title: WT_bio1_sRNA

city: Wuhan

first: Juxun

state: Hubei

address: No.1 of Shizishan street, Hongshan District

institute: Huazhong Agricultral University

data_processing:
For sequencing data of sRNA and degradome, low-quality tags were first filtered, leaving the remanent high-quality tags with no more than four positions with quality score lower than ten and no more than six positions with quality score lower than 13 between the 1st and the 30th nucleotide. Contaminants were further eliminated, including 5’ or 3’ adaptors, tags with no inserted sequence, tags with polyA sequence, tags shorter than 18 nt. Clean sRNA reads were finally obtained after the adaptors having been trimmed. For degradome sequencing result, the same procedure was used to filter out the contaminants. After ncRNAs and polyN sequences (polyA/T/C/G) eliminated, the remaining clean reads were regarded as clean degradome reads.
Genome_build: Citrus sinensis Annotation Project (CAP) (http://citrus.hzau.edu.cn/). Version CsiDB201301, released Jun. 10th, 2013.
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each read

source_name: fruit

growth_protocol: The WT ‘Fengjie 72-1’ orange (C. sinensis L. Osbeck) and its spontaneous late-ripening mutant (MT) ‘Fengwan’ were both cultivated in the same orchard (Fengjie, Chongqing City, China).

extract_protocol:
Approximate 2 to 3 g of powdered material was subjected to each RNA extraction, including 10 mL buffer extraction, 5 mL chloroform-isoamylalcohol extraction (twice), 5 mL isopropanol precipitation, 5 mL 75% ethanol cleaning and RNA purification as described by Camacho-Villasana YM et al.
For Small RNA library, the small RNAs (~18–30 nt) were purified from 10 μg of total RNA by polyacrylamide gel electrophoresis, and ligated first to a 5’ RNA adaptor and then to a 3’ RNA adaptor. A reverse transcription reaction was followed by several cycles of PCR to obtain sufficient product for Sequencing by Synthesis (SBS) sequencing via Solexa technology. For degradome library, poly(A+) RNA molecules were isolated from 200 μg of total RNA using the Oligotex mRNA kit (Qiagen), and then a 5’ RNA oligonucleotide adaptor containing an MmeI recognition site was ligated to the 5’-phosphate of the poly(A+) RNA by T4 RNA ligase. This was followed by purification of the ligated products using the Oligotex kit. Subsequently, five PCR cycles were performed on the products of a reverse transcription reaction which were then digested with MmeI and ligated to a 3’ double DNA adaptor. Finally, the ligation products were amplified with 20 PCR cycles, gel-purified, and subjected to SBS  sequencing by the Illumina sequencer.

value: pulp

tag: development stage

value: 170 DAF

tag: cultivar

value: Fengjie 72-1' navel orange


title: MT_bio2_sRNA

status: Public on Feb 10 2017

type: SRA

last: Wu

country: China

library_source: transcriptomic

molecule: total RNA

organism: Citrus sinensis

tag: tissue

value: Fengwan' navel orange


title: WT_bio2_sRNA


title: P-13

city: Melbourne

first: Nicole

middle: Margaret

last: Haynes

state: Victoria

address: 305 Grattan Street

department: Sir Peter MacCallum Department of Oncology

country: Australia

institute: Peter MacCallum Cancer Centre

description: AU565(pv) tumour bearing SCID mice treated with Panobinostat alone (Panobinostat 15mg/kg days 0,1; PBS days 0)

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Reads were mapped to the mouse reference genome (mm10) using Tophat2 with default parameters.
Counts per gene were obtained using HTSeq with mode intersection-nonempty and Ensembl gtf.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file containing transcript counts for each Sample

organism: Mus musculus

source_name: AU565(pv) human breast tumor xenograft grown in the mammary fat pad of SCID mice

growth_protocol: 1.5x1E6 AU565(pv) tumor cells were injected into the mammary fat pad of SCID mice.  Established tumours (20-25mm2) were treated as outlined below.

extract_protocol:
Whole tumors were mashed and lysed in QIAzol (Qiagen). Total RNA was extracted using a Qiagen miRNeasy Mini Kit and cleaned and concentrated using a Qiagen RNeasy MinElute Cleanup Kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Vehicle and Drug treatments were administered intraperitoneally. Treatment Groups: Vehicle (D5W days 0,1; PBS days 0), Trastuzumab (D5W days 0,1; Trastuzumab 10mg/kg days 0), Panobinostat (Panobinostat 15mg/kg days 0,1; PBS days 0), Panobinostat + Trastuzumab (Panobinostat 15mg/kg days 0,1; Trastuzumab 10mg/kg days 0)

tag: cell type

value: Whole AU565(pv) tumor:human tumour cells, mouse stroma, epithelial cells and immune cells

tag: origin

value: Mammary fat pad AU565(pv) xenograft, harvest 2-days post initiation of drug treatment

tag: strain

value: SCID mice


title: PE-11

description: AU565(pv) tumour bearing SCID mice treated with Panobinostat + Trastuzumab (Panobinostat 15mg/kg days 0,1; Trastuzumab 10mg/kg days 0)


title: C-6

description: AU565(pv) tumour bearing SCID mice treated with Vehicle (D5W days 0,1; PBS days 0)


title: P-7


title: E-15

description: AU565(pv) tumour bearing SCID mice treated with Trastuzumab alone (D5W days 0,1; Trastuzumab 10mg/kg days 0)


title: P-8


title: E-12


title: C-29


title: E-20


title: P-4


title: MT_bio1_sRNA


title: C-21


title: E-24


title: Small RNA cloning of 10-20 nt FLAG-dmDis3l2-CM-associated RNA_32613

city: Vienna

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

country: Austria

institute: IMBA

description: 10-20 nt size selection

data_processing:
The adapter (AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG) was cut once with cutadapt (v1.2.1). The random 4mers on 5' and 3' were removed with fastx_trimmer of the fastx-toolkit (v0.0.13). Summary statistics (length, nt count, nt composition from end) were computed with custom scripts for the range of 7-18nt.
Genome_build: Flybase r5.57
Supplementary_files_format_and_content: TXT (RPM): tab separated text containing 4mer and it's RPM (read per million); TXT (SEQCNT) tab separated text file containing alignment position, feature, tail statistics and count; XLSX: Excel file containing summary statistics (length, nt count, nt count from 3' to 5')

organism: Drosophila melanogaster

source_name: RNA associated with FLAG-dmDi3l2-CM expressed in Drosophila S2 cells

extract_protocol: Immunopurification of FLAG-dmDis3l2-CM o/n in the absence of EDTA, followed by CIP/PNK treatment and size selection of 10-20 nt RNA, RNA then subjected to small RNA cloning according to Reimao-Pinto et al, Molecular Cell, 2016

tag: sample group

tag: genotype/variation

value: stably expressing FLAG-dmDis3l2-CM under Actin5C promoter

tag: molecule subtype

value: RNA associated with dmDis3l2-CM


title: MT_WT_degradome

value: Fengwan' navel orange and 'Fengjie 72-1' navel orange


title: Pax6_sh_H3K4me2_ChIPseq

city: Bronx

first: Ales

last: Cvekl

state: NY

address: 1300 Morris Park Avenue, Ullman 123

department: The Departments Ophthalmology and Visual Sciences, Genetics

country: USA

institute: Albert Einstein College of Medicine

library_source: genomic

data_processing:
The ChIP-seq reads were aligned to the mouse genome (GRCm37/mm9).
Peak detection was performed with the MACS2 and SICER algorithms.
ChIP-seq peak calling: Pax6, Pol2, H3K4me1/2/3 peaks in Ctrl were called using Ctrl_input_ChIPseq as control. H3K4me1/2/3 peaks in Pax6_sh were called using Pax6_sh_input_ChIPseq. H3K4me2 peaks in lens were called using GSM1635083 (lens_input_2).
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: ChIP-seq: Tab-delimited text files include peaks for the samples.

molecule: genomic DNA

source_name: αTN4, Pax6 shRNA, H3K4me2 ChIP

growth_protocol: αTN4 cells were maintained in DMEM F-12 with 10% FBS.

extract_protocol:
ChIP-seq: The newborn (P1) lenses of CD-1 mice (Charles River Laboratories) were dissected, tissue was freshly crosslinked and homogenized. Sonicated lysates were clarified and histone-DNA complexes were isolated with antibody. αTN4 cells were freshly crosslinked and homogenized in the culture dish. Sonicated lysates were clarified and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: αTN4 cells were seeded in 24-well plates one day before infection. Lentivirus containing shRNA construct were added to αTN4 cells cultured in 24-well plate and selected with puromycin for 14 days. The stable cell lines were then maintained in DMEM F-12 with 10% FBS in the presence of puromycin.

tag: cell line

value: lens epithelial cell line

tag: shRNA

tag: chip antibody


title: Pax6_sh_H3K4me1_ChIPseq

source_name: αTN4, Pax6 shRNA, H3K4me1 ChIP


title: Pax6_sh_input_ChIPseq

source_name: αTN4, Pax6 shRNA, input


title: Control RPF

city: Munich

first: Markus

last: Pech

address: 25 Feodor-Lynen Str

department: Biochemistry

country: Germany

institute: Genzentrum, LMU

description: ribosome profiling

data_processing:
Library strategy: Ribo-seq
Demultiplexed reads were clipped for adapter sequences usinf FastX toolkit.
Reads mapping to ribosomal RNA, tRNA, small nuclear and nucleolar RNA were removed. Remaining reads were mapped to the yeast genome (R64-1-1, July19th, 2014) using Tophat(v2.0.8b).
Only unique reads are used for further bio-informatic processes.
Genome_build: sacCer3
Supplementary_files_format_and_content: Processed files contain per nucleotide coverage values generated using bedtools package. Strand specific files with values normalized to per million mapped reads are reported.

organism: Saccharomyces cerevisiae BY4741

source_name: yeast strain expressing C-terminally TAP (tandem affinity purification) tagged Ski3

growth_protocol: Cells were harvested at log phase around OD ~ 0.9 - 1. Harvested cells were immediately resuspended in ice-cold lysis buffer for extraction of the cell lysate.

extract_protocol: Ribosome Profiling (RNAse I digestion, sucrose gradient for collecting 80S fractions, pelleting 80S, splitting 80S and footprint isolation, size selection, end repair, adapter ligation, reverse transcription, circularization and PCR amplification for sequencing). For ribosome profiling of Ski samples, instead of sucrose gradient, 80S were directly pelleted by sucrose cushion after RNAse I digestion.

value: Ski3 TAP tag


title: Ski RNA

description: RNAseq

data_processing:
Demultiplexed reads were clipped for adapter sequences usinf FastX toolkit.
Reads mapping to ribosomal RNA, tRNA, small nuclear and nucleolar RNA were removed. Remaining reads were mapped to the yeast genome (R64-1-1, July19th, 2014) using Tophat(v2.0.8b).
Only unique reads are used for further bio-informatic processes.
Genome_build: sacCer3
Supplementary_files_format_and_content: Processed files contain per nucleotide coverage values generated using bedtools package. Strand specific files with values normalized to per million mapped reads are reported.

extract_protocol: Total RNA from the cell lysate, were extracted using Qiagen miRNA easy kit, followed by depletion of rRNA (ribosomal RNA) using Ribo-Zero rRNA removal kit from Epicentre. After rRNA depletion of the sample, processing of RNA-seq sample is followed as given in ARTseq Ribosome Profiling Kit (Heat fragmentation, end repair, adapter ligation, reverse transcription, circularization and PCR amplification for sequencing). For control RNA, RNA is extracted from cell lysate and for pulldown RNA, RNA is extracted from the Ski3 pulldown fraction.


