title: Male pravastatin treatment, biological replicate 1.

tag: gender


title: Male vehicle treatment, biological replicate 3.

status: Public on Apr 25 2018

type: SRA

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5150 Center Ave

department: BioMedical Informatics

country: USA

institute: University of Pittsburgh

description:
Re-analysis of GSM2508031
M61

library_source: transcriptomic

data_processing:
Reads were aligned to the GRCm38 genome using Tophat v 2.1.1 (default parameters)
Gene expression values were quantified using HTSeq with the union method
Differential expression was performed for genes with >1 CPM in at least 3 samples
Genome_build: GRCm38
Supplementary_files_format_and_content: Xlsx file contains results for all genes from three differential expression analyses: male pravastatin vs male vehicle, female pravastatin vs female vehicle, and all (male+female) pravastatin vs all (male+female) vehicle

molecule: total RNA

organism: Mus musculus

source_name: cerebral cortical neurosphere culture

growth_protocol: Cortex dissected from embryonic day 14.5 fetal mouse brain were dissociated into single cells and then cultured as neurospheres

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions
The Ilumina Stranded Total RNA-Seq Kit was used to construct the library according to the manufacturer's instructions

treatment_protocol: Neurospheres at third passage were treated with 10 uM pravastatin or equivalent volumes of vehicle for 24 hours

tag: age

value: embryonic day E14.5

value: Male

tag: treatment

value: Vehicle

tag: tissue

value: brain

tag: brain region

value: Cortex


title: TFAP2A-/- TFAP2C-/- Line 2 2i+LIF Replicate 1 RNA [RNA-Seq]

city: Montreal

first: William

middle: Abraham

last: Pastor

state: QC

address: 3655 Promenade Sir William Osler

department: Biochemistry

institute: McGill University

description: RNA (polyA enriched)

data_processing:
RNA-seq: RNA-seq reads were first aligned to the mm9 or hg19 gene annotation using Tophat, and reads that did not map to the gene annotation were mapped to the genome as a whole. Default parameters were used, except that the --no-coverage-search parameter was used. Readcounts for each gene were calculated using HTseq with default parameters, mapping to the UCSC hg19 (human) or mm9 Ensembl (mouse) annotations.
Genome_build: hg19 (human); mm9 (mouse)

source_name: TFAP2A/2C doubly deficient mESCs cultured for six passages in 2i+LIF

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and quantified using the Qubit RNA HS Assay kit (Thermo Scientific)
5ng to 50ng total RNA input was used to generate sequencing libraries using the Ovation Ultralow Library System V2 (Nugen) and then Ovation Rapid Library System (Nugen) protocols.

tag: cell type

tag: passage number

tag: library type

value: Ovation RNASeq System V2


title: Male vehicle treatment, biological replicate 2.

description:
Re-analysis of GSM2508029
M41


title: Serial Control Transfection Line 1 2i+LIF Replicate 2 RNA [RNA-Seq]

description: RNA (polyA enriched)

source_name: Control transfected (twice) V6.5 mESCs cultured for seven passages in 2i+LIF media


title: Female pravastatin treatment, biological replicate 3.

value: Female

value: Pravastatin


title: Male vehicle treatment, biological replicate 1.

description:
Re-analysis of GSM2508027
M31


title: Female pravastatin treatment, biological replicate 2.


title: Female vehicle treatment, biological replicate 3.

description:
Re-analysis of GSM2508025
F81


title: Female pravastatin treatment, biological replicate 1.


title: Male pravastatin treatment, biological replicate 2.


title: Female vehicle treatment, biological replicate 1.

description:
Re-analysis of GSM2508021
F51


title: Female vehicle treatment, biological replicate 2.

description:
Re-analysis of GSM2508023
F71


title: TFAP2C-/- Line 1 2i+LIF Replicate 2 RNA [RNA-Seq]

description: RNA (polyA enriched)

source_name: TFAP2C deficient mESCs cultured for seven passages in 2i+LIF media


title: 3632-ACP-0022

city: Nashville

first: Nathaniel

last: Hart

state: TN

address: 7465 Medical Research Building IV, 2215 Garland Ave.

department: Medicine

institute: Vanderbilt University Medical Center

description:
homozygous CFTR wt and Pdx1-Cre (+)
NEV_Mouse_RNAseq.xlsx

data_processing:
Following RNA sequencing, raw reads were mapped to reference mouse or human genome as appropriate using TopHat v2.0. Aligned reads were imported onto the Avadis NGS data analysis platform (Strand Scientific Intelligence, Bengalor). Reads were first filtered on their quality metrics, and then duplicate reads were removed. Normalized gene expression was quantified using the TMM (Trimmed Mean of M-values) algorithm. The transcriptional profile from each sample group was compared by principle component analysis (PCA) and hierarchal clustering analysis to determine the layout and spread of the samples. Differential expression between conditions was calculated on the basis of fold change (cutoff ≥ 2.0) and the p-value was estimated by z-score calculations (cutoff 0.05) as determined by the Benjamini Hochberg false discovery rate (FDR) method. Differentially expressed genes underwent gene set enrichment analysis (GSEA), gene ontology (GO) analysis, and pathway analysis using DAVID and Ingenuity Pathway Analysis.
Genome_build: hg19, mm9
Supplementary_files_format_and_content: Excel files include expression values for each Sample

source_name: Cftr wt/wt B6.FVB-Tg(PDX1-cre)6Tuv/J

extract_protocol:
RNAqueous Micro-Total RNA Isolation Kit (Ambion/Invitrogen). Trace contaminating DNA was removed with TURBO DNA-free (Ambion/Invitrogen).
Both murine and human islets were handpicked under microscope guidance, washed with PBS, and immediately frozen at -80 ºC. Islet RNA was extracted using the RNAqueous Micro-Total RNA Isolation Kit (Ambion/Invitrogen). Trace contaminating DNA was removed with TURBO DNA-free (Ambion/Invitrogen). RNA quality control quantification was performed using a Qubit Fluorometer (Invitrogen) and an Agilent 2100 Bioanalyzer. All RNA samples had an RNA integrity number (RIN) ≥6.0. RNA was amplified using the NuGEN Technologies Ovation RNA amplification kit optimized for RNA sequencing. Following amplification, the resulting cDNA was sheared to an average insert size of 300bp and used for library preparation. Sequencing was performed using standard Illumina methods.

tag: strain

tag: subject

tag: diagnosis

value: Pancreas

value: 10 week old

value: female

value: Islet of Langerhans


title: TFAP2C-/- Line 2 2i+LIF Replicate 2 RNA [RNA-Seq]

description: RNA (polyA enriched)

value: TFAP2C deficient mESCs cultured for seven passages in 2i+LIF media


title: 3632-ACP-0020

description:
homozygous CFTR exon 11 floxed and Pdx1-Cre (+)
NEV_Mouse_RNAseq.xlsx

value: 11 week old


title: Control Transfection Line 2 2i+LIF Replicate 2 RNA [RNA-Seq]

description: RNA (polyA enriched)

source_name: Control transfected V6.5 mESCs cultured for seven passages in 2i+LIF media


title: TFAP2C-/- Line 2 2i+LIF Replicate 1 RNA [RNA-Seq]

description: RNA (polyA enriched)

source_name: TFAP2C deficient mESCs cultured for six passages in 2i+LIF media


title: TFAP2C-/- Line 1 2i+LIF Replicate 1 RNA [RNA-Seq]

description: RNA (polyA enriched)

value: TFAP2C deficient mESCs cultured for six passages in 2i+LIF media


title: 3632-ACP-0019

value: male


title: Control Transfection Line 2 2i+LIF Replicate 1 RNA [RNA-Seq]

description: RNA (polyA enriched)

source_name: Control transfected V6.5 mESCs cultured for six passages in 2i+LIF media


title: 3632-ACP-0018


title: 3632-ACP-0010

description: Normalized expression values_mouse_3632ACP.xlsx

value: 16 week old

value: Tamoxifen


title: 3632-ACP-0016


title: 3632-ACP-0003

value: 17 week old


title: 3632-ACP-0009

value: 19 week old

value: Vehicle


title: Control Transfection Line 1 2i+LIF Replicate 1 RNA [RNA-Seq]

description: RNA (polyA enriched)

value: Control transfected V6.5 mESCs cultured for six passages in 2i+LIF media


title: TFAP2A-/- TFAP2C-/- Line 1 2i+LIF Replicate 1 RNA [RNA-Seq]

description: RNA (polyA enriched)

value: TFAP2A/2C doubly deficient mESCs cultured for six passages in 2i+LIF

value: Ovation RNASeq System V2


title: 3632-ACP-0001


title: 3632-ACP-0002

value: 14 week old


title: HUVEC_CTCF_senescent

city: Koeln

first: Milos

last: Nikolic

state: Nordrhein-Westfalen

address: Robert Koch Str. 21

country: Germany

institute: Center for Molecular Medicine Cologne

library_source: genomic

data_processing:
Library strategy: HiChIP
Raw reads processed using HiCpro software (Servant et al., 2015)
Loops were identified using HiChipper software (http://hichipper.readthedocs.io/en/latest/index.html)
Genome_build: hg19

molecule: genomic DNA

organism: Homo sapiens

source_name: human umbilical vein endothelial cells

growth_protocol: IMR90s (I90-10 and -79, passage 5; Coriell Biorepository) and HUVEC (passage 8 and 15) were continuously passaged to replicative exhaustion in MEM (M4655, Sigma-Aldrich) supplemented with non-essential amino acids and 20% FBS under 5% CO₂.

extract_protocol:
Hi-C was performed as previously described in Mumbach MR et al., 2016
HiChIP DNA was used as template for adding sequencing linkers via 12 PCR cycles. Then, Hi-C libraries were sequenced to generate at least 400 million paired-end reads (75-100 bp in length) per each donor/condition in a HiSeq4000 platform (Illumina).

treatment_protocol: Cell proliferation was monitored by MTT assays at different passages. In brief, ~5,000 cells are seeded in 96-well format plates in quadruplicates. On the next day, the medium is replaced with 100 µl fresh medium plus 10 µl of a 12 µM MTT stock solution (Invitrogen), and cells are incubated at 37°C for 4 h. Subsequently, all but 25 μl of the medium is removed from the wells, and formazan dissolved in 50 μl DMSO, mixed thoroughly and incubated at 37°C for 10 min. Samples are then mixed again and absorbance read at 530 nm. Measurements are taken at 24, 48 and 72 h post-seeding, background subtracted, and normalized to the 24 h time point. Senescence-associated β-galactosidase assay (Cell Signaling) was performed according to the manufacturer’s instructions to evaluate the fraction of senescent cells at different passages. Finally, DNA methylation at six selected CpG islands (Franzen et al. 2017) was measured by isolating genomic DNA at the different cell states and performing targeted pyrosequencing (Cygenia GmbH).Knockdown was performed using Accell siRNAs(Dharmacon) targeting HMGB2 or a control (NTC) on HUVEC according to the manufacturer’s instruction. RNA was isolated from cells 72h post transfection.

value: human umbilical vein endothelial cells

tag: donor

value: single donor

tag: genotype

value: WT

value: senescent


title: HUVEC_CTCF_proliferating

value: proliferating


title: Serial Control Transfection Line 1 2i+LIF Replicate 1 RNA [RNA-Seq]

description: RNA (polyA enriched)

source_name: Control transfected (twice) V6.5 mESCs cultured for six passages in 2i+LIF media


title: IMR90_HMGB1_ChIP (proliferating)

data_processing:
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and read statistics were obtained with SAMtools
Reads were mapped to the human reference assembly, version hg19, using BWA
Peaks were called using MACS2
Genome_build: hg19
Supplementary_files_format_and_content: peaks files

source_name: fetal lung fibroblast cells

growth_protocol: HUVECs from single, apparently healthy, donors (passage 2; Lonza Inc.) were continuously passaged to replicative exhaustion in complete Endopan-2 supplemented with 2% FBS under 5% CO₂. Cells were constantly seeded at ~10,000 cells/cm2, except late passages that were seeded at ~20,000 cells/cm2. Single-donor IMR90s (I90-10 and -79, passage 5; Coriell Biorepository) were continuously passaged to replicative exhaustion in MEM (M4655, Sigma-Aldrich) supplemented with non-essential amino acids and 20% FBS under 5% CO₂.

