title: GAF-RNAi replicate 1 (GRO-seq)

status: Public on Apr 04 2015

city: Ithaca

first: Nicholas

last: Fuda

state: New York

address: 417 Biotechnology Building, Cornell University

department: Molecular Biology and Genetics

institute: Cornell University

description:
Nuclear run on with 5-BromoUTP for immunopurification
nascent RNA

data_processing:
Library strategy: GRO-Seq
Barcode removed and read trimmed to 26nt
Adapter removed using cutAdapt with all possible combinations of VN and a threshold of 0.2
Aligned with bowtie to dm3, allowing two mismatches and requiring unique alignment (-m1).
converted bowtie .sam file to the .bed file standard.
normalized per million mapped reads
Genome_build: Release 5 (dm3)
Supplementary_files_format_and_content: bedgraph file; GRO-seq reads normalized to total number of mapped reads (either on the plus or minus strand) after they were trimmed to 26 nucleotides, and mapped to non-repetitive regions of the Drosophila genome using Bowtie.

source_name: S2 cell line

growth_protocol: Cells were grown in M3 media (Sigma) supplemented with bacto-peptone and yeast extract + 10% FBS

extract_protocol: Ten million nuclei were allowed to run-on for 10 minutes at 30°C in a reaction containing ATP, CTP, GTP, and BrUTP. The RNA was isolated using Trizol and acid phenol extractions. The RNAs were base hydrolyzed to an average length of 100-150 nucleotides, and RNAs with incorporated BrU were purified with 2 immunoprecipitations successive using Anti-BrdUTP agarose (Santa Cruz Biotechnology cat# sc32323 AC lot # I2111). The RNA was treated with PNK and polyadenylated using E. coli polyA polymerase to add 50-100 As to their 3’ ends. The polyadenylated RNA was reverse transcribed used with the following bar coded oligonucleotides (INOO3: 5’-pTAGAGATCGTCGGACTGTAGAACTCT-iSp18-CAAGCAGAAGACGGCATACGATTTTTTTTTTTTTTTTTTTTVN, INOO4: 5’-pTGATGATCGTCGGACTGTAGAACTCT-iSp18-CAAGCAGAAGACGGCATACGATTTTTTTTTTTTTTTTTTTTVN). The first 4 bases have the bar-code and iSp18 indicates an 18 carbon spacer between two oligo linkers used for Illumina sequencing. The resulting DNA was gel extracted and circularized using Epicentre CircLigase, and PCR amplified for 12-15 cycles. The cDNA was then sequenced on the Illumina Genome Analyzer.

treatment_protocol: cells untreated or treated with double-stranded RNA against Beta-galactosidase (LacZ-RNAi control) or GAGA factor

value: S2 cells

value: GAF-RNAi

tag: bru immunoprecipitation

value: Anti-BrdUTP agarose (Santa Cruz Biotechnology, catalog# sc32323 AC, lot# I2111)

tag: barcode

value: TCTA


title: Fibrous root_50dpi_HLB_RNA-Seq

type: SRA

city: Guangzhou

first: Chunzhen

last: Cheng

state: Guangdong

address: No.80 Dafeng No.2 street, Tianhe district, Guangzhou, China

department: Guangdong Academy of Agricultural Sciences

country: China

institute: Institute of fruit tree research

library_source: transcriptomic

data_processing:
The 90-bp raw paired end reads were generated by  Illumina HiSeq™ 2000 analyzed by Illumina HiSeq 2000 system.
Raw reads produced from sequencing machines contain dirty reads which contain adapters, unknown or low quality bases. These data will negatively affect following bioinformatics analysis. Therefore, dirty raw reads are discarded.
Clean reads were mapped to  Citrus clementina genome (Cclementina_165) and genes sequences respectively using SOAP2 (Li, 2009). Mismatches no more than m(m default is 5) bases were allowed in the alignment.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.The RPKM method is able to eliminate the influence of different gene length and sequencing discrepancy on the calculation of gene expression. Therefore, the calculated gene expression can be directly used for comparing the difference of gene expression among samples. If there are more than one transcript for a gene, the longest one is used to calculate its expression level and coverage.
In our analysis, we choose genes with FDR ≤ 0.001 and ratio larger than 2 as differentially expressed genes (DEGs).
Genome_build: Cclementina_165
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each citrus gene

molecule: total RNA

organism: Citrus reticulata

source_name: HLB-infected 'Sanhu' red tangerine fibrous root

extract_protocol:
Mature leaves and roots were collected from the CLas-inoculated and the control trees every ten days to detect for CLas by PCR. DNA used for PCR was extracted with the use of the Plant DNA isolation Kit (Trans, Beijing, China) according to manufacturer’s instructions. The fibrous roots of 3 CLas-positive and 3 control CLas-free trees were individually collected at 50 dpi (days post inoculation) when the HLB-inoculated trees became CLas-positive in both leaves and roots yet showed no visible chlorosis and other HLB symptoms. This should have allowed us not to miss too many early responsive genes but at the same time ensured that the trees were infected as expected. Total RNA was extracted from each sample using RNeasy plant mini kit (Qiagen, Valencia, CA) and further purified using the RQ1 Rnase Free Dnase Kit (Promega, Madison, USA). RNA quality and quantity were assessed by gel-electrophoresis and by absorbance at OD260/OD280, respectively. Aliquot RNA samples were stored at -80 ℃. For RNA-seq analysis, RNA samples from the three trees were mixed in equal amount and used for cDNA library construction following the Illumina mRNA-sequencing sample preparation protocol (Illumina, San Diego, CA). The 90-bp raw paired end reads were generated by Illumina HiSeqTM 2000 and analyzed by Illumina Genome Analyzer II system.
Beads with oligo(dT) were used to isolate poly(A) mRNA after total RNA was collected from eukaryote (prokaryocyte can be treated with kit to remove rRNA before next step). Fragmentation buffer was added for interrupting mRNA to short fragments. Taking these short fragments as templates, Random hexamerprimer hexamerprimer were used to synthesize the first-strand cDNA. The second-strand cDNA was synthesized using buffer, dNTPs, RNase H and DNA polymerase I,respectively. Short fragments were purified with QiaQuick PCR extraction kit and resolved with EB buffer for end reparation and adding poly(A). After that, the short fragments were connected with sequencing adaptors. And, for amplification with PCR, we selected suitable fragments, as templates, with respect to the result of agarose gel electrophoresis. At last, the library could be sequencing using Illumina HiSeq™ 2000 to generated the 90-bp raw paired end reads.

treatment_protocol: Two-year-old seedlings of ‘Sanhu’ red tangerine were grafted with buds from CLas-infected or CLas-free ‘Gonggan’ mandarin trees.

tag: cultivar

value: cv "Sanhu"

tag: tissue

value: fibrous root

tag: seedling age

tag: sample time

value: 50 days post grafting with buds from CLas-infected ‘Gonggan’ mandarin trees


title: LacZ-RNAi replicate 1 (GRO-seq)

country: USA

organism: Drosophila melanogaster

tag: cell type

tag: treatment

value: LacZ-RNAi


title: Fibrous root_50dpi_CK_RNA-Seq

source_name: healthy 'Sanhu' red tangerine fibrous root

value: 50 days post grafting with buds from CLas-free ‘Gonggan’ mandarin trees


title: Untreated replicate 2 (GRO-seq)

value: Untreated

value: ATCA


title: GAF-RNAi replicate 3 (H2AvD MNase-ChIP)

description:
MNase digested chromatin
H2AvD immunoprecipitated MNase digested cross-linked chromatin from GAF-RNAi S2 cells

library_source: genomic

data_processing:
Library strategy: MNase-ChIP-Seq
paired-end sequencing separated into individual libraries by bar-codes
reads filtered based sequencing quality filter
paired reads mapped using bowtie2 (--no-mixed --no-discordant)
reads 120-180bp selected
Genome_build: Release 5 (dm3)
Supplementary_files_format_and_content: bedgraph file of the complete paired-end reads

molecule: genomic DNA

extract_protocol: Ten million cross-linked nuclei were digested with MNase until about 80% of the material has mononucleosome-sized. For H2AvD nucleosomes, immunoprecipitated with 4ul Anti-H2AvD antisera (Glaser lab stock) from 75ul of digested material. Cross-links were reversed at 65°C and the DNA was extracted with phenol:chloroform and precipitated. 50ng of non-immunoprecipitated (MNase-seq) or immunoprecipitated (H2AvD) DNA was ligated to Tru-seq paired-end adapters. The resulting DNA was PCR amplified for 5 cycles and 200-400bp fragments were selected and PCR amplified for 12-15 cycles. The cDNA was then paired-end sequencing was performed (50 bases)  on the Illumina HiSeq 2500.

treatment_protocol: cells treated with double-stranded RNA against Beta-galactosidase (LacZ-RNAi control) or GAGA factor for 5 days

tag: cell line

tag: chip antibody

value: Anti-H2AvD antisera (Glaser lab stock)


title: Untreated replicate 1 (GRO-seq)


title: GAF-RNAi replicate 2 (H2AvD MNase-ChIP)


title: eIF3b library for replicate 2

status: Public on Apr 06 2015

city: Boston

first: Amy

middle: Si-Ying

last: Lee

state: MA

address: 450 Brookline Ave SM520

department: Cancer Immunology and Virology

institute: DFCI

description: Replicate 2 - eIF3b

data_processing:
Library strategy: PAR-CLIP
Raw illumina reads were collapsed using the fastx_collapser tool, and 3' adapters were removed using Cutadapt
Reads were mapped using Bowtie to the hg19 genome
Read clusters were identified using PARalyzer
Clusters were annotated using bedtools intersect
Genome_build: hg19
Supplementary_files_format_and_content: Reproducible cluster chromosomal locations, annotation, and number of supporting reads and T/C conversions from the union of the three replicates

organism: Homo sapiens

source_name: Human 293T cells

growth_protocol: 293T cells were grown in DMEM + 10% FBS

extract_protocol:
Cells were lysed in NP40 lysis buffer, and immunoprecipitation was performed using an eIF3b antibody. After a high salt wash, RNAs were digested with RNase T1, radiolabeled with T4 PNK, and protein-RNA complexes were excised after SDS-PAGE gel electrophoresis
cDNA libraries were constructed using a standard small RNA library protocol

treatment_protocol: Cells were treated with 100uM 4-thiouridine for 14h, and crosslinked on ice with 0.15 J cm-2

tag: par-clip antibody

value: anti-eIF3b (Bethyl A301-761A)


title: eIF3b library for replicate 1

description: Replicate 1 - eIF3b


title: LacZ-RNAi replicate 2 (H2AvD MNase-ChIP)

description:
MNase digested chromatin
H2AvD immunoprecipitated MNase digested cross-linked chromatin from LacZ-RNAi S2 cells


title: GAF-RNAi replicate 1 (H2AvD MNase-ChIP)


title: LacZ-RNAi replicate 3 (H2AvD MNase-ChIP)


title: GAF-RNAi replicate 3 (MNase-seq)

description:
MNase digested chromatin
formaldehyde cross-linked chromatin from GAF-RNAi S2 cells digested with micrococcal nuclease to mononucleosome sized fragments

data_processing:
paired-end sequencing separated into individual libraries by bar-codes
reads filtered based sequencing quality filter
paired reads mapped using bowtie2 (--no-mixed --no-discordant)
reads 120-180bp selected
Genome_build: Release 5 (dm3)
Supplementary_files_format_and_content: bedgraph file of the complete paired-end reads


title: GAF-RNAi replicate 2 (MNase-seq)


title: LacZ-RNAi replicate 2 (MNase-seq)

description:
MNase digested chromatin
formaldehyde cross-linked chromatin from LacZ-RNAi S2 cells digested with micrococcal nuclease to mononucleosome sized fragments


title: GAF-RNAi replicate 1 (MNase-seq)


title: GAF-RNAi replicate 2 (GRO-seq)


title: LacZ-RNAi replicate 1 (H2AvD MNase-ChIP)


title: LacZ-RNAi replicate 3 (MNase-seq)


title: siTFE3 construct2 rep2

status: Public on Apr 03 2015

first: Kenneth

middle: N

last: Ross

address: 450 Brookline Ave., Rm M640

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: 8988T PDA cells treated with siRNA against TFE3 (construct 2, replicate 2)

data_processing:
Reads trimmed with Trimmomatic version 0.30 in single end mode and trimming steps set to ILLUMINACLIP:illuminaAdapters.fa:  2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35
Reads aligned to human genome with tophat version 2.0.8 using UCSC hg19 gene annotation and default settings.
Aligned reads processed to Fragments Per Kilobase of exon per Million fragments mapped (FPKM) using cufflinks version 2.1.1 (http://cufflinks.cbcb.umd.edu/index.html) with the -G flag to use the hg19 reference annotation to estimate isoform expression and not assemble novel transcripts.
Genome_build: hg19
Supplementary_files_format_and_content: genes.fpkm_tracking files are tab delimited text files output by cufflinks in a generic FPKM tracking format with estimated gene-level expression values in the form of FPKM values

source_name: 8988T PDA Cell Line

growth_protocol: 8988T cells were cultured in DMEM supplemented with 10% FBS

extract_protocol:
Illumina TruSeq RNA Sample Prep Kit was used with >1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols at the Tufts University Bioinformatics Core (http://tucf-genomics.tufts.edu)

treatment_protocol: 8988T cells were transfected with siCTRL and 2 different siRNA targeting TFE3, 24 and 48hrs post-plating.  RNA was collected 48hrs following siRNA transfection.

