoma (Tubulopapillary type)

tag: er status

value: Negative

tag: her2 score (hercep test score)

tag: date of surgery

tag: date of death


title: Entorhinal_Cortex AsymAD (9031356102_K)

value: MALE

value: Subject  16


title: BRD4_ChIPSeq_DMSO_K562_rep1


title: BRD3_ChIPSeq_IBET151_5000nM_MV4;11_rep1

description:
BRD3_MV411_ChIP_BRD3_151_C_5000nM_RPGC_inputSub.bw
MV411_ChIP_BRD3_151_C_5000nM.bed

value: Biphenotypic B Myelomonocytic Leukemia

value: BRD3 (Bethyl Labs #A302-368A)


title: BRD3_ChIPSeq_IBET151_500nM_MV4;11_rep2

description:
BRD3_MV411_ChIP_BRD3_151_C_500nM_RPGC_inputSub.bw
MV411_ChIP_BRD3_151_C_500nM.bed


title: BRD3_ChIPSeq_IBET151_5000nM_MV4;11_rep2


title: BRD3_ChIPSeq_IBET151_500nM_MV4;11_rep1


title: CMT-136-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

value: Benign

tag: diagnosis

value: Simple adenoma

tag: Sex

value: Female

value: Intact

value: Absent

value: Yorkshire Terrier

value: Positive

tag: survival status (until 2018-08-01)

tag: survival (day)


title: BRD3_ChIPSeq_IBET151_50nM_MV4;11_rep1

description:
BRD3_MV411_ChIP_BRD3_151_C_50nM_RPGC_inputSub.bw
MV411_ChIP_BRD3_151_C_50nM.bed


title: Cerebellum AsymAD (9031356069_K)

tag: age

value: Cerebellum


title: input_DNA_ChIP_MV4;11_IBET_50_nM_rep1


title: BRD3_ChIPSeq_IBET151_50nM_MV4;11_rep2


title: CMT-142-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: tissue

value: Complex carcinoma

tag: neuter status

tag: lymphatic vessel invasion

tag: breed

value: Mixed

tag: er allred score

value: loss to follow-up


title: CMT-147-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue


title: Frontal_Cortex AsymAD (9031356052_K)

tag: gender

tag: individual

tag: disease state

value: AsymAD


title: BRD3_ChIPSeq_DMSO_MV4;11_rep2

description:
BRD3_MV411_ChIP_BRD3_DMSO_C_NA_RPGC_inputSub.bw
MV411_ChIP_BRD3_DMSO_C_NA.bed

tag: cell type

tag: chip antibody


title: Cerebellum control (9031356072_A)

value: FEMALE

value: Subject  15

value: control


title: Temporal_Cortex control (9031292037_A)


title: BRD3_ChIPSeq_DMSO_MV4;11_rep1

value: Biphenotypic B Myelomonocytic Leukemia

value: BRD3 (Bethyl Labs #A302-368A)


title: CMT-128-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: tumor grade

value: Benign

value: Complex adenoma

tag: er status

tag: her2 score (hercep test score)

tag: date of surgery

value: Y


title: Frontal_Cortex control (9031356077_A)


title: Entorhinal_Cortex control (9031356094_A)


title: BRD3_ChIPSeq_IBET151_5000nM_K562_rep1

description:
BRD3_K562_ChIP_BRD3_151_C_5000nM_RPGC_inputSub.bw
K562_ChIP_BRD3_151_C_5000nM.bed

value: Chronic Myelogenous Leukemia


title: CMT-124-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

tag: diagnosis

tag: Sex

value: Female

value: Intact

value: Absent

value: Yorkshire Terrier

tag: survival status (until 2018-08-01)


title: BRD3_ChIPSeq_IBET151_500nM_K562_rep2

description:
BRD3_K562_ChIP_BRD3_151_C_500nM_RPGC_inputSub.bw
K562_ChIP_BRD3_151_C_500nM.bed