extract_protocol:
For each batch of ChIP experiments approx. 25 million cells, cultured to >80% confluence in 15-cm dishes, were crosslinked in 15 mM EGS/PBS (ethylene glycol bis(succinimidyl succinate); Thermo Scientific) for 20 min at room temperature, followed by fixation for 40 min at 4°C in 1% PFA. From this point onwards, cells were processed using the ChIP-IT High Sensitivity kit (Active motif) as per manufacturer’s instructions. Chromatin was sheared to 200-500 bp fragments on a Bioruptor Plus (Diagenode; 2x 9 cycles of 30 sec on and 30 sec off, at the highest power setting), and immuno-precipitation was carried out by adding 4 μg of the appropriate antiserum (HMGB1: 4F10, DSHB, HMGB2: ab67282, Abcam; CTCF: 61311, Active motif) to approx. 30 μg of chromatin and incubating on a rotaror overnight at 4°C in the presence of protease inhibitors. Following addition of protein A/G agarose beads and washing, DNA was purified using the ChIP DNA Clean & Concentrator kit (Zymo Research).
DNA libraries were prepared using the Illumina TruSeq RNA sample preparation Kit v2 starting from the end repair step of the protocol. Up to 20 ng ChIP DNA was used as starting material. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified for 18 PCR cycles to create the final libraries.

treatment_protocol: Cell proliferation was monitored by MTT assays at different passages. In brief, ~5,000 cells are seeded in 96-well format plates in quadruplicates. On the next day, the medium is replaced with 100 µl fresh medium plus 10 µl of a 12 µM MTT stock solution (Invitrogen), and cells are incubated at 37°C for 4 h. Subsequently, all but 25 μl of the medium is removed from the wells, and formazan dissolved in 50 μl DMSO, mixed thoroughly and incubated at 37°C for 10 min. Samples are then mixed again and absorbance read at 530 nm. Measurements are taken at 24, 48 and 72 h post-seeding, background subtracted, and normalized to the 24 h time point. Senescence-associated β-galactosidase assay (Cell Signaling) was performed according to the manufacturer’s instructions to evaluate the fraction of senescent cells at different passages. Finally, DNA methylation at six selected CpG islands (Franzen et al. 2017) was measured by isolating genomic DNA at the different cell states and performing targeted pyrosequencing (Cygenia GmbH).

value: fetal lung fibroblast cells

tag: chip antibody

value: alpha-HMGB1, ab18256, Abcam


title: TFAP2C-/- 2d TFAP2C Induc TFAP2C ChIP [ChIP-Seq]

description: TFAP2C-/- UCLA1 hESCs transduced with a construct that allows doxycycline inducible expression of TFAP2C. These cells were cultured in primed conditions and induced for 48 hours with doxycycline

data_processing:
RNA-seq: RNA-seq reads were first aligned to the hg19 or mm9 gene annotation using Tophat, and reads that did not map to the gene annotation were mapped to the genome as a whole. Default parameters were used, except that the --no-coverage-search parameter was used. Readcounts for each gene were calculated using HTseq with default parameters, mapping to the UCSC hg19 (human) or mm9 Ensembl (mouse) annotations.
ATAC-seq: ATAC-seq reads were aligned to hg19 or mm9 using Bowtie with the parameters -X 2000 -m 1 -p 4 -S. All reads aligned to the + strands were offset by +4bp, and all reads aligned to the – strands were offset by -5bp to account for the pattern of primer insertion by the Tn5 transposase. The SAM files were converted to BAM using samtools and duplicated reads were removed with the samtools rmdup function. Processed bigwig files were generated using Deeptools with default settings.
ChIP-seq: ChIP-seq data was mapped using Bowtie2 with default settings and clonal reads were removed using samtools rmdup. Processed bigwig files were generated using Deeptools with default settings.
Genome_build: hg19/GRCh37 (human)
Genome_build: mm9/MGSCv37 (mouse)
Supplementary_files_format_and_content: RNA-seq: *_readsCount.txt: Readcount by gene.
Supplementary_files_format_and_content: ATAC-seq and ChIP-seq: *.bw: bigwig

source_name: TFAP2C-/- UCLA1 hESCs transduced with a construct that allows doxycycline inducible expression of TFAP2C; cells were cultured in primed conditions and induced for 48 hours with doxycycline

extract_protocol:
Cells were fixed with 1% paraformaldehyde (Sigma) and incubated with rotation for 10 minutes at room temperature. The paraformaldehyde was quenched by adding glycine to a final concentration of 0.14M and rotated another 10 minutes at room temperature. The cells were then centrifuged 735g for 5 minutes and then flash frozen with liquid nitrogen and stored at -80°C until ChIP was conducted. To lyse the cells for ChIP, cells were thawed and resuspended with 1mL lysis buffer (10mM TrisHCl pH 8.0, 0.25% Triton X-100, 10mM EDTA, 0.5mM EGTA, 1x Protease inhibitors (Roche) and 1mM PMSF), then rotated 15 minutes. Nuclei were pelleted by centrifugation at 1500g for 5 minutes at 4°C. Nuclei were then resuspended with 1mL 10mM TrisHCl pH 8.0, 200mM NaCl, 10mM EDTA, 0.5mM EGTA, 1x Protease inhibitor, 1mM PMSF and rotated 10 minutes. Nuclei were then pelleted and resuspended in 650μL 10mM TrisHCl pH 8.0, 10mM EDTA, 0.5mM EGTA,1x Protease inhibitor, 1mM PMSF and sonicated in a 12mm x 12mm Sonication Tube (Covaris) in a Covaris S2 (Intensity = 5; Cycles/burst = 200; Duty Cycle = 5%; 8x (30” on/30” off) for four minutes effective sonication). The sonicated lysate is then centrifuged for 10 minutes at 14200g, and the supernatant retained. 10% of the supernatant is saved as “Input”, the rest is used for ChIP. 30μL of Protein A Dynabeads (ThermoFisher) are washed three times with ChIP buffer (16.7mM TrisHCl pH 8.0, 0.01% SDS, 1.1 Triton X-100, 1.2mM EDTA, 167mM NaCl), each wash consisting of addition of 1mL of buffer and collection of the beads on a magnetic rack (Diagenode). The 30uL of beads were then resuspended in 650μL of ChIP buffer and combined with the ChIP sample to pre-Clear the sample. Beads and chromatin were rotated 2hrs at 4°C, and the beads were collected and the supernatant retained. 3μL of anti-TFAP2C antibody (Santa Cruz, sc-8977) was added to the ChIP sample. The samples were then rotated overnight at 4°C. 60μL of Protein A Dynabeads were then added to the ChIP samples and rotated 2 hours at 4°C. The beads were then washed 2x4 minutes with 500μL Wash Buffer A (50mM HEPES pH 7.9, 1% TritonX-100, 0.1% Deoxycholate, 1mM EDTA, 140mM NaCl), 500μL Wash Buffer B (50m HEPES pH 7.9, 0.1% SDS, 1% Triton X100, 0.1% Deoxycholate, 1mM EDTA, 500mM NaCl), and 500μL TE buffer (10mM TrisHCl pH 8.0, 1mM EDTA). Each wash consists of resuspension in 500μL buffer and rotation at 4 minutes, followed by collection of beads and removal of supernatant. DNA was eluted in 100μL elution buffer (50mM TrisHCl pH 8.0, 1mM EDTA, 1% SDS) at 65°C for 10 minutes in a ThermoMixer (Eppendorf) shaking at 1400RPM. The eluent was collected and the beads were subjected to a second round of elution with 150μL elution buffer. The ChIP eluants were pooled, and the input sample was diluted to 250μL with elution buffer. These samples was incubated 65°C overnight to promote decrosslinking. The samples were then allowed to cool to room temperature, 15μg of RNase A (Purelink, ThermoFisher) was added, and the samples were incubated 30 minutes at 37°C to degrade RNA. 100 μg Proteinase K was then added and the samples were incubated 56°C for two hours. DNA was purified using a MinElute PCR Purification kit (Qiagen).
DNA was sonicated again to 150bp average fragment size with a Covaris S2, concentrated with Agencourt AMPure XP beads (Beckman Coulter) and libraries were generated using the Ovation Ultralow Library System V2 (Nugen).

value: TFAP2C-/- 2d TFAP2C Induc TFAP2C ChIP

value: Ovation Ultralow Library System V2


title: Control Transfection Line 1 2i+LIF Replicate 2 RNA [RNA-Seq]

description: RNA (polyA enriched)

value: Control transfected V6.5 mESCs cultured for seven passages in 2i+LIF media


title: TFAP2C-/- 1d TFAP2C Induc TFAP2C ChIP [ChIP-Seq]

description: TFAP2C-/- UCLA1 hESCs transduced with a construct that allows doxycycline inducible expression of TFAP2C. These cells were cultured in primed conditions and induced for 24 hours with doxycycline

source_name: TFAP2C-/- UCLA1 hESCs transduced with a construct that allows doxycycline inducible expression of TFAP2C; cells were cultured in primed conditions and induced for 24 hours with doxycycline

value: TFAP2C-/- 1d TFAP2C Induc TFAP2C ChIP


title: TFAP2C-/- 2d TFAP2C Induc ChIP Input [ChIP-Seq]

value: TFAP2C-/- 2d TFAP2C Induc ChIP Input


title: TFAP2C-/- No Induc ChIP Input [ChIP-Seq]

description: TFAP2C-/- UCLA1 hESCs transduced with a construct that allows doxycycline inducible expression of TFAP2C. These cells were cultured in primed conditions and not induced

source_name: TFAP2C-/- UCLA1 hESCs transduced with a construct that allows doxycycline inducible expression of TFAP2C; cells were cultured in primed conditions and not induced

value: TFAP2C-/- No Induc ChIP Input


title: TFAP2C-/- 1d TFAP2C Induc ChIP Input [ChIP-Seq]

value: TFAP2C-/- 1d TFAP2C Induc ChIP Input


title: Primed TFAP2C ChIP Replicate 3 [ChIP-Seq]

description: Primed UCLA1 hESCs

source_name: Primed UCLA1 hESCs

value: Primed TFAP2C ChIP


title: Primed TFAP2C ChIP Replicate 2 [ChIP-Seq]

description: Primed UCLA1 hESCs


title: Primed TFAP2C ChIP Replicate 1 [ChIP-Seq]

description: Primed UCLA1 hESCs


title: TFAP2C-/- No Induc TFAP2C ChIP [ChIP-Seq]

value: TFAP2C-/- No Induc TFAP2C ChIP


title: Primed ChIP Input Replicate 3 [ChIP-Seq]

description: Primed UCLA1 hESCs

value: Primed ChIP Input


title: Serial Control Transfection Line 2 2i+LIF Replicate 1 RNA [RNA-Seq]

description: RNA (polyA enriched)

value: Control transfected (twice) V6.5 mESCs cultured for six passages in 2i+LIF media

value: Ovation RNASeq System V2


title: 3632-ACP-0017

value: Pancreas

value: 10 week old

value: male

value: Islet of Langerhans


title: Primed ChIP Input Replicate 2 [ChIP-Seq]

description: Primed UCLA1 hESCs


title: 3632-ACP-0004

value: 15 week old

value: Tamoxifen


title: Primed ChIP Input Replicate 1 [ChIP-Seq]

description: Primed UCLA1 hESCs

value: Ovation Ultralow Library System V2


title: TFAP2C-/- Line 2 Replicate 2 Embryoid Body [RNA-Seq]

description:
RNA (polyA enriched)
TFAP2C-/- Line 2 cells cultured in suspension for one day in mTESR media+ROCKi and then allowed to undergo 5 days of spontaneous differentiation as embryoid bodies

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and quantified using the Qubit RNA HS Assay kit (Thermo Scientific).
5ng to 50ng total RNA input was used to generate sequencing libraries using the Ovation Ultralow Library System V2 (Nugen) and then Ovation Rapid Library System (Nugen) protocols.

