title: U-2OS pmiR-null

status: Public on Aug 27 2016

city: Boston

first: Zhenfeng

last: Duan

state: Massachusetts

address: 55 Fruit Street Jackson Building

institute: Massachusetts General Hospital

description: Osteosarcoma cell line with pmiR-null.

hyb_protocol: Total RNA was processed and hybridized to Affymetrix Gene Chip U133 Plus 2.0 arrays (Affymetrix, Santa Clara, CA) by the Gene Array Technology Center at Harvard Medical School (http://genome.med.harvard.edu).

scan_protocol: GeneChip Scanner 3000 7G.

data_processing: The average expression value for each gene across the arrays was used to normalize the mRNA intensities. The CEL files were transformed into intensity information using the RMA normalization of Qlucore 3.2. Qlucore were used to analyze the microarray data (http://www.qlucore.com). Fold change in expression between miR-1 treated cell lines and control cell lines were evaluated using the Mann-Whitney test. A 1.2 fold change or greater change in intensity combined with a Mann-Whitney associated P value less than 0.05 was used as the criterion for inclusion in our filtered data set.

source_name: U-2OS osteosarcoma cells, miR-null

label_protocol: Labeled with biotin.

growth_protocol: The U-2OS and KHOS osteosarcoma cell lines were seeded onto the 100mm cell culture plate.

extract_protocol: Total RNA was collected from these cells using TRIzol® Reagent (GIBCO Grand Island, NY) according to the manufacturer’s instructions. To account for and eliminate biologic noise, RNA was isolated from three distinct flasks of each cell line and pooled together. RNA quality was determined via ethidium bromide staining following agarose/formaldehyde gel electrophoresis.

treatment_protocol: Cells were transfected with miRSelect pEP-miR-1 or miRSelect pEP-miR-Null using Lipofectamine LTX and Plus Reagent (Invitrogen) for 48 hours.

tag: cell line

tag: cell type

value: osteosarcoma cell line

tag: miRNA

value: miR-null


title: KHOS control

type: RNA

country: USA

description: Osteosarcoma cell line.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: KHOS osteosarcoma cells

value: KHOS


title: Ov_Tumor_Reference_Mix vs.  X4049

status: Public on Sep 30 2016

city: Santa Monica

first: Habib

last: Hamidi

state: CA

address: 2825 Santa Monica Blvd., Suite 200

institute: UCLA

description: reference_mix: The reference mix contained equal amounts of 106 ovarian samples including the following histologies: adenocarcinama=1, benign=4, clear cell= 3, endothelial=5, goblet cell=1, MMMT=5, mucinous=3. normal=7, serous=67, squamous=1, transitional

hyb_protocol: 825 ng each of labeled reference mix (cy3 label) and individual sample (cy5 label) were applied to Whole Human Genome 4X44 microarrays (Agilent G4112F) using the In Situ Hybridization Kit Plus (Agilent) protocol

scan_protocol: Slides were read on an Agilent G2505B scanner. All experiments were scanned with extended dynamic range enabled.

data_processing:
Agilent Feature Extraction Software (v9.5.1, 10.7, and 11.0) was used with no background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, error model used to determine
Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method.

source_name: 106 pooled ovarian samples

label_protocol: RNA were labeled with Cy3-CTP or Cy5-CTP using the Quick-Amp Labeling Kit (Agilent) following manufacturer's instructions

extract_protocol: Total RNA extracted using Qiagen RNeasy Kit following manufacturer's protocol.

tag: tissue

value: ovary

tag: control type

value: pooled reference sample

source_name: Ovarian Cancer Sample X4049


title: KHOS pmiR-null

description: Osteosarcoma cell line with pmiR-null.

source_name: KHOS osteosarcoma cells, miR-null


title: Ov_Tumor_Reference_Mix vs.  X4030

source_name: Ovarian Cancer Sample X4030


title: Ov_Tumor_Reference_Mix vs.  X4042

source_name: Ovarian Cancer Sample X4042


title: U-2OS control

description: Osteosarcoma cell line.

