title: Ad-SOX9-RNAseq_1

data_processing:
RNA-seq libraries were sequenced on Illumina Next-seq 500
Fastq output from sequencing were processed by RNA express (V1.0) App on Illumina basespace website using Deseq programs
Genome_build: Human genome hg19
Supplementary_files_format_and_content: Normalized sequences reads count in csv format; Gene fold enrichment comaprison in csv format

source_name: SOX9 adeno-viral overexpression hDFs

growth_protocol: Human dermal fibroblast cells (hDF) were maintained in DMEM/10%FBS with antibiotics.

extract_protocol:
Total RNAs were isolated with TRIZOL Reagent and treated with DNase I. Treated RNAs were then purified by RNeasy Mini Kit from Qiagen according to manufacturer's instruction
Library were constructed with Truseq Standard mRNA Sample Prep Kit Illumina according to manufacture's instruction

treatment_protocol: Adenoviral overexpressing SOX9 or eGFP were infected to hDF cells at MOI=50

value: dermal fibroblast cells (hDF)

tag: infected with

value: SOX9 adeno-virus

value: day 2 after infection


title: Wild type RNA-seq

status: Public on Jul 01 2015

type: SRA

city: Yangzhou

first: Bingwei

last: Zhang

state: JiangSu

address: 48 Wenhui East Road

department: Agricultural college

country: China

institute: Yangzhou University

description: processed data column: 4-ami-aa

library_source: transcriptomic

data_processing:
Rice genome and gene information was downloaded from the Rice Genome Annotation Project (http://rice.plantbiology.msu.edu). Raw image data derived from sequencing were transformed by culling into sequence data. Prior to mapping reads to the reference database, all sequences were filtered to remove adaptor sequences and low-quality sequences (the percentage of low quality bases with a quality value ≤5 was >50% in a read). The remaining reads were aligned to the rice genome using SOAPaligner/soap2, allowing up to two base mismatches.
ERANGE software (version 4.0) (http://woldlab.caltech.edu/gitweb/) was used to calculate gene expression levels by assigning reads to their site of origin and counting the number of reads. The expression levels of genes from RNA-Seq were normalized by reads per kilo-base per million reads (RPKM) values. For all RPKM values for each gene, the cutoff value for determining gene transcriptional activity was determined based on a 100% confidence threshold.
Genome_build: Rice Genome Annotation Project Reference 7
Supplementary_files_format_and_content: There are 3 columns in FPKM.txt, indicated gene name, FPKM of wild type and mutant, respectively.

molecule: polyA RNA

organism: Oryza sativa Indica Group

source_name: Transcriptome of Wild type

growth_protocol: All plants were grown in a paddy field under normal growth conditions at Yangzhou University, China.The Osam1 mutant, which was derived from an indica variety Zhongxian 3037, was previously induced by 60Co~γ ray radiation. Sequence analysis revealed a two-nucleotide deletion in the second exon of OsAM1, introducing a premature stop codon

extract_protocol:
Total RNA from young panicles in meiosis was prepared from both wild-type and Osam1 mutant plants using Trizol according to the manufacture’s protocol (Invitrogen, http://www.invitrogen.com).
An OligoTex mRNA mini kit (Qiagen) was used to isolate poly (A) mRNA and to prepare a nondirectional Illumina RNA-Seq library with an mRNA-Seq 8 Sample Prep Kit (Illumina). The gel extraction step was modified by dissolving excised gel slices at room temperature to avoid underrepresentation of AT-rich sequences. Purified DNA libraries were amplified by 18 cycles of PCR. The products were loaded onto an Illumina HiSeq2000 instrument and subjected to 100 cycles of paired-end (2×100 bp) sequencing.

tag: genotype/variation

value: wild type

tag: tissue

value: young panicles


title: Osam1 mutant RNA-seq

description: processed data column: 3-AmI-AA

source_name: Transcriptome of Osam1 mutant

value: Osam1 mutant


title: Ad-SOX9-RNAseq_3

city: Los Angeles

first: Xinjun

last: He

state: CA

address: 1425 San Pablo St

department: BROAD CIRM Center

country: USA

institute: University of Southern California

molecule: total RNA

organism: Homo sapiens

tag: cell type

tag: isolation stage


title: Ad-eGFP-RNAseq_3

source_name: eGFP adeno-viral overexpression hDFs

value: eGFP adeno-virus


title: TR2-90 - rep2 - 4% glucose

city: Leuven

first: Kevin

last: Verstrepen

address: Gaston Geenslaan 1

country: Belgium

institute: VIB/KULeuven

description:
glu4-TR2-90.2
TR2_90repeats_4%Glu_FC.txt

data_processing:
Raw reads were filtered using FASTX-Toolkit with Q30 cutoff.
Sequenced reads were trimmed to remove adaptor sequences and low quality reads and then aligned to the S. cerevisiae reference genome (GeneBank version 64) using Tophat 2.0.7 to obtain read numbers
The Trimmed Mean of M-values method (Robinson and Oshlack, Genome Biology 2010) was used to normalize the data and the edgeR Bioconductor package used to determine differentially expressed genes (in each TR2 variant relative to the WT - TR2-63)
Genome_build: SacCer_May2010
Supplementary_files_format_and_content: Tab delimited text files including Log2 fold change in gene expression relative to the WT sample (TR2-63)

organism: Saccharomyces cerevisiae

source_name: cells grown in glucose-rich medium

growth_protocol: Cells were grown  in YP medium supplemented with 4% glucose until exponential phase. Half the volume of each culture was harvested and the second half transferred to medium without glucose for 2 hours before harvest.

extract_protocol:
Cells were lysed with glass beads and total RNA was extracted using the Phenol-Chloroform standard method.
polyA RNA libraries were prepared from 1 ug total RNA using standard illumina protocols and sequenced on an Illumina HiSeq2000

tag: growth protocol

value: glucose-rich medium

tag: strain

tag: growth stage

value: exponential

tag: tandem repeat number

value: 90 repeats


title: Ad-eGFP-RNAseq_2


title: Ad-SOX9-RNAseq_2


title: U32-48K

city: Shanghai

first: shao

last: zhihui

address: Fenglin Road 300

institute: Institute of Plant Physiology & Ecology, SIBS, CAS

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GCF_000196835.1 whole genome using bowtie2(version:2.0.5)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a BEDTools (version:2.16.1) software.
Genome_build: GCF_000196835.1

organism: Amycolatopsis mediterranei U32

source_name: single microbial cell

growth_protocol: Amycolatopsis mediterranei U32 was cultivated in the Bennet medium supplemented with or without nitrate respectively

extract_protocol:
Amycolatopsis mediterranei U32 were centrifuged and then collected, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent and1 ug of  extraced total RNA for the construction of sequencing libraries.
cDNA libraries were prepared for sequencing using standard Illumina protocols

tag: medium

value: Bennet medium with 80mM nitrate

tag: developmental stage

value: 48hour (starionary phase)


title: U32-24K

value: 24hour (mid-log phase)


title: U32-48B

value: Bennet medium without nitrate


title: Control_grain_20 DAA

city: Zhengzhou

first: Jing

state: Henan

address: 95 Wenhua Road

institute: Henan Agricultural University

data_processing:
Illumina HiSeq™ 2000 System used for basecalling
Adaptor sequences, low quality tags (tags with unknown nucleotides N), empty reads and tags which were too long or too short, and tags with only one copy to get clean tags were removed. For annotation, all tags were mapped to the references sequence of Rice Database (http://rice.plantbiology.msu.edu).
Gene expression levels within a given samples were normalized as transcripts per million clean tags (TPM), pointing out the number of transcript copies in every 1 million clean tags.
Genome_build: TIGR 6.1
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...

source_name: grain

growth_protocol: The rice cultivar TN1 (Oryza sativa L.) was employed in this study. This cultivar has been previously shown to accumulate high As concentration in its brown rice (Zhang and Duan, 2008). A pot trial was carried out at the Scientific and Educational Farm of Henan Agricultural University (113°66’ E, 34°75’ N), Zhengzhou in central China. The background concentration of As in the soil was 2.78 mg/kg, and the soil pH was 7.2. For the 20As treatment, As was artificially added to soil with 20 mg/kg As (Na2AsO4.12H2O, 20As), another treatment was 20As+120S, sulfur (S) were supplied artificially with 120 mg/kg (Na2S2O3•5H2O) to the As-added soil (20As+120S).

extract_protocol:
Total RNA extraction was performed according to the manufacturer’s instructions of TRIzol (Invitrogen, USA) and was treated with RNase-free DNase I (Takara, Dalian, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The rice seeds were sown in a nursery plate and grown for 25 days. The pots were filled with 3.0 kg soil without a drainage hole at the bottom. The base fertilizers applied to each pot containing 0.40 g urea, 1.32 g monopotassium phosphate and 0.70 g potassium chloride. Urea of 0.90 g per pot was applied at the rate of 3 to 4 as top dressing at tillering stage and early panicle differentiation stage, respectively. Sulfur was mixed thoroughly with the soil containing base fertilizers, and As was added in liquid form. After a 2-week soil equilibration, the seedlings were transferred to the pots. Four replicates with one plant per pot were set for each treatment and the pots were placed randomly in the greenhouse.

tag: cultivar

value: 20 days after anthesis

value: seed

tag: treatment

value: 0 As, 0 S


title: 20As-S_grain_20 DAA


title: U32-24B


title: rdr2 (dsRNA)

status: Public on Jun 30 2015

city: University Park

first: Michael

middle: J

last: Axtell

state: PA

address: 280 Mueller Lab

department: Biology

institute: Pennsylvania State University

data_processing:
Raw FASTQ files were generated in the Illumina 1.5 format
FASTQ data were groomed with a custom script that 1) identified 3' adapter junctions ( the first occurrent of the sequence "TCGTATGCCG"), and trimmed them, including an additional 3nts of trimming, 2) Trimmed at the first occurrence of  a failed quality base ("B" in the Illumina 1.5 phred+64 encoding), 3) trimmed to remove any polyA (two or more A residues) at the right end of the read, 4) trimmed all reads at the right end to a maximum size of 80nts, and 5) suppressed all reads where the final trimmed size was less than 15 nts.
Groomed FASTQ data were aligned to the Physcomitrella version 1.6 genome assembly (Phytozome "Pp_152") including the plastid and mitochrondrial genomes. Alignments were performed with bowtie (version 0.12.9) using settings "-S -p 4 --best --phred64-quals", and the results passed through a samtools pipeline to create a sorted and indexed BAM alignment.
The counts of reads from each library that overlapped Physcomitrella patens version 2.0 small RNA gene annotations were determined. Reads per million (RPM) were calculated based on the number of aligned reads
Genome_build: Physcomitrella patens version 1.6 (Phytozome Pp_152)
Supplementary_files_format_and_content: Processed data files are tab-delimited text files giving 1) Locus coordinates, 2) Locus names, 3) Read counts, 4) Reads per Million (RPM)

organism: Physcomitrium patens

source_name: 10 day-old protonemata

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

extract_protocol:
Total RNA was extracted with Tri-Reagent (Sigma) per the manufacturer's instructions
dsRNAseq libraries for the Illumina GAIIx were prepared as described by Zheng et al. (2010) (PMID: 20941385). Brief method [excerpted from Zheng et al.]: Total RNA is subjected to one (1X Ribominus) or two (2X Ribominus) rounds of rRNA depletion as per manufacturer’s instructions (Ribominus, Invitrogen (Carlsbad, CA)). Next, these rRNA-depleted RNA samples are treated with a single-strand specific ribonuclease as per manufacturer’s instructions (RNase One, Promega (Madison, WI)). The RNA sample is then used as the substrate for sequencing library construction using the Small RNA Sample Prep v1.5 kit (Illumina, San Diego, CA) as per manufacturer’s instructions.

