title: ICL012_NS1trunc_18h_2

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including hybridization and array washing.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing:
Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol.
For the generation of the normalized data, the limma package was used. Background correction was performed (method=normexp, offset=1). Data was quantile normalized between arrays with the quantile normalization method and then log2 transformed.
R version 2.12.2 (2011-02-25)
Bioconductor package: limma (version: 3.6.9, date: 2010/12/01 version)

source_name: Calu-3, NS1trunc infected, 18h

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation.

growth_protocol: Calu-3 cells, a human lung adenocarcinoma cell line, were kindly provided by Dr. Raymond Pickles (University of North Carolina, Chapel Hill, NC) and were maintained in a 1:1 mixture of Dulbecco's Modified Eagle's Medium and Ham's F12 nutrient medium (DF12; Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum. All cells were grown at 37°C in an atmosphere of 5% CO2, with an antibiotic/antimycotic mixture (Invitrogen).

extract_protocol: At the indicated time points, triplicate wells of mock-infected or virus-infected Calu-3 monolayers were washed with 5 ml cold phosphate-buffered saline (PBS) and lysed directly with 1 ml of TRIzol (Invitrogen) according to the manufacturer's recommendation, and resulting lysates were stored at -80°C until further processing. All TRIzol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer's recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for quantitative real-time PCR (qPCR) and microarray analyses.

treatment_protocol: For RNA isolation, Calu-3 cells were seeded in 6-well plates (1 x 10^6 cells/well) two days prior to infection. Immediately preceding infection, monolayers were washed twice with DMEM/F12 supplemented with 0.3% bovine serum albumin (DF12-BSA), and inoculated with virus at an MOI of 1 in DF12-BSA for 50 minutes at 37°C. Mock-infected controls were inoculated with DF12-BSA only. Following inoculation, monolayers were washed once with DF12-BSA and incubated in DF12-BSA containing 0.5 μg/ml of TPCK-treated trypsin (Worthington Biochemical Corporation, Lakewood, NJ).

tag: cell line

tag: infection code

tag: time point

tag: biological replicate


title: ICL012_Mock_24h_2

status: Public on Jan 05 2013

type: RNA

country: USA

molecule: total RNA

organism: Homo sapiens

source_name: Calu-3, mock infected, 24h

value: mock


title: ICL012_VN1203_7h_3

source_name: Calu-3, VN1203 infected, 7h


title: Liver ANON2H-L

city: Woburn

first: Christos

last: Hatzis

state: MA

address: 400 West Cummings Park, Suite 5350

institute: Nuvera Biosciences

description: Liver biopsy

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized overnight at 46C on Affymetrix U133A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the diagnostic-grade Affymetrix scanner 3000DX

data_processing: Probe intensities were quantified with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.  CEL files were normalized using global scaling with a trimmed mean target intensity of each array arbitrarily set to 600 using the MAS5 algorithm from the simpleaffy package (http://bioconductor.org/packages/2.4/bioc/html/simpleaffy.html).

label: biotin

source_name: Liver ANON2H-L

label_protocol: A single-round T7 amplification was used to generate biotin-labeled cRNA for hybridization.  At least 1 ug of RNA is required for cRNA synthesis.

extract_protocol: Total RNA was extracted from tissue using Qiagen Rneasy columns

treatment_protocol: Patients prospectively consented to a research biopsy by fine needle aspiration (FNA) or  core biopsy (CBX) prior to any systemic therapy, and to the future assessment of pathologic  response and/or survival endpoints

tag: sample id

tag: sample cohort

tag: percent liver

tag: tissue

value: Liver biopsy


title: ICL012_NS1trunc_12h_1

source_name: Calu-3, NS1trunc infected, 12h


title: ICL012_NS1trunc_0h_1

source_name: Calu-3, NS1trunc infected, 0h


title: ICL012_Mock_0h_3

source_name: Calu-3, mock infected, 0h


title: ICL012_NS1trunc_18h_1


title: ICL012_NS1trunc_7h_1

source_name: Calu-3, NS1trunc infected, 7h


title: ICL012_Mock_7h_1

source_name: Calu-3, mock infected, 7h


title: ICL012_NS1trunc_0h_3


title: ICL012_VN1203_7h_1


title: ICL012_NS1trunc_0h_2


title: ICL012_NS1trunc_18h_3


title: ICL012_NS1trunc_12h_3


title: ICL012_NS1trunc_24h_1

source_name: Calu-3, NS1trunc infected, 24h


title: ICL012_Mock_12h_1

source_name: Calu-3, mock infected, 12h


title: ICL012_VN1203_24h_3

source_name: Calu-3, VN1203 infected, 24h


title: ICL012_NS1trunc_7h_2


title: ICL012_NS1trunc_3h_1

source_name: Calu-3, NS1trunc infected, 3h


title: ICL012_NS1trunc_24h_3


title: ICL012_VN1203_24h_1


title: ICL012_Mock_12h_2


title: ICL012_NS1trunc_24h_2


title: ICL012_Mock_18h_1

source_name: Calu-3, mock infected, 18h


title: ICL012_Mock_0h_2


title: ICL012_NS1trunc_7h_3


title: ICL012_Mock_24h_3


title: ICL012_Mock_3h_1

source_name: Calu-3, mock infected, 3h


title: ICL012_NS1trunc_3h_2


title: ICL012_Mock_18h_2


title: ICL012_Mock_18h_3


title: ICL012_Mock_7h_3


title: ICL012_Mock_12h_3


title: ICL012_NS1trunc_3h_3


title: ICL012_Mock_24h_1


title: ICL012_NS1trunc_12h_2


title: ICL012_Mock_7h_2


title: ICL012_VN1203_24h_2


title: ICL012_Mock_3h_3


title: ICL011_VN-PB1-F2-del_3h_2

source_name: Calu-3, VN-PB1-F2-del infected, 3h


title: ICL011_VN1203_7h_3


title: ICL011_Mock_24h_3


title: ICL011_VN-PB2-627E_24h_2

source_name: Calu-3, VN-PB2-627E infected, 24h


title: ICL011_VN-PB1-F2-del_24h_2

source_name: Calu-3, VN-PB1-F2-del infected, 24h


title: ICL011_Mock_0h_1


title: ICL011_VN-PB1-F2-del_24h_1


title: ICL011_VN-PB2-627E_0h_3

source_name: Calu-3, VN-PB2-627E infected, 0h


title: ICL011_Mock_24h_1

source_name: Calu-3, mock infected, 24h


title: ICL011_VN-PB2-627E_18h_1

source_name: Calu-3, VN-PB2-627E infected, 18h


title: ICL011_VN-PB1-F2-del_18h_3

source_name: Calu-3, VN-PB1-F2-del infected, 18h


title: ICL011_Mock_12h_3


title: ICL011_VN-PB2-627E_7h_2

source_name: Calu-3, VN-PB2-627E infected, 7h


title: ICL011_VN-PB1-F2-del_7h_1

source_name: Calu-3, VN-PB1-F2-del infected, 7h


title: ICL011_Mock_3h_3


title: ICL011_VN-PB1-F2-del_7h_3


title: ICL011_VN-PB1-F2-del_3h_1


title: IM005_PB2_627E_10^4pfu_4d_4

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 4X44K mouse genome (Design ID 014868) array.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages.

organism: Mus musculus

source_name: lung, PB2_627E-infected, 4d

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

extract_protocol:
Specific lobes of the lung from each animal were harvested and briefly rinsed in cold (4ºC) PBS. Following the RNAlater (Ambion) protocol, tissue was cut into small chunks (<0.5cm in any single dimension) and placed immediately into 10-20 volumes (w/v) (e.g., 100mg/ml) RNAlater. After a 4ºC incubation for overnight, samples were stored at -80ºC until further processing. Lung tissue was removed from RNAlater, washed in a small volume of Trizol, homogenized in 10-20 volumes (w/v) TRIzol and stored at -80°C until RNA isolation.
All TRIzol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer's recommended protocol (Qiagen, Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: Twenty-week-old C57BL/6 mice were infected by intranasal instillation of 10^4 PFU of PB2-627E: A/Vietnam/1203-CIP048_RG2/2004 (H5N1) in 50 µl of PBS or mock-infected with PBS alone. At days 1, 2, 4 and 7 days post-infection, lungs were harvested.

tag: strain

tag: gender

value: female

value: lung


title: ICL011_Mock_7h_3

source_name: Calu-3, mock infected, 7h


title: ICL011_VN-PB1-F2-del_0h_1

source_name: Calu-3, VN-PB1-F2-del infected, 0h


title: IM005_PB2_627E_10^4pfu_1d_1

source_name: lung, PB2_627E-infected, 1d


title: ICL012_Mock_3h_2


title: IM005_PB2_627E_10^4pfu_4d_5


title: IM005_mock_7d_2

source_name: lung, mock-infected, 7d


title: ICL011_VN-PB2-627E_3h_3

source_name: Calu-3, VN-PB2-627E infected, 3h


title: ICL012_VN1203_7h_2

source_name: Calu-3, VN1203 infected, 7h


title: ICL011_VN-PB2-627E_24h_1


title: IM005_PB2_627E_10^4pfu_7d_1

source_name: lung, PB2_627E-infected, 7d


title: ICL011_VN-PB1-F2-del_12h_2

source_name: Calu-3, VN-PB1-F2-del infected, 12h


title: ICL011_Mock_3h_1

source_name: Calu-3, mock infected, 3h


title: ICL011_VN1203_24h_1

source_name: Calu-3, VN1203 infected, 24h


title: ICL011_Mock_12h_2

source_name: Calu-3, mock infected, 12h


title: ICL011_VN-PB1-F2-del_0h_3


title: ICL011_VN1203_7h_2


title: IM005_mock_1d_2

source_name: lung, mock-infected, 1d


title: ICL011_VN1203_24h_2


title: ICL011_VN-PB2-627E_18h_3

source_name: Calu-3, VN-PB2-627E infected, 18h


title: Astrocytes2

type: genomic

city: Milan

first: Stefania

last: Corti

address: via F. Sforza 35

department: Neurological Sciences

country: Italy

institute: University of Milan

description: cells were detached from plates and pelleted

scan_protocol: Follow NimbleScan's default using Agilent Scanner (high-resolution NimbleGen MS 200 Microarray Scanner)

data_processing: Arrays were processed using Nimblegen's standard protocol:the data were analyzed using DEVA software and visualized using SignalMap software.

molecule: genomic DNA

source_name: Astro2 INPUT

label_protocol: samples were label NimbleGen Dual-Color DNA Labeling Kit According to standard NimbleGen Protocol

growth_protocol: Human cortical astrocytes were cultured in astrocyte medium (Science Cell)

extract_protocol: Qiagen’s DNeasy kit

value: astrocytes from brain cortex

tag: treatment

source_name: Astro2 MBD ENRICHED

treatment_protocol: We used a methyl CpG binding domain (MBD) precipitation of genomic DNA; we used recombinant MBD of MBD2 protein to precipitate densely methylated sequences. The procedure was done by Imagenes according to their standard operating procedures.


title: IM005_PB2_627E_10^4pfu_2d_5

source_name: lung, PB2_627E-infected, 2d


title: IM005_PB2_627E_10^4pfu_2d_1


title: IM005_PB2_627E_10^4pfu_2d_3


title: ICL011_VN-PB1-F2-del_18h_1

source_name: Calu-3, VN-PB1-F2-del infected, 18h


title: IM005_PB2_627E_10^4pfu_7d_4


title: ICL011_VN-PB1-F2-del_3h_3

source_name: Calu-3, VN-PB1-F2-del infected, 3h


title: IM005_PB2_627E_10^4pfu_7d_2


title: ICL011_Mock_18h_2

source_name: Calu-3, mock infected, 18h


title: ICL011_VN-PB1-F2-del_0h_2

source_name: Calu-3, VN-PB1-F2-del infected, 0h


title: IM005_mock_1d_3


title: ICL011_VN-PB2-627E_0h_2

source_name: Calu-3, VN-PB2-627E infected, 0h


title: IM005_mock_4d_1

source_name: lung, mock-infected, 4d


title: ICL011_Mock_7h_1

source_name: Calu-3, mock infected, 7h


title: ICL011_VN-PB2-627E_12h_1

source_name: Calu-3, VN-PB2-627E infected, 12h


title: ICL011_VN-PB2-627E_24h_3

source_name: Calu-3, VN-PB2-627E infected, 24h


title: Glioma #39 tumor

city: Salamanca

first: MariaDolores

last: Tabernero

address: Paseo San Vicente 58-182

country: Spain

institute: Hospital Universitario de Salamanca y Centro del Cáncer

hyb_protocol: Hybridizations were performed according to protocols from Affymetrix. Labeled RNA was hybridized to Human Genome U133Plus2.0 microarray, after quality checking on GeneChips Test 3 Arrays.

scan_protocol: Washing and scanning were performed using Fluidics Station 400 and GeneChip Scanner (Affymetrix Inc.).