source_name: U-2OS osteosarcoma cells


title: Ov_Tumor_Reference_Mix vs.  X4032

source_name: Ovarian Cancer Sample X4032


title: Ov_Tumor_Reference_Mix vs.  X4056

source_name: Ovarian Cancer Sample X4056


title: Ov_Tumor_Reference_Mix vs.  X4048

source_name: Ovarian Cancer Sample X4048


title: Ov_Tumor_Reference_Mix vs.  X4031

source_name: Ovarian Cancer Sample X4031


title: Ov_Tumor_Reference_Mix vs.  X4025

source_name: Ovarian Cancer Sample X4025


title: 6h_17a_rep2

status: Public on Jun 30 2016

city: Athens

first: Olga

last: Papadodima

address: 48, Vasileos Konstantinou av.

country: Greece

institute: National Hellenic Research Foundation

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: background corrected values were vst transformed and normalized using rsn method

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: HUVEC were  maintained in pooled cultures up to passage 4 in M199 including 15% FBS, 1% L-glutamine, 5U/ml heparin, 0.2mg/ml ECGS and antibiotics.

extract_protocol: Total RNA was isolated using the pureLink RNA Mini Kit (Ambion, Carlsbad, California, USA)

treatment_protocol: Serum-starved confluent HUVEC grown in 6-well plates were treated with 2μM of test compound or vehicle in presence of 2.5% FBS for 6 or 24 h.

value: Human Umbilical Vein Endothelial Cells (HUVEC)

tag: time point


title: 6h_18b_rep2


title: 24h_17a_rep1


title: 24h_17a_rep2


title: 24h_18b_rep2


title: 24h_18c_rep3


title: microRNA counts from H1-hESC (ENCLB795CMH)

status: Public on May 26 2016

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR408BER/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on human H1-hESC
experiment encode accession: ENCSR408BER
assay title: microRNA counts
assembly: GRCh38
encode release date: 2015-12-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB795CMH
size range: <30
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

hyb_protocol: Nanostring protocol

scan_protocol: Nanostring protocol

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens H1-hESC stem cell male embryo

label_protocol: Nanostring protocol

value: stem cell

tag: description

value: embryonic stem cells

tag: biosample encode accession

tag: age

value: unknown

tag: health state

value: healthy

tag: lab

value: Barbara Wold, Caltech

tag: dev stage

value: embryonic

tag: Sex

value: male

tag: link

value: ENCBS716AAA at ENCODE; https://www.encodeproject.org/ENCBS716AAA/

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/

value: ENCODE dbxrefs Cellosaurus CVCL_9771; http://web.expasy.org/cellosaurus/CVCL_9771

value: ENCODE dbxrefs H1-hESC; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=H1-hESC


title: microRNA counts from H1-hESC (ENCLB922NCX)

description:
https://www.encodeproject.org/experiments/ENCSR408BER/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on human H1-hESC
experiment encode accession: ENCSR408BER
assay title: microRNA counts
assembly: GRCh38
encode release date: 2015-12-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB922NCX
size range: <30
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

value: ENCBS051SJH at ENCODE; https://www.encodeproject.org/ENCBS051SJH/


title: 24h_18b_rep1


title: 24h_DMSO_rep3


title: 24h_DMSO_rep1


title: 6h_18c_rep3


title: 6h_17a_rep1


title: 24h_DMSO_rep2


title: 24h_18c_rep1


title: 6h_18b_rep1


title: MM.464-MM96db

status: Public on Mar 23 2016

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: Gene expression data from multiple myeloma newly-diagnosed primary tumor.

hyb_protocol: The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45°C on GeneChip Gene 1.0 ST array, according to the standard Affymetrix protocol, using the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning  of the arrays was performed using the GeneChip Scanner 7G.

