title: ARC-associated small RNAs

city: Paris

first: Daniel

last: Holoch

state: Cedex 05

address: 26 rue d'Ulm

department: Genetics and Developmental Biology Unit

country: France

institute: Institut Curie, Centre de Recherche

description: Immunoprecipitated and size-selected RNA

data_processing:
Base-calling was performed using CASAVA-1.8.2
Reads lacking the first 5 nt of the linker sequence (CTGTA), containing fewer than 17 nt before the CTGTA, or 10 or more consecutive A bases were removed.
Remaining reads were aligned to the Schizosccharomyces pombe genome using NovoAlign (http://www.novocraft.com/), with configurations -r random -s 1.
Reads aligning with more than one mismatch were removed and all remaining aligned reads were included in all further analyses.
These remaining reads were converted to an Integrated Genome Viewer (IGV)-viewable format.
Genome_build: ASM294v1, S. pombe h- (GCA_000002945.1)
Supplementary_files_format_and_content: IGV-viewable files are tab-delimited and include reads per million at each nucleotide position.

organism: Schizosaccharomyces pombe

source_name: TAP-arb1 3xFLAG-ago1 haploid cells

growth_protocol: Cells were grown in rich media (YES)

extract_protocol:
RNA was isolated from Tas3-TAP, TAP-Arb1 or 3xFLAG-Ago1 affinity purifications. Small RNAs were size-selected (18-28 nt) by polyacrylamide gel electrophoresis.
Library construction was conducted as described (Halic and Moazed, 2010, PMID 20178743). Small RNAs were ligated to a 3’ adaptor. The ligated species were size-selected on a 17.5% polyacrylamide/7M urea gel and ligated to a 5’ adaptor. RNA was then reverse transcribed into cDNA and PCR-amplified in a two-step process. Amplified cDNA was gel-purified and sequenced on the indicated Illumina platform.

value: h+ leu1-32 ade6-M210 ura4-DS/E otr1R(SphI)::ura4+ natMX6-3xFLAG-ago1 kanMX6-TAP-arb1


title: Quiescent

status: Public on Mar 01 2015

type: SRA

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA 1.8.1 (use only Illumin'a passed filter)
Reads were aligned to the Solanum lycopersicu (tomato) genome and to Colletotrichum gloeosporioides contigs (SUB133583, PRJNA176412)  release SL2.40 using TopHat V1.3.0 with the option --segment-mismatches 1
Transcripts were defined using cufflinks 1.1.0
Transcripts were quantified using Partek Genomics Suite V6.6 beta

molecule: total RNA

organism:
Solanum lycopersicum
Colletotrichum gloeosporioides

source_name: Fruit cuticle and parenchyma inoculated by fungi

growth_protocol: Tomato (Solanum lycopersicum) wild-type cultivars Motelle were grown in pots filled with a peat-vermiculite (4:1, v/v) mixture containing slow-release high-N Multicote 4 with microelements (0.3% w/w; Haifa Chemicals, Haifa Bay, Israel). Average temperatures in the greenhouse during the growth period fluctuated from 18 to 25˚C.

extract_protocol:
RNA was extracted from 100mg (dry weight) of C. gloeosporioides colonizing tomato fruit. Samples were ground into fine powder and were extracted using Tri-reagent 100 mg/ml (38% water saturated phenol, 0.8M Guanidine thiocyanate, 0.4M Ammonium thiocyanate, 0.1MSodium acetate pH=5, 5% glycerol). Aqueous phase was subsequently extracted twice with chloroform. Follow by isopropanol precipitation and two 70% ethenol washes, the RNA pellet was resuspended in DDW. The RNA was treated with DNase, Amplification Grade (Sigma, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tomato fruits cv. Mottel were inoculated with 7 µl, 106 conidia/ml at 30 inoculation spots per fruit on 5 different fruits per biological replicate with seven biological replicates per treatment. For necrotrophic stage growth a 10 mm2 of ripe tomato fruit cuticle was removed and inoculated with 70 µl of a conidial suspension (106 conidia/ml). Three inoculation spots on each of 10 different fruits were inoculated per biological replicate with seven biological replicate per treatment.

tag: cultivar/strain

value: Sl-Motelle

tag: fungal cultivar/strain

tag: fungal stage

value: Quiescent


title: RITS-associated small RNAs

source_name: tas3-TAP 3xFLAG-ago1 haploid cells

tag: strain

tag: genotype

value: h+ leu1-32 ade6-M216 ura4-D18 imr1R(NcoI)::ura4+ tas3-TAP-kanMX6 hphMX6-3xFLAG-ago1


title: 0001L_LL_rep_2

city: Seattle

first: Caroline

last: Harwood

state: WA

address: 1705 NE Pacific Street

department: Microbiology

country: USA

institute: University of Washington

description: low-light condition

data_processing:
All cDNA libraries were sequenced with an Illumina HiSeq at the University of Washington High Throughput Genomics Center
Raw sequencing data were processed by with the Xpression pipeline, as described in Phattarasukol, S., Radey, M. C., Lappala, C. R., Oda, Y., Hirakawa, H., Brittnacher, M. J., and Harwood, C. S. (2012) Identification of a p-coumarate degradation regulon in Rhodopseudomonas palustris by Xpression, an integrated tool for prokaryotic RNA-seq data processing. Appl. Environ. Microbiol. 78, 6812–8.
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each gene

organism: Rhodopseudomonas palustris

growth_protocol: Cells were grown anaerobically in light at 30°C in 10 ml non-nitrogen-fixing medium (PM) or nitrogen-fixing medium (NF and LL) containing 20 mM acetate, 10 μl VCl3, and Wolfe's vitamin solution (5 ml/l).

extract_protocol:
RNA was extracted and purified from 5 ml of the same cell suspensions and time points used for tracking the biomass composition.
The R. palustris-specific selective primers v2 were based on the genome sequences of six R. palustris strains (CGA009, TIE-1, HaA2, BisB5, BisB18, and BisA53). We used a pool of 1,203 selective primers with no perfect match to any rRNA genes (e.g., 5S, 16S, and 23S rRNA). An additional set of 200 primers that were responsible for the majority of rRNA-priming events in test libraries, was further removed, leaving a final set of 1,003 R. palustris-specific selective primers v2 (Table S1). For first strand cDNA synthesis, 500 ng of total RNA was mixed with 1 μl of 100 μM of R. palustris-specific selective primers v2 in 5 μl reaction volume, and incubated at 65 °C for 5 min. After snap chilling on ice, 2 μl of 5X First-Strand Buffer (Invitrogen, Carlsbad, CA), 2 μl of 10 mM dNTP mix (New England BioLabs, Ipswich, MA), 0.5 μl of 0.1 M DTT, 0.5 μl of SuperScript III Reverse Transcriptase (Invitrogen) were added, and the mixture was further incubated at 40°C for 90 min. To generate the second strand, 45.5 μl of water, 15 μl of 5X Second Strand Buffer (Invitrogen), 1.5 μl of 10 mM dNTP mix, 0.5 μl of Escherichia coli DNA Ligase (Invitrogen, 10 U/μl), 2 μl of DNA Polymerase I (Invitrogen, 10 U/μl), and 0.5 μl of RNase H (Invitrogen, 2 U/μl) were added to the reaction, and incubated at 16 °C for 2 h. The reaction was stopped by adding 25 μl of 20 mM EDTA, pH8.0.  Double stranded cDNA was then purified by using the MinElute PCR Purification Kit (QIAGEN, Valencia, CA) using 12 μl of Buffer EB. Finally, the cDNA library was constructed using the Ovation Ultralow DR Multiplex System (NuGEN, San Carlos, CA) following the manufacture’s instructions.

tag: treatment

value: low-light condition


title: 0001L_LL_rep_1

description: low-light condition


title: Bulk CRL2097

city: Philadelphia

first: Arjun

last: Raj

state: PA

address: 210 S. 33rd St., Ste. 240 Skirkanich Hall

department: Bioengineering

institute: University of Pennsylvania

description:
sample id: CRL2097-Total
Total ribo-depleted RNA

data_processing:
Aligned reads to genome using STAR
Assigned counts per gene using HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include counts for all genes and samples. All single-cell data is compiled into a single .tsv file, and there is a separate .txt file for the bulk data from each cell line.

organism: Homo sapiens

source_name: Primary foreskin fibroblast cells

extract_protocol:
RNA was harvested using Qiazol.
Used Ribo-Zero Gold and NEBNext Library Prep protocol.

tag: cell line

tag: cell type

value: bulk


title: Appressoria

value: Appressoria


title: Gene expression si_GFP BioRep2_seq

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

data_processing:
Illumina CASAVA version 1.8 used for basecalling.
Cutadapt was used to trim adaptors, reads mapping to rRNAs and tRNAs were removed, and the remaining reads were mapped to human genome (hg19) by TopHat 2 software version 2.0.9 with parameters -p 6 --b2-fast --library-type=fr-unstranded --no-novel-juncs --no-novel-indels --transcriptome-index
Cuffdiff was used to combine biological replicates and assign expression values (FPKM) for each RefSeq gene, run with parameters -p 1 -b -u
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values (value 1 and value 2) from cuffdiff combined biological replicates 1-3 for each treatment group and significance estimates comparing miR-191 transfection to control transfection

source_name: HeLa cell_siGFP_expression

growth_protocol: DMEM supplemented with 10% FBS

extract_protocol:
Lysates from each sample were split into 2 groups.  Group 1: Gene expression samples, total RNA was isolated with TRIzol.  Gene 2: Ago2 immunoprecipitation samples, Ago2 was immunoprecipated with an antibody against Ago2 and the associated RNA was isolated with TRIzol. In more detail, 24 hours post transfection, cells were washed 2X with PBS, 0.5 mL of lysis buffer was added to the plate, followed by incubation at 4°C for 30 minutes. Cell lysates were collected by scraping and debris cleared by centrifugation at 14,000 rpm at 4°C. 50 μl of the lysate was collected as input for total RNA profiling. Lysates were pre-cleared by incubating with 50 μl of protein-G beads (Roche) for 1 hour at 4°C and then collecting supernatants (pre-clearing). Pre-cleared lysates were then incubated with 15 μg of antibody against Argonaute-2 (AGO2)(ab57113, Abcam) at 4°C for 3 hours. AGO2 is a protein component of RISC. Following AGO2 antibody incubation, 50 μl of protein-G beads were added to the lysate and incubated for 1 hour at 4°C. Beads were washed 8 times with lysis buffer and RISC-RNA complexes were extracted by adding 1 mL TRIzol reagent (Invitrogen) directly to the beads. RNA extraction with TRIzol was carried out as per the manufacturers instructions.
rRNAs were removed using the Ribo-Zero rRNA Removal Kit (Epicentre). The remaining RNA was then fragmented with the NEBNext Magnesium RNA Fragmentation Module (New England BioLabs), and size selected using AMPure XP beads (Agencourt) at 1.8X volume. Ends of the fragmented RNAs were then prepared for adaptor ligation using T4 Polynucleotide Kinase (New England BioLabs). Libraries were prepared from the RNA using the NEBNext Small RNA Library Prep Set according to the manufacturers protocol (New England BioLabs). Libraries were cleaned and further size selected using 0.8X volume AMPure XP beads, and additional size selections with 1.0X beads were performed as necessary.

treatment_protocol: mature miR-191 duplex or control siRNA against GFP duplex was transfected with lipofectamine 2000 at a concentration of 100nM in the well

value: HeLa


title: Gene expression si_GFP BioRep3_seq


title: Necrotroph

source_name: Fruit parenchyma inoculated by fungi

value: Necrotroph


title: Gene expression si_GFP BioRep1_seq


title: embryos 24-48h_RNAseq_rep2

city: Pasadena

first: Maria

last: Ninova

state: CA

address: 1200 E California Blvd

department: Division of Biology and Biological Engineering

institute: Calfironia Institute of Technology

description: stranded polyA RNA library

data_processing:
For small RNA sequencing, adaptor sequences were removed using the cutadapt tool
Small RNA sequencing reads were mapped to the T. castaneum genome using Bowtie v1.0 allowing one mismatch; read counts per microRNA gene were calculated by a custom script accounting for multiple mapping positions
RNA-seq reads were mapped to the T. castaneum genome using Tophat, followed by htseq-count using Tcas 4.0 gene annotations
Genome_build: Tcas 4.0
Supplementary_files_format_and_content: tab-delimited file of genes/microRNAs and read counts

organism: Tribolium castaneum

source_name: embryos 24-48h

growth_protocol: Mixed sex adults (for embryonic samples) or virgin females (for oocytes) were maintained on whole grain flour and allowed to lay on white flour for the desired periods of time at 25°C.

