title: Myf5PBAT2

status: Public on Jan 07 2017

city: Dallas

first: Li

last: Li

state: TX

address: 5323 Harry Hines Boulevard

institute: UT Southwestern Medical Center

data_processing:
Sequencing libraries were generated using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB, USA) and 150 bp paired-end reads were sequenced on Illumina Hiseq2500 platform in Novogene company..
The paired-end clean reads were aligned to the reference genome using TopHat and each gene reads numbers were count by HTseq.
Differential expression analysis was performed by DEseq2 package in which gene length and dispersion bias was corrected.
The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate (FDR).
Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include readcount for each Sample.

source_name: Brown adipocytes

extract_protocol:
Total RNA were extract immediately by RNeasy Micro Kit (Qiagen) and the amplified cDNA samples were prepared by the SMART-Seq™ v4 Ultra™ Low Input RNA Kit for Sequencing (Clontech) and validated by the Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina HiSeq 2500 protocols

value: Brown adipocytes

value: 8-week old virgin


title: Ucp1NMyo1

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: Mammary myoepithelial cell

tag: cell type

value: Mammary myoepithelial cell

tag: strain

tag: age

value: lactation day 10

tag: genotype


title: Tgm odd probe

city: Augusta

first: Justin

last: Choi

state: GA

address: 1410 Laney Walker Blvd.

department: Cancer Center

institute: Georgia Regents University

description: Tg mouse chromosomal DNA captured by the Odd probe

library_source: genomic

data_processing:
Library strategy: ChIRP-Seq
TrimmomaticPE 0.32 trimmed sequencing adapters with ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 TRAILING:10 MINLEN:30.
BWA 0.7.10-r789 mapped read sequences to hg19 for the human samples and to mm10 and human hemoglobin locus for mouse trangenic samples.
Mapped reads were filtered if they were mapped to multiple locations and to unique location with 5% or more mismatches and indels of read lengths.
CHIRP-seq pipeline developed by  Howard Y. Chang was used to process BAM files.
Inhouse script merged wiggle files for even and odd probe samples.
Genome_build: hg19 for CD34
Genome_build: mm10 and human  beta-globin locus (chr11:5220000-5320000) in hg19 for Tgm
Supplementary_files_format_and_content: bigwig: binary wiggle file for each sample

molecule: genomic DNA

source_name: phenylhydrazine treated day 5 spleen erythroblast

growth_protocol: The CD34+ cells isolated from mobilized peripheral blood, were cultured in IMDM containing 4mM L-glutamine and 1% penicillin-streptomycin, 15%FBS, 15% human AB serum, SCF, 50 ng/ml, IL3, 10 ng/ml, and Epo, 2 units/ml. On day 7, the medium was replaced with fresh medium of the same composition, except that IL-3 was eliminated and SCF concentration was lowered to 25 ng/ml. On day 9 and 11, SCF concentration in the medium was lowered sequentially to 10 and 2 ng/ml. Cells were harvested on day 13 for subsequent assays.

extract_protocol:
Sonicated nuclei were incubated and hybridized with pooled biotinylated odd and even probes parallelly, and probe-lncRNA-DNA complexes were isolated with streptavidin beads. The pulled-down DNA was then eluted by Rnase A and Rnase H digestion.
Libraries were prepared according to NEBNext® Ultra™ DNA Library Prep Kit for Illumina (Part# E7370S).

treatment_protocol: 8 week old transgenic mice were weighed and injected intraperitoneally for two consecutive days with 15 mg/Kg body weight of phenylhydrazine (PHZ, Sigma-Aldrich, P-6926). Three days after the second PHZ administration, animals were sacrificed and spleen cells were harvested.

value: erythroblast

value: transgenic C57BL/6 mice with 100kb human globin locus


title: Tgm even probe

description: Tg mouse chromosomal DNA captured by the Even probe


title: Ucp1PBAT1


title: Myf5NMyo2


title: Ucp1NMyo2


title: Tgm Input

description: Tg mouse chromosomal DNA in the input control


title: E1_rep2 ATAC-seq

status: Public on Jan 08 2017

city: Philadelphia

first: Yijing

last: Su

state: PA

address: Levy 326

department: Department of Oral Medicine

institute: University of Pennsylvania

data_processing:
Illumina Casava1.7 software used for basecalling.
ATAC-seq reads were aligned to the mm9 genome assembly using Bowtie2 using default setting
peaks were called using MACS
Genome_build: mm9
Supplementary_files_format_and_content: bed/peak file

extract_protocol:
mice dentate gyrus were microdisected, ATAC-seq libraries were generated from each individuals
libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: dentate gyrus

value: adult 8 wks old


title: Ucp1PBAT2


title: Myf5PMyo2


title: Myf5PBAT1


title: Ucp1PMyo2


title: sh10 KD

description: Transcriptome analysis by RNA-seq

data_processing:
STAR 2.3.0e_r291 was used for mapping sequence reads to the human genome (hg19).
BedTools 2.16.2 and bedGraphToBigWig generated stranded binary wiggle files from BAM files
Cuffdiff 2.1.1 was used for differential expresion.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig: binary wiggle file for each sample
Supplementary_files_format_and_content: diff: differential expression for genes or isoforms (Cuffdiff output)
Supplementary_files_format_and_content: count_tracking: read counts of genes or isoforms for all samples (Cuffdiff output)
Supplementary_files_format_and_content: fpkm_tracking: FPKM of genes or isoforms for all samples (Cuffdiff output)

organism: Homo sapiens

source_name: erythroid cells

growth_protocol: The CD34+ cells isolated from mibilized peripheral blood, were cultured in IMDM containing 4mM L-glutamine and 1% penicillin-streptomycin, 15%FBS, 15% human AB serum, SCF, 50 ng/ml, IL3, 10 ng/ml, and Epo, 2 units/ml. On day 7, the medium was replaced with fresh medium of the same composition, except that IL-3 was eliminated and SCF concentration was lowered to 25 ng/ml. On day 9 and 11, SCF concentration in the medium was lowered sequentially to 10 and 2 ng/ml. Cells was harvested in day 13 for later assay.

extract_protocol:
RNA was isolated from cells with Trizol reagent.
Total cellular RNAs sheared to ~500 bp in lengths were constructed into cDNA libraries by HudsonAlpha using ribosomal RNA reduction and random prmer in cDNA synthesis.

treatment_protocol: On day 5, the cultured cells were transduced with lentivirus for sh5, sh10 and scramble ctrl, respectively. Puromycin selection was carried out on day 7 for 4 days until day 11 to select transcued cells.

value: Blood

tag: time

value: day 13 in culture


title: sh5 KD

description: Transcriptome analysis by RNA-seq


title: Myf5NMyo1


title: Scramble control

description: Transcriptome analysis by RNA-seq


title: SH-SY-IgG ChIPseq in SHSY5Y

city: Montreal

first: Panojot

last: Bifsha

state: QC

address: 3175 Chemin de la Côte Ste-Catherine

department: Pediatrics

country: Canada

institute: CHU Sainte-Justine

data_processing:
Sequence reads were trimmed for adapter sequences.
The resulting 50bp reads were trimmed to obtain high quality reads and then mapped to the hg19 human genome build using Bowtie
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using HOMER; Scores represent reads normalized per 10000000 reads

extract_protocol: ChIP experiment was performed as previously reported with few modifications (Langlais et al, Molecular Cell 2012). Briefly, human SHSY5Y cells stably expressing mouse Pitx3-3Fn were grown to 90% confluence, fixed in 1% formaldehyde/PBS for 5min at room temperature, washed, scraped off from the petri and sonicated to yield chromatin fragments with average size of 300-600bp. Sheared chromatin was incubated overnight at 4˚C along with 1:1 mix of Dynabeads-Protein A:Dynabeads-Protein G (Invitrogen) already coupled to primary antibody and thoroughly washed. Primary antibodies that were used were against the native form of Pitx3 (rabbit polyclonal, home-made) and Pitx3-Flag forms (mouse FlagM2, Sigma), including also rabbit (G2018, Sigma) or mouse (I5381, Sigma) IgG as controls for specific antibodies. Immunoprecipitated chromatin was washed, de-crosslinked, and then briefly treated with proteinase K and RNAse A. DNA from input, specific antibody and IgG was then purified using Qiaquick PCR purification kit (Qiagen). Immunoprecipitated DNA was sent for sequencing on Illumina GAIIx or Hi-Seq 2000 according to McGill University and Genome Quebec Innovation Centre protocols.

tag: cell line

value: Midbrain Dopamine Neurons

tag: chip antibody

value: IgG Sigma I5381


title: Pitx3 ChIPseq in human SHSY5Y cells stably expressing mouse Pitx3-3Fn

value: Pulichino et al. 2003


title: Myoblast rep4

city: Durham

first: Gregory

last: Crawford

state: NC

address: 101 Science Drive

department: Center for Genomic and Computational Biology

institute: Duke University

data_processing:
Single-end basecalls were done by using Illumina CASAVA 1.3 software.
After trimming bases with low quality score, reads were aligned to the UCSC Genes Hg19 reference transcriptome and filtering sequences containing no insertion, using Tophat with options −x 4 and −n 2 (23). Fragments Per Kilobase of exon per Million fragments mapped (FPKM) was estimated by Cufflinks and differential expression between normalized gene read counts in FPKM with significance threshold of FDR 0.05 by using Cuffdiff (24).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: cultured Myoblast cells

growth_protocol: Primary human dermal fibroblasts (Catalog ID: GM03348) were obtained from Coriell Institute (Camden, New Jersey) and were maintained in DMEM supplemented with 10% FBS and 1% penicillin streptomycin. All cells were cultured at 37 °C with 5% CO2. Three biological replicates of both the parental fibroblast cells and transduced fibroblast cells were were harvested on different days. Four replicates of Myoblasts were originally sampled and grown from four different patients, as described and published previously (PMID: 26041816).

extract_protocol:
RNA was extracted and purified by the methods in RNeasy Mini Handbook from Qiagen
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Fibroblasts cells were transfected with 20 µg of transfer vector(Tet-ON lentivirus that expresses a 3xFlag-tagged full-length MYOD1 cDNA ), 6 µg of pMD2G, and 10 µg psPAX2 using a calcium phosphate transfection. The media was changed 12-14 hours post transfection. The viral supernatant was collected 24 and 48 hours after this media change and pooled. For transduction, the cell medium was replaced with viral supernatant supplemented with 4 μg/mL polybrene. The viral supernatant was changed 24-48 hours later.

tag: transduced gene

value: cultured Myoblast cells


title: FS12

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: allFulSperm.results.csv.gz

data_processing:
Basic read quality was verified using summaries produced by FastQC
The reads for each sample for both CNV and DMR analyses were mapped to the zebra finch (Taenopygia guttata) genome using Bowtie2
The mapped read files were then converted to sorted BAM files using SAMtools
The MEDIPS R package was used to calculate differential coverage between sample groups. To identify DMR, the reference genome was broken into 100 bp windows. The edgeR Pvalue was used to determine the relative difference between the two sample groups for each genomic window. Windows with an edgeR P value less than 1e-3 were considered DMR. The DMR edges were extended until no genomic window with an edgeR P value less than 0.1 remained within 1000 bp of the DMR.
The DMR that included at least two windows with an edgeR P value < 1e-3 were then selected for further analysis and annotated.
Genome_build: taeGut3.2.4
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window as well as the calculated p-value and other summary values.

