title: Hepatocellular adenoma HCA-18-RA09065-830

city: Birmingham

first: Leda

last: Mirbahai

address: Edgbaston

department: Biosciences

institute: University of Birmingham

description:
Both samples are dissected from the same liver
insert size: 100-500 bp

data_processing: We assembled the MeDIP sequences to contigs to get methylated DNA fragments of dab fish. We identify the differential methylated DNA fragments between Hepatocellular adenoma and Healthy corresponding  surrounding tissue

organism: Limanda limanda

source_name: Liver

growth_protocol: Wild dab (Limanda limanda) were caught at South Cardigan Bay, UK in June, 2009. Liver was excised and tumour tissue dissected away from surrounding, apparently healthy, tissue. Tumour and surrounding tissue were stored at -80C until extraction. Presence/absence and type of lesions were confirmed by histopathology. Each liver was homogenised in 10 Î¼l/mg (wet tissue mass) water using a Precellys-24 ceramic bead-based homogeniser (Stretton Scientific Ltd.). Aliquot of the homogenised tissues (no less than 10 mg) were added to ice cold RLT (600 Î¼l) and Î²-mercaptoethanol (6 Î¼l) mixture. Following centrifugation and removal of lipid layer, RNA and DNA were extracted from the same sample using AllPrep DNA/RNA kit (Qiagen Ltd, West Sussex, UK) according to manufacturesâ guideline. The RNA and DNA purity and concentration was determined using the NanoDrop ND-1000 UV-VIS Spectrometer version 3.2.1 (Nanodrop, USA). The purity of RNA and DNA samples were assessed using the ratio A260/A280 as well as using 2100 Bioanalyzer (Agilent technologies, Berkshire, UK) for further RNA quality assessments. DNA samples form the HCA and surrounding tissue were used in DNA methylation immunoprecipitation combined to de novo high throughput sequencing using Illumina Whole Genome Analyser II.

extract_protocol: DNA samples extracted from one HCA sample and corresponding surrounding tissue (5 Î¼g) were sonicated. Fragmentation was carried out using a Covaris sonication system (16 cycles of duty cycle: 10%, intensity: 5, cycles/burst: 200, time: 960 s; Covaris, Inc, USA) which resulted in 100-500 bp rich DNA fragments. The Illumina Paired-end library preparation kit (Illumina, Inc, USA) and the protocol provided were used to generate adaptor-attached DNA fragments for sequencing. During this process the overhangs from fragmentation were converted into blunt ends using T4 DNA polymerase and Klenow polymerase.âAâ base was added to the 3' end of the blunt end phosphorylated DNA fragments which provided a recognition site for a single âTâ base overhang containing adaptors. Methylated adaptor ligated DNA fragments were separated from the un-methylated fragments using MagMeDIP kit (Diagenode, Belgium) according to the manufacturerâs instructions. The positive and negative control primers provided with the kit and the SYBR green mastermix (Applied Biosystems) with 40 cycles of 95Â°C for 15s and 60Â°C for 1 min were used for validation of the immunoprecipitation procedure. The methylated fractions were purified and eluted in EB buffer (27 Î¼l) using ZYMO DNA Clean & Concentrator-5 column following the manufacturerâs instructions. The eluted DNA was amplified by adaptor-mediated PCR in a final reaction volume of 50 Î¼l consisting of purified DNA (23 Î¼l), Phusion DNA polymerase mix (25 Î¼l) and PCR primers (2 Î¼l). Cycling parameters consisted of 94 Â°C 30 s, 16 cycles of 94 Â°C 30s, 60 Â°C 30 s, 72 Â°C 30 s with a final step of 1 min at 72 Â°C.

value: Hepatocellular adenoma

tag: gender

value: Female


title: Healthy surrounding tissue S.T-19-RA09065-830

status: Public on Nov 09 2011

type: SRA

country: United Kingdom

library_source: genomic

molecule: genomic DNA

tag: tissue

value: Healthy corresponding  surrounding liver tissue


title: WT mRNA-seq

status: Public on Nov 07 2011

city: Lausanne

first: Simon

last: Quenneville

address: station 15

country: Switzerland

institute: EPFL SV

library_source: transcriptomic

data_processing: Alignment: Sequence reads were obtained and mapped to the mouse genome (mm9) using the bowtie aligner. All reads mapping with three or fewer mismatches and reads not mapping to more than five locations in the genome were retained.

molecule: polyA RNA

organism: Mus musculus

source_name: WT ES cells

growth_protocol: Normal ES cell media

extract_protocol: RNA was extracted and polyA RNA were purified with oligodT beads.  RNA was fragmented and RT reaction was performed followed by sequencing

tag: cell type

value: embryonic stem (ES) cells

tag: genotype/variation

value: wildtype


title: KAP1 ChIP in E14 ES cells

description: Chromatin IP against RBCC (KAP1)

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm9) using the bowtie aligner. All reads mapping with three or fewer mismatches and reads not mapping to more than five locations in the genome were retained.
Peaks: Peak detection was performed with the ChIP-Seq Analysis Server (http://ccg.vital-it.ch/chipseq/)

source_name: KAP1 ChIP in E14 ES cells

extract_protocol: Lysates were clarified from paraformaldehyde sonicated nuclei and protein-DNA complexes were isolated with antibody.

tag: chip antibody

value: KAP1 (RBCC)

tag: expressed transgene


title: ZFP57 KO mRNA-seq

source_name: ZFP57 KO ES cells

value: ZFP57 KO


title: HA ChIP in ES cells expressing HAZFP57

description: Chromatin IP against HA

source_name: HA ChIP in ES cells expressing HAZFP57

value: HA

value: HA tagged ZFP57


title: HA ChIP in ES cells

description: Chromatin IP against HA

source_name: HA ChIP in ES cells


title: mRNA_mouse

city: Oxford

first: Yang

last: Li

address: 3 Fettlers House, Walton Wells Road

department: Nuffield Department of Medicine

institute: University of Oxford

description: Pooled from 3 males

data_processing:
mouse reads mapping: To map Solexa/Illumina 39bp and 76bp reads from wild-derived mouse liver, we constructed a reference library for mouse consisting of all mouse cDNA transcripts obtained from ENSEMBL. The reads were then mapped to this reference library with the short read mapper stampy (http://www.well.ox.ac.uk/project-stampy). All reads mapping outside of the 3' end of the cDNA, i.e. 1050 upstream from the cDNA end, were discarded. After this step, 13.4M out of the initial 24.3M mouse 76bp Solexa reads and 2.2M out of 6.2M mouse 39bp Solexa reads were successfully mapped to the mRNA reads with positive mapping scores.
naked mole-rat reads mapping: Solexa/Illumina naked mole-rat reads were first mapped onto the naked mole-rat transcriptome contigs (from the Platzer lab, not released) using stampy. Out of the 21.2M 76bp Solexa reads, 10.7M reads (50.2%) mapped successfully including 8.7M which had positive mapping scores while 2.5M (27.1%) reads out of 9.2M 39bp Solexa reads with 1.4M with positive mapping scores. The unaligned reads can be explained by the presence of many poly-T and poly-A reads generated by the PMAGE protocol which accounts for almost 50% of all the 39bp Solexa reads. The lower percentage of reads mapped compared to wild-derived mouse can be explained by the imperfect coverage of the naked mole-rat transcriptome assembly as opposed to using the high-quality reference mouse transcriptome. To determine the mouse orthologous gene associated to each naked mole-rat read, we employed BLAST to map the contigs of the assembly onto mouse and guinea pig cDNAs. A combination of mouse and guinea pig transcriptomes was used because the annotation of the mouse genome is better than that of the guinea pig while the guinea pig genome is more similar to that of the naked mole-rat. The mapping of 33,286 contigs out of the initial 77,086 were judged to be unambiguous and only contigs mapping unambiguously were used. A mapping is unambiguous if its BLAST map is either unique and its e-value is less than 0.05 or it is 2 orders of magnitude smaller than the one with the second smallest. Mouse and guinea pig mappings were combined by checking if the contigs map to orthologous genes in guinea pig and mouse.  If they do not map to the orthologous genes, the gene with the lowest e-value is used if it is 2 orders of magnitude smaller. Otherwise, the mapping is classified as ambiguous. Ultimately, out of the 8.7M reads mapped, 6.4M could be assigned to an orthologous gene in mouse or guinea pig reference genomes. For genes assigned to a guinea pig gene, the orthologous mouse gene was then used in subsequent steps for the purpose of comparing naked mole-rat and mouse gene expression patterns.

molecule: total RNA

extract_protocol: In the first step, liver tissues from three naked mole-rats and three wild-derived house mice (ID stock) were mixed separately in similar quantities, and mRNA was extracted from the two samples with DynabeadsÂ® mRNA DIRECTâ¢ Kit (Invitrogen, USA). Full-length mRNA was then converted to double-strand, full-length cDNA with SuperScriptÂ® Double-Stranded cDNA Synthesis Kit (Invitrogen, USA), in which the oligo dT was replaced by the following primer: 5â-biotin-GAGCTGATTCTGGAGTTTTTTTTTTTTTTTTTTVN-3â (BpmI recognizing site marked by underline, Agilent Technologies, USA). Exonuclease I (Epicenter, USA) digestion was then applied to remove biotin- BpmI-oligo-dT primer that did not participate in RT reaction and the products were then purified with QIAquick PCR Purification Kit (Qiagen, USA). In the second step, the purified double-strand, full-length cDNA was digested by NlaIII, and was then Qiagen purified. The resulted DNA-biotin complex was conjugated to M270 Dynabeads (Invitrogen, USA) and captured by a magnetic field. After being washed three times, the cDNA was released by being digested by BpmI, and was further Qiagen purified. In the third step, the resultant cDNA was blunted with End-Itâ¢ DNA End-Repair Kit (Epicenter, USA), and Qiagen purified. The libraries were then made according to the Illumina protocol and sequenced twice using the Illumina/Solexa platform,

tag: strain

value: Wild derived

value: Liver

tag: developmental stage

value: Middle aged


title: mRNA_nmr

description: Pooled from 3 males

organism: Heterocephalus glaber


title: Tat ChIP-seq

status: Public on Nov 06 2011

city: Los Angeles

first: Siavash

middle: K

last: Kurdistani

state: CA

address: 615 Charles E. Young Dr. South, 337

department: Biological Chemistry

country: USA

institute: University of California Los Angeles

description: chromatin ChIPed against HIV tat

data_processing:
Alignment: Sequence reads if 76 bp were obtained and mapped to the human hg19 genomes using the Bowtie 0.12.7.  All reads mapping with two or fewer mismatches were retained. Reads with more than one locations matched in the genome was discarded.  Sequence unable to align in the first alignment iteration was trimmed trimmed 25 bp away from 3' end of reads and re-aligned to the genome.
Each chromosome was divided into 100 bp windows.  Reads are normalized by total read counts.  Significant peaks were defined by comparing Tat ChIP read count versus input DNA read count using Poisson distribution to calculate  p-value enrichment.
final bed file used 10^-4 threshold requiring neighoring window also with p-value less than 10^-4

organism: Homo sapiens

source_name: Jurkat-Tat T cells

growth_protocol: Jurkat-Tat cells were maintained in RPMI supplemented with 10% fetal bovine serum, 1%penicillin and streptomycin and 800 microg/ml of G418

extract_protocol: Jurkat-Tat cells in exponential growth phase were fixed with 1% formaldehyde (v/v) for 10 min at 37Â°C.  Fixation was stopped by addition of glycine to a final concentration of 140mM. Cell were lysed and chromatin was digested with the micrococcal nuclease from S. aureus (Roche) for 90 min at 4Â°C according to the manufacturerâs instructions, resuspended in lysis buffer and sonicated with Misonix ultrasonic liquid processor . 1% of the lysate was used as an input control. Lysates were immunoprecipitated with 5Î¼g of anti-Tat antibodies (Abcam ab43014) using the standard ChIP protocol.

tag: expression

value: HIV Tat protein

value: Tat

tag: cell line

value: Jurkat

tag: chip antibody manufacturer

value: Abcam

tag: chip antibody catalog #


title: input DNA

description: input DNA


title: HeLa_SPT20-chip-seq

status: Public on Nov 05 2011

city: Strasbourg

first: Krishanpal

last: Karmodiya

email: krish@igbmc.fr, laszlo@igbmc.fr

address: 1 rue Laurent Fries / BP 10142

country: France

institute: Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)

description: Chromatin IP against SPT20

data_processing: ChIP-seq data were mapped using the ELAND software (Illumina) allowing one mismatch.

source_name: HeLa

growth_protocol: GM cells were grown according to the instructions of Coriell Cell Repositories

extract_protocol: ChIP DNA and input DNA were first band-isolated on a 2% agarose to obtain fragments between 150 and 350 base pairs and DNA was extracted using the QIAquick gel extraction kit (Qiagen) and eluted in 34 uL. For input DNA, because DNA amounts are higher than DNA recovered by ChIP, input DNA after gel extraction was diluted 1:5. After end-repair and addition of a single adenosine ("A") nucleotide, adapters were ligated to samples for 15 min at room temperature in the following fashion: the samples eluted from the MinElute column in 10 uL were ligated to 1 uL of adapters using 1.3 uL of LigaFast T4 DNA Ligase (3 Units/uL; Promega) and 12.3 uL Rapid Ligation Buffer (Promega). For DNA libraries, the Illumina genomic DNA adapters were diluted 1:10. After 15 min, samples were purified with the MinElute PCR purification kit (Qiagen).