extract_protocol:
Standard Trizol RNA extraction
Small RNA libraries were constructed according to the TruSeq Small RNA Sample Prep Kit instructions, and transcriptome libraries were constructed using the Illumina TruSeq Stranded mRNA Sample Prep Kit

treatment_protocol: Flour debri were manually, removed and embryos were dechorionated in 1% hypochlorite solution and washed with distilled water prior RNA extraction

tag: developmental stage

value: embryos 24-48h


title: RCH500_NF_rep_1

description: hydrogen-producing condition

value: hydrogen-producing condition


title: Gene expression miR-191 BioRep3_seq

source_name: HeLa cell_miR-191_expression


title: embryos 24-48h_RNAseq_rep1

description: stranded polyA RNA library


title: embryos 16-24h_RNAseq_rep2

description: stranded polyA RNA library

source_name: embryos 16-24h

value: embryos 16-24h


title: embryos 16-24h_RNAseq_rep1

description: stranded polyA RNA library


title: Ago2 IP siGFP BioRep2_seq

description: RNA isolated from Ago2 immunoprecipitation

source_name: HeLa cell_siGFP_Ago2IP

tag: antibody

value: AGO2 (ab57113, Abcam)


title: Gene expression miR-191 BioRep2_seq


title: 1a1_NF_rep_2

description: hydrogen-producing condition


title: embryos 8-16h_RNAseq_rep1

description: stranded polyA RNA library

source_name: embryos 8-16h

value: embryos 8-16h


title: Ago2 IP siGFP BioRep1_seq


title: oocytes_RNAseq_rep2

description: stranded polyA RNA library

source_name: oocytes

value: oocytes


title: embryos 8-16h_RNAseq_rep2

description: stranded polyA RNA library


title: Ago2 IP siGFP BioRep3_seq


title: Gene expression miR-191 BioRep1_seq


title: Bulk A549

description:
sample id: A549-Total
Total ribo-depleted RNA

source_name: Lung carcinoma cells


title: Ago2 IP miR-191 BioRep3_seq

source_name: HeLa cell_miR-191_Ago2IP


title: oocytes_smallRNA_rep2

description: small RNA library


title: Ago2 IP miR-191 BioRep1_seq


title: Target genes

city: Hangzhou

first: Xiangbin

last: Xu

address: Xiasha xuelin street 16

country: China

institute: Hangzhou Normal University

description:
cultivated for eight months
Table S4.xls

data_processing: A proprietary pipeline script, ACGT101-miR v4.2 (LC Sciences), was used for sequencing data analysis (Li et al. 2010; Wei et al. 2011). A Public software package, CleaveLand3.0 was used for analyzing Degradome sequencing data.

organism: Salvia miltiorrhiza

source_name: Mixture of root, stem, leaf and flower

extract_protocol: Total RNA was isolated with the Total RNA Purification Kit (Norgen Biotek Corporation, Thorold, Canada) according to the manufacturer’s instructions. Small RNA libraries were generated from the two samples using the Illumina Truseq Small RNA Preparation kit according to Illumina’s TruSeq Small RNA Sample Preparation Guide. The purified cDNA library was used for cluster generation on Illumina’s Cluster Station and then sequenced on Illumina HiSeq 2000 following vendor’s instruction for running the instrument. Raw sequencing reads were obtained using Illumina’s Sequencing Control Studio software version 2.8 (SCS v2.8) following real-time sequencing image analysis and base-calling by Illumina's Real-Time Analysis version 1.8.70 (RTA v1.8.70). A proprietary pipeline script, ACGT101-miR v4.2 (LC Sciences), was used for sequencing data analysis. Degradome library was constructed following with methods previously described by German et al.(2008).CleaveLand3.0 and LC Science’s ACGT301-DGEv1.0 program were used to detect potentially sliced targets of known and novel miRNA.

treatment_protocol: Salvia miltiorrhiza was cultivated in the experimental field of the Xiasha campus, Hangzhou normal university, China. The root, stem, leaf and flower were collected, immediately frozen and stored at -80 oC.

tag: development stage

value: Florescence

tag: tissue

value: Mixture of root, stem, leaf and flower


title: oocytes_smallRNA_rep1

description: small RNA library


title: Human Max protein

city: New York

first: Namiko

last: Abe

state: NY

department: Biochemistry and Molecular Biophysics

institute: Columbia University

description: Library strategy: SELEX-seq

library_source: genomic

data_processing:
Illumina 2500 fastq files were demultiplexed according to barcode (according to Riley et al, Methods in Molecular Biology, 2014)
12-mers were counted from Round 2 reads and Round 0 reads (according to Riley et al, Methods in Molecular Biology, 2014)
Round 2 12-mer counts were normalized to Round 0 expected counts derived from Markov Model (according to Riley et al, Methods in Molecular Biology, 2014)
Genome_build: Not applicable- SELEX reads are not aligned to reference genome
Supplementary_files_format_and_content: List of 12mers and their relative binding affinities derived from round 2 of SELEX-seq in a .txt file

molecule: genomic DNA

source_name: recombinant protein

growth_protocol: Plasmids were transformed into BL21 (DE3) expression strain of E. coli (New England BioLabs).  Overnight bacterial culture (5 mL) was diluted into 1 L LB (10 g BACTO Tryptone (BD); 5 g BACTO Yeast Extract (BD); 10 g NaCl; pH 7.5) and grown to OD 0.6 (600 nm visible light). Protein expression was then induced with 1 mM isopropyl β-D-1-thiogalactopyranoside (IPTG) for 3 hours at 37ºC. Cells were pelleted by centrifugation @ 12,000 rpm for 10 min and stored at -20ºC. Each pellet (from 1 L culture) was thawed in 15 ml lysis buffer (150 mM Tris-HCl, pH 8.0; 150 mM NaCl; 2 mM dithiothreitol (DTT); 1 tablet complete Mini, EDTA-free protease inhibitor cocktail (Roche, #11 836 170 001); 50 uM C4H10O6Zn (zinc acetate); 1 mg/ml chicken egg white lysozyme (Sigma, # L6876)) and subjected to two freeze-thaw cycles in dry ice/ethanol. To digest DNA, to each 15 ml lysis solution was added 10 uL recombinant, RNase-free DNAse I (Roche, #04 716 728 001, 10 U/ul), 30 uL 1 M MgCl2, and 2 mL 10% Triton X-100,  and digested at room temperature until solution was runny (~1 hr).  Solutions were centrifuged at 12,000 rpm for 25 min at 4ºC, and supernatant was used for protein purification.

extract_protocol:
Full-length open reading frames were cloned into the Gateway pDEST17 (N-terminal His-tag) expression vector by recombinational cloning from previously created pENTR clones. All proteins were produced by over-expression in E. coli BL21 (DE3) cells (New England BioLabs), and purified by FPLC (AKTAprime plus) using HisTrap FF affinity columns (GE Healthcare). Anti-His Western blots were performed to assess protein quality and concentration.
Hox and HM-Exd purification conditions, expression constructs, and EMSA conditions have been described previously (Joshi et al., 2010; Noro et al., 2006; Ryoo and Mann, 1999). AbdB (residue 224 to the C-terminus) and Pb (residues 126–306) were cloned in pET14b (Novagen) and pQE9 (Qiagen), respectively. For SELEX EMSA lanes, binding reactions were performed with 200 nM double stranded SELEX library, 67 nM Hox, and 33 nM HM-Exd in a final volume of 30 μl. Parallel DNA binding reactions using 32P labeled probes containing known Hox-Exd composite sites were used to track the mobility of Hox+HM-Exd+DNA complexes. Regions corresponding to the cooperative complex were cut out and eluted. The eluted DNA was purified, concentrated, and amplified by PCR. The PCR products were then purified and divided for the next round of SELEX or Illumina sequencing. Subsequent rounds of selection followed the same structure as the first round of SELEX.

tag: tag

value: histidine


title: embryos 20-24h_smallRNA

description: small RNA library

source_name: embryos 20-24h

value: embryos 20-24h


title: Leaf_miRNA

description:
cultivated for eight months
Table S1.xls

source_name: Leaf

value: Leaf


title: sample_M_head_7

city: Göttingen

first: Georg

last: Oberhofer

state: Lower Saxony

address: Justus von Liebig Weg 11

department: Developmental Biology

country: Germany

institute: University Göttingen

description: whole heads excluding the antennae, but with mouthparts

data_processing:
Sequence images were transformed with Illumina software BaseCaller to bcl files, which were demultiplexed to fastq files with CASAVA v1.8.2. Quality check was done via fastqc (v. 0.10.0, Babraham Bioinformatics).
Reference transcriptome: The preliminary au3.cds gene set supplemented with not covered genes from the OGS and manually curated candidates involved in olfaction (OR, GR, IR, SNMP, ODE, OBP...)  was used as the mapping reference. Isoforms were removed to avoid multiple mappings. The final transcriptome contained only t1 isoforms.
Reads were mapped to the reference using bowtie2 (version 2.1.0) with the these settings: -q -D 20 -R 3 -N 1 -L 20 -i S,1,0.50
Raw count tables were obtained with samtools (version 0.1.18).
Gene prediction set au3:  http://bioinf.uni-greifswald.de/tcas/genes/au3/ supplemented with gene models of the OGS and manually curated genes involved in olfaction
FastQC A Quality Control tool for High Throughput Sequence Data http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ by S. Andrews
Langmead, B., and Salzberg, S.L. (2012). Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359.
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., and Subgroup, 1000 Genome Project Data Processing (2009). The Sequence Alignment/Map format and SAMtools. Bioinforma. Oxf. Engl. 25, 2078–2079.
Supplementary_files_format_and_content: raw and normalized counts

source_name: sample M head 7

growth_protocol: Beatles were reared at 28 °C on full grain flour supplemented with 5% dry yeast, defined ages ranging from 0 to 21 days old were equaly pooled

extract_protocol:
Total RNA was extracted using ZR Tissue & Insect RNA MicroPrep™ (Zymo, #R2030) according to the manufacturers protocol.
Library preparation for RNA-Seq was performed using the TruSeq RNA Sample Preparation Kit (Illumina, Cat. N°RS-122-2002) starting from 400 ng of total RNA . Accurate quantitation of cDNA libraries was performed by using the QuantiFluor™ dsDNA System (Promega). The size range of final cDNA libraries was determined applying the DNA 1000 chip on the Bioanalyzer 2100 from Agilent (280 bp). cDNA libraries were amplified and sequenced by using the cBot and HiSeq2000 from Illumina (PairedRead; 2x100 bp).

treatment_protocol: Sex seperation and dissection of the different bodyparts

value: San Bernardino

value: head

tag: Sex

value: male

value: adult


title: sample_F_leg_4

source_name: sample F leg 4

value: leg

value: female


title: Flower_miRNA

source_name: Flower

value: Flower


title: sample_F_head_3

source_name: sample F head 3


title: Stem_miRNA

source_name: Stem

value: Stem


title: H4ac_HSPCcells_ChIPseq

city: Madrid

first: Sara

last: Alvarez

state: Madrid

address: C/Faraday 7

country: Spain

institute: NIMGenetics

data_processing:
Alignment was performed with BWA (Burrorws-Wheeler aligner software package) versus the human sequence assembly GRCh37/hg19 (Feb 2009)
MLL and AF9 peaks: Findpeaks was used to analyze the identified ChIP-seq MLL and AF9 binding regions. Calibration using input control was used, and peaks with a confidence less than 99.9 % for MLL and 99.0% for histone samples were rejected. Subpeaks (0.7) and trim (0.95) were enabled. The maximum number of genes associated to a peak is two (one in sense and the other in antisense)
MLL and AF9 peaks: A custom program was run to search Ensembl database and to find the first gene that lays in sense and antisense direction taking as reference point the defined peaks.a window of 5000 nt upstream and 200 nt downstream of the origin of transcription for each gene was defined
chromatin modifications: The SICER 1.1 was used following developer’s technical recommendations for histone modifications (200-bp window/ FDR≤ 0.01).
chromatin modifications: The software pipeline for finding differential peaks in pair-wise comparisons (HSPC-MA9 vs HSPC) was applied and significant ChIP-seq peaks were filtered at FC<1.5 and FDR ≤ 0.001.
Genome_build: hg19

source_name: umbilical cord blood

growth_protocol: Umbilical cord blood CD34+ cells were selected using immunomagnetic beads (Miltenyi Biotech) and stably transduced with retrovirus expressing empty vectors (HSPC control) or the MLL-AF9 (HSPC-MA9) fusion protein. Cells were cultured as described elsewhere (Wei et al., cell 2008).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
9 ng of ChIP DNA as quantitated by fluorometry was used. Electrophoretic fraction of 150 bp was processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq DNA Sample Preparation Guide" (part # 15005180 Rev. C). Adapter-ligated library was completed by limited-cycle PCR with Illumina PE primers (12 cycles). The resulting purified DNA library was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer's protocols.

