title: Endogenous small RNAs from synthetic allopolyploid, F1 generation, wild type, leaf (F1L)

status: Public on Jul 31 2009

city: Bethesda

first: Misook

last: Ha

address: NIH

institute: National Heart Lung Blood Institute

description:
F1 generation of synthetic allopolyploid derived from A. thaliana and A. arenosa
5' adaptor sequence:
ATCGTAGGCACCTGAAA

data_processing: The raw sequences were processed by identifying the barcodes, base call quality, and removing adaptor sequences. Each of the 10 libraries had a unique 4-nucleotide tag within the 5’-end adaptor sequences. After trimming adaptor sequences at both 5’ and 3’ ends, pyrosequenced cDNAs were aligned to full genomic sequences of A. thaliana. Sequences matching other cellular RNAs including pre-tRNAs, rRNAs, snoRNAs, and snRNAs were regarded as degradation products of other cellular RNAs and excluded for analysis. Also excluded were sequences matching genome sequences of mitochondria and chloroplasts. Remaining sequences 20-25-nt in length.

organism:
Arabidopsis thaliana
Arabidopsis arenosa

source_name: leaf, F1

extract_protocol:
Total RNA was isolated from leaves and flower buds using TRIZOL (Invitrogen) according to manufacturer’s instructions.
Small RNAs of 15-100-nt in size were purified in a 15% polyacrylamide gel and ligated to the 5’ and 3’ RNA adaptors, respectively. The resulting RNA bands ranged from 55- to 140-nt. The ligated RNAs from each sample were reverse-transcriptase transcribed, and the first-stranded cDNAs were amplified using the primer pair that contains 2 specific nucleotides (out of 4) as a “barcode”. A. arenosa and F1 leaf libraries were sequenced separately, and the remaining eight libraries were combined in two pools, and an aliquot of pooled DNA was cloned and sequenced to determine the quality and representation of inserts. After the quality control was done, the pooled DNA was subjected to high-through pyrosequencing, producing a total of ~1.5-million reads in eight runs.

tag: genotype/variation

value: synthetic allopolyploid F1


title: 23-29 nucleotide RNAs from Drosophila melanogaster ovaries

status: Public on Mar 08 2007

type: SRA

city: Cold Spring Harbor

first: Julius

last: Brennecke

state: NY

address: 1 Bungtown Road

country: USA

institute: Cold Spring Harbor Labs

description: cDNA library was prepared according to standard small RNA cloning procedures (Pfeffer S. et al. 2005; Nat. Methods)

library_source: transcriptomic

data_processing: library was sequenced at 454 Life Sciences and small RNA were extracted bioinformatically as the sequence flanked by the two cloning linkers.

molecule: total RNA

organism: Drosophila melanogaster

source_name: Hannon lab, Cold Spring Harbor Labs

extract_protocol: small RNA was isolated from dissected ovaries using TRIZOL and size separated on a 15% denaturing polyacrylamid gel.

tag: small RNAs (23-29nt) from total ovarian RNA, indicating the cloning frequency


title: Endogenous small RNAs from Arabidopsis suecica, wild type, leaf (AsL)

state: MD

description:
natural allopolyploid species derived from A. thaliana and A. arenosa
5' adaptor sequence:
GCCTCCCTCGCGCCATCAGgacgATCGTAGGCACCTGAAA
raw data file(s): EJSVVZQ01.sff, EJSVVZQ02.sff, EJSVYDC01.sff, EJSVYDC02.sff

organism: Arabidopsis suecica

source_name: leaf, A. suecica

value: natural allopolyploid derived from A. thaliana and A. arenosa


title: Endogenous small RNAs from synthetic allopolyploid, F7 generation, wild type, flower (F7F)

description:
F7 generation of synthetic allopolyploid derived from A. thaliana and A. arenosa
5'adoptor sequence: GCCTCCCTCGCGCCATCAGgctgATCGTAGGCACCTGAAA
raw data file(s): EJSVVZQ01.sff, EJSVVZQ02.sff, EJSVYDC01.sff, EJSVYDC02.sff

source_name: flower, F7

value: synthetic allopolyploid F7


title: Endogenous small RNAs from Arabidopsis suecica, wild type, flower (AsF)