value: pancreatic ductal adenocarcinoma


title: siTFE3 construct2 rep1

description: 8988T PDA cells treated with siRNA against TFE3 (construct 2, replicate 1)


title: E14.5 Post. Oral Rep. 3

city: Cincinnati

first: Steven

last: Potter

state: OH

address: 3333 Burnet Ave.

department: Developmental Biology

institute: Children's hospital Medical Center

data_processing:
Tophat version April 2012 was used for basecalling
Genespring 12.6.1 was used for analyzing Bam files
post alignment read metrics were used to remove reads that aligned to more than one place in the genome
Duplicate reads were filtered out
Genome_build: mouse genome build mm9
Supplementary_files_format_and_content: GeneSpring generated RPKM values

organism: Mus musculus

source_name: E14.5_posterior oral palate

extract_protocol:
isolation protocol: samples were isolated by laser capture microdissection from E14.5 embryos
Total RNA was extracted from laser capture samples using the Qiagen Rneasy Mini kit
RNA was amplified with NOvation® RNA-Seq System V2 (NuGen), Tagmented with Nextera, and libraries prepared according to Illumina HiSeq 2500 protocols

tag: strain

tag: developmental stage

tag: genotype/variation

value: wild type

tag: compartment

value: posterior oral palate


title: LacZ-RNAi replicate 2 (GRO-seq)


title: siTFE3 construct1 rep1

description: 8988T PDA cells treated with siRNA against TFE3 (construct 1, replicate 1)


title: E14.5 Post. Oral Rep. 2


title: siCTRL rep2

description: 8988T PDA cells treated with control siRNA (replicate 2)

value: siCTRL


title: E14.5 Post. Oral Rep. 1


title: siCTRL rep1

description: 8988T PDA cells treated with control siRNA (replicate 1)


title: E14.5 Ant. Oral Rep. 3

source_name: E14.5_anterior oral palate

value: anterior oral palate


title: E14.5 Ant. Oral Rep. 1


title: eIF3a library for replicate 3

description: Replicate 3 - eIF3a


title: E14.5 Ant. Oral Rep. 2


title: E14.5 Post. Nasal Rep. 2

source_name: E14.5_posterior nasal palate

value: posterior nasal palate


title: E14.5 Post. Nasal Rep. 1


title: E14.5 Post. Nasal Rep. 3


title: E14.5 Ant. Nasal Rep. 3

source_name: E14.5_anterior nasal palate

value: anterior nasal palate


title: E14.5 Antt. Nasal Rep. 4


title: E14.5 Ant. Nasal Rep. 2


title: E14.5 Ant. Nasal Rep. 1


title: E14.5 Post. Medial Rep. 2

source_name: E14.5_posterior medial palate

value: posterior medial palate


title: 38B9_Input ChIP-Seq

city: Seoul

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

country: South Korea

institute: Yonsei University

description: ChIP-Seq

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie with default parameters.
To call the peaks, MACS 1.4 software was used.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were converted from wiggle files generated by MACS 1.4 software.

source_name: pro B-Cell

growth_protocol: Cultures were maintained in RPMI medium 1640 supplemented with 10% FBS, 1% Pen/Strep and 55 μM 2-mercaptoethanol.

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with appopriate sizes were prepared for sequencing.
These libraries were made following the instructions of illumina Truseq DNA sample prep kit v2.

treatment_protocol: Cells were treated with DMSO or nothing before crosslinking. In brief, cells were crosslinked using 1% formaldehyde for 20 min at room temperature.

value: B cell leukemia

tag: antibody

tag: genotype

value: transformed pro B-Cell


title: E14.5 Post. Medial Rep. 1


title: LacZ-RNAi replicate 1 (MNase-seq)

value: S2 cells


title: E14.5 Post. Medial Rep. 3


title: siTFE3 construct1 rep2

description: 8988T PDA cells treated with siRNA against TFE3 (construct 1, replicate 2)


title: E14.5 Ant. Medial Rep. 2

source_name: E14.5_anterior medial palate

value: anterior medial palate


title: E14.5 Ant. Medial Rep. 1


title: E14.5 Post. Lateral Rep. 1

source_name: E14.5_posterior lateral palate

value: posterior lateral palate


title: E14.5 Ant. Medial Rep. 3


title: E14.5 Post. Lateral Rep. 2


title: E14.5 Ant. Lateral Rep. 3

source_name: E14.5_anterior lateral palate

value: anterior lateral palate


title: E14.5 Ant. Lateral Rep. 1


title: Stra8_deficient_mRNAseq_2

city: Cambridge

first: David

middle: C

last: Page

address: 9 Cambridge Center

institute: Whitehead Institute

description: mRNA from the whole testis of a one-year-old Stra8-deficient male mouse. The Stra8-deficient testis is grossly enlarged and consists mainly of cells that ressemble type-A spermatogonia. (Replicate 2)

data_processing:
Data were aligned to the genome with Tophat using the "-g 1" option
GTF file of RefSeq genes was downloaded from the UCSC genome browser, and reads in each gene were counted with htseq-count using the options: "-m intersection-strict -s no"
Differentially expressed genes were identified with edgeR, correcting for effective library size (using the calcNormFactors method), and fitting the GLM with tagwise dispersions
Differential expression statistics for each gene are provided in the supplementary file: stra8_deficient_vs_wildtype_edger.txt
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample

molecule: polyA RNA

source_name: Whole testis (grossly enlarged)

extract_protocol:
Testes were stripped of the tunica albuginea, placed in TRIzol (Invitrogen), homogenized, and stored at −20°C. Total RNAs were prepared according to the manufacturer's protocol. Total RNAs were then DNase-treated using DNA Free Turbo (Ambion)
Libraries were prepared using the Illumina mRNA-Seq Sample Preparation Kit (San Diego, CA) according to the manufacturer's protocol. Libraries were validated with an Agilent Bioanalyzer (Santa Clara, CA). Libraries were diluted to 10 pM and applied to an Illumina flow cell using the Illumina Cluster Station.

tag: strain background

tag: age

value: 1 year

value: Stra8 -/-

value: whole testis (grossly enlarged)


title: Wildtype_mRNAseq_1

description: mRNA from the whole testis of an adult wild-type male mouse.  (Replicate 1)

source_name: Whole testis

value: 2-4 months

value: Stra8 +/+

value: whole testis


title: Stra8_deficient_mRNAseq_3

description: mRNA from the whole testis of a one-year-old Stra8-deficient male mouse. The Stra8-deficient testis is grossly enlarged and consists mainly of cells that ressemble type-A spermatogonia. (Replicate 3)


title: Wildtype_mRNAseq_2

description: mRNA from the whole testis of an adult wild-type male mouse.  (Replicate 2)


title: Wildtype_mRNAseq_3

description: mRNA from the whole testis of an adult wild-type male mouse.  (Replicate 3)


title: E14.5 Ant. Lateral Rep. 2

value: wild type


title: Stra8_deficient_mRNAseq_1

description: mRNA from the whole testis of a one-year-old Stra8-deficient male mouse. The Stra8-deficient testis is grossly enlarged and consists mainly of cells that ressemble type-A spermatogonia. (Replicate 1)


title: ZG14 Control BR2

city: Pretoria

first: Ronishree

last: Mangwanda

address: Lynwood Road

country: South Africa

institute: University of Pretoria

description: processed data file: ZG14_Cuffdiff_gene_differential_expression_testing.txt

data_processing:
Quality control of the raw reads was performed using FASTQXC
Reads were mapped to the E. grandis genome using Tophat v2.0.4
FPKM values were generated using Cufflinks v1.0.3
Differential gene expression was performed using Cuffdiff v1.0.3
Genome_build: Eucalyptus grandis v1.1; http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Egrandis
Supplementary_files_format_and_content: Tabular cuffdiff gene lists of differentially expressed genes between the controls and inoculated samples in each genotype

organism: Eucalyptus grandis

source_name: ZG14 Control BR

extract_protocol:
RNA from the stem material was extracted using the CTAB protocol and purified with a Qiagen Rneasy mini kit
Library construction was performed at BGI

tag: clonal genotype

tag: response to c. austroafricana infection

value: susceptible

tag: inoculated with

value: C. austroafricana

tag: time point

value: 3 days post inoculation

value: stem


title: ZG14 Control BR3

tag: tissue


title: ZG14 Infected BR3

source_name: ZG14 Infected BR


title: ZG14 Infected BR1


title: TAG5 Infected BR2

description: processed data file: TAG5_Cuffdiff_gene_differential_expression_testing.txt

source_name: TAG5 Infected BR

value: tolerant


title: ZG14 Infected BR2


title: ZG14 Control BR1


title: TAG5 Infected BR1


title: TAG5 Control BR1

source_name: TAG5 Control BR


title: 20DAP_MATZ_r1

city: Gainesville

first: Karen

middle: E

last: Koch

state: Florida

department: Plant Molecular Cellular Biology

institute: University of Florida

data_processing:
Tophat 2/Bowtie 2
Cufflinks
Genome_build: B73 v2
Supplementary_files_format_and_content: Table of Cufflinks FPKM values for 39,424 maize gene models

