title: 60days-Mature roots

status: Public on Jun 22 2011

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description:
Nipponbare60 days Mature Roots- Sequencing technical replication -1
Library strategy: Illumina's Sequencing by Synthesis

data_processing:
Adapter sequences were removed using a Perl script, generating MmeI-derived tags initiated by a DpnII site (GATC). After this, the non-redundant sequences were generated with abundance for each distinct sequence. These were mapped to the Oryza sativa genome (v6.1 from MSU).
Alignment: Briefly, the "virtual" signatures were derived from the rice genome by extracting all occurrences of GATC plus the 16 nt sequence at the 3' terminus. These signatures were used for matching analysis with the experimental SBS signatures obtained from Illumina genome analyzer.
All the virtual genomic signatures derived from the rice genome were assigned a "class" based on the position of the signature relative to annotated genes. Signatures that did not match to the genome corresponded to the "Class 0" signatures and those that matched the genome corresponded to Classes 1 to 7. The bioinformatics pipeline for the SBS data analysis was performed similar to MPSS data analysis with few modifications (Meyers et al., 2004; Genome Research 14: 1641-1653; Nobuta et al. 2007; Nature Biotechnology 25(4) 473-477). For MC24 and MR24, raw files resulting from three separate runs were processed and concatenated to produce a single processed file.
For MC24 and MR24, raw files resulting from three separate runs were processed and concatenated to produce a single processed file.

organism: Oryza sativa

source_name: Roots

growth_protocol: Plants were grown in Conviron growth chambers at 26°C (day) and 20°C (night) (80% humidity, 12-hr-light/dark cycle; 700 µmol photons m-2 sec-1).

extract_protocol:
Total RNA for library construction was extracted using TriZol
Libraries were prepared according to Illumina's instructions accompanying the sample preparation kit (Catalog No. FC-102-1007). Isolate mRNA and synthesize first strand cDNA followed by second strand cDNA. Restriction digestion of the double stranded cDNA was done using DpnII enzyme. GEX DpnII Adapter 1 was ligated at the site of DpnII cleavage. Sixteen base pair tag was created by restriction digestion with MmeI. GEX adapter 2 was ligated at the site of MmeI cleavage. The GEX adapter 2 contains sequences complementary to the oligos attached to the flow cell surface. The adapter-ligated cDNA construct was selectively enriched using 15 cycles PCR. The amplified cDNA construct was purified and the purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: For biotic stress treatment; 3 weeks old rice plants were challenged with Magnaporthe oryzae (isolate KJ201) and leaves were collected post inoculation at 6, 12, 24 and 96hrs for total RNA isolation (both wild type Nipponbare and transgenic rice expressing Pi9 blast resistance gene). In case of insect infestation libraries; 2 months old rice plants were challenged with beet army worm and water weevil insects. Leaves were collected 24hr post infestation for total RNA isolation. For abiotic stress libraries, for cold treatment plants were stressed at 40C 24 h; for drought stress, plants were stressed without water for 5 d; for salt stress, plants were stressed by immersing in 250 mM NaCl solution for 24 h. All rice tissues were harvested when the plants were in darkness (4 hours after end of the ‘day’) to minimize to concentration of photosynthetic genes.

tag: cultivar

value: Nipponbare

tag: Stage

value: Developmental stage

value: Roots


title: Mature Sigma and Ovary

type: SRA

country: USA

description:
Nipponbare Mature Stigma and Ovary- Sequencing technical replication -1
Library strategy: Illumina's Sequencing by Synthesis

library_source: transcriptomic

molecule: total RNA

source_name: Flower

tag: tissue

value: Flower


title: cortex_MethylC-seq

status: Public on Jun 23 2011

city: Davis

first: Janine

last: LaSalle

state: CA

address: Medical Microbiology and Immunology

institute: UC Davis

description: MethylC-seq

library_source: genomic

data_processing: Fastq reads were aligned to the genome using BS-Seeker, allowing for up to two mismatches with the reference sequence. Custom perl scripts were used to calculate percent methylation for each genomic CpG site with read coverage. Methylation data for both DNA strands were combined. Only one read starting at a given genomic coordinate was kept to eliminate clonal replicates. Red=80-100% methylation, green=60-80%, blue=1-60%, black=0%

molecule: genomic DNA

organism: Homo sapiens

source_name: cerebral cortex

extract_protocol: Genomic DNA from frozen human cerebral cortex slices was purified using Qiagen's Puregene kit and fragmented to ~300bp using Diagenode's Bioruptor.  To create the sequencing libraries, 5 ug of DNA was end repaired using 1X T4 DNA ligase buffer, 400 uM dNTPs, 15 U T4 DNA polymerase (NEB), and 50 U PNK (NEB) for 30 minutes at 20 degrees Celsius. After PCR purifying (Qiagen), adenine bases were appended to the ends using 1X NEB 2 buffer, 200 uM dATP, and 15 U Klenow Fragment (3' to 5' exo-, NEB) for 30 minutes at 37 degrees Celsius. After another DNA purification using the PCR MinElute kit (Qiagen), 3 uL of Illumina's methylated sequencing adapters were ligated on using 1X ligase buffer and 5 uL Quick T4 DNA Ligase (NEB) for 30 minutes at room temperature. After a final PCR purification, 500 ng of library was bisulfite converted using Zymo's EZ DNA Methylation-Direct kit according to the manufacturer's instructions. The library was then amplified using 2.5 U PfuTurbo Cx Hotstart DNA Polymerase (Stratagene) for 12 cycles using Illumina's standard amplification protocol.

tag: tissue source

value: NICHD Brain and Tissue Bank for Developmental Disorders at the University of Maryland, Baltimore, MD

value: cerebral cortex, BA9

tag: age

value: 113 days old

tag: sex

value: male


title: YR15965-LowTaste-Developing seeds-6days-Rep2

description:
6 days old developing seeds were harvested from low taste quality cultivar- YRK- Sequencing technical replication -2
Library strategy: Illumina's Sequencing by Synthesis

source_name: Seed

value: Seed


title: SH-SY5Y_MethylC-seq

description: MethylC-seq

source_name: SH-SY5Y cells

growth_protocol: SH-SY5Y cells were grown in MEM media supplemented with 10% FBS and 1X Pen-Strep-Glut (Gibco).

extract_protocol: Genomic DNA from the SH-SY5Y cells and frozen human cerebral cortex slices was purified using Qiagen's Puregene kit and fragmented to ~300bp using Diagenode's Bioruptor.  To create the sequencing libraries, 5 ug of DNA was end repaired using 1X T4 DNA ligase buffer, 400 uM dNTPs, 15 U T4 DNA polymerase (NEB), and 50 U PNK (NEB) for 30 minutes at 20 degrees Celsius. After PCR purifying (Qiagen), adenine bases were appended to the ends using 1X NEB 2 buffer, 200 uM dATP, and 15 U Klenow Fragment (3' to 5' exo-, NEB) for 30 minutes at 37 degrees Celsius. After another DNA purification using the PCR MinElute kit (Qiagen), 3 uL of Illumina's methylated sequencing adapters were ligated on using 1X ligase buffer and 5 uL Quick T4 DNA Ligase (NEB) for 30 minutes at room temperature. After a final PCR purification, 500 ng of library was bisulfite converted using Zymo's EZ DNA Methylation-Direct kit according to the manufacturer's instructions. The library was then amplified using 2.5 U PfuTurbo Cx Hotstart DNA Polymerase (Stratagene) for 12 cycles using Illumina's standard amplification protocol.

tag: cell type

value: neuronal cells

tag: cell line


title: MEL_Input

city: Bronx

first: Sandeep

middle: Nagaraj

last: Wontakal

state: NY

address: 1300 Morris Park Ave Chanin 402

department: Cell Biology

institute: Albert Einstein College of Medicine

description: Input DNA that was used for chromatin immunoprecipitation

data_processing: Peak detection to mm9 was done using cisGenome and spp software.

organism: Mus musculus

source_name: Murine erythroleukemia (MEL) cells stably transfected with Gata-1 fused to ER

growth_protocol: MEL cells were grown in DMEM supplemented with 10% FBS (Gemini), 2mM L-glutamine, and 5mg/ml puromycin. ES-EPs were cultured in StemPro34 media (Invitrogen) supplmented with 2u/ml Epogen (Amgen), 40ng/ml hIGF-1 (Sigma), 10-6M dexamethosone (Sigma), 100ng/ml murine SCF (R&D Systems/Invitrogen), and 0.1% -mercaptoethanol (Gibco). ES-EP were maintained between 1-6x106 cells/ml by adding fresh media daily.

