title: Rela K.O.

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

description:
processed data file:
Rela.matrix.bgcorrected.deseqnorm_anno.txt

data_processing:
The samples were assessed for quality using FastQC. Trimmomatic version 0.33 was employed to trim reads after a quality drop below a mean of Q20 in a window of 5 nucleotides. Only reads above 30 nucleotides were cleared for further analyses. In order to normalize all samples to the same sequencing depth, 27 million reads per sample were randomly selected for further analysis. These were mapped versus the mm10 version of the mouse genome with STAR 2.4.2a using only unique alignments to exclude reads with unclear placing. The reads were further deduplicated using Picard 1.136 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format; http://broadinstitute.github.io/picard/) to avoid PCR artefacts leading to multiple copies of the same original fragment.
For Kindlin-2 samples the Macs2 peak caller version 2.1.0.20150731 was employed to identify peaks. The minimum qvalue was set to -1.5 and FDR was changed to 0.01. For Rela samples the MUSIC peakcaller (version from Dec. 2015) (Harmanci et al., MUSIC: identification of enriched regions in ChIP-Seq experiments using a mappability-corrected multiscale signal processing framework) was employed in punctate mode to accommodate for the range of peak widths typically expected for ATAC-seq. The maximum qvalue was set to 0.2 and the p-value normalization window length was changed to 1500. In order to determine thresholds for significant peaks, the data was manually inspected in IGV 2.3.52 (Robinson et al., Integrative Genomics Viewer). Peaks overlapping ENCODE blacklisted regions (known misassemblies, satellite repeats) were excluded.
In order to be able to compare peaks in different samples, the resulting lists of significant peaks were overlapped and unified to represent identical regions. After conversion of BAM files to BigWig format with deepTools bamCoverage (Ramirez et al., deepTools: a flexible platform for exploring deep-sequencing data), the counts per unified peak per sample were computed with BigWigAverageOverBed. Raw counts for unified peaks were submitted to DESeq2 for normalization (Anders et al., Differential expression analysis for sequence count data). Spearman correlations were produced to identify the degree of reproducibility between samples using R.
To permit a normalized display of samples in IGV, the raw BAM files were normalized for sequencing depth (number of mapped deduplicated reads per sample) and noise level (number of reads inside peaks versus number of reads not inside peaks). Two factors were computed and applied to the original BAM files using bedtools genomecov resulting in normalized BigWig files for IGV.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include library size normlized counts per peak

source_name: mouse fibroblasts

growth_protocol: cells were grown in Dulbecco's modified Eagle medium supplemented with 10% bovine calf serum (Hyclone, USA) and 50 U/ml penicillin and 50 μg/ml streptomycin (Sigma Aldrich, USA) at 37°C with 5% CO2.

extract_protocol: Cells were trypsinized and washed with PBS. Counting of cells was performed with MOXI Z Mini Automated Cell Counter Kit (Orflo) and 50.000 cells were used for ATAC Library preparation using Tn5 Transposase form Nextera DNA Sample Preparation Kit (Illumina). Cell pellet was resuspended in 50µl PBS annd mixed with 25µl TD-Buffer, 2.5µl Tn5, 0.5µl 10% NP-40 and 22µl water. Cell/Tn5 mixture was incubeated at 37°C for 30min with occasional snap mixing. Transposase treatment was followed by 30min incubation at 50°C together with 500mM EDTA pH8.0 for optimal recovery of digested DNA fragments. For neutralisation of  EDTA 100µl of 50mM MgCl2 was added followed by purification of the DNA fragments by MinElute PCR Purification Kit (Qiagen). Aplification of Library together with Indexing was performed as described elswere (Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. (2013) Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang & William J Greenleaf. Nature Methods. doi:10.1038/nmeth.2688). Libraries were mixed in equimolar ratios and sequenced on NextSeq500 platform using V2 chemistry.

tag: tissue source

value: embryo

tag: cell line

tag: cell type

value: mouse embryo fibroblast cell line

value: Rela K.O.

tag: passages


title: Rela wt

status: Public on Jan 17 2019

type: SRA

country: Germany

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: genotype/variation

value: Rela wt


title: Kindlin-2 K.O.

description:
processed data file:
K2.matrix.bgcorrected.deseqnorm_anno.txt

value: Kidney

value: mouse fibroblasts

value: Kindlin-2 K.O.


title: O6_iPS_b3

city: shanghai

first: You

last: Wu

address: 1239 siping road

department: school of life science and technology

country: China

institute: tongji university

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to hg19 reference genome using tophat v2.1.1 with default parameters.
Gene expression for each sample was quantified to FPKM using Cufflinks(v 2.2.1).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each transcript.

molecule: total RNA

organism: Homo sapiens

source_name: iPS cells

growth_protocol: The fibroblasts were cultured in Knockout DMEM supplemented with 10% fetal bovine serum, 1X nonessential amino acids, 1X GlutaMax, and 1X penicillin/streptomycin. Human iPSCs and ESCs were cultured on the Matrigel-coated plate with MEF-conditioned medium (MEF-CM) or on the CF1 feeder layer with hES medium consisted of DMEM/F12 supplemented with 20% knockout serum replacement, 1% NEAA, 1% GlutaMax, P/S, 100 μM 2-mercaptoethanol (Invitrogen), and 5 ng/ml bFGF. The MEF-CM was harvested after 24 hr incubation of hESC medium onto CF1 feeder cells, supplemented with additional 5 ng/ml bFGF and stored at -80 C until use. The MEF-CM was collected for 6 consecutive days.

extract_protocol:
The sorted TRA1-60+ cells during reprogramming were washed several times in 0.5% BSA-PBS (Sigma) solution and subsequently picked and transferred into lysate buffer by a mouth pipette with 50 cell for each tube.
The amplified cDNA was fragmented using Covaris sonicator (Covaris S220). To generate the sequence libraries, KAPA HyperPlus Library Preparation kit (KAPA KK8510) was used following the manufacturer’s instructions.

treatment_protocol: The reprogramming cells are digest to single cell and isolated by FACS analysis.APC anti-human CD13 , PE anti-human TRA-1-60  were used to obtain CD13- TRA-1-60+ cells for further analysis.

value: iPS cells

tag: time

tag: protocol

value: OCT6SKM reprogramming


title: shScrmbl_Replicate3

status: Public on Jan 18 2019

city: Boston

first: Michael

last: Wheeler

state: MA

address: 60 Fenwood Rd.

department: Neurology

country: USA

institute: Brigham and Women's Hospital

data_processing:
Reads were trimmed from 150bp to 50bp with Fastx (v0.0.13) fastx_trimmer.
Reads were aligned against the mm10 mouse genome with Bowtie (v2.3.0) in local mode with maximum fragment size 2000 (-X2000).
Alignments were sorted and filtered with SAMtools (v1.3.) to exclude reads with mapping quality <30, not properly aligned, aligned to the mitochondrial genome and/or aligned to ENCODE blacklist regions.
ATAC-Seq peaks were called for each replicate using MACS2 (v2.1.1).
Differential peaks were determined using DiffBind (v.2.6.1) for 600pb peak intervals and were selected with FDR<0.1.
Peaks were annotated using Bedtools (v2.26.0) closest.
Fold enrichment tracks were generated in MACS using bdgcmp and were visualized using IGV (v 2.3.59) and Sushi (v1.16.0).
Genome_build: mm10
Supplementary_files_format_and_content: Contains fold enrichment peaks provided by MACS2 bdgcmp

source_name: Flow cytometry sorted astrocytes

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by trypsinization, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, washed in PBS, and stained with primary antibodies for flow cytometry. Once cells were sorted, cells were pelleted, washed, and tagmented according to the ATAC-seq protocol (Buenrostro et al., Nature Methods 2013).
Nextera DNA Library Prep Kit

treatment_protocol: Induction of EAE in mice intracranially transduced with pLenti-Gfap-GFP-shScramble or pLenti-Gfap-GFP-shXbp1. EAE was induced by injecting 25 µg of MOG35-55 diluted in 100 µL of PBS emulsified in 100 µL of CFA per mouse.

tag: strain

value: WT

tag: lentivirus

value: pLenti-Gfap-GFP-shScramble

tag: Sex

value: Female

tag: age

tag: disease

value: EAE


title: O6_D16_4

source_name: reprogramming cells

value: TRA1-60+ reprogramming cells


title: O6_D16_2


title: O6_iPS_b1


title: O6_D16_3


title: BMAL_2

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

description: Bmalf/fxMrp8Cre neutrophils extracted at ZT5

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline.
Sequencing adaptor contaminations were removed from reads using cutadapt.
Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3.
Genome_build: Ensembl genebuild 76 (mouse assembly GRCm38).
Supplementary_files_format_and_content: matrix_table.xls file contains ENSEMBL gene Ids and TMM-Normalized counts per million for each sample.

molecule: polyA RNA

source_name: Neutrophils from blood

growth_protocol: SPF-kept mice, all donors were male  7-10 weeks of age.

extract_protocol:
Samples were amplified with the Ovation Single Cell kit (NuGen).
cDNA was prepared using the standard Ilumina TrueSeq RNAseq library preparation kit.

treatment_protocol: Freshly extracted blood samples were RBC-lysed and stained for Ly6G (1A8 clone) for sorting.

value: male

value: 7-10 weeks

tag: tissue

value: Blood

tag: genotype

value: BMALf/f x Mrp8Cre

tag: time of extraction


title: O6_D16_1


title: O6_D12_2


title: O6_D12_1


title: O6_D12_3


title: O6_D10_3


title: O6_D10_2


title: O6_D6_2


title: O6_D6_3


title: O6_D8_1


title: O6_D8_2


title: O6_D6_1


title: Kindlin-2 floxed

value: Kindlin-2 floxed


title: O6_D4_2


title: O6_iPS_b2


title: O6_D4_3


title: O4_D16_3

value: OCT4SKM reprogramming


title: O4_iPS_b3


title: O4_D16_2


title: O4_D12_2


title: O4_D12_3


title: O4_iPS_b2


title: O4_D16_1


title: O4_D10_2


title: O4_D10_1


title: O4_D8_b5


title: O4_D8_b3


title: O4_D8_b4


title: O4_D8_3


title: O4_D8_b2


title: O4_D8_2


title: O4_D8_1


title: O6_D4_1


title: O4_D6_3


title: O4_D6_b5


title: O4_D4_b1


title: O4_D6_b1


title: O4_D12_1


title: O4_D6_1


title: O4_D6_2


title: O4_D4_2


title: O4_D2_2


title: fib

source_name: fibroblast

value: fibroblast


title: O4_D2_1


title: O4_D4_1


title: oocyte_BCB_positive_3

city: Harbin

first: Zhi-Qiang

last: Du

address: 59 Mucai Street, XiangFang District

institute: Northeast Agricultural University

description:
single cell RNA-seq
15

data_processing:
Short reads were generated on the Illumina platform.
Clean reads were generated by removing low quality and adaptor sequence containing reads.
Clean reads were aligned to the Sscrofa10.2 genome assembly using BWA with default configurations.
After performing the assessment of sequence saturation and read distribution on reference genes, the expression levels of each gene were calculated as FPKM using the number of reads uniquely mapped to the specific gene and the total number of uniquely mapped reads in the sample using Cufflinks.
Genes and isoforms expression level are quantified by a software package: RSEM(RNASeq by Expectation Maximization).
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: text files containing gene and isoform expression levels.

organism: Sus scrofa

source_name: oocyte at geminal vesicle stage

growth_protocol: Pig ovaries were transported to the laboratory within 3 hours in a thermos bottle in physiological saline maintained at 30℃. Follicular fluid from 3- to 6-mm antral follicles were aspirated using an 18-gauge needle attached to a 10-ml disposable syringe. Cumulus-oocyte complexes (COCs) with at least three layers of intact cumulus cells and uniform ooplasm were selected for further procedure.

extract_protocol:
The whole oocyte lysate of three single BCB-negative (numbered as 1, 2 and 3) and three single BCB-positive (6, 7 and 15) oocytes without maturation culture were used to amplify and prepare the sequencing library as previously described (Tang et al., 2010).
The first-strand cDNA was synthesized from the whole oocyte lysate using the UP1 primer containing a 24-nt poly(dT) tail at the 3′end, which allowed all RNAs with poly(A) tails to be reverse transcribed. Then, the first-strand cDNA were amplified by PCR using hot start EX Taq and UP2 primer containing 24-nt poly(dT) at the 3′end to add a universal tail to the second-strand cDNA. Amplified cDNA were purified from gel and evaluated using Agilent’s Bioanalyzer (Agilent Technologies). The prepared cDNAs were sheared into fragments to use for preparation of deep-sequencing libraries. All libraries were sequenced with an Illumina HiSeq 2000 instrument in a single lane.

