title: MC3T3-E1 LIPUS-24 h 1

description:
US-1
MC3T3-E1 LIPUS + 24h culture at 37˚C-1.
MC3T3-E1 cell line: derived from the calvaria of 0-day-old newborn mice; fibroblast-like morphology; infinite lifespan.

tag: time


title: MC3T3-E1 (control-2)

status: Public on Mar 26 2013

type: RNA

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

country: Japan

institute: University of Toyama

description:
Ctr-2
MC3T3-E1 mock treatment (control-2).
MC3T3-E1 cell line: derived from the calvaria of 0-day-old newborn mice; fibroblast-like morphology; infinite lifespan.

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h. The arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: The arrays were scanned with a probe array scanner (Affymetrix).

data_processing: GeneChip Analysis Suite. RMA normalized.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Mouse preosteoblast MC3T3-E1 cells, mock treated

label_protocol: 500 ng of total RNA was used to synthesize cRNA with a GeneChip 3' IVT Express Kit (Affymetrix).

growth_protocol: The cells were cultured in MEMα supplemented with 10% fetal bovine serum (FBS) at 37˚C in humidified air with 5% CO2.

extract_protocol: Total RNA was extracted from cells using an RNeasy Total RNA Extraction kit (Qiagen), and treated with DNase I (Qiagen) for 15 min at room temperature to remove residual genomic DNA. RNA quality was analyzed using a Bioanalyzer 2100 (Agilent Technologies), producing RIN values between 9.5 and 10.

treatment_protocol: LIPUS treatment was applied by a sonic accelerated gracture-healing system (SAFHS) apparatus (SAFHS 4000J, Teijin Pharma Ltd., Tokyo, Japan). The signal had the SATA (spatial average, temporal average) intensity of 30 mW/cm2, with a frequency of 1.5 MHz in a pulsed-wave mode (0.2 s-burst sine waves repeated at 1.0 kHz). The cells were cultivated in MEMα supplemented with 10% FBS, 0.3 mM L-ascorbic acid and 10 mM β-glycerophosphate at 37˚C for 14 days. After trypsinization, the cells (5 x 10^5 cells) were seeded on 35-mm plastic culture dish (ASAHI GLASS Co., Ltd., Tokyo, Japan) and cultured at 37˚C for 24 h. LIPUS was transmitted through the bottom of the culture dish with standard ultrasound coupling gel (Teijin Pharma Ltd.). Attached cells in the dish with 2 ml of culture medium were sonicated for 20 min at 37˚C in a CO2 incubator. After sonication, cells were incubated at 37˚C in a CO2 incubator for 6 and 24 h. Mock-treated cells served as the control.

tag: cell line

tag: strain

tag: cell type

value: preosteoblasts

tag: treatment

value: mock

value: control


title: 3_206_T_R3

status: Public on Apr 01 2013

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

country: Germany

institute: RWTH Aachen University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute • Transfer 80μl of hyb solution to each array, then tape holes • Hybridize 16 hours at 45° at 60rpm • Fluidics washing is FS450_00007

scan_protocol: according to Affymetrix protocol - Affymetrix Gene ChIP Scanner 3000 7G

data_processing: normalization method: RMA; raw expression threshold: 150, dabg p: 0.05; expression data format: log2

source_name: Tak1 LPC-KO/Rip3-/- mice

label_protocol: Samples were amplified and labelled using the Ambion® WT Expression Kit, combined with the GeneChip® WT Terminal Labeling and Controls Kit according to the manufacturers instructions.

growth_protocol: Liver tissue, excised of 6 week old male mice

extract_protocol: RNA was extracted from snap frozen tissue using the Qiagen RNeasy Kit

tag: genotype

value: Tak1 LPC-KO/Rip3-/- mice

tag: gender

value: male

tag: tissue

value: liver

tag: age

value: 6 weeks


title: 2_205_T_R3


title: Normal breast Affymetrix 2

status: Public on Mar 01 2013

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

country: USA

institute: NCBI/NLM/NIH

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The data were analyzed with Partek GS 6.5 and GCRMA as normalization method.

organism: Homo sapiens

source_name: Normal Breast tissue

label_protocol: 1ng total RNA was used as input for the Pico amplification and 4ug of amplified cDNA was used for Exon Module amplification. cDNA amplification products were fragmented and labeled with biotin using the NuGEN FL module, hybridized to HG Gene 1.0 ST arrays (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix Hybridization Control Kit. And washed and stained using Affymetrix Wash and Stain kit. All steps were processed following the manufactures suggestions.

extract_protocol: RNA samples for amplification with the Pico kit were isolated from fresh tissues using the RNeasy Micro Kit (Qiagen) including the optional DNase treatment, according to the manufacturer's instructions. Total RNA was quantified using a Nanodrop Spectrophotometer 2000 (Thermo Scientific Inc., Waltham, MA, USA) and the quality confirmed on an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). RNA amplifications were carried out using Nugen Pico WTA amplification system according to the manufacturersâ€™ suggestions followed by an additional amplification step using Nugen Exon Module.

value: normal breast

tag: histological type

value: Normal

tag: age (y)

tag: grade

tag: site

tag: er   (1= positive, 0=nagative)

tag: pr   (1= positive, 0= negative)

tag: her2  (1=positive, 0=negative)

tag: triple negative (1= yes, 0= no)


title: 1_204_T_R3


title: pathologic_Alzheimer_3_hippocampus_rep2

status: Public on Jan 11 2013

city: São Paulo

first: Renato

middle: David

last: Puga

state: São Paulo

address: Dr Ovidio Pires de Campos,785

department: Instituto de Psiquiatria

country: Brazil

institute: Universidade de São Paulo

description: Reference RNA: Daudi (Burkitt's lymphoma), DLD-1 (colorectal adenocarcinoma), DU 145 (prostate carcinoma), FaDu (pharinx squamous cell carcinoma), GM-637 (fibroblast), H-146 (small cell lung carcinoma), HT-1080 (fibrosarcoma), HB4a (normal mammary luminal epithelium), HEK (human embryonic kidney), Jurkat (acute T cell leukemia), Saos-2 (osteosarcoma), SK-BR-3 (breast adenocarcinoma), SK-MEL-28 (melanoma), T24 (bladder transitional cell carcinoma), T98G (glioblastoma multiforme).

hyb_protocol: Hibridization - Solution: 5 X SSC; 0,1% SDS; 4 ug poly A DNA; 4 ug Cot1 DNA; 5X Denhardts ; 10 ug Esperma de salmao,  Formamida 25%. / Temperature:14 a 24 hs / Time:42 C / Touch Down: Washing - Round 1 - Solution: SSC 2x / Temperature:42 / Time:10 min. / Washing Number: 1 Washing - Round 2 - Solution: SSC 0,1x; SDS 0,1% / Temperature:42 / Time:10 min. / Washing Number: 2 Washing - Round 3 - Solution: SSC 0,1x / Temperature:42 / Time:10 min. / Washing Number: 2

scan_protocol: Hardware: Perkinelmer / Software: ScanArray

data_processing: Lowesss

source_name: Reference RNA

label_protocol: Protocol Cy3/Cy5

extract_protocol: Trizol

tag: RNA of 15 different cell lines

extract_protocol: kit Pico Pure RNA Isolation Kit

tag: braak

value: 6 CERAD:C CDR:0 Gender:male Age:72 years


title: pathologic_Alzheimer_3_hippocampus_rep1


title: biofilm_cells_a/alpha

status: Public on Jan 23 2013

type: SRA

city: Foster City

first: Brian

last: Tuch

state: CA

address: 850 Lincoln Center Dr.

institute: Life Technologies

description:
Strand-specific RNA-Seq.
Strain QMY23 (PMID: 17351132).
Poly(A) RNA.

library_source: transcriptomic

data_processing:
AB WT Analysis Pipeline.

The reads were aligned to the Candida albicans Assembly 21 (Ca21) genome (from Candida Genome Database [CGD]: www.candidagenome.org) using the alignment algorithm provided by the WT Pipeline v1.2 (Life Technologies) and documented in their manual. The reads were filtered against a database containing rDNA, tRNA, repetitive element, CEN and adapter sequences. Alignments are provided in MAX format. A MAX specification file is available on the Series GSE21291 record.

The WIG files were generated by counting the number of uniquely aligned reads covering each position in the genome. The coverage on the plus and minus strands are provided in the *plus.wig and *minus.wig files, respectively.

Genome_build: Ca21
Supplementary_files_format_and_content: MAX files: alignments. WIG files: Coverage on plus and minus strands.

organism: Candida albicans

source_name: Candida albicans biofilm a/alpha cells

growth_protocol: 37°C; spider medium (PMID: 7992058); biofilm growth.

extract_protocol:
Total RNA was extracted from the yeast cells (Hernday AD, Noble SM, Mitrovich QM, Johnson AD (2010) Genetics and Molecular Biology in Candida albicans. Methods in Enzymology: Elsevier Inc. pp. 737-758).

Two rounds of poly(A) selection with Poly(A)Purist MAG kit (Ambion). SOLiD whole transcriptome (WT) protocol applied to poly(A)-selected RNA.

treatment_protocol: None.

tag: strain

tag: isolate

value: MTLa/MTLalpha

tag: growth type

value: biofilm

tag: rna preparation

value: poly(A) RNA selection


title: 7_218_T_H

source_name: Tak1/Caspase8 LPC double knockout mice

tag: genotype

value: Tak1/Caspase8 LPC double knockout mice

tag: gender


title: MC3T3-E1 (control-3)

description:
Ctr-3
MC3T3-E1 mock treatment (control-3).
MC3T3-E1 cell line: derived from the calvaria of 0-day-old newborn mice; fibroblast-like morphology; infinite lifespan.

tag: cell line

tag: cell type

tag: treatment

tag: time


title: normal_brain_8_hippocampus_rep2

value: 2 CERAD:0 CDR:0 Gender:male Age:89 years


title: normal_brain_8_frontal_cortex_rep2


title: normal_brain_8_hippocampus_rep1


title: normal_brain_8_frontal_cortex_rep1


title: other_dementias_9_frontal_cortex_rep2

value: 0 CERAD:nd CDR:1 Gender:female Age:83 years


title: 75nm PVP_3

status: Public on May 31 2013

city: Durham

first: William

last: Ward

state: NC

address: 109 TW Alexander Dr

department: NHEERL

institute: United States EPA

description:
5665167004_D
replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with no background subtraction in Illumina GenomeStudio (V.2011.1).

organism: Rattus norvegicus

source_name: RBEC4_75nm PVP

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification kit for Illumina arrays

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit with DNase I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser and quantified by NanoDrop spectrophotometer.

value: Rat blood-brain barrier cells

tag: exposed to

value: 1.0 ppm PVP coated nanosilver particles (75nm)


title: pathologic_Alzheimer_3_frontal_cortex_rep2


title: normal_brain_6_frontal_cortex_rep1

value: 0 CERAD:0 CDR:0 Gender:female Age:65 years


title: other_dementias_9_hippocampus_rep2


title: other_dementias_9_frontal_cortex_rep1


title: normal_brain_7_frontal_cortex_rep1

value: 0 CERAD:0 CDR:0 Gender:female Age:59 years


title: pathologic_Alzheimer_3_frontal_cortex_rep1


title: normal_brain_7_frontal_cortex_rep2


title: normal_brain_6_hippocampus_rep1


title: normal_brain_7_hippocampus_rep1


title: normal_brain_6_hippocampus_rep2


title: normal_brain_7_hippocampus_rep2


title: pathologic_Alzheimer_2_hippocampus_rep2

value: 5 CERAD:C CDR:0 Gender:female Age:85 years


title: pathologic_Alzheimer_2_hippocampus_rep1


title: pathologic_Alzheimer_2_frontal_cortex_rep1


title: other_dementias_5_hippocampus_rep1

value: 0 CERAD:0 CDR:3 Gender:female Age:89 years


title: pathologic_Alzheimer_2_frontal_cortex_rep2


title: definitive_Alzheimer_3_hippocampus_rep1

value: 4 CERAD:C CDR:1 Gender:female Age:86 years


title: other_dementias_5_frontal_cortex_rep1


title: other_dementias_5_frontal_cortex_rep2


title: definitive_Alzheimer_3_hippocampus_rep2


title: normal_brain_6_frontal_cortex_rep2


title: definitive_Alzheimer_3_frontal_cortex_rep2


title: definitive_Alzheimer_3_frontal_cortex_rep1


title: other_dementias_9_hippocampus_rep1


title: normal_brain_5_hippocampus_rep2

value: 0 CERAD:0 CDR:0 Gender:male Age:57 years


title: other_dementias_8_frontal_cortex_rep1

value: 2 CERAD:0 CDR:2 Gender:female Age:85 years


title: HB1.F3

status: Public on May 23 2013

city: Daejeon

first: Sungsoo

last: Kang

address: 111 Gwahangno, Yuseong-gu

department: KOBIC

country: South Korea

institute: KRIBB

description: able to self-renew and differentiate into cells of neuronal and glial lineages both in vivo and in vitro

data_processing: Human genome assembly (hg18) and annotation tracks were downloaded from the UCSC Genome Browser, as of June 2008. Using BLAT, all the sequence reads from the Illumina 1G Genome Analyzer were mapped onto hg18.