extract_protocol: Libraries were prepared as recommended by Illumina.

tag: clone #

tag: chip antibody


title: Nipponbare-Control-Developing seeds-6days-Rep2

description:
6 days old developing seeds were harvested from Nipponbare cultivar-control- Sequencing technical replication -2
Library strategy: Illumina's Sequencing by Synthesis


title: YR15965-LowTaste-Developing seeds-6days-Rep1

description:
6 days old developing seeds were harvested from low taste quality cultivar- YRK- Sequencing technical replication -1
Library strategy: Illumina's Sequencing by Synthesis


title: Nipponbare-Control-Developing seeds-6days-Rep1

description:
6 days old developing seeds were harvested from Nipponbare cultivar-control- Sequencing technical replication -1
Library strategy: Illumina's Sequencing by Synthesis


title: LaGrue-LowMilling-Developing seeds-6days-Rep2

description:
6 days old developing seeds were harvested from low milling quality cultivar- LaGrue-- Sequencing technical replication -2
Library strategy: Illumina's Sequencing by Synthesis

value: LaGrue


title: Ilpumbyeo-HighTaste-Developing seeds-6days-Rep1

description:
6 days old developing seeds were harvested from high taste quality cultivar- Ilpumbyeo- Sequencing technical replication -1
Library strategy: Illumina's Sequencing by Synthesis

value: Ilpumbyeo


title: LaGrue-LowMilling-Developing seeds-6days-Rep1

description:
6 days old developing seeds were harvested from low milling quality cultivar- LaGrue- Sequencing technical replication -1
Library strategy: Illumina's Sequencing by Synthesis


title: Rice leaf- Mechanical damaged-24 hr-Rep2

description:
Nipponbare control leaves 24 hour after mechanical damage- Sequencing technical replication -2
Library strategy: Illumina's Sequencing by Synthesis

source_name: Leaves

value: Biotic stress

value: Leaves


title: Rice leaf-Water weevil damaged-24 hr-Rep2

description:
Rice water weevil (Lissorhoptrus oryzophilus) damaged 2 months old Nipponbare leaves 24 hours after infestation- Sequencing technical replication -2
Library strategy: Illumina's Sequencing by Synthesis


title: Cypress-HighMilling-Developing seeds-6days-Rep1

description:
6 days old developing seeds were harvested from high milling quality cultivar- Cypress- Sequencing technical replication -1
Library strategy: Illumina's Sequencing by Synthesis

value: Cypress


title: Rice leaf-beet armyworm damaged-24 hr- Rep1

description:
Beet armyworm (Spodoptera exigua) damaged 2 months old Nipponbare leaves 24 hours after infestation- Sequencing technical replication -1
Library strategy: Illumina's Sequencing by Synthesis


title: Untreated-leaves-2wks-Rep2

description:
2 weeks old Nipponbare plant leaves-untreated control- Sequencing technical replication -2
Library strategy: Illumina's Sequencing by Synthesis

value: Control-abiotic stress


title: Untreated-leaves-2wks-Rep1

description:
2 weeks old Nipponbare plant leaves-untreated control-Sequencing technical replication -1
Library strategy: Illumina's Sequencing by Synthesis


title: Salt Stress-Leaves-2wks-Rep1

description:
2 weeks old Nipponbare plant leaves- stressed in salt for 24 hours- Sequencing technical replication -1
Library strategy: Illumina's Sequencing by Synthesis

value: Abiotic stress


title: Ilpumbyeo-HighTaste-Developing seeds-6days-Rep2

description:
6 days old developing seeds were harvested from high taste quality cultivar- Ilpumbyeo- Sequencing technical replication -2
Library strategy: Illumina's Sequencing by Synthesis


title: Mature pollen

description:
Mature Pollen- Sequencing technical replication -1
Library strategy: Illumina's Sequencing by Synthesis

source_name: Pollen

value: Nipponbare

value: Pollen


title: Rice leaf-beet armyworm damaged-24 hr- Rep2

description:
Beet armyworm (Spodoptera exigua) damaged 2 months old Nipponbare leaves 24 hours after infestation- Sequencing technical replication -2
Library strategy: Illumina's Sequencing by Synthesis


title: Rice leaf-water weevil damaged-24 hr-Rep1

description:
Rice water weevil (Lissorhoptrus oryzophilus) damaged 2 months old Nipponbare leaves 24 hours after infestation- Sequencing technical replication -1
Library strategy: Illumina's Sequencing by Synthesis


title: 60 days-Mature leaves

description:
Nipponbare60 days Mature Leaves- Sequencing technical replication -1
Library strategy: Illumina's Sequencing by Synthesis

value: Developmental stage


title: Untreated-Roots-2wks-Rep1

description:
2 weeks old Nipponbare plant roots-untreated control- Sequencing technical replication -1
Library strategy: Illumina's Sequencing by Synthesis

value: Roots


title: Salt Stress-Roots-2wks-Rep1

description:
2 weeks old Nipponbare plant roots- stressed in salt for 24 hours- Sequencing technical replication -1
Library strategy: Illumina's Sequencing by Synthesis


title: 90 days-Immature panicle

description:
Nipponbare~90 days Immature Panicle- Sequencing technical replication -1
Library strategy: Illumina's Sequencing by Synthesis

source_name: Panicle

value: Panicle


title: Drought Stress-Roots-2wks-Rep1

description:
2 weeks old Nipponbare plant roots- stressed in drought for 24 hours- Sequencing technical replication -1
Library strategy: Illumina's Sequencing by Synthesis


title: 3 days-Germinating seed

description:
Nipponbare 3 days Germinating seed- Sequencing technical replication -1
Library strategy: Illumina's Sequencing by Synthesis


title: Salt Stress-Leaves-2wks-Rep2

description:
2 weeks old Nipponbare plant leaves- stressed in salt for 24 hours - Sequencing technical replication -2
Library strategy: Illumina's Sequencing by Synthesis


title: Drought Stress-Leaves-2wks-Rep2

description:
2 weeks old Nipponbare plant leaves- stressed in drought for 24 hours- Sequencing technical replication -2
Library strategy: Illumina's Sequencing by Synthesis


title: Cold Stress-Leaves-2wks-Rep2

description:
2 weeks old Nipponbare plant leaves- stressed in cold for 24 hours- Sequencing technical replication -2
Library strategy: Illumina's Sequencing by Synthesis


title: Cold Stress-Leaves-2wks-Rep1

description:
2 weeks old Nipponbare plant leaves- stressed in cold for 24 hours- Sequencing technical replication -1
Library strategy: Illumina's Sequencing by Synthesis


title: Drought Stress-Leaves-2wks-Rep1

description:
2 weeks old Nipponbare plant leaves- stressed in drought for 24 hours- Sequencing technical replication -1
Library strategy: Illumina's Sequencing by Synthesis


title: Rice leaf-Mechanical damaged-24 hr-Rep1

description:
Nipponbare control leaves 24 hour after mechanical damage - Sequencing technical replication -1
Library strategy: Illumina's Sequencing by Synthesis


title: M.oryzae-S-24h

description:
Leaves collected from 3 weeks old wild type Nipponbare plants 24 hours after rice blast (KJ201) inoculation - Sequencing technical replication -1
Library strategy: Illumina's Sequencing by Synthesis


title: 35 days-Callus

description:
Nipponbare 35 days Callus- Sequencing technical replication -1
Library strategy: Illumina's Sequencing by Synthesis

source_name: Callus

value: Callus


title: 60 days- Stem

description:
Nipponbare60 days Stem- Sequencing technical replication -1
Library strategy: Illumina's Sequencing by Synthesis

source_name: Stem

value: Stem


title: M.oryzae-S-12h

description:
Leaves collected from 3 weeks old wild type Nipponbare plants 12 hours after rice blast (KJ201) inoculation - Sequencing technical replication -1
Library strategy: Illumina's Sequencing by Synthesis


title: M.oryzae-S-6h

description:
Leaves collected from 3 weeks old wild type Nipponbare plants 6 hours after rice blast (KJ201) inoculation - Sequencing technical replication -1
Library strategy: Illumina's Sequencing by Synthesis