treatment_protocol: BCB-negative and BCB-positive oocytes were respectively denuded off cumulus cells by gentle vortexing in 0.1% hyaluronidase. Following four washes using DPBS containing 1% BSA, the zona pellucida of denuded oocytes was removed using pronase (0.5% in DPBS). The zona pellucida-free oocytes were washed three times in DPBS/1% BSA and then each single oocyte with minimal amount wash buffer (<0.5µL) was placed into 4.35µL cell lysis buffer in a 0.2mL tube using pulled glass pipette. The same volume of DPBS with 1% BSA wash buffer added into lysis buffer was used as negative control to ensure the absence of contamination. The collected single oocyte samples were stored at -80℃.

value: oocyte

tag: cell developmental stage

value: germinal vesicle

tag: bcb staining status

value: positive


title: oocyte_BCB_negative_3

description:
single cell RNA-seq
3

value: negative


title: oocyte_BCB_negative_2

description:
single cell RNA-seq
2


title: O4_D6_b4


title: isw1_isw2_rsc8_chd1_Rpb3_Input_B

status: Public on Jan 16 2019

city: Bethesda

first: Razvan

middle: V.

last: Chereji

state: Maryland

address: 6 Center Drive, Room 2A14

department: NICHD

institute: National Institutes of Health

description: Biological replicate 2

data_processing:
Sequencing data was aligned to the yeast genome (SacCer3) using Bowtie2 with default settings.
Occupancy profiles in bedGraph format were generated using bedtools.
For further analyses the aligned reads were size-selected as described in the article.
Genome_build: SacCer3
Supplementary_files_format_and_content: Nucleosomal or Rpb3 coverage in each strain/sample

organism: Saccharomyces cerevisiae

growth_protocol: GAL-Rsc8 containing strains were grown in synthetic complete (SC) medium containing 2% galactose and then switched to glucose. Rsc8-depleted cells were harvested when their growth reached a plateau after 7.5 hours. Wild-type cells and null mutants were grown to mid-log phase in SC medium containing 2% glucose.

extract_protocol:
In MNase-seq experiments, nuclei were prepared from unfixed yeast cells and then digested with Mnase. Mono-nucleosomal DNA was gel-purified (~150 bp) as described previously (Cole et al. 2012, PMID: 25348398; Ganguli et al. 2014, PMID: 25015381). In ChIP-seq experiments, cells were formaldehyde cross-linked before harvasting. The IP was performed with anti-Rpb3 antibody from Neoclone (cat: WP012, lot: A5081456)
The DNA was repaired using the DNA repair kit from New England Biolabs. The repaired DNA was processed for paired-end sequencing according to the Illumina protocol.

value: YJO493 (isw1D isw2D rsc8 chd1D)

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+ isw1-delta::ADE2 isw2-delta::LEU2 rsc8::KanMX-GALp-HA3-RSC8  chd1-delta::HIS5


title: isw1_isw2_rsc8_chd1_Rpb3_Input_A

description: Biological replicate 1


title: oocyte_BCB_positive_1

description:
single cell RNA-seq
6


title: rsc8_Rpb3_IP_B

description: Biological replicate 2

value: YPE468 (rsc8)

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+ rsc8::KanMX-GALp-HA3-RSC8

tag: chip antibody

value: anti-Rpb3 antibody

tag: chip antibody vendor

value: Neoclone

tag: chip antibody cat. #

tag: chip antibody lot #


title: rsc8_Rpb3_Input_B

description: Biological replicate 2

tag: genotype/variation


title: isw1_isw2_rsc8_chd1_Rpb3_IP_B

description: Biological replicate 2


title: rsc8_Rpb3_Input_A

description: Biological replicate 1


title: isw1_isw2_rsc8_chd1_B

description: Biological replicate 2

source_name: isw1_isw2_rsc8_chd1_nucleosome core particles (MNase)


title: rsc8_chd1_B

description: Biological replicate 2

source_name: rsc8_chd1_nucleosome core particles (MNase)

value: YJO494 (rsc8 chd1D)

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+ rsc8::KanMX-GALp-HA3-RSC8  chd1-delta::HIS5


title: rsc8_chd1_A

description: Biological replicate 1


title: isw2_rsc8_chd1_A

description: Biological replicate 1

source_name: isw2_rsc8_chd1_nucleosome core particles (MNase)

value: YJO492 (isw2D rsc8 chd1D)

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp-1 ura3-1 RAD5+ isw2-delta::LEU2 rsc8::KanMX-GALp-HA3-RSC8  chd1-delta::HIS5


title: isw2_rsc8_chd1_B

description: Biological replicate 2


title: isw1_isw2_rsc8_chd1_Rpb3_IP_A

description: Biological replicate 1


title: O4_D2_3

tag: cell type

value: TRA1-60+ reprogramming cells

tag: time


title: isw1_isw2_rsc8_chd1_A

description: Biological replicate 1

tag: strain


title: isw1_rsc8_chd1_B

description: Biological replicate 2

source_name: isw1_rsc8_chd1_nucleosome core particles (MNase)

value: YJO490 (isw1D rsc8 chd1D)

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+ isw1-delta::ADE2 rsc8::KanMX-GALp-HA3-RSC8  chd1-delta::HIS5


title: isw1_rsc8_chd1_A

description: Biological replicate 1


title: oocyte_BCB_positive_2

description:
single cell RNA-seq
7

value: oocyte


title: rsc8_B

description: Biological replicate 2

source_name: rsc8_nucleosome core particles (MNase)


title: oocyte_BCB_negative_1

description:
single cell RNA-seq
1

value: germinal vesicle


title: isw1_isw2_rsc8_B

description: Biological replicate 2

source_name: isw1_isw2_rsc8_nucleosome core particles (MNase)

value: YPE466 (isw1D isw2D rsc8)

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+ isw1-delta::ADE2 isw2-delta::LEU2, rsc8::KanMX-GALp-HA3-RSC8


title: isw2_rsc8_B

description: Biological replicate 2

source_name: isw2_rsc8_nucleosome core particles (MNase)

value: YPE464 (isw2D rsc8)

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+ isw2-delta::LEU2, rsc8::KanMX-GALp-HA3-RSC8


title: rsc8_A

description: Biological replicate 1

value: YPE468 (rsc8)


title: isw1_isw2_rsc8_A

description: Biological replicate 1


title: isw2_rsc8_A

description: Biological replicate 1


title: isw1_rsc8_B

description: Biological replicate 2

source_name: isw1_rsc8_nucleosome core particles (MNase)

value: YPE462 (isw1D rsc8)

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1ura3-1 RAD5+ isw1-delta::ADE2, rsc8::KanMX-GALp-HA3-RSC8


title: rsc8_Rpb3_IP_A

description: Biological replicate 1

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+ rsc8::KanMX-GALp-HA3-RSC8

value: anti-Rpb3 antibody

value: Neoclone


title: dim1_N5801_H3K9me3_ChIPseq

city: Colorado Springs

first: Andrew

middle: David

last: Klocko

state: Colorado

address: 278 Centennial Hall, 1420 Austin Bluffs Pkwy

department: Chemistry and Biochemistry

institute: University of Colorado Colorado Springs

description: genomic DNA ChIPseq libraries

data_processing:
To make the merged data files, the two replicate .fastq files were combined using the cat command; WT H3K9me3 ChIPseq replicate#1 dataset from GEO submission GSE68897.
To make ChIPseq enrichment files for display in Integrative Genomics Viewer (IGV, Robinson et al, 2011, Nat. Biotechnol.), reads were mapped with bowtie2 to the nc12-fixed genome (Galazka et al., 2016) using default parameters, and reads were converted to .bam files, sorted, and indexed. The .bam files (and the corresponding .bai index files) were counted with the "Count" command of igvtools, using the mean window function and 200bp windows. Output file was a .tdf file, displayable on IGV.
Genome_build: Neurospora crassa assembly 12 Fixed (files: neurospora_crassa_or74a_12_genome_FIXED.fasta, and neurospora_crassa_or74a_12_transcripts_FIXED.gtf; files are found in GEO submission GSE71024)
Supplementary_files_format_and_content: For ChIP-seq files: The tdf files were generated using the "count" function in igvtools (Integrative Genomics Viewer; Broad Institute, Robinson et al, 2011), using a window size of 200bp (.tdf files are binary files that shows enrichment peaks for each ChIP sample and have been processed for faster display of the data in IGV). The bcf files were produced from bam files (mapped to the Neurospora crassa assembly 12 Fixed by samtools), and report enrichment values.

organism: Neurospora crassa

source_name: germinated conidia

extract_protocol:
Cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 16 hours at 32oC. Mycelia were washed in PBS prior to crosslinking. Mycelia were cross-linked for 10 min in 0.5% formaldehyde for histone modification ChIP. Tissue added to ChIP lysis buffer (50mM Hepes pH 7.5, 90mM NaCl, 1mM EDTA, 1% triton + proteinase inhibitors) and was disrupted by sonication for thirty pulses before chromatin was sheared using a Bioruptor (Diagenode) for 15 min with a cycle of 30 sec on followed by 30 sec off, at high power. Lysates were cleared by centrifugation, 1/20th Input was saved, and histone modification antibody was added (typically 1uL) and samples were rotated overnight at 4oC. The next day, equilibrated Protein A or Protein G slurry (agarose or magnetic beads) was added to bind the antibody, incubated for 3 hours at 4oC, and washed twice in cold ChIP Lysis buffer, once with ChIP Lysis buffer + 0.5M NaCl, once with LiCl was buffer (10mM Tris pH 8.0, 250mM LiCl, 1mM EDTA, 0.5% NP40), and DNA/protein was eluted with TES buffer (50mM Tris pH 8.0, 10mM EDTA, 1% SDS) and incubated at 65oC. Samples (IP and input) were decrosslinked at 65oC overnight. The next day, samples were proteinase K treated for 2 hours at 50oC, and DNA was purified using the QIAquick PCR purification kit and eluted in 30 μl of water. Approximately 10 ng of DNA was used to generate ChIP-Seq libraries.
Each library was prepared using the NEB Next Library Preparation Kit (New England Biolabs, #E6040L) according to the manufacturer’s instructions, except custom oligos were used for barcoding (UO Genomics core facility; gc3f.uoregon.edu. “Invisible” fragments between 250-400 bp were excised and purified using the MinElute gel extraction kit (Qiagen, 28606). Final libraries were PCR-amplified using one cycle at 98 °C for 30 sec, 8 cycles at 98 °C for 10 sec, 60 °C for 30 sec and 72 °C for 30 sec and a final extension at 72 °C for 5 min.

