title: 11FTreg08

tag: donor id

tag: Sex

tag: donor group


title: 11FTreg07

status: Public on Nov 17 2020

type: SRA

city: Berkeley

first: Allon

last: Wagner

state: CA

address: 378 Stanley Hall

country: USA

institute: UC Berkeley

library_source: transcriptomic

data_processing:
Reads were pseuoaligned with Kallisto v0.46.0 to the Ensembl v96 human transcripome
Transcript TPMs were aggregated and summed for gene-level analysis, and then log2-transformed; non-protein-coding transcripts were excluded
Genome_build: GRCh38.96
Supplementary_files_format_and_content: linear-scale count matrix in csv format

molecule: total RNA

organism: Homo sapiens

source_name: iTreg

extract_protocol:
PBMCs were isolated from peripheral blood and Treg cells were single sorted into 96-well plates by FACS using CD4+CD25hiCD127lo/neg antibodies. For adipose tissue, we first performed collagenase digestion. Next, the lymphocytes were isolated from the sample by Ficoll gradient and centrifugation (as done with PBMC isolation) in a ratio of 9 mL of sample to 4 mL of Ficoll. The lymphocyte layer was removed and washed. The Treg cells were then single sorted by FACS using CD4+CD25hiCD127lo/neg antibodies.
Illumina TruSeq Stranded mRNA kit was used for library prep, and sequenced with a 2 × 100 bp paired-end protocol on the HiSeq 2000 Sequencing System (Illumina).

tag: tissue

value: Fat

tag: age at procedure

tag: date of procedure

tag: year diagnosed

tag: height (cm)

tag: weight (kg)

tag: bmi

value: F


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_A12_AD002

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

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

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J P56 Mouse Brain

growth_protocol: All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee. The knock-in mouse line, R26R-CAG-loxp-stop-loxp-Sun1-sfGFP-Myc (INTACT) was used for most experiments4 and they were maintained on a C57BL/6J background. 42-49 day old adult male and female INTACT mice were used for the retrograde labeling experiment.

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq215 (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.). The snmC-Seq2 libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

treatment_protocol: To label neurons projecting to regions of interest, injections of rAAV2-retro-Cre (produced by Salk Vector Core or Vigene, 2x10^12 to 1x10^13 viral genomes/ml, produced with capsid from Addgene plasmid #81070 packaging pAAV-EF1a-Cre from Addgene plasmid #55636) were made into both hemispheres of the INTACT mice. Animals were anesthetized with either ketamine/xylazine or isoflurane, placed in a stereotaxic frame, and 0.1 to 0.5 microliters of AAV was injected by pressure into stereotaxic coordinates corresponding to the desired projection target.

tag: strain

tag: age

value: brain

tag: source

value: MOp

tag: target

value: TH

tag: gender

value: female


title: 11FTreg06


title: singleCell_spheroid_plate2_D15_S168

city: Stanford

first: Rachel

last: Agoglia

address: 371 Jane Stanford Way

institute: Stanford University

data_processing:
Remove sequencing adapters with SeqPrep version 1.2
Map reads to GRCh38 and PanTro5 with STAR version 2.5.1b
Remove duplicate reads withSamtools version 0.1.19 with randomized discarding of duplicates
Remove reads which exhibit mapping bias with WASP (Hornet)
Count allele specific and total reads
Genome_build: Human: GRCh38; Chimpanzee: PanTro5
Supplementary_files_format_and_content: Counts matrix with total and allele-specific raw read counts (rows are genes, there are 3 columns per sample: total, human and chimpanzee read counts); matrix text files are provided for samples mapped on both the human and chimpanzee genomes; text files with sample meta data are also included for each data set

molecule: polyA RNA

organism:
Pan troglodytes
Homo sapiens

source_name: iPSC-derived cortical spheroid

extract_protocol:
Qiagen Rneasy Mini Kit with on-column DNAse digestion (Qiagen)
Illumina TruSeq Stranded mRNA library prep kit (Illumina)

tag: cell type

value: iPSC-derived cortical spheroid

tag: cell line

tag: differentiation id

tag: age (days)


title: singleCell_spheroid_plate2_D14_S167


title: 11FTreg04

tag: donor id

tag: Sex

tag: donor group


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_A12_AD001

tag: tissue

value: male


title: 11FTreg05

tag: age at procedure

tag: date of procedure

tag: year diagnosed


title: 11FTreg03

tag: height (cm)

tag: weight (kg)

tag: bmi


title: 11FTreg02


title: singleCell_spheroid_plate2_D13_S166


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_A11_AD008

tag: strain

tag: age

tag: source

value: SSp


title: 11BTreg96

value: Blood


title: 11BTreg95


title: 11FTreg01


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_A11_AD006

tag: target

tag: gender


title: 11BTreg94


title: singleCell_spheroid_plate2_D12_S165

tag: cell type

tag: cell line

tag: differentiation id


title: singleCell_spheroid_plate2_D11_S164

tag: age (days)


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_A11_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_A11_AD002


title: 11BTreg93

tag: donor id

tag: Sex

tag: donor group


title: singleCell_spheroid_plate2_D10_S163


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_A10_AD004

tag: tissue


title: 11BTreg92

tag: age at procedure

tag: date of procedure

tag: year diagnosed


title: singleCell_spheroid_plate2_C9_S139


title: 11BTreg91

tag: height (cm)

tag: weight (kg)

tag: bmi


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_H9_AD006

tag: strain

tag: age

tag: source

value: VIS

value: STR


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_H9_AD004

tag: target

tag: gender


title: singleCell_spheroid_plate2_C8_S138

tag: cell type

tag: cell line

tag: differentiation id


title: singleCell_spheroid_plate2_C7_S137

tag: age (days)


title: 11BTreg90

tag: donor id

tag: Sex

tag: donor group


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_H9_AD002

tag: tissue


title: 11BTreg89

tag: age at procedure

tag: date of procedure

tag: year diagnosed


title: singleCell_spheroid_plate2_C6_S136


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_H9_AD001


title: singleCell_spheroid_plate2_C5_S135


title: 11BTreg88

tag: height (cm)

tag: weight (kg)

tag: bmi


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_H7_AD006

tag: strain

tag: age

tag: source


title: 11BTreg87


title: singleCell_spheroid_plate2_C4_S134

tag: cell type


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_H7_AD002

tag: target

tag: gender


title: 11BTreg86


title: tumor tissue from patient 038

type: RNA

city: Shenzhen

first: Renling

last: Li

address: 3002 Lantian Road, Pingshan District, Shenzhen Guangdong, China

country: China

institute: Shenzhen Technology University

hyb_protocol: 15µg fragmented cRNA, with control oligo B2 and eukaryotic hybridization controls (bioB, bioC, bioD, cre) was hybridized to each GeneChip array at 45 °C for 16 hours (Affymetrix GeneChipHybridization Oven 640) according to manufacturer’s instructions.

scan_protocol: The GeneChip arrays were washed, and then stained with streptavidin phycoerythrinonan (SAPE) with Affymetrix Fluidics Station 450 followed by scanning with the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The hybridization data were analyzed using Affymetrix GeneChip Command Console Software (AGCC) and normalized using the Robust Multiarray Average (RMA) method.

label: biotin

source_name: ESCC patient

label_protocol: 100ng of total RNA was used for cDNA synthesis, and produce biotin-tagged cRNA with GeneChip IVT Labeling kit (Affymetrix).

extract_protocol: Total RNAs were extracted from tissues using Trizol reagent (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions, and digested with DNase I at 37 °C for 15 min to remove any contaminating DNA. The RNA was cleaned up with RNeasy Kit (Qiagen, Hilden, Germany) and the quantities and qualities were determined by spectrophometer, 1% formaldehyde denaturing gel electrophoresis and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). The samples with both bright bands of ribosomal 28S to18S RNA in a ratio >1.5:1 and RIN > 7 were used for microarray analysis.

treatment_protocol: tissues were collected within 10 minutes after surgical resection and immersed in RNAlater Stabilization Solution (AM7021, Ambion)  and stored at -80°C until use.

