title: Basal Region rep BR2

city: Kelowna

first: Michael

middle: K

last: Deyholos

state: British Columbia

address: 1177 Research Road

institute: University of British Columbia, Okanagan

data_processing:
Raw reads from all runs were filtered to remove adapter sequences, contamination, and low-quality reads, and the filtered raw reads were deposited in the SRA archive.
Clean sequencing reads  were mapped to the flax reference genome (downloaded from Phytozome 9 as Lusitatissimum_200.fa) using Tophat2  and the accepted hits were used as input for Cufflinks, with default parameters. The resulting assemblies were merged and with the reference genome annotation (downloaded from Phytozome 9 as Lusitatissimum_200_gene.gff3) with Cuffmerge, and finally Cuffdiff was used to calculate differential transcript abundance between the samples.
Genome_build: Lusitatissimum_200.fa, downloaded from Phytozome v9, as described in Wang et al. 2012 (Plant Journal), and associated Lusitatissimum_200_gene.gff3 file from Phytozome v9
Supplementary_files_format_and_content: cuffdiff output (gene_exp.diff), where expression ratios are log2(BR/AR)

organism: Linum usitatissimum

source_name: stem, no leaves, from 1 cm below apex, to base

growth_protocol: Grown in potting mix in an environmental chamber at 22°C, with a cycle of 16 hours light and 8 hours dark.

extract_protocol:
Samples were manually dissected and frozen immediately, then extracted with RNeasy Micro Kit (Qiagen), and digested with TURBO DNA-free™ Kit (Life Technologies).
oligoDT magnetic beads were used to isolate mRNA, which was used as a template for cDNA sysnthesis primed by random hexamers, followed by adapter ligation, size selection (200bp insert),

treatment_protocol: No special treatments.

value: stem segment (basal)

tag: variety

value: CDC Bethune


title: SF-10-48hr [RMB113]

status: Public on Apr 27 2016

type: SRA

city: Singapore

first: Ahmad Nazri

last: Mohamed Naim

address: 60 Biopolis Street, Genome, #02-01

department: Infectious disease

country: Singapore

institute: Genome institute of Singapore

library_source: transcriptomic

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to CDC1551 (NC_002755) whole genome using CLCgenomics workbench 6.5 with parameters: unspecific match limit = 10, additional upstream bases = 0, count paired reads as two = Yes, minimum exon coverage fraction = 0.2, minimum length fraction (long reads) = 0.9, minimum similarity fraction (long reads) = 0.8
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from CLC genomics workbench 6.5
Genome_build: ASM858v1; CDC1551 (NC002755)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

molecule: total RNA

organism: Mycobacterium tuberculosis CDC1551

source_name: cultured bacteria

growth_protocol: In vitro cultures of M. tuberculosis CDC1551 wildtype strain were grown to mid-log phase.

extract_protocol:
Treated bacterial cells were treated with RNAprotect Bacteria reagent (Qiagen), followed by extraction of total RNA using RNeasy Minikit (Qiagen) according to the manufacturer’s instructions. rRNA was depleted with Ambion’s MICROBExpress Kit (AM1905) as per the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina TRUseq version 2 protocols

treatment_protocol: Bacterial cells were co-incubated with lysosomal soluble fraction at non-inhibitory (10 μg/ml SF, 24hrs), sub-inhibitory (10 μg/ml SF, 48hrs) and inhibitory (20 μg/ml SF, 48hrs)

tag: concentration

value: soluble fraction (SF) 10 ug/ml

tag: time point

value: 48hour exposure


title: SF-20-48hr [RMB114]

value: soluble fraction (SF) 20 ug/ml


title: SF-10-48hr [RMB108]


title: SF-10-24hr [RMB111]

value: 24hour exposure


title: SF-0-48hr [RMB112]

value: soluble fraction (SF) 0 ug/ml


title: 21_Minus

city: Aurora

first: Lee

last: Niswander

state: Colorado

address: 12801 E. 17th Ave Bld RC1 South 12400

department: Pediatrics

country: USA

institute: UC Denver Anschutz Medical Campus

data_processing:
Sequenced reads were mapped to mm9 using Tophat v1.3.2
Transcripts were assembled and FPKM determined using Cufflinks v2.0.2
Genome_build: mm9
Supplementary_files_format_and_content: Cuffdiff analysis was performed to show differences in expression level between non-neural ectoderm (21_Plus, "Value_1)" and remaining neural tissue (21_Minus, "Value 2") samples to identify genes that are significantly enriched in non-neural ectoderm cells.

organism: Mus musculus

source_name: all remaining neural tube cells after removal of non-neural ectoderm

extract_protocol:
embryos were dissected at embryonic day 9.5 and non-neural tube tissue was dissected away. Embryos were dissociated with collagenase IV/Trypsin/EDTA to generate a single cell suspension and treated with DNAse. Cells were FACS sorted into two pools of GFP+ and RFP+ from the live singlet population. RNA was isolated immediately from sorted cells using the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems).
RNA libraries were generated from 1ug total RNA using the TruSeq RNA Sample Preparation Kit from Illumina according to the standard kit protocol

tag: strain

value: mTmG X Grhl3-cre; both C57BL/6 background

tag: developmental stage

value: 21-25 somite embryos


title: ago1-36

city: Beijing

first: xiaofeng

last: cao

address: West Lincui Road, Chaoyang District

department: State Key Laboratory of Plant Genomics

country: China

institute: Institute of Genetics and Developmental Biology

data_processing:
RNA-seq reads were aligned to the Arabidopsis genome (TAIR10) by Tophat (v2.0.11) with default parameters.
Gene expression was measured as reads per kilobase of exon model per million mapped reads (RPKM). GFold (v1.1.2) was used to identify differentially expressed genes (RPKM >5, fold-change >1.5).
Genome_build: TAIR10
Supplementary_files_format_and_content: The tab-delimited text file include RPKM and fold-change (ago1/wt) values for each gene.

organism: Arabidopsis thaliana

source_name: ago1-36 mutant seedlings

growth_protocol: Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates with 3% Sucrose for 12 days at 23°C under standard long-day condition (16 h of light followed by 8 h of darkness), and then were collected for RNA-seq.

extract_protocol:
Total RNAs from wild-type and ago1-36 seedlings were isolated using TRIzol (Invitrogen) following manufacturer’s instructions.
RNA-seq libraries were constructed using SMART approach (Levin et al,2010,Nature Methods).

tag: genotype/variation

value: ago1-36 mutant

tag: tissue

value: seedlings


title: Dmau_TAM16_repE

city: Göttingen

first: Nico

last: Posnien

address: Justus-von-Liebig-Weg 11

department: Department of Developmental Biology

country: Germany

institute: University of Göttingen

description:
Counts_Length_Published_DmauDsim.txt
Counts_Length_Direct_DmauDsim.txt
Counts_Length_Reciprocal_DmauDsim.txt

data_processing:
Illumina Casava1.8.2 software used for basecalling.
100 bp PE RNA-seq reads (from D. mauritiana replicates D, E and F and from D. simulans A, B and C) were split into two 50 bp reads each. Left and right reads were merged into a single fastq file to be equivalent to single-end reads.
Bowtie2 with parameters –very-sensitive-local –N 1 was used to map the RNA-seq reads to the respective references: D. melanogaster reads were mapped to the published CDS set (Flybase, r5.55, only longest transcript) and to our novel reciprocally re-annotated transcript set. D. mauritiana and D. simulans reads were mapped to the respective published transcript sets, to the directly re-annotated transcript sets and to the reciprocally re-annotated transcript sets.
The number of reads mapping to each transcript were summarized using samtools v0.1.19. Transcript length was also obtained using samtools.
Genome_build: This study was perfomed with the aim of showing the bias introduced to differential expression analysis by using non-comparable species-specific mapping references. Therefore the RNA-seq reads were mapped to different transcriptomic references already published or generated in this study. D. melanogaster reads were mapped to the published CDS set (Flybase, r5.55, only longest transcript) and to our novel reciprocally re-annotated transcript set. D. mauritiana and D. simulans reads were mapped to the respective published transcript sets (Nolte, V. et al. 2013 and Hu, T.T. et al. 2013, respectively), to the directly re-annotated transcript sets and to the reciprocally re-annotated transcript sets. All re-annotated references are available upon request.
Supplementary_files_format_and_content: Files are in tab-delimited text format. The row names are the FlyBase ID of all orthologs present in the annotated transcript set for each pair of species (D. mauritiana and D. melanogaster or D. mauritiana and D. simulans). The first three columns contain the raw counts of mapped reads to the D. mauritiana references (replicates A, B and C for the comparison to D. melanogaster and replicates D, E and F for the comparison to D. simulans). Columns four to six contain the raw counts of mapped reads to D. melanogaster or D. simulans references. Column seven contains the length (in bp) of the transcript in the D. mauritiana reference and column eight contains the length (in bp) of the transcript in the D. melanogaster or D. simulans reference.

organism: Drosophila mauritiana

source_name: eye-antennal imaginal disc

growth_protocol: flies were raised at 25ºC and 12h:12h dark/light cycle in density‐controlled conditions (30 freshly hatched LI larvae per vial).

extract_protocol:
Female LIII larvae were dissected and eye-antennal imaginal discs were stored in RNALater at 120 h after egg laying. 40-50 discs were dissected per sample. Total RNA was isolated using the Trizol  and the samples were DNAse I treated in order to remove DNA contamination.
Library preparation for RNA-Seq was performed using the TruSeq RNA Sample Preparation Kit starting from 500 ng of total RNA. Accurate quantitation of cDNA libraries was performed by using the QuantiFluor™dsDNA System . The size range of final cDNA libraries was determined applying the DNA 1000 chip on the Bioanalyzer 2100 from Agilent (280 bp). cDNA libraries were amplified and sequenced by using cBot and HiSeq 2000 (Illumina):single-end reads were generated for D. mauritiana (replicates A, B and C) and for D. melanogaster samples (1x50 bp) and paired-end reads were generated for D. mauritiana (replicates D, E and F) and for D. simulans samples (2x100 bp).

tag: species

value: Drosophila mauritiana

tag: Sex

value: female

value: late L3 larva

value: eye-antennal imaginal disc


title: Apical Region rep AR4

country: Canada

description: SRR1056624, SRR1056625

source_name: stem, no leaves, apex to 0.5mm below apex

tag: age

value: stem segment (apical)


title: SF-20-48hr [RMB104]


title: M4_Control_line_b_day_3

city: Okazaki

first: Yasuhiro

last: Go

address: 38 Nishigonaka Myodaiji

department: Department of Brain Sciences, Center for Novel Science Initiatives

country: Japan

institute: National Institutes of Natural Sciences

data_processing:
Mouse reference genome was complemented with the human genomic region inserted into GLUD2 transgenic mice to construct a custom reference genome
STAR was used to align the reads to the reference genome with parameters: --outFilterMultimapNmax 1 --outFilterMatchNmin 95 --outFilterMismatchNmax 1 --outFilterIntronMotifs RemoveNoncanonical
Reads per kilobase per million mapped reads (RPKM) was calculated for each gene based on mapping alignments and mouse GENCODE vM1 gene annotation.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each sample

molecule: polyA RNA

source_name: Control, line b, day 3

extract_protocol:
The poly(A)+ RNA fraction was isolated and processed for sequencing
cDNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A human bacterial artificial chromosome containing the GLUD2 gene (RP11-610G22) was linearized by NotI and injected into the male pronucleus of C57Bl/6 mice.

value: Control

tag: line

value: b

value: day 3

value: F

value: prefrontal cortex


title: 21_Plus

source_name: non-neural ectoderm cells


title: Dmau_TAM16_repF


title: Basal Region rep BR1

value: stem segment (basal)

value: CDC Bethune


title: wild-type

source_name: wild type seedlings

value: wild-type


title: SF-0-48hr [RMB102]

value: soluble fraction (SF) 0 ug/ml

value: 48hour exposure


title: Apical Region rep AR3

description: SRR1056622, SRR1056623


title: Dmau_TAM16_repC

description:
Counts_Length_Published_DmauDmel.txt
Counts_Length_Direct_DmauDmel.txt
Counts_Length_Reciprocal_DmauDmel.txt


title: SF-10-48hr [RMB103]

value: soluble fraction (SF) 10 ug/ml


title: SF-0-24hr [RMB110]

value: 24hour exposure


title: SF-20-48hr [RMB109]

value: soluble fraction (SF) 20 ug/ml


title: SF-0-48hr [RMB107]


title: Apical Region rep AR2

description: SRR1056620, SRR1056621


title: SF-10-24hr [RMB101]


title: Dmau_TAM16_repB

value: Drosophila mauritiana

value: female


title: Dmau_TAM16_repA

value: late L3 larva

value: eye-antennal imaginal disc


title: Anaerobic 1

status: Public on Apr 26 2016

city: Palmerston North

first: Christina

last: Moon

address: Tennent Drive

country: New Zealand

institute: AgResearch Ltd

data_processing:
Sequence data from BGI had been filtered to remove reads containing ≥ 10% unreadable bases, ≥ 20% low quality (≤ Q20) bases, adapter contamination or duplicate read-pairs
The quality of reads was assessed by using FastQC (Andrews S, 2010) and any reads with a quality score ≤  Q28 were trimmed using Trim Galore! (Krueger F, 2013 ).
Bowtie 2 (Langmead B & Salzberg SL, 2012) was used with default parameters, to remove any sequence reads aligning to ribosomal RNA, transfer RNA and non-coding RNA sequences.
RNA-Seq reads were mapped to the reference genome using EDGE-Pro (Magoc T, Wood D and Salzberg SL, 2013) ) with default parameters
Differential expression between aerobic and anaerobic environments was identified by using DESeq2 (Love M, Huber W and  Anders S, 2014)
Genome_build: Escherichia coli B str. REL606; NC_012967.1
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample

organism: Escherichia coli

source_name: Cultured cells

growth_protocol: Aerobic and anaerobic cultures were grown in 600 mL aliquots of DM25 and incubated at 37°C with an orbital shaking of 150 RPM and inoculated with 1/100th volume of overnight culture. Aerobic cultures were grown for 9 h while anaerobic cultures were grown for 16 h.