title: BRD3_ChIPSeq_IBET151_50nM_K562_rep1

description:
BRD3_K562_ChIP_BRD3_151_C_50nM_RPGC_inputSub.bw
K562_ChIP_BRD3_151_C_50nM.bed


title: CMT-129-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: tissue

tag: age

value: Spindle cell carcinoma (Malignant myoepithelioma)

tag: neuter status

value: Neutered

value: Shih Tzu

value: Negative

tag: survival (day)


title: BRD3_ChIPSeq_IBET151_500nM_K562_rep1


title: BRD3_ChIPSeq_DMSO_K562_rep2

description:
BRD3_K562_ChIP_BRD3_DMSO_C_NA_RPGC_inputSub.bw
K562_ChIP_BRD3_DMSO_C_NA.bed


title: BRD3_ChIPSeq_IBET151_50nM_K562_rep2


title: Temporal_Cortex control (9031356081_A)

tag: gender

value: FEMALE


title: CMT-121-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

value: Complex carcinoma

tag: lymphatic vessel invasion

tag: breed

value: Mixed

tag: er allred score

value: Positive

value: N

tag: date of death


title: CMT-121-normal

description: processed data file: CMT_222S_FPKM.csv

value: mammary normal tissue

tag: tumor grade


title: BRD2_ChIPSeq_IBET151_5000nM_MV4;11_rep2

description:
BRD2_MV411_ChIP_BRD2_151_C_5000nM_RPGC_inputSub.bw
MV411_ChIP_BRD2_151_C_5000nM.bed

tag: cell type

value: Biphenotypic B Myelomonocytic Leukemia

tag: chip antibody

value: BRD2 (Bethyl Labs #A302-583A)


title: BRD3_ChIPSeq_DMSO_K562_rep1

value: Chronic Myelogenous Leukemia

value: BRD3 (Bethyl Labs #A302-368A)


title: BRD2_ChIPSeq_IBET151_5000nM_MV4;11_rep1


title: CMT-118-tumor

description: processed data file: CMT_222S_FPKM.csv

value: Female

value: Intact

value: Absent

value: Schnauzer

tag: er status

tag: her2 score (hercep test score)

tag: date of surgery

value: Y


title: CMT-112-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

tag: diagnosis

value: Fibrosarcoma

tag: Sex

value: Maltese

value: Not applicable


title: BRD2_ChIPSeq_IBET151_50nM_MV4;11_rep2

description:
BRD2_MV411_ChIP_BRD2_151_C_50nM_RPGC_inputSub.bw
MV411_ChIP_BRD2_151_C_50nM.bed


title: BRD2_ChIPSeq_IBET151_500nM_MV4;11_rep1

description:
BRD2_MV411_ChIP_BRD2_151_C_500nM_RPGC_inputSub.bw
MV411_ChIP_BRD2_151_C_500nM.bed


title: BRD2_ChIPSeq_IBET151_500nM_MV4;11_rep2


title: Temporal_Cortex AD (9031292027_F)

value: FEMALE

tag: age

tag: individual

value: Subject  14

tag: tissue

tag: disease state

value: AD


title: BRD2_ChIPSeq_IBET151_50nM_MV4;11_rep1


title: Temporal_Cortex AsymAD (9031292027_K)

tag: gender

value: MALE

value: Subject  16

value: AsymAD


title: Cerebellum AD (9031356069_F)

value: Cerebellum


title: BRD2_ChIPSeq_DMSO_MV4;11_rep2

description:
BRD2_MV411_ChIP_BRD2_DMSO_C_NA_RPGC_inputSub.bw
MV411_ChIP_BRD2_DMSO_C_NA.bed

value: Biphenotypic B Myelomonocytic Leukemia

value: BRD2 (Bethyl Labs #A302-583A)


title: BRD2_ChIPSeq_DMSO_MV4;11_rep1


title: CMT-111-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

value: Carcinoma in benign mixed tumor

value: Female

tag: neuter status

value: Neutered

tag: lymphatic vessel invasion

tag: breed

value: Shih Tzu

value: Positive

tag: survival status (until 2018-08-01)

tag: survival (day)