data_processing:
CEL files were analyzed using R and Bioconductor software tools. The Bioconductor packages used for RMA normalization were:
library(limma)
library(affy)
library(hgu133plus2)

source_name: Brain tissue from glioma patient

label_protocol: Labeling were performed according to protocols from Affymetrix. Briefly,total RNA was amplified and labeled using the GeneChip two-cycle cDNA synthesis kit and GeneChip IVT labeling kit.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Quiagen, Valencia, CA). The RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

tag: age

tag: histology

value: Mixed Anaplastic Oligoastrocytoma

tag: who grade

value: III

tag: karnofsky index(%)


title: Glioma #37 tumor

value: male

value: Anaplastic Oligodendroglioma


title: IM005_mock_4d_2


title: Glioma #36 tumor

value: Oligodendroglioma

value: II


title: Glioma #40 tumor


title: ICL011_VN-PB1-F2-del_12h_1

source_name: Calu-3, VN-PB1-F2-del infected, 12h


title: Glioma #38 tumor


title: IM005_PB2_627E_10^4pfu_1d_4

source_name: lung, PB2_627E-infected, 1d


title: Human Neural Stem Cells (HNSC) derived from astrocytes reprogramming 2

hyb_protocol: According to standard NimbleGen Protocol

source_name: HNSCNanog 1 INPUT

growth_protocol: Neural stem cells from reprogrammed astrocytes

treatment_protocol: cells were detached from plates and pelleted

value: NSC from reprogrammed astrocytes

source_name: HNSCNanog 2 MBD ENRICHED

value: methyl CpG binding domain (MBD) precipitation


title: ICL011_Mock_3h_2

source_name: Calu-3, mock infected, 3h


title: Glioma #34 tumor

value: Gliosarcoma

value: IV


title: ICL011_VN-PB1-F2-del_24h_3

source_name: Calu-3, VN-PB1-F2-del infected, 24h


title: IM005_mock_2d_1

source_name: lung, mock-infected, 2d


title: Human Neural Stem Cells (HNSC) derived from astrocytes reprogramming 3

source_name: HNSCNanog 1 MBD ENRICHED


title: Glioma #33 tumor

value: Glioblastoma multiforme


title: Glioma #35 tumor


title: IM005_mock_4d_3


title: Human Neural Stem Cells (HNSC) derived from astrocytes reprogramming 1


title: Astrocytes3

source_name: Astro3 INPUT

source_name: Astro3 MBD ENRICHED


title: Glioma #31 tumor


title: Astrocytes4

source_name: Astro4 INPUT

source_name: Astro4 MBD ENRICHED


title: IM005_PB2_627E_10^4pfu_2d_4

source_name: lung, PB2_627E-infected, 2d


title: Glioma #28 tumor


title: IM005_PB2_627E_10^4pfu_7d_3

source_name: lung, PB2_627E-infected, 7d


title: ICL011_Mock_18h_1

source_name: Calu-3, mock infected, 18h


title: ICL011_VN-PB2-627E_7h_3

source_name: Calu-3, VN-PB2-627E infected, 7h


title: Glioma #32 tumor

source_name: Brain tissue from glioma patient


title: Glioma #29 tumor


title: Glioma #26 tumor


title: ICL011_VN-PB2-627E_3h_2

source_name: Calu-3, VN-PB2-627E infected, 3h


title: Glioma #30 tumor


title: Glioma #27 tumor


title: IM005_PB2_627E_10^4pfu_1d_3

source_name: lung, PB2_627E-infected, 1d


title: IM005_mock_1d_1

source_name: lung, mock-infected, 1d


title: ICL011_Mock_0h_3

source_name: Calu-3, mock infected, 0h


title: Glioma #22 tumor


title: ICL011_VN-PB1-F2-del_7h_2

source_name: Calu-3, VN-PB1-F2-del infected, 7h


title: Glioma #18 tumor


title: IM005_mock_7d_3

source_name: lung, mock-infected, 7d


title: Glioma #23 tumor


title: Glioma #19 tumor


title: Glioma #20 tumor


title: Glioma #21 tumor


title: IM005_PB2_627E_10^4pfu_4d_2

source_name: lung, PB2_627E-infected, 4d


title: ICL011_VN-PB1-F2-del_12h_3

source_name: Calu-3, VN-PB1-F2-del infected, 12h


title: Glioma #16 tumor


title: ICL011_Mock_24h_2

source_name: Calu-3, mock infected, 24h


title: IM005_PB2_627E_10^4pfu_1d_2


title: Glioma #14 tumor


title: Glioma #13 tumor


title: Glioma #17 tumor


title: Glioma #12 tumor


title: Glioma #25 tumor


title: IM005_mock_2d_2

source_name: lung, mock-infected, 2d


title: Glioma #15 tumor


title: ICL011_Mock_0h_2


title: IM005_PB2_627E_10^4pfu_7d_5


title: IM005_mock_2d_3


title: IM005_PB2_627E_10^4pfu_4d_1


title: Glioma #24 tumor


title: Glioma #11 tumor


title: ICL011_Mock_7h_2

source_name: Calu-3, mock infected, 7h


title: ICL011_VN-PB1-F2-del_18h_2

source_name: Calu-3, VN-PB1-F2-del infected, 18h


title: ICL011_VN-PB2-627E_7h_1


title: Glioma #8 tumor


title: ICL011_VN-PB2-627E_3h_1


title: IM005_PB2_627E_10^4pfu_1d_5


title: ICL011_VN-PB2-627E_12h_2

source_name: Calu-3, VN-PB2-627E infected, 12h


title: IM005_mock_7d_1


title: Glioma #6 tumor

value: Anaplastic Astrocytoma


title: IM005_PB2_627E_10^4pfu_4d_3


title: Glioma #1 tumor

value: Pilocytic Astrocytoma

value: I


title: Glioma #2 tumor

value: female


title: Glioma #7 tumor


title: ICL011_Mock_18h_3

value: mock


title: ICL011_VN1203_24h_3

source_name: Calu-3, VN1203 infected, 24h


title: ICL011_Mock_12h_1

source_name: Calu-3, mock infected, 12h


title: Glioma #4 tumor

value: Diffuse Astrocytoma


title: Glioma #5 tumor


title: Glioma #10 tumor


title: ICL011_VN-PB2-627E_18h_2

source_name: Calu-3, VN-PB2-627E infected, 18h


title: RA P100_1

city: Berlin

first: Sven

last: Geissler

state: Berlin

address: Augustenburger Platz 1

department: Julius Wolff Institute and BCRT

country: Germany

institute: Charite - Universitaetsmedizin Berlin

description:
replicate 1
SAMPLE 16

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Illumina BeadStudio software version 3

organism: Rattus norvegicus

source_name: 12 months-old_rats_MSCs_passage 100

label_protocol: Illumina Gene Expression protocols contain a first- and second-strand reverse transcription step, followed by a single in vitro transcription (IVT) amplification that incorporates biotin-labeled nucleotides. Subsequent steps include array hybridization, washing, blocking, and streptavadin-Cy3 staining. Fluorescence emission by Cy3 is quantitatively detected for downstream analysis.

extract_protocol: The RNA was isolated using RNeasy Mini Kit (Quiagen), and DNase digestion (RNase-free DNase Set, Quiagen) has been applied on the columns during isolation.

value: Sprague Dawley

value: 12 months

tag: tissue source

value: bone marrow

tag: cell type

value: mesenchymal stromal cells (MSCs)

tag: passage

value: passage 100


title: RA P100_3

description:
replicate 3
SAMPLE 18


title: RJ P100_3

description:
replicate 3
SAMPLE 15

source_name: 3 wks-old_rats_MSCs_passage 100

value: 3 weeks


title: RJ P100_2

description:
replicate 2
SAMPLE 14


title: ICL011_VN-PB2-627E_0h_1

source_name: Calu-3, VN-PB2-627E infected, 0h

tag: cell line

tag: infection code


title: Glioma #9 tumor

source_name: Brain tissue from glioma patient


title: RA P100_2

description:
replicate 2
SAMPLE 17


title: 1203_DKO

city: Helsinki

first: Gulayse

last: Ince Dunn

state: Finland

address: Haartmaninkatu 8

department: Stem Cells and Metabolism Program

country: Finland

institute: University of Helsinki

description: P0 forebrain Elavl3/Elavl4 double knockout

hyb_protocol: 5 microgram of biotinylated target was hybridized to Affymetrix Mouse Exon 1.0 ST array for 16 hours at 45°C. After hybridization, gene chips were stained with streptavidin-phycoerythrin, followed by anti-streptavidin and second streptavidin-phycoerythrin solution.  All liquid handling was performed by GeneChip Fluidics Station 450.

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

data_processing:
RMA values for gene-level analysis were calculated using Expression Console software.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm8.core.mps

source_name: Elavl3/Elavl4 double knockout forebrain

label_protocol: 1 microgram of total RNA was used to prepare biotin-labelled target fro the exon array experiment using the GeneChip Whole Transcript Sense Target Labelling Assay as described by the manufacturer (P/N 900652, Affymetrix, Santa Clara, CA).

growth_protocol: Mouse forebrain dissected from postnatal day 0 pups

extract_protocol: Wild-type and Elavl3/4 doulbe knockout mice were identifed by manual genotyping.  Forebrain tissue was dissected out in ice-cold PBS and immediately dissociated in Trizol. Total RNA was extracted using Trizol Plus RNA Purification Kit (Invitrogen).

value: forebrain

value: C57BL/6 and CD-1 mixed

tag: genotype


title: 685_DKO


title: Glioma #3 tumor


title: LPS+VD3-2

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

description:
14125718
Array covering Sanger miRBase 12.0 and Exiqon miRPlus mature miRNAs.

hyb_protocol: Using Tecan hybridization stations according to the manufacturer's protocol.

scan_protocol: The arrays were scanned with a GenePix 4000B scanner using the manufacturer's recommended settings.

data_processing: The raw data was extracted using GenePix Pro and imported into GeneSpring GX10 for analyses. Raw data were normalized using VSN normalization. The normalized data are log2 transformed. The Sample data table includes data for only mouse miRNA probes.

source_name: RAW264.7 cells, LPS+VD3

label_protocol: Using the miRCURY™ LNA Array Power labeling kit according to the manufacturer's protocol.

extract_protocol: Total cellular RNAs were extracted from the cell lysates using TRIzol reagents (Invitrogen, Carlsbad, CA).

treatment_protocol: RAW264.7 cells were treated with vehicle, or LPS (100ng/ml) in the presence or absence of 1,25(OH)2D3 (20 nM) overnight.

value: macrophages

value: lipopolysaccharide (LPS) + 1,25-dihydroxyvitamin D (VD3)

tag: treatment duration

value: overnight


title: 1152_DKO


title: LPS2

description:
14125716
Array covering Sanger miRBase 12.0 and Exiqon miRPlus mature miRNAs.

source_name: RAW264.7 cells, LPS

value: lipopolysaccharide (LPS)


title: C2

description:
14125714
Array covering Sanger miRBase 12.0 and Exiqon miRPlus mature miRNAs.

source_name: RAW264.7 cells, vehicle

value: vehicle


title: RJ P100_1

description:
replicate 1
SAMPLE 13


title: RA P30_3

description:
replicate 3
SAMPLE 12

source_name: 12 months-old_rats_MSCs_passage 30

value: passage 30


title: ICL011_VN-PB2-627E_12h_3

tag: time point

tag: biological replicate


title: RJ P30_1

description:
replicate 1
SAMPLE 7

source_name: 3 wks-old_rats_MSCs_passage 30


title: RJ P30_2

description:
replicate 2
SAMPLE 8


title: 1147_DKO

tag: tissue


title: RA P30_2

description:
replicate 2
SAMPLE 11

tag: strain


title: RA P30_1

description:
replicate 1
SAMPLE 10


title: RJ P30_3

description:
replicate 3
SAMPLE 9


title: LPS1

description:
14125705
Array covering Sanger miRBase 12.0 and Exiqon miRPlus mature miRNAs.


title: LPS+VD3-1

description:
14125706
Array covering Sanger miRBase 12.0 and Exiqon miRPlus mature miRNAs.


title: 803_Cont

description: P0 forebrain wild-type

source_name: wild-type forebrain

value: Wild-type


title: C1

description:
14125704
Array covering Sanger miRBase 12.0 and Exiqon miRPlus mature miRNAs.


title: 806_DKO


title: RA P2_2

description:
replicate 2
SAMPLE 5

source_name: 12 months-old_rats_MSCs_passage 2

value: passage 2


title: 1207_Cont

description: P0 forebrain wild-type


title: 688_Cont

description: P0 forebrain wild-type


title: RJ P2_1

description:
replicate 1
SAMPLE 1

source_name: 3 wks-old_rats_MSCs_passage 2


title: RA P2_1

description:
replicate 1
SAMPLE 4


title: 1150_Cont

description: P0 forebrain wild-type


title: 1145_Cont

description: P0 forebrain wild-type


title: RJ P2_2

description:
replicate 2
SAMPLE 2


title: RJ P2_3

description:
replicate 3
SAMPLE 3


title: MC2A_WT_YJL9293_9147-3hr_sample 332

status: Public on Jan 04 2013

city: San Francisco

first: Kenneth

middle: J

last: Finn

state: CA

address: 600 16th Street

department: Department of Biochemsitry and Biophysics

institute: University of California, San Francisco

description: Table S4

hyb_protocol: Hybridization was performed in 3X SSC + 25mM HEPES pH7.0 + 0.25% SDS at 63C for 18-48 hours.

scan_protocol: Arrays were scanned with an Axon 3000B scanner using GenePix4.0 or GenePixPro6.0.

data_processing: Data were filtered in GenePix to flag as bad features that had : (1) obvious defects; (2) saturated pixels; (3) regression r^2 values less than 0.5; (4) fewer than 55% of their pixels with flourescence intensity greater than 2 standard deviations above background. BLAST analysis was used to generate a filter that would flag as bad elements whose PCR product were excessively repetitive. Raw Cy5/Cy3 median of ratios values were normalized such that the average ratio was equal to 1.  VALUE is the log2 of the normalized ratio of Cy3 to Cy5; note that to convert to usable copy number profiles raise two to the indicated value.

organism: Saccharomyces cerevisiae

source_name: non-re-replicating strain (wild-type)

label_protocol: amino-allyl-dUTP incorporation with Klenow. Chemical coupling of dye to aa-dUTP labelled DNA.

