title: Cas9-BE3-2_2+Cas9-BE3-3_2

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 106-150
FANCF, RUNX1 Cas9-BE3 DNA replicate 2 and  CDKN2A, DYRK1A Cas9-BE3 DNA replicate 3

data_processing:
Basecalling using Illumina Casava1.8.2 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Reads were aligned against the GRCh37/hg19 human reference genome using BWA-MEM 0.7.9a-r786.
Genome_build: hg19 for human samples
Supplementary_files_format_and_content: Excel for Indels and Base Subtitutions

source_name: 293FT cells

growth_protocol: 293FT from ATCC were maintained in DMEM (10566, Gibco/Thermo Fisher Scientific) + 10% FBS (16000-044, Gibco/Thermo Fisher Scientific) and have been tested for mycoplasma contamination free.

extract_protocol:
For DNA, 72 hr after transfection, the genomic DNA was extracted from the cells with QuickExtractTM DNA Extraction Solution (QE09050, Epicentre).
For DNA, DNA-seq libraries were prepared with Illumina TruSeq ChIP Sample Preparation Kit. Deep sequencing was performed on Illumina Hiseq 2500 and Hiseq X ten at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.

treatment_protocol: For base editing in genomic DNA, cells were seeded in a 24-well plate at a density of 200,000 per well and transfected with 500 μl serum-free Opti-MEM that contained 5.04 μl LIPOFECTAMINE LTX (Life, Invitrogen), 1.68 μl LIPOFECTAMINE plus (Life, Invitrogen), 1 μg pCMV-dCpf1-BE0 (pCMV-dCpf1-BE, pCMV-dCpf1-BE-YE, pCMV-dCpf1-BE-YEE, pCMV-dCpf1-eBE, pCMV-dCpf1-eBE-YE, pCMV-BE2 or pCMV-BE3), and 0.68 μg crRNA or sgRNA-expressing plasmid. After 72 hr, the genomic DNA was extracted from the cells with QuickExtractTM DNA Extraction Solution (QE09050, Epicentre).

tag: cell line

tag: type

value: DNA

tag: treatment


title: NT-2_4

status: Public on Oct 16 2018

type: SRA

country: China

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 106-150
CDKN2A, DNMT1, DYRK1A, Site4 NT DNA replicate 2

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

value: NT


title: NT-2_1+NT-3_4

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 106-150
FANCF NT DNA replicate 2 and CDKN2A, DNMT1, DYRK1A, Site4 NT DNA replicate 3


title: Cas9-BE3-3_2

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 121-150
RUNX1, FANCF Cas9-BE3 DNA replicate 3


title: NT-3_2

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 131-150
FANCF, RUNX1 NT DNA replicate 3


title: Cas9-BE3-1_2+Cas9-BE3-2_2+Cas9-BE3-3_1

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 106-150
FANCF, RUNX1 Cas9-BE3 DNA replicate 1 and CDKN2A, DYRK1A Cas9-BE3 DNA replicate 2 and DNMT1 Cas9-BE3 DNA replicate 3


title: NT-1_1

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 126-150
RUNX1 NT DNA replicate 1


title: NT-1_5+NT-2_1

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 116-150
CDKN2A, DNMT1, DYRK1A, FANCF, Site4 NT DNA replicate 1 and RUNX1 NT DNA replicate2


title: Cas9-BE3-1_2+Cas9-BE3-2_1

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 116-150
CDKN2A, DYRK1A Cas9-BE3 DNA replicate 1 and DNMT1 Cas9-BE3 DNA replicate 2


title: Cas9-BE3-1_1

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 126-150
DNMT1 Cas9-BE3 DNA replicate 1


title: TetO-YAP H3K27ac

status: Public on Oct 18 2018

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

data_processing:
Adapter trimming with skewer (https://github.com/kendomaniac/docker4seq, skewer function, min.length=40)
mapping with BWA (https://github.com/kendomaniac/docker4seq, bwa function, mm10 UCSC mouse assembly)
peack calling woth MACS  (TEAD4 - parameters: macs.min.mfold=10, macs.max.mfold=30, macs.pval=1e-20  and YAP - parameters: macs.min.mfold=10, macs.max.mfold=30, macs.pval=1e-5) or SICER (H3K27 acetilation - prameters: sicer.wsize=600, sicer.gsize=200, sicer.fdr=0.10)  (https://github.com/kendomaniac/docker4seq, chipseq function)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

organism: Mus musculus

source_name: liver

extract_protocol:
Cells were cross-linked in 1% formaldehyde for 10 min at room temperature after which the reaction was stopped by addition of 0.125M glycine. Cells were lysed and harvested in ChIP buffer (100 mM Tris at pH 8.6, 0.3% SDS, 1.7% Triton X-100, and 5 mM EDTA) and the chromatin disrupted by sonication using a Diagenode Bioruptor sonicator UCD-200 to obtain fragments of average 200-500 bp in size. Suitable amounts of chromatin were incubated with specific antibodies overnight. Immunoprecipitated complexes were recovered on Protein-A/G agarose beads (Pierce) and, after extensive washes, DNA was recovered by reverse crosslinking and purification using QIAquick PCR purification kit (QIAGEN).
Libraries for ChIP-sequencing were generated by using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) and barcoded added using NEBNext Multiplex Oligos for Illumina (Index Primers Set 1) (NEB) according to manufacturer’s recommendation.

treatment_protocol: Tetracycline-inducible YAPS127A expression mice were previously described (Camargo et al., 2007). AAV8-TBG-Cre were obtained by University of Pennsylvania Vector Core. 1x10^11 pfu of AAV viruses are injected retro-orbitally. For TetOYAP overexpression, 3 days after AAV-Cre delivery, mice were administered doxycycline (1 mg/ml) ad libitum in their water.

tag: genotype/variation

value: Tetracycline-inducible YAPS127A

tag: sample type

value: strain described in Camargo et al Curr Biol. 2007 Dec 4;17(23):2054-60

tag: antibody

value: anti-acetilate H3K27 (Abcam ab4729)


title: Cas9-BE2-1_2+Cas9-BE2-2_1

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 116-150
CDKN2A, DYRK1A Cas9-BE2 DNA replicate 1 and DNMT1 Cas9-BE2 DNA replicate 2


title: Cas9-BE2-1_1

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 126-150
DNMT1 Cas9-BE2 DNA replicate 1


title: Cas9-BE2-2_3

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 106-150
FANCF, RUNX1, DYRK1A Cas9-BE2 DNA replicate 2


title: Cpf1-eBE-YE-1_1

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 106-150
FANCF Cpf1-eBE-YE DNA replicate 1


title: Cas9-BE2-3_5

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 121-150
CDKN2A, DNMT1, DYRK1A, FANCF, RUNX1 Cas9-BE2 replicate 3


title: Cpf1-eBE-YE-3_2

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 131-150
DYRK1A, RUNX1 Cpf1-eBE-YE DNA replicate 3


title: Cpf1-eBE-YE-1_2+Cpf1-eBE-YE-2_1

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 121-150
DYRK1A, RUNX1 Cpf1-eBE-YE DNA replicate 1 and FANCF Cpf1-eBE-YE DNA replicate 2


title: Cpf1-eBE-YE-2_2+Cpf1-eBE-YE-3_1

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 131-150
DYRK1A, RUNX1 Cpf1-eBE-YE DNA replicate 2 and FANCF Cpf1-eBE-YE replicate 3


title: Cpf1-eBE-3_3

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 131-150
DYRK1A, FANCF, RUNX1 Cpf1-eBE DNA replicate 3


title: Cpf1-eBE-2_1

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 131-150
DYRK1A Cpf1-eBE DNA replicate 2


title: Cpf1-eBE-1_2

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 106-150
FANCF, RUNX1 Cpf1-eBE DNA replicate 1


title: Cpf1-eBE-1_1+Cpf1-eBE-2_2

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 121-150
DYRK1A  Cpf1-eBE DNA replicate 1 and FANCF, RUNX1 Cpf1-eBE DNA replicate 2


title: Cpf1-BE-YE-1_2+Cpf1-BE-YE-2_3

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 121-150
RUNX1, Site4 Cpf1-BE-YE DNA replicate 1 and CDKN2A, DYRK1A, FANCF Cpf1-BE-YE replicate 2


title: Cpf1-BE-YEE-3_4

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 131-150
CDKN2A, DYRK1A, RUNX1, Site4 Cpf1-BE-YEE DNA replicate 3


title: Cpf1-BE-YEE-2_4+Cpf1-BE-YEE-3_1

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 131-150
CDKN2A, DYRK1A, RUNX1, Site4 Cpf1-BE-YEE DNA replicate 2 and FANCF Cpf1-BE-YEE DNA replicate 3


title: Cpf1-BE-YEE-1_1+Cpf1-BE-YEE-2_1

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 121-150
CDKN2A Cpf1-BE-YEE DNA replicate 1 and FANCF Cpf1-BE-YEE replicate 2


title: Cas9-BE2-1_2+Cas9-BE2-2_1_a

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 106-150
FANCF, RUNX1 Cas9-BE2 DNA replicate 1 and CDKN2A Cas9-BE2 DNA replicate2


title: 20d

city: Chengdu

first: Yao

last: Ma

state: Sichuan

address: Huiming road #211

institute: Sichuan Agricultural University

description: micRNA-derived exosome in 20d pigeon milk

library_source: transcriptomic

data_processing:
Initial sequence was subjected to a series of stringent filters (such as removing low quality-reads, repeated sequences and adaptor sequences) and the output was called clean data. Filtered sequences then were mapped to pigeon reference genome (https://www.ncbi.nlm.nih.gov/assembly/GCA_001887795.1) with stringent criteria (0 mismatch in the first 18bp) using Bowtie software
Since no exact annotation of pigeon miRNA was recorded in miRBase 21.0, we performed alignment between the extended genomic sequence of all mappable reads and mature miRNA sequences of chicken (Gallus gallus), zebra finch (Taeniopygia guttata) and other mammals allowing no mismatch. Besides, novel miRNAs were further predicted using the miRDeep2 core algorithm.
For each sample, counts were first normalized by the total count of mappable reads which is denoted as reads per million (RPM), then standardized by the formula log2 (RPM+1), which allowed unbiased comparison among samples.
Genome_build: Genome database:pigeon genome (assembly GCA_001887795.1); miRbase version: V21.0
Supplementary_files_format_and_content: Identified miRNAs in each library with count reads and normalized data

molecule: total RNA

organism: Columba livia

source_name: exosome

extract_protocol:
The total RNA was harvested using Trizol-LS reagent.
The integrity of total RNA was determined by theAgilent 2100 Bioanalyzer and RNA 6000  Nano LabChip Kit with suitable RNA samples having an RNA integrity number > 6.5. Approximately, 15 μg of small RNA-enriched total RNA was prepared for high-throughput sequencing. For each library, small RNA ranging from 15 to 35 nt was purified by 15% Tris-bora-EDTA polyacrylamide gel electrophoresis, and 3´ and 5´ adaptors were ligated with unique small RNA fractions. The modified small RNA was then reverse-transcribed and amplified by reverse transcription-PCR. Finally, the enriched cDNA was sequenced on a Illumina HiSeq 2500 according to the manufacturer’s instructions.

treatment_protocol: First of all, pigeon milk was got rid of impurities and stirred in phosphate buffered saline (PBS). ‘Milk’ samples were cleared of large aggregates as well as cells by sequential centrifugation at 2000 ×g for 30 min at 4 °C. The supernatant was sequentially subjected to centrifugations at 12,000×g for 45 min at 4 °C to remove remaining other debris. It was applied filtration procedures with syringe filters (0.22μm) before the supernatant was prepared by ultracentrifugation at 160,000×g for 90 min. The final fraction was resuspended in 250ul of PBS.