value: TFAP2C-/- Line 2


title: Control Cells (UCLA1) Replicate 2 Embryoid Body Assay [RNA-Seq]

description:
RNA (polyA enriched)
UCLA1 cells cultured in suspension for one day in mTESR media+ROCKi and then allowed to undergo 5 days of spontaneous differentiation as embryoid bodies

value: Control Cells (UCLA1)


title: Control Cells (Line 1) Replicate 2 Embryoid Body Assay [RNA-Seq]

description:
RNA (polyA enriched)
Control nucleofected UCLA1 line cultured in suspension for one day in mTESR media+ROCKi and then allowed to undergo 5 days of spontaneous differentiation as embryoid bodies

value: Control Cells (Line 1)


title: TFAP2C-/- Line 1 Replicate 2 Embryoid Body [RNA-Seq]

description:
RNA (polyA enriched)
TFAP2C-/- Line 1 cells cultured in suspension for one day in mTESR media+ROCKi and then allowed to undergo 5 days of spontaneous differentiation as embryoid bodies

value: TFAP2C-/- Line 1


title: TFAP2C-/- Line 2 Replicate 1 Embryoid Body [RNA-Seq]

source_name: TFAP2C-/- Line 2 cells cultured in suspension for one day in mTESR media+ROCKi and then allowed to undergo 5 days of spontaneous differentiation as embryoid bodies


title: Control Cells (UCLA1) Replicate 1 Embryoid Body [RNA-Seq]

source_name: UCLA1 cells cultured in suspension for one day in mTESR media+ROCKi and then allowed to undergo 5 days of spontaneous differentiation as embryoid bodies


title: TFAP2C-/- Line 1 Replicate 1 Embryoid Body [RNA-Seq]

source_name: TFAP2C-/- Line 1 cells cultured in suspension for one day in mTESR media+ROCKi and then allowed to undergo 5 days of spontaneous differentiation as embryoid bodies


title: Control Cells (Line 1) Replicate 1 Embryoid Body [RNA-Seq]

source_name: Control nucleofected UCLA1 line cultured in suspension for one day in mTESR media+ROCKi and then allowed to undergo 5 days of spontaneous differentiation as embryoid bodies


title: TFAP2C-/- Line 2 5iLAF 5% O2 SSEA4 Minus Reversion 2 [RNA-Seq]

description:
RNA (polyA enriched)
TFAP2C-/- UCLA1 line 2, cultured for six passages (38d) in 5iLAF in 5% O2. TRA-1-85+ cells (human) were then sorted into SSEA4 negative and positive cell populations.


title: Control Line 1 5iLAF 5% O2 SSEA4 Plus Reversion 2 [RNA-Seq]

description:
RNA (polyA enriched)
Control nucleofected UCLA1 line cultured for five passages (38d) in 5iLAF in 5% O2. TRA-1-85+ cells (human) were then sorted into SSEA4 negative and positive cell populations.


title: TFAP2C-/- Line 1 5iLAF 5% O2 SSEA4 Plus Reversion 2 [RNA-Seq]

description:
RNA (polyA enriched)
TFAP2C-/- UCLA1 line 1, cultured for six passages (38d) in 5iLAF in 5% O2. TRA-1-85+ cells (human) were then sorted into SSEA4 negative and positive cell populations.


title: TFAP2C-/- Line 1 5iLAF 5% O2 SSEA4 Plus Reversion 1 [RNA-Seq]

description:
RNA (polyA enriched)
TFAP2C-/- UCLA1 line 1, cultured for five passages (34d) in 5iLAF in 5% O2. TRA-1-85+ cells (human) were then sorted into SSEA4 negative and positive cell populations.


title: Control Line 1 5iLAF 5% O2 SSEA4 Minus Reversion 1 [RNA-Seq]

description:
RNA (polyA enriched)
Control nucleofected UCLA1 line cultured for five passages (34d) in 5iLAF in 5% O2. TRA-1-85+ cells (human) were then sorted into SSEA4 negative and positive cell populations.


title: TFAP2C-/- Line 1 5iLAF 5% O2 SSEA4 Minus Reversion 1 [RNA-Seq]

source_name: TFAP2C-/- UCLA1 line 1, cultured for five passages (34d) in 5iLAF in 5% O2. TRA-1-85+ cells (human) were then sorted into SSEA4 negative and positive cell populations.


title: TFAP2C-/- Dox inducible 0.50 μg/mL Dox d19 5iLAF [RNA-Seq]

description:
RNA (polyA enriched)
TFAP2C-/- UCLA1 hESCs transduced with a construct that allows doxycycline inducible expression of TFAP2C. These cells were treated for 19 days with 5iLAF media and 0.5μg/mL doxycycline, then TRA-1-85+ (human) cells were sorted and harvested.

source_name: TFAP2C-/- UCLA1 hESCs transduced with a construct that allows doxycycline inducible expression of TFAP2C; cells treated for 19 days with 5iLAF media and 0.5μg/mL doxycycline, then TRA-1-85+ (human) cells were sorted and harvested.

value: TFAP2C-/- Dox inducible 0.50 ug/mL Dox d19 5iLAF


title: Control Line 1 5iLAF 5% O2 SSEA4 Minus Reversion 2 [RNA-Seq]

source_name: Control nucleofected UCLA1 line cultured for five passages (38d) in 5iLAF in 5% O2. TRA-1-85+ cells (human) were then sorted into SSEA4 negative and positive cell populations.


title: Control Line 1 5iLAF 5% O2 SSEA4 Plus Reversion 1 [RNA-Seq]

source_name: Control nucleofected UCLA1 line cultured for five passages (34d) in 5iLAF in 5% O2. TRA-1-85+ cells (human) were then sorted into SSEA4 negative and positive cell populations.


title: TFAP2C-/- Dox inducible 0.25 μg/mL Dox d19 5iLAF [RNA-Seq]

description:
RNA (polyA enriched)
TFAP2C-/- UCLA1 hESCs transduced with a construct that allows doxycycline inducible expression of TFAP2C. These cells were treated for 19 days with 5iLAF media and 0.25μg/mL doxycycline, then TRA-1-85+ (human) cells were sorted and harvested.

source_name: TFAP2C-/- UCLA1 hESCs transduced with a construct that allows doxycycline inducible expression of TFAP2C; cells treated for 19 days with 5iLAF media and 0.25μg/mL doxycycline, then TRA-1-85+ (human) cells were sorted and harvested.

value: TFAP2C-/- Dox inducible 0.25 ug/mL Dox d19 5iLAF


title: TFAP2C-/- Dox inducible 1d 0.5μg/mL Dox Primed [RNA-Seq]

description:
RNA (polyA enriched)
TFAP2C-/- UCLA1 hESCs transduced with a construct that allows doxycycline inducible expression of TFAP2C. These cells were cultured in primed conditions and induced for 24 hours with doxycycline

value: TFAP2C-/- Dox inducible 1d 0.5ug/mL Dox Primed


title: Naïve TFAP2C ChIP Replicate 3 [ChIP-Seq]

data_processing:
ChIP-seq: ChIP-seq data was mapped using Bowtie2 with default settings and clonal reads were removed using samtools rmdup. Processed bigwig files were generated using Deeptools with default settings.
Genome_build: hg19 (human); mm9 (mouse)

source_name: UCLA1 hESCs cultured 37 passages in naïve (5iLAF) conditions

extract_protocol:
Cells were fixed with 1% paraformaldehyde (Sigma) and incubated with rotation for 10 minutes at room temperature. The paraformaldehyde was quenched by adding glycine to a final concentration of 0.14M and rotated another 10 minutes at room temperature. The cells were then centrifuged 735g for 5 minutes and then flash frozen with liquid nitrogen and stored at -80°C until ChIP was conducted. To lyse the cells for ChIP, cells were thawed and resuspended with 1mL lysis buffer (10mM TrisHCl pH 8.0, 0.25% Triton X-100, 10mM EDTA, 0.5mM EGTA, 1x Protease inhibitors (Roche) and 1mM PMSF), then rotated 15 minutes. Nuclei were pelleted by centrifugation at 1500g for 5 minutes at 4°C. Nuclei were then resuspended with 1mL 10mM TrisHCl pH 8.0, 200mM NaCl, 10mM EDTA, 0.5mM EGTA, 1x Protease inhibitor, 1mM PMSF and rotated 10 minutes. Nuclei were then pelleted and resuspended in 650μL 10mM TrisHCl pH 8.0, 10mM EDTA, 0.5mM EGTA,1x Protease inhibitor, 1mM PMSF and sonicated in a 12mm x 12mm Sonication Tube (Covaris) in a Covaris S2 (Intensity = 5; Cycles/burst = 200; Duty Cycle = 5%; 8x (30” on/30” off) for four minutes effective sonication). The sonicated lysate is then centrifuged for 10 minutes at 14200g, and the supernatant retained. 10% of the supernatant is saved as “Input”, the rest is used for ChIP. 30μL of Protein A Dynabeads (ThermoFisher) are washed three times with ChIP buffer (16.7mM TrisHCl pH 8.0, 0.01% SDS, 1.1 Triton X-100, 1.2mM EDTA, 167mM NaCl), each wash consisting of addition of 1mL of buffer and collection of the beads on a magnetic rack (Diagenode). The 30uL of beads were then resuspended in 650μL of ChIP buffer and combined with the ChIP sample to pre-Clear the sample. Beads and chromatin were rotated 2hrs at 4°C, and the beads were collected and the supernatant retained. 3μL of anti-TFAP2C antibody (sc-8977) was added to the ChIP sample. The samples were then rotated overnight at 4°C. 60μL of Protein A Dynabeads were then added to the ChIP samples and rotated 2 hours at 4°C. The beads were then washed 2x4 minutes with 500μL Wash Buffer A (50mM HEPES pH 7.9, 1% TritonX-100, 0.1% Deoxycholate, 1mM EDTA, 140mM NaCl), 500μL Wash Buffer B (50m HEPES pH 7.9, 0.1% SDS, 1% Triton X100, 0.1% Deoxycholate, 1mM EDTA, 500mM NaCl), and 500μL TE buffer (10mM TrisHCl pH 8.0, 1mM EDTA). Each wash consists of resuspension in 500μL buffer and rotation at 4 minutes, followed by collection of beads and removal of supernatant. DNA was eluted in 100μL elution buffer (50mM TrisHCl pH 8.0, 1mM EDTA, 1% SDS) at 65°C for 10 minutes in a ThermoMixer (Eppendorf) shaking at 1400RPM. The eluent was collected and the beads were subjected to a second round of elution with 150μL elution buffer. The ChIP eluants were pooled, and the input sample was diluted to 250μL with elution buffer. These samples was incubated 65°C overnight to promote decrosslinking. The samples were then allowed to cool to room temperature, 15μg of RNAse A (Purelink, ThermoFisher) was added, and the samples were incubated 30 minutes at 37°C to degrade RNA. 100 μg Proteinase K was then added and the samples were incubated 56°C for two hours. DNA was purified using a MinElute PCR Purification kit (Qiagen).
DNA was sonicated again to 150bp average fragment size with a Covaris S2, concentrated with Agencourt AMPure XP beads (Beckman Coulter) and libraries were generated using the Ovation Ultralow Library System V2 (Nugen).

value: UCLA1 hESCs cultured 37 passages in naive (5iLAF) conditions


title: TFAP2C-/- Dox inducible 2d 0.5μg/mL Dox Primed [RNA-Seq]

description:
RNA (polyA enriched)
TFAP2C-/- UCLA1 hESCs transduced with a construct that allows doxycycline inducible expression of TFAP2C. These cells were cultured in primed conditions and induced for 48 hours with doxycycline

value: TFAP2C-/- Dox inducible 2d 0.5ug/mL Dox Primed


title: Naïve TFAP2C ChIP Replicate 1 [ChIP-Seq]


title: TFAP2C-/- Dox inducible 0.125 μg/mL Dox d19 5iLAF [RNA-Seq]

description:
RNA (polyA enriched)
TFAP2C-/- UCLA1 hESCs transduced with a construct that allows doxycycline inducible expression of TFAP2C. These cells were treated for 19 days with 5iLAF media and 0.125μg/mL doxycycline, then TRA-1-85+ (human) cells were sorted and harvested.

source_name: TFAP2C-/- UCLA1 hESCs transduced with a construct that allows doxycycline inducible expression of TFAP2C; cells treated for 19 days with 5iLAF media and 0.125μg/mL doxycycline, then TRA-1-85+ (human) cells were sorted and harvested.

value: TFAP2C-/- Dox inducible 0.125 ug/mL Dox d19 5iLAF

value: Ovation RNASeq System V2


title: 5iLAF d5 TFAP2C ChIP [ChIP-Seq]

source_name: UCLA1 hESCs cultured for five days in 5iLAF media


title: TFAP2C-/- Dox inducible No Dox Primed [RNA-Seq]

description:
RNA (polyA enriched)
TFAP2C-/- UCLA1 hESCs transduced with a construct that allows doxycycline inducible expression of TFAP2C. These cells were cultured in primed conditions and not induced

value: TFAP2C-/- Dox inducible No Dox Primed


title: TFAP2C-/- Line 2 5iLAF 5% O2 SSEA4 Plus Reversion 2 [RNA-Seq]

source_name: TFAP2C-/- UCLA1 line 2, cultured for six passages (38d) in 5iLAF in 5% O2. TRA-1-85+ cells (human) were then sorted into SSEA4 negative and positive cell populations.