extract_protocol: NaN3 was added to a final concentration of 0.1% to 250 mL or 450 mL cultures that were arrested with nocodazole (final concentration = 15 ug/mL).  NaN3 treated cultures were added to 25 mL or 50 mL (for 250 mL or 450 mL cultures, respectively) of frozen, -80C, 0.2 M EDTA, 0.1% NaN3.  Cells were pelleted, washed with 50 mL of 4C TE (10 mM Tris-Cl, 1 mM EDTA pH 7.5) and stored frozen at -80C.  Pellets were resuspended in 4 mL lysis buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM Tris-Cl, 1 mM EDTA pH 8.0) and mixed with 4 mL of phenol:CHCl3:isoamyl alcohol (25:24:1) and 8 mL of acid-washed 0.5 mm glass beads (BioSpec Products, Inc., Bartlesville, OK). The suspension was vortexed seven times for 2-3 min separated by 2-3 min intervals at RT to get at least 95% of the cells lysed.  The lysate was diluted with 8 mL phenol:CHCl3:isoamyl alcohol (25:24:1) and 8 mL TE, vortexed once more, and then centrifuged at 18,500 x g for 15 min at RT.  After collecting the aqueous phase, the interphase was re-extracted with 8 mL TE, and the second aqueous phase from this re-extraction pooled with the first.  The combined aqueous phases were extracted with an equal volume of CHCl3.  The bulk of the RNA in the extract was selectively precipitated by addition of 0.01 volume 5 M NaCl (to a final concentration of 50 mM) and 0.4 volumes isopropanol followed by centrifugation at 9,000 x g for 15 min at RT.  The RNA pellet was discarded and an additional 0.4 volumes of isopropanol was added to the supernatant to precipitate the DNA.  Following centrifugation at 9,000 x g for 15 min at RT, the pellet was washed with 70% ethanol, dried, and resuspended with 3.5 mL of 10 mM Tris-Cl (pH 8), 1 mM EDTA.  RNase A (Qiagen, Valencia, CA) was added to 340 ug/mL and the sample incubated at 37C for 30-60 min.  Then Proteinase K was added to 555 ug/mL followed by another incubation at 55C for 30-60 min.  Finally, 0.5 mL of 10% (w/v) Cetyltrimethylammonium Bromide (CTAB, Sigma H6269), 0.9 M NaCl (prewarmed to 65C) and 0.9 mL of 5 M NaCl was added.  The sample was incubated for 20 min at 65C before being extracted with 8 mL CHCl3:isoamyl alcohol (24:1) and centrifuged at 6000 x g for 15-180 min at RT.  The DNA in the aqueous phase was precipitated with 0.8 volumes isopropanol at RT, washed with 70% ethanol, dried, and resuspended in 6 mL of 25 mM Tris-Cl (pH 7), 1 mM EDTA.  RNase A (Qiagen, Valencia, CA) was added to 33 ug/mL and the sample incubated at 37C for 15 min.  Then the following were added to the sample in the order listed: 1) 1.5 mL of 5 M NaCl; 2) 0.5 mL of 1M MOPS (pH 7); 3) 0.5 mL of Triton X-100 (3% vol/vol); 4) 1.5 mL of isopropanol.  The sample was then mixed by vortexing, then purified on a Qiagen Genomic-tip 100/G column as per the manufacturer's instructions (Qiagen, Valencia, CA).  The eluted DNA was precipitated with 0.8 volumes isopropanol at 4C, washed with 70% ethanol, dried, and resuspended in 275 uL of 2 mM Tris-Cl pH 7.8.  Genomic DNA was then sheared by sonication with a Branson Sonifier 450 to an average fragment size of 500 bp.

tag: sample type

value: reference DNA (G2/M arrested with nocodazole)

source_name: wild-type MC2A strain with ARS317 at ChrIV_567kb

extract_protocol: Isolates from the uracil prototrophy assay were cultured in SDC-Ura media until they reached saturation (so that most cells were in stationary phase with a 1C DNA content), or alpha factor was added to a final concentration of 100 ng/uL (to arrest cells with a 1C DNA content).  ~25 OD units of cells were harvested and suspended in 1 mL of sterile water in microfuge tubes.  Cells were then vortexed to wash and pelleted.  The water was then aspirated off and the cell pellets were snap-frozen in liquid nitrogen.  Cell pellets were thawed and resuspended in 200 uL of lysis buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM Tris-Cl, 1 mM EDTA (pH 8.0)).  To this suspension 200 uL of phenol:chloroform:isoamyl alcohol (25:24:1) and 200 uL of acid washed glass beads (0.5 mm) were added (BioSpec Products, Inc., Bartlesville, OK).  Cells were then lysed at room temperature using a Vortex-Genie 2 (Scientific Industries, NY) at top speed for 10 minutes.  To the lysate 450 uL of 10 mM Tris-Cl, 1 mM EDTA (pH 7.5) was added, and the mixture was vortexed for 30 seconds.  The mixture was then centrifuged at room temperature for 3 minutes at 20,800 x g.  500 uL of the aqueous phase was transferred to a new microfuge tube, to which 1 uL of 100 mg/mL RNase A (Qiagen, CA) was added.  Samples were incubated at 37C for 1-5 hours to allow digestion of the RNA.  300 uL of phenol:CHCl3:isoamyl alcohol (25:24:1) was added to each sample, which were then mixed at room temperature for 5 minutes on a multi-mixer (Tomy Tech USA, CA), then centrifuged at room temperature for 3 minutes at 20,800 x g.  400 uL of the aqueous phase was transferred to a new microfuge tube. 300 uL of CHCl3:isoamyl alcohol (24:1) was added to each sample.  Samples were mixed by shaking at room temperature and were then centrifuged at room temperature for 3 minutes at 20,800 x g.  300 uL of the aqueous phase was transferred to a new microfuge tube, to which 750 uL of 100% Ethanol and 3 uL of 10N NH4OAC (pH 7).  Samples were vortexed then centrifuged at room temperature for 7 minutes at 20,800 x g to pellet the DNA.  Pellets were washed with 70% Ethanol the air dried.  The DNA was suspended in 50 uL of 2 mM Tris-Cl (pH 7.8).

value: uracil prototroph isolate arising after re-replication from ARS317 at ChrIV_567kb (YJL9147-3 hr)


title: MC2A_WT_YJL9283_9130-3hr_sample 329

description: Table S4

label_protocol: amino-allyl-dUTP incorporation with Klenow.  Chemical coupling of dye to aa-dUTP labelled DNA.

value: uracil prototroph isolate arising after re-replication from ARS317 at ChrIV_567kb (YJL9130-3 hr)


title: MC2A_WT_YJL9289_9142-3hr_sample 333

description: Table S4

value: uracil prototroph isolate arising after re-replication from ARS317 at ChrIV_567kb (YJL9142-3 hr)


title: RA P2_3

description:
replicate 3
SAMPLE 6

value: Sprague Dawley

value: 12 months

value: bone marrow

value: mesenchymal stromal cells (MSCs)


title: MC2A_WT_YJL9284_9133-3hr_sample 330

description: Table S4

data_processing: Data were filtered in GenePix to flag as bad features that had : (1) obvious defects; (2) saturated pixels; (3) regression r^2 values less than 0.5; (4) fewer than 55% of their pixels with flourescence intensity greater than 2 standard deviations above background. BLAST analysis was used to generate a filter that would flag as bad elements whose PCR product were excessively repetitive. Raw Cy5/Cy3 median of ratios values were normalized such that the average ratio was equal to 1.  VALUE is the log2 of the normalized ratio of Cy5 to Cy3; note that to convert to usable copy number profiles raise two to the indicated value.

value: uracil prototroph isolate arising after re-replication from ARS317 at ChrIV_567kb (YJL9133-3 hr)


title: MC2A_WT_YJL8474_8364-3hr_sample 322

description: Table S4

value: uracil prototroph isolate arising after re-replication from ARS317 at ChrIV_567kb (YJL8364-3 hr)


title: MC2A_WT_YJL9291_9145-3hr_sample 331

description: Table S4

value: uracil prototroph isolate arising after re-replication from ARS317 at ChrIV_567kb (YJL9145-3 hr)


title: MC2A_WT_YJL9277_9118-3hr_sample 326

description: Table S4

value: uracil prototroph isolate arising after re-replication from ARS317 at ChrIV_567kb (YJL9118-3 hr)


title: MC2A_WT_YJL9286_9136-3hr_sample 324

description: Table S4

value: uracil prototroph isolate arising after re-replication from ARS317 at ChrIV_567kb (YJL9136-3 hr)


title: MC2A_WT_YJL9275_9115-3hr_sample 325

description: Table S4

value: uracil prototroph isolate arising after re-replication from ARS317 at ChrIV_567kb (YJL9115-3 hr)


title: MC2A_WT_YJL9287_9139-3hr_sample 323

description: Table S4

value: uracil prototroph isolate arising after re-replication from ARS317 at ChrIV_567kb (YJL9139-3 hr)


title: MC2A_WT_YJL9279_9121-3hr_sample 327

description: Table S4

value: uracil prototroph isolate arising after re-replication from ARS317 at ChrIV_567kb (YJL9121-3 hr)


title: S. boulardii cells in H2O vs. S. boulardii cells in H2O+HCl rep1

city: Providence

first: David

last: Laprade

state: RI

address: 1 Cunningham Sq.

institute: Providence College

description: Biological replicate 1 of 2

hyb_protocol: 300 ng of the relevant Cy3- and Cy5-stained cDNAs (control and experiment) were then pooled in a total volume of 25μL ddH2O and denatured at 95°C for 3 min. Following denaturation, 25 μL of 2x HiRPM gene expression and hybridization buffer (Agilent) was added to each sample. These cDNA solutions were then applied to the microarray slide and incubated at 65°C for ~17 hr in a hybridization oven, as per the manufacturer’s instructions. The slides were then sequentially washed in a row of Agilent Wash Buffer I, Agilent Wash Buffer II, and acetonitrile (Sigma), and dried using Agilent drying and stabilization buffer.

scan_protocol: Slides were scanned using an Axon 4000B scanner (Molecular Devices) and fluorescence was quantified using GENE Pix Pro 3.0 software (Molecular Devices).

data_processing: Data was normalized using the Goulphar transcriptome platform (http://transcriptome.ens.fr/goulphar/index.php), and log2 values were calculated using Excel.

source_name: Cells in H2O

label_protocol: cDNA was generated from 10 μg aliquots of purified RNA by first annealing hand-mixed random oligonucleotides (pdN9, 6.3 μg) and oligo(dT)19V (8.3 μg) obtained from IDT (Integrated DNA Technologies). First strand cDNA synthesis was then performing using Super Script III reverse transcriptase (Invitrogen) in a reaction containing 0.25 mM DTT 195 and 0.5 mM total deoxynucleoside triphosphates (amino-allyl-dUTP and deoxynucleoside triphosphates) in a ratio of 3:2 aa-dUTP. After synthesis for 3 hr at 42°C, the cDNA was hydrolyzed with 0.3 M NaOH and 0.03 M EDTA. The reaction was then neutralized with 0.3 M HCl to pH 7.0. Following this, cDNA was purified using a 25ug capacity DNA Concentrator and Cleanup Kit (Zymo), dried using a Speed-vac, resuspended in ddH2O (2 μg cDNA per 9 μl water), and stored at -80°C. Dye coupling was achieved by adding 1 μL of 1.0 M NaHCO3 solution (pH 9.0) and 1.25 μL of either Cy3 or Cy5 Amersham monoreative dye (GE Healthcare; dissolved in DMSO) to each 9 μL aliquot of cDNA, then incubating for 1 hr at room temperature in darkness. Unincorporated dye was removed and the samples purified using the Zymo cleanup kit

growth_protocol: S. boulardii cells were cultured in rich YPD media overnight, resuspended in fresh media, and allowed to reach exponential phase (an approximate OD600 value of 0.2).

extract_protocol: Total RNA was extracted using a RiboPure Yeast Kit (Ambion) and purified of gDNA with Turbo DNase (Ambion) according to manufacturer’s specifications.

treatment_protocol: Cells were resuspended in ddH2O.

value: Florastor, Lot No. 107538

source_name: Cells in H2O+HCl

treatment_protocol: Cells were resuspended in ddH2O + 50mM HCl.