title: M.oryzae-R-24h

description:
Leaves collected from 3 weeks old Pi9 transgenic plants 24 hours after rice blast (KJ201) inoculation - Sequencing technical replication -1
Library strategy: Illumina's Sequencing by Synthesis

value: Nipponbare transformed with Pi9 gene


title: M.oryzae-R-6h

description:
Leaves collected from 3 weeks old Pi9 transgenic plants 6 hours after rice blast (KJ201) inoculation - Sequencing technical replication -1
Library strategy: Illumina's Sequencing by Synthesis


title: M.oryzae-R-12h

description:
Leaves collected from 3 weeks old Pi9 transgenic plants 12 hours after rice blast (KJ201) inoculation - Sequencing technical replication -1
Library strategy: Illumina's Sequencing by Synthesis


title: Mock treatment-24hr

description:
Leaves collected from 3 weeks old Pi9 transgenic plants 24 hours after water spray-Mock treatment - Sequencing technical replication -1
Library strategy: Illumina's Sequencing by Synthesis

value: Control-Biotic Stress


title: RNA_12hr_nitrogen_step_down

city: La Jolla

first: James

middle: W

last: Golden

address: 9500 Gilman Dr. MC 0116

department: Biological Sciences

institute: UCSD

data_processing: CLC Genomics Workbench 4.0 was used to align reads to the NCBI Nostoc 7120 gbk file for the chromosome and each of seven plasmids with 2 mismatches allowed. Reads with more than 10 total matches were removed from the dataset, as were reads that aligned to the rRNA and tRNA annotated sequences.

organism: Nostoc sp. PCC 7120 = FACHB-418

source_name: whole filament

growth_protocol: For deep sequencing, total RNA was prepared from Anabaena cultures grown in 100 ml flasks in the presence or absence of combined nitrogen as previously described . Briefly, 100 ml of cells were grown to an OD750 of 0.5 in BG11 medium lacking sodium nitrate and containing 5 mM MOPS (pH 8.0) and 2.5 mM ammonium chloride.

extract_protocol: RNA was isolated with the Ambion RiboPure RNA isolation kit according to the manufacturer's protocol and total RNA (with ribosomal RNA) was sent for deep sequencing.  We chose to include ribosomal RNA to minimize the depletion of coding transcripts by the rRNA removal protocols. In addition, we did not multiplex to avoid bias from using different adapters for different time points, as is required when multiplexing with different data sets. Therefore, a directional RNA sequencing library was prepared from 1 µg of total RNA from each sample (0, 6, 12, 21). The samples were purified using a Qiagen RNeasy MinElute Cleanup Kit, fragmented for 180 seconds using a Covaris S2 set at 10% duty cycle, 5 Intensity, 200 cycles/burst in 120µl Tris-EDTA pH 8.0 and purified again using a Qiagen RNeasy MinElute Cleanup Kit. The fragmented RNA (100 ng) was dephosphorylated using antarctic phosphatase (2 units, 37 °C, 30 min), 5' phosphorylated using T4 polynucleotide kinase (20 units, 37 °C, 60 min) and purified using a Qiagen RNeasy MinElute Cleanup Kit. After this, cDNA library preparation steps were performed as described in the Illumina “Small RNA v1.5 Sample Preparation Guide.” For sequencing, the cDNA library was denatured in 0.1N NaOH and diluted to a final concentration of 9 pM before being loaded onto the Illumina single read flow-cell.

treatment_protocol: Cells were collected for the 0 hr time point before nitrogen step down, or washed 3 times in BG11 N- and diluted ten fold for diazotrophic growth for 6, 12, or 21 hours. At 6 hours cells are beginning to establish a pattern of proheterocysts, at 12 hours cells are committed to becoming heterocysts, and at 21 hours filaments have fully formed nitrogen-fixing heterocysts. Cells were then collected by cooling 50 ml of culture over 100 g ice and centrifugation at 4,000 x g for 10 minutes at 4°C. Pellets were transferred to a 2 ml tube and spun at 11,500 x g for 2 minutes at 4°C. Excess BG11 was removed and pellets were flash frozen in liquid nitrogen for storage at -80°C.

value: whole filament

tag: strain


title: RNA_21hr_nitrogen_step_down


title: RNA_0hr


title: RNA_6hr_nitrogen_step_down


title: TN_RNA_a

status: Public on Jun 21 2011

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing: 2007 M. musculus genome assembly (mm9) was used as a basis for all analyses. Low-complexity reads were filtered out based on their dinucleotide entropy (removing <1% of the reads). Alignments to the M. musculus genome were performed by the software bowtie (Langmead et al. 2009) with parameters -v 2 -a -m 100, tracking up to 100 best alignment positions per query and allowing at most two mismatches.

source_name: Terminally differentiated Neurons (TN)

growth_protocol: Wild-type embryonic stem cells (129Sv-C57Bl/6) were cultured and differentiated as previously described (M. Bibel, J. Richter, E. Lacroix, Y. A. Barde, Nat Protoc 2, 1034 (2007)) and differentiated to Neuronal  Progenitors and further to Terminally differentiated Neurons (TN). Mouse embryonic fibroblasts were isolated from wild-type embryos (C57Bl/6).

extract_protocol: RNA was isolated using RNeasy Mini Kit (Invitrogen) following the manufacturer's instructions. Libraries for sequencing were prepared with the Illumina mRNA-Seq 8-Sample Prep Kit (Cat# RS-100-0801) according to Illumina's instructions. After adapter ligation library fragments of ~250 bp were band isolated from an agarose gel. The DNA was PCR amplified with Illumina primers for 15 cycles, purified and loaded on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.

value: Terminally differentiated Neurons (TN)


title: TN_RNA_b


title: ES_RNA_a

source_name: Embryonic Stem Cells (ESCs)

value: Embryonic Stem Cells (ESCs)


title: M.oryzae-S-96h

description:
Leaves collected from 3 weeks old wild type Nipponbare plants 96 hours after rice blast (KJ201) inoculation- Sequencing technical replication -1
Library strategy: Illumina's Sequencing by Synthesis

value: Biotic stress


title: TN_H3K4me2

growth_protocol: Wild-type embryonic stem cells (129Sv-C57Bl/6) were cultured and differentiated as previously described (M. Bibel, J. Richter, E. Lacroix, Y. A. Barde, Nat Protoc 2, 1034 (2007))

extract_protocol: ChIP experiments were performed as described before (F. Mohn et al., Mol Cell 30, 755 (Jun 20, 2008)), starting with 70 µg of chromatin and 5 µg of the following antibodies: anti-trimethyl-H3K27 (Upstate, no. 07-449), anti-dimethyl-H3K4 (Upstate, no. 07-030). The ChIP libraries were prepared with the Illumina ChIP-Seq DNA Sample Prep Kit (Cat# IP-102-1001) according to Illumina's instructions and sequenced on the Genome Analyzer 2 following the manufacturer's protocols.

tag: antibody

tag: vendor

value: Upstate

tag: no


title: MEF_RNA_b

source_name: Embryonic Fibroblasts

value: Embryonic Fibroblasts


title: TN_H3K27me3_technical_replicate_a1


title: TN_H3K27me3_technical_replicate_a2


title: Input


title: MEF_RNA_a


title: ES_H3K27me3_biological_replicate_b


title: TN_H3K27me3_biological_replicate_b


title: ES_H3K4me2


title: ES_H3K27me3_technical_replicate_a2


title: Cold Stress-Roots-2wks-Rep1

description:
2 weeks old Nipponbare plant roots- stressed in cold for 24 hours- Sequencing technical replication -1
Library strategy: Illumina's Sequencing by Synthesis


title: ES_H3K27me3_technical_replicate_a1


title: MixedSamplesPairedEnd120nt_1

status: Public on Jun 16 2011

city: Aurora

first: Jianbin

last: Wang

state: CO

address: 12801 East 17th Ave

department: Biochemistry and Molecular Genetics

institute: University of Colorado Denver

description: Ascaris mixed samples of germlines and embryos, full length cDNA sheared

data_processing: Following removal of the adaptor sequences from the sequence reads, high quality reads with >= 36 nt in length were selected.

