title: body column endodermal epithelium  -rep 2 (endo1)

description:
Endo1_S32_L003
processed data file: DGE_ecto_endo_aepLRv2.matrix

data_processing:
library strategy: Tag-seq
Poly-A stretches and sequencing adapters were trimmed using the script bbduk.sh (Joint Genome Institute) using the following parameters: k=13 ktrim=r forcetrimleft=11 useshortkmers=t mink=5 qtrim=t trimq=10 minlength=20. Ribosomal reads were excluded using bbduk.sh and a set of Hydra rRNA sequences. Epithelium specific expression levels were estimated using RSEM v1.2.31 and bowtie v1.1.2.
genome build: Hydra vulgaris AEP transcriptome (aepLRv2) (https://research.nhgri.nih.gov/hydra/)
Supplementary_files_format_and_content: tab-delimited text file of isoform level expression estimates for endoderm and ectoderm (DGE_ecto_endo_aepLRv2.txt)

source_name: body column endodermal epithelium

extract_protocol:
Trizol (Invitrogen)
QuantSeq 3‘ mRNA-Seq Library Prep Kit for Illumina (FWD) (Lexogen)

treatment_protocol: Viable Hydra endoderm and ectoderm layers were obtained as described previously (Lesh-Laurie, 1983). Hydra were allowed to relax for approximately 30 sec to 1 min in M solution (Muscatine, 1961) that was adjusted to pH 2.5. The head was then excised by a cut directly below the tentacle ring, followed by the excision of the lower peduncle. The remaining cylinder of tissue was transferred to Haynes solution (Davis et al. 1966). Shortly after being placed in Haynes solution the ectoderm contracts until it forms a small ring surrounding a column of extended endodermal tissue. The ectodermal annulus and the endodermal tissue were immediately transferred to Trizol (Invitrogen). Eight to ten tissue samples were pooled prior to total RNA extraction.

value: Hydra vulgaris AEP (transgenic line expressing RFP in ectoderm, GFP in endoderm, Glauber et al., 2013)

value: endoderm


title: 1753890

status: Public on Nov 07 2018

type: RNA

city: Little Rock

first: Brian

last: Walker

state: AR

address: 4301 W Markham St.

country: USA

institute: University of Arkansas for Medical Sciences

description:
CD138+
Gene expresion data from newly diagnosed Smouldering patient

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on human GeneChip. U133 plus 2.0 chips are washed and stained further in affymetrix fluidics station

scan_protocol: Chips were scanned using the HG-U133 Plus 2.0 v2.2 on a Affymetrix Genechip scanner

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: CD138+ selected bone marrow plasma cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from200ng  total RNA

extract_protocol: RNA extraction and isolation was performed with the AllPrep kit by Qiagen

tag: patient id

tag: swog id

tag: patient group

value: AMM

tag: patient disease timepoint

value: Baseline

tag: sample type

value: RNAS-Random Aspirate

tag: molecular subgroup

tag: gep70 score


title: homeostatic Hydra, female spike-in (D03-FM)

status: Public on Nov 02 2018

type: SRA

city: Davis

first: Celina

middle: E

last: Juliano

state: California

address: 149 Briggs Hall

department: MCB

institute: University of California Davis

description:
D03-FM_S3
processed data file: Hydra_DS_genome_UMICounts.txt, Hydra_DS_transcriptome_UMICounts.txt

library_source: transcriptomic

data_processing:
library strategy: Drop-seq
Data was processed using Drop-seq tools v1.01, according to Drop-seq protocol v3.1 (http://www.dropseq.org/). Read 2 was aligned with Bowtie2 v 2.2.6 to 1) the Hydra vulgaris 105 2.0 genome using 2.0 genome gene models and 2) a Hydra vulgaris AEP transcriptome reference (aepLRv2)(references available at https://research.nhgri.nih.gov/hydra/). Each aligned read was tagged with its mate-pair UMI and cell barcode (which comprise Read 1). Each aligned exonic read was tagged with a gene name. Cell barcodes were corrected for synthesis errors. A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells, and rows are genes. The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample. Genome UMI counts are provided in supplementary file Hydra_DS_genome_UMICounts.txt. Transcriptome UMI counts are provided in supplementary file Hydra_DS_transcriptome_UMICounts.txt.
genome build: Hydra vulgaris 2.0 genome, Hydra vulgaris AEP transcriptome (aepLRv2)(https://research.nhgri.nih.gov/hydra/)
Supplementary_files_format_and_content: tab-delimited text files of UMI counts for genome mapping (Hydra_DS_genome_UMICounts.txt) and transcriptome mapping (Hydra_DS_transcriptome_UMICounts.txt)
Supplementary_files_format_and_content: tab-delimited text file of isoform level expression estimates

molecule: polyA RNA

organism: Hydra vulgaris

source_name: cell suspension from homeostatic Hydra vulgaris AEP

growth_protocol: Hydra vulgaris AEP were cultured according to standard protocol (Lenhoff, 1983)  at 18˚C.

extract_protocol:
Cells were encapsulated using a standard Drop-seq apparatus. Lysis occurred in droplets in Drop-seq lysis buffer (www.drop-seq.org).
Libraries were prepared according to Drop-seq Protocol v3.1 (12/28/2015), with 14 cycles of PCR amplification and 148 STAMPs per PCR reaction.

treatment_protocol: Prior to Drop-seq cells were dissociated for 90min using Pronase E (VWR, E629-1G) as described previously (Greber et al.,1992) at a concentration of ~75u/mL. 40-50 Hydra were washed twice in sterile filtered Hydra medium and transferred into a 1.5mL eppendorf tube. The medium was removed and 1mL Pronase solution was added. Cells were dissociated for 90min at room temperature (22-24C) with agitation on a nutator. Cells were washed twice and resuspended in resuspended in a salt-adjusted Hydra-PBS (10 mM PO43−, 2mM NaCL, 0.1mM KCl, 0.05% BSA, pH7.6).

tag: strain

value: Hydra vulgaris AEP (transgenic line nGreen, Robert E. Steele)

tag: tissue

value: whole animal


title: body column endodermal epithelium  -rep 1 (endo)

description:
Endo_S31_L003
processed data file: DGE_ecto_endo_aepLRv2.matrix

treatment_protocol: Viable Hydra endoderm and ectoderm layers were obtained as described previously (Lesh-Laurie, 1983). Hydra were allowed to relax for approximately 30 sec to 1 min in M solution (Muscatine, 1961) that was adjusted to pH 2.5. The head was then excised by a cut directly below the tentacle ring, followed by the excision of the lower peduncle. The remaining cylinder of tissue was transferred to Haynes solution (Davis et al. 1966). Shortly after being placed in Haynes solution the ectoderm contracts until it forms a small ring surrounding a column of extended endodermal tissue. The ectodermal annulus and the endodermal tissue were immediately transferred to Trizol (Invitrogen)


title: body column ectodermal epithelium  -rep 1 (ecto1)

description:
Ecto1_S34_L003
processed data file: DGE_ecto_endo_aepLRv2.matrix

source_name: body column ectodermal epithelium

value: ectoderm


title: body column ectodermal epithelium  -rep 2 (ecto2)

description:
Ecto2_S35_L003
processed data file: DGE_ecto_endo_aepLRv2.matrix


title: body column ectodermal epithelium  -rep 3 (ecto3)

description:
Ecto3_S36_L003
processed data file: DGE_ecto_endo_aepLRv2.matrix


title: homeostatic Hydra -rep 4 (D02-P1)

description:
D02-P1_S3
processed data file: Hydra_DS_genome_UMICounts.txt, Hydra_DS_transcriptome_UMICounts.txt

extract_protocol:
Cells were encapsulated using a standard Drop-seq apparatus. Lysis occurred in droplets in Drop-seq lysis buffer (www.drop-seq.org).
Libraries were prepared according to Drop-seq Protocol v3.1 (12/28/2015), with 12 cycles of PCR amplification and 296 STAMPs per PCR reaction.

value: Hydra vulgaris AEP


title: homeostatic Hydra -rep 6 (D03-KI)

description:
D03-KI_S1
processed data file: Hydra_DS_genome_UMICounts.txt, Hydra_DS_transcriptome_UMICounts.txt

extract_protocol:
Cells were encapsulated using a standard Drop-seq apparatus. Lysis occurred in droplets in Drop-seq lysis buffer (www.drop-seq.org).
Libraries were prepared according to Drop-seq Protocol v3.1 (12/28/2015), with 13 cycles of PCR amplification and 148 STAMPs per PCR reaction.


title: Replicate 3 - ATACseq reads generated for whole homeostatic Hydra

description:
ATAC-3
processed data file: consensus_peak.bed

library_source: genomic

data_processing:
Nextera adapters and unpaired reads were removed using trimmomatic 0.36. Reads were mapped using bowtie 2.2. PCR duplicates were removed using Picard 2.17.8. Peaks were called using MACS2 2.1.1.
genome build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)
Supplementary_files_format_and_content: Bed file. Consensus peak list consisting of all peaks that passed an IDR threshold of 0.1 for at least one pairwise comparison among the three biological replicates

molecule: genomic DNA

source_name: Hydra vulgaris 105 (nuclei)

growth_protocol: Hydra vulgaris 105 were cultured according to standard protocol (Lenhoff, 1983)  at 18˚C.

extract_protocol:
5 whole Hydra were homogenized using a dounce homogenizer and cells were lysed using a cocktail of mild detergents. ~50000 nuclei were then spun down and used for tagmentation.
OMNI-ATACseq (Corces et al. 2017)

value: Hydra vulgaris 105


title: body column endodermal epithelium  -rep 3 (endo3)

description:
Endo3_S33_L003
processed data file: DGE_ecto_endo_aepLRv2.matrix


title: homeostatic Hydra -rep 3 (D02-CO)

description:
D02-CO_S2
processed data file: Hydra_DS_genome_UMICounts.txt, Hydra_DS_transcriptome_UMICounts.txt

extract_protocol:
Cells were encapsulated using a standard Drop-seq apparatus. Lysis occurred in droplets in Drop-seq lysis buffer (www.drop-seq.org).
Libraries were prepared according to Drop-seq Protocol v3.1 (12/28/2015), with 15 cycles of PCR amplification and 296 STAMPs per PCR reaction.


title: homeostatic Hydra -rep 2 (D01-P2)

description:
D01-P2_S4
processed data file: Hydra_DS_genome_UMICounts.txt, Hydra_DS_transcriptome_UMICounts.txt

extract_protocol:
Cells were encapsulated using a standard Drop-seq apparatus. Lysis occurred in droplets in Drop-seq lysis buffer (www.drop-seq.org).
Libraries were prepared according to Drop-seq Protocol v3.1 (12/28/2015), with 12 cycles of PCR amplification and 100 STAMPs per PCR reaction.