tag: genotype

value: protonemal tissue


title: rdr6 (dsRNA)


title: Wild-Type (dsRNA)

value: wild-type


title: TR2-14 - rep2 - 4% glucose

description:
glu4-TR2-14.2
TR2_14repeats_4%Glu_FC.txt

value: 14 repeats


title: rdr2 (small RNA)

data_processing:
Raw FASTQ files were generated in the Illumina 1.5 format
FASTQ data were groomed by removal of 3' adapter sequences using ShortStack (version 1.1.0) with adapter sequence "ATCTCGTA". The right-most exact match to this sequence was inferred to be the 3' adapter junction, and was the site of trimming. Reads < 15 after trimming, and reads where the adapter was not found were discarded.
Trimmed FASTQ data was counted to make a table giving the frequencies of each unique small RNA sequence in tab-delimited text format.
Genome_build: n/a
Supplementary_files_format_and_content: Processed data files are tab-delimited text files giving 1) Small RNA sequences, 2) Frequencies

extract_protocol:
Total RNA was extracted with Tri-Reagent (Sigma) per the manufacturer's instructions
small RNA-seq libraries for the Illumina GAII were prepared as described by Zheng et al. (2010) (PMID: 20941385).


title: Wild-Type (small RNA)


title: rdr6 (small RNA)


title: non-responder TAG# 4647

city: Leiden

first: Ron

middle: P

last: Dirks

address: Sylviusweg 74

country: Netherlands

institute: Future Genomics Technologies BV

description: Origin of specimen: commercial eel farm (Passie voor Vis, Sevenum, The Netherlands)

data_processing: Supplementary_files_format_and_content: Microsoft Office Excel file (.xlsx) with the following columns: id; Name; Best hit; Description; Alternate descriptions; Min e-value; Similarity; GO molecular function; GO biological process; GO cellular component; Transcripts; Longest transcript length; Total length; sample 1; sample 2; sample 3; sample 4; sample 5; sample 6; BaseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj

organism: Anguilla anguilla

source_name: ovary

extract_protocol:
Tissues were taken from anterior, posterior and middle parts of gonad from each individual, and stored in RNAlater (Ambion) at -80ºC till RNA extraction. The different parts of gonad tissue of each individual were pooled. Total RNA was isolated from the pooled samples using the Qiagen miRNeasy kit according to the manufacturer’s instructions (Qiagen), and analyzed with an Agilent Bioanalyzer 2100 total RNA Nano series II chip (Agilent). A transcriptome library for each individual was prepared from 1 microgram total RNA, using the Illumina mRNAseq Sample Preparation Kit following the manufacturer’s instructions (Illumina Inc.).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ovary

tag: phenotype

value: non-responder


title: responder TAG# F8E1

value: responder


title: responder TAG# 1305


title: responder TAG# EA90


title: responder TAG# FEB6


title: Nr4a1_ChIPSeq

city: Ichikawa

first: Takashi

last: Sekiya

state: Chiba

address: 1-7-1 Kohnodai

country: Japan

institute: National Center for Global Health and Medicine

description: Regulatory T cells freshly prepared from spleens and lymph nodes

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm10 genome assembly using CLC Genomics Work Bench 6.0.5.
Data were filtered using the specifications; Filter peaks on probability of identical locations of forward and reverse reads, with maximum probability 0.01.
peaks were called using ChIP-seq analysis tool equipped in CLC Genomics Works Bench, with following parameters: with window size 250 bp, maximum false discovery rate 1%.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file includes output of peak callers.

molecule: genomic DNA

organism: Mus musculus

source_name: Regulatory T (Treg) cells

growth_protocol: Cells were freshly prepared by sorting, using FACSAria II (BD).

extract_protocol:
Lysates were clarified from sonicated nuclei and Nr4a1-DNA complexes were isolated with antibody (anti-NR4A1 antibody, clone H1648, cat#PP-H1648-00, lot#A-1, Perseus Proteomics).
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Sample Prep Kit (Cat# IP-202-1012). Briefly, DNA was end-repaired, then protruding 3- 'A' bases were ligated to Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of 250~350 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation, using TruSeq SR Cluster Kit vs-cBot-HS (Cat#GD-401-3001). Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols, Using TruSeq SBS Kit v3-HS (Cat#FC-401-3002).

value: Regulatory T cells

value: spleens and lymph nodes

tag: chip antibody

value: anti-NR4A1 antibody, clone H1648 (Perseus Proteomics, catalog# PP-H1648-00, lot# A-1)


title: Endoderm_Input_ChIPseq

city: Stanford

first: Se-Jin

last: Yoon

address: 300 Pasteur Drive, Alway M311

department: Genetics

institute: Stanford University

description: Input DNA

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequence reads were aligned to the mouse reference genome (mm9; July 2007) using the DNAnexus pipeline.
Peaks called using QuEST 2.4 (Valouev et al., 2008) in the DNAnexus platform (https://dnanexus.com) using a “transcription factor” setting (bandwidth of 30 bp, regions size of 300 bp) and 25-fold ChIP to input enrichment for seeding the regions at less than 0.001 FDR.
Genome_build: mm9
Supplementary_files_format_and_content: peaks called from ChIP samples, in TSV format

source_name: ESC-derived endoderm

growth_protocol: Mouse embryonic stem cells (ESCs) were cultured on gelatin coated plates in the absence of feeder cells. ESC medium was prepared by supplementing knockout DMEM (Invitrogen) with 15% FBS, 1 mM glutamax, 0.1 mM nonessential amino acids, 0.1 mM 2-mercaptoethanol and 1000 units of LIF (Millipore). To inhibit TGF-beta signaling pathway, ESCs were treated with 10 µM SB431542 (Tocris Bioscience) for 24 hours. For endoderm differentiation, ESCs were dissociated by TrypLE Express and cultured in serum-free defined differentiation media consisting of 75% Iscove’s modified Dulbecco’s medium and 25% Ham’s F12 media supplemented with 0.5x of both N2 and B27 (without retinoic acid), 0.05% BSA and 50 µg/ml ascorbic acid (Sigma). At day 2, human Activin A (100 ng/ml; R&D systems) was added to induce endoderm differentiation without dissociation/reaggregation. After 48 hours (day 4), ESC-derived endoderm samples were performed for ChIP-Seq. To inhibit TGF-beta signaling pathway, Activin A was treated with 10 µM SB431542 at day 2, then cultured for 48 hours to get day 4, ESC-derived differentiated samples.

extract_protocol:
Lysates were clarified from sonicated nuclei and ChIP-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Catalog # FC-102-1001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 200~400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.

treatment_protocol: not applicable

value: ESC-derived endoderm

tag: passages


title: Endoderm+SB_HEB_ChIPseq

description: ChIP DNA

value: HEB (Santa Cruz, sc-357, lot G0209)


title: ESC+SB_Input_ChIPseq

description: Input DNA

source_name: Embryonic stem cells

value: Embryonic stem cells


title: ESC+SB_HEB_ChIPseq

description: ChIP DNA


title: MCF7_input

city: London

first: Yichen

last: Xu

address: Du Cane Rd

country: United Kingdom

institute: Imperial College London

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie
peaks were called using MACS1.4 with the default settings
Genome_build: hg19
Supplementary_files_format_and_content: bed and wig files were generated using MACS1.4

source_name: breast cancer cells_MCF7_input

growth_protocol: MCF7 and MDA-MB-231 cells were cultured in DMEM medium supplied with 10% fetal calf serum (FCS) and 1% penicillin and streptomycin

extract_protocol:
Lysates were clarified from sonicated nuclei and LMTK3-DNA complexes were isolated with antibody.
libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: breast cancer cells


title: ESC_SMAD2/3_ChIPseq

description: ChIP DNA

value: SMAD2/3 (R&D Systems, AF3797, lot XHY01)


title: ESC_HEB_ChIPseq

description: ChIP DNA


title: Endoderm+SB_Input_ChIPseq

description: Input DNA


title: non-responder TAG# EC42


title: MDA231_input

source_name: breast cancer cells_MDA231_input


title: V2/xeno/A/A1

city: Rochester

first: Hugues

last: Sicotte

state: MN

address: 200 first street SW

department: Health Sciences Research

institute: Mayo Clinic

description:
Second visit
V2_xeno_A_A1

data_processing:
Image data were processed using the Illumina Standard Pipeline.
Base-calling was performed using Illumina’s RTA version 1.17.21.3.
Xenograft reads were pre-processed using Xenome, with default settings and trained using human hg19 and mouse NOD.CB17-Prkdcsid/J (http://cgd.jax.org/tools/Seqnature.shtml) as the backgound strain, this strain being closest to the SCID mouse used for the Xenograft. Only reads classified as host were kept.
Reads were aligned by TopHat 2.0.6 11 using the hg19 genome. TopHat:--keep-fasta-order, --keep-tmp, --no-coverage-search, --bowtie1, --library-type fr-unstranded, --max-multihits 20, --solexa1.3-quals, --fusion-search, --fusion-ignore-chromosomes chrM, --fusion-min-dist 50000.
HTseq software (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html) from Illumina gene annotation files (http://cufflinks.cbcb.umd.edu/igenomes.html).
Gene fusions were detected using Tophat-Fusion algorithm.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files (Gene counts and RPKM) contain 7 tab separated fields: Chr(Chromosome starting with letters chr), GeneID (Hugo Gene Symbol), Start(1-base coordinates start of Gene), Stop (end coordinate of gene), CodingLength (total size of coding region of gene), GeneCount, RPKM. The last two columns have headers corresponding the sample id followed by _GeneCount and _RPKM respectively.

source_name: Metastasized prostate cancer (xenograft)

growth_protocol: Methods for grafting in NOD SCID mice: All the procedures were performed in accordance with the protocols and guidelines approved by the Institutional Animal Care and Use Committee of Mayo Clinic. Male 4- to 6-week old nonobese diabetic, severe combined immuno-deficient mice (NOD.CB17-Prkdcscid/J) (Jackson Laboratory, Bar Harbor, Maine) were used to generated the PDX models.  The patient biopsy sample for grafting was immersed in CNT-52 medium (Zen-Bio, Research Triangle Park, NC, USA) and immediately transferred to animal surgery room within 1 hour.  Approximately 5 mm3 tissue sample (bone biopsy) mixed with 100 uL Matrigel (Corning, Tewksbury, MA, USA) was implanted under the renal capsule (ref).  The 25 mg 2-month releasing testosterone pellet (Innovative research of America, FL, USA) was subcutaneously injected under the skin between the neck and shoulder and repeated every 2 months.  Four to six months later, once the tumor grows, the grafted mice were euthanized by CO2 inhalation for necropsy and samples were collected for pathology and molecular analysis.

extract_protocol:
Cells were flash frozen on dry ice, and RNA was harvested using Rneasy Plus Mini Ki t(Qiagen). Ribo-zero rRNA remove Kit was used. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used
RNA libraries were prepared according to the manufacturer’s instructions for the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA).  The liquid handling Eppendorf (Hamburg, GER) EpMotion 5075 robot was employed for TruSeq library construction.  All AMPure bead clean up, mRNA isolation, end repair and A-tailing reactions was completed on the 5075 robot.  Reverse transcription and adaptor ligation steps were performed manually.    Briefly, poly-A mRNA was purified from total RNA using oligo dT magnetic beads. The purified mRNA was fragmented at 95°C for 8 minutes, eluted from the beads and primed for first strand cDNA synthesis. The RNA fragments were then copied into first strand cDNA using SuperScript III reverse transcriptase and random primers (Invitrogen, Carlsbad, CA).  Next, second strand cDNA synthesis was performed using DNA polymerase I and RNase H. The double-stranded cDNA was purified using a single AMPure XP bead (Agencourt, Danvers, MA) clean-up step.   The cDNA ends were repaired and phosphorylated using Klenow, T4 polymerase, and T4 polynucleotide kinase followed by a single AMPure XP bead clean-up.  The blunt-ended cDNAs were modified to include a single 3’ adenylate (A) residue using Klenow exo- (3’ to 5’ exo minus).  Paired-end DNA adaptors (Illumina) with a single “T” base overhang at the 3’ end were immediately ligated to the ‘A tailed’ cDNA population.  Unique indexes, included in the standard TruSeq Kits (12-Set A and 12-Set B) were incorporated at the adaptor ligation step for multiplex sample loading on the flow cells.  The resulting constructs were purified by 2 consecutive AMPure XP bead clean-up steps.   The adapter-modified DNA fragments were enriched by 12 cycles of PCR using primers included in the Illumina Sample Prep Kit. The concentration and size distribution of the libraries were determined on an Agilent Bioanalyzer DNA 1000 chip (Santa Clara, CA).  A final quantification, using Qubit fluorometry (Invitrogen, Carlsbad, CA), was done to confirm sample concentration.    mRNA libraries are loaded 2 per lane onto Illumina TruSeq v3 paired end flow cells at concentrations of 9 pM to generate cluster densities of 600,000-800,000/mm2 following Illumina’s standard protocol using the Illumina cBot and TruSeq Rapid Paired end cluster kit version 3.