title: C-3


title: Ctrl_H3K4me3_ChIPseq

source_name: αTN4, control shRNA, H3K4me3 ChIP

value: control


title: Ski RPF

description: ribosome profiling


title: Lens_H3K4me2_ChIPseq

source_name: newborn lens, H3K4me2 ChIP

tag: strain/background

value: newborn lens

tag: age


title: Cloning of total RNA_39892

data_processing:
Only the second read of a pair was used. The random 4mers on the 5' were removed with fastx_trimmer of the fastx-toolkit (v0.0.13). The sequences were reverse complemented. The reads were aligned with tailor (v1.1) with a minimal prefix match length of 18 and a mismatch allowed in the middle of the query. Counts were calculated with htseq-count (v0.6.1p1). The parameters were stranded=yes and  “intersection-nonempty”. A GTF containing the FlyBase r5.57 annotation supplemented with cisNATs and structured loci was used. The pre-miRNA annotation was split in two halves assigned to 5' and 3' of each miRNA region, respectively. Reads with multiple alignments were counted as their fraction to each location/feature. Feature types are summarized by following hierarchy (AS = antisense): mitochondrial mapping, rRNA, rRNA_AS, tRNA, tRNA_AS, pre_miRNA_5p3p, pre_miRNA_5p3p_AS, pre_miRNA, pre_miRNA_AS, transposable_element, transposable_element_AS, __no_feature, cisNATs, cisNATs_AS, structured_loci, structured_loci_AS, pseudogene, pseudogene_AS, ncRNA, ncRNA_AS, snoRNA, snoRNA_AS, snRNA, snRNA_AS, mRNA, mRNA_AS, intron, intron_AS.
Genome_build: Flybase r5.57
Supplementary_files_format_and_content: TXT (RPM): tab separated text containing 4mer and it's RPM (read per million); TXT (SEQCNT) tab separated text file containing alignment position, feature, tail statistics and count; XLSX: Excel file containing summary statistics (length, nt count, nt count from 3' to 5')

source_name: total RNA from Drosophila S2 cells

extract_protocol: Total RNA extracted from Drosophila S2 cells, 3´ adapter ligation and library generation using Lexogen FLEX Kit (Lexogen, Vienna, Austria)

value: Total RNA from Drosophila S2 cells

value: wild type

value: total RNA


title: Ctrl_H3K4me1_ChIPseq

source_name: αTN4, control shRNA, H3K4me1 ChIP


title: Pax6_sh_RNAseq_r

description: Processed data file: αTN4_RNAseq_matrix.diff

data_processing:
The RNA-seq reads were aligned to the mouse genome (GRCm37/mm9) using TopHat (v2).
The Cuffdiff tool in the Cufflinks package (v2) was used to determine RPKM (Reads Per Kb exons per Million mapped reads).
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: RNA-seq: aTN4_RNAseq_matrix.diff: Tab-delimited text files include RPKM.

source_name: αTN4, Pax6 shRNA

extract_protocol:
RNA-seq: αTN4 cells were lysed by Trizol reagent, and total RNA was extracted.
Libraries were prepared according to Illumina's instructions.


title: Ctrl_input_ChIPseq

source_name: αTN4, control shRNA, input


title: CVB2 wt 48h

city: Kalmar

first: Michael

last: Lindberg

address: Smalandsgatan 24

country: Sweden

institute: Linnaeus University

data_processing:
Sequence reads were trimmed with Nesoni clip (v0.115), with adaptors as well as beginnings and ends of quality lower than Q10 (1 error per 10 bases) removed
With TopHat (v2.0.11), the trimmed reads were aligned separately to the human genome, release GRCh37, and the virus genome of CVB2Owt (GenBank accession number AF081485.1)
Using Cufflinks(v2.2.1), reads were assembled into transcripts whose expression was quantified. With Cuffcompare and Cuffdiff, component tools of Cufflinks, expression levels were compared across samples and conditions
Genome_build: GRCh37 (human) and Genbank:AF081485.1 (virus)
Supplementary_files_format_and_content: gene_exp.txt, tab-delimited text file, comparing the FPKM values for genes of each sample to the values of each other sample with statistical data included.  The file is sorted by comparisons with all genotypes represented in either the "sample_1" or "sample_2" column.   Human and virus rna percent 20141023.txt, tab-delimited text file, one line per pair of raw data files, with percentages of number of reads that aligned to the human or virus genomes.

molecule: cytoplasmic RNA

organism:
Homo sapiens
Coxsackievirus B2 (strain Ohio-1)

source_name: rhabdomyosarcoma

growth_protocol: RD cells were maintained in Dulbecco’s modified Eagle’s Medium (Sigma-Aldrich) supplemented with 10 % newborn calf serum, 2 mM L-glutamine, 100 U/ml penicillin and 0.1 mg/ml streptomycin at 37 °C, 5 % CO2

extract_protocol:
Briefly, the cells were washed with PBS and detached from the culturing flask by trypsinization. The trypsin was neutralized with serum and the cells spun down at 300 x g for 5 min, after which the supernatant was removed. The cells were lysed with the RLT buffer and homogenized through the use of QIAshredder spin column (Qiagen). 70 % ethanol was added and the sample was loaded on the RNeasy spin column and successively washed with RW1 and RPE buffer. The RNA was eluted with 50 µl nuclease-free water.
The sequences were clustered using cBot and sequenced on HiSeq2500 (HiSeq Control Software 2.0.12.0/RTA 1.17.21.3) with a 2x101 setup in HighOutput mode. Bcl to Fastq conversion was performed using bcl2Fastq v1.8.3 from the CASAVA software suite. The quality scale is Sanger / phred33 / Illumina 1.8+

treatment_protocol: The cells were infected through incubation with the virus, diluted in a serum-free version of the cell culture medium described above, at room temperature for one hour. After the incubation the supernatants were removed, fresh medium added and the infections were incubated at 37 °C, 5 % CO2 until set time point.

value: RD

value: rhabdomyosarcoma

tag: pathogen

value: coxsackievirus B2 Ohio

tag: virus strain

tag: incubation


title: Control RNA

description: RNAseq


title: Ctrl_RNAseq_r

source_name: αTN4, control shRNA


title: C1

city: Cuernavaca

first: Veronica

last: Jimenez-Jacinto

state: Morelos

address: Av. Universidad 2001. Col. chamilpa

department: Unidad Universitaria de Secuenciación Masiva y Bioinformática

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

description: yA2, pabaA

data_processing:
Base call performed using CASAVA-1.8.2
Quality report perfomed using FastQC
Alignment made with Smalt version 0.7.6
The counts and calculations of coverage were done with BEDTools-2.16.2
Normalization, scatter calculations and differential expression analysis with EdgeR
Genome_build: Aspergillus nidulans fgsc a4 1
Supplementary_files_format_and_content: Sample.txt: tabulator-separated values with transcript_id and raw data, Sample_Norm.txt: tabulator-separated values with transcript_id and normalized data

organism: Aspergillus nidulans

source_name: asexual spores

growth_protocol: Asexual spores (conidia) were harvested from six day-old cultures in minimal medium

extract_protocol:
Conidia from 6-day old cultures from strains CLK43 (WT) and CFL7 (ΔnapA) were collected and washed 3 times with 10 ml of cold water. Excess liquid was removed by centrifugation and conidia were immediately frozen with liquid nitrogen. Total RNA was extracted by cryogenic grinding using the Tissue Lyser (Qiagen) and purified using the RNAeasy Mini kit (Qiagen), following the manufacturer’s protocol.
Libraries were constructed using the TruSeq Stranded mRNA Library Prep Kit, following the manufacture's recommendations

tag: genotype

value: yA2, pabaA

value: 6 days


title: Ctrl_RNAseq


title: T2D3-hiPSC-Plan C

city: Guangzhou

first: qianyu

last: chen

address: 190 Kai Yuan Avenue, Science Park

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie
Transcripts Per Million were  calculated using a protocol from RSEM
Genome_build: hg19
Supplementary_files_format_and_content: TPM

organism: Homo sapiens

source_name: induced pluripotent stem cell

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line/strain

value: induced pluripotent stem cell


title: Mock 48h

value: not infected


title: A1

description: yA2, pabaA


title: T2D4-hiPSC-Plan C


title: Ctrl_Pol2_ChIPseq

source_name: αTN4, control shRNA, Pol2 ChIP

value: Pax6 (Millipore, AB2237, lot# 2506390)


title: E1

description: ∆napA, yA2, pabaA

value: deltanapA, yA2, pabaA


title: F1

description: ∆napA, yA2, pabaA


title: CVB2 VP1Q164K 24h


title: CVB2 VP1Q164K 48h


title: ΔgaaR strain grows on medium with SBP for 24h_replicate2

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

country: Netherlands

institute: Centre of fungal biodiversity

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and removed for low-quality sequence, then mapped to Aspergillus niger NRRL3  whole genome using Bowtie2 (Langmead B et al., Genome Biology, 2009) and BWA software (Li H & Durbin R, Bioinformatics, 2009).
“Fragments per kilobase of exon model per million mapped reads” (FPKM) was calculated using RSEM tool (Li B & Dewey CN, BMC bioinformatics, 2011).
Genome_build: Aspergillus niger NRRL3 (http://genome.jgi.doe.gov/Aspni_NRRL3_1)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Aspergillus niger

source_name: Mycelium sample

growth_protocol: Freshly harvested spores were inoculated with a final concentration of 106 spores/ml in 100 ml complete medium (CM) (pH 5.8) with 2% (w/v) D-fructose (Sigma-Aldrich) and were pre-grown for 16h. Mycelium was harvested by filtration through sterile myracloth, washed twice with MM with no carbon sources (pH 6) and 2.5 g of pre-grown mycelia were transferred to 50 ml MM (pH 6) with 25 mM GA and incubated for 2h or to 50 ml MM with 1% SBP and incubated for 2, 8 or 24h. All incubations were performed in rotary shaker at 30°C and 250 rpm.

extract_protocol:
The mycelium of CBS-141257 (reference strain) and CBS-141258 (ΔgaaR) was ground in Tissue Lyser II (Qiagen) and RNA was extracted using TRIzol reagent (Invitrogen) and purified with NucleoSpin RNA Clean-up kit (Macherey-Nagel) with rDNase treatment. RNA quantity of the samples was checked with a NanoDrop-1000 spectrophotometer and the quality by RNA gel electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sampling time

value: 24 hour

value: deltagaaR

tag: agent

value: medium with SBP


title: Ctrl_H3K4me2_ChIPseq

source_name: αTN4, control shRNA, H3K4me2 ChIP

tag: cell type

value: lens epithelial cell line

value: control


title: ΔgaaR strain grows on medium with SBP for 24h_replicate1

tag: strain


title: Reference strain grows on medium with SBP for 24h_replicate2

value: Reference


title: HM1-hiPSC-Plan B


title: Reference strain grows on medium with SBP for 24h_replicate1


title: Ctrl_Pax6_ChIPseq

source_name: αTN4, control shRNA, Pax6 ChIP

value: RNA polymerase II (Abcam, ab817, lot# GR153063-402)


title: Pax6_sh_RNAseq


title: ΔgaaR strain grows on medium with SBP for 8h_replicate2

value: 8 hour


title: CP_CON

city: SEOUL

first: Jang-Seu

last: Ki

state: SEOUL

address: 20, Hongimun 2-Gil, Jongno-gu

department: Department of Life Science, College of Natural Sciences

country: South Korea

institute: Sangmyung University

data_processing:
Illumina Casava software used for basecalling.
The quality of raw reads was checked with FastQC_v0.10.0 . The raw data were cleaned and trimmed by removing adaptor and low quality reads, and then reads were assembled using Trinity software
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated  by using RSEM (Li and Dewey, 2011)
Supplementary_files_format_and_content: excell file  include FPKM values for each Sample .

organism: Margalefidinium polykrikoides

source_name: Marine dinoflagellate cells

growth_protocol: C. polykrikoides cultures cultured in f/2 medium at 20°C under a 12:12-h light-dark cycle with a photon flux density of about 65 mol photons m-2 s-1.

extract_protocol:
C. polykrikoides cultures were harvested using centrifugation at 1,000 g for 6 min, immediately frozen in liquid nitrogen, and stored at -80°C until RNA extraction. Preserved cells were physically broken by freeze-thawing in liquid nitrogen, and further homogenized with a mini-beadbeater (BioSpec Products Inc., Bartlesville, OK) with zirconium beads (0.1 mm diameter). Total RNA was isolated using TRIzol (Invitrogen, Carlsbad, CA), and purified using Mini Spin Columns from RNeasy Mini Kits (Qiagen, Valencia, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment

value: untreated cells that harvest in stationary phase


title: Reference strain grows on medium with SBP for 8h_replicate2

tag: genotype/variation


title: CP_1mg_CuSO4_24h

value: the cells were treated with 1 mg CuSO4 and harvested at 24 h after expousre to CuSO4 (exponential stage of growth)


title: CP_1mg_CuSO4_48h

value: the cells were treated with 1 mg CuSO4 and harvested at 12 h after expousre  to CuSO4


title: CP_1mg_CuSO4_12h

value: the cells were treated with 1 mg CuSO4 and harvested at 12 h after expousre  to CuSO4 (exponential stage of growth)


title: Reference strain grows on medium with SBP for 8h_replicate1


title: small RNAs in the dicer-2[null] rescued by the transgenic Dicer-2 [D1217A,D1476A]

city: BALTIMORE

first: Ryuya

last: Fukunaga

state: MD

address: 725 N. Wolfe St. 521A Physiology Bldg

department: Department of Biological Chemistry

institute: Johns Hopkins University School of Medicine

description: small RNAs in fly heads

data_processing:
Basecalls performed using bcl2fastq version 2.16
Sequenced reads were trimmed for adaptor sequence.
Genome_build: dm3
Supplementary_files_format_and_content: [.txt] Tab-delimited text file. Length of the read, Number of the read, Sequence of the read.