organism: Ascaris suum

source_name: Ascaris sample

growth_protocol: For the germinal zone of the testis and ovary, the distal 5 cm of the gonad was isolated from live worms and stored at -80°C. Other regions of the gonads were dissected from live worms and either frozen immediately at -80°C or lysed by homogenization in Trizol and then frozen. Ascaris fertilized eggs were harvested from 4 regions of female uteri (Zygote 1-4) by treatment with 0.5 N NaOH, followed by extensive washing in water, and then stored at 4 °C with 5 volumes of PBS (pH 2.0). For embryonation, the fertilized eggs from final proximal region of the uterus (Zygote-4 = 0 hr embryos) were incubated at 30 °C in PBS (pH 2.0) with constant (100 rpm) shaking for the desired time. The outer shell/membranes were de-coated with 0.4 N KOH/1.4% sodium hypochlorite at 4 °C (zygotes from regions 1-4) or 30°C (developing embryos and larvae) for 180 or 90 minutes, respectively, prior to RNA preparation. RNA from fertilized eggs in the uterus and early embryos (0 hr to 8 days) were extracted directly with Trizol (Invitrogen). Frozen L1, L2, testis and ovary samples were first ground with a mortar and pestle in liquid nitrogen and then extracted with Trizol.

extract_protocol: cDNA libraries were prepared from polyadenylated RNA (2x oligo-dT purified using μMACS™ mRNA Isolation Kit, Miltenyi Biotec). Two types of libraries were prepared: 1) sheared, full-length cDNA synthesized using a combination of oligo-dT and random hexamer priming and 2) cDNA prepared from RNA first chemically sheared and then double-stranded cDNA prepared using ramom hexamer priming. For the chemically sheared library, RNA was treated for 75-150 sec with RNA fragmentation buffer (Ambion) at 70°C to generate RNA fragments 150-400 nt in length. First stand cDNA was prepared by random priming (3-6 µg random hexamers/1 µg of A+ RNA) and second stranded cDNA synthesis was carried out using a SuperScript® Double-Stranded cDNA Synthesis Kit (Invitrogen).  Solexa paired-end adaptors were added to the blunt cDNA as described by Illumina, cDNA fragments of 300-400 bp in length were gel purified, the fragments amplified using 17 PCR cycles, and paired-end, 76-120 nt reads were generated as described on the Illumina GAII.

tag: library preparation

value: Paired-end 120 nt (insert:200-300 nt)

tag: library id


title: FemaleReproductivePairedEnd120nt_1

description: Ascaris complete female reproductive system

value: complete female reproductive system


title: WholeMalePairedEnd120nt_1

description: Ascaris whole male

value: whole male


title: RRB-Seq of Apis Mellifera sperm

city: London

first: Guillermo

last: Carbajosa

address: 4 Newark Street

department: Diabetes

country: United Kingdom

institute: Blizard Institute

description: bisulfite converted DNA

data_processing: 2 bp were trimmed at both ends of each reads before aligning. Raw reads were aligned using the MAQ methylation mode. Reads with a mapping quality of less than 10 were filtered. Reads that with none of their ends aligned further than 1 bp away from a restriction enzyme site were filtered. Only CpG sites with at least 5X coverage were retained for further analyses.

organism: Apis mellifera

source_name: Sperm

extract_protocol: A. mellifera drones were obtained in Sussex, UK. The sperm was collected from 6 mature drones as they were preparing for mating-flights. Drone heads were crushed, provoking the eversion of the genitalia, and sperm collected with a Pasteur pipette. Approximately 1 Âµl of semen was obtained per drone and then immediately frozen prior to DNA extraction. DNA was extracted using a standard phenol/chloroform method. Reduced Representation Bisulfite Sequencing was performed according to the protocol reported in Reference 7 of Nanty L. et al., 2011, Genome Research. Briefly, we performed two different digestions in parallel on 1 Âµg of genomic DNA using MspI/BsoBI for the first and TaqÎ±I for the second. MspI/BsoBI and TaqÎ±I libraries were admixed at 1:3 ratio prior to sequencing. Raw reads were aligned using the MAQ methylation mode. Only CpG sites with at least 5X coverage were retained for further analyses. The average insert size (fragment length) was 76.2 bp and the standard deviation 26.1

value: freshly isolated sperm


title: ES_RNA_b


title: EmbryoPairedEnd76nt_1

description: Ascaris mixed samples from 0 - 64 hr embryos

value: Paired-end 76 nt (insert:200-300 nt)

value: mixed samples from 0 - 64 hr embryos


title: EmbryoPairedEnd114nt_1

value: Paired-end 114 nt (insert:200-300 nt)


title: EmbryoSingleEnd2

value: Single end


title: EmbryoSingleEnd3


title: TestisPairedEnd114nt_1

description: Ascaris testis germinal zone

value: testis germinal zone


title: EmbryoSingleEnd1


title: TestisSingleEnd4

description: Ascaris testis germinal zone


title: TestisSingleEnd3

description: Ascaris testis germinal zone


title: TestisSingleEnd2

description: Ascaris testis germinal zone


title: Testis-G_5monophosphate3modified

description: Ascaris testis germinal zone

data_processing: Following removal of the adaptor sequences from the sequence reads, reads were collapsed to non-redundant datasets and then short reads (<= 17 bp) and low complexity reads were removed. Processed files are in fasta format, with the description of each unique sequence as >number1_number2, where number1 is a unique id and number2 is the total count of the sequence in the library. Note spike sequences are excluded in the processed files, but their number can be found in the raw data and our paper.

extract_protocol: We constructed three types of small RNA libraries: 1) libraries of 18-34 or 18-40 nt RNAs with a 5’ monophosphate (5’ monophosphate libraries), 2) libraries of 18-34 nt RNAs with a 5’ monophosphate but treated with periodate to enrich for small RNAs with 3’ end modifications (5’ monophosphate, 3’ end modified), and 3) libraries of 18-28 or 18-40 nt RNAs with a 5’ triphosphate, diphosphate, or monophosphate (5’ All-phosphate). Prior to gel purification of the RNAs, two small RNA spikes (p-AACUGUGUCUUUUCUGAAUAGA and p-UAUUUAGAAUGGCGCUGAUCUG) were added to the samples for subsequent library read normalization.

value: 5’ monophosphate, 3’ end modified


title: 128cell-L2_5allphosphate

description: Ascaris mixed samples from 128 cells - L2

value: 5’ allphosphate

value: mixed samples from 128 cells - L2


title: 128cell-L2_5monophosphate3modified


title: 0-64cell_5monophosphate3modified


title: Ovary-G-old_5monophosphate3modified

description: Ascaris ovary germinal zone

value: ovary germinal zone


title: 0-64cell_5allphosphate


title: LarvaePairedEnd120nt_1


title: OvaryPairedEnd120nt_1

description: Ascaris ovary germinal zone


title: Zygote-2_with_wall_5allphosphate

description: Ascaris zygotes from region 3 of the uterus, with undigested wall


title: Globo_HP_s1

status: Public on Jun 20 2011

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

institute: Radboud University

description: Assembly of sequenced data

data_processing:
Reads were assembled using Edena with parameters m=16 and M=16
Sequence reads were obtained using the Illumina Genome Analyzer Pipeline 1.4

organism: Globobulimina pseudospinescens

source_name: Whole living organisms

growth_protocol: Foraminifera were hand-picked from the sediment

extract_protocol:
Standard manufacturer (Illumina) protocol.
(mixed genomic and mitochondrial with possible bacterial contamination)
The complete info for the DNA extraction kit:
QIAamp DNA Micro Kit (50)
For 50 DNA preps: 50 QIAamp MinElute Columns, Proteinase K, Carrier RNA, Buffers, Collection Tubes (2 ml)
Cat number: 56304