tag: tissue

value: pigeon milk exosomes

tag: developmental stage


title: 10d

description: micRNA-derived exosome in 10d pigeon milk


title: Cpf1-BE-YE-1_3

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 106-150
CDKN2A, DYRK1A, FANCF Cpf1-BE-YE DNA replicate 1


title: Cpf1-BE-1_1+Cpf1-BE-2_5

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 121-150
RUNX1 Cpf1-BE DNA replicate 1 and CDKN2A, DNMT1, DYRK1A, FANCF, Site4 Cpf1-BE replicate 2


title: Cpf1-BE-YE-2_2+Cpf1-BE-YE-3_2

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 131-150
RUNX1, Site4 Cpf1-BE-YE DNA replicate 2 and CDKN2A, FANCF Cpf1-BE-YE DNA replicate 3


title: 15d

description: micRNA-derived exosome in 15d pigeon milk


title: 1d-3

description: micRNA-derived exosome in 1d pigeon milk


title: 5d

description: micRNA-derived exosome in 5d pigeon milk


title: 1d-2


title: Cpf1-BE-3

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 131-150
CDKN2A, DNMT1, DYRK1A, FANCF, RUNX1, Site4 Cpf1-BE DNA repllicate 3


title: Cpf1-BE-YE-3_3

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 131-150
DYRK1A, Site4, RUNX1 Cpf1-BE-YE DNA replicate 3


title: Cpf1-BE0-1_1+Cpf1-BE0-2_4

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 106-150
DNMT1 Cpf1-BE0 DNA replicate 1 and CDKN2A, DYRK1A, FANCF, RUNX1 Cpf1-BE0 DNA replicate 2


title: Cpf1-BE0-3

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 131-150
CDKN2A, DNMT1, DYRK1A, FANCF, RUNX1, Site4 Cpf1-BE0 DNA replicate 3


title: 1d-1


title: Cpf1-BE-1_2

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 106-150
DNMT1, DYRK1A Cpf1-BE DNA replicate 1


title: Cpf1-BE-1_3+Cpf1-BE-2_1

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 116-150
CDKN2A, FANCF, Site4 Cpf1-BE DNA replicate 1 and RUNX1 Cpf1-BE DNA replicate 2


title: Cpf1-BE-YEE-1_4

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 106-150
DYRK1A, FANCF, RUNX1, Site4 Cpf1-BE-YEE DNA replicate 1


title: Cpf1-BE0-2_1

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 126-150
Site4 Cpf1-BE0 DNA replicate 2


title: H3K79me2, ChIPseq, Mus Musculus CGN SGC0946, biological replicate 2

status: Public on Oct 15 2018

city: Freiburg

first: Patrick

middle: Piero

last: Bovio

address: Albertstr. 19

department: Department of Molecular Embryology

country: Germany

institute: Albert-Ludwigs University Freiburg, Institute of Anatomy and Cell Biology

data_processing:
Sequencer: HiSeq2500, 2 lanes,  200 M reads per lane, read length: 50bp paired end, multiplexing run
Raw data processed with Illumina bcl2fastq2 v1.8.4 to fastq files
Reads were directly mapped with Bowtie2 v2.2.0 without trimming
Picard MarkDuplicates v1.136.0 was used to remove read duplicates before peak calling with MACS2 broad peak v2.1.0 and DiffBind v2.1.0
Genome_build: UCSC mm10
Supplementary_files_format_and_content: bigwig

source_name: cerebellum, granular neurons

extract_protocol:
Roidl et al, Stem Cells. 2016 Jan;34(1):233-45. doi: 10.1002/stem.2187.
1 - NEBNext® Ultra DNA Library Prep Kit for Illumina® Minus Size Selection (E7370S/L)

treatment_protocol: CGNP (+SHH) DIV1, 4 h or CGN (+FBS) DIV2, 44 h after DOT1L inhibition with SGC0946; each compared to DMSO control. Cells derived from murine cerebellum of P7 NMRI WT mice

tag: agent

value: CGN SGC0946

tag: strain

value: NMRI

value: P7, DIV2

tag: genotype

value: Wildtype


title: Input, Mus Musculus CGN SGC0946, biological replicate 2

value: none, Input


title: Cpf1-BE0-1_4+Cpf1-BE0-2_1

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 116-150
CDKN2A, DYRK1A, FANCF, RUNX1 Cpf1-BE0 DNA replicate 1 and DNMT1 Cpf1-BE0 DNA replicate 2


title: Cpf1-BE0-1_1

description:
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 126-150
Site4 Cpf1-BE0 DNA replicate 1


title: H3K79me2, ChIPseq, Mus Musculus CGN SGC0946, biological replicate 1


title: Input, Mus Musculus CGN DMSO, biological replicate 2

value: CGN DMSO


title: H3K79me2, ChIPseq, Mus Musculus CGN DMSO, biological replicate 2


title: Input, Mus Musculus CGN DMSO , biological replicate 1


title: Input, Mus Musculus CGN SGC0946 , biological replicate 1


title: H3K79me2, ChIPseq, Mus Musculus CGNP SGC0946, biological replicate 2

source_name: cerebellum, granular neuron progenitors

value: CGNP SGC0946

value: P7, DIV1


title: H3K79me2, ChIPseq, Mus Musculus CGN DMSO, biological replicate 1


title: H3K79me2, ChIPseq, Mus Musculus CGNP SGC0946, biological replicate 1


title: Input, Mus Musculus CGNP DMSO, biological replicate 2

value: CGNP DMSO


title: H3K79me2, ChIPseq, Mus Musculus CGNP DMSO, biological replicate 2


title: H3K79me2, ChIPseq, Mus Musculus CGNP DMSO, biological replicate 1


title: Control 1

city: Houaton

first: Rainer

middle: B

last: Lanz

state: TX

address: One Baylor Plaza

department: Molecular and Cellular biology

country: USA

institute: Baylor College of Medicine

data_processing:
In order to increase the mappability, we trimmed 11 low-quality nucleotides from the 5’ ends of the reads.
The resulting 90-nucleotide pair-ended reads were mapped to the mouse genome (UCSC mm9) using STAR (Dobin et al., 2013) with NCBI RefSeq genes as the reference.
In order to reduce possible PCR biases, we removed the read duplicates using picard tools (http://broadinstitute.github.io/picard/)
HTseq (http://www-huber.embl.de/users/anders/HTSeq) was used to determine the number of reads falling in the known genes.
EdgeR (Robinson et al., 2010) was used to analyze the gene-based read counts to detect differentially expressed genes between the control and treatment groups.
Genome_build: mm9
Supplementary_files_format_and_content: EdgeR_KO.vs.WT_DE.txt reports Symbol, rawMeanCount_WT, rawMeanCount_KO, FC_edgeR, log2CPM_edgeR, PV_edgeR, FDR_edgeR, EntrezGene, geneName2.

source_name: Foxo1f/f, uterus

growth_protocol: standard chow

extract_protocol:
RNA was isolated using the Qiagen RNeasy Kit
Illumina TruSeq RNA Sample Preparation Protocol

treatment_protocol: Control Foxo1f/f and conditional knock out PgrCre/+ Foxo1f/f female mated with vasectomized males. Uteri harvest at day 4.5 of pseudopregnancy. Serum progesterone levels used to confirm stage of pregnancy.

tag: age

value: 8 weeks

value: Pseudo pregnancy day 4.5

value: uterus


title: Conditional Foxo1 knock-out 2

source_name: PgrCre/+ Foxo1f/f, uterus

value: PgrCre/+ Foxo1f/f


title: Conditional Foxo1 knock-out 3


title: SIR3Δ 2

city: Paris

first: Antonin

last: Morillon

address: 26 rue d'Ulm

country: France

institute: Institut Curie

data_processing:
Mapping with tophat 1.4.1 with default parameters
Readcount with in-house scripts
Normalization on total mapped read numbers
Genome_build: S288C saccharomyces cerevisiae R64-1-1 downloaded from SGD on september 25th 2011
Supplementary_files_format_and_content: tab delimited file containing genomic feature annotations and normalized read counts

organism: Saccharomyces cerevisiae

source_name: SIR3Δ_exponentially growing yeast cells

growth_protocol: Exponentially growing yeasts

extract_protocol:
Phenol-chloroform
Banks were constructed using the kit SOLiD Total RNA-Seq, with minor modifications : RNA are Zinc fragmented and fragments with size ranging form 100 to 200 nt selected by gel purification.
After reverse transcription only fragment of size > 150nt are kept. Paired end (50 + 35 ) sequencing was done by the Institut Curie plateform.

tag: strain background

value: SIR3{delta}; sir3-delta strain


title: Control 3


title: Input, Mus Musculus CGNP SGC0946 , biological replicate 1


title: Conditional Foxo1 knock-out 1


title: Input, Mus Musculus CGNP DMSO , biological replicate 1


title: GPD-SIR3 2

source_name: GPD-SIR3_exponentially growing yeast cells

value: GPD-SIR3; overexpressing SIR3


title: SIR3Δ 1


title: Control 2


title: GPD-SIR3-A2Q 2

source_name: GPD-SIR3-A2Q_exponentially growing yeast cells

value: GPD-SIR3-A2Q; overexpressing the SIR3-A2Q point mutation


title: GPD-SIR3 1


title: WT 1

source_name: WT_exponentially growing yeast cells

value: WT; wild-type


title: WT control  in E. coli

city: Hangzhou

first: Fei

last: Xu

address: 198 Shiqiao Road

institute: Zhejiang Academy of Agricultural Sciences

description:
processed data file: Ec_exp.txt
Ec_CK RPKM

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mo8 whole genome using CLC Genomics Workbench with default parameters
Reads Per Kilobase of exon per Million mapped reads (RPKM) for gene were calculated using CLC Genomics Workbench with default parameters
Genome_build: E. coli reference genome: DH10B, NC_010473.1
Genome_build: P. aeruginosa reference genome: PAO1, NC_002516.2
Supplementary_files_format_and_content: abundance measurements

organism: Escherichia coli

source_name: bacteria

growth_protocol: Endolysin wild type and mutant were expressed in E. coli and P. aeruginosa after 8-10 hours of arabinose induction

extract_protocol:
RNA was extracted by RNA extract kit,and MICROBExpress™ is designed to rapidly enrich bacterial mRNA from  purified total RNA by removing the 16S and 23S ribosomal RNAs  (rRNA).
Samples were barcoded and sequenced using the PE100 protocol on a HiSeq2000 sequencer, and RNA sequencing was performed by staff at Zhejiang Tianke (Hangzhou, China).Reads trimming and mapping were done using the CLC Genomics Workbench (QIAGEN, http://www.clcbio.com/). Default parameters were used if not specified. Reads of different samples were trimmed with maximal allowed ambiguous nucleotides of 2.

value: wild type (control)

tag: induced with

value: none (control)


title: Mutant endolysin expressed  in  P. aeruginosa

description:
processed data file: Pa_exp.txt
Pa_E12 RPKM

organism: Pseudomonas aeruginosa

value: expressing mutant endolysin

value: arabinose for 8-10hrs


title: Mutant endolysin expressed  in E. coli

description:
processed data file: Ec_exp.txt
Ec_E12 RPKM


title: WT control  in P. aeruginosa

description:
processed data file: Pa_exp.txt
Pa_CK RPKM


title: WT endolysin expressed  in P. aeruginosa

description:
processed data file: Pa_exp.txt
Pa_E RPKM

value: expressing WT endolysin


title: WT endolysin expressed  in E. coli

description:
processed data file: Ec_exp.txt
Ec_E RPKM


title: Repeat Treated Timepoint 5

status: Public on Oct 13 2018

city: East Lansing

first: George

last: Mias

address: 775 Woodlot Drive, Rm1319

department: Biochemistry and Molecular Biology

institute: Michigan State University

data_processing:
Data QC using FastQC, and reads trimmed 15 from the left and 15 from the right
Trimmed paired reads mapped using Tophat 2.1.0 (using --no-coverage-search --library-type fr-firststrand)
Mapped files quantitated using Cufflinks (--no-effective-length-correction, using hg38 annotation)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample corresponding to Cufflinks output.

source_name: Primary B Cells

growth_protocol: The Primary B cells (Stemcell technologies, Catalog # 70023.1, Lot # 1606290232) were grown to a a density of 0.6-0.8 x 10^6/mL in X VIVO-15 Serum free media

extract_protocol:
For RNA-Seq, total RNA was extracted using the Qiagen RNeasy kit (Qiagen) and treated with RNAse-free DNase (Qiagen). RNA from ~2 million cells was extracted, with concentration measured on a Qubit (Life Technologies). Additionally, RNA integrity was checked on a Bioanalyzer (Agilent, Santa Clara CA) and only RNA with an RNA integrity number (RIN) of > 7 was used for subsequent library construction. Library QC included Qubit, Bioanalyzer and PCR.
Libraries were constructed using Illumina's TruSeq kits following the manufacturer's protocol. cDNA was quantitated on a Bioanalyzer (Agilent).