organism: Zea mays

source_name: Maternal transfer zone

growth_protocol: ears harvested from field grown plants at 8DAP, 14DAP and 20DAP

extract_protocol:
total RNA extraction
Illumina standard protocol

treatment_protocol: tissues separated by cryomicrodissection

value: Maternal transfer zone

value: 20 days post pollination

value: W22 inbred


title: TAG5 Control BR3


title: TAG5 Infected BR3


title: 14DAP_BETL_r2

source_name: Basal endosperm transfer layer

value: Basal endosperm transfer layer

value: 14 days post pollination


title: 20DAP_MATZ_r2


title: 14DAP_BETL_r1


title: E14.5 Post. Lateral Rep. 3

value: posterior lateral palate


title: 20DAP_BETL_r1


title: 20DAP_BETL_r2


title: 14DAP_MATZ_r2


title: 14DAP_MATZ_r1


title: 8DAP_MATZ_r2

value: 8 days post pollination


title: prmt4a;4b mutant rep 3

city: Buenos Aires

first: Marcelo

last: Yanovsky

state: Ciudad Autonoma de Buenos Aires

address: Av. Patricias Argentinas 435

country: Argentina

institute: Fundación Instituto Leloir. IIBBA- CONICET

data_processing:
Basecalling done with Bustard Illumina Pipelline
Sequence reads were mapped to Arabidopsis thaliana TAIR10 genome using TopHat v2.0.9 with default parameters, except of maximum intron length set in 5000
Count tables for different feature levels were obtained from bam files using custom R v3.0.2 scripts.
Differential gene expression was estimated using edgeR package version 3.4.2 and resulting p-values were adjusted using false discovery rate (fdr) criterion.
The transcriptome was partitioned into subgenic joint features called bins and labeled as exon-bin, intron-bin or alternative-splicing (AS) bins. In addition AS-bins were further classified as exon skipping (ES), 5’ or 3’ alternative (5´alt, 3´alt), intron retention (IR) or multiple. Bins from monoexonic genes and with mean count values lower than 5 reads per condition were discarded.
Genome_build: We used edgeR exactTest for the identification of differential usage of bins corresponding to AS events or introns, and fdr corrected p-values. We also computed read densities in order to have a relationship between the bin and its corresponding gene. A Splicing Index was calculated as bin read density/gene read density, and the Splicing Index Ratio was calculated as Splicing Index in mutants/Splicing Index in WT plants. Only genes with read densities greater than 0.1 in all genotypes, and Splicing Indexes greater than 0.05 in at least one genotype, were used for the analysis. AS events as well as all introns with an absolute Log2 FC (bin read density in the mutant/bin read density in WT) value greater than 0.58, with fdr values lower than 0.15, and an abosolute Log2 Splicing Index Ratio (Splicing Index in the mutant/Splicing Index in WT) greater than 0.58, were deemed as differentially spliced.
Genome_build: TAIR10
Supplementary_files_format_and_content: Comprehensive spreadsheets with the results of the analysis of differential expression and differential splicing detailed above

organism: Arabidopsis thaliana

source_name: pool of tissues

growth_protocol: For WT (Col), prmt5 and prmt4a;4b mutants, seeds were grown on Murashige and Skoog medium containing 0.8% agarose, stratified for 4 d in the dark at 4 °C, and then grown at 22 °C in continuous light.

extract_protocol:
Total RNA was extracted with RNeasy Plant Mini Kit (QIAGEN) following the manufacturer’s protocols. To estimate the concentration and quality of samples, NanoDrop 2000c (Thermo Scientific) and gel electrophoresis were used, respectively.
Libraries were prepared following the TruSeq RNA Sample Preparation Guide (Illumina). Briefly, 3 μg of total RNA was polyA-purified and fragmented, and first-strand cDNA synthesized by reverse transcriptase (SuperScript II; Invitrogen) and random hexamers. This was followed by RNA degradation and second-strand cDNA synthesis. End repair process and addition of a single A nucleotide to the 3′ ends allowed ligation of multiple indexing adapters. Then, an enrichment step of 12 cycles of PCR was performed. Library validation included size and purity assessment with the Agilent 2100 Bioanalyzer and the Agilent DNA1000 kit (Agilent Technologies)

treatment_protocol: Whole plants were harvested after 15 d.

tag: ecotype

value: Col

value: prmt4a;4b double mutant


title: prmt4a;4b mutant rep 1


title: prmt5 mutant rep 3

value: prmt5 mutant


title: prmt4a;4b mutant rep 2


title: TAG5 Control BR2


title: WT Col rep 3

value: Wild type


title: prmt5 mutant rep 2


title: WT Col rep 2


title: WT Col rep 1


title: KR2-37

status: Public on Apr 02 2015

city: Madison

first: Federico

last: Rey

state: WI

address: 1550 Linden Dr.

institute: University of Wisconsin-Madison

data_processing:
Library strategy: COPRO-Seq
Demultiplexing: sequences were demultiplexed by 4 nt barcode, requiring an exact match (sequences without a barcode match were excluded from the analysis)
Trimming: after demultiplexing, all sequences were trimmed to 25 bases to eliminate low-quality bases at the ends of each read
Mapping: sequences were aligned to the reference genomes of the 13 bacteria included in the study using Illumina's ELAND aligner (as provided in GAPipeline-1.4.0). Only perfect, non-redundant matches were carried forward in the analysis.
Normalization: raw counts were normalized based on the informative genome size (IGS) of each organism included in the analysis, as described by McNulty et al. in a previous publication (PMID: 22030749).
Summarization: the proportional representation of each organism in the analysis was determined by dividing its normalized counts within a sample by the total normalized counts for all organisms within that sample.
Genome_build: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482, Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33656, Clostridium_sporogenes_ATCC_15579, Anaerococcus_hydrogenalis_DSM_7454, Clostridium_asparagiforme_DSM_15981, Clostridium_hathewayi_DSM13749, Edwardsiella_tarda_ATCC23685, Escherichia_fergusoni_ATCC_35469, Proteus_penneri_ATCC_35198, Providencia_rettgeri_DSM_1131
Supplementary_files_format_and_content: Excel file. The column header (B1-BE1) specifies the sample from which data were derived. Subsequent rows specify the organism/reference genome, raw counts, and normalized relative proportion for each taxon included in the alignment. Small intestine samples with less then 1000 reads (total raw counts) were not used in final analysis. Cecum and large intestine samples with less than 10,000 reads (total raw counts) were not used for final analysis. These samples are marked in red.
Supplementary_files_format_and_content: KR_Norm_Decimal_Percent_w_Raw_Counts.xlsx [Samples KR1 to KR56]
Supplementary_files_format_and_content: KR2_Norm_Decimal_Percent_w_Raw_Counts.xlsx [Samples KR2-1 to KR2-60]

organism: mouse metagenome

source_name: Distal Small Intestine

growth_protocol: Bacteria from frozen culture stocks were introduced as an artificial community (AC) into 6-24 week old male and female gnotobiotic C57BL/6J and NMRI mice.  Cells were therefore maintained over the course of the experiment within mice until sampling occurred.

extract_protocol:
DNA was extracted from intestinal samples using mechanical disruption (bead-beating with 0.1 mm zirconium beads) in phenol:chloroform:IAA in the same manner as described by McNulty et al. in a previous publication (PMID: 22030749).
Libraries were prepared according to a slightly modified version of the protocol accompanying the Illumina Genomic DNA Sample Prep Kit. Briefly, total bacterial gDNA was sonicated in a BioRuptor XL water bath sonicator, cleaned up and concentrated using a Macherey-Nagel PCR Purification column. DNA was blunted and poly-A tailed. The A-tailed molecules were ligated to the relevant barcoded Illumina adapter sequence.  Adaptered-DNA was then size-selected by agarose gel electrophoresis.  Fragments of the appropriate size were PCR amplified and purified, after which the purified PCR products were give to the University of Wisconsin-Madison Biotechnology Center for quality assurance and library sequencing following the manufacturer's protocols (Illumina MiSeq 1x50bp).

treatment_protocol: Immediately after collection, samples were subjected to flash-freezing in ethanol chilled with dry ice and stored at -80 C until total community DNA extractions could be performed.

value: NMRI

tag: gender

value: Male

tag: community composition

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33656, Clostridium_sporogenes_ATCC_15579, Anaerococcus_hydrogenalis_DSM_7454, Clostridium_asparagiforme_DSM_15981, Clostridium_hathewayi_DSM13749, Clostridium_hathewayi_DSM13749, Edwardsiella_tarda_ATCC23685, Escherichia_fergusoni_ATCC_35469, Proteus_penneri_ATCC_35198, Providencia_rettgeri_DSM_1131

tag: diet

value: Choline +

tag: mouse number


title: KR2-36

source_name: Distal Large Intestine

tag: strain


title: KR2-34


title: prmt5 mutant rep 1


title: KR2-32

source_name: Cecum


title: KR2-35


title: KR2-30


title: KR2-29


title: KR2-26


title: KR2-24

value: Choline -


title: KR2-27


title: KR2-28


title: KR2-25


title: KR2-23


title: 8DAP_BETL_r1

value: wild type


title: KR2-22


title: KR2-18


title: KR2-20


title: KR2-19


title: KR2-33


title: KR2-17


title: KR2-16


title: KR2-13


title: KR2-14


title: KR2-15


title: KR2-31


title: KR2-12


title: KR2-11


title: KR2-9


title: KR2-10


title: KR2-3


title: KR2-8


title: KR2-7


title: KR2-2


title: KR2-6


title: KR2-1


title: KR2-5


title: KR56

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33671


title: KR54

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33669


title: KR2-4


title: KR2-21


title: KR53

source_name: Proximal Small Intestine

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33668


title: KR52

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33667


title: KR50

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33665


title: KR48

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33663


title: KR46

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33661


title: KR44

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33659


title: KR51

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33666


title: KR49

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33664


title: KR47

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33662


title: KR45

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33660


title: KR42

value: Male

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33657


title: KR43

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33658

value: Choline +


title: KR55

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33670


title: KR33

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33656, Clostridium_sporogenes_ATCC_15579, Anaerococcus_hydrogenalis_DSM_7454, Clostridium_asparagiforme_DSM_15981, Clostridium_hathewayi_DSM13749, Clostridium_hathewayi_DSM13749, Edwardsiella_tarda_ATCC23685, Escherichia_fergusoni_ATCC_35469, Proteus_penneri_ATCC_35198, Providencia_rettgeri_DSM_1131


title: KR34


title: KR29


title: KR27


title: KR32


title: KR37


title: KR24


title: KR40


title: KR39


title: KR38


title: KR35


title: KR26


title: KR36


title: KR31


title: KR25


title: KR28


title: KR30


title: KR23


title: KR22


title: KR41

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33656


title: KR20

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33656, Clostridium_sporogenes_ATCC_15598


title: KR16

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33656, Clostridium_sporogenes_ATCC_15594


title: KR19

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33656, Clostridium_sporogenes_ATCC_15597


title: KR15

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33656, Clostridium_sporogenes_ATCC_15593


title: KR17

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33656, Clostridium_sporogenes_ATCC_15595


title: KR12

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33656, Clostridium_sporogenes_ATCC_15590


title: KR11

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33656, Clostridium_sporogenes_ATCC_15589


title: KR10

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33656, Clostridium_sporogenes_ATCC_15588


title: KR9

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33656, Clostridium_sporogenes_ATCC_15587


title: KR8

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33656, Clostridium_sporogenes_ATCC_15586


title: KR21

value: Male


title: KR5

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33656, Clostridium_sporogenes_ATCC_15583


title: KR7

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33656, Clostridium_sporogenes_ATCC_15585


title: KR6

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33656, Clostridium_sporogenes_ATCC_15584

value: Choline +


title: KR3

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33656, Clostridium_sporogenes_ATCC_15581


title: KR2

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33656, Clostridium_sporogenes_ATCC_15580


title: KR18

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33656, Clostridium_sporogenes_ATCC_15596


title: Input DNA for ChIPs, lin-35 mutant extract IL3

first: Przemyslaw

middle: Aleksander

last: Stempor

state: United Kingdom

address: Tennis Court Road

department: The Gurdon Institute

country: United Kingdom

institute: University of Cambridge

description: Sample name: input_lin35_IL051_IL3

data_processing:
ChIP-seq and RNA-seq reads were aligned to the WS220 assembly of the C. elegans genome using BWA (Li and Durbin, 2010) with default settings.
ChIP-seq data were normalized using BEADS algorithm (Cheung et al, 2011).
ChIP-seq signals were exported to bigWig tracks at native resolution.
RNA-seq tag counts for each gene were extracted from BAM alignment files using HTSeq method working in ”union” mode. An exon model based on WS235 genes (taken from Ensembl Gene 74 December 2013) was lifted over to ce10/WS220.
RNA-seq tag counts were used to build the expression matrix. Differential gene expression between N2, lin-35 mutant, and htz-1 mutant was tested using DESeq2
Genome_build: ce10/WS220
Genome_build: http://ws220.wormbase.org/
Genome_build: http://hgdownload.soe.ucsc.edu/goldenPath/ce10/bigZips/
Supplementary_files_format_and_content: "linear" scores in bigWig tracks represent BEADS values; files were generated using BEADS normalization pipeline in R
Supplementary_files_format_and_content: "zscore" scores in bigWig tracks represent standardized BEADS values; files were generated using BEADS normalization pipeline in R
Supplementary_files_format_and_content: xslx spreadsheet contains: reads per kilobase (kb) of transcript per millions reads in library (RPKM) for all RNA-seq experiments, averaged RPKM values for replicates, plus log2 fold changes, p-values and adjusted p-values (FDR) calculated with DEseq2 for gene knock-out replicates versus N2 (wild-type) replicate

organism: Caenorhabditis elegans

source_name: L3 larvae

growth_protocol: Worm_L3_growth_and_harvest_vPK1. About 2-7 million of worms are bleached and then hatched in M9 for 24-42 hrs. About 100 embryos are seeded onto the plate to test for contamination and hatching efficiency. Remaining hatched L1 larvae are inoculated in a proper volume of liquid culture. Next day when larvae reach the L3 stage they are cleaned by M9 washes and sucrose gradient and collected by freezing in liquid nitrogen. Just before collection DIC pictures are taken and about 50ul of worms are stained for DAPI to assess the stage.