value: HeLa cells

tag: antibody

value: Rabbit polyclonal

tag: vendor

value: Laszlo Tora


title: abdomen bees not parasitized by varroa not fed with pollen

city: Avignon

first: Cédric

last: Alaux

address: Domaine Saint-Paul

department: UMR 406 Abeilles et Environnement

institute: INRA

data_processing:
removal of linker : by perl script
alignment : eland
analysis : SAGE Genie

organism: Apis mellifera

growth_protocol: One-day-old bees were held for 8 days in cages and in the dark at 28°C and 70% relative humidity. They were fed ad libitum with candy (30% honey, 70% powdered sugar) and water. Caged bees were also exposed to a Beeboost® (Pherotech, Delta, BC, Canada) releasing one queen-equivalent of queen mandibular pheromone per day.

extract_protocol: Library was constructed according to Illumina's protocole « GeneExp_DpnII_Sample_Prep_OligoOnly » (ref.1003653_Rev_A)

treatment_protocol: Before emergence bees were collected and the presence (V+) or absence of varroa (V-) in the cells was checked. Bees that were parasitized by varroa or not at the pupae stage were then fed or not with pollen for 8 days.

tag: parasite

tag: treatment

value: not fed with pollen

tag: enzyme

value: DPNII

value: abdomen


title: abdomen bees not parasitized by varroa  fed with pollen

value: fed with pollen


title: abdomen bees parasitized by varroa not fed with pollen

value: varroa


title: abdomen bees parasitized by varroa  fed with pollen


title: Unlabelled DNA rep2

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

data_processing: Alignment: Sequence reads were obtained and mapped to the TAIR8 Arabidospis genome using SeqMap. Uniquely mapping with three or fewer mismatches were retained.

organism: Arabidopsis thaliana

source_name: MM2d cells

extract_protocol: The DNA libraries for both BrdU DNA and unlabelled DNA were generated and sequenced on Genome Analyzer II as per the manufacturer instructions.

tag: label

value: unlabelled


title: BrdU labelled DNA rep2

value: BrdU


title: L3_STAGE_GVL4R4202

status: Public on Nov 04 2011

city: Ann Arbor

first: Ryan

last: Mills

state: MI

address: 100 Washtenaw Ave

department: Computational Medicine and Bioinformatics

institute: University of Michigan

data_processing:
GRAVID_STAGE_GVOZ88J02.fna: is an intermediate, tab-delimited file derived from the GRAVID_STAGE_GVOZ88J02.sff raw sequence read file with the format: 454 Read ID, full read sequence, and linker-removed sequence. Linker sequence was removed using a custom Perl script.
mya-3__PABP_L2_STAGE_GVL4R4201.fna: is an intermediate, tab-delimited file derived from the mya-3__PABP_L2_STAGE_GVL4R4201.sff raw sequence read file with the format: 454 Read ID, full read sequence, and linker-removed sequence. Linker sequence was removed using a custom Perl script.
L3_STAGE_GVL4R4202.fna: is an intermediate, tab-delimited file derived from the L3_STAGE_GVL4R4202.sff raw sequence read file with the format: 454 Read ID, full read sequence, and linker-removed sequence. Linker sequence was removed using a custom Perl script.
L4_STAGE_GVOZ88J01.fna: is an intermediate, tab-delimited file derived from the L4_STAGE_GVOZ88J01.sff raw sequence read file with the format: 454 Read ID, full read sequence, and linker-removed sequence. Linker sequence was removed using a custom Perl script.
fasta_PABP_Run2-seq.txt: is a consolidation of all four sequence libraries into a single, uniqued (based on sequence) FASTA-formatted sequence file, suitable for input to BLAT for alignment to the C. elegans genome (version WS190). Sequence reads less than 15 nt in length, and those reads with no discernable linker sequence were discarded prior to consolidation of the four sequence libraries. Identical reads (based on sequence identity) were collapsed into a single, unique read. All reads were assigned a unique identifier.
fasta_PABP_Run2-seq.txt.2bit.psl: The consolidated read file fasta_PABP_Run2-seq.txt was aligned to the WS190 C. elegans genome using the BLAST-Like Alignment Tool (description here: http://genome.ucsc.edu/FAQ/FAQblat.html) with a maximum intron of 1000, minimum window size of 5, and maximum gap of 6. Best matches were selected, and multiple alignments reported if present in more than one genomic location.

organism: Caenorhabditis elegans

growth_protocol: myo-3-FLAG-PABP-SL2-GFP::unc-54 3’UTR transgenics worms were grown on 15cm2NGM (Nematode Growth Media) plates seeded with HB101 and synchronized by alkaline/hypochride. Starved L1 larvae were then plated on 15 cm2 plates (HB101 as food) raised at 20°C. Samples were taken at ~20hr (L2), ~30hr (L3), ~45hr (L4), ~72hr (gravids). Worms were collected in M9, washed 1X with M9 for 15 min to remove residue bacteria and then with milliQ water for 5 min.

extract_protocol: Worms were lysed in lysis buffer (50mM HEPES-KOH pH7.4, 1mM EDTA, 140mM KCL, 10% Glycerol, 0.5% NP-40, 1mM DTT, Protease inhibitor cocktail tablet, 1000U/ml of ribonuclease inhibitor and 20mM RVS, Sigma). Worm debris were removed by spinning at 18,000g for 20 min. The clear supernatant was then transferred to new tube and protein concentration was adjusted to 10mg/ml and incubated with 100ul of anti-FLAG M2 beads (Sigma) for 2 hrs at 4°C on nutator. After 2hrs of incubation the lysates washed with lysis buffer (3X), then with wash buffer (2X) and finally with TE buffer (1X). Elution was done using 100ul of elution buffer (2X) by incubation at 65°C for 5 min in a thermo-mixer. The eluted complex was then incubated for 6hrs at 65°C to reverse formaldehyde crosslinking. Proteins were digested using 10mg/ml of proteinase K by incubating at 37°C for 30min. Nucleic acid was extracted using TRI-Reagent (Applied Biosystems) followed by isopropanol extraction and ethanol precipitation. 3’UTR libraries were made using the protocol published in The Landscape of C. elegans 3′UTRs . Mangone, et al., 329 (5990): 432-435.

treatment_protocol: To crosslink poly(A) RNA with FLAG-PABP, worms were treated with 1% for-maldehyde in M9 for 15 min at 20°C . The formaldehyde was then inactivated by washing with 125 mM glycine for 5 min at 20°C and then with TBS (4X). The worms were then stored frozen until library preparation.

tag: purification method

value: myo-3::PABP pulldown

tag: tissue

value: muscle


title: L4_STAGE_GVOZ88J01


title: GM_SPT20-chip-seq r1

description: Chromatin IP against SPT20

tag: cell type

value: B lymphoblasts


title: GRAVID_STAGE_GVOZ88J02

source_name: gravid

value: gravid


title: mya-3__PABP_L2_STAGE_GVL4R4201


title: FB2 RNA_seq

status: Public on Nov 08 2011

city: Shanghai

first: Chengshu

last: Wang

address: 300 Fenglin Road

department: Institute of Plant Physiology and Ecology

country: China

institute: Shanghai Institutes for Biological Sciences, CAS

description: Cordyceps militaris growth on silkmoth pupae for 29 days.

data_processing: After base calling by transforming the raw image data into sequence data, the 3' adaptor was cleaned and the tags with "N" or the tags with only one copy were removed to generate clean tags. All clean tags were mapped onto the Cordyceps militaris genome (AEVU00000000.1) by allowing no more than 1nt mismatch. Clean tags mapping to the reference genome in multiple places were filtered. The remaining clean tags were designed as unambiguous clean tags. The number of unambiguous clean tags for each gene was calculated and then normalized to TPM (number of transcripts per million clean tags).

organism: Cordyceps militaris

source_name: Middle-term fruiting-bodies

growth_protocol: The conidia of Cordyceps militaris were injected into Chinese Tussah silkmoth (Antheraea pernyi) pupae and incubated at 22 Â°C, 12:12 hr light:dark control for up to 29 days. The samples were harvested for RNA extraction and RNA-seq analysis.

extract_protocol: Total RNA was extracted using Qiagen's RNeasy kit. Messenger RNA was purified from 6 ug of the total RNA from each sample using Oligo (dT) magnetic beads and reversely transcribed into cDNA. The generation of 5' CATG ends of tags was conducted using the endonuclease NlaIII and the Illumina adapter 1 was added to the 5' ends. The combination of the Illumina adapter 1 and CATG site is the recognition site of MmeI, which cuts the cDNA at 17bp downstream of the CATG site, producing tags with adapter 1. After removing 3' fragments with magnetic beads precipitation, the Illumina adapter 2 was introduced at the 3' ends of each tag to generate the tag libraries. After 15 cycles of linear PCR amplification, 85 base strips were purified by 6% TBE PAGE Gel electrophoresis and the single-chain molecules fixed onto the Solexa Sequencing Chip (flowcell) for sequencing with the method of sequencing by synthesis (SBS). Each tunnel generated millions of raw reads with sequencing length of 35bp.

value: Cm 01

tag: growth medium

value: silkmoth pupae

tag: growth duration

value: 29 days

value: middle-term fruiting bodies


title: SDB RNA_seq

description: Cordyceps militaris growth in a Sabouraud dextrose broth for 3 days.

source_name: Fungal mycelia grown in SDB culture

growth_protocol: The conidia from day 14 potato dextrose agar were inoculated into Sabouraud dextrose broth (SDB) and incubated at 25Â°C, 180 rpm for 3 days. The samples were harvested for RNA extraction and RNA-seq analysis.

tag: strain

value: liquid broth

value: 3 days

value: mycelia


title: FB3 RNA_seq

description: Cordyceps militaris growth on silkmoth pupae for 59 days.

source_name: Mature fruiting-bodies

growth_protocol: The conidia of Cordyceps militaris were injected into Chinese Tussah silkmoth (Antheraea pernyi) pupae and incubated at 22 Â°C, 12:12 hr light:dark control for up to 59 days. The samples were harvested for RNA extraction and RNA-seq analysis.

value: 59 days

tag: developmental stage

value: mature fruiting bodies


title: FB1 RNA_seq

description: Cordyceps militaris growth on silkmoth pupae for 14 days.

source_name: Newly formed fruiting-bodies

growth_protocol: The conidia of Cordyceps militaris were injected into Chinese Tussah silkmoth (Antheraea pernyi) pupae and incubated at 22 Â°C, 12:12 hr light:dark control for up to 14 days. The samples were harvested for RNA extraction and RNA-seq analysis.

value: 14 days

value: newly formed fruiting bodies


title: ES cell feeder-free, w/ LIF none ribo_mesc_nochx Illumina GAII

status: Public on Nov 03 2011

city: Berkeley

first: Nicholas

middle: T

last: Ingolia

email: ingolia@berkeley.edu, nick@ingolia.org

address: 1 Barker Hall # 3202

department: Molecular and Cell Biology

institute: University of California, Berkeley

description: Ribosome Profiling

data_processing: Alignment to transcriptome (mm9) using 25nt seed and extension to linker sequence

source_name: ES cell

growth_protocol: feeder-free, with LIF

extract_protocol: Rnase I footprinting, ribosome pelleting, RNA extraction, preadenylated linker ligation, reverse transcription, cDNA circularization, PCR amplification

value: ES cell feeder-free, w/ LIF

tag: genetic background


title: ES cell feeder-free, w/ LIF 60 s CYH (100 ug/ml) ribo_mesc_yeslif Illumina GAII

description: Ribosome Profiling

treatment_protocol: 60 s cycloheximide (100 ug/ml)

tag: cell line


title: ES cell 36 hours in low-adhesion dishes w/o LIF 60 s CYH (100 ug/ml) ribo_mesc_nolif Illumina GAII

description: Ribosome Profiling

growth_protocol: 36 hours in low-adhesion dishes without LIF


title: ES cell feeder-free, w/ LIF 120 s HRT (1 ug/ml) then 60 s CYH (100 ug/ml) ribo_mesc_harr120s Illumina GAII

description: Ribosome Profiling

extract_protocol: Rnase I footprinting, ribosome pelleting, RNA extraction, enzymatic polyadenylation, dT-primed reverse transcription, cDNA circularization, PCR amplification

treatment_protocol: 120 s harringtonine (1 ug/ml) followed by 60 s cycloheximide (100 ug/ml)


title: ES cell feeder-free, w/ LIF 150 s HRT (1 ug/ml) then 60 s CYH (100 ug/ml) ribo_mesc_harr150s Illumina GAII

description: Ribosome Profiling

treatment_protocol: 150 s harringtonine (1 ug/ml) followed by 60 s cycloheximide (100 ug/ml)


title: ES cell feeder-free, w/ LIF 180 s HRT (0.5 ug/ml) then 60 s CYH (100 ug/ml) ribo_mesc_harr180s Illumina GAII

description: Ribosome Profiling

treatment_protocol: 180 s harringtonine (0.5 ug/ml) followed by 60 s cycloheximide (100 ug/ml)


title: ES cell feeder-free, w/ LIF 60 s CYH (100 ug/ml) ribo_mesc_chx Illumina GAII

description: Ribosome Profiling


title: Cdk9_0hr_ChIPSeq

city: Kansas CIty

first: Alexander

middle: (Garrett)

last: Garruss

state: Missouri

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

description: Chromatin IP against Cdk9

data_processing:
Alignment: Sequencing reads were acquired through the primary Solexa image analysis pipeline, where bases were called and reads were filtered for quality, according to default Solexa standards. Filtered reads were then aligned to the mouse genome (NCBI build 37, UCSC mm9) or the human genome (UCSC hg19) using the bowtie (Langmead et al., 2009) alignment tool, version 0.12.7. Only those sequences that matched uniquely to the genome with up to two mismatches were retained.
Peaks: Enriched regions of ChIP-seq signal were determined by the ‘MACS’ (Zhang et al.,2008) peak-finding program, version 1.4.0rc2. Sequence reads for each ChIP-seq dataset and their associated whole-cell extract controls were used for the input and control file, respectively. The effective genome size was configured appropriately for mouse and human datasets, and the p-value cutoff was set to 1.00e-08 or FDR <= 1%, and a foldchange greater than five.