treatment_protocol: The patient presented with recurrent urinary obstructive symptoms in June 2010. Investigative workup revealed a hard and enlarged prostate and transurethral resection demonstrated an adenocarcinoma with an initial Gleason score (GS) 9 and a presenting PSA (June 2010) of 0.95 ng/dl. He underwent nerve-sparing radical resection of the prostate on October 4, 2010, with final pathology, Gleason 9; pT3b (bilateral seminal vesicles involvement); N0 (0 of 20 lymph nodes positive for metastases) stage and several positive margins. He received adjuvant radiation combined with LHRH analogues for a year. Post therapy his PSA remained undetectable until August 2012 when it increased to 2.9 ng/dl. Staging bone and CT scan abdomen and pelvis were non-revealing for metastasis, but an acetyl choline PET-CT demonstrated multiple sites of bony metastasis. He was re-started on Lupron in October 2012, with bicalutamide for hormone sensitive stage but repeat scans showed progression in February, 2013 to CRPC stage. Prior to initiating therapy for CRPC stage, he underwent a research study biopsy of a metastatic rib lesion for sequencing and developing PDX models. He was treated with Enzalutamide in combination with sipuleucel -T and indoximod on a clinical research trial and underwent a second research biopsy after 12 weeks of continuous treatment with the above combination. At 12 weeks he was found to have image based progressive disease resulting in change of therapy to systemic docetaxel chemotherapy for 4.5 months and subsequently to carboplatin based chemotherapy after further progression on docetaxel.

tag: tumor stage

value: castrate-resistant prostate cancer

tag: mice generation

value: 2nd generation Xenograft

tag: xenograft host

value: NOD SCID mice

tag: tumor treatment stage

value: Post-treatment


title: V2/xeno/A/A2

description:
Second visit
V2_xeno_A_A2


title: V2/xeno/A/B

description:
Second visit
V2_xeno_A_B


title: LMTK3_ChIP_MCF7

source_name: breast cancer cells_LMTK3_ChIP_MCF7

tag: cell type

value: LMTK3 monoclonal antibody (M02), clone 2H6 (Abnova, H00114783-M02)


title: V2/xeno/A

description:
Second visit
V2_xeno_A

value: 1st generation Xenograft


title: Endoderm_HEB_ChIPseq

description: ChIP DNA

tag: strain


title: V1/xeno/B/A

description:
First visit
V1_xeno_B_A

value: Pre-treatment


title: V1/xeno/C/A

description:
First visit
V1_xeno_C_A


title: V1/xeno/B

description:
First visit
V1_xeno_B


title: V1/xeno/C

description:
First visit
V1_xeno_C


title: V1/xeno/A/A

description:
First visit
V1_xeno_A_A


title: ESC_Input_ChIPseq

description: Input DNA


title: V2/met

description:
Second visit
V2_met

source_name: Metastasized prostate cancer (bone)

value: Patient bone tissue


title: V1/met

description:
First visit
V1_met


title: LMTK3_ChIP_MDA231

source_name: breast cancer cells_LMTK3_ChIP_MDA231


title: U8

city: Cold Spring Harbor

first: Wen-Wei

last: Liao

state: New York

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

data_processing:
BS-seq reads were aligned to the hg19 reference genome using the modified bisulfite aligner, BS Seeker2, and only uniquely mapped reads were kept.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data (CGmap) is in text format  containing methylation level per cytosine.  column 1=chromosome id; column 2=C/G (G stands for C on the opposite strand); column 3= chromosomal location; column 4=sequence context (CG/CHG/CHH); column 5=sequence context (CA/CT/CC/CG); column 6=methylation fraction #C/(#C+#T); column 7=number of C (#C); column 8 #C+#T.

source_name: placenta

extract_protocol:
Genomic DNA was extracted from placental tissue using QIAmp DNA mini kit (Qiagen).
Genomic DNA was digested with MspI. They were then ligated with Illumina adaptors, and size selected. Fragments from 40 to 220 bases were selected. These fragments were denatured and treated with sodium bisulfite. Libraries were sequenced using the Solexa sequencing technology (Illumna Hiseq 2000 sequencers). The reads were aligned to the reference genome (hg19) using the modified bisulfite aligner, BS Seeker2.

tag: tissue

value: whole placenta

tag: offspring

value: IUGR


title: FLAG::hrde-1_prg-1_male_herm_input

city: Fort Collins

first: Taiowa

middle: A

last: Montgomery

state: CO

address: 1878 Campus Delivery

department: Department of Biology

institute: Colorado State University

description:
18-30 nt small RNAs
RNA 5' Polyphosphatase Treated RNA

data_processing:
Base calling and fastq files were generated using Illumina software.
A Phred score cutoff is applied.
Small RNA sequences are parsed from adapters.
The number of reads for each sequence is calculated.
The data is formatted as sequence tab reads.
Supplementary_files_format_and_content: Tab-separated (TSV) files containing each sequence, regardless of whether or not they aligned to the genome, and total number of reads were generated using custom perl scripts.

organism: Caenorhabditis elegans

source_name: prg-1; FLAG::hrde-1 (RNAi reset in the absence of piRNAs), input (cell lysate)

growth_protocol: Animals were grown at 20˚C on E. coli strain OP50.

extract_protocol:
Total RNA from cell lysates or FLAG::HRDE-1-bound RNA was isolated by Trizol extraction followed by two rounds of chloroform extractions and precipitated using isopropanol.
Small RNAs were size selected, tobacco acid pyrophosphatase (TAP) or RNA 5' polyphophatase treated to remove 5’ di- and triphosphate groups, ligated to 5’ and 3’ adapters, subjected to reverse transcription, amplified by PCR, and gel purified in preparation for sequencing.

value: Gravid Adults

value: prg-1(n4357) I; FLAG::hrde-1 II


title: U5/Y5


title: FLAG::hrde-1_prg-1_male_IP

source_name: prg-1; FLAG::hrde-1 (RNAi reset in the presence of piRNAs, prg-1+/-), FLAG::HRDE-1 co-IP


title: FLAG::hrde-1_prg-1_male_herm_IP

source_name: prg-1; FLAG::hrde-1 (RNAi reset in the absence of piRNAs), FLAG::HRDE-1 co-IP


title: FLAG::hrde-1_IP

source_name: FLAG::hrde-1 (RNAi reset in the presence of piRNAs), FLAG::HRDE-1 co-IP

value: FLAG::hrde-1 II


title: V1/xeno/A

description:
First visit
V1_metxeno_A


title: Endoderm_SMAD2/3_ChIPseq

description: ChIP DNA

value: ESC-derived endoderm


title: FLAG::hrde-1_input

source_name: FLAG::hrde-1 (RNAi reset in the presence of piRNAs), input (cell lysate)


title: FLAG::hrde-1_prg-1_male_input

source_name: prg-1; FLAG::hrde-1 (RNAi reset in the presence of piRNAs, prg-1+/-), input (cell lysate)


title: U10/Y10


title: U4


title: mut-14smut-1_x_mut-16

description:
18-30 nt small RNAs
TAP Treated RNA

source_name: mut-14 smut-1 x mut-16, F1 progeny


title: prg-1_x_prg-1

description:
18-30 nt small RNAs
TAP Treated RNA

source_name: prg-1 x prg-1, F1 progeny


title: IP control XEN2

first: Kathy

last: Niakan

address: Mill Hill

institute: The Francis Crick Institute

description: processed data file: Gata6_ChIP-seq_peaks_XEN_cells2.xlsx

data_processing:
ChIP-seq data was assessed using the FASTQC program for quality (Babraham Bioinformatics). Any residual adapters were removed using Trim Galore! (Babraham Bioinformatics). Read were aligned to the UCSC mouse mm9 or mm10 reference genomes using Bowtie2 (Langmead and Salzberg, 2012). Only uniquely matched reads were retained using a sed command. Aligned reads (SAM files) were then transformed into a BED format and subsequently used to generate bigwig files. The bigwig files were visualized using the IGV browser (Robinson et al., 2011). Gata6 36-hour post doxycycline or eXEN cell replicates were compared using wigcorrelate and individual BAM files were merged. Candidate peaks were obtained using either CisGenome or MACS2 with an FDR <0.01. Peaks were called relative to input control samples. Gene annotation was performed using HOMER (Heinz et al., 2010).
genome build: mm9
processed data files format and content: Excel file Gata6 binding enrichment over input control: Gata6_ChIP-seq_peaks_XEN_cells2.xlsx

source_name: Extraembryonic endoderm stem cell line2

growth_protocol: XEN media: RPMI 1640, 15% fetal bovine serum (Hyclone), 2mM L-glutamine; 0.1mM B-mercaptoethanol, 1% penicillin/streptomycin

extract_protocol:
Immunoprecipitation was performed on 1-2 x107 XEN cells as described (Vokes et al., 2007) no primary antibody control. Sonication was performed using a Covaris sonicator.
Indexed libraries were prepared using the Illumina TruSeq ChIP Sample Preparation Kit according to the standard protocol. The libraries were sequenced on an Illumina HiSeq2000 with 50bp paired-end reads.

treatment_protocol: Standard XEN media

value: extraembryonic endoderm stem cell

value: Input control XEN cell line2 in standard maintenance media


title: U3/Y3


title: Ad-eGFP-RNAseq_1

source_name: eGFP adeno-viral overexpression hDFs

value: dermal fibroblast cells (hDF)

tag: infected with

value: eGFP adeno-virus

tag: isolation stage

value: day 2 after infection


title: wt_x_wt

description:
18-30 nt small RNAs
TAP Treated RNA

source_name: wild type x wild type, F1 progeny

tag: developmental stage


title: U2


title: IP control XEN1

description: processed data file: Gata6_ChIP-seq_peaks_XEN_cells.xlsx

data_processing:
ChIP-seq data was assessed using the FASTQC program for quality (Babraham Bioinformatics). Any residual adapters were removed using Trim Galore! (Babraham Bioinformatics). Read were aligned to the UCSC mouse mm9 or mm10 reference genomes using Bowtie2 (Langmead and Salzberg, 2012). Only uniquely matched reads were retained using a sed command. Aligned reads (SAM files) were then transformed into a BED format and subsequently used to generate bigwig files. The bigwig files were visualized using the IGV browser (Robinson et al., 2011). Gata6 36-hour post doxycycline or eXEN cell replicates were compared using wigcorrelate and individual BAM files were merged. Candidate peaks were obtained using either CisGenome or MACS2 with an FDR <0.01. Peaks were called relative to input control samples. Gene annotation was performed using HOMER (Heinz et al., 2010).
genome build: mm9
processed data files format and content: Excel file Gata6 binding enrichment over input control: Gata6_ChIP-seq_peaks_XEN_cells.xlsx

source_name: Extraembryonic endoderm stem cell line1

tag: treatment

value: Input control XEN cell line1 in standard maintenance media


title: Gata6 ChIP XEN2

value: Gata6 ChIP XEN cell line2 in standard maintenance media

tag: antibody

value: anti-Gata6 (R&D, catalog number AF1700)


title: Gata6 ChIP XEN1

value: Gata6 ChIP XEN cell line1 in standard maintenance media


title: G6L1 IP control 36h+d Line2

description: processed data file: Gata6_ChIP-seq_peaks_36h_post_dox.xls

data_processing:
ChIP-seq data was assessed using the FASTQC program for quality (Babraham Bioinformatics). Any residual adapters were removed using Trim Galore! (Babraham Bioinformatics). Read were aligned to the UCSC mouse mm9 or mm10 reference genomes using Bowtie2 (Langmead and Salzberg, 2012). Only uniquely matched reads were retained using a sed command. Aligned reads (SAM files) were then transformed into a BED format and subsequently used to generate bigwig files. The bigwig files were visualized using the IGV browser (Robinson et al., 2011). Gata6 36-hour post doxycycline or eXEN cell replicates were compared using wigcorrelate and individual BAM files were merged. Candidate peaks were obtained using either CisGenome or MACS2 with an FDR <0.01. Peaks were called relative to input control samples. Gene annotation was performed using HOMER (Heinz et al., 2010).
genome build: mm10
processed data files format and content: Excel file FLAG-tagged Gata6 binding enrichment over input control: Gata6_ChIP-seq_peaks_36h_post_dox.xls

source_name: Mouse embryonic stem cell line2

growth_protocol: KSR+LIF media: Advanced DMEM/F12, 20% Knockout serum replacer, 2mM L-glutamine; 0.1mM B-mercaptoethanol, 1% penicillin/streptomycin, 10ng/mL LIF

extract_protocol:
Immunoprecipitation was performed on 1-2 x107 cells as described (Vokes et al., 2007) no primary antibody control. Sonication was performed using a Misonix 4000 (28 cycles: 15 seconds on and 45 seconds off at an intensity of 70%) with a Microtip Probe (Misonix, Farmingdale, NY).
Indexed libraries were prepared using the Illumina TruSeq ChIP Sample Preparation Kit according to the standard protocol. The libraries were sequenced on an Illumina HiSeq2000 with 50bp paired-end reads.