value: CD34+ cells

tag: transduction

value: control

tag: chip antibody

value: H4ac (Millipore 06-598)


title: Input DNA


title: H4ac_HSPC-MA9cells_ChIPseq


title: Ago2 IP miR-191 BioRep2_seq

value: HeLa

value: AGO2 (ab57113, Abcam)


title: oocytes_RNAseq_rep1

description: stranded polyA RNA library

value: oocytes


title: sample_M_mand_12

description: most anterior part of the head, including mandibles, palps, labrum and labium

source_name: sample M mand 12

value: mouthparts


title: sample_SB_mand_5

source_name: sample SB mand 5

value: mixed


title: H3K79me2_HSPCcells_ChIPseq

value: H3K79me2 (Millipore 04-835)


title: H3K4me3_HSPCcells_ChIPseq

value: H3K4me3 (Millipore 17-614)


title: Root_miRNA

source_name: Root

value: Florescence

value: Root


title: Newman_rep3

city: RENNES

first: Yoann

last: AUGAGNEUR

address: 2 Avenue du Pr Leon Bernard

department: Pharmaceutical Biochemistry

institute: University Rennes 1

description: ribosomal-depleted RNA

data_processing:
Sequenced reads were verified by a fastqc report
reads were mapped using the BWA aligner
Reads were filtered for reads properly paired and sorted by pairs
Read pairs were counted using HTSeq count
Genome_build: Staphylococcus aureus subps, aureus N315 or Newman
Supplementary_files_format_and_content: file includes raw counts

organism: Staphylococcus aureus

source_name: RNA cell extract

growth_protocol: exponential phase of growth

extract_protocol:
Cells were lyzed with glass beads in a Fast Prep instrument and RNAs extract with Phenol/Chloroform. Ribosomal RNAs were depleted using the Ribo-zero rRNA remmoval kit (bacteria).
NEBNext ultra directional RNA library prep kit (E7420)

value: Newman


title: N315_rep2

description: ribosomal-depleted RNA


title: Newman_rep2

description: ribosomal-depleted RNA


title: N315_rep3

description: ribosomal-depleted RNA


title: sample_F_mand_11

source_name: sample F mand 11

value: San Bernardino

value: adult


title: H3K79me2_HSPC-MA9cells_ChIPseq


title: N315_rep1

description: ribosomal-depleted RNA


title: H3K4me3_HSPC-MA9cells_ChIPseq


title: dcr1∆ arb1∆ Ago1-associated small RNAs

source_name: dcr1∆ arb1∆ 3xFLAG-ago1 haploid cells

value: h+ leu1-32 ade6-M210 ura4-DS/E otr1R(SphI)::ura4+ …


title: sample_M_body_6

description: whole body excluding legs and heads

source_name: sample M body 6

value: body

value: male


title: sample_L_body_9

description: whole body including legs, without head

source_name: sample L body 9

value: larva


title: sample_L_head_10

description: whole head including antennae and mouthparts

source_name: sample L head 10

value: head


title: dcr1∆ Ago1-associated small RNAs

source_name: dcr1∆ 3xFLAG-ago1 haploid cells

value: h+ leu1-32 ade6-M210 ura4-DS/E otr1R(SphI)::ura4+ natMX6-3xFLAG-ago1 dcr1Δ::kanMX6


title: AF9_HSPC-MA9cells_ChIPseq

value: CD34+ cells

value: AF9 C-terminus (Bethyl 597A)


title: sample_M_leg_8

source_name: sample M leg 8

value: legs


title: MLL_HSPC-MA9cells_ChIPseq

value: MLL N-terminus (Bethyl 086A)


title: sample_F_body_2

description: whole body excluding legs and heads

source_name: sample F body 2

value: female


title: sample_F_ant1_1

source_name: sample F ant1 1

value: antenna


title: sample_F_ant3_3

source_name: sample F ant3 3


title: arb1∆ Ago1-associated small RNAs

source_name: arb1∆ 3xFLAG-ago1 haploid cells

value: h+ leu1-32 ade6-M210 ura4-DS/E otr1R(SphI)::ura4+ arb1Δ::kanMX6 hphMX6-3xFLAG-ago1


title: sample_M_ant3_5

source_name: sample M ant3 5


title: Newman_rep1

description: ribosomal-depleted RNA


title: sample_M_ant1_4

source_name: sample M ant1 4


title: sample_F_ant2_2

source_name: sample F ant2 2


title: SS

status: Public on Feb 28 2015

city: New Delhi

first: Ashwani

last: Pareek

state: Delhi

address: New Mehrauli Road

department: School of Life Sciences

country: India

institute: Jawaharlal Nehru University

data_processing:
After assessing the quality of the reads and removing low-quality reads, high-quality (Phred Score >20) paired-end and orphan reads were merged together and aligned to B. rapa genome using Tophat aligner
The aligned and unaligned reads were separately subjected to de novo assembly using Trinity software (http://trinityrnaseq.sourceforge.net/) with default k mer size set to 25 bp
To generate non-redundant full-length transcriptome (unigenes), the assembled transcripts with sequence length longer than 300 bp and >70% identity were clustered together using CD-HIT-EST v 4.6.1 clustering tool
Reads were aligned using Bowtie with default parameters (http://bowtie-bio.sourceforge.net/index.shtml
Transcripts with ≤70% mapping coverage were discarded from the final assembly.
Mapped reads were further normalized using DESeq method
Genome_build: BRAD (http://Brassicadb.org/) and de novo assembly. FASTA file of assembled transcripts is available on the series record.
Supplementary_files_format_and_content: text file with Normalized RPKM Values in both the libraries

organism: Brassica juncea

source_name: Salt stress-treated two-weeks-old seedlings

growth_protocol: Two-weeks-old seedlings were subjected to 200 mM salinity stress for 24 h. After 24 h, tissue from about 10 randomly selected seedlings was pooled to minimize biological variability for each sample and frozen in liquid nitrogen. Tissue from plants maintained in water was simultaneously collected as control.

extract_protocol:
Total RNA was extracted from the frozen tissue using TRIzol reagent and purified using oligo dT beads (TruSeq RNA Sample Preparation Kit, Illumina). The purified mRNA was fragmented at elevated temperature (90°C) in the presence of divalent cations and reverse transcribed with Superscript II Reverse Transcriptase (Invitrogen Life Technologies) by priming with random hexamers. Second strand cDNA was synthesized in the presence of DNA polymerase I and RNaseH. The cDNA was cleaned using Agencourt Ampure XP SPRI beads (Beckman Coulter). Illumina adapters were ligated to the cDNA molecules after end repair and addition of an ‘A’ base followed by SPRI clean-up. The resultant cDNA library was amplified using PCR for enrichment of adapter ligated fragments, quantified using a Nanodrop spectrophotometer (Thermo Scientific) and validated for quality with a Bioanalyzer (Agilent Technologies). It was then sequenced using the Illumina’s Hi-Seq 2000 platform.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Seeds of B. juncea var. CS52 were washed with de-ionized water and germinated in a hydroponic system with continuous air bubbling for 48 h in dark and then transferred to light for further growth (25 ± 2ºC, 12 h light and dark cycle) in plant growth room.

tag: cultivar

value: seedlings

value: Salt Stress


title: Ago1-associated small RNAs

source_name: 3xFLAG-ago1 haploid cells

value: h+ leu1-32 ade6-M210 ura4-DS/E otr1R(SphI)::ura4+ natMX6-3xFLAG-ago1


title: S2 repB light digest 0.5 h

city: Tallahassee

first: Jonathan

middle: H

last: Dennis

state: FL

address: 319 Stadium Dr

department: Biological Science

institute: Florida State Unversity

data_processing:
Illumina adapters were clipped from the 3' ends of reads with cutadapt 1.7.
MNase-seq reads were aligned to the Drosophila reference genome UCSC.dm3 using bowtie2 2.1.0
Bed files correspond to inferred fragment coordinates based on concordant mate-pair alignments to the dm3 reference assembly
Genome_build: UCSC.dm3
Supplementary_files_format_and_content: bed files include genome-wide nucleosome positions for each sample

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: S2 cells were maintained at 28oC in Schneider's Drosophila medium (Invitrogen), supplemented with 10% heat inactivated fetal bovine serum (Life Technologies).

extract_protocol:
MNase-digested DNA samples were resolved on 2% agarose gel. DNA band containing mononucleosomal DNA (<=200bps) was excised and purified by the freeze-squeeze method.
A mononucleosomal DNA library was prepared using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB #E7370S/L) according to manufacturer’s instructions. Each reaction used 30ng of mononucleosomal DNA. After end prep, adaptor ligation and indexing (NEB #E7335S/L, NEB #E7500S/L), the samples were cleaned with AMPure XP beads (Beckman Coulter, Inc. #A63881) without size selection. The library was amplified by 10 cycles of PCR, and again cleaned with AMPure XP beads. The quantity and quality of the library were checked with Qubit 2.0 Fluorometer (Life Sciences) and Agilent 2100 Bioanalyzer (Agilent Technologies). Paired-end 50bps sequencing was performed using cBOT cluster generation in Illumina HiSeq 2500.

treatment_protocol: Heat-killed S.aureus was added to S2 cells at a final concentration of 107 cells/ml. Samples of 3 × 107 S2 cells were harvested at 0, 30 minutes, 1 hour, and 4 hours after stimulation, and cross-linked in 1% formaldehyde at room temperature for 10 minutes. Cells were digested with either 200U/ml (heavy digest) or 40U/ml MNase (light digest).

value: hemocyte-like cell line

tag: time


title: CTRL

source_name: wild type two-weeks-old seedlings

value: Control


title: Ago1 F276A Y513A K517A-associated small RNAs

source_name: 3xFLAG-ago1-F276A Y513A K517A haploid cells

value: h+ leu1-32 ade6-M210 ura4-DS/E otr1R(SphI)::ura4+ trp1+::natMX6-3xFLAG-ago1-F276A Y513A K517A


title: S2 repB heavy digest 1 h

value: 1 h


title: S2 repB heavy digest 4 h

value: 4 h


title: S2 repA light digest 4 h


title: S2 repB heavy digest 0.5 h


title: S2 repB heavy digest 0 h

value: 0 h


title: S2 repA light digest 1 h


title: S2 repB light digest 0 h


title: S2 repA light digest 0 h


title: S2 repA light digest 0.5 h


title: S2 repA heavy digest 4 h


title: S2 repA heavy digest 1 h


title: S2 repA heavy digest 0.5 h


title: S2 repA heavy digest 0 h


title: Precursor

city: Newark

first: Bruce

last: Boman

state: DE

address: 4701, ogletown-stanton road

department: CTCR

institute: Helen F Graham Cancer Center and Research Institute

data_processing:
base calling was done using bcl2fastq_1.8.3
Sequenced reads were trimmed for adapter sequence and mapped to hg19 whole genome using Tophat v2.0.11, with 1 mismatch, gtf file gencode.v11.annotation.gtf, --no-novel-juncs
Transcript abundance (fpkm) was calculated using Cufflinks V2.2.0 using compatible hits normalization and compared using the cuffdiff program
Genome_build: hg19
Supplementary_files_format_and_content: cuffdiff output diff file

source_name: HT29 colon cancer cells

growth_protocol: HT29 cells were plated on 100 mm dish using McCoy medium (containing 5% FBS and 1% Pennicllin/Streptomycin) to reach a confluency of 90% at the day of transfection.

extract_protocol:
RNA was isolated 48 hours post transfection using Trizol method.
RNA libraries were prepared using the standard Illumina protocols.  HSA672 tag ATCACG.  HSA673 tag CGATGT.  HSA674 tag TTAGGC.  HSA674 tag TGACCA.

treatment_protocol: Cells were transfected with 50nm of MiR23b Prec, Antimir and their respective controls using Lipofectamine 2000 as a transfection reagent. Media was changed 24 hours post tranfection.

tag: sirna treated

value: High miR23b

tag: passages

value: Passages 12 -13

value: colon cancer


title: Antimir Control

value: Low miR23b Control


title: Antimir

value: Low miR23b


title: S2 repB light digest 1 h


title: Precursor Control

value: High mIR23b Control


title: CKO-Blastocyst-rep1

city: Boston

first: Li

last: Shen

address: 200 Longwood Ave

institute: HHMI/Boston Children's Hospital/Harvard Medical School

data_processing:
We first extracted discernible paternal reads from the total reads using SNP information between the CAST and C57BL/6J mice.  These paternal RRBS reads were then mapped to the mouse genome (mm9) using Bismark v0.10.1 (Babraham Bioinformatics) after adapter trimming by Trim Galore (Babraham Bioinformatics). The methylation level of each covered cytosine in CpG context was calculated as the number of reported C divided by the total number of reported C and T.
Genome_build: mm9
Supplementary_files_format_and_content: The processed data files are the coverage files generated by Bismark from the discernible paternal reads (chr, start, end, methylation%, number of reported C, number of reported T)

organism: Mus musculus

growth_protocol: MII oocytes were collected from 7-10 week-old superovulated females. They were transferred into HTF medium supplemented with 10 mg/ml bovine serum albumin (BSA; Sigma-Aldrich) and inseminated with activated spermatozoa collected from the caudal epididymides of adult CAST/EiJ male mice. Spermatozoa capacitation was attained by 1 h incubation in HTF medium. Five hours after fertilization, zygotes were transferred into KSOM. Zygotes and blastocysts were collected at 13 and 96 hours postfertilization, respectively and frozen at -80°C until use. Biological duplicates for each samples were used and each sample contains 40-50 zygotes or 4 blastocysts.