organism: Geospiza fuliginosa

source_name: Sperm

growth_protocol: Red blood cell and sperm samples were collected from wild finches

extract_protocol:
Genomic DNA from finch red blood cells (erythrocytes) was prepared using the Qiagen DNAeasy Blood and Tissue Kit (Qiagen, Valencia CA). The manufacturer’s instructions for nucleated blood samples were followed, but in the final DNA elution step H2O was used instead of the buffer provided in the kit. Genomic DNA from finch sperm was prepared as follows: collected sperm suspension was adjusted to 100 μl with 1 x Phosphate Buffered Saline (PBS) then 820 μl DNA extraction buffer (50mM Tris pH8, 10mM EDTA pH8, 0.5% SDS) and 80 μl 0.1 M dithiothreitol (DTT) were added and the sample was incubated at 65°C for 15 minutes. Next, 80 μl Proteinase K (20 mg/ml) were added and the sample was incubated on a rotator at 55°C for 2 hours. After incubation, 300 μl of protein precipitation solution (Promega, A795A) were added, then the sample was mixed and incubated on ice for 15 minutes, then spun at 4°C at 13,000 rpm for 20 minutes. The supernatant was transferred to a fresh tube, then precipitated over night with the same volume of 100% isopropanol and 2 μl glycoblue at -20°C. The sample was then centrifuged and the pellet washed with 75% ethanol, then air-dried and re-suspended in 100 μl H2O. DNA concentration was measured using a Nanodrop Spectrophotometer (Thermo Fisher).
The MeDIP pools were used to create libraries for next generation sequencing (NGS) at the University of Nevada, Reno Genomics Core Laboratory using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina®, starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA. After this step the manufacturer’s protocol was followed.

treatment_protocol: Samples from different cell types, species, and collection locations were compared.

value: Sperm

tag: developmental stage

value: Adult


title: scramble_rep3

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

description: chromatin associated RNA

data_processing:
Library strategy: RICh-Seq
MiSeq v2 reagents
Fastx toolkit (fastq_quality_trimmer) was used to trim bases fom the 3’ end of reads with a quality less than 10. Reads shorter than 20 nt were discarded
Fastx toolkit (fastx_clipper) was used to clip adapter sequences matching the string “AGATCGGAAGAGCACACGTCTGAACTCCAGTC”
STAR aligner was used to map reads to the human genome (Hg38 primary assembly from Ensembl) using version 78 gene annotations.
Featurecounts was used to count reads mapped to the correct strand with a minimum mapping quality of 10. Ensembl v78 GTF was used.
Genome_build: Hg38
Supplementary_files_format_and_content: Gene-wise raw read counts of gene expression

growth_protocol: Standard HeLa cell growth conditions

extract_protocol:
Crosslinked chromatin was isolated from cell monolayers as previously described (PMID:24732587). Chromatin was sheared using Diagenode BioRuptor sonicator. Biotin labeled locked nucleic acid probed were hybridised to the chromatin. Pulldown of probes and interacting chromatin was performed using streptavidin magnetic beads. RNA was isolated from the enriched fraction using Qiagen Rneasy Mini Kit.
NEB Next small RNA

tag: chromatin fraction

value: Scrambled probes pull-down


title: Myoblast rep3


title: FS10

description: allFulSperm.results.csv.gz


title: FS11

description: allFulSperm.results.csv.gz


title: Myoblast rep2


title: 6M2

city: Monterrey

first: Raquel

last: Cuevas Diaz Duran

address: Av Morones Prieto No. 3000, Colonia Los Doctores

department: Escuela de Medicina y Ciencias de la Salud

country: Mexico

institute: Tecnologico de Monterrey

data_processing:
Basecalling was performed with CASAVA v1.7 from Illumina
The 100-bp paired-end reads were aligned to the reference genome Rnor6 (downloaded from Ensembl) using TopHat v2.1.0 with default parameters.
Mapped reads were assembled using Cufflinks v2.2.1 and FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values were obtained for annotated genes and transcripts.
Read counts for annotated genes and transcripts were calculated using HTSeq-count
Genome_build: Rnor6

organism: Rattus norvegicus

source_name: Spinal cord

extract_protocol:
At 1 month, 3 months, and 6 months post-SCI, animals were intracardially perfused with 0.01M phosphate-buffered saline under anesthesia. A segment of the spinal cord tissue (0.5 mm) at the epicenter was dissected from each animal and snap-frozen in liquid nitrogen. Animals in the control group were sacrificed at 6 months post-SCI and a section of the spinal cord tissue at an equivalent location was collected. Total RNA was extracted from the spinal cord tissue using TRIzol reagent (Invitrogen) following the manufacturer’s instructions.  RNA quality was determined using a Bioanalyzer (Agilent), and all RNA integrity numbers (RINs) were greater than 8.  About 150–300 ng total RNA was used to construct each RNA-Seq library.
RNA samples were poly-A selected and paired-end sequencing libraries were constructed using the TruSeq RNA Sample Prep Kit, as described in the TruSeq RNA Sample Preparation V2 Guide (Illumina). Samples were then sequenced using the Illumina HiSeq 2000 sequencer.

value: Sprague-Dawley

tag: gender

value: female

value: Spinal cord

value: 12-14 weeks


title: Fd rep3

source_name: Fibroblast cells transfected with vectors carrying MyoD gene

value: human MyoD

value: Fibroblast cells


title: FS8

description: allFulSperm.results.csv.gz


title: Myoblast rep1


title: Myf5PMyo1

value: Mammary myoepithelial cell

value: lactation day 10


title: FS9

description: allFulSperm.results.csv.gz


title: 6M1


title: Ucp1PMyo1


title: 3M3


title: Fd rep2


title: NET_rep2

description: chromatin associated RNA

value: NET promoter pull-down


title: Fd rep1


title: scramble_rep1

description: chromatin associated RNA


title: FB12

description: allFulRBC.results.csv.gz

source_name: Red blood cell

value: Red blood cell


title: 3M1


title: 3M2


title: FS7

description: allFulSperm.results.csv.gz


title: NET_rep3

description: chromatin associated RNA


title: 1M3


title: Fb rep3

source_name: Cultured Fibroblast cells

value: Cultured Fibroblast cells


title: NET_rep1

description: chromatin associated RNA


title: FB11

description: allFulRBC.results.csv.gz


title: 1M2


title: Fb rep2


title: input_rep2

description: chromatin associated RNA

value: input chromatin


title: FB10

description: allFulRBC.results.csv.gz


title: 1M1


title: scramble_rep2

description: chromatin associated RNA


title: Fb rep1


title: Fd_input

data_processing:
Single-end basecalls were done by using Illumina CASAVA 1.3 software.
ChIP-seq raw reads were mapped to hg19 with bowtie-0.12.9, unique aligned, then bam files were converted to bed file by bedtools. After removing PCR artifacts bigWig files were created by using MACS2 (version 2.1.0)
Genome_build: hg19
Supplementary_files_format_and_content: peak calls

extract_protocol: cells were fixed with 1% formaldehyde (wt/vol) for 15 min, washed with 1 X PBS and lysed in buffer with 50 mM Tris(pH8), 1% SDS (wt/vol), and 10 mM EDTA. Lysed cells were sonicated with 30 s on/off cycles at high intensity by using a bioruptor (Diagenode).  Sonicated supernatants were diluted with buffer containing 16.7 mM Tris-HCl(pH8), 0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA and 167 mM NaCl. 10 ul of FLAG antibody (Monoclonal anti-FLAG M1 antibody produced in mouse, F3040, Sigma-Aldrich) was added into the diluted supernatants, and 60 ul of Dynabeads protein A beads were added and incubated for 3 hours at 4C. ChIP-seq libraries were made by using NEBNext Ultra DNA Library prep kit for Illumina


title: AMI-5_rep1

description:
processed data file: Okabe_AMI5_mRNA_counts.tsv
FC037_4_AMI5_rep1

data_processing:
OLB1.8
BWA alignment to human genome
Bedtools was used to count mapped reads with maping quality of 10 or higher. Gene annotations were obtained from GENCODE version 14.
Genome_build: Hg19
Supplementary_files_format_and_content: Gene-wise raw read counts of gene expression

growth_protocol: HMEC-1 cells grown in MCDB131 medium with normal glucose (5.5 mM)

extract_protocol:
Qiagen Rneasy Kit
Dynabead poly-A enrichment, Illumina mRNA-seq library preparation kit.

treatment_protocol: Cells were treated with either AMI-1 or AMI-5 at 100μM concentration in DMSO, or DMSO alone, for 16 hrs.

tag: delivered drug

value: AMI-5 100μM in DMSO, 16 h


title: FB8

description: allFulRBC.results.csv.gz


title: FB9

description: allFulRBC.results.csv.gz


title: Control2


title: AMI-5_rep2

description:
processed data file: Okabe_AMI5_mRNA_counts.tsv
FC038_3_AMI5_rep2


title: FS5

description: allForSperm.results.csv.gz

organism: Geospiza fortis


title: AMI-1_rep3

description:
processed data file: Okabe_AMI1_mRNA_counts.tsv
FC044_2_AMI1_rep3

value: AMI-1 100μM in DMSO, 16 h


title: AMI-5_rep3

description:
processed data file: Okabe_AMI5_mRNA_counts.tsv
FC044_3_AMI5_rep3


title: Fd_IP_rep2


title: Control1


title: input_rep3

description: chromatin associated RNA


title: Fd_IP_rep1


title: FB7

description: allFulRBC.results.csv.gz


title: CD34 even probe

description: Chromosomal DNA captured by the Even probe

source_name: day 13 erythroblast

value: erythroblast


title: Fd_IP_rep3


title: CD34 odd probe

description: Chromosomal DNA captured by the Odd probe


title: FS6

description: allForSperm.results.csv.gz

value: Sperm

value: Adult


title: AMI-1_rep2

description:
processed data file: Okabe_AMI1_mRNA_counts.tsv
FC038_2_AMI1_rep2


title: FS4

description: allForSperm.results.csv.gz


title: input_rep1

description: chromatin associated RNA


title: CD34 Input

description: Chromosomal DNA in the input control


title: Control3

value: Sprague-Dawley


title: AMI-1_rep1

description:
processed data file: Okabe_AMI1_mRNA_counts.tsv
FC037_3_AMI1_rep1


title: FS3

description: allForSperm.results.csv.gz


title: Fd_rep2

data_processing:
Single-end basecalls were done by using Illumina CASAVA 1.3 software.
First 20 bp of Dnase-seq raw reads were mapped to hg19 with bowtie-0.12.9, with 2 mismatches allowed, to generate bam files, then bam files were converted to bed file by bedtools. After removing PCR artifacts bigWig files were created by using MACS2(version 2.1.0) .
Genome_build: hg19
Supplementary_files_format_and_content: peak calls

extract_protocol:
Cells were Lysed and nuclei were digested according to the publication PMID: 20150147.
Libraries were prepared according to the publication PMID: 20150147.