value: germinated conidia

tag: antibody used


title: WT_N150_H3K9me3_ChIPseq

description: genomic DNA ChIPseq libraries


title: N1072_dim1-wg-seq

description: genomic DNA whole genome sequencing libraries

data_processing:
Library strategy: WGS
To begin, if data for the combined experiment (for both replicates) was to be analyzed, the replicate datasets were concatenated together with the "cat" command to make one .fastq file for each strain for each read direction (thus, two fastq files for each strain, since each paired-end experiment had R1 and R2 files; the combined files have the word "all" in the name). If the single replicates were to be analyzed independently, this step is omitted
To map the MNase-seq reads to the fixed version of the nc12 genome (Galazka et al)., paired end reads were mapped by bowtie with the following flags / parameters, per the protocols within the Nucwave program: "bowtie --suppress 1,6,7,8 -t --fr -p 6 -m 1 -v 2 -I 120 -X 180"; the -I and -X flags denote the distance between the two paired ends reads allowed for a mapped read pair to be recorded; the 120 to 180 basepair distance here is used to analyze only the mononucleosomes. The output file format is a .bowtie file.
The mapped paired-end read .bowtie file was run with the python program "nucwave_pe.py" with the "-w" flag to produce a .wig file. (instructions found at: http://nucleosome.usal.es/nucwave/, and are based on the manuscript:  "Luis Quintales, Enrique Vázquez and Francisco Antequera (2015) Comparative analysis of methods for genome-wide nucleosome cartography. Briefings in Bioinformatics 16: 576-587.")
To make ChIPseq enrichment files for display in Integrative Genomics Viewer (IGV, Robinson et al, 2011, Nat. Biotechnol.), reads were mapped with bowtie2 to the nc12-fixed genome (Galazka et al., 2016) using default parameters, and reads were converted to .bam files, sorted, and indexed.  The .bam files (and the corresponding .bai index files) were counted with the "Count" command of igvtools, using the mean window function and 200bp windows.  Output file was a .tdf file, displayable on IGV.
For Poly-A mRNA seq, high quality, adapter-less reads were identified (Stacks); Kmer filtering reduced sequencing errors. Reads were mapped (TopHat) to the modified Neurospora genome assembly 12, and sorted (SAMTools), and directionality-preserved read numbers were calculated at each gene ID (HTSeq), adding one read count to prevent abnormal fold changes. Differential gene expression analysis (DESeq) examined replicate differences and pair-wise analyses between WT and mutants.
For Bisulfite-seq files: The BRAT-BW software package (compbio.cs.ucr.edu/brat/; Harris et al, 2012) was used to prepare and map the reads to the N. crassa OR74A (annotation NC12) genome, which was converted to a four stranded reference genome to permit bisulfite mapping. BRAT-BW acgt-count “-B” option cytosine-only files produced for the forward and reverse strand reads were merged. The average 5mC level was determined for 25bp and 1bp  step-wise window size across the genome using the Methpipe program (http://smithlabresearch.org/software/methpipe/). The resulting file was renamed with a “.igv” file extension to allow display on the Integrated Genome Viewer (IGV; www.broadinstitute.org/igv/)
For Whole-genome-sequencing files: Single nucleotide polymorphisms (SNPs) in parental and dim-1 strains, relative to the Neurospora version 10 genome, were identified using Freebayes (Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907 [q-bio.GN] 2012), SNPs common between output vcf files were removed using vcf-isec within VCFtools (The Variant Call Format and VCFtools, Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A. Albers, Eric Banks, Mark A. DePristo, Robert Handsaker, Gerton Lunter, Gabor Marth, Stephen T. Sherry, Gilean McVean, Richard Durbin and 1000 Genomes Project Analysis Group, Bioinformatics, 2011 ), the genic mutations of SNPs were identified using SnpEFF ("A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92.), and those residing on LG III were filtered using SnpSift ("Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012.).
For whole genome sequencing to build a reference genome: fasta file was built by mapping reads to the Neurospora crassa genome, version 10, whereupon the resulting sam file was converted to a bam file and sorted, and the genome sequence determined by samtools mpileup tool with the "-uf" flag, and the output was viewed with the "-cg -" flags, and converted from a vcf file to a fastq, and edited in TextEdit to a fasta file.
Genome_build: Neurospora crassa assembly 12 Fixed (files: neurospora_crassa_or74a_12_genome_FIXED.fasta, and neurospora_crassa_or74a_12_transcripts_FIXED.gtf; files are found in GEO submission GSE71024)
Supplementary_files_format_and_content: For ChIP-seq files: The tdf files were generated using the "count" function in igvtools (Integrative Genomics Viewer; Broad Institute, Robinson et al, 2011), using a window size of 200bp (.tdf files are binary files that shows enrichment peaks for each ChIP sample and have been processed for faster display of the data in IGV). The bcf files were produced from bam files (mapped to the Neurospora crassa assembly 12 Fixed by samtools), and report enrichment values.
Supplementary_files_format_and_content: For RNA-seq files: the .txt files were generated by the program HTseq (using sequencing reads aligned to the Neurospora crassa assembly 12 Fixed genome with the program samtools). These HTseq.txt files report read number counts per gene for each replicate sample (two replicates total) from our four strains (WT N3752, delta set-7 N4718 and N4730, delta npf N4721, delta set-7;delta dim-5 N5916). The three Dataset.xls files were produced using the replicate HTseq.txt files in the program DESeq to determine genes that were differentially expressed > four fold and were significant (p < 0.05) in each mutant strain when compared to the WT N3752 reference expression datasets.
Supplementary_files_format_and_content: For MNase-seq files: The .wig files are single nucleotide resolution of the nucleosome signal enrichment (read in number of reads) genome-wide that have been smoothed with the Nucwave program.  Position .txt files for the nc12-fixed genome give the genome position, relative to each chromosome's left telomere, for either transcription start site (TSS) or the first nucleosome peak within that feature; position files are required as reference points to examine nucleosome position and enrichment changes.
Supplementary_files_format_and_content: For Bisulfite-seq files: .igv files displaying the % methylation over 25bp and 1bp windows where a score of 0 is a DNA region that has no cytosine methylation and a score of 1.0 is DNA where all of the cytosines are methylated in the region.  Values in between 0 and 1.0 represent partial methylation of a region.
Supplementary_files_format_and_content: For whole genome sequencing, the parental strain: the N200 strain, which is the parental strain, has a .fasta file that provides its genome sequence
Supplementary_files_format_and_content: For whole genome sequencing: the mutant strains have vcf files that detail the SNPs found in LGIII, what gene they are located in, and the subsequent change to the coding sequence.  These vcf files have intergenic and low-quality SNPs removed
Supplementary_files_format_and_content: For disiRNA-seq files: coordinates provided in GSE21175 were for the seventh version of the Neurospora genome. Data was downloaded and remapped to the nc12-fixed genome to make the .tdf file; the genome position coordinates for the Nc7 genome were reassigned to the locations in the nc12 version of the genome in the .bed file.

growth_protocol: Conidia flasks were inoculated and grown for 7-10 days, and subsequently used to inoculate an overnight 500mL culture grown 16 hours in Vogels medium and 1.5% sucrose. Cultures were harvested by Buchner funnel filtration, washed with dH2O, weighed, and frozen in liquid Nitrogen (LN2).

extract_protocol: Cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 48 hours at 32oC. Genomic DNA was isolated using a protocol modified from (Oakley et al, 1987). Whole genome sequencing was done with the Nextera kit (Illumina) following manufacturers’ protocol, except that after the PCR amplification step, libraries were purified using a Qiagen MinElute kit (PCR purification protocol), fragments between 350 – 550bp were size selected from a 2% TAE gel following gel electrophoresis, and final libraries were purified using a Qiagen MinElute kit (Gel Extraction protocol).

treatment_protocol: Frozen cultures were ground in a mortar and pestle kept cold with LN2, and resuspended with an equal volume (weight:volume) of Buffer A (1M sorbitol, 7% Ficoll, 20% Glycerol, 5mM Magnesium Acetate [MgAc2], 3mM CaCl2, 50mM Tris HCl pH7.5). Culture slurry was filtered through a cheesecloth funnel prewet with Buffer A.  Buffer B (10% Glycerol, 5mM MgAc2, 25mM Tris-HCl pH7.5) was added (2x the volume of buffer A) to the supernatant. Following overlaying of the solution on additional Buffer A:Buffer B solution (ratio 2.5:4), the supernatant containing cytoplasm and nuclei was centrifuged at 3000xg for 7 minutes in an HB-4 swinging bucket rotor at 4oC to pellet cell debris. Supernatant was overlaid onto ~1/7 total volume Buffer D (1M Sucrose, 10% Glycerol, 5mM MgAc2, 25mM Tris-HCl pH7.5), and centrifuged at 9400xg for 15 minutes in an HB-4 rotor. Supernatant was discarded and the pelleted nuclei were resuspended in Nuclei Storage Buffer (25% Glycerol, 5mM MgAc2, 0.1mM EDTA, 3mM DTT, 25mM Tris-HCl pH 7.5), flash frozen in LN2, and stored at -80°C for use in subsequent experiments.


title: N654het_dim1-wg-seq


title: N654microA_dim1-wg-seq


title: N5801_dim1-2_polyA_RNA

description: polyA+ RNAseq libraires

data_processing:
To begin, if data for the combined experiment (for both replicates) was to be analyzed, the replicate datasets were concatenated together with the "cat" command to make one .fastq file for each strain for each read direction (thus, two fastq files for each strain, since each paired-end experiment had R1 and R2 files; the combined files have the word "all" in the name). If the single replicates were to be analyzed independently, this step is omitted
To map the MNase-seq reads to the fixed version of the nc12 genome (Galazka et al)., paired end reads were mapped by bowtie with the following flags / parameters, per the protocols within the Nucwave program: "bowtie --suppress 1,6,7,8 -t --fr -p 6 -m 1 -v 2 -I 120 -X 180"; the -I and -X flags denote the distance between the two paired ends reads allowed for a mapped read pair to be recorded; the 120 to 180 basepair distance here is used to analyze only the mononucleosomes. The output file format is a .bowtie file.
The mapped paired-end read .bowtie file was run with the python program "nucwave_pe.py" with the "-w" flag to produce a .wig file. (instructions found at: http://nucleosome.usal.es/nucwave/, and are based on the manuscript:  "Luis Quintales, Enrique Vázquez and Francisco Antequera (2015) Comparative analysis of methods for genome-wide nucleosome cartography. Briefings in Bioinformatics 16: 576-587.")
To make ChIPseq enrichment files for display in Integrative Genomics Viewer (IGV, Robinson et al, 2011, Nat. Biotechnol.), reads were mapped with bowtie2 to the nc12-fixed genome (Galazka et al., 2016) using default parameters, and reads were converted to .bam files, sorted, and indexed.  The .bam files (and the corresponding .bai index files) were counted with the "Count" command of igvtools, using the mean window function and 200bp windows.  Output file was a .tdf file, displayable on IGV.
For Poly-A mRNA seq, high quality, adapter-less reads were identified (Stacks); Kmer filtering reduced sequencing errors. Reads were mapped (TopHat) to the modified Neurospora genome assembly 12, and sorted (SAMTools), and directionality-preserved read numbers were calculated at each gene ID (HTSeq), adding one read count to prevent abnormal fold changes. Differential gene expression analysis (DESeq) examined replicate differences and pair-wise analyses between WT and mutants.
For Bisulfite-seq files: The BRAT-BW software package (compbio.cs.ucr.edu/brat/; Harris et al, 2012) was used to prepare and map the reads to the N. crassa OR74A (annotation NC12) genome, which was converted to a four stranded reference genome to permit bisulfite mapping. BRAT-BW acgt-count “-B” option cytosine-only files produced for the forward and reverse strand reads were merged. The average 5mC level was determined for 25bp and 1bp  step-wise window size across the genome using the Methpipe program (http://smithlabresearch.org/software/methpipe/). The resulting file was renamed with a “.igv” file extension to allow display on the Integrated Genome Viewer (IGV; www.broadinstitute.org/igv/)
For Whole-genome-sequencing files: Single nucleotide polymorphisms (SNPs) in parental and dim-1 strains, relative to the Neurospora version 10 genome, were identified using Freebayes (Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907 [q-bio.GN] 2012), SNPs common between output vcf files were removed using vcf-isec within VCFtools (The Variant Call Format and VCFtools, Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A. Albers, Eric Banks, Mark A. DePristo, Robert Handsaker, Gerton Lunter, Gabor Marth, Stephen T. Sherry, Gilean McVean, Richard Durbin and 1000 Genomes Project Analysis Group, Bioinformatics, 2011 ), the genic mutations of SNPs were identified using SnpEFF ("A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92.), and those residing on LG III were filtered using SnpSift ("Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012.).
For whole genome sequencing to build a reference genome: fasta file was built by mapping reads to the Neurospora crassa genome, version 10, whereupon the resulting sam file was converted to a bam file and sorted, and the genome sequence determined by samtools mpileup tool with the "-uf" flag, and the output was viewed with the "-cg -" flags, and converted from a vcf file to a fastq, and edited in TextEdit to a fasta file.
Genome_build: Neurospora crassa assembly 12 Fixed (files: neurospora_crassa_or74a_12_genome_FIXED.fasta, and neurospora_crassa_or74a_12_transcripts_FIXED.gtf; files are found in GEO submission GSE71024)
Supplementary_files_format_and_content: For ChIP-seq files: The tdf files were generated using the "count" function in igvtools (Integrative Genomics Viewer; Broad Institute, Robinson et al, 2011), using a window size of 200bp (.tdf files are binary files that shows enrichment peaks for each ChIP sample and have been processed for faster display of the data in IGV). The bcf files were produced from bam files (mapped to the Neurospora crassa assembly 12 Fixed by samtools), and report enrichment values.
Supplementary_files_format_and_content: For RNA-seq files: the .txt files were generated by the program HTseq (using sequencing reads aligned to the Neurospora crassa assembly 12 Fixed genome with the program samtools). These HTseq.txt files report read number counts per gene for each replicate sample (two replicates total) from our four strains (WT N3752, delta set-7 N4718 and N4730, delta npf N4721, delta set-7;delta dim-5 N5916). The three Dataset.xls files were produced using the replicate HTseq.txt files in the program DESeq to determine genes that were differentially expressed > four fold and were significant (p < 0.05) in each mutant strain when compared to the WT N3752 reference expression datasets.
Supplementary_files_format_and_content: For MNase-seq files: The .wig files are single nucleotide resolution of the nucleosome signal enrichment (read in number of reads) genome-wide that have been smoothed with the Nucwave program.  Position .txt files for the nc12-fixed genome give the genome position, relative to each chromosome's left telomere, for either transcription start site (TSS) or the first nucleosome peak within that feature; position files are required as reference points to examine nucleosome position and enrichment changes.
Supplementary_files_format_and_content: For Bisulfite-seq files: .igv files displaying the % methylation over 25bp and 1bp windows where a score of 0 is a DNA region that has no cytosine methylation and a score of 1.0 is DNA where all of the cytosines are methylated in the region.  Values in between 0 and 1.0 represent partial methylation of a region.
Supplementary_files_format_and_content: For whole genome sequencing, the parental strain: the N200 strain, which is the parental strain, has a .fasta file that provides its genome sequence
Supplementary_files_format_and_content: For whole genome sequencing: the mutant strains have vcf files that detail the SNPs found in LGIII, what gene they are located in, and the subsequent change to the coding sequence.  These vcf files have intergenic and low-quality SNPs removed
Supplementary_files_format_and_content: For disiRNA-seq files: coordinates provided in GSE21175 were for the seventh version of the Neurospora genome. Data was downloaded and remapped to the nc12-fixed genome to make the .tdf file; the genome position coordinates for the Nc7 genome were reassigned to the locations in the nc12 version of the genome in the .bed file.