growth_protocol: Mouse embryonic stem cells (KH2) were cultured under feeder-free medium ESGRO (Millipore).  HCT-116 cells were grown in McCoy’s 5A medium supplemented with 10% FBS.

extract_protocol: Chromatin immunoprecipitation (ChIP) was performed according to previously described protocols (Wang et al. 2009 [MCB]).  Briefly,  ES cells were cross-linked by 1% formaldehyde and sonicated. 10 ug of antibodies were used in the ChIP assays. The ChIP Libraries were prepared with the Illumina DNA Sample Kit (Part# 0801-0303) according to Illumina's instructions and sequenced on the Genome Analyzer IIx following the manufacturer's protocols.  Antibodies for Pol II are from Covance, 8WG16, catalog #MMS-126R.  Other antibodies were sourced from the original work of Lin et al. 2010 (Mol. Cell)

treatment_protocol: For RA induction, mouse ES cells were treated with 0.3 uM of all-trans retinoic acid for 6 hours. For serum stimulation, cells were first starved by washing cells 2x in PBS, then culturing for 40 hours in McCoy’s 5A without serum. Cells were then either left untreated or treated with serum for 30 minutes before harvesting.

value: C57BL/6 (female)  x 129/S (male)

value: mES

tag: passages

value: passage 10-18

tag: chip antibody

value: His tag Cdk9(amino acids 204-372)


title: ES cell feeder-free, w/ LIF 60 s CYH (100 ug/ml) mrna_mesc_yeslif Illumina GAII

description: mRNA-Seq

extract_protocol: poly-(A) selection, fragmentation, enzymatic polyadenylation, dT-primed reverse transcription, cDNA circularization, PCR amplification


title: embryoid body 8d in low-adhesion dishes w/o LIF 60 s CYH (100 ug/ml) ribo_eb Illumina GAII

description: Ribosome Profiling

source_name: embryoid body

growth_protocol: 8 days in low-adhesion dishes without LIF


title: ES cell feeder-free, w/ LIF 90 s HRT (1 ug/ml) then 60 s CYH (100 ug/ul) ribo_mesc_harr90s Illumina GAII

description: Ribosome Profiling

treatment_protocol: 90 s harringtonine (1 ug/ml) followed by 60 s cycloheximide (100 ug/ul)


title: ES cell feeder-free, w/ LIF 60 s emetine ribo_mesc_emet Illumina GAII

description: Ribosome Profiling

treatment_protocol: 60 s emetine

value: ES cell feeder-free, w/ LIF 120 s HRT (1 ug/ml) then 60 s CYH (100 ug/ml)


title: ES cell 36 hours in low-adhesion dishes w/o LIF 60 s CYH (100 ug/ml) ribo_mesc_nolif Illumina HiSeq

description: Ribosome Profiling


title: ES cell 36 hours in low-adhesion dishes w/o LIF 60 s CYH (100 ug/ml) mrna_mesc_nolif Illumina GAII

description: mRNA-Seq


title: embryoid body 8d in low-adhesion dishes w/o LIF 60 s CYH (100 ug/ml) ribo_eb Illumina HiSeq

description: Ribosome Profiling


title: ES cell 36 hours in low-adhesion dishes w/o LIF 60 s CYH (100 ug/ml) mrna_mesc_nolif Illumina HiSeq

description: mRNA-Seq


title: Kns211_small RNAs

status: Public on Nov 02 2011

city: Beijing

first: Hu

last: Zheng

address: No.12 South Street, Zhongguancun, Haidian District

institute: Chinese Academy of Agricultural Sciences

description: Solexa small RNA sequencing

data_processing: Individual sequence reads with the base quality scores were produced by Illumina/Solexa. After removing the contaminant reads (the adapters, low quality and redundancy reads), the clean unique reads were mapped onto the Glycine max genome of Phytozome(http://www.phytozome.net/index.php) using the program SOAP (Li et al. 2008), and the perfectly mapped reads were scan against the Plant mature microRNA of Sanger miRBase (Release 13) (Griffiths-Jones et al. 2008) to identify the homologs of known microRNAs using the program Patscan (Dsouza et al. 1997) with two mismatches allowed. Then, the non-conserved unique reads were screened against the non-coding RNA databases (Griffiths-Jones et al. 2008) to remove the contaminated sequences of tRNA, rRNA, snoRNA, and other ncRNA using SOAP, and those reads that matched genome more than 20 times were also removed to avoid self-contradiction of microRNA prediction (Friedlander et al. 2008). Finally, the remaining reads, including the conserved reads and non-conserved reads filtered the non-coding RNA reads and those mapped onto genome > 20, were denoted as the microRNA potential reads and used for microRNA identification.As microRNA and microRNA* may be both sequenced and from the same precursor, and to avoid repeated predictions and to reduce the required amount of calculation, the potential microRNA reads were searched against the genome, and the candidate reads whose distance in the reference genome are less than 150 nt were jointed and examined as one genomic block. For each block, 150 nt of upstream and downstream extension, were extracted for secondary structure prediction. Firstly, the inverted repeats (IR) with characters of stem-loop or hairpin structure were identified by Einverted of Emboss (Drew et al. 2001), with the parameters threshold = 30, match score = 3, mismatch score = 3, gap penalty = 6, and maximum repeat length = 240 as described by Jones-Rhoades and Bartel (Jones-Rhoades and Bartel 2004). Then the secondary structure of IR was predicted by RNAfold (I. L. Hofacker 1994) with 10 nt extended of upstream and downstream, and evaluated by MirCheck (Bonnet et al. 2004). For the precursors (hairpins) of microRNA located by the non-conserved reads which sequenced more than twice, were inspected manually in order to remove the false prediction. Predicted precursors that microRNAs and microRNA* were found in their both arms, or with two or more unique reads located at mature position were deemed as high probability. When several length variants of the same microRNA were sequenced, only variants with the highest representation were considered.

organism: Glycine max

source_name: root, stem, leaf, and inflorescence

growth_protocol: Plant samples for RNA isolation were obtained from different development stages of the soybean cultivar Williams 82. Seeds were germinated in a 25°C growth cabinet without light. When the roots had grown to 2-3 cm, the plant material was collected for RNA isolation. Four-week-old seedlings and plants displaying inflorescence at mature stages were grown in a greenhouse under natural daylight conditions. Plant materials including the root, stem, leaf, and inflorescence were collected respectively for RNA isolation.

extract_protocol: Total RNA from different samples was isolated separately using TRIzol reagent (Invitrogen), according to the manufacturer's instructions. RNA was pooled with the equal quantity from different samples. The small RNAs were purified on a 15% (w/v) denaturing polyacrylamide gel, running overnight at 4°C in 0.4 M NaCl solution. The small RNAs were ligated with 3' and 5' adapters by T4 RNA ligase. Reverse transcription was performed using SuperScript III RT (Invitrogen), and they were PCR-amplified for sequencing.

tag: cultivar

value: Williams 82


title: RNA-Seq Neural progenitor cells, after 24h

status: Public on Nov 01 2011

city: Stockholm

first: Rickard

last: Sandberg

address: Berzelius vag 35

department: Department of Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

description:
Untransfected
library selection: Poly(A)-selection

data_processing:
Reads were aligned by Bowtie, with options -n 2 -m 1, against genome build mm9.
Expression values (FPKM) were calculated by rpkmforgenes.py (http://sandberg.cmb.ki.se/rnaseq/) with options -mRNAnorm -fulltranscript and RefSeq gene annotation downloaded from UCSC genome browser 1 July 2010.

source_name: Neural progenitor cells

growth_protocol: Mouse ES-cells were differentiated with B27 and N2 supplement (GIBCO) as monolayers on gelatinized cellbinding surface (Corning) with 0.5uM retinoic acid (all-trans, Sigma) at day 0 and day 2.

extract_protocol: Libraries were constructed from total RNA. Libraries were prepared according to Illumina's instructions accompanying the mRNA-Seq sample preparation kit (Part # 1004898 Rev.D). Briefly, the mRNA was purified from total RNA by PolyA selection. The mRNA was subjected to fragmentation using divalent cations under elevated temperature. cDNA synthesis was performed with fragmented RNA, and cDNA was end-repaired with 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 3? end. After adapter ligation, size   selection was achieved by excising a band of 200±25 bp from an agarose gel to remove excess adapters. The gel 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: siRNA transfection was done by Lipofectamine treatment. Magnetic beads was used for PSA NCAM sorting.

value: ES-cell derived neural progenitor cells

tag: differentiation

value: 4 days of differentiation

tag: modification

value: Untransfected, 24h


title: RNA-Seq Universal siRNA control in neural progenitor cells, after 48h

description:
Control transfected
library selection: Poly(A)-selection

value: Universal siRNA (Invitrogen) transfected, 48h


title: RNA-Seq Sox2/Sox3 siRNA in neural progenitor cells, after 48h

description:
Sox2/Sox3 knockdown
library selection: Poly(A)-selection

value: Sox2 and Sox3 siRNA (Invitrogen) transfected, 48h


title: Sox2 ChIP-Seq in neural progenitor cells, biol repl 3

description: Chromatin IP against Sox2

data_processing: Reads were aligned by Bowtie, with options -n 2 -m 1, against genome build mm9.

growth_protocol: Mouse ES-cells were differentiated with B27 and N2 supplement (GIBCO) as monolayers on gelatinized cellbinding surface (Corning) with 0.5uM retinoic acid (all-trans, Sigma) at day 0 and day 2. C2C12 cells were cultured with serum unless for 3h during lipofectamine transfection.

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Prep Kit (1003473).

treatment_protocol: Formaldehyde 1% crosslink 9min at 37°C. Cells were mechanically dissociated from the surface before lysis.

value: ES-derived neural progenitor cells

tag: differentiation specificity

value: 4 days in differentiation conditions with retinoic acid

value: Sox2 (Millipore)


title: embryoid body 8d in low-adhesion dishes w/o LIF 60 s CYH (100 ug/ml) mrna_eb Illumina GAII

description: mRNA-Seq

tag: treatment


title: 4X4_leaf_small_RNA_seq

status: Public on Nov 11 2011

city: Austin

first: Z Jeffrey

middle: Jeffrey

last: Chen

address: 2506 Speedway NMS 3.122 Stop A500

department: Molecular Biosciences

institute: The University of Texas at Austin

description:
balanced cross
small RNA sequencing

data_processing: Short reads (40-nt) were parsed to remove 3’ adaptors and mapped to Arabidopsis thaliana genome (TAIR9) using CASHX (http://asrp.cgrb.oregonstate.edu/db/download.html). To reduce ambiguity, only the perfectly matched reads were used for further analysis. The sequences from chloroplast and mitochondrial and structural non-coding RNAs including ribosomal RNAs, transfer RNAs, snoRNAs and snRNAs were excluded from the analysis.

source_name: rosette leaves

growth_protocol: Diploids (2n = 2x = 10) and tetraploids (2n = 4x = 20) of Arabidopsis thaliana Col-0 ecotype was grown under 16h light at 22°C and 8h darkness at 20°C.

extract_protocol: Total RNA was extracted from seeds and leaves using Plant RNA reagent (Invitrogen) and subjected to electrophoresis in a 15% urea-polyacrylamide gel. The small RNA fraction (18-30-nt) was recovered from the gel. The small RNAs were ligated to 5’ and 3’ RNA oligo adapters (Supplementary Table x3) and reverse-transcribed to produce first strand cDNAs, which were amplified by PCR and sequenced by Illumina Genome Analyzer II (at UC Davis Genome Center).

treatment_protocol: Reciprocal interploidy crosses were made by pollinating diploid flowers with tetraploid pollens (2x4) or tetraploid flowers with diploid pollens (4x2) 24h after manual emasculation. Diploid and tetraploid flowers were manually self-pollinated to serve as balanced dosage controls. Seeds were dissected from the siliques at 3, 4, 5, 6, 7 days after pollination (DAP) to eliminate maternal tissue contamination. Small RNA library construction and gene expression assays were performed using the seeds dissected at 6DAP.

tag: ecotype

tag: cross

value: 4x X 4x

value: rosette leaves

tag: Stage

value: Before bolting


title: RNA-Seq PSA NCAM+ neurons, biol repl 1

description:
RNA-Seq NCAM sorted neurons
library selection: Poly(A)-selection

source_name: PSA NCAM sorted neurons

tag: cell type

value: ES-cell derived neurons

value: 10 days of differentiation

value: PSA NCAM sorted (Chemicon antibody)


title: Control IgG ChIP-Seq in early formed neurons

description: Chromatin IP against IgG

source_name: Neurons

value: ES-derived neurons

value: 11 days in differentiation conditions with retinoic acid

value: IgG (Millipore)


title: Sox11 ChIP-Seq in early formed neurons, biol repl 2

description: Chromatin IP against Sox11

value: Sox11 (M. Wegner)


title: ES cell feeder-free, w/ LIF 60 s CYH (100 ug/ml) ribo_mesc_yeslif Illumina HiSeq

description: Ribosome Profiling


title: Sox11 ChIP-Seq in early formed neurons, biol repl 3

description: Chromatin IP against Sox11


title: Sox11 ChIP-Seq in early formed neurons, biol repl 1

description: Chromatin IP against Sox11


title: Sox2 ChIP-Seq in neural progenitor cells, biol repl 2

description: Chromatin IP against Sox2


title: Sox2 ChIP-Seq in neural progenitor cells, biol repl 1

description: Chromatin IP against Sox2


title: Sox3 ChIP-Seq in neural progenitor cells, biol repl 3

description: Chromatin IP against Sox3

value: Sox3 (T. Edlund)


title: Sox3 ChIP-Seq in neural progenitor cells, biol repl 1

description: Chromatin IP against Sox3


title: embryoid body 8d in low-adhesion dishes w/o LIF 60 s CYH (100 ug/ml) mrna_eb Illumina HiSeq

description: mRNA-Seq


title: USC_ChipSeq_MCF-7_GATA3_(SC-268)_UCDavis

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

tag: lab

value: USC

tag: lab description

value: Farnham - University of Southern California

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: human

tag: cell description

value: mammary gland, adenocarcinoma. (PMID:4357757), newly promoted to tier 2:not in 2011 analysis

tag: cell karyotype

value: cancer

tag: cell lineage

value: ectoderm

tag: cell sex

value: F

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

tag: antibody antibodydescription

value: Mouse monoclonal IgG raised against human recombinant GATA-3. Antibody Target: GATA3

tag: antibody targetdescription

value: This gene encodes a protein which belongs to the GATA family of transcription factors.  The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology.  Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq).