source_name: Female fly heads

extract_protocol:
Female fly heads were hand-dissected and RNAs were prepared using miRVana.
Libraries were prepared as previously described (Fukunaga et al, 2014 and Han et al, 2015).

value: wIR; dicer-2[null], Act5C-Gal4/dicer-2[null] ; UAST-HA-Dicer-2[D1217A,D1476A]/+

tag: sample type

value: in vivo


title: CP_CK_CuSO4

value: untreated cells that used as control (exponential stage of growth)


title: ΔgaaR strain grows on medium with SBP for 2h_replicate2

value: 2 hour


title: small RNAs in the dicer-2[null] rescued by the transgenic Dicer-2 [G31R]

description: small RNAs in fly heads

value: wIR; dicer-2[null], Act5C-Gal4/dicer-2[null] ; UAST-HA-Dicer-2[G31R]/+


title: ΔgaaR strain grows on medium with SBP for 2h_replicate1


title: Reference strain grows on medium with SBP for 2h_replicate2


title: HF1-hiPSC-Plan B

value: induced pluripotent stem cell


title: BMDM_WT_HP_0min_rep3

city: Blacksburg

first: Monica

last: Viladomiu

state: VA

address: 1015 Life Science Circle

department: Virginia Bioinformatics Institute

institute: Nutritional Immunology and Molecular Medicine Laboratory

data_processing:
Adapter trimming
Bowtie was used to map the reads to RefSeq sequences of mouse (downloaded from UCSC), and RSEM was used to calculate expression values for each gene. FPKM-transformed values were log-transformed followed by normal quantile transformation. Two methods of P-value adjustment (FDR & Bonferroni) were used. Kolmogorov-Smirnov test was used to test normality, followed by parametric 3-way ANOVA to obtain differential expression.
Genome_build: mm9

growth_protocol: femur and tibia were excised, washed in 70% EtOH and cold 1xPBS. BM progenitors were flushed out with cRPMI_M (RPMI 1640, 10% FBS, 2.5% Hepes, 1% Sodium pyruvate, 1% Pen/Strep, 1% L-Glutamine, 50uM 2-mercaptoethanol),  filtered through a 100µm cell strainer and centrifuged for 8 min at 1,200 rpm at 4°C. Red blood cells were eliminated by osmotic lysis and cell suspensions were filtered and centrifuged again as described above. BM progenitors were adjusted to 1x106 cells/mL with cRPMI_M containing 35ng/mL recombinant mouse M-CSF (Peprotech). Cells were plated in 100mm petri dishes and incubated at 37°C, 95% humidity and 5% CO2. Fresh media containing M-CSF was added on day 3. On day 6, non-adherent cells were removed and bone marrow derived macrophages (BMDM) were detached by incubation in ice cold 1xPBS at 4°-8°C for 10 minutes.  Cells were carefully removed from the dish by flushing them off the culture dish. BMDM were centrifuged, resuspended in fresh cRPMI_M without antibiotics and used for the Gentamicin infiltration assay.

extract_protocol:
After homogenization of tissue, total RNA was extracted and purified using the RNAeasy system according to manufacturer’s instructions (Qiagen Valencia, CA). The QIAGEN RNase-free DNase supplement kit was used to ensure that the RNA was free from DNA contamination.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
infection protocol: BMDM cell suspensions were resuspended in cRPMI_M without antibiotics and plated in triplicate in 12-well plates (2.5x105 for re-isolation experiments, 1x106 cells for RNA isolation). Cells were left to adhere overnight at 37°C, 95% humidity and 5% CO2. The following day, H. pylori SS1 was harvested from Columbia blood agar plates and resuspended in cRPMI_M w/o Ab to a concentration of 1x108 CFU/mL. H. pylori were added to BMDM at MOI 10 and plates were quick spun to ensure immediate contact. For iNOS inhibition experiments, cells were incubated with the selective iNOS inhibitor L-N6-(1-Iminoethyl)lysine dihydrochloride (L-NIL) at 100µM for 30 min. In some experiments, WT BMDM were treated with the PPARγ antagonist GW9662 (10µM) for 2 hours prior to bacterial co-culture. In the case of M1 induction BMDM were pre-treated with LPS (100ng/ml) and rIFN-γ (100ng/ml) overnight.   After 15 minutes of bacteria-macrophage co-culture at 37°C, 95% humidity, 5% CO2, the culture supernatant was removed and cells were washed three times with PBS/5% FBS/100ng/ml Gentamicin. Cells for time-point 0 were washed with 1xPBS and immediately collected for downstream assays.  The cells allocated for the remaining time points (15 min to 24 hours) were covered with culture media supplemented with 100ng/ml Gentamicin to kill extracellular H. pylori. Cells were incubated for the indicated time-points and then collected as described below.
BMDM were isolated from WT and PPARg-/- mice and cultured with M-CSF for 7 days to promote macrophage differentiation. Fully differentiation macrophages were challenged with H. pylori strains SS1 at an MOI of 10 for 15 minutes. Extracellular bacteria was then eliminated by gentamycin treatment. Cells were collected at 0, 60, 120, 240, 360 and 720 minutes post gentamycin treatment to ascertain whole transcriptome differential gene expression during infection.

tag: strain background

value: Wild-type

value: Bone marrow-derived macrophages (BMDM)

tag: infection status

value: H.pylori SS1-infected (MOI 10)

tag: collection time-point

value: 0min post gentamycin treatment


title: small RNAs in the dicer-2[null] rescued by the transgenic Dicer-2 [R943E,R956E]

description: small RNAs in fly heads

value: wIR; dicer-2[null], Act5C-Gal4/dicer-2[null] ; UAST-HA-Dicer-2[R943E,R956E]/+


title: CM

city: Nanjing

first: lifan

last: zhang

state: Jiangsu

address: No.6 Tongwei road

department: College of Animal Science and Technology

institute: Nanjing agricultural university

description: castrated male pigs (CM) from individuals pooled

data_processing:
Raw sequencing data was evaluated by FAST-QC
Raw reads after quality control testing were mapped to the reference pig genome version 10.2 (Sscrofa 10.2) using MapSplice program (v.2.1.8)
The normalized expression level of each gene was measured by Upper Quartile of Reads Per Kilobase per Million mapped reads (UQRPKM)
Genome_build: Sscrofa 10.2
Supplementary_files_format_and_content: tab-delimited text files include UQRPKM values for each gene

organism: Sus scrofa

source_name: visceral adipose

extract_protocol:
Visceral adipose tissue were subjected to total RNA extraction using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). Total RNA from IM, CM and CMT groups (4-6 individuals/group) was pooled in equal amounts to generate mixed sample respectively. Sequencing libraries were prepared using Ion Total RNA-Seq Kit v2.0 (Life Technologies, Carlsbad, CA, USA).
RNA libraries were prepared for sequencing using standard Ion protocols

treatment_protocol: Three groups of pigs were fed a high-fat and high-cholesterol diet

value: Chinese Wuzhishan miniature pigs

tag: tissue

value: visceral adipose

tag: Sex

value: male


title: small RNAs produced by Dicer-2 [R943E,R956E] in vitro

description:
small RNAs produced from 104 bp dsRNA in vitro
The sequences of strands 1 and 2 of the 104 bp dsRNAs are:
5'-GGGCCACAAGUUCAGCGUGUCCGGCGAGGGCGAGGGCGAUGCCACCUACGGCAAGCUGACCCUGAAGUUCAUCUGCACCACCGGCAAGCUGCCCGUGCCCUGGCCC-3'
and
5'-GCCAGGGCACGGGCAGCUUGCCGGUGGUGCAGAUGAACUUCAGGGUCAGCUUGCCGUAGGUGGCAUCGCCCUCGCCCUCGCCGGACACGCUGAACUUGUGGCCCAA-3'.
These two strands make 104 bp dsRNA with 3' 2-nt overhang at both ends.

molecule: other

organism: synthetic construct

source_name: 104 bp dsRNA

tag: proteins

value: in vitro


title: small RNAs in the dicer-2[null] rescued by the transgenic Dicer-2 [R943A,R956A]

description: small RNAs in fly heads

value: wIR; dicer-2[null], Act5C-Gal4/dicer-2[null] ; UAST-HA-Dicer-2[R943A,R956A]/+


title: IM

description: intact male pigs (IM) from individuals pooled


title: CMT

description: castrated male pigs with testosterone replacement (CMT) from individuals pooled


title: Reference strain grows on medium with SBP for 2h_replicate1

value: Reference

value: medium with SBP


title: ΔgaaR strain grows on medium with GA for 2h_replicate2

value: deltagaaR

value: medium with GA


title: small RNAs in the dicer-2[null] rescued by the transgenic Dicer-2 [wild-type]

description: small RNAs in fly heads

value: wIR; dicer-2[null], Act5C-Gal4/dicer-2[null] ; UAST-HA-Dicer-2[Wild-type]/+

value: in vivo


title: small RNAs produced by Dicer-2 [H743A,R752A,R759A,R943A,R956A] in vitro


title: ΔgaaR strain grows on medium with GA for 2h_replicate1

value: 2 hour


title: small RNAs produced by Dicer-2 [R943A,R956A] in vitro


title: ΔgaaR strain grows on medium with SBP for 8h_replicate1

value: 8 hour


title: small RNAs in the dicer-2[null] flies

description: small RNAs in fly heads

value: wIR; dicer-2[null], Act5C-Gal4/dicer-2[null] ; +


title: Pax6_sh_H3K4me3_ChIPseq

source_name: αTN4, Pax6 shRNA, H3K4me3 ChIP

tag: cell line

value: lens epithelial cell line

tag: shRNA

tag: chip antibody


title: Reference strain grows on medium with GA for 2h_replicate2


title: small RNAs produced by Dicer-2 [wild-type] in vitro

value: Dicer-2 [Wild-type]


title: small RNAs in the control flies

description: small RNAs in fly heads

value: wIR; dicer-2[null], Act5C-Gal4/CyO; +


title: NH-JS2_15d_2

city: Deajeon

first: Won Yong

last: Jung

state: N/A = Not Applicable

address: 125 Gwahak-ro, Yuseong-gu

institute: Korea Research Institute Bioscience and Biotechnology(KRIBB)

description: replicate, early bolting 15day

data_processing:
Trimming - SolexaQA package
Read mapping - bowtie2. Radish - WK10039 draft genome sequence (NCBI BioProject Accession: PRJNA239785).
DEG - R (EdgeR)
Genome_build: Radish - WK10039 draft genome sequence (NCBI BioProject Accession: PRJNA239785)
Supplementary_files_format_and_content: [.txt] edgeR normalized abundance measurements

molecule: polyA RNA

organism: Raphanus sativus

source_name: shoot tissue

growth_protocol: 23°C, 16 h light/8 h dark, for 2 weeks

extract_protocol:
Total RNAs were extracted using Trizol Reagent (Invitrogen, Carlsbad, CA, USA), and were then treated with DNase I (Fermentas, Pittsburgh, PA, USA) according to the manufacturers’ instructions.
Following the Illumina protocol(TruSeq RNA Library Prep Kit, TruSeq Stranded mRNA Sample Prep Kit)

treatment_protocol: cold(5±1°C), 12 h light/12 h dark, for 15 or 35 days

tag: breed

value: NH-JS

tag: line

value: shoot

tag: age

value: 2-week-old plants

tag: phenotype

value: early bolting

value: cold

tag: time

value: 15 days


title: NH-JS2_35d_2

description: replicate, early bolting 35day

tag: treatment

value: 35 days


title: NH-JS1_35d_2

description: replicate, late bolting 35day

value: late bolting


title: NH-JS2_0d_2

description: replicate, early bolting control

value: control

value: 0 days


title: small RNAs in the dicer-2[null] rescued by the transgenic Dicer-2 [H743A,R752A,R759A,R943A,R956A]