extract_protocol:
RNA was extracted from harvested cultures using a hot lysis buffer and acid phenol-based extraction method and isopropanol precipitation. Following RNA extraction, Turbo DNase (Ambion, USA) was used to treat the samples as per manufacturer’s instructions. Each sample was split into five 20 μL aliquots and two rounds of DNase treatment were performed on each aliquot. Following DNase treatment, RNA samples were purified using the RNeasy Mini kit (Qiagen, Germany) as per the manufacturer’s instructions. For each sample, the DNase-treated aliquots were pooled together before purification. RNA quality was measured using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA) with the RNA 6000 Nano Chip kit according to the manufacturer’s instructions while RNA was quantified using the Quant-iT RNA Assay kit (Life Technologies) and measured on a Qubit® 2.0 fluorometer. RNA was sequenced on the Illumina HiSeq 2000 platform  at BGI (Shenzen, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: growth phase

value: Stationary phase

tag: growth environment

value: Anaerobic


title: Anaerobic 3


title: SF-0-24hr [RMB105]


title: Aerobic 2

value: Aerobic


title: Aerobic 1


title: Aerobic 3


title: Apical Region rep AR1

value: stem segment (apical)


title: Q2

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

data_processing:
Reads were demultiplexed the reads into the different samples
Reads were aligned to the mm10 genome built and the sequences of the External RNA Control Consortium (ERCC) using Tophat (v2.0.10)
RSEM (v1.2.18) was used to quantify transcripts by directly running bowtie (v2.1.0). The quantification was done on gene structures of  RefSeq (mm10). Several transcripts used as spike-ins that were not present in the original gtf and were added.
For the RSEM run, the transcript library was prepared (rsem-prepare-reference) followed by rsem-calculate-expression (--bowtie2 --forward-prob 0 --paired-end).
Trinity’s  script abundance_estimates_to_matrix.pl was used to merge the abundance estimation of the different samples and to obtain TMM normalized FPKM matrix
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include TMM normalized FPKM values for each sample

source_name: RAday4 with mix2

growth_protocol: Embryoid Bodies (Ebs) where generated by plating R1 mouse ES cells into 6cm low cell binding dishes as a single cell suspension (35000cells/ml) in 5ml of mES growth medium without Lif and incubating them for 4 days.

extract_protocol:
RNA was prepared with RNeasy Mini kit (Qiagen)
Mouse IVT spike-in and ERCC mixes were added to the total RNA
1microgram of total RNA was processed using the Illumina TruSeq RNA Sample Preparation Kit v2 protocol and 700ng for the Illumina TruSeq Strand Specific total RNA with RiboZero Gold protocol (Illumina). Libraries were evaluated by Qubit and TapeStation. Sequencing libraries were constructed with barcodes to allow multiplexing of 9 samples on three lanes. Between 39-59 million paired-end 100-bp reads were sequenced per sample on Illumina HiSeq Rapid 2500 instrument using protocols RTA (1.17.21.3) and HCS (2.0.12.0).

treatment_protocol: Four days old Ebs where treated for the next 4 days with 2uM RA (Retinoic Acid, Sigma R2625). Day of RA addition corresponds to the sample name RAday0. Four days RA tratment corresponds to the sample name RAday4.

tag: cell type

value: Embryonic Stem Cells

tag: treatment

value: Day 4 - After the addition of retinoic acid

tag: mix of spikes

tag: ercc


title: R2

source_name: RAday4 with mix3


title: P2

source_name: RAday4 with mix1


title: M2


title: O2

source_name: RAday4 with mix4


title: L2


title: H2

source_name: RAday0 with mix2

value: Day 0 - Before the addition of retinoic acid


title: I2

source_name: RAday0 with mix3


title: PEP CLIPseq replicate input 1

city: New York

first: Hans-Hermann

last: Wessels

address: 101 Avenue of the Americas

institute: New York Genome Center

description: RNAseI-treated, ProteinaseK-treated, rRNA-depleted, size-selected (19-50nt) total RNA

data_processing: none provided by the submitter

organism: Drosophila melanogaster

source_name: S2 cells expressing inducible PEP

growth_protocol: Drosophila S2 cells have been stably transfected with FMO-plasmides retrieved from The Drosophila Genomics Resource Center  (DGRC) (PEP: FMO09119 and CG3800: FMO05319). After transfection, cells have been selected with Hygromycin B Gold solution (Invivogen) for > 5 passages and maintained at a concentration 100 micromolar Hygromycin in ExpressFive SFM medium containing 10% heat-inactivated fetal bovine serum (FBS) and supplemented with L-glutamine and Penicillin-Streptomycin.

extract_protocol:
CLIPseq was performed in biological replicates and was essentially described in (Hafner et al. 2010). Buffers and RNA digest were adapted from (Huppertz et al. 2014). The cell lysate was thawed on ice and RNAseI (333U/ml lysate; 1:333 (v/v)) and TurboDNAse (4U/ml lysate) treated for 3.5min at 37°C and 1100rmp and immediately replaced on ice for >3min. Lysates were cleared by centrifugation at 20,000g at 4°C. Immunoprecipitation (IP) was carried out with monoclonal FlagM2 (SIGMA) coated magnetic proteinG dynabeads (Life) on spin-cleared cell extracts for 2 h at 4ºC. Before IP, 50µl of the cleared lysate was taken, proteinase K treated and used for RNA extraction (Zymo DirectZol RNA-Mini Prep Kit). 2.5µg of this fragmented input total RNA was Ribozero treated. 100ng of rRNA-depleted, radioactively end-labeled input RNA was used to construct CLIP input libraries and resumed to CLIP cloning procedure at the step of 3’adapter ligation and was therefore subjected to the same RNA fragment size selection and adapter ligation procedures (see below).  After IP, CLIP samples were stringently washed 3 times with high salt buffer (1M NaCl). Samples were radioactively end-labeled with γ-32P-ATP (25min at 37°C and 1100rpm) and subsequent addition of 1µl high molar ATP for efficient 5’end phosphorylation. The crosslinked protein-RNA complexes were resolved on a 4-12% NuPAGE gel (Invitrogen). The SDS-PAGE gel was transferred to a nitrocellulose membrane (BioRad) and the protein-RNA complex migrating at an expected molecular weight was excised. RNA was isolated by Proteinase K (Roche) treatment and phenol-chloroform extraction, ligated to 3′ adapter (NNNN-TGGAATTCTCGGGTGCCAAGG) and 5′ adapter (GTTCAGAGTTCTACAGTCCGACGATC-NNNN), reverse transcribed, PCR-amplified (PCR cycles for libraries: PEP_CLIP_R1 und R2 18 x cycles; PEP_INPUT_R1 und R2 10 x cycles; CG3800_CLIP_R1 und R2 14 x cycles, CG3800_INPUT_R1 und R2 10 x cycles), and gel-excised. The amplified PEP cDNA was sequenced on HighSeq2000 (Illumina) with a 1x51 nt cycle. CG3800 cDNA was sequenced on NextSeq500 (Illumina) with 75 cycles single-end high output.
Each CLIP was conducted in a biological replicate including a sized-matched input RNA library.

treatment_protocol: For UV crosslinking, ~700*10e6 (at harvest) lowly passaged cells were cultured in ExpressFive SFM containing 100 microMolar Hygromycin B Gold solution and 300µM CuSO4 (last 18h before harvest) and collected by centrifugation (500×g for 5 min).  Cells were washed once with ice-cold PBS and irradiated on ice at UV 254 nm (400mJ/sqcm) in a Spectrolinker XL-1000. Cross-linked cells were collected by centrifugation at 500×g for 5 min and immediately lysed in NP40 and sodium deoxycholeate (SDC) containing lysis buffer (1ml lysis buffer per 150*10e6 cells) (including RNAse inhibitors), incubated on ice for 10 min, and stored at -80°C.

tag: uv crosslinking

value: 254nm 400mJ/sqcm Spectrolinker

tag: immunoprecipitated protein

value: FLAG/HA-tagged PEP

tag: adapter sequences


title: PEP CLIPseq replicate input 2

value: 3′ adapter (NNNN-TGGAATTCTCGGGTGCCAAGG) and 5′ adapter (GTTCAGAGTTCTACAGTCCGACGATC-NNNN)


title: PEP CLIPseq replicate 2

description: PEP ribonucleoprotein complexes


title: K2


title: F2

source_name: RAday0 with mix4


title: E2


title: SF-0-24hr [RMB100]

source_name: cultured bacteria

tag: concentration

value: soluble fraction (SF) 0 ug/ml

tag: time point


title: G2

source_name: RAday0 with mix1


title: PEP CLIPseq replicate 1

description: PEP ribonucleoprotein complexes


title: S2


title: D2


title: C2


title: Guide Only Control Rep2

city: Boston

first: Emma

middle: Joanna Katharina

last: Kowal

state: MA

address: 3 Blackfan Circle

department: Genetics

institute: Harvard Medical School

data_processing:
Reads were combined from the four different flow cells using a custom script
Reads were aligned to the hg19 UCSC Known Genes annotations using RSEM v1.2.1
Using paired end setting (not strand specific)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file of RSEM output with TPM, Expected counts, FPKM

organism: Homo sapiens

growth_protocol: HEK-293T cells were cultivated in Dulbecco’s Modified Eagle Medium (Life Technologies) with 10% FBS (Life Technologies) and Penicillin/Streptomycin (Life Technologies). Incubator conditions were 37 oC and 5% CO2.

extract_protocol:
Samples were lysed and RNA was extracted using the RNeasy Plus Mini Kit (Qiagen). For each sample, 200 ng of total RNA was polyA selected using Dynabeads mRNA Purification Kit (Life Technologies). The RNA was then DNAse treated with Turbo DNase (Life Technologies) and cleaned up with Agenocourt RNAClean XP Beads (Beckman Coulter).
RNA-Seq Libraries were constructed using Maxima H Minus First Strand Synthesis Kit (ThermoFisher Scientific) with random hexamers and then the NEBNext mRNA Second Strand Synthesis Module (New England Biolabs). The resulting cDNA then went into the Nextera XT DNA Library Prep Kit (Illumina)

treatment_protocol: Cells were transfected with Lipofectamine 2000 (Life Technologies)

tag: cell line


title: Suntag Rep1


title: SAM Rep2


title: SAM Rep1


title: Guide Only Control Rep1


title: Suntag Rep2


title: J2


title: VPR Rep1


title: W-2_15M.fastq

city: Taipei

first: Jeng-Shane

last: Lin

address: No. 1, Sec. 4, Roosevelt Road

department: Plant Biology

country: Taiwan

institute: National Taiwan University

data_processing:
Conventional base-calls
Sanger/Illumina 1.9 encoding was used for sequence quality trimming.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence.
Because limited data are available for the genomic sequences of sweet potato (Ipomoea batatas), the genomic sequences of Ipomoea in NCBI are used to blast sRNA sequencing from these deep sequencing data. In addition, many miRNAs are evolutionarily conserved. Plant miRNAs from mirBase version 16 are also used to blast these sRNA sequencing.

organism: Ipomoea batatas

source_name: sweet potato leaves

growth_protocol: Grown in a controlled environment (16 h/25°C day; 8 h/22°C night; humidity 70%; light 40 µmol photons m−2 s−1)

extract_protocol:
Total RNAs were isolated with Trizol reagent, and then total RNAs were treated with Dnase I
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Plants with six to eight fully developed leaves were used, and the third fully expanded leaves were wounded with tweezers.