treatment_protocol: Induction of mES cells was performed in pluripotency maintenance media (KSR+LIF) using doxycycline at a final concentration of 1 μg/mL

value: embryonic stem cell

value: Input control in FLAG-tagged Gata6 in embryonic stem cell line2 36h following Gata6 induction


title: prg-1mut-14smut-1_x_prg-1mut-16

description:
18-30 nt small RNAs
TAP Treated RNA

source_name: prg-1; mut-14 smut-1 x prg-1 mut-16, F1 progeny

tag: genotype


title: L6

value: whole placenta

value: LGA


title: G6L1 FLAG-ChIP 36h+d Line2

extract_protocol:
Immunoprecipitation was performed on 1-2 x107 cells as described (Vokes et al., 2007). Sonication was performed using a Misonix 4000 (28 cycles: 15 seconds on and 45 seconds off at an intensity of 70%) with a Microtip Probe (Misonix, Farmingdale, NY).
Indexed libraries were prepared using the Illumina TruSeq ChIP Sample Preparation Kit according to the standard protocol. The libraries were sequenced on an Illumina HiSeq2000 with 50bp paired-end reads.

value: ChIP for FLAG-tagged Gata6 in embryonic stem cell line2 36h following Gata6 induction

value: anti-FLAG (Sigma, catalog number F1804)


title: L4


title: L1


title: Nfix-/- rep2

city: Buffalo

first: Bo

last: Zhou

state: NY

address: 701 Ellicott st

department: Biochemistry

institute: University at Buffalo

data_processing:
Sequenced reads were trimmed for adaptor sequence, and mapped to mm9 whole genome using tophat 2.0.7 with parameters -G <uscs gene gtf file> -p 24
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks 1.3.0 with parameters -upper-quartile-norm, -frag-bias-correct <ucsc mm9 fasta file>, -multi-read-correct <ensembl Mus musculus gtf file>
Differential epression (Nfix-/- vs. WT) for each gene was tested based on the FPKM values in each sample using Cuffmerge and Cuffdiff included in the Cufflinks, following the paper <Trapnell, 2012, Nature Prodocols>
Genome_build: mm9
Supplementary_files_format_and_content: fpkm_tracking files contain tab-delimited text files include FPKM values for each sample; text file on series record contains differential expresssion testing for genes

source_name: brain SVZ-derived primary neural stem cells

growth_protocol: Cells were dissociated from postnatal day 10 SVZ, seeded on poly-l-lysine and Laminin treated wells and cultured in proliferation medium for 10 days. Medium consisted of DMEM/F12, B27, 2mM L-Glutamine, 20 ng/ml human EGF and 20ng/ml huamn FGF2

extract_protocol:
RNA was harvested and purified using Norgen total RNA purification micro kit. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared using illumina TruSeq RNA sample preparation kit

value: C57BL/6/129 F1 hybrid

value: brain

tag: Sex

value: female

tag: age

value: post natal day 10

value: Nfix-/-


title: Nfix-/- rep1

value: brain SVZ-derived primary neural stem cells

value: male


title: WT rep2

value: wild type


title: Nfix-/- rep3


title: C25

value: AGA


title: WT rep3


title: WT rep1


title: EB_activin+_shHEB_rep3

data_processing:
Basecalls performed using CASAVA version 1.8.2
Read sequences were trimmed to remove the 3SEQ adapters and leading or trailing low-quality bases using Trimmomatic 0.32 with parameters ILLUMINACLIP 2:30:5, LEADING:3, TRAILING:3
Trimmed reads were aligned by STAR 2.3.0e to the mm9 reference genome and a reference transcriptome prepared by combining Ensembl gene annotations with ENCODE RNA-seq data from E14 mouse ESCs using Cufflinks 2.2.1; candidate splice junctions that were both non-canonical and unannotated were discarded
Reads were counted in the last 1 kb of each transcript by the featureCounts tool in Subread 1.4.5,
Transcript read counts were tested for significant differences between HEB and control shRNA by DESeq2 1.2.8, analyzing each cell/treatment group indepedently; transcripts with no reads from any library were ignored
Genome_build: mm9
Supplementary_files_format_and_content: transcripts.gtf: transcript annotations from Ensembl + ENCODE RNA-seq, used for read alignment
Supplementary_files_format_and_content: transcripts_last1000.gtf: last 1 kb of each transcript annotation, used for read counting
Supplementary_files_format_and_content: transcript_counts.tsv: read counts from each library in each transcript's last 1 kb
Supplementary_files_format_and_content: DESeq2_analysis_*.tsv: results of DESeq2 analysis, including significance test and regularized log transformation of read counts

source_name: ESC-derived embryoid body

growth_protocol: Mouse embryonic stem cells (ESCs) were cultured on gelatin coated plates in the absence of feeder cells. ESC medium was prepared by supplementing knockout DMEM (Invitrogen) with 15% FBS, 1 mM glutamax, 0.1 mM nonessential amino acids, 0.1 mM 2-mercaptoethanol and 1000 units of LIF (Millipore). To inhibit TGF-beta signaling pathway, ESCs were treated with 10 µM SB431542 (Tocris Bioscience) for 24 hours. For defined embryoid body (EB) differentiation, ESCs were dissociated by TrypLE Express and cultured in serum-free defined differentiation media consisting of 75% Iscove’s modified Dulbecco’s medium and 25% Ham’s F12 media supplemented with 0.5x of both N2 and B27 (without retinoic acid), 0.05% BSA and 50 µg/ml ascorbic acid (Sigma).

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen), and messenger RNA (mRNA) was purified from the total RNA using Dynabeads Oligo(dT)25 (Invitrogen) according to the manufacturer's instructions.
RNA sequencing libraries were built using an approach which targets the 3′ end (3SEQ) as described previously (Beck et al., 2010). Heat sheared mRNA was reverse transcribed with the P7_oligo-dT Index primers. The P5 linker was then ligated to the free end, and the linker-ligated cDNA was size-selected for 200-350 bp fragments by 3% Nusieve agarose gels (Lonza). The selected DNA was amplified using primers P5 and P7_Index for 15 cycles, and the amplified product was second size-selected for 200-350 fragments. The purified library quality was assessed using Bioanalyzer and Qubit, and sequenced on the Illumina HiSeq 2000 with multiplexing.

treatment_protocol: At day 2, human Activin A (100 ng/ml; R&D systems) was added to induce endoderm differentiation without dissociation/reaggregation.

tag: passages

tag: activin treatment

value: yes


title: G6L1 FLAG-ChIP 36h+d Line1

source_name: Mouse embryonic stem cell line1

value: ChIP for FLAG-tagged Gata6 in embryonic stem cell line1 36h following Gata6 induction


title: EB_activin+_shHEB_rep1


title: C14

source_name: placenta


title: EB_activin+_shHEB_rep2


title: L7


title: EB_activin+_shControl_rep1


title: EB_activin-_shHEB_rep3

value: no


title: EB_activin-_shHEB_rep2


title: G6L1 IP control 36h+d Line1

value: embryonic stem cell

value: Input control in embryonic stem cell line1 36h following Gata6 induction


title: C1

value: whole placenta


title: EB_activin+_shControl_rep3


title: EB_activin-_shControl_rep3


title: EB_activin-_shHEB_rep1


title: M2

description: processed data file: RNA-seq_analysis_GATA6_induction_hESCs.xlsx

data_processing:
Paired-end reads were aligned to the human genome (hg19/GRCh37 ) using TopHat2 (Kim et al., 2013). BAM files were sorted and converted into SAM files using SAMtools (Li et al., 2009). The python package HTSeq (Anders et al., 2015) was then used to calculate read counts for each ensemble gene model (release 74), and these values were normalized by both gene length and sequencing depth to generate RPKM expression values.
genome build: hg19
processed data files format and content: Excel file containing RNAseq analysis of GATA6 induction in hES cells (day 6) and control hES cells in KSR or mTeSR media: RNA-seq_analysis_GATA6_induction_hESCs.xlsx

source_name: Human embryonic stem cells

growth_protocol: hESC media: H9 and H1 hES cells (WiCell) were cultured in mTeSR1 (Stemcell Technologies) on Matrigel (BD Biosciences) coated dishes.

extract_protocol:
Cells were trypsimized and 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

treatment_protocol: Uninduced control

value: hESC line2 in mTeSR media


title: C4


title: EB_activin-_shControl_rep2


title: M1

value: hESC line1 in mTeSR media


title: ESC_shHEB_rep3

source_name: Embryonic stem cells


title: C16


title: ESC_shHEB_rep2


title: K1

growth_protocol: hESC media: H9 and H1 hES cells (WiCell) were cultured in KSR media: Advanced DMEM/F12, 20% Knockout serum replacer, 2mM L-glutamine; 0.1mM B-mercaptoethanol, 1% penicillin/streptomycin,

value: hESC line1 in KSR media


title: EB_activin-_shControl_rep1


title: EB_activin+_shControl_rep2


title: ESC_shControl_rep2


title: G6 M2

value: Gata6 overexpressing hESC line2 in mTeSR media


title: ESC_shControl_rep3


title: RNA-seq_hlp1

city: Beijing

first: xiaofeng

last: cao

address: West Lincui Road, Chaoyang District

department: State Key Laboratory of Plant Genomics

institute: Institute of Genetics and Developmental Biology

data_processing:
Two independent CLIP-seq libraries (wild type HLP1 and △RRM) were sequenced on Illumina GAⅡ. 3'-end adaptors and the 5'-end four barcodes were removed using FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit). Tags less than 14 nt in length or adapter-only were discarded. Tags ranging from 14～19 nt (no mismatch allowed) and tags ≥ 20 nt (two mismatches allowed) were aligned to the Arabidopsis genome (TAIR10) using bowtie (0.12.7) (Langmead et al., 2009). The identical sequences with the same 4 nt random barcodes were regarded as one tag to exclude PCR duplication. The RNA-seq libraries for Col, hlp1-1, atprmt10-1 and double mutants were constructed according to strand-specific mRNA-Seq Sample Preparation Protocol. All the raw RNA-seq reads were aligned to the Arabidopsis genome (TAIR10) by using TopHat (1.3.0) (Trapnell et al., 2009) with no more than six mismatches. PAS-seq tags less than 20 nt were discarded. All tags more than 50nt were trimmed to 50 nt and reversely complemented because the tags were sequenced from 3' end of transcripts (Fu et al., 2011). Then trimmed tags were mapped to the Arabidopsis genome (TAIR10) using bowtie (0.12.7) (Langmead et al., 2009), allowing 2 mismatches. Only unique mapped tags from CLIP-seq/RNA-seq/PAS-seq were kept for downstream analyses and were tranfered into wiggle files which can be displayed in IGV (Robinson et al., 2011).
Genome_build: TAIR10

organism: Arabidopsis thaliana

growth_protocol: All of the Arabidopsis thaliana lines used in this study were in the Col background. Plant growth, flowering time analysis, and plant transformation were performed as reported previously (Pei et al., 2007).

