title: snoK:dox#3

city: Durham

first: Christopher

middle: L

last: Holley

state: NC

address: 2301 Erwin Rd

institute: Duke University

description:
cytoplasmic RNA
size 35-350nt

data_processing:
Demultiplexed data was uploaded to Galaxy for manipulation. FASTQ Groomer and Quality trimmer were applied and FASTQC was used to review raw data quality.  3' adapter sequences were removed using Clip.
Reads were mapped to rat genome (rn4) using Bowtie.  Resulting SAM files were converted to BAM format.
BAM files were imported to Partek Genomics Suite (6.6) for read annotation and quantification.
Read frequencies were normalized as RpM (reads per million) based on the total number of reads obtained per indexed sample (deposited as matrix_table.csv).
Genome_build: rn4 (Ensembl e69, RGSC3.4.69)
Supplementary_files_format_and_content: abundance measurements

source_name: H9c2 cells

growth_protocol: H9c2 cells (ATCC: CRL-1446) were maintained in DMEM/10% FBS at subconfluent density and low passage (<20)

extract_protocol:
Cells were collected by trypsinization and washed in PBS. Cytosol was isolated by plasma membrane permeabilization and differential centrifugation. Cytosolic RNA was isolated using Trizol LS.
Indexed RNA-seq libraries were made using the Illumina TruSeq Small RNA kit. Libraries were amplified with 14 cycles of PCR, pooled, and separated by PAGE.  Products from small RNA with input sizes of 35 to 350 nucleotides were excised, collected, and sequenced using an Illumina HiSeq 2500.

treatment_protocol: Cells were seeded in 10cm plates 24h prior to treatment; treatment was 1h with water, DPI (500nM), dox (20uM), or both DPI and dox.

value: cardiac ventricular myoblast


title: snoI:ctrl#3

status: Public on Mar 20 2015

type: SRA

country: USA

description:
cytoplasmic RNA
size 35-350nt

library_source: transcriptomic

molecule: total RNA

organism: Rattus norvegicus

tag: cell type


title: snoL:DPI/dox#3

description:
cytoplasmic RNA
size 35-350nt


title: MS04T65

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description: SC3seq amplified from single cell of hiPSC on SNL

data_processing:
All the reads were surveyed and the adaptor or the poly-A sequences were trimmed by cutadapt-1.3 with options "-c -m 30 -a CTCGAGGGCGCGCCGGATCCATATACGCCTTGGCCGTACAGCAG -g CTCGAGGGCGCGCCGGATCCATATACGCCTTGGCCGTACAGCAG -a AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA". The trimmed reads with less than 30 bp were discarded.
Untrimmed and trimmed reads of 30 bp or longer were mapped onto the mouse genome mm10 and the ERCC spike-in RNA sequences with tophat-1.4.1/bowtie1.0.1 with the “—no-coverage-search” option.
Mapped reads on the genome and the ERCC were separated, and the reads on the genome were converted into the expression levels by cufflinks-2.2.0 using the “—compatible-hits-norm”, “—no-length-correction” and “—library-type fr-secondstrand” options and mm10 reference gene annotations with extended TTSs. We also set the cufflinks option “—max-mle-iterations” to 50,000, because default iterations (5,000) resulted in “FAILED” when estimating the expression levels of some genes. For the reference gene annotations used in cufflinks, we extended the TTSs of the reference genes up to 10 kb downstream to correctly estimate the expression levels of genes whose transcripts are longer than the reference toward the 3 prime.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files with abundance measurements

organism: Homo sapiens

source_name: hiPSC on SNL

growth_protocol:
The mouse embryonic stem cell (mESC) line BVSC R8 was cultured in a 2i+LIF, feeder-free culture condition.
For the analysis of human iPSCs (hiPSCs), the two iPSC lines, 585A1 and 585B1, were cultured either under a conventional culture condition [DMEM/F12 [Life Technologies (11330-32), Carlsbad, CA] supplemented with 20% (vol/vol) Knockout Serum Replacement [KSR; Life Technologies (10828-028)], 1% (vol/vol) GlutaMax [Life Technologies (35050-061)], 0.1 mM nonessential amino acids [Life Technologies (11140-050)], 4 ng/ml recombinant human bFGF [Wako Pure Chemical Industries (064-04541), Osaka, Japan] and 0.1 mM 2-mercaptoethanol [Sigma-Aldrich (M3148)]] on the SNL feeder cells [Watanabe, K., et al. (2007). Nature Biotechnology, 25(6), 681.] or under a feeder-free condition as reported previously [Nakagawa, M., et al. (2014). Scientific Reports, 4, 3594.][Miyazaki, T., et al. (2012). Nature Communications, 3, 1236.].

extract_protocol:
Total RNAs from the mouse embryonic stem cell (mESC) line BVSC R8 were extracted using an RNeasy mini kit [Qiagen (74104), Hilden, Germany] according to the manufacturer’s instructions. The isolated RNAs were serially diluted by double-distilled water (DDW) to concentrations of 250 ng/μl, 25 ng/μl, 2.5 ng/μl, 250 pg/μl, and 25 pg/μl for use in evaluation of the quantitative performance of the SC3-seq.
For isolating mouse blastocysts, C57BL/6 mice were mated and noon of the day when a copulation plug was identified was designated as embryonic day (E) 0.5. At E4.5, peri-implantation blastocysts were flushed from the uteri by KSOM [Merck Millipore (MR-020P-5D), Darmstadt, Germany], and then they were bisected into a polar part containing an inner cell mass (ICM) and polar trophectoderm (pTE) and a mural part containing mural TE (mTE) by a glass needle under a dissection microscope [Leica Microsystems (M80), Wetzlar, Germany]. Each fragment was incubated with 0.25% trypsin/PBS [Sigma-Aldrich (T4799), St. Louis, MO] for around 10 min at 37°C, then dissociated into single cells by repeated pipetting, and dispersed in 0.1 mg/ml of PVA/PBS [Sigma-Aldrich (P8136)] in preparation for the SC3-seq analysis.
For the isolation of single hiPSCs cultured with the feeders, the culture was first treated with CTK solutions [0.25% Trypsin [Life Technologies (15090-046)], 0.1 mg/mL Collagenase IV [Life Technologies (17104-019)], 1 mM CaCl2 [Nacalai Tesque (06729-55)] (Fujioka, T., et al. (2004). Int.J.Dev.Biol., 48(10), 1149.)] for the removal of the feeder cells, then dissociated into single cells using Accutase [Innovative Cell Technologies, San Diego, CA]. For the preparation of single cells from a feeder-free system, the cells were dissociated into single cells with 0.5 × TrypLE Select [TrypLE Select [Life Technologies (12563011)] diluted 1:1 with 0.5 mM EDTA/PBS] [Nakagawa, M., et al. (2014). Scientific Reports, 4, 3594.]. Dissociated single hiPSCs were transferred several times into a pick-up medium consisting of 1% KSR/PBS containing 10 μM of the ROCK inhibitor Y-27632 [Wako Pure Chemical Industries (257-00511)] [Watanabe, K., et al. (2007). Nature Biotechnology, 25(6), 681–686.] in preparation for the SC3-seq analysis.
cDNA synthesis and amplification from isolated RNAs/single cells were perfomed essentially as reported in [Kurimoto, K.et.al., Nucleic Acids Research, 34(5), e42.] except that the spike-in RNAs developed by the External RNA Control consortium [ERCC; Life Technologies (4456740)] were used and different numbers of PCR cycles were employed for amplification depending on the amounts of starting total RNAs (total RNA 100 ng: 7 cycles; 10 ng: 11 cycles; 1 ng: 14 cycles; 100 pg: 17 cycles; 10 pg: 20 cycles). 5 ng of amplified and quality-checked cDNAs were added to the pre-amplification buffer [1 × ExTaq buffer [Takara Bio (RR006), Shiga, Japan], 0.2 μM of each dNTP [Takara Bio (RR006)], 0.01 μg/μl of the N-V3 (dT)24 primer (HPLC-purified, attachment of amine at the 5-prime end), 0.01 μg/μl of the V1(dT)24 primer (HPLC-purified), and 0.025 U/μl of ExTaqHS [Takara Bio (RR006)]], and were amplified by four cycles of PCR. The surplus primers and PCR byproducts such as primer dimers were removed by size selection through three rounds of purification using a 0.6 × volume of AMPureXP beads for each  round [Beckman Coulter (A63881), Tokyo, Japan] according to the manufacturer’s instructions. The purified cDNAs were diluted to 130 μl by double-distilled water (DDW) and fragmented by shearing with Covaris S2 or E210 (duty cycle: 10%; intensity: 5; cycles per burst: 200; duration: 50 seconds; an intensifier was installed in the case of E210) [Covaris, Woburn, MA], and then end-polished in the End-polish buffer [1 × NEBnext End Repair Reaction buffer [NEB (B6052S), Ipswich, MA], 0.01 U/μl of T4 DNA polymerase [NEB (M0203)], and 0.033 U/μl of T4 polynucleotide kinase [NEB (M0201)]] for 30 min at 20oC. After incubation, a 0.8 × volume of the AMPureXP was immediately added, the solution was mixed for more than 20 min, and then the supernatant was transferred to a 1.2 × volume of the AMPureXP reagent and the cDNAs were purified. Next, to provide the purified cDNAs with an Int-adaptor sequence, the cDNAs were incubated in 30 μl of the Internal adaptor extension buffer [1 × ExTaq Buffer, 0.23 mM of each dNTP, 0.67 μM of the IntV1 (dT)24 primer (HPLC-purified), 0.033 U/μl of ExTaqHS] using the following thermal cycler program: 95oC for 3 min, 67oC for 2 min, and 72oC for 2 min. The reactions were terminated by chilling in an ice-block, and after the addition of 20 μl of the P1-adaptor ligation buffer [a mixture of 10 μl of 5 × NEBNext Quick Ligation Reaction Buffer [NEB (B6058S)], 0.6 μl of 5 μM of the P1-T adaptor [Life Technologies (4464411)], and 1 μl of T4 ligase [NEB (M0202M)]], the solution was incubated for 15 min at 20oC and for 20 min at 72oC. After two rounds of cDNA purification by adding a 1.2 × volume of AMPure XP, the cDNAs were added into the Final amplification buffer [1 × ExTaq buffer, 0.2 mM of each dNTP, 1 μM of the P1 primer, 1 μM of the BarT0XX_IntV1 primer (HPLC-purified), 0.025 U/μl of ExTaqHS] and amplified by PCR using the following thermal cycler program: 95oC for 3 min; followed by 9 cycles of 95oC for 30 sec, 67oC for 1 min and 72oC for 1 min; with a final extension of 72oC for 3 min. Finally, the cDNA libraries were purified two times by using a 1.2 × volume of AMPureXP and dissolved in 20 μl of TE buffer. The quality and quantity of the constructed libraries were evaluated by LabChip GX or Bioanalyzer 2100, a Qubit dsDNA HS assay kit [Life Technologies (Q32851)], and a SOLiD Library TaqMan Quantitation kit [Life Technologies (4449639)]. The cDNA libraries were sequenced with an ABI SOLiD 5500XL system (Applied Biosystems) for 50-bp single-end reads according to the instructions of the manufacturer.

tag: cell line

value: hiPSC on SNL


title: snoH:DPI/dox#2

description:
cytoplasmic RNA
size 35-350nt


title: snoG:dox#2

description:
cytoplasmic RNA
size 35-350nt


title: snoB:DPI#1

description:
cytoplasmic RNA
size 35-350nt


title: snoD:DPI/dox#1

description:
cytoplasmic RNA
size 35-350nt


title: snoA:ctrl#1

description:
cytoplasmic RNA
size 35-350nt


title: snoC:dox#1

description:
cytoplasmic RNA
size 35-350nt


title: snoE:ctrl#2

description:
cytoplasmic RNA
size 35-350nt


title: snoF:DPI#2

description:
cytoplasmic RNA
size 35-350nt


title: MS04T74

description: SC3seq amplified from single cell of hIPSC, feeder free

source_name: hIPSC, feeder free

value: hIPSC, feeder free


title: Y^M_testis_rep3

city: Houston

first: Richard

last: Meisel

state: TX

address: 3455 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

data_processing:
Basecalls were performed using Casava 1.8.2
Reads were aligned to house fly genome assembly v2.0.2 and annotation release 100 using TopHat2 v2.0.8b and Bowtie v2.1.0.0 with the default parameters.
We tested for differential expression using the Cuffdiff2 program in the Cufflinks v2.2.1 package with the default parameters and a false discovery rate of 0.05.
Genome_build: Musca_domestica-2.0.2 (GCA_000371365.1)
Supplementary_files_format_and_content: alignments of reads to reference genome and annotation; expression level measurements (FPKM) and tests for differential expression

molecule: polyA RNA

organism: Musca domestica

source_name: testis

growth_protocol: Flies were kept at 25C with a 12:12 hour light:dark cycle. Larvae were reared in media made with 1.8 L water, 500 g calf manna (Manna Pro, St. Louis, MO), 120 g bird and reptile litter wood chips (Northeastern Products, Warrensburg, NY), 60 g dry active baker's yeast (MP Biomedical Solon, OH), and 1.21 kg wheat bran (Cargill Animal Nutrition, Minneapolis, MN).