extract_protocol: Cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 16 hours at 32oC. Mycelia were harvested and added to a tube containing ~300uL glass beads (260-300 micrometer, acid washed [Sigma Aldrich] and resuspended in sdH2O), 350uL NETS buffer (10mM Tris pH 7.5, 300mM NaCl, 1mM EDTA, 0.2% SDS) and 350uL phenol:chloroform:isoamyl alcohol (25:24:1) and lysed by a bead beater for 10 minutes at room temperature. Samples were cleared by centrifugation, and the aqueous (top) phase was added to 650uL cold 100% EtOH.  Samples were precipitated at -20oC, pelleted by centrifugation, washed with 70% EtOH, and resuspended in DEPC-treated dH2O. RNA was treated with DNAse (DNA-free™ DNA Removal Kit, Thermo Fisher Scientific), cleaned (Agencourt® RNAclean XP® beads, Beckman Coulter), and RNA-seq libraries were prepared (KAPA Stranded mRNA-seq kit, KAPA Biosystems)


title: N5801_dim1-1_polyA_RNA

description: polyA+ RNAseq libraires


title: N5801_dim1_H3K27me2me3

description: genomic DNA ChIPseq libraries

extract_protocol: Cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 16 hours at 32oC. Mycelia were washed in PBS prior to crosslinking. Mycelia were cross-linked for 10 min in 0.5% formaldehyde for histone modification ChIP.  Tissue added to ChIP lysis buffer (50mM Hepes pH 7.5, 90mM NaCl, 1mM EDTA, 1% triton + proteinase inhibitors) and was disrupted by sonication for thirty pulses before chromatin was sheared using a Bioruptor (Diagenode) for 15 min with a cycle of 30 sec on followed by 30 sec off, at high power. Lysates were cleared by centrifugation, 1/20th Input was saved, and histone modification antibody was added (typically 1uL) and samples were rotated overnight at 4oC. The next day, equilibrated Protein A or Protein G slurry (agarose or magnetic beads) was added to bind the antibody, incubated for 3 hours at 4oC, and washed twice in cold ChIP Lysis buffer, once with ChIP Lysis buffer + 0.5M NaCl, once with LiCl was buffer (10mM Tris pH 8.0, 250mM LiCl, 1mM EDTA, 0.5% NP40), and DNA/protein was eluted with TES buffer (50mM Tris pH 8.0, 10mM EDTA, 1% SDS) and incubated at 65oC.  Samples (IP and input) were decrosslinked at 65oC overnight.  The next day, samples were proteinase K treated for 2 hours at 50oC, and DNA was purified using the QIAquick PCR purification kit  and eluted in 30 μl of water.  Approximately 10 ng of DNA was used to generate ChIP-Seq libraries.  Each library was prepared using the Illumina Tru-Seq kits A and B (Illumina, IP-202-1012 and IP-202-1024) according to the manufacturer’s instructions.  “Invisible” fragments between 250-400 bp were excised and purified using the MinElute gel extraction kit (Qiagen, 28606).  Final libraries were PCR-amplified using one cycle at 98 °C for 30 sec, 8 cycles at 98 °C for 10 sec, 60 °C for 30 sec and 72 °C for 30 sec and a final extension at 72 °C for 5 min.


title: N1634_dim1_bisulfite

description: genomic DNA Bisulfite-seq libraries

source_name: germinated condia

extract_protocol: Cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 48 hours at 32oC. Genomic DNA was isolated using a protocol modified from (Oakley et al, 1987).  Genomic DNA (50ng) was treated with bisulfite using the EZ DNA Methylation LightningTM kit (ZYMO Research) per the manufacturer's protocol. Bisulfite-Seq Libraries were prepared for sequencing using the EpiGnomeTM Methyl-Seq Kit (Epicentre cat #EGMK91324) and EpiGnomeTM Index PCR Primers (Epicentre cat# EGIDX81312), the library was purified with Agencourt AMPure XP beads (Beckman Coulter), quantified using a Qubit HS Assay (Life Technologies), visualized on the Fragment AnalyzerTM (Advanced Analytical), and sequenced on a Illumina HiSeq 2000

value: germinated condia


title: N5801_delta-dim1_H3K9me3

description: genomic DNA ChIPseq libraries


title: N5801-dim1-1_MNase

description: genomic DNA MNase-seq libraries

source_name: nuclei from germinated condia

extract_protocol:
For MNase digestion: Frozen nuclei in storage buffer were defrosted and resuspended in MNase digestion buffer (10mM Hepes-NaOH pH 7.5, 10mM KCl, 1.5mM MgCl2, 50ug/mL Bovine Serum Albumin, Filter sterilized; β-merceptoethanol [5mM final], pepstatin [10ug/mL final], leupeptin [10ug/mL final], and PMSF [1mM final] were added prior to use), and a DNA concentration was determined by removing a 10uL fraction, adding SDS to 1% to solubilize nuclear membranes, and quantified with a Qubit HS in triplicate, using the mean concentration. Nuclei containing 16ug of DNA were brought up to 400uL with MNase digestion buffer, CaCl2 was added to a final concentration of 2mM, and MNase (New England Biolabs) was added to a final concentration of 0.5U/uL, and the reaction was digested at 37oC for 20 minutes. At two minute intervals, 1.2ug of DNA (30uL) was removed and added to an eppendorf tube containing 10mM EGTA to stop the reaction, and stored on ice until all timepoints were removed. RNaseA (5ug) was added to all samples and digested an additional 10 minutes at 37oC, and SDS was added to a final concentration of 1% to solubilize the nuclear membrane. DNA was purified from timepoint samples with a Qiagen MinElute Kit, and either used for Southern blotting or sequencing.
For MNase-seq, the mono- and di-nucleosome populations, as well as the corresponding linker DNA, of two independent biological replicates of the 8 and 10 minute timepoints were pooled for sequencing, reasoning that at earlier time points, we would capture both the slower-digested euchromatic and rapidly-digested heterochromatic regions. While mono- and di-nucleosome populations were analyzed first (both independently and combined), only mono-nucleosomes were analyzed in all figures for simplicity. Libraries were constructed using the Illumina TruSeq kit, following the manufacturer’s protocols with the following modifications. After End Repair, DNA was purified using a Qiagen MinElute Kit, as recommended by Lombardi et al, 2015. Libraries containing mono- and di-nucleosomes (and the fragments in between these two prominent bands) were size selected with 2% TAE gel electrophoresis following an eight-cycle PCR amplification step; the average size of mono-nucleosomes was ~270bp, while the average size of di-nucleosomes was ~490bp.

value: nuclei from germinated condia


title: N5801-dim1-2_MNase

description: genomic DNA MNase-seq libraries


title: N3752-WT_all_MNase

description: genomic DNA MNase-seq libraries


title: mitochondria rep1

city: Beijing

first: Fei

last: Chen

address: NO.1 Beichen West Road, Chaoyang District

institute: Beijing Institute of Genomics

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for  low-quality sequence, then mapped to hg38 whole genome.
The unmapped reads were extracted to identify junction sites of circRNAs, which was performed with two common pipelines, CIRI and CIRCexploer, following the suggested parameters by their respective developers. Only when the circRNAs were both detected in the two replicates of each fraction, they were believed to be indeed translocated to these subcellular fractions
CircRNAs normalization were performed as the number of back-splice junction spanning reads per ten million clean reads (RPTM). Since the quantitation of CIRCexplorer and CIRI were consistent, we took the mean of the two algorithms in the two replicates as the abundances of the circRNAs. If the circRNA could be detected by only one algorithm, we just took the mean RPTM value hereof in the two replicates as its abundance.
Genome_build: GENCODE v23
Supplementary_files_format_and_content: Excel files include the expression levels of six fraction circRNAs, the back-spliced reads of each method and each repeats are also included.

extract_protocol:
Total RNAs from HepG2 cells and its subcellular fractions were extracted using RNAiso Plus reagent (9108, TaKaRa, Dalian, China), and those except for exosomal RNAs were treated with Ribo-Zero Gold rRNA Removal Kit (MRZG12324, Illumina) to remove ribosomal RNA before constructing RNA-seq libraries.
Strand-specific RNA-seq libraries were prepared using Next® Ultra™ Directional RNA Library Prep Kit for Illumina (E7420, NEB, MA, USA) following the manufacturer’s instructions. Library quality was determined on Bioanalyzer 2100 (Agilent Technologies, CA, USA).

tag: cell line

tag: fractions

value: mitochondria


title: cytosol rep1

value: cytosol


title: mitochondria rep2


title: exosome rep2

value: exosome


title: exosome rep1


title: ribosome rep2

value: ribosome


title: cytoplasm rep2

value: cytoplasm


title: N3752-WT-2_MNase

description: genomic DNA MNase-seq libraries


title: cytosol rep2


title: ribosome rep1


title: N3752-WT-1_MNase

description: genomic DNA MNase-seq libraries


title: nucleus rep2

value: nucleus


title: cytoplasm rep1


title: N5496_delta-dim1_Bisulfite

description: genomic DNA Bisulfite-seq libraries


title: isw1_rsc8_A

description: Biological replicate 1


title: nucleus rep1


title: TAG_N200-parental-wg-seq


title: cell rep2

value: cell


title: N5801-dim1_all_MNase

description: genomic DNA MNase-seq libraries


title: cell rep1


title: SSX-IP2

status: Public on Jan 15 2019

city: Regensburg

first: Gerhard

last: Lehmann

address: Universitaetsstrasse 31

department: Biochemistry 1

institute: University of Regensburg

data_processing:
Illumina MiSeq System, MiSeq Control Software 2.6.2.1, RTA 1.18.54
Demultiplexing of samples on experiment barcode (nt 4 to 7), custom script
Introducing the unique molecular identifier sequence (nt 1 to 3, 8 and 9) to the fastq headerline, custom script
Trimming of unique molecular identifier and experiment barcode: 9 nt from the 5’ end of the sequences, custom script
3’ adapters were trimmed using Cutadapt v1.6, all untrimmed reads were discarded
Reads mapping to ribosomal RNA were removed using bowtie v0.12.7 (unique rRNA sequences from UCSC main table browser: BDGP6)
The remaining reads were aligned to the Drosophila BDGP6/dm6 genome sequence using bowtie v0.12.7
Duplicate reads based on mapping position and unique molecular identifier were removed, custom script
Overlapping reads were counted using R Bioconductor package GenomicRanges v1.26.3 against TxDb.Dmelanogaster.UCSC.dm6.ensGene v3.3.0
Differential expression was calculated using R Bioconductor package DEseq2 v1.14.1 on groups of annotations (5'UTR, inronic, CDS, 3'UTR)
Peaks were scored using ASPeak v2.0.0 (Kucukural et al. 2013)
30 nt up- and downstream of each peak were retrieved for motif analysis using MEME v4.11.3
Genome_build: D. melanogaster Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6)
Supplementary_files_format_and_content: Excel spreadsheet: DESeq results
Supplementary_files_format_and_content: Html: MEME motifs on ASPeak called peaks

organism: Drosophila melanogaster

source_name: SL2 cells

extract_protocol:
Protocol according to König et al. (2010). iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. NatStructMolBiol 17: 909-915.
Protocol according to König et al. (2010). iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. NatStructMolBiol 17: 909-915.
Protocol according to König et al. (2010). iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. NatStructMolBiol 17: 909-915.

