title: E11_5_15_GGACTCCT-CTCTCTAT_0


title: E11_5_13_AGGCAGAA-CTCTCTAT_0

status: Public on Oct 18 2018

type: SRA

city: Seattle

first: Raghav

last: Chawla

state: WA

address: 3720 15th Ave NE

department: Department of Genome Sciences

country: USA

institute: University of Washington

library_source: transcriptomic

data_processing:
Reads were aligned to the mouse reference genome build mm10 with TopHat (v2.0.13), which was provided with gene annotations from GENCODE (vM2).
Gene expression profiles for each cell were computed using Cufflinks (2.2.0).
Genome_build: mm10
Supplementary_files_format_and_content: The tarball includes gene and isoform FPKM tables, as well as samples annotations and gene attributes tables from the Cufflinks output.

molecule: total RNA

organism: Mus musculus

extract_protocol:
Single-cell suspensions were prepared from pancreata of Neurogenin 3-eGFP mouse embryos sacrificed at different days of embryonic development. Single eGFP-positive cells were FACS-sorted into 96-well plates, and single-cell cDNA was prepared using the SMART-seq protocol.
Single-cell sequencing libraries were generated using the Nextera XT DNA library preparation kit.

tag: tissue

value: Single-cell from pancreata of Neurogenin 3-eGFP mouse embryo

tag: developmental stage


title: HP-7

city: Durham

first: Integrative

last: Bioinformatics

state: NC

address: 111 TW Alexander Drive

department: BCBB

institute: NIEHS

description:
151HP_HF
processed data file: HP_NormalizedReadCounts.xls
11961X24_151210_D00294_0212_AC8B1PANXX_8

data_processing:
Fastq files were aligned to the human Hg38 reference genome with the STAR aligner using the Web interface application Oasis (https://oasis.dzne.de/index.php)
Raw read count files for known and novel small RNAs were generated using miRDeep2 as part of the online Oasis sRNA Detection application
Normalized read counts (counts per million reads (CPM)) and differentially expressed genes were determined using DESeq2 as part of the Oasis DE Analysis application
Genome_build: Homo sapiens Hg38
Supplementary_files_format_and_content: Excel file with small RNA IDs, predicted structure, chromosome coordinates, start and stop, strand and normalized read counts (CPM)

organism: Homo sapiens

source_name: Colon

extract_protocol:
DirectZOL (ZymoResearch)
Illumina TruSeq Small RNA Sample Prep (10613 experiment) and NEBNext Multiplex Small RNA Library Prep for Illumina (11961 and 13689 experiments)

tag: cohort

value: Sporadic

tag: tissue subtype

value: Hyperplastic polyp


title: HP-3

description:
132HP_S
processed data file: HP_NormalizedReadCounts.xls
10613X8_140320_SN141_0774_AC3RBEACXX_8


title: HP-6

description:
105HP_S
processed data file: HP_NormalizedReadCounts.xls
11961X23_151210_D00294_0212_AC8B1PANXX_8


title: E11_5_14_TCCTGAGC-CTCTCTAT_0

source_name: pancreata of Neurogenin 3-eGFP mouse embryo


title: HP-5

description:
76HP_S
processed data file: HP_NormalizedReadCounts.xls
11961X22_151210_D00294_0212_AC8B1PANXX_8


title: HP-2

description:
152HP_R
processed data file: HP_NormalizedReadCounts.xls
11961X48_151207_D00550_0309_BC8AP8ANXX_8

value: Serrated Polyposis


title: E11_5_10_CGAGGCTG-TAGATCGC_0


title: SSA/P-16

description:
314SSA/P_A
processed data file: SSAP_NormalizedReadCounts.xls
13689X48_161114_D00294_0271_ACAATKANXX_5

value: Sessile serrated adenoma/polyp


title: SSA/P-14

description:
304SSA/P_A
processed data file: SSAP_NormalizedReadCounts.xls
13689X17_161114_D00294_0271_ACAATKANXX_4


title: HP-1

description:
152HP_S
processed data file: HP_NormalizedReadCounts.xls
11961X47_151207_D00550_0309_BC8AP8ANXX_8


title: SSA/P-15

description:
195SSA/P_A
processed data file: SSAP_NormalizedReadCounts.xls
13689X34_161114_D00294_0271_ACAATKANXX_5


title: SSA/P-13

description:
157SSA/P_A
processed data file: SSAP_NormalizedReadCounts.xls
11961X46_151216_D00550_0312_BC8B1RANXX_8


title: 15% P 88.3

city: Fort Collins

first: Devin

last: Wahl

state: Colorado

address: 1582 Campus Delivery, Moby Reception

institute: Colorado State University

data_processing:
primary sequencing with Illumina bcl2fastq 2.18.0 12 pipeline
aligned against mus musculus mm10 and Tophat aligner (v2.0.14) used to reads genomic sequences
transcripts assembled with Stringtie tool v1.2.4
raw gene counts analysed by featurecounts (v.1.4.6) and differential gene expression by DESeq2 (v1.16.1) in R
GSEA completeled by setrank method and heatmaps generated in R.
Genome_build: Mus musculus genome (Build version mm10)
Supplementary_files_format_and_content: FPKM

source_name: Whole Hippocampus

extract_protocol:
RNA was isolated from total hippocampus with the trizol method, quantified with Qubit RNA Assay Kit (Life Technologies) and quality controlled with RNA6000 Nano Kit and BioAnalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA).
Approximately 300 ng was used as input for the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA), and sequencing libraries were created according to the manufacturer’s protocol. Briefly, poly-A containing mRNA molecules were purified using poly-dT magnetic beads. After purification, the mRNA was fragmented, and first-strand cDNA was produced using random primers and reverse transcriptase. Second-strand cDNA synthesis was then performed using DNA polymerase I and RNase H. The 3’ end of cDNAs was adenylated then ligated to indexed Illumina adapters and enriched with PCR to create the cDNA library. The library was then sequenced on a HiSeq 2500 (Illumina, Inc.) instrument as per manufacturer’s instructions with 100 cycles of single-end sequencing.

tag: Sex

value: Female

tag: age

value: 15 months


title: 15% P 85.3

value: Male


title: 15% P 44.3


title: HP-10

description:
303HP_S
processed data file: HP_NormalizedReadCounts.xls
13689X14_161114_D00294_0271_ACAATKANXX_4


title: 15% P 24.3


title: SSA/P-11

description:
100SSA/P_S
processed data file: SSAP_NormalizedReadCounts.xls
10613X10_140320_SN141_0774_AC3RBEACXX_8


title: 15% P 19.3


title: 15% P 43.4


title: 10% P 82.3


title: E11_5_16_TAGGCATG-CTCTCTAT_0


title: SSA/P-9

description:
17SSA/P_A
processed data file: SSAP_NormalizedReadCounts.xls
11961X21_151210_D00294_0212_AC8B1PANXX_8


title: E11_5_12_CGTACTAG-CTCTCTAT_0


title: E11_5_11_TAAGGCGA-CTCTCTAT_0


title: 10% P 79.3


title: 10% P 40.3


title: SSA/P-8

description:
14SSA/P_T
processed data file: SSAP_NormalizedReadCounts.xls
11961X20_151210_D00294_0212_AC8B1PANXX_8


title: 10% P 37.3


title: SSA/P-7

description:
14SSA/P_A
processed data file: SSAP_NormalizedReadCounts.xls
11961X19_151210_D00294_0212_AC8B1PANXX_8


title: 10% P 15.3


title: SSA/P-5

description:
13SSA/P_C
processed data file: SSAP_NormalizedReadCounts.xls
11961X17_151207_D00550_0309_BC8AP8ANXX_8


title: SSA/P-6

description:
14SSA/P_C
processed data file: SSAP_NormalizedReadCounts.xls
11961X18_151210_D00294_0212_AC8B1PANXX_8


title: HP-4

description:
111HP_R
processed data file: HP_NormalizedReadCounts.xls
10613X12_140320_SN141_0774_AC3RBEACXX_8


title: SSA/P-4

description:
11SSA/P_T
processed data file: SSAP_NormalizedReadCounts.xls
11961X16_151207_D00550_0309_BC8AP8ANXX_8


title: 10% P 14.3


title: 5% P 56.3


title: SSA/P-3

description:
15SSA/P_T
processed data file: SSAP_NormalizedReadCounts.xls
10613X6_140320_SN141_0774_AC3RBEACXX_8


title: SSA/P-12

description:
156SSA/P_A
processed data file: SSAP_NormalizedReadCounts.xls
11961X45_151216_D00550_0312_BC8B1RANXX_8


title: 5% P 55.3


title: SSA/P-2

description:
13SSA/P_A
processed data file: SSAP_NormalizedReadCounts.xls
10613X4_140320_SN141_0774_AC3RBEACXX_8


title: SSA/P-10

description:
152SSA/P_T
processed data file: SSAP_NormalizedReadCounts.xls
11961X44_151207_D00550_0309_BC8AP8ANXX_8


title: 5% P 8.3


title: 5% P 31.3


title: SSA/P-1

description:
11SSA/P_A
processed data file: SSAP_NormalizedReadCounts.xls
10613X2_140320_SN141_0774_AC3RBEACXX_8


title: G532_CT_3

city: Toronto

first: Xi

last: Huang

address: 686 Bay Street,

country: Canada

institute: SickKids

data_processing:
fastq reads were aligned to the hg19 transcriptome using kallisto 0.43.0 with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files containing transcript ID, transcript length, effective length, estimated counts, and abundance in TPM were generated using kallisto 0.43.0

molecule: polyA RNA

source_name: G532 with scrambled shRNA rep3

growth_protocol: G508 and G532 GBM stem cell lines were cultured using neural basal medium supplemented with glutamine, N2, B27, 25 ng/ml basic FGF and 25 ng/ml human EGF without addition of serum.

extract_protocol:
Total RNA was isolated from the cells using PureLinkTM RNA mini kit using manufacturer’s protocol (Thermo Fisher Scientific, Cat no. 12183018A).
polyA libraries were prepared according to manfacturer's instructions for the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® kit.

treatment_protocol: G508 and G532 GBM stem cell lines were treated with scrambled shRNA, shPIEZO1 #1, shPIEZO1 #2 and subjected to RNAseq analysis.

tag: cell line

tag: cell type

value: glioblastoma stem cells

tag: shRNA

value: scrambled shRNA


title: 5% P 32.3


title: G532_KD2_3

source_name: G532 with PIEZO1 shRNA #2 rep3

value: PIEZO1 shRNA #2


title: 5% P 7.3


title: ChowCR 121.3


title: ChowCR 122.3


title: ChowCR 100.3


title: G508_CT_3

source_name: G508 with scrambled shRNA rep3


title: G532_KD1_3

source_name: G532 with PIEZO1 shRNA #1 rep3

value: PIEZO1 shRNA #1


title: G508_KD2_3

source_name: G508 with PIEZO1 shRNA #2 rep3


title: ChowCR 99.3


title: ChowCR 97.3


title: ChowCR 98.3


title: Chow 49.3


title: G532_KD2_2

source_name: G532 with PIEZO1 shRNA #2 rep2


title: Chow 26.3


title: G532_KD1_2

source_name: G532 with PIEZO1 shRNA #1 rep2


title: G508_CT_2

source_name: G508 with scrambled shRNA rep2


title: G532_CT_2

source_name: G532 with scrambled shRNA rep2


title: Chow 50.3


title: Chow 25.3


title: G508_KD2_2

source_name: G508 with PIEZO1 shRNA #2 rep2


title: G532_CT_1

source_name: G532 with scrambled shRNA rep1


title: Chow 1.3


title: G532_KD1_1

source_name: G532 with PIEZO1 shRNA #1 rep1


title: G532_KD2_1

source_name: G532 with PIEZO1 shRNA #2 rep1


title: G508_CT_1

source_name: G508 with scrambled shRNA rep1


title: G508_KD2_1

source_name: G508 with PIEZO1 shRNA #2 rep1


title: G508_KD1_1

source_name: G508 with PIEZO1 shRNA #1 rep1


title: G508_KD1_3

source_name: G508 with PIEZO1 shRNA #1 rep3


title: G508_KD1_2

source_name: G508 with PIEZO1 shRNA #1 rep2


title: HS.3

city: Bethesda

first: Matthew

middle: J

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

description: iPSC derived neural stem cells from Hurler-Scheie replicate 3

data_processing:
Fastq files were generated from reads passing chastity filter.
Transcript level quantitation was performed using Kallisto v0.42.4 employing a merged transcript cDNA and ncRNA FASTA file downloaded from the Ensembl v82 ftp site.
Gene level quantification was generated by summarization of the transcript level quantitation using tximport v1.2 with the option “countFromAbundance=lengthScaledTPM”. The gene level count values were TMM normalized and converted to count per million (CPM) via edgeR v3.30.12.
Differential expression (DE) analysis of the organoid data was performed for each time-wise culturing condition using limma (3.24.15) with voom and eBayes functions. Genes having a mean of 10 counts-per-million (CPM) expression in at least one group were used in the analysis and those showing Benjamini-Hochberg false discovery rate (FDR) of < 1% and minimum fold change of 2 were considered in significant DE category.
Genome_build: GRCm38.p3 using Ensembl v82 annotation
Supplementary_files_format_and_content: Tab delimited text files containing transcript level counts, gene level counts, normalized gene level counts-per-million, or differential expression results.