source_name: neural stem cell

growth_protocol: HB1.F3 and F3.Olig2 cells were maintained in Dulbecco’s modified Eagles medium supplemented with 10% fetal bovine serum and 50 mg/ml gentamicin at 37°C and 5% CO2.

extract_protocol: RNA isolation with Qiazol (Qiagen) was performed according to the manufacturer’s instructions. Then, a small RNA library was prepared with a small RNA preparation kit according to the manufacturer's instructions (Illumina). Finally, a small RNA library was sequenced using an Illumina 1G Genome Analyzer.

value: neural stem cell


title: normal_brain_5_frontal_cortex_rep1


title: C2C12_G0_H3

status: Public on May 01 2013

type: genomic

city: Hyderabad

first: Rakesh

middle: K

last: Mishra

state: Andhra Pradesh

address: Uppal Road

country: India

institute: Centre for Cellular and Molecular Biology

description: C2C12 myoblasts were grown in suspension culture for 48h and harvested for chromatin preparation

hyb_protocol: 5 μg of each Cy3/Cy5-labeled samples were hybridized onto the mouse custom 1 Million ChIP-on-chip Array. Hybridization was performed in the hybridization oven at 65°C for 40 hours, followed by washes with Agilent ChIP-on-chip Wash buffer 1 and 2.

scan_protocol: The washed slides were scanned at 3 μm scan resolution using Agilent DNA microarray scanner as per Agilent Protocol.

data_processing: Data extraction was done using Agilent Feature extraction software and normalized using Agilent DNA Analytics software.

molecule: genomic DNA

label_protocol: 2ug of each DNA Sample was labeled using Agilent Genomic DNA labeling Kit (5190-0449). DNA yield and incorporation of label (specific activity) was measured using NanoDrop spectrophotometer.

extract_protocol: C2C12 myoblasts were maintained in growth medium and synchronized by subjecting subconfluent cells to suspension culture. Briefly, cells were harvested with trypsin and re-cultured as a single-cell suspension in DMEM containing 1.3% methyl cellulose, 20% FBS, 10 mM Hepes, and 1X Pen-strep. Suspended cells were harvested after 48 h by dilution with 1X PBS and centrifugation at 2500 rpm for 30 min at room temperature. Cells were washed well with 1X PBS and fixed using 1% formaldehyde in growth medium for 10 minutes at 37°C and quenched with 0.125M Glycine. Fixed cells were washed well with 1X PBS containing protease inhibitors at 4°C and resuspended in 2 ml lysis buffer (Upstate) supplemented with PMSF, DTT and protease inhibitor cocktail. Following 15 min incubation on ice, the sample was sonicated using Bioruptor (Diagnode) to obtain fragments in the average size range 200 bp – 600 bp. ChIP was performed using ChIP assay kit (Upstate, #17–295) on precleared chromatin from 1 million cells by incubation with rabbit polyclonal antibodies overnight at 4C as per manufacturer's instructions. Samples recovered from the enriched fraction along with Input DNA from two parallel experiments were pooled and processed for microarray hybridization.

value: C2C12 arrested myoblasts

tag: chip antibody

value: none, input DNA

source_name: C2C12_G0_PanH3 ChIP DNA

value: Histone H3 antibody


title: normal_brain_5_hippocampus_rep1


title: other_dementias_8_frontal_cortex_rep2


title: normal_brain_9_hippocampus_rep2

value: 0 CERAD:0 CDR:0 Gender:female Age:82 years


title: normal_brain_9_hippocampus_rep1


title: other_dementias_8_hippocampus_rep2


title: other_dementias_8_hippocampus_rep1


title: normal_brain_5_frontal_cortex_rep2


title: normal_brain_9_frontal_cortex_rep2


title: other_dementias_5_hippocampus_rep2


title: definitive_Alzheimer_6_hippocampus_rep1

value: 5 CERAD:B CDR:3 Gender:female Age:87 years


title: definitive_Alzheimer_5_frontal_cortex_rep2

value: 6 CERAD:C CDR:2 Gender:male Age:69 years


title: normal_brain_9_frontal_cortex_rep1


title: definitive_Alzheimer_5_hippocampus_rep1


title: other_dementias_4_frontal_cortex_rep2

value: 0 CERAD:0 CDR:1 Gender:male Age:61 years


title: other_dementias_4_hippocampus_rep2


title: definitive_Alzheimer_6_hippocampus_rep2


title: definitive_Alzheimer_6_frontal_cortex_rep1


title: definitive_Alzheimer_5_hippocampus_rep2


title: F3.Olig2

description: express oligodendrocyte markers and represent a model of neural stem cell differentiation

source_name: oligodendrocyte

value: oligodendrocyte


title: definitive_Alzheimer_6_frontal_cortex_rep2


title: other_dementias_4_frontal_cortex_rep1


title: other_dementias_4_hippocampus_rep1


title: definitive_Alzheimer_5_frontal_cortex_rep1


title: normal_brain_4_hippocampus_rep2

value: 1 CERAD:A CDR:0 Gender:male Age:77 years


title: C2C12_G0_H3K27me3

source_name: C2C12_G0_H3K27me3 ChIP DNA

value: H3K27me3 antibody


title: normal_brain_4_frontal_cortex_rep2


title: definitive_Alzheimer_2_frontal_cortex_rep1

value: 4 CERAD:B CDR:2 Gender:female Age:82 years


title: normal_brain_3_hippocampus_rep1

value: 1 CERAD:0 CDR:0 Gender:female Age:81 years


title: definitive_Alzheimer_2_frontal_cortex_rep2


title: definitive_Alzheimer_2_hippocampus_rep1


title: normal_brain_2_hippocampus_rep1

value: 1 CERAD:0 CDR:0 Gender:male Age:79 years


title: normal_brain_3_frontal_cortex_rep2


title: normal_brain_2_hippocampus_rep2


title: definitive_Alzheimer_2_hippocampus_rep2


title: normal_brain_4_frontal_cortex_rep1


title: normal_brain_4_hippocampus_rep1


title: normal_brain_10_frontal_cortex_rep1

value: 2 CERAD:0 CDR:0 Gender:female Age:94 years

tag: RNA pool of 15 different cell lines


title: normal_brain_2_frontal_cortex_rep1


title: normal_brain_3_frontal_cortex_rep1


title: normal_brain_3_hippocampus_rep2


title: normal_brain_2_frontal_cortex_rep2


title: pathologic_Alzheimer_1_frontal_cortex_rep2

value: 5 CERAD:C CDR:0 Gender:female Age:87 years


title: C2C12_G0_H3K4me3

source_name: C2C12_G0_H3K4me3 ChIP DNA

value: H3K4me3 antibody


title: normal_brain_10_hippocampus_rep1


title: other_dementias_7_hippocampus_rep1

value: 0 CERAD:nd CDR:2 Gender:female Age:76 years


title: pathologic_Alzheimer_1_hippocampus_rep2


title: normal_brain_10_hippocampus_rep2


title: pathologic_Alzheimer_1_hippocampus_rep1


title: other_dementias_7_frontal_cortex_rep2


title: normal_brain_10_frontal_cortex_rep2


title: other_dementias_7_frontal_cortex_rep1


title: other_dementias_7_hippocampus_rep2


title: definitive_Alzheimer_1_hippocampus_rep2

value: 5 CERAD:B CDR:3 Gender:female Age:99 years


title: pathologic_Alzheimer_1_frontal_cortex_rep1


title: definitive_Alzheimer_1_frontal_cortex_rep2


title: definitive_Alzheimer_1_hippocampus_rep1


title: other_dementias_3_hippocampus_rep2

value: 2 CERAD:A CDR:2 Gender:male Age:88 years


title: other_dementias_3_frontal_cortex_rep1


title: other_dementias_3_hippocampus_rep1


title: other_dementias_2_hippocampus_rep1

value: 2 CERAD:A CDR:1 Gender:male Age:80 years


title: other_dementias_2_frontal_cortex_rep2


title: other_dementias_6_frontal_cortex_rep2

value: 2 CERAD:A CDR:3 Gender:male Age:78 years


title: other_dementias_3_frontal_cortex_rep2


title: other_dementias_1_hippocampus_rep1

value: 2 CERAD:0 CDR:3 Gender:male Age:73 years


title: other_dementias_1_frontal_cortex_rep1


title: definitive_Alzheimer_1_frontal_cortex_rep1


title: other_dementias_2_hippocampus_rep2


title: other_dementias_1_hippocampus_rep2


title: other_dementias_6_frontal_cortex_rep1


title: normal_brain_1_frontal cortex_rep1

value: 0 CERAD:0 CDR:0 Gender:female Age:71 years


title: normal_brain_1_frontal cortex_rep2


title: definitive_Alzheimer_7_hippocampus_rep2

value: 5 CERAD:C CDR:2 Gender:female Age:82 years


title: other_dementias_1_frontal_cortex_rep2


title: definitive_Alzheimer_7_frontal_cortex_rep1


title: other_dementias_2_frontal_cortex_rep1


title: other_dementias_6_hippocampus_rep2


title: definitive_Alzheimer_7_frontal_cortex_rep2


title: pathologic_Alzheimer_4_hippocampus_rep1

value: 6 CERAD:C CDR:3 Gender:female Age:86 years


title: pathologic_Alzheimer_4_hippocampus_rep2


title: pathologic_Alzheimer_4_frontal_cortex_rep1

value: 6 CERAD:C CDR:0 Gender:female Age:86 years


title: pathologic_Alzheimer_4_frontal_cortex_rep2


title: definitive_Alzheimer_9_hippocampus_rep1

value: 6 CERAD:C CDR:3 Gender:female Age:83 years


title: normal_brain_1_hippocampus_rep2


title: definitive_Alzheimer_4_hippocampus_rep1

value: 5 CERAD:A CDR:3 Gender:female Age:83 years


title: GEK-54

status: Public on Jan 07 2013

city: Porto Alegre

first: Rogerio

last: Margis

state: RS

address: Av. Bento Goncalves 9500

department: Centro de Biotecnologia

institute: Universidade Federal do Rio Grande do Sul

data_processing:
Illumina Casava1.7 software used for basecalling.
low quality reads with 'n' were removed using PrinSeq script (Schmieder and Edwards, 2011)
Unique raw reads counted obtained with perl scripts
Supplementary_files_format_and_content: tab-delimited text files with abundance of unique sequences

organism: Eugenia uniflora

source_name: leaf

growth_protocol: Adult individual

extract_protocol: Total RNA was isolated from the leaf material using CTAB method (Gambino et al.,  2008) and the RNA quality was evaluated by electrophoresis on a 1% agarose gel. Total RNA (> 10 μg) was sent to Fasteris Life Sciences SA (Plan-les-Ouates, Switzerland) for processing. One mRNA library was constructed and it was sequenced by Illumina HiSeq2000. Briefly, the construction of the small RNA libraries consisted of the following successive steps: acrylamide gel purification of the RNA bands corresponding to the size range 20-30 nt, ligation of the 3p and 5p adapters to the RNA in two separate subsequent steps, each followed by acrylamide gel purification, cDNA synthesis followed by acrylamide gel purification, and a final step of PCR amplification to generate a cDNA colony template library for Illumina sequencing.