treatment_protocol: Cells were grown together and separated into two flasks at the beginning of the time course (corresponding to a “treated” and an “untreated” condition).  Both flasks were sampled simultaneously over 6 timepoints (0,1,2,4,7,15 hours). The difference between the conditions occurs at time point 1 (0 hours) where, after taking a sample, the cells corresponding to the “treated” condition were treated with Rituximab at a concentration of 20 micrograms/ml.  The experiment was repeated (samples names designated by R prefix)

value: B Cells

value: repeat treated

tag: timepoint


title: Repeat Treated Timepoint 6


title: Repeat Treated Timepoint 4


title: Repeat Treated Timepoint 3


title: WT 2


title: Repeat Untreated Timepoint 6

value: repeat untreated


title: Repeat Treated Timepoint 2


title: RepeatTreated Timepoint 1

description: treated right after sampling


title: GPD-SIR3-A2Q 1


title: Input, Mus Musculus CGNP SGC0946, biological replicate 2

value: none, Input

value: CGNP SGC0946

value: NMRI

value: P7, DIV1

value: Wildtype


title: Repeat Untreated Timepoint 5


title: Treated Timepoint 2

value: treated


title: Repeat Untreated Timepoint 3


title: Treated Timepoint 6


title: Treated Timepoint 5


title: Repeat Untreated Timepoint 2


title: Treated Timepoint 3


title: Untreated Timepoint 6

value: untreated


title: Untreated Timepoint 5


title: Treated Timepoint 1

description: treated right after sampling


title: Treated Timepoint 4


title: Untreated Timepoint 3


title: Untreated Timepoint 2


title: Untreated Timepoint 4


title: Repeat Untreated Timepoint 4


title: Repeat Untreated Timepoint 1


title: Untreated Timepoint 1


title: mouse_rnaseq_astrocyte_1

status: Public on Oct 12 2018

city: New York

first: Xiao

state: NY

address: 1230 York Ave

department: Laboratory of Molecular Biology

institute: The Rockefeller University

data_processing:
Data was mapped to the Mus musculus reference genome (mm10).
Analysis for RNA-seq datasets were performed as described in Xu et al., 2017
RNA-seq: Reads were aligned to the mm10 genome using STAR v2.4.2a (--outFilterMismatchNmax 999 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 35 --outFilterMismatchNoverLmax 0.05)
RNA-seq: Gene expression levels were estimated using featureCounts v1.5.2 (-C)
RNA-seq: Visualization tracks were generated using igvtools v2.3.32.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited txt format; Table of raw counts for all samples generated using species-specific annotations, mouse-rat-human ortholog annotations, or mouse-human ortholog annotations.

source_name: nuclear RNA from specific cell types obtained via the INSPECTION method

growth_protocol: All procedures involving mice were approved by The Rockefeller University Institutional Animal Care and Use Committee (IACUC) and were in accordance with the National Institutes of Health guidelines. Mice were housed in a specific-pathogen free facility, in groups of four to five per cage under a 12-h light-dark cycle with food and water ad libitum. Animals were sacrificed between 2-4 months of age.

extract_protocol:
Cerebellum was dissected and cell-type specific nuclei were isolated using the INSPECTION method or using FACS for GFP+ nuclei. Isolated nuclei were resuspended in Buffer PKD (INSPECTION) or RLT (GFP+) for RNA purification using the QNeasy FFPE kit or RNeasy Micro kit. Standard protocols were followed except with the following modifications for the FFPE kit: after Proteinase K digestion, RNA was spun at max speed for 15 minutes. The supernatant was removed and incubated at 65oC for 30 minutes, 70oC for 30 minutes, and 80oC for 15 minutes. An on-column DNase digestion was performed in place of the in-solution DNAase digestion. RNA quality was determined using Agilent 2100 Bioanalyzer.
Purified RNA was converted to cDNA and amplified using the Nugen Ovation RNA-seq System V2. Amplified cDNA was fragmented, end-repared, adpater ligated, fragment enriched, and sequenced on an Illumina HiSeq 2500 or NextSeq 500 instrument.

tag: brain region

value: cerebellum

tag: cell type

value: astrocyte

tag: target molecule

value: nuclear RNA


title: mouse_rnaseq_basket_3

value: basket


title: mouse_rnaseq_opc_1

value: OPC


title: mouse_rnaseq_cyt_1

source_name: cytoplasmic RNA from the cerebellum

value: mixed


title: mouse_rnaseq_oligo_1

value: oligodendrocyte - mature


title: mouse_rnaseq_basket_1


title: mouse_rnaseq_cyt_2


title: mouse_rnaseq_purkinje_3

value: Purkinje


title: mouse_rnaseq_purkinje_1


title: mouse_rnaseq_gfp_ntsr1_cthalamic_3

source_name: nuclear RNA from GFP+ nuclei

value: Corticothalamic


title: mouse_rnaseq_granule_1

value: granule


title: mouse_rnaseq_gfp_ntsr1_cthalamic_2


title: mouse_rnaseq_gfp_ntsr1_cthalamic_1


title: mouse_rnaseq_granule_3


title: mouse_rnaseq_opc_2


title: mouse_rnaseq_oligo_all_1

value: oligodendrocyte - all


title: human_rnaseq_glia_WI

data_processing:
Data was mapped to the Homo sapiens reference genome (hg38).
Analysis for RNA-seq datasets were performed as described in Xu et al., 2017
RNA-seq: Reads were aligned to the mm10 genome using STAR v2.4.2a (--outFilterMismatchNmax 999 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 35 --outFilterMismatchNoverLmax 0.05)
RNA-seq: Gene expression levels were estimated using featureCounts v1.5.2 (-C)
RNA-seq: Visualization tracks were generated using igvtools v2.3.32.
Genome_build: hg38
Supplementary_files_format_and_content: Tab delimited txt format; Table of raw counts for all samples generated using species-specific annotations, mouse-rat-human ortholog annotations, or mouse-human ortholog annotations.

extract_protocol:
Cell-type specific nuclei were isolated from post-mortem cerebellar tissue using the INSPECTION method. Isolated nuclei were resuspended in Buffer PKD (INSPECTION) for RNA purification using the QNeasy FFPE kit. Standard protocols were followed except with the following modifications: after Proteinase K digestion, RNA was spun at max speed for 15 minutes. The supernatant was removed and incubated at 65oC for 30 minutes, 70oC for 30 minutes, and 80oC for 15 minutes. An on-column DNase digestion was performed in place of the in-solution DNAase digestion. RNA quality was determined using Agilent 2100 Bioanalyzer.
Purified RNA was converted to cDNA and amplified using the Nugen Ovation RNA-seq System V2. Amplified cDNA was fragmented, end-repared, adpater ligated, fragment enriched, and sequenced on an Illumina HiSeq 2500 or NextSeq 500 instrument.

tag: gender

value: female

value: glia

value: nuclear rna


title: human_rnaseq_glia_TM


title: human_rnaseq_glia_WL

value: male


title: human_rnaseq_glia_OR


title: human_rnaseq_glia_LT


title: human_rnaseq_glia_SG


title: mouse_rnaseq_purkinje_2


title: mouse_rnaseq_oligo_2


title: human_rnaseq_glia_KQ


title: human_rnaseq_glia_KO


title: mouse_rnaseq_granule_2


title: human_rnaseq_basket_WI


title: human_rnaseq_basket_WL


title: human_rnaseq_basket_WC


title: human_rnaseq_glia_KE


title: human_rnaseq_basket_ZH


title: human_rnaseq_glia_ZH


title: human_rnaseq_glia_AI


title: human_rnaseq_basket_WO


title: human_rnaseq_basket_LT


title: human_rnaseq_basket_KQ


title: human_rnaseq_basket_VM


title: human_rnaseq_basket_TM


title: human_rnaseq_basket_OR


title: human_rnaseq_basket_KO


title: human_rnaseq_glia_VM


title: human_rnaseq_basket_AI


title: human_rnaseq_basket_KE


title: human_rnaseq_granule_ZH


title: human_rnaseq_granule_WO


title: human_rnaseq_granule_WI


title: human_rnaseq_granule_WC


title: human_rnaseq_granule_WL


title: human_rnaseq_basket_SG


title: human_rnaseq_granule_TM


title: human_rnaseq_granule_VM


title: human_rnaseq_granule_SG


title: human_rnaseq_granule_OR


title: human_rnaseq_granule_LT


title: human_rnaseq_granule_KQ


title: human_rnaseq_granule_KO


title: human_rnaseq_opc_XK


title: human_rnaseq_cyt_PK

value: cytoplasmic RNA


title: human_rnaseq_cyt_XK


title: human_rnaseq_granule_KE


title: human_rnaseq_opc_PK


title: human_rnaseq_oligo_XK

value: oligodendrocyte


title: human_rnaseq_astrocyte_PK

value: cerebellum


title: human_rnaseq_glia_XK


title: human_rnaseq_basket_XK


title: human_rnaseq_basket_PK


title: human_rnaseq_astrocyte_XK

value: astrocyte


title: human_rnaseq_granule_XK


title: rat_rnaseq_cyt_2

data_processing:
Data was mapped to the Rattus norvegicus reference genome (rn6).
Analysis for RNA-seq datasets were performed as described in Xu et al., 2017
RNA-seq: Reads were aligned to the rn6 genome using STAR v2.4.2a (--outFilterMismatchNmax 999 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 35 --outFilterMismatchNoverLmax 0.05)
RNA-seq: Gene expression levels were estimated using featureCounts v1.5.2 (-C) using annotation files for whole genes or exons
RNA-seq: Visualization tracks were generated using igvtools v2.3.32.
Genome_build: rn6
Supplementary_files_format_and_content: Tab delimited txt format; Table of raw counts for all samples generated using species-specific annotations, mouse-rat-human ortholog annotations, or mouse-human ortholog annotations.; tdf format for visualization in IGV.

organism: Rattus norvegicus

extract_protocol:
Cerebellum was dissected and cell-type specific nuclei were isolated using the INSPECTION method. Isolated nuclei were resuspended in Buffer PKD (INSPECTION) for RNA purification using the QNeasy FFPE kit. Standard protocols were followed except with the following modifications: after Proteinase K digestion, RNA was spun at max speed for 15 minutes. The supernatant was removed and incubated at 65oC for 30 minutes, 70oC for 30 minutes, and 80oC for 15 minutes. An on-column DNase digestion was performed in place of the in-solution DNAase digestion. RNA quality was determined using Agilent 2100 Bioanalyzer.
Purified RNA was converted to cDNA and amplified using the Nugen Ovation RNA-seq System V2. Amplified cDNA was fragmented, end-repared, adpater ligated, fragment enriched, and sequenced on an Illumina NextSeq 500 instrument.

value: Sprague Dawley


title: human_rnaseq_granule_PK


title: 24h tamoxifen-rep06

city: Cambridge

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

country: United Kingdom

institute: Cancer Research UK, Cambridge Institute

description: asynchronous MCF7 breast cancer cells treated with  OHT for 24h

data_processing:
Single-end 50-bp reads were aligned to the human genome version GRCh37.75 using TopHat v2.1.0
Read counts were then obtained using feature Counts function in Subread v1.5.2
Read counts was then normalized and tested for differential gene expression using the DESeq2 workflow
Genome_build: GRCh37.75

source_name: MCF7 breast cancer cell line

extract_protocol:
Total RNA was extracted using the RNeasy® kit (Qiagen, #74106)
Illumina TruSeq Stranded mRNA Library Prep Kit High Throughput

tag: cell line

value: Breast cancer

tag: time point


title: 6h tamoxifen-rep06

description: asynchronous MCF7 breast cancer cells treated with  OHT for 6h


title: human_rnaseq_granule_AI


title: rat_rnaseq_unsorted_2

source_name: nuclear RNA from unsorted cerebellar nuclei

value: nuclear RNA


title: rat_rnaseq_opc_2

value: Oligodendrocyte Precursor Cell


title: 2h tamoxifen-rep06

description: asynchronous MCF7 breast cancer cells treated with  OHT for 2h


title: rat_rnaseq_opc_1


title: rat_rnaseq_unsorted_1

value: mixed


title: vehicle-rep06

description: asynchronous MCF7 breast cancer cells treated with  ethanol for 24h

value: ethanol


title: rat_rnaseq_oligo_1

value: Oligodendrocyte


title: rat_rnaseq_basket_2

value: Basket


title: rat_rnaseq_astrocyte_1

value: Astrocyte


title: human_rnaseq_oligo_PK

value: female


title: human_rnaseq_glia_PK

value: glia


title: rat_rnaseq_astrocyte_2


title: rat_rnaseq_purkinje_2

value: Purkinje


title: rat_rnaseq_granule_2

value: Granule


title: rat_rnaseq_purkinje_1


title: 6h tamoxifen-rep05


title: rat_rnaseq_granule_1


title: 2h tamoxifen-rep05


title: vehicle-rep05


title: rat_rnaseq_cyt_1

value: cytoplasmic RNA


title: rat_rnaseq_oligo_2


title: 24h tamoxifen-rep04


title: 24h tamoxifen-rep05


title: 6h tamoxifen-rep04


title: mouse_rnaseq_basket_2

value: basket


title: 2h tamoxifen-rep04


title: vehicle-rep04


title: 24h tamoxifen-rep03


title: 6h tamoxifen-rep03


title: vehicle-rep03


title: rat_rnaseq_basket_1

value: cerebellum


title: 2h tamoxifen-rep02


title: 6h tamoxifen-rep02


title: vehicle-rep02


title: 24h tamoxifen-rep01


title: 2h tamoxifen-rep01


title: rat_atac_1

data_processing:
Adapter sequences were trimmed and reads were filtered depending on quality using Trim Galore! (trim_galore --stringency 3 --fastqc --paired *_R1_2.fastq.gz *_R2_2.fastq.gz).
Reads that passed the filter were aligned using Bowtie2 (Langmead and Salzberg, 2012) to the Rattus norvegicus reference genome (rn6).
Duplicate reads were removed using SAMtools (Li et al., 2009).
For data visualization, tdf files were generated using igvtools.
Genome_build: rn6
Supplementary_files_format_and_content: tdf format for visualization in IGV

source_name: unsorted nuclei from cerebellum

extract_protocol:
Cerebellum was dissected and nuclei were isolated. ATAC-seq libraries were prepared as described previously (Buenrostro et al., 2013; 2015) with the following modifications: nuclei were resuspended in ice-cold lysis buffer, omitting incubation step on ice and centrifuged. Transposition reaction was performed for 30 min at 37°C using Tn5 transposase from Nextera. DNA fragments were purified and size selected using AMPure XP beads to yield 100-700bp fragments.
Libraries were generated using the Nextera DNA Library Preparation Kit. ATAC-seq libraries from mouse and human cerebellum were sequenced on the Illumina HiSeq2500 to obtain 50bp paired-end reads, and libraries generated from rat cerebellum were sequenced on Illumina HiSeq 2500 NextSeq 500 to obtain 75bp paired-ended reads.