extract_protocol: Worm_L3_extraction_vPK1. Worms are frozen, ground, and crosslinked for 10 minutes in 1% formaldehyde. Formaldehyde is quenched and cross-linked tissue washed, then resuspended in FA buffer and subjected to sonication in Bioruptor (14 pulses of 30 seconds with 1 minute rests in between). Extracts are then spun down and soluble fraction is stored for quality tests and future ChIP.  Worm_chromatin_immunoprecipitation_vIL2. Appropriate amount of extract is incubated overnight with a proper amount of antibody (exceptional antibodies due to better results are incubated 2hrs). Afterwards, 40ul of equilibrated magnetic beads (either protein A or G, depending on antibody) are added and incubated for 2 hrs. Later, washes with FA, 500mM-salt FA, 1M salt FA, TEL, and TE buffer are performed and DNA is eluted in elution buffer (1% SDS in TE with 250 mM NaCl) two times with 57 ul volume each, at 65°C. Samples are treated with RNAse, proteinase K and then crosslinks are reversed overnight at 65°C. DNA is purified on Qiagen PCR purification columns, tested by q-PCR for ChIP quality, and stored at -20°C for future applications.  DNA was incubated with an enzyme mix (Klenow, T4 DNA polymerase and T4 PNK) to ensure blunt ends and then with Exo(-) Klenow fragment in the presence of dATP to add adenosine at the 3' ends. The DNA fragments were ligated with appropriate adaptor (Illumina) and then amplified by PCR. The amplicon was loaded into an agarose gel, and size-selected DNA was recovered from the gel.  Prepared sample are sequenced using Illumina GAIIx or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge.

value: whole larvae

tag: Stage

tag: genotype/variation

value: lin-35 mutant

tag: chip antibody


title: ChIP-seq of H4ac (tetraacetyl) in lin-35 mutant, replicate 2

description: Sample name: H4ac4_lin35_PK018_IL3_AR0109

treatment_protocol: Worms are frozen, ground, and crosslinked for 10 minutes in 1% formaldehyde. Formaldehyde is quenched and cross-linked tissue washed, then resuspended in FA buffer and subjected to sonication in Bioruptor (14 pulses of 30 seconds with 1 minute rests in between). Extracts are then spun down and soluble fraction is stored for quality tests and future ChIP.

value: anti-H4 tetraacetyl

tag: chip antibody supplier

value: Active Motif

tag: chip antibody catalog#


title: KR13

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33656, Clostridium_sporogenes_ATCC_15591


title: ChiP-seq of H3K4me3 in lin-35 mutant, replicate 1

description: Sample name: H3K4me3_lin35_IL050_IL3_WA305-34819

value: Wako


title: ChIP-seq of H4ac (tetraacetyl) in lin-35 mutant, replicate 1

description: Sample name: H4ac4_lin35_IL058_IL5_AR0109


title: ChiP-seq of HTZ-1 in lin-35 mutant, replicate 2

description: Sample name: HTZ-1_lin35_IL011_IL5_JA00001

value: Eurogentec


title: ChIP-seq of H3K36me3 in wild-type, replicate 2

description: Sample name: H3K36me3_N2_PK007_WA300-95259

growth_protocol: About 2-7 million of worms are bleached and then hatched in M9 for 24-42 hrs. About 100 embryos are seeded onto the plate to test for contamination and hatching efficiency. Remaining hatched L1 larvae are inoculated in a proper volume of liquid culture. Next day when larvae reach the L3 stage they are cleaned by M9 washes and sucrose gradient and collected by freezing in liquid nitrogen. Just before collection DIC pictures are taken and about 50ul of worms are stained for DAPI to assess the stage. http://wiki.modencode.org/project/index.php/Worm_L3_growth_and_harvest:JL:PK1

treatment_protocol: Worms are frozen, ground, and crosslinked for 10 minutes in 1% formaldehyde. Formaldehyde is quenched and cross-linked tissue washed, then resuspended in FA buffer and subjected to sonication in Bioruptor (14 pulses of 30 seconds with 1 minute rests in between). Extracts are then spun down and soluble fraction is stored for quality tests and future ChIP. http://wiki.modencode.org/project/index.php/Worm_L3_extraction:JL:PK1

value: wild-type


title: ChIP-seq of H3K4me3 in lin-35 mutant, replicate 2

description: Sample name: H3K4me3_lin35_IL071_IL5_WA305-34819


title: ChIP-seq of H3K36me3 in wild-type, replicate 1

description: Sample name: H3K36me3_N2_PK006_WA300-95259


title: ChiP-seq of HTZ-1 in lin-35 mutant, replicate 1

description: Sample name: HTZ-1_lin35_IL008_IL3_JA00001


title: Normal 2

city: Los Angeles

first: Michael

middle: James

last: Thompson

state: California

address: 610 Charles Young Drive East

department: Department of Molecular, Cell and Developmental Biology

institute: UCLA

data_processing:
Concatenate all qseq files for all lanes for a given sample
Map reads to genome with BS Seeker2 implementation of Bowtie
Call CpG sites and calculate methylation status with BS Seeker2
Genome_build: hg19
Supplementary_files_format_and_content: BS Seeker2 outputs CGmap files in text format
CGmap column headers: (1) chromosome (2) nucleotide on Watson (+) strand (3) position (4) context (CG/CHG/CHH) (5) dinucleotide-context (CA/CC/CG/CT) (6) methylation level (7) methylation counts (8) total counts

source_name: Pancreas

extract_protocol:
MagNA Pure Compact Nucleic Acid Isolation Kit (Roche)
Digests were performed with the methylation-insensitive restriction enzyme, MspI, and fragments ranging from 50 to 300 bases were selected to enrich for CpG rich regions. After digestion, samples were ligated with Illumina adaptors, size selected, denatured and treated with sodium bisulfite to reveal their methylation state.  Libraries were sequenced using Illumina Hiseq 2000 sequencers.

tag: donor age (years)

tag: disease-specific survival time (months)

tag: death censor

tag: tumor cellularity (%)


title: Pancreatitis 2


title: Normal 1


title: Pancreatitis 3


title: KR4

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33656, Clostridium_sporogenes_ATCC_15582


title: Tumor 11


title: Tumor 10


title: Tumor 8


title: Tumor 9


title: KR1

value: Male

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33656, Clostridium_sporogenes_ATCC_15579


title: Input DNA for ChIPs, lin-35 mutant extract IL5

description: Sample name: Input_lin35_IL063_IL5


title: Tumor 7


title: Tumor 5


title: Tumor 4


title: Tumor 3


title: KR14

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33656, Clostridium_sporogenes_ATCC_15592


title: Tumor 1


title: US-1422352

city: Columbus

first: James

last: Blachly

address: B305 Starling-Loving Hall

institute: The Ohio State University

data_processing:
Reads were quality and adapter trimmed by Sickle and Sythe, respectively
Transcriptomes were reconstructed with Trinity r2013_08_14
BLAST was used to select transcripts with homology to IGHV genes
A new reference transcriptome from the transcripts in the previous step was made with bowtie2- build
Reads were mapped to the IGHV transcriptome with bowtie2
Abundances were calculated with eXpress 1.5.1
IGH data were computed by feeding the transcripts into NCBI IgBLAST using the IMGT database
Genome_build: N/A
Supplementary_files_format_and_content: Matrix (igh.txt); eXpress quantification output files, tab delimited where rows represent IGH transcript candidates (SampleID_quant.txt).  See igh.txt for alleles.

source_name: PB

extract_protocol:
Total RNA was extracted with Trizol reagent
libraries were prepared with the Illumina Truseq mRNA kit

treatment_protocol: Ficoll gradient centrifugation and isolation of PBMCs

tag: disease

value: Chronic lymphocytic leukemia

tag: cell type

value: CLL cells


title: US-1422350


title: US-1422335


title: US-1422356


title: US-1422366


title: US-1422351


title: US-1422368


title: US-1422342


title: US-1422321


title: US-1422311


title: US-1422314


title: US-1422309


title: US-1422302


title: Tumor 6


title: RNA-seq in htz-1 mutants, replicate 2

description:
Sample name: htz1-1012_RNAseq_MC002
processed data file: N2_lin-35_htz-1_processed_RNAseq.xlsx

growth_protocol: Worms grown in liquid culture were bleached and then hatched in M9 for 24-42 hrs. Hatched L1 larvae were inoculated in a proper volume of liquid culture. Next day when larvae reached the L3 stage they were cleaned by M9 washes, sorted on a COPAS BIOSORT (Union Biometrica) to isolate non-GFP homozygous mutants, and collected by freezing in liquid nitrogen.

extract_protocol: Total RNA was used to make mRNA libraries using the TruSeq RNA Sample Preparation Kit according to the manufacturer's instructions (Illumina, Inc., San Diego, CA, USA).

treatment_protocol: Total RNA was extracted in TriPure Reagent according to manufacturer's protocol, treated with baseline-zero DNAse (Epicentre, Madison, WI, USA), and purified using the Qiagen Rneasy kit.

tag: tissue

value: htz-1 mutants


title: RNA-seq in lin-35 mutants, replicate 1

description:
Sample name: lin35_1109_RNAseq_MC005
processed data file: N2_lin-35_htz-1_processed_RNAseq.xlsx

growth_protocol: Worms grown in liquid culture were bleached and then hatched in M9 for 24-42 hrs. Hatched L1 larvae were inoculated in a proper volume of liquid culture. Next day when larvae reached the L3 stage they were cleaned by M9 washes and sucrose gradient and collected by freezing in liquid nitrogen.


