title: Subject 5038816-M, microRNA, Normal Pregnancy


title: Subject 4026626-M, microRNA, Normal Pregnancy

status: Public on Aug 24 2017

type: RNA

city: Boston

first: Alvin

middle: T.

last: Kho

state: MA

address: 320 Longwood Avenue

department: Informatics Program

country: USA

institute: Boston Children's Hospital

hyb_protocol: Not applicable.

scan_protocol: Not applicable.

data_processing:
Raw output values in triplets for each sample: Ct on base 2 exponent, Cq confidence Cq_Conf, amplification score Amp_Score. Triplets with any “Undetermined” value, or Cq-Conf<0.8, or Amp_Score<1.24 are disregarded in subsequent analyses.
In the Non-Normalized data matrix 3 values are given for each sample: CT values on base 2 exponent. Cq confidence CQ_CONF. Amplification score AMP_SCORE. In the Normalized data matrix, we have CT_QNORM which CT values from the Non-Normalized data matrix that have CQ_CONF>0.8 and AMP_SCORE>1.24 (otherwise they are null-valued) and then quantile normalized.

label: FAM

molecule: total RNA

organism: Homo sapiens

source_name: PAXgene whole blood

label_protocol: Not applicable.

growth_protocol: Not applicable.

extract_protocol: Total RNA from 1 mL of serum that was prepared from PAXgene whole blood of patients was isolated using the Plasma/Serum Circulating and Exosomal RNA Purification Kit (Norgen Biotek). We averaged around 4 ng/ul of total RNA in 20 ul measured by RiboGreen. Isolated RNA was reverse-transcribed and the product was pre-amplified using Megaplex PreAmp Primers and TaqMan PreAmp Master Mix (Applied Biosystems).

treatment_protocol: Not applicable.

tag: Sex

value: Female

tag: ethnicity

value: White

value: Normal


title: Subject 7066921-M, microRNA, Preeclampsia Pregnancy

value: Black or African American

value: Preeclampsia


title: Subject 9008893-M, microRNA, Normal Pregnancy


title: Subject 9034020-M, microRNA, Normal Pregnancy


title: Subject 6023219-M, microRNA, Preeclampsia Pregnancy


title: Subject 8011100-M, microRNA, Preeclampsia Pregnancy


title: Subject 6083937-M, microRNA, Preeclampsia Pregnancy


title: Subject 4043229-M, microRNA, Normal Pregnancy


title: Subject 4041299-M, microRNA, Normal Pregnancy


title: Subject 3040387-M, microRNA, Normal Pregnancy


title: Subject 6074068-M, microRNA, Preeclampsia Pregnancy

value: Other


title: Subject 3025567-M, microRNA, Preeclampsia Pregnancy


title: Subject 3025682-M, microRNA, Preeclampsia Pregnancy


title: Subject 9009710-M, microRNA, Preeclampsia Pregnancy


title: Subject 6009822-M, microRNA, Normal Pregnancy


title: Subject 2083037-M, microRNA, Preeclampsia Pregnancy


title: Subject 3025195-M, microRNA, Normal Pregnancy


title: Subject 2010858-M, microRNA, Normal Pregnancy


title: Subject 3039734-M, microRNA, Normal Pregnancy


title: Subject 3080235-M, microRNA, Normal Pregnancy


title: Subject 6082469-M, microRNA, Preeclampsia Pregnancy


title: Subject 3089596-M, microRNA, Normal Pregnancy


title: Subject 1075381-M, microRNA, Normal Pregnancy


title: Subject 8054547-M, microRNA, Normal Pregnancy


title: Subject 8084201-M, microRNA, Normal Pregnancy


title: Subject 8057476-M, microRNA, Normal Pregnancy


title: Subject 1089419-M, microRNA, Normal Pregnancy


title: Subject 7054360-M, microRNA, Normal Pregnancy


title: Subject 6037614-M, microRNA, Normal Pregnancy


title: Subject 1084308-M, microRNA, Preeclampsia Pregnancy


title: Subject 5087337-M, microRNA, Normal Pregnancy


title: Subject 7027740-M, microRNA, Preeclampsia Pregnancy

value: American Indian or Alaska


title: Subject 4078284-M, microRNA, Preeclampsia Pregnancy


title: Subject 3050398-M, microRNA, Preeclampsia Pregnancy


title: Subject 2055393-M, microRNA, Normal Pregnancy


title: Subject 7016015-M, microRNA, Preeclampsia Pregnancy


title: Subject 8012930-M, microRNA, Normal Pregnancy


title: Subject 4084584-M, microRNA, Preeclampsia Pregnancy


title: Subject 8023284-M, microRNA, Normal Pregnancy


title: Subject 5075311-M, microRNA, Preeclampsia Pregnancy


title: Subject 4015811-M, microRNA, Normal Pregnancy


title: Subject 6073211-M, microRNA, Normal Pregnancy


title: Subject 7050617-M, microRNA, Normal Pregnancy


title: Subject 6079515-M, microRNA, Preeclampsia Pregnancy


title: Subject 3092584-M, microRNA, Normal Pregnancy


title: Subject 7041367-M, microRNA, Normal Pregnancy


title: Subject 5019090-M, microRNA, Normal Pregnancy


title: Subject 4035971-M, microRNA, Normal Pregnancy


title: Subject 8009468-M, microRNA, Preeclampsia Pregnancy

value: Asian


title: Subject 5023045-M, microRNA, Normal Pregnancy


title: Subject 2002666-M, microRNA, Preeclampsia Pregnancy


title: Subject 3026263-M, microRNA, Normal Pregnancy


title: Subject 8097362-M, microRNA, Normal Pregnancy


title: Subject 4058470-M, microRNA, Normal Pregnancy


title: Subject 9026397-M, microRNA, Preeclampsia Pregnancy


title: Subject 6030914-M, microRNA, Normal Pregnancy


title: Subject 1091914-M, microRNA, Normal Pregnancy


title: Subject 5010120-M, microRNA, Normal Pregnancy


title: Subject 2098737-M, microRNA, Normal Pregnancy


title: Subject 7086373-M, microRNA, Normal Pregnancy


title: Subject 5097746-M, microRNA, Normal Pregnancy


title: Subject 6057555-M, microRNA, Normal Pregnancy


title: Subject 5031074-M, microRNA, Normal Pregnancy


title: Subject 6063221-M, microRNA, Normal Pregnancy


title: Subject 3024271-M, microRNA, Normal Pregnancy


title: Subject 5035754-M, microRNA, Preeclampsia Pregnancy


title: Subject 9078067-M, microRNA, Normal Pregnancy


title: Subject 7053108-M, microRNA, Normal Pregnancy


title: Subject 7008408-M, microRNA, Normal Pregnancy


title: Subject 6095056-M, microRNA, Normal Pregnancy


title: Subject 6051478-M, microRNA, Normal Pregnancy


title: Subject 4043864-M, microRNA, Normal Pregnancy


title: Subject 1020307-M, microRNA, Preeclampsia Pregnancy


title: Subject 6068170-M, microRNA, Preeclampsia Pregnancy


title: Subject 7061969-M, microRNA, Normal Pregnancy


title: Subject 6053558-M, microRNA, Normal Pregnancy


title: Subject 4018695-M, microRNA, Normal Pregnancy


title: Subject 5018713-M, microRNA, Normal Pregnancy


title: Subject 2032617-M, microRNA, Normal Pregnancy


title: Subject 2052394-M, microRNA, Preeclampsia Pregnancy


title: Subject 1086430-M, microRNA, Preeclampsia Pregnancy


title: Subject 4086732-M, microRNA, Preeclampsia Pregnancy


title: Subject 7000235-M, microRNA, Normal Pregnancy


title: Subject 6098802-M, microRNA, Normal Pregnancy


title: Subject 3064425-M, microRNA, Normal Pregnancy


title: Subject 3083249-M, microRNA, Preeclampsia Pregnancy


title: Subject 8071607-M, microRNA, Normal Pregnancy


title: Subject 4084871-M, microRNA, Normal Pregnancy


title: Subject 5079413-M, microRNA, Normal Pregnancy


title: Subject 7073579-M, microRNA, Normal Pregnancy


title: Subject 5034421-M, microRNA, Normal Pregnancy


title: Subject 4083145-M, microRNA, Normal Pregnancy


title: Subject 6074164-M, microRNA, Preeclampsia Pregnancy


title: Subject 7026812-M, microRNA, Preeclampsia Pregnancy


title: Subject 8050628-M, microRNA, Normal Pregnancy


title: Subject 2069323-M, microRNA, Normal Pregnancy


title: Subject 6094898-M, microRNA, Normal Pregnancy


title: Subject 2033556-M, microRNA, Preeclampsia Pregnancy


title: Subject 9050155-M, microRNA, Normal Pregnancy


title: Subject 6053887-M, microRNA, Preeclampsia Pregnancy


title: Subject 5005274-M, microRNA, Preeclampsia Pregnancy


title: Subject 3030282-M, microRNA, Normal Pregnancy


title: Subject 2006605-M, microRNA, Normal Pregnancy


title: Subject 5028464-M, microRNA, Normal Pregnancy


title: Subject 3017557-M, microRNA, Preeclampsia Pregnancy, Replicate 2


title: Subject 3017557-M, microRNA, Preeclampsia Pregnancy, Replicate 1


title: Subject 3040056-M, microRNA, Normal Pregnancy


title: Subject 7054702-M, microRNA, Preeclampsia Pregnancy


title: Subject 5014485-M, microRNA, Normal Pregnancy


title: Subject 3095818-M, microRNA, Normal Pregnancy


title: Subject 4012442-M, microRNA, Normal Pregnancy


title: Subject 9027966-M, microRNA, Preeclampsia Pregnancy


title: Subject 5027791-M, microRNA, Normal Pregnancy


title: Subject 3067074-M, microRNA, Normal Pregnancy


title: Subject 2012577-M, microRNA, Normal Pregnancy


title: Subject 9030732-M, microRNA, Normal Pregnancy


title: Subject 6061774-M, microRNA, Normal Pregnancy


title: Subject 4072444-M, microRNA, Preeclampsia Pregnancy


title: Subject 7081029-M, microRNA, Normal Pregnancy


title: Subject 8021460-M, microRNA, Normal Pregnancy


title: Subject 1050601-M, microRNA, Normal Pregnancy, Replicate 2


title: Subject 7045717-M, microRNA, Normal Pregnancy


title: Subject 3012659-M, microRNA, Preeclampsia Pregnancy


title: Subject 5037279-M, microRNA, Preeclampsia Pregnancy


title: Subject 3051856-M, microRNA, Normal Pregnancy


title: icSHAPE - 293T - DMSO rep2

status: Public on Apr 04 2016

type: SRA

city: Stanford

first: Zhipeng

last: Lu

state: CA

address: 269 Campus Drive

department: Department of Dermatology

institute: Stanford University

description:
RNA secondary Structure
processed data file: HS_293T_icSHAPE_InVitro_BaseReactivities.txt,HS_293T_icSHAPE_InVivo_BaseReactivities.txt