treatment_protocol: Washing with artificial sea water

value: 10,000 single-cell Globobulimina pseudospinescens organisms


title: Zygote-1_with_wall_5allphosphate

description: Ascaris zygotes from region 1 of the uterus, with undigested wall


title: Zygote-3_with_wall_5allphosphate

description: Ascaris zygotes from region 2 of the uterus, with undigested wall


title: Spermatids-old_5allphosphate

description: Ascaris spermatids

value: spermatids


title: Seminal_Vescile_5allphosphate

description: Ascaris seminal vescile

value: seminal vescile


title: Zygote-4_5allphosphate

description: Ascaris zygotes from region 4 of the uterus

value: zygotes from region 4 of the uterus


title: Testis-All_5allphosphate

description: Ascaris whole testis

value: whole testis


title: Zygote-3_5allphosphate

description: Ascaris zygotes from region 3 of the uterus

value: zygotes from region 3 of the uterus


title: TestisPairedEnd76nt_1

description: Ascaris testis germinal zone


title: Zygote-1_5allphosphate

description: Ascaris zygotes from region 1 of the uterus

value: zygotes from region 1 of the uterus


title: Zygote-2_5allphosphate

description: Ascaris zygotes from region 2 of the uterus

value: zygotes from region 2 of the uterus


title: Ovary-All_5allphosphate

description: Ascaris whole ovary

value: whole ovary


title: Ovary-G_5allphosphate

description: Ascaris ovary germinal zone


title: Ovary-G-old_5allphosphate

description: Ascaris ovary germinal zone


title: TestisSingleEnd1

description: Ascaris testis germinal zone


title: Spermatids_5allphosphate

description: Ascaris spermatids


title: Testis-2_5allphosphate

description: Ascaris testis region 2

value: testis region 2


title: Testis-G_5allphosphate

description: Ascaris testis germinal zone


title: Testis-1_5allphosphate

description: Ascaris testis region 1

value: testis region 1


title: Seminal_Vescile_5monophosphate

description: Ascaris seminal vescile

value: 5’ monophosphate


title: Zygote-3_with_wall_5monophosphate

value: zygotes from region 3 of the uterus, with undigested wall


title: LarvaeL2_5monophosphate

description: Ascaris Larvae L2 (21 day)

value: Larvae L2 (21 day)


title: Zygote-2_with_wall_5monophosphate

value: zygotes from region 2 of the uterus, with undigested wall


title: Testis-All_5monophosphate

description: Ascaris whole testis


title: Spermatids-old_5monophosphate

description: Ascaris spermatids


title: Zygote-1_with_wall_5monophosphate

value: zygotes from region 1 of the uterus, with undigested wall


title: LarvaeL1_5monophosphate

description: Ascaris Larvae L1 (10 day)

value: Larvae L1 (10 day)


title: 8D_5monophosphate

description: Ascaris 8 day embryo

value: 8 day embryo


title: 7D_5monophosphate

description: Ascaris 7 day embryo

value: 7 day embryo


title: 96hr_5monophosphate

description: Ascaris 96 hr embryo

value: 96 hr embryo


title: 6D_5monophosphate

description: Ascaris 6 day embryo

value: 6 day embryo


title: 116hr_5monophosphate

description: Ascaris 116 hr embryo

value: 116 hr embryo


title: 64hr_5monophosphate

description: Ascaris 64 hr embryo

value: 64 hr embryo


title: 24hr_5monophosphate

description: Ascaris 24 hr embryo

value: 24 hr embryo


title: 0hr_5monophosphate

description: Ascaris 0 hr embryo, same as zygotes from region 4 of the uterus


title: 46hr_5monophosphate

description: Ascaris 46 hr embryo

value: 46 hr embryo


title: Zygote-2_5monophosphate

value: zygotes from region 2 of the uterus


title: Zygote-1_5monophosphate

value: zygotes from region 1 of the uterus


title: Zygote-4_5monophosphate

value: zygotes from region 4 of the uterus


title: Ovary-All_5monophosphate

description: Ascaris whole ovary

value: 5’ monophosphate

value: whole ovary


title: Ovary-G_5monophosphate

description: Ascaris ovary germinal zone

value: ovary germinal zone


title: Ovary-G-old_5monophosphate

description: Ascaris ovary germinal zone


title: Testis-2_5monophosphate

description: Ascaris testis region 2

value: testis region 2


title: Testis-1_5monophosphate

description: Ascaris testis region 1

value: testis region 1


title: Spermatids_5monophosphate

description: Ascaris spermatids

value: spermatids


title: Testis-G_5monophosphate

description: Ascaris testis germinal zone

value: testis germinal zone


title: Mouse placenta RNAseq PWD/PhJ mother x AKR/J father AP

status: Public on Jun 15 2011

city: Ithaca

first: Andrew

last: Clark

address: 227 Biotech Building

institute: Cornell University

description: Illumina mRNA-seq

data_processing: Alignment: The reads were truncated to 40 bp and aligned to the mouse reference genome (NCBI B37/UCSC mm9) using BWA with a maximum of four mismatches. On average, 55.2% of the reads were mapped uniquely to the reference genome.

source_name: mouse embryonic day 17.5 placental tissue

extract_protocol: The mRNA-seq libraries were made with 5 ug of starting total RNA samples using the mRNA-Seq 8-Sample Prep Kit (Illumina Inc., CA), following the Illumina protocol for mRNA sequencing sample preparation.

value: PWD/PhJ mother x AKR/J father

value: placenta

tag: developmental stage


title: Fungal_mycelia_T37

city: Rockville

first: Ravi

last: Sanka

state: Maryland

address: 9704 Medical Center Drive

institute: JCVI

description:
polyA RNA from Aspergillus flavus grown at T37
sample T37

data_processing: Raw sequence data generated by GA II were processed, filtered and normalized using the Illumina pipeline (www.illumina.com) to generate raw sequence reads files. All reads were then filtered and aligned to the annotataed Aspergillus flavus NRRL3357 genome to calculate expression values for every gene in RPKM using CLC Bio Genomic Workbench with default parameters: minimum length fraction (0.9, minimum similarity fraction (0.8), maximum number of hits per read (10).

molecule: polyA RNA

organism: Aspergillus flavus

source_name: Mycelia

growth_protocol: Fungi were grown in GMS medium for 24 hours

extract_protocol: Each total RNA sample (20-50ug) was treated with DNase and enriched for mRNA using oligo (dT) tags.  Samples of poly (A) RNA (0.2- 1ug) were fragmented into smaller pieces (200-500 bp) and used to synthesize cDNA. Library construction was performed according to the Illumina protocol (www.illumina.com)

treatment_protocol: Mycelia were collected, fresh frozen with liquid nitrogen and grounded to a fine powder in liquid nitrogen. Total RNA was extracted from 100 mg of fungal tissue using TRIzolÂ® Reagent (Invitrogen) according to manufacturerâs instructions.


title: Fungal_mycelia_T30

description:
polyA RNA from Aspergillus flavus grown at T30
sample T30


title: Zygote-3_5monophosphate

value: zygotes from region 3 of the uterus


title: ACTIVEMOTIF_hmeDIPseq

status: Public on Jun 13 2011

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

data_processing: Sequenced reads were based-called using the standard Illumina software. Reads were trimmed down to 50 bases due to low quality base calls in the 3' end of reads, and aligned to hg18 with Bowtie (v.0.12.4) allowing up to 3 mismatches.

source_name: Embryonic stem cells

growth_protocol: HSF1 hESC line was cultured as previously described (Xiao et al. 1999 Embo J 18: 5943-5952).

extract_protocol: Illumina libraries were generated per manufacturer instructions (Illumina).

treatment_protocol: Hydroxymethyl-DNA immunoprecipitation (hmeDIP) experiments were performed on HSF1 hESCs as previously described(Zhang et al. Cell 2006 126(6):1189-201.) using commercial antibodies specific to 5hmC (Active Motif 39791 and Diagenode AF-110-0016), except that Illumina adapter ligated DNA fragments were used as the input for the IP.

tag: antibody manufacturer

value: Active Motif

tag: antibody catalog #


title: DIAGENODE_hmeDIPseq

value: Diagenode


title: sr-myc

city: Esch-Belval

first: Patrick

last: May

state: Luxembourg

address: 7, avenue des Hauts-Fourneaux

department: Luxembourg Centre for Systems Biomedicine

country: Luxembourg

institute: University of Luxembourg

description:
small RNA
processed data file: sequence counts

data_processing: Removed adaptores. Sequences without adapters were discarded. 3' adapter sequence: TCGTATGCCGTCTTCTGCTTGT

organism: Medicago truncatula

source_name: Medicago truncatula roots inoculated with Glomus intraradices (3wpi)

growth_protocol: Seeds of Medicago truncatula Jemalong A17 were germinated as described in. (Branscheid et al., 2010). Seedlings were grown in a sand: expanded clay substrate (1:1) under 16h light at 25°C and fertilized, unless otherwise noted, twice a week with half strengths Hoagland solution containing 20 µM phosphate. For inoculation with Glomus intraradices, an inoculum was added to the substrate at 10% (v/v). G. intraradices (strain BB-E, provided by Agrauxine, Dijon, France) was used.