title: MC2A_WT_YJL8472_8364-3hr_sample 320

description: Table S4

value: reference DNA (G2/M arrested with nocodazole)


title: MC2A_WT_YJL8471_8364-3hr_sample 319

description: Table S4


title: MC2A_WT_YJL8470_8364-3hr_sample 318

description: Table S4


title: MC2A_WT_YJL9281_9127-3hr_sample 328

description: Table S4

value: uracil prototroph isolate arising after re-replication from ARS317 at ChrIV_567kb (YJL9127-3 hr)


title: MC2A_WT_YJL8473_8364-3hr_sample 321

description: Table S4


title: MC2A_WT_YJL8468_8364-3hr_sample 316

description: Table S4


title: MC2A_WT_YJL8469_8364-3hr_sample 317

description: Table S4


title: MC2A_WT_YJL8465_8363-3hr_sample 313

description: Table S4

value: uracil prototroph isolate arising after re-replication from ARS317 at ChrIV_567kb (YJL8363-3 hr)


title: MC2A_WT_YJL8464_8363-3hr_sample 312

description: Table S4


title: MC2A_WT_YJL8461_8363-3hr_sample 309

description: Table S4


title: MC2A_WT_YJL8466_8363-3hr_sample 314

description: Table S4


title: MC2A_WT_YJL8460_8363-3hr_sample 308

description: Table S4


title: MC2A_WT_YJL8454_8113-3hr_sample 302

description: Table S4

value: uracil prototroph isolate arising after re-replication from ARS317 at ChrIV_567kb (YJL8113-3 hr)


title: MC2A_WT_YJL8458_8113-3hr_sample 306

description: Table S4


title: MC2A_WT_YJL8462_8363-3hr_sample 310

description: Table S4


title: MC2A_WT_YJL8463_8363-3hr_sample 311

description: Table S4


title: MC2A_WT_YJL8452_8113-3hr_sample 300

description: Table S4


title: MC2A_WT_YJL8451_8113-3hr_sample 299

description: Table S4


title: MC2A_WT_YJL8467_8364-3hr_sample 315

description: Table S4


title: MC2A_WT_YJL8450_8112-3hr_sample 298

description: Table S4

value: uracil prototroph isolate arising after re-replication from ARS317 at ChrIV_567kb (YJL8112-3 hr)


title: MC2A_WT_YJL8459_8363-3hr_sample 307

description: Table S4


title: MC2A_WT_YJL8449_8112-3hr_sample 297

description: Table S4


title: MC2A_WT_YJL8456_8113-3hr_sample 304

description: Table S4


title: S. boulardii cells in H2O vs. S. boulardii cells in H2O+HCl rep2

description: Biological replicate 2 of 2


title: MC2A_WT_YJL8457_8113-3hr_sample 305

description: Table S4


title: MC2A_WT_YJL8447_8112-3hr_sample 295

description: Table S4


title: MC2A_WT_YJL8446_8112-3hr_sample 294

description: Table S4


title: MC2A_WT_YJL8448_8112-3hr_sample 296

description: Table S4


title: ICL011_VN1203_7h_1

source_name: Calu-3, VN1203 infected, 7h


title: MC2A_WT_YJL8440_8364-0hr_sample 288

description: Table S4

value: uracil prototroph isolate arising without re-replication from ARS317 at ChrIV_567kb (YJL8364-0 hr)

extract_protocol: NaN3 was added to a final concentration of 0.1% to 250 mL or 450 mL cultures that were arrested with alpha-factor (final concentration = 50-100 ng/mL).  NaN3 treated cultures were added to 25 mL or 50 mL (for 250 mL or 450 mL cultures, respectively) of frozen, -80C, 0.2 M EDTA, 0.1% NaN3.  Cells were pelleted, washed with 50 mL of 4C TE (10 mM Tris-Cl, 1 mM EDTA pH 7.5) and stored frozen at -80C.  Pellets were resuspended in 4 mL lysis buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM Tris-Cl, 1 mM EDTA pH 8.0) and mixed with 4 mL of phenol:CHCl3:isoamyl alcohol (25:24:1) and 8 mL of acid-washed 0.5 mm glass beads (BioSpec Products, Inc., Bartlesville, OK). The suspension was vortexed seven times for 2-3 min separated by 2-3 min intervals at RT to get at least 95% of the cells lysed.  The lysate was diluted with 8 mL phenol:CHCl3:isoamyl alcohol (25:24:1) and 8 mL TE, vortexed once more, and then centrifuged at 18,500 x g for 15 min at RT.  After collecting the aqueous phase, the interphase was re-extracted with 8 mL TE, and the second aqueous phase from this re-extraction pooled with the first.  The combined aqueous phases were extracted with an equal volume of CHCl3.  The bulk of the RNA in the extract was selectively precipitated by addition of 0.01 volume 5 M NaCl (to a final concentration of 50 mM) and 0.4 volumes isopropanol followed by centrifugation at 9,000 x g for 15 min at RT.  The RNA pellet was discarded and an additional 0.4 volumes of isopropanol was added to the supernatant to precipitate the DNA.  Following centrifugation at 9,000 x g for 15 min at RT, the pellet was washed with 70% ethanol, dried, and resuspended with 3.5 mL of 10 mM Tris-Cl (pH 8), 1 mM EDTA.  RNase A (Qiagen, Valencia, CA) was added to 340 ug/mL and the sample incubated at 37C for 30-60 min.  Then Proteinase K was added to 555 ug/mL followed by another incubation at 55C for 30-60 min.  Finally, 0.5 mL of 10% (w/v) Cetyltrimethylammonium Bromide (CTAB, Sigma H6269), 0.9 M NaCl (prewarmed to 65C) and 0.9 mL of 5 M NaCl was added.  The sample was incubated for 20 min at 65C before being extracted with 8 mL CHCl3:isoamyl alcohol (24:1) and centrifuged at 6000 x g for 15-180 min at RT.  The DNA in the aqueous phase was precipitated with 0.8 volumes isopropanol at RT, washed with 70% ethanol, dried, and resuspended in 6 mL of 25 mM Tris-Cl (pH 7), 1 mM EDTA.  RNase A (Qiagen, Valencia, CA) was added to 33 ug/mL and the sample incubated at 37C for 15 min.  Then the following were added to the sample in the order listed: 1) 1.5 mL of 5 M NaCl; 2) 0.5 mL of 1M MOPS (pH 7); 3) 0.5 mL of Triton X-100 (3% vol/vol); 4) 1.5 mL of isopropanol.  The sample was then mixed by vortexing, then purified on a Qiagen Genomic-tip 100/G column as per the manufacturer's instructions (Qiagen, Valencia, CA).  The eluted DNA was precipitated with 0.8 volumes isopropanol at 4C, washed with 70% ethanol, dried, and resuspended in 275 uL of 2 mM Tris-Cl pH 7.8.  Genomic DNA was then sheared by sonication with a Branson Sonifier 450 to an average fragment size of 500 bp.

value: reference DNA (G1 arrested with alpha-factor)


title: MC2A_WT_YJL8445_8112-3hr_sample 293

description: Table S4


title: MC2A_WT_YJL8438_8363-0hr_sample 286

description: Table S4

value: uracil prototroph isolate arising without re-replication from ARS317 at ChrIV_567kb (YJL8363-0 hr)


title: MC2A_WT_YJL8455_8113-3hr_sample 303

description: Table S4


title: MC2A_WT_YJL8442_8364-0hr_sample 290

description: Table S4


title: MC2A_WT_YJL8444_8112-3hr_sample 292

description: Table S4


title: MC2A_WT_YJL8441_8364-0hr_sample 289

description: Table S4


title: MC2A_WT_YJL8443_8112-3hr_sample 291

description: Table S4


title: MC2A_WT_YJL8432_8112-0hr_sample 280

description: Table S4

value: uracil prototroph isolate arising without re-replication from ARS317 at ChrIV_567kb (YJL8112-0 hr)


title: MC2A_WT_YJL9542_8363-3hr_sample 278

description: Table S2

extract_protocol: Isolates from the sectoring assay were cultured in YEP + 8% Dextrose until they reached saturation (so that most cells were in stationary phase with a 1C DNA content).  ~25 OD units of cells were harvested and suspended in 1 mL of sterile water in microfuge tubes.  Cells were then vortexed to wash and pelleted.  The water was then aspirated off and the cell pellets were snap-frozen in liquid nitrogen.  Cell pellets were thawed and resuspended in 200 uL of lysis buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM Tris-Cl, 1 mM EDTA (pH 8.0)).  To this suspension 200 uL of phenol:chloroform:isoamyl alcohol (25:24:1) and 200 uL of acid washed glass beads (0.5 mm) were added (BioSpec Products, Inc., Bartlesville, OK).  Cells were then lysed at room temperature using a Vortex-Genie 2 (Scientific Industries, NY) at top speed for 10 minutes.  To the lysate 450 uL of 10 mM Tris-Cl, 1 mM EDTA (pH 7.5) was added, and the mixture was vortexed for 30 seconds.  The mixture was then centrifuged at room temperature for 3 minutes at 20,800 x g.  500 uL of the aqueous phase was transferred to a new microfuge tube, to which 1 uL of 100 mg/mL RNase A (Qiagen, CA) was added.  Samples were incubated at 37C for 1-5 hours to allow digestion of the RNA.  300 uL of phenol:CHCl3:isoamyl alcohol (25:24:1) was added to each sample, which were then mixed at room temperature for 5 minutes on a multi-mixer (Tomy Tech USA, CA), then centrifuged at room temperature for 3 minutes at 20,800 x g.  400 uL of the aqueous phase was transferred to a new microfuge tube. 300 uL of CHCl3:isoamyl alcohol (24:1) was added to each sample.  Samples were mixed by shaking at room temperature and were then centrifuged at room temperature for 3 minutes at 20,800 x g.  300 uL of the aqueous phase was transferred to a new microfuge tube, to which 750 uL of 100% Ethanol and 3 uL of 10N NH4OAC (pH 7).  Samples were vortexed then centrifuged at room temperature for 7 minutes at 20,800 x g to pellet the DNA.  Pellets were washed with 70% Ethanol the air dried.  The DNA was suspended in 50 uL of 2 mM Tris-Cl (pH 7.8).

value: red sector isolate arising after re-replication from ARS317 at ChrIV_567kb (YJL8363-3 hr)


title: MC2A_WT_YJL8453_8113-3hr_sample 301

description: Table S4


title: MC2A_WT_YJL8431_8112-0hr_sample 279

description: Table S4


title: MC2A_WT_YJL8434_8113-0hr_sample 282

description: Table S4

value: uracil prototroph isolate arising without re-replication from ARS317 at ChrIV_567kb (YJL8113-0 hr)


title: MC2A_WT_YJL9535_8363-3hr_sample 272

description: Table S2


title: IM005_PB2_627E_10^4pfu_2d_2

source_name: lung, PB2_627E-infected, 2d

tag: gender

value: female

value: lung


title: MC2A_WT_YJL8436_8113-0hr_sample 284

description: Table S4


title: MC2A_WT_YJL8439_8363-0hr_sample 287

description: Table S4


title: MC2A_WT_YJL9534_8363-3hr_sample 271

description: Table S2


title: MC2A_WT_YJL9536_8363-3hr_sample 273

description: Table S2


title: MC2A_WT_YJL9541_8363-3hr_sample 277

description: Table S2


title: MC2A_WT_YJL9539_8363-3hr_sample 275

description: Table S2


title: MC2A_WT_YJL8437_8363-0hr_sample 285

description: Table S4


title: MC2A_WT_YJL9537_8363-3hr_sample 274

description: Table S2


title: MC2A_WT_YJL9533_8363-3hr_sample 270

description: Table S2


title: MC2A_WT_YJL9531_8363-3hr_sample 268

description: Table S2


title: MC2A_WT_YJL8435_8113-0hr_sample 283

description: Table S4


title: MC2A_WT_YJL9532_8363-3hr_sample 269

description: Table S2


title: MC2A_WT_YJL8433_8112-0hr_sample 281

description: Table S4


title: MC2A_WT_YJL9530_8363-3hr_sample 267

description: Table S2


title: MC2A_WT_YJL9540_8363-3hr_sample 276

description: Table S2


title: MC2A_WT_YJL9529_8363-3hr_sample 266

description: Table S2


title: MC2A_WT_YJL9528_8363-3hr_sample 265

description: Table S2


title: MC2A_WT_YJL9527_8363-3hr_sample 264

description: Table S2


title: MC2A_WT_YJL9524_8363-0hr_sample 260

description: Table S2

value: red sector isolate arising without re-replication from ARS317 at ChrIV_567kb (YJL8363-0 hr)


title: MC2A_WT_YJL9523_8359-3hr_sample 259

description: Table S2

value: red sector isolate arising after re-replication from ARS317 at ChrIV_567kb (YJL8359-3 hr)


title: MC2A_WT_YJL9522_8359-3hr_sample 258

description: Table S2


title: MC2A_WT_YJL9526_8363-3hr_sample 263

description: Table S2


title: MC2A_WT_YJL9521_8359-3hr_sample 257

description: Table S2


title: MC2A_WT_YJL9520_8359-3hr_sample 256

description: Table S2


title: MC2A_WT_YJL9517_8359-3hr_sample 255

description: Table S2


title: MC2A_WT_YJL9516_8359-3hr_sample 254

description: Table S2


title: MC2A_WT_YJL9515_8359-3hr_sample 253

description: Table S2


title: MC2A_WT_YJL9512_8359-3hr_sample 250

description: Table S2


title: MC2A_WT_YJL9525_8363-0hr_sample 261

description: Table S2


title: MC2A_WT_YJL9510_8359-3hr_sample 248

description: Table S2


title: MC2A_WT_YJL9518_8359-0hr_sample 246

description: Table S2

value: red sector isolate arising without re-replication from ARS317 at ChrIV_567kb (YJL8359-0 hr)


title: MC2A_WT_YJL9509_8359-0hr_sample 245

description: Table S2


title: MC2A_WT_YJL9508_8355-3hr_sample 244

description: Table S2

value: red sector isolate arising after re-replication from ARS317 at ChrIV_567kb (YJL8355-3 hr)


title: MC2A_WT_YJL9507_8355-3hr_sample 243

description: Table S2


title: MC2A_WT_YJL9519_8359-0hr_sample 247

description: Table S2


title: MC2A_WT_YJL9514_8359-3hr_sample 252

description: Table S2


title: MC2A_WT_YJL9513_8359-3hr_sample 251

description: Table S2

value: reference DNA (G2/M arrested with nocodazole)


title: MC2A_WT_YJL9511_8359-3hr_sample 249

description: Table S2


title: MC2A_WT_YJL9502_8355-3hr_sample 238

description: Table S2


title: MC2A_WT_YJL9504_8355-3hr_sample 240

description: Table S2


title: MC2A_WT_YJL9503_8355-3hr_sample 239

description: Table S2


title: MC2A_WT_YJL9505_8355-3hr_sample 241

description: Table S2


title: MC2A_WT_YJL9500_8355-3hr_sample 236

description: Table S2


title: MC2A_WT_YJL9501_8355-3hr_sample 237

description: Table S2


title: MC2A_WT_YJL9506_8355-3hr_sample 242

description: Table S2


title: MC2A_WT_YJL9538_8363-0hr_sample 262

description: Table S2


title: MC2A_WT_YJL9499_8355-3hr_sample 235

description: Table S2


title: MC2A_WT_YJL8330_8112-3hr_sample 230

description: Table S2

value: red sector isolate arising after re-replication from ARS317 at ChrIV_567kb (YJL8112-3 hr)


