title: Bcells_DNaselHS

description: double strands

source_name: Bcells DNasel

growth_protocol: CD19+ IgM+ cells were isolated from C57/Bl6 spleen by FACS.

value: Splenic CD19+IgM+ B cells


title: genomic DNA from CD34+38- of AML patient SU001

status: Public on Oct 01 2015

type: genomic

city: Baltimore

first: Andrew

last: Feinberg

state: MD

address: 855 N. Wolfe St., Rangos 570

department: Medicine

country: USA

institute: Johns Hopkins University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan using standard recommended Illumina scanner setting

data_processing: Minfi v1.8.9; beta values not normalized

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: CD34+38- of AML patient

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from AML and normal bone marrow samples using Epicentre Kit according to standard instructions

tag: subject id

tag: subject status

value: AML

tag: gender

value: female

tag: phenotype

value: BLAST (blast cells)


title: AT cell D6 5665175063_A

status: Public on Apr 15 2013

type: RNA

city: Duarte

first: Crystal

middle: N

last: Marconett

email: cmarcone@usc.edu, cmarconett@coh.org

state: CA

address: 1500 E Duarte Rd

department: Integrative Translational Sciences

institute: City of Hope

description: AT cell D6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: BeadStudio was used to convert images to raw signal data.

data_processing: Using R (version 2.11.1), normalization was performed with VSN using LUMI (Du et al., 2008) to allow for a large number of significantly differentially expressed genes. Statistical analyses were performed using LIMMA (Smyth, 2004). The most variant probes were selected and a linear regression model was fitted over the time-course of differentiation. Technical replicates were removed, and T-tests were performed between Day 0 samples and Day 8 samples. P-values were controlled for false-discovery using the Benjamini-Hochberg (BH) correction (Benjamini & Hochberg, 1995).

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: Alveolar Epithelial type 2 (AT2 cell)

label_protocol: IlluminaTotalPrep RNA kit

growth_protocol: Rat AT2 cells were isolated as previously described (Zhou et al., 2008; Borok et al., 1998).

extract_protocol: RNA was extracted with the Illustra TriplePrep Kit (GE LifeSciences, Piscataway, NJ).

treatment_protocol: Differentiating in culture over time, no extra treatments added.

tag: time

tag: cell type

value: AT cell

tag: Sex

value: male