source_name: iPSC derived neural stem cells

growth_protocol: Control human iPSC-derived NSCs were obtained from xCell Science (Novato, CA). All NSCs were cultured in StemPro® NSC SFM media (Thermo Fisher cat #A10509-01- 500ml KnockOut DMEM/F-12 basal medium + 10 ml StemPro NSC SFM Supplement + 10 µg FGF Basic Recombinant Human & 10 µg EGF Recombinant Human). For generating MPS I syndrome specific iPSCs, we obtained the following skin fibroblasts from Coriell Cell Repository (Camden, NJ) (Fig. 1A): GM00415, Hurler Syndrome,4 year old male but mutation not listed;  GM00963, Hurler-Scheie Syndrome, 5 year old Caucasian but no mutation listed;  GM01256, Scheie Syndrome, 12 year old male carrying compound heterozygous mutations – G>A transition in intron 5 at position -7 from exon 6 (IVS5AS-7G>A) and G>A at nucleotide 1293 in exon 9 [Trp402Ter (W402X)]. Fibroblast lines were reprogrammed to iPSCs using the non-integrating CytoTune-iPSC Sendai Reprogramming Kit (Thermo Fisher) as described (Beers et al., 2015).

extract_protocol:
RNeasy Midi kit (cat #75144) from Qiagen (Gaithersburg, MD) was used for total RNA isolation from human NSCs cultured in 6-well plates.
TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego CA)

treatment_protocol: The iPSCs were expanded and differentiated into NSCs using the PSC Neural Induction medium (Thermo Fisher, cat #A1647801). Briefly, high quality human iPSCs were rinsed with PBS and dislodged with 0.5 mM EDTA for 4-5 minutes. Cells were triturated, counted, and seeded in freshly coated Matrigel 6-well plates at 1x106 cells/ml in Essential 8 medium supplemented with 10 µM Rock Inhibitor to prevent cell death. The following day cells were induced in PSC Neural Induction medium and continued culture for 5 to 7 days. NSCs were harvested and expanded for 5 passages in Neural Induction medium containing neurobasal medium and 1X neural induction supplement (Thermo Fisher, cat #A1647801) and later switched to StemPro® NSC SFM media.

value: iPSC derived neural stem cells

tag: disease state

value: Hurler-Scheie


title: H.1

description: iPSC derived neural stem cells from Hurler replicate 1

value: Hurler


title: HS.2

description: iPSC derived neural stem cells from Hurler-Scheie replicate 2


title: HS.1

description: iPSC derived neural stem cells from Hurler-Scheie replicate 1


title: S.1

description: iPSC derived neural stem cells from Scheie replicate 1

value: Scheie


title: H.2

description: iPSC derived neural stem cells from Hurler replicate 2


title: RAG_CTCF_2

city: Edinburgh

first: nick

last: gilbert

address: Crewe Rd

department: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: University of Edinburgh

library_source: genomic

data_processing:
Trim Galore (v0.4.1) was used to remove adapter sequence from paired end fastq files.
Trimmed reads were “in silico digested” using a custom script to split fastq records at GATC; for each paired end read this gives a group of shorter sequences.
Bowtie (v 1.1.1) was used to map each fragement in “single end” mode.
Groups of mapped fragments originating from the same pair of reads were identified, and a custom script used to remove duplicates, and identify target-report pairs.
Custom scripts were used to generate pile-ups of informative reads, and generate binned and smoothed interaction profiles for each target.
Genome_build: mm9
Supplementary_files_format_and_content: BedGraphs of raw pile-up of interactions, and binned and smoothed interaction profiles for each target.

molecule: genomic DNA

source_name: RAG cells

growth_protocol: β-TC3, MV+ and RAG cells were cultured in Dulbecco’s Modified Eagle Medium (ThermoFisher) supplemented with 10% fetal calf serum and 1% Penicillin-Streptomycin at 37°C in 5% CO2

extract_protocol:
Cells were further lysed by re-suspension in water, and then in 0.5 % SDS at 62 C for 10 min. Each replicate was split between three tubes, re-suspend in 800 l 1 DpnII buffer (NEB) with 1.6 % TritonX100, and digested with 3 sequential additions of 750 units DpnII enzyme at 37 C 1200rpm over 24 hours. Samples were heat inactivated at 65 C for 20 min, and 3 samples from each replicate combined into 7 ml with 1T4 DNA Ligase Buffer (NEB), with 1 % TritonX100, and 12,000 units of T4 DNA ligase at 16 C overnight. Samples were treated with Protinease K at 65 C overnight and RNase A/T1 (ThermoFisher) at 37 C for 1 hour, before a standard Phenol Chloroform/Chloroform extraction and ethanol precipitation was performed. Complete digestion and ligation was assessed by gel electrophoresis. Purified 3C DNA from each sample was sonicated to 200-400 bp with a Soniprep 150 probe sonicator at 4 C, and purified with a standard Ampure XP Bead protocol (Beckman Coulter) using a 1/1.5 DNA to bead ratio.  Two Illumina sequencing libraries were prepared per capture pool replicate, with 6 g of starting DNA in each, and generated using NebNext DNA Library Prep Kit (NEB), with samples indexed with unique barcodes using NebNext Multiplex Oligos for Illumina (NEB). Two separate capture pools were designed to the following Pax6 locus elements: CTCF/Cohesin binding sites, known and predicted enhancer clusters, and the multiple promoters of three genes in the locus Pax6, Elp4 and Rcn1 (a full list of targeted restriction enzyme fragments is given in Suppl. Table 1). Capture oligos were designed to each end of the targeted DpnII fragments as described by in Ref. (Davies, 2016), and each synthesised as a separate 4 nM reaction, with a 5 Biotin label on a 120 bp Ultramer (IDT). All capture oligos from each of the two capture pools were mixed at equimolar amounts and pooled to a final concentration of 13 pmol in a volume of 4.5 l per sequence capture. Libraries where sized and quality controlled on a D1000 Tapestation tape (Agilent).
NG Capture-C sequence capture was performed using SeqCap EZ HE-Oligo Kit A or B (dependent on the multiplex barcode) and SeqCap EZ Accessory Kit (Nimblegen) as described in Ref. (Davies, 2016), using each of the two capture pools, with 1.5-2 g 3C library DNA per hybridisation reaction. Each hybridisation reaction was performed on a thermocycler at 47 C and incubated for between 66 and 72 hours. Each hybridisation reaction was then bound to streptavidin beads from SeqCap EZ Pure Capture Bead Kit and washed with SeqCap EZ Hybridization and Wash Kit (Nimblegen), following the manufacture's protocol. Hybridization reactions were split into two and libraries re-amplified using Post LM-PCR oligos (Nimblegen) and Q5 High-Fidelity DNA polymerase (NEB) directly from the beads, and then the DNA was purified using Ampure XP Bead 1/1.8 DNA to bead ratio. A second hybridisation reaction was performed as above on the re-amplifed 3C libraries with two reactions pooled together (∼1 g in each) and incubated for 22-24 hours. Washed and re-amplified double captured libraries where sized and quality controlled on a D1000 Tapestation tape (Agilent), and paired-end sequenced on an Illumina Hi-seq 2500 or Hi-seq 4000.
Capture-C

treatment_protocol: Two replicates of  cells where processed for each cell type, fixed with 2 % formaldehyde, and lysed for 15 min with standard 3C lysis buffer before snap freezing at -80 °C.

value: RAG


title: S.2

description: iPSC derived neural stem cells from Scheie replicate 2


title: RAG_PROM_2


title: H.3

description: iPSC derived neural stem cells from Hurler replicate 3


title: Chow 2.3

source_name: Whole Hippocampus


title: S.3

description: iPSC derived neural stem cells from Scheie replicate 3


title: Cntl.2

description: iPSC derived neural stem cells from contol replicate 2

value: control


title: Cntl.3

description: iPSC derived neural stem cells from contol replicate 3


title: Cntl.1

description: iPSC derived neural stem cells from contol replicate 1


title: RAG_CTCF_1

description: proccessed data files are pileup bdg file from all combined replicates for each capture position and cell line


title: RAG_PROM_1


title: BTC3_PROM_2

source_name: β-TC3 cells


title: MV_CTCF_2

source_name: MV+ cells

value: MV+


title: MV_PROM_1


title: BTC3_CTCF_1


title: BTC3_PROM_1


title: ATAC_RAG2

data_processing:
Cram files where converted to two fastq files (one for each read pair). Adapter trimming of nextera adapters was performed on raw files using trim galore (v0.4.1) using (--paired --nextera).
Paired end fastq files where aligned to a mm9 bowtie2 index with Bowtie2 (v2.2.6) (-X2000), and processed (filtered for aligned reads only) into a sorted and indexed Bam file with Samtools (v1.6)
Bedtools genome coverage tool was used to visualise raw read pileups as bdg files.
Macs2 (v2.1.1) call peak was used (paired end -nomodel -q 0.05 --SPMR ) on the two replicates per cell line, to generate narrowPeaks and peak coordinates..
Genome_build: mm9
Supplementary_files_format_and_content: Macs2 data includes an Excel file of peaks from each cell line, a narrowPeak track of called peaks and a bdg read pile up normalized by sequencing depth in million reads.

extract_protocol:
Protocol for transposition reaction and PCR based on (Buenrostro et al., 2013). 50,000 nuclei per condition where pelleted and resuspend in 1XTD Buffer (Illumina) with 2.5ul Tn5 transposase (Illumina) in 50µl volume, at 37°C 300rpm for 30min.
DNA was purified by MiniElute PCR purification (Qiagen), before test amplification to calculate library amplification cycle number with NEBNext® Ultra™ II Q5 Master Mix (NEB), Sybre green and customized Nextera PCR Primers (Buenrostro et al., 2013) using a LightCycler480 (Roche). ATAC-seq libraries where uniquely indexed with customized Nextera PCR Primers and amplified with 11 cycles of amplification before QIAquick PCR purification (Qiagen), and Ampure XP Bead (Beckman Coulter) size selection, and sequenced on an Illumina HiSeq 4000 75bp PE sequencing.

treatment_protocol: A nuclei purification protocol was used on the two single cell suspensions of each cell line. Cell’s were pelleted at 1400rpm and resuspend in 2ml cold NBA buffer and mixed with 2ml of cold NBB buffer for 2min at 4°C (MV+ NBB 0.2% NP40, β-TC3 & RAG NBB 0.1% NP40), and centrifuged at 2000rpm before washing in 2ml NBR 4°C, centrifuged again and resuspend in 1ml NBR. Nuclei where checked for purity, and cells counted. Buffer: NBA (85 mM NaCl, 5.5% Sucrose, 10 mM TrisHCl  pH 7.5, 0.2 mM EDTA, 0.2 mM PMSF, 1 mM DTT, 1X Protease Inhibitors), NBB (as NBA + 0.1 or 0.2% NP40), NBR 85 mM NaCl, 5.5% Sucrose, 10 mM TrisHCl  pH 7.5, 3 mM MgCl2, 1.5 mM CaCl2, 0.2 mM PMSF, 1 mM DTT).