title: MC2A_WT_YJL9496_8355-0hr_sample 232

description: Table S2

value: red sector isolate arising without re-replication from ARS317 at ChrIV_567kb (YJL8355-0 hr)


title: MC2A_WT_YJL9497_8355-3hr_sample 233

description: Table S2


title: MC2A_WT_YJL9495_8355-0hr_sample 231

description: Table S2


title: MC2A_WT_YJL8323_8112-3hr_sample 223

description: Table S2


title: MC2A_WT_YJL8183_8112-3hr_sample 221

description: Table S2


title: MC2A_WT_YJL8325_8112-3hr_sample 225

description: Table S2


title: MC2A_WT_YJL8176_8112-3hr_sample 214

description: Table S2


title: MC2A_WT_YJL8326_8112-3hr_sample 226

description: Table S2


title: MC2A_WT_YJL8177_8112-3hr_sample 215

description: Table S2


title: MC2A_WT_YJL8184_8112-3hr_sample 222

description: Table S2


title: MC2A_WT_YJL8327_8112-3hr_sample 227

description: Table S2


title: MC2A_WT_YJL8182_8112-3hr_sample 220

description: Table S2


title: MC2A_WT_YJL8329_8112-3hr_sample 229

description: Table S2


title: MC2A_WT_YJL8179_8112-3hr_sample 217

description: Table S2


title: MC2A_WT_YJL8178_8112-3hr_sample 216

description: Table S2


title: MC2A_WT_YJL8286_8112-0hr_sample 210

description: Table S2

value: red sector isolate arising without re-replication from ARS317 at ChrIV_567kb (YJL8112-0 hr)


title: MC2A_WT_YJL8324_8112-3hr_sample 224

description: Table S2


title: MC2A_WT_YJL8173_8112-3hr_sample 211

description: Table S2


title: MC2A_WT_YJL8181_8112-3hr_sample 219

description: Table S2


title: MC2A_WT_YJL8172_8112-0hr_sample 208

description: Table S2

value: red sector isolate arising aithout re-replication from ARS317 at ChrIV_567kb (YJL8112-0 hr)


title: MC2A_WT_YJL8175_8112-3hr_sample 213

description: Table S2


title: MC2A_WT_YJL8180_8112-3hr_sample 218

description: Table S2


title: MC2A_WT_YJL8174_8112-3hr_sample 212

description: Table S2


title: MC2A_WT_YJL8285_8112-0hr_sample 209

description: Table S2


title: MC2A_WT_YJL8318_8108-3hr_sample 202

description: Table S2

value: red sector isolate arising after re-replication from ARS317 at ChrIV_567kb (YJL8108-3 hr)


title: MC2A_WT_YJL8320_8108-3hr_sample 204

description: Table S2

value: reference DNA (G1 arrested with alpha-factor)


title: MC2A_WT_YJL8321_8108-3hr_sample 205

description: Table S2


title: MC2A_WT_YJL8319_8108-3hr_sample 203

description: Table S2


title: MC2A_WT_YJL8322_8108-3hr_sample 206

description: Table S2


title: MC2A_WT_YJL8317_8108-3hr_sample 201

description: Table S2


title: MC2A_WT_YJL8314_8108-3hr_sample 198

description: Table S2


title: MC2A_WT_YJL8312_8108-3hr_sample 196

description: Table S2


title: MC2A_WT_YJL8313_8108-3hr_sample 197

description: Table S2


title: MC2A_WT_YJL8169_8108-3hr_sample 191

description: Table S2


title: MC2A_WT_YJL8165_8108-3hr_sample 187

description: Table S2


title: MC2A_WT_YJL8170_8108-3hr_sample 192

description: Table S2


title: MC2A_WT_YJL8315_8108-3hr_sample 199

description: Table S2


title: MC2A_WT_YJL8166_8108-3hr_sample 188

description: Table S2


title: MC2A_WT_YJL8316_8108-3hr_sample 200

description: Table S2


title: MC2A_WT_YJL8163_8108-3hr_sample 185

description: Table S2


title: MC2A_WT_YJL8310_8108-3hr_sample 194

description: Table S2


title: MC2A_WT_YJL8167_8108-3hr_sample 189

description: Table S2


title: MC2A_WT_YJL8168_8108-3hr_sample 190

description: Table S2


title: MC2A_WT_YJL8164_8108-3hr_sample 186

description: Table S2


title: MC2A_WT_YJL8309_8108-3hr_sample 193

description: Table S2


title: MC2A_WT_YJL9498_8355-3hr_sample 234

description: Table S2


title: MC2A_WT_YJL8158_8108-3hr_sample 180

description: Table S2


title: MC2A_WT_YJL8159_8108-3hr_sample 181

description: Table S2


title: MC2A_WT_YJL8171_8112-0hr_sample 207

description: Table S2


title: MC2A_WT_YJL8160_8108-3hr_sample 182

description: Table S2


title: MC2A_WT_YJL8161_8108-3hr_sample 183

description: Table S2


title: MC2A_WT_YJL8308_8104-3hr_sample 177

description: Table S2

value: red sector isolate arising after re-replication from ARS317 at ChrIV_567kb (YJL8104-3 hr)


title: MC2A_WT_YJL8311_8108-3hr_sample 195

description: Table S2


title: MC2A_WT_YJL8307_8104-3hr_sample 176

description: Table S2


title: MC2A_WT_YJL8162_8108-3hr_sample 184

description: Table S2


title: MC2A_WT_YJL8284_8108-0hr_sample 178

description: Table S2

value: red sector isolate arising without re-replication from ARS317 at ChrIV_567kb (YJL8108-0 hr)


title: MC2A_WT_YJL8306_8104-3hr_sample 175

description: Table S2


title: MC2A_WT_YJL8305_8104-3hr_sample 174

description: Table S2


title: MC2A_WT_YJL8157_8108-3hr_sample 179

description: Table S2


title: MC2A_WT_YJL8156_8104-3hr_sample 163

description: Table S2


title: MC2A_WT_YJL8302_8104-3hr_sample 171

description: Table S2


title: MC2A_WT_YJL8296_8104-3hr_sample 165

description: Table S2


title: MC2A_WT_YJL8295_8104-3hr_sample 164

description: Table S2


title: MC2A_WT_YJL8297_8104-3hr_sample 166

description: Table S2


title: MC2A_WT_YJL8301_8104-3hr_sample 170

description: Table S2


title: MC2A_WT_YJL8300_8104-3hr_sample 169

description: Table S2


title: MC2A_WT_YJL8303_8104-3hr_sample 172

description: Table S2


title: MC2A_WT_YJL8154_8104-3hr_sample 161

description: Table S2


title: MC2A_WT_YJL8153_8104-3hr_sample 160

description: Table S2


title: MC2A_WT_YJL8147_8104-3hr_sample 154

description: Table S2


title: MC2A_WT_YJL8304_8104-3hr_sample 173

description: Table S2


title: MC2A_WT_YJL8299_8104-3hr_sample 168

description: Table S2


title: MC2A_WT_YJL8328_8112-3hr_sample 228

description: Table S2


title: MC2A_WT_YJL8151_8104-3hr_sample 158

description: Table S2


title: MC2A_WT_YJL8150_8104-3hr_sample 157

description: Table S2


title: MC2A_WT_YJL8298_8104-3hr_sample 167

description: Table S2


title: MC2A_WT_YJL8146_8104-3hr_sample 153

description: Table S2


title: MC2A_WT_YJL8149_8104-3hr_sample 156

description: Table S2


title: MC2A_WT_YJL8143_8104-3hr_sample 150

description: Table S2


title: MC2A_WT_YJL8145_8104-3hr_sample 152

description: Table S2


title: MC2A_WT_YJL8152_8104-3hr_sample 159

description: Table S2


title: MC2A_WT_YJL8155_8104-3hr_sample 162

description: Table S2


title: MC2A_WT_YJL8142_8104-0hr_sample 149

description: Table S2

value: red sector isolate arising without re-replication from ARS317 at ChrIV_567kb (YJL8104-0 hr)


title: MC2A_WT_YJL8141_8104-0hr_sample 148

description: Table S2


title: MC2A_WT_YJL8140_8104-0hr_sample 147

description: Table S2


title: MC2A_WT_YJL8144_8104-3hr_sample 151

description: Table S2


title: MC2A_WT_YJL9494_8100-3hr_sample 146

description: Table S2

value: red sector isolate arising after re-replication from ARS317 at ChrIV_567kb (YJL8100-3 hr)


title: MC2A_WT_YJL8148_8104-3hr_sample 155

description: Table S2


title: MC2A_WT_YJL9486_8100-3hr_sample 138

description: Table S2


title: MC2A_WT_YJL9491_8100-3hr_sample 143

description: Table S2


title: MC2A_WT_YJL9489_8100-3hr_sample 141

description: Table S2


title: MC2A_WT_YJL9488_8100-3hr_sample 140

description: Table S2


title: MC2A_WT_YJL9484_8100-3hr_sample 136

description: Table S2


title: MC2A_WT_YJL9490_8100-3hr_sample 142

description: Table S2


title: MC2A_WT_YJL8293_8100-3hr_sample 133

description: Table S2


title: MC2A_WT_YJL9487_8100-3hr_sample 139

description: Table S2


title: MC2A_WT_YJL9485_8100-3hr_sample 137

description: Table S2


title: MC2A_WT_YJL9483_8100-3hr_sample 135

description: Table S2


title: MC2A_WT_YJL8294_8100-3hr_sample 134

description: Table S2


title: MC2A_WT_YJL8290_8100-3hr_sample 130

description: Table S2


title: MC2A_WT_YJL8291_8100-3hr_sample 131

description: Table S2


title: MC2A_WT_YJL8292_8100-3hr_sample 132

description: Table S2


title: MC2A_WT_YJL9492_8100-3hr_sample 144

description: Table S2


title: MC2A_WT_YJL8288_8100-3hr_sample 128

description: Table S2


title: MC2A_WT_YJL9493_8100-3hr_sample 145

description: Table S2


title: MC2A_WT_YJL8287_8100-3hr_sample 127

description: Table S2


title: MC2A_WT_YJL8137_8100-3hr_sample 124

description: Table S2


title: MC2A_WT_YJL8138_8100-3hr_sample 125

description: Table S2


title: MC2A_WT_YJL8134_8100-3hr_sample 121

description: Table S2


title: MC2A_WT_YJL8136_8100-3hr_sample 123

description: Table S2


title: MC2A_WT_YJL8131_8100-3hr_sample 118

description: Table S2


title: MC2A_WT_YJL8135_8100-3hr_sample 122

description: Table S2


title: MC2A_WT_YJL8132_8100-3hr_sample 119

description: Table S2


title: MC2A_WT_YJL8289_8100-3hr_sample 129

description: Table S2


title: MC2A_WT_YJL8139_8100-3hr_sample 126

description: Table S2


title: MC2A_WT_YJL8133_8100-3hr_sample 120

description: Table S2


title: MC2A_WT_YJL8130_8100-3hr_sample 117

description: Table S2


title: MC2A_rad51_YJL7898_7451-3hr_sample 111

description: Table S2

source_name: non-re-replicating strain (MpGAL + ARS317 at ChrIV_567kb)

source_name: rad51 MC2A strain with ARS317 at ChrIV_567kb

value: red sector isolate arising after re-replication from ARS317 at ChrIV_567kb (YJL7451-3 hr)


title: MC2A_rad51_YJL7899_7451-3hr_sample 112

description: Table S2


title: MC2A_WT_YJL9482_8100-0hr_sample 114

description: Table S2

value: red sector isolate arising without re-replication from ARS317 at ChrIV_567kb (YJL8100-0 hr)


title: MC2A_WT_YJL8128_8100-3hr_sample 115

description: Table S2


title: MC2A_WT_YJL8129_8100-3hr_sample 116

description: Table S2


title: MC2A_rad51_YJL7892_7451-3hr_sample 105

description: Table S2


title: MC2A_rad51_YJL7893_7451-3hr_sample 106

description: Table S2


title: MC2A_rad51_YJL7891_7451-3hr_sample 104

description: Table S2


title: MC2A_rad51_YJL7894_7451-3hr_sample 107

description: Table S2


title: MC2A_rad51_YJL7895_7451-3hr_sample 108

description: Table S2


title: MC2A_rad51_YJL7896_7451-3hr_sample 109

description: Table S2


title: MC2A_rad51_YJL7888_7451-3hr_sample 101

description: Table S2


title: MC2A_rad51_YJL7889_7451-3hr_sample 102

description: Table S2


title: MC2A_rad51_YJL7885_7451-3hr_sample 98

description: Table S2


title: MC2A_rad51_YJL7886_7451-3hr_sample 99

description: Table S2


title: MC2A_rad51_YJL7884_7451-3hr_sample 97

description: Table S2


title: MC2A_rad51_YJL7897_7451-3hr_sample 110

description: Table S2


title: MC2A_WT_YJL8283_8100-0hr_sample 113

description: Table S2


title: MC2A_rad51_YJL7829_7451-3hr_sample 96

description: Table S2


title: MC2A_rad51_YJL7887_7451-3hr_sample 100

description: Table S2


title: MC2A_rad51_YJL7827_7451-3hr_sample 94

description: Table S2


title: MC2A_rad51_YJL7825_7451-3hr_sample 92

description: Table S2


title: MC2A_rad51_YJL7826_7451-3hr_sample 93

description: Table S2


title: MC2A_rad51_YJL7821_7451-3hr_sample 88

description: Table S2


title: MC2A_rad51_YJL7823_7451-3hr_sample 90

description: Table S2


title: MC2A_rad51_YJL7890_7451-3hr_sample 103

description: Table S2


title: MC2A_rad51_YJL7824_7451-3hr_sample 91

description: Table S2


title: MC2A_rad51_YJL7822_7451-3hr_sample 89

description: Table S2


title: MC2A_rad51_YJL7819_7451-3hr_sample 86

description: Table S2


title: MC2A_rad51_YJL7812_7451-3hr_sample 79

description: Table S2


title: MC2A_rad51_YJL7820_7451-3hr_sample 87

description: Table S2


title: MC2A_rad51_YJL7810_7451-3hr_sample 77

description: Table S2


title: MC2A_rad51_YJL7817_7451-3hr_sample 84

description: Table S2


title: MC2A_rad51_YJL7816_7451-3hr_sample 83

description: Table S2


title: MC2A_rad51_YJL7828_7451-3hr_sample 95

description: Table S2


title: MC2A_rad51_YJL7883_7451-0hr_sample 76

description: Table S2

value: red sector isolate arising without re-replication from ARS317 at ChrIV_567kb (YJL7451-0 hr)