tag: cultivar

value: cv. Tainung 57

tag: tissue

value: leaves

value: unwound


title: VP64 Rep2


title: VPR Rep2


title: W+2_15M.fastq

value: wound for 0.5 hour


title: Dmau_TAM16_repD

source_name: eye-antennal imaginal disc

tag: strain

tag: species

value: Drosophila mauritiana

tag: Sex

value: female

tag: developmental stage

value: late L3 larva


title: pold2_RNA_rep2

first: Jinkui

last: Cheng

address: No.2 Yuanmingyuan West Road

institute: China Agricultural University

data_processing:
For ChIP-seq analysis, reads were mapped to the Arabidopsis genome (TAIR10) using bowtie1 (version 0.12.9) allowing two nucleotide mismatches using following parameters: bowtie -q -k 1 -n 2 -l 36 --best -S -p 2. Mapped reads were de-duplicated and sorted by samtools (version 0.1.19-44428cd)  Peaks were found using MACS software (version 1.4.2) using H3 as a background. For H3K27me3 peaks finding in the wild type as an example, the parameters were as follow: macs14  -t WT_K27ME3.sorted.bam –c WT_H3.sorted.bam –f  BAM -g 1.30e+8  -n WT_K27ME3 --shiftsize 73 --pvalue 1e-5 --bw=300 --mfold=10,30
For RNA-seq process, paired-end reads were selected and aligned to the Arabidopsis reference genome (version: TAIR10), using TopHat (v2.1.1) and Cuffdiff (v2.1.1).
For Bisulfite-seq analysis, high-throughput sequencing of the BS-seq library was performed on the Illumina NextSeq 500 System with single-end 75-bp reads. The raw sequence data were demultiplexed and converted to fastq files using bcl2fastq2 Conversion Software (version v2.16.0) under default parameters. Mapping, deduplication, and methylation extraction were performed using bismark software (V0.7.4),of which mapping using bowtie2 (2.0.5) to TAIR10.
Genome_build: tair10

source_name: young seedlings

growth_protocol: Seeds were grown on MS medium plates supplemented with 20 g/L sucrose and 0.8% agar at 22°C under long-day (23 h) illumination

extract_protocol:
Genomic DNAs were extracted from seedlings using the DNeasy Plant Mini Kit (QIAGEN)；total RNAs extracted from seedlings using the RNeasy Plant Mini Kit (QIAGEN)
For ChIP-seq library, a 10-ng quantity of ChIP or input DNA was used to prepare a high-throughput sequencing library. End repair, dA-tailing, adapter ligation, and amplification were carried out using the NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina (E6240, NEB) according to the manufacturer’s protocol. Index primers used for each sample were as follows: ATCACG for WT-H3K27me3, CGATGT for WT-H3K4me3, TTAGGC for WT-H3K9me2, TGACCA for WT-H3, ACAGTG for WT-Input, GCCAAT for pold2-H3K27me3, CAGATC for pold2-H3K4me3, ACTTGA for pold2-H3K9me2, GATCAG for pold2-H3, and TAGCTT for pold2-Input.
For Bisulfite-seq, a 2-μg quantity of genomic DNAs was sonicated (20 cycles of 30 s on, 30 s off, at low intensity) into 200-bp fragments with a Bioruptor (Diagenode, USA), end repaired, 3’-dA-tailed and ligated to methylated adapters. After purification, the ligated DNA fragments were treated with the EZ Methylation-Gold Kit (Zymo Research). The eluted bisulfite-treated DNAs were amplified using barcoded primers for sequencing (CGCTGT for the wild type and ACAGTG for the pold2 mutant)

treatment_protocol: No treatment

value: 10-day-old whole seedlings

tag: ecotype

tag: genotype

value: pold2 mutant


title: pold2_RNA_rep3


title: VP64 Rep1


title: pold2_RNA_rep1


title: WT_RNA_rep3

value: wild type


title: WT_RNA_rep1


title: at-endosperm-BS_replicate1_ler_x_col

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

country: Sweden

institute: SLU

description: Arabidopsis thaliana F1-endosperm of Landsberg-0 (female) crossed with Columbia-0 INT dde-2 (male)

library_source: genomic

data_processing:
ChIP-Seq: Reads were treated as single-ended. Reads passing a quality control and trimmed to 100-bp long were pooled together replicate-wise and mapped to the to the A. thaliana (TAIR10) genome using Bowtie allowing for up to two mismatches. Parental-of-origin alleles were identified by mapping the reads to the TAIR10 for Col and to the Ler-0 genome and not allowing for mismatches. Only reads aligning exclusively to one of the parental genomes were considered as parental specific. Genomic positions in Ler specific reads were converted to TAIR10 genomic coordinates for further analysis using the liftOver tool from UCSC. Reads that changed more than 10% were removed.  Mapped reads were deduplicated and extended to the estimated average length of the genomic fragments (270 bp), coverage was estimated and normalized to 10 millions of reads. ChIP signals were normalized with H3 ChIP by taking the log2 ratio in 50-bp bins across the genome. Enriched regions in any particular histone mark were defined by calculating the log2 ratios in 150-bp bins. These data were standardized and normalized for comparative purposes across samples with a Z score transformation applying a cutoff of z ≥ 1. Enriched regions consisting of bins with low H3 coverage (≤ 1st quartile) and/or situated >150 bp away from another enriched region were not considered.
BS-seq: Reads passing a quality control and trimming  were mapped to the TAIR 10.0 version of the Arabidopsis reference genome with bowtie as implemented in Bismark version 0.7.8, allowing up to two mismatches per read. Alignments were deduplicated using perl scripts. Methylated cytosine-calls were performed using the methylation extractor in Bismark version 0.7.8.
Genome_build: TAIR10
Supplementary_files_format_and_content: <chromosome> <position> <strand> <count_methylated> <count_unmethylated> <C_context> <trinucleotide_context>

molecule: genomic DNA

source_name: AT F1-Endosperm Landsberg x  Columbia

growth_protocol: All seeds were surface sterilized (5% sodium hypochlorite and 0.01% Triton X-100), stratified for 2 days at 4°C and germinated on half-strength Murashige and Skoog medium (1% sucrose) in long-day conditions (16 h light/8 h darkness; 21°C). Plants were transferred to soil after 10 to 12 days and grown under long day conditions.

extract_protocol:
Genomic DNA of INTACT-purified endosperm nuclei from 150-300 mg siliques was purified using MagJET Plant Genomic DNA kit (Thermo Fisher Scientific) and sonicated for 30 cycles (30 sec ON, 30 sec OFF at high power) using a Bioruptor (Diagenode). The bisulfite conversion was done using the EpiTect Fast DNA Bisulfite Kit (Qiagen, city, country) during the library preparation.
Bisulfite libraries were generated using Ovation Ultralow Methyl-Seq Library Systems (NuGEN) following the manufacturer's protocol using 10 g of starting DNA.

treatment_protocol: Material for Ler x Col cross was generated by pollinating pi/- mutants with pollen of Col-0 INT plants.

value: endosperm


title: WT_RNA_rep2


title: at-endosperm-BS_replicate2_col_x_ler

description: Arabidopsis thaliana F1-endosperm of Columbia-0 INT dde-2 (female) crossed with Landsberg-0 (male)

source_name: AT F1-Endosperm Columbia x Landsberg

treatment_protocol: Material for Col x Ler was generated by manually pollinating dde2; INT with pollen of Ler plants.


title: at-endosperm-BS_replicate1_col_x_ler


title: at-endosperm-BS_replicate2_ler_x_col


title: Vnt2_Ribodpl

city: La Jolla

first: Luke

last: Thompson

state: CA

address: 9500 Gilman Dr

institute: UC San Diego

data_processing:
Single-end fastq files were trimmed using Trimmomatic v.0.33 using the parameters ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 (the file TruSeq3-SE.fa contained TruSeq3 indexed and universal adapters as well as poly-A and poly-T sequences).
Reads from each sample were mapped to the Vibrio fischeri ES114 genome (NC_006840.2) using bwa v.0.6.2 (Burrows-Wheeler Aligner) using commands index, aln, and samse, generating SAM files.
SAM files were processed with SAMtools (Li et al., 2009) to generate BAM files.
Number of reads mapping to coding (CDS) and rRNA genes were calculated using the htseq-count command of HTSeq v.0.6.1p1.
Genome_build: Vibrio fischeri ES114 genome (NC_006840.2)
Supplementary_files_format_and_content: Tabular format of processed .csv files contains the following fields: 1. CDS number, 2. VF number, 3. Gene length (bp), 4. Description, 5 to end. CDS count from BWA for each CDS (row) and treatment (column)

organism: Aliivibrio fischeri ES114

source_name: Vented from squid Euprymna scolopes

growth_protocol: Vibrio fischeri ES114 cells were grown in Luria-Bertani salt (LBS) broth (10 g/L tryptone, 5 g/L yeast extract, 20 g/L NaCl) or seawater-based tryptone (SWT) broth (5 g/L tryptone, 3 g/L yeast extract, 0.3% glycerol, 700 mL Instant Ocean (IO; Aquarium Systems, Mentor, OH, USA) at 33-35 ppt, 300 mL water) as indicated, at 28 °C with shaking. Planktonic V. fischeri were generated by culturing to mid-log phase in SWT media, then inoculating filter-sterilized Instant Ocean with approximately 2x108 CFU and allowing the solution to incubate at room temperature (~23 °C) overnight.

extract_protocol:
For cultured bacterial samples, bacteria were grown to OD600 = ~0.5, then collected via centrifugation at 12,000 rpm for 2 min (Eppendorf centrifuge) prior to immediate RNA purification (Zymo micro-RNA prep kit). Planktonic samples were prepared as described above, then collected via centrifugation at 12,000 rpm for 2 min (Eppendorf centrifuge) prior to immediate RNA purification (Zymo micro-RNA prep kit).
Starting with total RNA, ribosomal RNA was removed using the Ribo-Zero Gold Epidemiology Kit (Epicentre), which removed both prokaryotic (Vibrio fischeri) and eukaryotic (Euprymna scolopes) rRNA. Ribo-depleted RNA was then used for library preparation using the TruSeq RNA sample preparation kit (Illumina). Libraries were sequenced using Illumina HiSeq 2500 with high output, V4 chemistry, and 100-bp single-end reads.

treatment_protocol: Freshly hatched juvenile squid were collected into V. fischeri free Instant Ocean from the UW-Madison aquaria facility. Animals were subsequently exposed to approximately 5000 CFU per mL of V. fischeri cells for 3 h, and then transferred to fresh V. fischeri free water. Animals were kept together in batches of approximately 30-35 animals to minimize deviations in colonization between individual animals. After ~36 h, colonization of the animals was verified by checking for bioluminescence using a luminometer (Turner TD 20/20). At approximately 48 h post-colonization, at the end of 12 h of darkness, animals were collected in batches of 100 into 80 mL of filter-sterile Instant Ocean and exposed to light for 15 min to induce venting of their bacterial population. Squid were subsequently removed to fresh water, and the vented bacteria were collected via centrifugation at 12,000 rpm for 10min at room temperature (Sorval centrifuge). The Instant Ocean was then removed, and total RNA was immediately purified (Zymo micro-RNA prep kit). In all cases, total time from initial light exposure to bacterial lysis for RNA purification was <30 min.

tag: medium

value: Vented

tag: total rna input (ng)

tag: ribodepletion

tag: library pcr amplification cycles

tag: replicate


title: Vnt3_Ribodpl

value: Ribo-Zero Gold Epidemiology Kit (Epicentre)


title: at-endosperm-Input_2_replicate_2_col_x_ler

description:
Arabidopsis thaliana F1-endosperm of Columbia-0 INT dde-2 (female) crossed with Landsberg-erecta (male)
none

source_name: AT F1-Endosperm Columbia x  Landsberg

extract_protocol:
INTACT-purified endosperm nuclei from 600-800 mg siliques were cross-linked 8 min with 1% formaldehyde and sonicated in 100 μl of NLB (Nuclei Lysis Buffer, 50 mM Tris-HCl pH8.0, 10 mM EDTA, 1% SDS, supplemented with Complete protease inhibitors) using a Bioruptor (Diagenode). 900 μl of ChIP dilution buffer (1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.0, 167 mM NaCl, containing Complete protease inhibitors (Roche)) was added and chromatin was divided in different aliquots for an overnight incubation with antibodies. The following antibodies were used in this study: anti-Histone H3 (Sigma, #H9289,), anti-H3K27me3 (Millipore, #07-449), H3K9me2 (Diagenode, #C15410060) and H3K27me1 (Diagenode, # C15410045). Antibodies IP were performed using Dynabeads (Invitrogen). DNA elution, de-crosslinking and purification steps were done using the IPure kit (Diagenode).
ChIP-seq libraries were generated using the Microplex Library Preparation kit (Diagenode) following the manufacturer's protocol using 1 ng of starting material.

treatment_protocol: Plant material of the cross combination Col x Ler was generated by manually pollinating dde2; INT with pollen of Ler plants.

tag: antibody

value: none (Input)


title: at-endosperm-Input_2_replicate_1_ler_x_col

description:
Arabidopsis thaliana F1-endosperm of Landsberg-erecta pi-1 (female) crossed with Columbia-0  INT (male)
none

source_name: AT F1-Endosperm Landsberg x Columbia

treatment_protocol: Material for Ler x Col cross was generated by pollinating pi mutants with pollen of Col-0 INT plants.