tag: sample

value: single

tag: age

value: adult

tag: tissue

value: leaf

tag: molecue subtype

value: Small RNA


title: definitive_Alzheimer_7_hippocampus_rep1

tag: braak


title: definitive_Alzheimer_9_hippocampus_rep2


title: definitive_Alzheimer_9_frontal_cortex_rep2


title: definitive_Alzheimer_4_frontal_cortex_rep2


title: normal_brain_1_hippocampus_rep1


title: NS012_Castrate-resistant(CR)_Input

status: Public on Jan 04 2013

city: Cambridge

first: Suraj

last: Menon

address: Li Ka Shing Center, Robinson Way

country: United Kingdom

institute: Cambridge Research Institute, Cancer Research UK

description:
Input DNA
Illumina Genome Analyzer IIx

library_source: genomic

data_processing:
Alignments (tumour samples): Single-end 36-bp ChIP-seq data was generated by the Illumina analysis pipeline version 1.6.1, and reads were aligned to the Human Reference Genome (assembly hg18, NCBI Build 36.1, March 2008) using BWA version 0.5.5 4. Reads were filtered by alignment quality score, removing all reads with a score less than 15 and exact duplicate reads were removed such that no single read start position was represented more than once
Alignments (cell lines): sequence reads were generated by the Illumina analysis pipeline version 1.3.4 and 1.4.0 and aligned to the Human Reference Genome (assembly hg18, NCBI Build 36.1, March 2008) using MAQ 5. They were filtered by alignment quality score, removing all reads with a MAQ score less than 20, and exact duplicate reads were removed
Peaks (tumour samples): Enriched regions of the genome were identified by comparing the ChIP samples to input samples using the SWEMBL peak caller version 3.2 (http://www.ebi.ac.uk/~swilder/SWEMBL/) with default parameters and R = 0.005. Only those peaks that were present in two or more samples in each treatment group (untreated, TR and CR) were used for further analyses
Peaks (cell lines): Enriched regions of the genome were identified by comparing the ChIP samples to input samples using two independent peak calling algorithms: MACS6 and ChIPSeqMini 7, taking only those regions identified by both algorithms.

source_name: Human prostate tumour sample

extract_protocol:
ChIP Protocol was as described in Wilson, M.D., Barbosa-Morais, N.L., Schmidt, D., Conboy, C.M., Vanes, L., Tybulewicz, V.L., Fisher, E.M., Tavare, S., and Odom, D.T. (2008). Species-specific transcription in mice carrying human chromosome 21. Science 322, 434-438.
Genomic DNA was isolated using phenol:chloroform:isopropanol (25:24:1, Invitrogen), back-extracted with 200 ul of TE, precipitated with isopropanol, washed with 75% ethanol, air-dried and resuspended in 60 ul 10 mM Tris-HCl pH 8.
Antibody info: Santa Cruz Biotechnology Rabbit polyclonal AR antibody, Clone number: (AR(N20)X), Product code: sc-816X
54 ul of ChIP DNA or 50 ng of total input control DNA were subjected to end-repair using T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase, before purification using the DNA Clean and concentrator-5 kit (Zymo Research).  Adenine overhangs were added using Klenow 5'-3' exo-minus, Illumina Solexa sequencing adapters were ligated using T4 DNA ligase and amplified with 18 PCR cycles using Phusion DNA polymerase (Finnzymes) and Illumina Solexa sequencing primers 1.1 and 2.1.  Libraries were size selected by electrophoresis, excising the DNA smear between 200-300 bp on a Dark Reader non-UV transilluminator, purified using a Qiagen gel-extraction mini-elute kit and quantified using an Agilent Bioanalyser. 36 bp sequence reads were generated using an Illumina (Solexa) Genome Analyzer II and these reads were mapped back to the reference human genome before peak calling.

value: Human prostate tumour

value: HRPC

tag: tumor status

value: Castrate-resistant(CR)


title: 22Rv1_AR_Input

description:
Input DNA
Illumina Genome Analyzer IIx

source_name: 22Rv1 cell line

value: AR-stimulated


title: NS022_Castrate-resistant(CR)_Input

description:
Input DNA
Illumina Genome Analyzer IIx


title: AR_consensus_LNCaP_AR_R2_LNCaP_Input2

description:
Chromatin IP against AR
Illumina Genome Analyzer IIx

source_name: LNCaP cell line

value: LNCaP


title: NS020_Castrate-resistant(CR)_Input

description:
Input DNA
Illumina Genome Analyzer IIx


title: 22Rv1_AR_Vehicle

value: Vehicle


title: definitive_Alzheimer_8_hippocampus_rep2

value: 4 CERAD:A CDR:3 Gender:Female Age:77 years


title: 22Rv1_AR_AR-stimulated


title: NS019_Castrate-resistant(CR)_Input

description:
Input DNA
Illumina Genome Analyzer IIx

value: LHRH


title: definitive_Alzheimer_4_hippocampus_rep2


title: definitive_Alzheimer_4_frontal_cortex_rep1


title: NS013_Treatment-responsive(TR)_Input

description:
Input DNA
Illumina Genome Analyzer IIx

value: Treatment-responsive(TR)


title: definitive_Alzheimer_8_hippocampus_rep1


title: NS018_untreated_Input

description:
Input DNA
Illumina Genome Analyzer IIx

value: untreated


title: definitive_Alzheimer_8_frontal_cortex_rep1


title: AR_consensus_VCaP_AR_R_VCaP_Input

source_name: VCaP cell line

value: VCaP


title: other_dementias_6_hippocampus_rep1

value: 2 CERAD:A CDR:3 Gender:male Age:78 years


title: definitive_Alzheimer_9_frontal_cortex_rep1

value: 6 CERAD:C CDR:3 Gender:female Age:83 years


title: definitive_Alzheimer_8_frontal_cortex_rep2


title: NA_Treatment-responsive(TR)_Input

description:
Input DNA
Illumina Genome Analyzer IIx


title: ARM003_Castrate-resistant(CR)_Input

description:
Input DNA
Illumina Genome Analyzer IIx


title: ARM002_untreated_Input

description:
Input DNA
Illumina Genome Analyzer IIx


title: ARM009_untreated_Input

description:
Input DNA
Illumina Genome Analyzer IIx


title: NS013_Treatment-responsive(TR)


title: NS022_Castrate-resistant(CR)


title: NS012_Castrate-resistant(CR)


title: NA_Treatment-responsive(TR)


title: ARM002_untreated


title: NS020_Castrate-resistant(CR)


title: ARM009_untreated


title: SG_pupa

status: Public on Dec 30 2012

city: Beijing

first: Pengcheng

last: Yang

address: Datun Road

country: China

institute: Institute of Zology, Chinese Academy of Sciences

data_processing:
Sequencing-received raw image data were transformed by base calling into raw sequence data. Clean tags were obtained after raw sequences were filtered to remove adaptor sequences, empty tags (sequences with only adaptor sequences but no tags), low quality tags (tags with unknown sequences ‘N’), tags that were too long or too short, and tags with a copy number of 1 (probably a sequencing error). The distribution of clean tags was used to evaluate the normality of the whole data. Saturation analysis was performed to determine whether or not the number of detected genes continues to increase when the sequencing amount increases. Pearson correlation analysis of two parallel libraries was performed to evaluate the reliability and operational stability of the experimental results.  A preprocessed database of all possible CATG+17 nucleotide tag sequences was created using C. p. quinquefasciatus whole genome reference sequences at the Broad Institute (http://www.broadinstitute.org/annotation/genome/culex_pipiens). All clean tags were mapped to the reference sequences and allowed no more than 1 nucleotide mismatch. Clean tags mapped to multiple genes were filtered and the remaining clean tags were designed as unambiguous tags. The number of unambiguous clean tags for each gene was calculated and then normalized to TPM (number of transcripts per million clean tags). When the expression of a gene was not detected, TPM was set to 0.01.
Genome Build:
SG_pupa.txt: CpipJ1

molecule: polyA RNA

organism: Culex quinquefasciatus

growth_protocol: The mosquitoes were maintained at 26 °C ± 1 °C and a long-day photoperiod (14 h light/10 h darkness cycle)

extract_protocol: Six micrograms of total RNA from each of the above five mosquito samples were isolated using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. Tag library preparation was performed with an Illumina Gene Expression Sample Prep Kit. mRNA was purified from total RNA using Oligo (dt) magnetic beads. Double-stranded cDNA was synthesized and subsequently digested with NlaIII, which recognized the CATG site. Illumina adapter 1 was added to the 5’ ends of cDNA fragments. The junction of Illumina adapter 1 and CATG site is the recognition site of MmeI, which cuts at 17 bp downstream of the CATG site, producing tags with adapter 1. Illumina adapter 2 was introduced at the 3’ ends of tags, acquiring tags with different adapters at both ends to form a tag library. After 15 cycles of linear PCR amplification, 85 base strips were purified and then digested. Single-chain molecules were fixed onto the Solexa Sequencing Chip and grown into sequencing templates through Situ amplification. Four types of nucleotides, labeled with four colors, were added and synthesis sequencing was performed. Each tunnel generated millions of raw reads with sequencing length of 35 bp.

tag: developmental stage

value: pupa

tag: strain

value: SG, insecticide resistant strain, a field population collected in Foshan, Guangdong Province, in 2007 and constantly treated with parathion at the laboratory

value: whole body


title: SG_third_instar_larvae

data_processing:
Sequencing-received raw image data were transformed by base calling into raw sequence data. Clean tags were obtained after raw sequences were filtered to remove adaptor sequences, empty tags (sequences with only adaptor sequences but no tags), low quality tags (tags with unknown sequences ‘N’), tags that were too long or too short, and tags with a copy number of 1 (probably a sequencing error). The distribution of clean tags was used to evaluate the normality of the whole data. Saturation analysis was performed to determine whether or not the number of detected genes continues to increase when the sequencing amount increases. Pearson correlation analysis of two parallel libraries was performed to evaluate the reliability and operational stability of the experimental results.  A preprocessed database of all possible CATG+17 nucleotide tag sequences was created using C. p. quinquefasciatus whole genome reference sequences at the Broad Institute (http://www.broadinstitute.org/annotation/genome/culex_pipiens). All clean tags were mapped to the reference sequences and allowed no more than 1 nucleotide mismatch. Clean tags mapped to multiple genes were filtered and the remaining clean tags were designed as unambiguous tags. The number of unambiguous clean tags for each gene was calculated and then normalized to TPM (number of transcripts per million clean tags). When the expression of a gene was not detected, TPM was set to 0.01.
Genome Build:
SG_larvae.txt: CpipJ1

value: third instar larvae


title: SG_adult

data_processing:
Sequencing-received raw image data were transformed by base calling into raw sequence data. Clean tags were obtained after raw sequences were filtered to remove adaptor sequences, empty tags (sequences with only adaptor sequences but no tags), low quality tags (tags with unknown sequences ‘N’), tags that were too long or too short, and tags with a copy number of 1 (probably a sequencing error). The distribution of clean tags was used to evaluate the normality of the whole data. Saturation analysis was performed to determine whether or not the number of detected genes continues to increase when the sequencing amount increases. Pearson correlation analysis of two parallel libraries was performed to evaluate the reliability and operational stability of the experimental results.  A preprocessed database of all possible CATG+17 nucleotide tag sequences was created using C. p. quinquefasciatus whole genome reference sequences at the Broad Institute (http://www.broadinstitute.org/annotation/genome/culex_pipiens). All clean tags were mapped to the reference sequences and allowed no more than 1 nucleotide mismatch. Clean tags mapped to multiple genes were filtered and the remaining clean tags were designed as unambiguous tags. The number of unambiguous clean tags for each gene was calculated and then normalized to TPM (number of transcripts per million clean tags). When the expression of a gene was not detected, TPM was set to 0.01.
Genome Build:
SG_adult.txt: CpipJ1

value: adult


title: NS019_Castrate-resistant(CR)

value: Human prostate tumour


title: plusRA_RNA-seq

status: Public on Dec 29 2012

city: La Jolla

first: MICHAEL

middle: G

last: ROSENFELD

address: 9500 Gilman Drive

institute: HHMI/UCSD

data_processing:
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline.
To quantify the gene expression, the counts/RPKM values for were computed by using SeqMap and rSeq
To identify the Alu elements with a DR2 sequence motif, Alu sequences were scanned with a DR2 position weighted matrix (PWM) (PAZAR database) using PATSER at distinct mapping scores. The potentially induced DR2 Alu elements were identified on the basis of the difference of normalized read counts (–atRA compared to +atRA). To quantify the DR2 Alu expression levels, the 72-nt sequencing reads were aligned to the hg18 assembly using Bowtie. Both uniquely aligned reads and those aligned to less than 10, 100, 1,000 or 10,000 locations were considered in the analysis. For reads aligned to multiple regions, a single location was chosen on the basis of a Gibbs sampling algorithm using five or ten iterations. The sequencing reads count on DR2 Alu was computed using intersectBed tool in BedTools and normalized to the sequencing depth. Globally, the induction of DR2-Alu was assessed by Z-test.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample, and a list of potentially induced DR2-Alu

source_name: NTera2/D1 cells

growth_protocol: Ntera2/D1 cells (American Type Culture Collection) were kept in minimum essential medium α (Invitrogen) plus 10% FBS.