extract_protocol: 5 µl of lysis buffer (20 mM Tris-EDTA [pH 8.0], 20 mM KCl, and 0.3% Triton X-100, 1 mg/ml QIAGEN Protease) was directly added to the frozen samples (in < 1µl PBS) followed by 3 hours of incubation at 50 ℃ and 30 minutes of inactivation at 75 ℃. Then to the same tube, 13 µl of MspI digestion master mix containing 10 units of MspI (Thermo Scientific) and 1.8 µl 10x Buffer Tango (Thermo Scientific) was added followed by 3 hours of incubation at 37 ℃ and 20 minutes of inactivation at 80 ℃. The digested DNA was then filled-in and tailed with an extra A to the 3’ end by adding 2 µl of end-preparation master mix containing 5 units of Klenow Fragment (exo-; Thermo Scientific), 1.8 µl of 10x Buffer Tango, 0.4 mM dATP, and 0.04 mM each of dGTP and dCTP (Thermo Scientific), followed by 40 minutes of incubation at 37 ℃ and 15 minutes of inactivation at 75 ℃. Adaptor ligation was then performed by adding 5 µl of ligation master mix, which contains 30 Weiss Units of T4 DNA Ligase (HC, Thermo Scientific), 0.5 µl of 10x Buffer Tango, 5mM ATP (Thermo Scientific), and 150 nM of methylated custom adaptor (Forward: 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATC*T-3’, Reverse: 5’-/5Phos/GATCGGAAGAGCACACGTCTGAACTCCAGTC-3’, where * indicates phosphorothioate bond). After three incubation steps (16 ℃ for 30 min, 4 ℃ overnight, and 65 ℃ for 20 min), the reaction mix was subjected to EpiTect Fast Bisulfite Conversion Kit (QIAGEN) following manufacturer’s low-concentration protocol. The bisulfite converted DNA was immediately subjected to PCR amplification using KAPA HiFi HotStart Uracil+ ReadyMix (Kapa Biosystems) and NEBNext Primers for Illumina (New England Biolabs). After amplification, final libraries were obtained by size selection of 150-500 bp DNA fragments using SPRIselect beads (Beckman Coulter).

tag: cell

value: blastocyst

tag: strain

value: C57BL/6J x CAST/EiJ

value: maternal Tet3 KO


title: Protoplast reprogramming_24h

city: Beijing

first: Lihong

last: Xiao

address: No.105 North Road of West 3rd-ring Road.Haidian District

institute: Capital Normal University

data_processing:
Adaptor tags, low quality tags and tags of copy number=1 were filtered,then the distinct clean tags were aligned to the reference P.patens database by Bowtie. The P.patens reference to which our clean tags were aligned was downloaded from JGI database (http://www.jgi.doe.gov/).  The genome build version: V7.0, and the FTP download address is ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v7.0/Ppatens/annotation/.
Genome Build:
24h.GeneExpression.txt: JGI v7.0

organism: Physcomitrium patens

source_name: P. patens protoplast cultures at 24 hours

growth_protocol: samples taken from P. patens protoplast cultures at 0, 24 48 and 72 hours after protoplastes isolated.

extract_protocol: Illumina HiSeq 2000 DGE

value: protoplast

tag: time (culture)


title: Protoplast reprogramming_72h

data_processing:
Adaptor tags, low quality tags and tags of copy number=1 were filtered,then the distinct clean tags were aligned to the reference P.patens database by Bowtie. The P.patens reference to which our clean tags were aligned was downloaded from JGI database (http://www.jgi.doe.gov/).  The genome build version: V7.0, and the FTP download address is ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v7.0/Ppatens/annotation/.
Genome Build:
72h.GeneExpression.txt: JGI v7.0

source_name: P. patens protoplast cultures at 72 hours


title: CKO-Blastocyst-rep2

tag: genotype


title: S2 repB light digest 4 h

tag: cell type

tag: cell line


title: WT-Blastocyst-rep1

value: WT


title: CKO-Zygote-rep2

value: zygote


title: WT-Blastocyst-rep2


title: WT-Zygote-rep1


title: CKO-Zygote-rep1


title: CAST-Sperm-rep2

value: sperm

value: CAST/EiJ


title: CAST-Sperm-rep1


title: WT-Zygote-rep2


title: NAc projector, experiment-1: NAc_671

status: Public on Feb 27 2015

first: Suzuko

last: Yorozu

state: Massachusettes

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: Experiment-1, NAc

data_processing:
Sequencing reads were aligned using Tophat version 2.0.10 against the Mus musculus UCSC version mm10 genome and the mm10 RefSeq transcriptome.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

source_name: Brain tissue (BLA), NAc-projector, Experiment-1

extract_protocol:
Total RNA was isolated using Arcturus PicoPure RNA isolation kit (Life Technologies).
Double stranded cDNA was generated from total RNA using a DNA-RNA chimeric primer mix and reverse transcriptase, and cDNA was amplified by the SPIA amplification process developed by NuGEN (Ovation RNA-Seq System V2 kit (Neugen)).
The amplified double stranded cDNA was fragmented to an average size of 200 bases using Covaris S-S series sonication system. The fragmented cDNA was end-repaired, and adaptors and barcodes were ligated before PCR-based library preparation using Ovation Ultralow DRMultiplex Systems (Nugen).

treatment_protocol: In order to label the BLA neurons projecting to the NAc or CeM, red retrobeads (Lumafluor Inc.) were injected into the NAc and CeM of the adult mice brains.  Two weeks after retrobeads injection, the retrobeads are traveled to the BLA, and the brain was quickly removed for acute 330 μm coronal brain slices for subsequent dissociation and isolation of retrobeads labeled BLA neurons. After dissociation of the retrobeads labeled BLA neurons, 30-60 retrobeads-positive neurons were isolated under a fluorescent dissecting microscope for subsequent RNA extraction.

value: male

tag: developmental stage

value: basolateral amygdala complex neurons


title: NAc projector, experiment-1: NAc_703

description: Experiment-1, NAc


title: Protoplast reprogramming_48h

data_processing:
Adaptor tags, low quality tags and tags of copy number=1 were filtered,then the distinct clean tags were aligned to the reference P.patens database by Bowtie. The P.patens reference to which our clean tags were aligned was downloaded from JGI database (http://www.jgi.doe.gov/).  The genome build version: V7.0, and the FTP download address is ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v7.0/Ppatens/annotation/.
Genome Build:
48h.GeneExpression.txt: JGI v7.0

source_name: P. patens protoplast cultures at 48 hours


title: CeM projector, experiment-1: CeM_709

description: Experiment-1, CeM

source_name: Brain tissue (BLA), CeM-projector, Experiment-1


title: WT

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

description: Sample 9

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were mapped to the reference genome (GRCm38.70) using bowtie 0.12.7 with -m 1
Sample 9 "WT" was used to generate the 5 pseudo-replicates of WT (i.e., samples "A_WT" to "E_WT") by random sub-sampling. However, sample 9 was not directly used for the analysis.
Peaks were called using macs2 2.0.10.20130520 with -p 0.001 using NLRC5 as control
Genome_build: GRCm38.70
Supplementary_files_format_and_content: bigwig and bed files report peaks

source_name: WT T-cells

growth_protocol: Sex and age-matched 6 to 12 week-old mice were used. Five mice were pooled for each genotype.

extract_protocol:
Chromatine was isolated, fragmented by sonication and immunoprecipitated it with anti Nlrc5 antibody
Libraries were prepared according to Illumina's instructions using the Truseq ChIP-seq protocol.

value: C57Bl/6 (H2b) background

value: T-cells

tag: genotype/variation

value: Rabbit polyclonal anti-mouse NLRC5 (aa 1–139) custom antibody generated by Adipogen


title: NAc projector, experiment-1: NAc_704

description: Experiment-1, NAc

tag: tissue


title: CeM projector, experiment-1: CeM_713

description: Experiment-1, CeM

tag: tag


title: NAc projector, experiment-1: NAc_666

description: Experiment-1, NAc

tag: Sex


title: CeM projector, experiment-1: CeM_721

description: Experiment-1, CeM


title: Protoplast reprogramming_0h

data_processing:
Adaptor tags, low quality tags and tags of copy number=1 were filtered,then the distinct clean tags were aligned to the reference P.patens database by Bowtie. The P.patens reference to which our clean tags were aligned was downloaded from JGI database (http://www.jgi.doe.gov/).  The genome build version: V7.0, and the FTP download address is ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v7.0/Ppatens/annotation/.
Genome Build:
0h.GeneExpression.txt: JGI v7.0

source_name: P. patens protoplast cultures at 0 hours


title: E_WT

description: Sample 5


title: RFX5

description: Sample 7

source_name: Rfx5-/- T-cells

value: mixed Sv129/C57Bl/6 (H2b) background


title: D_WT

description: Sample 4


title: B_WT

description: Sample 2


title: FL

description: Sample 8

source_name: Nlrc5F/F T-cells


title: A_WT

description: Sample 1


title: C_WT

description: Sample 3


title: CeM projector, experiment-1: CeM_722

description: Experiment-1, CeM


title: Unstimulated Mouse Bone Marrow Derived Dendritic Cells (t0)

city: Worcester

first: Manuel

last: Garber

state: Massachusetts

address: 55 Lake Ave North Worcester

department: Bioinformatics and Integrative Biology

institute: University of Massachusetts Medical School

data_processing:
Genome Alignment (TopHat 1.4.1)
Picard to Mark PCR duplicates
Igvtools count -w to generate big wig file
Scripture for transcript reconstruction
Scripture for quantification using the constituent exon model
Genome_build: mm9
Supplementary_files_format_and_content: bam, BigWig, bed

source_name: bone marrow

growth_protocol: Briefly, 6-8 week old female C57BL/6J mice were obtained from the Jackson Laboratories. RPMI medium (Invitrogen) supplemented with 10% heat inactivated FBS (Invitrogen), β-mercaptoethanol (50uM, Invitrogen), L-glutamine (2mM, VWR) penicillin/streptomycin (100U/ml, VWR), MEM non-essential amino acids (1X, VWR), HEPES (10mM, VWR), sodium pyruvate (1mM, VWR), and GM-CSF (20 ng/ml; Peprotech, Rocky Hill, NJ) was used throughout the study. At day 0, bone marrow-derived dendritic cells (BMDCs) were collected from femora and tibiae and plated on twenty (per mouse), 100mm non-tissue culture treated plastic dishes using 10ml medium per plate. At day 2, cells were fed with another 10ml medium per dish. At day 5, cells were harvested from 15ml of the supernatant by spinning at 1400rpm for 5 minutes; pellets were resuspended with 5ml medium and added back to the original dish. Cells were fed with another 5ml medium at day 7. At Day 8, all non-adherent and loosely bound cells were collected and harvested by centrifugation. Cells were then resuspended with medium, plated at a concentration of 15x106 cells in 10ml medium per 100mm dish. At day 9, cells were stimulated for various time points with LPS (100ng/ml, rough, ultra-pure E. coli K12 strain, Invitrogen).

extract_protocol:
Total RNA was extracted with QIAzol reagent following the miRNeasy kit’s procedure (Qiagen), and sample quality was tested on a 2100 Bioanalyzer (Agilent). We prepared the RNA-A+-Seq libraries using the ‘dUTP second strand (strand specific) protocol as described in (Levine et al 2010). Briefly, extracts were treated with DNase (Ambion 2238). Polyadenylated RNAs were selected using Ambion's MicroPoly(A)Purist kit (AM1919M) and RNA integrity confirmed using Bioanalyzer (Agilent).
RNA was fragmented by incubation in RNA fragmentation buffer (Affymetrix) at 80 degrees for 4 minutes. Fragmented RNA was mixed with 3 μg random hexamers (Invitrogen), incubated at 70 °C for 10 min, and placed on ice briefly before starting cDNA synthesis. We synthesized first-strand cDNA with this RNA primer mix by adding 4 μl 5× first-strand buffer, 2 μl 100 mM DTT, 1 μl 10 mM dNTPs, 4 μg of actinomycin D, 200 U SuperScript III and 20 U SUPERase-In, incubating at room temperature for 10 min followed by 1 h at 55 °C. We synthesized second-strand cDNA by adding 4 μl of 5× first-strand buffer, 2 μl of 100 mM DTT, 4 μl of 10 mM dNTPs with dTTP replaced by dUTP (Sigma), 30 μl of 5× second-strand buffer, 40 U of Escherichia coli DNA polymerase, 10 U of E. coli DNA ligase and 2 U of E. coli RNase H, and incubating at 16 °C for 2 h. cDNA was eluted using the Qiagen MiniElute kit with 30 μl of the manufacturer's EB buffer. DNA ends were repaired using dNTPs and T4 polymerase (NEB), followed by purification using the MiniElute kit. Adenine was added to the 3′ end of the DNA fragments using dATP and Klenow exonuclease (NEB; M0212S) to allow adaptor ligation, and fragments were purified using MiniElute. Adaptors were ligated and incubated for 15 min at room temperature (25 °C). Phenol/chloroform/isoamyl alcohol (Invitrogen 15593-031); extraction followed to remove the DNA ligase. The pellet was then resuspended in 10 μl EB buffer. The sample was run on a 3% agarose gel (Nusieve 3:1 agarose, Lonza) and a 160–380 base pair fragment was cut out and extracted. PCR was performed with Phusion High-Fidelity DNA Polymerase with the manufacturer's GC buffer (New England Biolabs) and 2 M betaine (Sigma). PCR conditions were 30 s at 98 °C; 16 cycles of 10 s at 98 °C, 30 s at 65 °C, 30 s at 72 °C; 5 min at 72 °C; forever at 4 °C. Products were run on a polyacrylamide gel for 60 min at 120 V. The PCR products were cleaned up with Agencourt AMPure XP magnetic beads (A63880) to completely remove primers and the product was submitted for Illumina sequencing.