description: small RNAs in fly heads

tag: genotype/variation

value: wIR; dicer-2[null], Act5C-Gal4/dicer-2[null] ; UAST-HA-Dicer-2[H743A,R752A,R759A,R943A,R956A]/+

value: in vivo


title: NH-JS1_15d_2

description: replicate, late bolting 15day


title: NGR 234 traI/ngrI double mutant with 1 µM apigenin R2

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

data_processing:
FastQ quality trimming using FastX (version 0.0.13)  and a cut-off value of 20
Fastq to fasta conversion using FastX  FastX (version 0.0.13)
Size filtering: discarding reads shorter than 20 nt (READemption version 0.3.5)
Read mapping using segemehl version 0.2.0  (READemption version 0.3.5)
Coverage calculation and normalisation (READemption version 0.3.5)
Genome_build: NC_000914.2, NC_012586.1, NC_012587.1
Supplementary_files_format_and_content: Read coverages normalized by total number of aligned reads multiplied by 1 M in wiggle format (counts per million). Files contain wiggle-formatted alignment data  for accessions NC_000914.2, NC_012586.1, and NC_012587.1

organism: Sinorhizobium fredii NGR234

growth_protocol: Sinorhizobium fredii NGR234 was grown at 30°C in liquid TY medium (0.5% tryptone, 0.25% yeast extract, 10 mM CaCl2, pH 7.0) at 200 rpm and supplemented with rifampicin (25 µg/ml). NGR234 QS double deletion mutant was cultivated under same condition as the NGR234 wild type strain, but the TY medium was additionally supplemented with gentamycin (10 µg/ml).

extract_protocol:
Total RNA was isolated using the hot phenol method followed by two chloroform-isoamyl alcohol treatments and precipitation with sodium acetate and ethanol.
The libraries were generated by Vertis Biotechnologie AG (Munich, Germany). The samples were poly(A)-tailed by using poly(A) polymerase. The 5'-PPP were removed using tobacco acid pyrophosphatase (TAP) followed by the ligation of the RNA adapter to the 5'-monophosphate of the RNA. First-strand cDNA synthesis was performed with an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNA was PCR-amplified to reach a concentration of 20-30 ng/μl using a high fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis. The primers used for PCR amplification were designed for TruSeq sequencing according to the instructions of Illumina

treatment_protocol: Precultures were established from cryocultures in 5 mL liquid TY medium and cultivated at 30°C and 200 rpm until they reached an OD600 of >3. For the cultures 50 mL liquid TY medium were inoculated with freshly grown precultures of NGR234 wild type as well as the double mutant strain. One culture of NGR234 wild type as well as the double mutant strain was supplemented with 1 µM apigenin and the control was treated with an equal aliquot of KOH. Cultures were allowed to grow for 48 h, were then harvested and transferred into falcon tubes with 10 mL ethanol/phenol (95:5). Samples were mixed well, directly frozen in liquid nitrogen and stored at -70°C until further use.

tag: strain


title: NGR 234 traI/ngrI double mutant with 1 µM apigenin R3


title: RNAseq-5azadC+VX680 rep2

city: Boston

first: Chunyao

last: Wei

state: MA

address: 185 Cambridge St

department: Molecular Biology

institute: Mass General Hospital

description:
Processed data files:
azavx680VSctl.mus.DEgenes.txt
azavx680VSctl.cas.DEgenes.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
Custom cas and mus genome were prepared using mm9 as genome template, combined with substitution of known SNPs and changes of known Indels and insertions reported for Mus musculus and Mus castaneus, respectively (Pinter SF, et al. (2012),Genome Biology).
Sequenced reads were trimmed for adaptor sequence, PCR duplicates, and masked for low-complexity or low-quality sequence, then mapped to custom cas and mus genome repectively using Tophat v2.0.10 (-g 1 –no-coverage-search–read-edit-dist 3 –read-mismatches 3 –read-gap-length 3 –b2-very-sensitive–mate-inner-dist 50 –mate-std-dev 50 –library-type fr-firststrand)
allelic origin of each mappable reads were then determined using in-house algorithms and the alignment coordinate of each read was adjusted to match mm9 mouse genome. Discordant pairs and multimapped reads were discarded.
gene expression levels within each library were quantified using Homer v4.8 (rna mm9 -count exons -strand + -noadj -condenseGenes)
normalized allelic differential expression analyses across samples were performed by using EdgeR
Genome_build: mm9
Supplementary_files_format_and_content: [.txt] tab-delimited text files include Raw count values and normalized value (RPM) for each Sample, and

organism: Mus musculus musculus x Mus musculus castaneus

growth_protocol: 700K cells were plated in 15 cm plate at 37C, Let grow 72h. Then Trizol applied directly to plate for RNA prep

extract_protocol:
Total RNAs were extracted using Trizol from cells
dUTP mediated directional RNAseq from NEBNext ultra directioanl preparation protocol

treatment_protocol: Drugs added 24 hr after plating. DMSO added to media so that volume of DMSO+Drug = same for all conditions (if 5 ulVX680 & 5 ul Aza added for dual treatment, 10 uL DMSO added for untreated media)

tag: animal

value: F1 hybrid of Mus musculus and Mus castaneus

tag: gender

value: female

tag: cell type

value: tail fibroblast

value: both 5-azadC and VX680


title: NH-JS2_0d_1

description: early bolting 0day (non treatment)

tag: tissue


title: NGR 234 traI/ngrI double mutant without apigenin R2


title: NH-JS2_15d_1

description: early bolting 15day


title: NH-JS2_35d_1

description: early bolting 35day


title: NH-JS1_0d_2

description: replicate, bolting 0day (non treatment)


title: NGR 234 traI/ngrI double mutant without apigenin R1


title: NH-JS1_15d_1

description: late bolting 15day


title: RNAseq-VX680 rep1

description:
Processed data files:
vx680VSctl.mus.DEgenes.txt
vx680VSctl.cas.DEgenes.txt


title: Reference strain grows on medium with GA for 2h_replicate1

tag: sampling time

value: 2 hour

value: Reference

tag: agent

value: medium with GA


title: RNAseq-VX680 rep2


title: RNAseq-5azadC+VX680 rep1


title: NGR 234_WT with 1 µM apigenin R2


title: RNAseq-5azadC rep1

description:
Processed data files:
azaVSctl.mus.DEgenes.txt
azaVSctl.cas.DEgenes.txt


title: RNAseq-5azadC rep2


title: NH-JS1_0d_1

description: late bolting 0day (non treatment)

value: NH-JS

value: shoot

value: 2-week-old plants


title: RNAseq-WT rep2

source_name: RNAseq-WT

value: untreated


title: NGR 234 traI/ngrI double mutant without apigenin R3


title: RNAseq-WT rep1


title: S. acidocaldarius L7Ae Co-IP small RNA

city: Marburg

last: Daume

state: Hessen

address: Karl-von-Frisch-Strasse 10

department: Prokaryotic Small RNA Biology

institute: Max Planck Institute for Terrestrial Microbiology

description: Sample 2

data_processing:
CLC Genomics Workbench 9.5.3
The raw data files were imported using the Illumina Import option (Illumina Pipeline 1.8 and removal of failed reads).
The raw data files were processed by quality score trimming (quality score trimming limit: 0.05; max. number of ambiguities: 2) and NEBNext 3' RNA adapter (AGACGTGTGCTCTTCCGATCT) trimming (strand: minus; action: remove adapter; mismatch cost: 3; gap cost: 5; cutoff internal end matches: 10 ; minimum end matches score: 5). The processed sequences were filtered by length (15 nt cutoff)
The trimmed sequences were mapped to the S. acidocaldarius reference genome (CP000077) using CLC default settings and saved as a read track file. The mapped reads (between 6 to 12 million reads per file) were extracted and sampled to 1.000.000 reads. These 1.000.000 reads were again mapped to the genome using CLC default settings.
Genome_build: S. acidocaldarius reference genome (GenBank accession CP000077.1)
Genome_build: The processed data files are in .wig (wiggle) format. They contain the mapping graphs of the three samples (each 1.000.000 mapped reads) which were created from the coverage plots of the generated read track files. Furthermore, the reference genome (Sulfolobus acidocaldarius DSM 639 (CP000077)) is included as .gkb (genbank) file, which is needed for the illustration of the mapping graph track.
instructions for .wig file importing: When working with CLC Genomics Workbench, import the .gkb file of S. acidocaldarius (genome file) via standard import. Rename the file to "Sulfolobus acidocaldarius DSM 639 (CP000077)" (remove understrikes). This step is critical for the illustration of the mapping graph. Convert the renamed file to a genome track (Toolbox -> Track tools -> Convert to Tracks -> Choose renamed file -> Create sequence track and save). Import the .wig file (via Import -> Tracks) and choose the converted genome track as reference track.

organism: Sulfolobus acidocaldarius

source_name: liquid culture

growth_protocol: Cells were grown in Brock medium to logarithmic phase.

extract_protocol:
Sample 1: Cells were lysed by homogenization and small RNAs were isolated according to the mirVana miRNA Isolation Kit (Ambion). The small RNA isolate was used for cDNA library preparation. Samples 2 and 3: In order to obtain L7Ae-interacting RNAs, cells with a C-terminal Flag-HA tag on the single L7Ae gene (saci_1520) in S. acidocaldarius were lysed by a French Pressure Cell Press and the protein was purified by two consecutive immunoprecipitation steps using the Flag-HA tandem purification Kit (Sigma). The urea eluate contained co-immunoprecipitated RNA. One sample was fragmented by ZnCl2 (10 mMZnCl2, 20 mM Tris pH 6.8) and treated with T4 PNK to cure the RNA termini. The two RNA samples (L7Ae co-IP small RNA and fragmented RNA) were then used for cDNA library preparation.
cDNA libraries were prepared according to the NEBNext Small RNA Library Prep Set for Illumina.

value: DSM 639

tag: phase

value: logarithmic phase


title: NGR 234_WT with 1 µM apigenin R1


title: S. acidocaldarius small RNA

description: Sample 1


title: NGR 234_WT with 1 µM apigenin R3


title: NGR_234_WT without apigenin R1


title: BMA01-C7

status: Public on Feb 09 2017

city: Cleveland

first: Jonathan

middle: D

last: Kenyon

state: OH

address: 2103 Cornell

department: Pathology

institute: Case Western Reserve University

description: bisulfite modified PCR amplified genomic DNA

data_processing:
version 2.6 of gsRunProcessor
doValleyFilterTrimBack>true<
vfBadFlowThreshold>4<
vfLastFlowToTest>320<
vfMaxFailedPercent>100<
vfTrimBackMinimumLength>84<
vfTrimBackScaleFactor>0.7<
if test="Run.Flow.CycleCount > 299"><vfTrimBackScaleFactor>2.2</vfTrimBackScaleFactor>
vfScanLimit>4096</vfScanLimit
computeUopt>false</computeUopt><scaleMultimers>false</scaleMultimers>
doQScoreTrim>true<
errorQscoreWindowTrim>0.010</
QScoreTrimNukeWindowSize>40<
QScoreTrimBackScaleFactor>0.9<
if test="starts-with(InstrumentModel,'GSJUNIOR_A')"><QScoreTrimBackScaleFactor>1.2</
if test="Run.Flow.CycleCount > 299"><QScoreTrimBackScaleFactor>1.5</
enable>true</enable><options>--fna --qual --454BaseCallerMetrics.txt --454BaseCallerMetrics.csv --454RuntimeMetricsAll.txt --454RuntimeMetricsAll.csv --454QualityFilterMetrics.txt --454QualityFilterMetrics.csv --454AllControlMetrics.txt --454AllControlMetrics.csv
sequence reads were next screened by barcode and compared to a hypothetical bisulfite modified 100% unmethylated sequence. All sequences with less than 70% homology to the hypothetical sequence were discarded.
Each CpG within sequence reads was then scored 0 for unmethylated or 1 for methylated. Frequency of methylation at each CpG was next calculated for each sample.
Supplementary_files_format_and_content: .tab processed files are the sequence reads obtained for each barcode from the raw data and screened (70% cutoff) for homology to a theoretical 100% bisulfite (BS) converted sequence of the hMLH1 promoter PCR amplification products from the given primers in the spreadsheet. The first column contains the unique sequence read name (G6ZBNM301CO5B5 for instance) which was generated by the run and plate location. The second column are the sequence reads with the barcodes trimmed (this was done to facilitate the 70% homology screen).
Supplementary_files_format_and_content: .csv files contain the CpG methylation scoring and frequencies. Three regions of the hMLH1 gene were amplified and sequenced (fragments were named A, B, C). The first row is a header, subsequent rows contain sequence read specific data. The first column of these files is the sequence read name, followed by the read length, then several columns of scores (1 = methylated or 0 = unmethylated) for each CpG within the amplified product, the next column shows the aveidentity (% sequence homology to hypothetical BS converted), and the last column is the sequence of bases observed at the CpG sites for that sequence read (A;A;R;A.... etc. for instance indicates the third CpG site was methyated).