title: ATAC_RAG1


title: ATAC_MV_2


title: MV_CTCF_1


title: BTC3_CTCF_2


title: ATAC_MV_1


title: B_L5e: healthy control cortical interneurons RNAseq

city: Greenville

first: Weihua

state: North Carolina

address: 600 Moye Blvd, Brody 7S-24

department: Pathology

institute: East Carolina University

data_processing:
Kallisto for pseudo-alignment to transcriptome of hg38
Sleuth for differential gene expression
Genome_build: hg38
Supplementary_files_format_and_content: An Excel file including TPM of each gene for all 28 samples

source_name: iPSC-derived interneurons

growth_protocol: interneurons were generated from iPSCs according to previously published protocols (Kim, T.G., et al. Efficient specification of interneurons from human pluripotent stem cells by dorsoventral and rostrocaudal modulation. Stem cells 32, 1789-1804, 2014), and were harvested for RNA preparation after 8 weeks of differentiation.

extract_protocol:
Samples were harvested using Trizol reagent (Invitrogen).
TruSeq Stranded LT mRNA kit

tag: diagnosis

value: healthy control

value: cortical interneurons


title: MV_PROM_2


title: B_L5d: healthy control cortical interneurons RNAseq


title: B_pyaumc: healthy control cortical interneurons RNAseq


title: ATAC_BTC3_2

source_name: Beta-TC3 cells


title: B_pyauma: healthy control cortical interneurons RNAseq


title: B_L9c: healthy control cortical interneurons RNAseq


title: HA-AB1_C17-TCF3_CHA replicate 2

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

description: TCF3-ZNF384 Fusion

data_processing:
we mapped 50bp single-end reads to mouse genome mm9(MGSCv37) with BWA (version 0.7.12-r1039),
marked duplicated reads with Picard and only unique mapped reads extracted by Samtools (version 1.2) were kept for analysis.
We extend each read to estimated fragment size by SPP (version 1.1) and generated bigwig files scaled the track normalized to 15M unique mapped reads.
Review each sample find they have clear peaks by IGV (3.0.beta) and consistent between anti-HA samples and anti-ZNF384 samples.
Later we performed analysis only used the anti-HA samples since their peaks are stronger and most have ZNF384 motif where anti-ZNF384 samples were weak.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

growth_protocol: Cells were derived from C57BL/6 Arf-/- BM cells as described (Randle et al, PNAS, 2001). Cells were transduced with lentiviral supernatants of ZNF384-HA, TAF15-ZNF384-HA, or TCF3-ZNF384-HA.

extract_protocol:
Chromatin was prepared as described (Zhang et.al, Nature Genetics, 2016). Breifly, 20 X 10^6 cells were crosslinked with 1% formaldehyde for 10 minutes. Cells were washed 3 times with PBS and lysed on ice for 10 minutes with lysis buffer. Chromatin was washed twice in wash buffer and once in shearing buffer before resuspending in 1ml of shearing buffer. Chromatin was sonicated with a Covaris E210 instrument and resuspended in dilution buffer. Finally, immunoprecipiation was performed with anti-HA antibody.
To prepare ChIP-seq libraries, 10 ng of ChIP DNA was end repaired and adaptor ligation was performed using the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina (New England BioLabs). Libraries were purified after 14 rounds of PCR amplification with Q5 DNA Hot-Start polymerase (New England BioLabs). Each ChIP-seq library underwent 50-cycle single-end sequencing using TruSeq SBS kit v3 on an Illumina HiSeq 2000.

value: pre-B cells Arf-/-

tag: strain

tag: passages

value: TCF3-ZNF384 Fusion

tag: chip antibody


title: HA-AB1_C16-TCF3_CHA replicate 1

description: TCF3-ZNF384 Fusion


title: ATAC_BTC3_1


title: HA-AB1_C13-TAF15_CHA replicate 1

description: TAF15-ZNF384 Fusion

value: TAF15-ZNF384 Fusion


title: HA-AB1_C6-ZNF384WT-CHA replicate 3

description: ZNF384 Wild Type

value: ZNF384 Wild Type


title: B_L7b: healthy control cortical interneurons RNAseq


title: B_367b: healthy control cortical interneurons RNAseq


title: B_L7a: healthy control cortical interneurons RNAseq


title: HA-AB1_C14-TAF15_CHA replicate 2

description: TAF15-ZNF384 Fusion


title: B_L9a: healthy control cortical interneurons RNAseq


title: HA-AB1_C11-ZNF384WT-CHA replicate 2

description: ZNF384 Wild Type


title: HA-AB1_C10-ZNF384WT-CHA replicate 1

description: ZNF384 Wild Type


title: INPUT_C15-TCF3_CHA

description: TCF3-ZNF384 Fusion


title: INPUT_C12-TAF15_CHA

description: TAF15-ZNF384 Fusion


title: B_365a: healthy control cortical interneurons RNAseq


title: B_365b: healthy control cortical interneurons RNAseq


title: B_317c: healthy control cortical interneurons RNAseq


title: INPUT_C4-ZNF384WT-CHA

description: ZNF384 Wild Type


title: B_317b: healthy control cortical interneurons RNAseq


title: B_292b: healthy control cortical interneurons RNAseq


title: B_272c: healthy control cortical interneurons RNAseq


title: B_272b: healthy control cortical interneurons RNAseq


title: B_226b: healthy control cortical interneurons RNAseq


title: P45 Hippocampus WT #1

city: Irvine

first: Robert

last: Hunt

state: CA

address: 110 Irvine Hall

institute: University of California, Irvine

description: rawcounts.txt

data_processing:
Software  used: FASTQC, Trimmomatic, Tophat2 (version 2.1.1), Samtools, and DESeq2.
Raw reads were trimmed using quality threshold of 15 and Truseq adapter sequences. Trimmed reads shorter than 20bp were discarded.
Reference genome sequence mm10 and its transcriptome annotation were collected and indexed for mapping (tophat iGenome website version).
Trimmed reads were mapped to reference sequences with gene annotations.
Mapping obtained were analyzed and gene expression level were quantified.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes raw counts for each sample.

source_name: P45 Hippocampus WT

extract_protocol:
MGE, cortex, and hippocampus were dissected and total RNA was extracted using Trizol reagent. For the library preparation kit, NEBNext Ultra RNA Library Preparation kit with Poly A selection was used.
NEBNext Ultra RNA Library Preparation kit with Poly A selection was used. RNA libraries were prepared for sequencing using standard manufacturer's  protocol.

tag: genotype

value: wildtype

value: Hippocampus


title: P45 Hippocampus HET #1

description: rawcounts.txt

source_name: P45 Hippocampus HET

value: Chd2 het


title: P45 Hippocampus HET #3

description: rawcounts.txt


title: P45 Hippocampus HET #2

description: rawcounts.txt


title: P45 Hippocampus WT #3

description: rawcounts.txt


title: E13.5 Cortex HET #3

description: rawcounts.txt

source_name: E13.5 Cortex HET

value: Cortex


title: B_292a: healthy control cortical interneurons RNAseq


title: B_190c: healthy control cortical interneurons RNAseq


title: E13.5 Cortex WT #3

description: rawcounts.txt

source_name: E13.5 Cortex WT


title: B_367a: healthy control cortical interneurons RNAseq


title: E13.5 Cortex WT #2

description: rawcounts.txt


title: B_190b: healthy control cortical interneurons RNAseq


title: B_139a: healthy control cortical interneurons RNAseq


title: E13.5 Cortex HET #2

description: rawcounts.txt


title: E13.5 Cortex HET #1

description: rawcounts.txt


title: B_107c: healthy control cortical interneurons RNAseq


title: B_107b: healthy control cortical interneurons RNAseq


title: E13.5 MGE HET #3

description: rawcounts.txt

source_name: E13.5 MGE HET

value: MGE


title: B_99b: healthy control cortical interneurons RNAseq


title: E13.5 MGE HET #2

description: rawcounts.txt


title: B_99c: healthy control cortical interneurons RNAseq


title: E13.5 MGE HET #1

description: rawcounts.txt


title: A_1442e: schizophrenia cortical interneurons RNAseq

value: schizophrenia


title: B_226c: healthy control cortical interneurons RNAseq


title: P45 Hippocampus WT #2

description: rawcounts.txt


title: E13.5 MGE WT #2

description: rawcounts.txt

source_name: E13.5 MGE WT


title: A_1442d: schizophrenia cortical interneurons RNAseq


title: A_L10b: schizophrenia cortical interneurons RNAseq


title: A_L8c: schizophrenia cortical interneurons RNAseq


title: E13.5 MGE WT #1

description: rawcounts.txt


title: A_L8a: schizophrenia cortical interneurons RNAseq


title: A_L10a: schizophrenia cortical interneurons RNAseq


title: RNA-seq_RAG_r2

data_processing:
Reads where aligned to mm9 genome index using TopHat v2 and processed with Samtools v1.6
Subread v1.5 feature counts was used to generate read counts and then FPKM scores calculated for each gene using mm9 RefSeq genes.gtf file.
Genome_build: mm9
Supplementary_files_format_and_content: Table of feature counts output, which contains read distrubution for each replicate over mm9 RefSeq gene and then an additional FPKM calculation for each gene (using total number of aligned of reads and gene length).

growth_protocol: MV+ and RAG cells were cultured in Dulbecco’s Modified Eagle Medium (ThermoFisher) supplemented with 10% fetal calf serum and 1% Penicillin-Streptomycin at 37°C in 5% CO2. Three experimental replicates where generated with three separe T25 culture flask of each cell type cultured to ~70% confluency.

extract_protocol:
Total RNA was prepared using the Qiagen RNeasy mini kit (Qiagen) with an on-column DNase I digestion using the Qiagen RNase-Free DNase set as the manufactures guidelines
Ribosomal RNA was depleted using the RiboMinus Eukaryote Kit for RNA-Seq (Life Technology) and RiboMinus Concentration module as manufactures’ guidelines.
Sequencing libraries where prepared using NEBNext mRNA Library Prep Master Mix Set (NEB), following the manufactures protocol, with all size selection performed using Agencourt AMPure XP beads (Beckman Cutler). Samples where multiplexed using the NEBNext Multiplex Oligos for Illumina kit to barcode each sample and amplified for 11 cycles. Sequnced using an Illumina Hi-Seq 2000 single end 50bp reads

value: RAG cells


title: B_139c: healthy control cortical interneurons RNAseq


title: RNA-seq_RAG_r1


title: E13.5 Cortex WT #1

description: rawcounts.txt


title: RAG H3K27ac Rep1

type: genomic

description: Raw array files from slide scanner of Input and ChIP samples

hyb_protocol: ChIP samples (Cy5) and Input samples (Cy3) were hybridized using a NimbleGen Hybridization and Sample Tracking Control Kit (Roche Cat. 05993776001) according to the manufacturer’s instructions. Slides were washed (NimbleGen Wash Buffer Kit, Roche Cat. 0558450700).

scan_protocol: Microarray slides were scanned at 2 µm resolution on a MS 200 Microarray Scanner (Nimblegen). Images were processed using Nimblescan version 2.5 and the Cy3 and Cy5 images were aligned with the NimbleGen design file (ndf) and a pair file generated of the intensity values.

data_processing: Ringo (Bioconductor) was used for pre-processing, normalisation, combining replicates and peak calling of ChIP-chip data. Ringo Probe annotation was performed on pair files using “posToProbeAnno” with following position file ("110505_AB_MM9_regions_ChIP.pos" provided, using mm9 genome. RG data was then background corrected using “minimum” method, and preprocessed using “loess” method and data normalised using “normalizedBetweenArrays” function.   Data was smoothed using “ computeRunningMedians” with winHalfSize=250, and min.probes=1, and replicates combined. Data was written out as a bedgraph file of log2 ratio ChIP/Input.

source_name: H3K27ac Input DNA RAG

label_protocol: ChIP and Input samples where whole genome amplified (GenomePlex, Sigma), purified (QIAquick, Qiagen) and labelled (NimbleGen Dual-Colour Labelling Kit, Roche Cat. 06370250001).