value: male, see Schneider's Drosophila Line 2 [D. Mel. (2), SL2] (ATCC CRL-1963)

tag: antibody

value: polyclonal Ssx-antibody, rabbit


title: SSX-IP1

description: Protocol according to König et al. (2010). iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. NatStructMolBiol 17: 909-915.


title: Ctrl-IP2

value: rabbit IgG


title: Ctrl-IP1


title: 12-gt-cre-321

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

country: United Kingdom

institute: Newcastle University

description: C57BL/6 wild type

data_processing:
Trimming - trimmomatic (v0.32). ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:12 TRAILING:1
Alignment - STAR (v2.5.2b).
Splicing Changes - MAJIQ
Gene counts - HTSEQ-count. -f bam -r name -s reverse -a 4 -i gene_id -m union
Genome_build: mm10
Supplementary_files_format_and_content: Count table (txt)

source_name: Testes

extract_protocol:
Testes were homogenized in RLTplus buffer from Qiagen before purification with the Rneasy kit. The RNA was then repurified with the kit before Dnase digestion.
Libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina), according to manufacturer's instructions. 75 bp paired-end reads were sequenced on a NextSeq 500.(Illumina).

treatment_protocol: [knockout protocol] None

value: wild type

tag: tissue

value: Testes


title: 8-gt-cre-279

description: C57BL/6 wild type

tag: genotype


title: 7-gt-cre-263

description: HnRNPGT Cre-Lox knockout

treatment_protocol: [knockout protocol] A targeting construct in which the Hnrnpgt open reading frame was flanked by LoxP sites was made using standard molecular biology techniques, and electroporated into ES129 cells (by Ozgene, Australia). Positive clones were injected into blastocyst to create chimaeras, and bred to yield agouti pups heterozygous for the targeted locus. The original mice containing the Neomycin gene (Figure 1B) were crossed to FlpE mice to remove the Neo gene and generate the HnrnpgtLoxP conditional allele (Figure 1C). Mice containing the HnrnpgtLoxP conditional allele were crossed with mice expressing PGKCre, resulting in deletion of the Hnrnpgt reading frame.

value: Hnrnpgt-/-


title: 11-gt-cre-320

description: HnRNPGT Cre-Lox knockout


title: GFP-flagIP 2

data_processing:
Illumina HiSeq
Trimming of Pico Input SMARTer Stranded Total RNA-Seq Kit Adapter: Trimmomatic headcrop 3 nt at the 5'-end of the forward read
Adapter clipping with Trimmomatic: ILLUMINACLIP:TruSeq_HT_PE.fa:2:30:15:2:true TRAILING:26 MINLEN:27
Aligment with Tophat2 against Drosophila_melanogaster.BDGP6.30 (Ensembl): option -library-type fr-secondstrand
Reads were summarized per gene using featureCounts (Rsubread, R-Bioconductor), annotation: Drosophila_melanogaster_BDGP6_30.gtf: option strandspecific 1
Differential enrichment of genes bound to Sxl and Ssx vs GFP were analysed using DESeq2 (R-Bioconductor)
Genome_build: ftp://ftp.ensemblgenomes.org/pub/release-30/metazoa/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.30.dna.genome.fa.gz
Supplementary_files_format_and_content: Excel spreadsheet: DESeq results, significantly upregulated genes

source_name: transfected SL2 cells

extract_protocol:
RNA extraction, rRNA depletion
Pico Input SMARTer Stranded Total RNA-Seq Kit (Clontech)
RNA-seq, paired-end 51 nt

tag: tag

tag: ip-antibody

value: anti-FLAG M2, mouse monoclonal


title: 010813 Adult Retina RNA

city: Cambridge

first: Aurora

last: Gomez-Duran

state: Cambridge

address: Welcome Trust/MRC Building

department: Department of Clinical Neurosciences

institute: Cambridge University

data_processing:
Trimming: Trimmomatic 0.3.5
Alignment: Star 2.5.2b
Counting: HTSeq-count 0.6.1
Differential expression analysis: DESeq2
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: Tab delimited raw counts and normalised counts

source_name: Adult Retina

extract_protocol:
Eyes or retinas were removed and stored in RNAlater, RNA was then extraxted using QIAGEN RNeasy kits as outlined in the manufacturer’s guidelines. RNA was then analysed for integrity and yeild before proceeding with library preparation.
Illumina TruSeq Stranded Total RNA Sample Prep Kit was used following the manufacturer’s guidelines.

value: Adult Retina

tag: post conception week

tag: developmental stage

value: Adult


title: Naïve KB5, rep3

city: Worcester

first: Dr Yvonne

last: Edwards

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

description:
untreated.CD8Tcell.rep3
Processed data file: mouse.gene.CD8Tcell.master_update_GEO_MATRIX.txt

data_processing:
Three independent libraries were examined for each condition. The cDNA libraries were sequenced using the Illumina Hi-Seq 2000 platform with a paired-end 50-bp format. Reads from each sample were aligned to the mouse genome (UCSC genome browser mm10 build) using TopHat2 (Kim et al., 2013). The expression value for each gene was summarized using BedTools to count the number of aligned reads overlapping with exons of any annotated splice isoform in the RefSeq database (Quinlan et al., 2010). Gene expression values were quantified as reads per kilobase of gene length per million mapped reads (RPKM). Differentially expressed genes were further calculated using the DESeq R package (Anders and Huber, 2010) with the read count of the longest isoform of each gene as the input.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: mouse.gene.CD8Tcell.master_update_GEO_MATRIX.txt: Tab-delimited text file includes counts of raw reads that mapped to reads.

source_name: Naïve KB5 CD8 T cells

extract_protocol:
RNA was recovered from the purified cells. Extraction of total RNA from cultured mouse embryonic fibroblasts was performed using the RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's instructions. DNA was eliminated by on-column RNase-free DNase treatment. RNA quality was verified (RNA integrity number >8.5) using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Messenger RNA was isolated, converted to cDNA, and amplified using the mRNA Purification Kit (Illumina, San Diego, CA) according to the manufacturer's instructions. An Illumina library was built and used to generate clusters on the Illumina flow cell according to the Illumina protocol and sequenced using a HiSeq 2000 (Illumina). Three independent libraries were examined for each condition.

treatment_protocol: For donor-specific transfusion (DST), mice were injected IV with 10 million C57BL/6 splenocytes. For anti-CD154, mice were injected IP with 0.5 mg of the antibody. For LPS, mice were injected IP with 100 ug. Spleens were recovered from treated mice at 12 hours post treatment and stained with antibodies against the KB5 TCR and CD8. Cells were sorted to a 95% purity level.

tag: strain/background

value: CBA/J

value: KB5 CD8 T cells

tag: treatment

value: untreated


title: Activated KB5 (DST), rep1

description:
DST.CD8Tcell.rep1
Processed data file: mouse.gene.CD8Tcell.master_update_GEO_MATRIX.txt

source_name: Activated KB5 CD8 T cells

value: H2b antigens from C57BL/6 mice


title: Naïve KB5, rep2

description:
untreated.CD8Tcell.rep2
Processed data file: mouse.gene.CD8Tcell.master_update_GEO_MATRIX.txt


title: Naïve KB5, rep1

description:
untreated.CD8Tcell.rep1
Processed data file: mouse.gene.CD8Tcell.master_update_GEO_MATRIX.txt


title: Activated KB5 (DST), rep2

description:
DST.CD8Tcell.rep2
Processed data file: mouse.gene.CD8Tcell.master_update_GEO_MATRIX.txt


title: Tolerized KB5 (DST+antiCD154), rep1

description:
DSTMR1.CD8Tcell.rep1
Processed data file: mouse.gene.CD8Tcell.master_update_GEO_MATRIX.txt

source_name: Tolerized KB5 CD8 T cells

value: H2b antigens from C57BL/6 mice + anti-CD154


title: 10-gt-cre-293

description: HnRNPGT Cre-Lox knockout


title: Tolerized KB5 (DST+antiCD154), rep3

description:
DSTMR1.CD8Tcell.rep3
Processed data file: mouse.gene.CD8Tcell.master_update_GEO_MATRIX.txt


title: Tolerized KB5 (DST+antiCD154), rep2

description:
DSTMR1.CD8Tcell.rep2
Processed data file: mouse.gene.CD8Tcell.master_update_GEO_MATRIX.txt


title: Inflamed KB5 (DST+antiCD154+LPS), rep3

description:
DSTMR1LPS.CD8Tcell.rep3
Processed data file: mouse.gene.CD8Tcell.master_update_GEO_MATRIX.txt

source_name: Inflamed KB5 CD8 T cells

value: H2b antigens from C57BL/6 mice + anti-CD154 + LPS


title: Inflamed KB5 (DST+antiCD154+LPS), rep2

description:
DSTMR1LPS.CD8Tcell.rep2
Processed data file: mouse.gene.CD8Tcell.master_update_GEO_MATRIX.txt


title: Inflamed KB5 (DST+antiCD154+LPS), rep1

description:
DSTMR1LPS.CD8Tcell.rep1
Processed data file: mouse.gene.CD8Tcell.master_update_GEO_MATRIX.txt


title: 9-gt-cre-288

description: C57BL/6 wild type


title: 12663 Foetal 10 Retina RNA

source_name: Foetal Retina

value: Foetal Retina


title: 230113 Adult Retina RNA


title: SSX-flagIP 2


title: 191115 Adult Retina RNA


title: SSX-flagIP 1


title: GFP-flagIP 1


title: 13172 Foetal 9 Retina RNA


title: 12xxx4 Foetal 9 Retina RNA


title: Activated KB5 (DST), rep3

description:
DST.CD8Tcell.rep3
Processed data file: mouse.gene.CD8Tcell.master_update_GEO_MATRIX.txt


title: SSX-flagIP 3


title: 13132 Foetal 8 Retina RNA


title: SXL-flagIP 1


title: 12410 Foetal 8 Retina RNA


title: SXL-flagIP 2


title: 12638 Foetal 8 Retina RNA


title: Input_ctrl


title: 12xxx3 Foetal 7 Retina RNA


title: 12xxx1 Foetal 7 Retina RNA


title: 13186 Foetal 6 Retina RNA


title: 12xxx5 Foetal 6 Retina RNA


title: 13149 Foetal 1 Retina RNA


title: 12774 Foetal 2 Retina RNA


title: 12552 Foetal 6 Retina RNA


title: 1940 Foetal 4 Retina RNA


title: 13159 Foetal 1 Retina RNA


title: 12xxx2 Foetal 7 Retina RNA


title: 12467 Foetal 5 Retina RNA


title: 1897 Embryonic CS22 Retina RNA

source_name: Embryonic Retina

value: Embryonic Retina


title: 12915 Foetal 5 Retina RNA


title: 12527 Embryonic CS20 Eye RNA

source_name: Embryonic Eye

value: Embryonic Eye


title: 12675 Embryonic CS18 Eye RNA


title: 12612 Embryonic CS18 Eye RNA


title: 12556 Embryonic CS16 Eye RNA


title: 12354 Embryonic CS14 Eye RNA


title: 921376_SJRHB010470_C10-Rh18-SUD-8h-rep2

status: Public on Jan 14 2019

city: Memphis

first: Timothy

middle: Isham

last: Shaw

state: TN

address: 262 Danny Thomas Pl

department: Computational Biology

institute: St Jude Children's Research Hospital

data_processing:
fastq files were mapped by STAR mapping.
HT-seq was used to produce the gene level read count using GENCODE annotation.
Genome_build: hg19

source_name: pediatric alveolar rhabdomyosarcoma

extract_protocol:
RNAs were extracted by Trizol (Invitrogen)
Poly-A enriched protocol was used to prepare the RNA library.