title: mouse_rnaseq_gfp_colgalt2_cpontine_2

value: Corticopontine


title: mouse_rnaseq_gfp_sept4_bglia_3

value: Bergmann glia


title: 6h tamoxifen-rep01

value: Breast cancer


title: mouse_rnaseq_gfp_sept4_bglia_2

value: nuclear RNA


title: mouse_rnaseq_gfp_sept4_bglia_4


title: mouse_rnaseq_gfp_sept4_bglia_1


title: mouse_rnaseq_gfp_pcp2_purkinje_4


title: mouse_rnaseq_gfp_pcp2_purkinje_3


title: mouse_rnaseq_gfp_pcp2_purkinje_2


title: mouse_rnaseq_gfp_neurod1_granule_3

value: granule


title: mouse_rnaseq_gfp_pcp2_purkinje_1


title: 2h tamoxifen-rep03


title: mouse_rnaseq_gfp_neurod1_granule_2


title: 24h tamoxifen-rep02


title: mouse_rnaseq_gfp_neurod1_granule_1


title: mouse_rnaseq_gfp_colgalt2_cpontine_3


title: mouse_rnaseq_gfp_colgalt2_cpontine_1


title: JYAC2 untreated DREADS Biological Replicate B

status: Public on Oct 11 2018

city: Boston

first: Zarmik

last: Moqtaderi

state: MA

address: 240 Longwood Avenue C2-355

department: BCMP

institute: Harvard Medical School

data_processing:
python scripts: remove 4 random nt from each read, count and remove initial Ts from R1 reads, discard any reads containing Ns, truncate remainder of each read to 17nt max (starting at nt 2 for the R2 side), discard reads with fewer than 9nt remaining after T removal.
bowtie: map to genome using bowtie with one mismatch and m1, X1000
python: screen the mapped reads to determine which initial Ts arose from genomically encoded As vs As added after cleavage
Microsoft Excel: normalize to equal number of total processed reads per sample
python: readjust mapped first position of R2 back 2nt: one nt to compensate for having started mapping from nt 2, and one more because the potential DMS-modified nt is 1 nt upstream of the last reverse-transcribed position
python: For DREADS samples, consolidate instances of every possible DMS-modfied position (mapped R2 read start position minus 2) for every 3' isoform
python: For every isoform, compare A and C positions of DMS-treated and control samples, subtracting read count of control from DMS sample to obtain net reads for the position
python: Obtain Winsorized reactivity values for every isoform by averaging the top 15 net reads values in the 300-nt window, assigning this averaged top value a score of 1, and scaling all other net reads values relative to this.
RNAStructure: predict folding of mRNA isoforms (assuming a 30-nt poly(A) tail) with and without considering the DMS reactivity values. (parameters: 30°C, 200 nt maximum pairing window)
Genome_build: S. cerevisiae build SacCer 3;  S. pombe build EF2; D. hansenii Deha2; K. lactis Klla0
Supplementary_files_format_and_content: Tab-delimited text files containing consolidated reads for each 3' isoform

source_name: Saccharomyces cerevisiae host harboring Kluyveromyces lactis chromosome segment on a YAC; sample spiked with a small amount of Schizosaccharomyces pombe

growth_protocol: Cells were cultured in YPD medium to mid-log phase prior to treatment and harvesting

extract_protocol:
Hot acidic phenol extraction of total RNA, followed by purification on Qiagen Rneasy columns with Dnase I treatment
DREADS/SHREADS library protocol: 25 µg mRNA was purified from total RNA samples with oligo dT(25) magnetic beads (NEB), and was then bound to beads pre-coated with a U45T5 biotinylated mRNA capture oligonucleotide1.  Immobilized mRNA tails were trimmed with RNase H to generate shortened poly(A) sequences averaging ~ 5 A’s as described1.  After ligation of 5’ pre-adenylated adapter A to the trimmed mRNA 3’ ends, mRNAs were reverse transcribed with Superscript III (Life Technologies) using primer B1.  cDNAs were ligated with T4 DNA Ligase to splint adapter C, and the single-stranded DNA products (110 – 500 nt) were purified on 6% polyacrylamide-urea gels.  DNA fragments were amplified by 18 cycles of PCR with barcoded oligonucleotides as described1.  Amplified libraries were purified with SizeSelector-I beads (Aline Biosciences) as described1. Adapter A: 5′-/5rApp/NNNNGATCGTCGGACTGTAGAACTCTGAAC/3ddC/-3′  Primer B: 5′ -GTTCAGAGTTCTACAGTCCGACGATC-3′  Splint Adapter: This is a double-stranded adapter where Z is the double-stranded equivalent of N.                                      5’ – ZZZZTGGAATTCTCGGGTGCCAAGG – 3’                     3’ – NNNNNNZZZZACCTTAAGAGCCCACGGTTCC – 5’  1. Jin, Y. et al. Mapping 3' mRNA isoforms on a genomic scale. Curr. Protoc. Mol. Biol. 110, 4.23.21-24.23.17 (2015)

treatment_protocol: Some samples were treated with dimethyl sulfate or NAI as described in the methods

tag: library strategy

value: DREADS


title: JYAC2 DMS-treated DREADS Biological Replicate A


title: JYAC7 untreated DREADS Biological Replicate B

source_name: Saccharomyces cerevisiae host harboring Debaryomyces hansenii chromosome segment on a YAC; sample spiked with a small amount of Schizosaccharomyces pombe


title: JYAC7 DMS-treated DREADS Biological Replicate B


title: vehicle-rep01

value: ethanol


title: JYAC2 DMS-treated DREADS Biological Replicate B


title: JYAC7 untreated DREADS Biological Replicate A


title: 2_CCR2NEGCD11CLO

city: Beijing

first: Xiangxiang

last: Jiang

state: Beijing

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Raw reads were filtered into clean reads by software SOAPnuke 1.5.6.
After filtering, BWA 0.7.10-r789 was used to map clean reads to genome reference and Bowtie 2.2.5 was used to map to gene references.
Genes expression level is quantified by a software package called  RSEM v1.1.17.
Genome_build: hg19
Supplementary_files_format_and_content: Text files include expected counts and FPKM values for each Sample

source_name: decidua

growth_protocol: isolated directly from decidua or peripheral blood without culture.

extract_protocol:
When primary cells were isolated by FACS or MACS, cells were precipitated. RNA was harvested using Trizol reagent. RNA concentration and quality were tested by Agilent 2100.  0.2 ug of total RNA was utilized for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment

tag: Stage

value: first trimester

value: decidua

value: decidual macrophages


title: 2_CCR2POSCD11CHI

tag: tissue

value: female


title: 3_CCR2NEGCD11CHI


title: 3_CCR2NEGCD11CLO


title: 2_CCR2NEGCD11CHI


title: H3K27ac_SiPrdm9_2

city: Mainz

first: Abhijeet

last: Pataskar

address: Ackermannweg 4

institute: Institute of Molecular Biology

description:
in-vitro
processed data file: SiPrdm9.wig.gz

data_processing:
The FASTQ files were aligned human genome (mm9) using TopHat v2.0.8 for RNAseq and Bowtie for ChIPseq
Samtools v0.1.19 was used for File format conversions (bam to sam)
Reads at transcripts were counted using HTSeq (v0.5.4p1) for RNASeq and QuaSR for ChIPseq at peaks called by MACS
Normalization (for library size) was done using DESeq
Differential expression analysis was done using DESeq
Genome_build: mm9
Supplementary_files_format_and_content: Excel file containing normalized read counts, MACS PEAK FILE AND WIGGLE FILES

growth_protocol: ES cell–derived aNPC cells were cultured in DMEM-F12 media supplemented with N2 and 10 ng/ml of both EGF and FGF-2. These aNPCs are differentiated into astrocytes for 1 day (eA), 5 days (lA_1) and 21 days (lA_2) in differentiation media comprising DMEM, 1% FBS and LIF.

extract_protocol:
For RNA-seq, RNA was harvested using Trizol reagent. For ChIP-seq, lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody against H3K27ac and H3K4me1 histone marks.
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For siRNA experiments, cells were transfected with corresponding siRNAs using Lipofecatmine RNAimax by following manufacturer's protocol in suspension culture. Cells were treated re-transfected with siRNA after 2 days for maintaining the culture and depletion for 5 days.

value: mature astrocytes  (lA)

tag: genotype/variation

tag: chip antibody

value: Anti-Histone H3 (acetyl K27) antibody (Abcam ab4729)


title: H3K27ac_SiPrdm9_1


title: 1_CCR2NEGCD11CLO


title: 1_CCR2POSCD11CHI


title: 1_CCR2NEGCD11CHI


title: 1_MO

source_name: peripheral blood

value: peripheral blood

value: peripheral monocytes


title: H3K27ac_SiStat3_1

description:
in-vitro
processed data file: SiStat3.wig.gz

value: early astrocytes (eA)


title: H3K27ac_SiRunx2_2

description:
in-vitro
processed data file: SiRunx2_lA.wig.gz


title: H3K27ac_SiStat3_2


title: JYAC7 DMS-treated DREADS Biological Replicate A


title: JYAC2 untreated DREADS Biological Replicate A


title: mouse_rnaseq_astrocyte_2

tag: strain

value: cerebellum

value: astrocyte


title: H3K27ac_SiRunx2_1


title: 3_MO


title: H3K27ac_SiNfia_2

description:
in-vitro
processed data file: SiNfia_eA.wig.gz

value: SiNfia


title: H3K27ac_Control_lA_2

description:
in-vitro
processed data file: Control_lA.wig.gz


title: H3K27ac_Control_lA_1


title: 2_MO


title: H3K27ac_SiAtf3_2

description:
in-vitro
processed data file: SiAtf3_eA.wig.gz


title: H3K27ac_SiNfia_1


title: H3K27ac_Control_eA_1

description:
in-vitro
processed data file: Control_eA.wig.gz


title: RNA_SiRunx2_2

description:
in-vitro
SiAtf3_D1_2
processed data file: NTC_2.xls


title: H3K27ac_SiAtf3_1


title: H3K27ac_Control_eA_2


title: RNA_SiRunx2_1

description:
in-vitro
SiAtf3_D1_1
processed data file: NTC_2.xls


title: RNA_SiNfia_1

description:
in-vitro
SiNfia_D1_1
processed data file: NTC_2.xls


title: RNA_SiAtf3_2

description:
in-vitro
CntD1_2
processed data file: NTC_2.xls


title: RNA_SiNfia_2

description:
in-vitro
SiNfia_D1_2
processed data file: NTC_2.xls


title: RNA_Control_lA_2

description:
in-vitro
siRunx2_D5_2
processed data file: NTC_2.xls


title: RNA_Control_eA_2

description:
in-vitro
CntD5_1
processed data file: NTC_2.xls


title: H3K4me1_lA_1

description:
in-vitro
processed data file: 5D_H3K4me1_peaks.encodePeak.txt


title: RNA_Control_eA_1


title: H3K4me1_lA_2


title: 3_CCR2POSCD11CHI


title: RNA_Control_lA_1

description:
in-vitro
siRunx2_D5_1
processed data file: NTC_2.xls


title: H3K4me1_eA_2

description:
in-vitro
processed data file: 1D_H3K4me1_peaks.encodePeak.txt


title: H3K4me1_eA_1


title: H3K27ac_lA_2

description:
in-vitro
processed data file: 5D_H3K27ac_peaks.encodePeak.txt


title: H3K4me1_aNPC_2

description:
in-vitro
processed data file: NPC_H3K4me1_peaks.encodePeak.txt

value: ES-derived neural progenitor cells (aNPC)