title: BRD2_ChIPSeq_IBET151_5000nM_K562_rep2

description:
BRD2_K562_ChIP_BRD2_151_C_5000nM_RPGC_inputSub.bw
K562_ChIP_BRD2_151_C_5000nM.bed

tag: cell type

value: Chronic Myelogenous Leukemia

tag: chip antibody


title: BRD2_ChIPSeq_IBET151_50nM_K562_rep2

description:
BRD2_K562_ChIP_BRD2_151_C_50nM_RPGC_inputSub.bw
K562_ChIP_BRD2_151_C_50nM.bed


title: BRD4_ChIPSeq_IBET151_500nM_K562_rep1

value: BRD4 (Bethyl labs #A301-985A)


title: CMT-107-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: tumor grade

value: Intact

value: Absent

value: Maltese

tag: er allred score

tag: er status

tag: her2 score (hercep test score)

value: Y


title: BRD2_ChIPSeq_IBET151_500nM_K562_rep2

description:
BRD2_K562_ChIP_BRD2_151_C_500nM_RPGC_inputSub.bw
K562_ChIP_BRD2_151_C_500nM.bed


title: BRD2_ChIPSeq_IBET151_5000nM_K562_rep1


title: Temporal_Cortex AD (9031292037_E)

value: FEMALE

value: Subject  13

value: AD


title: CMT-169-normal

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

value: mammary normal tissue

tag: diagnosis

value: Complex carcinoma

tag: Sex

value: Mixed

tag: date of surgery


title: Frontal_Cortex control (9216457020_H)

tag: age

tag: individual

value: Subject  15

tag: tissue

tag: disease state

value: control


title: Temporal_Cortex AD (9031356081_E)

tag: gender


title: CMT-106-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

value: Benign

value: Simple adenoma

value: Female

tag: neuter status

tag: lymphatic vessel invasion

tag: breed

value: Yorkshire Terrier

tag: survival status (until 2018-08-01)


title: Cerebellum AD (9031356072_E)

value: Cerebellum


title: BRD2_ChIPSeq_IBET151_50nM_K562_rep1

tag: cell type

value: Chronic Myelogenous Leukemia

tag: chip antibody

value: BRD2 (Bethyl Labs #A302-583A)


title: Frontal_Cortex AD (9031356077_E)


title: CMT-105-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: tumor grade

value: Simple carcinoma (Solid type)

value: Neutered

value: Present

tag: er allred score

tag: er status

value: Negative

value: N

tag: date of death

tag: survival (day)


title: BRD2_ChIPSeq_DMSO_K562_rep2

description:
BRD2_K562_ChIP_BRD2_DMSO_C_NA_RPGC_inputSub.bw
K562_ChIP_BRD2_DMSO_C_NA.bed


title: CMT-109-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

tag: diagnosis

value: Simple carcinoma (Tubulopapillary type)

tag: Sex

value: Intact

value: Absent

value: Positive

tag: her2 score (hercep test score)

tag: date of surgery

value: loss to follow-up


title: BRD2_ChIPSeq_IBET151_500nM_K562_rep1


title: CMT-107-normal

description: processed data file: CMT_222S_FPKM.csv

tag: tissue

value: mammary normal tissue

tag: age

value: Carcinoma in benign mixed tumor

value: Maltese

value: Y


title: Temporal_Cortex AD (9031356085_E)

tag: gender

value: FEMALE

tag: individual

value: Subject  12

tag: disease state

value: AD


title: CMT-105-normal

description: processed data file: CMT_222S_FPKM.csv

value: Simple carcinoma (Solid type)

value: Female

tag: neuter status

tag: lymphatic vessel invasion

tag: breed

value: Mixed

tag: survival status (until 2018-08-01)


title: Entorhinal_Cortex AD (9216457002_E)


title: Entorhinal_Cortex AD (9031356088_E)


title: CMT-103-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

tag: tumor grade

value: Benign

value: Simple adenoma

tag: er allred score

tag: er status


title: Cerebellum AD (9031356073_E)