title: Ctrl_rep3

description:
processed data file: Okabe_AMI1_mRNA_counts.tsv, Okabe_AMI5_mRNA_counts.tsv
FC044_1_Ctrl_rep3

value: vehicle control (DMSO)


title: 8h_3

city: Guangzhou

first: Daxiang

last: Chen

state: Guangdong

address: 1838 N. Guangzhou Avenue

country: China

institute: Southern Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to  the hg19 human reference genome using TopHat version 2, allowing for 2 nt of mismatch.
Fragments Per Kilobase of transcript per Megabper Million mapped reads (FPKM) were calculated using a protocol from Mortazavi et al., Mapping and quantifying mammalian transcriptomes by RNA-Seq, 2008.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include counts and FPKM values for each Sample

source_name: human foreskin fibroblast cells

growth_protocol: HFF-1 cells were cultured at 37°C in DMEM complemented with 15% FBS (Gemini, USA), containing penicillin (100 U/ml) and streptomycin (100µg/ml).

extract_protocol:
Following the incubation, total RNA was extracted using TRIZOL Reagent (Life Technologies, USA), according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HFF-1 cells were stimulated for 0, 3 or 8 hours with live ORFV OV-GO at a multiplicity of infection (MOI) of 5.

value: Skin

value: Newborn

tag: agent

value: ORFV

tag: time point


title: Fd_rep1

value: human MyoD

value: Fibroblast cells


title: Ctrl_rep2

description:
processed data file: Okabe_AMI1_mRNA_counts.tsv, Okabe_AMI5_mRNA_counts.tsv
FC038_1_Ctrl_rep2


title: FS2

description: allForSperm.results.csv.gz


title: 8h_2


title: 8h_1


title: Fb_rep3


title: FS1

description: allForSperm.results.csv.gz


title: Fd_rep3


title: 3h_3


title: NTC_rep3

treatment_protocol: Cells were transfected with lentivirus construct delivering either non-targeting shRNA or Set7 targeting shRNA

tag: delivered shrna construct

value: Non-targeting control


title: Fb_rep1


title: Fb_rep2


title: Ctrl_rep1

description:
processed data file: Okabe_AMI1_mRNA_counts.tsv, Okabe_AMI5_mRNA_counts.tsv
FC037_2_Ctrl_rep1


title: NTC_rep2


title: FB5

description: allForRBC.results.csv.gz


title: FB6

description: allForRBC.results.csv.gz


title: FB4

description: allForRBC.results.csv.gz


title: 3h_2


title: FB3

description: allForRBC.results.csv.gz


title: Myoblast_rep3

value: cultured Myoblast cells


title: Set7KD_rep3

value: Set7 knock-down


title: Myoblast_rep2


title: 0h_3


title: FB2

description: allForRBC.results.csv.gz

value: Red blood cell


title: NTC_rep1


title: Set7KD_rep2


title: 0h_2


title: Myoblast_rep1


title: FB1

description: allForRBC.results.csv.gz


title: 0h_1


title: 3h_1


title: Set7KD_rep1


title: wild_HU_Input

status: Public on Jan 06 2017

city: Tokyo

first: Yutaka

last: Kanoh

address: 2-1-6 Kamikitazawa, Setagaya-ku

department: Genome Medicine

country: Japan

institute: Tokyo Metropolitan Institute of Medical Science

data_processing:
All fastq files were aligned to S.pombe reference genomic ASM294v2 from Pombase by Bowtie1.0.0 with defalt setting.
The generated SAM files by Bowtie were converted to BAM and sorted by Samtools.
Peaks were called with Model-based analysis of ChIP-seq (MACS2.0.10) using following parameters; macs2 callpeak -t ChIP.sam -c Input.sam -f SAM -g 1.4e107 -n result_file -B -q 0.01 --nomodel
The generated treat_pileup.bedgraph files were loaded on Integrated Genome Browser.
Genome_build: ASM294v2

organism: Schizosaccharomyces pombe

source_name: yeast

growth_protocol: The stains were grown until mid log phase in YES medium at 30ºC. Cells containing nda3-KM311 mutation were arrested at M-phase at 20ºC for 5 hr. Cells were released into sequential cell cycle at 30ºC.

extract_protocol:
Protocol 1: The cell wall was disrupted by zirconia beads and multi-beads shocker (Yasui Kikai Co.). Lysates were prepared by sonication and clarified by centrifugation. Protein and DNA complexes were immuno-precipitated by antibody conjugated with Protein G Dynabeads.
Protocol 2: BrdU-incorporated genomic DNA was purified by Qiagen Genomic-tip and genomic buffer set. Purified genomic DNA was sheared by sonication. The fragmented DNA was heat-denatured and BrdU-substituted DNA was immuno-precipitated by Anti-BrdU antibody conjugated with anti-IgG1a-dynabeads.
ChIP, BrdUIP, and Input DNA was sheared to around 150bp by S220 Focused-ultrasonicators (COVARIS, INC.). The fragmented DNA were end-repaired, ligated to sequencing adapters and amplified according to the protocol of NEBNext® ChIP-Seq Library Prep Master Mix Set and NEBNext Multiplex Oligos for Illumina (New England Biolabs) to prepare library. The size and concentration of libraries were checked by Bioanalyzer 2000 and real-time PCR using KAPA Library Quantification Kits, respectively.

treatment_protocol:
Protocol 1: Cells during G1 phase were fixed with 1% Formaldehyde at 20min after release.
Protocol 2: Cells were arrested at early S-phase in 25mM HU at 60min after release from M-phase arrest and then the early replicated regions were labeled with 200µg/ml BrdU.

value: Wild Type

tag: tag or genetic characteristics

value: adh1-thymidine kinase-Ent1

tag: antibody


title: mrc1_3A_HU_BrdUIP

description: wild_HU_Input used as control

tag: strain

value: Anti-bromodeoxyuridine (MBL), Subclass; mouse IgG1, Clone; 2B1, Cat No.; MI-11-3,


title: mrc1_dhbs_HU_BrdUIP

description: wild_HU_Input used as control


title: T1_F_C

city: New York

first: Doron

last: Betel

state: NY

address: 1305 York Avenue (Box 140)

department: Medicine

institute: Weill Cornell Medical College

data_processing:
Basecall performed using Casava 1.7
Alignment performed using TopHat version 1.3.1
Gene counts were performed using GenomicRanges R package using refseq annotation file and lincRNA from PUBMED ID 22196729
Differential expression performed using edgeR-2.612 and limma-3.12.3
Genome_build: mm9
Supplementary_files_format_and_content: Read counts table

source_name: Frontal Cortex, Fear conditioning, 1hr

extract_protocol:
Prefrontal cortex (PFC) was dissected from 7-9 weeks old C57Bl6 mice (Jackson Laboratories) and polyribosome associated mRNAs were isolated using Trizol (Invitrogen). Polyribosome associated RNAs were prepared from context alone control (n=4) and fear conditioned mice (after one and six hours of contextual fear conditioning, n=4) for RNAseq analysis
Beginning with 200 ng RNA sample, the sample is reverse transcribed with random hexamer and poly A primers after removing ribosomal RNAs using Ribo minus kit (Invitrogen). This product is converted into double stranded cDNA, followed by SPIA amplification. After purification the sample is end repaired and then has specific adapters ligated to the 5’ and 3’ ends. These products are then PCR amplified to enrich for the ligated products (Nugen San Diego, CA). The amplified samples are then purified and diluted down to a 10µM library.

value: Frontal Cortex


title: T1_F_H

source_name: Hippocampus, Fear conditioning, 1hr

value: Hippocampus


title: T2_C_C

source_name: Frontal Cortex, Control, 6hr


title: T2_F_C

source_name: Frontal Cortex, Fear conditioning, 6hr


title: T1_C_H

source_name: Hippocampus, Control, 1hr


title: dmrc1_HU_BrdUIP

description: wild_HU_Input used as control


title: Mcm4ChIP_G1

description: wild_Input_metaphase used as control

value: ANTI-FLAG M2 Monoclonal Antibody(Sigma), Subclass; IgG1, Clone; M2, Cat No.; F1804


title: Myoblast_rep4

tag: cell type


title: T2_F_H

source_name: Hippocampus, Fear conditioning, 6hr


title: T1_C_C

source_name: Frontal Cortex, Control, 1hr


title: Non-progressor (81_L7.LB16)

city: Seattle

first: Daniel

middle: Edward

last: Zak

address: 307 Westlake Ave N, Suite 5

institute: Seattle Biomedical Research Institute

description: Processed data: primarySampleJunctions.xlsx - Sheet2

data_processing:
Alignment GSNAP version 2012-06-20
Sequenced reads were filtered for low-quality sequence and the presence of 'N's, then mapped to hg19 whole genome using gsnap v0.12.2
Junctions counts were calculated by using an in house script to count the number of reads mapped to all splice junctions in the genome
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file including the raw junction counts for all the detected junctions in the genome (number of reads mapped to the splice junctions in all samples)

source_name: Blood, control

extract_protocol:
Paxgene RNA
GlobinClear Globin transcript reduction followed by Illumina mRNA-Seq

tag: group

value: control (non-progressor)

tag: bin

tag: age

value: male

tag: ethnicity

value: coloured

tag: previousdiagnosisoftb

value: n

tag: tst

tag: qft

value: blood


title: SORT4_S4.fastq.gz

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description:
genomic DNA
HEK293 cells expressing Halo-tagged MLL protein. Cells were transfected with a pooled shRNA library comprised of TRC1 (81,041 shRNAs) and TRC1.5 (17,563 shRNAs) before sorting cells exhibiting higher Halo signal by FACS.

data_processing:
Basecalls performed using bcl2fastq v2.17.1.14 or CASAVA 1.8
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 or mm9 using Bowtie version 1.1.2.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.1.0.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: UCSC hg19, mm9
Supplementary_files_format_and_content: bigwig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate. RNAseq bigwigs are split by strand.

source_name: shRNA screen

growth_protocol: 293 and MEF cells were cultured in Dulbecco's Modified Eagle Medium (DMEM, catalog No. 11995, Gibco) supplemented with 10% fetal bovine serum (FBS, catalog No. F6178, Sigma). SEM and REH leukemia cells were maintained in Iscove's Modified Dulbecco's Medium (IMDM) with 10% FBS. REH and MM6 cells were maintained in RPMI-1640 medium supplemented with 10% FBS.

extract_protocol:
RNA was extracted using Trizol and QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit

treatment_protocol: Treatment with IRAK1/4 or IRAK4 inhibitors was administrated only once

tag: cell line

value: Human embryonic kidney cells


title: SORT3_Split2_S3.fastq.gz


title: SORT1_Split1_S1.fastq.gz


title: SORT2_Split2_S2.fastq.gz


title: SORT2_Split1_S2.fastq.gz


title: AEC RNAseq_f9c8_4025

first: Carole

last: Ober

address: 920 E 58TH ST

department: Human Genetics

institute: The University of Chicago

data_processing:
cDNA libraries were constructed using the TruSeq RNA Sample Preparation v2 according to manufacturer’s instructions
reads were mapped to the transcriptome (HG19) using BWA
sequences that overlapped with protein coding regions were determined using BEDTools
gene counts were adjusted for gene lengh
expression estimates were filtered to genes with at least 5 reads in 2 individuals and were annotated in biomart
factors of unwanted variation were identified and expression estimates were corrected for these estimates using RUVSeq
Genome_build: hg19
Supplementary_files_format_and_content: text file with normalized counts

source_name: Airway Epithelial cells

extract_protocol:
AECs were harvested via bronchial brushing and DNA/RNA was extracted consecutively using the AllPrep kit from QIAgen
Library construction protocol not provided.