source_name: A single colony forming unit grown from human bone marrow aspirate donation

extract_protocol:
DNA from individual CFU, CD34+, or RKO cells was harvested by Qiagen genomic DNA kit. DNA was next bisulfite modified and PCR amplified with forward oligonucleotides MLH1-AF (5' [Linker/spacer][barcode]actcaaaatcctctaccttataatatc 3'),  MLH1-BF (5' [Linker/spacer][barcode]acaaaccaaacacaaaaccccat 3'), MLH1-CF (5' [Linker/spacer][barcode] tcacctcaacaaaaacacacaaac 3') when [linker/spacer]= (5' CGTATCGCCTCCCTCGCGCCATCAG 3') and [barcode] was sample specific. Negative oligonucleotides used were: MLH1-AR (5'[Linker/spacer][barcode]ttaaaagaagtaagatggaag 3'),  MLH1-BR (5' [Linker/spacer][barcode]tttagttaataggagtagagatg 3'), MLH1-CR (5' [Linker/spacer][barcode]GTTAAATTTTTTAATTTTGTGGGTTGTTGGG 3') when [linker/spacer]= (5' CTATGCGCCTTGCCAGCCCGCTCAG 3') and [barcode] was sample specific.
Amplified products were run on an 1.5% agarose gel and appropriate sized bands excized. DNA fragments were purified from gel fragments and submitted for 454 sequencing. In parallel 1/2 of each sample was processed for RNA extracts. Total RNA was generated for each sample and used as the template for cDNA synthesis by a single cycle of reverse transcriptase activity followed by RNA digestion. Expression of the human gene hMLH1 (in parallel with human beta actin as a control) was next assessed for each cDNA sample generated by QRT-PCR on an Applied biosystems RT-PCR 7500 fast machine. Threshold values were automatically generated according to the manufacturers protocol. Gene expression for hMLH1 (scored as 1) was considered observed if amplification products broke threshold for both hMLH1 and beta actin. However, loss of hMLH1 (scored as 0) gene expression was defined as the observation of detectable amplification products for beta actin but not hMLH1

tag: donor number

tag: donorid

tag: donor age

value: hematiopoietic progenitor

tag: hmlh1 expression

tag: barcode

value: TTGCTAGGT


title: Unmethylated

source_name: Enzymatically unmethylated human DNA

value: TGTGTGTTC


title: UCB02-CD34

source_name: Immunomagnetic seperated CD34+ cells from human umbilical cord blood 02 (UCB02)

value: TTACGTGTA


title: BMA03-T2C1

value: TGAGCATGG


title: BMA03-T2C9

value: TCTAATGTT


title: BMA03-T1C1

value: TCTCCACAG


title: BMA06-CD34

source_name: Immunomagnetic seperated CD34+ cells from human bone marrow donor 06 (BMA06)

value: TCGGAACGA


title: BMA04-C6

value: TGCCGGATA


title: BMA01-C3

value: TCCTTAGCT


title: BMA07-CD34

source_name: Immunomagnetic seperated CD34+ cells from human bone marrow donor 07 (BMA07)

value: TCTGACCAC


title: NGR_234_WT without apigenin R3


title: BMA02-T1C4

value: TACGCTGGA


title: S. acidocaldarius L7Ae Co-IP fragmented RNA

description: Sample 3


title: BMA01-C1

value: GTTTACAGT


title: BMA03-T2C7

value: TCCTTCTGG


title: RKO cell line

source_name: The human colon cancer cell line RKO

value: RKO cells

value: GTTCTTGTT


title: BMA01-C8

value: GTTATGTAT


title: BMA04-C13

value: hematiopoietic progenitor

value: GTAGCCTCG


title: NGR_234_WT without apigenin R2


title: NGR 234 traI/ngrI double mutant with 1 µM apigenin R1


title: NH-JS1_35d_1

description: late bolting 35day

tag: breed

value: NH-JS

tag: line

value: shoot

tag: age

value: 2-week-old plants

tag: phenotype

value: late bolting

value: cold

value: 35 days


title: BMA02-T2C7

value: GACACCGGT


title: BMA02-T1C12

value: GTACTCATG


title: BMA02-T1C8

value: CGTGTACGC


title: BMA05-CD34

source_name: Immunomagnetic seperated CD34+ cells from human bone marrow donor 05 (BMA05)

value: CCCGCTGCC


title: BMA01-C4

value: GAGACGTAA


title: BMA02-T1C6

value: GGGCCATTG


title: BMA02-T1C1

value: GAGTAGGCA


title: BMA01-C11

value: CAATCCCTC


title: BMA01-C2

value: CCACGGCCG


title: BMA01-C13

value: hematiopoietic progenitor

value: ATATCTCAA


title: 1:1 (Methylated:Unmethylated)

source_name: 1:1 molar mixture of enzymatically methylated and unmethylated human DNA

value: ACGCGTTAA


title: Methylated

source_name: Enzymatically methylated human DNA

value: AACGGACCC


title: UCB01-CD34

source_name: Immunomagnetic seperated CD34+ cells from human umbilical cord blood 01 (UCB01)

value: AGTAGAAGA


title: BMA03-T2C4

value: CAGAGTGTT


title: BMA03-T2C5

value: AACCGCGTT


title: BMA03-T1C5

value: AACCCAAGA


title: BMA02-T2C8

value: ACCAACCTT


title: BMA04-C14

value: AATGGCTTA


title: BMA02-T1C9

value: ACTCCGAGT


title: BMA04-C7

value: CCCAAGGTG


title: BMA01-C14

value: ACTAGGTCC


title: NUR2

city: Avignon

first: Cedric

last: Alaux

address: Domaine Saint Paul, Site Agroparc

country: France

institute: INRA

description: Pseudo_Counts_FOR-NUR_RLE_RNA-Seq_Alaux.xls

data_processing:
Image analyses and basecalling were performed using the HiSeq Control Software (HCS 2.2.38) and Real-Time Analysis component (RTA 1.18.61).
Demultiplexing was performed using Illumina's sequencing analysis software (CASAVA 1.8.2). The quality of the data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequence Analysis Viewer).
A splice junction mapper, TopHat2 (with bowtie 2.2.3), was used to align RNA-seq reads to Apis mellifera genome (Amel 4.5 NCBI) with a set of gene model annotations (ref_Amel_4.5_top_level.gff3 downloaded from NCBI on June 18, 2014). Final read alignments having more than 3 mismatches are discarded.
Counting was performed with HTSeq-count 0.6.1p1 (union mode). The data is from a strand-specific assay, the read has to be mapped to the opposite strand of the gene.
Differentially expressed genes were identified using the Bioconductor package edgeR (v3.4.0). Genes with less than 15 reads (cumulating all the analysed samples) for NUR and FOR conditions, and 20 reads for VSH and NVS conditions, were filtered and thus removed from the analysis. Data were normalized using Relative Log Expression (RLE) normalization factors. Genes with adjusted p-value less than 5% (according to the FDR method from Benjamini-Hochberg) were declared differentially expressed.
Genome_build: Amel_4.5 [Apis mellifera 4.5 (NCBI)]
Supplementary_files_format_and_content: Excel files with 3 columns for gene identification : the first one is the NCBI Gene ID (mandatory), the second one is the gene symbol (if any), and the third one is the BeeBase ID (if any). The next columns correspond to the normalized abundance measurements (RLE normalization using edgeR statistical package) for each sample.

organism: Apis mellifera

source_name: Antennae

extract_protocol:
Bees were collected and flash frozen in liquid nitrogen, antennae were cut-off and RNA was isolated using Trizol reagent and following the Purelink Micro kit (Invitrogen) instructions.
RNA-Seq libraries were prepared with the 'TruSeq Stranded RNA sample preparation Kit' (Illumina) according to the manufacturer's instructions.

value: Nurse

tag: mean age

value: unknown

value: 4 pairs of antennae


title: FOR2

value: Forager


title: NUR1


title: NUR3


title: FOR3


title: NVS4

description: Pseudo_Counts_VSH-NVS_RLE_RNA-Seq_Alaux.xls

value: non-VSH


title: NVS3


title: NVS2


title: VSH4

value: VSH


title: NVS1


title: VSH3


title: VSH1


title: BMA01-C5

value: hematiopoietic progenitor

value: ACGGCCCTA


title: P0_Root

city: Beijing

first: WEIMIN

last: LI

address: No.12 Zhongguancun St.

institute: Biotechnology Research Institute, CAAS

data_processing:
Illumina GA Pipeline v1.6 software used for basecalling.
The raw reads were first processed through in-house perl scripts to filter high-quality clean reads by removing low quality reads as well as reads containing adaptor or unknown nucleotides larger than 10 %.
Clean reads derived from libraries of P-0h, P-6h, P-24h and Rh-6h were pooled and de novo assembled into transcripts using Trinity method (Grabherr et al., 2011. Nat Biotechnol 29: 644-652) with optimized K-mer length of 25 and coverage cut-off value of 2.
The clean reads from each RNA-seq library were mapped backed onto the assembled transcriptome using RSEM with a maximum of no more than 2 nucleotides mismatches (Li and Dewey, 2011. BMC Bioinformatics 12: 323). The resulting readcount for each matched unigene was normalized with FPKM (expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) as described (Trapnell et al., 2010. Nat Biotech 28: 511-515) to measure its expression level.
Genome_build: The transcriptome of A. sparsifolia primary roots constructed in the current work
Supplementary_files_format_and_content: Text file includes FPKM values for each sample

organism: Alhagi sparsifolia

source_name: untreated primary roots

growth_protocol: The A. sparsifolia seeds with similar size were first treated with concentrated sulfuric acid (98%) for 20 min, and immersed in sterile distilled water for 30 min preceded by 6 rinses with distilled water. After that, the seeds were placed in 12 cm Petri dishes containing 2-layer fully wetted filter paper, and cultured in the dark at 25℃ for 24 h. The properly germinated seeds were selected and transferred to Petri dishes with 2-layer fully wetted filter paper for additional 24h. The 2-day-old seedlings were then selected to be treated with PEG-6000.

extract_protocol:
Total RNA was extracted from P-0h, P-6h, P-24h and Rh-6h, respectively, by using TRIzol® reagent (Invitrogen, USA)
Total RNA was first assessed with NanoPhotometer® spectrophotometer (IMPLEN, USA) and RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, USA) to ensure the quality and integrity, and then processed with NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s instruction. Briefly, poly(A) mRNA was first isolated from 3 μg of total RNA using oligo (dT) magnetic beads (Invitrogen, USA), and then was fragmented into smaller pieces at 70℃ for 5min in the fragmentation buffer (Ambion, USA). Taking these mRNA fragments as templates, the first-strand cDNA was synthesized with M-MuLV Reverse Transcriptase (RNase H-) and random hexamer primer, and second strand cDNA synthesis was subsequently performed using DNA polymerase I (Invitrogen, USA) and RNaseH (Invitrogen, USA). The resulting double-stranded cDNA fragments were purified with AMPure XP system (Beckman Coulter, USA) followed by end repair, 3′ poly(A) addition, and NEBNext Adaptor ligation. The cDNA fragments of ~200 bp in length were selected and further enriched with PCR amplification to generate the cDNA libraries of P-0h, P-6h, P-24h and Rh-6h for Illumina sequencing. The library quality was evaluated on the Agilent Bioanalyzer 2100 system.