extract_protocol: 12-day-old seedlings (from MS plates containing 3% sucrose grown under LD at 23°C) expressing either CFP-HLP1 or CFP-HLP1ΔRRM were soaked in ice-cold PBS buffer and irradiated twice for 400 mJ/cm2 in the Hoefer UVC 500 Ultraviolet Crosslinker (GE). CLIP experiment was performed as described (Licatalosi et al., 2008; Xue et al., 2009). Poly(A) site sequencing was performed as described (Fu et al., 2011; Shepard et al., 2011). Briefly, poly(A) RNAs were purified using the mRNA purification kit (Invitrogen), and heat fragmented at 95°C for 30 min. Reverse transcription (Superscript Ⅱ, Invitrogen) was performed using our modified HITS-3’ adaptor at 42°C for 30 min, then add the HITS-5’ adaptor (a SMART oligo) and incubated for additional 30 min. The cDNAs were purified using the Qiagen PCR Cleanup kit and the second strand cDNAs were synthesized by 3 cycles PCR using Phusion DNA polymerase (NEB) and the PE1.0 and PE2.0 primers. The PCR products were separated by 2% agarose gel and the 200-300 bp bands were excised and purified. Gel-extracted DNAs were further amplified by a 13-cycle PCR. The PCR products were purified using the Qiagen PCR Cleanup kit. TA-cloning was performed before Illumina GA Ⅱ sequencing.

treatment_protocol: The seedlings were ground into fine power in liquid nitrogen and RNA was extracted by TRNzol reagent (Tiangen).

value: seedlings

tag: tag


title: 20As_grain_20 DAA

data_processing:
Illumina HiSeq™ 2000 System used for basecalling
Adaptor sequences, low quality tags (tags with unknown nucleotides N), empty reads and tags which were too long or too short, and tags with only one copy to get clean tags were removed. For annotation, all tags were mapped to the references sequence of Rice Database (http://rice.plantbiology.msu.edu).
Gene expression levels within a given samples were normalized as transcripts per million clean tags (TPM), pointing out the number of transcript copies in every 1 million clean tags.
Genome_build: TIGR 6.1
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...

source_name: grain

extract_protocol:
Total RNA extraction was performed according to the manufacturer’s instructions of TRIzol (Invitrogen, USA) and was treated with RNase-free DNase I (Takara, Dalian, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: 20 days after anthesis

value: seed


title: ESC_shHEB_rep1


title: G6 M1

value: Gata6 overexpressing hESC line1 in mTeSR media


title: G6 K1

value: Gata6 overexpressing hESC line1 in KSR media


title: CLIP-seq_HLP1

data_processing:
Library strategy: CLIP-Seq
Two independent CLIP-seq libraries (wild type HLP1 and △RRM) were sequenced on Illumina GAⅡ. 3'-end adaptors and the 5'-end four barcodes were removed using FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit). Tags less than 14 nt in length or adapter-only were discarded. Tags ranging from 14～19 nt (no mismatch allowed) and tags ≥ 20 nt (two mismatches allowed) were aligned to the Arabidopsis genome (TAIR10) using bowtie (0.12.7) (Langmead et al., 2009). The identical sequences with the same 4 nt random barcodes were regarded as one tag to exclude PCR duplication. The RNA-seq libraries for Col, hlp1-1, atprmt10-1 and double mutants were constructed according to strand-specific mRNA-Seq Sample Preparation Protocol. All the raw RNA-seq reads were aligned to the Arabidopsis genome (TAIR10) by using TopHat (1.3.0) (Trapnell et al., 2009) with no more than six mismatches. PAS-seq tags less than 20 nt were discarded. All tags more than 50nt were trimmed to 50 nt and reversely complemented because the tags were sequenced from 3' end of transcripts (Fu et al., 2011). Then trimmed tags were mapped to the Arabidopsis genome (TAIR10) using bowtie (0.12.7) (Langmead et al., 2009), allowing 2 mismatches. Only unique mapped tags from CLIP-seq/RNA-seq/PAS-seq were kept for downstream analyses and were tranfered into wiggle files which can be displayed in IGV (Robinson et al., 2011).
Genome_build: TAIR10


title: G6 K2

value: Gata6 overexpressing hESC line2 in KSR media


title: RNA-seq_col

value: col


title: OA chondrocyte 4 (OA4)

first: Nidhi

last: Bhutani

state: California

address: 300 Pasteur Drive, R164 Edwards Bldg

department: Orthopaedic Surgery

data_processing:
Library strategy: hMe-Seal/5hmC-seq
QC and filtering: Good-quality reads were obtained by an iterative quality check (FastQC http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and filtering procedure, with trimming of the first 6 bases (Cutadapt http://code.google.com/p/cutadapt/).
Alignment: The Burrows-Wheeler Aligner, version 0.7.5a-r405 (http://bio-bwa.sourceforge.net/) (Li and Durbin 2009), was used with default parameters to align the filtered and trimmed reads to the human reference genome (hg19). Alignments with a MAPQ score of greater than 5 were used for downstream analyses.
Peak calling: diffReps (Shen et al. 2013) was used for peak calling with default settings. The 4 normal samples were treated as biological replicates for the control group and the 4 OA samples were treated as biological replicates for the treatment group.
Data visualization: To identify the distribution of 5hmC throughout the gene body and around the TSS, ngs.plot (Shen et al. 2014) was used with default settings.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: The processed data file is a tab-delimited text file that contains peak calls generated using diffReps.

source_name: OA chondrocytes

growth_protocol: Human chondrocytes were isolated from patients undergoing TKR (OA samples) or ACL revisions (normal samples). Additional normal samples were obtained commercially. Cells were expanded for two passages in standard chondrocyte growth medium, before DNA extraction.

extract_protocol:
Total DNA was extracted and enriched for 5hmC using the Hydroxymethyl Collector (Active Motif) as per manufacturer's guidelines.
Libraries were prepared using enriched DNA and the NEBNext DNA Library Prep Master Mix Set for Illumina (NEB) as per manufacturer's guidelines. 500ng of enriched DNA was used for each library.

tag: donor disease status

value: osteoarthritis

value: chondrocytes

tag: enrichment type

tag: method for enrichment

value: Hydroxymethyl Collector (Active Motif)


title: OA chondrocyte 2 (OA2)

tag: cell type


title: OA chondrocyte 3 (OA3)


title: Normal chondrocyte 3 (N3)

source_name: Normal chondrocytes

value: normal


title: Normal chondrocyte 4 (N4)


title: K2

value: embryonic stem cell

value: hESC line2 in KSR media


title: Normal chondrocyte 1 (N1)


title: Normal chondrocyte 2 (N2)


title: C7

tag: tissue

value: whole placenta

tag: offspring

value: AGA


title: ESC_shControl_rep1

tag: strain

value: no


title: CNE1-BART1

city: Guangzhou

first: Xin

last: Li

state: Province

address: Southern medical university

department: Cancer research institute

institute: Southern medical university

description: Sample 2

data_processing:
The original image data is transfered into sequence data by base calling, which is defined as raw data or raw reads and saved as fastq files.
To get the clean reads, removing the dirty raw reads is needed before data analysis. Filter steps: 1. Remove reads with adaptors; 2. Remove reads in which unknown bases are more than 10%; 3. Remove low quality reads (the percentage of the low quality bases of quality value <5 is more than 50% in a read)
Clean reads were mapped to reference sequences using SOAPaligner/soap2. Mismatches no more than 2 bases were allowed in the alignment.
Genome_build: hg19
Supplementary_files_format_and_content: RPKM values for each Sample .

growth_protocol: Human nasopharyngeal carcinoma cell line CNE1 was cultured in RPMI 1640 with 10% new born cow serum.

extract_protocol:
Total RNA isolated with TRIzol reagent was treated with RNase-free DNase (NEB) at 37 oC for 10 minutes. The Dynabeads mRNA Purification Kit (Life Technologies) was used to isolate mRNA from the total RNA samples.
According to the manufacturer’s instructions, the mRNA was chemically fragmented by the use of divalent cations and converted into single-stranded cDNA using random hexamer primers and SuperscriptⅡ reverse transcriptase (Life Technologies). The second strand was generated to create double-stranded cDNA using RNase H (Enzymatics) and DNA polymerase. The cDNA products was purified by Ampure beads XP (Beckman).After converting the overhangs into blunt ends using T4 DNA polymerase and Klenow DNA polymerase, an ‘A’ base was added to the 3’ end of the DNA fragments by the polymerase activity of Klenow fragment. Sequencing adapters were subsequently ligated to the ends of the cDNA fragments using T4 DNA Ligase (Enzymatics). The fragments of 200bp were selected by Ampure beads XP (Beckman) and enriched by 12 cycles of PCR. The PCR products were loaded into flowcell to generate clusters and then sequenced by Hiseq 2000 (Illumina).

treatment_protocol: CNE1 cells were infected with EBV-miR-BART1/3/7 and their control lentivirus seperately according to the manufacture's protocol.

tag: cell line

value: human nasopharyngeal carcinoma cells

tag: infected with

value: EBV-miRNA-BART1 lentivirus


title: CNE1-MOCK

description: Sample 1

value: control lentivirus


title: Wild-type small RNAs - "old wild-type" - batch 1, biological rep 1 of 2

description: 3' adapter: TGGAATTC; barcode index: 10

data_processing:
For barcoded samples, libraries were deconvoluted using the Illumina pipeline
FASTQ files were trimmed to remove 3' adapters and converted to FASTA format using the script "trim_illumina_sRNA_fastq.pl", version 0.4 (available at http://axtell-lab-psu.weebly.com/tools.html) with settings -e 1 -q N -a TGGAATTC.
The frequency of each unique trimmed read was then counted
Genome_build: N/A
Supplementary_files_format_and_content: Processed files are simple tab-delimited text files with column1 being the sequence and column two being the frequency of occurence for the sequence.

source_name: 10-day old protonemata

growth_protocol: Plants were blended in water and grown on a cellophane overlaid-minimal BCD medium supplemented with 50 uM ammonium tartrate under 16h light/8h dark regime in 25 °C for 10 days.

extract_protocol:
Total RNA was isoated using miRNeasy Mini kit (Qiagen) following the manufacturer's instructions.
Samples were prepared with the Illumia TruSeq Small RNA sample prep kit per the manufacturer's instructions, and were barcoded.

value: Gransden, old

tag: developmental stage

value: 10-day old protonemata


title: Wild-type small RNAs - "old wild-type" - batch 1, biological rep 2 of 2

description: 3' adapter: TGGAATTC; barcode index: 11


title: CNE1-BART3

description: Sample 3

value: EBV-miRNA-BART3 lentivirus


title: Wild-type small RNAs - "2009 wild-type" - batch 3, biological rep 2 of 2, technical replicate 2

description: 3' adapter: TGGAATTC; barcode index: 5

value: Gransden, 2009 collection


title: CNE1-BART7

description: Sample 4

value: EBV-miRNA-BART7 lentivirus


title: Wild-type small RNAs - "2009 wild-type" - batch 3, biological rep 1 of 2, technical replicate 2

description: 3' adapter: TGGAATTC; barcode index: 4


title: rdr6_Apr1N

data_processing:
FASTQ data were groomed by removal of 3' adapter sequences using ShortStack (version 1.1.0) with adapter sequence "ATCTCGTA". The right-most exact match to this sequence was inferred to be the 3' adapter junction, and was the site of trimming. Reads < 15 after trimming, and reads where the adapter was not found were discarded.
Trimmed FASTQ data was counted to make a table giving the frequencies of each unique small RNA sequence in tab-delimited text format.
Genome_build: n/a
Supplementary_files_format_and_content: Processed data files are tab-delimited text files giving 1) Small RNA sequences, 2) Frequencies

source_name: 10 day-old protonemata

extract_protocol:
Total RNA was extracted with Tri-Reagent (Sigma) per the manufacturer's instructions
small RNA-seq libraries for the Illumina HiSeq2500 were prepared using the Illumina TruSeq Small RNA protocol, as described by the manufacturer

tag: genotype

value: protonemal tissue


title: Wild-type small RNAs - "old wild-type" - batch 2, biological rep 2 of 2, technical replicate 2

description: 3' adapter: TGGAATTC; barcode index: 12


title: Wild-type small RNAs - "old wild-type" - batch 2, biological rep 1 of 2, technical replicate 2

description: 3' adapter: TGGAATTC; barcode index: 11


title: OA chondrocyte 1 (OA1)

value: osteoarthritis

value: chondrocytes


title: rdr6_Apr1M


title: rdr6_Apr1K


title: rdr6_Apr1L


title: Wild-type small RNAs - "2009 wild-type" - batch 3, biological rep 2 of 2

description: 3' adapter: TGGAATTC; barcode index: 5

data_processing:
For barcoded samples, libraries were deconvoluted using the Illumina pipeline
FASTQ files were trimmed to remove 3' adapters and converted to FASTA format using the script "trim_illumina_sRNA_fastq.pl", version 0.4 (available at http://axtell-lab-psu.weebly.com/tools.html) with settings -e 1 -q N -a TGGAATTC.  For sample WT_old_1, the -a option was -a ATCTCGTA instead.
The frequency of each unique trimmed read was then counted
Genome_build: N/A
Supplementary_files_format_and_content: Processed files are simple tab-delimited text files with column1 being the sequence and column two being the frequency of occurence for the sequence.