title: MC2A_rad51_YJL7882_7451-0hr_sample 75

description: Table S2


title: MC2A_rad51_YJL7878_7451-0hr_sample 71

description: Table S2


title: MC2A_rad51_YJL7813_7451-3hr_sample 80

description: Table S2


title: MC2A_rad51_YJL7879_7451-0hr_sample 72

description: Table S2


title: MC2A_rad51_YJL7881_7451-0hr_sample 74

description: Table S2


title: MC2A_rad51_YJL7814_7451-3hr_sample 81

description: Table S2


title: MC2A_rad51_YJL7877_7451-0hr_sample 70

description: Table S2


title: MC2A_rad51_YJL7876_7451-0hr_sample 69

description: Table S2


title: MC2A_rad1_YJL7875_7445-3hr_sample 68

description: Table S2

source_name: rad1 MC2A strain with ARS317 at ChrIV_567kb

value: red sector isolate arising after re-replication from ARS317 at ChrIV_567kb (YJL7445-3 hr)


title: MC2A_rad51_YJL7811_7451-3hr_sample 78

description: Table S2


title: MC2A_rad1_YJL7874_7445-3hr_sample 67

description: Table S2


title: MC2A_rad1_YJL7873_7445-3hr_sample 66

description: Table S2


title: MC2A_rad51_YJL7818_7451-3hr_sample 85

description: Table S2


title: MC2A_rad1_YJL7870_7445-3hr_sample 63

description: Table S2


title: MC2A_rad1_YJL7872_7445-3hr_sample 65

description: Table S2


title: MC2A_rad1_YJL7869_7445-3hr_sample 62

description: Table S2


title: MC2A_rad1_YJL7808_7445-3hr_sample 59

description: Table S2


title: MC2A_rad51_YJL7880_7451-0hr_sample 73

description: Table S2


title: MC2A_rad1_YJL7868_7445-3hr_sample 61

description: Table S2


title: MC2A_rad1_YJL7807_7445-3hr_sample 58

description: Table S2


title: MC2A_rad1_YJL7809_7445-3hr_sample 60

description: Table S2


title: MC2A_rad1_YJL7804_7445-3hr_sample 55

description: Table S2


title: MC2A_rad1_YJL7803_7445-3hr_sample 54

description: Table S2


title: MC2A_rad1_YJL7805_7445-3hr_sample 56

description: Table S2


title: MC2A_rad1_YJL7802_7445-3hr_sample 53

description: Table S2


title: MC2A_rad1_YJL7800_7445-3hr_sample 51

description: Table S2


title: MC2A_rad1_YJL7806_7445-3hr_sample 57

description: Table S2


title: MC2A_rad1_YJL7799_7445-3hr_sample 50

description: Table S2


title: MC2A_rad1_YJL7795_7445-3hr_sample 46

description: Table S2


title: MC2A_rad1_YJL7796_7445-3hr_sample 47

description: Table S2


title: MC2A_rad1_YJL7867_7445-0hr_sample 40

description: Table S2

value: red sector isolate arising without re-replication from ARS317 at ChrIV_567kb (YJL7445-0 hr)


title: MC2A_rad1_YJL7797_7445-3hr_sample 48

description: Table S2


title: MC2A_rad1_YJL7794_7445-3hr_sample 45

description: Table S2


title: MC2A_rad1_YJL7790_7445-3hr_sample 41

description: Table S2


title: MC2A_rad1_YJL7791_7445-3hr_sample 42

description: Table S2


title: MC2A_rad1_YJL7793_7445-3hr_sample 44

description: Table S2


title: MC2A_rad1_YJL7865_7445-0hr_sample 38

description: Table S2


title: MpGAL_WT_YJL7901_6974-3hr_sample 37

description: Table S2

source_name: wild-type MpGAL strain with ARS317 at ChrIV_567kb

value: red sector isolate arising without re-replication from ARS317 at ChrIV_567kb (YJL6974-3 hr)


title: MC2A_rad1_YJL7792_7445-3hr_sample 43

description: Table S2


title: MC2A_rad1_YJL7866_7445-0hr_sample 39

description: Table S2


title: MC2A_rad51_YJL7815_7451-3hr_sample 82

description: Table S2


title: MC2A_rad1_YJL7798_7445-3hr_sample 49

description: Table S2


title: MC2A_rad1_YJL7801_7445-3hr_sample 52

description: Table S2


title: MpGAL_WT_YJL7788_6974-3hr_sample 34

description: Table S2

source_name: wild-type MpGALstrain with ARS317 at ChrIV_567kb


title: MC2A_rad1_YJL7871_7445-3hr_sample 64

description: Table S2


title: MpGAL_WT_YJL7789_6974-3hr_sample 35

description: Table S2


title: MpGAL_WT_YJL7900_6974-3hr_sample 36

description: Table S2


title: MC2A_WT_YJL7863_6558-3hr_sample 32

description: Table S2

value: red sector isolate arising after re-replication from ARS317 at ChrIV_567kb (YJL6558-3 hr)


title: MC2A_WT_YJL7784_6558-3hr_sample 26

description: Table S2


title: MC2A_WT_YJL7861_6558-3hr_sample 30

description: Table S2


title: MC2A_WT_YJL7787_6558-3hr_sample 29

description: Table S2


title: MC2A_WT_YJL7785_6558-3hr_sample 27

description: Table S2


title: MC2A_WT_YJL7782_6558-3hr_sample 24

description: Table S2


title: pol32_MC2A_YJL8421_3 hr Re-rep_sample 22

description: Figure S4

data_processing: Data were filtered in GenePix to flag as bad features that had : (1) obvious defects; (2) saturated pixels; (3) regression r^2 values less than 0.5; (4) fewer than 55% of their pixels with flourescence intensity greater than 2 standard deviations above background. BLAST analysis was used to generate a filter that would flag as bad elements whose PCR product were excessively repetitive. Raw Cy5/Cy3 median of ratios values were normalized such that the average ratio was equal to 2.  VALUE is the log2 of the normalized ratio of Cy5 to Cy3; note that to convert to usable copy number profiles raise two to the indicated value.

source_name: pol32 MC2A strain with ARS317 at ChrIV_567kb

extract_protocol: NaN3 was added to a final concentration of 0.1% to 250 mL cultures (arrested with nocodazole and induced with 2.7% galactose to re-replicate for 3 hr).  NaN3 treated cultures were added to 25 mL of frozen, -80C, 0.2 M EDTA, 0.1% NaN3.  Cells were pelleted, washed with 50 mL of 4C TE (10 mM Tris-Cl, 1 mM EDTA pH 7.5) and stored frozen at -80C.  Pellets were resuspended in 4 mL lysis buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM Tris-Cl, 1 mM EDTA pH 8.0) and mixed with 4 mL of phenol:CHCl3:isoamyl alcohol (25:24:1) and 8 mL of acid-washed 0.5 mm glass beads (BioSpec Products, Inc., Bartlesville, OK). The suspension was vortexed seven times for 2-3 min separated by 2-3 min intervals at RT to get at least 95% of the cells lysed.  The lysate was diluted with 8 mL phenol:CHCl3:isoamyl alcohol (25:24:1) and 8 mL TE, vortexed once more, and then centrifuged at 18,500 x g for 15 min at RT.  After collecting the aqueous phase, the interphase was re-extracted with 8 mL TE, and the second aqueous phase from this re-extraction pooled with the first.  The combined aqueous phases were extracted with an equal volume of CHCl3.  The bulk of the RNA in the extract was selectively precipitated by addition of 0.01 volume 5 M NaCl (to a final concentration of 50 mM) and 0.4 volumes isopropanol followed by centrifugation at 9,000 x g for 15 min at RT.  The RNA pellet was discarded and an additional 0.4 volumes of isopropanol was added to the supernatant to precipitate the DNA.  Following centrifugation at 9,000 x g for 15 min at RT, the pellet was washed with 70% ethanol, dried, and resuspended with 3.5 mL of 10 mM Tris-Cl (pH 8), 1 mM EDTA.  RNase A (Qiagen, Valencia, CA) was added to 340 ug/mL and the sample incubated at 37C for 30-60 min.  Then Proteinase K was added to 555 ug/mL followed by another incubation at 55C for 30-60 min.  Finally, 0.5 mL of 10% (w/v) Cetyltrimethylammonium Bromide (CTAB, Sigma H6269), 0.9 M NaCl (prewarmed to 65C) and 0.9 mL of 5 M NaCl was added.  The sample was incubated for 20 min at 65C before being extracted with 8 mL CHCl3:isoamyl alcohol (24:1) and centrifuged at 6000 x g for 15-180 min at RT.  The DNA in the aqueous phase was precipitated with 0.8 volumes isopropanol at RT, washed with 70% ethanol, dried, and resuspended in 6 mL of 25 mM Tris-Cl (pH 7), 1 mM EDTA.  RNase A (Qiagen, Valencia, CA) was added to 33 ug/mL and the sample incubated at 37C for 15 min.  Then the following were added to the sample in the order listed: 1) 1.5 mL of 5 M NaCl; 2) 0.5 mL of 1M MOPS (pH 7); 3) 0.5 mL of Triton X-100 (3% vol/vol); 4) 1.5 mL of isopropanol.  The sample was then mixed by vortexing, then purified on a Qiagen Genomic-tip 100/G column as per the manufacturer's instructions (Qiagen, Valencia, CA).  The eluted DNA was precipitated with 0.8 volumes isopropanol at 4C, washed with 70% ethanol, dried, and resuspended in 275 uL of 2 mM Tris-Cl pH 7.8.  Genomic DNA was then sheared by sonication with a Branson Sonifier 450 to an average fragment size of 500 bp.

value: 3 hr re-replication induction in G2/M

value: reference DNA (G2/M arrested with nocodazole)


title: MC2A_WT_YJL7783_6558-3hr_sample 25

description: Table S2


title: MC2A_WT_YJL7860_6558-0hr_sample 23

description: Table S2

data_processing: Data were filtered in GenePix to flag as bad features that had : (1) obvious defects; (2) saturated pixels; (3) regression r^2 values less than 0.5; (4) fewer than 55% of their pixels with flourescence intensity greater than 2 standard deviations above background. BLAST analysis was used to generate a filter that would flag as bad elements whose PCR product were excessively repetitive. Raw Cy5/Cy3 median of ratios values were normalized such that the average ratio was equal to 1.  VALUE is the log2 of the normalized ratio of Cy3 to Cy5; note that to convert to usable copy number profiles raise two to indicated value.

value: red sector isolate arising without re-replication from ARS317 at ChrIV_567kb (YJL6558-0 hr)


title: pol32_MC2A_YJL8422_3 hr Re-rep_sample 21

description: Figure S4


title: MC2A_WT_YJL7862_6558-3hr_sample 31

description: Table S2


title: rad1_MC2A_YJL8416_3 hr Re-rep_sample 15

description: Figure S4


title: msh3_MC2A_YJL8419_3 hr Re-rep_sample 18

description: Figure S4

source_name: msh3 MC2A strain with ARS317 at ChrIV_567kb


title: msh3_MC2A_YJL8418_3 hr Re-rep_sample 17

description: Figure S4


title: msh3_MC2A_YJL8418_3 hr Re-rep_sample 19

description: Figure S4


title: pol32_MC2A_YJL8421_3 hr Re-rep_sample 20

description: Figure S4


title: MC2A_WT_YJL7786_6558-3hr_sample 28

description: Table S2


title: rad51_MC2A_YJL8413_3 hr Re-rep_sample 12

description: Figure S4


title: rad51_MC2A_YJL8412_3 hr Re-rep_sample 13

description: Figure S4


title: rad1_MC2A_YJL8415_3 hr Re-rep_sample 14

description: Figure S4


title: rad52_MC2A_YJL8410_3 hr Re-rep_sample 9

description: Figure S4

source_name: rad52 MC2A strain with ARS317 at ChrIV_567kb


title: rad52_MC2A_YJL8409_3 hr Re-rep_sample 10

description: Figure S4


title: dnl4_MC2A_YJL8407_3 hr Re-rep_sample 7

description: Figure S4

source_name: dnl4 MC2A strain with ARS317 at ChrIV_567kb


title: rad52_MC2A_YJL8409_3 hr Re-rep_sample 8

description: Figure S4


title: rad51_MC2A_YJL8412_3 hr Re-rep_sample 11

description: Figure S4


title: rad1_MC2A_YJL8415_3 hr Re-rep_sample 16

description: Figure S4


title: dnl4_MC2A_YJL8408_3 hr Re-rep_sample 6

description: Figure S4


title: dnl4_MC2A_YJL8407_3 hr Re-rep_sample 5

description: Figure S4


title: MC2A_WT_YJL7864_6558-3hr_sample 33

description: Table S2


title: MC2A_WT_YJL8363_3 hr Re-rep_sample 1

description: Figure S4


title: MC2A_WT_YJL8364_3 hr Re-rep_sample 4

description: Figure S4


title: MC2A_WT_YJL8364_3 hr Re-rep_sample 2

description: Figure S4


title: iPS cells-derived motorneuron, treated SMA patient cells-03

hyb_protocol: The hybridization and scan protocols, suitable for Human Exon 1.0 ST microarrays, were provided by Affymetrix.