extract_protocol:
Total RNA was extracted from untreated and RA-treated NTera2 cells using the Trizol reagent (Invitrogen) and reverse-transcribed with SuperScript III kit (Invitrogen).
10 µg total RNAs were subjected to magnetic oligo(dT) beads for selecting poly(A)-tailed RNAs. The resultant RNA samples were then fragmented into small pieces by heating to 94°C, followed by EtOH precipitation. The fragmented RNAs were reverse-transcribed to the first strand of cDNAs by using the Superscript III kit (Invitrogen). The second strand of cDNAs was then synthesized by RNA Pol I. The double-stranded cDNAs were end-repaired by T4 DNA polymerase and Klenow polymerase. The blunt-ended double-stranded cDNAs were added an "A" base by Klenow fragment. The adaptors were added to the double-stranded cDNAs by the T4 DNA ligase. By separating the sample on 2% agarose gel, gel slice around 200 bp was cut out and subjected to gel extraction. The extracted cDNAs were amplified by PCR to obtain the library.

treatment_protocol: For induction, the cells were treated with 1 μM atRA (Sigma) for 2 days.

value: RA


title: NS018_untreated


title: Pooled tissue resistant

status: Public on Jan 01 2013

city: Ås

first: Matthew

last: Baranski

address: Osloveien 1

country: Norway

institute: Nofima Marin

data_processing: Residual adapter and poor quality sequences (quality score threshold of 10) were trimmed from the raw data using the FASTX toolkit  and reads shorter than 20bp were discarded. Fastq files were converted to fasta files and Trimest used to trim poly A/T tails from the sequence. De novo assembly of joint data with CLC Assembly Cell, then realignment of reads from resistant and susceptible flow cell lanes to joint reference with CLC Assembly Cell.

organism: Labeo rohita

source_name: liver, intestine, muscle, kidney, spleen, brain tissues

extract_protocol: RNA extracted using TriZOL. RNA was further purified by chloroform extraction followed by precipitation using isopropanol and one wash with 70% ethanol. RNA was resuspended in 25Âµl of RNase-free water. Only samples with optimal purity (OD260/280 >1.8 and <2.2; OD260/230>1.0 and <2.4) and concentration (>50 ng/microlitre and <2500 ng/microlitre), estimated using UV spectrophotometry (Nanodrop) and capillary electrophoresis (Agilent Bioanalyser), were utilized for sequencing. Samples were prepared using the Illumina protocol outlined in "Preparing Samples for Sequencing of mRNA" (Part# 1004898 Rev. A September 2008).  mRNA was purified from total RNA using magnetic oligo(dT) beads and fragmented using divalent cations under elevated temperature.  cDNA was synthesized from the fragmented mRNA using Superscript II (Invitrogen, USA), followed by 2nd strand synthesis.  cDNA fragment ends were repaired and phosphorylated using Klenow, T4 DNA Polymerase and T4 Polynucleotide Kinase.  Next, an 'A' base was added to the 3' end of the blunted fragments, followed by ligation of Illumina adapters via T-A mediated ligation.  The ligated products were size selected by gel purification and then PCR amplified using Illumina primers.  The library size and concentration were determined using capillary electrophoresis (Agilent Bioanalyzer, Agilent Technologies, USA). Fragments of 200Â±25 base pairs were gel purified for sequencing after adapter ligation, and a final enrichment of purified cDNA templates was performed using PCR as per the Illumina protocol. No RNA normalization was performed.

tag: phenotype

value: resistant  to Aeromonas hydrophila


title: small_RNA-seq_plusRA

data_processing:
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline.
The 3′ adaptor sequence was removed using FASTX .
The clipped reads were aligned to a custom DR2-Alu sequence database by using Novoalign.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text file that lists small RNA-seq reads that align to a custom database of DR2-Alu sequences

extract_protocol: 10 µg total RNAs were first added the SRA 3' and 5' adaptors by T4 RNA Ligase 2, truncated and T4 RNA ligase, respectively. The ligated product was then reverse-transcribed with the provided RT primers (Illumina) by using the SuperScript III kit (Invitrogen). The RT product was then subjected to PCR amplification with the provided PCR primers (Illumina). The separation of the PCR products was done in the 6% TBE gel. The gel slice corresponding to 100 -150 bp was cut out and passed through punched eppendorf tubes by centrifugation. The PCR products were eluted out of the gel with the SRA NaCl solution overnight. After EtOH precipitation, the library was ready for use.

treatment_protocol: For induction, the cells were treated with 1 μM atRA (retinoic acid) for 2 days.


title: ARM003_Castrate-resistant(CR)

value: HRPC

value: Castrate-resistant(CR)


title: Pooled tissue susceptible

value: liver, intestine, muscle, kidney, spleen, brain tissues

value: susceptible to  to Aeromonas hydrophila


title: S-lab_third_instar_larvae

data_processing:
Sequencing-received raw image data were transformed by base calling into raw sequence data. Clean tags were obtained after raw sequences were filtered to remove adaptor sequences, empty tags (sequences with only adaptor sequences but no tags), low quality tags (tags with unknown sequences ‘N’), tags that were too long or too short, and tags with a copy number of 1 (probably a sequencing error). The distribution of clean tags was used to evaluate the normality of the whole data. Saturation analysis was performed to determine whether or not the number of detected genes continues to increase when the sequencing amount increases. Pearson correlation analysis of two parallel libraries was performed to evaluate the reliability and operational stability of the experimental results.  A preprocessed database of all possible CATG+17 nucleotide tag sequences was created using C. p. quinquefasciatus whole genome reference sequences at the Broad Institute (http://www.broadinstitute.org/annotation/genome/culex_pipiens). All clean tags were mapped to the reference sequences and allowed no more than 1 nucleotide mismatch. Clean tags mapped to multiple genes were filtered and the remaining clean tags were designed as unambiguous tags. The number of unambiguous clean tags for each gene was calculated and then normalized to TPM (number of transcripts per million clean tags). When the expression of a gene was not detected, TPM was set to 0.01.
Genome Build:
S-lab_larvae.txt: CpipJ1

value: S-lab, which was OP-susceptible and reared at the laboratory without any contact with insecticides for many years


title: SG_egg

data_processing:
Sequencing-received raw image data were transformed by base calling into raw sequence data. Clean tags were obtained after raw sequences were filtered to remove adaptor sequences, empty tags (sequences with only adaptor sequences but no tags), low quality tags (tags with unknown sequences ‘N’), tags that were too long or too short, and tags with a copy number of 1 (probably a sequencing error). The distribution of clean tags was used to evaluate the normality of the whole data. Saturation analysis was performed to determine whether or not the number of detected genes continues to increase when the sequencing amount increases. Pearson correlation analysis of two parallel libraries was performed to evaluate the reliability and operational stability of the experimental results.  A preprocessed database of all possible CATG+17 nucleotide tag sequences was created using C. p. quinquefasciatus whole genome reference sequences at the Broad Institute (http://www.broadinstitute.org/annotation/genome/culex_pipiens). All clean tags were mapped to the reference sequences and allowed no more than 1 nucleotide mismatch. Clean tags mapped to multiple genes were filtered and the remaining clean tags were designed as unambiguous tags. The number of unambiguous clean tags for each gene was calculated and then normalized to TPM (number of transcripts per million clean tags). When the expression of a gene was not detected, TPM was set to 0.01.
Genome Build:
SG_egg.txt: CpipJ1

value: egg


title: minusRA_RNA-seq


title: PM10_outdoor_24h_3.rma-Signal

status: Public on Dec 21 2012

city: Erlangen

first: Roland

last: Lang

address: Wasserturmstr. 3-5

institute: University Hospital Erlangen

hyb_protocol: Biotinylated cRNA was hybridized on Affymetrix HG U133A 2.0 GeneChips, that were stained, washed and scanned following Affymetrix standard procedures.

data_processing: The probe level data (CEL files) were processed for global normalization and generation of expression values using the robust multi-array average algorithm (RMA) of the “affy package” in the R software environment (http://www.R-project.org).

label: Biotin

label_protocol: Per sample, 200 ng total RNA was processed using Ambion’s MessageAmp II Biotin Enhanced labeling kit according to the manufacturer’s instructions.

growth_protocol: Human immortalized bronchial epithelial BEAS-2B cells were cultured in bronchial epithelial cell basal medium (BEBM®; Bronchial Epithelial Cell Basal Medium; Clonetics®, Lonza Inc., Walkersville, USA) with 100 units/ml penicillin/streptomycin and bovine pituitary extract, hydrocortisone, hEGF, epinephrine, transferrin, insulin, retinoic acid, triiodothyronine in manufacturer-recommended concentrations (BEGM® SingleQuots®, Lonza). To improve cell adherence, culture plates were pre-coated with 0.01 mg/ml fibronectin, 0.03 mg/ml bovine collagen Type 1 and 0.01 mg/ml BSA. Exponential growing cells were sustained at 37°C, 90% relative humidity and 5% CO2.

extract_protocol: Subsequentially total RNA was extracted (RNeasy Micro Kit; Qiagen) and its concentration (Nanodrop, PeqLab) and quality (Bioanalyzer, Agilent Inc.) were tested.

treatment_protocol: For genome-wide gene expression analysis BEAS-2B cells (passage 41) were incubated with 10µg/ml PM10 (school 4 indoor and outdoor) for 4, 10 or 24h, all in triplicate.

value: bronchial epithelial cells

tag: passage

value: passage 41


title: PM10_indoor_24h_2.rma-Signal

scan_protocol: Biotinylated cRNA was hybridized on Affymetrix HG U133A 2.0 GeneChips, that were stained, washed and scanned following Affymetrix standard procedures.

tag: cell line


title: untreated_24h_2.rma-Signal

tag: cell type


title: PM10_outdoor_24h_2.rma-Signal


title: PM10_indoor_24h_3.rma-Signal


title: PM10_outdoor_24h_1.rma-Signal


title: untreated_10h_2.rma-Signal


title: input_1

status: Public on Dec 11 2012

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

description: service: Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Nijmegen, Netherlands

data_processing:
Sequenced reads were mapped to dm3 whole genome using bowtie version 0.12.7 with parameters  -m 1 (single reads) and --trim3 65 -X 1500 (paired end reads)
calculation of genomic coverage vectors for each sample using a 150 bp read extension for single read samples
arcsine transformation of coverages
averaging of replicate samples
subtraction of common background (input)
Genome_build: dm3
Supplementary_files_format_and_content: bedgraph files of the mean genomic coverage

organism: Drosophila melanogaster

source_name: Input

extract_protocol: As performed by sequencing service

tag: ip antibody

value: none (input)

tag: shearing technologie

value: Bioruptor

tag: chromatin size (bp)


title: untreated_24h_3.rma-Signal


title: PM10_Untreated_4h_2.rma-Signal


title: PM10_outdoor_10h_2.rma-Signal


title: untreated_24h_1.rma-Signal


title: PM10_Indoor_10h_3.rma-Signal


title: Mnase-seq_h4v86a

status: Public on Dec 05 2012

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

institute: KAIST

data_processing:
Sequence reads were mapped to the yeast genome (NCBI June 2008) by means of the Illumina sequencing pipeline. The sequencing tags were extended to the average size of fragments in the library (150 bp) and the number of overlapping sequence reads was obtained at 200-bp intervals across the genome.
Description of BED files ; First column: The name of chromosome, Second column: The starting position of the aligned tag, Third column: The ending position of the aligned tag, Fourth and fifth columns: No specific meanings, Sixth column: the strand definition (either '+'or '-').