library_source: transcriptomic

data_processing:
Library strategy: icSHAPE
After demultiplexing, reads were stripped adaptors (PMID: 25411354) and mapped to the Homo Sapiens transcriptome - GRCh37.74 (hg19) using Bowtie2.
All samples have a 13nt barcode on the 5'end which needs to be trimmed before mapping to the transcriptome
icSHAPE reverse transcriptase (RT)  stops were isolated as the first nucleotide after the 5'end barcode. RT stops were used to calculated icSHAPE reactivity scores
Genome_build: Homo sapiens - GRCh37.74 (hg19)
Supplementary_files_format_and_content: 2 Tables (one each for In Vitro and In Vivo modified samples) of icSHAPE reactivities across human transcripts measured. Format: Transcript ID, Transcript Length (in nucleotides), RPKM value, icSHAPE reactivity scores per base for the length of each transcript (NULL values denote bases not measured by the icSHAPE experiment)

source_name: Embryonic Kidney cells

extract_protocol:
HEK293T cells were grown, treated with DMSO or NAI-N3, and RNA collected with TRIzol as previously described (PMID: 25799993).  Protocol: icSHAPE
Deep sequencing libraries were prepared using 3'end RNA ligation, cDNA synthesis with SuperScript III, cDNA circularization, and subsequent PCR amplification

tag: cell line


title: EBF1-ChIP-Rep1

status: Public on May 06 2016

city: Freiburg

first: Senthilkumar

last: Ramamoorthy

address: Stübeweg 51

department: Cellular & Molecular Immunology

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description: EBF1 ChIP in Rag2 (-/-) pro-B cells

library_source: genomic

data_processing:
Basecalling and fastq files generation was performed by using Illumina bcl2fastq 1.8.4 (RTA 1.18.64)
The reads were aligned to the mm9 genome assembly using bowtie2 with default configurations
Duplicated reads were filtered and blacklisted regions were removed using samtools and Picard.
Peaks were identified using MACS2 (v2.1.0.20150731) with q-value cutoff 0.01 and further filtered for p-value 10^-10 and fold change 4
Genome_build: mm9
Supplementary_files_format_and_content: The processed bigwig files were generated using deeptools (v1.5.11) by normalizing to 1x coverage for the genome size 2150570000 and a binsize of 50

molecule: genomic DNA

organism: Mus musculus

source_name: Rag2(-/-)  pro-B cells

growth_protocol: Rag2(-/-) pro-B cells were derived from mouse fetal liver and cultured on OP9 cells for short term

extract_protocol:
Cells were crosslinked  with formaldehyde, lysed and DNA was fragmented to an average size of 300bp by sonication. Chromatin was precipitated with a specific antibody (EBF1, produced "in house") and protein A-coupled sepharose beads. After elution from the beads, chromatin was decrosslinked and purified via QIAquick PCR Purification Kit according to the manufacturer's manual.
Library preparation for ChIP analysis was performed with the NEBNext Ultra DNA Library Prep Kit  according to the manufacturer’s protocol. No size selection was used and amplification was performed for 10 PCR cycles.

tag: cell type

value: pro-B cells

tag: genotype

tag: strain

tag: tissue

value: fetal liver


title: EBF1-ChIP-Rep2

description: EBF1 ChIP in Rag2 (-/-) pro-B cells


title: Subject 7029286-M, microRNA, Normal Pregnancy


title: cell number 83

status: Public on Feb 29 2016

city: Madison

first: Xinyu

last: Zhao

state: Wisconsin

address: 1500 HIghland Ave, Wiasman Center North Tower T513

institute: University of Wisconsin Madison

description: FACS sorted individual DCX-dsRed+ cells

data_processing:
RSEM was used to align read pairs to the transcriptome and estimate gene expression levels. The following command was used to execute alignment and quantification: rsem-calculate-expression --paired-end --bowtie2 -p 8 $sample_forward.fastq $sample_reverse.fastq $rsem_index $sample_output.
A table of RSEM’s “expected counts” was used as expression values in downstream analyses.
Outliers were detected using Fluidigm's SINGuLAR Analysis Toolset in R. The "identifyOutliers()" command was used in this step.
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited text files containing 3 columns: (1) Refseq accession numbers, (2) gene symbols, and (3) expected counts calculated by RSEM.

molecule: polyA RNA

source_name: individual immature neuron

extract_protocol:
Dentate gyrus was microdissected and cell populations were isolated into single cells using a Becton Dickinson FACS. Immediately after FACS, collected cells were centrifuged and then resuspended in cell culture medium at a concentration of 500 cells/μl. The cell suspension was then mixed with C1 Cell Suspension Reagent (Fluidigm, 634833) at the recommended ratio of 3:2 immediately before loading 5 μl of this final mix on the C1 Integrated Fluidic Circuit (IFC). Single cells were capture and RNA extraction was performed by the Fluidigm C1 IFC.
mRNA amplification was performed on the C1 Single-Cell Auto Prep Integrated Fluidic Circuit (IFC) following the methods described in the protocol (PN 100-7168). The cDNA products were quantified using the Quant-iT PicoGreen double-stranded DNA (dsDNA) Assay Kit (Life Technologies) and high-sensitivity (HS) DNA chips (Agilent). All samples assayed had material present in the 1000-3000bp range with concentrations varied from ~160pg/μl to 1.5ng/µl.  The cDNA samples were diluted to less than 0.3ng/μl and 2ul of diluted cDNA reaction prod¬ucts were then converted into libraries using the Nextera XT DNA Sample Preparation Kit (Illumina, FC-131-1096 and FC-131-1002) following the manufacturer’s instruction. Briefly, 12 Cycles of PCR Amplification were used. After the PCR step, samples were pooled, cleaned with 0.9× Agencourt AMPure XP SPRI beads (Beckman Coulter lot#14669400 X2), eluted in Tris + EDTA buffer and quantified using a HS DNA chip (Agilent).

value: brain

tag: tissue compartment

value: Dentate gyrus

value: Dcx-dsRed

tag: age

value: 6-7 weeks


title: cell number 81

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 80

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 79

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 76

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 78

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 75

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 73

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 72

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 70

description: FACS sorted individual DCX-dsRed+ cells


title: Subject 4031608-M, microRNA, Normal Pregnancy


title: Subject 7029676-M, microRNA, Preeclampsia Pregnancy


title: cell number 67

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 68

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 64

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 63

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 62

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 61

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 60

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 59

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 57

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 55

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 54

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 52

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 53

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 51

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 49

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 47

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 71

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 65

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 69

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 45

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 66

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 46

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 43

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 41

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 39

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 38

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 35

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 31

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 24

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 23

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 21

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 20

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 17

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 16

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 48

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 15

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 18

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 13

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 14

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 12

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 11

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 9

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 8

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 6

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 5

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 4

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 22

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 7

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 3

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 2

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 1

description: FACS sorted individual DCX-dsRed+ cells


title: cell number 44

description: FACS sorted individual DCX-dsRed+ cells


title: HC [9963831032_D]

status: Public on Oct 07 2015

city: Toronto

first: Eric

last: Gracey

state: ON

address: 60 Leonard Ave

department: Immunology

country: Canada

institute: University of Toronto

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was checked for quality using Biocunductor/LUMI in R v3.0.2 and normalised using quantile normalisation in GeneSpring v12.6.1

label: biotin

source_name: Whole blood RNA

label_protocol: cRNA was prepared with the TotalPrep RNA kit Illumina kits

extract_protocol: Whole blood RNA was extracted using Tempus blood RNA isolation kits (ThermoFisher). Quality control was performed by analysis with NanoVue and Agilent Bioanalyser.

tag: age (yr)

tag: hla-b27 (1=positive, 0=negative)

value: unknown

tag: disease

value: healthy control


title: Subject 1050601-M, microRNA, Normal Pregnancy, Replicate 1


title: HC [9965280090_F]


title: HC [9963831051_J]

value: Male


title: HC [9963831045_E]


title: HC [9963831045_I]

value: Female


title: HC [9963831051_I]


title: HC [9963831033_K]


title: HC [9965280090_B]


title: HC [9963831032_K]


title: HC [9965280090_K]


title: HC [9965280034_I]


title: HC [9963831051_H]


title: HC [9963831051_K]


title: HC [9965280034_D]


title: HC [9965280034_A]


title: HC [9963831033_G]


title: HC [9963831032_C]


title: AS [9963831045_J]

value: Ankylosing Spondylitis


title: icSHAPE - 293T - DMSO rep1


title: AS [9965280034_G]


title: AS [9963831033_I]


title: AS [9963831045_L]


title: HC [9963831045_B]


title: AS [9963831045_D]


title: AS [9965280034_C]


title: HC [9963831032_A]


title: HC [9963831051_C]


title: AS [9963831032_H]


title: cell number 56

description: FACS sorted individual DCX-dsRed+ cells


title: AS [9963831051_L]


title: AS [9963831032_J]


title: AS [9963831051_D]


title: AS [9965280090_E]


title: AS [9965280034_J]


title: AS [9963831033_J]


title: AS [9965280034_H]


title: AS [9965280034_E]


title: AS [9963831032_E]


title: AS [9963831032_G]


title: AS [9963831032_B]


title: AS [9965280090_A]


title: cell number 77

description: FACS sorted individual DCX-dsRed+ cells


title: AS [9965280034_K]


title: AS [9963831045_G]


title: AS [9963831045_K]


title: AS [9963831051_F]


title: AS [9963831045_C]


title: AS [9965280090_G]


title: AS [9965280090_J]


title: AS [9963831033_H]


title: AS [9963831045_A]


title: AS [9965280090_D]


title: AS [9965280090_L]


title: AS [9965280034_F]


title: AS [9963831051_E]


title: AS [9965280090_I]


title: AS [9963831033_F]


title: AS [9965280034_L]


title: AS [9963831033_B]


title: AS [9965280090_H]


title: AS [9963831033_E]


title: AS [9963831032_I]


title: AS [9963831033_L]


title: AS [9963831051_B]


title: AS [9963831033_C]


title: AS [9963831045_F]


title: AS [9965280090_C]


title: AS [9963831051_G]


title: AS [9965280034_B]


title: AS [9963831032_L]


title: AS [9963831045_H]


title: AS [9963831051_A]


title: AS [9963831033_A]


title: Jemalong_root nodule_rep3

status: Public on Jun 01 2015

first: Melanie

middle: J

last: Barnett

address: 371 Jane Stanford Way

department: Biology

description: Root nodule harvested from Medicago truncatula Jemalong 21 days after inoculation with Sinorhizobium meliloti CL150

hyb_protocol: Twenty micrograms of biotinylated aRNA was hybridized to each chip at 48 degrees celsius for 16 hours as described by Barnett et al. 2004. GeneChips were washed and stained in the Affymetrix Fluidics Station

scan_protocol: Chips were scanned at the Stanford PAN facility using an Affymetrix scanner 3000 7G

data_processing: Affymetrix CEL files were analyzed using R and BIOCONDUCTOR software packages (Gentleman et al. 2004, Genome Biol 5:R80). Probe summarization and normalization were carried out with the AFFY package and the RMA algorithm (Irizarry et al. 2003, Biostatistics 4: 249-264). Since the proportion of plant to bacterial RNA varied between different root nodule zones and between nodules of different plant mutants. To account for varying plant to bacterial RNA ratios in different samples, normalization was done separately for M. truncatula and S. meliloti probe sets.