value: tumor tissue

tag: Stage

value: IIIB

value: Male

tag: smoking history

value: 50 years

tag: drinking history

value: Seldom

tag: disease history

value: Hypertension, coronary heart disease, cerebral  infarction

tag: family history of cancer

value: ESCC


title: tumor tissue from patient 036

tag: tissue

value: 40 years

value: cancer


title: tumor tissue from patient 133

value: 20 years


title: tumor tissue from patient 037

value: Female

value: Cerebral  infarction


title: singleCell_spheroid_plate2_C3_S133

value: iPSC-derived cortical spheroid

tag: cell line

tag: differentiation id

tag: age (days)


title: tumor tissue from patient 035

value: Lymphoma


title: 11BTreg85

tag: donor id

value: Blood

tag: age at procedure

tag: date of procedure

tag: year diagnosed

tag: height (cm)

tag: weight (kg)

tag: Sex

value: F

tag: donor group


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_H7_AD001

tag: strain

tag: age

value: brain

tag: source

value: VIS

tag: target

value: STR

tag: gender

value: male


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_H6_AD006

tag: tissue

value: female


title: 11BTreg83

tag: bmi


title: singleCell_spheroid_plate2_C2_S132

tag: cell type

tag: cell line

tag: differentiation id


title: singleCell_spheroid_plate2_C22_S152

tag: age (days)


title: tumor tissue from patient 031

value: tumor tissue

tag: Stage

value: IIIA

value: Male

tag: smoking history

tag: drinking history

value: Seldom

tag: disease history

tag: family history of cancer

value: Gastric cancer


title: 11BTreg82

tag: donor id

tag: age at procedure

tag: date of procedure

tag: year diagnosed

tag: height (cm)

tag: weight (kg)

tag: Sex

tag: donor group


title: singleCell_spheroid_plate2_C21_S151

tag: cell type


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_H6_AD002

tag: strain

tag: age

tag: tissue

tag: source

tag: target

tag: gender


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_H6_AD004


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_H6_AD001


title: 11BTreg81

tag: bmi


title: singleCell_spheroid_plate2_C20_S150

tag: cell line

tag: differentiation id

tag: age (days)


title: singleCell_spheroid_plate2_C1_S131


title: 11BTreg80

tag: donor id

tag: age at procedure

tag: date of procedure


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_H5_AD006


title: tumor tissue from patient 125

tag: Stage

value: II

tag: smoking history

tag: drinking history

tag: disease history

tag: family history of cancer


title: tumor tissue from patient 032

value: IIIB

tag: age

value: 40 years


title: singleCell_spheroid_plate2_C23_S153

tag: cell type

value: iPSC-derived cortical spheroid


title: 11BTreg79

tag: tissue

tag: year diagnosed

tag: height (cm)

tag: weight (kg)

tag: Sex

tag: donor group


title: 11BTreg78

tag: bmi


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_H5_AD004

tag: strain

tag: source

tag: target

tag: gender


title: singleCell_spheroid_plate2_C17_S147

tag: cell line

tag: differentiation id

tag: age (days)


title: tumor tissue from patient 124

tag: Stage

value: Female

tag: smoking history

tag: drinking history

tag: disease history

tag: family history of cancer


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_H5_AD002

tag: age

tag: tissue


title: 11BTreg84

tag: donor id

value: Blood

tag: age at procedure

tag: date of procedure

tag: year diagnosed

tag: height (cm)

tag: weight (kg)

tag: Sex


title: tumor tissue from patient 121

tag: gender


title: 11BTreg76

tag: bmi

value: F

tag: donor group


title: singleCell_spheroid_plate2_C16_S146

tag: cell type

tag: cell line

tag: differentiation id

tag: age (days)


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_H4_AD006

tag: strain

value: brain

tag: source

tag: target


title: tumor tissue from patient 033

tag: tissue

tag: Stage

tag: age

tag: smoking history

value: 30 years

tag: drinking history

tag: disease history

value: Cerebral  infarction

tag: family history of cancer


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_H5_AD001

value: VIS

value: STR

tag: gender

value: male


title: tumor tissue from patient 126

value: tumor tissue


title: tumor tissue from patient 122

value: Male


title: tumor tissue from patient 024

value: IIA

value: ESCC


title: tumor tissue from patient 027

value: IIB

value: 20 years

value: Colorectal cancer


title: tumor tissue from patient 026

value: 40 years

value: Hypertension


title: tumor tissue from patient 025

value: Female

value: Breast cancer


title: singleCell_spheroid_plate2_C15_S145

value: iPSC-derived cortical spheroid


title: 11BTreg74

tag: donor id

value: Blood

tag: age at procedure

tag: date of procedure

tag: year diagnosed

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: Sex

value: F


title: singleCell_spheroid_plate2_C18_S148

tag: cell type

tag: cell line

tag: differentiation id

tag: age (days)


title: singleCell_spheroid_plate2_C14_S144


title: tumor tissue from patient 023

tag: tissue

tag: Stage

tag: age

tag: smoking history

value: 30 years


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_H4_AD001

tag: strain

value: brain

tag: source

value: VIS

tag: target

value: STR

tag: gender


title: 11BTreg77

tag: donor id

tag: age at procedure

tag: date of procedure

tag: year diagnosed

tag: donor group


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_H4_AD004

value: female


title: 11BTreg72

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: Sex


title: singleCell_spheroid_plate2_C11_S141

tag: cell type

tag: cell line

tag: differentiation id

tag: age (days)


title: 11BTreg71

tag: tissue


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_H3_AD006

tag: strain

tag: age

tag: source


title: 11BTreg75

tag: donor id


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_H3_AD004

tag: target

tag: gender


title: tumor tissue from patient 021

value: tumor tissue

tag: Stage

value: IIA

value: Male

tag: smoking history

value: 50 years

tag: drinking history

value: Seldom

tag: disease history

tag: family history of cancer


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_H3_AD002

value: male


title: 11BTreg70

tag: age at procedure

tag: date of procedure

tag: year diagnosed

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: Sex

tag: donor group


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_H3_AD001

tag: strain

tag: age

tag: tissue

tag: source


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_H2_AD006

tag: target

tag: gender


title: singleCell_spheroid_plate2_C10_S140

tag: cell type

tag: cell line

tag: differentiation id

tag: age (days)


title: tumor tissue from patient 112

tag: Stage

value: IA

tag: smoking history

tag: drinking history

tag: disease history

value: Hypertension

tag: family history of cancer

value: ESCC


title: tumor tissue from patient 113

value: I


title: tumor tissue from patient 115


title: 11BTreg69

tag: donor id

value: Blood

tag: age at procedure

tag: date of procedure

tag: year diagnosed

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: Sex


title: singleCell_spheroid_plate2_B9_S116

tag: cell type

value: iPSC-derived cortical spheroid


title: tumor tissue from patient 016

tag: tissue

value: IB

tag: age

tag: gender

value: 36 years

value: liver cancer


title: tumor tissue from patient 111

tag: Stage

value: Female


title: singleCell_spheroid_plate2_C13_S143

tag: cell line

tag: differentiation id

tag: age (days)


title: 11BTreg73

value: F

tag: donor group


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_H2_AD004

tag: strain

value: brain

tag: source

value: VIS

tag: target

value: STR

value: female


title: singleCell_spheroid_plate2_B8_S115


title: singleCell_spheroid_plate2_C19_S149


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_H2_AD002


title: singleCell_spheroid_plate2_C12_S142


title: 11BTreg67

tag: donor id

tag: age at procedure

tag: date of procedure

tag: year diagnosed


title: tumor tissue from patient 015

value: tumor tissue

tag: smoking history

tag: drinking history

tag: disease history

tag: family history of cancer

value: lung cancer


title: singleCell_spheroid_plate2_B7_S114

tag: cell type


title: 11BTreg66

tag: tissue

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: Sex


title: singleCell_spheroid_plate2_B6_S113

tag: cell line

tag: differentiation id

tag: age (days)


title: tumor tissue from patient 014

tag: Stage

tag: age

tag: gender

value: Male

value: 20 years


title: tumor tissue from patient 013

value: 30 years

value: Seldom


title: 11BTreg64

tag: donor id

value: Blood

tag: age at procedure

tag: date of procedure

tag: year diagnosed

tag: donor group


title: 11BTreg68


title: singleCell_spheroid_plate2_B5_S112

tag: cell type

value: iPSC-derived cortical spheroid


title: 11BTreg63

tag: tissue


title: tumor tissue from patient 012

value: IB

tag: smoking history

tag: drinking history

tag: disease history

tag: family history of cancer

value: ESCC


title: singleCell_spheroid_plate2_B3_S110

tag: cell line


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_H1_AD002

tag: strain

tag: source

tag: target

value: male


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_H1_AD004

tag: age


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_H1_AD001

tag: gender


title: 11BTreg62

tag: donor id

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: Sex


title: singleCell_spheroid_plate2_B23_S130

tag: cell type

tag: differentiation id

tag: age (days)


title: singleCell_spheroid_plate2_B2_S109


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_H12_AD006

tag: tissue


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_H2_AD001


title: singleCell_spheroid_plate2_B22_S129


title: 11BTreg60

tag: age at procedure

tag: date of procedure

tag: year diagnosed

tag: donor group


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_H1_AD006

tag: strain

tag: source


title: 11BTreg65


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_H12_AD004

tag: age

tag: target


title: singleCell_spheroid_plate2_B4_S111

tag: cell line


title: 11BTreg59

tag: donor id

tag: height (cm)


title: singleCell_spheroid_plate2_B21_S128


title: paratumor tissue from patient 038

value: paratumor tissue

tag: Stage

value: IIIB

tag: gender

tag: smoking history

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tag: disease history

tag: family history of cancer


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_F7_AD001

tag: strain

tag: source

tag: target


title: 11BTreg07

tag: age at procedure

tag: date of procedure

tag: year diagnosed

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: Sex


title: normal tissue from patient 012

tag: tissue

tag: Stage

tag: age

tag: gender


title: singleCell_spheroid_plate1_P17_S241

tag: cell type

value: iPSC-derived cortical spheroid

tag: cell line

tag: differentiation id

tag: age (days)


title: 11BTreg06

tag: donor id

tag: donor group


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_F6_AD002

tag: strain

tag: source

tag: target


title: singleCell_spheroid_plate1_P16_S240


title: singleCell_spheroid_plate1_P15_S239


title: 11BTreg05

tag: age at procedure

tag: date of procedure

tag: year diagnosed

tag: height (cm)