title: H3K4me1_aNPC_1


title: RNA_SiAtf3_1

description:
in-vitro
CntD1_1
processed data file: NTC_2.xls


title: H3K27ac_eA_2

description:
in-vitro
processed data file: 1D_H3K27ac_peaks.encodePeak.txt


title: H3K27ac_lA_1


title: H3K27ac_aNPC_2

description:
in-vitro
processed data file: NPC_H3K27ac_peaks.encodePeak.txt


title: H3K27ac_eA_1


title: H3K27ac_aNPC_1


title: RNA_lA_2_1

description:
in-vitro
D21_R1
processed data file: NTC_1.xls


title: RNA_lA_2_2

description:
in-vitro
D21_R2
processed data file: NTC_1.xls


title: RNA_lA_2_3

description:
in-vitro
D21_R3
processed data file: NTC_1.xls


title: RNA_lA_1_2

description:
in-vitro
D5_R2
processed data file: NTC_1.xls


title: RNA_eA_3

description:
in-vitro
D1_R3
processed data file: NTC_1.xls


title: RNA_eA_2

description:
in-vitro
D1_R2
processed data file: NTC_1.xls


title: RNA_lA_1_3

description:
in-vitro
D5_R3
processed data file: NTC_1.xls


title: RNA_lA_1_1

description:
in-vitro
D5_R1
processed data file: NTC_1.xls


title: RNA_eA_1

description:
in-vitro
D1_R1
processed data file: NTC_1.xls


title: RNA_aNPC_3

description:
in-vitro
NPCs_R3
processed data file: NTC_1.xls


title: RNA_aNPC_2

description:
in-vitro
NPCs_R2
processed data file: NTC_1.xls


title: RNA_aNPC_1

description:
in-vitro
NPCs_R1
processed data file: NTC_1.xls


title: RNA_ES_3

description:
in-vitro
ES_R3
processed data file: NTC_1.xls

value: ES


title: RNA_ES_1

description:
in-vitro
ES_R1
processed data file: NTC_1.xls


title: RNA_ES_2

description:
in-vitro
ES_R2
processed data file: NTC_1.xls


title: L3_rep1 [ATAC-Seq]

city: Barcelona

first: Montserrat

last: Corominas

state: Catalonia

address: Diagonal 643

department: Genètica, Microbiologia i estadística

country: Spain

institute: University of Barcelona

data_processing:
Reads were continuously mapped to the fly genome (dm6) using STAR 2.4.0j software. Only uniquely aligned reads to canonical chromosomes were selected
To generate the nucleosome position data, reads below 100 bps were considered nucleosome free and reads between 180 and 247 bps were considered to be mononucleosomes
Peaks were called using paired-end mode of MACS2 software
Genome_build: dm6
Supplementary_files_format_and_content: raw data in fastq, process data in bigWig

organism: Drosophila melanogaster

source_name: Undamaged Wing Disc

growth_protocol: Flies were grown on standard media

extract_protocol:
We used 10 wing discs of each genotype (regeneration and control) and condition (0h, 15h, 25h) as well as third instar larva (L3). Samples were lysed in Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40) by gently pipetting. Lysates were centrifuged for 10min at 500g to isolate the nuclei. Nuclei were resuspended and incubated for 30 min at 37⁰C in transposition reaction mix (Illumina). Right after the transposition reaction, samples were purified using Qiagen MinElute Kit and eluted in Elution Buffer (10mM Tris buffer, pH8). For library preparation we amplified the transposed DNA fragments by running a conventional PCR (5 min at 72⁰C, 2.5 min at 95 ⁰C, thermoycling 13 cycles 20 sec at 98⁰C, 15 sec at 63⁰C and 1 min at 72⁰C) with Nextera barcoded primers. Libraries were purified using Qiagen PCR CleanUP Kit and eluted in Elution Buffer.
Illumina Nextera

tag: developmental stage

value: Third instar larvae

value: wing disc


title: 25h_reg_rep2 [ATAC-Seq]

source_name: Regenerating Wing Disc


title: L3_rep2 [ATAC-Seq]


title: 25h_reg_rep1 [ATAC-Seq]


title: 25h_ctrl_rep1 [ATAC-Seq]


title: 15h_reg_rep2 [ATAC-Seq]


title: 15h_ctrl_rep2 [ATAC-Seq]


title: 15h_reg_rep1 [ATAC-Seq]


title: 15h_ctrl_rep1 [ATAC-Seq]


title: 0h_reg_rep2 [ATAC-Seq]


title: 0h_reg_rep1 [ATAC-Seq]


title: 0h_ctrl_rep1 [ATAC-Seq]


title: 0h_ctrl_rep2 [ATAC-Seq]


title: 25h_reg_rep1 [RNA-Seq]

data_processing:
Data was processed using grape-nf (available at https://github.com/guigolab/grape-nf).
RNA-seq reads were aligned to the fly genome (dm6) using STAR 2.4.0j software with up to 4 mismatches per paired alignment using the FlyBase genome annotation r6.05
Gene and transcripts FPKMs were quantified using RSEM.
Genome_build: dm6
Supplementary_files_format_and_content: raw data in fastq, process data in bigWig

molecule: polyA RNA

extract_protocol:
We used 40 wing discs of each genotype (regeneration and control) and condition (0h, 15h, 25h). Two replicates of each sample were done. RNA was extracted with ZR RNA microprep and RNA clean and concentrator Kit from (Zymo Research).
Illumina truSeq


title: 25h_ctrl_rep1 [RNA-Seq]


title: 25h_reg_rep2 [RNA-Seq]


title: 15h_reg_rep1 [RNA-Seq]


title: 15h_reg_rep2 [RNA-Seq]


title: 15h_ctrl_rep1 [RNA-Seq]


title: 25h_ctrl_rep2 [RNA-Seq]


title: 15h_ctrl_rep2 [RNA-Seq]


title: 0h_reg_rep1 [RNA-Seq]


title: 0h_ctrl_rep2 [RNA-Seq]


title: 25h_ctrl_rep2 [ATAC-Seq]


title: 0h_ctrl_rep1 [RNA-Seq]


title: CLIP-READS Pab1-3-V5 strain anti-V5 IP

source_name: Saccharomyces cerevisiae spiked with Schizosaccharomyces pombe

extract_protocol:
Jin, Y. et al. Mapping 3' mRNA isoforms on a genomic scale. Curr. Protoc. Mol. Biol. 110, 4.23.21-24.23.17 (2015)
Hot acidic phenol extraction of total RNA, followed by purification on Qiagen Rneasy columns with Dnase I treatment

value: CLIP-READS


title: CLIP-READS Pab1-3-myc strain input control Rep B


title: CLIP-READS Pab1-3-V5 strain input control


title: CLIP-READS Pab1-3-myc strain input control Rep A


title: DREADS In vitro + DMS, Biological Replicate B

value: DREADS


title: CLIP-READS Pab1-3-myc strain anti-myc IP Rep A


title: H3pS10 ChIP cdc15-1 37 degres

city: Oslo

first: Pierre

last: Chymkowitch

address: Blindernveien 31

department: Biosciences

country: Norway

institute: University of Oslo

description: H3pS10 ChIP in cdc15-1 cells heat treated

data_processing:
reads aligned to reference using bowtie version 2.2.9 using parameters –best
bigWig files were generated by getting a ratio of IP over Input in 1 kb bins
Files with file name containing "E2" were aligned to SCerevisiae_after.genome (attached to this submission). Other files were aligned to SCerevisiae_before.genome (also attached to this submission).
Genome_build: Custom genomes attached to this submission
Supplementary_files_format_and_content: bigWig files for viewing in Genome Browser

source_name: Saccharomyces cerevisiae

growth_protocol: Cells were grown in YPD or Drop-out medium -Ade -Met

extract_protocol:
Chymkowitch et al, Genome Res., 2015.
Libraries were prepared at BGI or Novogene according to the illumina protocol

treatment_protocol: Cells were treated or not with 1nM beta-estradiol (E2) during 3 hours. Cells were heat treated at 37 celcius for 90 min.


title: DREADS YPD + DMS Biological Rep B, Library Prep 2

description:
2 sets of fastq files because more was sequenced in a second run for extra depth
JGY2000_B_DMS_5'endfreqs_Normalized_0.998xTo50M.txt


title: H3pS10 ChIP WT 37 degres

description: H3pS10 ChIP in WT cells heat treated


title: DREADS In vitro, Biological Replicate A


title: DREADS YPD + DMS Biological Rep B, Library Prep 1


title: DREADS In vitro + DMS, Biological Replicate A


title: H3 ChIP cdc15-1 37 degres

description: H3 ChIP cdc15-1 in cells heat treated


title: DREADS In vitro, Biological Replicate B


title: DREADS YPD Biological Rep B, Library Prep 1

description:
2 sets of fastq files because more was sequenced in a second run for extra depth
JGY2000_B_untreated_5'endfreqs_Normalized_0.996xTo50M.txt


title: 0h_reg_rep2 [RNA-Seq]


title: H3pS10 ChIP #3

description: H3pS10 ChIP in WT cells #3


title: input WT 37

description: input WT cells heat treated


title: DREADS YPD + DMS Biological Rep A, Library Prep 2

description:
2 sets of fastq files because more was sequenced in a second run for extra depth
JGY2000_A_DMS_5'endfreqs_Normalized_0.882xTo50M.txt


title: H3 ChiP WT 37

description: H3 ChiP in WT cells heat treated


title: DREADS YPD Biological Rep B, Library Prep 2


title: DREADS YPD + DMS Biological Rep A, Library Prep 1


title: DREADS YPD Biological Rep A, Library Prep 2

description:
2 sets of fastq files because more was sequenced in a second run for extra depth
JGY2000_A_untreated_5'endfreqs_Normalized_1.05xTo50M.txt


title: H3 ChIP E2 #3

description: H3 ChIP in WT cells treated with E2 #3


title: H3pS10 ChIP E2 #3

description: H3pS10 ChIP in WT cells treated with E2 #3


title: H3 ChIP #3

description: H3 ChIP in WT cells  #3


title: input E2 #3

description: input WT cells treated with E2 #3


title: CLIP-READS Pab1-3-myc strain anti-myc IP Rep B


title: DREADS YPD Biological Rep A, Library Prep 1


title: input cdc15-1 37 degres

description: input cdc15-1 cells heat treated


title: input #3

description: input WT cells #3


title: H3 ChIP E2 #2

description: H3 ChIP in WT cells treated with E2 #2


title: H3pS10 ChIP E2 #2

description: H3pS10 ChIP in WT cells treated with E2 #2


title: H3pS10 ChIP #2

description: H3pS10 ChIP in WT cells #2


title: input E2 #2

description: input WT cells treated with E2 #2


title: input #2

description: input WT cells #2


title: H3 ChIP #2

description: H3 ChIP in WT cells  #2


title: H3pS10 ChIP E2 #1

description: H3pS10 ChIP in WT cells treated with E2 #1


title: H3pS10 ChIP #1

description: H3pS10 ChIP in WT cells #1


title: H3 ChIP E2 #1

description: H3 ChIP in WT cells treated with E2 #1


title: input E2 #1

description: input WT cells treated with E2 #1


title: H3 ChIP #1

description: H3 ChIP in WT cells  #1


title: Rep3_H29

city: Qingdao

first: Yanhai

last: Gong

address: No.189 Songling Road

department: single cell center

institute: qibebt, cas

data_processing:
FASTQ sequencing files were generated using the Illumina CASAVA software and internally quality filtered based on Illumina’s chastity filtering procedure, then PF reads (raw reads) were used for further analysis.
Scripts bundled with Trinity software were mainly adopted to quantify the transcripts and find the differentially expressed subset.
Genome_build: Trinity.fasta (reference transcriptome)
Supplementary_files_format_and_content: raw count matrix was generated using Trinity.

organism: Ettlia oleoabundans

source_name: fed-batch cultured cells

growth_protocol: Experiments were performed in 1.7L flat panel air-lift photobioreactors (Labfors 5 Lux, Infors HT, Switzerland) at pH 7.5 and 25ºC, and sparged with 2% CO2 at an air flow of 1.2 L min-1 and photon flux density (PFD) of 800 µmol s-1 m-2 at a 12:12 day:night cycle.