data_processing: Log2-transformed expression values were extracted from CEL files raw data and normalized using RMA procedure in the affy package for Bioconductor and the Transcript Cluster Annotations included in the cdf definition files version 18 available at the Brainarray portal at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/18.0.0/version.html

source_name: Newly-diagnosed MM patient 464

label_protocol: Biotinylated single stranded cDNA samples were prepared starting from 100 nanograms of purified total RNA, according to the standard Affymetrix protocol (GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Gibco BRL). RNA was purified using the Rneasy Mini Kit according to the manufacturer's instruction (Qiagen).

treatment_protocol: Plasma cells were purified from bone marrow samples using CD138 immunomagnetic microbeads according to the manufacturer's instructions (MidiMACS system, Miltenyi Biotec); the purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases.

tag: translocation

tag: disease state

value: multiple myeloma primary tumor


title: 6h_18c_rep1


title: MM.449-MM96db

source_name: Newly-diagnosed MM patient 449


title: MM.437-MM96db

source_name: Newly-diagnosed MM patient 437


title: 6h_DMSO_rep1


title: MM.433-MM96db

source_name: Newly-diagnosed MM patient 433


title: MM.434-MM96db

source_name: Newly-diagnosed MM patient 434


title: MM.447-MM96db

source_name: Newly-diagnosed MM patient 447


title: MM.431-MM96db

source_name: Newly-diagnosed MM patient 431


title: MM.435-MM96db

source_name: Newly-diagnosed MM patient 435


title: MM.429-MM96db

source_name: Newly-diagnosed MM patient 429


title: 6h_DMSO_rep3


title: MM.425-MM96db

source_name: Newly-diagnosed MM patient 425


title: MM.424-MM96db

source_name: Newly-diagnosed MM patient 424


title: 6h_DMSO_rep2


title: MM.430-MM96db

source_name: Newly-diagnosed MM patient 430


title: MM.423-MM96db

source_name: Newly-diagnosed MM patient 423


title: MM.422-MM96db

source_name: Newly-diagnosed MM patient 422


title: MM.448-MM96db

source_name: Newly-diagnosed MM patient 448


title: MM.407-MM96db

source_name: Newly-diagnosed MM patient 407


title: MM.411-MM96db

source_name: Newly-diagnosed MM patient 411


title: MM.402-MM96db

source_name: Newly-diagnosed MM patient 402


title: MM.413-MM96db

source_name: Newly-diagnosed MM patient 413


title: MM.406-MM96db

source_name: Newly-diagnosed MM patient 406


title: MM.414-MM96db

source_name: Newly-diagnosed MM patient 414


title: MM.392-MM96db

source_name: Newly-diagnosed MM patient 392


title: MM.398-MM96db

source_name: Newly-diagnosed MM patient 398


title: MM.382-MM96db

source_name: Newly-diagnosed MM patient 382


title: MM.375-MM96db

source_name: Newly-diagnosed MM patient 375


title: MM.335-MM96db

source_name: Newly-diagnosed MM patient 335


title: MM.330-MM96db

source_name: Newly-diagnosed MM patient 330


title: MM.362-MM96db

source_name: Newly-diagnosed MM patient 362


title: MM.314-MM96db

source_name: Newly-diagnosed MM patient 314


title: MM.317-MM96db

source_name: Newly-diagnosed MM patient 317


title: MM.310-MM96db

source_name: Newly-diagnosed MM patient 310


title: MM.340-MM96db

source_name: Newly-diagnosed MM patient 340


title: MM.313-MM96db

source_name: Newly-diagnosed MM patient 313


title: MM.302-MM96db

source_name: Newly-diagnosed MM patient 302