extract_protocol: H3K27ac ChIP was performed largely as described in Creyghton et al., 2010. One T75 flask was used per replicates with cells at ~80% confluency, MV+ cells (lens epithelium) and RAG cells (renal adenocarcinoma). Culture media was aspirated and replaced with 20 ml of fresh DMEM with no additives and 550 μl of 37% Formaldehyde was added to each flask for 10 min, before 2 ml of 2 M glycine solution was added to quench the formaldehyde and flasks were incubated at 4°C for 5 min. Flasks were washed with ice cold PBS twice, rocking for 10 min at 4 °C. A cell scrapper was used to remove the adherent cell layer in 10 ml cold PBS and the cells pooled in a 50 ml conical tube. Fixed cells were centrifuged for 5 min, supernatant removed and the pellet resuspended in 3 ml of cold Cell Lysis Buffer (50 mM HEPES pH 6.8, 140 mM NaCl, 10% (v/v) glycerol, 0.5% (v/v) IPEGAL, 0.25% (v/v) Triton X, 1mM EDTA, 0.25 mM PMSF) and a 21G needle and syringe used to resuspend completely before samples incubated on ice 10 min. Samples were centrifuged for 5 min, supernatant removed and the pellet resuspended in 3-10 ml Pre ChIP Wash buffer (200 mM NaCl, 10 mM Tris pH 8, 1 mM EDTA, 0.5 mM EGTA, 0.25 mM PMSF) and incubated 5 min on ice. Samples were centrifuged and resuspended in ~2.5 ml of Sonication buffer (100 mM NaCl, 0.1% (v/v) Na deoxycholate, 0.5 % N-lauroylsarcosine 10 mM Tris pH8, 1 mM EDTA, 0.5 mM EGTA, 0.25 mM PMSF). Samples were sonicated for 13 min, 30 sec on, 30 sec off (rest 2 min after 8 min), at 50% amplitude with a Soniprep 150 probe sonicator, to achieve a size range of ~300-500 bp. 10 µl of H3K27ac antibody (Abcam Cat#ab4729) was used per sample, with Protein G Dyna beads (ThermoFisher Cat#10003D). IP bound beads were washed in 5x RIPA Buffer (50 mM HEPES (pH 7.6), 1 mM EDTA, 0.7% Na deoxycholate (v/v),1% (v/v) Nonidet P-40, and 0.5 M LiCl), and 2x ChIP Wash 4(TE, 50 mM NaCl). Chromatin was eluted from beads, in 400 µl elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS), shaking at 65°C overnight along with a 10% Input sample to reverse the cross-linking.  DNA was treated with RNaseA (0.2 μg/μl final) for 2 h at 37°C, followed by proteinase K (0.2 μg/μl final) for 2 h at 50°C. Two phenol chloroform extractions were performed with 2 ml Phase lock tubes (5 prime). Resulting DNA was purified using a PCR clean up kit (Qiagen), with a double 50 µl final elution and stored at -20°C. Two experimental replicates where performed for each ChIP.

treatment_protocol: Xlinked ChIP

value: cell line

source_name: H3K27ac ChIP DNA RAG


title: A_755a: schizophrenia cortical interneurons RNAseq


title: RAG H3K27ac Rep2


title: RNA-seq_MV+_r2

value: MV+ cells


title: A_755c: schizophrenia cortical interneurons RNAseq


title: A_689b: schizophrenia cortical interneurons RNAseq


title: β-TC3 Rad21 Rep2

source_name: ChIP Input DNA beta-TC3

label_protocol: ChIP and Input samples where whole genome amplified (GenomePlex, Sigma), Rad21 and Inputs had a second amplification (GenomePlex Whole Genome Reamplification Kit, Sigma)  purified (QIAquick, Qiagen) and labelled (NimbleGen Dual-Colour Labelling Kit, Roche Cat. 06370250001).

extract_protocol: CTCF and Rad21 ChIP was performed as follows. One T75 flask was used per replicates with cells at ~80% confluency, β-TC3 cells (pancreatic insulinoma), MV+ cells (lens epithelium) and RAG cells (renal adenocarcinoma). Culture media was aspirated and replaced with 20 ml of fresh DMEM with no additives and 550 μl of 37% Formaldehyde was added to each flask for 10 min, before 2 ml of 2 M glycine solution was added to quench the formaldehyde and flasks were incubated at 4°C for 5 min. Flasks were washed with ice cold PBS twice, rocking for 10 min at 4 °C. A cell scrapper was used to remove the adherent cell layer in 10 ml cold PBS and the cells pooled in a 50 ml conical tube. Fixed cells were centrifuged for 5 min, supernatant removed and the pellet resuspended in 3 ml of cold Cell Lysis Buffer (50 mM HEPES pH 6.8, 140 mM NaCl, 10% (v/v) glycerol, 0.5% (v/v) IPEGAL, 0.25% (v/v) Triton X, 1mM EDTA, 0.25 mM PMSF) and a 21G needle and syringe used to resuspend completely before samples incubated on ice 10 min. Samples were centrifuged for 5 min, supernatant removed and the pellet resuspended in 3-10 ml Pre ChIP Wash buffer (200 mM NaCl, 10 mM Tris pH 8, 1 mM EDTA, 0.5 mM EGTA, 0.25 mM PMSF) and incubated 5 min on ice. Samples were centrifuged and resuspended in ~2.5 ml of Sonication buffer. Samples were sonicated for 13 min, 30 sec on, 30 sec off (rest 2 min after 8 min), at 50% amplitude with a Soniprep 150 probe sonicator, to achieve a size range of ~300-500 bp. 10µl of capture antibody (CTCF antibody D31H2 XP Rabbit mAb #3418), and Rad21 antibody (Abcam Ab992) was used per sample, with Protein G Dyna beads (ThermoFisher Cat#10003D). IP bound beads were washed sequentially at 4°C in 1 ml each of ChIP wash buffers, 1x ChIP wash 1, 3x ChIP wash 2, 1x ChIP wash 3, beads were transferred to a new tube, and washed 2x ChIP Wash 4, 10 min 4°C, and 2x ChIP Wash 4 (TE, 50 mM NaCl).  Buffers: Sonication buffer (100 mM NaCl, 0.1% (v/v) Na deoxycholate, 0.5 % N-lauroylsarcosine 10 mM Tris pH8, 1 mM EDTA, 0.5 mM EGTA, 0.25 mM PMSF). ChIP Wash 1 (25 mM Tris pH 8, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA, 0.25 mM PMSF ), ChIP Wash 2 (25 mM Tris pH 8, 500 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA, 0.25 mM PMSF), ChIP Wash 3 (10 mM Tris pH8, 250 mM LiCl, 1% Triton X-100, 1% IPEGAL, 1% sodium deoxycholate, 2 mM EDTA, 0.25 mM PMSF), ChIP Wash 4 (TE, 50 mM NaCl). Chromatin was eluted from beads, in 400 µl elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS), shaking at 65°C overnight along with a 10% Input sample to reverse the cross-linking.  DNA was treated with RNaseA (0.2 μg/μl final) for 2 h at 37°C, followed by proteinase K (0.2 μg/μl final) for 2 h at 50°C. Two phenol chloroform extractions were performed with 2 ml Phase lock tubes (5 prime). Resulting DNA was purified using a PCR clean up kit (Qiagen), with a double 50 µl final elution and stored at -20°C. Two experimental replicates where performed for each ChIP.

source_name: Rad21 ChIP DNA beta-TC3


title: RNA-seq_MV+_r1


title: β-TC3 Rad21 Rep1


title: CD4 XBP1 knock out, replicate 3

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description:
CD45+CD3+CD4+ peritoneal wash samples of or Xbp1f/f Cd4cre mice
KO_CD4_3

data_processing:
Reads produced from 51bp single end sequencing runs were aligned against mouse genome (mm9) using Bowtie v0.12.8 algorithm. Mouse mm9 transcriptome information was obtained from UCSC Genome Browser and the RSEM algorithm was used to calculate number of aligned tags for each gene
Differential expression between two groups were tested by EdgeR
Genome_build: mm9
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene

extract_protocol:
Tumor infiltrating CD4+ T cells sorted from peritoneal wash samples of Xbp1f/f (WT) or Xbp1f/f Cd4cre (KO) female mice bearing aggressive ID8-Defb29/Vegf-A ovarian cancer for 20 days. miRVana miRNA isolation kit (Ambion) and RNeasy MinElute kit (Qiagen) were used for total RNA isolation and concentration
Library preparation was performed using the UltraLowRNAseq RNA Library Prep Kit

tag: genotype/variation

value: XBP1 KO

tag: replicate


title: MV+ H3K27ac Rep1

source_name: H3K27ac Input DNA MV+

source_name: H3K27ac ChIP DNA MV+


title: A_689a: schizophrenia cortical interneurons RNAseq

tag: tissue


title: CD4 XBP1 knock out, replicate 4

description:
CD45+CD3+CD4+ peritoneal wash samples of or Xbp1f/f Cd4cre mice
KO_CD4_4


title: E13.5 MGE WT #3

description: rawcounts.txt


title: CD4 XBP1 knock out, replicate 2

description:
CD45+CD3+CD4+ peritoneal wash samples of or Xbp1f/f Cd4cre mice
KO_CD4_2


title: RNA-seq_RAG_r3

source_name: RAG cells


title: CD4 XBP1 knock out, replicate 1

description:
CD45+CD3+CD4+ peritoneal wash samples of or Xbp1f/f Cd4cre mice
KO_CD4_1


title: MV+ H3K27ac Rep2


title: A_483c: schizophrenia cortical interneurons RNAseq


title: RNA-seq_MV+_r3


title: CD4 XBP1 wild type, replicate 4

description:
CD45+CD3+CD4+ peritoneal wash samples of Xbp1f/f mice
WT_CD4_4

value: WT


title: RAG Rad21 Rep2

source_name: ChIP Input DNA RAG

source_name: Rad21 ChIP DNA RAG


title: RAG Rad21 Rep1


title: MV+ Rad21 Rep2

source_name: ChIP Input DNA MV+

source_name: Rad21 ChIP DNA MV+


title: A_483b: schizophrenia cortical interneurons RNAseq

source_name: iPSC-derived interneurons


title: CD4 XBP1 wild type, replicate 2

description:
CD45+CD3+CD4+ peritoneal wash samples of Xbp1f/f mice
WT_CD4_2


title: CD4 XBP1 wild type, replicate 3

description:
CD45+CD3+CD4+ peritoneal wash samples of Xbp1f/f mice
WT_CD4_3


title: MV+ Rad21 Rep1


title: A_285b: schizophrenia cortical interneurons RNAseq


title: β-TC3 CTCF Rep2

source_name: CTCF ChIP DNA beta-TC3


title: CD4 XBP1 wild type, replicate 1

description:
CD45+CD3+CD4+ peritoneal wash samples of Xbp1f/f mice
WT_CD4_1


title: A_285a: schizophrenia cortical interneurons RNAseq


title: A_282b: schizophrenia cortical interneurons RNAseq


title: β-TC3 CTCF Rep1


title: A_282a: schizophrenia cortical interneurons RNAseq


title: mTEC_hi_2

city: Montreal

first: Krystel

last: Vincent

state: Quebec

address: 2950, chemin de la Polytechnique, Marcelle-Coutu Pavilion

institute: Institute for Research in Immunology and Cancer

data_processing:
Basecalls performed using CASAVA-1.8.2 for HiSEQ 2000 data and bcl2fastq version 2.19 for NextSeq 500 data
Sequenced reads were trimmed for sequencing adapters and low quality extremities using Trimmomatic version 0.35
Expression values were estimated using kallisto version 0.43.1 for each sample with replicates pooled into one sample
Genome_build: GRCm38 using transcript annotations from Ensembl 87
Supplementary_files_format_and_content: Tab-delimited files where columns are described in the header and are standard kallisto output: Ensembl transcript identifier, transcript length, eff_length, estimated counts, TPM values.