extract_protocol:
Samples were homogonized in TRIzol and RNA was extracted on QIAGEN RNeasy columns with gDNA elimination.
Barcoded mRNA-seq libraries were prepared using the Illumina TruSeq kit following the manufacturer's instructions.

treatment_protocol: Dissections were performed on living, non-anesthetized 4-6 day old unmated adult flies. Gonad dissections were performed in Ringer's solution (182 mM KCl, 46 mM NaCl, 3 mM CaCl2, 10 mM Tris-Cl in ddH2O).

tag: strain

value: CSaY (Y^M)

tag: Sex

value: male

tag: tissue

value: testis


title: Y^M_testis_rep1


title: Y^M_testis_rep2


title: ovary_rep1

source_name: ovary

value: CS (III^M)

value: female

value: ovary


title: III^M_testis_rep2


title: III^M_testis_rep3


title: III^M_testis_rep1


title: female_head_rep2

source_name: head

value: head


title: Y^M_male_head_rep1


title: Y^M_male_head_rep3


title: female_head_rep1


title: III^M_male_head_rep3


title: snoJ:DPI#3

description:
cytoplasmic RNA
size 35-350nt


title: III^M_male_head_rep2


title: III^M_male_head_rep1


title: ovary_rep2


title: GFP-only control sample 1

city: New york

first: Julia

last: Kaltschmidt

address: 1275 York Av

institute: Sloan-Kettering Institute

data_processing:
Illumina Casava v1.8.2 software used for basecalling.
Reads were mapped to mm9 genome and transcript assembly was performed using Tophat (v2.0.8) with –no-novel-juncs option and other default parameters
BAM files from the above step were used to call the differentially regulated genes using cuffdiff module in Cufflinks (v2.1.1) with -u option and other default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: Tab separeted file containing FPKM values, log2 fold change values, and qvalues for all genes in the genome.

organism: Mus musculus

source_name: Cortical pyramidal cells

extract_protocol:
RNA from dissociated FACS-purified GFP-expressing embryonic cortical pyramidal cells was extracted using TRIzol RNA Isolation Reagents (Life Technologies). Quality of RNA was ensured before amplification by analyzing 20–50 pg of each sample using the RNA 6000 pico kit and a bioAnalyzer (Agilent).
2.1 to 7.8 ng of high quality (RIN>8) total RNA was subsequently amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing (Clonetech Laboratory) according to instructions provided by the manufacturer. The sequencing library was prepared using Kapa HTP library preparation kit (Kapa Biosystems), adaptors were diluted 1/30 fold, and amplification was set for 10 cycles. Barcoded samples were then run on a Hiseq 2500 in a 50bp/50bp paired end run, using the TruSeq SBS Kit v3 (Illumina).

value: cortex

tag: electroporation age

tag: harvest age

value: embryonic cortical pyramidal cells


title: Ptf1a-misexpression sample 2


title: Ptf1a-misexpression sample 1


title: METTL3_CLIP_rep3

city: New York

first: Claudio

last: Alarcon

state: New York

address: 1230 York Ave

department: Systems Cancer Biology

institute: The Rockefeller University

description: METTL3 co-immunoprecipitated RNA

data_processing:
After linker sequence removal and quality trimming, sequence mapping was performed using Bowtie with default parameters (build hg19).
The binding sites were identified using the CIMS package (Zhang and Darnell, Nature biotech, 2011).
Genome_build: hg19
Supplementary_files_format_and_content: bed files marking the genomic coordinates of the identified peaks

source_name: HeLa

growth_protocol: Cells were grown in DMEM-based media supplemented with 10% FBS, 1% L-glutamine, 1% Sodium Pyruvate, and 1% Pen/Strep

extract_protocol:
cells were UV cross-linked and prepared as described previously (Licatalosi D, et al. 2008, Nature 456:464-U22).
Samples were prepared for sequencing as described previously (Licatalosi D, et al. 2008, Nature 456:464-U22).

treatment_protocol: After cells underwent selection no further treatment was performed

tag: replicate

value: HeLa


title: BCL6_REP2_INPUT

first: Katerina

last: Hatzi

state: NY

address: 413 E 69th Street, BB-1462

department: Hematology/Oncology

institute: WCMC

description: Input chromatin matching BCL6 ChIP-seq experiment (REP2)

library_source: genomic

data_processing:
Primary image analysis and basecalling were conducted using the Illumina pipeline and the generated reads were mapped to the human genome (UCSC hg18) using ELAND. Only sequences mapped uniquely to the genome with no more than 2 mismatches were accepted.
Read density tracks were visualized using the UCSC browser and ChIPseeqer algorithm (Giannopoulou and Elemento, 2011) was used for BCL6 peak calling, compared to total input control.
Clonal reads (reads mapping to the same exact location) were excluded from peak calling and generation of read density tracks as amplification artifacts. For peak calling each read was in silico extended to 158bp based at the corresponding DNA strand.
Genome_build: hg18
Supplementary_files_format_and_content: "Read_density-wig" files are wig tracks  generated using ChIPseeqerMakeReadDensityTrack of the ChIPseqer package. (http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqerMakeReadDensityTrack).They represent the average ChIPseq read density, normalized to the total number of reads. Wgl tracks called "peaks" are the peak locations called for every experiment by our peakcaling algorithm and they were generated using ChIPseeqer (http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_PeaksTrack). For every experiment peaks were called with ChIPs matched their own input chromatin.

molecule: genomic DNA

source_name: Primary CXCR5hi CD4 T cells isolated from human tonsils

extract_protocol:
Tfh cell sorts were initially gated on CD4+CD19-, then CD45RO+, then as CXCR5hi (GC Tfh). The following anti-human Abs were used: CD45RO (clone UCHL1), CD19 (clone HIB19), CD4 (clone RPA-T4) (eBioscience, San Diego, CA); CXCR5 (clone RF8B2).
GC Tfh (CXCR5hi PD1hi CD45RO+ CD4+ T cells, CD19‑) were isolated from human tonsils, fixed with 1% formaldehyde, lysed and sonicated to generate fragments less than 500bp. Chromatin immunoprecipitation was performed by incubation of the chromatin with antibodies against BCL6 (Santa Cruz, sc-858), H3K4me3(Abcam, ab8580), H4K4me1(Abcam, ab8895) and H3K27ac (Abcam, ab4729). Immunocomplexes were pulled down using protein A beads and after increasing stringency washes 10ng of ChIP DNA was recovered and used to generate a BCL6 ChIP-seq library according to Illumina ChIP-seq Library preparation Kit. A negative control library was prepared in parallel using 10ng of input chromatin DNA. Libraries were quantified and validated using Agilent Technologies 2100 Bioanalyser for size, concentration and purity. Both libraries were sequenced using HiSeq 2000 for 50 cycles.

treatment_protocol: Fresh human tonsils were obtained from Rady Children’s Hospital of San Diego. Informed consent was obtained from all donors. Tonsils were homogenized using wire mesh and passed through a cell strainer to make a single-cell suspension. Mononuclear cells were isolated using Histopaque 1077 (Sigma-Aldrich, St. Louis, MO). All protocols were approved by the La Jolla Institute for Allergy and Immunology (LJI), University of California, San Diego (UCSD) and Rady Children’s Hospital of San Diego.

value: tonsil

value: CXCR5hi PD1hi CD45RO+ CD4+ T cells, CD19-

tag: antibody

value: none (input)


title: BCL6_REP2_ChIPSeq

description: ChIP-seq using human Tfh cells (REP2)

value: BCL6 (Santa Cruz, sc-858)


title: GFP-only control sample 2


title: METTL3_CLIP_rep2

description: METTL3 co-immunoprecipitated RNA


title: METTL3_CLIP_rep1

description: METTL3 co-immunoprecipitated RNA


title: Ptf1a-misexpression sample 3


title: G9a ChIP-seq result

city: Duarte

first: Xiaochun

last: Yu

state: CA

address: 1500 E. Duarte Rd, Rm 202, Lippman-Graff Bldg

department: Internal Medicine

institute: city of hope

description: Home-made

data_processing:
The read quality of each sample was determined by FastQC software. After prefiltering the raw data by removing sequenced adapters and low quality reads, the tags were mapped to the human genome (assembly hg19) by Bowtie software. Parameter settings were as follows: -v, 3 (reported alignments with at most 3 mismatches), -5, 3 and -3, 3 (trim3 bases from 5' and 3' end to remove low-quality bases). Peak detection was performed using MACS software from Galaxy browser (www.galaxy.psu.edu). Parameters settings were as follows: tag size with 25bp, band width with 300bp, P-value cutoff for peak detection was set to 1e-03. The peaks obtained from ChIP sequencing were matched to the annotated reference genome (mouse mm9) using Cisgenome 2.0
Genome_build: hg19
Supplementary_files_format_and_content: bed

source_name: HEK 293T cells

growth_protocol: All procedures are to be done under sterile conditions in a laminar flow hood using sterile instruments and detergent-free glassware. Dulbecco’s modified Eagle’s media (DMEM) is used for 293T cell culture

extract_protocol:
293T cells were crosslinked with formaldehyde treatment. The chromatin were isolated from 1 × 108 cells and fragmented to 200 to 400 bp by sonication.
DNA were repaired to blunt ends by T4 DNA polymerase and phosphorylated with T4 polynucleotide kinase using the END-IT kit (Epicentre). A single “A” base was added to 3’ end with Klenow. Double-stranded adaptors were ligated to the fragments with DNA ligase. Ligation products between 200 and 600 bp were gel purified on 2% agarose to remove unligated adaptors and subjected to 20 PCR cycles.Following ligation of a pair of adaptors to the repaired ends, the fragments around 160 bp to 370 bp were isolated from agarose gel.

treatment_protocol: No special treatment

value: HEK 293T

tag: chip antibody


title: ZNF644 ChIP-seq result

description: Home-made


title: Y^M_male_head_rep2


title: WIZ ChIP-seq result

description: Home-made

value: WIZ


title: INPUT2_ChIPSeq

description: Input chromatin matching Histone modification ChIP-seq experiment REP2


title: H3K4me3_REP2_ChIPSeq

description: ChIP-seq using human Tfh cells

value: H3K4me3(Abcam, ab8580)


title: H3K27ac_REP2_ChIPSeq

description: ChIP-seq using human Tfh cells

value: H3K27ac (Abcam, ab4729)


title: INPUT1_ChIPSeq

description: Input chromatin matching Histone modification ChIP-seq experiment REP1


title: H3K4me3_REP1_ChIPSeq

description: ChIP-seq using human Tfh cells


title: BCL6_REP1_INPUT

description: Input chromatin matching BCL6 ChIP-seq experiment


title: H3K4me1_REP1_ChIPSeq

description: ChIP-seq using human Tfh cells

value: H4K4me1(Abcam, ab8895)


title: BCL6_REP1_ChIPSeq

description: ChIP-seq using human Tfh cells


title: ΔBbGPCR3TRE

status: Public on Mar 19 2015

city: Hangzhou

first: Shenghua

last: Ying

state: Zhejiang

address: Yu-hang-tang Road 688

country: China

institute: Zhejiang University

data_processing:
Illumina HiSeq™ 2000 used for sequencing
The sequenced tags were filtered to remove low-quality tags, empty tags and tags with a copy number of <2. All the clean tags vectoring the CATG and 49 bp tag fragments were mapped to the sequenced genome of Bb2860 or M. robertsii ARSEF23 with the precision of no more than two nucleotide mismatch.
Reads Per Kilobase of exon per Megabase of library size (RPKM) 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.
Screening of differentially expressed genes in WTSDB/BbGPCR3SDB comparison and BbGPCR3SDB/BbGPCR3TRE comparison. FDR (False Discovery Rate) is a method to determine the threshold of P-value in multiple tests (Benjamini, Y. and Yekutieli D. The Annals of Statistics. 2001, 29: 1165-1188).
Genome_build: ASM28067v1
Supplementary_files_format_and_content: Excel files include GeneID, gene_length, RPKM values, log2(fold change) and false discovery rate (FDR)  for each paired sample.