tag: disease status

value: Asthma

value: Airway Epithelial cells


title: AEC RNAseq_f964_47ea


title: AEC RNAseq_fb20_4736


title: AEC RNAseq_fff9_43b1


title: 293_NT86_IRAK_inhibitor

description: fragmented genomic DNA

tag: drug treatment

value: IRAK1/4 inhibitor

tag: chip antibody

value: MLL NT86


title: SORT3_Split1_S3.fastq.gz


title: T2_C_H

source_name: Hippocampus, Control, 6hr

tag: tissue


title: wild_HU_BrdUIP

description: wild_HU_Input used as control


title: AEC RNAseq_f5d3_41dd


title: AEC RNAseq_efe7_4deb


title: AEC RNAseq_e207_4fcd


title: AEC RNAseq_e089_4cc0

value: Control


title: AEC RNAseq_e549_49d1


title: AEC RNAseq_cf2d_4e5f


title: AEC RNAseq_e380_4917


title: AEC RNAseq_f0b3_4ef4


title: AEC RNAseq_ed81_42cb


title: AEC RNAseq_dd18_4326


title: SORT1_Split2_S1.fastq.gz


title: AEC RNAseq_c3df_4109


title: AEC RNAseq_cd0c_4cca


title: 293_NT86_DMSO

description: fragmented genomic DNA

value: DMSO


title: AEC RNAseq_d93e_43a4


title: AEC RNAseq_bf1e_4b60


title: AEC RNAseq_b75e_4b56


title: AEC RNAseq_b9fb_4080


title: AEC RNAseq_b3c4_45a5


title: AEC RNAseq_b3ae_412f


title: AEC RNAseq_a8b2_474d


title: AEC RNAseq_a7d1_4fec


title: AEC RNAseq_acb6_4308


title: AEC RNAseq_ad5c_4ce5


title: AEC RNAseq_a6d0_4327


title: AEC RNAseq_f4fe_4560


title: AEC RNAseq_9c8b_4a61


title: AEC RNAseq_9c18_4eb2


title: AEC RNAseq_8ebb_4e23


title: AEC RNAseq_86b9_4119


title: AEC RNAseq_8d5d_424a


title: AEC RNAseq_84e5_4094


title: AEC RNAseq_b65a_44b4


title: AEC RNAseq_7ed8_4eff


title: AEC RNAseq_87f0_42ad


title: AEC RNAseq_7bfd_4bf0


title: AEC RNAseq_7a9e_4793


title: AEC RNAseq_75cf_477a


title: AEC RNAseq_767f_4e2a


title: AEC RNAseq_8cd5_4d95


title: AEC RNAseq_74f3_4f8a


title: AEC RNAseq_ae28_4608


title: AEC RNAseq_86aa_4206


title: AEC RNAseq_6ebc_47ef


title: AEC RNAseq_78d1_4946


title: AEC RNAseq_690e_45c3


title: AEC RNAseq_5e70_4f6c


title: AEC RNAseq_44df_487e


title: AEC RNAseq_53ff_4183


title: AEC RNAseq_502d_4e7d


title: AEC RNAseq_5f2e_48a8


title: AEC RNAseq_4c83_4965


title: AEC RNAseq_3d3b_40f5


title: AEC RNAseq_411a_4fba


title: AEC RNAseq_4ba3_4efe


title: AEC RNAseq_39e9_4475


title: AEC RNAseq_3b7f_4689


title: AEC RNAseq_3a8f_4120


title: AEC RNAseq_36b7_4822


title: AEC RNAseq_6132_4c18


title: AEC RNAseq_2cfc_42e1


title: AEC RNAseq_273e_4084


title: AEC RNAseq_1ca9_4a88


title: AEC RNAseq_22ea_40a1


title: AEC RNAseq_1ba9_4d79


title: AEC RNAseq_2239_4ef1


title: AEC RNAseq_2d00_4023


title: AEC RNAseq_15e4_4e17


title: AEC RNAseq_1f64_4727


title: AEC RNAseq_179c_43ec


title: AEC RNAseq_154f_455f


title: AEC RNAseq_06f5_4503


title: AEC RNAseq_0447_47e4


title: AEC RNAseq_0610_40f0


title: AEC RNAseq_1c7d_4407


title: AEC RNAseq_07f4_4e79


title: AEC RNAseq_1299_419b


title: AEC RNAseq_107e_4776


title: 24hr m7G pulldown

city: Lebanon

last: Cole

state: NH

address: One Medical Center Dr

institute: Geisel School of Medicine at Dartmouth

description:
Methyl-capped mRNA pulldown
barcode: CTTGTA

data_processing:
Library strategy: RNA pulldown
RNA-seq reads were aligned against the hg38 genome assembly using STAR aligner to yield .bam output files.
Partek Genomics Suite was used to convert .bam files to .reads or .rpkm files
Reads of <5 were removed from further analysis. Inputs were considered "control" files and pulldowns were considered "treatment" files; all parameters were used in "default" mode.
Genome_build: hg38
Supplementary_files_format_and_content: Txt files were generated from the read and rpkm files from Partek Genomics Suite and listed in the file for each sample are: # of alignments, reads or rpkm per gene per sample.

source_name: P493-6 cells

growth_protocol: Cell lines were cultured in RPMI with 15% FBS and 1% pen/strep.

extract_protocol:
Total RNA was isolated from a T25 flask containing 1-2 x 10^6 cells and m7G mRNA was extracted using a recombinant protein, GST-eIF4E. m7G mRNA was separated from GST-eIF4E using TRIzol.
Libraries were prepared at Global Biologics (Missouri) using the Illumina RNA-seq kit, beginning with 9-13ng of methyl-capped mRNA (pulldown) or 1ug total RNA (input). RiboZero was used to remove ribosomal RNA from input samples. Barcodes were used to multiplex the sequencing run and the barcodes used were the following: CGATGT, GCCAAT, TGACCA, CAGATC, ACAGTG, CTTGTA. Libraries were sequenced on the HiSeq2000 according to the manufacturer's protocols at the University of Delaware.

treatment_protocol: The MYC transgene was silenced by treating cells with 0.1ug/mL tetracycline for 72 hours and was induced by resuspending the cells in fresh medium for 0, 1, or 24 h following 3 washes.

value: Human Burkitt lymphoma cell line

tag: fusion protein

value: GST-eIF4E (E. coli)


title: 24hr Input

description:
Input RNA
barcode: ACAGTG


title: 0hr m7G pulldown

description:
Methyl-capped mRNA pulldown
barcode: GCCAAT


title: 1hr Input

description:
Input RNA
barcode: TGACCA


title: AEC RNAseq_3348_4c75


title: AEC RNAseq_307c_4037


title: AEC RNAseq_29ed_4409


title: AEC RNAseq_2800_4691


title: 0hr Input

description:
Input RNA
barcode: CGATGT


title: SEM_DMSO_AFF4

description: fragmented genomic DNA

value: B cell precursor leukemia

value: homemade AFF4NT


title: SEM_IRAK14_inhibitor_AFF4

description: fragmented genomic DNA


title: SEM_IRAK14_inhibitor_AFF1CT

description: fragmented genomic DNA

value: homemade AFF1CT


title: SEM_IRAK4_inhibitor_AFF1CT

description: fragmented genomic DNA

value: IRAK4 inhibitor


title: GRO-seq control sample

city: La Jolla

first: Long

last: Vo ngoc

state: California

address: 9500 Gilman Dr

institute: UCSD

description: run-on RNA

data_processing:
Library strategy: GRO-Seq
Adapter sequences were removed from reads with homerTools trim.
The resulting reads were mapped to the hg19 human genome by using Bowtie2 with the default settings.
Genome_build: hg19

source_name: human breast carcinoma cells

growth_protocol: MCF-7 cells (ATCC) were maintained in DMEM (ATCC) supplemented with 10% FBS (ATCC), 15 μg/mL bovine insulin (Sigma-Aldrich), 50 U/mL penicillin (ThermoFisher), and 50 μg/mL streptomycin (ThermoFisher).

extract_protocol:
Two 5’-GRO-seq and one GRO-seq experiments were carried out by variation of the procedure described in Duttke et al. (2015) and Hetzel et al. (2016). We were curious with regard to whether the RNA fragmentation step would affect the 5'-GRO-seq data, and we therefore performed one experiment with the RNA fragmentation and other experiment without the RNA fragmentation. As shown in Supplemental Fig. S2, we obtained similar results from the two experiments, and thus used both datasets for our analyses. For each experiment, nuclear run-on reactions were performed with 107 MCF-7 nuclei in the presence of BrUTP (Sigma Aldrich) for labeling of the RNA. Trizol LS (Fisher Scientific) was used to terminate the reaction and to extract the RNA.
For 5’-GRO-seq with fragmentation, RNA was hydrolyzed by Zn(II)-mediated fragmentation (Ambion). BrU-labeled transcripts were immunoprecipitated with anti-BrdU agarose beads (Santa Cruz Biotech) and extracted with Trizol LS. The resulting RNA was incubated with T4 polynucleotide kinase (NEB) in low pH buffer followed by treatment with calf intestinal alkaline phosphatase (CIP; NEB) to achieve 5’ and 3’ dephosphorylation. A second BrU enrichment was performed, and 5’-monophosphate-RNAs were removed with Terminator 5’-phosphate-dependent exonuclease (Epicentre), as described in Hetzel et al. (2016). The RNA was subjected to a second round of dephosphorylation with CIP (NEB). Decapping and library preparation were performed as described in Hetzel et al. (2016). For GRO-seq, the dephosphorylation steps were replaced by phosphorylation steps using T4 PNK, and the Terminator digestion ommited.
The Small RNA Library Prep Set (New England Biolabs) was used for final library preparation with modifications as described in Hetzel et al. 2016


title: SEM-hUBE2O-4587-REP2-DAY4

description:
total RNA
cells lentiviral infected with shRNA targeting UBE2O


title: CBFbeta-LysM1

city: Charlottesville

first: Thomas

last: Braciale

state: Virginia

address: 345 Crispell Dr

department: Pathology

institute: University of Virginia

description: Day 2 post influenza infection

data_processing:
Base-Calling was performed at sequencing facility and fastq files were given.
Reads were aligned to the NCBI genome build of GRCm38 using Tophat Software and corresponding GTF file.
Using Cuffdiff, differential expression analysis was carried out.
Genome_build: GRCm38
Supplementary_files_format_and_content: Table of read counts for each transcript.