title: MM.286-MM96db

source_name: Newly-diagnosed MM patient 286


title: MM.295-MM96db

source_name: Newly-diagnosed MM patient 295


title: MM.268-MM96db

source_name: Newly-diagnosed MM patient 268


title: MM.282-MM96db

source_name: Newly-diagnosed MM patient 282


title: MM.269-MM96db

source_name: Newly-diagnosed MM patient 269


title: MM.267-MM96db

source_name: Newly-diagnosed MM patient 267


title: MM.300-MM96db

source_name: Newly-diagnosed MM patient 300


title: MM.301-MM96db

source_name: Newly-diagnosed MM patient 301


title: MM.327-MM96db

source_name: Newly-diagnosed MM patient 327


title: MM.308-MM96db

source_name: Newly-diagnosed MM patient 308


title: MM.261-MM96db

source_name: Newly-diagnosed MM patient 261


title: MM.263-MM96db

source_name: Newly-diagnosed MM patient 263


title: MM.262-MM96db

source_name: Newly-diagnosed MM patient 262


title: MM.321-MM96db

source_name: Newly-diagnosed MM patient 321


title: MM.280-MM96db

source_name: Newly-diagnosed MM patient 280


title: MM.278-MM96db

source_name: Newly-diagnosed MM patient 278


title: MM.274-MM96db

source_name: Newly-diagnosed MM patient 274


title: MM.253-MM96db

source_name: Newly-diagnosed MM patient 253


title: MM.239-MM96db

source_name: Newly-diagnosed MM patient 239


title: MM.243-MM96db

source_name: Newly-diagnosed MM patient 243


title: MM.219-MM96db

source_name: Newly-diagnosed MM patient 219


title: MM.154-MM96db

source_name: Newly-diagnosed MM patient 154


title: MM.206-MM96db

source_name: Newly-diagnosed MM patient 206


title: MM.229-MM96db

source_name: Newly-diagnosed MM patient 229


title: MM.159-MM96db

source_name: Newly-diagnosed MM patient 159


title: MM.179-MM96db

source_name: Newly-diagnosed MM patient 179


title: MM.087-MM96db

source_name: Newly-diagnosed MM patient 087


title: MM.123-MM96db

source_name: Newly-diagnosed MM patient 123


title: MM.177-MM96db

source_name: Newly-diagnosed MM patient 177


title: MM.104-MM96db

source_name: Newly-diagnosed MM patient 104


title: MM.066-MM96db

source_name: Newly-diagnosed MM patient 066


title: MM.055-MM96db

source_name: Newly-diagnosed MM patient 055


title: MM.143-MM96db

source_name: Newly-diagnosed MM patient 143


title: MM.056-MM96db

source_name: Newly-diagnosed MM patient 056


title: MM.131-MM96db

source_name: Newly-diagnosed MM patient 131


title: MM.212-MM96db

source_name: Newly-diagnosed MM patient 212


title: MM.074-MM96db

source_name: Newly-diagnosed MM patient 074


title: MM.050-MM96db

source_name: Newly-diagnosed MM patient 050


title: MM.049-MM96db

source_name: Newly-diagnosed MM patient 049


title: MM.052-MM96db

source_name: Newly-diagnosed MM patient 052


title: MM.115-MM96db

source_name: Newly-diagnosed MM patient 115


title: MM.213-MM96db

source_name: Newly-diagnosed MM patient 213


title: MM.078-MM96db

source_name: Newly-diagnosed MM patient 078


title: MM.043-MM96db

source_name: Newly-diagnosed MM patient 043


title: MM.039-MM96db

source_name: Newly-diagnosed MM patient 039


title: MM.069-MM96db

source_name: Newly-diagnosed MM patient 069


title: MM.042-MM96db

source_name: Newly-diagnosed MM patient 042


title: MM.025-MM96db

source_name: Newly-diagnosed MM patient 025


title: mirMM.448-MM96db

status: Public on Dec 08 2015

description: microRNA expression data from multiple myeloma newly-diagnosed primary tumor.