title: Replicate 2 - ATACseq reads generated for whole homeostatic Hydra

description:
ATAC-2
processed data file: consensus_peak.bed


title: Replicate 1 - ATACseq reads generated for whole homeostatic Hydra

description:
ATAC-1
processed data file: consensus_peak.bed


title: homeostatic Hydra -rep 1 (D01-D1)

description:
D01-D1_S1
processed data file: Hydra_DS_genome_UMICounts.txt, Hydra_DS_transcriptome_UMICounts.txt


title: twF

status: Public on Sep 15 2018

city: Stanford

first: Natalina

last: Quarto

state: CA

address: 257 Campus Drive

department: Surgery - Plastic and Reconstructive Surgery

institute: Stanford University School of Medicine

data_processing:
RNA-Seq alignment to the reference was performed using STAR v2.4.2a using default conditions as described in Dobin et al., Bioinformatics, 2013.
Normalized transcript abundances (FPKM) were calculated and differential expression analyses for RNA-Seq were performed using the Cuffdiff program from the Cufflinks v2.2.1 suite using default conditions as described in Trapnell et al., Nature Biotechnology, 2013. The bias detection and correction algorithm was used to significantly improve accuracy of transcript abundance estimates as described in Roberts et al., Genome Biology, 2011. The initial estimation procedure was used to more accurately weight reads mapping to multiple locations in the genome.
Exploration, analysis and visualization of Cuffdiff results were performed using the CummeRbund v2.12.1 R package installed in R v3.2.2 as described in Trapnell et al., Nature Protocols, 2012.
Genome_build: mm9
Supplementary_files_format_and_content: transcript abundance FPKM measurements

organism: Mus musculus

source_name: Twist1+/-_Calvarial frontal bone

extract_protocol:
Total RNAs isolated from wild-type and Twist1+/- frontal and parietal bones (mice = 12/each strain) were purified using a Qiagen MiRNeasy Kit (Cat #217004) following the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain background

tag: genotype/variation

tag: age

value: post natal day 21

value: bone

tag: tissue subtype

value: Calvarial frontal bone


title: twP

source_name: Twist1+/-_Calvarial parietal bone

value: Calvarial parietal bone


title: wtF

source_name: wild type_Calvarial frontal bone

value: wild type


title: homeostatic Hydra -rep 5 (D02-PB)

description:
D02-PB_S4
processed data file: Hydra_DS_genome_UMICounts.txt, Hydra_DS_transcriptome_UMICounts.txt


title: CD A1b L1 rep49

status: Public on Aug 01 2018

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: Ileal biopsy from Female CD patient aged 16.9166666666667 years at diagnosis with L1 location and Paris age A1b

data_processing:
Sequencing was peformed on the Illumina HiSeq2000
Reads were quantified using kallisto with  Gencode v23 as the reference genome, with transcripts per million as the output.
Genome_build: Gencode v23
Supplementary_files_format_and_content: Tab delimited files with gene symbol and TPM

source_name: Ileal biopsy

extract_protocol:
Ileal biopsies were obtained at diagnostic colonoscopies and stored in RNALater at -80.  RNA was isolated using Qiagen AllPrep RNA/DNA MiniKiet.
Poly-A-RNA selection, fragmentation, cDNA synthesis, adaptor ligation, and library preparation were performed using TruSeq RNA Sample preparation (Illumina)

tag: diagnosis

value: CD

tag: location

tag: Sex

value: Female

tag: age at diagnosis in years

tag: paris age


title: CD A1b L3 rep99

description: Ileal biopsy from Male CD patient aged 16.75 years at diagnosis with L3 location and Paris age A1b

value: Male


title: CD A1b L3 rep100


title: CD A1b L3 rep97

description: Ileal biopsy from Male CD patient aged 16.5 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep98


title: CD A1b L3 rep95


title: 3012729

description:
CD138+
Gene expresion data from newly diagnosed Smouldering patient

tag: patient id

tag: swog id


title: CD A1b L1 rep45

description: Ileal biopsy from Female CD patient aged 16.5 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L1 rep46

description: Ileal biopsy from Male CD patient aged 16.5 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L3 rep96

description: Ileal biopsy from Female CD patient aged 16.5 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L1 rep44

description: Ileal biopsy from Male CD patient aged 16.4166666666667 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L3 rep94

description: Ileal biopsy from Female CD patient aged 16.25 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep93

description: Ileal biopsy from Male CD patient aged 16.25 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep101

description: Ileal biopsy from Male CD patient aged 16.8333333333333 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep91

description: Ileal biopsy from Male CD patient aged 16.1666666666667 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep87

description: Ileal biopsy from Male CD patient aged 16.0833333333333 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep89

description: Ileal biopsy from Female CD patient aged 16.0833333333333 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep86

description: Ileal biopsy from Female CD patient aged 15.9166666666667 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L1 rep43

description: Ileal biopsy from Male CD patient aged 15.9166666666667 years at diagnosis with L1 location and Paris age A1b


title: wtP

source_name: wild type_Calvarial parietal bone


title: CD A1b L1 rep42

description: Ileal biopsy from Female CD patient aged 15.8333333333333 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L1 rep41


title: 3942942

tag: patient group

tag: patient disease timepoint


title: CD A1b L1 rep48

description: Ileal biopsy from Female CD patient aged 16.6666666666667 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L1 rep40

description: Ileal biopsy from Female CD patient aged 15.75 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L3 rep85

description: Ileal biopsy from Male CD patient aged 15.75 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep84

description: Ileal biopsy from Male CD patient aged 15.6666666666667 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep83

description: Ileal biopsy from Female CD patient aged 15.5833333333333 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep81

description: Ileal biopsy from Male CD patient aged 15.5 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L1 rep39

description: Ileal biopsy from Female CD patient aged 15.5833333333333 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L1 rep38

description: Ileal biopsy from Female CD patient aged 15.4166666666667 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L3 rep82


title: CD A1b L3 rep80

description: Ileal biopsy from Female CD patient aged 15.5 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep90


title: CD A1b L3 rep78

description: Ileal biopsy from Male CD patient aged 15.3333333333333 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L1 rep37

description: Ileal biopsy from Male CD patient aged 15.1666666666667 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L3 rep79

description: Ileal biopsy from Female CD patient aged 15.4166666666667 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep77


title: CD A1b L1 rep36

description: Ileal biopsy from Female CD patient aged 15.1666666666667 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L3 rep76

description: Ileal biopsy from Female CD patient aged 15.1666666666667 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L1 rep35

description: Ileal biopsy from Male CD patient aged 15 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L1 rep47

description: Ileal biopsy from Male CD patient aged 16.6666666666667 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L3 rep75


title: CD A1b L1 rep34

description: Ileal biopsy from Female CD patient aged 15 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L3 rep74

description: Ileal biopsy from Female CD patient aged 14.9166666666667 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep73

description: Ileal biopsy from Male CD patient aged 14.9166666666667 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep71

description: Ileal biopsy from Male CD patient aged 14.8333333333333 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep70

description: Ileal biopsy from Female CD patient aged 14.75 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L1 rep31

description: Ileal biopsy from Male CD patient aged 14.5833333333333 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L3 rep69

description: Ileal biopsy from Male CD patient aged 14.5833333333333 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L1 rep30

description: Ileal biopsy from Male CD patient aged 14.4166666666667 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L3 rep67

description: Ileal biopsy from Male CD patient aged 14.4166666666667 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep72


title: CD A1b L3 rep62

description: Ileal biopsy from Female CD patient aged 14.0833333333333 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep68


title: CD A1b L3 rep60

description: Ileal biopsy from Female CD patient aged 13.9166666666667 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep61

description: Ileal biopsy from Male CD patient aged 13.9166666666667 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep65

description: Ileal biopsy from Male CD patient aged 14.3333333333333 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L1 rep29

description: Ileal biopsy from Male CD patient aged 13.9166666666667 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L3 rep58

description: Ileal biopsy from Male CD patient aged 13.6666666666667 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L1 rep28

description: Ileal biopsy from Male CD patient aged 13.5833333333333 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L3 rep55

description: Ileal biopsy from Male CD patient aged 13.5 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep53

description: Ileal biopsy from Male CD patient aged 13.25 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L1 rep26

description: Ileal biopsy from Male CD patient aged 13.4166666666667 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L3 rep51


title: CD A1b L3 rep56

description: Ileal biopsy from Male CD patient aged 13.5833333333333 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep54

description: Ileal biopsy from Male CD patient aged 13.4166666666667 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep49

description: Ileal biopsy from Female CD patient aged 13.25 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L1 rep25

description: Ileal biopsy from Female CD patient aged 13.1666666666667 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L1 rep24

description: Ileal biopsy from Male CD patient aged 13.1666666666667 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L3 rep46

description: Ileal biopsy from Female CD patient aged 13.0833333333333 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L1 rep23

description: Ileal biopsy from Male CD patient aged 13.0833333333333 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L1 rep20

description: Ileal biopsy from Female CD patient aged 12.8333333333333 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L1 rep19


title: CD A1b L3 rep66

description: Ileal biopsy from Female CD patient aged 14.3333333333333 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep44

description: Ileal biopsy from Male CD patient aged 12.75 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep64

description: Ileal biopsy from Male CD patient aged 14.25 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep43


title: CD A1b L3 rep42

description: Ileal biopsy from Male CD patient aged 12.5833333333333 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep39

description: Ileal biopsy from Female CD patient aged 12.4166666666667 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep41


title: CD A1b L3 rep38

description: Ileal biopsy from Male CD patient aged 12.4166666666667 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep59

description: Ileal biopsy from Male CD patient aged 13.75 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep40

description: Ileal biopsy from Female CD patient aged 12.5 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep35

description: Ileal biopsy from Female CD patient aged 12.1666666666667 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep52

description: Ileal biopsy from Male CD patient aged 13.25 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L1 rep18

description: Ileal biopsy from Female CD patient aged 12.5 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L3 rep33

description: Ileal biopsy from Female CD patient aged 12.0833333333333 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep31

description: Ileal biopsy from Female CD patient aged 12 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L1 rep17

description: Ileal biopsy from Female CD patient aged 12.1666666666667 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L3 rep29

description: Ileal biopsy from Male CD patient aged 11.9166666666667 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L1 rep15

description: Ileal biopsy from Male CD patient aged 12 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L3 rep34

description: Ileal biopsy from Male CD patient aged 12.0833333333333 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L1 rep16

description: Ileal biopsy from Female CD patient aged 12.0833333333333 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L1 rep12