tag: treatment

value: LPS

value: 0 h

value: bone marrow-derived dendritic cells


title: s_RM27_bas

city: Scottsdale

first: Lawrence

middle: J

last: Mandarino

state: Arizona

address: 13400 E. Shea Boulevard

department: Researcg

institute: Mayo Clinic in Arizona

data_processing:
Basecalls were performed using CASAVA 1.7
The Read1 FASTQ files for each sample were trimmed of their NEB Next adapters using Cutadapt 0.9.5, discarding any reads shorter than 17bps after trimming. The reads were aligned to the human miRBase release18 miRNA sequences using bowtie 0.12.7 and quantified with miRDeep2 2.0.0.5. The miRDeep2 per-sample raw and Counts Per Million abundance measures were combined into the supplemental tables of miRNA_expression_raw.txt and miRNA_expression_norm.txt.
Genome_build: hg19 and miRBase release 18
Supplementary_files_format_and_content:
miRNA_expression_raw.txt: Raw Read Counts
miRNA_expression_norm.txt: Counts Per Million Read Counts

source_name: at rest (0 min)_muscle

extract_protocol:
RNA was extracted from tissue using the Qiagen miRNEasy kit following the manufacturer's protocol.
Small RNA libraries were prepared according to manufacturer’s instructions for the NEBNext Multiplex Small RNA Kit (New England Biolabs; Ipswich, MA).  Briefly, adaptors were ligated to the 3’ and 5’ ends of the miRNAs as part of total RNA samples.  A complementary primer was annealed to 3’ adaptor sequences followed by reverse transcriptase (Superscript III; Invitrogen; Carlsbad, CA) to generate a cDNA library of small RNAs.  The library was enriched by 12-15 cycles of PCR employing a common 5’ primer and up to 24 unique Index primers (3’ adaptor complement; equivalent to Illumina TruSeq Small RNA sequences).  PCR products were assessed for miRNA products by Agilent Bioanalyzer DNA 1000 (Santa Clara, CA) analysis.  The 130-155bp fraction was quantitated by region analysis to determine equimolar amounts of libraries to pool.  Pooled PCR reactions were purified and concentrated using a Qiagen MinElute protocol and eluted in 30ul nuclease-free dH2O. Small RNA libraries were fractionated to extract an miRNA-enriched sample via 3% Pippin Prep gel cassettes (Sage Science, Beverly, MA).  The 125-160bp recovered fraction was purified by Qiagen MinElute and recovered in 10ul nuclease-free dH2O. Individual or pooled miRNA fractions were assessed by a second Agilent DNA 1000 assay. A predominant peak at 140-150bp is evidence that the miRNA-modification molecular biology and size selection steps have performed as expected. The final concentration of each library or pool was determined by Qubit fluorometry using the Broad Range or High Sensitivity reagents (Invitrogen). Libraries were then loaded onto paired end flow cells at concentrations of 8-10 pM to generate cluster densities of 700,000/mm2 following Illumina’s standard protocol using the Illumina cBot and cBot Paired end cluster kit version 3.

tag: subject status

value: healthy participant

tag: time point

value: at rest (0 min)

value: muscle


title: CeM projector, experiment-1: CeM_710

description: Experiment-1, CeM


title: d7 CGN DNase-seq Rep 1

city: Durham

first: Christopher

middle: L

last: Frank

state: NC

address: 101 Science Dr.

institute: Duke University

data_processing:
Basecalls performed using CASAVA v1.8
First 20bp of DNase-seq reads mapped to NCBI37/mm9 with BWA, RNA-seq mapped to NCBI37/mm9 with Tophat v2.0.8b; ChIP-seq mapped to NCBI37/mm9 with Bowtie v1.0.0; in all cases up to 2 mismatches were allowed
Putative PCR artifacts filtered from mapped DNase-seq and ChIP-seq prior to peak calls
DNase-seq peaks called with F-seq v1.84, ChIP-seq peaks called with MACS v1.4, FPKM expression values estimated by Cufflinks v2.0.2
Genome_build: mm9
Supplementary_files_format_and_content: DNase-seq .npf (narrow peak format with chromosome, start, stop, name, score, p-value) contain top 100,000 DHS peaks identified by F-seq ; RNA-seq Cufflinks text files contain gene FPKM abundances ; ChIP-seq .bed files contain all MACS peak calls and scores with default significance threshold.

source_name: cultured cerebellar granule neurons

growth_protocol: Cerebellae from a litter of P7 mice were chopped into small pieces then digested at 37°C for 30 min in 10 U/ml papain (Worthington), 200g/ml L-cysteine (Sigma), and 250 U/ml DNase (Sigma) in PBS. The tissue was mechanically triturated in PBS with trypsin inhibitor and 250 U/ml DNase then centrifuged and resuspended in PBS/BSA. The cell suspension was passed through a cell strainer (Becton Dickinson), layered on a step gradient of 35% and 65% Percoll (Sigma), and centrifuged at 2500 rpm for 12 min at room temperature. Granule Neuron Precursors (GNPs) were harvested from the 35/65% interface, washed in PBS/BSA, resuspended in Neurobasal medium with B27 supplements and 2% fetal bovine serum and plated on poly-D-lysine coated dishes.

extract_protocol:
15-30 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Digestions were checked by pulse field gel electrophoresis and material was pooled from 3 different DNase concentrations (extent of digestion matched between samples) in equimolar amounts following blunt-ending reactions. This was followed by ligation to adapters, MmeI digestion, streptavidin bead-based enrichment, 14 cycles of PCR amplification, and separation from linker-only bands on a gel.
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis

value: cultured cerebellar granule neurons

value: GNP + 7DIV


title: d0 CGN DNase-seq Rep 1

value: Granule Neuron Precursors (GNPs)


title: s_RM27_30min

source_name: 30 min after a single acute exercise bout _muscle

value: 30 minutes after a single acute exercise bout


title: s_JN32-bas


title: d3 CGN DNase-seq Rep 1

value: GNP + 3DIV


title: s_RL26_30min


title: s_JN32-30min


title: s_JG34-bas


title: s_JG34-30min


title: NLRC5

description: Sample 6

source_name: Nlrc5-/- T-cells

tag: chip antibody


title: s_AC30-bas


title: s_AC30-30min


title: s_GC48-bas


title: ribo_tmisrib_b

city: Berkeley

first: Anna

middle: M

last: McGeachy

state: California

address: 416 Barker Hall

department: MCB

institute: UC Berkeley

description: Ribosome Profiling

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
rRNA alignment with bowtie v1.0.0
Transcriptome alignment with TopHat v2.0.10 (mRNA), TopHat v2.0.7 (footprints)
Read quantitation using custom scripts
Genome_build: hg19 with Gencode v17 transcripts
Supplementary_files_format_and_content: tab-delimited text files contain 3 columns: 1. feature name; 2. CDS size; 3. read counts on the CDS from without the first 15 of last 5 codons

growth_protocol: maintained at 37o C, 5% CO2 in DMEM media supplemented with 10% FBS, L-glutamine and antibiotics (penicillin and streptomycin)

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

value: 1μg/ml of tunicamycin and ISRIB (200 nM) for 1 hour


title: ribo_tm_a

description: Ribosome Profiling

value: 1μg/ml of tunicamycin for 1 hour


title: ribo_untr_a

description: Ribosome Profiling

value: untreated


title: ribo_isrib_b

description: Ribosome Profiling

value: ISRIB (200 nM) for 1 hour


title: mrna_tmisrib_b

description: RNA-seq

extract_protocol:
library construction: IlluminaTruSeqstranded prep
RNA extraction, preadenylated linker ligation, reverse transcription, cDNA circularization, PCR amplification


title: mrna_tmisrib_a

description: RNA-seq


title: mrna_tm_b

description: RNA-seq


title: ribo_isrib_a

description: Ribosome Profiling


title: mrna_tm_a

description: RNA-seq


title: mrna_untr_b

description: RNA-seq


title: ribo_untr_b

description: Ribosome Profiling


title: mrna_isrib_b

description: RNA-seq


title: mrna_isrib_a

description: RNA-seq


title: Control Pre [Sample_93_1]

first: Michael

middle: S

last: Breen

address: 1468 Madison Ave

department: Depts. of Psychiatry, Genetics and Genomic Sciences

institute: Ichan School of Medicine at Mount Sinai

data_processing:
Illumina Casava1.7 software used for basecalling as provided by Expression Analysis (EA) Inc.
Sequenced reads were trimmed for adapter sequence, and masked for low-complexity or low-quality sequence using FastqMcf provided by EA Inc (http://code.google.com/p/ea-utils/wiki/FastqMcf). Remaining reads were then mapped to hg19 UCSC human genome using RSEM v1.1.13 with parameters.
Genes with low counts were removed by unspecific filtering. Following, voom transformation was performed on raw counts as described by Law et al., Genome Biology 2014.
Genes which were found in common with Microarray accession no. were used in the final analysis and are provided in the normalized filtered matrix.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include raw count values and VOOM transformed values for each sample are provided.

source_name: Human peripheral blood leukocytes

extract_protocol:
RNA was isolated from peripheral blood leukocytes using LeukoLOCK Total RNA isolation.
RNA libraries were prepared for sequencing using stranded Illumina Tru-Seq protocols using the Illumina HiSeq 2000.

treatment_protocol: Each whole blood sample (10ml) was collected into an EDTA-coated collection tube.

tag: condition

value: Control

tag: time-point

value: Pre-deployment


title: Control Post [Sample_94_3]

value: Post-deployment


title: Control Post [Sample_92_3]


title: Control Pre [Sample_94_1]


title: Control Pre [Sample_92_1]


title: Control Post [Sample_93_3]


title: Control Post [Sample_91_3]


title: Control Post [Sample_90_3]


title: ribo_tmisrib_a

description: Ribosome Profiling


title: mrna_untr_a

description: RNA-seq


title: s_GC48-30min


title: s_RL26_bas


title: ribo_tm_b

description: Ribosome Profiling


title: Control Pre [Sample_90_1]


title: Control Post [Sample_89_3]


title: Control Pre [Sample_89_1]


title: Control Pre [Sample_88_1]


title: Control Post [Sample_88_3]


title: Control Post [Sample_87_3]


title: Control Post [Sample_86_3]


title: Control Pre [Sample_87_1]


title: Control Pre [Sample_86_1]


title: Control Pre [Sample_85_1]


title: Control Post [Sample_85_3]


title: Control Post [Sample_84_3]


title: Control Pre [Sample_84_1]


title: Control Post [Sample_82_3]


title: Control Pre [Sample_82_1]


title: Control Pre [Sample_91_1]


title: Control Post [Sample_80_3]


title: Control Pre [Sample_81_1]


title: Control Post [Sample_79_3]


title: Control Post [Sample_78_3]


title: Control Pre [Sample_79_1]


title: Control Pre [Sample_77_1]


title: Control Pre [Sample_76_1]


title: Control Pre [Sample_80_1]


title: Control Pre [Sample_75_1]


title: Control Post [Sample_76_3]


title: Control Pre [Sample_78_1]


title: Control Pre [Sample_74_1]


title: Control Post [Sample_74_3]


title: Control Post [Sample_73_3]


title: Control Pre [Sample_73_1]


title: Control Post [Sample_72_3]


title: Control Post [Sample_71_3]


title: Control Post [Sample_69_3]


title: Control Pre [Sample_71_1]


title: Control Pre [Sample_83_1]


title: Control Pre [Sample_72_1]


title: Control Pre [Sample_69_1]


title: Control Post [Sample_68_3]


title: Control Post [Sample_70_3]


title: Control Pre [Sample_70_1]


title: Control Pre [Sample_67_1]


title: Control Pre [Sample_68_1]


title: Control Post [Sample_75_3]


title: Control Post [Sample_64_3]