title: at-leaf-Input_2_replicate_1

description:
Arabidopsis thaliana leaf of Columbia-0
none

source_name: AT F1-Leaf Columbia x Columbia

extract_protocol:
Leaf nuclei extraction was performed using 300 mg starting material. Purified nuclei were sonicated in 100 μl of NLB (Nuclei Lysis Buffer, 50 mM Tris-HCl pH8.0, 10 mM EDTA, 1% SDS, supplemented with Complete protease inhibitors) using a Bioruptor (Diagenode). Afterwards, 900 μl of ChIP dilution buffer (1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.0, 167 mM NaCl, containing Complete protease inhibitors (Roche)) was added and chromatin was divided in different aliquots for an overnight incubation with antibodies. The following antibodies were used in this study: anti-Histone H3 (Sigma, #H9289,), anti-H3K27me3 (Millipore, #07-449), H3K9me2 (Diagenode, #C15410060) and H3K27me1 (Diagenode, # C15410045). Antibodies IP were performed using Dynabeads (Invitrogen). DNA elution, de-crosslinking and purification steps were done using the IPure kit (Diagenode).
ChIP-seq libraries were generated using the Microplex Library Preparation kit (Diagenode) following the manufacturer's protocol using 1 ng of starting material.

treatment_protocol: Leaf material was harvested from 20 day old Col-0 plants by specifically selecting leaf number 5 and 6.

value: leaf


title: at-endosperm-Input_2_replicate_1_col_x_ler


title: at-leaf-Input_1_replicate_2

extract_protocol:
Leaf nuclei extraction was performed using 300 mg starting material. Purified nuclei were sonicated in 100 μl of NLB (Nuclei Lysis Buffer, 50 mM Tris-HCl pH8.0, 10 mM EDTA, 1% SDS, supplemented with Complete protease inhibitors) using a Bioruptor (Diagenode). Afterwards, 900 μl of ChIP dilution buffer (1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.0, 167 mM NaCl, containing Complete protease inhibitors (Roche)) was added and chromatin was divided in different aliquots for an overnight incubation with antibodies. The following antibodies were used in this study: anti-Histone H3 (Sigma, #H9289,), anti-H3K27me3 (Millipore, #07-449), H3K9me2 (Diagenode, #C15410060) and H3K27me1 (Diagenode, # C15410045). Antibodies IP were performed using Dynabeads (Invitrogen). DNA elution, de-crosslinking and purification steps were done using the IPure kit (Diagenode).
ChIP-seq libraries were generated using Ovation Ultralow Library System (NuGEN, San Carlos, USA) using 1 ng of starting material.


title: Swt3_Ribodpl

source_name: SWT rich medium culture

value: SWT


title: at-endosperm-Input_1_replicate_2_col_x_ler


title: at-endosperm-Input_1_replicate_1_ler_x_col

description:
Arabidopsis thaliana F1-endosperm of Landsberg-erecta pi-1 (female) crossed with Columbia-0  INT (male)
h3k9m2_MX_ler_col.peaks_TOTAL.bed
h3k9m2_MX_ler_col.peaks_COL.bed
h3k9m2_MX_ler_col.peaks_LER.bed


title: M9_Control_line_a_day_10

source_name: Control, line a, day 10

tag: genotype/variation

value: Control

tag: line

value: a

tag: age

value: day 10

value: F

value: prefrontal cortex


title: at-endosperm-Input_1_replicate_2_ler_x_col


title: Plk2_Ribodpl

source_name: Planktonic seawater culture

value: Planktonic


title: Plk3_Ribodpl


title: Swt1_Ribodpl


title: Plk1_Ribodpl


title: at-endosperm-Input_1_replicate_1_col_x_ler


title: 1ng_Ribodpl_15cyc

description: Low-biomass test with 1ng total RNA and ribodepletion


title: at-endosperm-H3K9m2_2_replicate_2_col_x_ler

description:
Arabidopsis thaliana F1-endosperm of Columbia-0 INT dde-2 (female) crossed with Landsberg-erecta (male)
h3k9m2_MX_col_ler.peaks_TOTAL.bed
h3k9m2_MX_col_ler.peaks_COL.bed
h3k9m2_MX_col_ler.peaks_LER.bed


title: 1ng_Ribodpl_17cyc

description: Low-biomass test with 1ng total RNA and ribodepletion (2 additional cycles)


title: at-endosperm-H3K9m2_2_replicate_1_col_x_ler


title: at-endosperm-H3K9m2_2_replicate_1_ler_x_col


title: 2ng_Ribodpl_15cyc

description: Low-biomass test with 2.5ng total RNA and ribodepletion


title: 2ng_Ribodpl_17cyc

description: Low-biomass test with 2.5ng total RNA and ribodepletion (2 additional cycles)


title: Vnt1_Ribodpl


title: 5ng_Ribodpl_15cyc

description: Low-biomass test with 5ng total RNA and ribodepletion


title: Swt2_Ribodpl


title: at-leaf-H3K9m2_1_replicate_2

description:
Arabidopsis thaliana leaf of Columbia-0
h3k9m2_MX_col_col_LEAVES.peaks_TOTAL.bed


title: at-leaf-Input_1_replicate_1


title: at-endosperm-H3K9m2_1_replicate_2_ler_x_col


title: CG3800 CLIPseq replicate input 2

source_name: S2 cells expressing inducible CG3800

tag: uv crosslinking

value: 254nm 400mJ/sqcm Spectrolinker

tag: immunoprecipitated protein

value: FLAG/HA-tagged CG3800

tag: adapter sequences

value: 3′ adapter (NNNN-TGGAATTCTCGGGTGCCAAGG) and 5′ adapter (GTTCAGAGTTCTACAGTCCGACGATC-NNNN)


title: 10ng_Ribodpl

description: Low-biomass test with 10ng total RNA and ribodepletion


title: 5ng_Ribodpl_17cyc

description: Low-biomass test with 5ng total RNA and ribodepletion (2 additional cycles)


title: 25ng_Ribodpl

description: Low-biomass test with 25ng total RNA and ribodepletion


title: at-endosperm-H3K27m3_1_replicate_2_ler_x_col

description:
Arabidopsis thaliana F1-endosperm of Landsberg-erecta pi-1 (female) crossed with Columbia-0  INT (male)
h3k27m3_MX_ler_col.peaks_TOTAL.bed
h3k27m3_MX_ler_col.peaks_COL.bed
h3k27m3_MX_ler_col.peaks_LER.bed

tag: tissue


title: at-leaf-H3K9m2_1_replicate_1


title: at-endosperm-H3K27m3_1_replicate_2_leaf

description:
Arabidopsis thaliana leaf of Columbia-0
h3k27m3_MX_col_col_LEAVES.peaks_TOTAL.bed


title: CG3800 CLIPseq replicate input 1

description: RNAseI-treated, ProteinaseK-treated, rRNA-depleted, size-selected (19-50nt) total RNA


title: CG3800 CLIPseq replicate 1

description: CG3800 ribonucleoprotein complexes


title: CG3800 CLIPseq replicate 2

description: CG3800 ribonucleoprotein complexes


title: 50ng_Ribodpl

description: Low-biomass test with 50ng total RNA and ribodepletion


title: at-endosperm-H3K27m3_1_replicate_2_col_x_ler

description:
Arabidopsis thaliana F1-endosperm of Columbia-0 INT dde-2 (female) crossed with Landsberg-erecta (male)
h3k27m3_MX_col_ler.peaks_TOTAL.bed
h3k27m3_MX_col_ler.peaks_COL.bed
h3k27m3_MX_col_ler.peaks_LER.bed


title: pold2_INPUT

value: 10-day-old whole seedlings

value: pold2 mutant


title: at-endosperm-H3K27m3_1_replicate_1_ler_x_col

value: endosperm


title: at-leaf-H3K27m3_1_replicate_1


title: pold2_H3


title: pold2_H3K9me2


title: 100ng_NoRibo

description: Low-biomass test with 100ng total RNA and no ribodepletion

value: no ribodepletion


title: at-endosperm-H3K27m1_2_replicate_2_col_x_ler

description:
Arabidopsis thaliana F1-endosperm of Columbia-0 INT dde-2 (female) crossed with Landsberg-erecta (male)
h3k27m1_MX_col_ler.peaks_TOTAL.bed
h3k27m1_MX_col_ler.peaks_COL.bed
h3k27m1_MX_col_ler.peaks_LER.bed


title: 500ng_NoRibo

description: Low-biomass test with 500ng total RNA and no ribodepletion


title: at-endosperm-H3K27m3_1_replicate_1_col_x_ler


title: 1000ng_NoRibo

description: Low-biomass test with 1000ng total RNA and no ribodepletion


title: pold2_H3K4me3


title: at-endosperm-H3K27m1_2_replicate_1_ler_x_col

description:
Arabidopsis thaliana F1-endosperm of Landsberg-erecta pi-1 (female) crossed with Columbia-0  INT (male)
h3k27m1_MX_ler_col.peaks_TOTAL.bed
h3k27m1_MX_ler_col.peaks_COL.bed
h3k27m1_MX_ler_col.peaks_LER.bed


title: pold2_H3K27me3


title: at-leaf-H3K27m1_2_replicate_1

description:
Arabidopsis thaliana leaf of Columbia-0
h3k27m1_MX_col_col_LEAVES.peaks_TOTAL.bed


title: 6434

city: Nanchang

first: chenlong

last: liu

state: Jiangxi province

address: Lushanzhong street NO.888, Nanchang, China

department: Animal science and technology department

institute: Jiangxi Agricultural University

data_processing:
Illumina GA Pipeline v1.5 software used for basecalling.
Bowtie2_build was used to build a Sscrofa 10.2 genome index file
TopHat was used to align cleaned RNA-seq reads to reference genome to identify alternative splicing with parameters -o -p 20 --microexon-search --library-type fr-unstranded --mate-inner-dist 20 --solexa1.3-quals, Cuffdiff was used to calculate differential expression genes and transcripts with parameters
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: RPKMs

organism: Sus scrofa

source_name: QQ, ear tissue

extract_protocol:
Ear tissues were removed from RNAlater reagent, and total RNA isolated with TRIzol reagent. Illumina HiSeq 2000 was used for RNA-Seq.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Sutai

value: ear

value: new born

value: QQ


title: 6415


title: 6185STQ


title: 1000ng_Ribodpl

description: Low-biomass test with 1000ng total RNA and ribodepletion

value: SWT

value: Ribo-Zero Gold Epidemiology Kit (Epicentre)


title: at-endosperm-H3K27m1_2_replicate_1_col_x_ler

description:
Arabidopsis thaliana F1-endosperm of Columbia-0 INT dde-2 (female) crossed with Landsberg-erecta (male)
h3k27m1_MX_ler_col.peaks_TOTAL.bed
h3k27m1_MX_ler_col.peaks_COL.bed
h3k27m1_MX_ler_col.peaks_LER.bed


title: WT_H3

tag: developmental stage

value: wild type


title: WT_H3K9me2

tag: ecotype


title: 6407

source_name: qq, ear tissue

tag: genotype

value: qq


title: at-endosperm-H3K27m1_1_replicate_2_ler_x_col

description:
Arabidopsis thaliana F1-endosperm of Landsberg-erecta pi-1 (female) crossed with Columbia-0  INT (male)
h3k27m1_MX_col_ler.peaks_TOTAL.bed
h3k27m1_MX_col_ler.peaks_COL.bed
h3k27m1_MX_col_ler.peaks_LER.bed


title: Mated male reproductive tract 1 day after mating [Sample_Male2]

first: Ingrid

last: Curril

state: Niedersachsen

department: Developmental Biology

institute: Georg-August-Universität Göttingen

data_processing:
Sequence images were transformed with Illumina software BaseCaller to bcl files, which were demultiplexed to fastq files with CASAVA v1.8.2. Quality check was done via fastqc (v. 0.10.0, Babraham Bioinformatics).
Raw RNAseq reads were quality filtered with the NGSQC Toolkit. All reads containing ambiguous  reads were removed with 'AmbiguityFiltering.pl'. Next, reads ends were trimmed if phred score was <28 with
TrimmingReads.pl'. Finally, only reads with >95% of the read having a phred score >28 were retained with 'IlluQC_PRLL.pl
Reads were normalized with the 'normalize_by_kmer_coverage.pl' script from the Trinity pipeline.
Normalized reads were then assembled with the Trinity pipeline, all settings default.
For differential expression analysis the 50 bp SE reads were mapped back to the Trinity assembly with the Trinity pipeline, align_and_estimate_abundance.pl
Statistical analysis was performed in R with DESeq
Supplementary_files_format_and_content: Trinity.fasta.gz :gzip compressed fasta file
best_candidates.eclipsed_orfs_removed.pep.gz: all the peptide sequences of the assembly in fasta format.
best_candidates.eclipsed_orfs_removed.cds.gz: all the coding sequences of the assembly in fasta format.
ic_nov2013_table.tsv :read count table, tab separated values

organism: Ceratitis capitata

growth_protocol: Medflies were kept at 28-29 °C with 78% humidity and constant light (24 hours) and reared according to standard laboratory conditions as used in Saul 1982 (DOI: http://dx.doi.org/10.1093/aesa/75.4.480 480-483).