organism:
Sinorhizobium meliloti
Medicago truncatula

source_name: wild type (Jemalong)

label_protocol: One microgram template RNA was amplified and biotin-labeled using the MessageAmp Bacteria kit (Ambion). Amplified RNA (20 µg) was fragmented in 40 µl 200 mM Tris-Acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate at 94 degree centigrade for 35 min. The reaction was brought to 78.5 µl with water and hybridized to Affymetrix GeneChips as described previously (Barnett et al. 2004, PNAS, 101:16636-16641)

growth_protocol: Medicago truncatula [Gaertn.] cv Jemalong, A-17 and dnf plant seeds were lightly scratched with sandpaper and sterilized in undiluted bleach for 5 min. Seeds were rinsed with sterile water and imbibed for 8 h at room temperature and 48 h at 4°C, germinated overnight in inverted petri dishes in the dark, and planted into pre-sterilized vermiculite in cone-tainer tubes (Stuewe & Sons). Plants were watered every third day with 5 ml 0.1x BNM. Five day old seedlings were inoculated with 5 ml of a suspension (OD600 = 0.1) of CL150 in 0.1x Buffered Nodulation Medium (BNM) (Ehrhardt et al. 1992)(Barnett et al. 2004 Proc Natl Acad Sci USA 101:16636-16641). Cultures of S. meliloti CL150 were prepared for plant inoculation as described previously (Mitra and Long 2004, Plant Physiol.134: 595-604).

extract_protocol: The nodules were ground with a microcentrifuge tube pestle as the buffer thawed. The lysate was brought to a volume of 450 µl with RLT buffer and processed through a Qiashredder column (Qiagen) and an RNeasy Mini spin column (Qiagen). The RNA was DNase-treated (DNase I, Thermo Fisher Scientific) in the presence of RNase inhibitor (SuperaseIN, Ambion) (Barnett et al. 2004, PNAS, 101:16636-16641). The DNase-treated RNA was re-purified using RNeasy MinElute columns (RNeasy MinElute Kit, Qiagen).

treatment_protocol: Root nodules from dnf mutants and wild type cultivars Jemalong and A17 were placed in 30 µl of RLT buffer (RNeasy Mini Kit, Qiagen) and frozen in liquid nitrogen.

value: Root nodule


title: A17_root nodule_rep3

description: Root nodule harvested from Medicago truncatula A-17 21 days after inoculation with Sinorhizobium meliloti CL150

source_name: wild type (A17)


title: Jemalong_root nodule_rep1


title: A17_root nodule_rep2


title: AS [9963831032_F]


title: DNF4_root nodule_rep2

description: Root nodule harvested from Medicago truncatula dnf4 21 days after inoculation with Sinorhizobium meliloti CL150


title: DNF3_root nodule_rep2

description: Root nodule harvested from Medicago truncatula dnf3 21 days after inoculation with Sinorhizobium meliloti CL150


title: Jemalong_root nodule_rep2


title: DNF4_root nodule_rep3


title: AS [9963831033_D]


title: DNF4_root nodule_rep1


title: A17_root nodule_rep1


title: DNF3_root nodule_rep1


title: DNF3_root nodule_rep3


title: DNF7_root nodule_rep3

description: Root nodule harvested from Medicago truncatula dnf7 21 days after inoculation with Sinorhizobium meliloti CL150


title: Gran2D_PU1

status: Public on Jul 28 2014

city: Charlottesville

first: Chongzhi

last: Zang

state: VA

institute: University of Virginia

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie with -m 1 and default parameters
Uniquely aligned reads were filtered using SICER v1.1 to keep up to 2 copies at each genomic location
Wiggle files for histone modifications were generated using NPS with default parameters
Wiggle files for progenitor cells' H3K4me2 and transcription factors were generated using MACS v1.4
Genome_build: mm9

source_name: Immature granulocytes

growth_protocol: Single-cell suspensions of mouse fetal livers collected on gestational day 14 were prepared by passage through 40 μm filters and 18- to 23-gauge needles. Mature erythrocytes were lysed in Ammonium Chloride Potassium (ACK) buffer and cells were cultured in Dulbecco’s Modified Eagle Medium supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Individual lineages were isolated by depleting other lineages using TER119, GR1, CD41, and CD11b (B-D Pharmingen) monoclonal antibodies (mAb) and immunomagnetic Dynabeads (Invitrogen) or by positive selection using GR1 or TER119 mAb for flow cytometry. MK isolations included additional passage over triple (4%, 3%, 1.5%) gradients of bovine serum albumin, with collection of the supernatant (IMM cells) or pellet (MAT cells). Cell isolations were monitored by viewing May-Grünwald-Giemsa stains of cytocentrifuged preparations with an Olympus BX41 microscope and by flow cytometry using the above-listed mAb. Chromatin marks were pulled down with H3K4me2 or H3K27ac antibodies after MNase digestion or crosslinking + sonication of the cells. Transcription factors were pulled down with the respective antibodies after crosslinking + sonication of the cells
At least 20 ng of precipitated or input DNA from pools of at least 3 replicates was processed for deep sequencing using different library preparation kits for IMM or MAT cells (TruSeq, Illumina) and progenitors (TruPLEX-FD, Rubicon Genetics), following the manufacturers’ instructions. ChIP-seq libraries were sequenced using Illumina HiSeq2000 and tags were mapped to mouse genome build mm9.

treatment_protocol: To expand erythroid cells, granulocytes, and MKs, cultures were supplemented, respectively, with Stem Cell Factor (SCF, R&D Systems, 0.02 mg/10 mL) and erythropoietin (EPO, R&D Systems, 0.02 mg/10 mL); SCF and granulocyte-colony stimulating factor (G-CSF, R&D Systems, 0.05 mg/10 mL); or thrombopoietin (TPO, 1/100 dilution of producer cell supernatant [Villeval, 1997 #2788]). To enrich hematopoietic progenitors, short-term cultures were supplanted with SCF and interleukin-3 (R&D Systems, 0.05 mg/10 mL). Progenitors were harvested after 1 day of culture, IMM lineages after 2 days, and MAT cells after 4 (erythroid, granulocyte) or 5 days (MKs).

value: liver

value: Immature granulocytes

tag: genome/variation

value: wild-type

tag: antibody

value: PU.1, antibody vendor, cat #, lot #:Santa Cruz, sc-352, D2011


title: Gran2D_H3K27ac

value: H3K427ac, antibody vendor, cat #, lot #:Abcam, ab4729, 509313


title: DNF1_root nodule_rep1

description: Root nodule harvested from Medicago truncatula dnf1 21 days after inoculation with Sinorhizobium meliloti CL150


title: DNF5_root nodule_rep2

description: Root nodule harvested from Medicago truncatula dnf5 21 days after inoculation with Sinorhizobium meliloti CL150


title: DNF7_root nodule_rep1


title: DNF2_root nodule_rep2

description: Root nodule harvested from Medicago truncatula dnf2 21 days after inoculation with Sinorhizobium meliloti CL150


title: DNF1_root nodule_rep2


title: DNF2_root nodule_rep1


title: DNF1_root nodule_rep3


title: DNF5_root nodule_rep1


title: DNF2_root nodule_rep3


title: DNF7_root nodule_rep2


title: BMM_RANKL 3day_rep2

status: Public on Jul 30 2014

city: Los Angeles

first: Kyunghwan

last: Kim

state: California

address: 1450 Biggy Street NRT6517

department: Biochemistry and Molecular Biology

institute: University of Southern California

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were processed and anlayzed by the Array Pipe software.

source_name: Bone marrow-derived macrophage cells

label_protocol: Biotinylated cRNA was prepared with the Ambion MessageAmp kit for Illumina array.

growth_protocol: Bone marrow (BM) cells were collected by flushing femurs and tibias from 6- to 8-week-old C57BL/6 mice. Cells were cultured in α-minimum essential medium (α-MEM) supplemented with 10% FBS and M-CSF (5 ng/ml) for 16 h.  Non-adherent cells were harvested and cultured with M-CSF (30 ng/ml) for 3 days. Floating cells were removed and adherent cells were used as bone marrow-derived macrophage (BMM) cells.

extract_protocol: Total RNA was isolated using the TRIzol reagent according to the manufacturer's instructinos.

treatment_protocol: To generate osteoclasts, BMMs were cultured in the presence of M-CSF (30 ng/ml) and RANKL (50 ng/ml).

tag: cell culture type

value: Primary cells

value: Bone marrow-derived macrophage cells

value: 6-8 weeks


title: BMM_RANKL 3day_rep1

description: replicate 1


title: BMM_RANKL 0day_rep2

description: replicate 2


title: BMM_RANKL 0day_rep1

description: replicate 1


title: DNF5_root nodule_rep3


title: mPFC_maternal_rep4

status: Public on Feb 28 2014

hyb_protocol: Samples were hybridized to arrays at 45 degrees C for 16 hours following procedures outlined in the GeneChip WT Terminal Labeling and Hybridization Use Manual , Rev. 4.

scan_protocol: Arrays were scanned on the Affymetrix GC3000 G7 scanner, and data were extracted and processed using Affymetrix Command Console v3.1.1.1229.

data_processing: Raw array data were normalized and summarized at the probeset level using Affymetrix Power Tools v1.12.0 with default settings for PLIER with GC-bin background correction. Summarized data were analyzed using limma for BioConductor v3.6.9

label: Biotin

source_name: lactating maternal adult female_medial prefrontal cortex

label_protocol: 200ng of each total RNA sample were labeled with an Ambion GeneChip WT Expression Kit (Ambion, Austin, TX, USA) according to the manufacturer's specifications.

growth_protocol: The strain of mice used was outbred hsd:ICR mice purchased from Harlan labs (Madison, WI).  Maternal were housed with a breeder male for two weeks while virgin mice were co-housed with two other female mice for the same time period.  After the mating period, all females from both groups were individually housed through parturition until tissue collection (postpartum day 7).  Each virgin control sample was collected on the same day as a postpartum day 7 maternal sample.

extract_protocol: Total RNA was extracted using the Aurum Total RNA Fatty and Fibrous Tissue Kit (Bio-Rad, Hercules, CA, USA), which uses a guanidinium thiocyanate-phenol-chloroform extraction followed by a spin column cleanup and purification. RNA purity and concentration were assessed using a NanoDrop spectrophotometer, and RNA integrity was assessed using an RNA Pico Chip on an Agilent BioAnalyzer 2100.