extract_protocol:
Samples were centrifuged and cell pellets snap frozen in liquid nitrogen and stored at -80ºC.Total RNA was extracted from microalgal cells (~100-200 mg wet weight) by cell disruption by bead-beating in bead-beater tubes (Lysing Matrix E; MP Biomedicals, Santa Ana, CA, USA) for 1x10 sec at 5500 rpm in a Precellys® 24 bead beater (Bertin Technologies), in the presence of RLT buffer with β-mercaptoethanol (Qiagen). Subsequently, tubes were placed on ice and spun down for 2 min at 13.000 x g. RNA was further cleaned using the RNeasy Plant Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A nitrogen-replete batch pre-culture of N. oleoabundans (250 mL) was used to inoculate the photobioreactors, and microalgae were further batch cultivated until a biomass concentration of 2 g dry weight (DW) / L was reached. Subsequently, fed-batch cultivation was continued for several days until a stable biomass concentration was maintained. For the nitrogen starvation experiment biomass from the nitrogen-replete fed-batch culture was collected, spun down, rinsed and resuspended in nitrogen-free BBM medium. The reactors were rinsed with distilled water, filled with nitrogen-free BBM medium and inoculated with the same volume of the collected microalgae. During the nitrogen-depleted phase, the reactors were run in fed-batch mode. Medium was fed at 800 mL/d to compensate for the volume-loss due to sampling. Samples for biomass and molecular analysis were collected at short and long intervals during 4 days of nitrogen starvation.

value: UTEX 1185

tag: treatment

value: nitrogen starvation

tag: time

value: 29 hrs


title: Rep3_H53

value: 53 hrs


title: Rep3_H99

value: 99 hrs


title: Rep2_H53


title: Rep3_H10

value: 10 hrs


title: input #1

description: input WT cells #1


title: Rep2_H29


title: H3pS10 ChIP sgo1-TeTR

description: H3pS10 ChIP in sgo1-TetR-mCh cells


title: Rep3_H2

value: 2 hrs


title: Rep2_H99


title: Rep2_H10


title: Rep3_H-19

value: nitrogen repletion

value: -19 hrs


title: Rep3_H6

value: 6 hrs


title: H3pS10 ChIP sgo1-TeTR E2

description: H3pS10 ChIP in sgo1-TetR-mCh cells treated with E2


title: Rep2_H6


title: input sgo1-TetR

description: input sgo1-TetR-mChg cells


title: Rep2_H2


title: Rep2_H0

value: 0 hrs


title: Rep2_H-15

value: -15 hrs


title: H3 ChIP sgo1-TetR

description: H3 ChIP in sgo1-TetR-mCh cells


title: input sgo1-TetR E2

description: input sgo1-TetR-mCh cells treated with E2


title: Rep3_H0


title: H3 ChIP sgo1-TetR E2

description: H3 ChIP in sgo1-TetR-mCh cells treated with E2


title: H3pS10 ChIP sgo1 delta

description: H3pS10 ChIP in sgo1 delta cells


title: Rep2_H-19


title: H3 ChIP sgo1 delta

description: H3 ChIP in sgo1 delta cells


title: Rep1_H99


title: Rep1_H53


title: Rep1_H29


title: H3 ChIP sgo1 delta E2

description: H3 ChIP in sgo1 delta celles treated with E2


title: H3pS10 ChIP sgo1 delta E2

description: H3pS10 ChIP in sgo1 delta cells treated with E2


title: input sgo1 delta

description: input sgo1 delta cells


title: H3pS10 ChIP ipl1ts

description: H3pS10 ChIP in ipl1-321 cells heat treated


title: input ipl1ts

description: input ipl1-321 cells heat treated


title: H3pS10 ChIP S10A

description: H3pS10 ChIP in H3-S10A cells


title: Rep1_H-19


title: Rep1_H-15


title: Rep1_H0


title: Rep1_H2


title: Rep1_H6


title: H3pS10 ChIP S10A E2

description: H3pS10 ChIP in H3-S10A cells treated with E2


title: H3 ChIP S10A E2

description: H3 ChIP in H3-S10A cells treated with E2


title: H3 ChIP S10A

description: H3 ChIP in H3-S10A cells


title: Rep3_H-15


title: D. hansenii untreated DREADS Biological Replicate B

organism: Debaryomyces hansenii

source_name: Debaryomyces hansenii spiked with Schizoshaccaromyces pombe


title: K. lactis DMS-treated DREADS Biological Replicate B

organism: Kluyveromyces lactis

source_name: Kluyveromyces lactis spiked with Schizoshaccaromyces pombe


title: D. hansenii DMS-treated DREADS Biological Replicate B


title: input S10A

description: input H3-S10A cells


title: Input Ipl1-TetR E2

description: input Ipl1-TetR-mCh cells treted with E2


title: K. lactis untreated DREADS Biological Replicate B


title: K. lactis DMS-treated DREADS Biological Replicate A


title: H3 ChIP ipl1ts

description: H3 ChIP in ipl1-321 cells heat treated


title: H3pS10 ChIP Ipl1-TetR

description: H3pS10 ChIP in ipl1-TetR-mCh cells


title: Rep1_H10


title: input Ipl1-TetR

description: input Ipl1-TetR-mCh cells


title: H3pS10 ChIP Ipl1-TetR E2

description: H3pS10 ChIP in ipl1-TetR-mCh cells treated with E2


title: K. lactis untreated DREADS Biological Replicate A


title: D. hansenii untreated DREADS Biological Replicate A


title: H3 ChIP Ipl1-TetR

description: H3 ChIP in ipl1-TetR-mCh cells


title: MT_LEC

status: Public on Oct 10 2018

city: Seoul

first: Chanhyeok

last: Park

address: 5, Hwarang-ro 14-gil

department: Brain Science Institute

country: South Korea

institute: KIST (Korea Institute of Science and Technology)

data_processing:
Paired-end sequencing reads were mapped to mm9 mouse genome using STAR tool(v2.5.2b).
After mapping, fragments per kilobase million (FPKM) was calculated by Cufflinks (v2.2.1) tool using the following strand-specific Cuffnorm option: --library-type=fr-second strand.
Functional annotation of differentially expressed genes (DEGs) and enrichment analyses were performed using DAVID (v6.8) and Gene Set Enrichment Analysis (GSEA, v2.2.4), respectively, and genes were considered differentially expressed at the fold change > 3 and FPKM > 5. R (v3.3.2) package was used for statistical analyses and scatter plot generation, and RNA-Seq results were visualized using Integrative Genomics Viewer (IGV).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Lymphatic endothelial cell

growth_protocol: Primary mouse dermal LECs derived from C57BL/6 embryos were obtained and maintained in complete mouse endothelial cell media with supplements (C57-6064L & M1168, Cell Biologics). All the in vitro cell culture experiments was performed within passage 5.

extract_protocol:
RNA-Seq experiments with pooled RNA samples extracted from 2-3 biological replicates were performed. Total RNA was extracted from control and Dot1lΔEC skin LECs using RNeasy Plus Mini Kit (74134, Qiagen) and its amount and quality of the total RNA were evaluated using Bioanalyzer (Agilent). RNA samples with >7.0 RNA Integrity Number (RIN) value were used for RNA-Seq library preparation with the ScriptSeq v2 kit (Illumina) according to manufacturer’s instruction.
Libraries were prepared for sequencing using standard Illumina protocols

value: Skin

tag: age

tag: genotype

value: Dot1l Knockout


title: input sgo1 delta E2

description: input sgo1 delta treated with E2


title: Cont_LEC

value: Wild type


title: D. hansenii DMS-treated DREADS Biological Replicate A


title: CD14_M [215a_CD14]

city: Baltimore

first: Yuji

last: Zhang

state: MD

address: 660 W. Redwood Street

institute: University of Maryland

description:
CD14_isoform_exp.diff
CD14_gene_exp.diff

data_processing:
Blood was drawn into sodium heparin tubes (APP Pharmaceuticals, NDC 63323-540-11); CD4+, CD8+, and CD14+ cells were isolated from whole blood using anti-CD4/CD8/CD14 microbeads (Miltenyi Biotec) and MS column purification as per the manufacturer’s instructions. A small portion of the cell isolate was set aside for flow cytometry using anti CD3 APC-H7 and anti CD4/CD8/CD14 PE-Cy7 (BD PharMingen) to assess purity. Isolated cells were re-suspended at 1 million/ml in RPMI containing 10 % FBS and either immediately lysed in 0.7 ml QIAzol lysis reagent (Qiagen) or incubated for 4 h at 37 °C with 25 μl/ml anti-CD3/antiCD28 Human T-Activator Dynabeads (Invitrogen) prior to lysis. Lysates were stored at −80 °C until processing for RNAseq.
RNA integrity values of  ≥7.0 by Agilent Bioanalyzer (Santa Clara, CA) were processed by the Mayo Clinic Medical Genome Facility Gene Expression Core into TruSeq libraries according to the manufacturer’s instructions (RNA Prep Kit v2, Illumina, San Diego, CA) and published elsewhere [25]. Paired-end DNA adaptors (Illumina) with a single “T” base overhang at the 3’end were immediately ligated to the “A-tailed” cDNA population. Unique indexes, included in the standard TruSeq Kits (12-Set A and 12-Set B), were incorporated at the adaptor ligation step for multiplex sample loading on the flow cells. Libraries (8–10 pM) were loaded onto paired-end flow cells to generate cluster densities of 700,000/mm2 following Illumina’s standard protocol for cBot and cBot paired-end cluster kit version 3. The flow cells were sequenced as 51 X 2 paired-end reads on an Illumina HiSeq 2000 using TruSeq SBS sequencing kit version 3 and HCS v2.0.12 data collection software. Base-calling was performed using RTA version 1.17.21.3.
All biological samples were sequenced using Illumina HiSeq™ 2000 platform (Illumina) with 50-bp pair-end sequencing protocol in the Mayo DNA Sequencing Core Facility. Raw RNA-seq reads from each RNA-seq library were assessed for duplication rate and gene coverage using FastQC.
Trimmed reads were aligned to the human genome (GRCh38) with the GENCODE annotation (gencode.v23.annotation.gtf) by TopHat (Version 2.0.12). Using the mapping results from TopHat, the transcriptomes were reconstructed by Cufflinks (Version 2.2.1).
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files of Cufflinks include FPKM values for each Sample

source_name: CD14+ PBL

extract_protocol:
Participant recruitment and blood sample collection were conducted using protocols approval by the Mayo Clinic Institutional Review Board (IRB#12-002580 and IRB#13-002293).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: peripheral blood cells

tag: cell subtype

value: CD14+ monocytes

tag: tumor stage

value: the stage IV melanoma


title: CD14_M [210a_CD14]

tag: cell type


title: CD14_M [211b_CD14]


title: input S10A E2

description: input H3-S10A cells treated with E2


title: CD14_M [210b_CD14]


title: CD14_M [211a_CD14]


title: CD14_M [214b_CD14]


title: CD14_M [209b_CD14]


title: CD14_M [215b_CD14]


title: CD14_M [207b_CD14]


title: CD14_M [209a_CD14]


title: CD14_M [204b_CD14]


title: CD14_M [204a_CD14]


title: H3 ChIP Ipl1-TetR E2

description: H3 ChIP in ipl1-TetR-mCh cells treated with E2


title: CD14_M [203a_CD14]


title: CD14_M [201b_CD14]


title: CD14_M [202a_CD14]


title: CD14_M [202b_CD14]


title: CD14_H [0121k]

value: health


title: CD14_H [0121j]


title: CD14_M [214a_CD14]


title: CD14_H [0120k]


title: CD14_H [0120j]


title: CD14_H [0116k]


title: CD14_H [0117j]


title: CD14_H [0117k]


title: CD14_H [0116j]


title: CD14_H [0114j]


title: CD14_H [0114k]


title: CD14_H [0112k]


title: CD14_M [207a_CD14]


title: CD14_H [0113j]


title: CD14_H [0111k]


title: CD14_H [0110j]


title: CD14_H [0110k]


title: CD14_H [0107j]


title: CD14_H [0112j]


title: CD14_H [0111j]


title: CD14_H [0106k]


title: CD14_M [203b_CD14]


title: CD14_H [0106j]


title: CD14_M [201a_CD14]


title: CD14_H [0113k]


title: CD8_M [215a_CD8]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff

source_name: CD8+ PBL

value: CD8+ T cell


title: CD8_M [214b_CD8]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_M [214a_CD8]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD14_H [0101k]


title: CD8_M [211b_CD8]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_M [211a_CD8]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_M [215b_CD8]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_M [209b_CD8]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_M [208b_CD8]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD14_H [0101j]


title: CD8_M [210a_CD8]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD14_H [0107k]