title: Control Post [Sample_65_3]


title: Control Pre [Sample_64_1]


title: Control Pre [Sample_65_1]


title: Control Post [Sample_63_3]


title: Control Post [Sample_83_3]


title: Control Post [Sample_67_3]


title: Control Post [Sample_77_3]


title: Control Pre [Sample_63_1]


title: Control Post [Sample_62_3]


title: Control Post [Sample_81_3]


title: Control Post [Sample_61_3]


title: Control Pre [Sample_66_1]


title: Control Pre [Sample_61_1]


title: Control Post [Sample_60_3]


title: Control Pre [Sample_60_1]


title: Control Pre [Sample_58_1]


title: Control Post [Sample_58_3]


title: Control Pre [Sample_59_1]


title: Control Post [Sample_57_3]


title: Control Pre [Sample_57_1]


title: Control Post [Sample_66_3]


title: Control Post [Sample_56_3]


title: Control Pre [Sample_56_1]


title: Control Pre [Sample_55_1]


title: Control Post [Sample_54_3]


title: Control Post [Sample_55_3]


title: Control Post [Sample_53_3]


title: Control Pre [Sample_54_1]


title: Control Pre [Sample_50_1]


title: Control Post [Sample_50_3]


title: Control Post [Sample_51_3]


title: Control Post [Sample_49_3]


title: Control Pre [Sample_49_1]


title: Control Pre [Sample_52_1]


title: Control Pre [Sample_51_1]


title: Control Pre [Sample_48_1]


title: Case Post [Sample_47_3]

value: Case (PTSD)


title: Control Post [Sample_59_3]


title: Case Pre [Sample_47_1]

value: Case (PTSD risk)


title: Control Post [Sample_48_3]


title: Case Pre [Sample_46_1]


title: Case Post [Sample_45_3]


title: Case Post [Sample_44_3]


title: Case Pre [Sample_45_1]


title: Case Post [Sample_42_3]


title: Case Post [Sample_43_3]


title: Case Pre [Sample_44_1]


title: Control Pre [Sample_62_1]


title: Case Pre [Sample_43_1]


title: Case Pre [Sample_42_1]


title: Case Pre [Sample_41_1]


title: Control Post [Sample_52_3]


title: Control Pre [Sample_53_1]


title: Case Post [Sample_41_3]


title: Case Pre [Sample_40_1]


title: Case Post [Sample_40_3]


title: Case Pre [Sample_38_1]


title: Case Pre [Sample_39_1]


title: Case Post [Sample_38_3]


title: Case Post [Sample_46_3]


title: Case Post [Sample_36_3]


title: Case Pre [Sample_37_1]


title: Case Pre [Sample_36_1]


title: Case Pre [Sample_35_1]


title: Case Post [Sample_37_3]


title: Case Pre [Sample_34_1]


title: Case Post [Sample_35_3]


title: Case Post [Sample_34_3]


title: Case Pre [Sample_33_1]


title: Case Post [Sample_33_3]


title: Case Pre [Sample_32_1]


title: Case Post [Sample_32_3]


title: Case Post [Sample_30_3]


title: Case Pre [Sample_31_1]


title: Case Pre [Sample_30_1]


title: Case Post [Sample_29_3]


title: Case Pre [Sample_29_1]


title: Case Post [Sample_39_3]


title: Case Post [Sample_27_3]


title: Case Post [Sample_28_3]


title: Case Pre [Sample_28_1]


title: Case Post [Sample_24_3]


title: Case Pre [Sample_26_1]


title: Case Pre [Sample_27_1]


title: Case Post [Sample_25_3]


title: Case Pre [Sample_24_1]


title: Case Post [Sample_23_3]


title: Case Pre [Sample_21_1]


title: Case Pre [Sample_22_1]


title: Case Pre [Sample_20_1]


title: Case Post [Sample_20_3]


title: Case Post [Sample_19_3]


title: Case Post [Sample_22_3]


title: Case Pre [Sample_23_1]


title: Case Post [Sample_18_3]


title: Case Pre [Sample_18_1]


title: Case Post [Sample_21_3]


title: Case Post [Sample_31_3]


title: Case Post [Sample_26_3]


title: Case Post [Sample_14_3]


title: Case Post [Sample_15_3]


title: Case Pre [Sample_17_1]


title: Case Pre [Sample_14_1]


title: Case Post [Sample_13_3]


title: Case Post [Sample_16_3]


title: Case Pre [Sample_13_1]


title: Case Post [Sample_17_3]


title: Case Pre [Sample_25_1]


title: Case Post [Sample_12_3]


title: Case Pre [Sample_15_1]


title: Case Pre [Sample_12_1]


title: Case Pre [Sample_16_1]


title: Case Pre [Sample_11_1]


title: Case Post [Sample_11_3]


title: Case Pre [Sample_19_1]


title: Case Post [Sample_8_3]


title: Case Pre [Sample_10_1]


title: Case Pre [Sample_9_1]


title: Case Post [Sample_7_3]


title: Case Pre [Sample_7_1]


title: Case Post [Sample_6_3]


title: Case Post [Sample_5_3]


title: Case Pre [Sample_6_1]


title: Case Pre [Sample_5_1]


title: Case Post [Sample_4_3]


title: Case Pre [Sample_4_1]


title: Case Pre [Sample_3_1]


title: Case Pre [Sample_2_1]


title: Case Post [Sample_10_3]


title: Case Post [Sample_3_3]


title: RNA-seq-METTL14KD-rep1

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

description:
Sample 17
processed data file: Processed_location_m6A-switch.xlsx

data_processing:
The control and IP samples from PARCLIP-MeRIP experiments (same case for the control and knockdown samples from METTL knockdown experiments) were sequenced together in one flowcell on two lanes, and the reads from two lanes of each sample were combined for remaining analysis. The raw seq data was trimmed using the Trimmomatic computer program version 0.30 to remove adaptor sequences, and mapped to the Human genome version hg19 by Bowtie 1.0.0 without any gaps and allowed for at most two mismatches. For each genomic site, we calculated the average read counts within an 11-nt window centered at that site, as the normalized read counts for that site. This normalization smoothed the raw mapping curves, and facilitated identification of peaks within each mapping cluster. To correct for changes in sequencing depth or expression levels between samples, we then normalized the read counts at each genomic site to the total number of read counts on the respective gene. hnRNP C binding sites were identified by PARalyzer v1.1 with default settings.
Detection of PARCLIP-MeRIP peaks involves comparing the read counts of the IP sample with that of the control (Ctrl) sample as follows: (i) we identified all peaks within hnRNP C binding sites in the IP sample; (ii) we performed transcriptome-wide scanning to compare read counts of each identified peak in (i) with read counts at same genomic locations in the Ctrl sample to calculate the fold change score, score = log2(HIP/HCtrl). The score threshold was set to be 1, corresponding to a twofold increase compared with control. Detection of decreased hnRNP C binding sites involved comparing hnRNP C occupancies in the METTL3/14 knockdown (KD) sample with that in control as follows: (i) we identified all peaks within hnRNP C binding sites in the METTL3/14 knockdown sample; (ii) we performed transcriptome-wide scanning to compare read counts of each identified peak in (i) with read counts at the same genomic locations in control to calculate the fold change score, score = log2(HKD/HCtrl). The score threshold was set to be -1, corresponding to a twofold decrease compared with control.
RNA-seq experiments were performed on two replicate RNA samples from HNRNPC, METTL3, METTL14 KD as well as control HEK293T cells (48 hours after transfection). Total RNA samples were extracted according to RNeasy plus kit (Catalog # 74104, Qiagen). Libraries were prepared according to the TruSeq Stranded mRNA LT Sample Prep Kit (Catalog # RS-122-9005DOC). KD and control samples were sequenced together in one flowcell on four lanes, respectively. All samples were sequenced by illumina Hiseq 2000 with pair end 100-bp read length. The reads from the four lanes of each samples were combined for all analysis. The RNA-seq data was mapped using the splice-aware alignment algorithm TopHat version 1.1.4 based on the following parameters: tophat –num-threads 8 –mate-inner-dist 200 –solexa-quals –min-isoform-fraction 0 –coverage-search-segment-mismatches 1. Cufflinks was used to predict exons and cuffdiff was used to detect isoform expression level changes. Analysis of differential gene expression were performed using DESeq based on Ensembl gene annotations. Differential splicing was determined using DEXSeq based on Cufflinks-predicted, nonoverlapping exons.
Genome_build: hg19
Supplementary_files_format_and_content: Excel files with the m6A-switches sites in chromosome and transcript

growth_protocol: Embryonic kidney cell line HEK293T (CRL-11268) were obtained from American Type Culture Collection (ATCC) and were cultured under standard conditions

extract_protocol:
All PAR-CLIP RNA samples (samples 1-10) were extracted following normal PAR-CLIP procedures; the total RNA samples (samples 11-18) were extracted according to RNeasy plus kit (Catalog # 74104, Qiagen).
PAR-CLIP and PARCLIP-MeRIP libraries (Samples 1-10) were prepared using TruSeq Small RNA Sample Preparation Kit (RS-200-0012, Illumina) according to the manufacturer’s instructions, and then sequenced by Illumina Hiseq 2000 with single end 50-bp read length; RNA-seq libraries (Samples 11-18) were prepared according to the TruSeq Stranded mRNA LT Sample Prep Kit (Catalog # RS-122-9005DOC). KD and control samples were sequenced together in one flowcell on four lanes, respectively. The reads from the four lanes of each samples were combined for all analysis.

value: embryonic kidney cells

value: METTL14 Knockdown


title: RNA-seq-METTL3KD-rep2

description:
Sample 16
processed data file: Processed_location_m6A-switch.xlsx

value: METTL3 Knockdown


title: RNA-seq-METTL14KD-rep2

description:
Sample 18
processed data file: Processed_location_m6A-switch.xlsx


title: RNA-seq-METTL3KD-rep1

description:
Sample 15
processed data file: Processed_location_m6A-switch.xlsx


title: RNA-seq-HNRNPCKD-rep2

description:
Sample 14
processed data file: Processed_location_m6A-switch.xlsx

source_name: RNA-seq-HNRNPCKD

value: HNRNPC Knockdown


title: RNA-seq-control-rep2

description:
Sample 12
processed data file: Processed_location_m6A-switch.xlsx

source_name: RNA-seq-control

value: wild type


title: RNA-seq-control-rep1

description:
Sample 11
processed data file: Processed_location_m6A-switch.xlsx


title: Case Post [Sample_9_3]


title: RNA-seq-HNRNPCKD-rep1

description:
Sample 13
processed data file: Processed_location_m6A-switch.xlsx


title: hnRNPC-PAR-CLIP-METTL14KD-rep1

data_processing:
The control and IP samples from PARCLIP-MeRIP experiments (same case for the control and knockdown samples from METTL knockdown experiments) were sequenced together in one flowcell on two lanes, and the reads from two lanes of each sample were combined for remaining analysis.
The raw seq data was trimmed using the Trimmomatic computer program version 0.30 to remove adaptor sequences, and mapped to the Human genome version hg19 by Bowtie 1.0.0 without any gaps and allowed for at most two mismatches.
For each genomic site, we calculated the average read counts within an 11-nt window centered at that site, as the normalized read counts for that site. This normalization smoothed the raw mapping curves, and facilitated identification of peaks within each mapping cluster. To correct for changes in sequencing depth or expression levels between samples, we then normalized the read counts at each genomic site to the total number of read counts on the respective gene.
hnRNP C binding sites were identified by PARalyzer v1.1 with default settings.
Detection of PARCLIP-MeRIP peaks involves comparing the read counts of the IP sample with that of the control (Ctrl) sample as follows: (i) we identified all peaks within hnRNP C binding sites in the IP sample; (ii) we performed transcriptome-wide scanning to compare read counts of each identified peak in (i) with read counts at same genomic locations in the Ctrl sample to calculate the fold change score, score = log2(HIP/HCtrl). The score threshold was set to be 1, corresponding to a twofold increase compared with control. Detection of decreased hnRNP C binding sites involved comparing hnRNP C occupancies in the METTL knockdown (KD) sample with that in control as follows: (i) we identified all peaks within hnRNP C binding sites in the METTL knockdown sample; (ii) we performed transcriptome-wide scanning to compare read counts of each identified peak in (i) with read counts at the same genomic locations in control to calculate the fold change score, score = log2(HKD/HCtrl). The score threshold was set to be -1, corresponding to a twofold decrease compared with control.
Genome_build: hg19
Supplementary_files_format_and_content: Excel files with the m6A-switches sites in chromosome and transcript

source_name: Embryonic kidney cells

extract_protocol:
All PAR-CLIP RNA sample were extracted following normal PAR-CLIP procedures
Libraries were prepared using TruSeq Small RNA Sample Preparation Kit (RS-200-0012, Illumina) according to the manufacturer’s instructions, and then sequenced by Illumina Hiseq 2000 with single end 50-bp read length

value: HEK293T cells

tag: par-clip antibody

value: hnRNPC (sc-32308, Santa Cruz)


title: hnRNPC-PAR-CLIP-METTL14KD-rep2


title: hnRNPC-PAR-CLIP-Control-rep2


title: hnRNPC-PAR-CLIP-METTL3KD-rep2


title: Case Pre [Sample_8_1]


title: hnRNPC-PAR-CLIP-Control-rep1


title: hnRNPC-PAR-CLIP-METTL3KD-rep1


title: PARCLIP-MeRIP-IP-rep2


title: PARCLIP-MeRIP-IP-rep1


title: PARCLIP-MeRIP-Input-rep2


title: PARCLIP-MeRIP-Input-rep1


title: Dmrt1 Mutant Granulosa Cell C9 (paired-end)