description: Ileal biopsy from Male CD patient aged 11.5 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L3 rep28


title: CD A1b L3 rep23

description: Ileal biopsy from Male CD patient aged 11.5 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep24

description: Ileal biopsy from Male CD patient aged 11.5833333333333 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep27

description: Ileal biopsy from Female CD patient aged 11.75 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L1 rep11

description: Ileal biopsy from Male CD patient aged 11.4166666666667 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L1 rep13

description: Ileal biopsy from Female CD patient aged 11.5833333333333 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L3 rep30


title: CD A1b L3 rep21

description: Ileal biopsy from Male CD patient aged 11.25 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L1 rep8

description: Ileal biopsy from Male CD patient aged 11.25 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L1 rep7

description: Ileal biopsy from Male CD patient aged 11.1666666666667 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L3 rep22

description: Ileal biopsy from Female CD patient aged 11.25 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep19

description: Ileal biopsy from Female CD patient aged 11 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep17

description: Ileal biopsy from Female CD patient aged 10.8333333333333 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep18


title: CD A1b L3 rep15

description: Ileal biopsy from Male CD patient aged 10.8333333333333 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L1 rep6

description: Ileal biopsy from Male CD patient aged 10.75 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L3 rep16


title: CD A1b L3 rep14

description: Ileal biopsy from Female CD patient aged 10.75 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep13

description: Ileal biopsy from Male CD patient aged 10.75 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep12

description: Ileal biopsy from Female CD patient aged 10.6666666666667 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L1 rep5

description: Ileal biopsy from Male CD patient aged 10.6666666666667 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L3 rep9

description: Ileal biopsy from Male CD patient aged 10.5833333333333 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep10


title: CD A1b L3 rep7

description: Ileal biopsy from Female CD patient aged 10.3333333333333 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L1 rep10

description: Ileal biopsy from Male CD patient aged 11.3333333333333 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L3 rep6

description: Ileal biopsy from Male CD patient aged 10.3333333333333 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L1 rep3

description: Ileal biopsy from Male CD patient aged 10.3333333333333 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L1 rep9


title: CD A1b L1 rep1

description: Ileal biopsy from Female CD patient aged 10.1666666666667 years at diagnosis with L1 location and Paris age A1b


title: CD A1b L3 rep5


title: CD A1b L3 rep4

description: Ileal biopsy from Female CD patient aged 10.1666666666667 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L3 rep3

description: Ileal biopsy from Male CD patient aged 10.1666666666667 years at diagnosis with L3 location and Paris age A1b


title: CD A1b L1 rep2


title: CD A1b L3 rep2

description: Ileal biopsy from Female CD patient aged 10.0833333333333 years at diagnosis with L3 location and Paris age A1b


title: CD A1a L3 rep41

description: Ileal biopsy from Male CD patient aged 9.83333333333333 years at diagnosis with L3 location and Paris age A1a


title: CD A1b L3 rep20

description: Ileal biopsy from Male CD patient aged 11.1666666666667 years at diagnosis with L3 location and Paris age A1b


title: CD A1a L3 rep38

description: Ileal biopsy from Male CD patient aged 9.75 years at diagnosis with L3 location and Paris age A1a


title: CD A1a L3 rep39


title: CD A1a L3 rep34

description: Ileal biopsy from Female CD patient aged 9.5 years at diagnosis with L3 location and Paris age A1a


title: CD A1a L3 rep33

description: Ileal biopsy from Male CD patient aged 9.41666666666667 years at diagnosis with L3 location and Paris age A1a


title: CD A1a L1 rep7

description: Ileal biopsy from Female CD patient aged 9.41666666666667 years at diagnosis with L1 location and Paris age A1a


title: CD A1b L3 rep11

description: Ileal biopsy from Male CD patient aged 10.6666666666667 years at diagnosis with L3 location and Paris age A1b


title: CD A1a L3 rep37

description: Ileal biopsy from Male CD patient aged 9.58333333333333 years at diagnosis with L3 location and Paris age A1a


title: CD A1a L3 rep28

description: Ileal biopsy from Female CD patient aged 9.16666666666667 years at diagnosis with L3 location and Paris age A1a


title: CD A1a L3 rep30

description: Ileal biopsy from Male CD patient aged 9.25 years at diagnosis with L3 location and Paris age A1a


title: CD A1a L3 rep31


title: CD A1a L1 rep6

description: Ileal biopsy from Female CD patient aged 8.91666666666667 years at diagnosis with L1 location and Paris age A1a


title: CD A1a L3 rep25

description: Ileal biopsy from Female CD patient aged 9 years at diagnosis with L3 location and Paris age A1a


title: CD A1a L3 rep26

description: Ileal biopsy from Male CD patient aged 9.16666666666667 years at diagnosis with L3 location and Paris age A1a


title: CD A1a L3 rep27


title: CD A1a L3 rep24

description: Ileal biopsy from Male CD patient aged 8.91666666666667 years at diagnosis with L3 location and Paris age A1a


title: CD A1a L1 rep5

description: Ileal biopsy from Female CD patient aged 8.83333333333333 years at diagnosis with L1 location and Paris age A1a


title: CD A1a L3 rep20

description: Ileal biopsy from Male CD patient aged 8.83333333333333 years at diagnosis with L3 location and Paris age A1a


title: CD A1a L1 rep4

description: Ileal biopsy from Male CD patient aged 8.75 years at diagnosis with L1 location and Paris age A1a


title: CD A1a L3 rep17

description: Ileal biopsy from Female CD patient aged 8.66666666666667 years at diagnosis with L3 location and Paris age A1a


title: CD A1a L3 rep19

description: Ileal biopsy from Male CD patient aged 8.75 years at diagnosis with L3 location and Paris age A1a


title: CD A1a L3 rep13

description: Ileal biopsy from Male CD patient aged 8.41666666666667 years at diagnosis with L3 location and Paris age A1a


title: CD A1a L3 rep12


title: CD A1a L1 rep2

description: Ileal biopsy from Male CD patient aged 7.91666666666667 years at diagnosis with L1 location and Paris age A1a


title: CD A1a L3 rep10

description: Ileal biopsy from Male CD patient aged 8 years at diagnosis with L3 location and Paris age A1a


title: CD A1a L3 rep11

description: Ileal biopsy from Male CD patient aged 8.16666666666667 years at diagnosis with L3 location and Paris age A1a


title: CD A1a L3 rep8

description: Ileal biopsy from Male CD patient aged 7.66666666666667 years at diagnosis with L3 location and Paris age A1a


title: CD A1a L3 rep9

description: Ileal biopsy from Male CD patient aged 7.91666666666667 years at diagnosis with L3 location and Paris age A1a


title: CD A1a L3 rep6

description: Ileal biopsy from Male CD patient aged 7.33333333333333 years at diagnosis with L3 location and Paris age A1a


title: CD A1a L3 rep4

description: Ileal biopsy from Male CD patient aged 6.5 years at diagnosis with L3 location and Paris age A1a


title: CD A1a L3 rep1

description: Ileal biopsy from Female CD patient aged 6.16666666666667 years at diagnosis with L3 location and Paris age A1a


title: CD A1b L2 rep43

description: Ileal biopsy from Male CD patient aged 16.9166666666667 years at diagnosis with L2 location and Paris age A1b


title: CD A1b L2 rep38

description: Ileal biopsy from Male CD patient aged 15.8333333333333 years at diagnosis with L2 location and Paris age A1b


title: CD A1a L3 rep2

description: Ileal biopsy from Male CD patient aged 6.25 years at diagnosis with L3 location and Paris age A1a


title: CD A1a L3 rep23

description: Ileal biopsy from Female CD patient aged 8.91666666666667 years at diagnosis with L3 location and Paris age A1a


title: CD A1b L2 rep28

description: Ileal biopsy from Male CD patient aged 14.8333333333333 years at diagnosis with L2 location and Paris age A1b


title: CD A1b L2 rep35

description: Ileal biopsy from Male CD patient aged 15.75 years at diagnosis with L2 location and Paris age A1b


title: CD A1a L3 rep7

description: Ileal biopsy from Male CD patient aged 7.58333333333333 years at diagnosis with L3 location and Paris age A1a


title: CD A1b L2 rep34

description: Ileal biopsy from Male CD patient aged 15.4166666666667 years at diagnosis with L2 location and Paris age A1b


title: CD A1a L3 rep18

description: Ileal biopsy from Male CD patient aged 8.75 years at diagnosis with L3 location and Paris age A1a


title: CD A1a L3 rep15

description: Ileal biopsy from Female CD patient aged 8.58333333333333 years at diagnosis with L3 location and Paris age A1a


title: CD A1b L2 rep29


title: CD A1b L2 rep26

description: Ileal biopsy from Female CD patient aged 14.25 years at diagnosis with L2 location and Paris age A1b


title: CD A1b L2 rep27

description: Ileal biopsy from Male CD patient aged 14.75 years at diagnosis with L2 location and Paris age A1b


title: CD A1b L2 rep19

description: Ileal biopsy from Male CD patient aged 13.5833333333333 years at diagnosis with L2 location and Paris age A1b


title: CD A1a L3 rep14

description: Ileal biopsy from Female CD patient aged 8.5 years at diagnosis with L3 location and Paris age A1a


title: CD A1b L2 rep14

description: Ileal biopsy from Male CD patient aged 12.5833333333333 years at diagnosis with L2 location and Paris age A1b


title: CD A1b L2 rep10

description: Ileal biopsy from Male CD patient aged 11.8333333333333 years at diagnosis with L2 location and Paris age A1b


title: CD A1b L2 rep21

description: Ileal biopsy from Male CD patient aged 13.8333333333333 years at diagnosis with L2 location and Paris age A1b


title: CD A1b L2 rep39

description: Ileal biopsy from Male CD patient aged 15.9166666666667 years at diagnosis with L2 location and Paris age A1b


title: CD A1a L3 rep5

description: Ileal biopsy from Male CD patient aged 7.16666666666667 years at diagnosis with L3 location and Paris age A1a


title: CD A1b L2 rep5

description: Ileal biopsy from Male CD patient aged 10.6666666666667 years at diagnosis with L2 location and Paris age A1b


title: CD A1a L2 rep5

description: Ileal biopsy from Female CD patient aged 8 years at diagnosis with L2 location and Paris age A1a


title: CD A1a L2 rep10

description: Ileal biopsy from Female CD patient aged 9.16666666666667 years at diagnosis with L2 location and Paris age A1a


title: CD A1a L2 rep11

description: Ileal biopsy from Female CD patient aged 9.5 years at diagnosis with L2 location and Paris age A1a