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

tag: control

value: UCDavis

tag: control description

value: Input library was prepared at UC Davis.

tag: controlid

tag: replicate

tag: replicate description

value: tier 1


title: LY2_INPUT_CONTROL

city: Cork

first: Ailis

last: Fagan

address: University College Cork

country: Ireland

institute: University College Cork

description:
Input DNA.

Input-Control
Both replicates are in the same fastq file under different barcodes. They had even number of reads and weren't split for the analysis.

data_processing:
Alignment: Sequence reads were obtained and mapped to the h19 genome using Bowtie. All unique reads mapping with two or fewer mismatches were retained. The Bowtie alignments are in the *map files.

Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm version 1.3.7.1 (http://liulab.dfci.harvard.edu/MACS/). The MACS analyses are in the *wig files.

source_name: Mammary gland epithelial cells, input

growth_protocol: The LY2 cells were maintained in phenol red-free Eagle's minimum essential medium with 2mM L-glutamine and supplemented with charcoal dextran stripped fetal bovine serum, 10% (Invitrogen, Paisley, UK) and were incubated at 37C under 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer, followed by disruption with a Dounce homogenizer (cells) or motor  pestle (tissue). Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield.

DNA libraries were generated from 10 ng of ChIP output DNA by adaptor ligation, gel purification, and cycles of PCR as described by Illumina.

treatment_protocol: Cells were maintained in steroid-depleted medium for 72 h before treatment with a vehicle control or 4-OHT [4-hydroxytamoxifen 10-7 mol/L; Sigma Aldrich] for 45 minutes, and then immunoprecipitated with anti-SRC-1 (Santa Cruz, sc-8995) antibody.

tag: cell line

tag: cell type

value: mammary gland epithelial cells

tag: treatment

value: vehicle control

tag: chip antibody

tag: read length


title: LY2_SRC1_TAMOX

description:
Chromatin IP against SRC1.

Tamox-1 and Tamox-2.
This Sample represents 2 replicates. The reads for each replicate were aligned separately by Bowtie, but the replicates were combined for MACS analysis.

source_name: Mammary gland epithelial cells, tamoxifen treated, SRC1 ChIP

value: tamoxifen

tag: antibody vendor

value: Santa Cruz

tag: antibody catalog number

tag: antibody lot


title: RNA-Seq Sox2/Sox3 siRNA in neural progenitor cells, after 24h

value: ES-cell derived neural progenitor cells

tag: differentiation

value: 4 days of differentiation

tag: modification

value: Sox2 and Sox3 siRNA (Invitrogen) transfected, 24h


title: LY2_SRC1_UNTREAT

description:
Chromatin IP against SRC1.

Untreat-1 and Untreat-2.
This Sample represents 2 replicates. The reads for each replicate were aligned separately by Bowtie, but the replicates were combined for MACS analysis.

source_name: Mammary gland epithelial cells, untreated, SRC1 ChIP


title: RNA-Seq PSA NCAM+ neurons, biol repl 2

value: ES-cell derived neurons

value: 10 days of differentiation

value: PSA NCAM sorted (Chemicon antibody)


title: Sox3 ChIP-Seq in neural progenitor cells, biol repl 2

description: Chromatin IP against Sox3

value: ES-derived neural progenitor cells

tag: differentiation specificity

value: 4 days in differentiation conditions with retinoic acid

value: Sox3 (T. Edlund)


title: Control 2 [RNA-Seq]

city: North Adelaide

first: Jozef

last: Gecz

state: South Australia

address: 72 King William Rd

department: Genetics Medicine

country: Australia

institute: SA Pathology

data_processing:
The first and last 14 bases of all reads were trimmed to improve alignment and error rate. Reads were aligned to the human genome HG19, splice junctions database, mitochondrion DNA and rRNA. Splice junctions were built from exon annotation which comprises of 45 bases on each side of the exon-exon junction (see supplementary file 'Splice_Sites_45.fa.txt' on Series GSE27199 record). If the exon is less than 45 bp, the whole exon is included. Reads were mapped using ELAND (Illumina). Mapped reads with more than 2 mismatches were excluded from downstream analysis.
Description of *_HG19_Aligned.txt file:
1. Machine
2. Run number
3. Lane
4. Tile
5. X coordinate of cluster
6. Y coordinate of cluster
7. Index value (0 for a non-indexed run)
8. Read number (1 or 2 for paired-read analysis, 0 for single read analysis)
9. Read sequence
10. Quality string--In sym,bolic ASCII format (ASCII character code = quality value +64)
11. Match chromosome
12. Match contig
13. Match position--Always with respect to forward strand, number starts at 1
14. Match strand
15. Match descriptor--Concise description of alignment (Number denotes a run of matching bases, letter denotes substitution of a nucleotide)
16. Single read alignment score

source_name: Lymphoblastoid cell line

growth_protocol: The Epstein-Barr virus (EBV) immortalized B- cell lines (B-LCL) used in this study were established from peripheral blood lymphocytes of patients and controls. Once established the LCL cell lines were cultured in RPMI 1640 (Sigma) supplemented with 10% FCS, 2mM L-Glutamine, 0.017mg/ml benzylpenicillin and grown at 37 0 C with 5% CO2

extract_protocol: Total RNA was extracted from lymphoblastoid cell lines using Trizol (Inivtrogen) and RNeasy mini-kit (QIAGNE). PolyA+ RNA was purified from total RNA using oligo-dT magnetic beads. RT-PCR was performed to make cDNA with random primers. All outlined steps are part of the mRNA-seq 8 sample preparation kit (cat# RS-100-0801, Illumina) and were performed by Geneworks (Australia). ds-cDNA was sequenced using Illumina Genome Analyzer II as recommended my manufacturer, and was also performed by Geneworks (Australia).

treatment_protocol: No treatment

tag: individual

value: Control 2

value: Lymphoblastoid cell line

tag: disease state

value: Control


title: Patient 2 [RNA-Seq]

value: Patient 2

value: UPF3B mutation


title: Control 1 [RNA-Seq]

value: Control 1


title: Patient 1 [RNA-Seq]

value: Patient 1


title: Patient 3 [RNA-Seq]

value: Patient 3


title: Patient 6 [RNA-Seq]

value: Patient 6


title: 2X2_leaf_small_RNA_seq

description:
balanced cross
small RNA sequencing

tag: ecotype

tag: cross

value: 2x X 2x

tag: tissue

value: rosette leaves

tag: Stage

value: Before bolting


title: in vitro culture NM1200_InVitro_5_E3t2

city: Saint Louis

first: Nathan

middle: P

last: McNulty

state: MO

address: 4444 Forest Park Ave. (5th Floor)

department: Center for Genome Sciences and Systems Biology

institute: Washington University School of Medicine

description:
Bifidobacterium animalis subsp. lactis CNCM I-2494,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519,Lactococcus lactis subsp. cremoris CNCM I-1631,Streptococcus thermophilus CNCM I-1634
rRNA-depleted total RNA
RNA isolated from a milk fermentation reaction 3 hours after inoculation of the milk.  The milk in these reactions included a B. animalis subsp. lactis growth-enhancing ingredient.  B. animalis subsp. lactis represents approximately 44% of the total CFUs in these samples.  Biological replicate #2 of 3.

data_processing: After parsing each sequencing lane's data by barcode (where appropriate), we excised the barcodes and mapped the reads to an appropriate set of reference genomes using the ssaha2 algorithm.  Minimum score thresholds for ssaha were selected based on the distribution of scores for all mapped reads of a 32-nt barcoded sample and a 36-nt non-barcoded sample (29 was selected as the minimum score for 32-nt barcoded samples; 33 was the minimum score used for 36-nt and 76-nt non-barcoded samples). Although an 18-nt read is sufficient to map more than 90% of the sequencing reads, even at 32-36 nucleotides a large fraction of reads map to multiple locations (within a genome and/or across genomes). Reads that map non-uniquely were added to each gene in proportion to each gene's fraction of unique-match counts (e.g., a non-unique read that maps equally well to gene A with 18 unique reads and gene B with 2 unique reads will result in 0.9 counts being tallied to gene A and 0.1 counts being tallied to gene B). We added a pseudocount (i.e. added a value of 1) to each gene count prior to normalization to account for differences in sampling depth, although clearly a more appropriate model-based approach to smooth lower expression values is needed in the future, particularly with mixed species samples where one or more species is clearly undersampled. Raw counts were ultimately normalized to reads/kb gene length/million mapped reads (RPKM) following gene count assignments.

organism:
Lactobacillus delbrueckii subsp. bulgaricus
Lactococcus lactis subsp. lactis CNCM I-1631
Bifidobacterium animalis subsp. lactis CNCM I-2494
Streptococcus thermophilus CNCM I-1630

source_name: in vitro culture

extract_protocol: Libraries were prepared according a slightly modified version of the protocol accompanying the Illumina Genomic DNA Sample Prep Kit. Briefly, cDNA was sonicated in a BioRuptor XL water bath sonicator, cleaned up and concentrated using a Qiagen PCR Purification column, and end-repaired using Klenow DNA polymerase. The blunt DNA was treated with Klenow fragment (exo minus) to add an adenine overhang, and the A-tailed molecules were ligated to the relevant Illumina adapter sequence (with or without a 4-nt barcode).  Adaptered-DNA was then size-selected by agarose gel electrophoresis.  Fragments of the appropriate size were PCR amplified and purified, after which the purified PCR products were loaded on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer (IIx) following the manufacturer's protocols.