description:
natural allopolyploid species derived from A. thaliana and A. arenosa
5' adaptor sequence:
GCCTCCCTCGCGCCATCAGatgaATCGTAGGCACCTGAAA
raw data file(s): EJSVV8G01.sff, EJSVV8G02.sff, EJS6HNP01.sff, EJS6HNP02.sff, EJ4IYVT01.sff, EJ4IYVT02.sff

source_name: flower, A. suecica


title: Endogenous small RNAs from synthetic allopolyploid, F7 generation, wild type, leaf (F7L)

description:
F7 generation of synthetic allopolyploid derived from A. thaliana and A. arenosa
5'adoptor sequence: GCCTCCCTCGCGCCATCAGtactATCGTAGGCACCTGAAA
raw data file(s): EJSVVZQ01.sff, EJSVVZQ02.sff, EJSVYDC01.sff, EJSVYDC02.sff

source_name: leaf, F7


title: Endogenous small RNAs from Arabidopsis thaliana ler, wild type, flower (AtF)

description:
progenitor species
5' adaptor sequence:
GCCTCCCTCGCGCCATCAGctgcATCGTAGGCACCTGAAA
raw data file(s): EJSVV8G01.sff, EJSVV8G02.sff, EJS6HNP01.sff, EJS6HNP02.sff, EJ4IYVT01.sff, EJ4IYVT02.sff

organism: Arabidopsis thaliana

source_name: flower, A. thaliana

value: progenitor species


title: Endogenous small RNAs from Arabidopsis arenoa, wild type, flower (AaF)

description:
progenitor species
5' adaptor sequence:
GCCTCCCTCGCGCCATCAGtgatATCGTAGGCACCTGAAA
raw data file(s): EJSVV8G01.sff, EJSVV8G02.sff, EJS6HNP01.sff, EJS6HNP02.sff, EJ4IYVT01.sff, EJ4IYVT02.sff

organism: Arabidopsis arenosa

source_name: flower, A. arenosa


title: piRNAs associated with Ago3 from Drosophila melanogaster ovaries

extract_protocol: small RNA was isolated from Ago3 immunoprecipitates and size separated on a 15% denaturing polyacrylamid gel.

tag: small RNAs from Ago3 immunoprecipitates, indicating the cloning frequency


title: piRNAs associated with Piwi from Drosophila melanogaster ovaries

extract_protocol: small RNA was isolated from Piwi immunoprecipitates and size separated on a 15% denaturing polyacrylamid gel.

tag: Piwi associated small RNAs isolated from ovary extracts, indicating the cloning frequency


title: piRNAs associated with Aubergine from Drosophila melanogaster ovaries

extract_protocol: small RNA was isolated from Aubergine immunoprecipitates and size separated on a 15% denaturing polyacrylamid gel.

tag: small RNAs isolated from Aubergine immuno-precipitates, indicating the cloning frequency


title: Endogenous small RNAs from Arabidopsis arenoa, wild type, leaf (AaL)

description:
progenitor species
5' adaptor sequence:
ATCGTAGGCACCTGAAA

source_name: leaf, A. arenosa


title: Endogenous small RNAs from synthetic allopolyploid, F1 generation, wild type, flower (F1F)

description:
F1 generation of synthetic allopolyploid derived from A. thaliana and A. arenosa
5' adaptor sequence:
GCCTCCCTCGCGCCATCAGcgacATCGTAGGCACCTGAAA
raw data file(s): EJSVVZQ01.sff, EJSVVZQ02.sff, EJSVYDC01.sff, EJSVYDC02.sff

source_name: flower, F1


title: Endogenous small RNAs from Arabidopsis thaliana ler, wild type, leaf (AtL)

description:
progenitor species
5' adaptor sequence:
GCCTCCCTCGCGCCATCAGactaATCGTAGGCACCTGAAA
raw data file(s): EJSVV8G01.sff, EJSVV8G02.sff, EJS6HNP01.sff, EJS6HNP02.sff, EJ4IYVT01.sff, EJ4IYVT02.sff

source_name: leaf, A. thaliana


title: rdr6-19 rep2

status: Public on Dec 19 2008

city: University Park

first: Michael

middle: J

last: Axtell

state: PA

address: 280 Mueller Lab

department: Biology

institute: Pennsylvania State University

description: See Cho et al. for details

data_processing:
Small RNAs were sequenced using a Solexa GA.  Three different linkers were used for different samples and mixed prior to sequencing.  Raw data was filtered to identify small RNAs associated with each linker.  Subsequently, small RNAs were filtered to remove rRNA fragments.  The remainder were mapped to the Physcomitrella patens draft genome version 1.2 (using oligomap) and filtered to retain only those with one or more perfect match.  This sample is all small RNA sequences from the second (of two) technical replicates from 10 day old rdr6-19 mutants.  See Cho et al. for details.
Data are the raw number of reads for the indicated sequence in this replicate