title: CD A1a L2 rep1

description: Ileal biopsy from Male CD patient aged 6.58333333333333 years at diagnosis with L2 location and Paris age A1a


title: CD A1b L2 rep1

description: Ileal biopsy from Male CD patient aged 10.4166666666667 years at diagnosis with L2 location and Paris age A1b


title: D6I_464

status: Public on Jun 22 2018

city: Montpellier

first: Jamal

last: Tazi

address: 1919 Route de Mende

country: France

institute: CNRS

description: blood

data_processing:
Sequencing quality control: Image analysis and base calling were performed using the HiSeq Control Software and Real-Time Analysis component. Demultiplexing was performed using Illumina's sequencing analysis software. The quality of the data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequence Analysis Viewer). Potential contaminants were investigated with the FastQ Screen software from the Babraham Institute.
The reads were subjected to standard quality control (QC) and filter criteria according to the following parameters: (1) trimming and cleaning reads that aligned to primers and/or adaptors,(2) reads with over 50% of low-quality bases (quality value ≤15) in one read, and (3) reads with over 10% unknown bases (N bases). We have used a software called Trimmomatic to remove primers and also to remove bad quality reads. After filtering, we removed short reads (<36bp), the remaining reads are called "clean reads" and stored as FASTQ format.
Once we did confident in the quality of our sequencing data, we proceeded to align the clean reads within FASTQ files to a reference sequence. Alignments have been performed using TopHat2 v2.0.8b tool against human GRCh38 reference genome. Tophat2 is a splice-aware aligner that use bowtie2 aligner to align the data before counting the reads that have mapped to all the genes. Bowtie2 behavior was adjusted to support local alignment by set to sensitive. TopHat2 ouputs were stored in BAM files (accepted_hits.bam typically) which contain all the alignments. TopHat2 output also report statistics on alignments.  As SAM file format were then required to count reads, BAM files have been sorted by name and converted to SAM format using samtools-1.3.1 software. To compute gene level raw counts from mapped reads in each library we used the tool htseq-count v0.6.1p1 of the Python package HTSeq, using the default union-counting mode. HTSeq package produced raw counts table per library, raw counts were needed to operate gene’s expression level. DEGs (Differentially Expressed Genes) screening is aimed to find differential expressed genes between samples and perform further function analysis on them.
Genome_build: GRCh38
Supplementary_files_format_and_content: One text file by sample (tab delimited) with a first column for gene identification. The next column corresponds to the raw read counts (non-normalized).

source_name: PBMCs

extract_protocol:
Total RNA extraction was performed according to the Qiagen miRNeasy kit. RNA concentrations were determined using Qubit fluorometric quantification and purity by the RNA 6000 Bioanalyzer kit (Agilent)
RNA-Seq libraries were constructed with the Truseq stranded mRNA sample preparation (Low throughput protocol) kit from Illumina.    Poly-A based mRNA enrichment: 1.2µg of total RNA was used for the construction of the libraries.
 Using poly-T oligo attached magnetic beads, 1,2µg of total RNA was purified in order to obtain only poly-A mRNA.    Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature.  The cleaved RNA fragments are copied into first strand cDNA using SuperScript II reverse transcriptase, Actinomycin D and random hexamer primers. The Second strand cDNA was synthesized by replacing dTTP with dUTP. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with 15 cycles of PCR. The final cDNA libraries were validated with a Fragment Analyzer (Advanced Analytical, Ankeny, IA) and quantified with a KAPA qPCR kit (Kapa Biosystems, Wilmington, MA).    Library sequencing: On 8 sequencing lane of a flowcell V4, the 32 libraries were pooled in equal proportions by sets of 4 libraries per lane, denatured with NaOH and diluted to 16 pM before clustering. Cluster formation, primer hybridization and single-end read, 50 cycles sequencing were performed on cBot and HiSeq2500 (Illumina, San Diego, CA) respectively.

treatment_protocol: The CD4 T cells were uninfected or infected with the YU2 strain and were untreated or treated for 6 days

tag: yu2 strain infection

value: Infected

tag: cell type

value: purified CD4+ T cells

value: PBMCs

tag: treatment


title: Input

status: Public on May 19 2018

city: Illkirch

first: Peggy

last: Kirstetter

address: 1, rue Laurent Fries

department: Functional Genomic and Cancer

institute: Institut de Génétique et de Biologie Cellulaire et Moléculaire

data_processing:
Illumina Casava software used for basecalling.
Sequence reads were mapped to reference genome mm9/NCBI37 using Bowtie v0.12.7 with the following parameters -m 1 --strata --best.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b)

source_name: BH1 cell line

growth_protocol: BH1 cell line were grown in IMDM 10%  heat inactivated FCS, 100U/ml Pen/Strep, 2mM Glutamine, 50uM beta-mercaptoethanol, 8% Il-7 (supernatant from J558L cell line).

extract_protocol:
The ChIP protocol was adapted from the Millipore ChIP Assay Kit (17-295) with minor modifications. Cells were washed in PBS and 100 000 000 cells were cross-linked at 37° C for 10 min in 5ml PBS/0.5%BSA/1% ultra-pure formaldehyde(Electron Microscopy Sciences). Quenching with 125mM glycine and a cold PBS wash (containig 1 protease inhibitor cocktail (PIC); Roche) was followed by cell lysis in 5ml of 1% Triton X-100, 50mM MgCl2, 100mM Tris-HCl pH 7.1, 11% sucrose, 1 PIC for 10 min on ice. Nuclei were pelleted and were lysed in 500 ml of 1% SDS, 50mM Tris-HCl, 10mM EDTA, 1 PIC. Chromatin was sonicated to 500–300 bp using a Bioruptor 200 (Diagenode), cleared by centrifugation and sonication efficiency was verified.
Libraries were prepared according to standard Illumina protocols and were validated with the Agilent Bioanalyzer

treatment_protocol: BH1 cells were grown 24h without IL7 supernatant in the presence of 100nM of 4OH-Tamoxifen.

tag: cell line

value: Pre B cell line (BH1)

tag: strain

tag: chip antibody


title: Vian-2018-HIC039

status: Public on May 10 2018

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

data_processing:
The paired end reads were aligned separately using BWA against the mm9 mouse build or the b37 human build
PCR duplicates, low mapping quality and unligated reads were removed using Juicer (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016)
Contact matrices were constructed at various resolutions and normalized using Juicer (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016)
loops were annotated using HiCCUPS (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016), domains were annotated using Arrowhead (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016)
Genome_build: mm9 (mouse), b37 (human)
Supplementary_files_format_and_content: .hic file (contains contact matrices at various resolutions in an easy to visualize and access format) (see Durand, Robinson, et al Cell Systems 2016)

source_name: B-lymhoblastoids

extract_protocol:
Cells were crosslinked and then lysed with nuclei permeabilized but still intact. DNA was then restricted and the overhangs filled in incorporating a biotinylated base. Free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and then biotinylated ligation junctions were recovered with streptavidin beads.
standard Illumina library construction protocol, Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 8-12 cycles and library fragments of 400-600 bp (insert plus adaptor and PCR primer sequences) were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeqX Ten, NextSeq 500, or HiSeq 2500 following the manufacturer's protocols

tag: genotype

value: WT

tag: protocol

value: in situ Hi-C


title: CD A1b L2 rep25

description: Ileal biopsy from Female CD patient aged 14.1666666666667 years at diagnosis with L2 location and Paris age A1b

tag: diagnosis


title: Vian-2018-HIC037


title: Vian-2018-HIC038


title: Ikraos-ChIP

value: anti-Ikaros Polyclonal rabbit made in house


title: Vian-2018-HIC041


title: bulk_7160c5_no2

status: Public on Apr 28 2018

city: New York

first: Jinyang

last: Li

state: New York

address: 1230 York Ave

institute: The Rockefeller University

data_processing:
Alignment using STAR aligner with default settings
Raw counts calling using featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: text file including raw counts of each gene for all samples

source_name: bulk T cell intermediate tumors

growth_protocol: T cell low or high pancreatic tumor cells were subcutaneously implanted into C57BL/6 mice. Bulk tumor samples were prepared from tumors 3 weeks following implantation.

extract_protocol:
RNA was extracted using Qiagen Rneasy Micro Kit.
500 ng of total RNA was used for the preparation of sequencing libraries using NEB RNA-seq library preparation kit with standard protocol. RNA-seq libraries were sequenced on an Illumina Nextseq 550 high-throughput sequencer.

treatment_protocol: no treatment administrated

tag: sample type

value: bulk tumors

tag: t cell phenotype

value: intermediate


title: bulk_7160c2_no2

source_name: bulk T cell high tumors

value: high


title: bulk_7160c5_no1


title: bulk_7160c2_no1


title: bulk_7062c3_no2

source_name: not used


title: CD A1b L2 rep17

description: Ileal biopsy from Male CD patient aged 12.8333333333333 years at diagnosis with L2 location and Paris age A1b

tag: location

tag: Sex

tag: age at diagnosis in years


title: Vian-2018-HIC040


title: bulk_6883c4_no1


title: bulk_6694c2_no2

source_name: bulk T cell low tumors

value: low


title: Vian-2018-HIC036


title: bulk_6883c1_no1


title: bulk_6620c1_no1


title: bulk_6620c1_no2


title: bulk_6694c2_no1


title: bulk_6555c3_no2


title: bulk_6556c4_no2


title: bulk_6556c3_no2


title: D6_DMSO

description: blood

value: Not Infected

tag: tissue

value: DMSO


title: bulk_6556c4_no1


title: bulk_6499c4_no1


title: bulk_6555c3_no1


title: bulk_6556c3_no1


title: bulk_6422c5_no1


title: bulk_6421c2_no1


title: bulk_6499c3_no2


title: bulk_6421c2_no2


title: bulk_6422c1_no1


title: bulk_6419c5_no1


title: bulk_6499c3_no1


title: bulk_2838c3_no3


title: bulk_2838c3_no2


title: bulk_2838c3_no1


title: bulk_6422c5_no2


title: bulk_6419c5_no2


title: bulk_6419c1_no2


title: bulk_2669c4_no4


title: bulk_2669c4_no2


title: BM1077-MEP-Frozen-160107-72

status: Public on Apr 26 2018

city: Cambridge

first: Jason

middle: Daniel

last: Buenrostro

state: MA

address: 415 Main Street

institute: Broad Institute

description: No raw data is available for this cell (it was not included in the final analysis)

data_processing:
Adapter sequences were trimmed from FASTQs using custom python scripts to enable mapping fragments with sequences containing adapters. Paired-end reads were aligned to hg19 or mm10 using BOWTIE2 using the parameter –X2000 allowing fragments of up to 2 kb to align. Duplicates were removed using PICARD tools. Reads were subsequently filtered for alignment quality of >Q30 and were required to be properly paired. Reads mapping to the mitochondria, unmapped contigs and chromosome Y were removed and not considered.
We used MACS2 to call all reported ATAC-seq peaks. MACS2 was used with the following parameters (--nomodel --nolambda --keep-dup all --call-summits). Peaks were filtered using the consensus excludable ENCODE blacklist (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/) and a custom blacklist, designed to remove high-signal causing repeats and mitochondrial homologues. For all subsequent analysis we discarded peaks falling within these regions.
Genome_build: hg19
Supplementary_files_format_and_content: Bam files across single-cells representing identical biological conditions have been merged. Reads pertaining to individual cells can be identified by their unique RGID tag corresponding to each assayed well. Bed files represent 500 bp peak summits as described above.