organism: Beauveria bassiana ARSEF 2860

growth_protocol: Conidia suspension (500 μl,107 conidia ml-1) of WT and ΔBbGPCR3 of Beauveria bassiana were  inoculated into 50ml Sabouraud dextrose broth (SDB) or Trelalose-midified SDB at 25 °C for 2-day with shaking (180 r.p.m).

extract_protocol: Total RNA was isolated from frozen mycelial powder using TRIzol® Reagent (Invitrogen, Carlsbad, CA, USA), double-stranded cDNA were prepared with the Illumina gene expression sample prep kit for Illumina arrays.

treatment_protocol: Resultant mycelia of each strain were harvested and washed in sterile water twice.

tag: medium

value: TRE

tag: culture time

value: 2 days

value: mycelia

tag: genotype


title: WTSDB

source_name: BbWT

value: SDB

value: WT


title: ΔBbGPCR3SDB


title: ScxGFP+ cells, E15.5, hindlimb

city: cincinnati

first: HAN

last: LIU

state: oh

address: 3333 burnet avenue

department: DEVELOPMENTAL BIOLOGY

institute: CINCINNATI CHILDREN'S HOSPITAL

data_processing:
Illumina offline basecaller v1.9.0.
Sequenced reads were masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.7
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.Implanted in tophat 1.4.1 using parameters:tophat -G mm9.gtf -o tophat -p 4 -r 0 mm9 reads.fastq. 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 RPKM values for each Sample ...

source_name: embryonic hindlimb

extract_protocol:
GFP+ cells were FACS sorted using BD FACSAria II, cells were immediately frozen at -80℃
Total RNA was extracted by using RNeasy micro kit from Qiagen.cDNA was made by the NuGEN Ovation RNA-Seq v2 Assay.

tag: strain background

value: mixed

tag: age

value: embryonic day E15.5

value: embryonic hindlimb

tag: cell population

value: ScxGFP positive cells


title: ScxGFP+ cells, E11.5, hindlimb

value: embryonic day E11.5


title: ScxGFP+ cells, E13.5, forelimb

data_processing:
Illumina offline basecaller v1.9.0.
Sequenced reads were masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.7
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.Implanted in tophat 1.4.1 using parameters:tophat -G mm9.gtf -o tophat -p 4 -r 0 mm9 reads.fastq. 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 Sample ...

source_name: embryonic forelimb

extract_protocol:
Both GFP+ and GFP- cells were FACS sorted using BD FACSAria II, cells were immediately frozen at -80℃
Total RNA was extracted by using RNeasy micro kit from Qiagen.cDNA was made by the NuGEN Ovation RNA-Seq v2 Assay.

value: embryonic day E13.5

value: embryomic forelimb


title: Tumor_2 _B

city: Cold Spring Harbor

first: Simon

middle: Robert Vincent

last: Knott

address: 1 Bungtown Rd

department: Biology

institute: Cold Spring Harbor Laboratory

description: processed data file: All_Clones_Normalized.txt

data_processing:
1) Reads were alligned to the mm10 genome using bowtie-2.
2) Each gene's read counts were determined using htseq -count (python) function.
3) Reads were normalized across samples using DESeq (bioconductor)
Genome_build: mm10
Supplementary_files_format_and_content: All_Clones_Normalized.txt: The first field is the RefSeq gene symbol. All other fields are the normalized read counts for a sample. Samples are indicated in the headers.
Supplementary_files_format_and_content: Clone_4T1-T_shRNA_Normalized.txt: The first field is the RefSeq gene symbol. All other fields are the normalized read counts for a sample. Samples are indicated in the headers

source_name: 4T1 Mammary Cancer Cell Line

growth_protocol: DMEM high glucose (Life Technologies) supplemented with 5% fetal bovine serum (Thermo Scientific), 5% fetal calf serum (Thermo Scientific), non-essential amino acids (Life Technologies) and penicillin streptomycin (Life Technologies)

extract_protocol:
RNA was purified and DNAse treated using the Qiagen RNeasy Mini Kit
The NuGEN Ovation RNA-Seq V2 protocol was carried out on 100 ng of total RNA. cDNA was fragmented using the Covaris LE220 sonicator according to the manufacturer’s instruction to yield a target fragment size of 200 bp. The fragmented cDNA was subsequently processed using the NuGEN Ovation Ultralow DR Multiplex System.
Libraries were analyzed on an Illumina Hiseq-2.0 using 76bp reads.

value: Orthotopic Tumor


title: Tumor_1 _B


title: H3K27ac_REP1_ChIPSeq

description: ChIP-seq using human Tfh cells

value: tonsil

value: CXCR5hi PD1hi CD45RO+ CD4+ T cells, CD19-


title: Lung_1 _B

value: Lung Metastasis


title: Lung_1 _A


title: Lung_2 _B


title: ScxGFP- cells, E13.5, forelimb

value: ScxGFP negative cells


title: Clone 4T1-W_A

tag: clone

value: Clone 4T1-W (derived From Single Cell)

tag: intravasating capacity

value: Non-Intravasating


title: Lung_2 _A


title: Tumor_2 _A


title: Clone 4T1-S_B

value: Clone 4T1-S (derived From Single Cell)


title: Clone 4T1-U_B

value: Clone 4T1-U (derived From Single Cell)


title: Clone 4T1-V_A

value: Clone 4T1-V (derived From Single Cell)


title: Tumor_1 _A


title: Clone 4T1-T_B

value: Clone 4T1-T (derived From Single Cell)

value: Intravasating


title: ScxGFP+ cells, E13.5, hindlimb

value: mixed

value: embryonic hindlimb


title: H3K4me1_REP2_ChIPSeq

description: ChIP-seq using human Tfh cells

tag: cell type

value: H4K4me1(Abcam, ab8895)


title: Clone 4T1-U _A

value: Clone 4T1-U  (derived From Single Cell)


title: Clone 4T1-W_B


title: Clone 4T1-S_A


title: Clone 4T1-R_B

value: Clone 4T1-R (derived From Single Cell)


title: Clone 4T1-Q_A

value: Clone 4T1-Q (derived From Single Cell)


title: Clone 4T1-Q_B


title: EpiLC_H3K27ac_2

data_processing:
Read data were mapped on mouse mm9 genome by bowtie v0.12.9 with "-n 3 -m 1" option.
Mapped reads were sorted and format converted using samtools v0.1.18 and picard-tools v1.85.
Tdf files are made using igvtools v2.3.5.
Peak calling for EGFP-BLIMP1, T, H3K4me3, and H3K27ac were performed using MACS v1.4.2 with default setting.
To enable comparison of peaks in different samples, we scanned all peaks throughout the genome, and considered peaks detected in proximities (within 1 Kb) as a single peak.
Genome_build: mm9
Supplementary_files_format_and_content: Tdf files are made using igvtools v2.3.5 with "-w 25 -e 250" setting
Supplementary_files_format_and_content: Bed files of H3K27me3 and H3K9me2 were made by counting fpkm in 2kb-bin at every 1kb on the genome. Fpkm values were divided by that of input value and subsequently normalized by QPCR data.
Supplementary_files_format_and_content: Bed files for H3K27ac_all_peaks and H3K4me3_all_peaks were made as follows: we scanned all peaks in all samples throughout the genome, and considered peaks detected in proximities (within 1 Kb) as a single peak to be able to compare read  intensity among samples.

source_name: EpiLC

growth_protocol: BVSC and EGFP-Blimp1 knock-in ESC lines were induced into EpiLCs as described for 48 hrs (BVSC) or 36 hrs (EGFP-Blimp1 knock-in).  The EpiLCs were then cultured under a floating condition by plating 2-3×103 cells per well of lipidure-coated U-bottom 96-well plate (Thermo Scientific) in the GK15 medium containing LIF (1000 U/mL) for induction of d2 LIF aggregate (d2 LIF Ag), LIF and BMP4 (500 ng/mL) for d2 PGCLCs, and LIF, BMP4, BMP8a (500ng /mL), SCF (100 ng/mL), and EGF (50 ng/mL) for d6 PGCLCs, respectively.

extract_protocol:
Cells were suspended in 1 mL of phosphate buffered saline (PBS) and fixed by adding 27 mL of 36.5% formalin (Sigma) for 10 min at room temperature.  Fixation was terminated by adding 110 mL of 1.5 mM glycine.  The fixed cells were washed twice in PBS containing 0.1% bovine serum albmin (BSA), and were lysed in 400 mL SDS-lysis buffer [50 mM Tris-HCl (pH 8.0) containing 1% SDS, 10 uM EDTA, and 1 mM PMSF] on ice for 10 min.  Chromatins were then solubilized using Bioruptor UCD250 with ice-chilled water, with 15 cycles of 30 sec sonication at the high power and 60 sec interval.  The sonication products were centrifuged at 16,000 g for 5 min.  The supernatants were diluted in 1 mL ChIP dilution buffer [16.7 mM Tris-HCl (pH 8.0), 0.01% SDS, 1.1% Triton X100, 1.2 mM EDTA, 167 mM NaCl, 1 mM SDS, 200 mg/mL tRNA (Roche)], and were divided into 0.1 mL as input DNA and 1.3 mL as ChIP samples.  The ChIP samples were mixed with the Dynabeads-antibody complexes and rotated at 4 ºC overnight.  The ChIP-ed Dynabeads were recovered using the DynaMag-2 magnet (Life Technologies), and washed with 200 mL of low salt buffer [20mM Tris-Cl (pH 8.0), containing 0.1% SDS, 1% Triton X100, 2 mM EDTA, and 150 mM NaCl], high salt buffer [20mM Tris-Cl (pH 8.0), containing 0.1% SDS, 1% Triton X100, 2 mM EDTA, and 500 mM NaCl], RIPA buffer [10mM Tris Cl (pH8.0), containing 1% Sodium deoxycholate, 1% NP40, 250 mM LiCl, and 1 mM EDTA], and TE buffer [10 mM Tris Cl (pH8.0), containing 1 mM EDTA].  The ChIP-ed Dynabeads were then incubated in new tubes containing 50 mL of Elution buffer (0.1 mM NaHCO3, 1% SDS, 10 mM DTT, and 0.06 mM tRNA) for 15 min at room temperature.  The supernatants were collected using DynaMag-2, and were reverse-crosslinked by adding 8 mL of 2.5 M NaCl and incubating at 65 ºC overnight.  Then, 2 mL of 0.5 M EDTA and 4 mL of 0.645 mg/mL proteinase K solution were added to reaction mixture, and further incubated at 45 ºC for 1 hr.  The ChIP-ed DNAs were then purified with Qiaquick PCR purification columns, using the buffer EB supplemented with 4 ng/mL tRNA (Qiagen).
The ChIP-ed and Input DNAs were sheared to an average size of about 150 bp by ultra-sonication (Covaris, Woburn, MA).  ChIP-ed DNAs obtained from 1×106 cells were then subjected to the procedures for SOLiD Fragment Library Preparation (Life Technologies) according to the manufacture’s instruction except for the ligation reaction that was performed overnight.  The libraries were amplified with 11-13 cycles of PCR for H3K4me3 and H3K27ac or 8 cycles for H3K9me2 and H3K27me3.
ChIP-ed DNA for histone modifications from 1×105 cells were subjected to the procedures for SOLiD Fragment Library Preparation with a modification where the size fractionation step using AMPure XP beads (Agencourt) was omitted and ligation reaction was performed overnight.  The libraries were amplified with 12-16 cycles of PCR for H3K27ac or 8 cycles for H3K9me2 and H3K27me3.
We developed a new method to prepare and precisely amplify libraries of ChIPed DNA from a small number of cells, and applied this method to H3K4me3 from 1 x 105 cells and transcription factors from 3×105 ~ 1×106 cells.  A modified adaptor for SOLiD library was prepared by annealing 50 mM each of P1-T Adaptor/F (CCACTACGCCTCCGCTTTCCTCTCTATGGGCAGTCGGTGAT) and Barcode-Internal+12mer/R (TCACCGACTGCCACGCCTTGGCCGTACAGCAGCCTCTTACACAGAG, with Phosphorylated 5'-end) in 1×Linker buffer [50 mM Tris-HCl (pH 8.0) containing 100 mM NaCl and 1 mM EDTA] with a step-wise cooling procedure (95 ºC, 70 ºC, 50 ºC, 40 ºC and 25 ºC for 15 min, respectively).  The sheared DNAs were end-repaired using End-It DNA End-Repair Kit (Epicentre) in a 120 mL scale according to the manufacture’s instruction, and purified using MinElute PCR purification kit (Qiagen) with 540 mL of binding buffer PB3 (5.6 M Gu HCl, 33.3% isopropanol) supplemented with 10 ng/mL tRNA and 10 mL of elution buffer EB (Qiagen) with 4 ng/mL tRNA.  The end-repaired DNAs were incubated in 20 mL of dA tailing mixture [0.2 mM dATP (GE Healthcare), 1×High Yield buffer (Greiner), 4 ng/mL tRNA 2.5 unit of Taq DNA polymerase (Greiner)], for 10 min at 70 ºC, and purified using MinElute PCR purification kit with buffers PB (Qiagen) and EB (11 mL) supplemented with tRNA.  The dA-tailed DNAs were incubated in 15 mL ligation mixture [1×DNA Ligase Reaction Buffer (Life Technologies), 0.1 mM the modified adaptor, and 2.5 unit ExpressLink T4 DNA Ligase (Life Technologies)] at 16 ºC for more than 22 hr.  The adaptor-ligated DNAs were then amplified using the Platinum Taq DNA Polymerase in a 50 mL reaction scale (Life Technologies) with 1 mM each of Library PCR primer 1 (Life Technologies) and Library PCR primer Barcode001+Internal adaptor (CTCTGTGTAAGAGGCTGCTGTACGGCC).  PCR was performed with 8 cycles for ChIP-ed DNAs of H3K4me3 and with 10 cycles for those of EGFP-BLIMP1.  PCR products were purified using 50 mL AMPure XP beads supplemented with 3.33 mL of 25% PEG8000 and 13.7 mL of 2.5 M NaCl, and eluted in 30 mL of buffer EB supplemented with tRNA.  The PCR products were then subjected to another 5-cycle PCR using 1 mM each of Library PCR Primer 1 and P2-Barcode-N-Internal primer [CTGCCCCGGGTTCCTCATTCTCT (N10) CTGCTGTACGGCCAAGGCGT, where N10 corresponds to SOLiD barcode sequences other than barcode 1; e.g., AGGGAGTGGT for barcode 2], and purified twice with AMPure XP beads supplemented with PEG8000 and NaCl.