extract_protocol:
Total RNA was isoated using miRNeasy Mini kit (Qiagen) following the manufacturer's instructions.
Sample WT_old_1 was generated with the Illumina small RNA Prep kit per the manufacturer's instructions.  All other samples were prepared with the Illumia TruSeq Small RNA sample prep kit per the manufacturer's instructions, and were barcoded.


title: rdr2_Apr1F


title: Wild-type small RNAs - "old wild-type" - batch 2, biological rep 1 of 2

description: 3' adapter: TGGAATTC; barcode index: 11


title: Wild-type small RNAs - "old wild-type" - batch 2, biological rep 2 of 2

description: 3' adapter: TGGAATTC; barcode index: 12


title: CLIP-seq_HLP1_del_RRM

value: seedlings


title: rdr2_Apr1E


title: rdr2_Apr1D


title: rdr2_Apr1C


title: L2

value: LGA


title: rdr2_1D


title: nrpd1_Apr1S


title: rdr2_1C


title: nrpe1a_Apr1P


title: mDCL_Apr1Z

value: mDCL


title: mDCL_Apr2B


title: nrpd1_Apr1T


title: Wild-type small RNAs - "2009 wild-type" - batch 3, biological rep 1 of 2

description: 3' adapter: TGGAATTC; barcode index: 4


title: nrpe1a_1O


title: nrpe1a_1P


title: mDCL_Apr1Y


title: mDCL_1Z


title: mDCL_2A


title: mDCL_1Y


title: dcl4_Apr2E


title: dcl3_Apr1J


title: dcl4_Apr2F


title: dcl3_Apr1I


title: dcl3_Apr1H


title: PAS-seq_hlp1_mutant_rep1

description: high-throughput profiling of polyadenylation in hlp1 (mutant)

data_processing:
library strategy: PAS-seq
Tags less than 20 nt after removal of the 3’ linker and 4 nt random barcodes were discarded. All tags were reverse-complemented because the tags were sequenced from 3'-end of transcripts (Fu et al., 2011). Trimmed tags were then mapped to the Arabidopsis genome (TAIR10) using Bowtie (0.12.7) (Langmead et al., 2009), allowing 2 mismatches. Only uniquely mapped tags were kept for downstream analyses. Uniquely located tags with six or more continuous adenines downstream from the poly(A) junction in a 10-nt window were identified as internal priming tags and discarded (Shepard et al., 2011).
Genome_build: TAIR10
Supplementary_files_format_and_content: wig files were generated using MACS program

growth_protocol: All of the Arabidopsis thaliana lines used in this study were in the Col background. Plant growth, flowering time analysis, and plant transformation were performed as reported previously (Pei et al., 2007). The atprmt10-1 (Niu et al., 2007) and flc-3 (Michaels and Amasino, 1999) mutants were described previously. The hlp1-1 mutant was isolated from the SALK collection (SALK_021452). Seedlings were grown on Murashige and Skoog (MS) plates containing 3% sucrose.

extract_protocol:
The seedlings were ground into fine power in liquid nitrogen and RNA was extracted by TRNzol reagent (Tiangen).
Poly(A) site sequencing was performed as described with modifications at the HITS-3’ adaptor and sequencing primer (Fu et al., 2011; Shepard et al., 2011). Briefly, poly(A) RNAs were purified using a mRNA purification kit (Invitrogen), and heat fragmented at 95°C for 30 min. Reverse transcription (Superscript, Invitrogen) was carried out using our modified HITS-3’ adaptor at 42°C for 30 min, then the HITS-5’ adaptor (a SMART oligo) was added and incubated for an additional 30 min. The cDNAs were purified using a Qiagen PCR Cleanup kit and second strand cDNAs were synthesized by 3 cycles of PCR using Phusion DNA polymerase (NEB) and the PE1.0 and PE2.0 primers. The PCR products were separated on a 2% agarose gel and the 200-300 bp bands were excised and purified. Gel-extracted DNAs were further amplified by a 13-cycle PCR. The PCR products were purified using a Qiagen PCR Cleanup kit.

tag: background

value: col

tag: genotype/variation

value: hlp1 mutant


title: PAS-seq_col_rep1

description: high-throughput profiling of  in col (wild type)

value: wild type


title: PAS-seq_col_rep2


title: dcl3_Apr1G

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


title: clec12AKO_BMDMs_+_Salmonella_T24_rep3

city: Boston

first: Ramnik

last: Xavier

state: MA

address: 185 Cambridge Street

institute: Massachusetts General Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were aligned to mouse genome (mm10) using BWA-0.7.4 which uses the Burrows-Wheeler transform as described by Li H. and Durbin R. (Bioinformatics 2009, 25:1754-60.)
RSEM-based quantification using known transcripts was performed using protocol described by Li et al (BMC Bioinformatics 2011, 12:323)
The raw count matrix was then further processed with DESeq2 (Anders et al., Genome Biology 2010, 11:R106) and edgeR (Robinson et al., Bioinformatics 2010, 26, pp. -1.): The data was normalized by library size followed by variance estimation and evaluation of pairwise differential expression based on a negative binomial distribution model.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files contain matrix of UMI counts. (Normalized using rLog method in DESeq2)

growth_protocol: Cell were cultured in RPMI with 10% heat-inactivated FBS with pen-strep and 20ng/ml recombinant murine MCSF

extract_protocol:
Cells were washed in 1X PBS and lysed directly in Ambion mRNA direct lysis buffer.
RNA libraries were prepared as described in http://biorxiv.org/content/early/2014/03/05/003236
Stranded 3' digital gene expression

treatment_protocol: BMDMs were infected for 30 minutes with Salmonella strain SL1344 in RPMI without antibitic at an MOI of 10, washed with media containing 20ug/ml gentamicin and cultured for the indicated number of hours.

tag: strain background

value: CLEC12A KO

tag: gender

value: male

tag: age

value: 8 weeks old

value: S. enterica serovar Typhimurium

tag: time point

value: 24hrs post-infection

value: Bone Marrow

value: bone marrow derived macrophages (BMDM)


title: mDCL_2B


title: mDCL_Apr2A


title: clec12AKO_BMDMs_+_Salmonella_T24_rep2


title: PAS-seq_hlp1_mutant_rep2


title: clec12AKO_BMDMs_+_Salmonella_T24_rep1


title: clec12AKO_BMDMs_+_Salmonella_T6_rep1

value: 6hrs post-infection


title: clec12AKO_BMDMs_+_Salmonella_T6_rep3


title: clec12AKO_BMDMs_+_Salmonella_T6_rep2


title: nrpe1a_Apr1O

value: protonemal tissue


title: clec12AKO_BMDMs_+_Salmonella_T3_rep3

value: 3hrs post-infection


title: clec12AKO_BMDMs_+_Salmonella_T3_rep2


title: Clec12aKO_BMDMs_+_Listeria_T24_rep3

value: L. monocytogenes


title: clec12AKO_BMDMs_+_Salmonella_T3_rep1


title: Clec12aKO_BMDMs_+_Listeria_T24_rep1


title: Clec12aKO_BMDMs_+_Listeria_T6_rep2


title: Clec12aKO_BMDMs_+_Listeria_T24_rep2


title: Clec12aKO_BMDMs_+_Listeria_T3_rep3


title: Clec12aKO_BMDMs_+_Listeria_T6_rep1


title: Clec12aKO_BMDMs_+_Listeria_T3_rep1


title: Clec12aKO_BMDMs_T0_rep2

value: 0hr post-infection


title: Clec12aKO_BMDMs_+_Listeria_T3_rep2


title: Clec12aKO_BMDMs_T0_rep3


title: Clec12aKO_BMDMs_T0_rep1


title: WT_BMDMs_+_Salmonella_T24_12A_rep2


title: WT_BMDMs_+_Salmonella_T24_12A_rep3


title: WT_BMDMs_+_Salmonella_T24_12A_rep1


title: WT_BMDMs_+_Salmonella_T6_12A_rep2


title: Braswt-3

city: Honolulu

first: Yangrae

last: Cho

state: HI

address: 3190 Maile Way, St John 317

department: Plant and Environmental Protection Sciences

institute: University of Hawaii at Manoa

data_processing:
The sequenced reads were mapped to the genome sequence of Al. brassicicola (http://jgi.doe.gov/Abrassicicola) and the latest genome release of Ar. thaliana (TAIR10 ) (ftp://ftp.arabidopsis.org/home/tair/Genes/) using the programs Tophat 1.3.1 (Trapnell et al., 2009) and Bowtie 0.12.7 (Langmead et al., 2009).
The program Cuffdiff version 1.0.3 (which is part of Cufflinks, (Trapnell et al., 2010)) was used to identify reads overlapping with previously predicted genes.
The expression levels of each predicted gene were determined and normalized by the mapped Fragments Per Kilobase of exon model per Million (FPKM).  Differentially expressed genes between the wild type and the mutant were determined by comparing FPKM from three biological replicates for both the wild type and the mutant.  We also applied a cutoff of at least a two-fold change in expression value for differential expression.  The bias correction method was used while running Cuffdiff (Roberts et al., 2011).
Supplementary_files_format_and_content: ProteinId
Supplementary_files_format_and_content: A12F2 (normalized expression level of gene in the abpf2 mutant Alternaria)
Supplementary_files_format_and_content: A12W (normalized expression level of gene in the wild type Alternaria)

organism: Alternaria brassicicola

source_name: mycelia

extract_protocol:
Either myceila or mycelia plant tissue mixture were harvested, flash frozen in liquid nitrogen, and RNA was extracted using RNeasy kit (Qiagen).
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries, following Illumina protocols.

tag: medium

value: GYEB

tag: chemical treatment

value: 0.1uM brassinin

tag: treatment

value: 4 hours


title: 44hpiWt-1

value: Host plant, Brassica oleraceae

value: 44 hours


title: Braswt-2

value: wild type


title: 44hpiWt-2


title: 44hpiFtf1-2


title: WT_BMDMs_+_Salmonella_T3_12A_rep3

value: male

tag: cell type


title: Braswt-1


title: 44hpiWt-3


title: 44hpiFtf1-1


title: 44hpiFtf1-3


title: Clec12aKO_BMDMs_+_Listeria_T6_rep3

value: CLEC12A KO

value: 8 weeks old

tag: tissue


title: WT_BMDMs_+_Salmonella_T3_12A_rep2

value: S. enterica serovar Typhimurium


title: WT_BMDMs_+_Salmonella_T6_12A_rep3

value: Bone Marrow


title: BrasFtf1-2


title: BrasFtf1-1


title: WT_BMDMs_+_Salmonella_T3_12A_rep1

value: bone marrow derived macrophages (BMDM)


title: WT_BMDMs_+_Listeria_T24_rep2

value: 24hrs post-infection


title: WT_BMDMs_+_Listeria_T24_rep3


title: WT_BMDMs_+_Listeria_T6_rep2

value: 6hrs post-infection


title: WT_BMDMs_+_Listeria_T6_rep3


title: WT_BMDMs_+_Listeria_T3_rep3

value: 3hrs post-infection


title: WT_BMDMs_+_Listeria_T3_rep2

value: L. monocytogenes


title: WT_BMDMs_+_Listeria_T3_rep1


title: WT_BMDMs_+_Salmonella_T6_12A_rep1


title: WT_BMDMs_T0_rep3

value: 0hr post-infection


title: WT_BMDMs_T0_rep2


title: WT_BMDMs_T0_rep1


title: BrasFtf1-3

value: GYEB


title: fully expanded leaves

city: Yangzhou

first: Biao

last: Jin

state: Jiangsu

address: Wenhui east road no. 48

department: College of Horticulture and Plant Protection

institute: Yangzhou University

data_processing:
Illumina Casava1.7 software used for basecalling.
Removed reads with adaptor sequence, low-quality sequence and the percentage of unknown bases (N) is greater than 10%. At last, the obtained “clean reads” (or “clean data”) for further analysis
Clean reads were mapped to reference sequences and/or reference gene set using SOAPaligner/SOAP2 (No more than 2 mismatches were allowed in the alignment)
Reads Per kb per Million reads(RPKM) were calculated using a protocol from Mortazavi et al., Nature Methods, 2008. The RPKM method is able to eliminate the influence of different gene length and sequencing discrepancy on the calculation of gene expression level. Therefore, the RPKM values can be directly used for comparing the difference of gene expression among samples.
Screening of differentially expressed genes were preformed based on poisson distribution model
Genome_build: Reads_alignment_target.fa.gz
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Ginkgo biloba