extract_protocol:
Total RNA was extracted with the use of ZR Tissue & Insect RNA MicroPrep Catalog No. R2030, (Zymo Research) according to the manufacturers protocol.
Library preparation for RNA-Seq was performed using the TruSeq RNA Sample Preparation Kit (Illumina, Cat. N°RS-122-2002) starting from 400 ng of total RNA . Accurate quantitation of cDNA libraries was performed by using the QuantiFluor™ dsDNA System (Promega). The size range of final cDNA libraries was determined applying the DNA 1000 chip on the Bioanalyzer 2100 from Agilent (280 bp). cDNA libraries were amplified and sequenced by using the cBot and HiSeq2000 from Illumina (SingleRead; 1x50 bp and 1x100bp).

treatment_protocol: All flies were sexed 1 day after pupa emerging and placed on separate cages to guarantee their virginity prior to their inclusion in the mating assays. Virgin fies were dissected at either 1 day  or 4 days after pupa emerging.  To achieve a once-mated assay, about 400 sexually matured virgin medflies (4 days after pupa emerging) from both sexes were placed on a medium cage (25^3 cm) containing water and normal adult medfly food (sugar/yeast paste). Mating couples that formed were carefully extracted from the cage and placed into small individual conical vials where they stayed connected for at least 60 minutes and were allowed to terminate their copulation naturally. In order to guarantee a once-mating event, after copulation ended, flies were immediately separated by sexes and placed on normal adult rearing cages with food and water.

tag: strain

value: Egypt II wild type

value: testis, male accessory glands

value: 5 day old adult

tag: type


title: Mated male reproductive tract 1 day after mating [Sample_Male3]


title: Mated male reproductive tract 1 day after mating [Sample_Male1]


title: 500ng_Ribodpl

description: Low-biomass test with 500ng total RNA and ribodepletion

tag: medium

tag: total rna input (ng)

tag: ribodepletion


title: at-endosperm-H3_2_replicate_2_col_x_ler

description:
Arabidopsis thaliana F1-endosperm of Columbia-0 INT dde-2 (female) crossed with Landsberg-erecta (male)
none

tag: antibody


title: WT_H3K4me3


title: 6165ST


title: at-endosperm-H3_2_replicate_1_ler_x_col

description:
Arabidopsis thaliana F1-endosperm of Landsberg-erecta pi-1 (female) crossed with Columbia-0  INT (male)
none


title: WT_H3K27me3


title: WT_INPUT


title: Mated female reproductive tract 1 day after mating [Sample_Female5]

value: spermatheca, female accessory glands and uterus


title: at-leaf-H3_2_replicate_1

description:
Arabidopsis thaliana leaf of Columbia-0
none

value: leaf


title: Virgin female lower Reproductive tract 1 day after pupae emerging [Sample_Female3]

value: 4 day old adult


title: Mated female reproductive tract 1 day after mating [Sample_Female4]


title: at-endosperm-H3_2_replicate_1_col_x_ler


title: pold2_bisulfite sequencing

value: 10-day-old whole seedlings

value: pold2 mutant


title: WT_bisulfite sequencing


title: at-endosperm-H3_1_replicate_2_ler_x_col

value: endosperm


title: Mated female reproductive tract 1 day after mating [Sample_Female6]


title: Virgin female lower Reproductive tract 1 day after pupae emerging [Sample_Female1]


title: Virgin Female Gastrointestinal tract [Sample_C3]

source_name: Virgin Female Gastrointestinal tract

value: gastrointestinal tract


title: at-leaf-H3_1_replicate_2


title: Virgin female lower Reproductive tract 1 day after pupae emerging [Sample_Female2]


title: at-endosperm-H3_1_replicate_1_ler_x_col


title: E16.5-WT-UGS

city: Urbana

first: Lisa

middle: J

last: Stubbs

state: IL

address: 1206 West Gregory Drive | MC-195

department: IGB

institute: University of Illinois Urbana-Champaign

data_processing:
Fastq files were generated with the software Casava 1.8.2 (Illumina)
Illumina adapters including barcodes were trimmed using Trimmomatic v0.30
read alignment: Tophat 2.1.0, default parameters
differential expression: Cufflinks 2.2.1, default parameters
Genome_build: mouse NCBI version 37.2
Supplementary_files_format_and_content: Tbx18-E16E18-expressionmatrix.txt: FPKM values for each gene in each sample in a tab-delimited table in .txt format

source_name: urogenital sinus

growth_protocol: Embryos were collected from timed matings at either E16.5 or E18.5 after detection of the copulatory plug.  UGS was collected from embryos identified as mutants (Tbx18Gfp/Gfp) or WT by PCR.

extract_protocol:
Whole urogenital sinuses were dissected from male mouse embryos at embryonic day E16.5 and E18.5. Tissues were homogenized in Trizol and RNA was isolated. RNA was treated with NEB DNase I, then analyzed on a Bioanalyzer for quality.  RNA extracted from three mutant and three WT embryos from each stage were pooled for library construction.
RNA-Seq libraries were prepared with KAPA Biosystems KAPA Stranded mRNA-Seq Kit for Illumina Platform (KR0960 - V2.14).

tag: embryonic stage

value: urogenital sinus


title: E16-Tbx18Gfp/Gfp-UGS


title: Virgin Female Gastrointestinal tract [Sample_C1]


title: E18-Tbx18Gfp/Gfp-UGS


title: Virgin Female Gastrointestinal tract [Sample_C2]


title: E18.5-WT-UGS


title: Mated male reproductive tract 4 days after mating [Sample_MoMa96h]

value: 8 day old adult


title: 6161ST

value: Sutai

value: ear

value: new born


title: at-leaf-H3_1_replicate_1


title: at-endosperm-H3_1_replicate_1_col_x_ler


title: at-endosperm-H3_1_replicate_2_col_x_ler


title: Mated male reproductive tract 1 day after mating [Sample_MoMa24h]

value: wild type


title: 4 month-BPA/DMBA

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

description:
Sample_338_342_MMS_MRU
Basal cell formed spheres.

data_processing:
Libraries were sequenced on an Illumina HiSeq™ 2000 using a standard single-end 50 bp sequencing protocol.
The fastq reads were generated by CASAVA v1.8.2, and those reads with 'Y' in <is filtered> identifier were removed.
The reads were aligned to the reference mouse genome (UCSC build MM9) byTopHat with no more than 2 mismatches allowed in the alignment.
HTseq (http://www-huber.embl.de/users/anders/HTSeq/) was used to count gene expression (reads).
DEseq was used to find differentially expressed genes after performing median normalization. Differential expressed genes were identified with adjusted p-value < 0.05 with Benjamini-Hochberg false discovery controlled and sequence read abundance per gene above 40% within each sample.
Clustering was done by R/heatmap2, and DAVID (http://david.abcc.ncifcrf.gov/home.jsp) was used to determine common and unique functions and processes.
Genome_build: MGSCv37
Supplementary_files_format_and_content: Tab-delimited text files include count values of each gene.

source_name: mammospheres, BPA+DMBA

growth_protocol: Sorted basal cells were cultured in ultralow attachment 96-well plates (Corning) with mouse EpiCult-B medium (150 μL per well) supplemented with 2% B27 (Invitrogen), 20 ng/mL bFGF, 20 ng/mL EGF, 10 µg/mL heparin, 10 µg/mL insulin, 1 µg/mL hydrocortisone, and 50 µg/mL gentamicin for 7 days.

extract_protocol:
Total RNA was isolated using miRNeasy Mini kit (Qiagen, cat #217004).
Sequencing libraries were constructed using the Illumina TruSeq RNA sample preparation protocol (Illumina, Catalog no. RS-122-2002).

treatment_protocol: Balb/C mice of 21 days old were intragastrically gavaged daily with sesame oil (vehicle control) or BPA at 25 μg/kg/day for 3 weeks. Beyond puberty, all mice were continued on low-phytoestrogen diet until the end of the experiment. At 2 months of age, a subgroup of vehicle control and pubertal BPA-treated mice were given a single oral gavage of 7,12-dimethylbenz[a]anthracene (DMBA) at 30 mg/kg. Mammary glands were harvested at 4 months of age for FACS analysis and sorting. Sorted basal cells were then used for mammosphere culture. Spheres were harvested at day 7 for RNA extraction.

tag: strain/background

value: Balb/C

value: 4 months

value: mammary gland

tag: cell type

value: FACS-sorted basal cells

tag: treatment

value: BPA+DMBA


title: 4 month-DMBA

description:
Sample_332_337_MMS_MRU
Basal cell formed spheres.

source_name: mammospheres, DMBA

tag: age

value: DMBA


title: 4 month-Control

description:
Sample_322_326_MMS_MRU
Basal cell formed spheres.

source_name: mammospheres, control

value: control


title: Virgin female reproductive tract 4 days after pupae emerging [Sample_ViFe96h]

value: Egypt II wild type

value: spermatheca, female accessory glands and uterus

value: 4 day old adult


title: Virgin male reproductive tract 4 days after pupae emerging [Sample_ViMa96h]

value: testis, male accessory glands


title: Mated female reproductive tract 1 day after mating [Sample_MoFe24h]

value: 5 day old adult


title: Virgin male reproductive tract 1 day after pupae emerging [Sample_ViMa24h]

value: 1 day old adult


title: Virgin female lower Reproductive tract 1 day after pupae emerging [Sample_ViFe24h]


title: Virgin female gastrointestinal tract control  [Sample_CoFe6uts]

value: gastrointestinal tract


title: S_aureus_TSB

status: Public on Apr 25 2016

city: Tampa

first: Andy

last: Weiss

state: Florida

address: 4202 East Fowler Avenue, ISA2015

department: Department of Cell Biology, Microbiology and Molecular Biology

institute: University of South Florida

description: rRNA-depleted

data_processing:
Raw data files (.fastq) were imported into the CLC Genomics Workbench software platform for analysis
Expression values were caculated using the "RNA-Seq Analysis" function in CLC Genomics Workbench
Expression values were exported into excel files
Genome_build: The genome files used as references for each sample were: S_aureus_TSB: https://dx.doi.org/10.6084/m9.figshare.2061132.v1; S_epidermidis_TSB:  https://dx.doi.org/10.6084/m9.figshare.2072890; S_carnosus_TSB:  https://dx.doi.org/10.6084/m9.figshare.2072890
Supplementary_files_format_and_content: Expression values calculated for small non-coding transcripts are presented as RPKM values in excel format

organism: Staphylococcus aureus

source_name: Bacterial cells, pelleted

growth_protocol: Strains were grown in TSB medium at 37°C with shaking

extract_protocol:
Total bacterial RNA was isolated utilizing the Qiagen RNeasy mini kit and contaminating DNA was removed by treatment with Ambio Turbo DNA-free kit
Library construction was performed using the Ion Total RNA-Seq v2 Kit from Life Technologies

treatment_protocol: Samples were stored at -80°C prior to RNA extraction

value: USA300 Houston

value: wild-type

tag: growth medium

value: TSB

tag: growth conditions (time/temp/shaking)


title: HuR irCLIP - 100K cells - Rep1 and 2

city: Stanford

first: Ryan

middle: Alexander

last: Flynn

address: 380 Roth Way, Room 265

institute: Stanford University

description: library strategy: CLIP-seq

data_processing:
FASTQ files first demultiplexed by sample, PCR duplicates removed, and all adaptor sequences trimmed as previously described (PMID: 25411354).
Processed sequencing reads were mapped to human genome indices, RT stop positions extracted, and replciate experiments intersected to obtain highly reproducible binding sites for further analysis as per FAST-iCLIP (PMID: 25411354)
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files containing RT stops of irCLIP datasets mapped to the hg19 build of the human genome. Add data are normalized to a library depth of 10,000,000 reads.

source_name: HeLa Cells

growth_protocol: HeLa were grown under standard tissue culture conditions

extract_protocol:
Cells were lysed, clarified, and specific RBPs were isolated using antibody enrichment
RNA ligation for library construction was performed on affinity beads and RNA was subsequently transformed into dsDNA libraries using RT, cDNA circularization, and PCR amplification

treatment_protocol: Cells were UV-C crosslinked to fix in vivo RNA-protein interactions

tag: cell line

value: HeLa

value: HuR, Santa Cruz biotechnology N-16, sc-5483


title: hnRNP-C irCLIP - 100K cells - Rep1 and 2

description: library strategy: CLIP-seq

value: hnRNPC, Santa Cruz biotechnology, sc-32308


title: 4 month-BPA

description:
Sample_327_331_MMS_MRU
Basal cell formed spheres.