treatment_protocol: d2 and d6 PGCLCs of the BVSC line were purified with Fluorescence-activated cell sorter (FACS) (ARIA III; BD Biosciences) by fluorescence of BV.  For the EGFP-BLIMP1 knock-in line, d2 PGCLCs were purified with FACS using anti-Kit antibody and d6 PGCLCs using anti-SSEA1 and anti-Integrin b3 antibodies.

tag: strain

value: anti H3K27ac, MsIgG, CMA309

tag: genotype/variation

value: Blimp1-mVenus reporter (BV),Prdm14-mVenus reporter (PV)


title: Clone 4T1-V_B


title: Clone 4T1-P_A

value: Clone 4T1-P (derived From Single Cell)


title: Clone 4T1-P_B


title: Clone 4T1-O_B

value: Clone 4T1-O (derived From Single Cell)


title: Clone 4T1-O_A


title: Clone 4T1-T_A


title: Clone 4T1-M_B

value: Clone 4T1-M (derived From Single Cell)


title: Clone 4T1-N_B

value: Clone 4T1-N (derived From Single Cell)

value: Non-Intravasating


title: Clone 4T1-N_A


title: Clone 4T1-K_A

value: Clone 4T1-K (derived From Single Cell)


title: Clone 4T1-M_A


title: Clone 4T1-J_A

value: Clone 4T1-J (derived From Single Cell)


title: Clone 4T1-H_B

value: Clone 4T1-H (derived From Single Cell)


title: Clone 4T1-L_B

value: Clone 4T1-L (derived From Single Cell)


title: Clone 4T1-L_A


title: Clone 4T1-G_B

value: Clone 4T1-G (derived From Single Cell)


title: Clone 4T1-G_A


title: Clone 4T1-R_A


title: Clone 4T1-F_A

value: Clone 4T1-F (derived From Single Cell)


title: Clone 4T1-J_B


title: Clone 4T1-F_B


title: Clone 4T1-E_B

value: Clone 4T1-E (derived From Single Cell)

value: Intravasating


title: Clone 4T1-K_B


title: Clone 4T1-E_A


title: Clone 4T1-I_B

value: Clone 4T1-I (derived From Single Cell)


title: Clone 4T1-D_A

value: Clone 4T1-D (derived From Single Cell)


title: Clone 4T1-D_B


title: Clone 4T1-C_B

value: Clone 4T1-C (derived From Single Cell)


title: Clone 4T1-B_B

value: Clone 4T1-B (derived From Single Cell)


title: Clone 4T1-A_B

value: Clone 4T1-A (derived From Single Cell)


title: Clone 4T1-I_A


title: Clone 4T1-B_A


title: Clone 4T1-C_A


title: Clone 4T1-H_A


title: Clone 4T1-A_A


title: H3K27AcIP_H3K27Ac_ChIP_WT_Retina1

city: Seattle

first: Timothy

middle: J

last: Cherry

state: WA

department: Developmental Biology and Regenerative Medicine

institute: Seattle Children's Research Institute

data_processing:
Base calling was performed using CASAVA software.
Illumina raw reads in .fastq files were aligned to mouse mm9 reference genome with bwa 0.6.2. Uniquely mapped reads  were extended in silico to reflect average fragment size  of the input DNA(~250bp).
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files of unnormalized histograms for mapped, in silico extended reads

source_name: retina

growth_protocol: Mice were housed under standard conditions in the animal facility and dissected at the same time point in the light-dark cycle for each dissection.

extract_protocol:
MEF2D ChIP from mouse retinas was performed as previously described for brain tissue (Hong et al., 2008) with the following modifications: p11 mouse retinas were dissected in ice-cold HBSS prior to homogenization and crosslinking. 4μg of anti-MEF2D antibody was pre-bound to 15μl of Protein A dynabeads (Life Technologies) per immunoprecipitation (IP) from approximately 100 million retinal cells. H3K27Ac ChIP was performed as described above with the following modifications: 10 mM sodium butyrate was added to all solutions until post-IP washes with the exception of cross-linking buffer. Chromatin was fragmented for H3K27Ac ChIP by brief sonication followed by MNase (New England Biolabs) digestion for 8 minutes at 37C to generate mononucleosomes. 0.25μg of anti-H3K27Ac antibody was used per IP from 10 million retinal cells. After reverse crosslinking all samples were purified using phenol/chloroform/isoamyl alcohol followed by column clean up.
Single-end short read sequencing libraires were prepared using standard protocols, following the manufacturers instructions. 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.

treatment_protocol: Retinae were dissected from p11 knockout or wild-type littermate controls.

tag: tissue

value: retina

value: wild type

value: postnatal day 11

value: anti-H3K27Ac (Abcam AB4729)


title: INPUT_Mef2d_ChIP_CrxKO_Retina3

value: Crx KO

value: anti-MEF2D (Flavell et al., 2008)


title: INPUT_Mef2d_ChIP_WT_Retina3


title: H3K27AcIP_H3K27Ac_ChIP_Mef2dKO_Retina1

value: Mef2d KO


title: Mef2dIP_Mef2d_ChIP_WT_stim_Ctx2

value: postnatal day 13


title: INPUT_H3K27Ac_ChIP_Mef2dKO_Retina1


title: Mef2dIP_Mef2d_ChIP_WT_unstim_Ctx2

value: postnatal day 12


title: INPUT_Mef2d_ChIP_WT_stim_Ctx1


title: Mef2dIP_Mef2d_ChIP_WT_Retina2


title: INPUT_H3K27Ac_ChIP_WT_Retina1


title: INPUT_Mef2d_ChIP_WT_Retina2


title: INPUT_Mef2d_ChIP_Mef2dKO_Retina2


title: INPUT_Mef2d_ChIP_WT_unstim_Ctx1


title: INPUT_Mef2d_ChIP_WT_Retina1


title: Mef2dIP_Mef2d_ChIP_Mef2dKO_Retina2


title: Mef2dIP_Mef2d_ChIP_WT_unstim_Ctx1


title: Mef2dIP_Mef2d_ChIP_WT_Retina3


title: pifq_D-3

city: Beijing

first: Xu

middle: Zhao

last: Gao

state: Beijing

address: The Summer Palace Road No. 5

department: College of Biological Sciences

institute: Peking University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Tair10 whole genome using tophat with parameters -p -r -G -o genome C1_R1.fq
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks.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: Tair10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

organism: Arabidopsis thaliana

growth_protocol: Seeds were vernalized for 3 d at 4 °C after surface sterilization. Then seeds were exposed to light for 12 h and grown in darkness for 4 days.

extract_protocol:
Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 4-day-old dark grown seedlings were either kept in darkness (D) or exposured to white light for 6 h (DL6h).

value: plant seedling

value: pifq


title: Mef2dIP_Mef2d_ChIP_WT_Retina1


title: P11_Crx_KO_Retina_1

description:
Total RNA was depleted of rRNA by hybridization (using RiboZero) and heat fragmented. Strand-specific RNA-Seq libraries were prepared using the dUTP method, and sequenced on an Illlumina Hiseq instrument
Andzelm-Cherry_CRX_Retina_Exon_Densities.txt

data_processing:
Base calling was performed using standard approaches.
Illumina raw reads in .fastq files were aligned using bwa 0.6.2.  Target sequences included (1) mm9  autosomal and sex chromosomes plus (2) a read-length-dependent splice library (~3M sequences, each 50-98bp).  The latter comprised all possible minimal intragenic sequences of two or more exons (based on the RefSeq annotation) for which one or more exon-exon junctions could be crossed by reads of the required length.  After bwa-indexing the targets with the bwtsw algorithm, reads were aligned with zero trimming, zero gaps, and allowing up to 5 mismatches. The sam/bam files output by bwa were indexed and sorted and served as input for further processing.
Aligned reads were minimally filtered for QC, removing any reads with uncalled bases or with unmapped or nonuniquely mapped sequences.
Employing "MAPtoFeatures" perl scripts, the loci of uniquely mapped reads were compared to the loci of all genic features (exons, introns, UTRs, CDSs, etc., and all junctions between them) of (1) all genes based on the RefSeq annotation and (2) all rRNA genes based on RepeatMasker, for the alignment target genome. Average exon Density (read coverage per bp) was calculated, equal to rdbp per feature length.  Each sample's Densities were renormalized from total reads not in noncoding genes and not in rRNA to a standard total of 10M reads, and to a standard read length of 35bp.  With these conventions, units of Density always equal RPKM times 0.35.  Quantile normalized exon densities were treated as expression levels comparable among all samples.  For paired-end samples only "L" files were considered for determining exon densities.
Genome_build: For all samples mm9 (NCBI37, Jul7. 2007).
Supplementary_files_format_and_content: Entrez gene ID, refseq gene name, chromosome, orientation (strand), gene start, gene stop, refseq number and exon densities are listed for each of the  genes analyzed across expression platforms in this study.

source_name: Retina, postnatal day 11, male

extract_protocol:
Retinae were dissected from p11 knockout or wild-type littermate controls. Both retinae from each animal were pooled for each sample.  RNA was extracted using trizol and Qiagen Rneasy purification with on-column DNase digestion.
Illumina library construction and sequencing was carried out as follows: total RNA was depleted of ribosomal RNA using the Ribozero rRNA removal kit (Epicentre), heat-fragmented to 200-700 bp in length and cloned using Uricil-N-Glycosylase-based strand-specific cloning. cDNA fragments were sequenced using an Illumina HiSeq 2000
Strand-specific, rRNA depleted total RNA, Paired (WT vs. Mef2d KO) or single-end (WT vs. Crx KO) 49 bp sequencing

tag: gender

value: male


title: P11_WT_Retina_4

source_name: Retina, postnatal day 11, female

value: female


title: det1-1_D-2


title: pifq_D-2


title: P11_WT_Retina_3


title: P11_Crx_KO_Retina_2


title: pifq_D-1


title: ChIP-seq_Bapx1_ 3T3

city: Potsdam

first: Thomas

last: Lufkin

address: 8 Clarkson Avenue

institute: Clarkson University

description: invitro ChIP-seq of Bapx1 in NIH_3T3 cells. V5 tagged Bapx1 was overexpressed in 3T3 cells and pulled down with V5 antibody

data_processing:
The sequenced tags were aligned to mouse genome (mm9) and the peak detection was done using MACS.
Genome Build: mm9
CMM070-Bapx1_peaks.txt
CMM070-6cols-Bapx1-3T3.tags.txt
CMM070-3T3-Bapx1-6cols.tags.wig

source_name: In-vitro cell culture of NIH_3T3 cell

extract_protocol: Standard ChIP DNA extraction methods as described here-( Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT: ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods 2009, 48(3):240-248.). Standard Illumina single end read library was prepared as per as manufacturer's instruction to be sequenced on a GAII sequencer (14 round amplification cycle was used)

value: 3T3 cell line

tag: ChIP

value: V5 tagged Bapx1 over expressed in NIH_3T3 cells [V5- Abcam (ab15828)]


title: Input_ 3T3

description: input control in NIH_3T3 cell line. Empty pcDNA6 vector was tranfected in 3T3 cells and pulled down with V5 antibody.