source_name: Bone Marrow CD34+

extract_protocol:
Single cells were captured using the C1 Single-Cell Auto Prep IFC microfluidic chips and assayed using the single-cell ATAC-seq protocol. All cells described here were FACS sorted prior to performing the assay.
In a 96-well plate, 10 µL of harvested libraries were amplified in 50 µL PCR for an additional 14 cycles (1.25 µM custom Nextera dual-index PCR primers (Supplementary Table 1) in 1x NEBnext High-Fidelity PCR Master Mix) using the following PCR conditions: 72°C for 5min; 98°C for 30 s; and thermocycling at 98°C for 10 s, 72°C for 30 s, and 72°C for 1 min. The PCR products were pooled creating a final volume of ~4.8 mL. The pooled library was purified on a single MinElute PCR purification column (Qiagen) yielding libraries at an approximate concentration of ~1 µM. Libraries were quantified using qPCR prior to sequencing.

value: CD34+ Bone Marrow

value: MEP


title: BM1077-MEP-Frozen-160107-67


title: bulk_6499c4_no2


title: bulk_2669c4_no1


title: bulk_2669c4_no3


title: BM1077-MEP-Frozen-160107-63


title: BM1077-MEP-Frozen-160107-65


title: iEAF2-1B

status: Public on Apr 25 2018

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

data_processing:
Reads of each sample were aligned to reference using Salmon (v0.7.2) to produce quant files
Counts of transcripts from quant files, were converted to genes using tximport (v1.4.0) R package
edgeR (v3.18.1) package was used to idenity the differentially expressed genes
genome build: GRCh38
processed data files format and content: Tab delimited files which shows quantification values of transcripts as produced by salmon

source_name: C4-2 prostate cancer cell line

extract_protocol:
Total RNA was isolated from the testes using TRIzol reagent. TruSeq Stranded Total RNA library preparation was performed using 1ug total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: siRNA knockdown of EAF2 and/or tp53 was performed for 24 h, followed by treatment with 2 nM R1881 for an additional 48 h

value: prostate

tag: sirna target gene

value: wild type


title: Mock-1B

value: Mock


title: DKD-1B

value: EAF2 and tp53


title: iP53-1B


title: bulk_6419c1_no1


title: B00EWA9

status: Public on Mar 01 2018

city: Lausanne

first: Gregory

last: Lefebvre

address: EPFL Scientific Parc

country: Switzerland

institute: Nestlé Institute of Health Science

description: Submitter cannot provide additional metadata due to legal reasons, contact submitter directly for further information

data_processing:
Basecalling and Demultiplexing were carried out with Illlumina Cassava software
Mapping was performed with rna-star  (version 2.2.0) using default parameters
Sequence quality was evaluated using FastQC
Mapping quality was assessed using Rsamtools R package (version 1.18.2).
Inserts mapping onto genes was retrieved using GenomicAlignments R package (version 1.2.1).
Mapping quality was assessed using Rsamtools R package (version 1.18.2) and AnnotationDbi R package (version 1.28.1)
Genome_build: GRCh37 assembly
Supplementary_files_format_and_content: tab-delimted file. Columns are sample names. Rows are genes. Values are non-normalized counts

source_name: Adipose Tissue

extract_protocol:
Illumina manufacturer’s standard protocols.
Illumina manufacturer’s standard protocols.

value: Adipose Tissue

tag: gender

value: F

tag: age

tag: time

value: CID2 is after 8 weeks of LCD


title: B00EWAF

value: M


title: B00EWEV

value: CID1 is for the baseline without LCD


title: B00EWA1


title: B00EW9V


title: B00EWA6


title: B00EW9N


title: B00EW9Z


title: B00EW9T


title: B00EW9Y


title: B00EW9J


title: B00EWA3


title: BM1077-MEP-Frozen-160107-66

tag: cell type


title: iCon-1B

value: non-targeted control


title: B00EWK0


title: B00EWA7


title: B00EWAE


title: B00EW9I


title: B00EW8G


title: B00EW9C


title: B00EW8B


title: B00EW98


title: B00EW8N


title: B00EW8E


title: B00EW89


title: B00EW61


title: B00EW87


title: B00EW83


title: B00EW7S


title: B00EW7V


title: B00EW7R


title: B00EW86


title: B00EW7K


title: B00EW5X


title: B00EW60


title: B00EW5Y


title: B00EW5Z


title: B00EW5W


title: B00EW5T


title: Focal Cortical Dysplasia Tissue 3 (F9)

status: Public on Mar 10 2018

type: genomic

city: NEW DELHI

first: APARNA

middle: BANERJEE

last: DIXIT

state: AIIMS

address: Room No 7003, 7th Floor, Convegence Block, AIIMS, ANSARI, NAGAR

department: A collaborative project between NBRC & AIIMS

country: India

institute: NATIONAL BRAIN RESERACH CENTRE

hyb_protocol: Labeled DNAs were hybridized to Human DNA methylation Microarray slides (G4495A, AMADID 023795) containing the annotated human 27,627 expanded CpG islands, 5081 UMR regions, 237,227 biological probes with median probe spacing of 97bp followingthe microarray manufacturer’s instructions.

scan_protocol: The slides were subsequently washed and scanned using Agilent scanner P/N G2565BA

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: Focal Cortical Dysplasia tissue_MeDIP-WGA

label_protocol: 2μg of DNA from the WGAamplified sample (MeDIP-WGA), along with their corresponding whole genomic DNA (input), were labeled usingthe SureTag DNA labeling kit (5190-3400, Agilent)

growth_protocol: Tissues resected from 2 autopsy , 3 MTLE and 4 FCD type II were used for isolating Genomic DNA

extract_protocol: Genomic DNA was extracted using genomic DNAextraction kit (Qiagen, Hilden, Germany) and Methylated DNA was immunoprecipitated using standard protocols  with some modifications.  Briefly, 4 µg MseI digested genomic DNA was immunoprecipitated with 10 µg of monoclonal mouse anti 5-methylcytidine antibody (New England Biolab, Pickering, Ontario and Abcam Inc.Cambridge, MA 02139) a negative control normal mouse IgG (Abcam, ab81032) in a final volume of 500 μl IP buffer (10 mM sodium phosphate (pH 7.0), 140 mM NaCl, 0.05% Triton X-100). We incubated the mixture with 40 μl of Dynabeads and M-280 sheep antibody to mouse IgG (Dynal Biotech) for 12 hr at 4°C and washed it seven times with 700 μl of IP buffer. We then treated the beads with proteinase K for 4 hr at 50°C and recovered the methylated DNA by phenol-chloroform extraction followed by ethanol precipitation. The immunoprecipitated DNA and a sample of input DNA were amplified using GenomePlex Complete Whole Genome Amplification (WGA) kit (Sigma-Aldrich, Saint Louis, Missouri 63103 USA). At each step DNA integrity was analyzed by agarose gel electrophoresis.

treatment_protocol: autopsy were used as non-epileptic controls and MTLE  and FCD tissues were epileptic tissues

tag: subject status

value: Focal cortical dysplasia (FCD) type II patient

value: MALE

value: brain

source_name: Focal Cortical Dysplasia input DNA

value: whole genomic DNA (input)


title: Autopsy Control Tissue 1 (A1)

source_name: Autopsy Control tissue_MeDIP-WGA

value: control; non-epileptic post mortem cases without any brain pathology

source_name: Autopsy Control input DNA


title: Autopsy Control Tissue 2 (A2)

value: FEMALE


title: B00EW5P


title: B00EW5L


title: B00EW5M


title: B00EW5C


title: B00EW5K


title: B00EW5B


title: B00EW5G


title: B00EW5A


title: B00EW57


title: B00EW5E


title: B00EW56


title: B00EW51


title: B00EW52


title: B00EW4X


title: B00EW55


title: B00EW54


title: B00EW4S


title: B00EW81


title: Focal Cortical Dysplasia Tissue 2 (F2)


title: B00EW4R


title: B00EW4W


title: B00EW4A


title: B00EW4D


title: B00EW42


title: B00EW41


title: B00EW46


title: B00EW3X


title: B00EW3Z


title: B00EW3U


title: B00EW3V


title: B00EW8I


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title: B00EW34


title: B00EW2Y


title: B00EW36


title: B00EW2R


title: B00EW32


title: B00EW2W


title: Focal Cortical Dysplasia Tissue 1 (F1)


title: B00EW3J


title: B00EW2Q


title: B00EW2O


title: B00EW2K


title: B00EW2L


title: B00EW2V


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title: B00EVDY


title: B00EVDZ


title: B00EVDQ


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title: B00EVE1


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title: B00EVD5


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title: B00EVD3


title: B00EVD2


title: B00EVCV


title: B00EVD0


title: B00EVCU


title: B00EVCY


title: B00EVCQ


title: B00EVCL


title: B00EVCO


title: B00EVCT


title: B00EVDB


title: B00EVCS


title: B00EVDW


title: B00EVCE


title: B00EVCF


title: B00EVCA


title: B00EVC9


title: B00EVCI


title: B00EVC7


title: B00EVC4


title: B00EVBY


title: B00EVCK


title: B00EVDH


title: B00EVBV


title: B00EVC2


title: NG-18_siIRF9-IFN-TNF

status: Public on Feb 28 2018

city: Montreal

first: Nathalie

last: Grandvaux

address: 2900, boul. Édouard-Montpetit

country: Canada

institute: University of Montreal

description: mRNASeq stranded

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh37
Supplementary_files_format_and_content: comma-delimited text files include Raw reads and RPKM values for each Sample ...

source_name: U3A cell line

growth_protocol: Cells were grown in DMEM medium supplemented with 10% Heat-Inactivated-FBS or Heat-Inactivated-Fetal Clone III (HI-FCl) and 1% L-glutamine