hyb_protocol: Byotin-labeled RNA samples were hybridized for 16 hours  at 48°C on GeneChip miRNA 3.0 array, according to the standard manifacturer's protocol, using the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: Raw data were extracted from CEL files and then normalized using robust multi-array average (RMA) procedure in the affy package for Bioconductor and the miRbase Release 18 annotations included in the corresponding cdf definition files available at the University of Michigan Brainarray portal at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/18.0.0/version.html). Annotations were then updated to miRBase Release 20 definition using the mirna.diff files available at the miRbase website

source_name: Newly-diagnosed MM patient 448

label_protocol: 500 ng of total RNA were converted to biotin-labeled RNA using the FlashTag Biotin HSR Labeling kit, according to Affimetrix protocol.

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


title: mirMM.447-MM96db

source_name: Newly-diagnosed MM patient 447


title: mirMM.449-MM96db

source_name: Newly-diagnosed MM patient 449


title: mirMM.437-MM96db

source_name: Newly-diagnosed MM patient 437


title: MM.035-MM96db

source_name: Newly-diagnosed MM patient 035


title: MM.026-MM96db

source_name: Newly-diagnosed MM patient 026


title: mirMM.435-MM96db

source_name: Newly-diagnosed MM patient 435


title: MM.040-MM96db

source_name: Newly-diagnosed MM patient 040


title: mirMM.434-MM96db

source_name: Newly-diagnosed MM patient 434


title: MM.027-MM96db

source_name: Newly-diagnosed MM patient 027


title: mirMM.431-MM96db

source_name: Newly-diagnosed MM patient 431


title: mirMM.433-MM96db

source_name: Newly-diagnosed MM patient 433


title: mirMM.429-MM96db

source_name: Newly-diagnosed MM patient 429


title: MM.021-MM96db

source_name: Newly-diagnosed MM patient 021


title: mirMM.425-MM96db

source_name: Newly-diagnosed MM patient 425


title: mirMM.430-MM96db

source_name: Newly-diagnosed MM patient 430


title: mirMM.424-MM96db

source_name: Newly-diagnosed MM patient 424


title: MM.016-MM96db

source_name: Newly-diagnosed MM patient 016


title: MM.036-MM96db

source_name: Newly-diagnosed MM patient 036


title: mirMM.423-MM96db

source_name: Newly-diagnosed MM patient 423


title: mirMM.422-MM96db

source_name: Newly-diagnosed MM patient 422


title: mirMM.464-MM96db

source_name: Newly-diagnosed MM patient 464


title: MM.030-MM96db

source_name: Newly-diagnosed MM patient 030


title: MM.004-MM96db

source_name: Newly-diagnosed MM patient 004


title: MM.034-MM96db

source_name: Newly-diagnosed MM patient 034


title: MM.015-MM96db

source_name: Newly-diagnosed MM patient 015


title: MM.387-MM96db

source_name: Newly-diagnosed MM patient 387


title: MM.385-MM96db

source_name: Newly-diagnosed MM patient 385


title: mirMM.413-MM96db

source_name: Newly-diagnosed MM patient 413


title: mirMM.414-MM96db

source_name: Newly-diagnosed MM patient 414


title: mirMM.387-MM96db


title: mirMM.385-MM96db


title: mirMM.392-MM96db

source_name: Newly-diagnosed MM patient 392


title: mirMM.406-MM96db

source_name: Newly-diagnosed MM patient 406


title: mirMM.398-MM96db

source_name: Newly-diagnosed MM patient 398


title: mirMM.402-MM96db

source_name: Newly-diagnosed MM patient 402


title: mirMM.407-MM96db

source_name: Newly-diagnosed MM patient 407


title: mirMM.411-MM96db

source_name: Newly-diagnosed MM patient 411


title: mirMM.382-MM96db

source_name: Newly-diagnosed MM patient 382


title: mirMM.340-MM96db

source_name: Newly-diagnosed MM patient 340


title: mirMM.362-MM96db

source_name: Newly-diagnosed MM patient 362


title: mirMM.375-MM96db

source_name: Newly-diagnosed MM patient 375


title: mirMM.317-MM96db

source_name: Newly-diagnosed MM patient 317