data_processing:
The sequenced tags were aligned to mouse genome (mm9) and the peak detection was done using MACS.
Genome Build: mm9
CMM069-6cols-Input-3T3.tags.txt
CMM069-3T3-input-6cols.tags.wig

value: Wild type 3t3 pulled down with V5 antibody [V5- Abcam (ab15828)]


title: Input_ VC

description: input for Sox9  vertebral column ChIP. IgG control.

data_processing:
The sequenced tags were aligned to mouse genome (mm9) and the peak detection was done using MACS.
Genome Build: mm9
CME061-6cols-input.tags.txt
CME061-input.tags.wig

source_name: Embryonic day 12.5 vertebral column pulled down with IgG

value: E12.5 vertebral column and limb

value: IgG


title: ChIP-seq_Sox9_VC

description: invivo ChIP-seq of Sox9 in Vertebral column of E12.5 wild type embryos. Sox9 antibody was used

data_processing:
The sequenced tags were aligned to mouse genome (mm9) and the peak detection was done using MACS.
Genome Build: mm9
CME060-sox9_peaks.txt
CME060-6cols-sox9.tags.txt
CME060-sox9.tags.wig

source_name: Embryonic day 12.5 vertebral column

value: Sox9 [R&D system (AF3075)]


title: det1-1_D-1


title: ChIP-seq_Bapx1_VC

description: invivo ChIP-seq of Bapx1 in Vertebral Column of E12.5 mouse embryo. Endogenous Bapx1 was tagged with S-Peptide and pulled down with S-peptide antibody

data_processing:
The sequenced tags were aligned to mouse genome (mm9) and the peak detection was done using MACS.
Genome Build: mm9
CME207-Bapx1_peaks.txt
CME207-6cols-Bapx1-VC.tags.txt
CME207-Bapx1.tags.wig

value: E12.5 vertebral column

value: S-peptide tagged Bapx1 [S-Pepetide - Bethyl laboratories (A-190-134A)]


title: P11_WT_Retina_1

description:
Total RNA was depleted of rRNA by hybridization (using RiboZero) and heat fragmented. Strand-specific RNA-Seq libraries were prepared using the dUTP method, and sequenced on an Illlumina Hiseq instrument
Andzelm-Cherry_MEF2D_Retina_Exon_Densities.txt

value: wild type

value: retina

value: postnatal day 11


title: det1-1_D-3


title: Col_DL6h-3


title: Mef2dIP_Mef2d_ChIP_CrxKO_Retina3

value: Crx KO

value: anti-MEF2D (Flavell et al., 2008)


title: Input l_VC

description: Background control for S-peeptide tagged Bapx1 ChIP. Vertebral column from wild type E12.5  embryos were pulled down with S-peptide antibody

data_processing:
The sequenced tags were aligned to mouse genome (mm9) and the peak detection was done using MACS.
Genome Build: mm9
CME206-6cols-Input-VC.tags.txt
CME206-input.tags.wig

source_name: Embryonic day 12.5 vertebral column of wild type mice

value: S-pepetide in wild type embryo [S-Pepetide - Bethyl laboratories (A-190-134A)]


title: P11_WT_Retina_2


title: m6A #1

data_processing:
Paired reads were mapped to the human genome (build hg19) using bowtie2 with “sensitive-local” option (doi:10.1038/nmeth.1923)
Consistent reads were converted into genomic intervals (bed format).
ChIPseeqer (doi:10.1186/1471-2105-12-277) was used to detect statistically significant peaks that were present in the m6A co-precipitation samples and not the IgG control. The following parameters were used: -t 10 –fold_t 2 –minlen 20.
Genome_build: hg19
Supplementary_files_format_and_content: bed files marking the genomic coordinates of the identified peaks

molecule: nuclear RNA

extract_protocol:
Cells were lysed using LB1 buffer, the nuclear fraction was then lysed with M-PER (Thermo Scientific) buffer and diluted 10-fold in dilution buffer before the immunoprecipitation. Rabbit α-m6A antibody (Synaptic Systems) and rabbit IgG control bound to protein A Dynabeads were used for the immunoprecipitations. The immunoprecipitated RNA was eluted with N6-methyladenosine (Sigma-Aldrich), ethanol precipitated and resuspended in water.
RNA was barcoded using ScriptSeq V2 kit (Epicentre) and sent for sequencing.

tag: cell line


title: Col_DL6h-1

value: plant seedling


title: Col_DL6h-2


title: IgG control


title: P11_Mef2d_KO_Retina_1

value: Mef2d KO

value: male


title: Col_D-1


title: TAC_H3K27ac_ChIP-seq

city: Tarrytown

first: Rene

middle: Christian

last: Adam

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals

description: Chromatin IP against H3K27ac

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm9, build 37) using the Bowtie program (Version 0.1.2.7). Unique reads mapped to a single genomic location (allowing two mismatches) were kept for peak identification.
Peak detection was performed with the software MACS (Version 1.4.2) with input as controls.
wig files created using IGVtools with 25bp windows with no extension to reads.
Genome_build: mm9
Supplementary_files_format_and_content: wig files; enrichment values in 25bp windows

source_name: Mouse back skins

growth_protocol: HFSCs and TACs were FACS-purifed from the back skins of indicated ages of mice

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 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 25 cycles and library fragments of 150-300 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.

treatment_protocol: No treatment

value: Female

value: K14-H2BGFP (Tumbar et al., 2004)

tag: sorting markers

value: GFP, integrin α6, CD34 and Sca1

value: H3K27ac (abcam, catalog# ab4729, lot# GR132150-1)

value: back skin

value: TACs


title: HFSC_invitro_Input_DNA

description: input DNA

source_name: primary HFSCs

tag: passage

value: integrin α6, CD34 and Sca1, iRFP

tag: chip antibody

value: cultured HFSCs


title: Tel Bulge_H3K4me1_ChIP-seq

description: Chromatin IP against H3K4me1

value: integrin α6, CD34 and Sca1

value: H3K4me1 (abcam, catalog# ab8895, lot# GR114298-1)

value: HFSCs


title: TAC_Input_DNA

description: input DNA


title: Tel Bulge_Med1_ChIP-seq

description: Chromatin IP against Med1

value: Med1 (Crsp1/Trap220, Bethyl Laboratories, catalog# A300-793A, lot# A300-793A-2)


title: m6A #2


title: Tel Bulge_H3K27ac_ChIP-seq

description: Chromatin IP against H3K27ac


title: TAC_H3K4me1_ChIP-seq

description: Chromatin IP against H3K4me1


title: Col_D-3

value: wild type


title: TAC_Med1_ChIP-seq

description: Chromatin IP against Med1


title: non-silencing control siRNA technical replicate 3

city: Philadelphia

first: Sylvia

middle: T

last: Nurnberg

state: PA

address: 3400 Civic Center Blvd

department: Medicine

institute: University of Pennsylvania

data_processing:
alignment: tophat
alignment: bowtie
transcript assembly: cufflinks
differential assembly: cuffdiff
genome build: Hg19 male
processed data files format and content: bed

source_name: in vitro cultured primary coronary artery smooth muscle cells

growth_protocol: SmGM-2 Smooth Muscle Growth Medium-2 including hEGF, insulin, hFGF-B and FBS, but without antibiotics

extract_protocol:
Total RNA from cultured HCASMCs was obtained by direct lysis using the QIAGEN miRNeasy Mini Kit (Qiagen #217004) according to manufacturer’s instructions.
Total RNA of 3 samples each either siTCF21 or siControl treated samples was depleted for ribosomal RNA with the Ribo-Zero magnetic kit from epicentre (Illumina #MRZH116), libraries generated with the epicentre ScriptSeq v2 RNA-Seq library preparation kit (Illumina #SSV21106).
Libraries were sequenced as 100bp paired-end reads on an Illumina HiSeq 2000 instrument.

treatment_protocol: HCA-SMCs were transfected with 300 nM TCF21 Trilencer-27 Human siRNA (OriGene #SR304753C) or Trilencer-27 Universal Scrambled Negative Control siRNA (OriGene #SR30004) at 80% confluence using the Amaxa Basic Nucleofector Kit for Primary Mammalian Smooth Muscle Cells (Lonza #VPI-1004). Cells were transfected following the Lonza Optimized Protocol for Primary Mammalian Smooth Muscle cells at a density of 1 x 106 cells per 100 µL sample using Nucleofector Program U-025. Cells were changed to medium without supplements at 18 hours post-transfection and cultured for an additional 48 hours.

tag: transfection

value: non-silencing control siRNA


title: TCF21 knockdown siRNA technical replicate 2

value: in vitro cultured primary coronary artery smooth muscle cells

value: TCF21 knockdown siRNA


title: non-silencing control siRNA technical replicate 1


title: embryonic stem cells

status: Public on Mar 18 2015

city: Duesseldorf

first: Ulf

last: Tiemann

address: Moorenstrasse 5

department: Institute for Stem Cell Research and Regenerative Medicine

country: Germany

institute: Heinrich Heine University Duesseldorf

data_processing:
Detected adapter and primer sequences were removed from the sequence reads. Further, poor quality bases (below phred-quality Q15) were trimmed off from the sequence reads.
Reference mapping was done using the BISMARK/Bowtie2 alignment tool with the default parameters. Sequence alignments were further refined by local realignment and recalibration  using Bis-SNP adopted GATK modules.
Reference related CpG island annotations were obtained from the UCSC genome browser and gene annotations were obtained from NCBI's RefSeq database.
The R-package methylKit was used for comparative methylation analyses (differential methylation relative to the defined control sample ESC)
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: comma separated value (.csv) tables; containing lists of identified differentially methylated regions (DMRs, one file each for hyper- and hypomethylated regions) in the samples GSC1, iPSC1, iPSC2, gPSC1, and gPSC2, all relative to the control sample ESC; indicated for each DMR are: position within the genome, genomic feature (exon, intron, promoter, or intergenic), annotated gene identifiers (if applicable), methylation rate relative to ESC control, q-value (Fisher's exact test, corrected for false discovery rate by the SLIM method)

source_name: mouse in vitro cell line

extract_protocol:
DNA was isolated using the QIAamp DNA Mini Kit (Qiagen)
Libraries were prepared by GATC Biotech using standard protocols

value: ESC


title: germline-derived pluripotent stem cell line 2

value: gPSC


title: TCF21 knockdown siRNA technical replicate 3


title: induced pluripotent stem cell line 1

value: iPSC


title: germline stem cells

value: GSC


title: TCF21 knockdown siRNA technical replicate 1


title: v65 polyA(+) icSHAPE in vivo NAI-N3 Biological Replicate 2

city: Stanford

first: Ryan

middle: Alexander

last: Flynn

address: 380 Roth Way, Room 265

institute: Stanford University

description: protocol: icSHAPE

data_processing:
Raw sequencing reads were removed of PCR duplicates based on the randomized sequencing the 5’ barcode. The 5’ and 3’ barcodes/adaptors were then trimmed and reads were mapped to the mouse transcriptome (Ensembl annotation build GRCm38.74) using Bowtie2. For reads that can be mapped to multiple locations of the transcriptome, we randomly distribute them to ten different locations. The first nucleotide of each sequencing read from the NAI-N3 libraries are identified as the base directly 3’ of the icSHAPE modification.
Genome_build: Ensembl GRCm38.74 (mouse)
Supplementary_files_format_and_content: bigWig : the bigWig file provided contains processed Crosslinked nucleotides from the icSHAPE experiment. Data presented is an intersection of the two biological replicates

source_name: v6.5 mouse ES cells

growth_protocol: v6.5 cells were grown in typical mES cell culture conditions off MEFs on gelatin with serum and LIF

extract_protocol:
Mock or icSHAPE modified cells were harvested using Trizol LS, total RNA purified using RNeasy columns and processed for icSHAPE library construction.
Total or polyA selected RNA was first reacted with DIBO-Biotin (Life Technologies) to CLICK biotin to icSHAPE modified transcripts. RNA was then fragmented with RNA Fragmentation Reagent (Ambion) to sizes ranging between 25-150 nts. Fragmented RNA was 3’end repaired with T4 PNK (NEB) and 3’ adaptors ligated with T4 RNL2tr (NEB). cDNA synthesis was achieved with SuperScriptIII (Life Technologies) and icSHAPE modified transcripts were captured with MyOne C1 Streptavidin beads (Life Technologies). Enriched icSHAPE modified cDNAs were circularized and amplified using quantitative PCR before deep sequencing.