title: RNA-seq in wild-type, replicate 2

description:
Sample name: N2_0910_RNAseq_MC003
processed data file: N2_lin-35_htz-1_processed_RNAseq.xlsx


title: US-1422282


title: RNA-seq in lin-35 mutants, replicate 2

description:
Sample name: lin35_0910_RNAseq_MC006
processed data file: N2_lin-35_htz-1_processed_RNAseq.xlsx


title: RNA-seq in wild-type, replicate 1

description:
Sample name: N2-1109_RNAseq_MC004
processed data file: N2_lin-35_htz-1_processed_RNAseq.xlsx


title: Tumor 2


title: US-1422278


title: ChIP-seq of histone H3 in lin-35 mutant, replicate 2

description: Sample name: H3_lin35_AA223_IL10_ab1791

value: Abcam


title: 8DAP_MATZ_r1

value: Maternal transfer zone

tag: age

value: 8 days post pollination

tag: genotype

value: wild type

value: W22 inbred


title: US-1422333


title: ChIP-seq of histone H3 in wild-type, replicate 1

description: Sample name: H3_N2_AA220_IL2_ab1791

value: whole larvae


title: 8DAP_BETL_r2

value: Basal endosperm transfer layer


title: ChIP-seq of histone H3 in lin-35 mutant, replicate 1

description: Sample name: H3_lin35_AA222_IL3_ab1791

value: lin-35 mutant


title: ChIP-seq of histone H3 in wild-type, replicate 2

description: Sample name: H3_N2_AA221_IL7_ab1791


title: S95N

first: Luz

last: Orozco

state: CA

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

data_processing:
Basecalls perfromed with Illumina RTA
Reads aligned to mm9 genome using BS-Seeker2 and Bowtie as base aligner
Methylation calling using BS-Seeker2
Genome_build: mm9
Supplementary_files_format_and_content: .CGmap files containg methylation calls.

source_name: Liver

extract_protocol:
We isolated genomic DNA from flash frozen livers using a phenol-chloroform extraction
We digested 1μg of DNA with MspI restriction enzyme (NEB, Ipswich, MA, USA), carried out end-repair/adenylation (NEB) and ligation with TruSeq barcoded adapters (Illumina, San Diego, CA, USA). We selected DNA fragments of size range 200-300bp with AMPure magnetic beads (Beckman Coulter, Brea, CA, USA), followed by bisulfite treatment on the DNA (Millipore, Billerica, MA, USA), and PCR amplification (Bioline, Taunton, MA, USA ). We sequenced the libraries by multiplexing two libraries per lane in an Illumina HiSeq sequencer, with 100bp reads.

tag: Sex

value: 16 weeks old


title: S96N


title: RNA-seq in htz-1 mutants, replicate 1

description:
Sample name: htz1-0812_RNAseq_MC001
processed data file: N2_lin-35_htz-1_processed_RNAseq.xlsx


title: S92N


title: US-1422294


title: S93N


title: INPUT8 pcf11-13 37C

city: Oxford

first: Michal

middle: R.

last: Gdula

address: South Parks Road

institute: Oxford University

description: INPUT8 pcf11-13 37C

data_processing:
ChIP-seq reads were aligned to the saccharomyces cerevisiae (Yeast) full genome as provided by UCSC (sacCer3, April 2011) using Stampy.
Genome coverage was calculated, read count information was binned into 20bp intervals, read count normalized and eventuallu log2 of IP/input ratios were calculated. Such procesed signals were used for all further analysis discribed in the paper.
bedgraph files were generated from the ChIP and input genome coverage files binned into 10 bp bins. Log2 valuses of the ratio of ChIP and input in corresponding bins were calculated.
Genome_build: sacCer3, April 2011
Supplementary_files_format_and_content: tab-delimited text files (bedGraph format) include log2(IP/input) values for each Sample

organism: Saccharomyces cerevisiae

source_name: cell culture

growth_protocol: Strains were grown in YPD (1% yeast extract, 2% Bacto-peptone, 2% glucose)

extract_protocol:
Lysates were clarified from 1% formaldehyde fixed, sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP DNA was end-repaired, A-tailed and adaptor ligated before amplification and size selection. Prepared libraries after quality control were multiplexed and single-end sequenced over one "rapid" run on HiSeq sequencer.

value: pcf11-13 mutant

tag: growth temperature

value: grown at 37C

value: CMA601 antibody

tag: chip antibody reference


title: Wt

city: Hangzhou

first: Fangfang

last: Wang

address: No.1 Xueshi Road.

institute: Zhejiang University

data_processing:
Basecalls performed using HCS1.5.15.1+RTA1.13.48+OLB1.9.4.
Sequenced reads were mapped to the human genome (hg19) by SOAP2.21.
Raw data were filtered by SOAPnuke, one read will be removed if it matches any condition shows bellow: 1. contain adapter read；2. N base is more than 10% of read；3. bases with quality low than 20 is more than 50% of read.
Peaks were called using MACS-1.4.0alpha2.
Genome_build: hg19
Supplementary_files_format_and_content: Bed files were generated by MACS after soap alignment, the columns represent chromsome, start positon and end position in chromsome respectively.

source_name: GC

growth_protocol: GCs of infertile women with tubal factor were isolated and cultured.

extract_protocol:
Lysates were clarified from sonicated nuclei and AR-HA-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: DHT treatment

tag: transduction

value: Wt AR-HA

value: primary ovarian granulosa cells

tag: chip-antibody

value: HA


title: Del

value: Del AR-HA


title: Ins

value: Ins AR-HA


title: ChIP-seqpcf11-13 37C

description: ChIP-seqpcf11-13 37C

tag: genotype/variation

tag: chip antibody


title: Knockdown

city: Tianjin

first: Xuexia

last: Zhou

address: 154 Anshan Road

department: Tianjin Neurological Institute

institute: Tianjin Medical University General Hospital

description: Sample 2

data_processing:
Images generated by sequencers are converted by base calling into nucleotide sequences.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
The clean reads were then aligned to the reference human genome and the corresponding annotated genes using the TopHat.
In the alignment, preliminary experiments were performed to optimize the alignment parameters to provide the most information on the alternative splicing events.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited excel file includes gene name, the splicing loci on chromosome, the number of mapping reads supporting exon skipping and inclusion separated by the symbol "::" in KD and WT samples, the number of reads supporting the alternative splicing exons (or part of exons) and supporting the expressed gene separated by the symbol "::" in KD and WT samples, statistically P-value and FDR values for alternative splicing events between the two samples, and their corresponding splicing types

source_name: RKO cells

growth_protocol: Human colon cancer RKO cells were cultured in Dulbecco's modified eagle medium (DMEM),supplemented with 10% fetal bovine serum(FBS), 100 U/mL penicillin, and 100 μg/mL streptomycin.

extract_protocol:
Cells were harvested and total RNA was extracted by Trizol reagent. Beads with oligo(dT) were used to isolate poly(A) mRNA after total RNA was collected.
Libraries for paired-end sequencing were prepared using mRNA-Seq Sample Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: Different siRNA oligos were ordered from Gene Pharma (Shanghai, China). Transfection was performed using Lipofectamine RNAiMAX, according to the manufacturer’s instructions.

tag: cell line

value: RKO

value: colon carcinoma epithelial cells

value: colon

value: SRSF10 knockdown


title: Control

description: Sample 1

value: control


title: S90N

tag: strain

value: Male


title: jarid KD R5

city: Parkville

first: Marnie

last: Blewitt

state: VIC

address: 1G Royal Parade

department: Molecular Medicine Division

country: Australia

institute: WEHI

data_processing:
The RNA-sequencing reads were aligned to mm10 using TopHat version 2.0.8 with the -- b2-very-sensitive preset
Aligned reads were then summarised over exons using featureCounts from the Rsubread package.
Differential analysis was done using Voom (Law et al., 2014) together with Limma (Smyth, 2004) on genes with a count per million (cpm) larger than 1 in at least 2 samples.
Read counts were divided by total exon length giving RPKM.
Genome_build: mm10
Supplementary_files_format_and_content: csv files with rpkm and differential expression for the groups.

source_name: Jarid2 knockdown_HSPC

growth_protocol: Experimental protocols were approved by the Walter and Eliza Hall Institute Animal Ethics Committee. Retroviral supernatants were prepared as described in Majewski et al., 2008. Gene-specific short hairpin RNA sequences (Supplementary Table) were designed using the DSIR website (http://biodev.cea.fr/DSIR/DSIR.html) (Vert et al., 2006) and subcloned into the LMS-GFP or LMP-BFP vectors that drive expression of a modified microRNA (mir30 backbone) adapted from Dickins et al., 2005 with selectable markers EGFP or EBFP/puromycin, respectively. E14.5 FL cell transduction and transplantation was performed as described in Majewski et al., 2010. Lethally irradiated (11Gy) secondary transplant recipients were injected with 1-3 x 10^6 BM cells isolated from FL primary recipients, with 2 or 3 secondary recipients per donor. Adult BM was harvested from the iliac, femur and tibia bones of CD45.1+ C57BL/6 donor mice. Cells were stained with rat monoclonal antibodies against mature lineage markers (Ter119, B220, CD19, Mac1, Gr1, CD2, CD3, CD8) and then incubated with BioMag goat anti-rat IgG beads (Qiagen) for depletion using a Dynal magnet (Invitrogen). Lineage-depleted cells were stained with fluorophore-conjugated anti-rat IgG, c-Kit and Sca-1 and flow sorted on the FACSAria or BD InFlux (BD Biosciences). Sorted HSPCs were incubated for 16hrs in StemSpan SFEM (StemCell Technologies) with cytokines (50ng/ml SCF, 10ng/ml each of TPO, IL6 and Flt3), placed on viral coated dishes and incubated for a further 24hrs prior to cell collection and intravenous injection into lethally irradiated CD45.2+ recipients with buffer whole BM cells.

extract_protocol:
Donor+ Lineage- c-Kit+ Sca-1+ GFP+/BFP+ HSPCs were isolated from BM of recipient mice with 30,000 to 100,000 HSPCs pooled from 6 to 10 recipients used per sample. In total, we generated 5 shRNA-Nons, 4 shRNA-Suz12, 4 shRNA- Jarid2.1 and 3 shRNA-Jarid2.2 transduced HSPC samples.
Sequencing libraries were prepared using the TruSeq mRNA Sample Prep Kit (Illumina).
100bp single-end read sequencing was performed on a HiSeq2000 or HiSeq2500 (Illumina) by the Australian Genome Research Facility.

tag: strain background

value: Jarid2 knockdown

value: hematopoietic stem and progenitor cell (HSPC)


title: S91

value: A/J

value: 16 weeks old


title: S9


title: jarid KD R4


title: ChIP-seq pcf11-9 37C

description: ChIP-seq pcf11-9 37C

value: pcf11-9 mutant

value: grown at 37C


title: jarid KD R3


title: S89N


title: S94N


title: INPUT6 pcf11-2 37C

description: INPUT6 pcf11-2 37C

value: pcf11-2 mutant

value: CMA601 antibody


title: jarid KD R2


title: S88N

value: KK/HlJ


title: suz KD R3

source_name: Suz12 knockdown_HSPC

value: Suz12 knockdown


title: S87N

value: PL/J


title: INPUT5 WT 37C

description: INPUT5 WT 37C

value: wild type cells


title: ChIP-seq WT 37C

description: ChIP-seq WT 37C


title: S86N


title: suz KD R1


title: INPUT4 pcf11-13 24C

description: INPUT4 pcf11-13 24C

value: pcf11-13 mutant

value: grown at 25C


title: suz KD R2


title: S85NR


title: nons R4

value: non-silencing


title: INPUT7 pcf11-9 37C

description: INPUT7 pcf11-9 37C


title: ChIP-seq pcf11-9 25C

description: ChIP-seq pcf11-9 25C


title: ChIP-seq pcf11-13 24C

description: ChIP-seq pcf11-13 24C


title: S84N


title: INPUT2 pcf11-2 25C

description: INPUT2 pcf11-2 25C


title: nons R1


title: S83N


title: nons R3


title: nons R2


title: S82N


title: jarid KD R1


title: S81NR


title: ChIP-seq pcf11-2 25C

description: ChIP-seq pcf11-2 25C


title: S80NR


title: ChIP-seq pcf11-2 37C

description: ChIP-seq pcf11-2 37C


title: S8


title: INPUT1 WT 25C

description: INPUT1 WT 25C


title: S79N

value: SJL/J


title: ChIP-seq WT 25C

description: ChIP-seq WT 25C


title: INPUT3 pcf11-9 25C

description: INPUT3 pcf11-9 25C


title: S78N

value: Male


title: S77N


title: S76N

value: LG/J


title: INPUT_2

city: los angeles

first: matteo

last: pellegrini

address: 610 charles young drive east

data_processing:
Obtained reads were first mapped against the yeast (sacCer3) using bowtie v0.12.8 (Langmead et al., 2009)
Aligned reads were processed according to Ferrari et al. (Ferrari et al., 2012)
Genome_build: sacCer3
Supplementary_files_format_and_content: wig

source_name: yeast cell culture

growth_protocol: All the yeast strains were grown at 30 C in SC + Galactose 2% without uracil (Sunrise Science, cat 1652 and 1485-100) overnight. The next morning, cells were diluted to 0.3 OD600/ml and grown to mid-log phase (0.8-1 OD600/ml) or to stationary phase (5-6 OD600/ml or for 24-30 h).