molecule: polyA RNA

source_name: Alveolar type-1 cells

extract_protocol:
Samples were shipped in Trizol to sequencing facility where RNA was extracted.
RNA library were prepped using the SMARTer Low Input RNA Kit

value: Lung

value: Alveolar type-1

tag: genotype


title: SEM-shUBE2O-4587-REP1-DAY4


title: CBFbeta-LysM2

description: Day 2 post influenza infection


title: SEM_DMSO_AFF1CT

description: fragmented genomic DNA


title: AEC RNAseq_0d7e_4fec


title: SEM-shGFP-2-DAY4

description:
total RNA
cells lentiviral infected with control vector


title: SEM-shGFP-1-DAY4


title: WT2

description: Day 2 post influenza infection

value: WT


title: WT1

description: Day 2 post influenza infection


title: SEM-shAFF4-426769-DAY4

description:
total RNA
cells lentiviral infected with shRNA targeting AFF4


title: WT3

description: Day 2 post influenza infection


title: SEM-GFPi-1-DAY4


title: SEM-shAFF4-15825-DAY4


title: MEF_KO_INPUT

description: fragmented genomic DNA

source_name: MLL knockout MEF

value: Mouse embryonic fibroblasts


title: MEF_WT_INPUT

description: fragmented genomic DNA

source_name: MLL wild-type MEF


title: 293_AFF1CT

description: fragmented genomic DNA

value: Human embryonic kidney cells


title: 293_MLLAFF1_AFF4NT

description:
fragmented genomic DNA
HEK293 cells ectopically expressing MLL-AFF1


title: SEM_IRAK4_inhibitor_AFF4

description: fragmented genomic DNA


title: 293_MLLAFF1_D2N1D

value: MLL D2N1D


title: 293_D2N1D

description: fragmented genomic DNA


title: 1hr m7G pulldown

description:
Methyl-capped mRNA pulldown
barcode: CAGATC


title: MEF_MLL_KO_D2N1D

description: fragmented genomic DNA


title: 293_AFF4NT

description: fragmented genomic DNA


title: 293_MLLAFF1_D2M7U

value: MLL D2M7U


title: 293_D2M7U

description: fragmented genomic DNA


title: 293_D2M7U_IRAK_inhibitor_2_INPUT

description: fragmented genomic DNA

value: IRAK1/4 inhibitor


title: MEF_MLL_KO_D2M7U

description: fragmented genomic DNA


title: 293_D2M7U_IRAK_inhibitor_1_INPUT

description: fragmented genomic DNA


title: 293_D2M7U_DMSO_2_INPUT

description: fragmented genomic DNA


title: MEF_MLL_WT_D2M7U

description: fragmented genomic DNA


title: 293_MLLAFF1_AFF1CT


title: SEM-GFPi-2-DAY4


title: MEF_MLL_KO_N20

description: fragmented genomic DNA

value: Pol II N20


title: MEF_NT86

description: fragmented genomic DNA

value: MLL NT86


title: 293_D2M7U_DMSO_1_INPUT

description: fragmented genomic DNA

value: DMSO


title: SEM_IRAK_inhibitor_1

description: total RNA


title: SEM_DMSO_1

description: total RNA


title: SEM_IRAK4_inhibitor_2

description: total RNA


title: SEM_DMSO_2

description: total RNA


title: SEM_IRAK_inhibitor_2

description: total RNA


title: REH_IRAK_inhibitor_2

description: total RNA

source_name: REH


title: SEM_IRAK4_inhibitor_1

description: total RNA


title: MEF_MLL_WT_N20

description: fragmented genomic DNA


title: REH_DMSO_2

description: total RNA


title: REH_IRAK_inhibitor_1

description: total RNA


title: REH_IRAK4_inhibitor_1

description: total RNA


title: MM6_IRAK_inhibitor_2

description: total RNA

value: Acute monocytic leukemia


title: BFU-E cells_47

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

data_processing:
alignment TopHat v2.0.12
subRead featureCounts v1.4.6
Genome_build: mm10
Supplementary_files_format_and_content: comma-delimited gene counts/normalized counts

source_name: blood cells from fetal liver

growth_protocol: Mouse fetal liver BFU-E and CFU-E isolation and human cord blood BFU-E purification. Purification of BFU-E and CFU-E cells from murine fetal livers was performed as described before. Briefly, fetal liver erythroid cells were isolated between embryonic days 14.5 (E14.5) to E15.5. A pure erythroid progenitor population containing more than 90% of BFU-E and CFU-E cells were obtained through a negative magnetic bead selection for lineage markers including Ter119, B220, Mac-1, CD3, Gr-1, Sca-1, CD16/CD32, CD41, CD34 and positive selection for c-Kit. Afterwards c-Kit+ BFU-E (CD71 10% low) and CFU-E (CD71 20% high) cells were separated by flow cytometry. Purified BFU-E or CFU-E cells were seeded in serum-free erythroid liquid expansion medium (SFELE) (StemSpanTM SFEM with 100 ng/mL rmSCF, 40 ng/mL rmIGF-1, and 2 U/mL rhEpo) alone, or SFELE containing 100 nM DEX ± TGF inhibitors with indicted concentrations. Erythroblasts produced from purified BFU-E and CFU-E were analyzed over time by FACS and benzidine-Giemsa staining as described. For human BFU-E isolation, the cultured cells were negatively selected for lineage markers including Lin, Thy, CD45RA, FLT3, CD7, CD10, CD123, CD36 and positive selection for CD34 and CD38 double positive cells, which accounts for 15% of total population. CD34+CD38+ were further gated by CD71 and TβRIII surface markers. CD71loTβRIII10%lo and CD71loTβRIII10%hi cells were isolated by FACS sorting.

extract_protocol:
Single-cell whole transcriptome amplification (WTA) was performed using the Fluidigm C1 Single-Cell Auto Prep System (C1 System) as per the manufacturer’s recommendations (full details available at Fluidigm.com). Briefly, flow-sorted mouse BFU-E cells were resuspended at a concentration of 250 cell per μL of complete media, mixed 7:3 with C1 suspension reagent (Fluidigm), and loaded onto C1 Single-Cell Auto Prep chips (C1 chips; Fluidigm). After loading, each of the cell isolation chambers on the C1 chip was optically inspected for the presence of a cell. Subsequently, these cells were lysed and SMART-Seq (Ramskold et al., 2012) whole transcriptome amplified (WTA) products were prepared with the C1 System using the SMARTer Ultra Low RNA Kit for Illumina Sequencing (Clontech) and protocols provided by Fluidigm.
WTA products were harvested from the C1 chip, diluted to a concentration of 0.15 ng/μL, and cDNA libraries were prepared using Nextera XT DNA Sample preparation reagents (Illumina) as per the manufacturer’s recommendations, with minor modifications. Specifically, reactions were run at ¼ the recommended volume, the tagmentation step was extended to 10 minutes, and the extension time during the PCR step was increased from 30s to 60s. After the PCR step, all 96 samples were pooled without library normalization, cleaned twice with 0.9x AMPure XP SPRI beads (Beckman Coulter), and eluted in buffer TE. The pooled libraries were quantified using Quant-IT DNA High-Sensitivity Assay Kit (Invitrogen) and examined using a high-sensitivity DNA chip (Agilent). Finally, samples were sequenced deeply using either a HiSeq 2000 or a HiSeq 2500 sequencer (50-75 bp paired-end reads or single end). Single-cell samples were sequenced to an average depth of 1.5 million reads per cell.

value: BFU-E

tag: tissue source

value: fetal liver

tag: developmental stage


title: BFU-E cells_48

tag: cell type


title: BFU-E cells_46


title: REH_IRAK4_inhibitor_2

description: total RNA

value: B cell precursor leukemia


title: BFU-E cells_45


title: MEF_MLL_WT_D2N1D

description: fragmented genomic DNA


title: REH_DMSO_1

description: total RNA


title: MM6_DMSO_2

description: total RNA


title: BFU-E cells_44


title: MM6_IRAK4_inhibitor_2

description: total RNA


title: 293_D2M7U_IRAK_inhibitor_1

description: fragmented genomic DNA


title: BFU-E cells_42


title: BFU-E cells_43


title: BFU-E cells_41


title: MM6_IRAK4_inhibitor_1

description: total RNA


title: Adult_naive

city: Ithaca

first: Andrew

last: Grimson

address: 445 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University

data_processing:
Nucleotides with Phred scores <20 were trimmed from read ends
Trimmed reads >18 nt in length were aligned to the genome with Tophat v2.1.1
Aligned reads were quantified and differnetial expression was found using CuffDiff v2.2.1
Genome_build: mm9
Supplementary_files_format_and_content: CuffDiff output file. Columns include gene name, sample 1 name, sample 2 name, test status, sample 1 FPKM value, sample 2 FPKM value, log2 fold-change, test statistic, p value, q value, and if signficant at a FDR of 5%

source_name: Single positive CD8+ T cells from the spleen

extract_protocol:
Total RNA was isolated using Trizol from purified cell populations
NEBNext Ultra RNA Library Kit (NEB) was used on 25-200 ng RNA

tag: mouse age

value: 2-4 months (adult)

value: Spleen

tag: isolation protocol

value: Positive immunomagnetic selection for CD8, followed by FACS sorting for CD44lowCD122low cells


title: Adult_innate_memory

value: Positive immunomagnetic selection for CD8, followed by FACS sorting for CD44highCD122high cells


title: Neonatal_thymus

source_name: Single positive CD8+ T cells from the thymus

value: 6-8 days (neonate)

value: Thymus

value: Depleted CD4+ thymocytes with negative immunomagnetic selection; FACS sorted for CD8+ cells


title: Neonatal_spleen

value: Positive immunomagnetic selection for CD8


title: Neonatal_innate_memory


title: BFU-E cells_40


title: Neonatal_naive


title: Adult_spleen


title: Adult_thymus


title: MM6_IRAK_inhibitor_1

description: total RNA


title: BFU-E cells_38


title: Day 4 EB rep 2 Trp53-/-,p63shp73sh RNA-Seq

city: Hangzhou

first: Yilong

last: Zou

state: Zhejiang

address: Shilongshan Road #18, Cloud Town, Xihu District

department: School of Life Sciences

institute: Westlake University

description: p53KO.p63sh.p73sh.RNASeq.count.table.txt

data_processing:
Sequencing data quality control: reads pairs in FASTQ format (50bp/50bp) were quality assessed by FastQC v0.11.3 for sequencing integrity and completeness
Read mapping: RNA-Seq reads were mapped to mouse genome mm9 (NCBI build 37, Jul/2007) with STAR2.3.0e using standard settings for paired reads. In average 82% of raw reads were uniquely mapped. For ChIP-Seq, paired-end (50/50bp) FASTQ reads were mapped to mouse genome mm9 (NCBI build 37, Jul/2007) with Bowtie2 with default filtering criteria. Resulted SAM files were converted to BAM files though Samtools 0.1.19. BAM files were sorted and indexed with Samtools.
RNA-Seq read counting: Uniquely mapped reads were counted to each gene with HTSeq v0.5.4 with default settings.
RNA-Seq data normalization and differential expression analysis: Read counts were normalized by library size through the “DESeq2” package deposited in Bioconductor. Differential gene expression analysis between any two conditions was perform based on a model utilizing the negative binomial distribution.
ChIP-Seq data visualization: To visualize ChIP-Seq data, BAM files were converted to TDF file by IGV Tools 2.3.32 using the command “igvtools count -z 5 -w 25 -e 250”, specifying the coverage window size to be 25bp and average fragment size of 250bp.
Genome_build: mm9, NCBI build 37, July/2007
Supplementary_files_format_and_content: TDF files are contain whole-genome coverage data for eac ChIP-Seq sample. This file data can be loaded to IGV genome browser and visualize ChIP-Seq peak distribution.
Supplementary_files_format_and_content: Txt files contain normalized read counts of each gene in each sample from RNA-Seq experiments. Read counts are normalized to library size in each experiment.