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_F5_AD006

tag: tissue


title: 11BTreg04

tag: weight (kg)

tag: bmi

tag: Sex


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_F5_AD004

tag: age

tag: gender


title: 11BTreg03


title: singleCell_spheroid_plate1_P13_S237

tag: cell type

tag: cell line

tag: differentiation id


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_F5_AD002


title: TamR4 KD

city: Odense

first: Henrik

last: Ditzel

state: Denmark

address: J.B. Winsløwsvej 25

country: Denmark

institute: University of Southern Denmark

description: Gene expression data in tamoxifen-resistant cell line (TamR4) following MCM3 gene knockdown.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Partek Genomic suite version 6.0 (PGS 6.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Tamoxifen-resistant MCF7 cell line (TamR4) transfected with MCM3 specific siRNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Tamoxifen-sensitive MCF7 cells were grown in DMEM medium containing 1% FBS, 6ng/ml insulin and 2.5mM glutamax. The tamoxifen-resistant cell lines (TamR1, TamR4 and TamR7) were grown in similar medium containing 10e6mM tamoxifen.

extract_protocol: Cells were harvested from culture plate and total RNA was extracted using Trizol RNA extraction method.

treatment_protocol: Cells grown under standard culture conditions were harvested at 80% confluence. Cells (2 x 10e6) were transfected with a combination of two or a single small interfering RNAs (siRNAs) (300nM) in 100µl nucleofector solution v (Cell Line Nucleofector® Kit V, Amaxa) using electroporation P20 (nucleofector® II, Amaxa) at room temperature according to manufacturer’s protocol. MCM3-specific siRNAs were obtained from Qiagen: SI02664879, SI00037009, while Control siRNA (siControl) was obtained from Sigma; MISSION® siRNA Universal Negative Control: sic001. Transfected cells were cultured in standard culture medium. Gene knockdown efficiency was evaluated at 48 hours using RT-qPCR.

tag: tamoxifen sensitivity

value: Resistant

tag: sirna


title: 11BTreg02

tag: donor id

tag: donor group


title: singleCell_spheroid_plate1_P12_S236

tag: age (days)


title: TamR4 Ctrl

description: Gene expression data in tamoxifen-resistant cell line (TamR4) following control siRNA transfection.

source_name: Tamoxifen-resistant MCF7 cell line (TamR4) transfected with control siRNA

value: Control


title: TamR7 Ctrl

description: Gene expression data in tamoxifen-resistant cell line (TamR7) following control siRNA transfection.

source_name: Tamoxifen-resistant MCF7 cell line (TamR7) transfected with control siRNA


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_F3_AD002

tag: strain

value: brain

tag: source

tag: target


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_F5_AD001

tag: tissue

value: VIS


title: 11BTreg01

tag: age at procedure

tag: date of procedure

tag: year diagnosed

tag: height (cm)

tag: weight (kg)


title: singleCell_spheroid_plate1_P11_S235

tag: cell type


title: singleCell_spheroid_plate1_P10_S234

tag: cell line


title: 10FTreg96

value: Fat

tag: bmi

tag: Sex

value: M


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_F3_AD001

tag: age

value: STR

tag: gender


title: 10FTreg95

tag: donor id

tag: donor group


title: TamR7 KD

description: Gene expression data in tamoxifen-resistant cell line (TamR7) following MCM3 gene knockdown.

source_name: Tamoxifen-resistant MCF7 cell line (TamR7) transfected with MCM3 specific siRNA

tag: tamoxifen sensitivity

tag: sirna


title: singleCell_spheroid_plate1_O9_S209

tag: differentiation id

tag: age (days)


title: 10FTreg94

tag: tissue

tag: age at procedure


title: singleCell_spheroid_plate1_P14_S238


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_F1_AD004

tag: strain

tag: source

tag: target


title: 10FTreg93

tag: date of procedure

tag: year diagnosed

tag: height (cm)

tag: weight (kg)


title: singleCell_spheroid_plate1_O7_S207

tag: cell type

tag: cell line


title: singleCell_spheroid_plate1_O6_S206


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_F11_AD004

tag: age

tag: gender


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_F1_AD006


title: singleCell_spheroid_plate1_O8_S208


title: MCF7 Ctrl

description: Gene expression data of tamoxifen-sensitive MCF7 cell line following control siRNA transfection.

source_name: Tamoxifen-sensitive MCF7 breast cancer cell line transfected with control siRNA

tag: tamoxifen sensitivity

value: Sensitive


title: healthy [GSM02052029]

city: Basel

first: Lukas

middle: Walter Andreas

last: Roth

address: Postfach

country: Switzerland

institute: Novartis Institiues for Biomedical Research

description: Comparison between lesional and non-lesional skin samples from patients and healthy holunteers.

hyb_protocol: An amount of biotin-labelled cDNA of approximately 3.41 μg for each sample was hybridized for approximately 16 to 18 hours at 45°C on an array. The array was washed and stained using Affymetrix Fluidics Workstation 450.

scan_protocol: The array was scanned using an Affymetrix Scanner 3000 and the image was processed using AGCC software

data_processing: The data were analyzed with GeneSpring 14.9 importing .cel files and using RMA normalization

source_name: Total RNA extracted from OCT block sections

label_protocol: Target preparation was performed with a starting amount of 50 ng of total RNA using the Nugen Ovation RNA Amplification System V2, the Ovation WB reagent and the FL-Ovation cDNA Biotin Module.

growth_protocol: OCT embedded skin blocks

extract_protocol: Qiagen RNeasy mini kit

treatment_protocol: no treatment

value: skin

tag: patient

tag: Sex


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_F1_AD001


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_F12_AD001


title: MCF7 KD

description: Gene expression data of tamoxifen-sensitive MCF7 cell line following MCM3 gene knockdown.

source_name: Tamoxifen-sensitive MCF7 breast cancer cell line transfected with MCM3 specific siRNA

tag: sirna


title: 10FTreg92

tag: donor id

tag: tissue

tag: bmi

tag: donor group


title: TamR1 Ctrl

description: Gene expression data in tamoxifen-resistant cell line (TamR1) following control siRNA transfection.

source_name: Tamoxifen-resistant MCF7 cell line (TamR1) transfected with control siRNA


title: lesional [GSM02052028]


title: lesional [GSM02052027]


title: TamR1 KD

description: Gene expression data in tamoxifen-resistant cell line (TamR1) following MCM3 gene knockdown.

source_name: Tamoxifen-resistant MCF7 cell line (TamR1) transfected with MCM3 specific siRNA


title: lesional [GSM02052024]


title: lesional [GSM02052026]


title: 10FTreg91

tag: age at procedure


title: singleCell_spheroid_plate1_O5_S205

tag: differentiation id

tag: age (days)


title: 10FTreg90

tag: date of procedure

tag: year diagnosed

tag: height (cm)


title: singleCell_spheroid_plate1_O4_S204

tag: cell type

tag: cell line


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_F10_AD006

tag: strain

tag: age

tag: source

tag: target

tag: gender


title: singleCell_spheroid_plate1_O3_S203


title: lesional [GSM02052022]

tag: patient

tag: Sex


title: 10FTreg89

tag: donor id

tag: tissue

tag: weight (kg)

tag: bmi


title: 10FTreg88

tag: age at procedure

tag: donor group


title: 10FTreg87

tag: date of procedure

tag: year diagnosed


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_E9_AD006


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_E9_AD004


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_F10_AD004


title: singleCell_spheroid_plate1_O24_S224

tag: cell type

tag: differentiation id

tag: age (days)


title: singleCell_spheroid_plate1_O2_S202

tag: cell line


title: 10FTreg85

tag: height (cm)


title: lesional [GSM02052020]

tag: age


title: singleCell_spheroid_plate1_O23_S223


title: 10FTreg86


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_E9_AD002

tag: strain

tag: source

tag: target

tag: gender


title: singleCell_spheroid_plate1_O22_S222


title: lesional [GSM02052021]

tag: tissue

tag: patient

tag: Sex


title: healthy [GSM02052018]


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_E9_AD001


title: 10FTreg84

tag: donor id

tag: age at procedure

tag: weight (kg)

tag: bmi


title: singleCell_spheroid_plate1_O21_S221

tag: cell type


title: healthy [GSM02052019]


title: 10FTreg83

tag: date of procedure

tag: year diagnosed

tag: donor group


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_E7_AD006


title: singleCell_spheroid_plate1_O20_S220

tag: cell line

tag: differentiation id

tag: age (days)