tag: sample type

value: milk fermentation reaction

tag: source


title: human feces TSDA2.4

description:
Akkermansia muciniphila ATCC BAA-835,Bacteroides caccae ATCC 43185,Bacteroides thetaiotaomicron VPI-5482,Bacteroides vulgatus ATCC 8482,Bifidobacterium longum NCC2705,Bifidobacterium longum DJO10A,Bifidobacterium adolescentis ATCC 15703,Bacteroides fragilis YCH46,Bacteroides fragilis NCTC 9343,Bacteroides ovatus ATCC 8483,Bacteroides uniformis ATCC 8492,Blautia hydrogenotrophica DSM 10507,Bryantella formatexigens DSM 14469,Clostridium scindens ATCC 35704,Clostridium spiroforme DSM 1552,Collinsella aerofaciens ATCC 25986,Dorea longicatena DSM 13814,Escherichia coli str. K-12 substr. MG1655,Eubacterium eligens ATCC 27750,Eubacterium rectale ATCC 33656,Faecalibacterium prausnitzii A2-165,Faecalibacterium prausnitzii M21/2,Helicobacter pylori HPAG1,Lactobacillus reuteri DSM 20016,Methanobrevibacter smithii ATCC 35061,Methanosphaera stadtmanae DSM 3091,Parabacteroides distasonis ATCC 8503,Lactococcus lactis subsp. lactis Il1403,Streptococcus thermophilus LMG 18311,Streptococcus thermophilus CNRZ1066,Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842,Lactobacillus casei ATCC 334,Lactococcus lactis subsp. cremoris SK11,Streptococcus thermophilus LMD-9,Lactococcus lactis subsp. cremoris MG1363,Escherichia fergusonii ATCC 35469,Bifidobacterium animalis subsp. lactis AD011,Ruminococcus obeum ATCC 29174,Ruminococcus torques ATCC 27756,Vibrio cholerae O1 biovar eltor str. N16961 chromosome I,Vibrio cholerae O1 biovar eltor str. N16961 chromosome II,Clostridium bolteae ATCC BAA-613,Clostridium sporogenes ATCC 15579,Bacteroides dorei DSM 17855,Bifidobacterium catenulatum DSM 16992,Clostridium asparagiforme DSM 15981,Bifidobacterium adolescentis L2-32,Alistipes putredinis DSM 17216,Ruminococcus lactaris ATCC 29176,Anaerococcus hydrogenalis DSM 7454,Bifidobacterium angulatum DSM 20098,Catenibacterium mitsuokai DSM 15897,Bacteroides capillosus ATCC 29799,Anaerotruncus colihominis DSM 17241,Coprococcus comes ATCC 27758,Bifidobacterium gallicum DSM 20093,Blautia hansenii DSM 20583,Ruminococcus gnavus ATCC 29149,Anaerofustis stercorihominis DSM 17244,Citrobacter youngae ATCC 29220,Collinsella intestinalis DSM 13280,Bifidobacterium breve DSM 20213,Anaerostipes caccae DSM 14662,Bacteroides coprocola DSM 17136,Butyrivibrio crossotus DSM 2876,Providencia alcalifaciens DSM 30120,Bacteroides cellulosilyticus DSM 14838,Eubacterium ventriosum ATCC 27560,Parabacteroides merdae ATCC 43184,Clostridium sp. L2-50,Eubacterium dolichum DSM 3991,Clostridium leptum DSM 753,Parvimonas micra ATCC 33270,Coprococcus eutactus ATCC 27759,Clostridium bartlettii DSM 16795,Clostridium ramosum DSM 1402,Bacteroides stercoris ATCC 43183,Clostridium sp. SS2/1,Providencia stuartii ATCC 25827,Streptococcus infantarius subsp. infantarius ATCC BAA-102,Bacteroides intestinalis DSM 17393,Bifidobacterium animalis subsp. lactis HN019,Providencia rustigianii DSM 4541,Bifidobacterium pseudocatenulatum DSM 20438,Dorea formicigenerans ATCC 27755,Bacteroides plebeius DSM 17135,Bacteroides eggerthii DSM 20697,Proteus penneri ATCC 35198,Mitsuokella multacida DSM 20544,Clostridium nexile DSM 1787,Bacteroides finegoldii DSM 17565,Collinsella stercoris DSM 13279,Desulfovibrio piger ATCC 29098,Parabacteroides johnsonii DSM 18315,Clostridium hylemonae DSM 15053,Roseburia intestinalis L1-82,Eubacterium biforme DSM 3989,Methanobrevibacter smithii DSM 2374,Methanobrevibacter smithii DSM 2375,Bacteroides fragilis 3_1_12,Bacteroides sp. D1,Prevotella copri DSM 18205,Holdemania filiformis DSM 12042,Providencia rettgeri DSM 1131,Fusobacterium sp. 4_1_13,Shigella sp. D9,Clostridium methylpentosum DSM 5476,Eubacterium hallii DSM 3353,Bacteroides sp. D2,Bacteroides sp. 1_1_6,Fusobacterium varium ATCC 27725,Actinomyces odontolyticus ATCC 17982,Victivallis vadensis ATCC BAA-548,Clostridium hiranonis DSM 13275,Subdoligranulum variabile DSM 15176,Clostridium sp. M62/1,Bacteroides coprophilus DSM 18228,Bacteroides WH2,Bifidobacterium dentium,Bacteroides thetaiotaomicron 3731,Bacteroides thetaiotaomicron 7330,Bacteroides xylanisolvens XB1A,Clostridium symbiosum,Desulfovibrio piger GOR1,Enterobacter cancerogenus,Eubacterium rectale DSM17629,M23A,Ruminococcus bromiiL263,Lactobacillus casei DN114001,Lactobacillus delbrueckii DN100107,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519,Lactococcus lactis subsp. cremoris CNCM I-1631,Streptococcus thermophilus DN001147,Streptococcus thermophilus CNCM I-1630,Bifidobacterium animalis subsp. lactis CNCM I-2494
rRNA-depleted total RNA
RNA isolated from the feces of a human subject (subject F1T2, timepoint "FMP1") who had been consuming 2 servings of a fermented milk product (Danone, Activia) daily for 1 week. Read length is 36 nucleotides.

organism: human gut metagenome

source_name: human feces

value: feces of a human subject


title: human feces TSDA2.4_long

description:
Akkermansia muciniphila ATCC BAA-835,Bacteroides caccae ATCC 43185,Bacteroides thetaiotaomicron VPI-5482,Bacteroides vulgatus ATCC 8482,Bifidobacterium longum NCC2705,Bifidobacterium longum DJO10A,Bifidobacterium adolescentis ATCC 15703,Bacteroides fragilis YCH46,Bacteroides fragilis NCTC 9343,Bacteroides ovatus ATCC 8483,Bacteroides uniformis ATCC 8492,Blautia hydrogenotrophica DSM 10507,Bryantella formatexigens DSM 14469,Clostridium scindens ATCC 35704,Clostridium spiroforme DSM 1552,Collinsella aerofaciens ATCC 25986,Dorea longicatena DSM 13814,Escherichia coli str. K-12 substr. MG1655,Eubacterium eligens ATCC 27750,Eubacterium rectale ATCC 33656,Faecalibacterium prausnitzii A2-165,Faecalibacterium prausnitzii M21/2,Helicobacter pylori HPAG1,Lactobacillus reuteri DSM 20016,Methanobrevibacter smithii ATCC 35061,Methanosphaera stadtmanae DSM 3091,Parabacteroides distasonis ATCC 8503,Lactococcus lactis subsp. lactis Il1403,Streptococcus thermophilus LMG 18311,Streptococcus thermophilus CNRZ1066,Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842,Lactobacillus casei ATCC 334,Lactococcus lactis subsp. cremoris SK11,Streptococcus thermophilus LMD-9,Lactococcus lactis subsp. cremoris MG1363,Escherichia fergusonii ATCC 35469,Bifidobacterium animalis subsp. lactis AD011,Ruminococcus obeum ATCC 29174,Ruminococcus torques ATCC 27756,Vibrio cholerae O1 biovar eltor str. N16961 chromosome I,Vibrio cholerae O1 biovar eltor str. N16961 chromosome II,Clostridium bolteae ATCC BAA-613,Clostridium sporogenes ATCC 15579,Bacteroides dorei DSM 17855,Bifidobacterium catenulatum DSM 16992,Clostridium asparagiforme DSM 15981,Bifidobacterium adolescentis L2-32,Alistipes putredinis DSM 17216,Ruminococcus lactaris ATCC 29176,Anaerococcus hydrogenalis DSM 7454,Bifidobacterium angulatum DSM 20098,Catenibacterium mitsuokai DSM 15897,Bacteroides capillosus ATCC 29799,Anaerotruncus colihominis DSM 17241,Coprococcus comes ATCC 27758,Bifidobacterium gallicum DSM 20093,Blautia hansenii DSM 20583,Ruminococcus gnavus ATCC 29149,Anaerofustis stercorihominis DSM 17244,Citrobacter youngae ATCC 29220,Collinsella intestinalis DSM 13280,Bifidobacterium breve DSM 20213,Anaerostipes caccae DSM 14662,Bacteroides coprocola DSM 17136,Butyrivibrio crossotus DSM 2876,Providencia alcalifaciens DSM 30120,Bacteroides cellulosilyticus DSM 14838,Eubacterium ventriosum ATCC 27560,Parabacteroides merdae ATCC 43184,Clostridium sp. L2-50,Eubacterium dolichum DSM 3991,Clostridium leptum DSM 753,Parvimonas micra ATCC 33270,Coprococcus eutactus ATCC 27759,Clostridium bartlettii DSM 16795,Clostridium ramosum DSM 1402,Bacteroides stercoris ATCC 43183,Clostridium sp. SS2/1,Providencia stuartii ATCC 25827,Streptococcus infantarius subsp. infantarius ATCC BAA-102,Bacteroides intestinalis DSM 17393,Bifidobacterium animalis subsp. lactis HN019,Providencia rustigianii DSM 4541,Bifidobacterium pseudocatenulatum DSM 20438,Dorea formicigenerans ATCC 27755,Bacteroides plebeius DSM 17135,Bacteroides eggerthii DSM 20697,Proteus penneri ATCC 35198,Mitsuokella multacida DSM 20544,Clostridium nexile DSM 1787,Bacteroides finegoldii DSM 17565,Collinsella stercoris DSM 13279,Desulfovibrio piger ATCC 29098,Parabacteroides johnsonii DSM 18315,Clostridium hylemonae DSM 15053,Roseburia intestinalis L1-82,Eubacterium biforme DSM 3989,Methanobrevibacter smithii DSM 2374,Methanobrevibacter smithii DSM 2375,Bacteroides fragilis 3_1_12,Bacteroides sp. D1,Prevotella copri DSM 18205,Holdemania filiformis DSM 12042,Providencia rettgeri DSM 1131,Fusobacterium sp. 4_1_13,Shigella sp. D9,Clostridium methylpentosum DSM 5476,Eubacterium hallii DSM 3353,Bacteroides sp. D2,Bacteroides sp. 1_1_6,Fusobacterium varium ATCC 27725,Actinomyces odontolyticus ATCC 17982,Victivallis vadensis ATCC BAA-548,Clostridium hiranonis DSM 13275,Subdoligranulum variabile DSM 15176,Clostridium sp. M62/1,Bacteroides coprophilus DSM 18228,Bacteroides WH2,Bifidobacterium dentium,Bacteroides thetaiotaomicron 3731,Bacteroides thetaiotaomicron 7330,Bacteroides xylanisolvens XB1A,Clostridium symbiosum,Desulfovibrio piger GOR1,Enterobacter cancerogenus,Eubacterium rectale DSM17629,M23A,Ruminococcus bromiiL263,Lactobacillus casei DN114001,Lactobacillus delbrueckii DN100107,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519,Lactococcus lactis subsp. cremoris CNCM I-1631,Streptococcus thermophilus DN001147,Streptococcus thermophilus CNCM I-1630,Bifidobacterium animalis subsp. lactis CNCM I-2494
rRNA-depleted total RNA
RNA isolated from the feces of a human subject (subject F1T2, timepoint "FMP1") who had been consuming 2 servings of a fermented milk product (Danone, Activia) daily for 1 week. Read length is 76 nucleotides.


title: in vitro culture NM1200_InVitro_4_E2t2

description:
Bifidobacterium animalis subsp. lactis CNCM I-2494,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519,Lactococcus lactis subsp. cremoris CNCM I-1631,Streptococcus thermophilus CNCM I-1633
rRNA-depleted total RNA
RNA isolated from a milk fermentation reaction 3 hours after inoculation of the milk.  The milk in these reactions included a B. animalis subsp. lactis growth-enhancing ingredient.  B. animalis subsp. lactis represents approximately 44% of the total CFUs in these samples.  Biological replicate #1 of 3.


title: in vitro culture NM1200_InVitro_5_E4t2

description:
Bifidobacterium animalis subsp. lactis CNCM I-2494,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519,Lactococcus lactis subsp. cremoris CNCM I-1631,Streptococcus thermophilus CNCM I-1635
rRNA-depleted total RNA
RNA isolated from a milk fermentation reaction 3 hours after inoculation of the milk.  The milk in these reactions included a B. animalis subsp. lactis growth-enhancing ingredient.  B. animalis subsp. lactis represents approximately 44% of the total CFUs in these samples.  Biological replicate #3 of 3.


title: human feces TSDA2.8

description:
Akkermansia muciniphila ATCC BAA-835,Bacteroides caccae ATCC 43185,Bacteroides thetaiotaomicron VPI-5482,Bacteroides vulgatus ATCC 8482,Bifidobacterium longum NCC2705,Bifidobacterium longum DJO10A,Bifidobacterium adolescentis ATCC 15703,Bacteroides fragilis YCH46,Bacteroides fragilis NCTC 9343,Bacteroides ovatus ATCC 8483,Bacteroides uniformis ATCC 8492,Blautia hydrogenotrophica DSM 10507,Bryantella formatexigens DSM 14469,Clostridium scindens ATCC 35704,Clostridium spiroforme DSM 1552,Collinsella aerofaciens ATCC 25986,Dorea longicatena DSM 13814,Escherichia coli str. K-12 substr. MG1655,Eubacterium eligens ATCC 27750,Eubacterium rectale ATCC 33656,Faecalibacterium prausnitzii A2-165,Faecalibacterium prausnitzii M21/2,Helicobacter pylori HPAG1,Lactobacillus reuteri DSM 20016,Methanobrevibacter smithii ATCC 35061,Methanosphaera stadtmanae DSM 3091,Parabacteroides distasonis ATCC 8503,Lactococcus lactis subsp. lactis Il1403,Streptococcus thermophilus LMG 18311,Streptococcus thermophilus CNRZ1066,Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842,Lactobacillus casei ATCC 334,Lactococcus lactis subsp. cremoris SK11,Streptococcus thermophilus LMD-9,Lactococcus lactis subsp. cremoris MG1363,Escherichia fergusonii ATCC 35469,Bifidobacterium animalis subsp. lactis AD011,Ruminococcus obeum ATCC 29174,Ruminococcus torques ATCC 27756,Vibrio cholerae O1 biovar eltor str. N16961 chromosome I,Vibrio cholerae O1 biovar eltor str. N16961 chromosome II,Clostridium bolteae ATCC BAA-613,Clostridium sporogenes ATCC 15579,Bacteroides dorei DSM 17855,Bifidobacterium catenulatum DSM 16992,Clostridium asparagiforme DSM 15981,Bifidobacterium adolescentis L2-32,Alistipes putredinis DSM 17216,Ruminococcus lactaris ATCC 29176,Anaerococcus hydrogenalis DSM 7454,Bifidobacterium angulatum DSM 20098,Catenibacterium mitsuokai DSM 15897,Bacteroides capillosus ATCC 29799,Anaerotruncus colihominis DSM 17241,Coprococcus comes ATCC 27758,Bifidobacterium gallicum DSM 20093,Blautia hansenii DSM 20583,Ruminococcus gnavus ATCC 29149,Anaerofustis stercorihominis DSM 17244,Citrobacter youngae ATCC 29220,Collinsella intestinalis DSM 13280,Bifidobacterium breve DSM 20213,Anaerostipes caccae DSM 14662,Bacteroides coprocola DSM 17136,Butyrivibrio crossotus DSM 2876,Providencia alcalifaciens DSM 30120,Bacteroides cellulosilyticus DSM 14838,Eubacterium ventriosum ATCC 27560,Parabacteroides merdae ATCC 43184,Clostridium sp. L2-50,Eubacterium dolichum DSM 3991,Clostridium leptum DSM 753,Parvimonas micra ATCC 33270,Coprococcus eutactus ATCC 27759,Clostridium bartlettii DSM 16795,Clostridium ramosum DSM 1402,Bacteroides stercoris ATCC 43183,Clostridium sp. SS2/1,Providencia stuartii ATCC 25827,Streptococcus infantarius subsp. infantarius ATCC BAA-102,Bacteroides intestinalis DSM 17393,Bifidobacterium animalis subsp. lactis HN019,Providencia rustigianii DSM 4541,Bifidobacterium pseudocatenulatum DSM 20438,Dorea formicigenerans ATCC 27755,Bacteroides plebeius DSM 17135,Bacteroides eggerthii DSM 20697,Proteus penneri ATCC 35198,Mitsuokella multacida DSM 20544,Clostridium nexile DSM 1787,Bacteroides finegoldii DSM 17565,Collinsella stercoris DSM 13279,Desulfovibrio piger ATCC 29098,Parabacteroides johnsonii DSM 18315,Clostridium hylemonae DSM 15053,Roseburia intestinalis L1-82,Eubacterium biforme DSM 3989,Methanobrevibacter smithii DSM 2374,Methanobrevibacter smithii DSM 2375,Bacteroides fragilis 3_1_12,Bacteroides sp. D1,Prevotella copri DSM 18205,Holdemania filiformis DSM 12042,Providencia rettgeri DSM 1131,Fusobacterium sp. 4_1_13,Shigella sp. D9,Clostridium methylpentosum DSM 5476,Eubacterium hallii DSM 3353,Bacteroides sp. D2,Bacteroides sp. 1_1_6,Fusobacterium varium ATCC 27725,Actinomyces odontolyticus ATCC 17982,Victivallis vadensis ATCC BAA-548,Clostridium hiranonis DSM 13275,Subdoligranulum variabile DSM 15176,Clostridium sp. M62/1,Bacteroides coprophilus DSM 18228,Bacteroides WH2,Bifidobacterium dentium,Bacteroides thetaiotaomicron 3731,Bacteroides thetaiotaomicron 7330,Bacteroides xylanisolvens XB1A,Clostridium symbiosum,Desulfovibrio piger GOR1,Enterobacter cancerogenus,Eubacterium rectale DSM17629,M23A,Ruminococcus bromiiL263,Lactobacillus casei DN114001,Lactobacillus delbrueckii DN100107,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519,Lactococcus lactis subsp. cremoris CNCM I-1631,Streptococcus thermophilus DN001147,Streptococcus thermophilus CNCM I-1630,Bifidobacterium animalis subsp. lactis CNCM I-2494
rRNA-depleted total RNA
RNA isolated from the feces of a human subject (subject F1T2, timepoint "Post2") 2 weeks after their completion of a 7-week consumption regimen consisting of two daily servings of a fermented milk product (Danone, Activia).  Read length is 36 nucleotides.