source_name: mouse embroid bodies

growth_protocol: mESCs E14Tg2a.IV were maintained on gelatin (0.1%, Millipore, ES-006-B) coated plates with LIF-supplemented medium at 37°C with 5% CO2. Basic ES cell medium included 80% Knockout DMEM (Life Technologies, 10829-018), 15% Fetal Bovine Serum (HyClone, SH30071), 50U Penicillin and 50ug/ml Streptomycin (Cellgro, 30-001-CI), 1% Non-essential Amino acids (Life Technologies, 11140-050), 1% L-Glutamine (Life Technologies, 25030081), 100μM β-Mercaptoethanol (Sigma-Aldrich, M6250), 1000 U/ml mLIF (Gemini Bio-Products, 400-495). Mouse ESCs Trp53+/+ and Trp53-/- cell lines were kindly provided by Jing Huang lab (NIH/NCI) and maintained in N2B27 LIF+2i (PD0325901, 1μM, Cayman; CHIR99021, 3 μM, Cayman) medium. EB formation and differentiation were carried out as described by the supplier (ATCC).

extract_protocol:
For RNA-Seq samples,  2 million ES or EB cells were collected at the indicated time point and extracted with PrepEase RNA spin kit (Affymetrix). For ChIP-Seq sample preparation, ES or EB cells are treated with Activin or SB431542 as indicated, fixed and quenched, sonicated to average fragment size of 250bp in 1% SDS lysis buffer, and incubated with 60ul Dynabeads protein G conjugated with 3-5ug of indicated antibodies. 2% pre-cleared chromatin prior to primary antibody addition was kept as input DNA. Magnetic beads were washed, chromatin was eluted, and reverse crosslinked ChIP DNA was dissolved in 10 mM Tris pH 8.0 buffer for further analysis.
For RNA-Seq library construction, total RNA purified from mES and mEB was quantified by Ribogreen and quality assessed by Agilent BioAnalyzer 2000. 500ng RNA with integrity number (RIN) > 9.5 from each sample was used for library construction with TruSeq RNA Sample Prep Kit v2 (Illumina) according to manufacturer’s instructions.  For ChIP-Seq library construction, ChIP-Seq DNA samples were quantified and quality assessed by Ribogreen and Agilent Bioanalyzer. DNA fragments range from 200-600bp were selected constructed for ChIP-Seq library with TruSeq ChIP Sample Prep Kit (Illumina) according to manufacturer’s instructions.
Multiplexed sequencing libraries were ran on a Hiseq2500 platform and more than 40million raw paired-end reads were generated for each sample.

treatment_protocol: Recombinant human Activin A (R&D Systems, 338-AC) were used at 50ng/ml. SB431542 (Tocris, #1614) were used at 10μM

value: Mouse ES cells

tag: genetic background

value: Trp53-/-, p63shRNA, p73shRNA


title: MM6_DMSO_1

description: total RNA


title: BFU-E cells_37


title: BFU-E cells_35


title: Day 4 EB rep 1 Trp53-/-,p63shp73sh RNA-Seq


title: Day 4 EB rep 2 Trp53+/+ RNA-Seq

value: wild type


title: 293_D2M7U_DMSO_1

description: fragmented genomic DNA

value: Human embryonic kidney cells

value: MLL D2M7U


title: BFU-E cells_36


title: Day 3 EB rep2 RNA-Seq

description: E14.diff.time_course.RNASeq.count.table.txt


title: Day 4 EB rep2 RNA-Seq


title: Day 4 EB rep1 RNA-Seq


title: BFU-E cells_34


title: BFU-E cells_33


title: Day 2 EB rep2 RNA-Seq


title: Day 3 EB rep1 RNA-Seq


title: BFU-E cells_39


title: Day 2 EB rep1 RNA-Seq


title: Day 1 EB rep2 RNA-Seq


title: Day 1 EB rep1 RNA-Seq


title: Day 0 ES rep1 RNA-Seq

source_name: mouse embryonic stem cells


title: BFU-E cells_32


title: BFU-E cells_31


title: BFU-E cells_30


title: Input sample day 3 EB_Trp53-/-,p73sh_Activin

description: Sonicated chromatin DNA

value: Trp53-/-, p73shRNA

tag: antibody


title: Smad2/3 ChIP-Seq day 3 EB_Trp53-/-,p73sh_SB431542

tag: antibody vendor/catalog

value: Cell Signaling Technology/8685


title: Smad2/3 ChIP-Seq day 3 EB_Trp53-/-,p73sh_Activin


title: Day 4 EB rep 1 Trp53+/+ RNA-Seq


title: BFU-E cells_29

value: BFU-E

value: fetal liver


title: Input sample day 3 EB_Trp53+/+_Activin

description: Sonicated chromatin DNA


title: BFU-E cells_28


title: BFU-E cells_27


title: Smad2/3 ChIP-Seq day 3 EB_Trp53+/+_SB431542


title: BFU-E cells_26


title: Input sample for p53 ChIP-Seq day 3 EB_Activin

description: Sonicated chromatin DNA


title: p53 ChIP-Seq day 3 EB_Activin

value: anti-p53(FL-393) and anti-p53(M19)

value: Santa Cruz Biotechnology/sc-6243X and sc-1312


title: Smad2/3 ChIP-Seq day 3 EB_Trp53+/+_Activin


title: p53 ChIP-Seq day 3 EB_SB431542


title: BFU-E cells_25


title: Tcf3 ChIP-Seq day 0 ES

value: Santa Cruz Biotechnology/sc-8635X


title: Input sample day 0 ES

description: Sonicated chromatin DNA


title: BFU-E cells_24


title: Input sample day 3 EB_Activin

description: Sonicated chromatin DNA


title: Tcf3 ChIP-Seq day 3 EB_Activin


title: Day 0 ES rep2 RNA-Seq


title: Smad2/3 ChIP-Seq day 3 EB_SB431542


title: BFU-E cells_21


title: BFU-E cells_22


title: BFU-E cells_23


title: Smad2/3 ChIP-Seq day 3 EB_Activin


title: BFU-E cells_20


title: BFU-E cells_19


title: Nat1-/- C3 Total rep3

city: Kyoto

first: Shinya

last: Yamanaka

address: 53 Kawahara-machi, Shogoin, Sakyo-ku

institute: Center for iPS Cell Research and Applicaton (CiRA), Kyoto University

description:
C3_Total
Nat1-null mouse embryonic stem cells cultured with LIF, replicate 3.
Total RNA
Processed data file: NormalizedCounts.txt

data_processing:
Fastq files were generated with bcl2fastq v2.17 (Illumina). Bases with low quality scores and the adapters in all the sequenced reads were trimmed with cutadapt-1.9.1. The trimmed reads were mapped to mouse rRNA and tRNA sequences with Bowtie2 version 2.2.8, and the reads aligned to rRNA or tRNA were excluded from further analysis. The remaining reads were mapped to mouse genome (mm10) using tophat-2.1.0 with GENECODE annotation (GRCm38.p4, Release M10). The number of reads mapped to each gene was counted by HTSeq-0.6.1 software and normalized with the DESeq2 R/Bioconductor package (v. 1.10.1) for RPF and total RNA independently.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: NormalizedCounts.txt: Tab-delimited text file contains the normalized counts data.

source_name: C3, Nat1-null mouse embryonic stem cell line, LIF, Total RNA

growth_protocol: Standard mouse ESC medium on gelatin-coated plates at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol:
RNA was extracted using the TruSeq Ribo Profile Mammalian Kit (Illumina) according to the manufacturer's instruction.
Libraries were prepared using the TruSeq Ribo Profile Mammalian Kit (Illumina) according to the manufacturer's instruction.

treatment_protocol: Mouse embryonic stem cells were treated with LIF.

tag: genotype/variation

value: mouse embryonic stem cell line

tag: treatment

value: LIF


title: Nat1-/- C3 RPF rep3

description:
C3_RPF
Nat1-null mouse embryonic stem cells cultured with LIF, replicate 3.
RPF
Processed data file: NormalizedCounts.txt

data_processing:
Library strategy: Ribo-Seq
Fastq files were generated with bcl2fastq v2.17 (Illumina). Bases with low quality scores and the adapters in all the sequenced reads were trimmed with cutadapt-1.9.1. The trimmed reads were mapped to mouse rRNA and tRNA sequences with Bowtie2 version 2.2.8, and the reads aligned to rRNA or tRNA were excluded from further analysis. The remaining reads were mapped to mouse genome (mm10) using tophat-2.1.0 with GENECODE annotation (GRCm38.p4, Release M10). The number of reads mapped to each gene was counted by HTSeq-0.6.1 software and normalized with the DESeq2 R/Bioconductor package (v. 1.10.1) for RPF and total RNA independently.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: NormalizedCounts.txt: Tab-delimited text file contains the normalized counts data.

source_name: C3, Nat1-null mouse embryonic stem cell line, LIF, RPF


title: BFU-E cells_16


title: BFU-E cells_17


title: BFU-E cells_15


title: Nat1+/- C1 Total rep3

description:
C1_Total
Nat1 heterozygous mouse embryonic stem cells cultured with LIF, replicate 3.
Total RNA
Processed data file: NormalizedCounts.txt

source_name: C1, Nat1 heterozygous mouse embryonic stem cell line, LIF, Total RNA

value: Nat1 heterozygous


title: Smad2/3 ChIP-Seq day 0 ES

tag: cell line


title: Nat1-/- B12 RPF rep1

description:
B12_RPF
Nat1-null mouse embryonic stem cells cultured with LIF, replicate 1.
RPF
Processed data file: NormalizedCounts.txt

source_name: B12, Nat1-null mouse embryonic stem cell line, LIF, RPF


title: Nat1-/- B12 Total rep1

description:
B12_Total
Nat1-null mouse embryonic stem cells cultured with LIF, replicate 1.
Total RNA
Processed data file: NormalizedCounts.txt

source_name: B12, Nat1-null mouse embryonic stem cell line, LIF, Total RNA


title: BFU-E cells_13


title: BFU-E cells_14


title: Nat1+/- C1 RPF rep3

description:
C1_RPF
Nat1 heterozygous mouse embryonic stem cells cultured with LIF, replicate 3.
RPF
Processed data file: NormalizedCounts.txt

source_name: C1, Nat1 heterozygous mouse embryonic stem cell line, LIF, RPF


title: Nat1+/- B4 Total rep2

description:
B4_Total
Nat1 heterozygous mouse embryonic stem cells cultured with LIF, replicate 2.
Total RNA
Processed data file: NormalizedCounts.txt

source_name: B4, Nat1 heterozygous mouse embryonic stem cell line, LIF, Total RNA


title: Nat1+/- B4 RPF rep2

description:
B4_RPF
Nat1 heterozygous mouse embryonic stem cells cultured with LIF, replicate 2.
RPF
Processed data file: NormalizedCounts.txt

source_name: B4, Nat1 heterozygous mouse embryonic stem cell line, LIF, RPF


title: BFU-E cells_10


title: Nat1-/- B2 Total rep2

description:
B2_Total
Nat1-null mouse embryonic stem cells cultured with LIF, replicate 2.
Total RNA
Processed data file: NormalizedCounts.txt

source_name: B2, Nat1-null mouse embryonic stem cell line, LIF, Total RNA


title: BFU-E cells_9


title: BFU-E cells_8


title: BFU-E cells_12


title: BFU-E cells_18


title: Nat1+/- A7 Total rep1

description:
A7_Total
Nat1 heterozygous mouse embryonic stem cells cultured with LIF, replicate 1.
Total RNA
Processed data file: NormalizedCounts.txt

source_name: A7, Nat1 heterozygous mouse embryonic stem cell line, LIF, Total RNA


title: BFU-E cells_7


title: Nat1+/- A7 RPF rep1

description:
A7_RPF
Nat1 heterozygous mouse embryonic stem cells cultured with LIF, replicate 1.
RPF
Processed data file: NormalizedCounts.txt

source_name: A7, Nat1 heterozygous mouse embryonic stem cell line, LIF, RPF


title: BFU-E cells_6


title: WT Total rep2

description:
WTex2_Total
Wild-type mouse embryonic stem cells cultured with LIF, replicate 2.
Total RNA
Processed data file: NormalizedCounts.txt

source_name: RF8, wild-type mouse embryonic stem cell line, LIF, Total RNA

value: wild-type


title: piPSCs P10 (Rex1-)_rep2

first: Jian

last: Mao

address: 2318 Yuhangtang Rd

institute: Hangzhou Normal University

data_processing:
Quality control of raw data (FASTQ format) was firstly processed through in-house Perl scripts.
Clean data (clean reads) were obtained by removing reads with adapter and poly-N, as well as low abundant reads from raw data. Subsequent analyses were based on the clean data with high quality.
Index of the reference genome was built using Bowtie v2.0.6 which is an ultrafast, memory-efficient short read aligner. Paired-end clean reads were aligned to the reference genome using TopHat v2.0.9 which is a fast splice junction mapper for RNA-seq reads.
Multi-array log2 transformation, normalization, and t-test were performed to identify the differentially expressed genes between any two selected samples using genomic analysis software suite (http://www.geworkbench.org).
Fragments per kilobase of exon per million fragments mapped (FPKM) were calculated for each gene. Hierarchical clustering was built using Pearson’s Correlation and total linkage algorithms.
Genome_build: susScr3
Supplementary_files_format_and_content: Excel includes FPKM values for each Sample.