extract_protocol:
Chromatin immunoprecipitation experiments were conducted according to Kitada et al. (Kitada et al., 2012), with minor modifications. Briefly, 50 OD of yeast cells are crosslinked using 1% formaldehyde for 15 minutes at room temperature and quenched with glycine 125 mM for 5 minutes at room temperature. After two washes with ice-cold PBS, the cells are resuspended in yeast lysis buffer (with 140 mM NaCl for DNMT3b and RNApolII or 500 mM NaCl for histone post-translational modifications) and the same volume of acid-washed glass beads. We disrupted the cells by vortexing for 5 minutes in a Disruptor Genie at 4°C and incubating in iced-water for 2 minutes. We repeated the cycle an additional five times. We collected the lysate by centrifugation after creating a hole on the bottom of the tube with a 25-G needle. We transferred a fraction of the lysate into a microTube (AFA filter – Covaris) and proceeded with the sonication using the Covaris S2 system according to the following parameters: 14 cycles of 30 sec ON, 30 sec OFF; Duty Cycle=5%; Intensity=5%; Cycles/Burst=200. The sonicated lysate is clarified via centrifugation and 50 μl of the supernatant are incubated over night at 4°C with a specific antibody (Supplementary File 6, Panel D). 10 μl of the clarified lysate are used as input control. The next day, immunoprecipitations are incubated 2 hours at 4°C with Protein A Dynabeads. Each wash is performed twice in the following order: low-salt buffer (50mM HEPES pH 7.5, SDS 0.1%, 1% Triton X-100, 0.1% Deoxycholate, 1mM EDTA, 140mM NaCl), high salt buffer (50mM HEPES pH 7.5, SDS 0.1%, 1% Triton X-100, 0.1% Deoxycholate, 1mM EDTA, 500 mM NaCl), LiCl buffer (10 mM Tris-HCl pH 8, 250 mM LiCl, 5mM EDTA, 1% Triton-X, 0.5% NP-40), TE buffer (100 mM Tris-HCl pH 8, 10 mM EDTA). Elution is performed at 65°C with TE/SDS buffer (100 mM Tris-HCl pH 8, 10 mM EDTA, 1% SDS). Tubes containing the eluted immunoprecipitations and input controls (additioned of TE/SDS buffer) are incubated overnight at 65°C to reverse the cross-links. RNase treatment is performed at 37°C for 1 hour, followed by a proteinase K treatment for 1 hour at 60°C. Each reaction is then purified using 1.8 volumes of AMPure XP beads according to manufacturer’s instructions.
Libraries were prepared with Ovation Ultralow DR kit (Nugen Technologies) starting from 1 ng of purified DNA according to the protocol.

tag: growth phase

value: stationary growth phase

tag: strain - genotype

tag: salt concentration used for the extraction (mm)


title: H3K4me1

value: ab8895 (Abcam)


title: polII

value: MMS-126R-200 (Covance)


title: S75NR

value: 16 weeks old


title: H3K4me3

value: 39159 (Active Motif)


title: H3K36me3

value: ab9050 (Abcam)


title: DNMT3b

value: ab2851 (Abcam)


title: S71N


title: S72NR

value: NZW/LacJ


title: Pancreatitis 1

tag: donor age (years)

tag: disease-specific survival time (months)

tag: death censor

tag: tumor cellularity (%)


title: S74NR

value: BTBR T<+> tf/J

tag: Sex

tag: age


title: S73N


title: INPUT_1


title: 3b_strain_3

data_processing:
Reads were aligned against sacCer3 genome assemblies using STAR v2.3.1 (Dobin et al., 2013) with the following parameters: --outFilterMismatchNoverLmax 0.04 --outFilterMultimapNmax 1.
Genome_build: sacCer3

extract_protocol:
RNA was collected from 5 OD of yeast cells (Collart and Oliviero, 2001) .
Approximately 500-1000 ng of extracted yeast RNA are used to prepare RNA-seq libraries using Illumina TruSeq mRNA Library Prep Kit v2 according to manufacturer’s instructions.

tag: genotype

value: wild-type


title: S7


title: 3b_strain_2


title: S69NR

value: NOD/ShiLtJ


title: S67N


title: S68NR

value: SM/J


title: EV_strain_4


title: 3b_strain_1

description: MNase-digested chromatin

data_processing:
Reads from both naked and nucleosomal DNA sequencing were aligned using bowtie v0.12.8 (Langmead et al., 2009) against the sacCer3 genome assembly, allowing up to 2 mismatches
Nucleosome calling was performed using DANPOS v2.1.3 (Chen et al., 2013) subtracting the naked DNA-derived reads from the nucleosomal reads and using the  “-k1 -e1” parameters
Genome_build: sacCer3
Supplementary_files_format_and_content: wig files

extract_protocol:
Nucleosome mapping has been performed according to Rando O.  (Rando, 2010) with minor modifications. Stationary phase yeast culture (≈6 OD/ml) is cross-linked with 1% formaldehyde for 20 minutes with occasional rotation at room temperature. The reaction is quenched with glycine for 5 min at room temperature. About 60 OD of yeast cells are washed twice with PBS buffer and then resuspended in 2 ml of Z buffer (1M sorbitol, 50 mM Tris-HCl pH 7.4 with freshly added 10 mM β-mercaptoethanol) containing 3.6 mg of Zymolyase-20T (from Arthrobacter luteus, AMS Biotechnology) and incubated at 37°C in agitation. After 45 min the same amount of Zymolyase is added and each sample which is incubated for an additional 45 min at 37°C in agitation. Spheroplasts are then pelleted by centrifugation for 5 min at 4°C at 1,500 g. The pellet is washed once with NP-buffer, then resuspended in 1.6 ml of NP-buffer and divided in 3 tubes. An increasing amount of MNase (Sigma, N3755) is added to each tube: 0.25 U, 0.5 U and 1 U. After incubation for 20 min at 37°C, each reaction is stopped by the addition of SDS and EDTA to a final concentration of 1% and 10 mM, respectively. The reaction is then treated with 0.2 mg/mg of Proteinase K (NEB) at 65°C overnight. The sample is then purified with 2 rounds of phenol:chloroform (1:1) and the aqueous solution precipitated. The resuspended DNA pellet is treated for 1 h with RNase A at 37°C. For the naked DNA digestion, 200 ng of extracted DNA are incubated at 37°C with 0.01 U of MNase. After 7 minutes the reaction is stopped as described before. Both naked and RNaseA-treated nucleosomal DNAs are then purified using 1.8 volumes of AMPure XP beads
Libraries were prepared using NEBNext DNA Library Prep Master Mix Set for Illumina (NEB, E6040S) with few modifications of the manufacturer’s protocol. Only the digestion pattern obtained with 0.5 U of MNase was used for the library preparation. The DNA is end-repaired (in half of the suggested volume), dA-tailed and 1 μl of Illumina TruSeq Adapters is added to a 40 μl ligation reaction. Purification after each step are performed using AMPure XP beads according to the protocol. The size selection step is carried out with 0.8x of AMPure beads in the first step and 0.2x of AMPure XP beads in the second step. Half of the DNA is amplified using Illumina PCR Master Mix and Illumina TruSeq PCR Primer Cocktail (TruSeq DNA Sample Prep kit v2) with the following protocol: initial denaturation at 98°C for 30 seconds; 12 cycles of 98°C for 15 seconds, 60°C for 30 seconds, 72°C for 30 seconds; final extension at 72°C for 5 minutes. The final product is purified using AMPure XP beads before being submitted for sequencing.


title: EV_strain_3


title: S65N


title: 3b_strain_4


title: EV_strain_1

description: MNase-digested chromatin


title: 3b strain 1_naked

description: MNase-digested genomic DNA


title: S64


title: EV strain 1_naked

description: MNase-digested genomic DNA


title: S70N


title: S62NR

value: BALB/cJ


title: dot1delta replicate 2

data_processing:
Reads from bisulfite-treated yeast genomic DNA were aligned using BS-Seeker2 v2.0.3 (Guo et al., 2013) against the sacCer3 and mm9 genome assemblies, respectively. Up to 4 mismatches were allowed and bowtie (v0.12.8) was specified as the aligner.
Methylation was called using default parameters of BS-Seeker2.
Genome_build: sacCer3
Supplementary_files_format_and_content: wig

extract_protocol:
5 OD600 of yeast cells were disrupted by vortexing for 6 minutes in a Disruptor Genie (Scientific Industries, Inc.) in the presence of an equal volume of breaking buffer, acid-washed glass beads and phenol:chloroform (1:1). After the addition of TE buffer, aqueous phase is transferred into a new tube and precipitated with ethanol. The nucleic acid pellet is resuspended in TE buffer and treated for 1 hour at 37°C with RNase A, followed by incubation for 1 hour with 2 mg/ml Proteinase K in the presence of 1% SDS at 60°C. The resulting solution is treated twice with phenol:chloroform (1:1), once with chloroform and ethanol precipitated. The DNA pellet is resuspended in EB buffer (Qiagen).
Between 500-1000 ng of extracted yeast DNA are added to 2 ng of λ unmethylated DNA (Promega, D1521) and the mixture is sonicated with a Covaris S-2 to obtain fragments in the 200-300 bp range [Total Time: 6 minutes; Duty Cycle: 10%; Intensity: 5; Cycles/Burst: 200; Mode: Frequency Sweeping]. The reagents used in the library preparation are from the Illumina TruSeq DNA Sample Prep kit v2. End-Repair, purification and dA-tailing steps are performed according to manufacturer’s instructions. Ligation is performed according to the protocol except that 1 μl of Illumina TruSeq Adapters is used in the final reaction. The ligation reaction is purified using 1.2 volumes of AMPure XP beads (Beckman Coulter Inc.) and DNA fragments with a 170-350 bp range are enriched using 0.7 and 0.3 volumes of AMPure XP beads in the first and second size-selection step, respectively. Samples are treated with bisulfite (EpiTect kit, QIAGEN) according to manufacturer’s protocol, except that two consecutive rounds of conversion are performed, for a total of 10 h of incubation. Half of the converted DNA is amplified using MyTaq Mix (Bioline) and Illumina TruSeq PCR Primer Cocktail according to the following protocol: initial denaturation at 98°C for 30 seconds; 12 cycles of 98°C for 15 seconds, 60°C for 30 seconds, 72°C for 30 seconds; final extension at 72°C for 5 minutes. The final product is purified using AMPure XP beads before being submitted for sequencing.