source_name: mammospheres, BPA

value: Balb/C

value: 4 months

tag: tissue

value: mammary gland

value: FACS-sorted basal cells

value: BPA


title: hnRNP-C irCLIP - 20K cells - Rep1 and 2

description: library strategy: CLIP-seq


title: Xeno_FF_1_Input_1

first: Ramesh

last: Shivdasani

address: 450 Brookline Ave. Dana 720D

department: Medical Oncology

institute: Dana Farber Cancer Institute

data_processing:
Alignment: For ChIPseq experiments we used Bowtie2 (2.1.0) with settings (--no-unal). For RNAseq we used Tophat, version 2.0.9, default options.
For big wiggle generation we used MACS analysis.
RNAseq analyses: normalized and differential expression: Cufflinks, version 2.2.1; settings: -b, -u, and default; Cuffmerge was used with reference gtf and default settings; Cuffquant was used with default settings; Cuffnorm was used with default settings; Cuffdiff was used with -b, -u and default settings.
Supplementary_files_format_and_content: RNAseq: Individual samples have an FPKM gene tracking file from Cufflinks, estimating transcript abundance for that sample, along with confidence intervals.  There are two processed data matrices that apply to all the samples.
Genome_build: Hg19
Supplementary_files_format_and_content: Bigwiggle files

extract_protocol: For ChIPseq:ThruPLEX-FD kits (Rubicon Genomics) was used and 75 bp single-end reads were sequenced on a NextSeq 500 instrument (Illumina). For RNAseq: TruSeq RNA Sample Preparation Kit (Illumina) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

treatment_protocol: 15 sections of 10 μm thickness were scraped into plastic tubes sonicated. DNA libraries were prepared using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a Nextseq 500 instrument (Illumina)

value: Snap-frozen tissue


title: SM_1_FFPE_Input

source_name: Seminoma

treatment_protocol:
sections of 10 Î¼m thickness were scraped into plastic tubes
FiT-Seq protocol was performed and 10 µg Ab was used.

value: FFPE


title: Xeno_FFPE_Input_1


title: SM_3_FFPE_Input


title: CRC_6_FFPE_Input

source_name: Primary colorectal carcinoma


title: CRC_7_FFPE_Input


title: CRC_9_FF_Input

treatment_protocol: sections of 10 μm thickness were scraped into plastic tubes sonicated. DNA libraries were prepared using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a Nextseq 500 instrument (Illumina)


title: CRC_5_FF_Input


title: Mated female reproductive tract 4 days after mating [Sample_MoFe96h]

value: Egypt II wild type

value: spermatheca, female accessory glands and uterus

value: 8 day old adult

value: wild type


title: CRC_4_FFPE_Input


title: SM_2_FFPE_Input


title: CRC_6_FF_Input


title: CRC_3_FFPE_Input


title: CRC_5_FFPE_Input


title: CRC_3_FF_Input


title: CRC_14_FF_Input


title: CRC_2_FF_Input


title: CRC_13_FF_Input


title: CRC_12_FF_Input


title: PTBP1 irCLIP - 100K cells - Rep1 and 2

description: library strategy: CLIP-seq

value: PTBP1, Santa Cruz biotechnology N-20, sc-16547


title: CRC_11_FF_Input


title: CRC_8_FFPE_Input


title: CRC_1_FF_Input


title: CRC_1_FFPE_Input


title: CM_9_FF_Input

description: H3K4me2 bw file in colonic mucosa from patient 9 CRC

source_name: Primary colonic mucosa


title: CM_8_FFPE_Input

description: H3K4me2 bw file in colonic mucosa from patient 8 CRC


title: CM_2_FFPE_Input

description: H3K4me2 bw file in colonic mucosa from patient 2 CRC


title: CM_12_FF_Input

description: H3K4me2 bw file in colonic mucosa from patient 12 CRC


title: CM_7_FFPE_Input

description: H3K4me2 bw file in colonic mucosa from patient 7 CRC


title: CM_6_FFPE_Input

description: H3K4me2 bw file in colonic mucosa from patient 6 CRC


title: CM_11_FF_Input

description: H3K4me2 bw file in colonic mucosa from patient 11 CRC


title: BrCa_3  - FFPE Input

source_name: Primary breast cancer

treatment_protocol: sections of 10 μm thickness were scraped into plastic tubes , FiT-Seq protocol was performed no antibody was used. Libraries were prepared with ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a Nextseq 500 instrument (Illumina)


title: BlCa_6  - FFPE Input

source_name: Primary bladder cancer


title: BrCa_2  - FFPE Input


title: BlCa_2  - FFPE Input


title: BlCa_4  - FFPE Input


title: CM_14_FF_Input

description: H3K4me2 bw file in colonic mucosa from patient 14 CRC


title: BlCa_5  - FFPE Input


title: xeno_48h - FFPE H3K4me2-ChIPseq_PK10

description: MCF7 xenograft FFPE fixed for 48h 10 minutes PK treatment pair end_R1

value: H3K4me2 (Millipore, 07-030)


title: CRC_2_FFPE_Input


title: CRC_4_FF_Input


title: BlCa_3  - FFPE Input


title: xeno_48h - FFPE H3K4me2-ChIPseq

description: MCF7 xenograft FFPE fixed for 48h no PK treatment pair end_R1

treatment_protocol: sections of 10 Î¼m thickness were scraped into plastic tubes , FiT-Seq protocol was performed without PK and 10 µg Ab was used. Libraries were prepared with ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a Nextseq 500 instrument (Illumina)


title: xeno_168h - FFPE H3K4me2-ChIPseq

description: MCF7 xenograft FFPE fixed for 168h no PK treatment single end


title: SM3 - FFPE H3K4me2_ChIPseq

description: H3K4me2 bw file for FFPE SM3


title: xeno - FF H3K4me2-ChIPseq

description: MCF7 xenograft FF (2 samples from pair ended) R1

treatment_protocol: sections of 10 Î¼m thickness were scraped into plastic tubes sonicated, followed by ChIP with 10 µg Ab. DNA libraries were prepared using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a Nextseq 500 instrument (Illumina)


title: SM2 - FFPE H3K4me2_ChIPseq

description: H3K4me2 bw file for FFPE SM2


title: xeno_168h - FFPE H3K4me2-ChIPseq_PK10

description: MCF7 xenograft FFPE fixed for 168h 10 minutes PK treatment pair end_R1


title: CRC8 - FFPE H3K4me2_ChIPseq-rep2

description: H3K4me2 bw file for FFPE CRC8_replicate 2


title: SM1 - FFPE H3K4me2_ChIPseq

description: H3K4me2 bw file for FFPE SM1


title: CM_13_FF_Input

description: H3K4me2 bw file in colonic mucosa from patient 13 CRC


title: CM_10_FF_Input

description: H3K4me2 bw file in colonic mucosa from patient 10 CRC


title: CRC8 - FFPE H3K4me3_ChIPseq

description: H3K4me3 bw file for FFPE CRC8

value: H3K4me3 (Diagenode C15410003)


title: CRC8 - FFPE H3K4me2_ChIPseq-rep1

description: H3K4me2 bw file for FFPE CRC8_replicate 1


title: CRC8 - FFPE H3K36me3_ChIPseq

description: H3K36me3 bw file for FFPE CRC8

value: H3K36me3 (Abcam ab9050)


title: CRC7 - FFPE H3K4me2_ChIPseq

description: H3K4me2 bw file for FFPE CRC7


title: CRC5 - FFPE H3K4me2_ChIPseq

description: H3K4me2 bw file for FFPE CRC4


title: CRC4 - FFPE H3K4me2_ChIPseq-heat

description: H3K4me2 bw file for FFPE CRC4_heating


title: CRC6 - FF H3K4me2_ChIPseq

description: H3K4me2 bw file for FF CRC6


title: CRC4 - FFPE H3K4me2_ChIPseq

description: H3K4me2 bw file for FFPE CRC4_


title: CRC4 - FFPE H3K4me2_ChIPseq-5minPK

description: H3K4me2 bw file for FFPE CRC4_5'PK


title: CRC4 - FF H3K4me2_ChIPseq

description: H3K4me2 bw file for FF CRC4


title: CRC3- FFPE RNAseq

description: FPKM in FFPE CRC 3

treatment_protocol: 5 sections of 10 μm thickness were scraped into plastic tubes and RNA was isolated with trizol


title: CRC3 - FF H3K4me2_ChIPseq

description: H3K4me2 bw file for FF CRC3


title: CRC2 - FFPE RNAseq

description: FPKM in FFPE CRC 2


title: CRC4 - FFPE RNAseq

description: FPKM in FFPE CRC 4


title: CRC3 - FFPE H3K4me2_ChIPseq

description: H3K4me2 bw file for FFPE CRC3


title: CRC2 - FFPE H3K4me2_ChIPseq

description: H3K4me2 bw file for FFPE CRC2


title: CRC2 - FF H3K4me2_ChIPseq

description: H3K4me2 bw file for FF CRC2


title: CRC9 - FF H3K4me2_ChIPseq

description: H3K4me2 bw file for FF CRC9


title: CRC13 - FF H3K4me2_ChIPseq

description: H3K4me2 bw file for FF CRC13

treatment_protocol: DNA libraries were prepared from micrococcal nuclease digested chromatin using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina).


title: CRC14 - FF H3K4me2_ChIPseq

description: H3K4me2 bw file for FF CRC14


title: CRC12 - FF H3K4me2_ChIPseq

description: H3K4me2 bw file for FF CRC12


title: CRC10 - FF H3K4me2_ChIPseq

description: H3K4me2 bw file for FF CRC10


title: CRC11 - FF H3K4me2_ChIPseq

description: H3K4me2 bw file for FF CRC11


title: CRC1 - FFPE H3K4me2_ChIPseq

description: H3K4me2 bw file for FFPE CRC1


title: CRC1 - FF H3K4me2_ChIPseq

description: H3K4me2 bw file for FF CRC1


title: CM9 - FF H3K4me2_ChIPseq

description: H3K4me2 bw file in colonic mucosa from patient 9 CRC


title: CRC6 - FFPE H3K4me2_ChIPseq

description: H3K4me2 bw file for FFPE CRC5


title: CM7 - FFPE H3K4me2-ChIPseq


title: CM8 - FFPE H3K4me2 ChIPseq

description: H3K4me2 bw file in colonic mucosa from patient 8 CRC


title: CRC4 - FFPE H3K4me2_ChIPseq-10minPK

description: H3K4me2 bw file for FFPE CRC4_10'PK


title: CRC5 - FFPE RNAseq

description: FPKM in FFPE CRC 5


title: CM5 - FFPE RNAseq

description: H3K4me2 bw file in colonic mucosa from patient 5 CRC

source_name: Primary colorectal cancer


title: CM6 - FFPE H3K4me2-ChIPseq


title: CRC5 - FF H3K4me2_ChIPseq

description: H3K4me2 bw file for FF CRC5


title: CM5 - FFPE H3K4me2_ChIPseq


title: CM4 - FFPE H3K4me2_ChIPseq

description: H3K4me2 bw file in colonic mucosa from patient 4 CRC


title: CM3 - FFPE H3K4me2-ChIPseq

description: H3K4me2 bw file in colonic mucosa from patient 3 CRC


title: CM3 - FFPE RNAseq


title: CM14 - FF H3K4me2-ChIPseq

description: H3K4me2 in H3K4me2 bw file in colonic mucosa from patient 14 CRC

treatment_protocol: sections of 10 Î¼m thickness were scraped into plastic tubes and treated with 0.2 U micrococcal nuclease (Sigma Aldrich) for 8 min at 37oC, followed by ChIP with 10 µg H3K4me2 Ab. DNA libraries were prepared using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a HiSeq2000 instrument (Illumina)


title: CM4 - FFPE RNAseq


title: SF-10-24hr [RMB106]

city: Singapore

first: Ahmad Nazri

last: Mohamed Naim

address: 60 Biopolis Street, Genome, #02-01

institute: Genome institute of Singapore

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to CDC1551 (NC_002755) whole genome using CLCgenomics workbench 6.5 with parameters: unspecific match limit = 10, additional upstream bases = 0, count paired reads as two = Yes, minimum exon coverage fraction = 0.2, minimum length fraction (long reads) = 0.9, minimum similarity fraction (long reads) = 0.8
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from CLC genomics workbench 6.5
Genome_build: ASM858v1; CDC1551 (NC002755)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: cultured bacteria

extract_protocol:
Treated bacterial cells were treated with RNAprotect Bacteria reagent (Qiagen), followed by extraction of total RNA using RNeasy Minikit (Qiagen) according to the manufacturer’s instructions. rRNA was depleted with Ambion’s MICROBExpress Kit (AM1905) as per the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina TRUseq version 2 protocols

treatment_protocol: Bacterial cells were co-incubated with lysosomal soluble fraction at non-inhibitory (10 μg/ml SF, 24hrs), sub-inhibitory (10 μg/ml SF, 48hrs) and inhibitory (20 μg/ml SF, 48hrs)