title: human feces TSDA9.4_long

description:
Akkermansia muciniphila ATCC BAA-835,Bacteroides caccae ATCC 43185,Bacteroides thetaiotaomicron VPI-5482,Bacteroides vulgatus ATCC 8482,Bifidobacterium longum NCC2705,Bifidobacterium longum DJO10A,Bifidobacterium adolescentis ATCC 15703,Bacteroides fragilis YCH46,Bacteroides fragilis NCTC 9343,Bacteroides ovatus ATCC 8483,Bacteroides uniformis ATCC 8492,Blautia hydrogenotrophica DSM 10507,Bryantella formatexigens DSM 14469,Clostridium scindens ATCC 35704,Clostridium spiroforme DSM 1552,Collinsella aerofaciens ATCC 25986,Dorea longicatena DSM 13814,Escherichia coli str. K-12 substr. MG1655,Eubacterium eligens ATCC 27750,Eubacterium rectale ATCC 33656,Faecalibacterium prausnitzii A2-165,Faecalibacterium prausnitzii M21/2,Helicobacter pylori HPAG1,Lactobacillus reuteri DSM 20016,Methanobrevibacter smithii ATCC 35061,Methanosphaera stadtmanae DSM 3091,Parabacteroides distasonis ATCC 8503,Lactococcus lactis subsp. lactis Il1403,Streptococcus thermophilus LMG 18311,Streptococcus thermophilus CNRZ1066,Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842,Lactobacillus casei ATCC 334,Lactococcus lactis subsp. cremoris SK11,Streptococcus thermophilus LMD-9,Lactococcus lactis subsp. cremoris MG1363,Escherichia fergusonii ATCC 35469,Bifidobacterium animalis subsp. lactis AD011,Ruminococcus obeum ATCC 29174,Ruminococcus torques ATCC 27756,Vibrio cholerae O1 biovar eltor str. N16961 chromosome I,Vibrio cholerae O1 biovar eltor str. N16961 chromosome II,Clostridium bolteae ATCC BAA-613,Clostridium sporogenes ATCC 15579,Bacteroides dorei DSM 17855,Bifidobacterium catenulatum DSM 16992,Clostridium asparagiforme DSM 15981,Bifidobacterium adolescentis L2-32,Alistipes putredinis DSM 17216,Ruminococcus lactaris ATCC 29176,Anaerococcus hydrogenalis DSM 7454,Bifidobacterium angulatum DSM 20098,Catenibacterium mitsuokai DSM 15897,Bacteroides capillosus ATCC 29799,Anaerotruncus colihominis DSM 17241,Coprococcus comes ATCC 27758,Bifidobacterium gallicum DSM 20093,Blautia hansenii DSM 20583,Ruminococcus gnavus ATCC 29149,Anaerofustis stercorihominis DSM 17244,Citrobacter youngae ATCC 29220,Collinsella intestinalis DSM 13280,Bifidobacterium breve DSM 20213,Anaerostipes caccae DSM 14662,Bacteroides coprocola DSM 17136,Butyrivibrio crossotus DSM 2876,Providencia alcalifaciens DSM 30120,Bacteroides cellulosilyticus DSM 14838,Eubacterium ventriosum ATCC 27560,Parabacteroides merdae ATCC 43184,Clostridium sp. L2-50,Eubacterium dolichum DSM 3991,Clostridium leptum DSM 753,Parvimonas micra ATCC 33270,Coprococcus eutactus ATCC 27759,Clostridium bartlettii DSM 16795,Clostridium ramosum DSM 1402,Bacteroides stercoris ATCC 43183,Clostridium sp. SS2/1,Providencia stuartii ATCC 25827,Streptococcus infantarius subsp. infantarius ATCC BAA-102,Bacteroides intestinalis DSM 17393,Bifidobacterium animalis subsp. lactis HN019,Providencia rustigianii DSM 4541,Bifidobacterium pseudocatenulatum DSM 20438,Dorea formicigenerans ATCC 27755,Bacteroides plebeius DSM 17135,Bacteroides eggerthii DSM 20697,Proteus penneri ATCC 35198,Mitsuokella multacida DSM 20544,Clostridium nexile DSM 1787,Bacteroides finegoldii DSM 17565,Collinsella stercoris DSM 13279,Desulfovibrio piger ATCC 29098,Parabacteroides johnsonii DSM 18315,Clostridium hylemonae DSM 15053,Roseburia intestinalis L1-82,Eubacterium biforme DSM 3989,Methanobrevibacter smithii DSM 2374,Methanobrevibacter smithii DSM 2375,Bacteroides fragilis 3_1_12,Bacteroides sp. D1,Prevotella copri DSM 18205,Holdemania filiformis DSM 12042,Providencia rettgeri DSM 1131,Fusobacterium sp. 4_1_13,Shigella sp. D9,Clostridium methylpentosum DSM 5476,Eubacterium hallii DSM 3353,Bacteroides sp. D2,Bacteroides sp. 1_1_6,Fusobacterium varium ATCC 27725,Actinomyces odontolyticus ATCC 17982,Victivallis vadensis ATCC BAA-548,Clostridium hiranonis DSM 13275,Subdoligranulum variabile DSM 15176,Clostridium sp. M62/1,Bacteroides coprophilus DSM 18228,Bacteroides WH2,Bifidobacterium dentium,Bacteroides thetaiotaomicron 3731,Bacteroides thetaiotaomicron 7330,Bacteroides xylanisolvens XB1A,Clostridium symbiosum,Desulfovibrio piger GOR1,Enterobacter cancerogenus,Eubacterium rectale DSM17629,M23A,Ruminococcus bromiiL263,Lactobacillus casei DN114001,Lactobacillus delbrueckii DN100107,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519,Lactococcus lactis subsp. cremoris CNCM I-1631,Streptococcus thermophilus DN001147,Streptococcus thermophilus CNCM I-1630,Bifidobacterium animalis subsp. lactis CNCM I-2494
rRNA-depleted total RNA
RNA isolated from the feces of a human subject (subject F5T1, timepoint "FMP1") who had been consuming 2 servings of a fermented milk product (Danone, Activia) daily for 1 week. Read length is 76 nucleotides.


title: in vitro culture NM1200_InVitro_4_T4t2

description:
Bifidobacterium animalis subsp. lactis CNCM I-2494,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519,Lactococcus lactis subsp. cremoris CNCM I-1631,Streptococcus thermophilus CNCM I-1632
rRNA-depleted total RNA
RNA isolated from a fermented milk product (Danone, Activia) at the end of product fermentation (3 hours after initial inoculation of the milk), prior to cooling and packaging.  B. animalis subsp. lactis represents approximately 9% of the total CFUs in these samples.  Biological replicate #3 of 3.

value: fermented milk product


title: 2X2_seed_DAP6_small_RNA_seq

description:
balanced cross
small RNA sequencing

source_name: DAP6 seeds

value: dissected seeds

value: 6 Days After Pollination


title: 2X4_seed_DAP6_small_RNA_seq

description:
imbalanced cross
small RNA sequencing

value: 2x X 4x


title: 4X2_seed_DAP6_small_RNA_seq

description:
imbalanced cross
small RNA sequencing

value: 4x X 2x


title: human feces TSDA5.6

description:
Akkermansia muciniphila ATCC BAA-835,Bacteroides caccae ATCC 43185,Bacteroides thetaiotaomicron VPI-5482,Bacteroides vulgatus ATCC 8482,Bifidobacterium longum NCC2705,Bifidobacterium longum DJO10A,Bifidobacterium adolescentis ATCC 15703,Bacteroides fragilis YCH46,Bacteroides fragilis NCTC 9343,Bacteroides ovatus ATCC 8483,Bacteroides uniformis ATCC 8492,Blautia hydrogenotrophica DSM 10507,Bryantella formatexigens DSM 14469,Clostridium scindens ATCC 35704,Clostridium spiroforme DSM 1552,Collinsella aerofaciens ATCC 25986,Dorea longicatena DSM 13814,Escherichia coli str. K-12 substr. MG1655,Eubacterium eligens ATCC 27750,Eubacterium rectale ATCC 33656,Faecalibacterium prausnitzii A2-165,Faecalibacterium prausnitzii M21/2,Helicobacter pylori HPAG1,Lactobacillus reuteri DSM 20016,Methanobrevibacter smithii ATCC 35061,Methanosphaera stadtmanae DSM 3091,Parabacteroides distasonis ATCC 8503,Lactococcus lactis subsp. lactis Il1403,Streptococcus thermophilus LMG 18311,Streptococcus thermophilus CNRZ1066,Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842,Lactobacillus casei ATCC 334,Lactococcus lactis subsp. cremoris SK11,Streptococcus thermophilus LMD-9,Lactococcus lactis subsp. cremoris MG1363,Escherichia fergusonii ATCC 35469,Bifidobacterium animalis subsp. lactis AD011,Ruminococcus obeum ATCC 29174,Ruminococcus torques ATCC 27756,Vibrio cholerae O1 biovar eltor str. N16961 chromosome I,Vibrio cholerae O1 biovar eltor str. N16961 chromosome II,Clostridium bolteae ATCC BAA-613,Clostridium sporogenes ATCC 15579,Bacteroides dorei DSM 17855,Bifidobacterium catenulatum DSM 16992,Clostridium asparagiforme DSM 15981,Bifidobacterium adolescentis L2-32,Alistipes putredinis DSM 17216,Ruminococcus lactaris ATCC 29176,Anaerococcus hydrogenalis DSM 7454,Bifidobacterium angulatum DSM 20098,Catenibacterium mitsuokai DSM 15897,Bacteroides capillosus ATCC 29799,Anaerotruncus colihominis DSM 17241,Coprococcus comes ATCC 27758,Bifidobacterium gallicum DSM 20093,Blautia hansenii DSM 20583,Ruminococcus gnavus ATCC 29149,Anaerofustis stercorihominis DSM 17244,Citrobacter youngae ATCC 29220,Collinsella intestinalis DSM 13280,Bifidobacterium breve DSM 20213,Anaerostipes caccae DSM 14662,Bacteroides coprocola DSM 17136,Butyrivibrio crossotus DSM 2876,Providencia alcalifaciens DSM 30120,Bacteroides cellulosilyticus DSM 14838,Eubacterium ventriosum ATCC 27560,Parabacteroides merdae ATCC 43184,Clostridium sp. L2-50,Eubacterium dolichum DSM 3991,Clostridium leptum DSM 753,Parvimonas micra ATCC 33270,Coprococcus eutactus ATCC 27759,Clostridium bartlettii DSM 16795,Clostridium ramosum DSM 1402,Bacteroides stercoris ATCC 43183,Clostridium sp. SS2/1,Providencia stuartii ATCC 25827,Streptococcus infantarius subsp. infantarius ATCC BAA-102,Bacteroides intestinalis DSM 17393,Bifidobacterium animalis subsp. lactis HN019,Providencia rustigianii DSM 4541,Bifidobacterium pseudocatenulatum DSM 20438,Dorea formicigenerans ATCC 27755,Bacteroides plebeius DSM 17135,Bacteroides eggerthii DSM 20697,Proteus penneri ATCC 35198,Mitsuokella multacida DSM 20544,Clostridium nexile DSM 1787,Bacteroides finegoldii DSM 17565,Collinsella stercoris DSM 13279,Desulfovibrio piger ATCC 29098,Parabacteroides johnsonii DSM 18315,Clostridium hylemonae DSM 15053,Roseburia intestinalis L1-82,Eubacterium biforme DSM 3989,Methanobrevibacter smithii DSM 2374,Methanobrevibacter smithii DSM 2375,Bacteroides fragilis 3_1_12,Bacteroides sp. D1,Prevotella copri DSM 18205,Holdemania filiformis DSM 12042,Providencia rettgeri DSM 1131,Fusobacterium sp. 4_1_13,Shigella sp. D9,Clostridium methylpentosum DSM 5476,Eubacterium hallii DSM 3353,Bacteroides sp. D2,Bacteroides sp. 1_1_6,Fusobacterium varium ATCC 27725,Actinomyces odontolyticus ATCC 17982,Victivallis vadensis ATCC BAA-548,Clostridium hiranonis DSM 13275,Subdoligranulum variabile DSM 15176,Clostridium sp. M62/1,Bacteroides coprophilus DSM 18228,Bacteroides WH2,Bifidobacterium dentium,Bacteroides thetaiotaomicron 3731,Bacteroides thetaiotaomicron 7330,Bacteroides xylanisolvens XB1A,Clostridium symbiosum,Desulfovibrio piger GOR1,Enterobacter cancerogenus,Eubacterium rectale DSM17629,M23A,Ruminococcus bromiiL263,Lactobacillus casei DN114001,Lactobacillus delbrueckii DN100107,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519,Lactococcus lactis subsp. cremoris CNCM I-1631,Streptococcus thermophilus DN001147,Streptococcus thermophilus CNCM I-1630,Bifidobacterium animalis subsp. lactis CNCM I-2494
rRNA-depleted total RNA
RNA isolated from the feces of a human subject (subject F3T1, timepoint "FMP4") who had been consuming 2 servings of a fermented milk product (Danone, Activia) daily for 4 weeks. Read length is 36 nucleotides.