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
Transfection: IRF9-targeting siRNA using Oligofectamine
Stimulation : IFNb (1000U/ml) +TNFa (10ng/ml)

tag: cell line

value: Human U3A cell line. The STAT1-deficient U3A cells were obtained by mutagenesis of 2ftGH cells originally derived from HT1080 fibrosarcoma cells (McKendry R, et al.Proc Natl Acad Sci U S A. 1991;88(24):11455-9)

value: epithelial

value: Connective tissue

tag: disease

value: Fibrosarcoma

value: Male

tag: ethnicity

value: Caucasian


title: NG-15_siSTAT2-NS

description: mRNASeq stranded

treatment_protocol:
Transfection: STAT2-targeting siRNA using Oligofectamine
Stimulation : none


title: NG-14_siCtrl-IFN-TNF

description: mRNASeq stranded

treatment_protocol:
Transfection: control non-targeting siRNA using Oligofectamine
Stimulation : IFNb (1000U/ml) +TNFa (10ng/ml)


title: NG-16_siSTAT2-IFN-TNF

description: mRNASeq stranded

treatment_protocol:
Transfection: STAT2-targeting siRNA using Oligofectamine
Stimulation : IFNb (1000U/ml) +TNFa (10ng/ml)


title: NG-17_siIRF9-NS

description: mRNASeq stranded

treatment_protocol:
Transfection: IRF9-targeting siRNA using Oligofectamine
Stimulation : none


title: NG-13_siCtrl-NS

description: mRNASeq stranded

treatment_protocol:
Transfection: control non-targeting siRNA using Oligofectamine
Stimulation :none


title: NG-2_siCtrl-IFN-TNF

description: mRNASeq stranded


title: NG-4_siSTAT2-IFN-TNF

description: mRNASeq stranded


title: NG-3_siSTAT2-NS

description: mRNASeq stranded


title: NG-1_siCtrl-NS

description: mRNASeq stranded

treatment_protocol:
Transfection: control non-targeting siRNA using Oligofectamine
Stimulation : none


title: NG-8_siCtrl-IFN-TNF

description: mRNASeq stranded


title: NG-7_siCtrl_NS

description: mRNASeq stranded


title: NG-5_siIRF9-NS

description: mRNASeq stranded


title: Ov/Ob Pre

status: Public on Dec 30 2017

city: Shreveport

first: Tara

middle: M

last: Henagan

state: LA

address: 1501 Kings Hwy

department: Medical School

institute: Louisiana State University Health Sciences Center - Shreveport

description: Mononucelosomal DNA

data_processing:
Reads were trimmed for the adaptor sequence and aligned to the human (hg38) genome using Bowtie version 2.2.6.2, while allowing 0 mismatches in a seed alignment during multiseed alignment. On average, ~98% of sequenced reads aligned to genome.
Peaks were called using HOMER software using the following parameters: -fdr 0.05 -size 147 -minDist 162 -tagThreshold 4 -L 0 -C 0 -F 0 -o auto (read count ≥4; false discovery rate = 0.05; peak size = 147; minimum distance between peaks = 162; genome size = 4,000,000,000; number of tags used for normalization = 10,000,000; size of region used for local filtering = 0; Poisson p-value over local region = 1.00e-04).
Genome_build: hg38
Supplementary_files_format_and_content: Text files were generated using HOMER and are formatted as follows: PeakID (column 1), chromosome (column 2), start (column 3), end (column 4), strand (column 5), peak score (column 6), focus ratio/region size (column 7), annotation (column 8), detailed annotation (column 9), distance to transcription start site (column 10), nearest promoter ID (column 11), Entrez ID (column 12), nearest Unigene (column 13), nearest Refseq (column 14), nearest Ensembl (column 15), gene name (column 16), gene alias (column 17), gene description (column 18), gene type (column 19).

source_name: Vastus Lateralis Muscle

extract_protocol:
Skeletal muscle biopsies were obtained from the vastus lateralis muscle using the percutaneous muscle biopsy technique before (Pre) and immediately following (Post) the exercise testing trial. Briefly, 2.5 mL of a 1% lidocaine solution was injected into the thigh and a 6 mm Bergstrom biopsy needle (Pelomi Medical, Denmark) under suction was used collect the muscle sample. The collected sample was quickly rinsed in PBS and blotted to remove any blood prior to freezing. Pre biopsy samples were taken from the participant’s non-dominant leg, whereas Post biopsies were obtained from the dominant leg. Samples were then flash frozen in liquid nitrogen and stored at −80°C until further processing. Mononucleosomal DNA was isolated from approximately 10 mg of skeletal muscle (n=5 per group). Briefly, the samples were homogenized using a dounce homogenizer in a 0.25 M sucrose buffer (0.25 M sucrose, 10 mM Tris-acetate pH 8.1, 1 mM EDTA, 1 mM DTT, 1 mM sodium orthovanadate, and 1 1X complete protease inhibitor tablet (Roche, Indianapolis, USA). The pellets were washed and resuspended in 0.25 sucrose buffer containing 0.1 mM CaCl2 and 4 mM MgCl2 and incubated with micrococcal nuclease (MNase; Roche, Indianapolis, USA) for isolation of mononucleosomal DNA for 15 min at 37°C. Then, EDTA was added (final concentration: 5 mM). After centrifugation, the resulting pellets were suspended in with 0.25 M lysis buffer (50 mM Tris, pH 8.1, 10 mM EDTA, 1% SDS, and 1 1X complete protease inhibitor tablet (Roche, Indianapolis, USA). Samples were treated with 0.1 mg/mL of proteinase K (Qiagen, Germantown, MD) overnight at 37°C.
Mononucleosomal DNA sequencing was performed by the Genomics Core Facility at Pennington Biomedical Research Center. The NEB ultra II DNA library prep kit and NEBNext multiplex oligos for Illumina index primer sets 1 and 2 (New England Biolabs, Ipswich, MA) were used for library construction, per the manufacturer’s protocol. Sequencing was completed using the NextSeq 500 Sequencing System (Illumina, San Diego, CA) to generate 75 nucleotides long single-end reads, with an average of ~387 million reads per treatment group.

treatment_protocol: 30 men, aged 19-30 years, were recruited and divided into two groups: lean (BMI<25, 18.5- 24.1 kg/m2, n=15) and Ov/Ob (BMI≥25, 25.5- 36.9 kg/m2, n=15). Participants were instructed to refrain from vigorous physical activity for 24 h prior to the exercise testing trial. Following an overnight fast, participants reported to the Purdue University Nutrition Science Bionutrition Core between 0700 and 1000 h where they sat quietly for 15 min prior to quadriceps muscle biopsy sampling (Pre samples).  Participants then consumed a standardized, high carbohydrate meal (7 kcal/kg; 60% carbohydrate, 25% fat, 15% protein) under the supervision of a registered dietician. Following the meal, participants were asked to refrain from eating or drinking, with the exception of water, and to refrain from physical activity for the next 4 h, at which time they reported back to the laboratory for the exercise testing trial. For the exercise testing trail, each participant completing a 2 min warm up at a self-selected intensity not exceeding 100W on the stationery cycle ergometer. Participants then cycled at the workload equal to their previously measured 50% VO2 max. Between minutes 5-8 of the exercise testing trial, steady-state oxygen consumption was measured using the TrueOne 2400 Metabolic Measurement System (Parvo Medics, Utah, USA). Measured values were compared with the participant’s expected 50% VO2 max. Workload was adjusted as necessary to obtain the expected oxygen consumption necessary for the participants to expend 650 kcal upon completion of the exercise testing trial. Immediately following the exercise testing trial, a second quadriceps muscle biopsy were obtained from each participant (Post samples).

value: Vastus Lateralis Muscle

tag: group

value: Pre-exercise


title: Lean Post

description: Mononucelosomal DNA

value: Post-exercise


title: Lean Pre

description: Mononucelosomal DNA


title: Ov/Ob Post

description: Mononucelosomal DNA


title: B00EVC0

value: Adipose Tissue

value: M

value: CID1 is for the baseline without LCD


title: NG-6_siIRF9-IFN-TNF

description: mRNASeq stranded


title: NG-11_siIRF9-NS

description: mRNASeq stranded


title: NG-12_siIRF9-IFN-TNF

description: mRNASeq stranded

tag: ccell line


title: NG-10_siSTAT2-IFN-TNF

description: mRNASeq stranded

treatment_protocol:
Transfection: STAt2n-targeting siRNA using Oligofectamine
Stimulation : IFNb (1000U/ml) +TNFa (10ng/ml)


title: NG-9_siSTAT2-NS

description: mRNASeq stranded


title: Regional - Duodenum M1

status: Public on Nov 06 2017

city: Boston

first: Adam

last: Haber

state: Massachusetts

address: 665 Huntington Ave, HSPH Building 1, Room 305

institute: Harvard T. H. Chan School of Public Health

description:
3' polyA RNA-seq. The expression levels for each gene (rows) in each single cell (column) in UMI counts as calculated using the CellRanger pipeline. Each column header provides the sequencing batch id, the cell barcode, and the cell type as identified by cluster analysis. Each ID is seperated by '_'
Regional_UMIcounts.txt
EEC_UMIcounts.txt

data_processing:
3' polyA RNA-seq
CellRanger 1.0
PCA (prcomp in R)
kNN-based graph clustering (R code)
Supplementary_files_format_and_content: UMI count expression values for each gene (rows) in each cell (columns)

source_name: Intestinal epithelial cells extracted from from WT mouse duodenum

extract_protocol:
3' polyA RNA seq
10X Genomics Chromium Prep

tag: strain

value: Wild type

tag: agent

value: Regional - Duodenum


title: Regional - Duodenum M2


title: SchB_1

status: Public on Dec 20 2017

city: Seoul

first: Ju-Hong

last: Jeon

state: Seoul

address: 28 Yongon-Dong, Chongno-Gu

department: Department of Physiology and Biomedical Sciences

country: South Korea

institute: Seoul National University College of Medicine

description:
A7r5 rat aortic smooth muscle cell
A7r5 cells are to study signal transduction and electrophysiological characteristics of vascular smooth muscle

hyb_protocol: Following fragmentation, 5.5 ug of framented cDNA were hybridized for about 17 hr at 45℃ on Affymetrix Rat Genome 230 2.0 Array. The hybridized probe arrays were stained and washed with GeneChip® Hybridization, Wash and Stain Kit using the Fluidics Station 450 (Affymetrix).

scan_protocol: The stained GeneChips were scanned with a GeneChip® Scanner 3000+ 7G(Affymetrix) a 570 nm.