extract_protocol: Total RNA was isolated using the mirVana miRNA isolation kit (Ambion) in combination with the Plant RNA Isolation Aid (Ambion). 10 µg RNA were used for small RNA library construction using the Digital Gene Expression Small RNA Sample Prep Kit (Illumina).

tag: ecotype

value: Jemalong A17


title: sr-nm

source_name: Medicago truncatula roots


title: no antibody

tag: sample type

value: input DNA eluted from beads without antibodies


title: input DNA

value: input DNA


title: microRNA expression in Ter119+ mature erythroblasts

status: Public on Jun 09 2011

city: Cambridge

first: Lingbo

last: Zhang

address: Nine Cambridge Center

institute: Whitehead Institute for Biomedical Research and MIT Department of Biology

data_processing: Alignment: Sequence reads were obtained and mapped to the mouse (mm9) genome as well as miRBase miRNA Sequences using the ELAND. The number of mapped positions for the genome alignment were used to normalize the number of counts per miRNA.

source_name: Erythoid cells

growth_protocol: CFU-E erythroid progenitors were isolated from E14.5 fetal liver as the Ter119, B220, Mac-1, CD3 and Gr-1 negative, C-Kit positive and 20% high CD71 population. Mature Ter119+ erythroblasts were isolated from E14.5 fetal liver as C-Kit negative and Ter119 positive population.

extract_protocol: Samples prepared were prepared by using the Small RNA Sample Prep Kit (Illumina) according to instruction.

tag: genetic background

value: Ter119+ mature erythroblasts


title: microRNA expression in CFU-E late erythroid progenitors

value: CFU-E late erythroid progenitors


title: deg-myc

description:
degradome
processed file: tag count data

extract_protocol: Total RNA was isolated using the mirVana miRNA isolation kit (Ambion) in combination with the Plant RNA Isolation Aid (Ambion). Poly(A) RNA was isolated from total RNA using the Oligotex mRNA Kit (Qiagen). The degradome libraries from 1 µg poly(A)- enriched RNA were generated according to (German et al., 2009).


title: deg-nm


title: Breast_Normal_99B

status: Public on Jun 07 2011

city: New York

first: Thalia

last: Farazi

address: 1230 York Ave, BOX 186

department: Lab of RNA Molecular Biology

institute: Rockefeller University

description:
99
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information

data_processing:
We processed all samples by 3'-adapter barcoded small RNA cDNA library Solexa sequencing (library construction). 61,319,767 sequence reads were extracted from barcodes yielding a median of 134,022 reads per sample (range: 7,403-1,608,855); these reads were mapped to the genome allowing one mismatch/insertion/deletion and then to our non-coding RNA and miRNA databases allowing up to two mismatches or one insertion/deletion (22). We constructed a miRNA read database from over 1,000 human samples sequenced in the Tuschl laboratory, defined prototypical miRNAs (557 precursors, corresponding to 1112 mature and star sequences, miR-451 and miR-618 being the only miRNAs without a star sequence), added 269 not yet reported star sequences, ignored putative miRNAs from miRBase for which we did not obtain read evidence and renamed specific miRNAs according to the read ratio between mature/star sequences (Tuschl, unpublished data).
Note: Not all subsamples from each sequencing run were used for this project. We did not include these subsamples in the unassigned read files if they contained a barcode. Unasigned reads are reads that were not able to be mathced to any barcode. Unassigned read files are attached to the Series record.

source_name: Breast tissue

growth_protocol: Tissues Collected from patients; Cell lines grown according to ATCC recommendations.

extract_protocol: Fresh-frozen (frozen immediately after surgery and stored at -80C) normal and tumor tissue was collected. RNA was isolated from approximately thirty 30-um cryosections corresponding to approximately 20 mg of tissue, using the first and last section to assess tumor content; only samples containing more than 50% tumor were further characterized. The tissues were homogenized in Trizol using a Polytron instrument (polytron, PT, MR2100, Kinematica AG, Luzern) for 1 min and total RNA was isolated by a modified Trizol protocol (acidic phenol:chloroform:IAA (25:24:1) extraction, precipitated with 2M NaOAc pH 4.2 and Ethanol). Quality of isolated RNA was assessed on a 1% agarose gel based on the relative abundance of 18S and 28S subunits of ribosomal RNA. We used a barcoded small RNA sequencing approach (Hafner 2011). Briefly, in a total reaction volume of 20 ul, 2 ug total RNA was ligated to 100 pmol adenylated 3' adapter containing a unique pentamer barcode (App-(Barcode)TCGTATGCCGTCTTCTGCTTGT), 1 ug Rnl2(1-249)K227Q (plasmid for expression of recombinant ligase is available at www.addgene.org) in 50 mM Tris-HCl, pH 7.6, 10 mM MgCl2, 10 mM 2-mercaptoethanol, 0.1 mg/ml acetylated BSA (Sigma, St. Louis, MO), and 15% DMSO for 16 h on ice. Barcodes are listed in this table. Following 3' adapter ligation, 20 barcoded samples were pooled and products were purified on a 15% denaturing polyacylamide gel. Small RNAs, measuring 45-50 nt in length, were excised from the gel, eluted, and ligated to 100 pmol 5' oligoribonucleotide adapter (GUUCAGAGUUCUACAGUCCGACGAUC) in a 20 ul reaction volume using 1 ug Rnl1 RNA ligase in 50 mM Tris-HCl, pH 7.6, 10 mM MgCl2, 10 mM 2-mercaptoethanol, 0.2 mg/ml acetylated BSA, 0.1 mg/ml acetylated BSA, 0.2 mM ATP, and 15% DMSO for 1 h at 37C. Ligated small RNAs were purified on a 12% polyacrylamide gel, reverse transcribed using SuperScript III Reverse Transcriptase (Invitrogen, Carlsbad, CA), and amplified by PCR using appropriate primers (forward primer: AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA; RT and reverse primer: CAAGCAGAAGACGGCATACGA). cDNA libraries were sequenced by Solexa technology at the Rockefeller University Genomics Resource Center. To selected samples we added in total 2.5 or 3.4 fmol of a cocktail of 10 calibrator oligoribonucleotides per ug of total RNA (for sequences see (Hafner 2011)).

tag: tissue

value: Breast

tag: disease status

value: Normal

tag: ID

tag: esr/er ihc (1=positive, 0=negative)

tag: pgr/pr ihc (1=positive, 0=negative)

tag: erbb2 ihc (1=positive, 0=negative)


title: Breast_IDC_78B

description:
78
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information

value: IDC


title: Breast_DCIS_9B

description:
9
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information

value: DCIS


title: Breast_DCIS_5B

description:
5
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_70B

description:
70
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_52B

description:
52
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_75C

description:
75
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Normal_105B

description:
105
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_45C

description:
45
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_36B

description:
36
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_32C

description:
32
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_31C

description:
31
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_DCIS_18B

description:
18
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_DCIS_16B

description:
16
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Normal_98C

description:
98
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_148B

description:
148
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_92C

description:
92
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Normal_104C

description:
104
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_66C

description:
66
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Cell Line_193A

description:
193
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information

source_name: Breast cell line

value: Cell Line


title: Breast_Cell Line_192A

description:
192
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_94B

description:
94
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Cell Line_195A

description:
195
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Normal_103B

description:
103
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_57B

description:
57
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_167B

description:
167
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_65B

description:
65
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_175B

description:
175
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Metaplastic_166B

description:
166
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information

value: Metaplastic


title: Breast_IDC_74

description:
74
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_71

description:
71
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_60

description:
60
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_90

description:
90
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_58

description:
58
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_89A

description:
89
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_79

description:
79
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Cell Line_194A

description:
194
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Gastrula_dorsal_explant

status: Public on Jun 18 2011

city: Santiago

first: Juan

last: Larrain

address: Alameda 340

department: Cell and Molecular Biology

country: Chile

institute: P. Universidad Catolica de Chile

description: DMZ

data_processing: After removing the adapters (using a set of in-house scripts) and merging identical reads, the sequences were filtered by length (20 - 32nt), sequence complexity and then mapped to the Xenopus tropicalis genome (Assembly 4.1v) allowing only exact matches. This will consolidate the summary table for each library. Each summary table contains two columns: (1) Nucleotide sequence, and (2) Counts of the sequence in the library.