organism: Physcomitrium patens

source_name: Physcomitrella patens 10day rdr6-19 Protonemata

growth_protocol: protonemal tissue was grown on cellophane-overlaid BCD media {Ashton, 1977} supplemented with 50mM ammonium tartarate under 16hr days, 8hr nights at 22ºC.

extract_protocol: Total RNA was extracted with Tri-Reagent (Sigma), fractionated on PAGE in the presence of radiolabeled 21 and 24nt standards, and the ~20-25nt size regions eluted.  Eluted RNAs were than adapter ligated, reverse transcribed, and sequenced as described in Cho et al.

treatment_protocol: No treatment

tag: Small RNAs


title: dcl3-10

description: See Cho et al. for details

data_processing:
Small RNAs were sequenced using a Solexa GA.  Three different linkers were used for different samples and mixed prior to sequencing.  Raw data was filtered to identify small RNAs associated with each linker.  Subsequently, small RNAs were filtered to remove rRNA fragments.  The remainder were mapped to the Physcomitrella patens draft genome version 1.2 (using oligomap) and filtered to retain only those with one or more perfect match.  This sample is all small RNA sequences from 10 day old dcl3-10 mutants.  See Cho et al. for details.
Data are the raw number of reads for the indicated sequence in this replicate

source_name: Physcomitrella patens 10day dcl3-10 Protonemata


title: dcl3-5

description: See Cho et al. for details

data_processing:
Small RNAs were sequenced using a Solexa GA.  Three different linkers were used for different samples and mixed prior to sequencing.  Raw data was filtered to identify small RNAs associated with each linker.  Subsequently, small RNAs were filtered to remove rRNA fragments.  The remainder were mapped to the Physcomitrella patens draft genome version 1.2 (using oligomap) and filtered to retain only those with one or more perfect match.  This sample is all small RNA sequences from 10 day old dcl3-5 mutants.  See Cho et al. for details.
Data are the raw number of reads for the indicated sequence in this replicate

source_name: Physcomitrella patens 10day dcl3-5 Protonemata


title: rdr6-19 rep1

description: See Cho et al. for details

data_processing:
Small RNAs were sequenced using a Solexa GA.  Three different linkers were used for different samples and mixed prior to sequencing.  Raw data was filtered to identify small RNAs associated with each linker.  Subsequently, small RNAs were filtered to remove rRNA fragments.  The remainder were mapped to the Physcomitrella patens draft genome version 1.2 (using oligomap) and filtered to retain only those with one or more perfect match.  This sample is all small RNA sequences from the first (of two) technical replicates from 10 day old rdr6-19 mutants.  See Cho et al. for details.
Data are the raw number of reads for the indicated sequence in this replicate


title: WT_rep2

description: See Cho et al. for details

data_processing:
Small RNAs were sequenced using a Solexa GA.  Three different linkers were used for different samples and mixed prior to sequencing.  Raw data was filtered to identify small RNAs associated with each linker.  Subsequently, small RNAs were filtered to remove rRNA fragments.  The remainder were mapped to the Physcomitrella patens draft genome version 1.2 (using oligomap) and filtered to retain only those with one or more perfect match.  This sample is all small RNA sequences from the second (of two) technical replicates from 10 day old Wild-Type.  See Cho et al. for details.
Data are the raw number of reads for the indicated sequence in this replicate

source_name: Physcomitrella patens 10day Wild-Type Protonemata


title: WT_rep1

description: See Cho et al. for details

data_processing:
Small RNAs were sequenced using a Solexa GA.  Three different linkers were used for different samples and mixed prior to sequencing.  Raw data was filtered to identify small RNAs associated with each linker.  Subsequently, small RNAs were filtered to remove rRNA fragments.  The remainder were mapped to the Physcomitrella patens draft genome version 1.2 (using oligomap) and filtered to retain only those with one or more perfect match.  This sample is all small RNA sequences from the first (of two) technical replicates from 10 day old Wild-Type.  See Cho et al. for details.
Data are the raw number of reads for the indicated sequence in this replicate