value: Cerebellum


title: BRD2_ChIPSeq_DMSO_K562_rep1

tag: cell type

value: Chronic Myelogenous Leukemia

tag: chip antibody

value: BRD2 (Bethyl Labs #A302-583A)


title: CMT-103-normal

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

tag: diagnosis

tag: Sex

value: Intact

value: Absent

value: Positive

tag: survival (day)


title: Nppb KO mut4_LV

description:
CRISPR deletion in exon 2 of Nppb
Nppb-KO-RNA-seq-counts.xlsx

data_processing:
RNA-seq: reads were mapped to mm10 build of the mouse transcriptome using STAR (Dobin et al., 2013).
RNA-seq: Differential expression analysis was performed using the DESeq2 package based on a model using the negative binomial distribution (Love et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: Nppb-KO-RNA-seq-counts.xlsx (Excel file with raw and normalized (DESeq2) count data per gene & differential expression analysis).

source_name: HOM

extract_protocol:
Total RNA was isolated from left ventricular tissue of Nppb KO mutants and wildtype littermates using Tri Reagent (Sigma Aldrich) according to the manufacturer’s protocol (Sigma Aldrich) and further purified using Nucleospin RNA Clean-up Kit with DnaseI treatment (Macherey-Nagel)
cDNA was prepared with the Truseq Stranded Total RNA Library Preparation Kit (Illumina, Part# 15031048 Rev. E). Total RNA (900 ng) was purified and sheared into small fragments followed by cDNA synthesis and ligation of the adapter. The quality and size distribution of the cDNA library templates were validated with Agilent DNA 1000 on 2100 Bioanalyzer (Agilent Technologies). cDNA samples were pooled per lane of paired-end 125 bp sequencing on an Illumina HiSeq 2500 instrument.

tag: strain

value: FVB

tag: age

value: 8-12 weeks

tag: tissue

value: Left ventricle

tag: genotype/variation

value: Nppb KO


title: CMT-102-tumor

description: processed data file: CMT_222S_FPKM.csv

value: Benign mixed tumor

tag: neuter status

value: Maltese

tag: her2 score (hercep test score)

tag: date of surgery

value: Y


title: Nppb KO mut3_LV


title: CMT-100-tumor

description: processed data file: CMT_222S_FPKM.csv

value: Carcinoma in benign mixed tumor

value: Female

tag: lymphatic vessel invasion

tag: breed

value: Cocker Spaniel

tag: survival status (until 2018-08-01)


title: Low Fat Diet, Mouse 4

city: New York

first: Akanksha

last: Verma

state: New York

address: 1300, York Avenue

department: Department of Physiology and Biophysics

institute: Weill Cornell Medical College

hyb_protocol: Samples were hybridized to the Affymetrix Genechip Mouse Gene 2.0.ST Arrays (Santa Clara, CA) following the manufacturer’s instructions at the Genomics Resources Core Facility at Weill Cornell Medicine.

scan_protocol: GeneChip arrays were scanned by GeneChip Scanner 3000 7G (GC30007G) according the manufacturer’s instructions. Affymetrix GeneChip Command Console Software was used for image acquisition.

data_processing: Raw image data were background corrected, normalized and summarized into probeset expression values using the Robust Multichip Average (RMA) algorithm within GeneSpring 12.6 Software (Agilent Technologies). Log2 transformed expression values for within-array replicate probes were condensed by their average. Differential gene expression analyses were carried out using limma package in R 3.5.0 (R Foundation for Statistical Computing, Vienna, Austria). Genes with false discovery rate < 0.05 and fold change > 2 in between-group comparisons were considered significantly differentially expressed.

source_name: Peri-prostatic fat

label_protocol: Samples were labeled and hybridized to the Affymetrix Genechip Mouse Gene 2.0.ST Arrays (Santa Clara, CA) following the manufacturer’s instructions at the Genomics Resources Core Facility at Weill Cornell Medicine.

growth_protocol: All animals were housed in the Weill Cornell Medicine vivarium under standard temperature controlled conditions with a 12-hour light-dark cycle. Animals had ad libitum access to their respective diets (low fat or high fat).