treatment_protocol: On postpartum day 0, pups were culled, if necessary, to standardize litter size to 11.  Tissue was collected on postpartum day 7.

value: Outbred hsd:ICR

tag: maternal state

value: lactating maternal

value: microdissected medial prefrontal cortex


title: mPFC_maternal_rep2


title: mPFC_maternal_rep5


title: mPFC_maternal_rep1


title: mPFC_virgin_rep3

source_name: virgin adult female_medial prefrontal cortex

value: virgin


title: mPFC_virgin_rep2


title: mPFC_maternal_rep3


title: mPFC_virgin_rep4


title: mPFC_virgin_rep1


title: 009-282-012-TP15 [5356583031F]

status: Public on Apr 19 2013

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

description:
Test_Set_Vein
5356583031F

hyb_protocol: Hybridization to HumanHT-12 v3 Expression BeadChip as per Illumina protocol

scan_protocol: Illumina BeadStation 500 SentrixScanVersion 2.3.0.13

data_processing: Following background subtraction, the raw signal intensities extracted with Illumina Genome Studio v2010.1 Gene Expression 1.6.0 software were scaled to the mean intensity of the dataset.

source_name: Whole Blood

label_protocol: Biotinylated cRNA were generated following manufacturer protocols using the Illumina TotalPrep Amplification Kit from Ambion

extract_protocol: RNA was isolated using the MagMAX™-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion, Austin, TX, USA) according to the manufacturer's instructions

tag: subject id

tag: day

tag: vaccine

value: Saline

tag: blood source

value: Vein

tag: gender

value: M

tag: race

value: Caucasian

value: Non Hispanic or Latino

tag: sample set


title: 009-282-012-TP14 [5356583036L]

description:
Test_Set_Vein
5356583036L

tag: ethnicity


title: 009-282-012-TP9 [5356583045B]

description:
Test_Set_Vein
5356583045B


title: 009-282-012-TP1 [5356583045G]

description:
Test_Set_Vein
5356583045G


title: mPFC_virgin_rep5

tag: strain

tag: tissue


title: 009-282-012-TP7 [5356583030J]

description:
Test_Set_Vein
5356583030J

tag: age


title: 009-282-012-TP12 [5356583040C]

description:
Test_Set_Vein
5356583040C


title: 009-282-004-TP2 [5447320040I]

description:
Test_Set_Finger
5447320040I

value: PNEUM

value: Finger

value: F


title: 009-282-011-TP1 [5447320040H]

description:
Test_Set_Finger
5447320040H

value: African American


title: 009-282-021-TP13 [5447320040A]

description:
Test_Set_Finger
5447320040A


title: 009-282-011-TP13 [5447320040E]

description:
Test_Set_Finger
5447320040E


title: 009-282-012-TP2 [5356583035L]

description:
Test_Set_Vein
5356583035L


title: 009-282-026-TP1 [5447320037K]

description:
Test_Set_Finger
5447320037K


title: 009-282-021-TP2 [5447320037L]

description:
Test_Set_Finger
5447320037L


title: 009-282-011-TP2 [5447320038A]

description:
Test_Set_Finger
5447320038A


title: 009-282-026-TP2 [5447320038L]

description:
Test_Set_Finger
5447320038L


title: 009-282-021-TP1 [5447320037J]

description:
Test_Set_Finger
5447320037J


title: 009-282-014-TP2 [5447320040G]

description:
Test_Set_Finger
5447320040G

value: NS


title: 009-282-004-TP13 [5447320035F]

description:
Test_Set_Finger
5447320035F


title: 009-282-026-TP13 [5447320038I]

description:
Test_Set_Finger
5447320038I


title: 009-282-007-TP13 [5447320039E]

description:
Test_Set_Finger
5447320039E


title: 009-282-015-TP1 [5447320037E]

description:
Test_Set_Finger
5447320037E

value: Hispanic


title: 009-282-004-TP1 [5447320040F]

description:
Test_Set_Finger
5447320040F


title: 009-282-020-TP2 [5447320037D]

description:
Test_Set_Finger
5447320037D


title: 009-282-006-TP2 [5447320036I]

description:
Test_Set_Finger
5447320036I


title: 009-282-013-TP13 [5447320039C]

description:
Test_Set_Finger
5447320039C


title: 009-282-020-TP13 [5447320040B]

description:
Test_Set_Finger
5447320040B


title: 009-282-003-TP13 [5447320038B]

description:
Test_Set_Finger
5447320038B


title: 009-282-014-TP13 [5447320036K]

description:
Test_Set_Finger
5447320036K


title: 009-282-007-TP2 [5447320035D]

description:
Test_Set_Finger
5447320035D


title: 009-282-013-TP2 [5447320035K]

description:
Test_Set_Finger
5447320035K


title: 009-282-006-TP1 [5447320035J]

description:
Test_Set_Finger
5447320035J


title: 009-282-008-TP13 [5447320039L]

description:
Test_Set_Finger
5447320039L

value: FLUZONE


title: 009-282-006-TP13 [5447320035E]

description:
Test_Set_Finger
5447320035E


title: 009-282-013-TP1 [5447320036L]

description:
Test_Set_Finger
5447320036L


title: 009-282-007-TP1 [5447320035H]

description:
Test_Set_Finger
5447320035H


title: 009-282-003-TP2 [5447320035L]

description:
Test_Set_Finger
5447320035L


title: 009-282-015-TP13 [5447320036F]

description:
Test_Set_Finger
5447320036F


title: 009-282-014-TP1 [5447320037C]

description:
Test_Set_Finger
5447320037C


title: 009-282-018-TP13 [5447320039K]

description:
Test_Set_Finger
5447320039K


title: 009-282-024-TP2 [5447320039I]

description:
Test_Set_Finger
5447320039I

value: Asian


title: 009-282-008-TP1 [5447320039F]

description:
Test_Set_Finger
5447320039F


title: 009-282-001-TP1 [5447320039D]

description:
Test_Set_Finger
5447320039D


title: 009-282-024-TP13 [5447320038F]

description:
Test_Set_Finger
5447320038F


title: 009-282-022-TP13 [5447320038G]

description:
Test_Set_Finger
5447320038G


title: 009-282-003-TP1 [5447320038K]

description:
Test_Set_Finger
5447320038K


title: 009-282-010-TP2 [5447320036J]

description:
Test_Set_Finger
5447320036J


title: 009-282-018-TP2 [5447320035B]

description:
Test_Set_Finger
5447320035B


title: 009-282-022-TP2 [5447320037F]

description:
Test_Set_Finger
5447320037F


title: 009-282-010-TP1 [5447320035G]

description:
Test_Set_Finger
5447320035G


title: 009-282-001-TP13 [5447320037B]

description:
Test_Set_Finger
5447320037B


title: 009-282-024-TP1 [5447320036A]

description:
Test_Set_Finger
5447320036A


title: 009-282-018-TP1 [5447320036C]

description:
Test_Set_Finger
5447320036C


title: 009-282-001-TP2 [5447320038E]

description:
Test_Set_Finger
5447320038E


title: 009-282-010-TP13 [5447320036B]

description:
Test_Set_Finger
5447320036B


title: 009-282-020-TP4 [5326907020J]

description:
Training_Set_Finger
5326907020J


title: 009-282-020-TP8 [5326907022F]

description:
Training_Set_Finger
5326907022F


title: 009-282-022-TP1 [5447320038C]

description:
Test_Set_Finger
5447320038C


title: 009-282-020-TP11 [5324338030B]

description:
Training_Set_Finger
5324338030B


title: 009-282-020-TP5 [5324338024C]

description:
Training_Set_Finger
5324338024C


title: 009-282-020-TP3 [5324338024J]

description:
Training_Set_Finger
5324338024J


title: 009-282-020-TP9 [5326907019H]

description:
Training_Set_Finger
5326907019H


title: 009-282-020-TP7 [5326907022J]

description:
Training_Set_Finger
5326907022J


title: 009-282-020-TP2 [5326907025G]

description:
Training_Set_Finger
5326907025G


title: 009-282-014-TP11 [5324338024F]

description:
Training_Set_Finger
5324338024F


title: 009-282-020-TP6 [5326907021D]

description:
Training_Set_Finger
5326907021D


title: 009-282-014-TP9 [5324338023G]

description:
Training_Set_Finger
5324338023G


title: 009-282-014-TP4 [5324338023I]

description:
Training_Set_Finger
5324338023I


title: 009-282-014-TP8 [5324338001H]

description:
Training_Set_Finger
5324338001H


title: 009-282-014-TP10 [5324338022I]

description:
Training_Set_Finger
5324338022I


title: 009-282-014-TP7 [5322244024D]

description:
Training_Set_Finger
5322244024D


title: 009-282-014-TP5 [5324338003C]

description:
Training_Set_Finger
5324338003C


title: 009-282-014-TP3 [5324338023B]

description:
Training_Set_Finger
5324338023B


title: 009-282-020-TP10 [5326907022K]

description:
Training_Set_Finger
5326907022K


title: 009-282-012-TP13 [5356583031C]

description:
Test_Set_Vein
5356583031C


title: 009-282-014-TP2 [5324338003H]

description:
Training_Set_Finger
5324338003H


title: 009-282-014-TP1 [5324338001F]

description:
Training_Set_Finger
5324338001F


title: 009-282-014-TP6 [5322244023D]

description:
Training_Set_Finger
5322244023D


title: 009-282-013-TP11 [5326907019D]

description:
Training_Set_Finger
5326907019D


title: 009-282-013-TP4 [5322244024K]

description:
Training_Set_Finger
5322244024K


title: 009-282-006-TP10 [5324338022E]

description:
Training_Set_Finger
5324338022E


title: 009-282-013-TP2 [5324338001L]

description:
Training_Set_Finger
5324338001L


title: 009-282-013-TP9 [5324338002D]

description:
Training_Set_Finger
5324338002D


title: 009-282-006-TP4 [5307141015L]

description:
Training_Set_Finger
5307141015L


title: 009-282-003-TP11 [5322244023G]

description:
Training_Set_Finger
5322244023G


title: 009-282-013-TP7 [5324338023E]

description:
Training_Set_Finger
5324338023E


title: 009-282-013-TP5 [5324338022H]

description:
Training_Set_Finger
5324338022H


title: 009-282-006-TP9 [5307141023C]

description:
Training_Set_Finger
5307141023C


title: 009-282-013-TP1 [5322244023H]

description:
Training_Set_Finger
5322244023H


title: 009-282-006-TP5 [5307141014A]

description:
Training_Set_Finger
5307141014A


title: 009-282-006-TP11 [5322244023B]

description:
Training_Set_Finger
5322244023B


title: 009-282-006-TP2 [5307141008D]