title: Naïve TFAP2C ChIP Replicate 2 [ChIP-Seq]


title: 5iLAF d5 Input [ChIP-Seq]

value: UCLA1 hESCs cultured for five days in 5iLAF media


title: Naïve ChIP Input Replicate 1 [ChIP-Seq]


title: TFAP2C-/- Line 2 5d 5iLAF Replicate 1 RNA [RNA-Seq]

description: RNA (polyA enriched)

source_name: TFAP2C-/- UCLA1 hESCs cultured for five days in 5iLAF media


title: Naïve ChIP Input Replicate 2 [ChIP-Seq]


title: Control transfected cells 5d 5iLAF Replicate 2 RNAv

description: RNA (polyA enriched)

source_name: Control transfected UCLA1 hESCs cultured for five days in 5iLAF media


title: TFAP2C-/- Line 1 5d 5iLAF Replicate 2 RNA [RNA-Seq]

description: RNA (polyA enriched)

value: TFAP2C-/- UCLA1 hESCs cultured for five days in 5iLAF media


title: Naïve ChIP Input Replicate 3 [ChIP-Seq]


title: Primed 5% O2 (control for reversion 2) [RNA-Seq]

description:
RNA (polyA enriched)
Primed SSEA4+ UCLA1 hESCs, transitioned to 5% O2 for one passage before harvest

value: Primed 5% O2 (control for reversion 2)


title: Primed control for 5% O2 reversion 1 [RNA-Seq]

description:
RNA (polyA enriched)
Primed SSEA4+ UCLA1 hESCs

source_name: Primed SSEA4+ UCLA1 hESCs

value: Primed control for 5% O2 reversion 1


title: Control transfected cells 5d 5iLAF Replicate 1 RNA [RNA-Seq]

description: RNA (polyA enriched)

value: Control transfected UCLA1 hESCs cultured for five days in 5iLAF media


title: Untransfected cells 5d 5iLAF Replicate 1 RNA [RNA-Seq]

description: RNA (polyA enriched)

source_name: Untransfected UCLA1 hESCs cultured for five days in 5iLAF media


title: mTFAP2A-/- mTFAP2C-/- Line 2 2i+LIF Replicate 2 ATAC [ATAC-Seq]

data_processing:
ATAC-seq: ATAC-seq reads were aligned to hg19 or mm9 using Bowtie with the parameters -X 2000 -m 1 -p 4 -S. All reads aligned to the + strands were offset by +4bp, and all reads aligned to the – strands were offset by -5bp to account for the pattern of primer insertion by the Tn5 transposase. The SAM files were converted to BAM using samtools and duplicated reads were removed with the samtools rmdup function. Processed bigwig files were generated using Deeptools with default settings.
Genome_build: hg19 (human); mm9 (mouse)

source_name: Control transfected (twice) V6.5 mESCs cultured for eight passages in 2i+LIF media

extract_protocol:
FACS collected cells were spun 500g x 5 minutes at 4°C. Cells were resuspended in 50μL lysis buffer (10mM Tris pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP40, 1x Complete Protease Inhibitor(Roche)) and spun 10 minutes 500g 4°C to collect nuclei. The nuclei were resuspended in 50μL Transposase reaction (25μL 2xTagmentation buffer, 22.5μL water, 2.5μL Tn5 Transposase enzyme) and reacted for 30 minutes at 37°C on a PCR machine. The material was purified using a Qiagen MinElute protocol, eluting with 14μL EB.
The eluted material was amplified in 50μL volume using 1.25μM primer concentration and a 1x concentration NEBNext High-Fidelity Master-Mix (NEB) (Program: 72°C 5:00, 98°C 30s, 5x (98°C 10s, 63°C 30s, 72°C 1 minute), 4°C hold). After these 5 cycles of amplification, the tube was kept on ice. A 5μL aliquot was then removed and used to perform a 15 μL side reaction with identical concentrations of primer and enzyme, except that 0.6x SYBR Green (Invitrogen S-7563) was included to monitor amplification. This side reaction was amplified on a Stratagene Mx3005p qPCR (Agilent) system with the following amplification conditions (98°C 30s, 20x (98°C 10s, 63°C 30s, 72°C 1:00)). The number of additional cycles ‘N’ required to reach ¼ maximum fluorescence was observed. The remaining 45μL of the reaction was then further amplified (98°C 30s, N x (98°C 10s, 63°C 30s, 72°C 1:00), 4°C) and the libraries were purified by a Qiagen MinElute kit eluting with 20 μL volume.

value: Nextera ATAC-seq


title: 554 small RNA-Seq

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

description: Processed with kit "TruSeq Small RNA Sample Prep Kit" (Illumina part # RS-930-1012)

data_processing:
small-RNA-seq analysis:
Image analysis and per-cycle basecalling was performed with Illumina Real Time Analysis software (RTA1.9) (Illumina). Conversion to FASTQ read format was performed by CASAVA-1.8 (Illumina). Small-RNA-seq libraries were sequenced as 40 and 50bp single-end reads (Illumina Genome Analyzer IIx, GAIIx). Sequenced reads were quality-checked with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).  Small-RNA-seq read adapter sequences were firstly removed with cutadapt v1.2.1 and only those reads longer than 15bp and shorter than 35bp were kept for further analysis.  Reads were aligned to the human genome (GRCh37/hg19) with Bowtie 1.0.0 and Samtools 0.1.19 allowing no mismatches and a maximum of 1 alignment per read. Raw counts for miRNAs were obtained with HTSeq v0.5.3p9, using the miRBase v20 annotation for hg19. Differential expression was calculated with DESeq and edgeR. Normalized counts were used to filter out miRNAs with questionable expression and outliers. The following criteria were used: first, we required that a miRNA should have a minimal normalized count value of 15 in at least 5% of the samples. Second, miRNAs with normalized expression values across the samples that exceeded Q1-3*IQR or Q3+3*IQR were considered outliers and discarded.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Normalized counts calculated with DESeq

source_name: tumor

growth_protocol: No cultered cells were used.

extract_protocol:
Total RNA was obtained using TriPure Reagent (Roche Applied Science, Indianapolis, IN, USA), following manufacturer’s instructions.
Total RNA samples were used and sample RNA Integrity Numbers were in the range 7.3 to 8.45 (average 7.8) when assayed on an Agilent 2100 Bioanalyzer. Sample amounts were 1µg of total RNA. They were processed with kit "TruSeq Small RNA Sample Prep Kit" (Illumina part # RS-930-1012) by following manufacturer instructions (Truseq SmallRNA SamplePrep Guide 15004197-E). Briefly, samples were sequentially ligated to 3' and 5' adapters, with the truncated form of T4 RNA Ligase 2 and the T4 RNA ligase 1, respectively. Reverse transcription with SuperScript II Reverse Transcriptase followed, yielding cDNA adapter-ligated and indexed libraries that were amplified by PCR with Illumina RNA PCR primers (13 cycles). Amplified barcoded cDNA from different samples was pooled, and a polyacrylamide gel electrophoresis fraction of 145 to 150 bases was extracted. The purified fraction was applied to an Illumina flow cell for cluster generation, and sequenced on an Illumina Genome Analyzer IIx (GAIIx), by following manufacturer's protocols. Sequencing read ends are expected to contain a variable length of the 3' adaptor, whose sequence is TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC.

treatment_protocol: No treatment was used

value: T-cell lymphoblastic lymphoma


title: 840 small RNA-Seq


title: TFAP2C-/- Line 2 5d 5iLAF Replicate 2 RNA [RNA-Seq]

description: RNA (polyA enriched)


title: 521 small RNA-Seq


title: Serial Control Transfection Line 1 2i+LIF Replicate 2 ATAC [ATAC-Seq]

source_name: TFAP2A/2C doubly deficient mESCs cultured for eight passages in 2i+LIF


title: Serial Control Transfection Line 2 2i+LIF Replicate 2 ATAC [ATAC-Seq]

value: TFAP2A/2C doubly deficient mESCs cultured for eight passages in 2i+LIF


title: 460 small RNA-Seq


title: 408 small RNA-Seq


title: 405 small RNA-Seq

source_name: control

value: control thymus


title: mTFAP2A-/- mTFAP2C-/- Line 1 2i+LIF Replicate 1 ATAC [ATAC-Seq]

source_name: Control transfected (twice) V6.5 mESCs cultured for seven passages in 2i+LIF media


title: TFAP2C-/- Line 1 5d 5iLAF Replicate 1 RNA [RNA-Seq]

description: RNA (polyA enriched)


title: IMR90_CTCF_proliferating

source_name: fetal lung fibroblast cells

value: fetal lung fibroblast cells

value: single donor

value: WT

value: proliferating


title: IMR90_CTCF_senescent

value: senescent


title: mTFAP2A-/- mTFAP2C-/- Line 2 2i+LIF Replicate 1 ATAC [ATAC-Seq]

value: Control transfected (twice) V6.5 mESCs cultured for seven passages in 2i+LIF media


title: Serial Control Transfection Line 2 2i+LIF Replicate 1 ATAC [ATAC-Seq]

source_name: TFAP2A/2C doubly deficient mESCs cultured for seven passages in 2i+LIF


title: WT 5-d old plants, biological rep1

type: RNA

city: Amritsar

first: Brinderjit

last: Singh

state: Punjab

address: Amritsar

department: Biotechnology

country: India

institute: Guru Nanak Dev University

description: expression analysis

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Arabidopsis Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3300

data_processing: Raw data from the Feature Extraction software were obtained in .txt (Tab delimited) format and were normalized using GeneSpring GX v12.0. Normalization was performed by taking the 50th percentile for each sample. A baseline correction was applied to the median of all samples. The expected versus observed measurements of the hybridization control probes were compared for hybridization quality control for each sample. Hybridization quality control for replicate samples was performed by measuring the correlation co-efficient, performing a principle component analysis (PCA), creating scatter plots and creating an unsupervised condition tree of samples using the Pearson uncentered algorithm with average linkage rule.

label: biotin

organism: Arabidopsis thaliana

source_name: 5-d old wild type

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3ug total RNA

growth_protocol: Seeds were sterlised and grown on OS medium in the Arabidopsis culture room having 16h/8h light/dark cycle.

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

treatment_protocol: No specific treatment was given to the plants before processing.

value: whole plant

tag: genotype/variation

value: wild-type


title: 346 small RNA-Seq


title: TaVAPOE 5-d old plants, biological rep1

description: expression analysis

source_name: 5-d old wild type having TaVAP overexpression

value: TaVAPOE


title: 404 small RNA-Seq


title: Atvap Mutant 5-d old plants, biological rep1

description: expression analysis

source_name: 5-d old mutant

value: atvap mutant


title: WT 5-d old plants, biological rep2

description: expression analysis


title: Serial Control Transfection Line 1 2i+LIF Replicate 1 ATAC [ATAC-Seq]

value: TFAP2A/2C doubly deficient mESCs cultured for seven passages in 2i+LIF


title: Atvap Mutant 5-d old plants, biological rep2

description: expression analysis


title: TaVAPOE 5-d old plants, biological rep2

description: expression analysis


title: 238 small RNA-Seq


title: EpiSC Technical Replicate 2 ATAC [ATAC-Seq]

source_name: EpiSC line from P. Tesar

value: EpiSC line from P. Tesar


title: mTFAP2A-/- mTFAP2C-/- Line 1 2i+LIF Replicate 2 ATAC [ATAC-Seq]

value: Control transfected (twice) V6.5 mESCs cultured for eight passages in 2i+LIF media


title: 2i+LIF Technical Replicate 2 ATAC [ATAC-Seq]

source_name: V6.5 mESCs cultured in 2i+LIF conditions

value: Nextera ATAC-seq


title: EpiSC Technical Replicate 1 ATAC [ATAC-Seq]


title: 192 small RNA-Seq

value: T-cell lymphoblastic lymphoma


title: 4t1-control

city: Chengdu

first: Shengtao

last: Zhou

address: #17, Renmin South Road

department: Department of Obstetrics and Gynecology

country: China

institute: West China Second Hospital, Sichuan University

data_processing:
Basecalls performed using CASAVA version 1.8
RNA seq reads were adaptor-trimmed and mapped to mouse genome(mm9) by bowtie2 software with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: normalized counts

source_name: breast cancer cell

extract_protocol:
RNA extracted using Trizol by following manufacturer’s instruction (Invitrogen).
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA,  USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).