source_name: fully expanded leaves

extract_protocol:
Fresh fully expanded leaves and mature ovules were collected from the female trees in April 2012, and then were frozen in liquid nitrogen immediately after harvest and stored at -80°C until use. The total RNA were extracted from ovuels and leaves using modified CTAB method according to Wang et al., Biotechnol lett, 2005, respectively
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Sex

value: Female

value: fully expanded leaves (April)

value: Leaf


title: post-spawning matured eel

description: Origin of specimen: Lake Veerse, The Netherlands, 26 May 2010

data_processing:
Illumina Casava software used for basecalling: SCS2.7/RTA1.7
Reads were aligned to the draft genome sequence of the European eel (Henkel et al., 2012) using TopHat (version 2.0.5) (Trapnell et al., 2009)
The resulting files were filtered using SAMtools (version 0.1.18) (Li et al., 2009) to exclude secondary alignment of reads
Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq (Anders et al., 2014)
Differentially expressed genes were identified using DESeq (Anders and Huber, 2010) and data were further processed using Microsoft Excel
Genome_build: Anguilla_anguilla_genome_v1_09_nov_10
Supplementary_files_format_and_content: Microsoft Office Excel file (.xlsx) with the following columns: Gene Name; Best hit; Description; Alternate descriptions; Min e-value; Similarity; GO molecular function; GO biological process; GO cellular component; Transcripts; Longest transcript length; Total length; yellow_gonads_fulllength_unique_reads; yellow_gonads_fulllength_corrected_total_reads; yellow_gonads_fulllength_RPKM; silver_gonads_fulllength_unique_reads; silver_gonads_fulllength_corrected_total_reads; silver_gonads_fulllength_RPKM; spawned_gonads_fulllength_unique_reads; spawned_gonads_fulllength_corrected_total_reads; spawned_gonads_fulllength_RPKM; gonads_yellow_vs_silver_foldChange; gonads_yellow_vs_silver_adjlog2FC; gonads_yellow_vs_silver_pval; gonads_yellow_vs_silver_padj; gonads_silver_vs_spawned_foldChange; gonads_silver_vs_spawned_adjlog2FC; gonads_silver_vs_spawned_pval; gonads_silver_vs_spawned_padj; gonads_yellow_vs_spawned_foldChange; gonads_yellow_vs_spawned_adjlog2FC; gonads_yellow_vs_spawned_pval; gonads_yellow_vs_spawned_padj

source_name: ovary

extract_protocol:
Tissues were taken from anterior, posterior and middle parts of gonad from each individual, and stored in RNAlater (Ambion) at -80ºC till RNA extraction. The different parts of gonad tissue of each individual were pooled. Total RNA was isolated from the pooled samples using the Qiagen miRNeasy kit according to the manufacturer’s instructions (Qiagen), and analyzed with an Agilent Bioanalyzer 2100 total RNA Nano series II chip (Agilent). A transcriptome library for each individual was prepared from 10 microgram total RNA, using the Illumina mRNAseq Sample Preparation Kit following the manufacturer’s instructions (Illumina Inc.).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ovary


title: Mature ovules

source_name: Mature ovules

value: Mature (April)

value: Ovule


title: Cell exposed to 45C during 1W

city: Vienna

first: Hakim

last: Tafer

address: Muthgasse 18

country: Austria

institute: University of Natural Resources and Life Sciences Vienna

description:
Cell exposed to 45C during 1W
WT_45C1W

data_processing:
Trimming done by IonTorrent Server
Mapping done with Segemehl 1.9 and lack
Splice sites detection and classification was done with testrealign
Cuffdiff / cummerRbund differential expression
Genome_build: exophiala dermatitidis (CBS 525.76)  assembled by Broad Institute
Supplementary_files_format_and_content: Cuffdiff/cummeRbund output for WT_1C1W vs WT_1C1H

organism: Exophiala dermatitidis

source_name: exophiala dermatitidis

growth_protocol: Exophiala dermatitidis (CBS 525.76) was cultured in Malt extract agarose media (2% malt extract, 2% D-glucose, 0.1% bacto-peptone and 2% agar). For the RNA-seq experiment, the cells were grown in Petri dishes for 2 weeks at 37 °C and then as follows: one week at 37 °C (control, 37C), 1 week at 45°C (45C1W), 1 week at 37 °C plus 1 hour at 1 °C (1C1H) or at 45 °C (45C1H), 1 week at 1 °C (1C1W) and 1 week at 45 °C (45C1W), for a total of 4 treatments.

extract_protocol:
Total RNA was extracted with FastRNA PRO™ RED KIT (MP Biomedicals, Santa Ana, CA) according to the instructions of the manufacturer. The mRNA was isolated with the Dynabeads® mRNA DIRECT™ Micro Kit (Ambion by Life Technologies, Carlsbad, CA) and the following transcriptome library preparation was performed with the Ion Total RNA-Seq Kit v2 (Life Technologies, Carlsbad, CA).
Total RNA, isolated mRNA and the final cDNA library were all qualitatively and quantitatively evaluated by mean of Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). The RNA-seq was realized with the use of Ion Torrent™ technology coupled with the Ion Proton™ sequencer (Life Technologies, Carlsbad, CA). The average read length is 175 bp for all five samples. Total reads generated per sample varied between 57,611,573 and 99,965,344.

tag: strain

value: Exophiala dermatitidis (CBS 525.76)


title: Cell exposed to 45C during 1H

description:
Cell exposed to 45C during 1H
WT_45C1H


title: LCL19_Total

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

description: RNA-Seq, ncRNA-Seq

data_processing:
aligned reads >25 bases in length to hg19 genome reference first with tophat under default parameters, then aligning the unmapped reads using a local and very sensitive approach with bowtie
expression estimated with cufflinks v.2.1.1 for gencode v18 and lncipedia annotation for isoforms and gene. Whole gene expression calculated as sum of isoform with "OK" status
SNPs called using default conditions of mpileup with samtools and placed within UCSC annotated genes using annovar. AEI calculated by combining SNPs called as heterozygous in both total and polysome of a sample across a gene
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files with FPKM for each annotated isoform for each sample and vcf formatted SNP calls for each sample

source_name: Coriell lymphoblast cell line (LCL)

growth_protocol: cells were grown to 5x105 cells/mL density in T75 tissue culture flask and harvested.

extract_protocol:
RNA was isolated with Trizol reagent from the cytoplasm of the three LCLs (total cytosol content), and from pooled polysome sucrose fractions (>3 ribosomes; 250 µL). Two-step column purification and size separation were performed on each RNA sample. First, long RNA (>200 bases) was separated using SpinSmart RNA Purification column (Denville), and the flowthrough (<200 bases) was placed on a second column for small RNA (microRNA) separation with mirPremier microRNA isolation kit (Sigma-Aldrich, St. Louis, MO). RNA quality was evaluated on a Bioanalyzer.
Cytoplasmic (total) and polysome derived long RNA (25 ng each) was then converted to cDNA using the NuGen Ovation RNA-Seq System V2 (NuGen Technologies, San Carlos, CA), which uses both random hexamers and oligo-dT to amplify all RNA sequences, while suppressing cDNA formation from ribosomal RNA by >90%. ERCC RNA (External RNA Control Consortium, Ambion) controls were spiked into RNA prior to NuGen cDNA synthesis. The NuGen Ovation RNA-Seq kit produces non-stranded cDNA (3-5 microgram, measured with Qubit (Life Technologies, Foster City, CA)). The double-stranded cDNA derived from long RNAs was sheared to 150-200 bp fragments with a Covaris focused-ultrasonicator (Covaris, Inc. Woburn, MA) and recovered by centrifuging over an YM-30 spin filter (Amicon EMD Millipore Billerica, MA). Fragments longer than 100 bp were retained and eluted from the membrane.
We generated barcoded sequencing libraries from 100 ng of sheared cDNA using the NEBNext Fast DNA Library Prep Set for Ion Torrent sequencing (New England Biolabs, NEB, Ipswich, MA), as described [22,48]. In a separate step, purified small RNA fractions (containing 100 ng RNA) were used for library construction using Ion Total RNA-Seq Kit v2 for small RNAs (Life Technologies, Foster City, CA). Pooled barcoded RNA libraries were sequenced on the Ion Torrent Proton platform (Life Technologies, Foster City, CA).

tag: cell line

tag: fraction

value: total


title: LCL31_Polysome

description: RNA-Seq, ncRNA-Seq

value: polysome


title: WT_BMDMs_+_Listeria_T24_rep1

value: wild type

value: male

value: 8 weeks old

tag: infected with

value: Bone Marrow


title: LCL19_Polysome

description: RNA-Seq, ncRNA-Seq


title: LCL31_Total

description: RNA-Seq, ncRNA-Seq


title: yellow eel

first: Ron

last: Dirks

address: Sylviusweg 74

description: Origin of specimen: Lake Veerse, The Netherlands, 21 April 2010


title: LCL14_Polysome

description: RNA-Seq, ncRNA-Seq


title: LCL14_Total

description: RNA-Seq, ncRNA-Seq


title: prepubertal silver eel

description: Origin of specimen: Lake Grevelingen, The Netherlands, 7 December 2008


title: WT_BMDMs_+_Listeria_T6_rep1

value: 6hrs post-infection

value: bone marrow derived macrophages (BMDM)


title: Cell exposed to 1C during 1H

description:
Cell exposed to 1C during 1H
WT_1C1H


title: J215 WT replicate 2

status: Public on Jun 29 2015

city: Hanover

first: Deborah

last: Hogan

state: NH

address: Vail Building Rm 208

department: Microbiology and Immunology

institute: Geisel School of Medicine at Dartmouth

data_processing:
Reads were trimmed for adaptor sequences and mapped to the PAO1 whole genome with CLC Genomics Workbench platform (v7.5.1) using default parameters.
Mapped reads were quantile normalized to all reads using CLC Genomics Workbench.
Fold change values and significance statistics between RNA Seq samples were calculated using the 'Empirical analysis of DGE' algorithm in CLC Genomics Workbench, which is a re-implementation of the "Exact Test" from the EdgeR Bioconductor package (Robinson and Smyth, Biostatistics, 2008)(Robinson et al., Bioinformatics, 2010), and was conducted between all pairs.
Genome_build: ASM676v1; PAO1 NC_002516
Supplementary_files_format_and_content: Processed data file is a data matrix that contains raw unique gene reads, quantile normalized reads, and calculated fold changes between WT and ∆anr samples.

organism: Pseudomonas aeruginosa

source_name: J215 WT replicate 2

growth_protocol: Strains to be analyzed were grown overnight in LB, pelleted and washed, then resuspended to an OD600=1.0 in T-broth. 9, 5uL spots of this suspension were spotted onto T-broth agar and incubated at 1% O2, 5% CO2 for 12 h.

extract_protocol:
Colony biofilms of PAO1 and J215 wild type or Δanr were grown for 12 h, then harvested in 1 mL of PBS applied to the plate followed by recovery with an angled glass rod. Samples were pelleted by centrifugation and stored at -80°C. RNA was isolated from pelleted cells using the RNeasy mini kit (Qiagen), followed by treatment with RQ1 DNAase from Promega, both in accordance with manufacturers’ instructions. Ribosomal and transfer RNAs were removed using the MICROBExpress kit (Life Technologies) according to manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: WT

value: J215, Cystic fibrosis clinical isolate

tag: quorum sensing status


title: J215 ∆anr replicate 2

source_name: J215 ∆anr replicate 2

value: {delta}anr


title: J215 ∆anr replicate 1

source_name: J215 ∆anr replicate 1


title: 37C Control

description:
37C Control
WT_37CCTRL


title: J215 WT replicate 1

source_name: J215 WT replicate 1


title: Bt_mAb260.8plusmAb225.4_rep2

city: St. Louis

first: Joseph

middle: D

last: Planer

state: Missouri

address: 4444 Forest Park Ave

department: Pathology

institute: Washington University School of Medicine

description: Sample name: Bt_RNA_Seq_B_24

data_processing:
Short read alignment with Bowtie v1.1.0.
Removal of rRNA and intergenic reads.
Differential expression analysis with DESeq2 package in R version 3.1.2.
Genome_build: ASM1106v1 (NC_004663)
Supplementary_files_format_and_content: Raw counts.