scan_protocol: Affymetrix RUO platform

data_processing: RAW data were acquired by Affymetrix GCOS software. The 9 raw data files have been normalized with the RMA algorithm (Irizarry et al., 2003) to generate signal intensities for 17881 core transcripts: the core type consists of alignments of mRNA with annotated full-length CDS regions. The groups of interest have been compared using moderated t-test (Smyth, 2004). Prior to adjustment for multiple comparison (Benjamini and Hochberg, 1995), we have filtered out the less variable transcripts based on the inter-quantile range. 8940 tran- scripts have been kept. Differentially expressed transcripts have been defined as having an adjusted p-value < 0.05.

label: Biotin

label_protocol: Affymetrix GeneChip whole transcript (WT) Sense Taget (ST) labeling array and GeneChip Hybridization wash and stain Kit: ribosomal RNA was firstly reduced by using the RiboMinus human/mouse kit (Invitrogen) starting from 1 µg of total RNA. Subsequently, purified RNA was used ad a template in the synthesis of double strand cDNA according to the instructions provided by Affymetrix protocol. Double strand cDNA was in-vitro transcribed producing cRNA. Finally, cRNA was newly retro-transcribed (2nd cycle) and ss-cDNA obtained through this passage was purified, quantified by Nanodrop, biotin-labeled and fragmented according manufacturers protocols.

growth_protocol: We analyzed iPSC-derived motor neurons from SMA patient's fibroblast (n=3), iPSC-derived motor neurons from healthy father's fibroblast (n=3) and treated iPSC-derived motor neurons from SMA patient's fibroblast (n=3). Human iPS cells were expanded in the absence of mouse embryonic fibroblasts, only on matrigel coated plates in a feeder-independent medium for maintenance of undifferentiated human pluripotent stem cells (mTeRS).

extract_protocol: RNA extraction with RNeasy Mini Kit

treatment_protocol: We differentiated spinal motor neurons from iPSCs using a multistage differentiation protocol developed for human ES cells (Hu BY and Zhang SC, 2009). The procedure for motor neuron differentiation from iPSCs is schematically summarized. For the production of motor neurons from iPSCs-SMA, iPSCs-TR and iPSCs-WT, they were plated with neuronal medium made of DMEM/F12 (Gibco, Grand Island, NY,bhttp://www.invitrogen.com), supplemented with MEM non-essential amino acids solution, N2 and heparin (2 μg/ml; Sigma-Aldrich). After 10 days we added RA (0.1 μM, Sigma-Aldrich) for the neural caudalization. At day 17 (after one week) we collected the posteriorized neuroectodermal cells. These cluster were then suspended for a week in the same medium with RA (0.1 μM) and SHH (100–200 ng/ml; R&D Systems Inc.). On day 24, we added other grow factors like BDNF (brain-derived neurotrophic factor), GDNF (glial-derived neurotrophic factor), and IGF1 (insulin-like growth factor-1) (10 ng/ml; Peprotech).

tag: genotype/variation

value: SMN1-/-;SMN2+; SMN2(into1)

value: iPS cells-derived motorneurons


title: iPS cells-derived motorneuron, treated SMA patient cells-02


title: iPS cells-derived motorneuron, healthy father-03


title: iPS cells-derived motorneuron, treated SMA patient cells-01


title: MC2A_WT_YJL8363_3 hr Re-rep_sample 3

description: Figure S4


title: iPS cells-derived motorneuron, healthy father-01


title: prefrontal cortex_individual 2

city: Shanghai

first: Ning

last: Fu

address: 320# Yue-Yang Road

department: Shanghai Institute for Biological Sciences

country: China

institute: Chinese Academy of Sciences

hyb_protocol: Hybridization to Affymetrix® Human Exon 1.0 ST arrays was carried out following standard Affymetrix protocols.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneChip Scanner 3000.

data_processing: Prior to expression data analysis, we masked all probes that did not match reference human genomes perfectly (hg18) and did not map to a unique location within the human genome (http://hgdownload.cse.ucsc.edu/goldenPath/hg18/). To determine whether the signal intensity of a given probe was above the expected level of background noise, we compared the signal intensity for each probe to a distribution of signal intensities of the antigenomic probes with the same GC content. Antigenomic probes are specifically designed by Affymetrix to provide an estimate of the non-specific background hybridization (http://www.affymetrix.com/support/technical/whitepapers/exon_backgrou nd_correction_whitepaper.pdf) . To further remove any possible systematic experimental differences between the arrays, we performed a PM-GCBG correction and just selected the designed core probes according to Affymetrix Human Exon Array Whitepaper.The intensities of transcripts were summarized by median polish method.Prior to the quantile normalization using R package “affy”, all intensities were base-two-logarithm transformed. We removed the transcripts with average expression in each tissue less than 4.6 (the least expression value of a transcript with identified corresponding protein expression). This resulted in total of 18,044 mRNA transcripts with expression detected in at least one of the three human tissues.

source_name: Adult human prefrontal cortex:individual 2

label_protocol: Isolated RNA was reverse transcripted and resulted cDNA was fragmented to 100-300 bp pieces and labeled following the standard GeneChip® Whole Transcript (WT) Sense Target Labelling Assay (see manual, P/N 701880).

extract_protocol: Trizol extraction of total RNA from 100 mg of tissue was performed according to the manufacturer's instructions.

treatment_protocol: All human postmortem brain tissue samples were obtained from the NICHD Brain and Tissue Bank for Developmental Disorders (NICHDBB)(Baltimore, MD, USA). All subjects were defined as normal controls by forensic pathologists at the NICHDBB. No subjects with prolonged agonal state were used.

tag: sex

value: male

tag: age

value: Adult human prefrontal cortex


title: iPS cells-derived motorneuron, healthy father-02


title: prefrontal cortex_individual 3

source_name: Adult human prefrontal cortex:individual 3


title: liver_individual 2

source_name: Adult human liver:individual 2

value: Adult human liver


title: CLL B-cell, patient UM4_transfected (non targeting_RNAi)_stimulated cells_at 210min

city: Strasbourg

first: Laurent

last: Vallat

address: 1, Place de l'Hopital

department: Immunology

country: France

institute: Strasbourg University Hospital

description: CLL-UM4_Transfect-non target_S_T210

hyb_protocol: standard affymetrix

scan_protocol: standard affymetrix

data_processing: Data were normalized with the invariant set method and the model based expression index (MBEI) obtained by the PM-MM model (Li et al., PNAS 2001) using dChip software (dChip v.2006; www.dchip.org). The obtained expression values are preprocessed by truncating the value to less than or equal to 1.

source_name: CLL B-cell_transfected (non targeting_RNAi)_stimulated cells_210min

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

extract_protocol: At each time point 10^7 control US and S cells were washed and resuspended in 1 mL TRIzol (Invitrogen, Carlsbad, CA). Total RNA was purified using Promega columns (SV total isolation system, Promega corp. Madison, WI).

treatment_protocol:
cell isolation: B-cells were negatively selected from fresh blood samples using the Rosettesep B-cell enrichment cocktail (Stemcell Biotechnologies, Vancouver, Canada) and isolated by density gradient centrifugation over Ficoll-Paque plus (Pharmacia, Upsala, Sweden). Quality of the selection was assessed by flow cytometry on a Cytomics FC500 system (Beckman-Coulter, Fullerton, CA) after CD5-PE / CD19-FITC staining (BD Biosciences, Palo Alto, CA) and in all cases was greater than 93%, range from 93-98% (med. 96%). Cells were starved for 4 hr at 37degree C / 5% CO2 in RPMI 1640 media supplemented with 2 nM L-glutamine and 24 ug/mL gentamicin.
B-cells at a density of 10^7cells/mL were divided in two. One was used as unstimulated (US) control and the other stimulated (S) by goat F(ab’)2 anti human IgM-BIOT (Southern biotech, Birmingham, AL) at 20 mg/mL and cross-linked by 20 mg/mL of avidin (Sigma-Aldrich, St Louis, MO) on ice during 5 min, follow by incubation at 37degree C for 15 min. After washing, cells were cultured at 37degree C / 5% CO2 in RPMI 1640 media supplemented with 10% FBS, 2 nM L-glutamine and 24 ug/mL gentamicin.

tag: cell classification

value: aggressive leukemia

value: chronic lymphocytic leukemia B-cell

tag: unstimulated (us)/stimulated (s)

value: S

tag: time point (min)

tag: transfected with

value: non-targeting RNAi


title: cerebellum_individual 1

source_name: Adult human cerebellum:individual 1

value: Adult human cerebellum


title: CLL B-cell, patient UM4_transfected (non targeting_RNAi)_stimulated cells_at 90min

description: CLL-UM4_Transfect-non target_S_T90

source_name: CLL B-cell_transfected (non targeting_RNAi)_stimulated cells_90min

tag: cell type


title: liver_individual 3

source_name: Adult human liver:individual 3


title: iPS cells-derived motorneuron, SMA patient-02


title: CLL B-cell, patient UM4_transfected (non targeting_RNAi)_unstimulated cells_at 390min

description: CLL-UM4_Transfect-non target_US_T390

source_name: CLL B-cell_transfected (non targeting_RNAi)_unstimulated cells_390min

value: US


title: iPS cells-derived motorneuron, SMA patient-01


title: liver_individual 1

source_name: Adult human liver:individual 1


title: cerebellum_individual 2

source_name: Adult human cerebellum:individual 2


title: iPS cells-derived motorneuron, SMA patient-03


title: cerebellum_individual 3

source_name: Adult human cerebellum:individual 3


title: prefrontal cortex_individual 1

source_name: Adult human prefrontal cortex:individual 1


title: SpnD39_vicK_IU1781vsIU1896_BHI_rep2

city: Bloomington

first: Ho-Ching

middle: Tiffany

last: Tsui

state: IN

address: 1001 E. Third St.

department: Biology

institute: Indiana University

description: Independent biological replicate, dye swap

hyb_protocol: Performed as per microarray manufacturer’s recommendations (OciChip Application Guide from Ocimum Biosolutions). Fluorescently-labeled cDNAs were resuspended in the manufacturer’s salt-based hybridization buffer. Samples were heated for 3 min at 95C, then chilled on ice for 3 min before application to the microarray slide. Slides were hybridized at 42C overnight (~18 hrs). Slides were washed sequentially for 5 min in the following buffers pre-warmed to 30C: Buffer 1, 2X SSC, 0.1% SDS; Buffer 2, 1X SSC; Buffer 3, 0.1X SSC.

scan_protocol: Microarray slides were scanned on an Axon GenePix 4200A microarray scanner at 532 nm and 635nm. Slides were scanned at gain settings which balanced the signal acquired in both channels (pixel ratio~1.0). Images were analysed using GenePix Pro 5.0 software (molecular Devices)

data_processing: Data were normalized with BASE (Bioarray Software Environment) using the Lowess normalization method without background subtraction.

organism: Streptococcus pneumoniae

source_name: strain: IU1781, S. pneumoniae bacterial strain D39 rpsL1

label_protocol: Single strand cDNA synthesis and direct labeling performed using 30 micrograms of total RNA and superscript II reverse transcriptase (Invitrogen) as per microarray manufacturer’s recommendations (OciChip Application Guide from Ocimum Biosolutions)

growth_protocol: Bacterial strains were grown statically in brain heart infusion media (Bacto BHI, Becton Dickinson) at 37C and an atmosphere of 5% CO2 overnight. Overnight cultures which displayed no lysis were diluted to an OD620 of ~0.005 into BHI and grown at 37C and an atmosphere of 5% CO2. Growth was monitored by change in OD620 (13mm cuvette) as measured in a Spectronic 20 spectrophotometer.

extract_protocol: Total RNA was extracted from exponentially growing cultures (OD620~0.2) using a hot lysis/ acid phenol procedure followed by on-column DNase treatment and purification using the RNAeasy mini kit (Qiagen) as described in Robertson et al, J. Bact (2002) 184:3508-3520

value: IU1781  D39 rpsL1 (streptomycin resistant)

source_name: IU1896, S. pneumoniae bacterial strain D39 rpsL1∆vicK

value: IU1896 D39 rpsL1∆vicK (streptomycin resistant)

tag: type

value: vicK sequence is deleted except for the 60 nt at the 5’ and 3’ end.