data_processing: Raw data were normalized using the Single Channel Array Normalization (Piccolo et al. 2012, PMID: 22959562) method, which is implemented as a Bioconductor package (http://www.bioconductor.org/packages/release/bioc/html/SCAN.UPC.html). As part of the normalization process, a custom chip-definition file (CDF ver. 19) from the BrainArray (http://brainarray.mbni.med.umich.edu/brainarray/) resource was used to map genes based on updated genome mappings and excludes inaccurate or wrongly annotated probes.microarray probes to 13,877 genes.

organism: Rattus norvegicus

source_name: Schisandrin B treatment effect on gene expression profile in A7r5 cells

label_protocol: The Affymetrix GeneChip® procedure for generation of the biotin-labeled single-stranded cDNA by in vitro transcription were performed according to the manufacturer's instructions from 300ng total RNA(GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Rev.5). Protocol performed  using the Whole Transcript Sense Target Labeling and Control Reagents (Affymetrix 900652).

growth_protocol: The cells were maintained under DMEM medium containing 10% FBS.

extract_protocol: Total RNA was extracted from the cells and processed according to the manufacturer’s guideline (Affymetrix).

treatment_protocol: SCE and SchB were dissolved in DMSO

value: aortic smooth muscle


title: Regional - Jejunum M1

source_name: Intestinal epithelial cells extracted from from WT mouse jejunum

value: Regional - Jejunum


title: Regional - Jejunum M2


title: SchB-TGFb1_2

source_name: Schisandrin B + TGF-β1 treatment effect on gene expression profile in A7r5 cells


title: SchB-TGFb1_3


title: SchB_3


title: SCE-TGFb1_3

source_name: Schisandra chinensis extract + TGF-β1 treatment effect on gene expression profile in A7r5 cells


title: SCE-TGFb1_2


title: SchB_2


title: SCE_3

source_name: Schisandra chinensis extract treatment effect on gene expression profile in A7r5 cells


title: SCE-TGFb1_1


title: SCE_2


title: Vehicle_1

source_name: Vehicle effect on gene expression profile in A7r5 cells


title: Vehicle_2


title: SCE_1


title: TGFb1_3

source_name: TGF-β1 treatment effect on gene expression profile in A7r5 cells


title: TGFb1_2


title: Vehicle_3


title: RPZT12_2; ZT12, ribosome footprint, rep2

status: Public on Oct 14 2015

city: Lasuanne

first: David

last: Gatfield

address: UNIL CIG

department: CIG

institute: University of Lausanne

data_processing:
Base-calling: Casava 1.82
Adapter trimming: Adapter sequences were removed using cutadapt utility with following options: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --match-read-wildcards -m 6
Insert size filtering: Trimmed read sequences were filtered by their size using an in-house Python script with following inclusive ranges: [26,35] for footprints, [21,60] for total RNA
Alignment: Trimmed and filtered insert sequences were mapped sequentially to following databases: mouse rRNA, human rRNA, mt-tRNA, mouse tRNA, mouse cDNA (Ensembl.v.75) and mouse genome (GRCm38.p2). All but last one were mapped using bowtie (version 2.2.1) using following parameters: -p 2 -L 15 -k 20 –no-unal. Mapping against genomic sequence was performed using tophat (v2.0.11) with following parameters: --transcriptome-index=Mmusculus.GRCm38.75.dna.ensembl_data -p 2. After each alignment, only reads that were not aligned were used in the following mapping. For further analysis (processed data files), only alignments against mouse cDNA were used. Separately from this alignment strategy, each query set was also directly aligned against mouse genome using tophat with similar parameters (“global tophat”).
Post-alignment filtering: For each query sequence, only alignments with maximum score were kept. The output of “global tophat” alignment was used to estimate expressed transcript models using cufflinks (v2.2.1) with following parameters: --GTF Mus_musculus.GRCm38.75.gtf --frag-len-mean 37 --frag-len-std-dev 8 --compatible-hits-norm --multi-read-correct --upper-quartile-norm --frag-bias-correct Mmusculus.GRCm38.75.dna.ensembl.fa -p 3. Transcript FPKM estimates from all samples were merged using cuffcompare with following parameters: -r Mus_musculus.GRCm38.75.gtf -R -V. Resulting FPKM tracking information was parsed with an in-house Python script to filter out transcripts which were not found to have an FPKM > 0.1, a LOW95 > 0.05 and a FMI > 2.0 in at least 3 samples. A database of expressed transcripts was used in further analysis.
Abundance measurement: mRNA and RPF (ribosome protected fragment) levels were estimated per locus. An in-house Python script was used to count uniquely (by gene) mapped reads within each annotation feature (5'UTR, CDS, 3'UTR). For multi-isoform loci, preference order used was CDS, 5'UTR, 3'UTR.
Pre-normalization: Mappable and countable feature lengths (in bps) for each locus were calculated by means of generating all possible 21-, 30-, 45-, and 60-bp long reads in silico (faux reads) for each expressed transcript in the database and counting the faux reads through identical mapping and counting work flow used for real experimental reads. Weigthed averages of these mappable and countable lengths were later used in RPKM calculations.
Normalization: Read counts of total RNA and RPF were normalized with upper quantile method of R package edgeR. Prior to normalization, transcripts which did not have at least 10 counts in at least one third of the samples were removed from the datasets.
Normalization: RPKM values were calculated as the number of counted reads per 1000 mappable and countable bases per geometric mean of normalized read counts per million.
Genome_build: Genome Reference Consortium GRCm38.p2 (mm10)
Supplementary_files_format_and_content: rpkm files were generated with R; gene IDs are ENSEMBL-IDS

source_name: RPZT12_2; ZT12, ribosome footprint

extract_protocol:
Livers were homogenized in 3 volumes of lysis buffer (150 mM NaCl, 20 mM Tris-HCl pH7.4, 5 mM MgCl2, 5 mM DTT, 100 μg ml-1 cycloheximide, 1% Triton X-100, 0.5% Sodium deoxycholate, complete EDTA-free protease inhibitors (Roche) and 40 U ml-1 RNasin plus (Promega)) using a Teflon homogenizer. Lysates were incubated for 10 min on ice and cleared by centrifugation at 1000 x g, 4°C for 3 min in a tabletop centrifuge. Supernatants were flash-frozen and stored in liquid nitrogen. Lysates of two mice per timepoint were pooled. Total RNA-seq libraries were generated from the lysate pool. For ribosome profiling libraries, lysate pools (15 OD260) were digested with 650 U RNase I (Ambion) for 45 min at room temperature and passed over size exclusion columns for ribosome purification prior to RNA extraction and library preparation.
Sequencing libraries for total RNA and ribosome protected RNA were generated using Ribo-Zero (Epicentre) and ARTseq ribosome profiling kits (Epicentre).

value: male

value: 11-12 weeks

tag: timepoint

value: liver

tag: insert type

value: ribosome footprint

tag: molecule subtype

value: ribosome protected RNA


title: RPZT12_1; ZT12, ribosome footprint, rep1

source_name: RPZT12_1; ZT12, ribosome footprint

tag: tissue


title: RP_ZT0_1; ZT0, ribosome footprint, rep1

source_name: RP_ZT0_1; ZT0, ribosome footprint


title: RP_ZT2_1; ZT2, ribosome footprint, rep1

source_name: RP_ZT2_1; ZT2, ribosome footprint


title: RP_ZT2_2; ZT2, ribosome footprint, rep2

source_name: RP_ZT2_2; ZT2, ribosome footprint


title: TGFb1_1


title: RP_ZT0_2; ZT0, ribosome footprint, rep2

source_name: RP_ZT0_2; ZT0, ribosome footprint


title: MPP2

status: Public on Oct 04 2017

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

description:
Transformed E12 rat mescencephalic neuronal stem cells, dopamine producing, used for neurotoxin studies
C2

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60°C and hybridized on to a Agilent's Rat Gene Expression  8x60k Array (AMADID: 028279). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65° C for 16 hours.

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift normalization method.

source_name: Immortalized Rat mescencephalic dopaminergic neurons

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: N27 cells were grown in RPMI medium and passaged once in two days by trypsinization

extract_protocol: RNA extraction was performed by using Qiagen Rneasy mini kit with Dnase Treatment.

treatment_protocol: Cells were treated with 150 µM and 250 µM of Mn or MPP+ respectively, for 48 h

value: N27 Dopaminergic Neural Cell Line

tag: treatment

value: MPP+


title: MPP1

description:
Transformed E12 rat mescencephalic neuronal stem cells, dopamine producing, used for neurotoxin studies
C1


title: Mn1

description:
Transformed E12 rat mescencephalic neuronal stem cells, dopamine producing, used for neurotoxin studies
B1

value: Mn


title: SchB-TGFb1_1


title: Control1

description:
Transformed E12 rat mescencephalic neuronal stem cells, dopamine producing, used for neurotoxin studies
A1

value: Control


title: Control2

description:
Transformed E12 rat mescencephalic neuronal stem cells, dopamine producing, used for neurotoxin studies
A2


title: Mn2

description:
Transformed E12 rat mescencephalic neuronal stem cells, dopamine producing, used for neurotoxin studies
B2


title: biofilm_ribosome

status: Public on Oct 22 2013

city: Seattle

first: Arvind

middle: R

last: Subramaniam

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences Division

institute: Fred Hutchinson Cancer Center

description:
Ribosome protected mRNA
extracted at OD600 = 1.4

data_processing:
PolyA tails were trimmed by identifying a continuous run of 10 or more As
Reads aligning to rRNA, tRNA and non-coding RNA removed by aligning with bowtie 0.12.7 against NC_000964.frn sequences
Remaining reads aligning to genome were trimmed by 8nt on either side, weighted by the length of the fragment and assigned to the genomic coordinate
Genome_build: ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Bacillus_subtilis_168_uid57675/NC_000964.fna
Supplementary_files_format_and_content: Each line in the processed file has three columns: Col 1: Genomic coordinate based on NC_000964.fna, Col 2: Strand, Col 3: Total read weight assigned to the coordinate, Only genomic coordinates with non-zero read weight are included in the text file, Reads aligning to rRNA, tRNA and non-coding RNA are not included.

organism: Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10

source_name: whole cell lysate

growth_protocol: 30C, 200rpm shaking, minimal biofilm inducing medium (Msgg)

extract_protocol:
Rapid filtration followed by flash freezing of intact cells, cell lysis by glass bead beating, Micrococcal nuclease digestion of polysomes, purification of monosomes by sucrose-gradient centrifugation
Libraries were prepared using a modified small RNA library protocol, see Methods in  Subramaniam et al., in submission

treatment_protocol: Either biofilm induction by post-exponential growth or serine starvation, exponential phase sample and serine-rich sample are controls

value: {delta}epsH


title: serinerich_ribosome

description:
Ribosome protected mRNA
extracted at OD600 = 0.5, Serine present in growth medium

value: {delta}serA


title: exponential_mrna

description:
total mRNA
extracted at OD600 = 0.6


title: exponential_ribosome

description:
Ribosome protected mRNA
extracted at OD600 = 0.6


title: serinestarved_ribosome

description:
Ribosome protected mRNA
extracted at OD600 = 0.5 following 60 min of serine starvation


title: biofilm_mrna

description:
total mRNA
extracted at OD600 = 1.4


title: DGM-00663 [gene_expr]

status: Public on Jun 20 2012

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: small airway epithelium from healthy nonsmokers or healthy smokers