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

description: Cell C9

data_processing:
Reads were trimmed with Trimmomatic Version 0.32.
Reads were mapped to mm9 with STAR_2.3.0e.
Duplicates were removed with Picard 1.94.
Mapped reads were sorted and indexed with Samtools 0.1.18.
Features corresponding to Ensembl Genes were counted with the GenomicAlignments Package in Bioconductor.
Genome_build: mm9
Supplementary_files_format_and_content: The RNA-Seq data are summarized as a comma separated value text file for raw counts of Ensembl Genes.

source_name: P17 Ovaries

extract_protocol:
8-10 week gonad samples were harvested in Trizol.  For single cell RNA-Seq, CAG-Stop-Dmrt1-Gfp;Sf1-Cre ovaries at P17 were dissociated and ~0.5 million cells were FACS sorted based on forward- and side-scatter, GFP and the Zombie Aqua viability stain (Biolegend). Cells were captured with a 5-10μm cell capture cassette using the Fluidigm C1 instrument.
PolyA+ mRNA from 8-10 week tissue samples was subjected to Illumina TruSeq library creation. For single cell RNA-Seq, cDNA was synthesized using SMARTer-Seq (Clontech) and the Nextera XT (Illumina) protocols.

tag: strain

value: Mixed

tag: gender

value: Female

tag: tissue type

value: Ovary

tag: age


title: Case Post [Sample_2_3]


title: Dmrt1 Mutant Granulosa Cell C96 (paired-end)

description: Cell C96

tag: genotype


title: Case Post [Sample_1_3]


title: Case Pre [Sample_1_1]


title: Dmrt1 Mutant Granulosa Cells (Bulk) (paired-end)

description: Bulk


title: Dmrt1 Mutant Granulosa Cell C94 (paired-end)

description: Cell C94


title: Dmrt1 Mutant Granulosa Cell C93 (paired-end)

description: Cell C93


title: Dmrt1 Mutant Granulosa Cell C87 (paired-end)

description: Cell C87


title: Dmrt1 Mutant Granulosa Cell C92 (paired-end)

description: Cell C92


title: Dmrt1 Mutant Granulosa Cell C91 (paired-end)

description: Cell C91


title: Dmrt1 Mutant Granulosa Cell C89 (paired-end)

description: Cell C89


title: Dmrt1 Mutant Granulosa Cell C7 (paired-end)

description: Cell C7


title: Dmrt1 Mutant Granulosa Cell C78 (paired-end)

description: Cell C78


title: Dmrt1 Mutant Granulosa Cell C82 (paired-end)

description: Cell C82


title: Dmrt1 Mutant Granulosa Cell C84 (paired-end)

description: Cell C84


title: Dmrt1 Mutant Granulosa Cell C77 (paired-end)

description: Cell C77


title: Dmrt1 Mutant Granulosa Cell C79 (paired-end)

description: Cell C79


title: Dmrt1 Mutant Granulosa Cell C72 (paired-end)

description: Cell C72


title: Dmrt1 Mutant Granulosa Cell C73 (paired-end)

description: Cell C73


title: Dmrt1 Mutant Granulosa Cell C71 (paired-end)

description: Cell C71


title: Dmrt1 Mutant Granulosa Cell C74 (paired-end)

description: Cell C74


title: Dmrt1 Mutant Granulosa Cell C66 (paired-end)

description: Cell C66


title: Dmrt1 Mutant Granulosa Cell C65 (paired-end)

description: Cell C65


title: Dmrt1 Mutant Granulosa Cell C69 (paired-end)

description: Cell C69


title: Dmrt1 Mutant Granulosa Cell C67 (paired-end)

description: Cell C67


title: Dmrt1 Mutant Granulosa Cell C64 (paired-end)

description: Cell C64


title: Dmrt1 Mutant Granulosa Cell C63 (paired-end)

description: Cell C63


title: Dmrt1 Mutant Granulosa Cell C59 (paired-end)

description: Cell C59


title: Dmrt1 Mutant Granulosa Cell C62 (paired-end)

description: Cell C62


title: Dmrt1 Mutant Granulosa Cell C5 (paired-end)

description: Cell C5


title: Dmrt1 Mutant Granulosa Cell C57 (paired-end)

description: Cell C57


title: Dmrt1 Mutant Granulosa Cell C58 (paired-end)

description: Cell C58


title: Dmrt1 Mutant Granulosa Cell C53 (paired-end)

description: Cell C53


title: Dmrt1 Mutant Granulosa Cell C55 (paired-end)

description: Cell C55


title: Dmrt1 Mutant Granulosa Cell C56 (paired-end)

description: Cell C56


title: Dmrt1 Mutant Granulosa Cell C50 (paired-end)

description: Cell C50


title: Dmrt1 Mutant Granulosa Cell C44 (paired-end)

description: Cell C44


title: Dmrt1 Mutant Granulosa Cell C42 (paired-end)

description: Cell C42


title: Dmrt1 Mutant Granulosa Cell C52 (paired-end)

description: Cell C52


title: Dmrt1 Mutant Granulosa Cell C46 (paired-end)

description: Cell C46


title: Dmrt1 Mutant Granulosa Cell C47 (paired-end)

description: Cell C47


title: Dmrt1 Mutant Granulosa Cell C49 (paired-end)

description: Cell C49


title: Dmrt1 Mutant Granulosa Cell C43 (paired-end)

description: Cell C43


title: Dmrt1 Mutant Granulosa Cell C3 (paired-end)

description: Cell C3


title: Dmrt1 Mutant Granulosa Cell C37 (paired-end)

description: Cell C37


title: Dmrt1 Mutant Granulosa Cell C41 (paired-end)

description: Cell C41


title: Dmrt1 Mutant Granulosa Cell C2 (paired-end)

description: Cell C2


title: Dmrt1 Mutant Granulosa Cell C32 (paired-end)

description: Cell C32


title: Dmrt1 Mutant Granulosa Cell C33 (paired-end)

description: Cell C33


title: Dmrt1 Mutant Granulosa Cell C31 (paired-end)

description: Cell C31


title: Dmrt1 Mutant Granulosa Cell C36 (paired-end)

description: Cell C36


title: Dmrt1 Mutant Granulosa Cell C27 (paired-end)

description: Cell C27


title: Dmrt1 Mutant Granulosa Cell C28 (paired-end)

description: Cell C28


title: Dmrt1 Mutant Granulosa Cell C21 (paired-end)

description: Cell C21


title: Dmrt1 Mutant Granulosa Cell C22 (paired-end)

description: Cell C22


title: Dmrt1 Mutant Granulosa Cell C24 (paired-end)

description: Cell C24


title: Dmrt1 Mutant Granulosa Cell C75 (paired-end)

description: Cell C75


title: Dmrt1 Mutant Granulosa Cell C23 (paired-end)

description: Cell C23


title: Dmrt1 Mutant Granulosa Cell C20 (paired-end)

description: Cell C20


title: Dmrt1 Mutant Granulosa Cell C1 (paired-end)

description: Cell C1


title: Dmrt1 Mutant Granulosa Cell C19 (paired-end)

description: Cell C19


title: Dmrt1 Mutant Granulosa Cell C38 (paired-end)

description: Cell C38


title: Dmrt1 Mutant Granulosa Cell C18 (paired-end)

description: Cell C18


title: CA-CRTC-1S76A, S179A, rep3

city: Ann Arbor

first: Ana

middle: Rodrigues

last: Grant

state: MI

address: 100 Washtenaw Avenue

department: Computational Medicine & Bioinformatics

institute: University of Michigan

description:
TRA00009040
Poly-A selected RNA
Processed data file: WBM55norm.txt

data_processing:
Basecalls performed with CASAVA version 1.8.2.
Adapter sequences and poor quality bases (<20) were trimmed and filtered with CUTADAPT.
Reads (50b paired-end) were aligned to the Caernohadbitis elegans reference genome (ce6, WS238) using TopHat version 2.0.8 (Kim et al., 2013), with a median 35 million reads mapped in proper pairs.
The number of reads mapping to each gene was counted with htseq-count. Genes with less than 1 Count Per Million Reads (CPM) were discarded from further analysis. Counts were normalized for sequencing depth and RNA composition across all samples with edgeR. Genes were tested for differential expression between each mutant strain and wild-type using edgeR's glm method. For each comparison, genes with less than 5 CPM were filtered and those with at least 50% change and FDR of 1% or less were considered differentially expressed.
Genome_build: ce6
Supplementary_files_format_and_content: Tab-delimited text files with normalized expression measurements in all replicates for a strain.

organism: Caenorhabditis elegans

source_name: whole animals, WBM55

growth_protocol: Gravid adults grown at 20¡C on 100 mm NG plates seeded with OP50-1 E. coli were collected and treated with hypochlorite to release eggs. Eggs were incubated overnight in M9 media to obtain L1 synchronized populations. One thousand L1 larvae were grown on a 100 mm NG plate seeded with OP50-1 E. coli.

extract_protocol:
Worms were harvested for RNA extraction when L4 larval stage was reached. Animals were collected and washed extensively with M9 media to remove bacteria. Worms were then snap frozen in liquid nitrogen. RNA was extracted by five freeze/thaw cycles in Qiazol then purified by RNeasy mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.
RNA quality was checked using an Agilent Technologies 2100 Bioanalyzer. All samples had an RNA integrity number of 10. cDNA libraries were prepared from 4 μgs of total RNA using the TruSeq RNA Sample Preparation v2 kit (Illumina).
50-cycle paired-end sequencing was performed on an Illumina HiSeq 2000 by the Harvard Biopolymer Core.

tag: strain/background

value: CA-CRTC-1S76A, S179A

tag: developmental stage

value: L4 larva

value: whole body


title: N2, rep3

description:
TRA00009038
Poly-A selected RNA
Processed data file: N2norm.txt

source_name: whole animals, N2

tag: tissue


title: CA-AAK-2;CA-CRTC-1S76A, S179A, rep3

description:
TRA00009043
Poly-A selected RNA
Processed data file: WBM66norm.txt

source_name: whole animals, WBM66

tag: genotype/variation

value: CA-AAK-2;CA-CRTC-1S76A, S179A


title: CA-AAK-2;CA-CRTC-1S76A, S179A, rep2

description:
TRA00009037
Poly-A selected RNA
Processed data file: WBM66norm.txt


title: Dmrt1 Mutant Granulosa Cell C34 (paired-end)

description: Cell C34


title: CA-AAK-2, rep2

description:
TRA00009036
Poly-A selected RNA
Processed data file: WBM60norm.txt

source_name: whole animals, WBM60


title: CA-AAK-2, rep3

description:
TRA00009042
Poly-A selected RNA
Processed data file: WBM60norm.txt


title: N2, rep2

description:
TRA00009032
Poly-A selected RNA
Processed data file: N2norm.txt


title: N2, rep1

description:
TRA00009026
Poly-A selected RNA
Processed data file: N2norm.txt


title: Dmrt1 Mutant Granulosa Cell C26 (paired-end)

description: Cell C26


title: Dmrt1 Mutant Granulosa Cell C13 (paired-end)

description: Cell C13


title: CA-AAK-2, rep1

description:
TRA00009030
Poly-A selected RNA
Processed data file: WBM60norm.txt


title: Dmrt1 Mutant Granulosa Cell C11 (paired-end)

description: Cell C11


title: Dmrt1 Mutant Granulosa Cell C17 (paired-end)

description: Cell C17


title: Dmrt1 Mutant Granulosa Cell C16 (paired-end)

description: Cell C16


title: Dmrt1 Mutant Granulosa Cell C10 (paired-end)

description: Cell C10


title: CA-AAK-2;CA-CRTC-1S76A, S179A, rep1

description:
TRA00009031
Poly-A selected RNA
Processed data file: WBM66norm.txt


title: CA-CRTC-1S76A, S179A, rep1

description:
TRA00009028
Poly-A selected RNA
Processed data file: WBM55norm.txt


title: Dmrt1 Mutant Granulosa Cell C96 (single)

description: Cell C96


title: Dmrt1 Mutant Granulosa Cell C9 (single)

description: Cell C9


title: Dmrt1 Mutant Granulosa Cells (Bulk) (single)