description:
Training_Set_Finger
5307141008D


title: 009-282-015-TP2 [5447320040D]

description:
Test_Set_Finger
5447320040D


title: 009-282-006-TP3 [5307141023F]

description:
Training_Set_Finger
5307141023F


title: 009-282-013-TP10 [5322244024H]

description:
Training_Set_Finger
5322244024H


title: 009-282-006-TP1 [5307141024A]

description:
Training_Set_Finger
5307141024A


title: 009-282-006-TP7 [5307141014H]

description:
Training_Set_Finger
5307141014H


title: 009-282-006-TP6 [5307141015G]

description:
Training_Set_Finger
5307141015G


title: 009-282-013-TP8 [5324338022D]

description:
Training_Set_Finger
5324338022D


title: 009-282-013-TP6 [5322244024J]

description:
Training_Set_Finger
5322244024J


title: 009-282-006-TP8 [5307141022G]

description:
Training_Set_Finger
5307141022G


title: 009-282-003-TP10 [5307141024B]

description:
Training_Set_Finger
5307141024B


title: 009-282-013-TP3 [5322244023K]

description:
Training_Set_Finger
5322244023K


title: 009-282-003-TP9 [5307141024C]

description:
Training_Set_Finger
5307141024C


title: 009-282-003-TP2 [5307141022C]

description:
Training_Set_Finger
5307141022C


title: 009-282-003-TP7 [5322244022K]

description:
Training_Set_Finger
5322244022K


title: 009-282-003-TP5 [5307141022B]

description:
Training_Set_Finger
5307141022B


title: 009-282-003-TP8 [5307141023G]

description:
Training_Set_Finger
5307141023G


title: 009-282-026-TP10 [5326907021B]

description:
Training_Set_Finger
5326907021B


title: 009-282-003-TP1 [5307141023I]

description:
Training_Set_Finger
5307141023I


title: 009-282-026-TP4 [5326907019K]

description:
Training_Set_Finger
5326907019K


title: 009-282-026-TP9 [5326907021G]

description:
Training_Set_Finger
5326907021G


title: 009-282-003-TP6 [5307141015E]

description:
Training_Set_Finger
5307141015E


title: 009-282-026-TP3 [5324338030K]

description:
Training_Set_Finger
5324338030K


title: 009-282-003-TP4 [5307141008I]

description:
Training_Set_Finger
5307141008I


title: 009-282-026-TP8 [5326907025H]

description:
Training_Set_Finger
5326907025H


title: 009-282-026-TP6 [5326907022C]

description:
Training_Set_Finger
5326907022C


title: 009-282-021-TP9 [5324338024L]

description:
Training_Set_Finger
5324338024L


title: 009-282-021-TP5 [5324338030H]

description:
Training_Set_Finger
5324338030H


title: 009-282-026-TP5 [5326907022G]

description:
Training_Set_Finger
5326907022G


title: 009-282-021-TP2 [5326907024E]

description:
Training_Set_Finger
5326907024E


title: 009-282-026-TP2 [5326907021J]

description:
Training_Set_Finger
5326907021J


title: 009-282-021-TP3 [5326907025J]

description:
Training_Set_Finger
5326907025J


title: 009-282-026-TP1 [5326907021L]

description:
Training_Set_Finger
5326907021L


title: 009-282-021-TP11 [5326907020K]

description:
Training_Set_Finger
5326907020K


title: 009-282-021-TP10 [5326907024I]

description:
Training_Set_Finger
5326907024I


title: 009-282-021-TP4 [5326907020F]

description:
Training_Set_Finger
5326907020F


title: 009-282-003-TP3 [5307141015D]

description:
Training_Set_Finger
5307141015D


title: 009-282-021-TP7 [5326907020G]

description:
Training_Set_Finger
5326907020G


title: 009-282-026-TP7 [5326907019F]

description:
Training_Set_Finger
5326907019F


title: 009-282-021-TP8 [5326907021F]

description:
Training_Set_Finger
5326907021F


title: 009-282-021-TP6 [5324338024E]

description:
Training_Set_Finger
5324338024E


title: 009-282-021-TP1 [5326907022E]

description:
Training_Set_Finger
5326907022E


title: 009-282-026-TP11 [5324338030A]

description:
Training_Set_Finger
5324338030A


title: 009-282-015-TP11 [5324338030D]

description:
Training_Set_Finger
5324338030D


title: 009-282-015-TP8 [5324338001B]

description:
Training_Set_Finger
5324338001B


title: 009-282-015-TP6 [5322244024L]

description:
Training_Set_Finger
5322244024L


title: 009-282-015-TP9 [5324338002F]

description:
Training_Set_Finger
5324338002F


title: 009-282-015-TP1 [5324338022L]

description:
Training_Set_Finger
5324338022L


title: 009-282-011-TP7 [5322244024A]

description:
Training_Set_Finger
5322244024A


title: 009-282-015-TP4 [5324338023D]

description:
Training_Set_Finger
5324338023D


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Training_Set_Finger
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Training_Set_Finger
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Training_Set_Finger
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Training_Set_Finger
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Training_Set_Finger
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Training_Set_Finger
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Training_Set_Finger
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Test_Set_Vein
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Test_Set_Vein
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Test_Set_Vein
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Validation_Vein
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Test_Set_Vein
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Test_Set_Vein
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title: 009-282-015-TP9 [5356583039A]

description:
Test_Set_Vein
5356583039A


title: 009-282-004-TP15 [5356583043B]

description:
Test_Set_Vein
5356583043B


title: 009-282-011-TP9 [5356583034H]

description:
Test_Set_Vein
5356583034H


title: 009-282-004-TP14 [5356583034F]

description:
Test_Set_Vein
5356583034F


title: 009-282-004-TP12 [5356583032G]

description:
Test_Set_Vein
5356583032G


title: 009-282-007-TP7 [5356583030D]

description:
Test_Set_Vein
5356583030D


title: 009-282-004-TP13 [5356583037D]

description:
Test_Set_Vein
5356583037D


title: 009-282-004-TP7 [5356583035I]

description:
Test_Set_Vein
5356583035I


title: 009-282-004-TP9 [5356583045A]

description:
Test_Set_Vein
5356583045A


title: 009-282-024-TP14 [5356583049H]

description:
Test_Set_Vein
5356583049H


title: 009-282-004-TP2 [5356583040I]

description:
Test_Set_Vein
5356583040I


title: 009-282-024-TP15 [5356583038B]

description:
Test_Set_Vein
5356583038B


title: 009-282-024-TP12 [5356583035K]

description:
Test_Set_Vein
5356583035K


title: 009-282-004-TP1 [5356583040E]

description:
Test_Set_Vein
5356583040E


title: 009-282-024-TP13 [5356583039J]

description:
Test_Set_Vein
5356583039J


title: 009-282-022-TP15 [5356583045L]

description:
Test_Set_Vein
5356583045L


title: 009-282-022-TP2 [5356583037I]

description:
Test_Set_Vein
5356583037I


title: 009-282-022-TP7 [5356583036I]

description:
Test_Set_Vein
5356583036I


title: 009-282-022-TP14 [5356583042B]

description:
Test_Set_Vein
5356583042B


title: 009-282-022-TP9 [5356583040G]

description:
Test_Set_Vein
5356583040G


title: 009-282-024-TP1 [5356583044D]

description:
Test_Set_Vein
5356583044D


title: 009-282-022-TP13 [5356583031J]

description:
Test_Set_Vein
5356583031J


title: 009-282-018-TP13 [5356583041H]

description:
Test_Set_Vein
5356583041H


title: 009-282-022-TP12 [5356583032I]

description:
Test_Set_Vein
5356583032I


title: 009-282-024-TP9 [5356583043L]

description:
Test_Set_Vein
5356583043L


title: 009-282-018-TP1 [5356583036C]

description:
Test_Set_Vein
5356583036C


title: 009-282-010-TP14 [5356583042E]

description:
Test_Set_Vein
5356583042E


title: 009-282-024-TP2 [5356583039B]

description:
Test_Set_Vein
5356583039B


title: 009-282-022-TP1 [5356583043A]

description:
Test_Set_Vein
5356583043A


title: 009-282-010-TP12 [5356583034C]

description:
Test_Set_Vein
5356583034C


title: 009-282-018-TP15 [5356583041D]

description:
Test_Set_Vein
5356583041D


title: 009-282-010-TP13 [5356583045F]

description:
Test_Set_Vein
5356583045F


title: 009-282-018-TP14 [5356583038L]

description:
Test_Set_Vein
5356583038L


title: 009-282-018-TP12 [5356583034E]

description:
Test_Set_Vein
5356583034E


title: 009-282-018-TP7 [5356583049I]

description:
Test_Set_Vein
5356583049I


title: 009-282-018-TP9 [5356583035H]

description:
Test_Set_Vein
5356583035H


title: 009-282-024-TP7 [5356583049K]

description:
Test_Set_Vein
5356583049K


title: 009-282-010-TP15 [5356583039C]

description:
Test_Set_Vein
5356583039C


title: 009-282-018-TP2 [5356583042A]

description:
Test_Set_Vein
5356583042A


title: 009-282-010-TP7 [5356583045J]

description:
Test_Set_Vein
5356583045J


title: 009-282-010-TP2 [5356583045K]

description:
Test_Set_Vein
5356583045K


title: 009-282-008-TP15 [5356583031K]

description:
Test_Set_Vein
5356583031K


title: 009-282-008-TP14 [5356583042C]

description:
Test_Set_Vein
5356583042C


title: 009-282-010-TP9 [5356583039D]

description:
Test_Set_Vein
5356583039D


title: 009-282-008-TP9 [5356583040F]

description:
Test_Set_Vein
5356583040F


title: 009-282-008-TP7 [5356583030H]

description:
Test_Set_Vein
5356583030H


title: 009-282-010-TP1 [5356583030L]

description:
Test_Set_Vein
5356583030L


title: 009-282-001-TP9 [5356583049D]

description:
Test_Set_Vein
5356583049D


title: 009-282-008-TP1 [5356583036E]

description:
Test_Set_Vein
5356583036E


title: 009-282-001-TP13 [5356583038G]

description:
Test_Set_Vein
5356583038G


title: 009-282-008-TP2 [5356583039L]

description:
Test_Set_Vein
5356583039L


title: BAYVAC018T9 [5368138017I]

description:
Training_Set_Vein
5368138017I

value: saline

value: Not Hispanic or Latino


title: 009-282-001-TP7 [5356583031A]

description:
Test_Set_Vein
5356583031A


title: 009-282-001-TP14 [5356583049C]

description:
Test_Set_Vein
5356583049C


title: BAYVAC018T8 [5376074009J]

description:
Training_Set_Vein
5376074009J


title: 009-282-001-TP2 [5356583041E]

description:
Test_Set_Vein
5356583041E


title: 009-282-001-TP15 [5356583044C]