value: Human Rh18 RMS cell line

value: Sudemycin treated

tag: disease

value: pediatric alveolar rhabdomyosarcoma


title: 12301 Embryonic CS14 Eye RNA


title: 12773 Foetal 7 Retina RNA


title: 921373_SJRHB010470_C7-Rh18-DMSO-rep2

value: DMSO treated


title: 921372_SJRHB010470_C6-Rh18-DMSO-rep1


title: 921377_SJRHB010470_C11-Rh18-SUD-8h-rep3


title: 1901 Embryonic CS23 Eye RNA


title: 921374_SJRHB010470_C8-Rh18-DMSO-rep3


title: 13187 Embryonic CS22 Retina RNA


title: ovaRNAi_1

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

institute: NIBS

data_processing:
Illumina Casava1.8 software used for basecalling.
RNAseq sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to BDGP6 genome and Transposon elements sequence using STAR 2.5.2b with default parameters.
RPM (reads per million) was calculated for each transposon element.
Genome_build: Ensemble Drosophila melanogaster BDGP6
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample, and the distribution of abundance for small RNA samples.

extract_protocol:
RNA and library was prepared by following the manufacturer’s instructions
Libraries were prepared for sequencing using standard Illumina protocols

value: ova RNAi

tag: age

value: adult stage 5-7 days old

value: ovary


title: ovaRNAi_smallRNA


title: w1118_smallRNA

value: Wild type


title: ovaRNAi_2


title: w1118_3


title: ovaRNAi_3


title: Ly6Clow monocytes 16h_3_Pat

city: Montréal

first: Tarik

last: Moroy

state: Québec

address: 110 Avenue des Pins

country: Canada

institute: Institut de recherches cliniques de Montréal (IRCM)

data_processing:
Raw reads were trimmed with Trimmomatic v0.33 with the following parameters (PE -phred33 ILLUMINACLIP:adaptors.fa:2:30:10 TRAILING:30 MINLEN:36)
Trimmed reads were aligned with Tophat v.2.0.14 (using bowtie v.2.2.5) with default parameters
Transcript reconstruction was performed with Cufflinks v.2.21 using default parameters and UCSC mm10 annotation gtf.
Differential expression analysis was performed with Cuffdiff v.2.21 using default parameters
Genome_build: mm10
Supplementary_files_format_and_content: Differential expression analysis results with FPKM values, log2 fold change values, p-value and q-values.

source_name: Patrolling monocytes subtype

extract_protocol:
Total RNA was extracted from using TRI Reagent (Molecular Reasearch Center Inc, Cincinnati, OH, USA) according to the manufacturer’s instructions
Illumina RNA seq kit for sequence library preparation based on the Illumina TruSeq RNA Sample Preparation protocol was used

value: MDP


title: Ing5.Het1.Liver.RNAseq

city: Adelaide

first: Luke

middle: Thomas

last: Isbel

state: South Australia

address: 4 North Terrace, AHMS, Lvl 9

country: Australia

institute: SAiGENCI

data_processing:
For RNA-seq, sequenced reads were provided by the sequencing service provider (Australian Genome Research Facility) in a .fastq.gz format. Reads were mapped to the mouse mm9 genome using the program Tophat (version 2.0.11) with the following parameters: -I 100000 --library-type=fr-firststrand --read-edit-dist 3 --no-coverage-search --read-mismatches 3
For RNA-seq, read counts for gene exons were extracted using the program htseq-count (version 0.6.1) with the options "--idattr=gene_id --stranded=reverse -m intersection-strict". Normalization and differnetial gene expression was assessed using the R-package DEseq, with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: For processed RNA-seq data, the tab-delimited text file includes raw read counts for each of the samples

source_name: Ing5 Het1 Liver

extract_protocol:
Liver were removed from mice and flash frozen on dry ice, RNA was harvested using Trizol reagent. Libraries were constructed using the illumina TruSeq RNA Sample Preparation kit (cat Num RS-122-2201).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: FVB

value: Liver

value: 84 days post partum

tag: genotype/variation

value: Ing5 MommeD48/+


title: Ing5.Het3.Liver.RNAseq

source_name: Ing5 Het3 Liver


title: Ing5.WT1.Liver.RNAseq

source_name: Ing5 WT1 Liver


title: Ly6Clow monocytes 16h_2_Pat


title: Ing5.WT2.Liver.RNAseq

source_name: Ing5 WT2 Liver


title: Ing5.WT3.Liver.RNAseq

source_name: Ing5 WT3 Liver


title: Ing5.Het2.Liver.RNAseq

source_name: Ing5 Het2 Liver


title: crwn1 crwn2

city: Norwich

first: Pawel

last: Mikulski

address: Colney Lane

department: CDB

institute: John Innes Centre

data_processing:
2 x90bp paired-end raw sequencing reads were scored by quality, cleaned and trimmed from 5’ and 3’ends in Trimmomatic v0.35 and FastQC v0.10. Clean reads were aligned to TAIR10 reference genome by TopHat v2.0.12 with mate inner distance (-r ) = 20bp, segment length = 30bp  and minimal intron length (-i) = 20bp, according to: (Trapnell et al., 2009). Alignment files were processed in two different pipelines: 1) Cufflinks (Tuxedo protocol, (Trapnell et al., 2013)) and 2) EdgeR (Robinson et al., 2010). 1) FPKM values from mapped reads were calculated in Cufflinksv2.2.1 with enabled: reference annotation (-g), multi read correction (-u), fragment bias correction (-b) and minimal intron length set to 20 bp. Cufflinks output was used to create common transcript reference file in Cuffmerge v2.2.1.0 and perform DEG analysis in Cuffdiff v2.2.1 with multi read correction and fragment bias correction. 2) Mapped reads were transformed into counts using HTSeq v0.6.1 and used as input for edgeR v3.3. Features with less than 1 count per mln were discarded. For remaining features differential expression was computed with adjusted p-values <0.05. DEG analysis in either of pipelines concerned comparison between wildtype and mutant (pwo1 or crwn1/2) samples.  In order to ensure the stringency of the analysis, only those genes that were present in DEG lists from both pipelines were taken for subsequent steps.
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: Excel file with FPKM values obtained from Cufflinks v2 pipeline and counts obtained from Htseq + DiffBind v2 softwares for the genes scored as differentially expressed between wildtype and respective mutant by both pipelines.

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: Seeds of respective genotypes were sterilzed, then stratified for 2 days and sown to Petri dishes containing MS medium. Seedlings were grown vertically in long-day conditions.

extract_protocol:
Material was harvested at 2 week-old seedling stage. RNA was isolated according to Rneasy Plant Mini Prep Kit (Qiagen)
According to TruSeq RNA Library Prep Kit v2 (Illumina)

value: whole seedling

value: 14 day-old seedlings

value: crwn1 crwn2


title: pwo1


title: w1118_2


title: Col

value: Col-0 (wildtype)


title: Ly6Clow monocytes 16h_1_Pat


title: 12878 Embryonic CS14 Eye RNA

value: Embryonic Eye


title: 921375_SJRHB010470_C9-Rh18-SUD-8h-rep1

value: Human Rh18 RMS cell line

value: Sudemycin treated


title: Ly6Clow monocytes Naive_3_Pat

value: Placebo


title: w1118_1


title: lacI-HP1a_uas-ova_H3K4me2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to BDGP6 genome using Bowtie v1.1.2 with -v 3 -m 1 parameters.
Peaks were called using MACS version 1.4.2 with default parameters.
Genome_build: Ensemble Drosophila melanogaster BDGP6.
Supplementary_files_format_and_content: bigwig files were generated using Homer package.

extract_protocol:
Drosophila DamID was carried out according to iDamIDseq based on a method from Gutierrez-Triana JA et al.2016
Libraries were prepared for sequencing using standard Illumina protocols

tag: chip antibody

value: H3K4me2 (Abcam, ab7766)


title: Ly6Clow monocytes Naive_2_Pat

tag: strain


title: Ly6Clow monocytes Naive_1_Pat


title: lacI-HP1a_uas-ova_input

value: adult stage 5-7 days old


title: lacI-HP1a_H3K4me2

value: ovary


title: Ly6Chigh monocytes 16h_3_Infl

source_name: Inflammatory monocytes subtype


title: Ly6Chigh monocytes 16h_1_Infl


title: Ly6Chigh monocytes 16h_2_Infl


title: Ly6Chigh monocytes Naive_3_Infl


title: lacI-HP1a_input


title: lacO_input

value: lacO-GFP


title: ovaRNAi_polII

value: ova RNAi

value: polll (Abcam, ab817)


title: lacO_H3K4me2


title: ovaRNAi_H3K4me2


title: w1118_polII

value: Wild type


title: w1118_input


title: w1118_H3K4me2


title: ovaRNAi_input


title: Sample_LEPC_miR-93-5p_mutation_interact_mRNA

status: Public on Jan 12 2019

city: Shanghai

first: Ke

middle: Ai

state: Shanghai

address: 138 Yixueyuan Road

department: Liver Cancer Institute

institute: Zhonghai Hospital

data_processing:
RNA-Seq
Illumina Casava1.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using tophat2 with defalt parameters.
transciptome assemblied by cufflinks and differential expressed genes were identified by cuffdiff.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each genes.
ChIP-Seq
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie under default parameters.
peaks were called using MACS14 with the defalt parameters.
Genome_build: mm9
Supplementary_files_format_and_content: bed files include ChIP-seq peaks list;bedGraph files include the averaged ChIP-seq density.

source_name: LEPC cell line

growth_protocol: Mouse LEPCs cell line was maintained in Dulbecco’s modiﬁed MEM medium (DMEM) (Gibco, Gaithersburg, MD) supplemented with 10% FBS, 100 U/ml penicillin, and 0.1 mg/ml streptomycin.

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

tag: passages

value: overexpress miR-93-5p mutant


title: Sample_LEPC_Control_RNA-seq

value: scr


title: Ly6Chigh monocytes Naive_1_Infl


title: Sample_LEPC_OE-miR-93-5p_RNA-seq

value: overexpress miR-93-5p


title: Sample_LEPC_OE-miR-93-5p_Input

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.


title: Sample_LEPC_OE-miR-93-5p_H3K9me3

value: H3K9me3 (Abcam, ab8898)


title: Sample_LEPC_OE-miR-93-5p-mutation_RNA-seq


title: Sample_LEPC_miR-93-5p_interact_mRNA


title: Sample_LEPC_control_miRNA_interact_mRNA


title: Sample_LEPC_OE-miR-93-5p_H3K4me3


title: Sample_LEPC_Control_Input


title: Sample_LEPC_Control_H3K9me3


title: Sample_LEPC_Control_H3K4me3


title: Sample_LEPC_Control_H3K27me3


title: Ly6Chigh monocytes Naive_2_Infl


title: HCT116 Input

city: Xiamen

first: Min

last: Liu

state: Fujian

address: Rm.214, Bldg. Chaoyang Huang, Xiamen University-Xiang'an Campus

department: School of Life Sciences

institute: Xiamen University

description: ChIP antibody: None

data_processing:
Base-calling were performed by RiboBio Co. Ltd. （Guangzhou,China).
Raw ChIP-seq reads were trimmed for adaptor sequences and retained 46bp from the 3'-end.
Reads were then mapped to human genome (GRCh37/hg19) using Bowtie 1.1.1 (Langmead et al., 2009) with 3-mismatches.
Enriched Pol II binding peaks were identified and then annotated by HOMER v4.7 with default settings (Heinz et al., 2010; Wang et al., 2011a).
Genome_build: hg19
Supplementary_files_format_and_content: Bed files were generated by tagDir2bed.pl, which is converted from Homer tag file directories.

source_name: HCT116 cells - input

growth_protocol: HCT116 cells were maintained in McCoy's 5A medium (Sigma), supplemented with 10% FBS and 1xPSK (Gibco).

extract_protocol:
The nuclei were incubated with Micrococcal Nuclease (MNase) (10 μg DNA per 1 unit MNase) to digest genomic DNA to the optimal length (1-2 nucleosomes), followed by sonication to break the nuclear membrane, with the presence of 0.1% SDS. ChIP was performed with anti-Rpb1(Pol II) antibody.
Libraries were constructed by RiboBio Co. Ltd. （Guangzhou,China).