source_name: mature medullary thymic epithelial cells

extract_protocol:
KAPA RNA Stranded PolyA
TriZol + RNeasy mini Kit (Qiagen, #74106)
see SAMPLES section

value: thymus

value: 5-8 weeks

value: mTEChi


title: A_212b: schizophrenia cortical interneurons RNAseq

value: cortical interneurons


title: GFPhigh4abundance

city: Planegg

first: Jovica

last: Ninkovic

address: Grosshaderner strasse 9

country: Germany

institute: LMU Munich

data_processing:
FASTQ files were used for the transcript counting using kallisto pipeline (the reference transcriptome was Danio rerio full transcriptome (danrer10))
Sleuth pipeline was used for statistical analysis
Genome_build: danrer10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

organism: Danio rerio

source_name: GFP high

growth_protocol: cells are isolated from gfap:GFP transgenic animals using FACS protocol as previously described (Barbosa et al., Nat. Protocols, 2016)

extract_protocol:
RNA is isolated using PicoPure RNA isolation Kit (ThermoFisher; KIT0204) and cDNA was made using SMART-Seq v4 Ultra Low Input RNA Kit (Takara, Cat. No. 634888).
MicroPlex Library Preparation Kit v2 and processed according to the manufacturer ́s instruction. Deep sequencing was performed on Illumina HiSeq system with 100bp paired-end reads
cDNA library

treatment_protocol: no treatment

value: Ependymoglial cells


title: brain_5dpi_100μl/chicken PBS_rep1

type: RNA

city: Yangling

first: wenbin

last: wang

state: Shannxi

address: 22#, Xinong Road

department: College of Veterinary Medicine

country: China

institute: Northwest A&F University

description: Gene expression in brain after 5 day injected with PBS 100μl

hyb_protocol: 0.875 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 1x fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 μl of 2x GEx hybridization buffer was added to the fragmentation mixture and hybridized to Agilent chicken Oligo Microarrays(V2), 4x44(G2519F-26441) for 17 hours at 65℃ in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37℃ GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Ozone-Barrier Slide Cover (Agilent p/n G2505-60550) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5μm, Dye channel is set to Green and Green PMT is set to XDR Hi 100%, XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 026441_D_20140626) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Gallus gallus

source_name: spf chicken brain, 5dpi, 100μl/chicken PBS, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: All SPF white Leghorn chickens were raised in biosafety isolators.

extract_protocol: RNA was prepared using QIAGEN RNeasy Mini kit (QIAGEN) following the manufacturer's recommendations. RNA was quantified using a NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: The SPF chickens were infected with with F48E9 and LaSota viruses (100000 pfu/100μl/chicken) via intraocular-nasal route. The control group was inoculated with PBS. The F48E9 infected chickens were euthanized when they displayed severe neurological symptoms or moribund. The brains of each group for gene microarray analysis were collected at 5 dpi.

value: brain

tag: gender

value: female

value: 4 week


title: GFPlow4abundance

source_name: GFP low


title: GFPlow3abundance


title: brain_5dpi_100000 pfu/100μl/chicken LaSota_rep1

description: Gene expression in brain after 5 day injected with LaSota (100000 pfu/100μl/chicken )

source_name: spf chicken brain, 5dpi, 100000 pfu/100μl/chicken LaSota, replicate 1


title: brain_5dpi_100000 pfu/100μl/chicken F48E9_rep1

description: Gene expression in brain after 5 day injected with F48E9 (100000 pfu/100μl/chicken )

source_name: spf chicken brain, 5dpi, 100000 pfu/100μl/chicken F48E9, replicate 1


title: RAG CTCF Rep1

source_name: CTCF ChIP DNA RAG


title: GFPhigh3abundance


title: A_212a: schizophrenia cortical interneurons RNAseq


title: CT26

source_name: tumor cell line

value: Balb/c

value: colon

value: CT26 tumor cell line


title: GFPlow5abundance


title: MV+CTCF Rep2

source_name: CTCF ChIP DNA MV+


title: A_162b: schizophrenia cortical interneurons RNAseq

value: schizophrenia


title: mTEC_hi_1


title: MV+ CTCF Rep1


title: mTEC_hi_3


title: A_128c: schizophrenia cortical interneurons RNAseq


title: EL4

extract_protocol:
TruSEQ RNA stranded
TriZol + RNeasy mini Kit (Qiagen, #74106)
see SAMPLES section

value: T lymphocyte

value: EL4 tumor cell line


title: GFPhigh1abundance


title: GFPhigh2abundance


title: wild type_rep3

city: beijing

first: zhang

middle: yong

last: zhuo

address: Beijing Forestry University

institute: Beijing Forestry 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 containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based onthe clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
Supplementary_files_format_and_content: FPKM

organism: Arabidopsis thaliana

source_name: mature stem

growth_protocol: All the plants grew in greenhouse at 20 oC (16h light, 8h dark).

extract_protocol:
Total RNA was isolated from the main stem of different developmental stage of Arabidopsis plant, using EASYspin Plant RNA kit RN09 (Aidlab, China) according to the manufacturer's instructions.
In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: non-treatment

value: stem

tag: Stage

value: 35 days after flowering


title: RNA_C37-TCF3_CHA replicate 1

description:
RNASeq_counts.mm9.txt
counts.RNA_C37-TCF3_CHA-Rep3b

data_processing:
Paired-end 100-cycle sequencing was performed per the manufacturer’s directions (Illumina).
RNA-Seq was mapped as described previously (Downing et al., 2012)
HTSeq (version 0.6.1p1) were used to get gene-level count and estimated FPKM based on GENCODE (vM9).
Genome_build: mm9
Supplementary_files_format_and_content: gene-based rawcounts

extract_protocol:
Total RNA was isolated from GFP+ sorted cells using RNeasy Mini Kit (QIAGEN).
Libraries were prepared from total RNA with the TruSeq Stranded Total RNA Library Prep Kit (Illumina.)

value: pre-B cells Arf-/-

value: TCF3-ZNF384 Fusion


title: wild type_rep2


title: RAG CTCF Rep2

value: cell line


title: RNA_C36-TCF3_CHA replicate 2

description:
RNASeq_counts.mm9.txt
counts.RNA_C36-TCF3_CHA-Rep2b


title: wild type_rep1


title: A_117b: schizophrenia cortical interneurons RNAseq


title: RNA_C34-TAF15_CHA replicate 1

description:
RNASeq_counts.mm9.txt
counts.RNA_C34-TAF15_CHA-Rep3b

value: TAF15-ZNF384 Fusion


title: RNA_C33-TAF15_CHA replicate 2

description:
RNASeq_counts.mm9.txt
counts.RNA_C33-TAF15_CHA-Rep2b


title: hdt1 mutant_rep2


title: A_67b: schizophrenia cortical interneurons RNAseq

value: cortical interneurons


title: A_162a: schizophrenia cortical interneurons RNAseq


title: hdt1 mutant_rep1


title: RNA_C22-EV replicate 2

description:
RNASeq_counts.mm9.txt
counts.RNA_C22-EV

value: Empty Vector


title: A_67a: schizophrenia cortical interneurons RNAseq


title: RNA_C21-EV replicate 1

description:
RNASeq_counts.mm9.txt
counts.RNA_C21-EV


title: A_58b: schizophrenia cortical interneurons RNAseq


title: RNA_C31-ZNF384WT-CHA replicate 1

description:
RNASeq_counts.mm9.txt
counts.RNA_C31-ZNF384WT-CHA-Rep3b

value: ZNF384 Wild Type


title: A_58a: schizophrenia cortical interneurons RNAseq


title: RNA_C30-ZNF384WT-CHA replicate 2

description:
RNASeq_counts.mm9.txt
counts.RNA_C30-ZNF384WT-CHA-Rep2b


title: A_128a: schizophrenia cortical interneurons RNAseq


title: hdt1 mutant_rep3


title: A_117a: schizophrenia cortical interneurons RNAseq


title: nanoceria ground 1

city: Pontedera (PI)

first: Gianni

last: Ciofani

address: Viale Rinaldo Piaggio 34

country: Italy

institute: Istituto Italiano di Tecnologia

hyb_protocol: Each of the nine RNA samples was spotted on a single chip; hybridized arrays were then stained, washed and scanned using a GeneChip Fluidics Station 450, Command Console Software and GeneChip Scanner 3000 7G, generating a .cel file (Table 1) for each array (ThermoFisher Scientific)

scan_protocol: Images were scanned by Affymetrix GeneChip Command Console (ThermoFisher Scientific) and analyzed with the Affymetrix GeneChip Expression Console (ThermoFisher Scientific). The quality of the scanned data was first estimated by confirming the order of signal intensities of the Poly-A and Hybridization controls using Expression Console Software (ThermoFisher Scientific)

data_processing: Fluorescence intensities across samples were normalized (in perfect-match only conditions) using the robust multi-array average (RMA) algorithm. As an additional quality check for replicates belonging to the same experimental class, a principal component analysis was performed: those cartridges failing to pass this control step were removed from further analyses (a sample named B1508 was discarded after failing quality controls)

label: Biotin

organism: Rattus norvegicus

source_name: Cells grown on Earth and exposed to nanoceria

label_protocol: Gene expression was investigated with rat Clariom S Pico arrays (ThermoFisher Scientific 902936) by using 30 ng of total RNA for reverse transcription (with 500 pg of HeLa cell RNA as control), genomic reference Rnor_6.0. Reverse transcription was initiated at the poly-A tail and throughout the RNA length to ensure that both coding and multiple forms of non-coding RNA were captured. Complementary RNA (cRNA) amplification was obtained by low-cycle PCR followed by linear amplification through T7 in vitro transcription. Quantification of cRNA was performed with NanoDrop spectrophotometer. The cRNA (20 µg) was converted into biotinylated, double stranded cDNA (quantification reported in Supplementary Table 4), which was fragmented (all fragments were in the 25-200 nt range) and terminally labeled for hybridization to arrays

growth_protocol: H9c2 myoblasts (ATCC CRL 1446) at passage 6-12 were seeded at a density of 35,000 cells/cm2 on Thermanox coverslips (1×2.2 cm2, Nunc 174934). Kayser Italia Experiment Units (EUs, qualified for flight to the International Space Station) were loaded with cell culture media (100 µg/ml FBS-coated NC dispersion in one reservoir for two EUs), a saline solution (DPBS added with Ca2+/Mg2+) for cell rinse prior to fixation, and a fixative solution (RNAlater, Ambion AM7020) for nucleic acid stabilization. At day 1 after seeding, cell cultures were transferred to EUs, which were then positioned within Kayser Italia Experiment Containers (ECs) before being inserted into a soft pouch containing phase change materials pre-heated at 27°C. An iButton data logger recorded the temperature every minute until the end of the experiment. The experimental hardware was delivered to flight authorities at day 2; it was launched on a Dragon / Falcon 9 vector in the framework of the SpaceX CRS-12 mission at day 4, and reached the ISS at day 7 after seeding. Once on board the ISS, the ECs were manually inserted by an astronaut in the Kubik incubator set at 37°C, and the electronics was switched on. Fluidic activations were automatically performed at days 7, 8 and 9 after seeding. The last two activations were performed at day 10: in particular, fixation occurred after 5 min from rinse with saline solution. Samples were then manually transferred to MELFI refrigerator and stowed at -80°C until re-entry

extract_protocol: Samples were thawed, retrieved from EUs and imaged by optical microscopy in phase contrast mode with a Nikon Eclipse Ti microscope. Temperature profile was downloaded from data loggers on the ECs and was reproduced for experiment repetition on ground within six EUs (three treated with NC and three untreated) that were manually activated.  Cell culture samples were positioned in 2 ml test tubes, covered with their supernatant (composed by 70% RNAlater fixative, 21% DPBS and 9% cell culture medium) and centrifuged at 10,000 g for 15 min. The supernatant was carefully removed, and a volume of 100 μl was left in the tubes so as not to perturb cells potentially precipitated after detachment from the substrate. MirVana PARIS kit (Ambion AM1556) was used for cell lysis, as well as for following RNA extraction and purification procedures. Ice-cold cell disruption buffer (250 μl) was pipetted directly on the Thermanox substrates holding the H9c2 cell cultures three times. Cell lysis was also promoted by vortexing for 30 s and by placing cultures on ice every 10 s. An equal volume of 1.5% β-mercaptoethanol denaturing solution (350 μl) was added to each tube, and then the lysate was incubated on ice for 5 min. An equal volume of acid-phenol:chloroform solution (700 μl) was added to the lysate. Samples were thus vortexed for 1 min and centrifuged at 10,000 g for 10 min. The aqueous phase (600 μl) from each sample was transferred to another clean tube, and was added with 1.25 volumes of 99.9% ethanol (750 μl). Each solution was then loaded on a filter cartridge positioned in a collection tube, and was centrifuged at 10,000 g for 30 s. The eluate was discarded, and 700 μl of complete miRNA Wash Solution 1 were added to each filter cartridge for centrifugation at 10,000 g for 30 s. The eluate was again discarded, and 500 μl of complete wash solution 2/3 were added to each filter cartridge for centrifugation at 10,000 g for 30 s (this step was repeated twice). The eluate was once again discarded, and the tubes were centrifuged for 1 min in order to fully remove the wash solution. Thereafter, filter cartridges were transferred to clean collection tubes, and RNA was eluted with 40 μl of RNAse-free water pre-heated at 90° C. The tubes were incubated for 10 min and centrifuged at 10,000 g for 5 min. The eluate was used for RNA quality and yield assessment with NanoDrop spectrophotometer