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_F10_AD001

tag: strain

tag: age

tag: source


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_E7_AD004

tag: tissue

tag: target

tag: gender


title: healthy [GSM02052016]

tag: patient

tag: Sex


title: healthy [GSM02052017]


title: non-lesional [GSM02052013]


title: lesional [GSM02052014]


title: singleCell_spheroid_plate1_O1_S201


title: healthy [GSM02052015]


title: 10FTreg82

tag: donor id

tag: age at procedure

tag: height (cm)

tag: weight (kg)


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_E7_AD002


title: 10FTreg81

tag: date of procedure

tag: year diagnosed

tag: bmi


title: lesional [GSM02052011]


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_E6_AD006


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_E6_AD004


title: 10FTreg80

tag: donor group


title: 10FTreg79


title: singleCell_spheroid_plate1_O15_S215

tag: cell type

tag: cell line

tag: differentiation id

tag: age (days)


title: non-lesional [GSM02052010]

tag: tissue

tag: age


title: 10FTreg77


title: singleCell_spheroid_plate1_O17_S217


title: singleCell_spheroid_plate1_O18_S218


title: 10FTreg78


title: lesional [GSM02052007]


title: singleCell_spheroid_plate1_O19_S219


title: 10FTreg76


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_E6_AD001

tag: strain

tag: source

tag: target

tag: gender


title: singleCell_spheroid_plate1_O13_S213


title: non-lesional [GSM02052002]

tag: patient

tag: Sex


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_E5_AD006


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_E7_AD001


title: lesional [GSM02052009]


title: lesional [GSM02052005]


title: lesional [GSM02052004]


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_E5_AD004


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_E6_AD002


title: singleCell_spheroid_plate1_O12_S212


title: 10FTreg74

tag: donor id

tag: age at procedure

tag: height (cm)

tag: weight (kg)


title: singleCell_spheroid_plate1_O14_S214


title: singleCell_spheroid_plate1_O16_S216


title: singleCell_spheroid_plate1_O11_S211


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_E2_AD001


title: singleCell_spheroid_plate1_O10_S210


title: 10FTreg72

tag: date of procedure

tag: year diagnosed

tag: bmi

tag: donor group


title: lesional [GSM02051999]


title: 10FTreg75


title: singleCell_spheroid_plate1_N9_S185

tag: cell type

tag: cell line

tag: differentiation id

tag: age (days)


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_E1_AD004

tag: strain

tag: age

tag: tissue

tag: source


title: singleCell_spheroid_plate1_N8_S184


title: 10FTreg70

tag: Sex


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_E1_AD006

tag: target

tag: gender


title: non-lesional [GSM02051996]

tag: patient


title: lesional [GSM02051997]


title: lesional [GSM02052001]


title: lesional [GSM02051995]


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_E1_AD002


title: 10FTreg67

tag: donor id

tag: age at procedure

tag: height (cm)

tag: weight (kg)


title: singleCell_spheroid_plate1_N5_S181


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_E5_AD001


title: singleCell_spheroid_plate1_N7_S183


title: singleCell_spheroid_plate1_N6_S182


title: 10FTreg66

tag: date of procedure

tag: year diagnosed

tag: bmi

tag: donor group


title: 10FTreg69


title: 10FTreg68


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_E1_AD001


title: 10FTreg71


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_E12_AD004


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_E11_AD006


title: 10FTreg65


title: singleCell_spheroid_plate1_N3_S179

tag: cell type

tag: cell line

tag: differentiation id

tag: age (days)


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_E11_AD004

tag: strain

tag: age

tag: tissue

tag: source


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_E12_AD006

tag: target

tag: gender


title: non-lesional [GSM02051998]

tag: patient

tag: Sex


title: 10FTreg64

tag: donor id

tag: age at procedure

tag: height (cm)

tag: weight (kg)


title: singleCell_spheroid_plate1_N4_S180


title: 10FTreg63

tag: date of procedure

tag: year diagnosed

tag: bmi

tag: donor group


title: singleCell_spheroid_plate1_N24_S200

tag: cell type

tag: cell line

tag: differentiation id

tag: age (days)


title: non-lesional [GSM02051992]

tag: tissue

tag: age


title: lesional [GSM02051993]


title: healthy [GSM02051991]


title: non-lesional [GSM02051994]


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_E10_AD006

tag: strain

tag: source

tag: target

tag: gender


title: singleCell_spheroid_plate1_N23_S199


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_E10_AD004


title: 10FTreg62

tag: donor id

tag: age at procedure

tag: Sex


title: 276_control_3

city: Jacksonville

first: Yan

middle: W.

last: Asmann

state: FL

address: 4500 San Pablo Road South

institute: Mayo Clinic

description:
200514010030_L
replicate 3

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Standard Illumina protocol

source_name: GBM, untreated

label_protocol: Standard Illumina protocol

growth_protocol: Cells were maintained in DMEM/F12 media supplemented with 2% GEM21 Neuroplex, 1% antibiotic/antimycotic, 20 ng/mL human EGF and 20 ng/mL FGF.

extract_protocol: Total RNA was extracted using Trizol and RNeasy mini kit according to manufacturer's instructions

treatment_protocol: For CSF stimulation, cells were cultured on laminin-coated plates. 24 hours prior to experimentation, cells were maintained in media without EGF and FGF. CSF was utilized at a 1:100 dilution

tag: disease state

value: GBM

value: GBM cell line 276

tag: treatment

value: untreated

tag: subtype

value: mesenchymal


title: healthy [GSM02051990]

tag: patient

value: male


title: singleCell_spheroid_plate1_N22_S198

tag: cell type


title: 10FTreg61

tag: date of procedure

tag: year diagnosed

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: donor group


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_E10_AD002

tag: strain

tag: age

tag: tissue

tag: source


title: 276_control_2

description:
200514010030_J
replicate 2

tag: cell line

tag: gender

value: female


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_E10_AD001

tag: target


title: 10FTreg60

tag: donor id

tag: age at procedure

tag: Sex


title: 10FTreg59


title: singleCell_spheroid_plate1_N21_S197

tag: cell type

tag: differentiation id

tag: age (days)


title: singleCell_spheroid_plate1_N2_S178


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_D9_AD006


title: singleCell_spheroid_plate1_N20_S196


title: 276_control_1

description:
200514010030_H
replicate 1

tag: disease state

tag: treatment

tag: subtype


title: singleCell_spheroid_plate1_N1_S177


title: 276_slit_3

description:
200514010030_F
replicate 3

source_name: GBM, slit

value: slit


title: 10FTreg58

tag: date of procedure

tag: year diagnosed

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: donor group


title: 276_slit_2

description:
200514010030_D
replicate 2

tag: cell line

tag: gender


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_D9_AD004

tag: strain

tag: age

tag: tissue

tag: source

tag: target


title: singleCell_spheroid_plate1_N19_S195

tag: cell type

value: iPSC-derived cortical spheroid

tag: differentiation id

tag: age (days)


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_D9_AD001


title: 276_slit_1

description:
200514010030_B
replicate 1

tag: disease state

tag: treatment

tag: subtype


title: 10FTreg56

tag: donor id

tag: age at procedure

tag: date of procedure

tag: year diagnosed

tag: height (cm)

tag: Sex


title: singleCell_spheroid_plate1_N17_S193

tag: cell line


title: 10FTreg54

tag: weight (kg)

tag: bmi

tag: donor group


title: singleCell_spheroid_plate1_N16_S192


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_D7_AD004

tag: strain

tag: age

tag: tissue

tag: source

tag: target

tag: gender


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_D7_AD001


title: 10FTreg53


title: 276_GBM_-2

description:
200514010030_I
replicate 2

source_name: GBM, Cancer CSF

tag: disease state

tag: treatment

value: Cancer CSF

tag: subtype


title: 276_NPH_3

description:
200514010030_E
replicate 3

source_name: GBM, nonCancer CSF

value: nonCancer CSF


title: 276_GBM_3

description:
200514010030_K
replicate 3


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_D6_AD006

value: brain


title: 10FTreg57

source_name: iTreg

tag: donor id

tag: age at procedure

tag: date of procedure


title: 10FTreg52

tag: year diagnosed

tag: height (cm)

tag: Sex


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_D7_AD006

source_name: C57BL/6J P56 Mouse Brain

value: VIS


title: 10FTreg51

value: Fat

tag: weight (kg)

tag: bmi


title: singleCell_spheroid_plate1_N14_S190

source_name: iPSC-derived cortical spheroid

tag: cell type

tag: cell line

tag: differentiation id

tag: age (days)


title: singleCell_spheroid_plate1_N18_S194


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_D6_AD004

tag: strain

tag: age

tag: tissue

tag: source

tag: target


title: 10FTreg55

tag: donor id

value: M

tag: donor group


title: singleCell_spheroid_plate1_N13_S189


title: 10FTreg50

tag: age at procedure

tag: date of procedure


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_D5_AD006

value: STR

tag: gender


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_D6_AD001


title: singleCell_spheroid_plate1_N12_S188


title: 10FTreg49

tag: year diagnosed

tag: height (cm)

tag: Sex


title: singleCell_spheroid_plate1_N11_S187

tag: cell type


title: singleCell_spheroid_plate1_N15_S191

tag: cell line


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_D5_AD004


title: 276_NPH_1

description:
200514010030_A
replicate 1

tag: disease state

tag: treatment

tag: subtype


title: 10FTreg48

tag: weight (kg)

tag: bmi


title: singleCell_spheroid_plate1_N10_S186

tag: differentiation id

tag: age (days)