title: CD8_M [203b_CD8]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_M [202a_CD8]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_M [204a_CD8]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_M [202b_CD8]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_H [123_f_0]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_M [208a_CD8]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_M [201b_CD8]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_M [210b_CD8]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_H [123_e_0]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_H [122_e_0]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_M [203a_CD8]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_M [209a_CD8]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_H [121_e_0]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_H [122_f_0]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_H [120_e_0]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_H [117_f_0]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_H [120_f_0]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_M [204b_CD8]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_H [119_e_0]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_M [201a_CD8]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_H [121_f_0]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_H [118_e_0]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_H [115_e_0]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_H [115_f_0]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_H [111_f_0]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_M [207a_CD8]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_H [111_e_0]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_H [105_e_0]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_H [102_e_0]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_H [102_f_0]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_H [101_f_0]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_H [101_e_0]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_H [119_f_0]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD4_M [214a_CD4_0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff

source_name: CD4+ PBL

value: CD4+ T cell


title: CD4_M [215a_CD4_0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD4_M [215b_CD4_0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD4_M [214b_CD4_0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD8_H [117_e_0]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD4_M [210b_CD4_0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD4_M [211b_CD4_0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD4_M [210a_CD4_0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD4_M [209b_CD4_0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD4_M [208a_CD4_0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD4_M [207b_CD4_0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD4_M [208b_CD4_0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD4_M [203b_CD4_0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD4_M [204a_CD4_0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD4_M [204b_CD4_0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD4_M [202b_CD4_0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD8_M [207b_CD8]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD4_M [211a_CD4_0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD8_H [105_f_0]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD8_H [118_f_0]

description:
CD8_isoform_exp.diff
CD8_gene_exp.diff


title: CD4_M [202a_CD4_0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD4_H [112B_0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD4_H [111b-0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD4_H [112A_0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD4_M [201b_CD4_0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD4_H [110B_0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD4_H [111a-0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD4_M [209a_CD4_0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD4_H [108b-0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD4_H [110A_0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD4_H [108a-0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD4_H [107b-0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD4_M [203a_CD4_0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD4_H [104b-0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD4_H [103B_0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD4_H [101b-0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD4_H [102a-0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD4_H [109A_0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD4_H [102b-0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD4_H [101a-0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD4_M [207a_CD4_0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD4_M [201a_CD4_0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: Control-PFC-14235d [ctl_mirna23]

city: Shanghai

first: Xiling

last: Liu

address: 320 Yue Yang Road

institute: Partner Institute for Computational Biology

data_processing:
The raw sequencing reads were mapped to human genome using Bowtie, requiring perfect match.
Sequences with copy number ≥2 were retained.
sequences of mature miRNAs and miRNAs precursors based on miRBase version 17. All sequences with copy number ≥2 to map within three nucleotides up- / down-stream of the annotated 5'-position of the mature miRNAs were retained. The sequence with the maximal copy number was considered as the reference sequence for each miRNA.
The expression level of each miRNA was then calculated as a sum of the copy number of the reference sequence and the sequences mapping at the same 5'-end position as the reference sequence
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file shows expression values of each microRNA in each sample.

source_name: dissected control post-mortem superior frontal gyrus

extract_protocol:
Total RNA was isolated using Trizol® reagent (Invitrogen, Carlsbad, CA) and low molecular weight RNA was then isolated.
Sequencing libraries were prepared with TruSeq small RNA Sample Preparation Protocol (Illumina) without modification.

treatment_protocol: PFC dissections were made from the frontal part of the superior frontal gyrus.

tag: subject group

value: Control

tag: gender

value: male

value: superior frontal gyrus of the brain


title: Control-PFC-18250d [ctl_mirna24]


title: CD4_H [109B_0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: CD4_H [107a-0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff


title: Control-PFC-6205d [ctl_mirna19]

value: 6205 days


title: Control-PFC-4309d [ctl_mirna17]

value: 4309 days


title: Control-PFC-5105d [ctl_mirna18]

value: 5105 days


title: Control-PFC-2922d [ctl_mirna14]

value: 2922 days


title: Control-PFC-3134d [ctl_mirna15]

value: female

value: 3134 days


title: Control-PFC-2827d [ctl_mirna13]

value: 2827 days


title: Control-PFC-787d [ctl_mirna9]

value: 787 days


title: Control-PFC-1734d [ctl_mirna12]

value: 1734 days


title: Control-PFC-212d [ctl_mirna6]

value: 212 days


title: Control-PFC-1016d [ctl_mirna10]

value: 1016  days


title: CD4_H [103A_0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff

value: peripheral blood cells

value: health


title: Control-PFC-35d [ctl_mirna4]

value: 35 days


title: Control-PFC-5d [ctl_mirna2]

value: Control

value: 5 days


title: Control-PFC-1460d [ctl_mirna11]

value: 1460 days

value: superior frontal gyrus of the brain


title: Control-PFC-488d [ctl_mirna8]

value: male

value: 488 days


title: Control-PFC-3912d [ctl_mirna16]

value: 3912 days


title: Control-PFC-96d [ctl_mirna5]

value: 96 days


title: Control-PFC-22452d [ctl_mirna25]


title: Control-PFC-16d [ctl_mirna3]

value: female

value: 16 days


title: Autism-PFC-21900d [aut_mirna20]

source_name: dissected autism post-mortem superior frontal gyrus

value: autistic patient


title: Control-PFC-8352d [ctl_mirna20]

value: 8352 days


title: Autism-PFC-14235d [aut_mirna18]


title: Control-PFC-9897d [ctl_mirna21]

value: 9897 days


title: Autism-PFC-18980d [aut_mirna19]


title: Autism-PFC-10585d [aut_mirna16]


title: Autism-PFC-8030d [aut_mirna14]

value: 8030 days


title: Autism-PFC-6570d [aut_mirna12]

value: 6570 days


title: Autism-PFC-5236d [aut_mirna11]

value: 5236 days


title: Control-PFC-443d [ctl_mirna7]

value: 443 days


title: Autism-PFC-7300d [aut_mirna13]

value: 7300 days


title: Autism-PFC-4015d [aut_mirna10]

value: 4015 days


title: Control-PFC-2d [ctl_mirna1]

value: Control

value: 2 days


title: Autism-PFC-10950d [aut_mirna17]

value: male

value: superior frontal gyrus of the brain


title: Autism-PFC-2610d [aut_mirna6]

value: 2610 days


title: Autism-PFC-2045d [aut_mirna5]

value: 2045 days


title: Autism-PFC-3224d [aut_mirna8]

value: 3224 days


title: Autism-PFC-2920d [aut_mirna7]

value: 2920 days


title: Autism-PFC-3650d [aut_mirna9]

value: autistic patient

value: 3650 days


title: Autism-PFC-1825d [aut_mirna4]

value: female

value: 1825 days


title: Fry-MO

city: Pittsburgh

first: Neil

middle: A.

last: Hukriede

state: PA

department: Developmental Biology

institute: University of Pittsburgh

description: small RNA

data_processing:
The purified cDNA library was used for cluster generation on Illumina’s Cluster Station and then sequenced on Illumina GAIIx following vendor’s instruction for running the instrument.
Raw sequencing reads (40 nts) were obtained using Illumina’s Sequencing Control Studio software version 2.8 (SCS v2.8) following real-time sequencing image analysis and base-calling by Illumina's Real-Time Analysis version 1.8.70 (RTA v1.8.70).
The extracted sequencing reads were then used in the standard data analysis, which is described in the next Section
A proprietary pipeline script, ACGT101-miR v4.2 (LC Sciences), was used for sequencing data analysis
After the raw sequence reads, or sequenced sequences (sequ seqs) were extracted from image data, a series of digital filters (LC Sciences) were employed to remove various un-mappable sequencing reads
“mappings” were performed on unique seqs against pre-miRNA (mir) and mature miRNA (miR) sequences listed in the latest release of miRBase5 or genome based on the public releases of appropriate species. Mappings were also done on mirs of interest against genome sequence. Methods and criteria used for various mappings were documented in the ACGT-101 User’s Manual
Normalization of sequence counts in each sample (or data set) is achieved by dividing the counts by a library size parameter of the corresponding sample. The library size parameter is a median value of the ratio between the counts a specific sample and a pseudo-reference sample. A count number in the pseudo-reference sample is the count geometric mean across all samples
In-depth data analysis for mapping mappable reads to reference databases:various “mappings” were performed on unique seqs against pre miRNA (mir) and mature miRNA (miR) sequences listed in the latest release of miRBase or genome based on the public releases of appropriate species. Methods and criteria used for various mappings were documented in the ACGT101-miR bioinformatic tool.
Genome_build: miRNA database v20, genome and mRNA database JGI 08/2005
Supplementary_files_format_and_content: Excel file includes the library size of each data set, the miR sequence and name. For each miRNA, the raw and normalized sequence counts are listed. The number of read copies from each sample is tracked during mapping and normalized for comparison. The comparison results are consolidated in the file Report_miRNA seq_comparison.xls. Reads may be mapped to multiple entries of the reference database and the number of the read copies is divided by the number of mapped entries.

organism: Xenopus laevis

source_name: Xenopus S10.5 embryos

extract_protocol:
A total of 30 dorsal half embryos at stage 10.5 were cut, pooled and homogenized with a plastic microcentrifuge pestle in 500 ul of TRI reagent (Ambion), and total RNA was isolated using an RNeasy Micro Kit (Qiagen) per the manufacturer’s instructions.
A small RNA library was generated using the Illumina Truseq™ Small  RNA Preparation kit according to Illumina’s TruSeq™ Small RNA Sample Preparation Guide.

treatment_protocol: 4-cell Xenopus embryos processed for miRNA sequencing were injected into both dorsal blastomeres with 20 ng of Fry-MO or 400 pg of Lhx1-AS or left uninjected, embryos were incubated at 14°C until stage 10.5 in MMR and a total of 30 dorsal half embryos at stage 10.5 were pooled for miRNA seq

value: embryo


title: Autism-PFC-730d [aut_mirna1]

value: 730 days


title: Autism-PFC-1625d [aut_mirna2]

value: 1625 days


title: uninjected

description: small RNA


title: Autism-PFC-1825d [aut_mirna3]


title: Control-PFC-10220d [ctl_mirna22]


title: Lhx1-AS

description: small RNA


title: Scerevisiae_mutant_190min

city: Hanover

first: Christina

middle: M

last: Kelliher

state: NH

address: 7400 Hinman

department: Molecular & Systems Biology

institute: Geisel School of Medicine at Dartmouth

data_processing:
Sequenced reads mapped to the S288C reference genome using STAR with parameters --outFilterType BySJout --alignIntronMin 10 --alignIntronMax 3000 --outFilterIntronMotifs RemoveNoncanonical
Transcripts were quantified in Fragments Per Kilobase of transcript per Million mapped reads (FPKM) using Cufflinks with the S288C transcriptome GTF file (i.e. quantify one transcript per annotated gene, not gene isoforms). Values were normalized by gene size and by library size.
Time point samples were normalized together using the cuffnorm feature of Cufflinks (default parameters for stranded RNA-Seq)
A value of "1" was added to every FPKM value in each dataset; see manuscript for details
Genome_build: Saccharomyces cerevisiae S288C Ensembl R64-1-1 downloaded from Illumina iGenomes on 3-2-16
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

source_name: S. cerevisiae culture, clb1-6 mutant, 190 min

growth_protocol: YEPGalactose at 30c, alpha-factor arrest, YEPDextrose at 30c

extract_protocol:
KAPA Stranded mRNA-Seq Library Preparation Kit was used for the construction of sequencing libraries
Cells were removed at each time point and flash frozen on dry ice. RNA was harvested using standard yeast methods.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: synchronous G1 population collected by alpha-factor mating pheromone (30 ng/ml, 160 minutes) arrest-release

tag: strain genotype/variation

value: BF264-15D MATa bar1::hphMX4 arg4 clb1::URA3 clb2::LEU2 clb3::TRP1 clb4::HIS2 clb5::ARG4 clb6::ADE1 PGAL1-CLB1::LEU2