organism: Bacteroides thetaiotaomicron

source_name: Mid-log phase culture

growth_protocol: Cells were grown to mid-log phase in TYG medium.

extract_protocol:
Cells were extracted using acidic phenol:chlorophorm:isoamyl alcohol (125:24:1, pH 4.5). rRNA was removed using Ribo-zero.
Illumina adapters were ligated to the DNA with T4 DNA ligase and cDNAs were size-selected by 2% agarose gel electrophoresis. PCR of the adapter-ligated product was performed , and samples were pooled in equal proportion.

treatment_protocol: Cultures were grown to early log phase (OD600 ~0.1) and antibody or PBS (carrier control) was added to each culture tube. Tubes were then incubated until cultures reached OD600 0.5-0.7, when they were harvested into RNAprotect (Qiagen).

tag: mab

tag: od600 at harvest


title: Bt_PBSctl_rep2

description: Sample name: Bt_RNA_Seq_B_21


title: Bt_mAb260.8_rep2

description: Sample name: Bt_RNA_Seq_B_22


title: Bt_mAb225.4_rep2

description: Sample name: Bt_RNA_Seq_B_23


title: Bt_IgActl_rep1

description: Sample name: Bt_RNA_Seq_B_15


title: Bt_mAb260.8plusmAb225.4_rep1

description: Sample name: Bt_RNA_Seq_B_14


title: Bt_mAb225.4_rep1

description: Sample name: Bt_RNA_Seq_B_13


title: Cell exposed to 1C during 1W

description:
Cell exposed to 1C during 1W
WT_1C1W


title: Bt_PBSctl_rep1

description: Sample name: Bt_RNA_Seq_B_11


title: Bt_mAb260.8_rep1

description: Sample name: Bt_RNA_Seq_B_12


title: WTDRB3H

city: La Jolla

first: Xiang-Dong

last: Fu

address: 9500 Gilman Drive, Room 231

department: CMM

institute: UC San Diego

data_processing:
Library strategy: Gro-seq
Sequencing reads were trimmed by using cutadapt program (version 1.2.1) to remove 3' adaptor TCGTATGCCGTCTTCTGCTTG and then polyAs. Trimmed reads smaller than 16 nt were discarded.
Reads were mapped to the mouse genome by using Bowtie (version 0.12.7), with parameters "--best --strata -l25 -n2 -k1 -m10'. Only one read was kept for those reads mapped to the same location and strand.
For Gro-seq, the replicated samples were combined together. The genomic coverage signal were counted in forward and reverse strands separately and normalized to 1 million total reads.
Genome_build: mm9
Supplementary_files_format_and_content: The bigWig files are genomic coverage signals for Gro-seq samples.

source_name: Mouse embryonic stem cells isolated from inner cell mass of Tdgfl/fl embryos

growth_protocol: Cells were maintained in KnockoutTM DMEM (Life Technologies, Cat. NO: 10828-018) supplemented with 15% KnockoutTM Serum Replacement (Life Technologies, Cat. NO: 10828-028), 2 mM L-glutamine (Life Technologies, Cat. NO: 25030-081), 1X Non-essential amino acids (Life Technologies, Cat. NO: 11140-050), 1X Penicillin-Streptomycin (Life Technologies, Cat. NO: 15140-122), 0.1 mM  2-Mercaptoethanol (Life Technologies, Cat. NO: 21985-023), 1000 U/ml LIF (Millipore, Cat. NO: ESG1106), 3 µM CHIR99021 (Stemgent, Cat. NO: 04-0004) and 1 µM PD0325901 (Stemgent, Cat. NO: 04-0006).

extract_protocol:
~10 million cell nuclei from WT or TDG knockout cells were extracted and harvested.
The global nuclear run-on assay and was carried out and analyzed by deep sequencing using a published protocol (Wang et al., 2011).

treatment_protocol: Add DRB to the medium to 100 mM final concentration and incubate for 3 hours in the incubator.

value: ES cell line

tag: genotype/variation

value: Tdgfl/fl

tag: assayed molecule

value: nascent RNA


title: WTWASH10M

treatment_protocol: Add DRB to the medium to 100 mM final concentration and incubate for 3 hours in the incubator. Quickly wash cells 3 times with PBS to remove DRB, then add fresh medium and incubate for 10 min in the incubator.


title: KOWASH20M

source_name: Mouse embryonic stem cells isolated from inner cell mass of Tdg-/-  embryos

treatment_protocol: Add DRB to the medium to 100 mM final concentration and incubate for 3 hours in the incubator. Quickly wash cells 3 times with PBS to remove DRB, then add fresh medium and incubate for 20 min in the incubator.

value: ES cell line with TDG knockout

value: Tdg-/-


title: WTWASH30M

treatment_protocol: Add DRB to the medium to 100 mM final concentration and incubate for 3 hours in the incubator. Quickly wash cells 3 times with PBS to remove DRB, then add fresh medium and incubate for 30 min in the incubator.


title: KOWASH10M


title: U251 WT CLIP-seq Rep 2

city: Los Angeles

first: Philip

middle: James

last: Uren

address: 1050 Childs Way, RRI201

institute: University of Southern California

data_processing:
Raw reads were mapped using RMAP
Read counts per-gene and per-exon computed for RNA-seq data using in-house script
Peak calling pefformed in CLIP data using Piranha
Genome_build: hg18
Supplementary_files_format_and_content: Processed data files are raw read counts for exons and genes derived from RNA-seq and peak locations for iCLIP of MSI1

source_name: U251 WT CLIP-seq

growth_protocol: U251 cells were plated on 100-mm dishes and cross-linked when semi-confluent in 6mL PBS with a Spectrolinker XL-1500 two times at 100 mJ/cm2.

extract_protocol:
iCLIP was performed according to Konig et al using Abcam rabbit anti-MSI1 monoclonal antibody (ab52865) (Abcam, Cambridge, MA).
Samples were amplified, purified with Beckman Genomics Ampure XP beads (Beckman Coulter Genomics, Danvers, MA), and quantitated with an Agilent 2100 Bioanalyzer and DNA 1000 chips (Agilent Technologies, Santa Clara, CA). Three biologic replicates were combined and 50SE sequencing performed on an Illumina Hi-Seq 2000 (Illumina, Inc., San Diego, CA).

value: glioblastoma cells

value: wild type (control)

tag: iclip antibody

value: anti-MSI1 monoclonal antibody

tag: iclip antibody vendor

value: Abcam

tag: iclip antibody cat. #


title: U251 WT CLIP-seq Rep 1


title: KOWASH30M


title: KONODRB


title: WTNODRB


title: WTWASH20M


title: KODRB3H


title: U251 Msi1 KD Rep 2

source_name: U251 Msi1 KD

value: Msi1 KD


title: IFNg RPF replicate 2

city: New York

first: Xiaodi

last: Su

address: 535 East 70th Street

department: Arthritis and Tissue Degeneration Program

institute: Hospital for Special Surgery

data_processing:
For both RPF and RNA libraries the first seven degenerate nucleotides were trimmed from 5’end; the polyA adapters at 3’end was removed by Clip; low quality reads were filtered out (mean quality score<20). rRNA contamination of ribosome protected fragments (RPF) were removed by Bowtie2 using the default setting.
Both RPF and RNAseq reads were aligned to protein-coding gtf file described in the online methods with Tophat2;The BAM files generated from Tophat2 were annotated with Htseq. Reads that have multiple alignments were filtered out and cpm (counts per million) was calculated
Genome_build: hg19
Supplementary_files_format_and_content: excel file includes aligned read counts for each sample (8 in total)

source_name: human primary macrophages

growth_protocol: Cells were maintained in RPMI1640 supplemented with 10% FBS, P/S, 2mM L-Gln and 20ng/ml MCSF, under 5% CO2 at 37C.

extract_protocol:
For RNAseq total RNA was isolated via Trizol extraction; for RPF cell lysates were treated with micrococccal nuclease, and momosomes were purified by sucrose gradient followed by sucrose cushion; RPFs were extracted by Trizol
RPF and RNA libraries were prepared for sequencing using modified Illumina protocols with polyA selection (see online methods).

treatment_protocol: Cells cultured for 24h were stimulated with Pam3Cys (10ng/ml) for 4h

tag: tlr stimulation

value: TLR2 stimulated


title: U251 WT CLIP-seq Rep 3


title: Mock RNA replicate 2


title: Mock RPF replicate 2


title: U251 Msi1 KD Rep 3


title: Bt_IgActl_rep2

description: Sample name: Bt_RNA_Seq_B_25


title: IFNg RPF replicate 1


title: U251 Msi1 KD Rep 1


title: IFNg RNA replicate 1


title: Mock RNA replicate 1


title: U251 WT RNA-seq Rep 2

source_name: U251 WT RNA-seq


title: U251 WT RNA-seq Rep 1


title: Mock RPF replicate 1


title: IFNg RNA replicate 2


title: IFNg TLR replicate 2

data_processing:
Mirdeep2 was used to align the sequencing reads to human precursor miRNAs (miRBase release 21); allow one mismatch
Mirdeep2 was used to calculate the read counts and cpm for each miRNA
Genome_build: miRBase release 21
Supplementary_files_format_and_content: excel file includes cpm values for each sample (8 in total)

growth_protocol: Cells were maintained in RPMI1640 supplemented with 10% FBS and 20ng/ml MCSF, under 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted by using mirVana miRNA isolation kit
miRNA libraries were prepared by using TruSeq small RNA library prep kit (Illumina)

treatment_protocol: Cells cultured for 24h were stimulated with or without Pam3Cys (10ng/ml) for 4h


title: PAO1 ∆anr replicate 2

organism: Pseudomonas aeruginosa PAO1

source_name: PAO1 ∆anr replicate 2

value: Laboratory strain

value: Quorum sensing intact


title: IFNg UT replicate 2

value: unstimulated


title: Mock UT replicate 2


title: Round spermatids_RRBS

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

description: DNA methylation data from round spermatids

data_processing:
Basecalling using Illumina Casava1.8.2 software
Map the reads to mouse genome mm10 using Bismark v0.12.2
Ectract CpG sites by bismark methylation extractor script
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include methylated counts, unmethylated counts and methylated level for sequenced CpG sites

source_name: Round spermatids from testis

growth_protocol: Mouse androgenetic haploid embryonic stem cells (AG-haESCs) were cultured on feeder in ES medium supplemented with 2i.

extract_protocol:
Total DNA was extracted and purified using DNA extraction kit according to the manufacturer's instructions.
Genomic DNA was digested using MspI restriction enzyme, then repaired the end and ligated with methylated adapters. The ligation products were purified and size-selected by agarose gel electrophoresis. Purified DNA from gel fragment was bisulfite-treated followed by PCR amplification.

treatment_protocol: ES cells were washed by DPBS (GIBCO), trypsinized, and collected by centrifugation.

tag: passages

tag: type

value: Round spermatids


title: Mock TLR replicate 2


title: PAO1 WT replicate 2

source_name: PAO1 WT replicate 2

value: WT


title: U251 WT RNA-seq Rep 3

tag: cell type


title: Mock UT replicate 1


title: H19△DMR-IG△DMR-OG3-2_RRBS

description: DNA methylation data from  AG-haESCs

source_name: Haploid embryonic stem cells derived from  androgenetic blastocysts_DKO2

value: Embryonic stem cells


title: AGH-OG3_RRBS

description: DNA methylation data from  AG-haESCs

source_name: Haploid embryonic stem cells derived from  androgenetic blastocysts_wildtype


title: PAO1 WT replicate 1

source_name: PAO1 WT replicate 1


title: PAO1 ∆anr replicate 1

source_name: PAO1 ∆anr replicate 1

value: {delta}anr