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_D5_AD002

tag: strain

tag: age

tag: tissue

tag: source

tag: target


title: singleCell_spheroid_plate1_M9_S161


title: 10FTreg47

tag: donor id

tag: age at procedure

tag: date of procedure

tag: year diagnosed

tag: donor group


title: 10FTreg46

tag: height (cm)

tag: Sex


title: singleCell_spheroid_plate1_M8_S160

tag: cell type

tag: cell line


title: 612_control_2

description:
200162410039_J
replicate 2

tag: disease state

value: GBM cell line 612

tag: treatment

tag: gender

tag: subtype

value: proneural


title: 276_GBM_1

description:
200514010030_G
replicate 1

value: GBM


title: 612_control_3

description:
200162410039_L
replicate 3


title: 276_NPH_2

description:
200514010030_C
replicate 2

value: GBM cell line 276


title: 612_slit_3

description:
200162410039_F
replicate 3


title: 612_slit_1

description:
200162410039_B
replicate 1


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_D4_AD001

tag: strain

tag: age


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_D5_AD001

tag: tissue

tag: source


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_D1_AD004

tag: target


title: 612_control_1

description:
200162410039_H
replicate 1

value: untreated


title: 10FTreg45

tag: donor id

tag: age at procedure

tag: weight (kg)

tag: bmi


title: singleCell_spheroid_plate1_M7_S159

tag: differentiation id

tag: age (days)


title: singleCell_spheroid_plate1_M6_S158

tag: cell type


title: 10FTreg44

tag: date of procedure

tag: year diagnosed

tag: height (cm)

tag: Sex

tag: donor group


title: 10FTreg43


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_D12_AD004

tag: strain

tag: gender


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_D11_AD001

tag: age

tag: tissue


title: singleCell_spheroid_plate1_M5_S157

tag: cell line


title: 612_slit_2

description:
200162410039_D
replicate 2

tag: disease state

tag: treatment

tag: subtype


title: singleCell_spheroid_plate1_M4_S156


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_D10_AD006

tag: source

tag: target


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_D10_AD004


title: 10FTreg42

tag: donor id

tag: age at procedure

tag: weight (kg)

tag: bmi


title: 10FTreg41

tag: date of procedure

tag: year diagnosed

tag: height (cm)


title: 10FTreg40

tag: Sex

tag: donor group


title: singleCell_spheroid_plate1_M2_S154

tag: cell type

tag: differentiation id

tag: age (days)


title: singleCell_spheroid_plate1_M24_S176

tag: cell line


title: 10FTreg39

tag: tissue


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_D10_AD001

tag: strain

tag: age

tag: gender


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_C9_AD006

tag: source

tag: target


title: 18MMPN input

city: London

first: Kurt

last: Berger

state: Ontario

address: 800 Commissioner's Road E.

country: Canada

institute: UWO

description: ChIP-seq results

data_processing:
Aligned with Bowtie2
Peaks called with macs2
Annotated with Homer
Tracks generated with DeepTools
Genome_build: hg38
Supplementary_files_format_and_content: includes peak data and gene coordinate data used for further conclusions

source_name: Bone Marrow

growth_protocol: human Mononuclear cells extracted from bone marrow samples.

extract_protocol:
Mononuclear cells were extracted by standard Ficol procedures
Standard Illumina HiSeq Paired End library prep kit
Pooled all sample in 1:1:2 ratios for H3K4Me1:H3K4me3:H3K27Me3

treatment_protocol: these were untreated samples.

value: Mononuclear cells

tag: disease state

value: dysplastic chronic myelomonocytic leukemia

tag: genotype

value: RAS  pathway mutant

tag: antibody


title: 18MMPN H3K27ME3

description: ChIP-seq results


title: 612_NPH_3

description:
200162410039_E
replicate 3

tag: treatment

value: male

tag: subtype


title: 18MMPN H3K04ME3

description: ChIP-seq results


title: 10FTreg73

tag: donor id

tag: age at procedure

tag: date of procedure

tag: year diagnosed

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: Sex


title: singleCell_spheroid_plate1_M23_S175

tag: cell type

value: iPSC-derived cortical spheroid

tag: cell line

tag: differentiation id

tag: age (days)


title: 612_GBM_3

description:
200162410039_K
replicate 3

tag: disease state

value: Cancer CSF

tag: gender


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_C9_AD004

tag: strain

tag: age

tag: tissue

tag: source

tag: target

value: female


title: 10FTreg38

tag: donor id

tag: age at procedure

tag: date of procedure

tag: donor group


title: singleCell_spheroid_plate1_M22_S174


title: 18MMPN H3K04ME1

description: ChIP-seq results

tag: genotype

tag: antibody


title: 612_GBM_1

description:
200162410039_G
replicate 1

tag: treatment

tag: subtype


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_C9_AD002

value: brain


title: 10FTreg37

tag: year diagnosed

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: Sex


title: 13MMPN input

description: ChIP-seq results

tag: cell type

tag: disease state


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_C9_AD001

tag: strain

tag: age

tag: tissue

tag: source

value: VIS

tag: gender


title: 10FTreg36

tag: donor id

value: Fat

tag: age at procedure

tag: date of procedure

tag: donor group


title: 612_GBM_2

description:
200162410039_I
replicate 2

tag: cell line

tag: treatment

tag: subtype


title: 612_NPH_1

description:
200162410039_A
replicate 1

value: nonCancer CSF


title: 13MMPN H3K27ME3

description: ChIP-seq results

tag: genotype

tag: antibody


title: singleCell_spheroid_plate1_M21_S173

tag: differentiation id

tag: age (days)


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_C7_AD006

tag: target

value: STR


title: singleCell_spheroid_plate1_M20_S172

tag: cell type


title: 13MMPN H3K04ME3

description: ChIP-seq results

tag: disease state


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_C7_AD004

tag: strain

tag: age

tag: tissue


title: 10FTreg34

tag: donor id

tag: year diagnosed

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: Sex

value: M


title: 10FTreg35

tag: age at procedure

tag: date of procedure

tag: donor group


title: 10FTreg33


title: 13MMPN H3K04ME1

description: ChIP-seq results

tag: genotype

tag: antibody


title: singleCell_spheroid_plate1_M1_S153

tag: cell line

tag: differentiation id

tag: age (days)


title: singleCell_spheroid_plate1_M19_S171

tag: cell type


title: singleCell_spheroid_plate1_M3_S155


title: 12FMPN input

description: ChIP-seq results

tag: disease state


title: 10FTreg32

tag: tissue


title: 12FMPN H3K27ME3

description: ChIP-seq results


title: singleCell_spheroid_plate1_M18_S170


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_C7_AD001

tag: strain

tag: age

tag: source

tag: target

tag: gender


title: 10FTreg31

tag: donor id

tag: year diagnosed

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: Sex


title: singleCell_spheroid_plate1_M17_S169

tag: cell line


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_C6_AD006


title: 12FMPN H3K04ME3

description: ChIP-seq results

tag: genotype

tag: antibody


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_C6_AD004


title: singleCell_spheroid_plate1_M16_S168

tag: cell type

tag: differentiation id

tag: age (days)


title: 10FTreg30

tag: tissue

tag: age at procedure

tag: date of procedure

tag: donor group


title: 12FMPN H3K04ME1

description: ChIP-seq results

tag: disease state


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_C6_AD001

tag: strain

tag: age

tag: source

tag: target

tag: gender


title: 10FTreg29

tag: donor id

tag: year diagnosed

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: Sex


title: singleCell_spheroid_plate1_M15_S167

tag: cell type

tag: cell line

tag: differentiation id

tag: age (days)