value: control-treated 4T1 group


title: 2i+LIF Technical Replicate 1 ATAC [ATAC-Seq]

value: V6.5 mESCs cultured in 2i+LIF conditions


title: B16-treatment

source_name: melanoma cell

value: LY500307-treated B16 group


title: 4C-seq from rfng gene promoter in 24hpf zebrafish embryos, replicate 2

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

institute: CABD/CSIC

data_processing:
library strategy: 4C-seq
ATAC-seq:
Alignment: reads were aligned using danRer10 as reference genome and Bowtie2 software.
Filtering duplicates: duplicated pairs were removed using Samtools software.
Localization of the cleavage site: the enzyme cleavage site was determined as the position -4 (minus strand) or +5 (plus strand) from each read start, and this position was extended 5 bp in both directions.
Visualization: bigWig files were visualized using local browser
4C-seq:
Demultiplexing: different samples were demultiplexed using the primer sequences
Mapping: reads were mapped to the zebrafish genome (danRer10 assembly) using Bowtie software (http://bowtie-bio.sourceforge.net). Only uniquely mapped reads were kept.
Filtering: only those reads that mapped withing fragments with a DpnII at one end and a Csp6I at the other end were kept.
Raw reads were converted into reads/restriction fragment end, and a running 30 fragments-window smoothing algorithm was used to smooth the data.
Data visualization: data were uploaded to UCSC Browser for visualization.
Genome_build: danRer10/GRCz10
Supplementary_files_format_and_content:
ATAC-seq bigWig format for visualization
4C-seq bedGraph containing smoothed data that can be directly uploaded to UCSC for visualization.

organism: Danio rerio

growth_protocol: Embryos were raised at 28ºC untill they reached the desired developmental stage. They were dechorionated with pronase before fixation.

extract_protocol:
Chromatin was extracted from single cells preparations from different samples. DNA was digested with DpnII and ligated. Then sample was de-crosslinked, digested with Csp6I and ligated again.
Primers with Illumina adaptors were used to amplify the library. Different samples were multiplexed for sequencing.

treatment_protocol: No treatment

tag: developmental stage

value: whole embryos


title: ATAC-seq in hindbrain samples from 24hpf zebrafish embryos, replicate 2

data_processing:
ATAC-seq:
Alignment: reads were aligned using danRer10 as reference genome and Bowtie2 software.
Filtering duplicates: duplicated pairs were removed using Samtools software.
Localization of the cleavage site: the enzyme cleavage site was determined as the position -4 (minus strand) or +5 (plus strand) from each read start, and this position was extended 5 bp in both directions.
Visualization: bigWig files were visualized using local browser
4C-seq:
Demultiplexing: different samples were demultiplexed using the primer sequences
Mapping: reads were mapped to the zebrafish genome (danRer10 assembly) using Bowtie software (http://bowtie-bio.sourceforge.net). Only uniquely mapped reads were kept.
Filtering: only those reads that mapped withing fragments with a DpnII at one end and a Csp6I at the other end were kept.
Raw reads were converted into reads/restriction fragment end, and a running 30 fragments-window smoothing algorithm was used to smooth the data.
Data visualization: data were uploaded to UCSC Browser for visualization.
Genome_build: danRer10/GRCz10
Supplementary_files_format_and_content:
ATAC-seq bigWig format for visualization
4C-seq bedGraph containing smoothed data that can be directly uploaded to UCSC for visualization.

extract_protocol: Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-Seq) experiments were performed as described in Buenrostro et al., 2015. Curr. Protoc. Mol. Biol. 109, 21.29.1-9. doi:10.1002/0471142727.mb2129s109

value: whole embryos; hindbrain


title: 4C-seq from rfng gene promoter in 24hpf zebrafish embryos, replicate 1


title: ATAC-seq in hindbrain samples from 24hpf zebrafish embryos, replicate 1


title: PB-1_Panicle_Repl2 [RNA-seq]

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: GKVK Campus, Bellary road

department: Plant epigenetics

institute: National Center for Biological Sciences

data_processing:
Adapter was removed and low quality bases were trimmed from sequenced reads.
The processed reads were aligned to the rice genome using TopHat (v2.1.1).
Gene expressions were calculated using CuffLinks (v2.2.1) as mentioned in Cole Trapnell et al, 2012.
Genome_build: Oryza sativa japonica nipponbare genome – IRGSP1
Supplementary_files_format_and_content: Tab delimited text files including FPKM for each sample.

organism: Oryza sativa

source_name: Panicle

extract_protocol:
Total RNA from two different tissues, flagleaf and panicle of selected rice species were extracted using Trizol (Invitrogen) reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subspecies, cultivar

value: Genotype:Rice, Indica, Pusa Basmati 1 (PB-1)

value: panicle

tag: subspecies

value: Indica


title: B16-control

value: control-treated B16 group


title: PB-1_Panicle_Repl2  [ncRNA-seq]

data_processing:
3’ adapter (5’-TGGAATTCTCGGGTGCCAAGG-3’) was removed from sequenced reads using UEA small RNA workbench.
The small RNA reads of length 16nt-35nt were filtered and analyzed.
Supplementary_files_format_and_content: Text file containing 16nt-35nt long unique reads and their raw abundance after removal of adapter.

extract_protocol:
Total RNA from three different tissues, 4-week old seedling, flagleaf and panicle of selected rice species were extracted using Trizol (Invitrogen) reagent.
Size fractionation

value: Panicle


title: PB-1_Panicle_Repl1  [ncRNA-seq]


title: PB-1_Flagleaf_Repl2  [ncRNA-seq]

source_name: Flagleaf

value: Flagleaf


title: PB-1_Flagleaf_Repl1  [ncRNA-seq]


title: PB-1_Seedling_Repl2  [ncRNA-seq]

source_name: Four weeks old seedlings

value: Four weeks old seedlings


title: PB-1_Panicle_Repl1 [RNA-seq]


title: PB-1_Flagleaf_Repl2 [RNA-seq]

value: flagleaf


title: PB-1_Flagleaf_Repl1 [RNA-seq]


title: PB-1_Seedling_Repl1  [ncRNA-seq]


title: 4t1-treatment

value: LY500307-treated 4T1 group


title: HL-1 shRNA-3

city: Shanghai

first: deyong

last: xiao

address: Room 308, Mingdao building, Research Center For Birth Defects, School of Basic Medical Sciences,  Fudan University, 130 Dongan Road, Shanghai , China

institute: Fudan university

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
Genome_build: GRCm38

source_name: heart

extract_protocol:
Cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: heart

tag: shRNA


title: HL-1 shRNA-2

tag: tissue


title: Patient 9 CN-8

city: Wuhan

first: Yu

last: Wang

state: Hubei

address: 1095 Jiefang Dadao

institute: Institute of Pathology

description: paraffin tissue

hyb_protocol: Hybridization was performed overnight on a μParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) (1). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://www.mirbase.org/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 L 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics)

data_processing: Data were analyzed by first subtracting the background, then the signals were normalized using a Lowess (locally weighted regression) filter. The raw microarray data set was filtered according to a standard procedure to exclude spots with minimum intensity. It was arbitrarily set to an intensity parameter of P100 for the miRNA microarray data. Spots with diameters less than 10 μm and flagged spots were also excluded from the analyses.

source_name: CD117IHC-/wild-type GIST

label_protocol: Labeling of total RNA was performed according to the protocol from LC Science for a single-color experiment with no modification.

extract_protocol: Total RNA was isolated with the Total RNA Purification Kit (Norgen Biotek Corporation, Thorold, Canada) according to the manufacture's instructions

value: CD117IHC-/wild-type GIST

tag: status after 5 years

value: alive

tag: histology

value: spindle

tag: age

value: 64 years

tag: Sex

value: Male


title: HL-1 shRNA-1

tag: strain


title: HL-1 CTR-3

value: control shRNA


title: HL-1 CTR-1


title: Patient 10 CN-10

description: paraffin tissue

tag: cell type

value: 56 years

value: Female


title: Patient 7 CN-4

description: paraffin tissue

value: 62 years


title: Patient 8 CN-6

description: paraffin tissue

value: 55 years


title: Patient 6 CN-1

description: paraffin tissue

value: mixed

value: 46 years


title: Patient 5 CP-10

description: paraffin tissue

source_name: CD117IHC+/KITmutant GIST

value: CD117IHC+/KITmutant GIST

value: 42 years


title: Patient 4 CP-9

description: paraffin tissue

value: 49 years


title: Patient 3 CP-7

description: paraffin tissue

value: 72 years


title: Orufipogon_Panicle_Repl1  [ncRNA-seq]

organism: Oryza rufipogon

value: Panicle


title: Patient 1 CP-4

description: paraffin tissue


title: Patient 2 CP-5

description: paraffin tissue

value: 58 years


title: IMR90_input (proliferating)

value: fetal lung fibroblast cells

value: single donor

value: WT

tag: treatment

value: proliferating


title: Orufipogon_Flagleaf_Repl2  [ncRNA-seq]

value: Flagleaf


title: Orufipogon_Panicle_Repl2  [ncRNA-seq]


title: HUVEC_HMGB1_ChIP (proliferating)

source_name: human umbilical vein endothelial cells

value: human umbilical vein endothelial cells

tag: donor

value: alpha-HMGB1 (4F10), DSHB


title: IMR90_HMGB2_ChIP (proliferating)

tag: genotype

value: alpha-HMGB2, ab67282, Abcam, lot# GR149806


title: IMR90_HMGB2_ChIP (senescent)

value: senescent

tag: chip antibody


title: HUVEC_input (proliferating)


title: Orufipogon_Flagleaf_Repl1  [ncRNA-seq]


title: Onivara_Panicle_Repl1  [ncRNA-seq]

organism: Oryza nivara


title: Case 1_bladder cancer urine sample

city: Jinan

first: Lutao

last: Du

state: Shandong

address: 247 Beiyuan Street, Jinan 250033, Shandong, China

institute: The Second Hospital of Shandong University

description: Gene and lncRNA expression in Case 1 bladder cancer urine sample

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%)

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: Case 1, bladder cancer urine sample

label_protocol: each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Freshly voided urine samples were collected from bladder cancer patients and healthy controls.Cells and debris were removed from each urine sample by centrifugation at 1500 x g for 10 min and 13800 x g for 15 min at 4 °C and supernatant was stored at −80°C until further processing

extract_protocol: Total RNA was extracted from the tissues using Trizol reagent (Invitrogen).mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). RNA quantity and quality were measured by NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: No treatment of urine samples was conducted.

tag: disease state

value: Urothelial carcinoma

tag: sample type

value: bladder cancer urine sample


title: Orufipogon_Seedling_Repl1  [ncRNA-seq]

value: Four weeks old seedlings


title: Orufipogon_Seedling_Repl2  [ncRNA-seq]


title: Case 1_healthy control urine sample

description: Gene and lncRNA expression in Case 1 healthy control urine sample

source_name: Case 1, healthy control urine sample

value: healthy control

value: healthy control urine sample


title: Orufipogon_Panicle_Repl2 [RNA-seq]

value: panicle


title: Onivara_Panicle_Repl2  [ncRNA-seq]

value: Panicle


title: Orufipogon_Panicle_Repl1 [RNA-seq]


title: Orufipogon_Flagleaf_Repl2 [RNA-seq]

value: flagleaf


title: Orufipogon_Flagleaf_Repl1 [RNA-seq]


title: Onivara_Flagleaf_Repl1  [ncRNA-seq]


title: HL-1 CTR-2

value: heart

value: control shRNA


title: Onivara_Flagleaf_Repl2  [ncRNA-seq]


title: Onivara_Seedling_Repl2  [ncRNA-seq]


title: Onivara_Seedling_Repl1  [ncRNA-seq]


title: HUVEC_HMGB2_ChIP (proliferating)

value: single donor

value: WT


title: Onivara_Flagleaf_Repl1 [RNA-seq]


title: Onivara_Panicle_Repl2 [RNA-seq]


title: Onivara_Panicle_Repl1 [RNA-seq]


title: Onivara_Flagleaf_Repl2 [RNA-seq]


title: Cell384

status: Public on Apr 24 2018

city: St. Louis

first: Haojia

last: Wu

state: Missouri

address: 600 S Euclid Ave

department: Renal Division/Internal Medicine

institute: Washington University in St. Louis

data_processing: The resulting sequencing reads were demultiplexed by index with a custom Python demultiplexing script and further demultiplexed by barcode with a custom Perl demultiplexing script. The RNA-Seq reads were then aligned to the Mus musculus Ensembl release 76 top-level assembly with STAR version 3.0.4.b. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Sailfish version 0.6.3. was used to produce isoform estimated counts.