treatment_protocol: v6.5 cells were collected and incubated with either DMSO (mock modified) or NAI-N3 (icSHAPE modified) at 100mM final concentration in 10% final DMSO for 20 minutes at 37C.

value: embryonic stem cell


title: Col_D-2

value: plant seedling

tag: genotype


title: germline-derived pluripotent stem cell line 1


title: ioc3disw1d_NUCseq

city: Worcester

first: Oliver

last: Rando

state: MA

address: 364 Plantation St.

institute: UMass Medical School

data_processing:
OLB 1.9/CASAVA_v1.8.2 were used for base calling
barcoded libraries were separated by Novobarcode
reads were mapped to sacCer3 genome using bowtie2
the cross correlation between watson and crick reads was determined to define the fragment length and reads were extended to this fragment length and bedtools genomecoverage was used to count the read coverage at each base pair, which was normalized to one
gene alignments were performed using the edge of the +1 nucleosome (Tsankov et al., 2010)
nucleosome positions were determined by a template filtering algorithm (Weiner et al., 2010) and assigned to genes
Genome_build: S288C (sacCer3)
Supplementary_files_format_and_content: tab-delimited files presenting normalized count at base pairs -500 to +1000 surrounding the edge of the +1 nucleosome

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: 200mL cultures grown overnight in above media to approximately 0.5 OD

extract_protocol:
DNA was PCI extracted and ethanol precipitated followed by Rnase digestion
digested DNA was treated with calf intestinal phosphatase (NEB) and mononucleosomal DNA was gel purified (BioRad, Freeze N' Squeeze), which was blunt-ended, a-tailed, and ligated (Epicentre) to inline barcoded Illumina adapters and amplified with Illumina sequence primers

treatment_protocol: cell wall disruption via bead beating followed by micrococcal nuclease digestion to isolate mononucleosomes

tag: mutant

tag: media

value: SD+URA


title: v65 polyA(+) icSHAPE DMSO Biological Replicate 1

description: protocol: icSHAPE


title: KlacIOC3ISW1_NUCseq

value: IOC3 & ISW1 from K.lactis


title: v65 polyA(+) icSHAPE in vitro NAI-N3 Biological Replicate 1

description: protocol: icSHAPE


title: non-silencing control siRNA technical replicate 2


title: Tel Bulge_Input_DNA

description: input DNA

value: Female

tag: age

value: back skin


title: Zta Chip plus acyclovir

city: Brighton

first: Alison

middle: Jane

last: Sinclair

state: E. Sussex

address: University of Sussex

department: School of Life Sciences

country: United Kingdom

institute: University of Sussex

description:
Zta ChIP
with 0.125% rabbit anti-human IgG anti-IgG added 48 hours

data_processing:
Initial processing of sequencing images was carried out using the CASAVA pipeline. Base calling, and quality control statistics were performed using GOAT and Bustard modules.
Sequence reads were aligned to the hg19 release of the human genome with ELAND.
Bigwig files were generated by calculating tag density in 10-bp windows, normalizing per million total reads and subtracting the input signals using in-house R scripts.
Peak calling (p<10−7) was performed from a merged Bed file generated from the two ChIP datasets using MACS, with a merged input Bed file acting as background.
Genome_build: hg19
Supplementary_files_format_and_content: MACS output

source_name: Akata BL cell line_with_acyclovir

growth_protocol: RPMI medium supplemented with 10% (v/v) fetal bovine serum, 100units/ml penicillin, 100μg/ml streptomycin and 2mM L-glutamine

extract_protocol:
Chromatin was fixed by application of 1% (v/v) formaldehyde for 15 min  then sonnicated on ice (10 x 10s-pulses; 30% amplitude output on a Branson model 250 Microtip at setting 5 (Sonics Vibacell). The chromatin was pre-cleared with protein A/G-sepharose bead slurry (Sigma) that had been pre-blocked in 0.5% (w/v) fraction V BSA (Sigma) in DPBS. 2% (v/v) of the pre-cleared extract was retained as the input control sample while the remainder was incubated with 10μg of Zta-specific goat antibody (Santa Cruz # sc-17503) or control goat IgG for 1 h at 4oC]. The input control sample and the precipitated DNA were sequentially treated with 0.2μg/ml RNAse A and 0.2μg/ml Proteinase K and the DNA purified.
Sequencing libraries were prepared using 10ng of the input and ChIP DNA using a ChIP-Seq sample preparation kit (Illumina) following the manufacturer’s protocol, except that the library (150-350bp fragments) was purified from the gel after PCR-amplification. The DNA fragments were separated on a 2% agarose gel in TAE buffer, visualized using SYBR-safe stain and 150-300bp fragments were excised and purified using a gel extraction kit (Qiagen).

treatment_protocol: 0.125% rabbit anti-human IgG anti-IgG was added for 48 hours

tag: pathogen

value: Epstein-Barr virus

value: Akata

value: B lymphocytes

tag: acyclovir dose

value: with100uM acyclovir

tag: antibody

value: anti-Zta (BZLF1)

tag: antibody manufacturer

value: Santa Cruz

tag: antibody catalog number


title: induced pluripotent stem cell line 2

tag: strain

tag: cell type


title: BZLF1 B cell RNASeq biological replicate 2

description: processed data files: CONTROLvsBZLF1.RNASeq.genes.counts.tsv, CONTROLvsBZLF1.RNASeq.edgeR.DE_results.tsv

data_processing:
Alignments were performed to human RefSeq genes archived in the Illumina iGenomes resource using RSEM (version 1.2.4; Li and Dewey 2011).
An existing pipeline developed within the Trinity software package (Grabherr et al., 2011) was used to perform differential expression analysis with edgeR (Robinson et al., 2010) which is available as part of the Bioconductor project (Gentleman et al., 2004) developed within the R programming language (version 3.01).
Genes with a read count less than ten across all samples were removed before differential expression analysis with edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: CONTROLvsBZLF1.RNASeq.genes.counts.tsv:  Tab-delimited text file containing gene names as rows and columns that represent read counts generated by RSEM for all samples with respect to the RefSeq annotation.
Supplementary_files_format_and_content: CONTROLvsBZLF1.RNASeq.edgeR.DE_results.tsv:  Tab-delimited text file containing gene names as rows and columns that represent the output from edgeR.

source_name: modified Burkitt's lymphoma cell line

growth_protocol: Maintained in RPMI medium supplemented with 10% (v/v) fetal bovine serum, 100units/ml penicillin, 100_g/ml streptomycin and 2mM L-glutamine (Life Technologies) at 370C with 5% CO2.

extract_protocol:
Total cell RNA was prepared from the cells using RNAeasy reagents (Qiagen).
The RNA-Seq libraries were prepared with the Illumina stranded mRNA kit. The mRNA was purified using oligo-dT beads and fragmented using elevated temperatures. The first strand of cDNA is generated from the mRNA using random hexamer primers.  The second strand was synthesized without the use of dUTP so strand specificity is not encoded. Double stranded cDNA was ligated to standard Illumina adapters and amplified by PCR using 15 cycles of amplification. The libraries were subjected to cluster formation and then 100bp paired-end sequencing on the HiSeq 2500 using the v3 chemistry.

treatment_protocol: 500ng/ml doxycycline for 24h and enrichment on anti-NGFR MACS beads.

value: modified Burkitt's lymphoma cell line (Akata)

tag: genotype/variation

value: harboring BZLF1 tet inducible gene

tag: construct


title: Control B cell RNASeq biological replicate 2

tag: cell line

value: harboring control tet inducible gene


title: P11_Mef2d_KO_Retina_2

value: Mef2d KO

tag: tissue

value: retina

value: postnatal day 11

tag: gender

value: female


title: v65 polyA(+) icSHAPE in vivo NAI-N3 Biological Replicate 1

description: protocol: icSHAPE

value: embryonic stem cell


title: v65 polyA(+) icSHAPE DMSO Biological Replicate 2

description: protocol: icSHAPE


title: hho1d_NUCseq

value: SD+URA


title: HuR iCLIP Biological replicate 2

description:
Protein enriched RNA
HuR_iCLIP_v65.bw

data_processing:
Sequencing reads were trimmed of 3' adaptors, collapsed for PCR duplicates, stripped of the 5' barcode, and mapped to the mouse (mm9) genome using bowtie2
RT stop identificaiton, gene assignment, and peak calling was performed as in FAST-iCLIP (PMID: 25411354)
Genome_build: mm9
Supplementary_files_format_and_content: bigWig file containing high confidence RT stops from HuR iCLIP in mESCs generated from biological duplicates and mapped to the mm9 murine genome.

source_name: Embryonic Stem Cells

growth_protocol: mESCs were grown on gelatin plates with serum and LIF.

extract_protocol:
Lysates were clarified from sonicated mESCs and HuR-RNA complexes were isolated with anti-HuR (Santa Crus sc-5483) antibody.
Libraries were prepared according to the FAST-iCLIP protocol (PMID: 25411354)

treatment_protocol: Cells were UV crosslinked at 254nm for 0.3J/cm^2 to in vivo fix RNA-RBP interactions

value: ES cells

value: male

value: anti-HuR (Santa Crus sc-5483)


title: Day_19_L9_Biological_replicate_3

city: Fort Collins

first: Samuel

middle: Gebremedhn

last: Etay

state: CO

address: 1683 Campus Delivery

department: Biomedical Sciences

institute: Colorado State University

data_processing:
Base calling, data filtering and index sorting was performed by the CASAVA Pipeline version 1.8.0
Initial sequence quality; per base sequence quality, over represented sequences, quality score and GC content  were checked using FASTQC software.
CutAdapt software was used to remove 3´ and 5´ adaptors, PCR primers and their reverse complement, low Quality reads and over represented reads
Mapper.pl of miRDeep2 was used to align the sequence to the bovine reference genome. Mapper.pl uses BOWTIE to processed reads with the reference genome
Detection of both known and novel miRNAs were performed using miRDeep2 software package. Differential expression of miRNAs was done using DESeq2 in R-package
Genome_build: UMD3.1
Supplementary_files_format_and_content: CSV with average read count of each microRNA

organism: Bos taurus

source_name: Granulosa cells

extract_protocol:
miRNA enriched total RNA was extracted using miRNeasy Mini Kit (Qiagen GmbH, Hilden, Germany
MiRNA library preparation and sequencing the samples was performed by GATC BioTech AG (Konstanc, Germany) using the Illumina® TruSeq™ Small RNA sample preparation protocol

tag: follicle types

value: Preovulatory Dominant follicles

tag: developmental stage of follicles

value: Day 19 of the oestrous cycle


title: METTL3 KO polyA(+) icSHAPE NAI-N3 Biological Replicate 2

description:
PolyA (+) RNA, structure modified (NAI-N3)
LIB_METTL3KO_polyA_icSHAPE_reactivity.bw

data_processing:
Library strategy: icSHAPE
Raw sequencing reads were removed of PCR duplicates based on the randomized sequencing the 5’ barcode. The 5’ and 3’ barcodes/adaptors were then trimmed and reads were mapped to the mouse transcriptome (Ensembl annotation build GRCm38.74) using Bowtie2. For reads that can be mapped to multiple locations of the transcriptome, we randomly distribute them to ten different locations. The first nucleotide of each sequencing read from the NAI-N3 libraries are identified as the base directly 3’ of the icSHAPE modification.
Genome_build: Ensembl GRCm38.74 (mouse)
Supplementary_files_format_and_content: bigWig : the bigWig file provided contains processed data from the icSHAPE experiment. Data presented nucleotide reactivity at each base and is an intersection of the two biological replicates