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_C7_AD002

tag: tissue


title: 11MMPN input

description: ChIP-seq results

tag: disease state

tag: genotype

value: RAS wild type

tag: antibody


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_C12_AD006

tag: strain

tag: age

tag: source


title: 11MMPN H3K27ME3

description: ChIP-seq results


title: 10FTreg27

tag: donor id

tag: age at procedure

tag: date of procedure

tag: donor group


title: 612_NPH_2

description:
200162410039_C
replicate 2

value: GBM

value: GBM cell line 612

tag: treatment

tag: gender

tag: subtype

value: proneural


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_C12_AD004

tag: target


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_C12_AD001


title: singleCell_spheroid_plate1_M13_S165

tag: cell type

tag: cell line

tag: differentiation id


title: singleCell_spheroid_plate1_M12_S164

tag: age (days)


title: 11MMPN H3K04ME3

description: ChIP-seq results

value: Mononuclear cells

tag: disease state

tag: genotype


title: 10FTreg26

tag: tissue

tag: year diagnosed

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: Sex


title: 11MMPN H3K04ME1

description: ChIP-seq results

value: dysplastic chronic myelomonocytic leukemia

tag: antibody


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_C11_AD002

tag: strain

tag: age

tag: source


title: 10FTreg25

tag: donor id

tag: age at procedure

tag: date of procedure

tag: donor group


title: singleCell_spheroid_plate1_M11_S163

tag: cell type

tag: cell line

tag: differentiation id

tag: age (days)


title: 07FMDY input

description: ChIP-seq results

tag: disease state

tag: genotype


title: 07FMDY H3K27ME3

description: ChIP-seq results


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_C11_AD001

tag: tissue

tag: target

tag: gender


title: singleCell_spheroid_plate1_L9_S137


title: 10FTreg23

tag: year diagnosed

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: Sex


title: 07FMDY H3K04ME3

description: ChIP-seq results

tag: antibody


title: 10FTreg24

tag: donor id

tag: age at procedure

tag: date of procedure


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_C10_AD004

tag: strain

tag: age

tag: source


title: singleCell_spheroid_plate1_M10_S162

tag: cell type

tag: cell line

tag: differentiation id

tag: age (days)


title: 10FTreg28

tag: tissue

tag: donor group


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_C10_AD006

tag: target

tag: gender


title: singleCell_spheroid_plate1_M14_S166


title: singleCell_spheroid_plate1_L8_S136


title: 10FTreg22

tag: year diagnosed

tag: height (cm)

tag: weight (kg)

tag: bmi


title: 07FMDY H3K04ME1

description: ChIP-seq results

tag: disease state

tag: genotype

tag: antibody


title: singleCell_spheroid_plate1_L7_S135


title: 06MMDN input

description: ChIP-seq results


title: 10FTreg21

tag: donor id

tag: age at procedure

tag: date of procedure

tag: Sex


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_C10_AD001

tag: strain

tag: age

tag: source


title: 10FTreg20

tag: tissue

tag: donor group


title: 10FTreg19


title: singleCell_spheroid_plate1_L5_S133

tag: cell type

tag: cell line

tag: differentiation id

tag: age (days)


title: 06MMDN H3K04ME3

description: ChIP-seq results


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_B9_AD006

tag: target

tag: gender


title: 06MMDN H3K27ME3

description: ChIP-seq results

tag: disease state

tag: genotype


title: singleCell_spheroid_plate1_L6_S134


title: 10FTreg18

tag: donor id

tag: year diagnosed

tag: height (cm)

tag: weight (kg)

tag: bmi


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_B9_AD004

tag: strain

tag: age


title: singleCell_spheroid_plate1_L4_S132


title: singleCell_spheroid_plate1_L3_S131


title: 10FTreg17

tag: tissue

tag: age at procedure

tag: date of procedure

tag: Sex


title: 06MMDN H3K04ME1

description: ChIP-seq results

tag: cell type

tag: antibody


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_B9_AD002

tag: source

tag: target


title: 10FTreg16

tag: donor group


title: G477-WT_WGBS

city: Santiago de Compostela

first: Carmen

last: Rivas

address: Avda Barcelona

department: CIMUS

country: Spain

institute: Universidad de Santiago de Compostela

description: According to manufacturer's protocol

data_processing:
Raw reads from whole-genome bisulfite sequencing were aligned using BWA (version 0.6.1). Low-quality sequence at the 3′ ends were trimmed. After alignment, we filtered duplicated or poorly mapping reads (>2% mismatches or aberrant insert size). Samtools (version 0.1.18) in mpileup mode was applied to call CpG methylation. We used igvtools to generate the tdf files.
Genome_build: hg19
Supplementary_files_format_and_content: tdf

source_name: brain tumor derived cell line

growth_protocol: Tumor-derived cell lines were maintained in NeuroCult NS-A proliferation media (StemCell Technologies) supplemented with bFGF (10ng/mL) (StemCell Technologies), rhEGF (20 ng/mL) (StemCell Technologies) and heparin (0.0002%) (StemCell Technologies) on plates coated in poly-L-ornithine (0.01%) (Sigma) and laminin (0.01 mg/mL) (Sigma).

extract_protocol:
DNA was extracted from cell lines using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) following manufacturer instructions.
Whole-genome sequencing libraries were generated from 700 to 1000 ng of genomic DNA spiked with 0.1% (w/w) unmethylated λ DNA (Promega) previously fragmented to 300–400 bp peak sizes using the Covaris focused-ultrasonicator E210. Fragment size was controlled on a Bioanalyzer DNA 1000 Chip (Agilent) and the KAPA High Throughput Library Preparation Kit (KAPA Biosystems) was applied. End repair of the generated dsDNA with 3′ or 5′ overhangs, adenylation of 3′ ends, adaptor ligation, and clean-up steps were carried out as per KAPA Biosystems’ recommendations. The cleaned-up ligation product was then analyzed on a Bioanalyzer High Sensitivity DNA Chip (Agilent) and quantified by PicoGreen (Life Technologies). Samples were then bisulfite converted using the Epitect Fast DNA Bisulfite Kit (Qiagen) according to the manufacturer’s protocol. Bisulfite-converted DNA was quantified using OliGreen (Life Technologies) and, based on quantity, amplified by 9–12 cycles of PCR using the Kapa Hifi Uracil + DNA polymerase (KAPA Biosystems) according to the manufacturer’s protocol. The amplified libraries were purified using Ampure XP Beads (Beckman Coulter), validated on Bioanalyzer High Sensitivity DNA Chips, and quantified by PicoGreen.

tag: cell line

tag: genotype

value: H3 wild-type


title: singleCell_spheroid_plate1_L2_S130

tag: differentiation id

tag: age (days)


title: singleCell_spheroid_plate1_L24_S152


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_B9_AD001

tag: gender

value: male


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_B7_AD004


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_C10_AD002


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_B7_AD006


title: singleCell_spheroid_plate1_L23_S151

value: iPSC-derived cortical spheroid


title: singleCell_spheroid_plate1_L22_S150


title: 10FTreg15

tag: donor id

tag: year diagnosed

tag: height (cm)

tag: weight (kg)

tag: bmi


title: 10FTreg14

tag: tissue

tag: age at procedure

tag: date of procedure


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_B7_AD002

tag: strain

tag: age


title: HSJ019-K27M1_Input

description: According to manufacturer's protocol

data_processing:
Raw ChIP sequencing reads were aligned using BWA version 0.7.17 with default parameters. After alignment, we sorted the bam files using samtools, then igvtools was used to generate wig files (igvtools count -w 25 -e 200). Finally, bigWig files were obtained using wigToBigWig.
Genome_build: hg19 and dm6 for human and drosophila data, respectively
Supplementary_files_format_and_content: bigWig

source_name: brain tumor derived cell line & S2 cells (spike in)

growth_protocol: Tumor-derived cell lines were maintained in NeuroCult NS-A proliferation media (StemCell Technologies) supplemented with bFGF (10ng/mL) (StemCell Technologies), rhEGF (20 ng/mL) (StemCell Technologies) and heparin (0.0002%) (StemCell Technologies) on plates coated in poly-L-ornithine (0.01%) (Sigma) and laminin (0.01 mg/mL) (Sigma).  Drosophila S2 cells were cultured in Schneider's Drosophila Medium (Invitrogen) containing 10% heat-inactivated FBS.

extract_protocol:
Cells were fixed with 1% formaldehyde (Sigma). Fixed cell preparations were washed, pelleted and stored at -80°C. Sonication of lysed nuclei (lysed in a buffer containing 1% SDS) was performed on a BioRuptor UCD-300 for 60 cycles, 10s on 20s off, centrifuged every 15 cycles, chilled by 4°C water cooler. Samples were checked for sonication efficiency using the criteria of 150-500bp by gel electrophoresis. After the sonication, the chromatin was diluted to reduce SDS level to 0.1% and before ChIP reaction 2% of sonicated drosophila S2 cell chromatin was spiked-in the samples for quantification of total levels of histone mark after the sequencing. ChIP reaction for histone modifications was performed on a Diagenode SX-8G IP-Star Compact using Diagenode automated Ideal ChIP-seq Kit. 25ul Protein A beads (Invitrogen) or 70ul of sheep anti-mouse IgG beads (Invitrogen) were washed and then incubated with antibodies (protein A beads with: anti-H3K27me3 (1:40, CST 9733), anti-H3K27me2 (1:50, CST 9728), anti-H3K36me2 (1:50, CST 2901), anti-H3K9me3 (1:66, Abcam ab8898); anti-mouse IgG beads with: anti-H3K27me1 (1:50, Active Motif 61015), anti-H3K36me3 (1:100, Active Motif 61021)), and 2 million cells of sonicated cell lysate combined with protease inhibitors for 10 hr, followed by 20 min wash cycle with provided wash buffers. ChIP reaction for SUZ12 was performed as follows: antibodies (anti-SUZ12 (1:150, CST 3737)) were conjugated by incubating with 40ul protein A beads at 4°C for 6 hours, then chromatin from ~4 million cells was added in RIPA buffer, incubated at 4°C o/n, washed using buffers from Ideal ChIP-seq Kit (1 wash with each buffer, corresponding to RIPA, RIPA+500mM NaCl, LiCl, TE), eluted from beads by incubating with Elution buffer for 30 minutes at room temperature. Reverse cross linking took place on a heat block at 65°C for 4 hr. ChIP samples were then treated with 2ul RNase Cocktail at 65°C for 30 min followed by 2ul Proteinase K at 65°C for 30 min. Samples were then purified with QIAGEN MiniElute PCR purification kit as per manufacturers’ protocol. In parallel, input samples (chromatin from about 50,000 cells) were reverse crosslinked and DNA was isolated following the same protocol.
Library preparation was carried out using Kapa HTP or HyperPrep Illumina library preparation reagents, according to manufacturer's instructions.