treatment_protocol: Cerium oxide nanoparticles (nanoceria, Sigma 544841) were first dispersed at a concentration of 20 mg/ml in water, then they were incubated with 50% fetal bovine serum (FBS, Gibco 10082147) for 30 min. Subsequently, 0.5, 1 and 2 mg/ml NC dispersions with 10% FBS in CO2-independent medium (Gibco 18045088) were obtained for assessing antioxidant effect of nanoparticles by flow cytometry. These dispersions were finally ten-fold diluted in differentiation medium composed by CO2-independent medium at a final concentration of 1% FBS, with 1% insulin-transferrin-sodium selenite mixture (Sigma-Aldrich I3146), 2 mM L-glutamine (Gibco 25030149), 100 U/ml penicillin-100 μg/ml streptomycin (Gibco 15140122)

value: myoblast, muscle cell line

tag: treatment

value: cultured on Earth with nanoceria treatment


title: untreated ground 1

source_name: Cells grown on Earth and not exposed to nanoceria

value: cultured on Earth without nanoceria treatment


title: untreated ground 3


title: nanoceria space 1

source_name: Cells grown in space and exposed to nanoceria

value: cultured oaboard the International Space Station with nanoceria treatment


title: untreated space 1

source_name: Cells grown in space and not exposed to nanoceria

value: cultured aboard the International Space Station without nanoceria treatment


title: nanoceria ground 3


title: Differentiated_hiPSCs_on411

status: Public on Oct 17 2018

city: Suita

first: Shun

last: Shibata

state: Osaka

address: 2-2 Yamadaoka

country: Japan

institute: Osaka University

description: Gene expression after 3 days of ocular cell differentiation

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver2.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Differentiated hiPSCs on LN411E8

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was prepared using RNeasy Plus micro kit (QIAGEN) according to manufacturer's  protocol.

value: Human Induced Pluripotent Stem Cells


title: Differentiated_hiPSCs_on511

source_name: Differentiated hiPSCs on LN511E8


title: Differentiated_hiPSCs_on111

source_name: Differentiated hiPSCs on LN111E8


title: nanoceria ground 2


title: Differentiated_hiPSCs_on332

source_name: Differentiated hiPSCs on LN332E8


title: RAG Rad21 Rep2 ChIP ChIP Agilent

description: Biological replicates:Cy3_Cy5 data combined in single raw data file. Data in separte file: Rad21_ChIP_ChIP_log2IP_adam.j.buckle.txt

hyb_protocol: Standard Agilent protocols

scan_protocol: Standard Agilent protocols at the VU microarray facility Amsterdam.

data_processing: Ringo (Bioconductor) was used for pre-processing, normalisation, combining replicates and peak calling of ChIP-chip data. Ringo Probe annotation was was extracted from the micrarray files using Agilent mapping corindates “extractProbeAnno”  using mm9 genome. RG data was then, background corrected using “minimum” method, and preprocessed using Nimblgen method and data normalised using “normalizedBetweenArrays” function.   Data was smoothed using “ computeRunningMedians” with winHalfSize=250, and min.probes=5, and replicates combined. Data was written out as a bedgraph file of log2 ratio ChIP/Input.

source_name: ChIP Input DNA RAG

label_protocol: ChIP and Input samples where whole genome amplified (GenomePlex, Sigma), Rad21 and Inputs had a second amplification (GenomePlex Whole Genome Reamplification Kit, Sigma)  purified (QIAquick, Qiagen). Samples labeled using an ENZO labeling kit with Cy3 and Cy5.

growth_protocol: One T75 flask was used per replicates with cells at ~80% confluency RAG cells (renal adenocarcinoma)

extract_protocol: Rad21 ChIP was performed as follows. Culture media was aspirated and replaced with 20 ml of fresh DMEM with no additives and 550 μl of 37% Formaldehyde was added to each flask for 10 min, before 2 ml of 2 M glycine solution was added to quench the formaldehyde and flasks were incubated at 4°C for 5 min. Flasks were washed with ice cold PBS twice, rocking for 10 min at 4 °C. A cell scrapper was used to remove the adherent cell layer in 10 ml cold PBS and the cells pooled in a 50 ml conical tube. Fixed cells were centrifuged for 5 min, supernatant removed and the pellet resuspended in 3 ml of cold Cell Lysis Buffer (50 mM HEPES pH 6.8, 140 mM NaCl, 10% (v/v) glycerol, 0.5% (v/v) IPEGAL, 0.25% (v/v) Triton X, 1mM EDTA, 0.25 mM PMSF) and a 21G needle and syringe used to resuspend completely before samples incubated on ice 10 min. Samples were centrifuged for 5 min, supernatant removed and the pellet resuspended in 3-10 ml Pre ChIP Wash buffer (200 mM NaCl, 10 mM Tris pH 8, 1 mM EDTA, 0.5 mM EGTA, 0.25 mM PMSF) and incubated 5 min on ice. Samples were centrifuged and resuspended in ~2.5 ml of Sonication buffer. Samples were sonicated for 13 min, 30 sec on, 30 sec off (rest 2 min after 8 min), at 50% amplitude with a Soniprep 150 probe sonicator, to achieve a size range of ~300-500 bp. 10µl of capture antibody Rad21 antibody (Abcam Ab992) was used per sample, with Protein G Dyna beads (ThermoFisher Cat#10003D). IP bound beads were washed sequentially at 4°C in 1 ml each of ChIP wash buffers, 1x ChIP wash 1, 3x ChIP wash 2, 1x ChIP wash 3, beads were transferred to a new tube, and washed 2x ChIP Wash 4, 10 min 4°C, and 2x ChIP Wash 4 (TE, 50 mM NaCl).  Buffers: Sonication buffer (100 mM NaCl, 0.1% (v/v) Na deoxycholate, 0.5 % N-lauroylsarcosine 10 mM Tris pH8, 1 mM EDTA, 0.5 mM EGTA, 0.25 mM PMSF). ChIP Wash 1 (25 mM Tris pH 8, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA, 0.25 mM PMSF ), ChIP Wash 2 (25 mM Tris pH 8, 500 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA, 0.25 mM PMSF), ChIP Wash 3 (10 mM Tris pH8, 250 mM LiCl, 1% Triton X-100, 1% IPEGAL, 1% sodium deoxycholate, 2 mM EDTA, 0.25 mM PMSF), ChIP Wash 4 (TE, 50 mM NaCl). Chromatin was eluted from beads, in 400 µl elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS), shaking at 65°C overnight along with a 10% Input sample to reverse the cross-linking.  DNA was treated with RNaseA (0.2 μg/μl final) for 2 h at 37°C, followed by proteinase K (0.2 μg/μl final) for 2 h at 50°C. Two phenol chloroform extractions were performed with 2 ml Phase lock tubes (5 prime). Resulting DNA was purified using a PCR clean up kit (Qiagen), with a double 50 µl final elution and stored at -20°C. Two experimental replicates where performed for each ChIP.

value: RAG

source_name: Xlinked ChIP


title: Differentiated_hiPSCs_on211

source_name: Differentiated hiPSCs on LN211E8


title: Differentiated_hiPSCs_onVN

source_name: Differentiated hiPSCs on VN


title: nanoceria space 2


title: RAG Rad21 Rep1 ChIP ChIP Agilent


title: RRV replicate 2 latent oligo KT493

city: New Haven

first: Johanna

middle: B

last: Withers

state: CT

address: 295 Congress Ave

department: Molecular Biophysics and Biochemistry

institute: Yale University

description: CHART-enriched DNA

data_processing:
Library strategy: CHART
bowtie2 --q -x
samtools view -H input.bam > output.sam
samtools view input.bam | grep AS:i:0 | grep -v XS:i:0 >> output.sam
macs2 callpeak -t sample.sam -c input.sam -n SampleName -f SAM -g 2.7e9 -B --broad --verbose 0
bedtools multiinter -header -i
Genome_build: Human genome HG38; KSHV genome GQ994935; RRV genome AF210726
Supplementary_files_format_and_content: Broadpeak called from MACS2 analysis

source_name: BJAB-RRV cells

growth_protocol: BCBL-1 and BJAB-RRV cells were grown in RPMI supplemented with 20% fetal bovine serum, 5% L-glutamine and 1% pen/strep.

extract_protocol:
CHART samples were prepared as described in Simon 2013 PMID:23288463
NEB CHIP-seq library prep kit for illumina

treatment_protocol: To induce the virally-infected cells into the lytic phase, BCBL-1 cells were treated with valproic acid and BJAB-RRV cells were treated with TSA. Latent samples were untreated.

value: BJAB-RRV cells

tag: viral stage

value: latent

tag: viral lytic induction timepoint

value: 0 hr


title: RRV replicate 2 latent oligo TKV

description: CHART-enriched DNA

tag: cell line


title: RRV replicate 2 36 hr oligo TKV

description: CHART-enriched DNA

value: lytic

value: 36 hr


title: RRV replicate 2 36 hr oligo TKV Input

description: Genomic DNA


title: RRV replicate 2 latent oligo TKV Input

description: Genomic DNA


title: RRV replicate 2 36 hr oligo KT493 and No oligo Input

description: Genomic DNA


title: F/F EAE p50 Mic

city: Fukuoka

first: Ryo

last: Yamasaki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-Ku

department: Neurology

institute: Kyushu University

hyb_protocol: cRNA was hybridized to Affymetrix  Clariom D Assay Mouse array, washed and stained according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Affymetrix scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The data were analyzed with median polish summarization and quantile normalization by Affymetrix® Expression Console™ 1.1 software, and obtained normalized intensity values.

label: biotin

source_name: microglia, EAE mice CNS (p50)

label_protocol: The cRNA was amplified, labeled using GeneChip WT Pico Reagent Kit according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

value: microglia


title: icKO naive MG

source_name: microglia, Cx47 deficient mice CNS


title: RRV replicate 2 24 hr oligo TKV

description: CHART-enriched DNA

value: 24 hr


title: icKO EAE p50 Mic

source_name: microglia, Cx47 icKO EAE mice CNS (p50)


title: icKO EAE MG

source_name: microglia, Cx47 deficient mice CNS with EAE


title: icKO EAE MG IGU

source_name: microglia, Cx47 icKO mice EAE CNS, iguratimod treatment


title: FL EAE MG

source_name: microglia, EAE mice CNS


title: FL EAE MG IGU

source_name: microglia, wt mice EAE CNS, iguratimod treatment


title: FL naive MG

source_name: microglia, naive mice CNS


title: RRV replicate 2 18 hr oligo TKV

description: CHART-enriched DNA

value: 18 hr


title: RRV replicate 2 24 hr oligo KT493 and No oligo Input

description: Genomic DNA


title: RRV replicate 1 latent oligo TKV Input

description: Genomic DNA


title: RRV replicate 1 latent oligo KT493 and No oligo Input

description: Genomic DNA


title: RRV replicate 2 18 hr oligo TKV Input

description: Genomic DNA


title: RRV replicate 2 24 hr oligo TKV Input

description: Genomic DNA


title: RRV replicate 1 36 hr oligo TKV

description: CHART-enriched DNA


title: RRV replicate 1 latent oligo TKV

description: CHART-enriched DNA


title: RRV replicate 2 18 hr oligo KT493 and No oligo Input

description: Genomic DNA


title: RRV replicate 1 36 hr oligo TKV Input

description: Genomic DNA


title: Rbp53CrebbpTHY_T5

city: Seattle

first: David

last: MacPherson

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.2
Reads of low quality were filtered out prior to alignment to mm9 using TopHat v2.0.12.  Counts were generated from TopHat alignments at the gene-level  using the  “intersection-strict” overlap mode in HTSeq v0.6.1.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include counts generated at the gene-level by HTSeq-count v0.6.1

source_name: mouse thyroid carcinoma

extract_protocol:
Cells were lysed in TRIzol reagent with RNA isolated following manufacturers instructions.
RNA libraries were prepared using theNEBNext Ultra RNA Library Prep Kit for Illumina (catalog E7530L). Briefly, 500 ng total RNA was used to isolate mRNA with the NEB Next Oligo dT Magnetic Isolation Module (catalog E7490L). The isolated mRNA undergoes fragmentation, priming, cDNA synthesis and end repair/dA-tail. Individual index primers for multiplexing were added during PCR library enrichment after adaptor ligation.