source_name: Mouse kidney

extract_protocol:
Kidney dissociation protocol: Mice were euthanized and perfused with sterile PBS via the left ventricle and the kidneys were placed in PBS with 5% FBS. After thoroughly mincing the tissue/organ using a sterile scalpel (Feather), the tissue/organ was placed in gentleMACS C Tubes (Miltenyi Biotec) containing 1.5ml DMEM (Life Technologies) with 0.1mg/ml Liberase TL (Roche). The tissue was then dissociated using the D program of the gentleMacs dissociator (Miltenyi Biotec) followed by 30 min incubation at 37°C.
FACS-seq protocol: Single cell sorting was performed at the Siteman Flow Cytometry Core (Washington University) using an iCyt Synergy sorter (Sony). Single cells were sorted directly into 10x lysis buffer (Clontech) in 96well PCR plates. Data were analyzed by using Flow Jo software (Version 9.6.2, Tree Star Inc).  96-well plates with single cell in each well were sealed and sent to the sequencing core at Washington University in St Louis (Genome Technology Access Center, GTAC). RNA from individual wells were processed with the Clonetech Smarter system and ligated with unique barcodes. Each plate was then pooled into one library and the resulting pools were then ligated to adapters containing unique 7bp index sequences so that samples originating from a single plate can be identified by Illumina conventional indexing strategies and each individual well is defined by barcoades sequenced on the first read of a paired end read pair. All plates were pooled into a single library and subjected to Illumina sequencing (HiSeq2500 2x50bp).
RNA libraries were prepared for sequencing using standard FACS-seq procedure

tag: protocol

value: Single cell FACS-seq

value: 8 wks

tag: cell population

tag: batch


title: Cell382


title: Cell379


title: Cell381


title: Cell380


title: Cell375


title: Cell376


title: Cell374


title: Cell377


title: Cell378


title: Cell373


title: Cell371


title: Cell372


title: Cell369


title: Cell368


title: Cell370


title: Cell365


title: Cell366


title: Cell364


title: Cell363


title: Cell383


title: Cell362


title: Cell360


title: Cell359


title: cowpea vs adzuki bean

type: genomic

city: Hangzhou

first: Pei

last: Xu

address: 198 Shiqiao Rd

department: Vegetable Institute

institute: Zhejiang Academy of Agricultural Sciences

description: no replicate

hyb_protocol: Genomic DNA from cowpea and adzuki bean were mixed with SeqCap EZ Developer Reagent. The SeqCap EZ Developer Reagent is an alternative of human Cot-1 DNA specifically designed for plants to minimize non-specific binding of probes and DNA. After being denatured at 95°C, the mixture was applied to the microarray, and the hybridization was carried out at 57°C for 40 hours (Oligo aCGH hybridization kit, Agilent Technologies).

scan_protocol: After hybridization, the microarray was washed with OligoaCGH wash buffer at 37°C, and slides were then dried. The arrays were then scanned using an Agilent Scanner (Agilent Technologies)

data_processing: The log2-intensities were extracted from raw microarray image files using the Agilent Feature Extraction software version 9.0

organism: Vigna unguiculata

source_name: Cowpea leaf

label_protocol: Genomic DNA from cowpea and adzuki bean were labeled with fluorochromes Cy3 and Cy5, respectively

growth_protocol: Seedlings were grown in a growth chamber with the ambient temperature cycle of 28°C (day)/22°C (night) and 16h/8h of photoperiod.

extract_protocol: DNA was extratced using the CTAB method

tag: cultivar

tag: origin

value: China

value: leaf

organism: Vigna angularis

source_name: Adzuki bean leaf

value: Suxiaodou 12


title: Cell361


title: Cell358


title: Cell367


title: Cell356


title: Cell351


title: Cell349


title: Cell354


title: Cell347


title: Cell345


title: Cell346


title: Cell344


title: Cell355


title: Cell348


title: Cell352


title: Cell341


title: Cell342


title: Cell339


title: Cell340


title: Cell343


title: Cell337


title: Cell335


title: Cell336


title: Cell333


title: Cell334


title: Cell357


title: Cell350


title: Cell331


title: Human K562 LaminB1 replicate1

city: Urbana

first: Andrew

middle: S

last: Belmont

state: IL

address: 601 S Goodwin Ave, CLSL B509

institute: University of Illinois at Urbana-Champaign

hyb_protocol: The labeled MePCR DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, 80 μg per sample was combined into 33.6 μl water, and mixed with 2.4 μl Alignment oligo, 24 μl hybridization component A, and 60 μl 2x Hybridization Buffer. The entire 120 μl was used for hybridization in Tecan hybridization stations for 16-18 h at 42C. Arrays were then washed in 42 °C Nimblegen washbuffer1, and room temperature Nimblegen washbuffer 2 and 3. All buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Microarrays were scanned in a Agilent Scanner (Model G2505C, Serial number US22502518), which uses Scan Control software (Version A.8.1.3). Slides were first placed in a slide holder before putting it in the Scanner Carousel, which was installed in the scanner. Slides were double-pass scanned at maximum PMT for each channel, at a 2 um per pixel resolution

data_processing: Arrays were quantified with NimbleScan 2.5. Raw .pair files were read with the Ringo package for R and the loess normalized. Subsequently, single channel data was obtained and subjected to quantile-quantile normalisation over all available cell types and replicates. The score was calculated as the log2 Dam-LaminB1: Dam ratio of the loess-quantile normalized data.

source_name: Dam-LaminB1 DamID DNA from K562 Cells

label_protocol: 2.0 µg MePCR DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3/Cy5 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html). Labeling time was extended to 2 hours to increase yield.

extract_protocol: 1.5x10e6 cells were infected with lenti-virus expressing either Dam-LaminB1 or only Dam. After 48 hours gDNA was isolated with the Bioline ISOLATE II Genomic DNA Kit per the manufacturers protocol. The DNA was precipitated with ethanol. 1.5µg genomic DNA was treated for 1 hour with 5 units of Antarctic phosphatase (New England Biolabs, cat nr M0289S) in 20µl of 1X Antarctic Phosphatase Reaction Buffer (New England Biolabs) followed by ethanol precipitation.  100-500 ng of gDNA was digested with DpnI (New England Biolabs)), adapters were ligated with T4 ligase ((New England Biolabs)), and the ligation reaction was subsequently digested with DpnII ((New England Biolabs)). 50-200 ng of the DpnII digested material was used as input for a PCR amplification of methylated fragments (MePCR), see Vogel et al., 2008, Nature Protocols for details. MePCR fragments were purified by ISOLATE II PCR and Gel Kit (Bioline).

tag: cell line

tag: expression

source_name: Dam-only DamID DNA from K562 Cells

value: Dam


title: Cell330

tag: age


title: Cell329


title: Cell328


title: Cell327


title: Cell326


title: Cell323


title: Cell321


title: Cell320


title: Cell316


title: Cell314


title: Human K562 LaminB1 replicate2


title: Cell315


title: Cell332


title: Cell313


title: Cell312


title: Cell310


title: Cell311


title: Cell308


title: Cell306


title: Cell309


title: Cell307


title: Cell322


title: Cell324


title: Cell305


title: Cell325


title: Cell304


title: Cell303


title: Cell319


title: Cell318


title: Cell317


title: Cell298


title: Cell301


title: Cell299


title: Cell297


title: Cell353


title: Cell294


title: Cell296


title: Cell293


title: Cell291


title: Cell292


title: Cell288


title: Cell290


title: Cell287


title: Cell289


title: Cell286


title: Cell285


title: Cell284


title: Cell283


title: Cell281


title: Cell300


title: Cell278


title: Cell279


title: Cell280


title: Cell282


title: Cell277


title: Cell274


title: Cell275


title: Cell295


title: Cell272


title: Cell302


title: Cell271


title: Cell273


title: Cell269


title: Cell267


title: Cell268


title: Cell265


title: Cell266


title: Cell264


title: Cell262


title: Cell263


title: Cell260


title: Cell259


title: Cell258


title: Cell257


title: Cell256


title: Cell255


title: Cell252


title: Cell254


title: Cell250


title: Cell251


title: Cell253


title: Cell249


title: Cell248


title: Cell247


title: Cell270


title: Cell246


title: Cell245


title: Cell244


title: Cell243


title: Cell239


title: Cell242


title: Cell241


title: Cell261


title: Cell240


title: Cell238


title: Cell237


title: Cell236


title: Cell231


title: Cell232


title: Cell235


title: Cell276


title: Cell230


title: Cell228


title: Cell226


title: Cell229


title: Cell223


title: Cell225


title: Cell224


title: Cell217


title: Cell222


title: Cell220


title: Cell218


title: Cell221


title: Cell216


title: Cell215


title: Cell234


title: Cell214


title: Cell233


title: Cell212


title: Cell209


title: Cell210


title: Cell208


title: Cell206


title: Cell227


title: Cell204


title: Cell207


title: Cell203


title: Cell202


title: Cell199


title: Cell219


title: Cell200


title: Cell198


title: Cell201


title: Cell197


title: Cell192


title: Cell194


title: Cell193


title: Cell195


title: Cell213


title: Cell190


title: Cell191


title: Cell211


title: Cell186


title: Cell189


title: Cell187


title: Cell182


title: Cell183


title: Cell184


title: Cell180


title: Cell181


title: Cell338


title: Cell177


title: Cell175


title: Cell176


title: Cell196


title: Cell174


title: Cell172


title: Cell205


title: Cell173


title: Cell169


title: Cell168


title: Cell170


title: Cell171


title: Cell166


title: Cell167


title: Cell165


title: Cell188


title: Cell163


title: Cell160


title: Cell162


title: Cell179


title: Cell158


title: Cell161


title: Cell157


title: Cell159


title: Cell156


title: Cell185


title: Cell178


title: Cell152


title: Cell153


title: Cell150


title: Cell149


title: Cell155


title: Cell164


title: Cell144


title: Cell143


title: Cell145


title: Cell141


title: Cell142


title: Cell140


title: Cell139


title: Cell146


title: Cell138


title: Cell137


title: Cell148


title: Cell134


title: Cell133


title: Cell136


title: Cell135


title: Cell132


title: Cell151


title: Cell154


title: Cell131


title: mESC_ATAC_seq

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071

institute: University of California, San Diego School of Medicine

data_processing:
Reads were mapped to mm10 genome using bowtie
Then, we Filter reads, eliminate PCR duplicates and mitochondrial reads
Next ,we converted read ends to account for Tn5 insertion position by moving the read end position by 4bp  towards the center of the fragment.
We converted paired-end read ends to single-ended read ends.
Last, we used MACS2 (2.1.1.20160309 when I ran it) with flags “—nomodel —shift 37 —ext 73 —pval 1e-2 -B —SPMR —call-sumits" to generate signal track and peak calls. Check https://github.com/kundajelab/atac_dnase_pipelines for code and more details.
Genome_build: mm10
Supplementary_files_format_and_content: Signal track file in bigwig format (https://genome.ucsc.edu/goldenpath/help/bigWig.html) and peak calls in BED format (https://genome.ucsc.edu/FAQ/FAQformat.html)

source_name: embryonic stem cells

growth_protocol: Cells were cultured on MEF feeder cells in serum free media (DMEM 10013-cv supplemented with 15% KSR, 2 mM L-glutamine, 100 μM nonessential amino acids, 50 μM beta-mercaptoethanol, 1000 units ml⁻¹ leukemia inhibitory factor (LIF), 100 units ml⁻¹ penicillin, and 100 μg ml⁻¹ streptomycin.) at 37°C with 5%CO2.

extract_protocol:
Cells were trypsinized and disassociated into single cell suspension. 100,000 were collected and incubated in 1ml cold NPB (0.2%NP-40, 5% BSA, 1mM DTT, 1x proteinase inhibitor in PBS) for 15min. NPB treated cells were resuspended in Tagmentation buffer and incubated with 0.5 μl Tagment DNA Enzyme 1 (FC-121-1030, Illumina) for 30min at 37 °C. Tagmented DNA were purified with QIAGEN MiniElute columns.
Tagmented DNA were PCR (NEB Next 2x PCR master mix, catalog M0541S)  amplified for 8 cycles using Illumina Nextera adapters. PCR products were purified and size selected for 200~750bp with Agencourt AMPure XP beads.