tag: chip antibody


title: hctle-shstat2C

city: Philadelphia

first: Ana

middle: Maria

last: Gamero

state: PA

address: 3440 N. Broad St.

department: Biochemistry

institute: Temple University

data_processing:
FASTQ files were generated via BaseSpace cloud server during sequencing.
Single-end RNA-seq reads were aligned to human genome GRCh38 using STAR, version 2.5.2.
Reads were quantified with htseq-count, version 0.10.0, based on features in Ensembl reference Homo_sapiens.GRCh38.87.gtf.
Genome_build: GRCh38
Supplementary_files_format_and_content: *.combined.htseq.txt: Tab-delimited text files include abundance estimates.

source_name: HCT116 p53 null

growth_protocol: Subcutaneous implantation of tumor cells.

extract_protocol:
Trizol RNA extraction from snap frozen tumors.
Reagents: TruSeq stranded mRNA library kit, Hiseq rapid SR cluster kit, HiSeq rapid SBS kit (Illumina, CA); Equipment: HiSeq2500; Stranded mRNA-seq library: 1000ng total RNAs from each sample were used to make library according to the product guide. In short, mRNAs were enriched twice via poly-T based RNA purification beads, and subjected to fragmentation at 94 degree for 8 min via divalent cation method. The 1st strand cDNA was synthesized by SuperscriptII and random primers at 42 degree for 15 mins, followed by 2nd strand synthesis at 16 degree for 1hr. During second strand synthesis, the dUTP was used to replace dTTP, thereby the second strand was quenched during amplification. A single 'A' nucleotide is added to the 3' ends of the blunt fragments at 37 degree for 30 min. Adapters with illuminaP5, P7 sequences as well as indices were ligated to the cDNA fragment at 30 degree for 10 min. After Ampure bead (BD) purification, a 15-cycle PCR reaction was used to enrich the fragments. PCR was set at 98 degree for 10 sec, 60 degree for 30 sec and extended at 72 degree for 30 sec. Libraries were again purified using AmPure beads, had a quality check on bioanalyzer (Agilent) and quantified with Qubit (Invitrogen). Sample libraries were subsequently pooled and loaded to the sequencer. Single end reads at 50bp, 30 million reads per sample were generated for the bioinformatic analysis.

tag: transfection

value: pLKO.1 STAT2 shRNA

value: Tumor xenograft


title: 10FTreg11

tag: Sex

tag: donor group


title: singleCell_spheroid_plate1_L21_S149

tag: cell type

tag: cell line

tag: differentiation id


title: hctle-shstat2B


title: singleCell_spheroid_plate1_L1_S129

tag: age (days)


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_B7_AD001

value: brain

tag: source

tag: target

tag: gender


title: BT245-K27M_WGBS

description: According to manufacturer's protocol

tag: genotype


title: singleCell_spheroid_plate1_L20_S148


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_B6_AD006

tag: tissue

value: VIS

value: female


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_B6_AD001


title: 10FTreg10

tag: donor id

value: Fat

tag: age at procedure

tag: year diagnosed

tag: height (cm)

tag: weight (kg)

tag: bmi


title: singleCell_spheroid_plate1_L19_S147


title: hctle-EV-B

tag: transfection

value: pLKO.1 Control vector


title: hctle-EV-A


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_B6_AD004

tag: strain

tag: age

value: STR


title: 10FTreg13

tag: date of procedure

tag: Sex

value: M

tag: donor group


title: singleCell_spheroid_plate1_L18_S146

tag: cell type

tag: cell line

tag: differentiation id

tag: age (days)


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_B5_AD004

tag: tissue

tag: source

tag: target

tag: gender


title: 10FTreg08

tag: donor id

tag: age at procedure

tag: year diagnosed

tag: height (cm)


title: UTX-AB4-hNSC

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

description: UTX-hNSC.SICER.bed.gz

data_processing:
Basecalls performed using CASAVA
Single-end reads of 50bp were mapped human genome hg19(GRCh37-lite) by BWA (version  0.7.12-r1039, default parameter), duplicated reads were then marked with Picard(version  2.6.0-SNAPSHOT) and only non-duplicated reads have been kept by samtools (parameter “-q  1 -F 1024” version 1.2).
We followed ENCODE guideline for quality control of our data. For peak calling of H3K27ac, H3K4me3, we used MACS2(version 2.1.1.20160309). To assure the  replicability, we first finalized reproducible peaks for each group as only retained a peak if it called with stringent cutoff(macs2 -q 0.05) in one sample and at least called with lower  cutoff(macs2 -q 0.5) in the other sample. Peaks for H3K27me3 were called by reproducible peaks between SICER(V1.1) and MACS2. Correlation plots indicated the libraries are  reproducible between biological replicates.
Genome_build: hg19(GRCh37)
Supplementary_files_format_and_content: Peaks

source_name: Cell Line

growth_protocol: H7/WA07 (WiCell) and H9/WA09 cells (WiCell) were grown on Matrigel with reduced growth  factors (ThermoFisher Scientific, #354230) in mTeSR1 medium (STEMCELL Technologies,  #85850) at 37°C and 5% CO2. For neural differentiation, ES cells were seeded onto  AggreWell800 plates (STEMCELL Technologies, #34811) and fed with neural induction medium  (STEMCELL Technologies, #05835) to form uni-sized embryoid bodies (EBs).

extract_protocol:
Cells were harvested in PBS. Cytoplasmic fractions were extracted using buffer A with 1×  protease inhibitors and 1 mM DTT. Nuclear pellets were cross-linked by 1.1% formaldehyde in  buffer B with 1× protease inhibitors and 1 mM DTT; washed; and lysed in lysis buffer 3 with 1×  protease inhibitors, 1 mM DTT, and 1 mM PMSF. The fixed and lysed nuclear extract was  sonicated with Bioruptor® Pico (Diagenode) 10 times for 15 s each, with 45-s intervals.  Chromatin was added to Dynabeads™ (Life Technologies) prebound with 4 μg of antibodies.  For UTX chromatin immunoprecipitation (ChIP), chromatin and antibodies were incubated  overnight, followed by 4 h of recapture with Dynabeads™ the next day.
After incubation, beads were washed and immunoprecipitates were eluted. DNA from eluates was recovered by the  GeneJET FFPE DNA purification kit (ThermoFisher Scientific, #K0882).Libraries are prepared and sequenced at the St. Jude Hartwell Center.

treatment_protocol: On day 5, EBs were re-plated onto Matrigel-treated 6-well plates. Neural differentiation (STEMCELL  Technologies, #08500) started from day 11 to day 16. On day 17, cells were treated with  Accutase® (STEMCELL Technologies) and seeded and fed with neuronal maturation medium  (STEMCELL Technologies, #08510) till days 22–24.

value: Human Neural Stem Cells H9

tag: chip antibody


title: 10FTreg07

tag: weight (kg)

tag: bmi


title: 10FTreg12

tag: date of procedure

tag: Sex


title: DIPGXIII-K27M1_H3K36me2

description: According to manufacturer's protocol

value: SU-DIPGXIII

value: H3K36me2 (Cell Signaling Technology, #2901)

tag: genotype


title: hctle-EV-C

tag: transfection


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_B5_AD002

tag: strain

tag: age


title: singleCell_spheroid_plate1_L16_S144

tag: cell type

tag: cell line

tag: differentiation id

tag: age (days)


title: 10FTreg06

tag: donor id

tag: tissue

tag: donor group


title: INPUT-hNSC-H9-UTXKO-forK27me3

description: H3K27me3.hNSC-UTXKO.Rep.SharpBroad.bed.gz

value: Human Neural Stem Cells H9 UTXKO


title: UTX-AB3-hNSC

description: UTX-hNSC.SICER.bed.gz


title: 10FTreg09

tag: age at procedure

tag: year diagnosed

tag: height (cm)


title: 10FTreg05

tag: weight (kg)

tag: bmi


title: singleCell_spheroid_plate1_L15_S143


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_B5_AD001

tag: source

tag: target

tag: gender


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_B4_AD001

tag: strain


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_B3_AD001

tag: age


title: INPUT-hNSC-H7-WT-forK27me3

tag: cell type

value: Human Neural Stem Cells H7

tag: chip antibody


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_B5_AD006


title: INPUT-hNSC-H7-UTXKO-forK27me3

value: Human Neural Stem Cells H7 UTXKO


title: singleCell_spheroid_plate1_L14_S142

tag: cell line

tag: differentiation id


title: 10FTreg03

tag: donor id

tag: date of procedure

tag: Sex


title: H3K27me3-AB3-hNSC-H9-WT


title: singleCell_spheroid_plate1_L12_S140

tag: age (days)


title: 10FTreg04

tag: tissue

tag: age at procedure

tag: year diagnosed

tag: donor group


title: H3K27me3-AB3-hNSC-H9-UTXKO


title: singleCell_spheroid_plate1_L17_S145


title: 10FTreg02

tag: height (cm)

tag: weight (kg)

tag: bmi


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_B12_AD006

tag: strain

tag: source

tag: target

tag: gender


title: 10FTreg01


title: singleCell_spheroid_plate1_L11_S139

tag: cell type

tag: cell line


title: 10BTreg96

tag: donor id

value: Blood


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_B12_AD004

tag: age


title: H3K27me3-AB3-hNSC-H7-WT

tag: chip antibody


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_B11_AD006


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_B12_AD001

value: male


title: H3K27me3-AB3-hNSC-H7-UTXKO


title: singleCell_spheroid_plate1_K8_S112

value: iPSC-derived cortical spheroid

tag: differentiation id

tag: age (days)