description:
Test_Set_Vein
5356583044C


title: 009-282-008-TP13 [5356583034L]

description:
Test_Set_Vein
5356583034L


title: 009-282-001-TP12 [5356583040D]

description:
Test_Set_Vein
5356583040D


title: 009-282-008-TP12 [5356583040K]

description:
Test_Set_Vein
5356583040K


title: BAYVAC018T4 [5368138025G]

description:
Training_Set_Vein
5368138025G


title: BAYVAC018T7 [5368138047I]

description:
Training_Set_Vein
5368138047I


title: BAYVAC013T8 [5368138042B]

description:
Training_Set_Vein
5368138042B


title: BAYVAC018T3 [5368138026D]

description:
Training_Set_Vein
5368138026D


title: BAYVAC013T7 [5368138039B]

description:
Training_Set_Vein
5368138039B


title: 009-282-001-TP1 [5356583035D]

description:
Test_Set_Vein
5356583035D


title: BAYVAC018T2 [5368138046D]

description:
Training_Set_Vein
5368138046D


title: BAYVAC018T5 [5376074009H]

description:
Training_Set_Vein
5376074009H


title: BAYVAC018T0 [5376074001F]

description:
Training_Set_Vein
5376074001F


title: BAYVAC013T9 [5368138046H]

description:
Training_Set_Vein
5368138046H


title: BAYVAC013T4 [5376074001D]

description:
Training_Set_Vein
5376074001D


title: BAYVAC013T5 [5376074001K]

description:
Training_Set_Vein
5376074001K


title: BAYVAC013T6 [5368138047E]

description:
Training_Set_Vein
5368138047E


title: BAYVAC018T6 [5368138039C]

description:
Training_Set_Vein
5368138039C


title: BAYVAC013T2 [5368138041K]

description:
Training_Set_Vein
5368138041K


title: BAYVAC006T3 [5368138047B]

description:
Training_Set_Vein
5368138047B


title: BAYVAC013T0 [5368138041L]

description:
Training_Set_Vein
5368138041L


title: BAYVAC006T5 [5368138018E]

description:
Training_Set_Vein
5368138018E


title: BAYVAC006T4 [5368138026B]

description:
Training_Set_Vein
5368138026B


title: BAYVAC005T4 [5368138046J]

description:
Training_Set_Vein
5368138046J


title: BAYVAC006T6 [5368138046B]

description:
Training_Set_Vein
5368138046B


title: BAYVAC005T9 [5368138018I]

description:
Training_Set_Vein
5368138018I


title: BAYVAC005T7 [5368138047K]

description:
Training_Set_Vein
5368138047K


title: BAYVAC003T7 [5368138041C]

description:
Training_Set_Vein
5368138041C


title: BAYVAC006T9 [5368138041A]

description:
Training_Set_Vein
5368138041A


title: BAYVAC005T8 [5368138017L]

description:
Training_Set_Vein
5368138017L


title: BAYVAC013T3 [5368138056G]

description:
Training_Set_Vein
5368138056G


title: BAYVAC005T2 [5376074001C]

description:
Training_Set_Vein
5376074001C


title: BAYVAC003T8 [5368138042H]

description:
Training_Set_Vein
5368138042H


title: BAYVAC006T0 [5376074001G]

description:
Training_Set_Vein
5376074001G


title: BAYVAC003T6 [5368138027H]

description:
Training_Set_Vein
5368138027H


title: BAYVAC006T7 [5376074009K]

description:
Training_Set_Vein
5376074009K


title: BAYVAC005T5 [5368138042I]

description:
Training_Set_Vein
5368138042I


title: BAYVAC003T3 [5368138017J]

description:
Training_Set_Vein
5368138017J


title: BAYVAC005T3 [5368138026F]

description:
Training_Set_Vein
5368138026F


title: BAYVAC005T6 [5368138027A]

description:
Training_Set_Vein
5368138027A


title: BAYVAC003T9 [5368138026L]

description:
Training_Set_Vein
5368138026L


title: BAYVAC006T8 [5376074009E]

description:
Training_Set_Vein
5376074009E


title: BAYVAC003T2 [5368138040L]

description:
Training_Set_Vein
5368138040L


title: BAYVAC005T0 [5368138041I]

description:
Training_Set_Vein
5368138041I


title: BAYVAC003T0 [5376074001L]

description:
Training_Set_Vein
5376074001L


title: BAYVAC003T4 [5368138040C]

description:
Training_Set_Vein
5368138040C


title: BAYVAC003T5 [5376074009F]

description:
Training_Set_Vein
5376074009F


title: BAYVAC001T8 [5368138027G]

description:
Training_Set_Vein
5368138027G


title: BAYVAC001T7 [5368138039H]

description:
Training_Set_Vein
5368138039H


title: BAYVAC001T3 [5368138041B]

description:
Training_Set_Vein
5368138041B


title: BAYVAC001T5 [5368138026I]

description:
Training_Set_Vein
5368138026I


title: BAYVAC001T6 [5368138018A]

description:
Training_Set_Vein
5368138018A


title: BAYVAC001T9 [5368138056J]

description:
Training_Set_Vein
5368138056J


title: BAYVAC001T0 [5376074009G]

description:
Training_Set_Vein
5376074009G


title: BAYVAC025T7 [5368138027I]

description:
Training_Set_Vein
5368138027I

value: Flu


title: BAYVAC001T2 [5376074009I]

description:
Training_Set_Vein
5376074009I

value: Vein


title: BAYVAC001T4 [5368138017G]

description:
Training_Set_Vein
5368138017G


title: BAYVAC024T9 [5368138025E]

description:
Training_Set_Vein
5368138025E

value: M


title: BAYVAC025T5 [5368138047L]

description:
Training_Set_Vein
5368138047L


title: BAYVAC025T8 [5368138047C]

description:
Training_Set_Vein
5368138047C


title: BAYVAC025T0 [5368138039L]

description:
Training_Set_Vein
5368138039L


title: BAYVAC024T7 [5368138026H]

description:
Training_Set_Vein
5368138026H


title: BAYVAC025T6 [5368138039D]

description:
Training_Set_Vein
5368138039D


title: BAYVAC025T2 [5376074001I]

description:
Training_Set_Vein
5376074001I


title: BAYVAC024T2 [5368138047H]

description:
Training_Set_Vein
5368138047H


title: BAYVAC024T8 [5376074001B]

description:
Training_Set_Vein
5376074001B


title: BAYVAC025T3 [5368138042D]

description:
Training_Set_Vein
5368138042D


title: BAYVAC023T8 [5368138027K]

description:
Training_Set_Vein
5368138027K

value: Caucasian


title: BAYVAC023T7 [5376074009B]

description:
Training_Set_Vein
5376074009B


title: BAYVAC024T4 [5368138025F]

description:
Training_Set_Vein
5368138025F


title: BAYVAC024T0 [5368138039K]

description:
Training_Set_Vein
5368138039K


title: BAYVAC024T5 [5368138056I]

description:
Training_Set_Vein
5368138056I


title: BAYVAC023T6 [5368138018C]

description:
Training_Set_Vein
5368138018C


title: BAYVAC025T4 [5376074001E]

description:
Training_Set_Vein
5376074001E


title: BAYVAC024T6 [5368138039J]

description:
Training_Set_Vein
5368138039J


title: BAYVAC025T9 [5376074001A]

description:
Training_Set_Vein
5376074001A


title: BAYVAC024T3 [5368138040E]

description:
Training_Set_Vein
5368138040E


title: BAYVAC023T2 [5368138018F]

description:
Training_Set_Vein
5368138018F


title: BAYVAC023T5 [5368138046K]

description:
Training_Set_Vein
5368138046K


title: BAYVAC023T4 [5368138039F]

description:
Training_Set_Vein
5368138039F


title: BAYVAC023T3 [5368138018G]

description:
Training_Set_Vein
5368138018G


title: BAYVAC022T9 [5368138039G]

description:
Training_Set_Vein
5368138039G


title: BAYVAC023T9 [5376074001H]

description:
Training_Set_Vein
5376074001H


title: BAYVAC022T5 [5368138040H]

description:
Training_Set_Vein
5368138040H


title: BAYVAC023T0 [5368138046G]

description:
Training_Set_Vein
5368138046G


title: BAYVAC022T4 [5368138039A]

description:
Training_Set_Vein
5368138039A


title: BAYVAC022T3 [5368138046L]

description:
Training_Set_Vein
5368138046L


title: BAYVAC022T6 [5376074009C]

description:
Training_Set_Vein
5376074009C


title: BAYVAC022T7 [5368138041J]

description:
Training_Set_Vein
5368138041J


title: BAYVAC022T8 [5368138040D]

description:
Training_Set_Vein
5368138040D


title: BAYVAC022T0 [5368138046A]

description:
Training_Set_Vein
5368138046A


title: BAYVAC021T9 [5368138025I]

description:
Training_Set_Vein
5368138025I


title: BAYVAC022T2 [5368138017C]

description:
Training_Set_Vein
5368138017C


title: BAYVAC021T6 [5368138047D]

description:
Training_Set_Vein
5368138047D


title: BAYVAC021T5 [5368138042E]

description:
Training_Set_Vein
5368138042E


title: BAYVAC020T6 [5368138027L]

description:
Training_Set_Vein
5368138027L


title: BAYVAC020T9 [5368138026E]

description:
Training_Set_Vein
5368138026E


title: BAYVAC021T3 [5368138018B]

description:
Training_Set_Vein
5368138018B


title: BAYVAC021T8 [5368138025H]

description:
Training_Set_Vein
5368138025H


title: BAYVAC021T4 [5368138056D]

description:
Training_Set_Vein
5368138056D


title: BAYVAC021T7 [5368138025K]

description:
Training_Set_Vein
5368138025K


title: BAYVAC021T0 [5368138042J]

description:
Training_Set_Vein
5368138042J


title: BAYVAC018T9 [4835507058A]

description:
Training_Set_Vein
4835507058A

value: Saline


title: BAYVAC020T8 [5368138056A]

description:
Training_Set_Vein
5368138056A


title: BAYVAC021T2 [5368138017A]

description:
Training_Set_Vein
5368138017A


title: BAYVAC020T7 [5368138042K]

description:
Training_Set_Vein
5368138042K


title: BAYVAC020T5 [5368138017B]

description:
Training_Set_Vein
5368138017B


title: BAYVAC020T4 [5368138027B]

description:
Training_Set_Vein
5368138027B


title: BAYVAC018T8 [4835507051J]

description:
Training_Set_Vein
4835507051J


title: BAYVAC020T3 [5368138047G]

description:
Training_Set_Vein
5368138047G


title: BAYVAC018T7 [4835507054B]

description:
Training_Set_Vein
4835507054B


title: BAYVAC020T0 [5368138041H]

description:
Training_Set_Vein
5368138041H


title: BAYVAC020T2 [5368138018D]

description:
Training_Set_Vein
5368138018D


title: BAYVAC018T0 [4835507049G]