tag: cell type

value: Colon Cancer Cells

tag: cell line


title: shAFF4-HMBA

description: ChIP antibody: Rpb1 (Santa Cruz, sc-899X)

source_name: HCT116 cells - shAFF4 - HMBA


title: shGFP-HMBA

source_name: HCT116 cells - shGFP - HMBA


title: shBrd4-HMBA

source_name: HCT116 cells - shBrd4 - HMBA


title: shGFP-control

source_name: HCT116 cells - shGFP - control


title: Red1 ChIP for ndt80Δ T=6  rep2

status: Public on Jan 10 2019

city: New York

first: Andreas

last: Hochwagen

state: NY

address: 1009 Silver Center 100 Washington Square East

institute: New York University

description:
processed data file:
AH6179Red1T6rep-322-430-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph.gz

data_processing:
Illumina output reads were processed as described in (Paul et al., 2017). The reads were mapped to SK1 genome (Yue et al., 2017) using Bowtie (Langmead et al., 2009). Only reads that mapped to a single position and also matched perfectly to the SK1 genome were retrieved for further analysis.
3' ends of the reads were extended to a final length of 200bp using MACS2 2.1.1 (https://github.com/taoliu/MACS) and probabilistically determined PCR duplicates were removed. The input and ChIP pileups were SPMR-normalized (signal per million reads) and fold-enrichment of ChIP over input data was used for further analyses.
The input and ChIP pileups were SPMR-normalized (signal per million reads) and fold-enrichment of ChIP over input data was used for further analyses.
Bedgraph files were created from pooled replicates.
Genome_build: SK1 (Yue et al., 2017)
Supplementary_files_format_and_content: Bedgraph

source_name: Red1 ChIP for ndt80Δ T=6

growth_protocol: Synchronous meiosis was performed by first innoculating strains at OD600 = 0.3 in BYTA medium and grown for 16.5 hours at 30°C. Then cells were washed twice with sterile water and resuspended into SPO medium at OD600 = 2.0 at 30°C (details are described in (Blitzblau et al., 2012)).

extract_protocol:
25 ml of the meiotic cells were collected at different time points and fixed for 30 min in 1% formaldehyde. The formaldehyde was quenched with 125 mM glycine. Samples were processed as described in (Blitzblau et al., 2012).
Libraries for ChIP sequencing were prepared by PCR amplification with TruSeq adaptors (Illumina) as described in (Sun et al., 2015). Quality of the libraries was checked on 2100 Bioanalyzer or 2200 Tapestation. Libraries were quantified using qPCR prior to pooling. The ChIP libraries were sequenced on Illumina HiSeq 2500 or NextSeq 500 instruments at NYU Biology Genomics core to yield 50 or 51 bp single-end reads.

tag: meiotic time point

value: 6 hour


title: ndt80Δ T=3 input for Red1 rep2

description:
processed data file:
AH6179Red1T3rep-321-428-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph.gz

source_name: ndt80Δ T=3 input for Red1

value: 3 hour


title: Red1 ChIP for ndt80Δ T=3  rep2

source_name: Red1 ChIP for ndt80Δ T=3


title: spo11Δ ndt80Δ T=6 input for pH2A ChIP rep1

description:
processed data file:
AH6214pH2AT6rep-432-434-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph.gz

source_name: spo11Δ ndt80Δ T=6 input for pH2A ChIP


title: spo11Δ ndt80Δ T=6 input for pH2A ChIP rep2


title: pH2A ChIP for spo11Δ ndt80Δ T=6  rep2

source_name: pH2A ChIP for spo11Δ ndt80Δ T=6


title: pH2A ChIP for spo11Δ ndt80Δ T=6  rep1


title: Sample_LEPC_OE-miR-93-5p_H3K27me3

last: Wu

tag: antibody


title: Mek1 ChIP for ndt80Δ T=3  rep2

description:
processed data file:
AH6179Mek1T3rep-117-423-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph.gz

source_name: Mek1 ChIP for ndt80Δ T=3

tag: genotype


title: Rad51 ChIP for ndt80Δ T=8  rep2

description:
processed data file:
AH7137AH7121Rad51T8rep-360-362-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph.gz

source_name: Rad51 ChIP for ndt80Δ T=8

value: 8 hour


title: ndt80Δ T=8 input for Rad51 ChIP rep2

source_name: ndt80Δ T=8 input for Rad51 ChIP


title: Rad51 ChIP for ndt80Δ T=8  rep1


title: ndt80Δ T=3 input for Mek1 rep2

source_name: ndt80Δ T=3 input for Mek1


title: pH2A ChIP for ndt80Δ T=6  rep1

description:
processed data file:
AH6179pH2AT6rep-346-350-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph.gz

source_name: pH2A ChIP for ndt80Δ T=6


title: ndt80Δ T=6 input for pH2A ChIP rep2

source_name: ndt80Δ T=6 input for pH2A ChIP


title: ndt80Δ T=6 input for Mek1 rep2

description:
processed data file:
AH6179Mek1T6rep-120-425-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph.gz

source_name: ndt80Δ T=6 input for Mek1


title: Mek1 ChIP for ndt80Δ T=6  rep2

source_name: Mek1 ChIP for ndt80Δ T=6


title: ndt80Δ T=8 input for Rad51 ChIP rep1


title: Hop1 ChIP for wild type T=4 input rep2

description:
processed data file:
AH574Hop1T4rep-336-342-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph.gz

source_name: Hop1 ChIP for wild type T=4 input

value: 4 hour


title: wild type T=4 input rep2

source_name: wild type T=4 input


title: shAFF1&4-HMBA

source_name: HCT116 cells - shAFF1&4 - HMBA


title: pH2A ChIP for ndt80Δ T=6  rep2


title: ndt80Δ T=6 input for Red1 rep2

source_name: ndt80Δ T=6 input for Red1


title: Hop1 ChIP for wild type T=3 input rep2

description:
processed data file:
AH574Hop1T3rep-334-340-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph.gz

source_name: Hop1 ChIP for wild type T=3 input


title: wild type T=3 input re2

source_name: wild type T=3 input re2


title: Hop1 ChIP for wild type T=2 input rep2

description:
processed data file:
AH574Hop1T2rep-332-338-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph.gz

source_name: Hop1 ChIP for wild type T=2 input

value: 2 hour


title: Red1 ChIP for ndt80Δ T=3  rep1

source_name: Red1 ChIP for ndt80Δ T=3


title: ndt80Δ T=6 input for Red1 rep1


title: Red1 ChIP for ndt80Δ T=6  rep1

source_name: Red1 ChIP for ndt80Δ T=6


title: Hop1 ChIP for wild type T=4 input rep1


title: wild type T=4 input rep1


title: Zip1 ChIP for ndt80Δ T=6 rep2

description:
processed data file:
AH6179Zip1T6rep-306-305-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph.gz

source_name: Zip1 ChIP for ndt80Δ T=6

value: anti-Zip1 (abcam y300)


title: ndt80Δ T=6 input for pH2A ChIP rep1


title: wild type T=2 input rep2

source_name: wild type T=2 input


title: ndt80Δ T=6 input for Zip1

source_name: ndt80Δ T=6 input for Zip1


title: wild type T=2 input rep1


title: wild type T=3 input rep1

source_name: wild type T=3 input


title: Zip1 ChIP for ndt80Δ T=6 rep1

value: anti-Zip1 (abcam yC-19)


title: Hop1 ChIP for pch2Δ ndt80Δ T=6 input rep1

description:
processed data file:
AH6639Hop1T6rep-227-217-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph.gz

source_name: Hop1 ChIP for pch2Δ ndt80Δ T=6 input


title: Hop1 ChIP for ndt80Δ T=6 input rep2

description:
processed data file:
AH6179Hop1T6rep-121-215-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph.gz

source_name: Hop1 ChIP for ndt80Δ T=6 input


title: pch2Δ ndt80Δ T=6 input rep1

source_name: pch2Δ ndt80Δ T=6 input


title: Hop1 ChIP for wild type T=3 input rep1


title: Hop1 ChIP for pch2Δ ndt80Δ T=6 input rep2


title: pch2Δ ndt80Δ T=6 input rep2


title: Hop1 ChIP for wild type T=2 input rep1


title: ndt80Δ T=3 input for Red1 rep1

source_name: ndt80Δ T=3 input for Red1


title: ndt80Δ T=3 input rep2

description:
processed data file:
AH6179Hop1T3rep-118-214-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph.gz

source_name: ndt80Δ T=3 input


title: Hop1 ChIP for ndt80Δ T=3 input rep2

source_name: Hop1 ChIP for ndt80Δ T=3 input


title: Mek1 ChIP for ndt80Δ T=6 input rep1

source_name: Mek1 ChIP for ndt80Δ T=6 input


title: Hop1 ChIP for ndt80Δ T=6 input rep1


title: Hop1 ChIP for ndt80Δ T=3 input rep1


title: Mek1 ChIP for ndt80Δ T=3 input rep1

source_name: Mek1 ChIP for ndt80Δ T=3 input


title: ndt80Δ T=3 input rep1

description:
processed data file:
AH6179Hop1T3rep-118-214-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph.gz
AH6179Mek1T3rep-117-423-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph.gz


title: RNAseq_polyA_Cortex.e18.5_wildtype_3

status: Public on Jan 09 2019

first: Yuhki

last: Saito

address: 1230 York avenue

institute: The Rockefeller University

description:
processed data:
mm10.IR.265.xlsx

data_processing:
alignment with Olego or kallisto
inference of exon junctions (Bayesian method)
RNA abundance analysis (edgeR) and alternative splicing events analysis (Quantas)
Genome_build: mm10
Supplementary_files_format_and_content: file containing gene symbol, log2 fold change, pValue FDR, chr number, start and end positon, strand, dI, TPM

source_name: Cortex

growth_protocol: Mouse brain or spinal cord tissue from Nova2-cKO or wild-type mice

extract_protocol:
Trizol extraction
Illumina High-throughput TruSeq RNA Sample preparation: ribozero or poly(A) selection

tag: tissue

value: brain

value: embryonic day 18.5

value: wild-type


title: RNAseq_polyA_Cortex.e18.5_wildtype_1

description:
processed data:
mm10.IR.265.xlsx


title: RNAseq_polyA_AdultP90.Spinal.Cord_wildtype_2

description:
processed data:
mm10.AS.Quantas.spinalcord_exon.inclusion.rate.xlsx

source_name: Spinal cord

value: Spinal cord

value: Postnatal day 90


title: RNAseq_polyA_Cortex.e18.5_wildtype_2

description:
processed data:
mm10.IR.265.xlsx


title: ndt80Δ T=6 input rep2

source_name: ndt80Δ T=6 input


title: RNAseq_polyA_Cortex.e18.5_Nova2-ko_1

description:
processed data:
mm10.IR.265.xlsx


title: RNAseq_polyA_Cortex.e18.5_Nova2-ko_2

description:
processed data:
mm10.IR.265.xlsx


title: RNAseq_polyA_AdultP90.Spinal.Cord_wildtype_1


title: RNAseq_Ribo0_Cortex.e18.5_Nova2.Ptbp2-dko_3

description:
processed data:
mm10.BED12.AS.Quantas.Nova2.Ptbp2-dKO.FDR005_dI01.xlsx


title: RNAseq_Ribo0_Cerebellum.PurkinjeLayer_Pcp2Cre.Nova2cKO_2

description:
processed data:
mm10.AS.Quantas.Dissection.RNAseq.P28.Purkinje.Nova2cKO.FDR005_dI01.txt.gz
mm10.AS.Quantas.Dissection.RNAseq.P28.Purkinje.Nova2cKO.FDR005_dI01.txt.gz

source_name: Cerebellum_Purkinje cell layer

value: Postnatal day 28


title: RNAseq_Ribo0_Cerebellum.PurkinjeLayer_Pcp2Cre.Control_1

description:
processed data:
mm10.AS.Quantas.Dissection.RNAseq.P28.Purkinje.Nova2cKO.FDR005_dI01.txt.gz
mm10.Kallisto.GeneExpression.P28.PurkinjeLayer.wt_vs_Nova2cKO.Pcp2-Cre.xlsx.gz


title: RNAseq_Ribo0_Cortex.e18.5_Nova2.Ptbp2-dko_2


title: RNAseq_Ribo0_Cortex.e18.5_Nova2.Ptbp2-dko_1


title: RNAseq_Ribo0_Cerebellum.PurkinjeLayer_Pcp2Cre.Nova2cKO_3


title: RNAseq_Ribo0_Cerebellum.PurkinjeLayer_Pcp2Cre.Control_2


title: RNAseq_FACS_Ribo0_Cortex.e18.5_Gad2Cre.Nova2cKO_1

description:
processed data:
mm10.AS.Quantas.FACS.RNAseq.e18.5.Gad2-Cre.Ctl_vs_Nova2cko.FDR005_dI01.txt.gz
mm10.BED12.AS.Quantas.FACS.RNAseq.e18.5.Gad2-Cre.Ctl_vs_Nova2cko.FDR005_dI01.txt.gz