organism: Sus scrofa

source_name: iPSCs

extract_protocol:
RNA from PEF (at passage 5) and piPSCs (P5 Rex1+ and P10 Rex1-) was extracted using a RNeasy Mini Kit (Qiagen).
Libraries for sequencing were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB) following manufacturer’s instruction.

tag: passages

tag: strain

value: Small Xiang Pig

value: iPSCs


title: piPSCs P10 (Rex1-)_rep1


title: WT Total rep1

description:
WTex1_Total
Wild-type mouse embryonic stem cells cultured with LIF, replicate 1.
Total RNA
Processed data file: NormalizedCounts.txt


title: piPSCs P5 (Rex1+)_rep2


title: BFU-E cells_4

source_name: blood cells from fetal liver


title: BFU-E cells_3


title: BFU-E cells_11


title: WT RPF rep1

description:
WTex1_RPF
Wild-type mouse embryonic stem cells cultured with LIF, replicate 1.
RPF
Processed data file: NormalizedCounts.txt

source_name: RF8, wild-type mouse embryonic stem cell line, LIF, RPF


title: piPSCs P5 (Rex1+)_rep1


title: shTP53:RB1-2

city: Dallas

first: Ping

last: Mu

address: 6000 Harry Hines Blvd., NA6.308A

department: Human Oncology and Pathogenesis

institute: UT Southwestern Medical Center

description: cell line transduced with shTP53:RB1 hairpin, biological  replicate 2

data_processing:
Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (Bolger et al 2014).
The output data (FASTQ files) were mapped to the target genome using the rnaStar aligner that maps reads genomically and resolves reads across splice junctions.
HTSeq v0.5.4 is used for feature counting and generating  a matrix of fragments per kilobase of exon per million fragments mapped (RPKM)
Genome_build: GRCh37.75(hg19)
Supplementary_files_format_and_content: [.txt] normalized count table

source_name: shTP53:RB1, LNCaP/AR cell line

growth_protocol: LNCaP/AR prostate cells were transduced with either shNT or shTP53:RB1 hairpins and then harvested for RNA

extract_protocol:
Cells were collected from culture dish and RNA was extracted using Trizol reagent following standard protocol
SMART-seq V4 (Clonetech) ultra low input RNA kit was used for library preparation. 10 ng of amplified cDNA was used to prepare Illumina hiseq libraries with the Kapa DNA library preparation chemistry (Kapa Biosystems) using 8 cycles of PCR.

value: LNCaP/AR

tag: transduction

value: shTP53:RB1 hairpin


title: shTP53:RB1-1

description: cell line transduced with shTP53:RB1 hairpin, biological replicate 1


title: BFU-E cells_2


title: iLin28b_spleen

data_processing:
Adapters were trimmed using Cutadapt v1.8.3
Trimmed reads were mapped and quantified to miRNAs using Mirdeep2 and Bowtie (miRBase version 21)
Genome_build: mm9
Supplementary_files_format_and_content: Mirdeep2 output flle; contains miRNA, number reads mapped to the miRNA across samples, precursor-miRNA, total number reads, number reads per sample, and normalized (reads per million) reads per sample

source_name: splenic CD8+ T cells

extract_protocol:
Total RNA was isolated using Trizol from purified cell populations
NEBNext Multiplex Small RNA Library Prep Set for Illumina

treatment_protocol: Bone marrow cells from gBT-I mice, either WT or expressing inducible Lin28b, was infected in an adult mouse whose bone marrow had been irradiated. Mice then received doxycycline in their drinking water to induce Lin28b. Cells were used 8 weeks after reconstitution.

tag: exogenous expression

value: Human Lin28b

tag: tissue

value: Spleen


title: Nat1-/- B2 RPF rep2

description:
B2_RPF
Nat1-null mouse embryonic stem cells cultured with LIF, replicate 2.
RPF
Processed data file: NormalizedCounts.txt

source_name: B2, Nat1-null mouse embryonic stem cell line, LIF, RPF


title: shNT-2

description: cell line transduced with shNT hairpin, biological replicate 2

source_name: shNT, LNCaP/AR cell line

value: shNT hairpin


title: BFU-E cells_1


title: WT_spleen


title: BFU-E cells_5


title: shNT-1

description: cell line transduced with shNT hairpin, biological replicate 1


title: Ileum Input Rep1

status: Public on Jan 05 2017

city: Houston

first: Yuan-Hung

last: Lo

address: One Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Illumina HiSeq 2000 software used for basecalling.
Sequenced reads were mapped to mm9 whole genome using Bowtie2 with the preset --very-sensitive setting (specific parameters are -D 20 -R 3 -N 0 -L 20 -i S,1,0.50)
Using the mapping files, regions with enriched Atoh1 binding were called using macs14, parameters -g mm -p 1e-10
The input samples were used as the control in calling peaks from the Atoh1, methylation, or acylation markers in the histones.
Called peaks (Atoh1 binding regions) were then annotated with Homer using mouse mm9 gene model.
Genome_build: Ensembl mm9
Supplementary_files_format_and_content: wig files were generated on the mapped files, using igvtools count command, parameters -z 5 -w 20 -e 250

source_name: Mouse

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to  instructions of NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (NEB #E6240S/L)

value: distal small intestine [Ileum]

tag: chip antibody

value: input

tag: sample type

value: DNA control


title: Ileum Input Rep2


title: Ileum Input Rep3


title: wild_Input_metaphase

data_processing:
All fastq files were aligned to S.pombe reference genomic ASM294v2 from Pombase by Bowtie1.0.0 with defalt setting.
The generated SAM files by Bowtie were converted to BAM and sorted by Samtools.
Peaks were called with Model-based analysis of ChIP-seq (MACS2.0.10) using following parameters; macs2 callpeak -t ChIP.sam -c Input.sam -f SAM -g 1.4e107 -n result_file -B -q 0.01 --nomodel
The generated treat_pileup.bedgraph files were loaded on Integrated Genome Browser.
Genome_build: ASM294v2

source_name: yeast

value: Wild Type

tag: tag or genetic characteristics

value: No-tag


title: WT RPF rep2

description:
WTex2_RPF
Wild-type mouse embryonic stem cells cultured with LIF, replicate 2.
RPF
Processed data file: NormalizedCounts.txt

tag: cell type


title: Ileum H3K27Ac

value: open chromatin


title: Ileum H3K27me3

value: closed chromatin


title: PEF_rep2

source_name: fibroblasts

value: fibroblasts


title: Colon Atoh1 Rep2

value: colon

value: GFP

value: Atoh1 Binding sites


title: Colon Input Rep3


title: Ileum Atoh1 Rep1


title: Colon Input Rep2


title: Colon Input Rep1


title: Colon H3K27me3


title: Colon H3K27Ac


title: Colon Atoh1 Rep1


title: Ileum Atoh1 Rep2


title: Ileum WT Rep 2

data_processing:
Illumina HiSeq 2000 software used for basecalling.
Sequenced reads were mapped to mm9 whole genome using TopHat v1.4.1 with parameters -r 400 –p -8
Expression level, the raw counts, for each gene was estimated using htseq-count function of HTSeq program on mapped reads.
Genome_build: Ensembl mm9
Supplementary_files_format_and_content: Tab-deliminted raw counts for each gene, obtained from HTSeq; individual file for eah sample.

source_name: isolated from Atoh1 f/+; Vil CreERT2 mice

extract_protocol:
RNA was harvested using Trizol reagent followed by RNeasy Kit (QUIGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Atoh1 WT crypts

tag: genotype

value: WT


title: Ileum KO Rep 2

source_name: isolated from Atoh1 f/f ; VilCreERT2 mice

value: Atoh1 KO crypts

value: KO


title: PEF_rep1

value: Small Xiang Pig


title: Ileum KO Rep 1


title: Ileum WT Rep 1


title: Ileum GFP+ Rep 3

source_name: sorted from AtohGFP/GFP mice

value: Atoh1 GFP+ cells

value: GFP+


title: Ileum GFP+ Rep 1

value: distal small intestine [Ileum]


title: Ileum GFP+ Rep 2


title: Colon KO Rep 2


title: Colon WT Rep 1


title: Colon KO Rep 1


title: Colon WT Rep 2


title: Colon GFP+ Rep 2


title: Colon GFP+ Rep 3


title: Rnf40_KO_rep2

city: Göttingen, Niedersachsen

first: Steven

middle: A

last: Johnsen

state: Niedersachsen

address: Robert Koch Strasse 40

department: Clinic for General, Visceral and Pediatric Surgery

country: Germany

institute: University Medical Center Göttingen

data_processing:
Sequenced reads were  mapped to mouse reference transcriptome (UCSC mm9) using bowtie 2 (version 2.1.0) with parameters --threads 11 --very-sensitive --omit-sec-seq
Read counts for each sample and each gene were aggregated using a custom Ruby script
DESeq (version 1.14.0) was used for measuring differential expression
Genome_build: mm9
Supplementary_files_format_and_content: The table includes gene normalized counts for each sample

source_name: mouse embryonic fibroblasts

growth_protocol: Primary MEFs were cultured in high-glucose GlutaMAX™-DMEM (Invitrogen) supplemented with 10% FBS Superior (Biochrom), 1% penicillin–streptomycin (Sigma-Aldrich), and 1% non-essential amino acids (Invitrogen) at 37°C, 5% CO2.

extract_protocol:
total RNA was isolated using QIAzol Lysis Reagent (QIAGEN)
Libraries were prepared from 1 µg of total RNA using NEXTflex™ Rapid Directional RNA-Seq Kit according to the manufactures introduction (Bioo Scientific).

treatment_protocol: For RNF40 knockout, MEFs were passaged into GlutaMAX™-DMEM supplemented with 250nM of 4-hydroxitamoxifen (4-OHT) for 5 days, and then cultured for 3 days without 4-OHT.