title: SpnD39_VicK_IU1781 vs IU1896_BHI_rep3

source_name: IU1781, S. pneumoniae bacterial strain D39 rpsL1

value: IU1781 D39 rpsL1 (streptomycin resistant)


title: CLL B-cell, patient UM4_transfected (non targeting_RNAi)_stimulated cells_at 390min

description: CLL-UM4_Transfect-non target_S_T390

source_name: CLL B-cell_transfected (non targeting_RNAi)_stimulated cells_390min


title: CLL B-cell, patient UM4_transfected (non targeting_RNAi)_unstimulated cells_at 210min

description: CLL-UM4_Transfect-non target_US_T210

source_name: CLL B-cell_transfected (non targeting_RNAi)_unstimulated cells_210min


title: CLL B-cell, patient UM4_transfected (non targeting_RNAi)_stimulated cells_at 60min

description: CLL-UM4_Transfect-non target_S_T60

source_name: CLL B-cell_transfected (non targeting_RNAi)_stimulated cells_60min


title: SpnD39_vicK_IU1781vsIU1896_BHI_rep1

value: IU1896D39 rpsL1∆vicK (streptomycin resistant)


title: CLL B-cell, patient UM4_transfected (DUSP1_RNAi)_stimulated cells_at 90min

source_name: CLL B-cell_transfected (DUSP1_RNAi)_stimulated cells_90min

value: DUSP1 RNAi


title: CLL B-cell, patient UM4_transfected (non targeting_RNAi)_unstimulated cells_at 90min

description: CLL-UM4_Transfect-non target_US_T90

source_name: CLL B-cell_transfected (non targeting_RNAi)_unstimulated cells_90min


title: CLL B-cell, patient UM4_transfected (DUSP1_RNAi)_unstimulated cells_at 210min

source_name: CLL B-cell_transfected (DUSP1_RNAi)_unstimulated cells_210min


title: CLL B-cell, patient UM4_transfected (DUSP1_RNAi)_stimulated cells_at 210min

source_name: CLL B-cell_transfected (DUSP1_RNAi)_stimulated cells_210min


title: CLL B-cell, patient UM4_stimulated cells_at 390min

source_name: CLL B-cell_stimulated cells_390min


title: CLL B-cell, patient UM4_transfected (DUSP1_RNAi)_unstimulated cells_at 390min

source_name: CLL B-cell_transfected (DUSP1_RNAi)_unstimulated cells_390min


title: CLL B-cell, patient UM4_transfected (DUSP1_RNAi)_unstimulated cells_at 90min

source_name: CLL B-cell_transfected (DUSP1_RNAi)_unstimulated cells_90min


title: CLL B-cell, patient UM4_transfected (DUSP1_RNAi)_unstimulated cells_at 60min

source_name: CLL B-cell_transfected (DUSP1_RNAi)_unstimulated cells_60min


title: CLL B-cell, patient UM4_stimulated cells_at 60min

source_name: CLL B-cell_stimulated cells_60min


title: CLL B-cell, patient UM4_transfected (DUSP1_RNAi)_stimulated cells_at 60min

source_name: CLL B-cell_transfected (DUSP1_RNAi)_stimulated cells_60min


title: CLL B-cell, patient UM4_stimulated cells_at 210min

source_name: CLL B-cell_stimulated cells_210min


title: CLL B-cell, patient UM4_unstimulated cells_at 390min

source_name: CLL B-cell_unstimulated cells_390min


title: CLL B-cell, patient UM4_stimulated cells_at 90min

source_name: CLL B-cell_stimulated cells_90min


title: CLL B-cell, patient UM4_unstimulated cells_at 60min

source_name: CLL B-cell_unstimulated cells_60min


title: CLL B-cell, patient UM3_stimulated cells_at 90min


title: CLL B-cell, patient UM4_unstimulated cells_at 210min

source_name: CLL B-cell_unstimulated cells_210min


title: CLL B-cell, patient UM4_transfected (non targeting_RNAi)_unstimulated cells_at 60min

description: CLL-UM4_Transfect-non target_US_T60

source_name: CLL B-cell_transfected (non targeting_RNAi)_unstimulated cells_60min


title: CLL B-cell, patient UM4_transfected (DUSP1_RNAi)_stimulated cells_at 390min

source_name: CLL B-cell_transfected (DUSP1_RNAi)_stimulated cells_390min


title: CLL B-cell, patient UM3_stimulated cells_at 210min


title: CLL B-cell, patient UM3_stimulated cells_at 60min


title: CLL B-cell, patient UM3_unstimulated cells_at 390min


title: CLL B-cell, patient UM3_unstimulated cells_at 210min


title: CLL B-cell, patient UM3_unstimulated cells_at 90min

source_name: CLL B-cell_unstimulated cells_90min


title: CLL B-cell, patient UM3_stimulated cells_at 390min


title: CLL B-cell, patient UM2_stimulated cells_at 60min


title: CLL B-cell, patient UM2_unstimulated cells_at 90min


title: CLL B-cell, patient UM3_unstimulated cells_at 60min


title: CLL B-cell, patient UM2_stimulated cells_at 210min


title: CLL B-cell, patient UM2_stimulated cells_at 390min


title: CLL B-cell, patient UM1_stimulated cells_at 210min


title: CLL B-cell, patient UM2_unstimulated cells_at 390min


title: CLL B-cell, patient UM4_unstimulated cells_at 90min


title: CLL B-cell, patient UM2_stimulated cells_at 90min


title: CLL B-cell, patient UM2_unstimulated cells_at 210min


title: CLL B-cell, patient UM1_stimulated cells_at 390min


title: CLL B-cell, patient UM2_unstimulated cells_at 60min


title: CLL B-cell, patient UM1_unstimulated cells_at 390min


title: CLL B-cell, patient UM1_stimulated cells_at 90min


title: CLL B-cell, patient UM1_stimulated cells_at 60min


title: CLL B-cell, patient UM1_unstimulated cells_at 90min


title: CLL B-cell, patient M2_stimulated cells_at 390min


title: CLL B-cell, patient M2_stimulated cells_at 210min


title: CLL B-cell, patient M2_unstimulated cells_at 90min


title: CLL B-cell, patient M2_unstimulated cells_at 390min


title: CLL B-cell, patient M8_stimulated cells_at 210min

value: indolent leukemia


title: CLL B-cell, patient M2_stimulated cells_at 90min


title: CLL B-cell, patient M2_unstimulated cells_at 210min


title: CLL B-cell, patient UM1_unstimulated cells_at 60min


title: CLL B-cell, patient UM1_unstimulated cells_at 210min


title: CLL B-cell, patient M2_unstimulated cells_at 60min


title: CLL B-cell, patient M8_stimulated cells_at 90min


title: CLL B-cell, patient M8_stimulated cells_at 390min


title: CLL B-cell, patient M8_unstimulated cells_at 390min


title: CLL B-cell, patient M8_unstimulated cells_at 90min


title: CLL B-cell, patient M7_stimulated cells_at 390min


title: CLL B-cell, patient M8_unstimulated cells_at 210min


title: CLL B-cell, patient M7_unstimulated cells_at 390min


title: CLL B-cell, patient M7_unstimulated cells_at 210min


title: CLL B-cell, patient M8_stimulated cells_at 60min


title: CLL B-cell, patient M8_unstimulated cells_at 60min


title: CLL B-cell, patient M7_stimulated cells_at 210min


title: CLL B-cell, patient M7_stimulated cells_at 90min


title: CLL B-cell, patient M7_stimulated cells_at 60min


title: CLL B-cell, patient M7_unstimulated cells_at 90min


title: CLL B-cell, patient M7_unstimulated cells_at 60min


title: CLL B-cell, patient M6_stimulated cells_at 90min


title: CLL B-cell, patient M6_stimulated cells_at 210min


title: CLL B-cell, patient M6_unstimulated cells_at 390min


title: CLL B-cell, patient M6_stimulated cells_at 390min


title: CLL B-cell, patient M6_unstimulated cells_at 60min


title: Erythropoietic cells rep2

city: Bethesda

first: Jennifer

last: Barb

state: MD

address: 12 South Drive Bldg 12A Room 2001

department: DCB

institute: NIH

hyb_protocol: Each sample was hybridized to a GeneChip® miRNA Array (Affymetrix, Santa Clara, CA, USA) at 48°C and 60 rpm for 16 hours then washed and stained on Fluidics Station 450 and scanned on a GeneChip® Scanner 3000 7G (Affymetrix). The image data were analyzed with the miRNA QC Tool software for quality control (www.affymetrix.com/products_services/arrays/specific/mi_rna.affx#1_4).

scan_protocol: The raw data were preprocessing by Affymetrix miRNA QC Tool (Version 1.1.1.0) using robust multiarray analysis algrorithm for background correction, quantile normalization and median polish summarization. 4,592 unique mature human miRNAs probes were selected for hierarchical clustering analysis. The differential expression miRNA between cell groups were selected by moderated t-statistics with Benjamini-Hochberg multiple testing correction implemented in R bioconductor limma package.

data_processing: RMA was used to normalize the data. The differential expression miRNA between cell groups were selected by moderated t-statistics with Benjamini-Hochberg multiple testing correction implemented in R bioconductor limma package. Differentially expressed miRNA were selected with statistical filters of log 2 FC and FC greater than 2.0.

source_name: Erythropoietic cells rep2

label_protocol: Total RNA containing low molecular weight RNA was labeled using the Flashtag RNA labeling kit (Genisphere, Hatfield, PA, USA) according to the manufacturer's instructions. Briefly, for each sample, 2 µg total RNA were subjected a tailing reaction (2.5 mM MnCl2, ATP, Poly A Polymerase - incubation for 15 minutes at 37°) followed by ligation of the biotinylated signal molecule to the target RNA sample (1× Flash Tag ligation mix biotin, T4 DNA ligase - incubation for 30 minutes at RT) and adding of stop solution.

growth_protocol: CD34+ PBCs were cultured in X-VIVO10 (BioWhittaker, Walkersville, MD) supplemented with 1% human serum albumin (HSA).  At least 1 x 106 CD34+ cells were assayed in 6-well plates and incubated at 37°C and 5% CO2 in a fully humidified atmosphere in air.

extract_protocol: Total RNA enriched with microRNA was extracted using RNAeasy mini kit (Qiagen, Valencia, CA) following the manufacturer’s directions. The concentration of the isolated RNA was determined using the Nanodrop ND-100 spectrophotometer (Nanodrop Technologies, Wilmington, DE). Quality and integrity of the total RNA isolated was assessed on the Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: To induce lineage-specific differentiation, growth factors (R&D Systems, Wiesbaden-Nor-denstadt, Germany, were added as follows: for erythropoietic differentiation, SCF (50 ng/ml), Flt3-ligand (50 ng/ml), IL-3 (10 ng/ml), EPO (10 U/ml); for granulopoietic differentiation, SCF (50 ng/ml), Flt3-ligand (50 ng/ml), IL-3 (10 ng/ml), G-CSF, and GM-CSF (each, 10 ng/ml); for megakaryopoietic differentiation, SCF (50 ng/ml), Flt3-ligand (50 ng/ml), TPO (20 ng/ml). All growth factors were added at the beginning of culture. The cells were cultured in a final volume of 2 ml, in separate wells for each of the conditions and each of the time points.  The cells were inspected daily for 11 days and harvested on days 0, and 11.

value: Erythropoietic cells


title: CLL B-cell, patient M6_unstimulated cells_at 210min


title: Megakaryocytic cells rep1

source_name: Megakaryocytic cells rep1

value: Megakaryocytic cells


title: CLL B-cell, patient M6_stimulated cells_at 60min


title: CLL B-cell, patient M6_unstimulated cells_at 90min


title: Erythropoietic cells rep1

source_name: Erythropoietic cells rep1


title: CD34+ peripheral blood cells rep2

source_name: CD34+ peripheral blood cells rep2

value: CD34+ peripheral blood cells


title: CD34+ peripheral blood cells rep1

source_name: CD34+ peripheral blood cells rep1


title: CLL B-cell, patient M5_stimulated cells_at 390min

source_name: CLL B-cell_stimulated cells_390min


title: Megakaryocytic cells rep2

source_name: Megakaryocytic cells rep2


title: CLL B-cell, patient M5_unstimulated cells_at 90min


title: Granulopoietic cells rep2

source_name: Granulopoietic cells rep2

value: Granulopoietic cells


title: CLL B-cell, patient M5_stimulated cells_at 60min

source_name: CLL B-cell_stimulated cells_60min


title: CLL B-cell, patient M5_unstimulated cells_at 210min


title: CLL B-cell, patient M5_stimulated cells_at 210min

source_name: CLL B-cell_stimulated cells_210min


title: CLL B-cell, patient M5_stimulated cells_at 90min


title: Granulopoietic cells rep1

source_name: Granulopoietic cells rep1


title: CLL B-cell, patient M4_stimulated cells_at 90min

source_name: CLL B-cell_stimulated cells_90min


title: CLL B-cell, patient M5_unstimulated cells_at 390min

source_name: CLL B-cell_unstimulated cells_390min


title: CLL B-cell, patient M5_unstimulated cells_at 60min

source_name: CLL B-cell_unstimulated cells_60min


title: CLL B-cell, patient M4_stimulated cells_at 210min


title: CLL B-cell, patient M4_stimulated cells_at 390min


title: CLL B-cell, patient M4_unstimulated cells_at 390min


title: CLL B-cell, patient M4_unstimulated cells_at 60min


title: CLL B-cell, patient M4_unstimulated cells_at 210min

source_name: CLL B-cell_unstimulated cells_210min


title: CLL B-cell, patient M4_stimulated cells_at 60min


title: CLL B-cell, patient M1_stimulated cells_at 90min


title: Healthy B-cell, subject N6_unstimulated cells_at 390min

value: healthy control

value: Healthy B-cell


title: CLL B-cell, patient M1_unstimulated cells_at 90min

value: chronic lymphocytic leukemia B-cell


title: control, biological rep 9

city: Pittsburgh

first: Kusum

middle: Vijay

last: Pandit

state: PA

address: 200, Lothrop street, W1200-25A Biomedical Science Tower

department: Medicine-PACCM

institute: University of Pittsburgh

description: Lung tissue samples obtained from the University of Pittsburgh Health Sciences Tissue Bank. miRNA expression data from a control lung.

hyb_protocol: Labeled RNA was hybridized for 20 hr at 55C on Agilent 8X15K microRNA array. Arrays were washed according to the manufacturer's protocol.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15K array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters. The normalization algorithm used is quantile normalization.

source_name: Lung tissue, control, biological rep 9

label_protocol: Cy3 labeled RNA was prepared according to the standard Agilent protocol from 100ng total RNA

extract_protocol: Total RNA extracted using miRNeasy mini kit (Qiagen) according to the manufacturer's instructions.

value: whole lung

value: not available


title: control, biological rep 8

source_name: Lung tissue, control, biological rep 8


title: control, biological rep 12

source_name: Lung tissue, control, biological rep 12

value: male


title: Healthy B-cell, subject N6_stimulated cells_at 210min

source_name: Healthy B-cell_stimulated cells_210min

value: S