title: human feces TSDA9.3_long

description:
Akkermansia muciniphila ATCC BAA-835,Bacteroides caccae ATCC 43185,Bacteroides thetaiotaomicron VPI-5482,Bacteroides vulgatus ATCC 8482,Bifidobacterium longum NCC2705,Bifidobacterium longum DJO10A,Bifidobacterium adolescentis ATCC 15703,Bacteroides fragilis YCH46,Bacteroides fragilis NCTC 9343,Bacteroides ovatus ATCC 8483,Bacteroides uniformis ATCC 8492,Blautia hydrogenotrophica DSM 10507,Bryantella formatexigens DSM 14469,Clostridium scindens ATCC 35704,Clostridium spiroforme DSM 1552,Collinsella aerofaciens ATCC 25986,Dorea longicatena DSM 13814,Escherichia coli str. K-12 substr. MG1655,Eubacterium eligens ATCC 27750,Eubacterium rectale ATCC 33656,Faecalibacterium prausnitzii A2-165,Faecalibacterium prausnitzii M21/2,Helicobacter pylori HPAG1,Lactobacillus reuteri DSM 20016,Methanobrevibacter smithii ATCC 35061,Methanosphaera stadtmanae DSM 3091,Parabacteroides distasonis ATCC 8503,Lactococcus lactis subsp. lactis Il1403,Streptococcus thermophilus LMG 18311,Streptococcus thermophilus CNRZ1066,Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842,Lactobacillus casei ATCC 334,Lactococcus lactis subsp. cremoris SK11,Streptococcus thermophilus LMD-9,Lactococcus lactis subsp. cremoris MG1363,Escherichia fergusonii ATCC 35469,Bifidobacterium animalis subsp. lactis AD011,Ruminococcus obeum ATCC 29174,Ruminococcus torques ATCC 27756,Vibrio cholerae O1 biovar eltor str. N16961 chromosome I,Vibrio cholerae O1 biovar eltor str. N16961 chromosome II,Clostridium bolteae ATCC BAA-613,Clostridium sporogenes ATCC 15579,Bacteroides dorei DSM 17855,Bifidobacterium catenulatum DSM 16992,Clostridium asparagiforme DSM 15981,Bifidobacterium adolescentis L2-32,Alistipes putredinis DSM 17216,Ruminococcus lactaris ATCC 29176,Anaerococcus hydrogenalis DSM 7454,Bifidobacterium angulatum DSM 20098,Catenibacterium mitsuokai DSM 15897,Bacteroides capillosus ATCC 29799,Anaerotruncus colihominis DSM 17241,Coprococcus comes ATCC 27758,Bifidobacterium gallicum DSM 20093,Blautia hansenii DSM 20583,Ruminococcus gnavus ATCC 29149,Anaerofustis stercorihominis DSM 17244,Citrobacter youngae ATCC 29220,Collinsella intestinalis DSM 13280,Bifidobacterium breve DSM 20213,Anaerostipes caccae DSM 14662,Bacteroides coprocola DSM 17136,Butyrivibrio crossotus DSM 2876,Providencia alcalifaciens DSM 30120,Bacteroides cellulosilyticus DSM 14838,Eubacterium ventriosum ATCC 27560,Parabacteroides merdae ATCC 43184,Clostridium sp. L2-50,Eubacterium dolichum DSM 3991,Clostridium leptum DSM 753,Parvimonas micra ATCC 33270,Coprococcus eutactus ATCC 27759,Clostridium bartlettii DSM 16795,Clostridium ramosum DSM 1402,Bacteroides stercoris ATCC 43183,Clostridium sp. SS2/1,Providencia stuartii ATCC 25827,Streptococcus infantarius subsp. infantarius ATCC BAA-102,Bacteroides intestinalis DSM 17393,Bifidobacterium animalis subsp. lactis HN019,Providencia rustigianii DSM 4541,Bifidobacterium pseudocatenulatum DSM 20438,Dorea formicigenerans ATCC 27755,Bacteroides plebeius DSM 17135,Bacteroides eggerthii DSM 20697,Proteus penneri ATCC 35198,Mitsuokella multacida DSM 20544,Clostridium nexile DSM 1787,Bacteroides finegoldii DSM 17565,Collinsella stercoris DSM 13279,Desulfovibrio piger ATCC 29098,Parabacteroides johnsonii DSM 18315,Clostridium hylemonae DSM 15053,Roseburia intestinalis L1-82,Eubacterium biforme DSM 3989,Methanobrevibacter smithii DSM 2374,Methanobrevibacter smithii DSM 2375,Bacteroides fragilis 3_1_12,Bacteroides sp. D1,Prevotella copri DSM 18205,Holdemania filiformis DSM 12042,Providencia rettgeri DSM 1131,Fusobacterium sp. 4_1_13,Shigella sp. D9,Clostridium methylpentosum DSM 5476,Eubacterium hallii DSM 3353,Bacteroides sp. D2,Bacteroides sp. 1_1_6,Fusobacterium varium ATCC 27725,Actinomyces odontolyticus ATCC 17982,Victivallis vadensis ATCC BAA-548,Clostridium hiranonis DSM 13275,Subdoligranulum variabile DSM 15176,Clostridium sp. M62/1,Bacteroides coprophilus DSM 18228,Bacteroides WH2,Bifidobacterium dentium,Bacteroides thetaiotaomicron 3731,Bacteroides thetaiotaomicron 7330,Bacteroides xylanisolvens XB1A,Clostridium symbiosum,Desulfovibrio piger GOR1,Enterobacter cancerogenus,Eubacterium rectale DSM17629,M23A,Ruminococcus bromiiL263,Lactobacillus casei DN114001,Lactobacillus delbrueckii DN100107,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519,Lactococcus lactis subsp. cremoris CNCM I-1631,Streptococcus thermophilus DN001147,Streptococcus thermophilus CNCM I-1630,Bifidobacterium animalis subsp. lactis CNCM I-2494
rRNA-depleted total RNA
RNA isolated from the feces of a human subject (subject F5T1, timepoint "Pre1") 1 week prior to their first consumption of a fermented milk product (Danone, Activia). Read length is 76 nucleotides.


title: 4X4_seed_DAP6_small_RNA_seq

description:
balanced cross
small RNA sequencing

value: 4x X 4x


title: human feces TSDA2.3

description:
Akkermansia muciniphila ATCC BAA-835,Bacteroides caccae ATCC 43185,Bacteroides thetaiotaomicron VPI-5482,Bacteroides vulgatus ATCC 8482,Bifidobacterium longum NCC2705,Bifidobacterium longum DJO10A,Bifidobacterium adolescentis ATCC 15703,Bacteroides fragilis YCH46,Bacteroides fragilis NCTC 9343,Bacteroides ovatus ATCC 8483,Bacteroides uniformis ATCC 8492,Blautia hydrogenotrophica DSM 10507,Bryantella formatexigens DSM 14469,Clostridium scindens ATCC 35704,Clostridium spiroforme DSM 1552,Collinsella aerofaciens ATCC 25986,Dorea longicatena DSM 13814,Escherichia coli str. K-12 substr. MG1655,Eubacterium eligens ATCC 27750,Eubacterium rectale ATCC 33656,Faecalibacterium prausnitzii A2-165,Faecalibacterium prausnitzii M21/2,Helicobacter pylori HPAG1,Lactobacillus reuteri DSM 20016,Methanobrevibacter smithii ATCC 35061,Methanosphaera stadtmanae DSM 3091,Parabacteroides distasonis ATCC 8503,Lactococcus lactis subsp. lactis Il1403,Streptococcus thermophilus LMG 18311,Streptococcus thermophilus CNRZ1066,Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842,Lactobacillus casei ATCC 334,Lactococcus lactis subsp. cremoris SK11,Streptococcus thermophilus LMD-9,Lactococcus lactis subsp. cremoris MG1363,Escherichia fergusonii ATCC 35469,Bifidobacterium animalis subsp. lactis AD011,Ruminococcus obeum ATCC 29174,Ruminococcus torques ATCC 27756,Vibrio cholerae O1 biovar eltor str. N16961 chromosome I,Vibrio cholerae O1 biovar eltor str. N16961 chromosome II,Clostridium bolteae ATCC BAA-613,Clostridium sporogenes ATCC 15579,Bacteroides dorei DSM 17855,Bifidobacterium catenulatum DSM 16992,Clostridium asparagiforme DSM 15981,Bifidobacterium adolescentis L2-32,Alistipes putredinis DSM 17216,Ruminococcus lactaris ATCC 29176,Anaerococcus hydrogenalis DSM 7454,Bifidobacterium angulatum DSM 20098,Catenibacterium mitsuokai DSM 15897,Bacteroides capillosus ATCC 29799,Anaerotruncus colihominis DSM 17241,Coprococcus comes ATCC 27758,Bifidobacterium gallicum DSM 20093,Blautia hansenii DSM 20583,Ruminococcus gnavus ATCC 29149,Anaerofustis stercorihominis DSM 17244,Citrobacter youngae ATCC 29220,Collinsella intestinalis DSM 13280,Bifidobacterium breve DSM 20213,Anaerostipes caccae DSM 14662,Bacteroides coprocola DSM 17136,Butyrivibrio crossotus DSM 2876,Providencia alcalifaciens DSM 30120,Bacteroides cellulosilyticus DSM 14838,Eubacterium ventriosum ATCC 27560,Parabacteroides merdae ATCC 43184,Clostridium sp. L2-50,Eubacterium dolichum DSM 3991,Clostridium leptum DSM 753,Parvimonas micra ATCC 33270,Coprococcus eutactus ATCC 27759,Clostridium bartlettii DSM 16795,Clostridium ramosum DSM 1402,Bacteroides stercoris ATCC 43183,Clostridium sp. SS2/1,Providencia stuartii ATCC 25827,Streptococcus infantarius subsp. infantarius ATCC BAA-102,Bacteroides intestinalis DSM 17393,Bifidobacterium animalis subsp. lactis HN019,Providencia rustigianii DSM 4541,Bifidobacterium pseudocatenulatum DSM 20438,Dorea formicigenerans ATCC 27755,Bacteroides plebeius DSM 17135,Bacteroides eggerthii DSM 20697,Proteus penneri ATCC 35198,Mitsuokella multacida DSM 20544,Clostridium nexile DSM 1787,Bacteroides finegoldii DSM 17565,Collinsella stercoris DSM 13279,Desulfovibrio piger ATCC 29098,Parabacteroides johnsonii DSM 18315,Clostridium hylemonae DSM 15053,Roseburia intestinalis L1-82,Eubacterium biforme DSM 3989,Methanobrevibacter smithii DSM 2374,Methanobrevibacter smithii DSM 2375,Bacteroides fragilis 3_1_12,Bacteroides sp. D1,Prevotella copri DSM 18205,Holdemania filiformis DSM 12042,Providencia rettgeri DSM 1131,Fusobacterium sp. 4_1_13,Shigella sp. D9,Clostridium methylpentosum DSM 5476,Eubacterium hallii DSM 3353,Bacteroides sp. D2,Bacteroides sp. 1_1_6,Fusobacterium varium ATCC 27725,Actinomyces odontolyticus ATCC 17982,Victivallis vadensis ATCC BAA-548,Clostridium hiranonis DSM 13275,Subdoligranulum variabile DSM 15176,Clostridium sp. M62/1,Bacteroides coprophilus DSM 18228,Bacteroides WH2,Bifidobacterium dentium,Bacteroides thetaiotaomicron 3731,Bacteroides thetaiotaomicron 7330,Bacteroides xylanisolvens XB1A,Clostridium symbiosum,Desulfovibrio piger GOR1,Enterobacter cancerogenus,Eubacterium rectale DSM17629,M23A,Ruminococcus bromiiL263,Lactobacillus casei DN114001,Lactobacillus delbrueckii DN100107,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519,Lactococcus lactis subsp. cremoris CNCM I-1631,Streptococcus thermophilus DN001147,Streptococcus thermophilus CNCM I-1630,Bifidobacterium animalis subsp. lactis CNCM I-2494
rRNA-depleted total RNA
RNA isolated from the feces of a human subject (subject F1T2, timepoint "Pre1") 1 week prior to their first consumption of a fermented milk product (Danone, Activia). Read length is 36 nucleotides.