treatment_protocol: The well developed 2-day-old A. sparsifolia seedlings were selected and placed into 12 cm Petri dishes with 2-layer filter paper saturated with the 22% PEG-6000 solution. At 0 h, 6 h and 24 h post treatment, the primary roots were collected to generate an untreated sample (P-0h) as well as two other samples (P-6h and P-24h) that individually represent the early and late responses to water stress in primary roots. Moreover, the seedlings with 24 h of PEG treatment were thoroughly rinsed with sterile distilled water, and then re-transferred to Petri dishes but containing moist filter paper, and cultured for additional 6 h (in total, up to 30h of continuous treatment) to make the sample Rh-6h representing the response to post stress rehydration in primary roots. About 40 seedlings were used in each different treatment, and three independent experiments were performed. The samples were immediately frozen in liquid nitrogen and were stored at -80℃ until use.

tag: developmental stage

value: seedling

value: primary roots


title: P6_Root

source_name: primary roots subjected to 6h of PEG-6000 treatment


title: P24_Root

source_name: primary roots subjected to 24h of PEG-6000


title: Rh6_Root

source_name: primary roots subjected to 24h of PEG treatment following 6h of rehydration


title: 3,5-18 RNA-seq

city: HangZhou

first: Biaoyang

last: Lin

address: 866 Yu Hang Tang Road Zi Jin Gang Campus Zhejiang University.

department: ZCNI

institute: ZheJiang University

data_processing:
Base calling and quality scoring are performed by an updated implementation of Real-Time Analysis (RTA), called RTA v2
TopHat2 v2.0.7
Cufflinks 2.1.1
Genome_build: hg38
Supplementary_files_format_and_content: cufflinks output files, gene expression in fpkm

source_name: tumorigenic progeny of EP156T following EMT

growth_protocol: All cells were grown as monolayers in 6-well plates using standard and published growth conditions (QU, Y (2013) Cancer Research Dec 1;73(23):7090-100 for EP156T and EPT3-M1 and according to the ATCC recommendation for LNCaP, 22RV1 and VCaP cells). For experiments media in the wells were adjusted to the indicated concentrations and for the given time with synthetic androgen R1881 or DMSO vehicle for negative controls.

extract_protocol:
Cells were harvested by adding 700 microliters Trizol lysis buffer to each 6-well immediately following removal of growth medium. Total RNA was purified following the Qiagen miRNeasy protocol followed by DNAse treatment of total RNA.
Total RNA was treated according to STARSeq roitines (2014), including Agilent Bioanlyzer2100, all RIN values >10, rRNA depletion, cDNA synthesis, concentration and quality control (Qubit/Agilent Bioanalyzer), fragmentation and sizing (Covaris TMS2), sequencing preparation with barcoded adapters for muliplexing and Illumina NextSeq 500 sequencing, paired end read, 150 nt, 100 Mio reads.

tag: cell line

value: mesenchymal traits

tag: passages

tag: treatment

value: Treated with only DMSO vehicle


title: 5,9-19 RNA-seq

source_name: from prostate cancer mouse CWR22 xenograft

value: ATCC CRL-2505

tag: cell type

value: Treated with 1 nM R1881 24 hrs


title: 5,4-19 RNA-seq

value: Grown normal medium w/o R1881


title: VSH2

tag: tissue


title: 2,4-18 RNA-seq

source_name: hTERT immortalized prostate basal epithelial cells

value: prostate epithelial cell

value: Treated R1881 10 nM 48 hrs


title: 2,6-18 RNA-seq


title: 7,3-19 RNA-seq

source_name: from prostate cancer vertebral metastasis

value: ATCC CRL-2876

value: VCaP


title: 3,1-18 RNA-seq

source_name: from prostate cancer lymph node metastasis

value: ATCC CRL-1740

value: LNCaP

value: 33 (in our lab)


title: MycT_45751_Dox

city: Omaha

first: Kay-Uwe

last: Wagner

state: NE

address: 985950 Nebraska Medical Center

department: Eppley Institute for Cancer Research

institute: University of Nebraska Medical Center

data_processing:
Sequenced reads were trimmed for adaptor sequence using cutadapt, Sequenced reads were aligned to the mm9 genome assembly using the TopHat program
Fragment Per Kilobase of exon per million fragments mapped (FPKM) were calculated using a protocol. 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.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Pancreatic Tumor

extract_protocol:
Total RNA was extracted from flash-frozen pancreatic cancer tissues before or after doxycycline treatment of tumor transplanted athymic nude mice using the RNeasy Mini Kit (Qiagen).
RNA samples were processed using the TruSeq RNA Sample kit and sequenced using a HiSeq2000 sequencer (Illumina).

treatment_protocol: Orthotopically transplanted pancreatic tumor bearing athymic nude mice were treated with Doxycycline at 100 ug/ml concentration supplemented with 2.5% sucrose via drinking water for 2 weeks.

tag: strain

value: Athymic Nude

value: Pancreatic Tumor

tag: dox treatment days

value: 14 days


title: MycT_39643_NoDox

value: 0 days


title: ToxinSpecific_infected2

city: Sydney

first: Nandan

middle: P

last: Deshpande

state: NSW

address: Kensington Campus

department: School of Biotechnology and Biological Sciences

institute: Systems Biology Initiative

data_processing:
DynamicTrim.pl + LengthSort.pl
Mapped trimmed read to hg19 using tophat/2.0.4
Used htseq-count to get count values for individual samples
Genome_build: hg19
Supplementary_files_format_and_content: Combined counts file.

growth_protocol: Caco-2 cells were grown in Minimal Essential Media, supplemented with 10% v/v Fetal Bovine Serum, 1 mM sodium pyruvate, 0.1 mM non-essential amino acids, 2.25 mg l-1 sodium bicarbonate and 100 μg ml-1 penicillin and streptomycin

extract_protocol:
RNA extraction was performed using the Isolate II RNA Extraction Mini Kit (Bioline)
Illumina TruSeq RNA Sample Prep Kit (version 3) according to manufacturer's instructions, with 2 µg of total RNA being used per sample.

treatment_protocol: Exposure to zonula occludens toxin

value: exposure to zonula occludens toxin


title: ToxinSpecific_infected3


title: ToxinSpecific_Untreated3

treatment_protocol: control

value: control


title: 3,3-18 RNA-seq

value: mesenchymal traits


title: ToxinSpecific_Untreated1


title: MycT_45746_NoDox


title: KrasT_45976_Dox


title: ToxinSpecific_Untreated2


title: 6,7-19 RNA-seq


title: 2,8-18 RNA-seq


title: MycT_45744_Dox


title: G401-sg1-HOXB13

city: Los Angeles

first: Paul-Joseph

last: Aspuria

state: California

address: 8400 Beverly Blvd.

department: Women's Cancer Program

institute: Cedars-Sinai Medical Center

data_processing:
Torrent Suite™ Software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Bowtie
Fragments Per Kilobase of exon per Million reads (FPKM) were calculated using TopHAT and Cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: Excel files contain FPKM counts of each cell line

source_name: rhabdoid tumor of the kidney

growth_protocol: G401 cells were grown in RPMI + 15% FBS and harvested at 80% confluency

extract_protocol:
Qiagen RNeasy kit
Extracted RNA was enriched using the Ribominus™ Eukaryote Kit (Invitrogen). The Ion PI™ Template OT2 200 Kit (Invitrogen) was used to prepare the RNA library for sequencing.

value: kidney

tag: tumor type

value: rhabdoid


title: G401-sg-control


title: KrasT_42274_Dox


title: KrasT_45251_Dox


title: ToxinSpecific_infected1


title: KrasT_39868_NoDox


title: KrasT_45649_NoDox


title: Rop7-II biological replicate 3

city: London

first: Eva

last: Frickel

address: 1 Midland Road

department: Host-Toxoplasma Interaction Laboratory

country: United Kingdom

institute: The Francis Crick Institute

description: non strand-specific RNA-Seq

data_processing:
The RSEM package (version 1.2.11) (Li and Dewey, 2011) was used for the alignment and subsequent gene-level counting of the sequenced reads with respect to mm10 RefSeq genes downloaded from the UCSC Table Browser (Karolchik et al., 2004) on 27th May 2015.
Differential expression analysis between the triplicate groups was performed with DESeq2 (version 1.8.1) (Love et al., 2014) after removal of genes with a maximum transcript per million (TPM) value of 1 across all samples in the experiment.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file containing TPM values generated by RSEM where gene names are rows and columns represent all RNA-Seq samples generated in the study.

source_name: CD8 T-cells that harbour a T-cell receptor recognising the Toxoplasma epitope Rop7 on MHC I

growth_protocol: Cell were grown in RPMI medium 1640 supplemented with 10% fetal bovine serum, L-glutamine, penicillin/streptomycin, β-mercaptoethanol and recombinant mouse IL-2 (10 ng/ml).

extract_protocol:
RNA was isolated using Trizol and the RNeasy Micro-Kit (Qiagen).
A total of 200 ng of RNA was used to prepare the RNA library using TruSeq mRNA Library Prep Kit v2 (Illumina) according to the manufacturer’s recommendations.

treatment_protocol: Cells were incubated overnight at 37°C and 5% CO2. CD3+ CD8+ H-2Ld-Rop7+ cells were sorted, maintained at 4°C and purity determined to be 90-95%.

value: transnuclear mouse strain Rop7-II

value: CD8 T-cells


title: Rop7-III biological replicate 1

description: non strand-specific RNA-Seq

value: transnuclear mouse strain Rop7-III


title: Rop7-III biological replicate 3

description: non strand-specific RNA-Seq


title: Rop7-II biological replicate 2

description: non strand-specific RNA-Seq


title: Rop7-II biological replicate 1

description: non strand-specific RNA-Seq


title: Rop7-III biological replicate 2

description: non strand-specific RNA-Seq


title: Rop7-I biological replicate 2

description: non strand-specific RNA-Seq

value: transnuclear mouse strain Rop7-I


title: Rop7-I biological replicate 1

description: non strand-specific RNA-Seq


title: ATAC-seq_singleSort_nrlKOPhotoreceptor_2

city: St. Louis

first: Joseph

last: Corbo

address: 660 S. Euclid

institute: Washington University School of Medicine

description:
blueCone_2
Processed data file: ATAC-seq_singleSort_nrlKOPhotoreceptor_rep2.nfr.bw
Processed data file: ATAC-seq_countTable.txt
Processed data file: ATAC-seq_singleSort_nrlKOPhotoreceptor_IDR_peaks.narrowPeak

data_processing:
Library strategy: ATAC-Seq
ATAC-seq (alignment): paired-end reads were aligned to mm10 using Bowtie2 (v2.2.3) with a maximum insert size of 2000 (-X 2000).
ATAC-seq (sort): alignments were sorted in coordinate order using Picard (v1.121) SortSam.
ATAC-seq (merge): alignments for individual libraries run on multiple sequencing lanes were merged using Picard (v1.121) MergeSamFiles.
ATAC-seq (filter): alignments were filtered using SAMtools (v1.3) view to retain only properly paired reads (-f 0x0002) with minimum mapping quality 30 (-q 30) not aligning to unlocalized contigs, unassembled contigs, the mitochondrial genome, or ENCODE blacklist regions (-L <POSITION FILE>).
ATAC-seq (remove PCR duplicates): PCR duplicates were marked with Picard (v1.121) MarkDuplicates and removed with SAMtools (v1.3) view (-F 0x0400).
ATAC-seq (filter for nucleosome-free reads): alignments were filtered for fragments with an insert size less than 100 using SAMtools (v1.3) view and awk.
ATAC-seq (generate bedGraph): bedgraph files were generated using HOMER (v4.8) makeUCSCfile (-style DNase -fsize 5e8).
ATAC-seq (call peaks): consensus peaks for each pair of ATAC-seq biological replicates (filtered nucleosome-free reads) were generated using MACS2 (v2.1.0) callpeak (--nomodel --shift -100 --extsize 200 --keep-dup all --pvalue 1e-2 --call-summits) followed by thresholding using the irreproducible discovery rate (IDR) framework.
ATAC-seq (feature counts): 200 bp intervals centered on peak summits were merged across all peak call sets using bedops (v2.4.14) to generate a reference set of photoreceptor ATAC-seq peaks. Each of the resulting intervals was then scored for coverage using bedtools (v2.24.0) coverageBed to generate the ATAC-seq count table used for differential accessibility analysis.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bigWig (ATAC-seq): normalized ATAC-seq reads per genomic interval from filtered nucleosome-free alignment file.
Supplementary_files_format_and_content: narrowPeak (ATAC-seq): consensus (IDR-thresholded) peaks for each cell type.
Supplementary_files_format_and_content: txt (ATAC-seq): count table of ATAC-seq reads for each biological replicate overlapping photoreceptor ATAC-seq peaks.
Supplementary_files_format_and_content: bigWig (RNA-seq): normalized RNA-seq reads per genomic interval (3' bases are dropped from reads flanking exon-intron junctions).
Supplementary_files_format_and_content: txt (RNA-seq): count table of RNA-seq reads for each biological replicate overlapping RefSeq genes.