organism: Saccharomyces cerevisiae

source_name: histone mutant

growth_protocol: yeast cells were grown in YPD to an A600 OD of 1.5 at 200 rpm. Cells were fixed in 1% formaldehyde, and incubated for 30 minutes at room temperature, shaking, at 200 rpm. 2.5 M glycine was added to a final concentration of 125 mM to quench the formaldehyde. Cell pellet was resuspended in 10ml b-ME buffer (200mM EDTA, 0.7 M b-mercaptoethanol). After 30min of incubation at 30C, cell pellet were precipitated by 5 min of centrifugation at 3000 rpm.

extract_protocol: Spheroplast preparation was conducted at 30C for30 minutes in 10ml lyticase lysis buffer (1M sorbitol. 50mM Tris, pH 7.8; 5mM b-ME) using 10000 units of Lyticase (Sigma). After digesting cell walls, spheroplasts were spun down, washed twice with 1 M sorbitol. DNA digestion was conducted at 37C for 20 minutes in 1.6 ml of digestion buffer (1M sorbitol, 50mM NaCl, 10mM Tris-HCl at pH 7.5, 5 mM MgCl2, 1 mM CaCl2, 1mM b-mercaptoethanol, 0.5mM spermidine and 0.075% v/v NP40). 400uL aliquots of spheroplasts were digested with 3.5 units of MNase (Sigma).  Reaction was stopped by the addition of MNase stop buffer (5% SDS, 250mM EDTA). Samples were treated with 5uL of proteinase K (20mg/mL) at 37? for 5 hours, then phenol:chloroform extracted, ethanol precipitated, treated with RNase A, and  precipitated with ethanol.Digested DNA was purified and separated on a 1.5% agarose gel, and mononucleosomal DNA (~147 bp) was cut out of the gel. Mononucleosomal DNA fragments were sequenced by Illumina Genome Analyzer, subjected to 36 cycles of single-read sequencing.

tag: genotype/variation

value: histone mutant by substituting H4V86 to alanine


title: Mnase-seq_h4wt

source_name: hisotne h4 wild-type

value: hisotne h4 wild-type


title: PM10_Indoor_10h_2.rma-Signal


title: msl2_1

source_name: MSL2 ChIP-Seq

value: polyclonal rabbit MSL2, crude serum


title: PM10_Untreated_4h_1.rma-Signal


title: Mnase-seq_h3L61a

value: histone mutant by substituting H3L61 to alanine


title: Mnase-seq_h3wt

source_name: histone h3 wild-type

value: histone h3 wild-type


title: Mnase-seq_h3v46a

value: histone mutant by substituting H3V46 to alanine


title: untreated_10h_1.rma-Signal


title: PM10_Indoor_4h_2.rma-Signal


title: PM10_Untreated_4h_3.rma-Signal


title: Mnase-seq_h3k56r

value: histone mutant by substituting H3K56 to arginine


title: PM10_Outdoor_4h_3.rma-Signal


title: PM10_Indoor_4h_1.rma-Signal


title: PM10_Outdoor_4h_1.rma-Signal


title: PM10_Outdoor_4h_2.rma-Signal


title: PM10_Indoor_10h_1.rma-Signal


title: Untreated_10h_3.rma-Signal


title: PM10_Indoor_4h_3.rma-Signal


title: PM10_outdoor_10h_3.rma-Signal


title: Mnase-seq_h3k56a

value: histone mutant by substituting H3K56 to alanine


title: Whole seed 12-14 DAF

status: Public on Oct 09 2012

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

description: Williams (ii/ii yellow seed) whole seed 12-14 DAF

data_processing: Adapter trimming was performed using the first occurrences of substring TCG as the unique identifier for the beginning of the adapter (TCGTATGCCGTCTTCTGCTTG). The sizes of the small RNAs after adapter trimming ranged from 16 - 35 nt.

organism: Glycine max

source_name: Whole seed 12-14 DAF

growth_protocol: Plants were grown in the greenhouse and tissues harvested from at least four plants of each line. Leaves and stems were harvested from two to four-week-old plants. Stem samples consisted of one centimeter size fragments immediately underneath the base of the unifoliate leaves. The leaf sample was made of first trifoliate sampled over the course of one week. Germinating cotyledons were harvested from two weeks old seedling. The very young whole seeds were collected 12-14 days after flowering.

extract_protocol: Gel purification, cloning and sequencing of small RNAs from the multiple tissue samples was performed at Illumina Inc. (San Diego, CA) using the SBS (sequencing by synthesis) technology.

treatment_protocol: Optimal greenhouse growth conditions

tag: cultivar

value: Williams

tag: genotype

value: homozygous for the dominant ii allele that specifies yellow seed coat

tag: tissue and developemental stage

value: Whole seed 12-14 DAF


title: Vbr

status: Public on Oct 04 2012

city: Menlo Park

first: Tyson

middle: A

last: Clark

address: 1380 Willow Rd.

institute: Pacific Biosciences

description: Sample 3

data_processing:
Sequencing reads were processed and mapped to the respective reference sequences using the BLASR mapper (http://www.pacbiodevnet.com/SMRT-Analysis/Algorithms/BLASR) and the Pacific Biosciences' SMRT Analysis pipeline (http://www.pacbiodevnet.com/SMRT-Analysis/Software/SMRT-Pipe) using the standard mapping protocol.
To identify modified positions, we used Pacific Biosciences' SMRTPortal analysis platform, v. 1.3.1, which uses an in silico kinetic reference, and a t-test based kinetic score detection of modified base positions (details are available at http://www.pacb.com/pdf/TN_Detecting_DNA_Base_Modifications.pdf)
Supplementary_files_format_and_content: modifications.gff files are comma separated text files that contain data for genome positions with Qmod scores greater than 20; Data includes Qmod scores, IPD ratios, coverage, and sequence contexts for a +/- 20 nt window surrounding the modified position
Supplementary_files_format_and_content: modifications.csv files are comma separated text files that contain data for all positions (both strands) in the reference sequence; data includes Qmod score, IPD ratio, and coverage

organism: Vibrio breoganii

source_name: Bacterial gDNA

extract_protocol: Native gDNA was randomly sheared to an avearge size of approximately 800 bp, end repaired, and ligated to blunt end hairpin adapters for form standard SMRTbell templates


title: BceS

description: Sample 6

organism: Bacillus cereus


title: CjeN

description: Sample 5

organism: Campylobacter jejuni


title: CjeF

description: Sample 4

value: subsp. jejuni 81-176


title: Stem 2 week plants

source_name: Stem 2 week plants

value: Stem 2 week plants


title: Taxus chinensis cells_0h_RNA-seq

status: Public on Nov 16 2012

city: Wuhan

first: Longjiang

last: Yu

address: 1037 Luoyu Road

department: College of life science and technology

institute: Huazhong University of Science & Technology

description: RNA-seq of Taxus chinensis

data_processing:
Transcriptome de novo assembly was carried out with short reads assembling program- SOAP denovo. SOAPdenovo firstly combined reads with certain length of overlap to form longer fragments (contigs.) without N (N for unknown sequence). Then the reads were mapped back to contigs.; with paired-end reads it was able to detect contigs. from the same transcript as well as the distances between these contigs.
The average insert size of T0 is 667.

organism: Taxus chinensis

source_name: Taxus chinensis cells

extract_protocol: Filtered cells were ground in liquid nitrogen, and total RNA was isolated with TRIzol reagent (Invitrogen, USA) according to manufacturer's protocol, and then treated with RNase-free DNase I (Invitrogen, USA) to remove residual DNA. Beads with oligo (dT) were used to isolate poly(A) mRNA from the total RNA. Fragmentation buffer was added for interrupting mRNA to short fragments in 200 bp lengths. Taking these short fragments as templates, random hexamer-primers were used to synthesize the first-strand cDNA. The second-strand cDNA was synthesized using buffer, dNTPs, RNase H and DNA polymerase I, respectively. Short fragments were purified with QiaQuick PCR extraction kit (QIAGEN,Germany) and resolved with EB buffer for end reparation and adding poly(A). After that, the short fragments were connected with sequencing adapters. For amplification with PCR, the suitable fragments were selected as templates, with respect to the result of agarose gel electrophoresis. At last, the library could be sequencing using Illumina GA IIX by the Beijing Genomics Institute (commercial service).

tag: treatment

value: MeJA

tag: treatment time

tag: tissue

value: leave


title: Taxus chinensis cells_16h_RNA-seq

description: RNA-seq of Taxus chinensis treated with MeJA for 16h

data_processing:
Transcriptome de novo assembly was carried out with short reads assembling program- SOAP denovo. SOAPdenovo firstly combined reads with certain length of overlap to form longer fragments (contigs.) without N (N for unknown sequence). Then the reads were mapped back to contigs.; with paired-end reads it was able to detect contigs. from the same transcript as well as the distances between these contigs.
The average insert size of T16 is 658.


title: Csa

description: Sample 2

organism: Chromohalobacter israelensis


title: H3K4me1_ChIP-seq

status: Public on Sep 14 2012

first: David

last: Gorkin

state: California

address: 9500 Gilman Dr. CMM-East 2071

institute: Ludwig Institute for Cancer Research

description: This Sample represents 2 replicates.

data_processing:
EP300 peaks called with MACS.
H3K4me1 peaks called with CisGenome. The Two Sample Peak Calling option of CisGenome allows both replicates to be entered simultaneously, producing a single set of output files, which are provided here.
Genome_build: mm9
Supplementary_files_format_and_content: txt and wig files generated by MACS for EP300 and CisGenome for H3K4me1.

source_name: melan-a, H3K4me1 ChIP

growth_protocol: Cells were propagated according to guidelines from Bennet et al. 1987 (PMID 3102392). See http://www.sgul.ac.uk/depts/anatomy/pages/WTFGCB.htm.

extract_protocol: ChIP was performed as previously described (Lee et al. 2006 (PMID 17406303)), with some minor adjustments to buffers and sonication conditions. Alternative lysis buffers to those in the referenced protocol were used, as follows: Lysis buffer 1 (5mM PIPES, 85mM KCl, 0.5% NP-40, and 1x Roche Complete, EDTA-free protease inhibitor), lysis buffer 2 (50mM Tris-HCl, 10mM EDTA, 1% SDS, and 1x Roche Complete, EDTA-free protease inhibitor), and lysis buffer 3 (16.7mM Tris-HCl, 1.2mM EDTA, 167mM NaCl, 0.01% SDS, 1.1% Triton X-100, and 1x Roche Complete, EDTA-free protease inhibitor). Sonication was performed using a Bioruptor (Diagenode; Denville, NJ) with the following settings: high output; 30 second disruption; 30 second cooling; total sonication time of 35 min with addition of fresh ice and cold water to water bath every 10 minutes. 2ug of anti-H3K4me1 (Abcam ab8895; Lot 961715) and 10ug of anti-p300 antibody (Santa Cruz Biotechnology sc-585; Lot B2410) were used for H3K4me1 and EP300 ChIP, respectively. IP wash conditions were also adjusted from the above referenced protocol, as follows: Each IP was washed twice with low-salt wash buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl, 150mM NaCl), twice with high-salt wash buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl, 500mM NaCl), twice with cold LiCl wash buffer (0.25M LiCl, 1% IGEPAL CA630, 1% deoxycholic acid (sodium salt), 1mM EDTA, 10 mM Tris-HCl), and rinsed once with PBS, pH 7.4. No antibody was used for input samples (pre-IP).

value: melan-a

value: immortalized melanocytes

tag: chip antibody


title: EP300_ChIP-seq

description: This Sample represents 2 replicates.

source_name: melan-a, EP300 ChIP


title: Mnase-seq_h3k56q

value: histone mutant by substituting H3K56 to glutamine


title: Larix leptolepis miRNAs

status: Public on Sep 04 2012

first: Liwang

last: Qi

address: Xiang shan Road

department: The Research Institute of Forestry

institute: The Chinese Academy of Forestry

data_processing:
The raw data were obtained using Illumina's pipeline v1.5 software following sequencing image analysis by Pipeline Firecrest Module and base-calling by pipeline Bustard Module. The extracted sequencing reads were stored in file mylibrary 01_RawData.txt (not included here) and were then used in the standard data analysis. After the raw sequence reads were extracted from image data, a series of digital filters, namely the ACGT101-miR program (Version 3.5, LC Sciences), were employed to remove various un-mappable sequencing reads. Specifically, 533ADT, 53ADT, and junk sequences (>=80% A, C, G or T; >=3 N; only A, C, or only G, T) were initially filtered out, sequences possessing a length of < 15-nt were cut out, followed by "hit" mRNA, RFam including rRNA, tRNA, snRNA, and snoRNA, and Repbase. The resulting sequences were referred to as "Mappable sequences" and were saved in the file called mylibrary_FHG_db.fa (not included here), which is used for miRNA mapping.