tag: tissue

value: E14 mouse embryonic stem cells


title: Cell129


title: Cell130


title: Cell147


title: P5HET 2

city: London

first: Albert

last: Basson

address: Floor 27, Tower Wing, Guy's Hospital

department: Craniofacial Development and Stem Cell Biology

country: United Kingdom

institute: King's College London

description:
mRNA fraction selected from total RNA before conversion to cDNA
P5read_counts_chd8.txt

data_processing:
Quality of raw sequencing files was checked using FastQC version 0.11.2 and trimming of adaptor sequences was performed using Trim Galore! Version 0.4.1
Reads were aligned to mouse genome mm10 using TopHat version 2.1.0 with parameters  -bowtie1 -r 150, -mate-std-dev=50, -p 8
Reads were counted using FeatureCounts version 1.5.0 with parameters -p -T 8 -F GTF
Read counts from technical replicates (i.e. from both lanes) were summed using the Deseq2 version 1.10.1 CollapseReplicates function.  Deseq2 version 1.10.1 was used for differential expression testing, using the DESeq command.
Genome_build: mm10 (GRCm38.p4)
Supplementary_files_format_and_content: Text file containing read counts for all samples assigned to features (genes)

source_name: Cortex

extract_protocol:
Total RNA was extracted from brain tissue samples using Trizol Reagent. RNA was purified using the Direct-Zol RNA Miniprep Kit (Zymo Research, CA, USA; Catalogue No. R2050) according to the manufacturer's recommendations.
Library Prep was performed by the Oxford Genomics Centre (Oxford, United Kingdom). mRNA was selected from total RNA and converted to cDNA. dUTP was incorporated during second strand cDNA synthesis. CDNA was end-repaired, A-tailed and adaptor ligated. Uridine digestion was performed before amplification of samples. Prepared libraries were size selected and multiplexed and paired-end sequencing was performed across 2 lanes of a flow cell on the Illumina HiSeq 4000 platform.

value: Cortex

tag: strain background

value: Postnatal day 5


title: P5WT 3


title: P5WT 2


title: P5WT 1


title: P5HET 3


title: Cell128


title: Cell127


title: Cell119


title: Cell126


title: Cell117


title: Cell125


title: Cell118


title: Cell122


title: Cell116


title: Cell123


title: Cell121


title: Cell124


title: P5HET 1


title: Cell120


title: Cell115


title: Cell114


title: Cell113


title: Cell112


title: Cell110


title: iPS2.D21.1 (bulk)

city: Cambridge

first: Ralda

last: Nehme

state: Ma

address: 415 Main St

institute: Broad Institute

data_processing:
Single cell RNA sequencing libraries were prepared  according to the SmartSeq2 protocol (Picelli et al. 2014) with minor modifications  (Trombetta et al. 2014). All libraries were prepared by the Broad Technology Labs and  sequenced by the Broad Genomics Platform. Briefly, total RNA was purified using  RNA-SPRI beads. Poly(A)+ mRNA was converted to cDNA which was then amplified.  cDNA was subject to transposon-based fragmentation that used dual-indexing to barcode  each fragment of each converted transcript with a combination of barcodes specific to  each sample. Each cell was given its own combination of barcodes. Barcoded cDNA  fragments were then pooled prior to sequencing. Sequencing was carried out as pairedend  2x25bp with an additional 8 cycles for each index. To obtain expression values for  each cell, the data was separated by barcode and aligned using Tophat version 2.0.10  (Kim et al. 2013) with default settings. Transcripts were quantified by the BTL  computational pipeline using Cuffquant version 2.2.1 (Trapnell et al. 2012).
The total  population RNA-seq fastq data was aligned against ENSEMBL human reference genome  (build GRCh37/hg19) using STAR (v.2.4.0) (Dobin et al. 2013). Cufflinks (v.2.2.1)  (Trapnell et al. 2012) was used to derive normalized gene expression in fragments per  kilo base per million (FPKM). The following analysis only included genes that had an  average expression of more than 1 FPKM (N (genes)=17922).
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: hiPS derived Neurons

growth_protocol: NGN2 expression was induced in TetO-NGN2-T2A-PURO/TetO-GFP infected human stem cells by exposure to doxycycline one day after plating. To induce patterning toward a forebrain phenotype, cells  were neuralized by inhibiting TGFβ and BMP signaling (treatment with SB431542 and LDN193189), and dorsalized by inhibiting Wnt signaling (treatment with XAV939, a tankyrase inhibitor) for three days. Puromycin was then applied to select for cells expressing NGN2 . At 4 days post-dox induction (day 4), cells were co-cultured with mouse astrocytes to promote neuronal maturation and synaptic  connectivity.

extract_protocol:
RNA was extracted using the Qiagen RNeasy plus micro kit for the total population RNA seq. For single cell RNAseq (SmartSeq2 library prep), cells were single-cell sorted into 5 μl of 1xTCL buffer (Qiagen,  #1031576). After sorting, plates were immediately sealed, spun down for 5 minutes at 550g and  flash frozen on dry-ice. Sorted cells were then stored at -80°C. Details
Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold for bulk RNAseq.For single cell RNAseq, Smart-Seq2 libraries were  prepared by the Broad Technology Labs and sequenced by the Broad Genomics Platform.

tag: time

tag: cell type

value: hiPS derived Neurons

value: bulk RNA


title: Cell111


title: iPS2.D21.2 (bulk)


title: iPS2.D49.1 (bulk)


title: iPS1.Nv5_D2.2 (bulk)

source_name: hiPS derived Neuronal Progenitors

value: hiPS derived Neuronal Progenitors


title: iPS2.Nv5_D3.2 (bulk)


title: iPS1.Nv5_D1.1 (bulk)


title: iPS2.D0.1 (bulk)

source_name: Pluripotent Stem Cells (hiPSC)

value: Pluripotent Stem Cells (hiPSC)


title: iPS2.D49.2 (bulk)


title: iPS1.D21.2 (bulk)


title: iPS2.Nv5_D3.3 (bulk)


title: iPS1.Nv5_D1.3 (bulk)


title: iPS2.Nv5_D2.1 (bulk)


title: Cell109


title: Cell107


title: Cell108


title: iPS2.D4.3 (bulk)


title: Cell106


title: iPS2.Nv5_D1.3 (bulk)


title: Cell105


title: iPS1.Nv5_D3.3 (bulk)


title: iPS2.D0.2 (bulk)


title: Cell102


title: Cell104


title: iPS1.Nv5_D1.2 (bulk)


title: iPS1.D4.2 (bulk)


title: Cell101


title: iPS1.D21.3 (bulk)


title: iPS2.D28.2 (bulk)


title: Cell99


title: Cell98


title: Cell97


title: iPS2.Nv5_D0.2.3 (bulk)


title: Cell100


title: iPS2.D4.2 (bulk)


title: Cell95


title: iPS1.Nv5_D4.2 (bulk)


title: iPS1.Nv5_D0.1 (bulk)


title: Cell96


title: Cell93


title: iPS1.D28.2 (bulk)


title: Cell94


title: Cell103


title: iPS1.D49.2 (bulk)


title: iPS2.D28.1 (bulk)


title: iPS1.Nv5_D3.2 (bulk)


title: Cell91


title: Cell90


title: Cell89


title: Cell92


title: iPS1.Nv5_D3.1 (bulk)


title: iPS2.D28.3 (bulk)


title: Cell88


title: iPS1.D14.3 (bulk)


title: iPS2.D0.3 (bulk)


title: iPS1.D14.2 (bulk)


title: iPS1.D28.1 (bulk)


title: Cell86


title: Cell84


title: Cell87


title: iPS2.Nv5_D4.1 (bulk)


title: Cell82


title: Cell83


title: iPS1.D49.3 (bulk)


title: Cell85


title: iPS1.D28.3 (bulk)


title: iPS2.D4.1 (bulk)


title: iPS1.D0.3 (bulk)


title: Cell80


title: Cell79


title: Cell81


title: Cell78


title: iPS2.D49.3 (bulk)


title: Cell77


title: Cell76


title: iPS1.D0.2 (bulk)


title: iPS1.Nv5_D4.1 (bulk)


title: Cell75


title: iPS2.Nv5_D2.2 (bulk)


title: Cell74


title: iPS2.D21.3 (bulk)


title: iPS1.Nv5_D0.2.3 (bulk)


title: Cell73


title: iPS1.D21.1 (bulk)


title: iPS1.Nv5_D2.3 (bulk)


title: Cell71


title: Cell70


title: iPS2.Nv5_D1.2 (bulk)


title: iPS1.D49.1 (bulk)


title: iPS1.D4.3 (bulk)


title: iPS1.D14.1 (bulk)


title: iPS2.Nv5_D2.3 (bulk)


title: Cell69


title: Cell68


title: iPS1.Nv5_D2.1 (bulk)


title: Cell67


title: Cell66


title: iPS2.Nv5_D3.1 (bulk)


title: iPS2.D14.2 (bulk)


title: Cell64


title: Cell65


title: Cell63


title: iPS1.Nv5_D4.3 (bulk)


title: iPS2.Nv5_D1.1 (bulk)


title: iPS2.D14.3 (bulk)


title: Cell72


title: Cell61


title: iPS1.D0.1 (bulk)


title: Cell60


title: Cell62


title: Cell59


title: iPS2.Nv5_D0.1 (bulk)


title: iPS2.Nv5_D4.2 (bulk)


title: iPS1.D4.1 (bulk)


title: iPS2.Nv5_D4.3 (bulk)


title: Cell57


title: Cell55


title: iPS2.D14.1 (bulk)


title: Cell54


title: RIS_shHMGA1_R4

first: Shamith

last: Samarajiwa

address: ICTEM Building, Hammersmith Campus, Du Cane Road,

department: Genetics and Genomics Section  Department of Metabolism, Digestion and Reproduction

institute: Imperial College London

data_processing:
Reads were mapped to the Human reference genome hg19 with the STAR (version 2.5.0b) aligner
Low quality reads (mapping quality less than 20) as well as known adapter contamination were filtered out using Cutadapt (version 1.10.0)
Read counting was performed using Bioconductor package Rsubread and differential expression analysis with edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: Read counts per gene calculated using Rsubread.

extract_protocol:
RNA was prepared using the Qiagen RNeasy plus kit (74136, Qiagen) according to the manufacturer’s instructions and reverse-transcribed to cDNA using the Applied Biosystems High-Capacity Reverse Transcription Kit (43-688-13, Thermo Fischer).
Libraries were prepared from 6 biological replicates of each condition using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to manufacturers instructions and sequenced using the HiSeq-2500 platform (Illumina).

treatment_protocol: Cells were retrovirally infected with ER:HRAS(G12V) and either MSCV vector or MSCV miR30 shHMGA1. For RIS samples, cells are treated for 6 days with 4OHT.

tag: agent

tag: vector 1

tag: vector 2

value: MSCV miR30 shHMGA1

tag: passage


title: RIS_shHMGA1_R6


title: RIS_shHMGA1_R3


title: RIS_shHMGA1_R5


title: RIS_shHMGA1_R2


title: Cell52


title: Cell51


title: Cell50


title: RIS_Vector_R6

value: MSCV Vector


title: RIS_shHMGA1_R1


title: Cell58


title: RIS_Vector_R5


title: Cell56


title: Cell49


title: RIS_Vector_R4


title: Cell48


title: Cell53


title: RIS_Vector_R3


title: Cell47


title: Cell46


title: Growing_shHMGA1_R6


title: RIS_Vector_R1


title: Cell45


title: Cell44


title: Growing_shHMGA1_R5


title: Cell43


title: Growing_shHMGA1_R4


title: RIS_Vector_R2


title: Cell42


title: Growing_shHMGA1_R3


title: Cell41


title: Growing_shHMGA1_R2


title: Cell40


title: Growing_shHMGA1_R1


title: Cell39


title: Growing_Vector_R6


title: Growing_Vector_R5


title: Cell38


title: Cell37


title: colorectal carcinoma tissue-14

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

description: Gene expression data from colorectal carcinoma tissue

hyb_protocol: Following fragmentation(94 °C for 35 min), 10 ug of cRNA were hybridized for 16 hr at 45℃(60 rpm) on PrimeView™ Human Gene Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method.

source_name: colorectal carcinoma tissues

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol (Thermo Fisher Scientific) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Samples from colorectal cancer patients were processed with routine methods for snap frozen and stored in liquid nitrogen until use.

value: colorectal carcinoma


title: colorectal carcinoma tissue-11


title: colorectal carcinoma tissue-13


title: Growing_Vector_R4


title: colorectal carcinoma tissue-12


title: genomic DNA from bone marrow 31

city: Houston

first: Koichi

last: Takahashi

state: TX

address: 1881 East Road

institute: UT MD Anderson Cancer Center

description:
SAMPLE 31
200970090037_R01C01

hyb_protocol: genomic DNA from bone marrow samples was treated with sodium bisulfite and then processed by whole genome amplification, enzymatic fragmentation and hybridization to bead chips at 48ºC for 17 hours.