extract_protocol: Mice were euthanized by CO2 asphyxiation, periprostatic fat was harvested and snap frozen in liquid nitrogen prior to storage at -80C. Total RNA was extracted from frozen tissue using trizol reagent and the RNAeasy Mini Kit (Qiagen). RNA concentration (NanoDrop) and quality (Bioanalyzer) were measured. Only samples with RNA Integrity Number (RIN) >7 were used for microarray analysis.

treatment_protocol: Male C57BL/6J mice were obtained from The Jackson Laboratory and fed low fat diet  (10 kcal% fat, 12450Bi; Research Diets), n=4 or high fat diet (60 kcal% fat, D12492i), n=5 beginning at 6 weeks of age. The mice were continued on these diets for a total of 12 weeks before being sacrificed by CO2 asphyxiation at 18 weeks of age. Periprostatic fat was then harvested, snap frozen in liquid nitrogen, and stored at -80C until total RNA extraction.

value: Peri-prostatic fat

value: 18 weeks

tag: diet

value: Low fat diet, 10 kcal% fat


title: CMT-099-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

tag: tumor grade

value: Simple carcinoma (Tubulopapillary type)

tag: er allred score

tag: er status


title: Nppb KO mut2_LV


title: Low Fat Diet, Mouse 3


title: CMT-097-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

tag: diagnosis

value: Neutered

value: Absent

value: N

tag: date of death


title: High Fat Diet, Mouse 5

tag: strain

value: High fat diet, 60 kcal% fat


title: WT4_LV

description: Nppb-KO-RNA-seq-counts.xlsx

source_name: WT

value: FVB

tag: age

value: 8-12 weeks

value: Left ventricle

value: Wild type


title: Frontal_Cortex AsymAD (9344744089_F)

tag: gender

value: FEMALE

tag: individual

value: Subject  11

tag: tissue

tag: disease state

value: AsymAD


title: Frontal_Cortex AD (9031356076_E)

value: Subject  12

value: AD


title: Low Fat Diet, Mouse 1

value: Peri-prostatic fat

value: 18 weeks


title: High Fat Diet, Mouse 3


title: Entorhinal_Cortex AsymAD (9345344031_A)


title: Temporal_Cortex AsymAD (9345344009_A)


title: High Fat Diet, Mouse 2


title: Low Fat Diet, Mouse 2

value: Low fat diet, 10 kcal% fat


title: Frontal_Cortex AD (9031356076_F)

value: MALE

value: Subject  10


title: Cerebellum AD (9031356073_F)

value: Cerebellum


title: CMT-092-tumor

description: processed data file: CMT_222S_FPKM.csv

value: mammary tumor tissue

value: Benign

value: Simple adenoma

tag: Sex

value: Female

tag: neuter status

value: Intact

value: Absent

value: Schnauzer

value: Positive

tag: her2 score (hercep test score)

tag: date of surgery

value: Y

tag: survival (day)


title: High Fat Diet, Mouse 4

tag: diet

value: High fat diet, 60 kcal% fat


title: Nppb KO mut1_LV

value: FVB

value: 8-12 weeks

value: Left ventricle

tag: genotype/variation

value: Nppb KO


title: WT3_LV

description: Nppb-KO-RNA-seq-counts.xlsx

value: Wild type


title: CMT-096-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: tumor grade

value: Simple carcinoma (Tubulopapillary type)

value: Neutered

tag: lymphatic vessel invasion

tag: breed

value: Yorkshire Terrier

tag: er allred score

tag: er status

tag: survival status (until 2018-08-01)


title: CMT-091-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

value: mammary tumor tissue

value: Benign

tag: age

tag: diagnosis

value: Complex adenoma

value: Maltese


title: WT1_LV

description: Nppb-KO-RNA-seq-counts.xlsx

tag: strain

tag: tissue


title: CMT-091-normal

description: processed data file: CMT_222S_FPKM.csv

value: mammary normal tissue

tag: Sex

value: Female

tag: neuter status

value: Intact

value: Absent