title: mirMM.310-MM96db

source_name: Newly-diagnosed MM patient 310


title: mirMM.314-MM96db

source_name: Newly-diagnosed MM patient 314


title: mirMM.313-MM96db

source_name: Newly-diagnosed MM patient 313


title: mirMM.302-MM96db

source_name: Newly-diagnosed MM patient 302


title: mirMM.330-MM96db

source_name: Newly-diagnosed MM patient 330


title: mirMM.327-MM96db

source_name: Newly-diagnosed MM patient 327


title: mirMM.321-MM96db

source_name: Newly-diagnosed MM patient 321


title: mirMM.308-MM96db

source_name: Newly-diagnosed MM patient 308


title: mirMM.335-MM96db

source_name: Newly-diagnosed MM patient 335


title: mirMM.286-MM96db

source_name: Newly-diagnosed MM patient 286


title: mirMM.301-MM96db

source_name: Newly-diagnosed MM patient 301


title: mirMM.282-MM96db

source_name: Newly-diagnosed MM patient 282


title: mirMM.295-MM96db

source_name: Newly-diagnosed MM patient 295


title: mirMM.300-MM96db

source_name: Newly-diagnosed MM patient 300


title: mirMM.274-MM96db

source_name: Newly-diagnosed MM patient 274


title: mirMM.278-MM96db

source_name: Newly-diagnosed MM patient 278


title: mirMM.269-MM96db

source_name: Newly-diagnosed MM patient 269


title: mirMM.263-MM96db

source_name: Newly-diagnosed MM patient 263


title: mirMM.262-MM96db

source_name: Newly-diagnosed MM patient 262


title: mirMM.253-MM96db

source_name: Newly-diagnosed MM patient 253


title: mirMM.261-MM96db

source_name: Newly-diagnosed MM patient 261


title: mirMM.268-MM96db

source_name: Newly-diagnosed MM patient 268


title: mirMM.267-MM96db

source_name: Newly-diagnosed MM patient 267


title: mirMM.177-MM96db

source_name: Newly-diagnosed MM patient 177


title: mirMM.280-MM96db

source_name: Newly-diagnosed MM patient 280


title: mirMM.206-MM96db

source_name: Newly-diagnosed MM patient 206


title: mirMM.154-MM96db

source_name: Newly-diagnosed MM patient 154


title: mirMM.143-MM96db

source_name: Newly-diagnosed MM patient 143


title: mirMM.123-MM96db

source_name: Newly-diagnosed MM patient 123


title: mirMM.159-MM96db

source_name: Newly-diagnosed MM patient 159


title: mirMM.131-MM96db

source_name: Newly-diagnosed MM patient 131


title: mirMM.212-MM96db

source_name: Newly-diagnosed MM patient 212


title: mirMM.219-MM96db

source_name: Newly-diagnosed MM patient 219


title: mirMM.213-MM96db

source_name: Newly-diagnosed MM patient 213


title: mirMM.239-MM96db

source_name: Newly-diagnosed MM patient 239


title: mirMM.229-MM96db

source_name: Newly-diagnosed MM patient 229


title: mirMM.179-MM96db

source_name: Newly-diagnosed MM patient 179


title: mirMM.243-MM96db

source_name: Newly-diagnosed MM patient 243


title: mirMM.087-MM96db

source_name: Newly-diagnosed MM patient 087


title: mirMM.104-MM96db

source_name: Newly-diagnosed MM patient 104


title: mirMM.115-MM96db

source_name: Newly-diagnosed MM patient 115


title: mirMM.074-MM96db

source_name: Newly-diagnosed MM patient 074


title: mirMM.069-MM96db

source_name: Newly-diagnosed MM patient 069


title: mirMM.066-MM96db

source_name: Newly-diagnosed MM patient 066


title: mirMM.056-MM96db

source_name: Newly-diagnosed MM patient 056


title: mirMM.078-MM96db

source_name: Newly-diagnosed MM patient 078


title: mirMM.040-MM96db

source_name: Newly-diagnosed MM patient 040


title: mirMM.039-MM96db

source_name: Newly-diagnosed MM patient 039


title: mirMM.043-MM96db

source_name: Newly-diagnosed MM patient 043


title: mirMM.049-MM96db

source_name: Newly-diagnosed MM patient 049


title: mirMM.042-MM96db

source_name: Newly-diagnosed MM patient 042


title: mirMM.052-MM96db

source_name: Newly-diagnosed MM patient 052


title: mirMM.055-MM96db

source_name: Newly-diagnosed MM patient 055


title: mirMM.004-MM96db