description:
Training_Set_Vein
4835507049G


title: BAYVAC018T6 [4853887040J]

description:
Training_Set_Vein
4853887040J


title: BAYVAC018T5 [4835507049E]

description:
Training_Set_Vein
4835507049E


title: BAYVAC013T9 [4835507056D]

description:
Training_Set_Vein
4835507056D


title: BAYVAC018T3 [4835507045J]

description:
Training_Set_Vein
4835507045J


title: BAYVAC013T8 [4835507053A]

description:
Training_Set_Vein
4835507053A


title: BAYVAC013T3 [4835507059F]

description:
Training_Set_Vein
4835507059F


title: BAYVAC018T2 [4835507041B]

description:
Training_Set_Vein
4835507041B


title: BAYVAC013T5 [4853887042B]

description:
Training_Set_Vein
4853887042B


title: BAYVAC013T6 [4835507044J]

description:
Training_Set_Vein
4835507044J


title: BAYVAC013T2 [4835507059K]

description:
Training_Set_Vein
4835507059K


title: BAYVAC013T7 [4835507058D]

description:
Training_Set_Vein
4835507058D


title: BAYVAC018T4 [4835507052H]

description:
Training_Set_Vein
4835507052H


title: BAYVAC013T4 [4835507051I]

description:
Training_Set_Vein
4835507051I


title: BAYVAC013T0 [4835507056F]

description:
Training_Set_Vein
4835507056F


title: BAYVAC005T9 [4835507045I]

description:
Training_Set_Vein
4835507045I


title: BAYVAC006T6 [4856050004D]

description:
Training_Set_Vein
4856050004D


title: BAYVAC006T7 [4853887046B]

description:
Training_Set_Vein
4853887046B


title: BAYVAC005T8 [4835507045L]

description:
Training_Set_Vein
4835507045L


title: BAYVAC006T0 [4835507044K]

description:
Training_Set_Vein
4835507044K


title: BAYVAC006T4 [4835507053J]

description:
Training_Set_Vein
4835507053J


title: BAYVAC005T7 [4853887046E]

description:
Training_Set_Vein
4853887046E


title: BAYVAC005T5 [4835507059L]

description:
Training_Set_Vein
4835507059L


title: BAYVAC005T4 [4853887042F]

description:
Training_Set_Vein
4853887042F


title: BAYVAC006T8 [4835507052L]

description:
Training_Set_Vein
4835507052L


title: BAYVAC003T9 [4835507056J]

description:
Training_Set_Vein
4835507056J


title: BAYVAC006T3 [4835507053C]

description:
Training_Set_Vein
4835507053C


title: BAYVAC006T9 [4835507044I]

description:
Training_Set_Vein
4835507044I


title: BAYVAC003T3 [4835507058G]

description:
Training_Set_Vein
4835507058G


title: BAYVAC005T3 [4835507056C]

description:
Training_Set_Vein
4835507056C


title: BAYVAC005T0 [4853887042D]

description:
Training_Set_Vein
4853887042D


title: BAYVAC006T5 [4835507056K]

description:
Training_Set_Vein
4835507056K


title: BAYVAC005T6 [4835507054D]

description:
Training_Set_Vein
4835507054D


title: BAYVAC001T9 [4835507042F]

description:
Training_Set_Vein
4835507042F


title: BAYVAC003T2 [4835507054I]

description:
Training_Set_Vein
4835507054I


title: BAYVAC003T6 [4835507051K]

description:
Training_Set_Vein
4835507051K


title: BAYVAC001T7 [4853887047A]

description:
Training_Set_Vein
4853887047A


title: BAYVAC003T7 [4835507053L]

description:
Training_Set_Vein
4835507053L


title: BAYVAC001T8 [4856050004C]

description:
Training_Set_Vein
4856050004C


title: BAYVAC001T4 [4853887040D]

description:
Training_Set_Vein
4853887040D


title: BAYVAC001T6 [4853887040F]

description:
Training_Set_Vein
4853887040F


title: BAYVAC003T5 [4835507042B]

description:
Training_Set_Vein
4835507042B


title: BAYVAC016T8 [4856050004I]

description:
Training_Set_Vein
4856050004I


title: BAYVAC001T0 [4853887047D]

description:
Training_Set_Vein
4853887047D


title: BAYVAC003T0 [4835507042C]

description:
Training_Set_Vein
4835507042C


title: BAYVAC001T2 [4835507042J]

description:
Training_Set_Vein
4835507042J


title: BAYVAC003T8 [4835507051A]

description:
Training_Set_Vein
4835507051A


title: BAYVAC016T9 [4835507041I]

description:
Training_Set_Vein
4835507041I


title: BAYVAC005T2 [4853887040H]

description:
Training_Set_Vein
4853887040H


title: BAYVAC003T4 [4835507041D]

description:
Training_Set_Vein
4835507041D


title: BAYVAC001T5 [4835507058F]

description:
Training_Set_Vein
4835507058F


title: BAYVAC001T3 [4835507051H]

description:
Training_Set_Vein
4835507051H


title: BAYVAC016T5 [4853887047H]

description:
Training_Set_Vein
4853887047H


title: BAYVAC016T3 [4835507053K]

description:
Training_Set_Vein
4835507053K


title: BAYVAC016T4 [4835507058B]

description:
Training_Set_Vein
4835507058B


title: BAYVAC016T2 [4853887046G]

description:
Training_Set_Vein
4853887046G


title: BAYVAC016T7 [4835507044G]

description:
Training_Set_Vein
4835507044G


title: BAYVAC016T6 [4853887046H]

description:
Training_Set_Vein
4853887046H


title: BAYVAC016T0 [4853887042A]

description:
Training_Set_Vein
4853887042A


title: BAYVAC015T9 [4835507053B]

description:
Training_Set_Vein
4835507053B


title: BAYVAC015T4 [4835507042E]

description:
Training_Set_Vein
4835507042E


title: BAYVAC012T9 [4835507058C]

description:
Training_Set_Vein
4835507058C


title: BAYVAC015T7 [4835507045K]

description:
Training_Set_Vein
4835507045K


title: BAYVAC015T0 [4835507056L]

description:
Training_Set_Vein
4835507056L


title: BAYVAC015T6 [4835507054E]

description:
Training_Set_Vein
4835507054E


title: BAYVAC012T8 [4835507051G]

description:
Training_Set_Vein
4835507051G


title: BAYVAC015T2 [4835507042H]

description:
Training_Set_Vein
4835507042H


title: BAYVAC015T5 [4835507052C]

description:
Training_Set_Vein
4835507052C


title: BAYVAC012T3 [4835507056G]

description:
Training_Set_Vein
4835507056G


title: BAYVAC012T0 [4835507051L]

description:
Training_Set_Vein
4835507051L


title: BAYVAC015T3 [4853887047G]

description:
Training_Set_Vein
4853887047G


title: BAYVAC015T8 [4835507045E]

description:
Training_Set_Vein
4835507045E


title: BAYVAC010T8 [4853887042E]

description:
Training_Set_Vein
4853887042E


title: BAYVAC012T4 [4853887046D]

description:
Training_Set_Vein
4853887046D


title: BAYVAC010T4 [4835507049A]

description:
Training_Set_Vein
4835507049A


title: BAYVAC010T7 [4835507059I]

description:
Training_Set_Vein
4835507059I


title: BAYVAC010T5 [4835507044F]

description:
Training_Set_Vein
4835507044F


title: BAYVAC012T2 [4835507054J]

description:
Training_Set_Vein
4835507054J


title: BAYVAC010T2 [4835507045H]

description:
Training_Set_Vein
4835507045H


title: BAYVAC010T9 [4853887040A]

description:
Training_Set_Vein
4853887040A


title: BAYVAC010T3 [4835507059B]

description:
Training_Set_Vein
4835507059B


title: BAYVAC012T7 [4835507041A]

description:
Training_Set_Vein
4835507041A


title: BAYVAC012T5 [4835507042K]

description:
Training_Set_Vein
4835507042K


title: BAYVAC010T0 [4835507052B]

description:
Training_Set_Vein
4835507052B


title: BAYVAC010T6 [4835507059J]

description:
Training_Set_Vein
4835507059J


title: BAYVAC009T9 [4835507045D]

description:
Training_Set_Vein
4835507045D


title: BAYVAC009T8 [4835507044D]

description:
Training_Set_Vein
4835507044D


title: BAYVAC012T6 [4835507049H]

description:
Training_Set_Vein
4835507049H


title: BAYVAC009T7 [4835507053H]

description:
Training_Set_Vein
4835507053H


title: BAYVAC009T4 [4835507049J]

description:
Training_Set_Vein
4835507049J


title: BAYVAC009T6 [4853887046L]

description:
Training_Set_Vein
4853887046L


title: BAYVAC002T7 [4853887047E]

description:
Training_Set_Vein
4853887047E


title: BAYVAC002T4 [4853887047C]

description:
Training_Set_Vein
4853887047C


title: BAYVAC002T8 [4835507041H]

description:
Training_Set_Vein
4835507041H


title: BAYVAC009T5 [4853887042G]

description:
Training_Set_Vein
4853887042G


title: BAYVAC002T0 [4835507041F]

description:
Training_Set_Vein
4835507041F


title: BAYVAC009T0 [4856050004G]

description:
Training_Set_Vein
4856050004G


title: BAYVAC009T3 [4835507051B]

description:
Training_Set_Vein
4835507051B


title: BAYVAC002T5 [4835507042G]

description:
Training_Set_Vein
4835507042G


title: BAYVAC009T2 [4853887046F]

description:
Training_Set_Vein
4853887046F


title: BAYVAC002T6 [4853887040C]

description:
Training_Set_Vein
4853887040C


title: BAYVAC002T2 [4835507052A]

description:
Training_Set_Vein
4835507052A


title: LS_maternal_rep2

status: Public on Mar 26 2013

source_name: Lateral septum, lactating maternal adult female mouse

growth_protocol: The strain of mice used was outbred hsd:ICR mice purchased from Harlan labs (Madison, WI).  Maternal mice and pups removed mice were housed with a breeder male for two weeks while virgin mice were co-housed with 2 other female mice for the same time period.  After two weeks, the females from all three groups were individually housed.

treatment_protocol: On postpartum day 0, pups were culled, if necessary, to standardize litter size to 11.  For females in the pups removed group, pups were removed from the cage on pospartum day 2.