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: department of genetic medicine id

tag: smoking status

value: S


title: DGM-00641 [gene_expr]


title: DGM-00613 [gene_expr]


title: lymphoma_9250_ADR

status: Public on Jul 04 2013

city: Berlin

first: Maja

last: Milanovic

address: Augustenburgerplatz 1

department: Hematology and Oncology

country: Germany

institute: Charite University Medicine, Berlin

description: Primary lymphoma cells isolated from lymph nodes of Emu-myc; Suv39h1-/- mice with palpable lymphadenopathy.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on MOE430 2.0 Arrays (Affymetrix). GeneChips were washed and stained with standard protocols in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scanner G3000.

data_processing: Affymetrix CEL files were imported into Partek Genomic Suite Software (Version 6.5, Partek Inc., St. Louis, USA) and processed by the implemented RMA workflow (median polish probe set summarization, RMA background correction, quantile normalization).

source_name: Primary lymphoma cells, isolated from lymph nodes of Emu-myc,Suv39h1-/- mice and retrovirally transduced by Bcl2, ADR treated

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol (One Cycle Target labeling protocol) from 3 ug total RNA.

growth_protocol: Primary Emu-myc;Suv39h1-/- lymphoma cells were cultivated in B-cell medium (DMEM and IMDM in 1:1 ratio, 10%FBS, 4mM L-glutamine, 25µM beta-mercaptoethanol, 100U/ml penicilin/streptamycin) on gamma-irradiated (20Gy) NIH 3T3 cells as feeder.

extract_protocol: The total RNA from untreated or 5 days ADR treated Myc;Bcl2 lymphomas was prepared using an RNeasy Mini kit (QIAGEN, Valencia, California) according to the manufacturer's instructions.

treatment_protocol: Freshly isolated lymphoma cells were retrovirally transduced by Bcl2 (MSCVpuro) and selected with Puromycin for 48h. These Myc;Bcl2 cells were either left untreated or treated in vitro with 0.05µg/ml Adriamycin for 5 days.

tag: genotype

tag: transduction

value: primary lymphoma cells from lymph nodes

value: Adriamycin (ADR)


title: lymphoma_4936_ADR

tag: cell type


title: lymphoma_4936_nt

source_name: Primary lymphoma cells, isolated from lymph nodes of Emu-myc,Suv39h1-/- mice and retrovirally transduced by Bcl2, untreated


title: lymphoma_1032_ADR


title: lymphoma_9250_nt


title: lymphoma_7890_nt


title: lymphoma_5783_ADR


title: lymphoma_7890_ADR


title: RNA_Normal_W

status: Public on Jun 30 2012

city: Birmingham

first: Yan

last: Sanders

state: AL

address: 901 19th Street S

institute: University of Alabama at Birmingham

description: Normal

hyb_protocol: The cRNA was then hybridized to a human HT-12 BeadChip and stained with strepavidin-Cy3 for visualization.

scan_protocol: Scanned using the Illumina iScan.

data_processing: Quantile normalized, no background subtraction

source_name: Normal

label_protocol: Total RNA was converted to cDNA by reverse transcription, followed by second-strand synthesis to generate double-stranded cDNA.  After purification, the cDNA was converted to biotin-labeled cRNA.

extract_protocol: Rneasy

value: lung

tag: disease status

value: Normal


title: RNA_Normal_N

description: Normal


title: RNA_Normal_M

description: Normal


title: lymphoma_1032_nt


title: lymphoma_5783_nt


title: DGM-00732 [gene_expr]


title: DGM-00599 [gene_expr]


title: DGM-00914 [gene_expr]

value: Eur


title: DGM-00764 [gene_expr]

value: Afr


title: RNA_Normal_O

description: Normal


title: DGM-00797 [gene_expr]


title: DGM-00752 [gene_expr]


title: DGM-01089 [gene_expr]


title: DGM-00798 [gene_expr]


title: DGM-00583 [gene_expr]


title: DGM-00703 [gene_expr]


title: DGM-00413 [gene_expr]


title: DGM-00889 [gene_expr]


title: DGM-00708 [gene_expr]


title: DGM-00612 [gene_expr]


title: DGM-01589 [gene_expr]

value: NS


title: DGM-00593 [gene_expr]


title: DGM-00464 [gene_expr]


title: DGM-00537 [gene_expr]


title: DGM-00743 [gene_expr]


title: DGM-00300 [gene_expr]


title: DGM-00469 [gene_expr]


title: DGM-00332 [gene_expr]


title: DGM-00447 [gene_expr]


title: DGM-00474 [gene_expr]


title: DGM-00567 [gene_expr]


title: DGM-00552 [gene_expr]


title: DGM-00446 [gene_expr]


title: DGM-00273 [gene_expr]


title: DGM-00224 [gene_expr]


title: DGM-00761 [gene_expr]


title: DGM-00216 [gene_expr]


title: DGM-00451 [gene_expr]


title: DGM-00278 [gene_expr]


title: DGM-00206 [gene_expr]


title: DGM-00205 [gene_expr]


title: DGM-00193 [gene_expr]


title: DGM-00004 [gene_expr]


title: DGM-00774 [gene_expr]


title: DGM-00080 [gene_expr]


title: DGM-00013 [gene_expr]


title: DGM-00626 [gene_expr]


title: DGM-00814 [gene_expr]


title: DGM-00906 [gene_expr]

status: Public on Mar 05 2012


title: DGM-01141

tag: serum 25-oh-d

value: high vitamin D


title: DGM-00625

tag: ethnicity


title: DGM-01283_sm

value: low vitamin D


title: DGM-00778


title: DGM-00530


title: DGM-00052 [gene_expr]


title: DGM-00416


title: DGM-00069 [gene_expr]


title: DGM-01330

value: mid vitamin D


title: DGM-00936


title: DGM-01150


title: DGM-00548


title: DGM-00030


title: DGM-01540


title: DGM-00795


title: DGM-00078 [gene_expr]


title: DGM-00553 [gene_expr]


title: DGM-00757


title: DGM-00785_sm


title: RNA_Ago2_PAR-CLIP_mildMNase_repB

status: Public on May 15 2011

city: Rehovot

first: Jean

last: Hausser

address: Herzl St.

country: Israel

institute: Weizmann Institute of Science

data_processing: The raw reads were processed on the CLIPZ server (Khorshid et al., Nucleic Acids Research 2011, 39:D245)

molecule: cytoplasmic RNA

growth_protocol: HEK293 cells were routinely grown in DMEM supplemented with 10% FCS in the presence of antibiotics.

extract_protocol: CLIP, PAR-CLIP

treatment_protocol: For samples subjected to PAR-CLIP, 4-Thiouridine was added to cells grown in monolayer at 1mM final concentration 12-14 hours prior to crosslinking at 365 nm UV. For samples subjected to CLIP, the cells were directly crosslinked at 254 nm UV.

tag: cell line

tag: clip variant

value: PAR-CLIP

tag: enzymatic digestion

value: mild MNase digestion

tag: protein


title: DGM-00268_sm


title: DGM-01561


title: RNA_Ago2_PAR-CLIP_mildMNase_repA


title: DGM-00751 [gene_expr]


title: DGM-00685


title: DGM-00551 [gene_expr]


title: DGM-00244


title: DGM-00073 [gene_expr]


title: DGM-00041 [gene_expr]


title: DGM-00123 [gene_expr]


title: DGM-00044 [gene_expr]


title: DGM-00029 [gene_expr]


title: DGM-00036 [gene_expr]


title: DGM-00035 [gene_expr]


title: DGM-00249


title: DGM-00696 [gene_expr]


title: DGM-01521 [gene_expr]


title: DGM-00661


title: DGM-00465


title: DGM-00342_sm


title: DGM-00568_sm


title: DGM-00072 [gene_expr]


title: Native A7r5 gene expression (2)

status: Public on Aug 25 2010

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

institute: Vanderbilt University

description: Normoxic A7r5 vascular smooth muscle cells, approximately 50% confluent in 10% serum + DMEM, stably transfected with empty vector.

hyb_protocol: Standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Manual).

data_processing: Affymetrix CHP and CEL files. Data was normalized using RMA.

source_name: A7r5 vascular smooth muscle cells, native expression complement

extract_protocol: RNA was extracted from freshly cultured A7r5 cells using a Qiagen RNeasy kit.

value: vascular smooth muscle cells

tag: tranfection

value: empty vector


title: A7r5 stably transfected with wild-type BMPR2 (1)

description: Normoxic A7r5 vascular smooth muscle cells, approximately 50% confluent in 10% serum + DMEM, stably transfected with wild-type human BMPR2.

scan_protocol: Standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Manual).

source_name: A7r5 vascular SMC stably transfected with wild-type BMPR2

value: wild-type BMPR2


title: A7r5 stably transfected with CD mutant BMPR2 (1)

description: Normoxic A7r5 vascular smooth muscle cells, approximately 50% confluent in 10% serum + DMEM, stably transfected with BMPR2 bearing a 2579-2580delT (cytoplasmic tail domain, CD) mutation.

source_name: A7r5 vascular SMC stably transfected with CD mutant BMPR2

label_protocol: Standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Manual).

value: CD mutant BMPR2


title: A7r5 stably transfected with ED mutant BMPR2 (2)

description: Normoxic A7r5 vascular smooth muscle cells, approximately 50% confluent in 10% serum + DMEM, stably transfected with BMPR2 bearing a T354G (extracellular domain, ED) mutation.

source_name: A7r5 vascular SMC stably transfected with ED mutant BMPR2

value: ED mutant BMPR2


title: A7r5 stably transfected with KD mutant BMPR2 (2)

description: Normoxic A7r5 vascular smooth muscle cells, approximately 50% confluent in 10% serum + DMEM, stably transfected with BMPR2 bearing a C994T (kinase domain, KD) mutation.

source_name: A7r5 vascular SMC stably transfected with KD mutant BMPR2

value: KD mutant BMPR2


title: A7r5 stably transfected with CD mutant BMPR2 (2)


title: A7r5 stably transfected with wild-type BMPR2 (2)


title: A7r5 stably transfected with ED mutant BMPR2 (1)