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_B11_AD004

tag: tissue


title: singleCell_spheroid_plate1_K9_S113


title: H3K27me3-AB1-hNSC-H9-UTXKO


title: H3K27me3-AB1-hNSC-H9-WT


title: singleCell_spheroid_plate1_K7_S111


title: H3K27me3-AB1-hNSC-H7-WT


title: singleCell_spheroid_plate1_L13_S141


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_B11_AD002


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_B11_AD001


title: singleCell_spheroid_plate1_L10_S138


title: singleCell_spheroid_plate1_K5_S109


title: singleCell_spheroid_plate1_K6_S110


title: 10BTreg90

tag: age at procedure

tag: date of procedure

tag: year diagnosed

tag: Sex


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_B10_AD004


title: 10BTreg92

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: donor group


title: 10BTreg95


title: singleCell_spheroid_plate1_K4_S108


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_B10_AD006

tag: strain

tag: source

tag: target

tag: gender


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_B10_AD001

tag: age


title: 10BTreg94

tag: donor id


title: 10BTreg89


title: singleCell_spheroid_plate1_K3_S107

tag: cell type

tag: cell line

tag: differentiation id


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_A9_AD006

tag: tissue


title: 10BTreg87

tag: age at procedure

tag: date of procedure


title: 10BTreg88

tag: year diagnosed

tag: Sex


title: singleCell_spheroid_plate1_K2_S106

tag: age (days)


title: 10BTreg93

tag: height (cm)

tag: weight (kg)

tag: bmi


title: singleCell_spheroid_plate1_K23_S127


title: singleCell_spheroid_plate1_K24_S128


title: 10BTreg91

tag: donor group


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_A9_AD004

tag: strain

tag: source

tag: target


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_A7_AD006

tag: age

tag: gender


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_A9_AD001


title: singleCell_spheroid_plate1_K22_S126

tag: cell type

tag: cell line


title: 10BTreg85

tag: donor id

tag: tissue


title: 10BTreg84

tag: age at procedure

tag: date of procedure


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_A7_AD004


title: singleCell_spheroid_plate1_K21_S125

tag: differentiation id


title: Cardiomyocytes treated with DOX and IFN-γ rep2

city: ZhengZhou

first: Chen

last: Ni

state: Henan

address: NO.1 Jianshe East Road

department: Midical Research Center

institute: The First Affiliated Hospital of Zhengzhou University

description:
DOX + IFN-r 2
Expression data from differently treated mouse cardiomyocytes.

hyb_protocol: Following labeling, cDNA was hybridized on a GeneChip®Mouse Transcriptome Array 1.0.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Command Console installed in the GeneChip® Scanner 3000 7G.

data_processing: The data was analyzed with the Robust Multichip Analysis (RMA) algorithm, using the Affymetrix default analysis settings.

label_protocol: Biotinylated cDNA was prepared from 250 ng total RNA according to the manufacturer’s standard protocol (Affymetrix).

growth_protocol: The mouse cardiomyocyte cell line HL-1 was maintained in culture medium consisting of DMEM supplemented with 10% fetal bovine serum at 37℃.

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

treatment_protocol: Mouse cardiomyocytes dispensed in 10ml culture medium were cultured in 10-cm dishes at 80% confluence, DOX (0.3µM) and IFN-γ (20ng/ml) were added.

value: Cardiomyocyte cell line

tag: tissue derivation

value: Heart

tag: treatment

value: DOX and IFN-gamma


title: Cardiomyocytes treated with DOX and IFN-γ rep1

description:
DOX + IFN-r 1
Expression data from differently treated mouse cardiomyocytes.


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_A7_AD001

value: brain

value: VIS


title: Cardiomyocytes treated with DOX rep3

description:
DOX3
Expression data from differently treated mouse cardiomyocytes.

source_name: Cardiomyocytes treated with DOX

value: DOX


title: singleCell_spheroid_plate1_K20_S124

tag: age (days)


title: Cardiomyocytes treated with DOX and IFN-γ rep3

description:
DOX + IFN-r 3
Expression data from differently treated mouse cardiomyocytes.


title: 10BTreg83

tag: year diagnosed

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: Sex


title: Cardiomyocytes treated with DOX rep2

description:
DOX2
Expression data from differently treated mouse cardiomyocytes.


title: Cardiomyocytes treated with DOX rep1

description:
DOX1
Expression data from differently treated mouse cardiomyocytes.


title: Cardiomyocytes treated with PBS rep2

description:
Con2
Expression data from differently treated mouse cardiomyocytes.

source_name: Cardiomyocytes treated with PBS

value: PBS


title: 10BTreg82

value: M

tag: donor group


title: singleCell_spheroid_plate1_K1_S105


title: 10BTreg86


title: 10BTreg81


title: 10BTreg80


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_A6_AD004

tag: strain

tag: age

tag: source

tag: target

value: STR

tag: gender

value: female


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_A5_AD006

tag: tissue


title: singleCell_spheroid_plate1_K18_S122

tag: cell type

tag: cell line


title: HSJ019-KO2_RNA-seq rep1

data_processing:
Raw RNA sequencing reads were aligned using STAR version 2.5.3a with default parameters. After alignment, we sorted the bam files using samtools, then igvtools was used to generate wig files (igvtools count -w 25 -e 200). Finally, bigWig files were obtained using wigToBigWig.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

extract_protocol:
Total RNA was extracted from cell pellets and mouse tumors using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to instructions from the manufacturer.
Library preparation was performed with ribosomal RNA (rRNA) depletion according to instructions from the manufacturer (Epicentre) to achieve greater coverage of mRNA and other long non-coding transcripts.

tag: genotype

value: H3.3 (H3F3A) K27M-KO by introducing frameshift indel to the H3F3A allele carrying K27M mutation and leaving wild-type allele


title: 10BTreg79

tag: donor id

tag: age at procedure

tag: date of procedure


title: HSJ019-KO1_RNA-seq rep2


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_A6_AD006


title: HSJ019-KO2_RNA-seq rep2


title: singleCell_spheroid_plate1_K19_S123

tag: differentiation id

tag: age (days)


title: Cardiomyocytes treated with PBS rep1

description:
Con1
Expression data from differently treated mouse cardiomyocytes.

tag: tissue derivation

tag: treatment


title: Cardiomyocytes treated with PBS rep3

description:
Con3
Expression data from differently treated mouse cardiomyocytes.


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_A6_AD001


title: HSJ019-KO1_RNA-seq rep1


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_A5_AD004


title: singleCell_spheroid_plate1_K15_S119


title: HSJ019-K27M2_RNA-seq rep1


title: singleCell_spheroid_plate1_K16_S120


title: singleCell_spheroid_plate1_K17_S121


title: HSJ019-K27M2_RNA-seq rep2


title: 10BTreg78

tag: year diagnosed

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: Sex

tag: donor group


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_A5_AD002

tag: strain

tag: age

tag: tissue

tag: source

tag: target

tag: gender


title: singleCell_spheroid_plate1_K12_S116

tag: cell type

tag: cell line


title: HSJ019-K27M1_RNA-seq rep2

tag: genotype


title: 10BTreg77

tag: donor id

tag: age at procedure

tag: date of procedure


title: HSJ019-K27M1_RNA-seq rep1


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_A12_AD002


title: G477-K27R_RNA-seq rep1

value: H3.3 (H3F3A) K27R overexpression


title: singleCell_spheroid_plate1_K14_S118

tag: differentiation id

tag: age (days)


title: singleCell_spheroid_plate1_K13_S117


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_A12_AD004


title: G477-K27M_RNA-seq rep3

value: H3.3 (H3F3A) K27M overexpression


title: 10BTreg74

tag: year diagnosed

tag: height (cm)

tag: weight (kg)

tag: bmi