value: Microdissected lateral septum

value: Outbred hsd:ICR

value: Lactating maternal


title: LS_maternal_rep4


title: BAYVAC002T9 [4835507054C]

description:
Training_Set_Vein
4835507054C


title: BAYVAC002T3 [4835507049K]

description:
Training_Set_Vein
4835507049K


title: LS_virgin_rep5

source_name: Lateral septum, virgin adult female mouse

value: Virgin


title: LS_maternal_rep3


title: LS_virgin_rep4


title: LS_maternal_rep5


title: LS_maternal_rep1


title: LS_pupsremoved_rep4

source_name: Lateral septum, postpartum adult female mouse with pups removed

value: Postpartum, pups removed


title: LS_pupsremoved_rep2


title: LS_pupsremoved_rep6


title: LS_pupsremoved_rep3


title: LS_pupsremoved_rep1


title: LS_pupsremoved_rep5


title: LS_maternal_rep6


title: LS_virgin_rep3


title: PU.1_UT

status: Public on Jan 17 2013

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

description: Chromatin IP against PU.1

data_processing:
Reads quality filtered according to the Illumina pipeline
Reads were mapped to the mouse mm9 genome using Bowtie 0.12.7 (PMID: 19261174). All reads with a unique match to the genome with two or fewer mismatches were retained.
Peak calling was performed using MACS 1.4 (PMID 18798982) with default parameters and bw=100 (except for the pol_II for which a bw=300 was used). Each IP was compared to input DNA derived from BMDM (GSM487453).
Genome_build: mm9 (NCBI Build 37)
Supplementary_files_format_and_content: *_peaks.bed, list of the peaks called by MACS

source_name: Primary bone marrow-derived macrophages (BMDM)

growth_protocol: Bone marrow cells isolated from C57BL/6 mice were plated in 10 cm plates in 5ml of BM-medium (high glucose DMEM supplemented with 20% low endotoxin fetal bovine serum, 30% L929-conditioned medium, 1% glutamine, 1%, Pen/Strep, 0.5% Sodium Pyruvate, 0.1% β-mercaptoethanol). Cultures were fed with 2.5 ml of fresh medium every two days.

extract_protocol: ChIP lysates were generated from 2x10^8 cells. Cells were fixed in 1% formaldehyde for 10min.  Lysate was immunoprecipitated with 10ug of antibody. Antibodies were pre-bound overnight to 100ul of G protein-coupled paramagnetic beads in PBS/BSA 0.5%. Beads were then added to lysates (the preclearing step was omitted) and incubation was let to proceed overnight. Beads were washed 6 times in a modified RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and once in TE containing 50mM NaCl. DNA was eluted in TE containing 2% SDS and crosslinks reversed by incubation overnight at 65ºC. DNA was then purified by Qiaquick columns (Qiagen) and quantified using PicoGreen (Invitrogen). ChIP DNA was prepared for HiSeq 2000 Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection on gel and PCR with index primers. A mixture of T4 DNA polymerase, DNA polymerase I and T4 kinase was used according to manufacturer’s instruction. Library preparation is carried out on SPRIworks Fragment Library System.

treatment_protocol: Macrophages were subjected to different treatment (see individual samples for details)

tag: cell type

value: BMDM cells (7th day of differentiation)

value: Anti-PU.1 (in-house rabbit polyclonal against the N-Terminal (aa. 1-100))

tag: treatment

value: No treatment


title: H3K27ac_UT

description: Chromatin IP against H3K27ac

value: Anti-H3K27ac (Abcam # ab4729)


title: BMDM cells No treatment

data_processing:
Reads were quality filtered according to the Illumina pipeline
Reads were mapped to the mouse mm9 genome and transcripts using TopHat 1.3.1 (PMID: 19289445), allowing up to two mismatches and with a mean distance between pairs (-r) of 250bp
Transcripts abundance were quantified using Cufflinks 1.2.1 (PMID: 20436464)
Differentially expressed genes were called using Cuffdiff 1.2.1 (PMID: 20436464)
Genome_build: mm9 (NCBI Build 37), transcripts from Mus Musculus Ensembl Build 63
Supplementary_files_format_and_content: *.fpkm_tracking list the absolute value of expression (FPKM), *.diff list the statistics for differential expression compared to the untreated (refer to http://cufflinks.cbcb.umd.edu/manual.html for details)

extract_protocol: The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. 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 reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single A base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library.


title: LS_virgin_rep1


title: LS_virgin_rep2


title: LS_virgin_rep6


title: Osteoclastogenic cell line_stimulated RANKL_2 days_rep1

status: Public on Jan 29 2013

city: Toroto

first: Maayan

last: Inger

address: Fitzgerald Building 150 College Street, Room 221

description: H10 (1)

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: Expression Console

source_name: H10_RANKL stimulated_2 days

label_protocol: Ambion WT kit

growth_protocol: cells were plated on 60 mm tissue culture dishes at a density of 0.5 million  in a culture medium consisting of 8 ml of Dulbecco's Modified Eagle Medium (DMEM, Life Technologies, Grand Island, NY, USA) supplemented with 10% Fetal Bovine Serum (FBS) and 10% antibiotics (164 IU/mL of penicillin G, 50 mg/ml of gentamicin, and 0.25 mg/ml of fungizone).

extract_protocol: Qiagen RNeasy Minikit, Germantown, MD, USA

treatment_protocol: cells were stimulated for 2 days with purified recombinant RANKL (60ng/ml)

tag: cell line

value: osteoclastogenic cells

tag: stimuated with

value: purified recombinant RANKL (60ng/ml) for 2 days


title: Non Osteoclastogenic cell line_stimulated RANKL_2 days_rep3

description: C8 (3)

source_name: C8_RANKL stimulated_2 days

value: non-osteoclastogenic cells


title: Osteoclastogenic cell line_stimulated RANKL_2 days_rep2

description: H10 (2)


title: Osteoclastogenic cell line_stimulated RANKL_2 days_rep3

description: H10 (3)


title: Non Osteoclastogenic cell line_stimulated RANKL_2 days_rep2

description: C8 (2)


title: Mc3T3 AA_ 5day_rep2

status: Public on May 02 2012

first: Noushin

last: Nabavi

address: 1265 Military Trail

description:
Mc3T3-E1_T1-2
MOE4302_042809H_RH4_AA2
Gene expression data from Mc3T3-E1 cells stimulated with AA for 5 days

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Mouse MOE430 2.0 array.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000.

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. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Mc3T3 cells_treated with AA_5 days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: MC3T3-E1 subclone 4 was obtained from American Type Culture Collection (ATCC). The MC3T3-E1 steoblastic cell line was routinely cultured in α-MEM supplemented with heat inactivated 10% FBS and incubated in a humidified atmosphere at 37oC with 5% CO2.

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

treatment_protocol: MC3T3-E1 OB cells grown in 6-well plates and either left untreated or treated with 50 micrograms of Ascorbic Acid (AA) for 5 days.  Media was replenished every 2nd day.

value: osteoblastic cells

tag: treated with

value: 50µg of Ascorbic Acid (AA) for 5 days


title: Non Osteoclastogenic cell line_stimulated RANKL_2 days_rep1

description: C8 (1)


title: Mc3T3 control_ 5day_rep3

description:
Mc3T3-E1_T0-3
MOE4302_042809H_RH5_Ctl3
Gene expression data from control Mc3T3-E1 cells

source_name: Mc3T3_untreated_5 days


title: BC5486

status: Public on Oct 11 2011

city: Köln

first: Karsten

middle: Ernst

last: Weber

address: Nattermannallee 1

institute: Sividon Diagnostics GmbH

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 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. The trimmed mean target intensity of each array was set to 500.

source_name: primary breast cancer sample, fresh-frozen

label_protocol: from 5 µg total RNA, labeled cRNA was prepared using the Roche Microarray cDNA Synthesis, Microarray RNA Target Synthesis (T7) and Microarray Target Purification Kit (Roche Applied Science, Mannheim, Germany), according to the manufacturer’s instructions

growth_protocol: primary tumor tissue, fresh-frozen after surgery

extract_protocol: RNeasy kit, Qiagen. according to the manufacturer's instructions

tag: center/subcohort

value: Mainz

tag: metastasis (1

value: yes, 0:no/censored):1

tag: metastasis free interval (months)

tag: tumor size

tag: positive lymph nodes

tag: adjuvant patient treatment

value: Tamoxifen


title: BC5476

value: unknown


title: BC5472

value: yes, 0:no/censored):0


title: BC5491


title: BC5496


title: BC5480


title: BC5475


title: BC5493


title: BC5490


title: BC5600


title: Mc3T3 control_ 5day_rep1

description:
Mc3T3-E1_T0-1
MOE4302_042809H_RH1_Ctl1
Gene expression data from control Mc3T3-E1 cells


title: BC5470


title: BC5488


title: Mc3T3 AA_ 5day_rep1

description:
Mc3T3-E1_T1-1
MOE4302_042809H_RH2_AA1
Gene expression data from Mc3T3-E1 cells stimulated with AA for 5 days


title: BC5489


title: BC5482


title: Mc3T3 AA_ 5day_rep3

description:
Mc3T3-E1_T1-3
MOE4302_042809H_RH6_AA3
Gene expression data from Mc3T3-E1 cells stimulated with AA for 5 days


title: BC5468


title: BC5602


title: Mc3T3 control_ 5day_rep2

description:
Mc3T3-E1_T0-2
MOE4302_042809H_RH3_Ctl2
Gene expression data from control Mc3T3-E1 cells


title: BC5466


title: BC5463


title: BC5461


title: BC5462


title: BC5460


title: BC5453


title: BC5455


title: BC5446


title: BC5447


title: BC5456


title: BC5458


title: BC5451


title: BC5459


title: BC5444


title: BC5445


title: BC5464


title: BC5437


title: BC5441


title: BC5443


title: BC5429


title: BC5438


title: BC5452


title: BC5436


title: BC5457


title: BC5432


title: BC5434


title: BC5430


title: BC5431


title: BC5449


title: BC5427


title: BC5440


title: BC5422


title: BC5424


title: BC5425


title: BC5426


title: BC5418


title: BC5417


title: BC5414


title: BC5420


title: BC5415


title: BC5416


title: BC5413


title: BC5408


title: BC5407


title: BC5404


title: BC5412


title: BC5401


title: BC5392


title: BC5411


title: BC5410


title: BC5391


title: BC5400


title: BC5394


title: BC5397


title: BC5398


title: BC5390


title: BC5399


title: BC5395


title: BC5393


title: BC5385


title: BC5383


title: BC5379


title: BC5389


title: BC5406


title: BC5402


title: BC5377


title: BC5387


title: BC5388


title: BC5373


title: BC5371


title: BC5380


title: BC5378


title: BC5372


title: BC5376


title: BC5374


title: BC5386


title: BC5369


title: BC5384


title: BC5355


title: BC5370


title: BC5360


title: BC5375


title: BC5364


title: BC5368


title: BC5365


title: BC5362


title: BC5358


title: BC5359


title: BC5367


title: BC5350


title: BC5353


title: BC5357


title: BC5356


title: BC5352


title: BC5351


title: BC5354


title: BC5366


title: BC5349


title: BC5421


title: BC5347


title: BC5348


title: BC5346


title: BC5345


title: BC5343


title: BC5342


title: BC5330


title: BC5396


title: BC5327


title: BC5337


title: BC5315


title: BC5335