source_name: nrlKO blue cone photoreceptors

extract_protocol:
Retinas were harvested from eight-week-old mice, dissociated with trypsin, washed with calcium- and magnesium-free HBSS, and resuspended in FACS buffer (1% FBS, 0.1mM EDTA in calcium- and magnesium-free HBSS). GFP-positive cells were isolated via FACS and collected in 10% FBS in PBS.
ATAC-seq libraries were prepared using the standard protocol (Buenrostro et al. 2013).

tag: strain/background

tag: genotype/variation

value: Nrl-eGFP;NrlKO

value: blue cone photoreceptors

tag: purification

value: FACS single sort


title: RNA-seq_singleSort_rod_3

description:
Processed data file: RNA-seq_singleSort_rods_rep3.bw
Processed data file: RNA-seq_countTable.txt

data_processing:
RNA-seq (alignment): single-end RNA-seq reads were aligned to mm10 using STAR (v2.4.2a) (index prepared for mm10 with 50 bp reads and RefSeq gene model included in the iGenomes mm10 Annotations).
RNA-seq (generate bedGraph): bedgraph files were generated using HOMER (v4.8) makeUCSCfile (-fragLength given).
RNA-seq (feature counts): RNA-seq counts overlapping RefSeq genes were generated for each biological replicate using HTSeq (v0.6.1p1) htseq-count (-m union -r pos -i gene_name -a 10 --stranded=no). The resulting RNA-seq count table was used for differential expression analysis.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bigWig (ATAC-seq): normalized ATAC-seq reads per genomic interval from filtered nucleosome-free alignment file.
Supplementary_files_format_and_content: narrowPeak (ATAC-seq): consensus (IDR-thresholded) peaks for each cell type.
Supplementary_files_format_and_content: txt (ATAC-seq): count table of ATAC-seq reads for each biological replicate overlapping photoreceptor ATAC-seq peaks.
Supplementary_files_format_and_content: bigWig (RNA-seq): normalized RNA-seq reads per genomic interval (3' bases are dropped from reads flanking exon-intron junctions).
Supplementary_files_format_and_content: txt (RNA-seq): count table of RNA-seq reads for each biological replicate overlapping RefSeq genes.

source_name: rod photoreceptors

extract_protocol:
Retinas were harvested from eight-week-old mice, dissociated with trypsin, washed with calcium- and magnesium-free HBSS, and resuspended in FACS buffer (1% FBS, 0.1mM EDTA in calcium- and magnesium-free HBSS). GFP-positive cells were isolated via FACS and collected in Buffer RLT (Qiagen).
cDNA was prepared using the SMARTer Ultra Low RNA Kit for Illumina Sequencing - HV (Clontech) per manufacturer's instructions. Subsequent preparation of RNA-seq libraries was performed using standard Illumina protocols.

value: Nrl-eGFP

value: rod photoreceptors


title: RNA-seq_singleSort_nrlKOPhotoreceptor_1

description:
blueCone_1
Processed data file: RNA-seq_singleSort_nrlKOPhotoreceptor_rep1.bw
Processed data file: RNA-seq_countTable.txt


title: RNA-seq_singleSort_nrlKOPhotoreceptor_2

description:
blueCone_2
Processed data file: RNA-seq_singleSort_nrlKOPhotoreceptor_rep2.bw
Processed data file: RNA-seq_countTable.txt


title: RNA-seq_singleSort_nrlKOPhotoreceptor_3

description:
blueCone_3
Processed data file: RNA-seq_singleSort_nrlKOPhotoreceptor_rep3.bw
Processed data file: RNA-seq_countTable.txt


title: ATAC-seq_doubleSort_greenCone_4

description:
Processed data file: ATAC-seq_doubleSort_greenCones_rep4.nfr.bw
Processed data file: ATAC-seq_countTable.txt
Processed data file: ATAC-seq_doubleSort_greenCone_IDR_peaks.narrowPeak

source_name: green cone photoreceptors

extract_protocol:
Retinas were harvested from eight-week-old mice, dissociated with trypsin, washed with calcium- and magnesium-free HBSS, and resuspended in FACS buffer (1% FBS, 0.1mM EDTA in calcium- and magnesium-free HBSS). GFP-positive cells were isolated via FACS and collected in 10% FBS in PBS. Purified cells were sorted a second time to further enrich for GFP-positive cells.
ATAC-seq libraries were prepared using the standard protocol (Buenrostro et al. 2013).

value: green cone photoreceptors

value: FACS double sort


title: ATAC-seq_singleSort_greenCone_1

description:
Processed data file: ATAC-seq_singleSort_greenCones_rep1.nfr.bw
Processed data file: ATAC-seq_countTable.txt
Processed data file: ATAC-seq_singleSort_greenCone_IDR_peaks.narrowPeak


title: ATAC-seq_singleSort_nrlKOPhotoreceptor_1

description:
blueCone_1
Processed data file: ATAC-seq_singleSort_nrlKOPhotoreceptor_rep1.nfr.bw
Processed data file: ATAC-seq_countTable.txt
Processed data file: ATAC-seq_singleSort_nrlKOPhotoreceptor_IDR_peaks.narrowPeak


title: ATAC-seq_doubleSort_greenCone_3

description:
Processed data file: ATAC-seq_doubleSort_greenCones_rep3.nfr.bw
Processed data file: ATAC-seq_countTable.txt
Processed data file: ATAC-seq_doubleSort_greenCone_IDR_peaks.narrowPeak


title: ATAC-seq_singleSort_greenCone_2

description:
Processed data file: ATAC-seq_singleSort_greenCones_rep2.nfr.bw
Processed data file: ATAC-seq_countTable.txt
Processed data file: ATAC-seq_singleSort_greenCone_IDR_peaks.narrowPeak


title: RNA-seq_singleSort_rod_1

description:
Processed data file: RNA-seq_singleSort_rods_rep1.bw
Processed data file: RNA-seq_countTable.txt


title: type III ECs rep2

first: Mingzhao

last: Zhu

address: 15 Da Tun Rd, Chaoyang District

department: Key Laboratory of Infection and Immunity

institute: Institute of Biophysics, Chinese Academy of Sciences

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Adapter sequence and low-quality sequences were trimmed.
For RNA seq data, TopHat (version 2.0.10) were used for sequence alignment to mouse mm9 genome. Gene expression level (FPKM) were calculated using Cufflinks (version 2.1.1).
Genome_build: mm9
Supplementary_files_format_and_content: Cuffdiff exported, gene id,gene short name, locus and FPKM value.

source_name: Thymic sorted endothelial cells

growth_protocol: Subsets of thymic ECs were digested and sorted by FACS. The purity of each sample was at least 90%.

extract_protocol:
RNA was extracted using an RNeasy Plus Micro kit (Qiagen) according to the manufacturer’s instructions. The quality and quantity of the total RNA was assessed using a High Sensitivity NGS Fragment Analysis kit (DNF-486-0500).
The sequencing library was prepared using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB).

treatment_protocol: Thymus tissues were digested with 0.2 mg/ml collagenase I (Sigma), 1U/ml dispase I (Corning) and 0.06 mg/ml DNase I (Roche) in RPMI 1640 medium with 2% FBS for 1 h at 37°C. The digestion was washed with cold PBS and filtered through a 70-μm cell strainer (Biologix Group). The stromal cells were enriched by discontinuous density gradient centrifugation in Percoll (GE Healthcare) (bottom layer = 1.115 g/ml; middle layer =1.06 g/ml; top layer = 2% FBS RPMI 1640). The cells recovered from the upper interface were washed The samples were stained with antibodies against CD45 (30-F11), CD31 (MEC13.3), EpCAM (G8.8), P-selectin (RB40.34), and Ly6C (HK1.4). Dead cells were excluded by staining with propidium iodide (Sigma). Finally, the ECs were sorted as CD31+CD45－EpCAM－and further divided into 3 groups by Ly6C and Selp.

value: sorted endothelial cells

tag: background strain

tag: genotype

value: wildtype

tag: gender

value: Female

value: Thymus

value: 4-6 weeks

tag: surface markers

value: Ly6c-  Selp+


title: type II ECs rep2

tag: age

value: Ly6c+ Selp+


title: type II ECs rep1


title: ATAC-seq_singleSort_rod_2

description:
Processed data file: ATAC-seq_singleSort_rods_rep2.nfr.bw
Processed data file: ATAC-seq_countTable.txt
Processed data file: ATAC-seq_singleSort_rod_IDR_peaks.narrowPeak


title: type III ECs rep1


title: type I ECs rep2

value: Ly6c+ Selp-


title: KrasT_45530_NoDox

value: Athymic Nude

value: Pancreatic Tumor

value: 0 days


title: Rop7-I biological replicate 3

description: non strand-specific RNA-Seq

value: transnuclear mouse strain Rop7-I

value: CD8 T-cells


title: RNA-seq_singleSort_rod_2

description:
Processed data file: RNA-seq_singleSort_rods_rep2.bw
Processed data file: RNA-seq_countTable.txt

value: Nrl-eGFP

value: FACS single sort


title: ATAC-seq_singleSort_rod_1

description:
Processed data file: ATAC-seq_singleSort_rods_rep1.nfr.bw
Processed data file: ATAC-seq_countTable.txt
Processed data file: ATAC-seq_singleSort_rod_IDR_peaks.narrowPeak

value: rod photoreceptors


title: type I ECs rep1


title: R-12h

first: Yinxin

last: Li

address: Nanxincun No. 20, Xiangshan, Haidian District

department: Chinese Academy of Sciences

institute: Institute of Botany

data_processing:
Filtering out artifact sequences using BGI sRNA analysis pipeline.
Genome_build: S. europaea mRNA transcriptome database (NCBI SRA database with accession NO. SRX302090).
Supplementary_files_format_and_content: fasta files including sequence ID, sequence read count and sequence

organism: Salicornia europaea

source_name: root

growth_protocol: The seeds of  S. europaea were sown on vermiculite damped with tap water. After germination, the seedlings were grown in a greenhouse in Beijing Botanical Garden maintained at a thermo period of 25 °C /20 °C day/night temperature, photoperiod of 16 h, and a relative humidity of 50 ± 10%. The seedlings were irrigated weekly with half-strength Hoagland nutrient solution for 30 days.

extract_protocol:
Plant tissues were ground in liquid nitrogen and were added into two volume of extraction buffer containing 2 M NaCl, 25 mM EDTA, 200 mM Tris (pH 8.0), 20 mM sodium borate, 2% PVPP (w/v), 2% CTAB (w/v), 1% LSS (w/v), and 2% b-mercaptoethanol (v/v). The homogenate was then transferred into a sterile disposable polypropylene tube, vortexed vigorously, and incubated at 65°C in a water-bath shaker over 10 min with occasional shaking. Added one volume of chloroform/isoamyl alcohol (24:1, v/v) into the mixture, and then vortexed, followed by centrifuging at 15,000g for 15 min at 4°C. The resulting upper aqueous phase was transferred into another tube containing one volume of water-saturated phenol/chloroform/ isoamyl alcohol (25:24:1, v/v, pH 4.5). Following vortexing, the sample was then centrifuged at 12,000g for 10 min at 4°C. The above step was repeated until a clean interface was observed. The upper phase containing RNA extract was extracted with one volume of chloroform/isoamyl alcohol (24:1, v/v) and centrifuged at 12,000g for 10 min at 4°C. After the upper phase was transferred into another centrifuge tube, a volume of isopropyl alcohol was added into the tube. The mixture was incubated at-20 °C for at least 1 h or sometimes overnight, followed by centrifugation at 15,000g for 15 min at 4°C. Decant the supernatant immediately. The pellet was rinsed with 75% ethanol and collected by centrifugation at 12,000g for 5 min at 4°C for three times. The air-dried pellet was finally dissolved in DEPC-treated water and stored at -80°C.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
plants treated with 200 mM NaCl for 12 hours
The 30-days old S. europaea seedlings were salinized with 200 mM NaCl for 12 h and 7 d. The plants without NaCl treatment was used as control. To make sure all materials collected having the same biological age and growth rhythm, they were treated separately with NaCl at different time points while harvested at the same time.