title: human feces TSDA2.9

description:
Akkermansia muciniphila ATCC BAA-835,Bacteroides caccae ATCC 43185,Bacteroides thetaiotaomicron VPI-5482,Bacteroides vulgatus ATCC 8482,Bifidobacterium longum NCC2705,Bifidobacterium longum DJO10A,Bifidobacterium adolescentis ATCC 15703,Bacteroides fragilis YCH46,Bacteroides fragilis NCTC 9343,Bacteroides ovatus ATCC 8483,Bacteroides uniformis ATCC 8492,Blautia hydrogenotrophica DSM 10507,Bryantella formatexigens DSM 14469,Clostridium scindens ATCC 35704,Clostridium spiroforme DSM 1552,Collinsella aerofaciens ATCC 25986,Dorea longicatena DSM 13814,Escherichia coli str. K-12 substr. MG1655,Eubacterium eligens ATCC 27750,Eubacterium rectale ATCC 33656,Faecalibacterium prausnitzii A2-165,Faecalibacterium prausnitzii M21/2,Helicobacter pylori HPAG1,Lactobacillus reuteri DSM 20016,Methanobrevibacter smithii ATCC 35061,Methanosphaera stadtmanae DSM 3091,Parabacteroides distasonis ATCC 8503,Lactococcus lactis subsp. lactis Il1403,Streptococcus thermophilus LMG 18311,Streptococcus thermophilus CNRZ1066,Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842,Lactobacillus casei ATCC 334,Lactococcus lactis subsp. cremoris SK11,Streptococcus thermophilus LMD-9,Lactococcus lactis subsp. cremoris MG1363,Escherichia fergusonii ATCC 35469,Bifidobacterium animalis subsp. lactis AD011,Ruminococcus obeum ATCC 29174,Ruminococcus torques ATCC 27756,Vibrio cholerae O1 biovar eltor str. N16961 chromosome I,Vibrio cholerae O1 biovar eltor str. N16961 chromosome II,Clostridium bolteae ATCC BAA-613,Clostridium sporogenes ATCC 15579,Bacteroides dorei DSM 17855,Bifidobacterium catenulatum DSM 16992,Clostridium asparagiforme DSM 15981,Bifidobacterium adolescentis L2-32,Alistipes putredinis DSM 17216,Ruminococcus lactaris ATCC 29176,Anaerococcus hydrogenalis DSM 7454,Bifidobacterium angulatum DSM 20098,Catenibacterium mitsuokai DSM 15897,Bacteroides capillosus ATCC 29799,Anaerotruncus colihominis DSM 17241,Coprococcus comes ATCC 27758,Bifidobacterium gallicum DSM 20093,Blautia hansenii DSM 20583,Ruminococcus gnavus ATCC 29149,Anaerofustis stercorihominis DSM 17244,Citrobacter youngae ATCC 29220,Collinsella intestinalis DSM 13280,Bifidobacterium breve DSM 20213,Anaerostipes caccae DSM 14662,Bacteroides coprocola DSM 17136,Butyrivibrio crossotus DSM 2876,Providencia alcalifaciens DSM 30120,Bacteroides cellulosilyticus DSM 14838,Eubacterium ventriosum ATCC 27560,Parabacteroides merdae ATCC 43184,Clostridium sp. L2-50,Eubacterium dolichum DSM 3991,Clostridium leptum DSM 753,Parvimonas micra ATCC 33270,Coprococcus eutactus ATCC 27759,Clostridium bartlettii DSM 16795,Clostridium ramosum DSM 1402,Bacteroides stercoris ATCC 43183,Clostridium sp. SS2/1,Providencia stuartii ATCC 25827,Streptococcus infantarius subsp. infantarius ATCC BAA-102,Bacteroides intestinalis DSM 17393,Bifidobacterium animalis subsp. lactis HN019,Providencia rustigianii DSM 4541,Bifidobacterium pseudocatenulatum DSM 20438,Dorea formicigenerans ATCC 27755,Bacteroides plebeius DSM 17135,Bacteroides eggerthii DSM 20697,Proteus penneri ATCC 35198,Mitsuokella multacida DSM 20544,Clostridium nexile DSM 1787,Bacteroides finegoldii DSM 17565,Collinsella stercoris DSM 13279,Desulfovibrio piger ATCC 29098,Parabacteroides johnsonii DSM 18315,Clostridium hylemonae DSM 15053,Roseburia intestinalis L1-82,Eubacterium biforme DSM 3989,Methanobrevibacter smithii DSM 2374,Methanobrevibacter smithii DSM 2375,Bacteroides fragilis 3_1_12,Bacteroides sp. D1,Prevotella copri DSM 18205,Holdemania filiformis DSM 12042,Providencia rettgeri DSM 1131,Fusobacterium sp. 4_1_13,Shigella sp. D9,Clostridium methylpentosum DSM 5476,Eubacterium hallii DSM 3353,Bacteroides sp. D2,Bacteroides sp. 1_1_6,Fusobacterium varium ATCC 27725,Actinomyces odontolyticus ATCC 17982,Victivallis vadensis ATCC BAA-548,Clostridium hiranonis DSM 13275,Subdoligranulum variabile DSM 15176,Clostridium sp. M62/1,Bacteroides coprophilus DSM 18228,Bacteroides WH2,Bifidobacterium dentium,Bacteroides thetaiotaomicron 3731,Bacteroides thetaiotaomicron 7330,Bacteroides xylanisolvens XB1A,Clostridium symbiosum,Desulfovibrio piger GOR1,Enterobacter cancerogenus,Eubacterium rectale DSM17629,M23A,Ruminococcus bromiiL263,Lactobacillus casei DN114001,Lactobacillus delbrueckii DN100107,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519,Lactococcus lactis subsp. cremoris CNCM I-1631,Streptococcus thermophilus DN001147,Streptococcus thermophilus CNCM I-1630,Bifidobacterium animalis subsp. lactis CNCM I-2494
rRNA-depleted total RNA
RNA isolated from the feces of a human subject (subject F1T2, timepoint "Post4") 4 weeks after their completion of a 7-week consumption regimen consisting of two daily servings of a fermented milk product (Danone, Activia).  Read length is 36 nucleotides.


title: human feces TSDA2.2

description:
Akkermansia muciniphila ATCC BAA-835,Bacteroides caccae ATCC 43185,Bacteroides thetaiotaomicron VPI-5482,Bacteroides vulgatus ATCC 8482,Bifidobacterium longum NCC2705,Bifidobacterium longum DJO10A,Bifidobacterium adolescentis ATCC 15703,Bacteroides fragilis YCH46,Bacteroides fragilis NCTC 9343,Bacteroides ovatus ATCC 8483,Bacteroides uniformis ATCC 8492,Blautia hydrogenotrophica DSM 10507,Bryantella formatexigens DSM 14469,Clostridium scindens ATCC 35704,Clostridium spiroforme DSM 1552,Collinsella aerofaciens ATCC 25986,Dorea longicatena DSM 13814,Escherichia coli str. K-12 substr. MG1655,Eubacterium eligens ATCC 27750,Eubacterium rectale ATCC 33656,Faecalibacterium prausnitzii A2-165,Faecalibacterium prausnitzii M21/2,Helicobacter pylori HPAG1,Lactobacillus reuteri DSM 20016,Methanobrevibacter smithii ATCC 35061,Methanosphaera stadtmanae DSM 3091,Parabacteroides distasonis ATCC 8503,Lactococcus lactis subsp. lactis Il1403,Streptococcus thermophilus LMG 18311,Streptococcus thermophilus CNRZ1066,Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842,Lactobacillus casei ATCC 334,Lactococcus lactis subsp. cremoris SK11,Streptococcus thermophilus LMD-9,Lactococcus lactis subsp. cremoris MG1363,Escherichia fergusonii ATCC 35469,Bifidobacterium animalis subsp. lactis AD011,Ruminococcus obeum ATCC 29174,Ruminococcus torques ATCC 27756,Vibrio cholerae O1 biovar eltor str. N16961 chromosome I,Vibrio cholerae O1 biovar eltor str. N16961 chromosome II,Clostridium bolteae ATCC BAA-613,Clostridium sporogenes ATCC 15579,Bacteroides dorei DSM 17855,Bifidobacterium catenulatum DSM 16992,Clostridium asparagiforme DSM 15981,Bifidobacterium adolescentis L2-32,Alistipes putredinis DSM 17216,Ruminococcus lactaris ATCC 29176,Anaerococcus hydrogenalis DSM 7454,Bifidobacterium angulatum DSM 20098,Catenibacterium mitsuokai DSM 15897,Bacteroides capillosus ATCC 29799,Anaerotruncus colihominis DSM 17241,Coprococcus comes ATCC 27758,Bifidobacterium gallicum DSM 20093,Blautia hansenii DSM 20583,Ruminococcus gnavus ATCC 29149,Anaerofustis stercorihominis DSM 17244,Citrobacter youngae ATCC 29220,Collinsella intestinalis DSM 13280,Bifidobacterium breve DSM 20213,Anaerostipes caccae DSM 14662,Bacteroides coprocola DSM 17136,Butyrivibrio crossotus DSM 2876,Providencia alcalifaciens DSM 30120,Bacteroides cellulosilyticus DSM 14838,Eubacterium ventriosum ATCC 27560,Parabacteroides merdae ATCC 43184,Clostridium sp. L2-50,Eubacterium dolichum DSM 3991,Clostridium leptum DSM 753,Parvimonas micra ATCC 33270,Coprococcus eutactus ATCC 27759,Clostridium bartlettii DSM 16795,Clostridium ramosum DSM 1402,Bacteroides stercoris ATCC 43183,Clostridium sp. SS2/1,Providencia stuartii ATCC 25827,Streptococcus infantarius subsp. infantarius ATCC BAA-102,Bacteroides intestinalis DSM 17393,Bifidobacterium animalis subsp. lactis HN019,Providencia rustigianii DSM 4541,Bifidobacterium pseudocatenulatum DSM 20438,Dorea formicigenerans ATCC 27755,Bacteroides plebeius DSM 17135,Bacteroides eggerthii DSM 20697,Proteus penneri ATCC 35198,Mitsuokella multacida DSM 20544,Clostridium nexile DSM 1787,Bacteroides finegoldii DSM 17565,Collinsella stercoris DSM 13279,Desulfovibrio piger ATCC 29098,Parabacteroides johnsonii DSM 18315,Clostridium hylemonae DSM 15053,Roseburia intestinalis L1-82,Eubacterium biforme DSM 3989,Methanobrevibacter smithii DSM 2374,Methanobrevibacter smithii DSM 2375,Bacteroides fragilis 3_1_12,Bacteroides sp. D1,Prevotella copri DSM 18205,Holdemania filiformis DSM 12042,Providencia rettgeri DSM 1131,Fusobacterium sp. 4_1_13,Shigella sp. D9,Clostridium methylpentosum DSM 5476,Eubacterium hallii DSM 3353,Bacteroides sp. D2,Bacteroides sp. 1_1_6,Fusobacterium varium ATCC 27725,Actinomyces odontolyticus ATCC 17982,Victivallis vadensis ATCC BAA-548,Clostridium hiranonis DSM 13275,Subdoligranulum variabile DSM 15176,Clostridium sp. M62/1,Bacteroides coprophilus DSM 18228,Bacteroides WH2,Bifidobacterium dentium,Bacteroides thetaiotaomicron 3731,Bacteroides thetaiotaomicron 7330,Bacteroides xylanisolvens XB1A,Clostridium symbiosum,Desulfovibrio piger GOR1,Enterobacter cancerogenus,Eubacterium rectale DSM17629,M23A,Ruminococcus bromiiL263,Lactobacillus casei DN114001,Lactobacillus delbrueckii DN100107,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519,Lactococcus lactis subsp. cremoris CNCM I-1631,Streptococcus thermophilus DN001147,Streptococcus thermophilus CNCM I-1630,Bifidobacterium animalis subsp. lactis CNCM I-2494
rRNA-depleted total RNA
RNA isolated from the feces of a human subject (subject F1T2, timepoint "Pre2") 2 weeks prior to their first consumption of a fermented milk product (Danone, Activia). Read length is 36 nucleotides.


title: in vitro culture NM1200_InVitro_3_T2t2

description:
Bifidobacterium animalis subsp. lactis CNCM I-2494,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519,Lactococcus lactis subsp. cremoris CNCM I-1631,Streptococcus thermophilus CNCM I-1630
rRNA-depleted total RNA
RNA isolated from a fermented milk product (Danone, Activia) at the end of product fermentation (3 hours after initial inoculation of the milk), prior to cooling and packaging.  B. animalis subsp. lactis represents approximately 9% of the total CFUs in these samples.  Biological replicate #1 of 3.


title: 2X4_leaf_small_RNA_seq

description:
imbalanced cross
small RNA sequencing