scan_protocol: The hybridized chips were scanned on iScan (Illumina, San Deigo, CA) to generate IDAT files.

data_processing:
ChAMP R package was used for data processing and normalization following the program’s default procedures.
data normalization was performed using BMIQ method

label: cy3, cy5

source_name: bone marrow sample from MPAL patient

label_protocol: standard Illumina Protocol

extract_protocol: genomic DNA was extracted from diagnostic bone marrow aspirate using an Autopure extractor (QIAGEN/Gentra, Valencia, CA).

tag: subject status

value: mixed phenotype acute leukemia (MPAL) patient

tag: subject id

value: MPAL patient 31

value: bone marrow


title: genomic DNA from bone marrow 28

description:
SAMPLE 28
200970090029_R01C01

value: MPAL patient 28


title: Growing_Vector_R3


title: genomic DNA from bone marrow 22

description:
SAMPLE 22
200970090037_R05C01

value: MPAL patient 22


title: genomic DNA from bone marrow 29

description:
SAMPLE 29
200970090037_R07C01

value: MPAL patient 29


title: genomic DNA from bone marrow 25

description:
SAMPLE 25
200970090009_R01C01

value: MPAL patient 25


title: genomic DNA from bone marrow 23

description:
SAMPLE 23
200970090047_R01C01

value: MPAL patient 23


title: colorectal carcinoma tissue-9


title: genomic DNA from bone marrow 30

description:
SAMPLE 30
200970090047_R04C01

value: MPAL patient 30


title: Cell34

tag: protocol

value: Single cell FACS-seq

value: 8 wks

tag: cell population


title: Growing_Vector_R1


title: genomic DNA from bone marrow 26

description:
SAMPLE 26
200970090009_R05C01

value: MPAL patient 26


title: genomic DNA from bone marrow 18

description:
SAMPLE 18
200970090029_R03C01

value: MPAL patient 18


title: Cell36

tag: batch


title: genomic DNA from bone marrow 16

description:
SAMPLE 16
200970090037_R03C01

value: MPAL patient 16


title: colorectal carcinoma tissue-7


title: genomic DNA from bone marrow 13

description:
SAMPLE 13
200970090047_R06C01

value: MPAL patient 13


title: colorectal carcinoma tissue-10


title: genomic DNA from bone marrow 27

description:
SAMPLE 27
200970090009_R08C01

value: MPAL patient 27


title: genomic DNA from bone marrow 10

description:
SAMPLE 10
200970090029_R06C01

value: MPAL patient 10


title: genomic DNA from bone marrow 11

description:
SAMPLE 11
200970090037_R06C01

value: mixed phenotype acute leukemia (MPAL) patient

value: MPAL patient 11


title: Cell32


title: genomic DNA from bone marrow 21

description:
SAMPLE 21
200970090009_R04C01

value: MPAL patient 21

value: bone marrow


title: Cell35


title: genomic DNA from bone marrow 15

description:
SAMPLE 15
200970090009_R06C01

value: MPAL patient 15


title: genomic DNA from bone marrow 9

description:
SAMPLE 9
200970090029_R04C01

value: MPAL patient 9


title: genomic DNA from bone marrow 20

description:
SAMPLE 20
200970090047_R08C01

value: MPAL patient 20


title: genomic DNA from bone marrow 14

description:
SAMPLE 14
200970090009_R02C01

value: MPAL patient 14


title: colorectal carcinoma tissue-6

value: colorectal carcinoma


title: Cell31

value: Single cell FACS-seq


title: genomic DNA from bone marrow 8

description:
SAMPLE 8
200970090037_R08C01

value: MPAL patient 8


title: genomic DNA from bone marrow 12

description:
SAMPLE 12
200970090047_R02C01

value: MPAL patient 12


title: Cell33

value: 8 wks


title: genomic DNA from bone marrow 19

description:
SAMPLE 19
200970090029_R08C01

value: MPAL patient 19


title: genomic DNA from bone marrow 17

description:
SAMPLE 17
200970090009_R07C01

value: MPAL patient 17


title: Cell28


title: genomic DNA from bone marrow 7

description:
SAMPLE 7
200970090037_R04C01

value: MPAL patient 7


title: genomic DNA from bone marrow 24

description:
SAMPLE 24
200970090047_R05C01

value: MPAL patient 24


title: colorectal carcinoma tissue-5


title: Cell26


title: Cell30


title: Cell25


title: Cell24


title: colorectal carcinoma tissue-1


title: colorectal carcinoma tissue-4


title: non-cancerous surrounding tissue-13

description: Gene expression data from non-cancerous colorectal tissue

source_name: non-cancerous colorectal tissue

value: non-cancerous colorectal


title: colorectal carcinoma tissue-3


title: colorectal carcinoma tissue-2


title: Cell21


title: non-cancerous surrounding tissue-11


title: non-cancerous surrounding tissue-12


title: Cell27


title: Cell20


title: Growing_Vector_R2

value: MSCV Vector


title: Cell23


title: Cell18


title: Cell19


title: non-cancerous surrounding tissue-10


title: non-cancerous surrounding tissue-14


title: non-cancerous surrounding tissue-8


title: non-cancerous surrounding tissue-6


title: non-cancerous surrounding tissue-9


title: Cell17


title: Cell16


title: non-cancerous surrounding tissue-7


title: Cell15


title: Cell13


title: non-cancerous surrounding tissue-5


title: Cell14


title: Cell11


title: non-cancerous surrounding tissue-2


title: Cell9


title: non-cancerous surrounding tissue-1


title: non-cancerous surrounding tissue-4


title: non-cancerous surrounding tissue-3


title: Cell12


title: Cell8


title: colorectal carcinoma tissue-8


title: Cell7


title: Cell6


title: Cell5


title: Cell4


title: Cell2


title: Cell3


title: genomic DNA from bone marrow 4

description:
SAMPLE 4
200970090047_R03C01

value: mixed phenotype acute leukemia (MPAL) patient

value: MPAL patient 4


title: Cell22


title: genomic DNA from bone marrow 3

description:
SAMPLE 3
200970090029_R07C01

value: MPAL patient 3

value: bone marrow


title: genomic DNA from bone marrow 5

description:
SAMPLE 5
200970090047_R07C01

value: MPAL patient 5


title: Cell1


title: Cell29


title: iPS2 D28 Camk2A+ hpiNs (single cells; SSF899)

description:
iPS2_D28_Camk2A_hpiNs_SSF899.genes.fpkm_table.txt
SSF-899_fpkm_table_rawfiles_README.txt

value: hiPS derived Neurons

tag: sample type

value: single cell RNA


title: genomic DNA from bone marrow 6

description:
SAMPLE 6
200970090009_R03C01

value: MPAL patient 6


title: iPS1 D28 Camk2A+ hpiNs (single cells; SSF896)

description:
iPS1_D28_Camk2A_hpiNs_SSF896.genes.fpkm_table.txt
SSF-896_fpkm_table_rawfiles_README.txt

tag: cell line


title: iPS2 D28 hpiNs (single cells; SSF900)

description:
iPS2_D28_hpiNs_SSF900.genes.fpkm_table.txt
SSF-900_fpkm_table_rawfiles_README.txt


title: iPS1 D28 hpiNs (single cells; SSF897)

description:
iPS1_D28_hpiNs_SSF897.genes.fpkm_table.txt
SSF-897_fpkm_table_rawfiles_README.txt


title: genomic DNA from bone marrow 2

description:
SAMPLE 2
200970090029_R02C01

value: MPAL patient 2


title: genomic DNA from bone marrow 1

description:
SAMPLE 1
200970090037_R02C01

value: MPAL patient 1


title: Cell10

value: Single cell FACS-seq

value: 8 wks


title: Cetuximab resistant clones derived from SCC25, CTXR12

city: Baltimore

first: Elana

middle: Judith

last: Fertig

state: MD

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

hyb_protocol: Samples were loaded to the Beadchip and incubated in the Illumina Hybridization Oven, according to manufacturer's protocol

scan_protocol: Beadchips were scanned using the Methylation Module of GenomeStudio 1.0 of the Illumina HiScan equiptment.

data_processing: iDat files were loaded with minfi version 1.16.1 and used to compute beta values for each probe.

label: Cy5 and Cy3

source_name: SCC25 clone, PBS, CTXR12

label_protocol: Infinium Human MethylationEPIC Beadchip Kit (Illumina), following manufacturer's instructions.

extract_protocol: Dneasy Blood & Tissue Kit following manufacturer's instructions.

value: SCC25 cetuximab resistant clone 12

tag: generations

tag: treatment

tag: cetuximab resistant clone


title: WT Rep 4

city: Minneapolis

first: Christine

middle: M.

last: Henzler

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota, Twin Cities (Minneapolis, MN, US)

data_processing:
Illumina HiSeq 2000 software used for basecalling
Raw reads were first groomed by trimming the first 12bpfrom the 5'-ends with random base concentration, then mapped to UCSC mm10 using STAR aligner (STAR-2.5.3a)
Expression level for each gene was estimated using Python program HTSeq (Anders et al., Bioinformatics 2014). Specifically htseq-count function of HTSeq accumulated the number of aligned reads that falls under
Using the obtained read counts, differential gene analyses were carried out using the DESeq2 package in the R environment.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Text files inclue read counts value for each gene; individual file for each sample.

source_name: Brain cerebellar tissue

growth_protocol: standard animal house conditions

extract_protocol:
Mice were euthanized under anesthesia and cerebella were quickly dissected over ice. RNA was extracted following published protocols. Isolated RNA was submitted to the University of Minnesota Genomics Center. Sample quality checks using the NanoDrop spectrophotometer and Agilent Bioanalyzer 2100 were conducted.
Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3’ poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer’s protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.

tag: strain

value: FVB

tag: tissue

value: Cerebellum

tag: genotype


title: WT Rep 5


title: HNSCC sensitive cell line SCC25 baseline 2

source_name: cell line SCC25, parental cell line

value: SCC25 parental cell line


title: WT Rep 3


title: Cetuximab resistant clones derived from SCC25, CTXR11

source_name: SCC25 clone, PBS, CTXR11

value: SCC25 cetuximab resistant clone 11


title: WT Rep 2


title: WT Rep 1


title: 82Q Rep 4


title: Cetuximab resistant clones derived from SCC25, CTXR7

source_name: SCC25 clone, PBS, CTXR7

value: SCC25 cetuximab resistant clone 7


title: HNSCC sensitive cell line SCC25 treated with 100nM cetuximab, week 10

source_name: cell line SCC25,cetuximab,week 10

value: CTX generation 10 for SCC25 cetuximab resistant generations

value: 100nM Cetuximab


title: Cetuximab resistant clones derived from SCC25, CTXR9

source_name: SCC25 clone, PBS, CTXR9

value: SCC25 cetuximab resistant clone 9


title: Cetuximab resistant clones derived from SCC25, CTXR5

source_name: SCC25 clone, PBS, CTXR5

value: SCC25 cetuximab resistant clone 5


title: 82Q Rep 3


title: Cetuximab resistant clones derived from SCC25, CTXR1

source_name: SCC25 clone, PBS, CTXR1

value: SCC25 cetuximab resistant clone 1


title: 82Q Rep 5


title: Cetuximab resistant clones derived from SCC25, CTXR8

source_name: SCC25 clone, PBS, CTXR8

value: SCC25 cetuximab resistant clone 8


title: Cetuximab resistant clones derived from SCC25, CTXR2

source_name: SCC25 clone, PBS, CTXR2

value: SCC25 cetuximab resistant clone 2


title: HNSCC sensitive cell line SCC25 treated with PBS, week 9

source_name: cell line SCC25,PBS,week 9

value: PBS generation 9 for SCC25 cetuximab resistant generations

value: PBS


title: HNSCC sensitive cell line SCC25 baseline 1


title: 82Q Rep 1


title: HNSCC sensitive cell line SCC25 treated with 100nM cetuximab, week 11

source_name: cell line SCC25,cetuximab,week 11

value: CTX generation 11 for SCC25 cetuximab resistant generations


title: Cetuximab resistant clones derived from SCC25, CTXR3

source_name: SCC25 clone, PBS, CTXR3

value: SCC25 cetuximab resistant clone 3


title: Cetuximab resistant clones derived from SCC25, CTXR10

source_name: SCC25 clone, PBS, CTXR10

value: SCC25 cetuximab resistant clone 10