tag: concentration

value: soluble fraction (SF) 10 ug/ml

tag: time point

value: 24hour exposure


title: CM2 - FFPE RNAseq

description: H3K4me2 in H3K4me2 bw file in colonic mucosa from patient 2 CRC


title: CM11 - FF H3K4ME2-ChIPseq

description: H3K4me2 in H3K4me2 bw file in colonic mucosa from patient 11 CRC


title: CM12 - FF H3K4me2_ChIPseq

description: H3K4me2 in H3K4me2 bw file in colonic mucosa from patient 12 CRC


title: CM13 - FF H3K4me2 ChIPseq

description: H3K4me2 in H3K4me2 bw file in colonic mucosa from patient 13 CRC


title: BrCa_3 - FFPE H3K4me2_ChIPseq

description: H3K4me2 bw file for FFPE BrCa3


title: BrCa_2 - FFPE H3K4me2_ChIPseq

description: H3K4me2 bw file for FFPE BrCa2


title: BrCa_1 - FFPE H3K4me2_ChIPseq

description: H3K4me2 bw file for FFPE BrCa1


title: BlCa_6 - FFPE H3K4me3_ChIPseq

description: H3K4me3 bw file for FFPE BlCa6


title: BlCa_6 - FFPE H3K9ac_ChIPseq

description: H3K9ac bw file for FFPE BlCa6

value: H3K9ac (Abcam ab4441)


title: BlCa_6 - FFPE H3K36me3_ChIPseq

description: H3K36me3 bw file for FFPE BlCa6


title: BlCa_6 - FFPE H3K4me2_ChIPseq

description: H3K4me2 bw file for FFPE BlCa6


title: CM10 - FF H3K4me2_ChIPseq

description: H3K4me2 in H3K4me2 bw file in colonic mucosa from patient 10 CRC


title: BlCa_5 - FFPE H3K4me2_ChIPseq

description: H3K4me2 bw file for FFPE BlCa5


title: BlCa_6 - FFPE H3K27me3_ChIPseq

description: H3K27me3 bw file for FFPE BlCa6

value: H3K27me3( Cell Signaling C36811)


title: BlCa_4 - FFPE H3K4me2_ChIPseq

description: H3K4me2 bw file for FFPE BlCa4


title: BlCa_3 - FFPE H3K4me2_ChIPseq

description: H3K4me2 bw file for FFPE BlCa3


title: HSV effector memory CD8 T cells, spleen, rep2

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University

description: Spleen_TEM_Sort2_C6GUTANXX_GTCCGCAC_L003_R1

data_processing:
Two or more biological replicates were generated and sequenced for each sample. Sequence reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using the Subread aligner. Only uniquely mapped reads were retained. Genewise counts were obtained using featureCounts. Reads overlapping exons in annotation build 38.1 of NCBI RefSeq database were included.
Genes were filtered from downstream analysis if they failed to achieve a CPM (counts per million mapped reads) value of at least 1 in at least two libraries. Counts were converted to log2 counts per million, quantile normalized and precision weighted with the ‘voom’ function of the limma package.
A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. Genes were called differentially expressed if they achieved a false discovery rate of 0.05 or less and had an expression change of two folds or greater. The called differentially expressed genes must also have at least 8 RPKMs (reads per kilobase of exon length per million mapped reads) in one or both of the two cell types being compared.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized log2-FPKM values for each library. The supplementary file, Supp_Raw_Counts.txt, includes raw read counts for genes in each library.

source_name: HSV effector memory CD8 T cells_spleen

extract_protocol:
RNA purification was performed following the manufacturer's protocol using the RNAeasy Plus Mini Kit (Qiagen).
Libraries were generated using the Illumina Truseq RNA sample preparation kit following manufacturer instructions.

tag: strain background

tag: genotype/variation

value: Wild type

value: Spleen

value: Effector memory CD8 T cells

tag: infection

value: Herpes Simplex Virus (HSV)


title: BlCa_1 - FFPE H3K4me2_ChIPseq

description: H3K4me2 bw file for FFPE BlCa1

value: FFPE


title: BlCa_2 - FFPE H3K4me2_ChIPseq

description: H3K4me2 bw file for FFPE BlCa2


title: CM2 - FFPE H3K4ME2-ChIPseq


title: HSV central memory CD8 T cells, spleen, rep2

description: Spleen_TCM_Sort2_C6GUTANXX_CCGTCCCG_L003_R1

source_name: HSV central memory CD8 T cells_spleen

value: Central memory CD8 T cells


title: HSV tissue-resident memory CD8 T cells, skin, rep2

description: Skin_TRM_Sort2_C6GUTANXX_GTGAAACG_L003_R1

source_name: HSV tissue-resident memory CD8 T cells_skin

value: Skin

value: Tissue-resident memory CD8 T cells


title: HSV central memory CD8 T cells, spleen, rep1

description: Spleen_TCM_Sort1_C6GUTANXX_AGTCAACA_L003_R1


title: Naive CD8 T cells, spleen, rep3

description: Klaas_Sample1_C6GUTANXX_GGCTACAT_L003_R1

source_name: Naïve CD8 T cells_spleen

value: Naive CD8 T cells


title: LCMV nature killer T cells, liver, rep2

source_name: LCMV nature killer T cells_liver

value: Liver

value: Nature killer T cells

value: Lymphocytic Choriomeningitis Virus (LCMV)


title: LCMV tissue-resident nature killer cells, liver, rep2

source_name: LCMV tissue-resident nature killer cells_liver

value: Tissue-resident nature killer cells


title: LCMV conventional nature killer cells, liver, rep2

source_name: LCMV conventional nature killer cells_liver

value: Conventional nature killer cells


title: LCMV tissue-resident memory CD8 T cells, gut, rep2

source_name: LCMV tissue-resident memory CD8 T cells_gut

value: Gut


title: LCMV tissue-resident memory CD8 T cells, liver, rep2

source_name: LCMV tissue-resident memory CD8 T cells_liver


title: LCMV effector memory CD8 T cells, spleen, rep2

source_name: LCMV effector memory CD8 T cells_spleen


title: LCMV central memory CD8 T cells, spleen, rep2

source_name: LCMV central memory CD8 T cells_spleen


title: LCMV effector memory CD8 T cells, liver, rep2

source_name: LCMV effector memory CD8 T cells_liver


title: LCMV nature killer T cells, liver, rep1


title: LCMV tissue-resident memory CD8 T cells, gut, rep1


title: LCMV conventional nature killer cells, liver, rep1


title: LCMV tissue-resident nature killer cells, liver, rep1


title: LCMV tissue-resident memory CD8 T cells, liver, rep1


title: LCMV effector memory CD8 T cells, spleen, rep1


title: LCMV central memory CD8 T cells, spleen, rep1


title: HSV effector memory CD8 T cells, spleen, rep1

description: Spleen_TEM_Sort1_C6GUTANXX_AGTTCCGT_L003_R1


title: LCMV effector memory CD8 T cells, liver, rep1


title: Naive CD8 T cells, spleen, rep1


title: Naive CD8 T cells, spleen, rep4

description: Klaas_Sample2_C6GUTANXX_CTTGTAAT_L003_R1


title: Blimp1/Hobit double knockout rep3

source_name: Blimp1/Hobit double knockout _bone marrow

value: Blimp1/Hobit double knockout

value: Bone marrow

value: CD8 T cells


title: S_carnosus_TSB

description: rRNA-depleted

organism: Staphylococcus carnosus

source_name: Bacterial cells, pelleted

tag: strain

tag: genotype

value: wild-type

value: TSB


title: S_epidermidis_TSB

description: rRNA-depleted

organism: Staphylococcus epidermidis


title: HSV tissue-resident memory CD8 T cells, skin, rep1

description: Skin_TRM_Sort1_C6GUTANXX_ATGTCAGA_L003_R1

value: Wild type

value: Herpes Simplex Virus (HSV)


title: Wild type rep3

source_name: Wild type _bone marrow


title: CoMO_3

city: Aberdeen

first: Stefan

last: Hoppler

address: Foresterhill

department: Institute of Medical Sciences

country: United Kingdom

institute: University of Aberdeen

description: processed data file: CoMO_ucsc.bw

data_processing:
Sequenced reads were checked for the base qualities, trimmed where 20% of the bases are below quality score 20 and filtered sequences that were shorter than 20 bp using Fastx (Version 0.0.13).
Sequences were aligned to the X. tropicalis genome JGI 4.2/xenTro3 with gsnap (Wu and Watanabe, Bioinformatics, 2005).
Aligned reads were counted using HTSeq (version 0.5.4p2).
Genome_build: xenTro3
Supplementary_files_format_and_content: [RNA-seq] tab-delimited text for raw counts; bigWig

organism: Xenopus tropicalis

source_name: early gastrula embryos

growth_protocol: Embryos were raised in 0.1xMMR to early gastrula stage (stage 10.25 according to Nieuwkoop and Faber staging criteria)

extract_protocol:
Total RNA was extracted from whole embryos using RNeasy Mini Kit (QIAGEN, # 74104).
Illumina TruSeq RNA libraries were prepared according to Illumina's instructions using the TruSeq RNA Library Preparation Kit v2.

value: Stage 10.25

tag: experimental condition

value: standard control morpholino-injected


title: wnt8a_MO_3

description: processed data file: wnt8aMO_ucsc.bw

tag: embryonic stage

value: wnt8a morpholino-injected


title: Hobit knockout rep3

source_name: Hobit knockout _bone marrow

value: Hobit knockout


title: Blimp1/Hobit double knockout rep2


title: Hobit knockout rep2


title: Naive CD8 T cells, spleen, rep2

value: Spleen

value: Naive CD8 T cells


title: Blimp1 knockout rep3

source_name: Blimp1 knockout _bone marrow

value: Blimp1 knockout


title: wnt8a_MO-CSKAwnt8a_3

description: processed data file: wnt8aMO-CSKAwnt8a_ucsc.bw

value: wnt8a morpholino and wnt8a-expressing CSKA-wnt8a DNA co-injected


title: Uninjected_3

description: processed data file: Uninjected_ucsc.bw

value: uninjected


title: wnt8a_MO-CSKAwnt8a_2


title: Blimp1 knockout rep2


title: Wild type rep2


title: Blimp1/Hobit double knockout rep1


title: Dmel Input female

first: Friederike

last: Dündar

state: New York

address: 1300 York Ave

department: Physiology & Biophysics

institute: Weill Cornell Medicine

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were aligned to the genome (version dm3 for D. melanogaster samples; version Dvir1.2 for D. virilis samples) using bowtie (v2.0.5) with standard parameters.
Reads with mapping quality < 5 were discarded.10 bp) using the bamCoverage module of the deepTools suite (https://deeptools.github.io; PMID: 247994360
Peak calling was done with MACS2 (v. 2.0.10).
Genome_build: dm3; Dvir1.2
Supplementary_files_format_and_content: Bigwig files were generated using the bamCoverage module of deepTools (https://github.com/fidelram/deepTools), normalizing to 1x coverage with the parameters -f 200 --binSize 10 --normalizeTo1x [158736537 for D.mel | 189205863 for D. vir]

source_name: salivary gland

growth_protocol: Fly strains were reared at room temperature with standard medium. D. virilis stock number (UCSD): 15010-1051.00

extract_protocol: Libraries were prepared according to Illumina's instructions

tag: developmental stage

value: third instar

tag: Sex

value: male


title: wnt8a_MO_2

description: processed data file: wnt8aMO_ucsc.bw


title: CoMO_2

description: processed data file: CoMO_ucsc.bw


title: Blimp1 knockout rep1

value: Bone marrow

tag: cell type


title: Uninjected_2

description: processed data file: Uninjected_ucsc.bw


title: wnt8a_MO_1

description: processed data file: wnt8aMO_ucsc.bw


title: wnt8a_MO-CSKAwnt8a_1


title: Wild type rep1

value: CD8 T cells


title: Uninjected_1

description: processed data file: Uninjected_ucsc.bw


title: CoMO_1

description: processed data file: CoMO_ucsc.bw


title: wt/FVB week 28 replicate 1

city: Minneapolis

first: Christine

middle: M.

last: Henzler

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota, Twin Cities (Minneapolis, MN, US)

description:
cuffdiff_week28_ATXN1.82Q_ATXN1.30Q.D776_WTFVB_gene_exp.diff.txt
cuffnorm_ATXN1.82Q_ATXN1.30Q.D776_WTFVB_genes.fpkm_tracking.txt
cuffdiff_week5_vs_week12_vs_week28_FVB_gene_exp.diff.txt

data_processing:
Reads were aligned to the mouse reference genome (mm10) with Tophat2 (v. 2.0.11)  using all default parametersexcept setting mate inner distance and standard deviation to the data and only looking for junctions in the supplied gene annotation model (--no-novel-juncs setting). The annotation file used was the mm10 gtf file from iGenomes.
Gene expression was quantified using Cuffquant (in Cufflinks v. 2.2.1) using the bias correction (-b) and multi-read correction (-u) settings using the igenomes mm10 gtf file (for differential expression analysis). The inclusion of miRNAs and snoRNAs in the gtf file was later found to distort the PCA analysis, since miRNAs and snoRNAs are not captured completely by a total RNA library preparation and their quantification is consequently distorted in Cuffquant. Gene expression was re-quantified for CuffNorm using the same gtf with miRNAs and snoRNAs removed for the PCA analysis.
CuffDiff  (in Cufflinks v. 2.2.1) was used with default setttings to test for differential expression between samples.
CuffNorm (in Cufflinks v.2.2.1) was used to normalize data across all samples using the default settings except that output was in cuffdiff format
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files provide output of gene_exp.diff.txt files output from CuffDiff for each of the comparisons listed
Supplementary_files_format_and_content: tab-delimited text file gene.fpkm_tracking.txt provides normalized expression data for all genes (miRNAs and snoRNAs removed; see Cuffquant step above)

source_name: cerebellum

growth_protocol: Not applicable

extract_protocol:
Total RNA was isolated from dissected cerebella using TRIzol Reagent (Life Technologies, Carlsbad, California) following the manufacturer’s protocols. Cerebella were homogenized using an RNase-Free Disposable Pellet Pestles in a motorized chuck. For RNA-sequencing, RNA was further purified to remove any organic carryover using the RNeasy Mini Kit (Qiagen, Venlo, Netherlands) following the manufacturer’s RNA Cleanup protocol.
RNA libraries were constructed using standard Illumina protocols.