Homologous alignment of miRNAs: Various "mappings" were performed on unique sequences against pre-miRNA (mir) and mature miRNA (miR) sequences from plants and animals listed in the miRBase16.0, and the genomes of A. thaliana, P. trichocarpa, P. patens and ESTs of Pinus, Picea and Larix downloaded from the NCBI database.

GSM701474_FHG_uni_miRs.txt: includes all unique potential miRNAs

Unique sequences were further sorted based on their copy numbers:
GSM701474_FHG_hc.txt: contains sequences with >= 3 copies
GSM701474_FHG_lc.txt: contains sequences with <= 3 copies

organism: Larix kaempferi

source_name: embryogenic calli, somatic embryos

growth_protocol: Embryogenic callus tissues were induced from immature embryos of L. leptolepis on induction medium, followed by sub-culture, and culture on differentiation medium in a dark environment with a temperature of 25±2 degrees Celsius.

extract_protocol: Total RNA was extracted from the materials using the Total RNA Purification Kit according to the manufacturer's instructions (NORGEN Biotec Corporation, Canada). Purity/concentration and integrity of RNA were evaluated by NanoDrop 1000 and electrophoresis, respectively. Equal quantities of RNA from seven developmental stages were pooled for Illumina Genome Analyzer GA-IIx sequencing. The library construction, sequencing and initial data analysis were performed by LC Sciences.

value: embryonic calli and embryos

tag: development stage

value: seven stages during somatic embryogenesis

tag: line


title: sRNA cloned from AGO1

status: Public on Aug 04 2012

first: Xiuying

last: Liu

address: No. 1 West Beichen Road, Chaoyang District

department: Bioinformatics

institute: CAS

data_processing: After filtering internal controls and trimming adaptor sequences, clone reads with lengths between 19 and 28 nt were selected and mapped to the Arabidopsis genome (TAIR10 version). Only sRNAs with perfect genomic matches were used for further analysis. Detailed adaptors and processing can be found in the paper by Zhu, et al., 2011.

organism: Arabidopsis thaliana

source_name: inflorescence

growth_protocol: Plants were grown in LP5 Metromix (SunGro, Canada) in a walk-in growth chamber at 22°C with relative humidity of 50% under long-day conditions (16 h light/8 h dark) unless otherwise noted. Light illumination (110 mmol photons/m2s) was provided by a Spectralux T5 high-output lamp (Hydrowarehouse).

extract_protocol: Tandem-affinity purification of AGO complexes, sRNA cloning and illumina sequencing  are discribed in Hongliang Zhu, et al.,  2011. The Arabidopsis Argonaute 10 specifically recruits miR166/165 to maintain shoot apical meristem. Cell. 145:242-256

tag: ecotype

tag: complexes


title: PM10_indoor_24h_1.rma-Signal

tag: cell line

value: bronchial epithelial cells

tag: passage

value: passage 41


title: sRNA cloned from total RNA

value: none (total RNA)


title: Sample 38_Input DNA for NPAS2 ChIP-seq

status: Public on Aug 31 2012

city: Dallas

first: Joseph

middle: S

last: Takahashi

state: TX

address: 5323 Harry Hines Blvd., NA4.118

department: HHMI, Neuroscience

institute: University of Texas Southwestern Medical Center

description: Raw data file same as sample 37 [GSM982724]

data_processing:
Sequence reads were mapped to the mouse genome (NCBIm37/mm9) with Applied Biosystems BioScope v1.3.
In order to adjust for differences in sequencing depth among time samples, the sequence reads were “down sampled” to the lowest number of the uniquely mapped reads with duplicates among the six time points for each ChIP factor.
PCR duplicates were removed using Picard MarkDuplicates.
Genome_build: mm9
Supplementary_files_format_and_content: The .bw files show the sequence read density across the mm9 mouse genome. The bed files show where the transcription factors or histone marks bind.

organism: Mus musculus

source_name: Input DNA for NPAS2 ChIP-seq

growth_protocol: Male C57BL/6J at 8-12 weeks of age were housed in light-tight boxes and entrained to LD12:12 conditions. After a minimum of 7 days, animals were transferred to constant darkness (DD) conditions. Thirty-six hours after DD, liver samples (N=3 mice) were collected every 4 hrs.

extract_protocol:
The immunoprecipitated DNA fragments were repaired by the End-It DNA End Repair Kit (Epicentre Biotechnology) according to the manufacturer’s instructions. The end-repaired ChIP DNA fragments  ere purified by MinElute Reaction Cleanup Kit (Qiagen) and eluted in 20 μl in EB buffer.
The resulting DNA fragments were ligated with P1 and P2 adaptors for the Applied Biosystems SOLiD system for 20 min at room temperature using the Quick Ligase Kit (NEB), followed by purification using the MinElute Reaction Cleanup Kit (Qiagen).
The purified, adaptor-ligated ChIP DNA fragments were run on 5% native polyacrylamide gel electrophoresis (PAGE) for an in-gel PCR reaction. A gel slice containing 175–200 bp adaptor-ligated ChIP DNA fragments (corresponding to 115-140 bp genomic gment sizes) was cut and shredded.
PCR Platinum Supermix (100 μl, Invitrogen), 50 pmol of PCR primers with barcodes, 0.5 μl Taq DNA polymerase (NEB), and 0.15 μl p.f.u. Turbo DNA polymerase (Stratagene) were added into the shredded gel slice.
The adaptor-ligated ChIP DNA fragments were amplified by 14-19 cycles of in-gel PCR. After the PCR reaction, gel pieces were filtered out with a 0.45 μm filter spin column, and the amplified ChIP-seq library was purified by the MinElute PCR purification kit (Qiagen).
The library was purified by one more round of 5% PAGE. A gel slice containing 200-230 bp PCR products (110-130 bp fragment size) was cut and shredded, and the amplified library was extracted out of the gel by passive elution in elution buffer (2.5 M ammonium acetate in TE).
Gel pieces were removed with a spin column, and the resulting ChIP-seq library was purified using the QIAquick PCR purification kit (Qiagen).

tag: strain background

value: wild-type

tag: gender

value: male

value: liver

tag: time

value: mixture of CT0 to 20


title: Gme

description: Sample 1

organism: Geobacter metallireducens

tag: strain


title: Sample 110_Input DNA for H3K4me3 ChIP-seq

description: Raw data file same as sample 103 [GSM982790]

source_name: Input DNA for H3K4me3 ChIP-seq

tag: genotype/variation


title: sample86.flowcell312M0AAXX.lane8

status: Public on Jul 17 2012

city: Rochester

first: Brian

last: Bot

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

data_processing: The first five flow cells were processed using SCS v 2.01 and the last eight flow cells were processed with SCS v 2.4 which allowed for higher cluster densities and higher pass filter rates. The images from the sequencing cycles were processed using the Illumina Pipeline Software v1.5. Specifically, images were converted to signal intensities using Illumina Pipelineâs FireCrest program. Base calling from intensity values was performed, and the quality scores for every base were calculated using the Bustard program. Illuminaâs alignment tool, ELAND, was used to align the sequence reads to genome build 36 and exon junction databases. Illuminaâs CASAVA tool was used to summarize the alignment results using only reads that mapped to a unique genome location and CASAVA results were imported into Genome Studio to generate the count tables for genes, exons, and exon-junctions. Sequencing pass/fail quality was determined by cluster densities, percent of clusters passing filters, percent of reads aligning to the reference and percent error rate of the alignment.  As this exercise was method-development and evaluation, data is provided as blinded gene level count data so as to protect biological conclusions until clinical analyses are completed.

organism: Homo sapiens

source_name: PBMC

growth_protocol: frozen and thawed PBMC

extract_protocol: Total RNA was extracted from stabilized cells using RNeasy Plus mini kit (Qiagen, Valencia, CA). RNA concentration and quality were assessed by Nano Chip kit analysis on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA). Libraries were prepared using the mRNA-Seq Sample Prep Kit (Illumina, San Diego, CA) following the manufacturerâs instructions. Briefly, polyadenylated RNA was isolated from 1 (mu)g of total RNA using two rounds of hybridization to oligo-dT magnetic beads. The mRNA samples were chemically fragmented, reverse transcribed and converted into double stranded cDNA. Unique Illumina adaptors were ligated to the DNA fragments after end repair (to produce blunt ends) and A-base tailing. Fragments of approximately 200 bp were gel purified and amplified by PCR. The libraries were validated and quantified on Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) using the DNA 1000 Chip kits.

tag: sample

tag: flowcell

tag: lane

tag: pcrbatch

tag: outcome

value: H

tag: cell type

value: PBMC


title: sample6310.flowcell312M0AAXX.lane3

value: L


title: sample86.flowcell312M0AAXX.lane7


title: sample6310.flowcell312M0AAXX.lane4


title: sample7954.flowcell42KT7AAXX.lane8


title: sample7954.flowcell42KT7AAXX.lane7


title: sRNA cloned from AGO10


title: sample56.flowcell42KT7AAXX.lane3


title: T36_60hr, rep2

status: Public on Sep 01 2012

city: Boston

first: Youjin

last: Lee

state: MA

address: 4 Blackfan Circle, HIM#730

institute: Harvard Medical School/ Brigham Women's Hospital

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 in an Affymetrix GeneChip Hybridisation Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneTitan system.

data_processing: The data was normalized using the GenePattern software with the Robust Multi Array (RMA) algorithm.

source_name: Primary CD4 T cells, TGF-beta3/IL-6

label_protocol: Affymetrix 3' IVT Express kit (Affymetrix, 901228) using 100 ng total RNA as starting material for a single round of amplification using standard methods.

growth_protocol: Naïve CD4 T cells (CD4+, CD44low, CD62Lhigh) were sorted and cultured in tissue culture plates coated with anti-CD3/ anti-CD28 with their respective cytokines for 60 hours.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit according to the manufacturer's protocol (Qiagen).

treatment_protocol: Cells were differentiated with activation alone (no cytokines) or Th17 conditions (IL-1beta-IL-6+/-IL-23, TGF-beta1-IL-6+/-IL-23, TGF-beta3-IL-6+/-IL-23).

tag: Sex

value: female

tag: age

value: 6-8 weeks

value: primary CD4 T cells

tag: cytokine activation

value: TGF-beta3, IL-6

tag: activation duration

value: 60 hours


title: Human Islets 1

status: Public on Sep 09 2012

city: Toronto

first: Michael

last: Wheeler

state: Ontario

address: 1 King's College Circle

department: Physiology

country: Canada

institute: University of Toronto

description:
Human Islets 1
Adult Human Islets

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133 Plus 2.0 GeneChip. EukGE-WSv4_450 was used to stain and wash the arrays.