source_name: Newly-diagnosed MM patient 004


title: mirMM.015-MM96db

source_name: Newly-diagnosed MM patient 015


title: mirMM.036-MM96db

source_name: Newly-diagnosed MM patient 036


title: mirMM.050-MM96db

source_name: Newly-diagnosed MM patient 050


title: mirMM.016-MM96db

source_name: Newly-diagnosed MM patient 016


title: mirMM.035-MM96db

source_name: Newly-diagnosed MM patient 035


title: mirMM.034-MM96db

source_name: Newly-diagnosed MM patient 034


title: mirMM.030-MM96db

source_name: Newly-diagnosed MM patient 030


title: mirMM.027-MM96db

source_name: Newly-diagnosed MM patient 027


title: mirMM.025-MM96db

source_name: Newly-diagnosed MM patient 025


title: mirMM.021-MM96db

source_name: Newly-diagnosed MM patient 021


title: mirMM.026-MM96db

source_name: Newly-diagnosed MM patient 026


title: ChIP-Seq analysis of H3K4me1; chondr. dif cls; Lib:MC:20100726:09--ChIP:MC:20100713:09:chondrogenic dif cells

status: Public on Mar 31 2011

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

institute: Broad Institute

description:
sample_term_id: CL_0000138
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100726:09--ChIP:MC:20100713:09:chondrogenic dif cell
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5650
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5951
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM669909_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me1.58.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100726:09--ChIP:MC:20100713:09:chondrogenic dif cells:.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 58 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6515
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.4904
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.5252
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.9963
IROC_PERCENTILE: 79
POISSON_SCORE: 0.6278
POISSON_PERCENTILE: 79

**********************************************************************

ANALYSIS FILE NAME: GSM669909_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me1.58.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100726:09--ChIP:MC:20100713:09:chondrogenic dif cells:.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 58 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6725
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: CfBMDMSC H3K4me1 58
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 Donor 58 Library Lib:MC:20100726:09--ChIP:MC:20100713:09:chondrogenic dif cells EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.4904
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.5252
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.9963
IROC_PERCENTILE: 79
POISSON_SCORE: 0.6278
POISSON_PERCENTILE: 79

**********************************************************************

molecule: genomic DNA

source_name: chondrocytes derived via in vitro culture from mesenchymal stem cells; Lib:MC:20100726:09--ChIP:MC:20100713:09:chondrogenic dif cells

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

tag: molecule

value: genomic DNA

tag: disease

tag: markers

value: Medium:NA; Differentiation Method:alginate hydrogel scaffold (SR Herlofsen et al, Tissue Eng Part A. 2011)

value: chondrogenic dif cells

value: Unknown

value: Primary Cell Culture

value: Rikshospitalet University Hospital

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K4me1

value: Bioruptor


title: 611 2015 IFE

status: Public on Oct 01 2015

city: Brussels

first: Cédric

last: Blanpain

address: Route de Lennik 808

country: Belgium

institute: ULB

hyb_protocol: cDNA was hybridized to Affymetrix Mouse Genome 430PM strip arrays for 16 hours at 45ºC.Washing and staining of microarrays was performed using  the GeneAtlas Fluidics Station (Affymetrix, Santa Clara, CA)