value: cell-cycle-arrested B-type cyclin (clb1-6) mutant

tag: time point

value: 190 min


title: Scerevisiae_mutant_200min

source_name: S. cerevisiae culture, clb1-6 mutant, 200 min

value: 200 min


title: Scerevisiae_mutant_170min

source_name: S. cerevisiae culture, clb1-6 mutant, 170 min

value: 170 min


title: Scerevisiae_mutant_160min

source_name: S. cerevisiae culture, clb1-6 mutant, 160 min

value: 160 min


title: Scerevisiae_mutant_150min

source_name: S. cerevisiae culture, clb1-6 mutant, 150 min

value: 150 min


title: Scerevisiae_mutant_180min

source_name: S. cerevisiae culture, clb1-6 mutant, 180 min

value: 180 min


title: Scerevisiae_mutant_90min

source_name: S. cerevisiae culture, clb1-6 mutant, 90 min

value: 90 min


title: Scerevisiae_mutant_110min

source_name: S. cerevisiae culture, clb1-6 mutant, 110 min

value: 110 min


title: Scerevisiae_mutant_80min

source_name: S. cerevisiae culture, clb1-6 mutant, 80 min

value: 80 min


title: Scerevisiae_mutant_100min

source_name: S. cerevisiae culture, clb1-6 mutant, 100 min

value: 100 min


title: Scerevisiae_mutant_140min

source_name: S. cerevisiae culture, clb1-6 mutant, 140 min

value: 140 min


title: Scerevisiae_mutant_70min

source_name: S. cerevisiae culture, clb1-6 mutant, 70 min

value: 70 min


title: Scerevisiae_mutant_60min

source_name: S. cerevisiae culture, clb1-6 mutant, 60 min

value: 60 min


title: Scerevisiae_mutant_50min

source_name: S. cerevisiae culture, clb1-6 mutant, 50 min

value: 50 min


title: Scerevisiae_mutant_0min

source_name: S. cerevisiae culture, clb1-6 mutant, 0 min

value: 0 min


title: Scerevisiae_mutant_10min

source_name: S. cerevisiae culture, clb1-6 mutant, 10 min

value: BF264-15D MATa bar1::hphMX4 arg4 clb1::URA3 clb2::LEU2 clb3::TRP1 clb4::HIS2 clb5::ARG4 clb6::ADE1 PGAL1-CLB1::LEU2

value: 10 min


title: Scerevisiae_mutant_30min

source_name: S. cerevisiae culture, clb1-6 mutant, 30 min

value: cell-cycle-arrested B-type cyclin (clb1-6) mutant

value: 30 min


title: Scerevisiae_mutant_40min

source_name: S. cerevisiae culture, clb1-6 mutant, 40 min

value: 40 min


title: E2A-PBX_1

city: Frederick

first: Jack

last: Chen

address: SAIC-Frederick Miller Dr

institute: NIH

data_processing:
Sequences were aligned to mm10 using STAR aligner.
Reads were quantified to RefSeq release 11/1/16 using Partek E/M algorithm, and then normalized to fragments per kilobase of transcript per Million mapped reads (FPKM).
Genome_build: mm10
Supplementary_files_format_and_content: FPKMs

source_name: pre-B ALL

extract_protocol:
RNA samples were prepared using TRIzol reagent (Invitrogen) following the manufacturer’s recommended protocol.  Samples were evaluated using Fragment Analyzer and NanoDrop.
Indexed cDNA sequencing libraries were prepared using the TruSeq Stranded mRNA Sample Preparation Kit, and bar-coded with individual tags, following the manufactures recommendations. Library preparation was performed using a 96-well plate method. The libraries were quantified using Qubit fluoroscopy and the NGS kit for Fragment Analyzer. Any failed results from the fragment analyzer were repeated using 2100 Bioanalyzer. Indexed libraries were prepared as equimolar pools and run on HiSeq4000 (2x150 paired end runs) to generate 40 million paired-end reads per sample library.

value: Spleen


title: Eµ-RET_3

value: E{Mu}-RET


title: E2A-PBX_2


title: Eµ-RET_2


title: NP23_1873

source_name: Progenitor B-1 B cell ALL

value: Lymph node


title: Eµ-RET_1


title: NP23_752


title: NP23_724


title: NP23_633

value: Bone marrow


title: NP23_758


title: NP23_1450


title: WT FL CD19+B220+

source_name: fetal B cell progenitors

value: Fetal liver

value: WT


title: Scerevisiae_mutant_20min

source_name: S. cerevisiae culture, clb1-6 mutant, 20 min

value: 20 min


title: Scerevisiae_mutant_130min

source_name: S. cerevisiae culture, clb1-6 mutant, 130 min

value: 130 min


title: NP23_1533


title: Scerevisiae_mutant_120min

source_name: S. cerevisiae culture, clb1-6 mutant, 120 min

value: 120 min


title: Embryo2_circRNA

city: Yangling

first: Hui

last: Li

state: Shaanxi

address: College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China

institute: Northwest A&F University

description: circRNA

data_processing:
From the raw FASTQ files, adapter was removed using Trim Galore and filtered data were aligned to the Bos taurus reference genome (bosTau7) from UCSC (http://genome.ucsc.edu/) with TopHat2 (version 2.0.14)
Linear transcripts assembly and abundance estimation were first performed using CuffLinks, and then the reads of fusion transcripts, obtained from TopHat2, which did not align to the linear RNA were identified.
Then the program TopHat-Funsion was done with the fusion transcripts and the transcripts obtained from the assembled linear RNA to obtain back-spliced junctions reads. Only circRNAs within 100 kb, with two or more supporting reads, and with no more than two mismatches were kept.
CircRNAs were normalized as the number of uniquely mapped fragments per kilobase of exon per million fragments mapped (FPKM).
Genome_build: Btau_4.6.1
Supplementary_files_format_and_content: [Additional file 1] All circRNAs candidates
Supplementary_files_format_and_content: [Additional file 2] 1,287 circRNAs candidates contained at least one unique back-spliced read were videntified in bovine muscle tissues.
Supplementary_files_format_and_content: [Additional file 3] 589 circRNAs were found in mixed sample using  rRNA−&RNase R+ method.
Supplementary_files_format_and_content: [Additional file 4] List of differentially expressed circRNAs identified in skeletal muscle.
Supplementary_files_format_and_content: [Additional file 5] 537 terms enriched in molecular function of Gene Ontology enrichment (circRNA-hosting gene of all samples).
Supplementary_files_format_and_content: [Additional file 6] 330 terms enriched in cellular component of Gene Ontology enrichment (circRNA-hosting gene of all samples).
Supplementary_files_format_and_content: [Additional file 7] 1482 terms enriched in biological processes of Gene Ontology enrichment (circRNA-hosting gene of all samples).
Supplementary_files_format_and_content: [Additional file 8] 152 KEGG pathways were enriched in bovine muscle tissues (circRNA-hosting gene of all samples).

organism: Bos taurus

source_name: embryonic longissimus muscle

growth_protocol: Six longissimus muscle samples from Qinchuan cattles of two developmental states (embryonic, 90 d; and adult, 24 M old) were collected from Yiming abattoir, a local slaughterhouse of Xi’An, P.R. China. Tissue samples were snap-frozen in liquid nitrogen and stored at –80°C freezer until use.

extract_protocol:
Total RNA was assessed by electrophoresis on a denaturing agarose gel and quantified by NanoDrop spectrophotometer (NanoDrop, USA) and Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA). The total RNA samples (3 mg) were treated with the epicentre Ribo-ZeroTM Kit to remove rRNA before constructing the RNA-seq libraries. For RNase R treatment, ribosome-depleted RNA was incubated for 15 min at 37°C with 5 units μg−1 of RNase R (Epicentre Technologies, Madison, WI).
Then the rRNA depleted RNA samples or circRNAs samples were fragmented and used to synthesize first- and second-strand complementary DNA (cDNA) with random hexamer primers, dNTPs and DNA Polymerase I. The cDNA fragments were cleaned and concentrated using AMPure XP beads, then the ends were repaired and modified with T4 DNA polymerase Klenow DNA polymerase to add A and adapter at the 3’ end of the DNA fragments. The ligated cDNA products were purified with AMPure XP beads and treated with uracil DNA glycosylase to remove the second-strand cDNA.
Purified first-strand cDNA was subjected to PCR amplification, and the libraries were quality controlled with an Agilent 2100 Bioanalyzer and sequenced by HiSeq 2500 (Illumina, San Diego, CA) on a 150 bp paired-end (PE) run.

tag: breed

value: Qinchuan

value: skeletal muscle

value: embryo


title: Embryo3_circRNA

department: College of Animal Science and Technology

description: circRNA

tag: tissue


title: mLEC_EPZ5676_k79me2

data_processing:
ChIP-seq raw reads were aligned to mouse mm9 genome using Bowtie2 (v2.2.9).
SAMtools (v1.2) was used for the data arrangement.
ChIP-seq peaks were called using the following MACS2 (v2.1.0) parameters: -B --nomodel -f BAM -g mm --broad -p 1e-5.
Genome_build: mm9
Supplementary_files_format_and_content: The bigwig files were generated using bedGraphToBigWig

source_name: Lymphatic endothelial cell

growth_protocol: Primary mouse dermal LECs derived from C57BL/6 were were grown in CellBiologics culture medium (cat# M1168) supplemented with VEGF, ECGS, Heparin, EGF, Hydrocortisone, L-glutamine, Antbiotic-Antimycotic solution, FBS). Cells were maintained in a humidified incubator equilibrated with 5% CO2 at 37°C.

extract_protocol:
The primary mouse dermal LECs derived from C57BL/6 were were maintained in CellBiologics culture medium supplemented with VEGF, ECGS, Heparin, EGF, Hydrocortisone, L-glutamine, Antbiotic-Antimycotic solution, FBS). Approximately 1-3 x 10^7 cells were used for each ChIP-Seq assay. The chromatin was precipitated by H3K79me2 antibody (ab3594, Abcam) and immunoprecipitated DNAs were purified with treatment of proteinase K, phenol/chloroform and ethanol precipitation.
ChIP-Seq libraries were produced using Truseq ChIP Sample kit (Illumina) according to manufacturer’s instruction.

treatment_protocol: The primary mouse dermal LECs were treated with either DMSO or 2M of EPZ5676.

value: Skin

value: Mouse primary dermal lymphatic endothelial cell

tag: passages

value: anti-H3K79me2 (Abcam, catalog# ab3594, lot# GR290484)


title: Adult1_circRNA

description: circRNA

source_name: adult longissimus muscle

value: adult


title: Autism-PFC-10585d [aut_mirna15]

source_name: dissected autism post-mortem superior frontal gyrus

value: autistic patient

value: male

value: superior frontal gyrus of the brain


title: mLEC_DMSO_k79me2

value: DMSO

tag: chip antibody


title: BP_submerged_fast_pool4

type: RNA

city: Leioa

first: Daniel

last: Prieto

address: Barrio Sarriena s/n

institute: University of the Basque Country

description: HSF pool 4

hyb_protocol: Samples were manually hybridized with SureHyb hybridization chambers (Agilent technologies). Hybridization was done in the oven of Agilent technologies following the Agilent protocol. Characteristics: 600 ng of marked cRNA; 40 µl volume; 65 ºC temperature; 20 hours duration at 10 rpm in the hybridization

scan_protocol: The scanning was carried out on the DNA microarrays G2565CA scanner with ozone –barrier slide covers with the Scan control Software version 8.5.1., using the default protocol AgilentG3_GX_1Color. The Scanning resolution was 3 µm and green channel

data_processing: We used Agilent Feature Extraction Software (ver. 10.7.3.1) (Agilent Technologies) to process the microarray images and to quantify the fluorescence of the probes

organism: Mytilus galloprovincialis

source_name: F mussels reared in BP diet. Experiment I

label_protocol: We used “One-Color Microarray-Based Exon Analysis” marking protocol from Agilent. Samples were marked using “Low Input Quick Amp WT Labeling kit, One-Color” (p/n 5190-2943) kit.

growth_protocol: Mussels were reared in laboratory under different nutritional conditions

extract_protocol: The RNA was extracted with Ribopure system (Ambion kit). The analysis of the quality and integrity of RNA was checked with Fragment AnalyzerTM Automated CE System equipment from advanced analytical with DNF-471 Standard Sensitivity RNA Analysis kit, (15 nt) and Fragment AnalyzerTM 1.1.0.11 software version. RNA quality was checked using PROSize 2.0.

treatment_protocol: Fast and slow growing individuals were obtained in each rearing condition. Mussels were dissected and gills were obtained to extract the RNA. Samples were stored immersed in RNA later at -80 ºC until the RNA was extracted

tag: growth

value: F

tag: diet

value: BP

tag: emersion

value: submerged

value: Gill sample


title: BP_submerged_slow_pool2

description: HSS pool 2

source_name: S mussels reared in BP diet. Experiment I

value: S


title: AP_submerged_fast_pool2

description: LSF pool 2

source_name: F mussels reared in AP diet. Experiment I

value: AP


title: Embryo1_circRNA

description: circRNA

value: Qinchuan

tag: developmental stage


title: AP_submerged_slow_pool2

description: LSS pool 2

source_name: S mussels reared in AP diet. Experiment I


title: AP_submerged_slow_pool3

description: LSS pool 3


title: CD4_H [104a-0]

description:
CD4_isoform_exp.diff
CD4_gene_exp.diff

source_name: CD4+ PBL

value: peripheral blood cells

value: CD4+ T cell

value: health


title: AP_submerged_slow_pool4

description: LSS pool 4