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

data_processing: The data were analyzed with Affymetrix Expression Console (Version 1.1) using Affymetrix default analysis settings and RMA as normalization method.

source_name: Human Islets from Donor

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: hESC differentiated according to the 'Nostro Protocol' (Development, 2011) to day 22. Human Islets obtained from the Clinical Islet Laboratory, University of Alberta and hand-picked.

extract_protocol: Qiagen RNeasy Plus Mini Kit

treatment_protocol: As described in Nostro et al., Development, 2011

value: Pancreatic Islets


title: T36_60hr, rep1


title: sample1353.flowcell42KV5AAXX.lane8


title: T1623_60hr, rep1

source_name: Primary CD4 T cells, TGF-beta1/IL-6/IL-23

value: TGF-beta1, IL-6, IL-23


title: sample1353.flowcell42KV5AAXX.lane7


title: sample6044.flowcell42KV5AAXX.lane4


title: small RNAs from vegetative cells_SL14

status: Public on Aug 02 2012

first: Krys

last: Kelly

address: Downing Street

department: Plant Sciences

institute: University of Cambridge

description: SL14.trimmed_reads.fasta.txt: the fasta file initially derived from the SL14 fastq file.  This still has the illumina IDs in the description line for each sequence and has all sequences (i.e. they are not filtered), but the adaptor sequence 'TCGTATGCCGTCTTCTGCTTGT' has been removed.  The original sequence may be reconstituted by adding sufficient bases from the adaptor (beginning at the 3prime end) to make 35bp.  No further filtering has been done on this file.  There are no quality scores.

data_processing: Sequence reads were obtained using the Illumina Genome Analyzer Pipeline.  The 3 prime adaptor sequence was removed from the small RNA reads and the reads were aligned to the Chlamydomonas genome, assembly 4.  Only reads with 100% match to the genome were retained.

organism: Chlamydomonas reinhardtii

source_name: vegetative cells

growth_protocol: Chlamydomonas cells were grown in liquid culture.

extract_protocol: RNA was extracted using Trizol (Invitrogen) and small RNA isolated from the total RNA fraction using mirVana (Ambion),  adapter sequences appropriate Illumina sequencing were ligated.

treatment_protocol: Small RNAs were isolated from different strains of Chlamydomonas and from cells at different phases of the Chlamydomonas sexual cycle.  Genomic DNA was isolated from vegetative cells.

tag: 3prime adaptor

value: TCGTATGCCGTCTTCTGCTTGT


title: sample56.flowcell42KT7AAXX.lane4


title: Human Islets 3

description:
Human Islets 3
Adult Human Islets


title: sample6044.flowcell42KV5AAXX.lane3


title: T1623_60hr, rep2


title: sample98.flowcell428YAAAXX.lane3


title: sample6292.flowcell428YAAAXX.lane7


title: sample6370.flowcell429B4AAXX.lane6


title: sample98.flowcell428YAAAXX.lane4


title: sample6171.flowcell30609AAXX.lane1


title: sample6292.flowcell428YAAAXX.lane8


title: sample6311.flowcell30609AAXX.lane5


title: sample6370.flowcell429B4AAXX.lane5


title: sample8013.flowcell429B4AAXX.lane2


title: Human Islets 2

description:
Human Islets 2
Adult Human Islets


title: sample8013.flowcell429B4AAXX.lane1


title: sample6311.flowcell30609AAXX.lane6


title: sample6431.flowcell42CUCAAXX.lane6


title: sample6431.flowcell42CUCAAXX.lane5


title: sample6171.flowcell30609AAXX.lane2


title: sample6101.flowcell4297UAAXX.lane2


title: sample6101.flowcell4297UAAXX.lane1


title: sample2641.flowcell4297UAAXX.lane7


title: sample2641.flowcell4297UAAXX.lane8


title: sample2637.flowcell42CUCAAXX.lane3


title: sample6249.flowcell42DCLAAXX.lane8


title: sample2674.flowcell42DCLAAXX.lane2


title: sample5257.flowcell30WFYAAXX.lane5


title: sample5257.flowcell30WFYAAXX.lane6


title: sample6113.flowcell30WFYAAXX.lane4


title: sample2674.flowcell42DCLAAXX.lane1


title: sample6113.flowcell30WFYAAXX.lane3


title: sample1286.flowcell305TMAAXX.lane7


title: sample6249.flowcell42DCLAAXX.lane7


title: sample6045.flowcell30WP5AAXX.lane2


title: sample2550.flowcell305TMAAXX.lane3


title: sample4019.flowcell30WPLAAXX.lane6


title: sample4019.flowcell30WPLAAXX.lane5


title: sample6045.flowcell30WP5AAXX.lane1


title: sample1286.flowcell305TMAAXX.lane8


title: sample2550.flowcell305TMAAXX.lane4


title: small RNA from red blood cells (Sample 6)

status: Public on Jul 01 2012

city: Zurich

first: imane

last: azzouzi

address: Steinwiesstrasse 75

department: Haematology division

country: Switzerland

institute: Children's Hospital Zurich

description:
15-30 nucleotide small RNA
Small RNA from red blood cell from adult donor

source_name: adult

extract_protocol: Small RNA cDNA library was constructed using a protocol adapted from Hafner et al., 2008, Methods. Briefly total RNA from 9 individuals was size-fractionated via polyacrylamide gel electrophoresis and small RNAs corresponding in molecular weight to the mature miRNA population (15- 30-nucleotide fraction) were gel extracted. Small RNAs samples from the 4 healthy kids were pulled together to start with enough material. The 5 other samples were processed individually and all samples were then ligated to the 5' adaptor (Modban adenylated adaptor from IDT, San Jose, CA, USA) using the truncated RNL2 (NEB, Ipswich, MA, USA) and to a 3' adaptor (IDT, San Jose, CA, USA) sequentially using the T4 RNL1 (Promega, Dübendorf, Switzerland). The obtained cDNA samples were then RT-PCR amplified using the Superscript III Reverse transcriptase (Invitrogen AG, Basel, Switzerland) and Taq polymerase (Roche, Rotkreuz, Switzerland). The primers used for amplification included tails corresponding to the 454 adaptors and 3-nucleotide multiplexing tags. All samples were pulled into a single library for sequencing.

tag: library number

value: library 6

tag: tissue

value: red blood cell

tag: developmental stage

value: adult


title: small RNA from red blood cells (Sample 5)

value: library 5


title: small RNA from red blood cells (Sample 1'')

description:
15-30 nucleotide small RNA
Small RNA from red blood cell from child donor

source_name: child

value: library 1

value: child


title: small RNA from red blood cells (Sample 2)

value: library 2


title: small RNA from red blood cells (Sample 1''')


title: small RNA from red blood cells (Sample 1)


title: Adult Male Head (Replicate 2) extraction2_seq1 aliquote 1

status: Public on Aug 10 2012

first: DCC

last: modENCODE

address: MaRS Centre, South Tower, 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

description: Small RNA data.

data_processing: raw sequences were clipped by 3' linker sequences recognition, and select clipped sequences longer than 18 nt

source_name: Drosophila melanogaster adult male head

extract_protocol: total RNA from adult male head, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

value: male head


title: PM10_outdoor_10h_1.rma-Signal

tag: cell line

value: bronchial epithelial cells

tag: passage

value: passage 41


title: Somatosensory cortex_Postnatal day 28_Technical replicate_2

status: Public on Jun 26 2012

city: Shanghai

first: Maojin

last: Yao

address: 320# Yueyang Road

department: Neural circuit development

institute: Institute of Neurosciecne

data_processing: After removing low quality reads according to the criteria of Solexa, the full length unique small RNA tag were counted as their expression abundances. Those identical RNA tag were mapped to genome of Rat by SOAP software (Short Oligonucleotide Alignment Program) (http://soap.genomics.org.cn) to analyze their expression and distribution on the genome. Small RNA tags were aligned to the miRNA precursor and mature sequence from miRbase 14.0 (www.miRBase.org) to obtain the known miRNA counts and get rid of matched tags from unannotated tags. Then small RNA tags were aligned with the sequences of non-coding RNAs (rRNA, tRNA, scRNA,snRNA, snoRNA) from Rfam  http://www.sanger.ac.uk/software/Rfam) and the GenBank (http://www.ncbi.nlm.nih.gov/) to get rid of matched tags from unannotated tags. In addition, all sequences were searched for piRNA in NCBI database with screening program developed by Beijing Genomics Institute.To identify potential novel miRNA candidates, software Mireap (http://sourceforge.net/projects/mireap) developed by BGI was used to predict novel miRNA by exploring the secondary structure, the Dicer cleavage site and the minimum free energy of the unannotated small RNA tags which could be mapped to genome. In briefly, the sequence length should be between 18-26 nt, maximal free energy allowed for a miRNA precursor was -18 kcal/mol, maximal space between miRNA and miRNA* was 35 nt, and flank sequence length of miRNA precursor should be 10 nt. After filtering in above analysis pipeline, unannotated small RNA tags were aligned with mature miRNAs from miRBase14.0 to detect miRNA editing allowing one mismatch on certain position miRNAs.

organism: Rattus norvegicus

source_name: cortex

extract_protocol: Rat cortical tissues of various developmental stages (E10-P28) were dissected and total RNA was then extracted with TRIzol. Size-fractionation was performed on 15% polyacrylamide gel electrophoresis (PAGE) to collect the 16-35 nt fraction. Libraries were prepared according to Illumina's instructions. In briefly, adapters were ligated to the 5’ and 3’ termini of these small RNAs, which then were used as templates for cDNA synthesis. After producing libraries via PCR amplification, the purified PCR products were then sequenced using Illumina genome Analyzer II

value: cortex

value: Postnatal day 28

tag: strain

value: Sprague Dawley


title: Somatosensory cortex_Postnatal day 14_Technical replicate_1

value: Postnatal day 14


title: small RNA from red blood cells (Sample 4)

value: library 4


title: Somatosensory cortex_Postnatal day 14_Technical replicate_2


title: Somatosensory cortex_Postnatal day 7_Technical replicate_2

value: Postnatal day 7


title: 1st Instar Larvae (Replicate 2) extraction2_seq1 aliquote 1

description: Small RNA data.

source_name: Drosophila melanogaster 1st instar larvae

extract_protocol: total RNA from 1st instar larvae, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

tag: Stage

value: 1st instar larvae


title: 7mm length flower of hermaphrodite

status: Public on Jul 16 2012

city: Ueda

first: Hideo

last: Matsumura

state: Nagano

address: Tokita 3-15-1

department: Gene Research Center

institute: Shinshu University

description: digital trasncript profiling using 26-bp tags

data_processing: Once csfasta-formatted sequence files from SOLiD3 were converted to fasta-formatted files for further analysis. Sorting of sequence reads based on indexed sequences and the subsequent extraction of sequence tags from reads was conducted using a script written in Perl (Matsumura et al. 2010).

organism: Carica papaya

source_name: flower bud

growth_protocol: Plants were grown in greenhouse.

extract_protocol: Double-stranded cDNA was synthesized from total RNA using the biotinylated adapter-oligo dT primer. Purified cDNA was digested with NlaIII, resulting fragments were bound to streptavidin-coated beads, and non-biotinylated cDNA fragments were removed by washing.  Adapter-2SLD was ligated to cDNA fragments on the beads and after washing digested with EcoP15I. EcoP15I-digested and released fragments (adapter-2SLD-tags) were ligated to adapters-1SLD with defined index sequences for sample identification.  Tags sandwiched between two adapters were amplified by PCR.  The PCR regime consisted of 98oC for 1min, 12 cycles at 98oC for 30sec, and 60oC for 30sec.  Eight tubes from this PCR amplification (each 15ml) were pooled and concentrated PCR products were run on an 8% non-denaturing polyacrylamide gel.  The band at 160bp was cut out from the gel, and DNA purified after its elution from the gel pieces.  Equal concentrations of PCR products from all the samples were mixed and applied to SOLiD3 sequencing.

tag: cultivar

value: Sunrise solo

tag: gender

value: hermaphrodite


title: small RNA from red blood cells (Sample 1')

value: red blood cell


title: THP1_smallRNAseq

city: New York

last: Brown

state: NY

address: 1470 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Illumina Casava1.8 software used for basecalling.
The 3' linker was identified and stripped out of the raw reads.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes read counts for each sequence of the three protocols used

source_name: THP1 cells

growth_protocol: Cells were cultured in  RPMI 1640 media + 10% FBS + 2mM L-Glutamine + Pen/Strept +  0.05 mM betamercaptoethanol

extract_protocol:
Small RNA was extracted from 3x106 THP1 cells by using QIAGEN miRNeasy Mini Kit. Three different methods were used for the library construction (as in Jayaprakash, A. et al, Nucleic Acid Res, 2011):
"Illumina" protocol: Illumina TruSeq small RNA Sample Preparation Kit was used following manufacturer's instructions.
"Hannon" protocol: Adaptors containing the required sequences were ligated to each end, and then reverse transcribed and PCR amplified.
"Barcode" protocol: Pooled adaptors (to overcome ligation bias) containing the required sequences were ligated to each end, and then reverse transcribed and PCR amplified.