scan_protocol: GeneChips were scanned in a GeneAtlas Imaging Station (Affymetrix, Santa Clara, CA)

data_processing: RMA normalization method

label: Biotin

organism: Mus musculus

source_name: FACS sorted epidermal cells

label_protocol: 25 ng total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2) and 8 µg of cDNA were subsequently fragmented and labeled using GeneChip Human Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

extract_protocol: qiagen kit

tag: genotype/variation

tag: treatment

tag: isolation

value: FACS

tag: staining


title: Col WT, rep2

status: Public on Aug 31 2014

city: Singapore

first: Toshiro

last: Ito

address: 1 Research Link, National University of Singapore

country: Singapore

institute: Temasek Life Sciences Laboratory

description: Total RNA from wild-type plants were used in this experiment. This is the second sample of the two biological replicates.

hyb_protocol: Hybridization was performed  following NimbleGen standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed  following NimbleGen standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Arabidopsis thaliana

source_name: Col WT, 13 DAG

label_protocol: Labeling was performed following NimbleGen standard operating protocol. See www.nimblegen.com.

growth_protocol: The seeds of the indicated genotype were planted on soil, and grown at 22°C under long day (LD, 16 hour light, 8 hour dark) conditions. 13 DAG seedlings were harvested.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and DNA was removed by on-column DNaseI digestion with the RNase-Free DNase set (Qiagen).

treatment_protocol: No treatment applied.

tag: genetic background

tag: tissue

value: seedling

tag: genotype

value: wild-type

tag: phenotype

value: Normal flowering


title: 614 2015 BULGE


title: 609 2015 K14 Ep+

source_name: FACS sorted tumor cells

value: 2,5mg TAM

value: Epcam+/Lin-/DAPI-


title: 612 2015 BULGE


title: A1907-06 Lgr5 EP+ mixed

hyb_protocol: cDNA was hybridized to Affymetrix Mouse Genome 430 arrays for 16 hours at 45ºC.Washing and staining of microarrays was performed using  the GeneAtlas Fluidics Station (Affymetrix, Santa Clara, CA)

value: 10mg TAM


title: 606 2015 Lgr5 Ep- MIXED

value: Epcam-/Lin-/DAPI-


title: 613 2015 IFE


title: 1123 2014 Lgr5 Ep+ MIXED


title: Col WT, rep1

description: Total RNA from wild-type plants were used in this experiment. This is the first sample of the two biological replicates.


title: 35S-JMJ30-HA, rep1

description: Total RNA from 35S::JMJ30-HA transgenic plants were used in this experiment. This is the first sample of the two biological replicates.

value: Late flowering


title: 1122 2014 Lgr5 Ep- MIXED


title: 610 2015 K14 Ep+


title: 35S-JMJ30-HA, rep2

description: Total RNA from 35S::JMJ30-HA transgenic plants were used in this experiment. This is the second sample of the two biological replicates.


title: 605 2015 Lgr5 Ep+ MIXED


title: 608 2015 Lgr5 Ep- MIXED


title: 308 2014 K14 Ep+


title: A1907-07 Lgr5 EP- mixed


title: 5 wk old WT male 2

status: Public on Apr 07 2010

first: Hao

last: Zhu

address: 7th Floor Karp, 300 Longwood Ave.

department: Hematology/Oncology

institute: Children's Hospital of Boston

description: replicate 2

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Mouse quad muscle

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: strain

tag: age

value: 5 weeks

value: quadraceps muscle


title: 607 2015 Lgr5 Ep+ MIXED


title: 5 wk old Lin28A Tg male  2

description: replicate 2


title: 5 wk old Lin28A Tg male  1

description: replicate 1


title: 307 2014 K14 Ep+


title: 5 wk old WT male 1

description: replicate 1