organism: Xenopus tropicalis

source_name: Embryo, dorsal

extract_protocol: All samples were prepared and sequenced at GeneWorks (Adelaide, Australia), a commercial sequencing provider. Libraries were generated using the v1.5 Illumina small RNA sequencing kit (Part # 15002615) and adaptor (5' ATCTCGTATGCCGTCTTCTGCTTG 3') according to the manufacturer's instructions. Small RNA size selection was performed using a modified ladder, which has additional markers at 14, 18 and 21 bp to facilitate sequencing of very small RNA species.

value: gastrula

value: stage 10

tag: explant

value: dorsal


title: Breast_IDC_73

description:
73
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_84

description:
84
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_76

description:
76
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_72

description:
72
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_62A

description:
62
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_70A

description:
70
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_48

description:
48
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_69A

description:
69
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_53

description:
53
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_50A

description:
50
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Cell Line_196

description:
196
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Cell Line_197

description:
197
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_75A

description:
75
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Normal_98A

description:
98
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Normal_97

description:
97
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_59

description:
59
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_52A

description:
52
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Normal_95A

description:
95
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Normal_103A

description:
103
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Normal_102A

description:
102
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Normal_100A

description:
100
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Normal_104A

description:
104
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_86A

description:
86
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_85A

description:
85
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_78A

description:
78
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_66A

description:
66
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_54

description:
54
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_68

description:
68
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_63A

description:
63
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_56

description:
56
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_51

description:
51
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_93A

description:
93
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_46

description:
46
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Mouse placenta RNAseq AKR/J mother x PWD/PhJ father PA

description: Illumina mRNA-seq

tag: strain

value: AKR/J mother x PWD/PhJ father

value: placenta


title: Breast_IDC_94A

description:
94
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_82

description:
82
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_92A

description:
92
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_83A

description:
83
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_80

description:
80
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_77

description:
77
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_87

description:
87
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_65A

description:
65
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_61A

description:
61
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_57A

description:
57
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_45A

description:
45
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Cell Line_195B

description:
195
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Normal_96

description:
96
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Normal_99A

description:
99
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_42

description:
42
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_27A

description:
27
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_32A

description:
32
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_139A

description:
139
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Normal_105A

description:
105
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Normal_101

description:
101
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_155A

description:
155
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Atypical Medullary_126B

description:
126
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information

value: Atypical Medullary


title: Breast_IDC_152A

description:
152
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_124A

description:
124
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Round spermatids

status: Public on Jun 10 2011

city: Beijing

first: Chunsheng

last: Han

state: Beijing

address: 1-5 Beichen West Road, Chaoyang District

department: Institute of Zoology

country: China

institute: Chinese Academy of Sciences

description: small RNA sequencing; sample 3

data_processing: After clipping the adapter sequences, removing reads with Ns, reads were aligned to the reference genome (mm9) allowing zero mismatches by PASS [PASS: a program to align short sequences. PMID: 19218350. http://pass.cribi.unipd.it/cgi-bin/pass.pl].

source_name: male germ cell

extract_protocol: Illumina small RNA library preparation kit. Ten micrograms of total RNAs were separated by 15% denaturing PAGE gel, visualized by SYBR-gold staining, and small RNAs of 18-36 nt were gel-purified.

treatment_protocol: total RNA was size selected (18-36nt)

value: ICR

value: testis

tag: cell type

value: Round spermatids


title: Gastrula_ventral_explant

description: VMZ

source_name: Embryo, ventral

value: ventral


title: Breast_Atypical Medullary_64

description:
64
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_63B

description:
63
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_61B

description:
61
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Metaplastic_183

description:
183
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_45B

description:
45
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_49

description:
49
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_85B

description:
85
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_181B

description:
181
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Metaplastic_136

description:
136
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Atypical Medullary_134

description:
134
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Pachytene spermatocytes

description: small RNA sequencing; sample 2

value: Pachytene spermatocytes


title: Breast_Atypical Medullary_135

description:
135
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information

value: Breast


title: Breast_IDC_62B

description:
62
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Atypical Medullary_128

description:
128
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Metaplastic_132

description:
132
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Type A spermatogonia

description: small RNA sequencing; sample 1

value: Type A spermatogonia


title: Breast_IDC_121B

description:
121
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information

value: IDC


title: Breast_IDC_92B

description:
92
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_119B

description:
119
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_89B

description:
89
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_93B

description:
93
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_75B

description:
75
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_66B

description:
66
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_165

description:
165
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Metaplastic_130

description:
130
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_163

description:
163
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_164

description:
164
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_158

description:
158
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_156

description:
156
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_DCIS_4

description:
4
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information

value: DCIS


title: Breast_IDC_139B

description:
139
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_124B

description:
124
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_DCIS_10

description:
10
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_148A

description:
148
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_146

description:
146
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_DCIS_9A

description:
9
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Metaplastic_127

description:
127
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_153B

description:
153
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_DCIS_8

description:
8
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_107B

description:
107
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_DCIS_7

description:
7
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_DCIS_6

description:
6
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_83B

description:
83
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_DCIS_3

description:
3
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_DCIS_17

description:
17
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_162

description:
162
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_159

description:
159
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_157

description:
157
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_86B

description:
86
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Atypical Medullary_131

description:
131
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_152B

description:
152
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_161

description:
161
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_154

description:
154
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_150

description:
150
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_DCIS_15

description:
15
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_125

description:
125
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_DCIS_14

description:
14
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_147

description:
147
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Atypical Medullary_126A

description:
126
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_43B

description:
43
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_DCIS_11

description:
11
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_DCIS_5A

description:
5
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_31B

description:
31
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_DCIS_2

description:
2
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_30B

description:
30
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_DCIS_18A

description:
18
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_19B

description:
19
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_38B

description:
38
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_121A

description:
121
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_DCIS_16A

description:
16
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_119A

description:
119
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_118

description:
118
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Apocrine_117

description:
117
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information

value: Apocrine


title: Breast_IDC_155B

description:
155
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_116

description:
116
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_114

description:
114
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_115

description:
115
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_113

description:
113
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_112

description:
112
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_123

description:
123
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_111

description:
111
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_35A

description:
35
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_DCIS_12

description:
12
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_DCIS_1

description:
1
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_32B

description:
32
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_182

description:
182
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_28B

description:
28
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_33B

description:
33
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_180

description:
180
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_120

description:
120
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_145

description:
145
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_178

description:
178
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_144

description:
144
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_177

description:
177
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_179

description:
179
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_181A

description:
181
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_140

description:
140
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_110

description:
110
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_142

description:
142
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_109

description:
109
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_108

description:
108
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_107A

description:
107
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_106

description:
106
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Mucinous A_26

description:
26
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information

value: Mucinous A


title: Breast_IDC_176

description:
176
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Metaplastic_174

description:
174
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information

value: Metaplastic


title: Breast_IDC_175A

description:
175
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_27B

description:
27
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_172

description:
172
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Adenoid_171

description:
171
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information

value: Adenoid


title: Breast_IDC_169

description:
169
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_173

description:
173
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_143

description:
143
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_167A

description:
167
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Apocrine_160

description:
160
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_168

description:
168
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_153A

description:
153
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Apocrine_149

description:
149
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Metaplastic_166A

description:
166
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Metaplastic_129

description:
129
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_34

description:
34
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Metaplastic_122B

description:
122
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_41

description:
41
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Atypical Medullary_137

description:
137
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_39

description:
39
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_31A

description:
31
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_33A

description:
33
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_28A

description:
28
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_20

description:
20
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_21

description:
21
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_24

description:
24
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_19A

description:
19
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_67

description:
67
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Apocrine_170

description:
170
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_88A

description:
88
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_55A

description:
55
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_47A

description:
47
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_44

description:
44
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Metaplastic_122A

description:
122
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Adenoid_138

description:
138
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_ILC_40

description:
40
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information

value: ILC


title: Breast_IDC_36A

description:
36
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_43A

description:
43
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_Atypical Medullary_141

description:
141
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_38A

description:
38
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_30A

description:
30
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_37

description:
37
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_29

description:
29
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_35B

description:
35
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_23

description:
23
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_22

description:
22
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: Breast_IDC_25

description:
25
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: E2F6_K562_ChIP-seq_rep2 lane 1

city: Palo Alto

first: Philip

last: Cayting

address: 1501 S California Ave

department: Genetics

institute: Stanford University

description: Chromatin IP against E2F6

data_processing:
Alignment: Sequence reads were obtained and mapped to the human genome assembly hg18 (March, 2006) or hg19 (February, 2009) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.
Peaks were called with Sole-Search (http://chipseq.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi)