description: Bulk


title: Dmrt1 Mutant Granulosa Cell C94 (single)

description: Cell C94


title: Dmrt1 Mutant Granulosa Cell C93 (single)

description: Cell C93


title: Dmrt1 Mutant Granulosa Cell C12 (paired-end)

description: Cell C12


title: Dmrt1 Mutant Granulosa Cell C92 (single)

description: Cell C92


title: Dmrt1 Mutant Granulosa Cell C89 (single)

description: Cell C89


title: Dmrt1 Mutant Granulosa Cell C87 (single)

description: Cell C87


title: CA-CRTC-1S76A, S179A, rep2

description:
TRA00009034
Poly-A selected RNA
Processed data file: WBM55norm.txt


title: Dmrt1 Mutant Granulosa Cell C84 (single)

description: Cell C84


title: Dmrt1 Mutant Granulosa Cell C75 (single)

description: Cell C75


title: Dmrt1 Mutant Granulosa Cell C73 (single)

description: Cell C73


title: Dmrt1 Mutant Granulosa Cell C77 (single)

description: Cell C77


title: Dmrt1 Mutant Granulosa Cell C82 (single)

description: Cell C82


title: Dmrt1 Mutant Granulosa Cell C74 (single)

description: Cell C74


title: Dmrt1 Mutant Granulosa Cell C7 (single)

description: Cell C7


title: Dmrt1 Mutant Granulosa Cell C78 (single)

description: Cell C78


title: Dmrt1 Mutant Granulosa Cell C72 (single)

description: Cell C72


title: Dmrt1 Mutant Granulosa Cell C69 (single)

description: Cell C69


title: Dmrt1 Mutant Granulosa Cell C67 (single)

description: Cell C67


title: Dmrt1 Mutant Granulosa Cell C62 (single)

description: Cell C62


title: Dmrt1 Mutant Granulosa Cell C71 (single)

description: Cell C71


title: Dmrt1 Mutant Granulosa Cell C65 (single)

description: Cell C65


title: Dmrt1 Mutant Granulosa Cell C64 (single)

description: Cell C64


title: Dmrt1 Mutant Granulosa Cell C5 (single)

description: Cell C5


title: Dmrt1 Mutant Granulosa Cell C63 (single)

description: Cell C63


title: Dmrt1 Mutant Granulosa Cell C59 (single)

description: Cell C59


title: Dmrt1 Mutant Granulosa Cell C56 (single)

description: Cell C56


title: Dmrt1 Mutant Granulosa Cell C91 (single)

description: Cell C91


title: Dmrt1 Mutant Granulosa Cell C58 (single)

description: Cell C58


title: Dmrt1 Mutant Granulosa Cell C57 (single)

description: Cell C57


title: Dmrt1 Mutant Granulosa Cell C50 (single)

description: Cell C50


title: Dmrt1 Mutant Granulosa Cell C55 (single)

description: Cell C55


title: Dmrt1 Mutant Granulosa Cell C52 (single)

description: Cell C52


title: Dmrt1 Mutant Granulosa Cell C79 (single)

description: Cell C79


title: Dmrt1 Mutant Granulosa Cell C47 (single)

description: Cell C47


title: Dmrt1 Mutant Granulosa Cell C49 (single)

description: Cell C49


title: Dmrt1 Mutant Granulosa Cell C46 (single)

description: Cell C46


title: Dmrt1 Mutant Granulosa Cell C43 (single)

description: Cell C43


title: Dmrt1 Mutant Granulosa Cell C66 (single)

description: Cell C66


title: Dmrt1 Mutant Granulosa Cell C3 (single)

description: Cell C3


title: Dmrt1 Mutant Granulosa Cell C42 (single)

description: Cell C42


title: Dmrt1 Mutant Granulosa Cell C37 (single)

description: Cell C37


title: Dmrt1 Mutant Granulosa Cell C33 (single)

description: Cell C33


title: Dmrt1 Mutant Granulosa Cell C44 (single)

description: Cell C44


title: Dmrt1 Mutant Granulosa Cell C27 (single)

description: Cell C27


title: Dmrt1 Mutant Granulosa Cell C41 (single)

description: Cell C41


title: Dmrt1 Mutant Granulosa Cell C28 (single)

description: Cell C28


title: Dmrt1 Mutant Granulosa Cell C26 (single)

description: Cell C26


title: Dmrt1 Mutant Granulosa Cell C38 (single)

description: Cell C38


title: Dmrt1 Mutant Granulosa Cell C24 (single)

description: Cell C24


title: Dmrt1 Mutant Granulosa Cell C53 (single)

description: Cell C53


title: Dmrt1 Mutant Granulosa Cell C36 (single)

description: Cell C36


title: Dmrt1 Mutant Granulosa Cell C22 (single)

description: Cell C22


title: Dmrt1 Mutant Granulosa Cell C31 (single)

description: Cell C31


title: Dmrt1 Mutant Granulosa Cell C34 (single)

description: Cell C34


title: Dmrt1 Mutant Granulosa Cell C20 (single)

description: Cell C20


title: Dmrt1 Mutant Granulosa Cell C1 (single)

description: Cell C1


title: Dmrt1 Mutant Granulosa Cell C21 (single)

description: Cell C21


title: Dmrt1 Mutant Granulosa Cell C17 (single)

description: Cell C17


title: Dmrt1 Mutant Granulosa Cell C2 (single)

description: Cell C2


title: Dmrt1 Mutant Granulosa Cell C13 (single)

description: Cell C13


title: Dmrt1 Mutant Granulosa Cell C19 (single)

description: Cell C19


title: Dmrt1 Mutant Granulosa Cell C18 (single)

description: Cell C18


title: Dmrt1 Mutant Granulosa Cell C16 (single)

description: Cell C16


title: Dmrt1 Mutant Granulosa Cell C10 (single)

description: Cell C10


title: Dmrt1 Mutant Female Replicate 2

source_name: 8-10 week Ovary

value: 8-10 week


title: Dmrt1 Mutant Granulosa Cell C32 (single)

description: Cell C32


title: Dmrt1 Mutant Female Replicate 1


title: WT Female Replicate 1


title: Dmrt1 Mutant Granulosa Cell C23 (single)

description: Cell C23


title: WT Male Replicate 1

source_name: 8-10 week Testis

value: Male

value: Testis


title: WT Male Replicate 2


title: P60 Cortex Zic ChIP-seq Rep 1

source_name: cerebral cortex

growth_protocol: All animals were housed in groups of 4-5, given access to standard laboratory chow and water ad libitum and housed in a humidity and temperature-controlled room on a 14/10h light/dark cycle.

extract_protocol:
Crosslinked material was sonicated with a Bioruptor (Diagenode) with 30 sec. on/off cycles to an average size range of 150-350bp as visualized by agarose gel electrophoresis. Sonicated supernatants were diluted 10-fold in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2mM EDTA, 16.7mM Tris pH 8.1, 167mM NaCl) before immunoprecipitation. 6uL antibody (anti-Zic 1/2 C-terminus, or total rabbit IgG, Millipore, Cat. #12-370) was first incubated with 100uL Dynabeads Protein G (Invitrogen) beads for 4 h. at 4°C, then the antibody conjugate was added to 6 mL of cell lysis for overnight IP. Standard TruSeq adapters were ligated for library preparation using the MicroPlex Library Preparation Kit (Diagenode).
C57BL/6Ncrl male and female mice at P7 or P60 were deeply anesthetized with isofluorane and decapitated for brain harvesting. The cerebellar cortex was dissected, dounced in 1% formaldehyde PBS buffer, incubated at room temperature for 15 minutes, washed 2x with cold PBS, and then lysed in 600 uL lysis buffer (1% SDS, 10mM EDTA, 50mM Tris pH 8.1). We pooled cerebellum or cortex from three P7 mice or two P60 mice for each biological replicate.

value: cerebral cortex

value: Postnatal day 60 (P60)

tag: antibody


title: P60 Cerebellum IgG Cntrl ChIP-seq Rep 1

source_name: whole cerebellum

value: whole cerebellum

value: total rabbit IgG, Millipore, Cat. #12-370


title: SCC-SCs mCherry Neg_Exp2

city: New York

first: Naoki

last: Oshimori

state: New York

address: 1230 York Avenue

institute: The Rockefeller University/HHMI

data_processing:
The raw reads were aligned using Tophat to the mm9 build of the mouse genome.
Cufflinks was used to assemble transcripts and determine differential expression with the Ensemble mRNA transcripts reference as a guide.
CummeRbund was used to analyze the data.
Genome_build: mm9
Supplementary_files_format_and_content: fpmk

source_name: Primary skin SCCs

extract_protocol:
RNA samples were prepared using Direct-zol RNA MiniPrep Kit (Zymo Research) per manufacturer's instructions.
Library was prepared using the Illumina TrueSeq mRNA sample preparation kit at the Weill Cornell Medical College Genomic Core Facility.

tag: expression

value: absence of TGF-beta signaling

value: C57BL/6 X FBV

value: Skin epidermis-derived SCC

value: TetO-Hras + LV-rtTA3-TGF-beta reporter


title: SCC-SCs mCherry Pos_Exp1

value: presence of TGF-beta signaling


title: SCC-SCs mCherry Pos_Exp2


title: SCC-SCs mCherry Neg_Exp1


title: P60 Cerebellum Input Cntrl ChIP-seq Rep 1

value: none (input)


title: P7 Cerebellum IgG Cntrl ChIP-seq Rep 1

value: Postnatal day 7 (P7)


title: P7 Cerebellum Input Cntrl ChIP-seq Rep 1


title: P7 Cerebellum Zic ChIP-seq Rep 2

description: Reference for anti-Zic antibody: Borghesani, P.R. et al. BDNF stimulates migration of cerebellar granule cells. Development 129, 1435-1442 (2002).

value: anti-Zic 1/2 C-terminus


title: P60 Cerebellum Zic ChIP-seq Rep 2


title: P60 Cerebellum Zic ChIP-seq Rep 1


title: Dmrt1 Mutant Granulosa Cell C11 (single)

description: Cell C11

value: Mixed

value: Female

value: Ovary


title: d7 Zic1 KD CGN RNA-seq Rep 1

source_name: cultured cerebellar granule neurons

extract_protocol:
2μg of total RNA was used for standard TruSeq library preparation with polyA selection
RNA was isolated from P7, P14, or P60 C57BL/6 mouse cerebellar cortex or cultured mouse CGNs using the Absolutely RNA kit (Agilent). For in vivo samples, RNA from at least two cerebellae was pooled for each biological replicate, and in culture a single litter constituted a biological replicate of cultured CGNs.

value: cultured cerebellar granule neurons

value: GNP + 7DIV


title: P7 Cerebellum Zic ChIP-seq Rep 1


title: WT Female Replicate 2

value: wild type

value: 8-10 week


title: d7 KD Cntrl CGN RNA-seq Rep 2


title: d7 Zic2 KD CGN RNA-seq Rep 2


title: d7 KD Cntrl CGN RNA-seq Rep 1


title: d7 + BDNF CGN RNA-seq Rep 1


title: Dmrt1 Mutant Granulosa Cell C12 (single)

description: Cell C12


title: d7 Zic1 KD CGN RNA-seq Rep 2


title: d7 + BDNF CGN RNA-seq Rep 2


title: d3 CGN RNA-seq Rep 3

value: GNP + 3 DIV


title: d3 CGN RNA-seq Rep 2

value: GNP + 3DIV


title: d7 CGN RNA-seq Rep 1


title: d0 CGN RNA-seq Rep 3

value: Granule Neuron Precursors (GNPs)


title: d7 CGN RNA-seq Rep 2


title: d3 CGN RNA-seq Rep 1


title: d7 CGN RNA-seq Rep 3


title: d0 CGN RNA-seq Rep 2


title: d0 CGN RNA-seq Rep 1


title: P14 Cerebellum RNA-seq Rep 2

value: whole cerebellum

value: Postnatal day 14 (P14)


title: P14 Cerebellum RNA-seq Rep 3


title: P60 Cerebellum RNA-seq Rep 1

value: Postnatal day 60 (P60)


title: P14 Cerebellum RNA-seq Rep 1


title: Liver DNase-seq Rep1

source_name: liver tissue

extract_protocol:
25-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Digestions were checked by pulse field gel electrophoresis and material was pooled from 3 different DNase concentrations (extent of digestion matched between samples) in equimolar amounts following blunt-ending reactions. This was followed by ligation to adapters, MmeI digestion, streptavidin bead-based enrichment, 14 cycles of PCR amplification, and separation from linker-only bands on a gel.
C57BL/6 adult female mice were sacked and liver dissected and stored in liquid nitrogen.  0.5-1.0g of frozen tissue (1-2 livers) was ground to fine powder in liquid nitrogen, resuspended in ice cold 20mL nuclei isolation buffer (NIB), filtered through Miracloth, spun down, resuspended in NIB with 0.5% Triton X-100, and centrifuged again to obtain nuclei pellet.

value: liver

value: Adult