value: human monocytic leukemia


title: small RNA from red blood cells (Sample 3)

value: library 3

value: adult


title: Somatosensory cortex_Postnatal day 0_biological replicate_2_Technical replicate_2

value: Postnatal day 0


title: 20mm length flower of hermaphrodite


title: Somatosensory cortex_Postnatal day 0_biological replicate_2_Technical replicate_1


title: Somatosensory cortex_Postnatal day 0_biological replicate_1_Technical replicate_2


title: Somatosensory cortex_Postnatal day 3_Technical replicate_2

value: Postnatal day 3


title: Somatosensory cortex_Postnatal day 0_biological replicate_1_Technical replicate_1


title: Somatosensory cortex_Embryonic day 17_Technical replicate_2

value: Embryonic day 17


title: Forebrain_Embryonic day 13_Technical replicate_2

source_name: Forebrain

value: Forebrain

value: Embryonic day 13


title: Somatosensory cortex_Postnatal day 3_Technical replicate_1

value: cortex


title: Forebrain_Embryonic day 13_Technical replicate_1

value: Sprague Dawley


title: Forebrain_Embryonic day 10_Technical replicate_1

value: Embryonic day 10


title: Somatosensory cortex_Embryonic day 17_Technical replicate_1


title: N2 no RNAi 2

status: Public on Jun 22 2012

city: Pasadena

first: Diane

middle: E

last: Trout

address: 1200 E California Blvd M/C 156-29

department: Biology

institute: California Institute of Technology

description:
cDNA from mRNA
RNA-seq

data_processing:
Alignment: Sequence reads were obtained and aligned to the C. elegans genome using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml)
Peaks: Shifted peaks were identified using the software package Erange (http://woldlab.caltech.edu/rnaseq)

organism: Caenorhabditis elegans

source_name: embryo

growth_protocol: Worms were grown on NGM-special plates at 25ËC and fed RNAi expressing bacteria.

extract_protocol: Fixed animals were freeze-cracked, lysed, and the lysate purified. mRNA's were polyA selected. Libraries were constructed and sequenced as per Illumina's instructions.

treatment_protocol: Whole embryos were fixed in Trizol 400 minutes following adult bleaching.

tag: RNAi

value: embryo


title: RW364 no RNAi 2

description:
cDNA from mRNA
RNA-seq


title: N2 Triple RNAi

description:
cDNA from mRNA
RNA-seq

value: mex-3; skn-1; elt-1


title: 20mm length flower of female

value: female


title: RW364 no RNAi 1

description:
cDNA from mRNA
RNA-seq


title: RW364 mex-3 RNAi

description:
cDNA from mRNA
RNA-seq


title: RW364 Triple RNAi

description:
cDNA from mRNA
RNA-seq


title: 20mm length flower of male

value: male


title: 1st Instar Larvae (Replicate 1) extraction1_seq1 aliquote 1

description: Small RNA data.

organism: Drosophila melanogaster

value: 1st instar larvae


title: PD4605 mex-3 RNAi

description:
cDNA from mRNA
RNA-seq


title: N2 no RNAi 1

description:
cDNA from mRNA
RNA-seq


title: input DNA mex

description: input DNA

extract_protocol: Fixed animals were freeze-cracked, lysed, and sonicated, with the lysate then purified with the antibody. Libraries were constructed and sequenced as per Illumina's instructions.

treatment_protocol: Whole embryos were fixed in 2% formaldehyde 400 minutes following adult bleaching.

tag: antibody


title: PD4605 no RNAi

description:
cDNA from mRNA
RNA-seq


title: input DNA triple

description: input DNA


title: N2 mex-3 RNAi

description:
cDNA from mRNA
RNA-seq


title: 7mm length flower of male


title: antiHLH-1 triple RNAi ChIP-seq

description: Chromatin IP against HLH-1


title: sample2637.flowcell42CUCAAXX.lane4

tag: sample

tag: flowcell

tag: lane

tag: pcrbatch

tag: outcome

value: H

tag: cell type

value: PBMC


status: Public on Jun 14 2012

city: Auckland

first: Justin

middle: M.

last: O'Sullivan

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland

description:
Genome Conformation Capture performed on Glucose grown S. cerevisiae.
Replicate samples, Saccharomyces_cerevisiae_Glucose_GCC_Rep1 and Saccharomyces_cerevisiae_Glucose_GCC_Rep2, correlated well and were subsequently concatenated and analysed as one file. This is why there is only one processed data file: Glucose_2010Repeats.out.datcomb.txt (linked as a supplementary file on the Series record).

data_processing: Sequences were mapped onto the S. cerevisiae S288c genome sequence [June 2008 (SGD/sacCer2) assembly] using Topography v1.19 which is coupled to the SOAP algorithm (Li. R., et al 2008).  Topography is avaliable upon request from the corresponding author.

organism: Saccharomyces cerevisiae

source_name: Glucose grown S. cerevisiae

growth_protocol: S. cerevisiae strain (BY4741) was grown (30oC, 160 rpm) to an OD600 = 0.6 in synthetic complete media containing amino acid supplements and glucose (2% w/v).

extract_protocol: Genome Conformation Capture (GCC): Cells were cross-linked (2% v/v formaldehyde, 10 mins, room temperature, with stirring) and quenched (0.125M glycine). Samples (residuals of 108 cells in 52.6ul) were digested (37°C, 2hr) with MspI (100U, Fermentas) in a final volume of 100 ml.  MspI was inactivated by the addition of 1% SDS (final v/v) and incubation (65°C, 20mins). Reactions were diluted in 2ml T4 ligation buffer (NEB) containing 1% Triton X-100. T4 DNA Ligase (20U, Invitrogen) was added and the reaction incubated (16°C, 2hrs). Samples were reverse cross-linked (65°C, O/N) in the presence of Proteinase K (7-11ug, Roche), 20ul EDTA (0.5M), 12ul NaCl (5M), 1.2ul Tris-HCl (1M).  RNase (20ug) was added and incubated (37°C, 15mins) prior to three Phenol:Chloroform (1:1) extractions.  Samples were purified using Zymo Clean and Concentrator columns. Sequencing was performed (38 bp paired end) on an Illumina Genome Analyser (FMI, Basel, Switzerland).


title: PD4605 Triple RNAi

description:
cDNA from mRNA
RNA-seq


title: 7mm length flower of female

value: Sunrise solo


title: 0-1hr Embryo (Replicate 2) extraction2_seq1 aliquote 1

description: small RNAs

source_name: Drosophila melanogaster 0-1hr embryo

extract_protocol: total RNA from 0-1hr embryo, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

value: 0-1hr embryo


title: Fragment 2 4C PCR of tL(CAA)G3 tRNA replaced with SUP4-1 containing MspI fragment

description:
PCR Product: Nested inverse PCR primers were designed to amplify out of the "bait" MspI fragments that contained the intact tL(UAA)B2 or tL(CAA)G3 tRNA genes and the SUP4-1 replacement mutants.
Circular chromosome conformation capture of wildtype and two tRNA replacement mutants
Processed data file: yPH499-yDP84_dat_and_datcomb.txt
Processed data file: yPH77-yDP84_dat_and_datcomb.txt

data_processing:
Sequences were mapped onto the S. cerevisiae S288c genome sequence [June 2008 (SGD/sacCer2) assembly] using Topography v1.19. For analysis Fragment 1 and Fragment 2 need to be concatenated for each mutant and the unknown sequence ligated to the forward primer of fragment 1 needs to be re assigned to the forward primer of fragment 2. The same needs to be performed for the reverse primer of fragment 2 needs to be re-assigned to the reverse primer of fragment 1. This is because the SUP4-1 element which has replaced the wild type tRNA is a repetitive element meaning that during the Topography program analysis the 4C fragment cannot be uniquely positioned upon the reference genome without these reassignments.
Processed data file type: Alignment - Topography 1.19 Proprietary Software Output (see supplementary files on the Series record).

source_name: Saccharomyces cerevisiae

growth_protocol: S. cerevisiae strains (i.e. WT: yPH499, Mutants: yDP77 and yDP84) were grown (30oC, 160 rpm) to an OD600 = 0.6 in synthetic complete media containing amino acid supplements and glucose (2% w/v).

extract_protocol: Circular Chromosome Conformation Capture (4C): Cells were cross-linked (2% v/v formaldehyde, 10 mins, room temperature, with stirring) and quenched (0.125M glycine). Samples (residuals of 108 cells in 52.6ul) were digested (37°C, 2hr) with MspI (100U, Fermentas) in a final volume of 100 ml.  MspI was inactivated by the addition of 1% SDS (final v/v) and incubation (65°C, 20mins). Reactions were diluted in 2ml T4 ligation buffer (NEB) containing 1% Triton X-100. T4 DNA Ligase (20U, Invitrogen) was added and the reaction incubated (16°C, 2hrs). Samples were reverse cross-linked (65°C, O/N) in the presence of Proteinase K (7-11ug, Roche), 20ul EDTA (0.5M), 12ul NaCl (5M), 1.2ul Tris-HCl (1M).  RNase (20ug) was added and incubated (37°C, 15mins) prior to three Phenol:Chloroform (1:1) extractions.  Samples were purified by ethanol precipitation using LPA as a carrier. Nested inverse PCR primers were designed to amplify out of the "bait" MspI fragments that contained the intact tL(UAA)B2 or tL(CAA)G3 tRNA genes and the SUP4-1 replacement mutants. PCR conditions were as follows 1) first round (95°C, 2:00 min; 35x [95°C, 0:30 sec; 59°C, 0:30 sec; 72°C, 2:00 sec]; 72°C, 5:00) and 2) nested second round (95°C, 2:00 min; 35x [95°C, 0:30 sec; 62°C, 0:30 sec; 72°C, 2:00 sec]; 72°C, 5:00). The primer annealing temperatures for fragment 1 and 2 of the yDP77 strain were 68.1°C and 60°C, respectively. Nested primers contained unique 6 bp tags (TCTCTG [yPH499 wild type arrangement of the yDP84 strain], TGATGC [yDP84 fragment 1], and AGCACG [yDP84 fragment 2], AGAGAC [yPH499 wild type arrangement of the yDP77 strain], ACAGAG [yDP77 fragment 1], TAGATC [yDP77 fragment 2]) to enable pooling of the 4C PCR products for sequencing (100 bp paired end) on an Illumina Genome Analyser (Allan Wilson Centre, Massey University).

tag: genotype/variation

value: Mutant

tag: unique 6 bp tags to enable pooling of 4c pcr products for sequencing

value: AGCACG


title: Fragment 1 4C PCR of tL(UAA)B2 tRNA replaced with SUP4-1 containing MspI fragment

description:
PCR Product: Nested inverse PCR primers were designed to amplify out of the "bait" MspI fragments that contained the intact tL(UAA)B2 or tL(CAA)G3 tRNA genes and the SUP4-1 replacement mutants.
Circular chromosome conformation capture of wildtype and two tRNA replacement mutants
Processed data file: yPH499-yDP77_dat_and_datcomb.txt
Processed data file: yPH77-yDP84_dat_and_datcomb.txt

value: ACAGAG


title: Fragment 1 4C PCR of tL(CAA)G3 tRNA replaced with SUP4-1 containing MspI fragment

value: TGATGC


title: Saccharomyces_cerevisiae_Glucose_GCC_Rep2


title: antiHLH-1 mex-3 RNAi ChIP-seq

description: Chromatin IP against HLH-1

tag: tissue


title: 4C PCR of tL(CAA)G3 tRNA containing MspI fragment

description:
PCR Product: Nested inverse PCR primers were designed to amplify out of the "bait" MspI fragments that contained the intact tL(UAA)B2 or tL(CAA)G3 tRNA genes and the SUP4-1 replacement mutants.
Circular chromosome conformation capture of wildtype and two tRNA replacement mutants
Processed data file: yPH499-yDP77_dat_and_datcomb.txt
Processed data file: yPH499-yDP84_dat_and_datcomb.txt

value: Wildtype

value: TCTCTG


title: Somatosensory cortex_Postnatal day 7_Technical replicate_1

value: cortex

tag: age

value: Postnatal day 7

value: Sprague Dawley


title: 4C PCR of tL(UAA)B2 tRNA containing MspI fragment

value: AGAGAC