value: root


title: S-12h

source_name: shoot

value: shoot

value: plants treated with 200 mM NaCl for 12 hours


title: S-7d

treatment_protocol:
plants treated with 200 mM NaCl for 7 days
The 30-days old S. europaea seedlings were salinized with 200 mM NaCl for 12 h and 7 d. The plants without NaCl treatment was used as control. To make sure all materials collected having the same biological age and growth rhythm, they were treated separately with NaCl at different time points while harvested at the same time.


title: Freeze Stress (FS)

city: New Delhi

first: Prakash

middle: Chand

last: Sharma

state: Delhi

address: Sector 16-C, Dwarka

department: University School of Biotechnology

country: India

institute: GGS indraprastha University

description: Sample 3

data_processing:
BLAST（alignment software) (Blast v2.2.21), software（used for the annotation of GO and pathway)
BLAT（alignment software）(Blat v.34 software, used for removing the redundancy of the reference.
SOAP (soap v1.11)，Used for the alignment of Mitochondrial and chloroplast sequences.
Bowtie (bowtie v0.12.3), Used for genome alignment, and format the database.
Cluster (cluster v1.47),  clustering software
Java TreeView (Java TreeView v1.1.4r3), checking the cluster result
Medusa (Medusa v1.5.1), checking the mutual action network result.
Blast2GO Blast2GO, v2.3.5, to get the GO annotation from the blast result.
Genome_build: NCBI non reduntant (nr) database
Supplementary_files_format_and_content: txt including TPM value of tags and fold change of differentially expressed genes with gene id.

organism: Hippophae rhamnoides

source_name: Leaf tissues

growth_protocol: Seabuckthorn (H. rhamnoides L.) seeds were surface sterilized and germinated in dark at room temperature for 3 days. The seedlings were transferred to growth chamber, maintained at 28°C temperature, 55% relative humidity and photoperiod of sixteen hours light and eight hours dark.

extract_protocol:
Leaf tissues were harvested from control (CON) and stress subjected plants (CS and FS)and processed for RNA isolation.
Illumina Gene Expression Sample Prep Kit and Solexa Sequencing Chip (Flowcell) were used for tag preparation and the main instruments used for sequencing included Illumina Cluster Station and Illumina HiSeqTM 2000 System.

treatment_protocol: The 30 days old plantlets, at six leaves stage, were subjected to cold stress (CS) at 4°C and freeze stress (FS) at -10°C treatment for 6 hr. The seedlings grown at 28°C were taken as control (CON).

value: 30 days old plantelets

value: -10°C for 6 hr.

value: Leaf


title: R-7d

value: plants treated with 200 mM NaCl for 7 days


title: R-CK

treatment_protocol:
control plants
The 30-days old S. europaea seedlings were salinized with 200 mM NaCl for 12 h and 7 d. The plants without NaCl treatment was used as control. To make sure all materials collected having the same biological age and growth rhythm, they were treated separately with NaCl at different time points while harvested at the same time.

value: control plants


title: S-CK


title: Cold Stress (CS)

description: Sample 2

value: 4°C for 6 hr.


title: NextSeq_RRBS

city: Royal Parade

first: Andrew

last: Keniry

department: Molecular Medicine

institute: The Waler and Eliza Hall Institute of Medical Research

description: Bisulfite treated genomic DNA

data_processing:
For HiSeq200: Illumina Casava1.7 software used for basecalling.
For NextSeq500: Base calling and quality scoring: Real-Time Analysis v2.4.6,  FASTQ file generation and de-multiplexing: bcl2fastq conversion software v2.15.0.4
Trimming of adapters and low quality base calls was performed with trim_galore
Trimmed reads were then filtered for true RRBS reads (which contain an MspI cut site at the 5’ end of both read 1 and read 2) with trimRRBSdiversityAdaptCustomers.py (NuGEN)
To eliminate potential mapping bias between the alleles, sequencing reads were aligned to a bisulfite converted custom version of the mouse genome (mm10), where SNPs that exist between Mus musculus domesticus and Mus musculus castaneus have been N-masked, using bismark.
Methylation bias in the reads was determined using the bismark_methylation_extractor using the --mbias_only option, and methylation calls were made, excluding the 13 5’ bases of reads due to mbias, using bismark_methylation_extractor.
NOTE: For processing of the NextSeq sample, 6bp were removed from the 5' end of R2 to improve mapping, as discussed in the paper. The methylation calls provided here were produced using this method.
Genome_build: mm10
Supplementary_files_format_and_content: Text file containing methylation calls for each SNP.  Produced by the bismark_methylation_extractor.
Columns:
(1) seq-ID
(2) methylation state
(3) chromosome
(4) start position (= end position)
(5) methylation call
A more detailed description of the Bismark methylation extractor output can be found at:  http://www.bioinformatics.babraham.ac.uk/projects/bismark/Bismark_User_Guide.pdf.

organism: Mus musculus

source_name: E9.5 whole embryo

extract_protocol:
Pregnant females were sacrificed at E9.5 by CO2 asphyxiation and the embryos dissected from deciduae in PBS. Embryo samples were snap frozen in buffer RLT plus (Qiagen) and DNA was later extracted with the AllPrep DNA/RNA Mini Kit (Qiagen) using the manufacturer’s instructions. DNA was treated with RNase A then purified through the DNA Clean and Concentrator column (Zymo).
RRBS libraries were made from 100 ng of purified DNA using the Ovation RRBS Methyl-Seq System (NuGEN), according to the manufacturers recommendations, which includes use of the Qiagen Epitect kit for bisulfite conversion.

value: C57BL/6 x castaneous

value: whole embryo


title: PLC8024 CD133+

city: Hong Kong

first: Chi Ho

address: 6th Floor, The Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam

department: Centre for PanorOmic Sciences

country: Hong Kong

institute: The University of Hong Kong

data_processing:
Sequencing reads were first filtered for adapter and low quality sequences using Cutadapt (Martin 2011) and custom scripts. Low quality reads were defined as sequencing reads with more than 5% unknown bases (‘N’) and reads with more than 50% of the bases having a base quality value of ≤ 10. Reads with length < 40 bp were discarded.
Finally, sequencing reads were filtered for rRNA sequence and remaining high quality reads were used for downstream analysis. The high-quality reads were aligned against human genome assembly (NCBI Build 37.1/hg19) using TopHat v2.0.8b (Kim 2013). Expression estimation and tests for differential expression were processed by Cufflinks v2.0.2 (Trapnell 2013).
Genome_build: Human genome (hg19)

source_name: HCC

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Mini Kit according to the manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CD133+ and CD133- cells were sorted from Huh7 and PLC8024 HCC cells using flow cytometry cell sorting technique

tag: cell fraction


title: PLC8024 CD133-

tag: cell line


title: Huh7 CD133+


title: Huh7 CD133-


title: STAT3 input

first: Bruce

last: Horwitz

address: 77 Ave Louis Pasteur

institute: Brigham and Women's Hospital

description: input

data_processing:
Trim_galore
Bowtie2
MACS2
Genome_build: mm10
Supplementary_files_format_and_content: bigWig normalized read density

source_name: Bone Marrow Derived Macrophages

growth_protocol: Bone marrow precursors were grown in M-CSF conditioned media containing FBS for 5 days prior to stimulation

extract_protocol:
Macrophages were plated at 2 x 107 cells per condition and after stimulation fixed for 10 minutes in 1% formaldehyde.  Chromatin was isolated and sheared by sonication (10 cycles, 20 s on, 30 s rest).  After aliquoting an input fraction, 4 x 106 cells were incubated overnight at 4°C with Protein A Dynabeads pre-coupled with 300ng of anti-STAT3 Ab (Cell Signaling 12640).  After incubation, the beads were washed sequentially with a low salt buffer, high salt buffer, lithium chloride buffer, and TE buffer.  DNA-protein complexes were eluted from the beads with 1% SDS TE buffer at 65°C for 15 min.  Input and IP crosslinks were reversed by overnight incubation at 65°C.  DNA was treated with proteinase K and RNase A before purification with the QIAquick PCR Purification kit.
NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina

treatment_protocol: Untreated, IL-10 (1 ng/mL) for 30 min, LPS (1 ng/mL) for 195 min, LPS for 195 min and IL-10 for the last 30 min of the stimulation

value: Bone Marrow Derived Macrophage

tag: antibody

value: STAT3 (Cell Signaling 12640)


title: STAT3 30min IL-10

description: 30min IL-10


title: STAT3 195min LPS + 30min IL-10

description: 195min LPS + 30min IL-10


title: STAT3 195min LPS

description: 195min LPS


title: STAT3 Untreated

description: Untreated


title: H3K27ac 195minLPS+30min-a10 Rep3

description: 195min LPS +30min IL-10 (a10)

data_processing:
Trim_galore
Bowtie2
MACS2
DiffBind
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited txt of normalized peak values

extract_protocol:
Macrophages were plated at 2 x 107 cells per condition and after stimulation fixed for 10 minutes in 1% formaldehyde.  Chromatin was isolated and sheared by sonication (10 cycles, 20 s on, 30 s rest).  After aliquoting an input fraction, 4 x 10^6 cells were incubated overnight at 4°C with Protein A Dynabeads pre-coupled with 5 µg of anti-H3K27ac Ab (Abcam, ab4729).  After incubation, the beads were washed sequentially with a low salt buffer, high salt buffer, lithium chloride buffer, and TE buffer.  DNA-protein complexes were eluted from the beads with 1% SDS TE buffer at 65°C for 15 min.  Input and IP crosslinks were reversed by overnight incubation at 65°C.  DNA was treated with proteinase K and RNase A before purification with the QIAquick PCR Purification kit.
using NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina

treatment_protocol: Untreated, LPS (1 ng/mL)  for 195 min, LPS and IL-10 (1 ng/mL) for 195 min (c10), LPS for 195 min and IL-10 for the last 30 min of the stimulation (a10)

value: H3K27ac (Abcam ab4729)


title: H3k27ac input

description: Input


title: Control (CON)

description: Sample 1

tag: treatment

value: 28°C for 6 hr.


title: H3K27ac 195minLPS+30min-a10 Rep1

description: 195min LPS +30min IL-10 (a10)

tag: cell type


title: H3K27ac 195minLPS+IL-10-c10 Rep2

description: 195min LPS +c10


title: H3K27ac 195minLPS+IL-10-c10 Rep3

description: 195min LPS +c10


title: H3K27ac 195minLPS+IL-10-c10 Rep1

description: 195min LPS +c10


title: H3K27ac 195minLPS+30min-a10 Rep2

description: 195min LPS +30min IL-10 (a10)


title: 195minLPS+30min-a10 Rep2

description: 195min LPS +30min IL-10 (a10)

data_processing:
Trim_galore
Rbowtie
QuasR qCount
DESeq
Genome_build: mm10
Supplementary_files_format_and_content: csv of normalized expression values

extract_protocol:
Cells were rinsed in PBS and lysed in TRIzol, RNA was purified with qiagen RNeasy Columns
NEB next ribomal depletion followed by NEB Directional RNA Library Prep Kit

treatment_protocol: Untreated, LPS (1ng/mL)  for 195min, LPS and IL-10 (1ng/mL) for 195min (c10), LPS for 195min and IL-10 for the last 30min of the stimulation (a10)


title: H3K27ac untreated Rep3

description: Untreated


title: H3K27ac untreated Rep2

description: Untreated


title: H3K27ac untreated Rep1

description: Untreated


title: H3K27ac 195min  LPS Rep2

description: 195min LPS


title: H3K27ac 195min  LPS Rep3

description: 195min LPS


title: 195min LPS Rep1

description: 195min LPS


title: H3K27ac 195min  LPS Rep1

description: 195min LPS


title: 195minLPS+30min-a10 Rep1

description: 195min LPS +30min IL-10 (a10)


title: 195minLPS+c10 Rep1

description: 195min LPS + IL-10 (c10)


title: 195min LPS Rep2

description: 195min LPS