treatment_protocol: v6.5 cells were collected and incubated with either DMSO (mock modified) or NAI-N3 (icSHAPE modified) at 100mM final concentration in 10% final DMSO for 20 minutes at 37C


title: METTL3 KO polyA(+) icSHAPE DMSO Biological Replicate 2

description:
PolyA (+) RNA, mock modified (DMSO)
LIB_METTL3KO_polyA_icSHAPE_reactivity.bw


title: METTL3 KO polyA(+) icSHAPE NAI-N3 Biological Replicate 1


title: METTL3 KO polyA(+) icSHAPE DMSO Biological Replicate 1


title: KlacHHO1_NUCseq

tag: mutant

value: HHO1 from K.lactis


title: ChIP-seq:KAP1

city: Lausanne

first: Adamandia

last: Kapopoulou

address: Station 15

department: Sciences de la Vie

country: Switzerland

institute: EPFL

data_processing:
HCMV genome (TB40-BAC4 GenBank accession EF999921.1) using the bowtie short read aligner version 0.12.7 (Langmead et al., 2009) and allowing up to 3 mismatches over the whole length of the read
The signal of the total input was subtracted from the KAP1 IP signal using a custom made PERL program and regions with similar signal were merged together. The resulting regions were ranked according to their signal. The signal follows a normal distribution (tested with Shapiro-Wilk normality test) thus we considered as enriched regions the extreme right part of the distribution
Genome_build: TB40-BAC4 GenBank accession EF999921.1
Supplementary_files_format_and_content: bed file contains the peaks called

source_name: TB40-E HCMV strain infected CD34+ cells

growth_protocol: CD34+ are cultured in X-Vivo15 complemented with 25 ng/ml SCF, 50 ng/ml Flt3-ligand and 20 ng/ml thrombopoietin

extract_protocol:
For Chipseq CD34+ infected cells were crosslinked by 1% formaldehyde and sonicated, and chromatin was immunoprecipitated by using an affinity-purified rabbit polyclonal antibody raised against KAP1 aa 20–418, RBCC (F. R. Santoni de Sio et al.,. Blood 119, 4675 (2012)). Detailed protocols for ChIP are described in D. C. Schultz,. Genes Dev 15, 428 (2001).   Reverse cross-linking was performed overnight in the presence of proteinase K and RNase, followed by DNA extraction using the MinElute PCR purification kit (Quiagen) according to manufacturer protocol.
The library was generated from 10 ng total DNA using the TruSeq Illumina Preparation Kit.

treatment_protocol: CD34+ were infected by HCMV TB40-E strain during 5 days before fixation.

value: Human hematopoietic stem cells CD34+ freshly purified

tag: disease state

value: 5 days of HCMV infection

tag: sample pool

value: mixed patients

value: against KAP1


title: Day_19_S8_Biological_replicate_2

value: Anovulatory subordinate follicles


title: v65 polyA(+) icSHAPE in vitro NAI-N3 Biological Replicate 2

description: protocol: icSHAPE


title: BZLF1 B cell RNASeq biological replicate 1

value: modified Burkitt's lymphoma cell line (Akata)

value: harboring BZLF1 tet inducible gene


title: NG-6435_A26272_L6_lib18507_1362_3_1.fastq.bz2 Biological replicate 3

city: Bonn

first: Dessie

last: Salilew-Wondim

state: NRW

address: Endenicher Allee 15

department: Animal breeding and husbandry group

institute: University of Bonn

description: Biological replicate 3

data_processing:
Base calling, data filtering and index sorting was performed by the CASAVA Pipeline version 1.8.0
The basic statistics including the sequence quality, quality score, sequence content and GC content were analysed using FASTQC programm
Adapters and PCR primers were trimmed using cutadapt software
Mapper.pl script of miRDeep 2 was used to allign the read sequence to the bovine reference genome
Detection and quantification of miRNAs were perfomed using miRDeep software
Genome_build: Bos_taurus_UMD_3.1
Supplementary_files_format_and_content: miRNAs with their read counts

source_name: Granulosa cells from dominant follices (DF) collected at day 7 oestrous cycle

extract_protocol:
MiRNA enriched total RNA was extracted using miRNeasy Mini Kit (Qiagen GmbH, Hilden, Germany
MiRNA library preparation and sequencing of  the samples was performed by GATC BioTech AG (Konstanc, Germany) using the Illumina® TruSeq™ Small RNA sample preparation protocol

value: Granulosa cells from dominant follices collected at day 7 oestrous cycle


title: NG-6435_A26271_L5_lib18506_1362_3_1.fastq.bz2 Biological replicate 2

description: Biological replicate 2


title: NG-6435_A26269_L3_lib18504_1362_3_1.fastq.bz2 Biological replicate 3

description: Biological replicate 3

source_name: Granulosa cells from dominant follices (DF) collected at day 3 oestrous cycle

value: Granulosa cells from dominant follices collected at day 3 oestrous cycle


title: Zta chip

source_name: Akata BL cell line

tag: pathogen

value: Epstein-Barr virus

value: Akata

value: B lymphocytes

value: no acyclovir

value: anti-Zta (BZLF1)

value: Santa Cruz


title: HuR iCLIP Biological replicate 1

description:
Protein enriched RNA
HuR_iCLIP_v65.bw

value: ES cells

value: male

value: anti-HuR (Santa Crus sc-5483)


title: CHIP-seq:Ti

value: Human hematopoietic stem cells CD34+ freshly purified

value: 5 days of HCMV infection


title: Day_19_L8_Biological_replicate_2

value: Preovulatory Dominant follicles

value: Day 19 of the oestrous cycle


title: Day_19_L7_Biological_replicate_1


title: Day_19_S9_Biological_replicate_3

value: Anovulatory subordinate follicles


title: NG-6435_A26258_S1_lib18493_1362_3_1.fastq.bz2 Biological replicate 1

description: Biological replicate 1

source_name: Granulosa cells from subordinate follices (SF) collected at day 3 oestrous cycle

value: Granulosa cells from subordinate follices collected at day 3 oestrous cycle


title: input

description:
input
with 0.125% rabbit anti-human IgG anti-IgG added 48 hours

tag: acyclovir dose

value: none (input)


title: HFSC_invitro_H3K27ac_ChIP-seq

description: Chromatin IP against H3K27ac

value: Female

tag: passage

tag: sorting markers

value: integrin α6, CD34 and Sca1, iRFP

tag: chip antibody

value: H3K27ac (abcam, catalog# ab4729, lot# GR132150-1)

value: cultured HFSCs


title: NG-6435_A26270_L4_lib18505_1362_3_1.fastq.bz2 Biological replicate 1

description: Biological replicate 1

value: Granulosa cells from dominant follices collected at day 7 oestrous cycle


title: Day_19_S7_Biological_replicate_1


title: Col_Sun_4_replicate2

city: Davis

first: Kazunari

last: Nozue

state: California

address: One Shields Avenue

department: Plant Biology

institute: University of California Davis

data_processing:
Illumina Casava1.8 software used for basecalling.
By custom scripts, sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Arabidopsis thaliana whole genome using TopHat.
Differentially expressed genes were extracted by edgeR, a  R/bioconductor package.
Genome_build: Arabidopsis thaliana (TAIR10)
Supplementary_files_format_and_content: tab-delimited text files include normalized expression values (cpm) for each Sample

source_name: early shade responses in Arabidopsis adult plants (Col, 4 hr sun)

extract_protocol:
For RNA extraction, plants were treated with shade starting at ZT 4 or left in the sun. We prepared two replicates of each sample at 1 hour and 4 hours after sun and shade treatment and five plants were pooled for each replicate. Cotyledons, hypocotyls, and roots were removed from the samples, leaving leaves and apical tissue. Total RNA from the plants was extracted using RNeasy Plant Mini kit (Qiagen) with DNAse treatment (Qiagen).
Five μg total RNA was used to construct mRNA library using mRNA-Seq-8 sample Prep kit (Illumina).

tag: ecotype

value: Col


title: Col_Shade_1_replicate1

source_name: early shade responses in Arabidopsis adult plants (Col, 1 hr shade)


title: KlacCHD1plasmid_NUCseq

value: CHD1 plasmid from K.lactis

tag: media

value: SD+URA


title: NG-6435_A26268_L2_lib18503_1362_3_1.fastq.bz2 Biological replicate 2

description: Biological replicate 2

tag: cell type

value: Granulosa cells from dominant follices collected at day 3 oestrous cycle


title: NG-6435_A26263_S6_lib18498_1362_3_1.fastq.bz2 Biological replicate 3

description: Biological replicate 3

source_name: Granulosa cells from subordinate follices (SF) collected at day 7 oestrous cycle

value: Granulosa cells from subordinate follices collected at day 7 oestrous cycle


title: Control B cell RNASeq biological replicate 1

value: modified Burkitt's lymphoma cell line (Akata)

tag: genotype/variation

value: harboring control tet inducible gene

tag: construct


title: NG-6435_A26267_L1_lib18502_1362_3_1.fastq.bz2 Biological replicate 1

description: Biological replicate 1


title: Col_Sun_4_replicate1


title: NG-6435_A26260_S3_lib18495_1362_3_1.fastq.bz2 Biological replicate 3

description: Biological replicate 3


title: NG-6435_A26259_S2_lib18494_1362_3_1.fastq.bz2 Biological replicate 2

description: Biological replicate 2


title: Mef2dIP_Mef2d_ChIP_WT_stim_Ctx1

data_processing:
Base calling was performed using CASAVA software.
Illumina raw reads in .fastq files were aligned to mouse mm9 reference genome with bwa 0.6.2. Uniquely mapped reads  were extended in silico to reflect average fragment size  of the input DNA(~250bp).
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files of unnormalized histograms for mapped, in silico extended reads

source_name: retina

extract_protocol:
MEF2D ChIP from mouse retinas was performed as previously described for brain tissue (Hong et al., 2008) with the following modifications: p11 mouse retinas were dissected in ice-cold HBSS prior to homogenization and crosslinking. 4μg of anti-MEF2D antibody was pre-bound to 15μl of Protein A dynabeads (Life Technologies) per immunoprecipitation (IP) from approximately 100 million retinal cells. H3K27Ac ChIP was performed as described above with the following modifications: 10 mM sodium butyrate was added to all solutions until post-IP washes with the exception of cross-linking buffer. Chromatin was fragmented for H3K27Ac ChIP by brief sonication followed by MNase (New England Biolabs) digestion for 8 minutes at 37C to generate mononucleosomes. 0.25μg of anti-H3K27Ac antibody was used per IP from 10 million retinal cells. After reverse crosslinking all samples were purified using phenol/chloroform/isoamyl alcohol followed by column clean up.
Single-end short read sequencing libraires were prepared using standard protocols, following the manufacturers instructions. 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.

tag: tissue

value: retina

tag: genotype

value: wild type

tag: age

value: postnatal day 11

value: anti-MEF2D (Flavell et al., 2008)


title: NG-6435_A26261_S4_lib18496_1362_3_1.fastq.bz2 Biological replicate1

description: Biological replicate 1


title: Col_Sun_1_replicate1

source_name: early shade responses in Arabidopsis adult plants (Col, 1 hr sun)


title: Col_Shade_1_replicate2


title: Col_Shade_4_replicate2

source_name: early shade responses in Arabidopsis adult plants (Col, 4 hr shade)


title: KlacN1-194_NUCseq

value: CHD1 chimera with N-terminal 194bp from K.lactis

value: YPD


title: KlacCHD1_NUCseq

value: CHD1 from K.lactis


title: ScerCHD1_NUCseq

value: CHD1 wt


title: KlacN177-340_NUCseq

value: CHD1 chimera with K.lactis chromodomains (177-340)


title: chd1d_NUCseq


title: NG-6435_A26262_S5_lib18497_1362_3_1.fastq.bz2 Biological replicate 2

description: Biological replicate 2


title: Col_Sun_1_replicate2


title: KlacN195-340_NUCseq

value: CHD1 chimera with K.lactis chromodomains (195-340)


title: ScerCHD1plasmid_NUCseq

value: CHD1 wt plasmid


title: KlacCterm_NUCseq

value: CHD1 chimera with K.lactis C-terminus


title: Col_Shade_4_replicate1

value: Col


title: KlacCHD1plasmid2_NUCseq

value: CHD1 plasmid from K.lactis

value: SD+URA


title: KlacCHD12_NUCseq


title: ScerCHD12_NUCseq


title: chd1d2_NUCseq


title: KlacN+Cterm_NUCseq

value: CHD1 chimera with K.lactis N- & C-termini


title: yJC_rpb1-1_pA_8 (Run 2)

status: Public on Mar 17 2015

city: Cleveland

first: Jeffery

middle: Michael

last: Coller

state: OH

address: 2109 Adelbert Dr.