title: dot1delta replicate 1


title: S63NR

value: LP/J


title: S6


title: S60N

value: CBA/J


title: set2delta replicate 2


title: set1delta replicate 2


title: set2delta replicate 1


title: set1delta replicate 1


title: 3b strain 7


title: S5I

value: Male


title: 3b strain 8


title: S5L


title: S5G


title: S66NR


title: 3b strain 6


title: S5F


title: 3b strain 4


title: 3b strain 5


title: S5E


title: S5D


title: S61N

value: SWR/J


title: S5C


title: 3b strain 3

value: stationary growth phase


title: S59N

value: CAST/EiJ


title: 3b strain 1


title: 3b strain 2


title: S58N


title: 3b_exp

value: exponential growth phase


title: S57N

value: 16 weeks old


title: EV_strain 4


title: S5H


title: EV strain 3


title: S56N

value: AKR/J


title: EV_strain 2


title: S51N


title: S54N


title: S52N


title: S53N

value: BUB/BnJ


title: S49N


title: EV strain 1


title: S4B


title: S46N


title: S48N


title: S47N


title: S43N


title: S44N


title: S50N


title: S45N


title: S42N


title: S55N


title: S39N

value: CE/J


title: S36NR


title: S35N


title: S40N


title: S37N


title: S33NB


title: S38NC


title: S34NC

value: NON/ShiLtJ


title: S5


title: S32C


title: S29N


title: S31N


title: S30N


title: S3


title: S28NC


title: S28N


title: S25NC

value: SEA/GnJ


title: S2B


title: S20


title: S22


title: S21


title: S26


title: S24B


title: S27

value: RIIIS/J


title: S41N


title: S16


title: S17C


title: S14


title: S13C


title: S10


title: S23


title: S12


title: S1


title: INP_E13.5_male_germcells

data_processing:
Obtained reads were first mapped against the mouse (mm9) using bowtie v0.12.8 (Langmead et al., 2009)
Aligned reads were processed according to Ferrari et al. (Ferrari et al., 2012)
Genome_build: mm9
Supplementary_files_format_and_content: wig: IP over INPUT

source_name: embryonic testes FACS-sorted cells

extract_protocol:
Pregnant females were euthanized using CO2 and the embryos removed from the womb and stored on a 10cm dish filled with chilled 1xPBS. Testicles were removed from the embryos, placed in an individual 15ml falcon tube with 3mls of 0.25 % Trypsin with 3μl of DNAse I 1Unit/1μL (Life Technologies).  Testes were incubated for 15mins at 37C. After incubation the cells were agitated into suspension gently by pipetting. The trypsin was then quenched using 5mL DMEM/10% FBS (Life Technologies). The cells were centrifuged at 278g for 5 minutes and resuspended in 500uL FACS buffer (1xPBS 1% BSA). 7-AAD was added at a 1:50 dilution (BD Biosciences) and the cells strained through BD FACS tubes (Corning) before analysis. GFP positive cells were sorted for ChIP.
The ChIP-seq protocol was adapted from published sources (Ng et al., 2013, Pastor et al., 2014). FACS sorted cells from four male, E13.5 embryos were diluted to 292μL with room temperature 1xPBS. 8.11μL 37% Formaldehyde (Sigma) was added and the sample was incubated 10 minutes at room temperature with rocking. 48.8μL of 1M glycine was then added to yield a final concentration of 0.14M and the samples were quenched 30 minutes with rocking. Cells were then spun 425g for 10 minutes at RT. The cell pellet was flash frozen. After thawing, the cells were resuspended in 300μL Lysis buffer (50mM Tris-Cl pH 8.0, 20mM EDTA pH 8.0, 0.1% SDS, 1x Complete Protease Inhibitor (Roche)) and incubated on ice ten minutes. Samples were then sonicated by Covaris S2 (Intensity 5, cycles/burst=200, duty cycle=5%, 10x30s on 30s off sonication). Samples were spun 14000g 10 minutes to remove insoluble material. The soluble sample was diluted to 600μL with dilution buffer (16.7mM Tris pH 8, 0.01% SDS, 1.1% TritonX-100, 1.2mM EDTA, 167mM NaCl) and 10% of material was saved as input. Sample was precleared with 30μL Protein A Dynabeads (Life Technologies) and preincubated 1hr. The cleared material was incubated with 1μL L anti-H3K36me3 antibody (Abcam Ab9050) overnight. The samples were incubated with 30μL Protein A Dynabeads and the precipitated material was recovered with a magnet. The beads were washed 2x4 minutes with Buffer A (50mM HEPES pH 7.9, 1% Triton X-100, 0.1% Deoxycholate, 1mM EDTA, 140mM NaCl), 2x4 minutes with Buffer B (50mM HEPES pH 7.9, 0.1% SDS, 1% Triton X-100, 0.1% Deoxycholate, 1mM EDTA, 500mM NaCl) and 2x4 minutes with 10mM Tris/1mM EDTA. Bound material was eluted with 100μL Elution buffer (50mM Tris pH 8.0, 1mM EDTA, 1% SDS) at 65 C for ten minutes and then eluted a second time with 150μL elution buffer. The input samples were thawed and diluted with 200μL buffer. Crosslinking of ChIP and input samples was reversed by incubating 16 hours at 65C. Samples were cooled and treated with 1.5μl of 10mg/mL RNaseA (PureLink RNAse A, Invitrogen #12091-021) for thirty minutes at 37C. 100μg of Proteinase K was then added and the samples treated for 2hr at 56C. The samples were then purified using a Qiagen MinElute kit. Samples were amplified by a SeqPlex DNA Amplification kit (Sigma) and then converted to libraries using an Ovation Rapid Library kit.

tag: embryonic day

tag: sample

value: INPUT

tag: cell type

value: embryonic testes cells


title: S18


title: jarid KD R7

tag: genotype/variation

value: Jarid2 knockdown

value: hematopoietic stem and progenitor cell (HSPC)


title: K36me3_E13.5_male_germcells

value: IP

tag: chip antibody

value: ab9050 (Abcam)


title: suz KD R4

value: Suz12 knockdown


title: jarid KD R6


title: S19

tag: strain

value: Male


title: hMeDIP_pw3_1

city: Munich

first: Arshan

last: Perera

state: Bavaria

department: Pharmacology

country: Germany

institute: LMU Munich

data_processing:
Peak-calling was performed using MACS Version 1.4 (http://liulab.dfci.harvard.edu/MACS/)
Minimum criteria for peaks was 4 reads
Peaks have to overlap within the replicates
Overlapping peaks in all samples were defined as conserved peaks
If peaks only overlap at postnatal week 2, they were considered as lost peaks
If peaks only overlap at postnatal week 3, they were considered as gained peaks
Genome_build: mm9
Supplementary_files_format_and_content: wig files contain conserved, lost and gained 5hmC peaks

source_name: retina

extract_protocol:
Retinas were removed, flash frozen on dry ice and DNA fragmentation was performed as described in (Mohn, Weber, Schubeler, & Roloff, 2009).
Paired-end libraries were prepared using the paired-end TruSeq DNA sample prep kit

tag: hmedip antibody

value: hmC pAB (Active Motif)

value: postnatal week 3

tag: tissue

value: retina


title: hMeDIP_pw3_3


title: hMeDIP_pw2_1

value: postnatal week 2


title: hMeDIP_pw3_2


title: nons R5

tag: strain background

value: non-silencing


title: S15C

value: 16 weeks old


title: KR2-60

value: NMRI

tag: gender

value: Female

tag: community composition

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33656, Clostridium_sporogenes_ATCC_15579, Anaerococcus_hydrogenalis_DSM_7454, Clostridium_asparagiforme_DSM_15981, Clostridium_hathewayi_DSM13749, Clostridium_hathewayi_DSM13749, Edwardsiella_tarda_ATCC23685, Escherichia_fergusoni_ATCC_35469, Proteus_penneri_ATCC_35198, Providencia_rettgeri_DSM_1131

tag: diet

value: Choline +

tag: mouse number


title: H3A_shBRG1_rep2

city: Illkirch

first: Patrick

last: Laurette

address: 1 Rue Laurent Fries

country: France

institute: IGBMC

data_processing:
Illumina Casava v1.8 software was used for basecalling.
Sequence reads were mapped onto the hg19 assembly of the human human using Tophat v1.4.1 and the bowtie v0.12.7 aligner.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file corresponding to abundance measurements (raw read counts for each ensembl gene id) for each sample

source_name: Hermes 3A

extract_protocol:
Total RNA isolation from 501M or Hermes3A cells was performed according to standard procedure (Qiagen kit). 1,5 μg of RNA was reverse transcribed using a mix 1/1 of SuperScript II RNase H-reverse transcriptase (Invitrogen) and AMV retrotranscriptase (Roche) with 500 ng of oligodT22 primer, hexanucleotides or specific primers according to the manufacter’s instructions
Total RNA-seq libraries were prepared following the Illumina protocol with some modifications. Briefly, 2 µg of total RNA was hybridized with rRNA sequence-specific 5’biotin labeled oligonucleotide probes to selectively deplete ribosomal RNA. The rRNA/5’biotin labeled probe was removed from the sample with streptavidin-coated magnetic beads. (Ribominus Eukaryote kit for RNA-seq, #A10837-08, Invitrogen Corporation). The rRNA depleted RNAs were then fragmented using divalent cations at 95°C for 5 minutes and used to generate a reverse transcribed cDNA library. 100 ng of each DNA library was then denatured at 98°C for 2 minutes, incubated at 68°C for 5 hours and then incubated in the presence Duplex-Specific thermostable Nuclease enzyme (DSN, #EA001, Evrogen) for DSN normalization following the Illumina protocol. DSN treated libraries were purified using Agencourt AMPure XP beads, enriched by PCR (30 sec at 98°C; [10 sec at 98°C, 30 sec at 65°C, 30 sec at 72°C] x 6 cycles; 5 min at 72°C) and purified again using Agencourt AMPure XP beads.

tag: cell line

value: Hermes 3A

value: melanocyte

tag: knockdown


title: H3A_shBRG1_rep1


title: H3A_shMITF_rep2

value: shMITF


title: BRG1siSOX10_CHIP-seq

data_processing:
Image analysis and base calling were performed using RTA 1.17.21.3 and CASAVA 1.8.2
Sequenced reads were mapped to the reference genome Human, hg19 using Bowtie 1.0.0 that was run using the following arguments -m 1 --strata --best -y -S -l 40 -p 2.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200bp)

extract_protocol:
BRG1 ChIP experiments were performed on native Mnase-digested chromatin isolated from 501Mel cells (Kasinathan et al., 2014). SOX10 and 3HA-MITF ChIP experiments were performed on 0,4% PFA-fixed chromatin isolated from 501Mel and Cl8 cells respectively according to standard protocols as previously described (Strub et al., 2011). Up to 60 ug of chromatin was subjected to immunoprecipation with a specific antibody.
The libraries were sequenced on the Illumina Hiseq 2500 as single-end 50 base reads following Illumina’s instructions

value: melanoma

value: BRG1 :Abcam (clone EPNCIR111A, ab110641)


title: KR2-59

data_processing:
Library strategy: COPRO-Seq
Demultiplexing: sequences were demultiplexed by 4 nt barcode, requiring an exact match (sequences without a barcode match were excluded from the analysis)
Trimming: after demultiplexing, all sequences were trimmed to 25 bases to eliminate low-quality bases at the ends of each read
Mapping: sequences were aligned to the reference genomes of the 13 bacteria included in the study using Illumina's ELAND aligner (as provided in GAPipeline-1.4.0). Only perfect, non-redundant matches were carried forward in the analysis.
Normalization: raw counts were normalized based on the informative genome size (IGS) of each organism included in the analysis, as described by McNulty et al. in a previous publication (PMID: 22030749).
Summarization: the proportional representation of each organism in the analysis was determined by dividing its normalized counts within a sample by the total normalized counts for all organisms within that sample.
Genome_build: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482, Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33656, Clostridium_sporogenes_ATCC_15579, Anaerococcus_hydrogenalis_DSM_7454, Clostridium_asparagiforme_DSM_15981, Clostridium_hathewayi_DSM13749, Edwardsiella_tarda_ATCC23685, Escherichia_fergusoni_ATCC_35469, Proteus_penneri_ATCC_35198, Providencia_rettgeri_DSM_1131
Supplementary_files_format_and_content: Excel file. The column header (B1-BE1) specifies the sample from which data were derived. Subsequent rows specify the organism/reference genome, raw counts, and normalized relative proportion for each taxon included in the alignment. Small intestine samples with less then 1000 reads (total raw counts) were not used in final analysis. Cecum and large intestine samples with less than 10,000 reads (total raw counts) were not used for final analysis. These samples are marked in red.
Supplementary_files_format_and_content: KR_Norm_Decimal_Percent_w_Raw_Counts.xlsx [Samples KR1 to KR56]
Supplementary_files_format_and_content: KR2_Norm_Decimal_Percent_w_Raw_Counts.xlsx [Samples KR2-1 to KR2-60]

extract_protocol:
DNA was extracted from intestinal samples using mechanical disruption (bead-beating with 0.1 mm zirconium beads) in phenol:chloroform:IAA in the same manner as described by McNulty et al. in a previous publication (PMID: 22030749).
Libraries were prepared according to a slightly modified version of the protocol accompanying the Illumina Genomic DNA Sample Prep Kit. Briefly, total bacterial gDNA was sonicated in a BioRuptor XL water bath sonicator, cleaned up and concentrated using a Macherey-Nagel PCR Purification column. DNA was blunted and poly-A tailed. The A-tailed molecules were ligated to the relevant barcoded Illumina adapter sequence.  Adaptered-DNA was then size-selected by agarose gel electrophoresis.  Fragments of the appropriate size were PCR amplified and purified, after which the purified PCR products were give to the University of Wisconsin-Madison Biotechnology Center for quality assurance and library sequencing following the manufacturer's protocols (Illumina MiSeq 1x50bp).