tag: tissues

value: thyroid carcinoma

tag: tumor type

value: mouse neuroendocrine thyroid carcinoma


title: Rbp53CrebbpTHY_T3


title: Rbp53CrebbpTHY_T4


title: RRV replicate 1 36 hr oligo KT493 and No oligo Input

description: Genomic DNA


title: RRV replicate 1 24 hr oligo KT493 and No oligo Input

description: Genomic DNA


title: RRV replicate 1 24 hr oligo TKV

description: CHART-enriched DNA


title: Rbp53CrebbpTHY_T1


title: RRV replicate 1 24 hr oligo TKV Input

description: Genomic DNA


title: RRV replicate 1 18 hr oligo TKV

description: CHART-enriched DNA


title: Rbp53CrebbpTHY_T2


title: Rbp53THY_T7


title: Rbp53THY_T6


title: FL_EAE_Ast

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: Astrocyte, wt mice, EAE

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

value: Spinal cord

value: wild type


title: F/F EAE p50 Ast

source_name: Astrocyte, wt mice, EAE chronic phase


title: icKO_naive_Ast

source_name: Astrocyte, Cx47 deficient mice

value: Cx47 deficient


title: Rbp53THY_T5


title: RRV replicate 1 18 hr oligo KT493 and No oligo Input

description: Genomic DNA


title: KSHV replicate 2 48 hr  oligo set B

description: CHART-enriched DNA

source_name: BCBL-1 cells

value: BCBL-1 cells

value: 48 hr


title: icKO_EAE_Ast_IGU

source_name: Astrocyte, Cx47 deficient mice EAE, iguratiomod treatment


title: RRV replicate 1 18 hr oligo TKV Input

description: Genomic DNA


title: icKO_EAE_Ast

source_name: Astrocyte, Cx47 deficient mice, EAE


title: FL_EAE_Ast_IGU

source_name: Astrocyte, wt mice EAE, iguratiomod treatment


title: icKO EAE p50 Ast

source_name: Astrocyte, Cx47 deficient mice, EAE chronic phase


title: FL_naive_Ast

source_name: Astrocyte, wt mice


title: Rbp53THY_T2


title: KSHV replicate 2 24 hr  oligo set B

description: CHART-enriched DNA


title: preSC-shCrebbp-1

source_name: preSC cell line

extract_protocol:
Cells were lysed in TRIzol reagent with RNA isolated following manufacturers instructions.
RNA-seq libraries were prepared using theNEBNext Ultra RNA Library Prep Kit for Illumina (catalog E7530L). Briefly, 500 ng total RNA was used to isolate mRNA with the NEB Next Oligo dT Magnetic Isolation Module (catalog E7490L). The isolated mRNA undergoes fragmentation, priming, cDNA synthesis and end repair/dA-tail. Individual index primers for multiplexing were added during PCR library enrichment after adaptor ligation.

tag: cell type

value: precursor cell line of SCLC

tag: shRNA vectors


title: KSHV replicate 2 48 hr  oligo set A

description: CHART-enriched DNA


title: KSHV replicate 2 24 hr  input

description: Genomic DNA


title: preSC-shNS


title: KSHV replicate 2 16 hr  oligo set B

description: CHART-enriched DNA

value: 16 hr


title: preSC-shEmpty-2

value: pLKO.1-TRC-empty vector


title: KSHV replicate 2 24 hr  oligo set A

description: CHART-enriched DNA


title: preSC-shEmpty


title: KSHV replicate 2 16 hr  input

description: Genomic DNA


title: KSHV replicate 2 16 hr  oligo set A

description: CHART-enriched DNA


title: Rbp53CrebbpPIT_T8

source_name: mouse pituitary tumor

value: pituitary tumor

value: neuroendocrine pituitary tumor


title: Rbp53THY_T3


title: Rbp53CrebbpPIT_T7


title: KSHV replicate 2 latent oligo set A

description: CHART-enriched DNA

value: latent

value: 0 hr


title: KSHV replicate 2 latent input

description: Genomic DNA


title: Rbp53CrebbpPIT_T6


title: preSC-shCrebbp-5


title: Rbp53CrebbpPIT_T5


title: KSHV replicate 1 48 hr  input

description: Genomic DNA

value: lytic


title: Rbp53CrebbpPIT_T4


title: KSHV replicate 1 24 hr  input

description: Genomic DNA

value: 24 hr


title: Rbp53CrebbpPIT_T2


title: KSHV replicate 1 16 hr  input

description: Genomic DNA


title: Rbp53CrebbpPIT_T3


title: Rbp53CrebbpPIT_T1


title: Rbp53PIT_T8


title: Rbp53PIT_T5


title: KSHV replicate 1 latent input

description: Genomic DNA


title: Rbp53PIT_T6


title: Rbp53PIT_T7


title: Rbp53PIT_T4


title: Rbp53PIT_T2


title: Rbp53PIT_T1


title: KSHV replicate 2 latent oligo set B

description: CHART-enriched DNA


title: Rbp53PIT_T3


title: Rbp53CrebbpSCLC_T6

source_name: mouse SCLC primary tumor

value: primary SCLC

value: small cell lung cancer


title: Rbp53CrebbpSCLC_T4


title: Rbp53CrebbpSCLC_T3


title: Rbp53CrebbpSCLC_T7


title: Rbp53CrebbpSCLC_T5


title: Rbp53SCLC_T4


title: Rbp53SCLC_T7


title: Rbp53PIT_T9


title: Rbp53CrebbpSCLC_T1


title: Rbp53SCLC_T5


title: Rbp53SCLC_T6


title: Rbp53THY_T4

value: thyroid carcinoma

value: mouse neuroendocrine thyroid carcinoma


title: Rbp53SCLC_T2


title: Rbp53SCLC_T1


title: Rbp53SCLC_T3


title: Rbp53THY_T1


title: RRV replicate 2 latent No oligo

description: CHART-enriched DNA

source_name: BJAB-RRV cells

value: BJAB-RRV cells


title: RRV replicate 2 latent oligo KT493 and No oligo Input

description: Genomic DNA


title: Rbp53CrebbpSCLC_T2


title: RRV replicate 2 36 hr No oligo

description: CHART-enriched DNA

value: 36 hr


title: RRV replicate 2 24 hr oligo KT493

description: CHART-enriched DNA


title: RRV replicate 2 24 hr No oligo

description: CHART-enriched DNA


title: RRV replicate 2 18 hr No oligo

description: CHART-enriched DNA

value: 18 hr


title: RRV replicate 2 18 hr oligo KT493

description: CHART-enriched DNA


title: RRV replicate 1 24 hr No oligo

description: CHART-enriched DNA


title: RRV replicate 1 36 hr oligo KT493

description: CHART-enriched DNA


title: A549_vector control_H83

city: Wuhan

first: Chunhua

last: Wei

address: 1277 JieFang Avenue

institute: Huazhong University of Science and Technology

hyb_protocol: The pre-hybridization of HOA v7 arrays were rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, Cy5-labeled aaRNA was hybridize on MOA v2 in duplication (two arrays for each sample) at 50℃ for 16 hour in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Agilent G2505C scanner (635nm) and quantify the fluoresence intensity.

data_processing:
The data processing was processed by Rosetta Resolver® System (Rosetta Biosoftware, USA). We filtered the spots in which flag=-50 within all arrays and control probes. Probes passed filter were normalized by median scaling to remove systemic effect, then combine the duplicate data by averaging their intensity value.
The pairwised comparison were performed by Rosetta Resolver® System error-weighted modeling to find significant diffrential expressed probes (log2 |Fold change| ≥ 1 and P < 0.05).

source_name: NSCLC cells

label_protocol: aaRNAs were amplified using Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion #AM1753, CA, USA) from 1μg total RNA and directed labeled by NHS-CyDye (Cy5, Amershan) to uridine (dUTP).

growth_protocol: A549 cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum, 100 U/ml penicillin and 100 mg/ml streptomycin in humidified air at 37ºC with 5% CO2.

extract_protocol: RNA extraction by Trizol method. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧ 1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: A549 cell were transfected with lentivirus that knockdown of miR-330-3p and vector. 1 × 10^8 TU/ml lentivirus and 2 μg/ml polybrene were used to transfect A549 cells. Cells were incubated in 5% CO2 at 37 °C for 24 h. The medium was refreshed and cultured for another 48 h. Stable cell lines were selected by using puromycin.

value: non-small cell lung cancer (NSCLC)

value: vector control


title: A549_miR-330-3p_KD_H76

value: knockdown of miR-330-3p


title: A549_vector control_H79


title: Rbpj -/-_N3

city: Ulm

first: André

last: Lechel

address: Albert-Einstein-Allee 23

department: Department of Internal Medicine I

institute: University hospital Ulm

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s protocol. On completion of the fragmentation reaction, 25 µl of 2x Agilent HiRPM hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse GE 8x60K Microarrays (G4852A) for 17 hours at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C prewarmed GE Wash buffer 2 (Agilent) and 30 seconds with Acetonitril.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA microarray Scanner G2505B (3micron) with the the Agilent Scan Control Version A.8.5.1 .

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent). Further processing (background correction, percentile shift normalization, summarization, log2 transformation, median shift) was done following Agilent's quickstart guided workflow.

source_name: whole liver, cholestatic

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's protocol, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with a NanoPhotometer

growth_protocol: mice were kept in a pathogen-free environment

extract_protocol: RNA was isolated using the RNeasy Mini Kit (Qiagen) following the manufacturer's protocol. RNA was quantified using a NanoPhotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: mice are untreated, liver from Rbpj-/- mice were cholestatic

tag: strain

value: whole liver

value: Rbpj -/-

tag: disease state

value: cholestasis


title: Rbpj -/-_2866


title: Rbpj +/+_991

source_name: whole liver, wildtype

value: Rbpj +/+

value: no cholestasis


title: Rbpj -/-_N5


title: preSC-shCrebbp-2

value: precursor cell line of SCLC


title: RRV replicate 1 24 hr oligo KT493

description: CHART-enriched DNA

value: lytic

value: 24 hr


title: Rbpj +/+_1156


title: Rbpj +/+_1024


title: Rbpj +/+_1155


title: A549_miR-330-3p_KD_H74


title: A549_vector control_H81


title: RRV replicate 2 36 hr oligo KT493

description: CHART-enriched DNA


title: KSHV replicate 1 48 hr  oligo set B

description: CHART-enriched DNA

value: BCBL-1 cells

value: 48 hr


title: KSHV replicate 1 48 hr  mock

description: CHART-enriched DNA


title: KSHV replicate 1 48 hr  oligo set A

description: CHART-enriched DNA


title: RRV replicate 1 latent No oligo

description: CHART-enriched DNA

value: latent

value: 0 hr


title: RRV replicate 1 36 hr No oligo

description: CHART-enriched DNA

value: BJAB-RRV cells

value: 36 hr


title: RRV replicate 1 latent oligo KT493

description: CHART-enriched DNA


title: A549_miR-330-3p_KD_H72

value: non-small cell lung cancer (NSCLC)