department: Center for RNA Molecular Biology

institute: Case Western Reserve University

description:
Sample 34
Sample name: 7796

data_processing:
Basecalling was performed using Illumina CASAVA software
Reads were aligned to the reference genome using bowtie version 0.12.7 using parameters ‘-m 1 -v 2 -p 8’
Transcripts FPKMs from aligned reads were obtained using Cufflinks 1.3.0 using GTF provided by SGD (default parameters)
Unaligned reads from bowtie were aligned to control RNA sequences to obtain relative concentration
Genome_build: SacCer2
Supplementary_files_format_and_content: Processed data files listing all FPKMs used in final analysis

source_name: mid-log phase culture

growth_protocol: rpb1-1 mutant cells (yJC244) were grown to mid-log phase at 24C as described above. Cells were shifted to 37C, then cell aliquots were removed and total RNA was isolated. 10 time points were collected over 60 minutes, including an initial aliquot at time 0 collected before the temperature shift.

extract_protocol:
Cells were lysed by bead bashing in phenol and RNA was purified by acidic phenol-chlorofom extraction
Input RNA was spiked with control RNA and libraries were prepared using either Illumina TruSeq Stranded mRNA library prep kits or Illumina TruSeq Stranded Total RNA library prep kit as indicated above

treatment_protocol: Cells were transferred to non-permissive temperature (37C) to shut off transcription

tag: strain

value: rpb1-1 mutant

tag: mrna type

value: poly(A)+ mRNA

tag: time point (minutes)

tag: repeat


title: yJC_rpb1-1_pA_60 (Run 2)

description:
Sample 40
Sample name: 7802


title: yJC_rpb1-1_pA_6 (Run 2)

description:
Sample 33
Sample name: 7795


title: yJC_rpb1-1_pA_45 (Run 2)

description:
Sample 39
Sample name: 7801


title: KlacNterm_NUCseq

source_name: yeast

tag: mutant

value: CHD1 chimera with K.lactis N-terminus


title: yJC_rpb1-1_pA_20 (Run 2)

description:
Sample 37
Sample name: 7799


title: yJC_rpb1-1_pA_30 (Run 2)

description:
Sample 38
Sample name: 7800


title: yJC_rpb1-1_pA_15 (Run 2)

description:
Sample 36
Sample name: 7798


title: yJC_rpb1-1_RZ_45 (Run 2)

description:
Sample 29
Sample name: 7771

value: total mRNA


title: yJC_rpb1-1_RZ_30 (Run 2)

description:
Sample 28
Sample name: 7770


title: ScerCHD1plasmid2_NUCseq


title: yJC_rpb1-1_pA_10 (Run 2)

description:
Sample 35
Sample name: 7797


title: KlacN1-176_NUCseq

value: CHD1 chimera with N-terminal 176bp from K.lactis


title: yJC_rpb1-1_RZ_15 (Run 2)

description:
Sample 26
Sample name: 7768


title: yJC_rpb1-1_RZ_20 (Run 2)

description:
Sample 27
Sample name: 7769


title: yJC_rpb1-1_pA_0 (Run 2)

description:
Sample 31
Sample name: 7793


title: KlacATPase_NUCseq

value: CHD1 chimera with K.lactis ATPase domain


title: yJC_rpb1-1_RZ_6 (Run 2)

description:
Sample 23
Sample name: 7765


title: yJC_rpb1-1_RZ_10 (Run 2)

description:
Sample 25
Sample name: 7767


title: yJC_rpb1-1_RZ_3 (Run 2)

description:
Sample 22
Sample name: 7764


title: yJC_rpb1-1_RZ_0 (Run 2)

description:
Sample 21
Sample name: 7763


title: yJC_rpb1-1_pA_45 (Run 1)

description:
Sample 19
Sample name: 6550


title: yJC_rpb1-1_pA_3 (Run 2)

description:
Sample 32
Sample name: 7794


title: yJC_rpb1-1_pA_30 (Run 1)

description:
Sample 18
Sample name: 6549


title: yJC_rpb1-1_pA_20 (Run 1)

description:
Sample 17
Sample name: 6548


title: yJC_rpb1-1_RZ_60 (Run 2)

description:
Sample 30
Sample name: 7772


title: yJC_rpb1-1_pA_15 (Run 1)

description:
Sample 16
Sample name: 6547


title: yJC_rpb1-1_pA_8 (Run 1)

description:
Sample 14
Sample name: 6545


title: yJC_rpb1-1_pA_10 (Run 1)

description:
Sample 15
Sample name: 6546


title: ∆pnp_RNA-Seq

city: Oeiras

first: Cecilia

middle: M.

last: Arraiano

address: Av. Republica, Apt 127

country: Portugal

institute: Instituto de Tecnologia Quimica e Biologica (ITQB) / Univ. Nova de Lisboa

description: Sample 4

data_processing:
Vertis Biotechnologie AG bioinformatics department did a preliminary analysis of the high-throughput sequencing results which included the mapping of the reads against E. coli genome (NC_000913 downloaded from NCBI genome database).
We then used the mapped files to run Cufflinks (estimates the relative abundance of the transcripts) and after Cuffdiff to find significant changes in transcript expression when comparing two samples (Trapnell, Williams et al. 2010).
Genome_build: ASM584v2
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

organism: Escherichia coli

source_name: Culture cells

growth_protocol: Overnight cultures from isolated colonies were diluted in fresh medium to an initial OD600~0.03 and grown to exponential phase (OD600~0.3) at 37ºC, with shaking at 200 rpm in Luria-Bertani (LB) medium supplemented with thymine (50 mg ml-1). When required, antibiotics were present at the following concentrations: kanamycin, 50 mg ml-1; tetracycline, 20 mg ml-1; streptomycin/spectinomycin 20 µg ml-1.

extract_protocol:
RNA was isolated following cell lysis and phenol:chloroform extraction as previously described (Andrade, Pobre et al. 2012). After precipitation step in ethanol and 300 mM sodium acetate, RNA was resuspended in MilliQ-water. The integrity of RNA samples was evaluated by agarose gel electrophoresis. Turbo DNase (Ambion) treatment was used to remove contaminant DNA.
RNA libraries were prepared for sequencing by the company Vertis Biotechnologie AG in Germany

tag: growth phase

value: Exponential Phase

value: PNPase mutant


title: WT_RNA-Seq

description: Sample 1

value: Wild-type


title: ∆rnb_RNA-Seq

description: Sample 2

value: RNase II mutant


title: ∆rnr_RNA-Seq

description: Sample 3

value: RNase R mutant


title: yJC_rpb1-1_pA_0 (Run 1)

description:
Sample 11
Sample name: 6542


title: yJC_rpb1-1_RZ_60 (Run 1)

description:
Sample 10
Sample name: 6581


title: yJC_rpb1-1_pA_3 (Run 1)

description:
Sample 12
Sample name: 6543


title: yJC_rpb1-1_RZ_8 (Run 2)

description:
Sample 24
Sample name: 7766


title: yJC_rpb1-1_RZ_45 (Run 1)

description:
Sample 9
Sample name: 6580


title: yJC_rpb1-1_RZ_10 (Run 1)

description:
Sample 5
Sample name: 6576


title: yJC_rpb1-1_pA_60 (Run 1)

description:
Sample 20
Sample name: 6551


title: yJC_rpb1-1_RZ_20 (Run 1)

description:
Sample 7
Sample name: 6578


title: yJC_rpb1-1_RZ_15 (Run 1)

description:
Sample 6
Sample name: 6577


title: yJC_rpb1-1_RZ_3 (Run 1)

description:
Sample 2
Sample name: 6573


title: yJC_rpb1-1_RZ_8 (Run 1)

description:
Sample 4
Sample name: 6575


title: yJC_rpb1-1_RZ_6 (Run 1)

description:
Sample 3
Sample name: 6574


title: Angptl2-Input

status: Public on Mar 16 2015

city: Boston

first: Leonard

last: Zon

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

data_processing:
Images acquired from the Illumina/Solexa sequencer were processed through the bundled Solexa image extraction pipeline, which identified polony positions, performed base-calling, and generated QC statistics.
Sequences were aligned using ELAND software to NCBI Build 36 (UCSC hg18) of the human genome.
All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.
Genome_build: hg18
Supplementary_files_format_and_content: wiggle

source_name: Hematopoietic progenitor cells

growth_protocol: Human CD34+ cells expanded for 6 days in culture

extract_protocol:
Lysates were clarified from sonicated nuclei and Notch antibody bound genomic DNA complexes
Libraries were prepared as follows: DNA was end-repaired using End-It DNA Repair kit (Epicenter ER0720). The blunt, phosphorylated ends were treated with Klenow and dATP for ligation of Illumina's adapters. After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of ~250 bp were gel extracted and purified. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Hi-seq

treatment_protocol: Purified mANGPTL2 was added to cultured cells at 1ug/ml for 1 hour (the Notch antibody used in the ChIP-Seq analysis is a home-made antibody made in our collaborator's lab, Dr Jon Aster's lab).

value: CD34+ cells

tag: expansion

value: 6 days


title: Angptl2-Notch ChIPseq

value: Notch


title: yJC_rpb1-1_RZ_0 (Run 1)

description:
Sample 1
Sample name: 6572


title: input plus acyclovir

source_name: Akata BL cell line_with_acyclovir

tag: pathogen

value: Epstein-Barr virus

tag: cell line

value: Akata

value: B lymphocytes

tag: acyclovir dose

value: with 100uM acyclovir

tag: antibody

value: none (input)


title: hGFAP-Cre/Cx43fl/fl

city: Paris

first: Laurent

last: Jourdren

address: 46 rue d'Ulm

department: Biologie

country: France

institute: École Normale Supérieure

description: Sample 2

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
RNA-Seq data analysis was done using the Eoulsan software version 1.1.6. Before mapping, poly N read tails were trimmed, reads ≤11 bases were removed, and reads with quality mean ≤12 were discarded. Reads were then aligned against the Mus musculus genome (mm10 genome assembly from UCSC) using the Bowtie mapper (version 0.12.7). Alignments from reads matching more than once on the genome were removed. Mus musculus GFF3 genome annotation from UCSC (mm10) was used to compute gene expression. All overlapping regions between alignments and referenced exons were counted.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include transcripts counting (reads counts) for each Sample

source_name: Brain vessel

extract_protocol:
Total RNA was extracted using the Rneasy Lipid tissue kit (Qiagen). PolyA+ RNAs were purified from 1 µg of total RNA using oligo(dT)
Libraries were prepared using the bi-directional RNA-Seq library preparation TruSeq RNA Sample Prep Kits v2 (Illumina)

tag: genetic background


title: PAN02EXO

city: New York

first: David

last: Lyden

department: Departments of Pediatrics, Cell & Developmental Biology

institute: Weill Medical College of Cornell University

data_processing:
Illumina Casava v1.8.2 software used for basecalling.
Sequenced reads were trimmed for low-quality sequences by using fastq_quality_trimmer in the FASTX toolkit with parameters "-t 10 -l 45"; then mapped to the UCSC hg19 human reference genome using tophat v2.0.11 with default parameters.
Number of raw counts was calculated using the htseq-count script in the HTSeq package v0.6.1 with parameters "--stranded=no --mode=union --minaqual=10"; Genes with statistically significant changes in expression were selected by using the edgeR package v3.8.2.
Genome_build: hg19
Supplementary_files_format_and_content: Processed files including gene name, RefSeq id, raw counts and normalized counts of each sample, for each gene

source_name: Primary culture (Life technologies)

growth_protocol: RPMI + 10% exosome free FBS

extract_protocol:
RNeasy Mini Kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated in 6 wells plates with 5ug/mL of exosomes every other day for 14 days

tag: cell type

value: Human Kupffer cells

tag: treatment

value: Treatment with PAN02 exosomes


title: C57BL6-BALB/c

description: Sample 1

tag: genotype/variation

value: WT


title: yJC_rpb1-1_RZ_30 (Run 1)

description:
Sample 8
Sample name: 6579

value: rpb1-1 mutant

value: total mRNA


title: C57BL6

description: Sample 3


title: Human_Kupffer_Cells_BxPC3exo

value: Treatment with BxPC-3 exosomes