treatment_protocol: ATXN1[82Q] (Burright et al., 1995), ATXN1[30Q]-D776, ATXN1[82Q]-D776 (Duvick et al., 2010), conditional ATXN1[30Q]-D776 (Ebner et al., 2013), Pcp2-tTA (Zu et al., 2004) and FVB/NJ mice were housed and managed by Research Animal Resources under SPF conditions in an AAALAC-approved facility. Gene-off mice were given 1.5mg/ml doxycycline (dox) (purchased from the University of Minnesota Boynton Health Service Pharmacy) in a 4% sucrose solution in their drinking water. Gene-on animals were given 2% sucrose (to account for sucrose intake) for the same amount of time gene-off mice were administered dox. Pcp2 tTA/+ control mice were administered dox similar to the gene-on cohort. In all experiments involving the use of mice, animals of either sex were used.

value: FVB

value: cerebellum

tag: age

value: 28 weeks

value: wt/FVB


title: ATXN1[30Q]-D776 week 28 replicate 3

description:
cuffdiff_week28_ATXN1.82Q_ATXN1.30Q.D776_WTFVB_gene_exp.diff.txt
cuffnorm_ATXN1.82Q_ATXN1.30Q.D776_WTFVB_genes.fpkm_tracking.txt
cuffdiff_week5_vs_week12_vs_week28_ATXN1.30Q.D776_gene_exp.diff.txt


title: wt/FVB week 28 replicate 3


title: ATXN1[30Q]-D776 week 28 replicate 2


title: ATXN1[30Q]-D776 week 28 replicate 1


title: ATXN1[82Q] week 28 replicate 2

description:
cuffdiff_week28_ATXN1.82Q_ATXN1.30Q.D776_WTFVB_gene_exp.diff.txt
cuffnorm_ATXN1.82Q_ATXN1.30Q.D776_WTFVB_genes.fpkm_tracking.txt
cuffdiff_week5_vs_week12_vs_week28_ATXN1.82Q_gene_exp.diff.txt


title: ATXN1[82Q] week 28 replicate 3


title: ATXN1[82Q] week 28 replicate 1


title: Dmel Input male

source_name: salivary glands

value: female


title: Dmel MSL1 male

extract_protocol:
Chromatin was obtained from male 3rd instar larvae salivary glands as previously described (PMID: 16547175). In brief, collected salivary glands (10 per ChIP) were fixed, sonicated for 8 min (pulsed eight times for 30 sec, paused for 30 sec, high) in a Bioruptor (Cosmo Bio), and chromatin immunoprecipitated with the respective antibody.
Libraries were prepared according to Illumina's instructions

tag: chip antibody

value: polyclonal MSL1 antibody raised against the N-terminus (AA1-584)


title: wt/FVB week 12 replicate 2

description:
cuffdiff_week12_ATXN1.82Q_ATXN1.30Q.D776_WTFVB_gene_exp.diff.txt
cuffnorm_ATXN1.82Q_ATXN1.30Q.D776_WTFVB_genes.fpkm_tracking.txt
cuffdiff_week5_vs_week12_vs_week28_FVB_gene_exp.diff.txt

value: 12 weeks


title: ATXN1[82Q] week 12 replicate 2

description:
cuffdiff_week12_ATXN1.82Q_ATXN1.30Q.D776_WTFVB_gene_exp.diff.txt
cuffnorm_ATXN1.82Q_ATXN1.30Q.D776_WTFVB_genes.fpkm_tracking.txt
cuffdiff_week5_vs_week12_vs_week28_ATXN1.82Q_gene_exp.diff.txt


title: Hobit knockout rep1

value: Hobit knockout


title: ATXN1[82Q] week 12 replicate 1


title: wt/FVB week 12 replicate 1


title: RNA-seq HAF shPTB 6d rep1

first: Xiang-Dong

last: Fu

state: California

address: 9500 Gilman Drive

department: Department of Cellular and Molecular Medicine

institute: University of California, San Diego

data_processing:
Basecalls performed using CASAVA version 1.7
Raw reads were firstly trimmed by the command "fastx_trimmer -f 4 -l 40"
Trimmed reads were mapped to both the humane genome (hg19) and the transcriptome (refseq) using Tophat v2.0.9 with parameters "-G refseq.gtf --segment-length 15 --no-coverage-search"
All accepted hits from tophat were summaried using the function "multicov" in bedtools v2.17.0
The total read count of a gene is the sum of mapped reads to all its exons.
Genome_build: hg19
Supplementary_files_format_and_content: The summary file saves the read counts of mapped reads in each sample.

source_name: RNA-seq HAF shPTB 6d

growth_protocol: Human dermal fibroblasts  were grown in Dulbecco’s Modified Eagle Medium (DMEM)/F12 media (20% FBS, 1X Penicillin/streptomycin) or fibroblast media (DMEM/F12, 5ng/ml of recombinant bFGF, 1ug/ml of hydrocortisone, 50ug/ml of ascorbic acid, 5ug/ml of recombinant human insulin, 2% FBS).

extract_protocol:
Total RNA was extracted with Trizol (Life Technology), except that 10µg/ml of glycogen was used at the precipitation step to enrich for small RNAs
RNA-seq libraries were prepared with MAPS protocol developed by Dr.Xiang-Dong Fu lab

treatment_protocol: For neuronal reprogramming, human adult fibroblasts were first infected with shPTB lentivirus for 16 hrs. After selection with hygromycin B for 3 days, the cells were switched to N3 media (DMEM/F12 plus 25 μg/ml insulin, 50 μg/ml transferring, 30 nM sodium selenite, 20 nM progesterone, 100 nM putrescrine) for two weeks to induce neuronal morphology.

value: human adult fibroblasts (HAFs)

tag: treated with

value: PTB shRNA

value: 6 days after switching to N3 media

tag: barcode

value: ACCA


title: ATXN1[30Q]-D776 week 12 replicate 3

description:
cuffdiff_week12_ATXN1.82Q_ATXN1.30Q.D776_WTFVB_gene_exp.diff.txt
cuffnorm_ATXN1.82Q_ATXN1.30Q.D776_WTFVB_genes.fpkm_tracking.txt
cuffdiff_week5_vs_week12_vs_week28_ATXN1.30Q.D776_gene_exp.diff.txt

tag: tissue


title: RNA-seq HAF shPTB 6d rep2

value: ACGC


title: RNA-seq HAF hygro rep1

source_name: RNA-seq HAF hygro

value: control shRNA

value: 6 days after switching to N3 media without lentivirus

value: AACC


title: ATXN1[30Q]-D776 week 12 replicate 2


title: RNA-seq HAF shPTB 3w rep1

source_name: RNA-seq HAF shPTB 3w

value: 3 weeks after switching to N3 media

value: AGGA


title: RNA-seq HAF hygro rep2

value: AAGG


title: 10C_M6

city: Crawley

first: Mohammed

last: Alsaweed

state: WA

address: 35 stirling hwy

department: Biochemistry

institute: UWA

description:
Small RNA-seq
miRNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Cleaning reads: included getting rid of low-quality reads, reads with 5' primer contaminants, reads without 3' primer, reads without the insert tag, reads with poly A, and reads shorter than 18nt.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Length distribution of all clean reads.
Analysis of base composition and quality.
Map to human genome.
Reads aligned to miRBase 21.0 database.
Novel miRNA prediction.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text file includes reads for each identified SE50 molecule in each Sample.

source_name: Total human milk cells, month 6 of lactation

extract_protocol:
Human milk total cells and lipids were isolated by centrifugation of whole milk, then lipids were purified by further centrifugation. Total cells were washed three times using PBS, total RNA/miRNA was extracted using miRNeasy kit (Qiagen) for cells samples and Exiqon Biofluids kit was used for lipids samples.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: gender

tag: body fluid

value: breast milk

tag: fraction

value: total cell content

tag: collection time

value: during month 6 of lactation (week 20-24)

tag: individual identifier


title: 10F_M2

description:
Small RNA-seq
miRNA

source_name: Human milk lipids, month 2 of lactation

value: female

value: lipids

value: during month 2 of lactation (week 4-8)


title: 10C_M2

description:
Small RNA-seq
miRNA

source_name: Total human milk cells, month 2 of lactation


title: 10F_M6

description:
Small RNA-seq
miRNA

source_name: Human milk lipids, month 6 of lactation


title: 10C_M4

description:
Small RNA-seq
miRNA

source_name: Total human milk cells, month 4 of lactation

value: during month 4 of lactation (week 12-16)


title: 9F_M6

description:
Small RNA-seq
miRNA


title: 9F_M4

description:
Small RNA-seq
miRNA

source_name: Human milk lipids, month 4 of lactation


title: RNA-seq HAF shPTB 3w rep2

value: human adult fibroblasts (HAFs)

value: PTB shRNA

tag: time point

value: AGTC


title: 9C_M4

description:
Small RNA-seq
miRNA


title: 9C_M6

description:
Small RNA-seq
miRNA


title: 8F_M4

description:
Small RNA-seq
miRNA


title: 8C_M4

description:
Small RNA-seq
miRNA


title: 8C_M6

description:
Small RNA-seq
miRNA


title: 8F_M2

description:
Small RNA-seq
miRNA


title: 6F_M6

description:
Small RNA-seq
miRNA


title: 8C_M2

description:
Small RNA-seq
miRNA


title: 7C_M2

description:
Small RNA-seq
miRNA


title: 6C_M6

description:
Small RNA-seq
miRNA


title: 7C_M4

description:
Small RNA-seq
miRNA


title: 6F_M2

description:
Small RNA-seq
miRNA


title: 7C_M6

description:
Small RNA-seq
miRNA


title: 6F_M4

description:
Small RNA-seq
miRNA


title: 8F_M6

description:
Small RNA-seq
miRNA


title: 9F_M2

description:
Small RNA-seq
miRNA


title: 6C_M4

description:
Small RNA-seq
miRNA


title: 5C_M2

description:
Small RNA-seq
miRNA


title: 4F_M6

description:
Small RNA-seq
miRNA


title: 4C_M6

description:
Small RNA-seq
miRNA


title: 4F_M2

description:
Small RNA-seq
miRNA


title: 4C_M4

description:
Small RNA-seq
miRNA


title: 5C_M6

description:
Small RNA-seq
miRNA


title: ATXN1[30Q]-D776 week 12 replicate 1

tag: strain

value: FVB

value: cerebellum

value: 12 weeks

tag: genotype


title: 6C_M2

description:
Small RNA-seq
miRNA


title: 5C_M4

description:
Small RNA-seq
miRNA


title: 4F_M4

description:
Small RNA-seq
miRNA


title: 9C_M2

description:
Small RNA-seq
miRNA


title: 4C_M2

description:
Small RNA-seq
miRNA


title: Dvir Input male replicate B

organism: Drosophila virilis

source_name: third instar larva

value: third instar

value: male


title: Dvir MSL1 male replicate B

extract_protocol:
Inverted 3rd instar larva were fixed, dissolved in RIPA buffer and sonicated 16 x 30 sec using a Branson 250 sonicator at 40 pulse, intensity 5, and chromatin immunoprecipiatet with the respective antibody. (see PMID: 20620954 for details).
Libraries were prepared according to Illumina's instructions

value: polyclonal MSL1 antibody raised against the N-terminus (AA1-265)


title: 3C_M6

description:
Small RNA-seq
miRNA


title: 3C_M2

description:
Small RNA-seq
miRNA


title: 3C_M4

description:
Small RNA-seq
miRNA


title: Dvir Input male replicate A


title: Dmel Input mof2 mutant


title: Dvir MSL1 male replicate A


title: Dmel MSL1 mof2 mutant

value: polyclonal MSL1 antibody raised against the N-terminus (AA1-584)


title: wt/FVB week 28 replicate 2

value: 28 weeks

value: wt/FVB


title: 2C_M4

description:
Small RNA-seq
miRNA

value: breast milk

value: total cell content


title: 2C_M2

description:
Small RNA-seq
miRNA

value: female


title: 1C_M6

description:
Small RNA-seq
miRNA

value: during month 6 of lactation (week 20-24)