title: KSHV replicate 1 24 hr  mock

description: CHART-enriched DNA


title: RRV replicate 1 18 hr No oligo

description: CHART-enriched DNA

value: 18 hr


title: RRV replicate 1 18 hr oligo KT493

description: CHART-enriched DNA


title: KSHV replicate 1 16 hr  oligo set B

description: CHART-enriched DNA

value: 16 hr


title: KSHV replicate 1 24 hr  oligo set B

description: CHART-enriched DNA


title: KSHV replicate 1 24 hr  oligo set A

description: CHART-enriched DNA


title: KSHV replicate 1 16 hr  mock

description: CHART-enriched DNA


title: KSHV replicate 1 latent oligo set B

description: CHART-enriched DNA


title: Basic 2

first: Katrine

last: Whiteson

address: 3315 McGaugh Hall

description: ribosomal depleted RNA

data_processing:
Paired-end reads were quality-filtered and adaptors were trimmed with Trimmomatic version 0.35
Residual ribosomal RNA was removed with Deconseq version 0.4.3
Overlapping paired-end reads were joined to make single-end reads using PAIR (version 2015-04-09)
The overlapping reads and paired-end reads were aligned to the FLR19 genome using bowtie2 version 2.2.7
The number of reads that aligned to genes were counted using HT-Seq Count version 0.6.1
Differentially expressed genes were determined using the "edgeR" R package
Genome_build: assembled with A5 assembler, available on PATRIC 40324.190
Supplementary_files_format_and_content: excel sheet containg the read counts from HT-Seq for all samples

organism: Stenotrophomonas maltophilia

source_name: Bacterial cells

growth_protocol: pH-buffered todd-hewitt broth for 24h

extract_protocol:
Zymo Direct-zol miniprep kit and Ribo-Zero rRNA Removal kit
TruSeq RNA sample prep kit

treatment_protocol: phopshate-buffered pH 5, pH 7, or pH 9 media

tag: condition

value: basic pH

tag: isolation source

value: cystic fibrosis lungs

tag: incubation


title: Basic 1

description: ribosomal depleted RNA


title: Neutral 3

description: ribosomal depleted RNA

value: neutral pH


title: 4_HIF2A_KD_H

city: Oulu

first: Irina

last: Raykhel

address: Aapistie 5

department: FBMM

country: Finland

institute: University of Oulu

description: Gene expression data from Madin-Darby canine kidney epithelial cells, KD for HIF2A, in hypoxia

hyb_protocol: cRNA was hybridized on GeneChip Canine Genome 2.0 Array  plates according to manufacturer's instructions (wash_stain_scan_cartridge_arrays_manual.pdf, Chapter2; WASH, STAIN AND SCAN PROTOCOL WITH USERPREPARED REAGENTS)

scan_protocol: 7GGeneChips were scanned on Affymetrix GeneChip Scanner 3000 7G

data_processing: Data were normalized using pair-wise rank-invariant normalization in  software dchip_2010_01.exe.

organism: Canis lupus familiaris

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip® 3’ IVT Express Kit, Affymetrix)

growth_protocol: Madin-Darby canine kidney epithelial cells (MDCKII) were incubated 24h in normoxic condition then additionaly were incubated 24h in normoxic or hypoxic conditions

extract_protocol: Total RNA was extracted with RNeasy Kit (Qiagen) according to the manufacturer's instructions.

value: MDCKII cells (ATCC:CCL-34)

tag: genotype/variation

value: HIF2A knockdown

value: hypoxic


title: 3_HIF2A_WT_H

description: Gene expression data from Madin-Darby canine kidney epithelial cells, WT for HIF2A, in hypoxia

value: wild type


title: 1_HIF2A_WT_N

description: Gene expression data from Madin-Darby canine kidney epithelial cells, WT for HIF2A, in normoxia

value: normoxic


title: Neutral 1

description: ribosomal depleted RNA


title: KSHV replicate 1 latent oligo set A

description: CHART-enriched DNA

value: BCBL-1 cells


title: 2_HIF2A_KD_N

description: Gene expression data from Madin-Darby canine kidney epithelial cells, KD for HIF2A, in normoxia


title: KSHV replicate 1 latent mock

description: CHART-enriched DNA


title: Neutral 2

description: ribosomal depleted RNA


title: Acidic 1

description: ribosomal depleted RNA

value: acidic pH


title: Acidic 2

description: ribosomal depleted RNA


title: KSHV replicate 1 16 hr  oligo set A

description: CHART-enriched DNA

value: lytic


title: T-ALL_C28

status: Public on Oct 16 2018

city: Gent

first: Sofie

last: Peirs

address: De Pintelaan 185

country: Belgium

institute: Ghent University

description: primary T-ALL sample from patient C28 vs. gender-matched control

hyb_protocol: Samples were hybridized on Agilent SurePrint G3 Human CGH 4x180K microarrays (G4449A, design ID: 022060) for 24h at 65 °C.

scan_protocol: The samples were scanned at 2 µm resolution using a DNA microarray scanner G2505B (Agilent Technologies).

data_processing:
The scan images were analyzed using the feature extraction software 9.5.3.1 (Agilent Technologies).
Log2 of the ratio of the intensities (green channel/red channel)

source_name: primary T-ALL sample collected at diagnosis

label_protocol: 100 ng of genomic DNA (for sample D04 only 82 ng was used and for sample D09 78 ng was used) was labeled with Cy3-dCTP (Perkin Elmer, NEL620001KT) using a Bioprime Array CGH Labeling System (Invitrogen, 10297-018). In parallel, Kreatech gender-matched controls were labeled with Cy5-dCTP.

extract_protocol: DNA was extracted from T-ALL patient samples using the AllPrep DNA/RNA Mini Kit (Qiagen) according to the manufacturer’s instructions.

tag: age

value: Male

tag: white blood cell count

tag: treatment regimen

value: COG AALL0434

source_name: gender-matched control DNA

value: male


title: T-ALL_C30

description: primary T-ALL sample from patient C30 vs. gender-matched control

tag: gender

value: Female


title: T-ALL_D03

description: primary T-ALL sample from patient D03 vs. gender-matched control


title: T-ALL_D04

description: primary T-ALL sample from patient D04 vs. gender-matched control


title: T-ALL_D08

description: primary T-ALL sample from patient D08 vs. gender-matched control


title: T-ALL_D06

description: primary T-ALL sample from patient D06 vs. gender-matched control

value: female


title: T-ALL_C31

description: primary T-ALL sample from patient C31 vs. gender-matched control


title: T-ALL_C23

description: primary T-ALL sample from patient C23 vs. gender-matched control


title: T-ALL_C19

description: primary T-ALL sample from patient C19 vs. gender-matched control


title: T-ALL_C20

description: primary T-ALL sample from patient C20 vs. gender-matched control


title: T-ALL_C21

description: primary T-ALL sample from patient C21 vs. gender-matched control


title: T-ALL_C24

description: primary T-ALL sample from patient C24 vs. gender-matched control


title: T-ALL_C18

description: primary T-ALL sample from patient C18 vs. gender-matched control


title: T-ALL_C16

description: primary T-ALL sample from patient C16 vs. gender-matched control


title: T-ALL_C17

description: primary T-ALL sample from patient C17 vs. gender-matched control


title: T-ALL_C12

description: primary T-ALL sample from patient C12 vs. gender-matched control


title: T-ALL_C15

description: primary T-ALL sample from patient C15 vs. gender-matched control


title: T-ALL_C10

description: primary T-ALL sample from patient C10 vs. gender-matched control


title: T-ALL_C14

description: primary T-ALL sample from patient C14 vs. gender-matched control


title: T-ALL_C09

description: primary T-ALL sample from patient C09 vs. gender-matched control


title: T-ALL_C07

description: primary T-ALL sample from patient C07 vs. gender-matched control


title: T-ALL_C06

description: primary T-ALL sample from patient C06 vs. gender-matched control


title: T-ALL_C03

description: primary T-ALL sample from patient C03 vs. gender-matched control


title: T-ALL_C05

description: primary T-ALL sample from patient C05 vs. gender-matched control


title: T-ALL_C01

description: primary T-ALL sample from patient C01 vs. gender-matched control


title: T-ALL_D21

description: primary T-ALL sample from patient D21 vs. gender-matched control


title: SC_WT_1

city: Seoul

first: Chanhyeok

last: Park

address: 5, Hwarang-ro 14-gil

department: Brain Science Institute

country: South Korea

institute: KIST (Korea Institute of Science and Technology)

description: Gene expression data from postnatal day 14

hyb_protocol: Fifteen microgram of RNA were hybridized for 16 hour at 45 ℃ on GeneChip Mouse Genome 430 2.0 Arrays.

scan_protocol: GeneChips were washed and stained in the Affymetrix Fluidics Station 450. GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Microarray CEL files (3 biological replicates/each group) were background corrected, normalized RMA. Differential expression analysis was carried out using biocLite (affy, limma, GenomicRanges) of Bioconductor (v3.2). DEGs were determined at cutoff P value < 0.05.

source_name: postnatal day 14 mouse testis

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA (Affymetrix).

growth_protocol: All mice were maintained in control rooms with a 12 hour (h) light-dark cycle and provided food and water ad libitum.

extract_protocol: Total RNAs were extracted using RNeasy total RNA isolation kit (Qiagen) according to the manufacturer's instruction. Potential genomic DNAs were digested with RNase-free DNase (Qiagen) during RNA purification.

treatment_protocol: All mice were sacrificed on postnatal day 14 and genotyped with specific primers to distinguish control and conditional knockout. The testes were removed, washed with PBS and kept in liquid nitrogen until use.

tag: tissue

value: Testes

tag: genotype

value: Cfp1F/+ , Stra8-cre


title: SC_WT_3


title: SC_CO_1

value: Cfp1F/F , Stra8-cre


title: SC_WT_2


title: T-ALL_C02

description: primary T-ALL sample from patient C02 vs. gender-matched control


title: T-ALL_D11

description: primary T-ALL sample from patient D11 vs. gender-matched control


title: SC_CO_2


title: T-ALL_D15

description: primary T-ALL sample from patient D15 vs. gender-matched control


title: T-ALL_D12

description: primary T-ALL sample from patient D12 vs. gender-matched control


title: T-ALL_C11

description: primary T-ALL sample from patient C11 vs. gender-matched control


title: T-ALL_D10

description: primary T-ALL sample from patient D10 vs. gender-matched control


title: T-ALL_D16

description: primary T-ALL sample from patient D16 vs. gender-matched control


title: T-ALL_D09

description: primary T-ALL sample from patient D09 vs. gender-matched control


title: SC_CO_3


title: T-ALL_D13

description: primary T-ALL sample from patient D13 vs. gender-matched control


title: T-ALL_D20

description: primary T-ALL sample from patient D20 vs. gender-matched control


title: KSHV replicate 2 48 hr  input

description: Genomic DNA

source_name: BCBL-1 cells

tag: cell line

tag: viral stage

tag: viral lytic induction timepoint

value: 48 hr


title: F1-RM38 (patient derived xenograft)

city: Amsterdam

first: Sander

middle: Roeland

last: van Hooff

address: Meibergdreef 9

department: Center for Experimental and Molecular Medicine (CEMM),

country: Netherlands

institute: AUMC

hyb_protocol: Hybridization was performed according to the standard protocols of the Cologne Center for Genomics (CCG), University of Cologne, Germany.

scan_protocol: Samples were scanned using the Gene Titan Affymetrix instrument according to the standard protocols of the Cologne Center for Genomics (CCG), University of Cologne, Germany.

data_processing: Data were normalized by RMA using the Affy R package and batch effects were corrected using ComBat using the sva R package

source_name: Xenograft F1

label_protocol: Labeling was performed according to the standard protocols of the Cologne Center for Genomics (CCG), University of Cologne, Germany.

extract_protocol: Total RNA was extracted using the Nucleospin miRNA kit (Bioke, Leiden, The Netherlands) according to the supplier’s instruction.

value: CRC

value: Liver metastasis

tag: Stage

tag: cimp

tag: msi

tag: cms

tag: batch

tag: center

value: AMC


title: F2-RM38 (patient derived xenograft)

source_name: Xenograft F2

tag: disease state


title: F3-RM37 (patient derived xenograft)

source_name: Xenograft F3


title: F2-RM40 (patient derived xenograft)


title: F3-RM28 (patient derived xenograft)


title: F1-RM29 (patient derived xenograft)


title: F2-RM28 (patient derived xenograft)


title: F3-RM39 (patient derived xenograft)


title: F1-RM28 (patient derived xenograft)