source_name: chronic myeloid leukemia cell line

growth_protocol: All cells were grown according to ENCODE standards (http://genomewiki.ucsc.edu/EncodeDCC/index.php/Cell_lines)

extract_protocol: Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3 to 5 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3â end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: ChIP assay was performed following the ChIP protocol provided at: http://farnham.genomecenter.ucdavis.edu/pdf/FarnhamLabChIP%20Protocol.pdf

tag: cell-type

value: K562 cell line

tag: harvest date

tag: chip antibody

value: rabbit anti-E2F6 (Santa Cruz Biotechnology, catalog# sc-22823x)


title: L3MBTL2_K562_ChIP-seq_rep2

description: Chromatin IP against L3MBTL2

value: rabbit anti L3MBTL2 (Danny Reinberg's lab)


title: Breast_IDC_81A

description:
81
genomic small RNA (size selected RNA from total RNA)
See Supplementary Table S1 and S2 for further sample information


title: debarshi_1110_retina

city: Cleveland

first: Debarshi

last: Mustafi

state: OH

address: 2109 Aldelbert Rd

department: Pharmacology

institute: Case Western Reserve University

description:
Nrl _Retina
Isolated retina mRNA
library selection: Poly-A beads

data_processing:
Illumina Pipeline software - ELAND and CASAVA v1.7
processed data file build:  mm9
Base-calling and alignment were performed using the Illumina pipeline software ELAND v1.7.  Alignment was performed to the mouse genome assembly version mm9 and accompanying RefSeq annotation, downloaded from UCSC, and a splice-sites file downloaded from Illumina.  Alignment results from multiple lanes and/or runs were combined for analysis using the Illumina program CASAVA v1.7, which calculated FPKM (fragments per kilobase of exon model per million mapped reads) by gene, transcript, and exon.  ELAND and CASAVA were run with default settings.  The output from CASAVA was visualized with the GenomeStudio RNA Sequencing Module (Illumina), which allowed comparison between the samples based on the CASAVA output files.

source_name: Retina tissue

extract_protocol: Mice were euthanized by cervical dislocation. Eyes were enucleated and immediately placed in RNAlater stabilization reagent (Qiagen, Valencia, CA, USA) to preserve RNA content and integrity for whole eye runs. Alternatively, the retina was rapidly dissected out and similarly preserved. One mouse eye or two retinas were homogenized at once and passed through a QIAShredder column (Qiagen) as per manufacturer's directions to further homogenize the eye tissues. Total RNA was then purified by using the RNeasy Mini Kit (Qiagen) with on column DNase treatment (Qiagen) as per manufacturer's directions. Poly(A) RNA was isolated with the Oligotex kit (Qiagen) as per the manufacturer's instructions. Pooled total RNA samples of 5 Wt and 5 Nrl-/- female mice 4 weeks of age were used for the whole eye library preparation and pooled total RNA samples from 5 Wt and 5 Nrl-/- female mice at 4 weeks of age were used for the retina library preparation.   For first strand cDNA synthesis, instructions from the SuperScript III kit protocol (Invitrogen) were followed. About 400-450 ng of isolated poly(A) RNA was mixed with 50 ng of random primers and 1 mM deoxyribonucleotide triphosphate (dNTP), incubated at 65°C for 5 min and then placed on ice for 5 min. A reaction mixture comprising 5 mM MgCl2, 10 mM DTT, 40 U RNaseOUT, and 200 U SuperScript III reverse transcriptase was added to the initial mix to achieve a total volume of 20 µL. The mixture was incubated at 25°C for 10 min, followed by 50 min at 50°C. The reaction was terminated at 85°C for 5 min and then chilled on ice for 10 min. At this point, 2 U RNase H was added and the mix was incubated at 37°C for 20 min. The first strand cDNA synthesis reaction was immediately used for second strand synthesis. To the first strand product, 300 µM dNTP, E. coli DNA polymerase I buffer, and water was added to obtain a total volume of 95 µL and allowed to incubate on ice for 10 min. Then, 0.05 U E. coli DNA polymerase I (New England Biolabs, Beverly, MA, USA) was added and the mixture was incubated at 16°C for 2.5 h. The resulting double stranded cDNA was purified with the Wizard SV Gel and PCR Clean-up System (Promega, Madison, WI, USA) and eluted in 100 µL nuclease-free water and then fragmented by the Covaris S2 instrument (Woburn, MA, USA) to generate ~200 bp fragments as follows: 10% duty cycle, intensity of 5, 100 cycles per burst, with a bath temperature of 7.7°C and an acoustic power of 24 W.   The Illumina library was prepared according to the manufacturer's instructions and purified using the Wizard SV Gel and PCR Clean-up System (Promega). Overhangs were converted into blunt ends with T4 DNA polymerase and Klenow DNA polymerase by incubating the mixed sample at 20°C for 30 min. cDNA was purified and eluted in 32 µL of nuclease free water with the Wizard Plus Minipreps DNA purification system (Promega). The purified sample was then mixed with Klenow fragment (3' to 5' exo minus) and incubated at 37°C for 30 min to add an 'A' base to the 3' end of the blunt phosphorylated DNA fragments. The cDNA was then purified and eluted in 23 µL of nuclease free water with the Wizard Plus Minipreps DNA purification system (Promega). Eluted DNA was mixed with Illumina Adapter Oligo mix and T4 DNA ligase and incubated at room temperature for 15 min to ligate adapters to the ends of the DNA fragments to prepare them for hybridization to the flow cell. cDNA then was purified and eluted in 10 µL of nuclease free water with the Wizard Plus Minipreps DNA purification system (Promega). cDNAtemplates were purified by running samples on a 1% agarose gel at 120 V for 60 min and excising the region of the gel in the 200 bp range. The 200 bp cDNA enriched fragments were purified and eluted in 30 µL of nuclease free water with the Wizard PlusMinipreps DNA purification system (Promega). cDNA in the library was then amplified by a 15 cycle PCR with two primers that annealed to the ends of the adapters. The amplified cDNA was purified and eluted in 30 µL of nuclease free water with the Wizard Plus Minipreps DNA purification system (Promega). The size, purity and concentration of the final library was checked with the Bio-Rad Experion DNA specific chip prior to sequencing by using the Illumina Genome Analyzer IIx.

value: Retina

tag: genotype/variation

value: Nrl gene knockout


title: debarshi_111210_retina

description:
B6_Retina
Isolated retina mRNA
library selection: Poly-A beads

value: Wild type


title: L3MBTL2_K562_ChIP-seq_rep1

description: Chromatin IP against L3MBTL2


title: debarshi_B6_eye

description:
B6_Whole_eye
Isolated whole eye mRNA
library selection: Poly-A beads

source_name: Eye tissue

value: Whole Eye


title: debarshi_0525_3-5_eye

description:
Nrl _Whole_eye
Isolated whole eye mRNA
library selection: Poly-A beads


title: Basal cells, donor 1

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: Basal cells

data_processing: Data analysis was performed using rna2map software provide by SOLiD™ Software Development Community (http://solidsoftwaretools.com/gf/). This tool allows to identifies reads as miRNAs among a reference set miRNAs: here xtr mirbase_v14. Parameters of identification has been set as follows: 1 color mismatch in the miRNAs seed (first 18 bases) and 2 color mismatchs in the extension step. Following identification of miRNAs, a normalization to 1000000 miRNAs count was performed. See supplementary series file for original (unrounded) counts and miRNA names.

source_name: Basal cells

growth_protocol: HAECs were dissociated from nasal polyps for cell sorting by FACSaria.

extract_protocol: SREK was performed according to the manufacturer’s protocol (Ambion, Inc, Austin, TX).

treatment_protocol: Isolated HAECs were  incubated with both mouse monoclonal anti-CD151-PE (6 µl/106 cells) and monoclonal mouse anti-TF-FITC antibodies (3 µl/106 cells).Bright basal cells (CD151+/TF+) and negative columnar cells (CD151-/TF-) were selected and sorted using the cell sorter’s purity option at a rate of 5,000 events per second. Sorted populations were reanalyzed (3 x 104 events recorded) for purity and viability.

value: human nasal mucosa

value: Basal

tag: rin number

tag: bank concentration (ng/µl)