title: H3A_shMITF_rep3


title: S11

tag: Sex

tag: age


title: KR2-58

source_name: Distal Small Intestine


title: H3A_shMITF_rep1


title: KR2-57

source_name: Distal Large Intestine


title: KR2-56

source_name: Cecum


title: H3A_shSCR_rep1

value: shSCR


title: hMeDIP_pw2_2


title: H3A_shSCR_rep3


title: KR2-54


title: 501_shMITF_rep2


title: KR2-55


title: 501_shMITF_rep1


title: KR2-53


title: 501_shSCR2_rep2


title: KR2-52


title: KR2-51


title: 501_shSCR2_rep1


title: 501_shBRG1_rep2


title: 501_shBRG1_rep3


title: KR2-48


title: 501_shSCR1_rep3


title: 501_shBRG1_rep1


title: KR2-47


title: KR2-46


title: I. ricinus salivary glands

city: Maisons Alfort

first: Sarah

middle: Irene

last: Bonnet

address: 23 avenue du general de Gaulle

department: Animal Health

institute: INRA

data_processing:
After 454 sequencing with GS FLX Titanium and trimming, de novo assembly of all the reads was performed with GS De Novo Assembler Software version V2.5.3
Burrows-Wheeler Transform Aligner (BWA) was used to align polyA trimmed Illumina reads against the I. ricinus salivary glands reference transcriptome obtained in 454
To calculate relative expression profiles in infected ticks, Relative Abundance (RA) values were computed for each isotig per sample by dividing its sequence count by the total sequence count in the sample. Differentially expressed isotigs between infected and non-infected ticks were detected by using the R and χ2 test statistics with Bonferroni correction using the IDEG6 software (http://telethon.bio.unipd.it/bioinfo/IDEG6_form/). An isotig was considered to be significantly differentially expressed in response to B. henselae infection when its RA had a fold change (FC) ≥ 2.0 and both statistical tests yielded significant values at P ≤ 0.0001.
The Open Reading Frame (ORF) of differentially expressed isotigs was determined by using the ORF Finder web sever at www.ncbi.nlm.nih.gov/projects/gorf and the conserved domains searching for each differentially expressed isotig was done using Conserved Domains Database (CDD) web sever version (CDD v3.03) at www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml.
All the isotigs were imported into the BLAST2GO version 2.5.0 (www.blast2go.org) program for homology searches and Gene Ontology (GO) annotation.
Genome_build: de novo assembly from RNA-Seq data
Supplementary_files_format_and_content: NG-5717_comparative_table.tsv where 1minus corresponds  to count of sequences for non-infected ticks and 2plus corresponds to count of sequences for Bartonella-infected ticks; NG-5717_nr-blast_out_top5.txt contains the isotigs blast searches results

organism: Ixodes ricinus

source_name: transcriptome of non-infected salivary glands of female I. ricinus

extract_protocol:
RNA was extracted from tick salivary glands using TRIzol® Reagent (Invitrogen, USA)
not provided

tag: b. henselae infection

value: no

value: salivary gland

value: female


title: Input_SOX10


title: I. ricinus B. henselae infected and non-infected salivary glands

source_name: transcriptome of both B. henselae-infected and non-infected salivary glands of female I. ricinus

value: yes and no


title: 501_shSCR1_rep1


title: KR2-45

value: Male


title: I. ricinus B. henselae-infected  salivary glands

source_name: transcriptome of B. henselae-infected  salivary glands of female I. ricinus

value: yes


title: KR2-49


title: KR2-44


title: Input_MITF


title: H3A_shSCR_rep2


title: KR2-43


title: 501_shSCR1_rep2


title: GFPsiCTRL_CHIP-seq

value: GFP :IGBMC (2A3)


title: KR2-41

value: NMRI


title: SOX10_CHIP-seq


title: KR2-50

value: Female


title: BRG1siCTRL_CHIP-seq


title: KR2-40

value: Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33656, Clostridium_sporogenes_ATCC_15579, Anaerococcus_hydrogenalis_DSM_7454, Clostridium_asparagiforme_DSM_15981, Clostridium_hathewayi_DSM13749, Clostridium_hathewayi_DSM13749, Edwardsiella_tarda_ATCC23685, Escherichia_fergusoni_ATCC_35469, Proteus_penneri_ATCC_35198, Providencia_rettgeri_DSM_1131


title: BRG1siMITF_CHIP-seq


title: KR2-38

value: Choline +


title: KR2-39


title: WT heart

status: Public on Apr 01 2015

city: Shanghai

first: Ning

last: Wei

address: 320 Yueyang RD.

institute: Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

data_processing:
Illumina GA Pipeline v1.3 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi, 2008.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Embryonic heart at E13.5 were collected and frozened in Liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: BALB/c

value: WT

value: Embryonic day 13.5

value: heart


title: Mast cells stimulated

city: Mainz

first: Tobias

last: Bopp

address: Langenbeckstrasse 1

department: Institute for Immunology

institute: University Medical Center Mainz

description: BMMC stimulated for 24h with ionomycin [1µM]

data_processing:
Sequence reads were trimmed for adapter sequence and further processed using the software CLC genomics workbench (6.5; using CLC's default settings for RNA-Seq analysis). Reads were aligned to mm9 genome.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated employing CLC Genomics Workbench (6.5)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: BMMC

growth_protocol: For the generation of mast cells, mice were sacrificed by cervical dislocation. Intact femurs and tibias were removed and bone marrow was harvested by repeated flushing with MEM supplemented with 2% FCS. Mast cell cultures were established at a density of 2×106 cells/ml in IMDM supplemented with 10% FCS (inactivated at 56°C), 1% L-glutamine and Na-pyruvate, 1% penicillin/streptomycin, 20U/ml murine (m)IL-3, 50U/ml mIL-4, and 200ng/ml SCF. Nonadherent cells were transferred to fresh culture plates every 2–3 days for a total of at least 28 days to remove adherent macrophages and fibroblasts.

extract_protocol:
Mast cell total RNA was isolated using Trizol
Barcoded mRNA-seq cDNA libraries were prepared from 5ug of total RNA using a modified version of the Illumina mRNA-seq protocol. With the aid of Seramag Oligo(dT) magnetic beads (Thermo Scientific) mRNA was isolated and subsequently fragmented using divalent cations and heat resulting in fragments ranging from 160-220bp. Fragmented mRNA was converted to cDNA using random primers and SuperScriptII (Invitrogen) followed by second strand synthesis using DNA polymerase I and RNaseH. cDNA was end repaired using T4 DNA polymerase, Klenow DNA polymerase and 5’ phosphorylated using T4 polynucleotide kinase. Blunt ended cDNA fragments were 3’ adenylated using Klenow fragment (3’ to 5’ exo minus). 3’ single T-overhang Illumina multiplex specific adapters were ligated using a 10:1 molar ratio of adapter to cDNA insert using T4 DNA ligase. cDNA libraries were purified and size selected at 200-220bp using the E-Gel 2% SizeSelect gel (Invitrogen). Enrichment, adding of Illumina six base index and flow cell specific sequences were done by PCR using Phusion DNA polymerase (Finnzymes). Clean-up was done using 1,8x volume of AgencourtAMPure XP magnetic beads. All quality controls were done using Invitrogen’s Qubit HS assay and fragment size was determined using Agilent’s 2100 Bioanalyzer HS DNA assay. Barcoded RNA-Seq libraries were clustered on the cBot using Truseq SR cluster kit v2.5 using 7pM and 50bps were sequenced on the Illumina HiSeq2000 using Truseq SBS kit-HS 50bp. The raw output data of the HiSeq was preprocessed according to the Illumina standard protocol

value: bone marrow derived mast cell

tag: protocol

value: stimulated for 24h with ionomycin [1µM]


title: Mast cells stimulated in presence of sialostatinL

description: BMMC stimulated for 24h with ionomycin [1µM] in the presence of sialostatinL [3µM]

tag: cell type


title: AC rep 1 (Illumina HiSeq 2000)

city: Utrecht

first: Geert

last: Geeven

state: Utrecht

address: Uppsalalaan 8

department: Biomedical Genomics

country: Netherlands

institute: Hubrecht Institute

description: barcode: TG

data_processing:
Library strategy: 4C-Seq
sat4C reads were aligned to sequences flanking restriction sites in the mm9 genome assembly using a custom mapping pipeline written in Perl
Data from individual experiments were normalized for sequencing depth to the average number of mapped reads in all experiments
Genome-wide sat4C coverage profiles were calculated by averaging over running windows of 101 sat4C fragment and resulting sat4C profiles were quantile normalized
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using custom R script; Scores represent normalized sat4C coverage

source_name: Astrocyte cell line

growth_protocol: Thymus tissue was isolated from adult male mice (C57/Bl6) and disaggregated through a nylon cell strainer. Mouse embryonic stem cells (IB10) and neural precursor cells derived from these ESC were a gift from Bas van Steensel and maintained as previously described (Peric-Hupkes et al. 2010, Mol. Cell). Astrocytes were derived from these NPC in our own lab according to established protocols (Peric-Hupkes et al. 2010, Mol. Cell).

extract_protocol:
In general, satellite 4C follows the regular 4C protocol as detailed by Splinter et al. (2012, Methods) with several modifications. Chromatin is fragmented with ApoI and MfeI (both NEB), and subsequently ligated under diluted conditions. After reversal of the cross-links, the DNA is purified and treated with the NlaIII. After a second re-ligation step, the sample is purified and a 4C PCR is applied. 4C PCR samples were purified using Ampure beads (Beckman Coulter) and sent for next generation sequencing (illumina).
Library is generated by 4C PCR with primers carrying illumina adapter sequences

treatment_protocol: Approximately 10 million cells were crosslinked using 1% formaldehyde for 10minutes at room temperature


title: AC rep 2 (Illumina HiSeq 2000)

description: barcode: TC


title: NPC rep 1 (Illumina HiSeq 2000)

description: barcode: AC

source_name: Neural precursor cell line


title: NPC rep 2 (Illumina HiSeq 2000)

description: barcode: CT


title: Thymus rep 2 (Illumina HiSeq 2000)

description: barcode: GC

source_name: Adult thymus tissue


title: ESC rep 2 (Illumina HiSeq 2000)

description: barcode: CA

source_name: Embryonic stem cell line


title: Thymus rep 3 (Illumina HiSeq 2000)

description: barcode: GC


title: ESC rep 3 (Illumina HiSeq 2000)

description: barcode: GA