title: RNAseq_Ribo0_Cerebellum.PurkinjeLayer_Pcp2Cre.Control_3


title: RNAseq_FACS_Ribo0_Cortex.e18.5_Gad2Cre.Control_3

description:
processed data:
mm10.AS.Quantas.FACS.RNAseq.e18.5.Emx1-Cre_vs_Gad2-Cre.FDR005_dI01.txt.gz
mm10.BED12.AS.Quantas.FACS.RNAseq.e18.5.Emx1-Cre_vs_Gad2-Cre.FDR005_dI01.txt.gz


title: ndt80Δ T=6 input rep1

description:
processed data file:
AH6179Hop1T6rep-121-215-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph.gz
AH6179Mek1T6rep-120-425-Reps-SK1Yue-PM_B3W3_MACS2_FE.bedGraph.gz


title: RNAseq_FACS_Ribo0_Cortex.e18.5_Emx1Cre.Nova2cKO_3

description:
processed data:
mm10.AS.Quantas.FACS.RNAseq.e18.5.Emx1-Cre.Ctl_vs_Nova2cko.FDR005_dI01.txt.gz
mm10.BED12.AS.Quantas.FACS.RNAseq.e18.5.Emx1-Cre.Ctl_vs_Nova2cko.FDR005_dI01.txt.gz


title: RNAseq_FACS_Ribo0_Cortex.e18.5_Gad2Cre.Control_1


title: RNAseq_FACS_Ribo0_Cortex.e18.5_Emx1Cre.Nova2cKO_2


title: RNAseq_polyA_Cortex.e18.5_Nova2-ko_3

description:
processed data:
mm10.IR.265.xlsx


title: RNAseq_FACS_Ribo0_Cortex.e18.5_Emx1Cre.Nova2cKO_1


title: RNAseq_FACS_Ribo0_Cortex.e18.5_Emx1Cre.Control_3

description:
processed data:
mm10.AS.Quantas.FACS.RNAseq.e18.5.Emx1-Cre_vs_Gad2-Cre.FDR005_dI01.txt.gz
mm10.Kallisto.GeneExpression.e18.5.FACS.wt.Emx1-Cre_vs_Gad2-Cre.xlsx.gz


title: RNAseq_Ribo0_Cerebellum.PurkinjeLayer_Pcp2Cre.Nova2cKO_1


title: RNAseq_FACS_Ribo0_Cortex.e18.5_Emx1Cre.Control_2


title: PTBP2_CLIP_Nova2-ko_Cortex_3

description:
processed data file:
mm10.e18.5.Cortex.PTBP2-CLIP.Nova2-KO.bedgraph.gz

data_processing:
collapsing of exact sequences
stripping of degenerate linker (5nt; ends with a G)
removal of 3'adaptor (GTGTCAGTCACTTCCAGCGG)
alignment with novoalign (unambiguous mapping on mm10)
collapsing of PCR duplicates (unique CLIP tags)
clustering of unique reads
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files generated from NOVA2 cTag-CLIP unique tags for genome browser

extract_protocol:
Tissues were UV-irradiated and subjected to NOVA2 cTag-CLIP with mouse anti-GFP (Heiman et al., 2014), clones 19F7 and 19C8 (detailed desription in accompanying paper).
partial RNAse digestion, RNA linker ligation and PCR amplificiation. NOVA2-AcGFP bound fragments were ligated to a degenerate 5'linker and a 3'linker.


title: RNAseq_FACS_Ribo0_Cortex.e18.5_Gad2Cre.Nova2cKO_3


title: RNAseq_FACS_Ribo0_Cortex.e18.5_Emx1Cre.Control_1


title: PTBP2_CLIP_Nova2-ko_Cortex_2


title: RNAseq_FACS_Ribo0_Cortex.e18.5_Gad2Cre.Nova2cKO_2


title: PTBP2_CLIP_Nova2-ko_Cortex_1


title: Pcp2-Cre_NOVA2_cTag-CLIP_Cerebellum_1

description:
processed data file:
mm10.P28.Cerebellum.NOVA2-cTagCLIP.Pcp2-Cre.bedgraph.gz

source_name: Cerebellum


title: Pcp2-Cre_NOVA2_cTag-CLIP_Cerebellum_2


title: PTBP2_CLIP_wildtype_Cortex_wt3

description:
processed data file:
mm10.e18.5.Cortex.PTBP2-CLIP.wildtype.bedgraph.gz


title: vGlut1-Cre_NOVA2_cTag-CLIP_Cerebellum_2

description:
processed data file:
mm10.P28.Cerebellum.NOVA2-cTagCLIP.vGlut1-Cre.bedgraph.gz


title: Pcp2-Cre_NOVA2_cTag-CLIP_Cerebellum_3


title: vGlut1-Cre_NOVA2_cTag-CLIP_Cerebellum_1


title: CMV-Cre_NOVA2_cTag-CLIP_Cerebellum_3

description:
processed data file:
mm10.P28.Cerebellum.NOVA2-cTagCLIP.CMV-Cre.bedgraph.gz


title: CMV-Cre_NOVA2_cTag-CLIP_Cerebellum_2


title: vGlut1-Cre_NOVA2_cTag-CLIP_Cerebellum_3


title: RNAseq_FACS_Ribo0_Cortex.e18.5_Gad2Cre.Control_2


title: NOVA2_CLIP_Cerebellum_3

description:
processed data file:
mm10.P28.Cerebellum.NOVA2-CLIP.bedgraph.gz


title: CMV-Cre_NOVA2_cTag-CLIP_Cerebellum_1


title: NOVA2_CLIP_Cerebellum_1


title: RNAseq_polyA_AdultP90.Spinal.Cord_wildtype_3


title: Emx1-Cre_NOVA2_cTag-CLIP_Cortex_2

description:
processed data file:
mm10.e18.5.Cortex.NOVA2-cTagCLIP.Emx1-Cre.bedgraph.gz


title: Emx1-Cre_NOVA2_cTag-CLIP_Cortex_3


title: Emx1-Cre_NOVA2_cTag-CLIP_Cortex_1


title: PTBP2_CLIP_wildtype_Cortex_wt1


title: PTBP2_CLIP_wildtype_Cortex_wt2


title: Gad2-Cre_NOVA2_cTag-CLIP_Cortex_2

description:
processed data file:
mm10.e18.5.Cortex.NOVA2-cTagCLIP.Gad2-Cre.bedgraph.gz


title: Gad2-Cre_NOVA2_cTag-CLIP_Cortex_3


title: CMV-Cre_NOVA2_cTag-CLIP_Cortex_2

description:
processed data file:
mm10.e18.5.Cortex.NOVA2-cTagCLIP.CMV-Cre.bedgraph.gz


title: Gad2-Cre_NOVA2_cTag-CLIP_Cortex_1


title: CMV-Cre_NOVA2_cTag-CLIP_Cortex_1


title: Th9+TLA1 rep2

status: Public on Jan 08 2019

city: Los Angeles

first: Jie

last: Tang

address: 8700 Beverly Blvd

institute: Cedars Sinai Medical Center

data_processing:
Raw reads were filtered and trimmed by FASTX toolkit
Gene read counts were generated using HTSeq version 0.5.4 and then counts per million (CPM) were calculated by edgeR in Bioconductor.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized count values for each Sample

source_name: T cell, Th9+TLA1 condition

extract_protocol:
Total RNA was isolated from T cells using RNeasy kits (Qiagen, Valencia, CA) according to the manufacturer’s protocol
Clontech’s SMARTer® Ultra™ Low Input RNA Kit for Sequencing v3 was employed to generate double-stranded cDNA libraries from 1.5 to 2.5 ng total RNA from each sample per manufacturer’s recommendations. Double-stranded cDNA libraries were individually fragmented and ligated with Ion Torrent Ion Xpress™ Barcode Adapters using Ion Xpress™ Plus Fragment Library Kit with limited modifications including size-selected final libraries with a double bead clean-up and ½ volume of Ion Adapters.  RNA-Seq libraries were assessed for concentration and length using Invitrogen’s Qubit® dsDNA HS Assay Kit (Carlsbad, CA) and Agilent High Sensitivity DNA Kit respectively (Carlsbad, CA). Samples were multiplexed to obtain >10 million (11-15 million) reads each for sequencing. The pooled libraries were amplified onto Ion Sphere™ and sequenced using the Ion PI™ Sequencing 200 Kit v2, Ion Torrent™.

value: T cell

value: Th9+TLA1 condition


title: Th9 rep2

source_name: T cell, Th9 condition

value: Th9 condition


title: Th9+TLA1 rep1


title: Th9 rep1


title: RNA-seq for KRAS(G12D) mouse liver tumor 1

status: Public on Jan 07 2019

city: Stanford

first: Zhen

last: Shi

state: California

address: 279 Campus Drive

institute: Stanford

description: polyA RNA

data_processing:
For Ribo-seq, a layered alignment was performed to first discard reads mapping to mouse ribosomal RNA (rRNA) sequences using Burrows-Wheeler Aligner (BWA). Non-rRNA reads were then aligned against the mouse transcriptome (GRCm38 build 76) using RSEM and bowtie2. Reads were aligned strand-specifically to exclude anti-sense or other non-transcript reads. For each gene, total number of Ribosome Protected Fragments (RPFs) and RNA reads were counted and fed into the downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Text files include normalized read values for protein-coding genes

source_name: liver

extract_protocol:
Mouse liver tumours were micro-dissected immediately after animal euthanization. Liver perfusion (with ice cold PBS containing 10 mg/ml cycloheximide (CHX)) and placed in ice cold PBS containing 10 mg/ml CHX for 5 min. Tumours were minced into small pieces with a scalpel and incubated for 20 min in 0.5% collagenase supplemented with 10 mg/ml CHX. After spun down, tumour was resuspended in 4 ml trypsin containing 5 mg/ml CHX for 10 to 15 min at 37 °C, followed by filtering through a 40 m cell strainer and resuspension in the lysis buffer (20 mM Tris pH 7.5, 150 mM NaCl, 15 mM MgCl2, 100 μg/ml cycloheximide, 1 mM DTT, 0.5% Triton X-100, 0.1 mg/ml heparin, 8% glycerol, 20 U/ml TURBO™ DNase, 1x Combined Protease and Phosphatase Inhibitor)
All Ribo-Seq libraries were prepared as described in Ingolia, N. T., Brar, G. A., Rouskin, S., McGeachy, A. M. & Weissman, J. S. After removing the nuclei and mitochondria, lysate was treated with RNase A/T1 mix (0.5 mg RNase A (Ambion, AM2272) and 1,000 U RNase T1 (Life Technologies, 2280)) to digest mRNAs that are not protected by the ribosome. The digestion was stopped by adding SUPERase-In™ RNase Inhibitor (20 U/μl, Ambion, AM2696), followed by centrifuging to pellet ribosomes. Ribosome-protected fragments were purified by TRIzol®, and two biological replicates were performed for each type of Ribo-Seq and all Ribo-Seq libraries (three biological replicates for WT liver).

value: Alb Cre specific expression of LSL-KRAS(G12D)

tag: sample type

value: polyA RNA


title: Ribo-seq for MYC(Tg); KRAS(G12D) mouse liver tumor 1

description: ribosome protected RNA

data_processing:
Library strategy: Ribo-seq
For Ribo-seq, a layered alignment was performed to first discard reads mapping to mouse ribosomal RNA (rRNA) sequences using Burrows-Wheeler Aligner (BWA). Non-rRNA reads were then aligned against the mouse transcriptome (GRCm38 build 76) using RSEM and bowtie2. Reads were aligned strand-specifically to exclude anti-sense or other non-transcript reads. For each gene, total number of Ribosome Protected Fragments (RPFs) and RNA reads were counted and fed into the downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Text files include normalized read values for protein-coding genes

value: Alb Cre specific expression of HA-epitope tagged c-MYC (human) and LSL-KRAS(G12D)

value: ribosome protected RNA


title: RNA-seq for KRAS(G12D) mouse liver tumor 2

description: polyA RNA


title: Ribo-seq for KRAS(G12D) mouse liver tumor 2

description: ribosome protected RNA


title: Ribo-seq for MYC(Tg); KRAS(G12D) mouse liver tumor 2

description: ribosome protected RNA


title: Ribo-seq for WT mouse liver 2

description: ribosome protected RNA

value: Wild type


title: Ribo-seq for WT mouse liver 3

description: ribosome protected RNA


title: RNA-seq for WT mouse liver 3

description: polyA RNA


title: Ribo-seq for WT mouse liver 1

description: ribosome protected RNA