title: Rnf40_WT_rep2


title: Rnf40_KO_rep1


title: Rnf40_WT_rep3


title: Rnf40_WT_rep1


title: Rnf40_KO_rep3


title: Colon GFP+ Rep 1


title: day 16 Wheat bran replicate 1

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

country: Netherlands

institute: Centre of fungal biodiversity

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequence reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the genome sequence of D. squalens LYAD-421 SS1 v1.0 whole genome using SOAPALIGNER/SOAP2. No more than 2 mismatches allowed in the alignment.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., 2008.
Genome_build: Dichomitus squalens LYAD-421 SS1 v1.0
Supplementary_files_format_and_content: excel file include unique reads number, gene length, coverage, RPKM values and KEGG orthology annotation of genes for each sample.

organism: Dichomitus squalens

source_name: day 16 Wheat bran

growth_protocol: The fungus was cultivated for 4 days at 28ºC in 75 ml liquid low-nitrogen-asparagine-succinate medium (LN-AS) (pH 4.5) (Hatakka and Uusi-Rauva, 1983) supplemented with 6.8 mM glycerol in 250 ml Erlenmeyer flasks inoculated with five mycelium covered plugs (diameter 7 mm) from malt extract agar plates. A homogenized mycelial suspension was prepared as described previously (Mäkelä et al., 2002) of which 4 ml was used to inoculate 100 ml LN-AS culture medium supplemented with 1 g of spruce wood (Picea abies) sawdust, aspen wood (Populus tremula) sawdust, powdered wheat bran or powdered cotton seed hulls.

extract_protocol:
Total RNA was extracted from mycelia ground in liquid N2 with the N-cetyl-N,N,N-trimethylammonium bromide (CTAB, Sigma, Germany) method (Chang et al., 1993) and further purified with the RNeasy Plant Mini kit (Qiagen, Germany). Quantity and integrity of RNA were determined spectrophotometrically (NanoDrop ND-1000, NanoDrop Technologies Inc., USA) and with RNA6000 Nano Assay (Agilent 2100 Bioanalyzer, Agilent Technologies, USA). Purification of mRNA, synthesis of cDNA library and sequencing reactions were conducted in the BGI Tech Solutions Co., Ltd. (Hong Kong) as described previously (Patyshakuliyeva et al., 2015)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mycelium colonized different substrates were collected at the different growth stages of D. squalens. All samples were immediately frozen and processed according to the extraction protocol.

value: LYAD-421 SS1

tag: substrate

value: Wheat bran (powdered)

tag: sampling time

value: 16 days

value: Mycelium colonized substrate


title: day 9 Wheat bran replicate 1

source_name: day 9 Wheat bran

value: 9 days


title: day 9 Wheat bran replicate 2


title: day 16 Spruce replicate 2

source_name: day 16 Spruce

value: Spruce (sawdust)


title: day 9 Spruce replicate 2

source_name: day 9 Spruce


title: day 9 Spruce replicate 1


title: day 9 Cotton seed hulls replicate 2

source_name: day 9 Cotton seed hulls

value: Cotton seed hulls (powdered)


title: day 16 Cotton seed hulls replicate 2

source_name: day 16 Cotton seed hulls


title: day 16 Cotton seed hulls replicate 1


title: day 16 Aspen (sawdust) replicate 2

source_name: day 16 Aspen (sawdust)

value: Aspen (sawdust)


title: day 16 Aspen (sawdust) replicate 1


title: day 9 Aspen (sawdust) replicate 2

source_name: day 9 Aspen (sawdust)


title: day 9 Aspen (sawdust) replicate 1


title: Adult Male Capped RNA

city: Ipswich

first: Barton

last: Slatko

state: Massachusetts

address: 240 County Road

institute: New England Biolabs

data_processing:
Sequence reads from each sample were first trimmed and assessed for quality using Sickle (Galaxy v 1.0.0, default settings) and FastQC.
RNA-Seq reads from each sample were mapped to the genome of the Wolbachia endosymbiont of B. malayi, wBm (version 2.2) or to the B. malayi genome (Wormbase version WS236) using the default settings of Bowtie2 (Galaxy v 0.2)
Reads aligned using Bowtie2 were assembled into transcripts using the default settings of Cufflinks (Galaxy v 0.0.7)
Genome_build: Wolbachia endosymbiont of B. malayi, wBm (version 2.2); B. malayi genome (Wormbase version WS236)
Supplementary_files_format_and_content: tabular files include FPKM values for each sample

organism: Brugia malayi

source_name: Brugia malayi adult males

growth_protocol: Adult male B. malayi and microfilariae (mf) were obtained from the peritoneal cavity of one infected jird

extract_protocol:
RNA was harvested using Trizol reagent.
[Vaccinia Capping protocol] Total RNA from B. malayi microfilariae (25 μg) or adult males (1.5 µg) was incubated with 0.5 mM 3´ desthiobiotin-GTP, 0.1 mM S-adenosylmethionine (SAM) and 70 units of the Vaccinia Capping Enzyme in 1X Capping Buffer for 30 min at 37°C. RNA was then purified using the MEGAClear™ Transcription Cleanup Kit and eluted in 50 μL H2O.
[Capture of 3' desthiobiotin capped RNA protocol] Capped RNA was mixed with 100 μL of hydrophilic streptavidin magnetic beads. The RNA-bead mixture was incubated for 20 min at room temperature, washed and RNA eluted with the addition of 1 mM biotin. The RNA, containing the 3´ desthiobiotin capped transcripts was collected and cleaned up using the RNA Clean and Concentrator Kit and eluted in 10 μL H2O and stored at −80°C until further use (‘Capped RNA’ sample).
RNA libraries were prepared for sequencing using NEBNext RNA Ultra Prep Kit for Illumina

tag: developmental stage

value: adult

tag: gender

value: male


title: Adult Male Total RNA


title: day 16 Wheat bran replicate 2


title: Microfilarial Total RNA

source_name: Brugia malayi microfilariae

value: microfilariae


title: H3K4me3_KO_rep2

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 1.0.0
peaks were called using MACS version 1.0.0 with the following setting: Effective Genome Size (Mouse (mm9)), Tag size (25), Bandwidth (300), Pvalue (0.00001), Shift size (125).
Coverage was determined by normalizing the filtered reads per hundred million
bigwig files were generated using Wig/BedGraph-to-bigWig
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated from wig files using Wig/BedGraph-to-bigWig

source_name: Mouse embryonic fibroblasts

extract_protocol:
Cells were crosslinked with 1% Formaldehyde for 10  minutes and quenched with 1.25 M Glycine. The nuclear pellets were sonicated to the fragment range of 200-400 bp. Sonicated extracts were incubated with specific antibodies at 4˚C overnight and ChIP-immune complexes were pulled down using Protein A sepharose.
Library preparations were done using NEBnext Ultra DNA library preparation kit according to the manufacturer’s instructions.

value: H3K4me3 (Diagenode, pAb-003-050)


title: H3K4me3_KO_rep1


title: H3K4me3_WT_rep2


title: H3K4me3_WT_rep3


title: day 16 Spruce replicate 1


title: H3K4me3_WT_rep1


title: jac_NASH-129

city: College Station

first: Ivan

last: Rusyn

state: TX

address: 4458 TAMU

institute: Texas A&M University

data_processing:
Trimmomatic used to trim adapter sequences and low quality bases
TopHat v.2.0.13 was used to map to GRcm38/mm10 assembly
HTSeq was used to generate read counts per gene using the intersection-nonempty paramter to account for ambiguous read mappings
DESeq2 was used to generate normalized counts for each gene ( using the parameter normalized = TRUE)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files includeread counts for each sample (from HTSeq)

source_name: Liver left lobe (pulverized)

extract_protocol:
Total RNA was extracted from pulverized liver left lobe tissue using Qiagen miRNEasy kits
Libraries were prepared according to Illumina's instructions accompanying the commercially-available kit (Illumina TruSeq stranded mRNA HT kit cat# RS-122-2103)

treatment_protocol: C57Bl6/J male mice were fed a base diet (BD; 4% fat), high-fat diet (HFD; 31% fat), or high-fat (31%fat) diet deficient in methionine/choline/folate (MCD).

tag: Sex

value: Male

tag: diet

value: BD

value: Vehicle (5% Alkmauls El-620 in saline)

tag: duration

value: 24 hour post treatment


title: jac_NASH-130

tag: treatment


title: jac_NASH-126

tag: strain


title: jac_NASH-127


title: jac_NASH-060

value: HFD


title: day 9 Cotton seed hulls replicate 1

value: LYAD-421 SS1


title: jac_NASH-059


title: jac_NASH-128


title: jac_NASH-055

value: MCD


title: jac_NASH-054


title: jac_NASH-053


title: jac_NASH-051


title: Input_tag_4

city: Bethesda

first: Bertram

middle: J

last: Canagarajah

state: Maryland

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

description: ChIP-seq

data_processing:
ChIP-seq: Raw reads were processed with cutadapt v1.8.1 to remove adapters and perform quality trimming. Trimmed reads were mapped to the UCSC mm10 assembly using Bowtie with default parameters and only uniquely aligned sequences were retained.
genome build: mm10
processed data files format and content: ChIP-seq bigwigs were normalized to million mapped unique, non-duplicate reads.

source_name: testes

extract_protocol:
Testicular cells were collected by collagenase and trypsin treatment.
SimpleChIP Enzymatic Chromatin IP Kit was used to prepare ChIP-seq libraries.

tag: age

value: 3-4 weeks

value: transgenic

value: testes

value: C57BL/6 (B6) X 129/SvJ hybrid

tag: chip-antibody


title: P18_KO_s3

description: small RNA-seq

data_processing:
small RNA-seq: After removing adaptors, rRNA and tRNA sequences were filtered before analysis. Remaining reads with sizes from 26 to 31 bp were mapped to the UCSC mm10 assembly using TopHat and only uniquely mapped reads were used for further analysis.
genome build: mm10
processed data files format and content: counts table from featureCounts as tab-delimited text file

extract_protocol:
Total RNA was isolated from mouse testes using TRI Reagent and small RNA was enriched by size selection during library preparation.
NEBNext Multiplex Small RNA Library Prep Set for Illumina was used for small RNA-seq library construction.

value: post natal day 18

value: homozygous

tag: tissue


title: P18_KO_s2

description: small RNA-seq


title: jac_NASH-052


title: Microfilarial Capped RNA


title: IP_mCherry-FLAG_4

description: ChIP-seq

value: Mouse anti-FLAG (Sigma-Aldrich, F3165) and Rat anti-mCherry (ThermoFisher Scientific, M11217)


title: jac_NASH-056


title: jac_NASH-057


title: P18_KO_s1

description: small RNA-seq


title: P18_Con_s3

description: small RNA-seq

value: heterozygous


title: P18_Con_s1

description: small RNA-seq


title: P18_Con_s2

description: small RNA-seq


title: jac_NASH-058


title: IP_HET_POLII_2

description:
IP DNA
ChIP-seq

data_processing:
ChIP-seq and ATAC-seq: Raw reads were processed with cutadapt v1.8.1 to remove adapters and perform quality trimming. Trimmed reads were mapped to the UCSC mm10 assembly using Bowtie with default parameters and only uniquely aligned sequences were retained. ChIP-seq and ATAC-Seq peaks were called with MACS2 v2.1.0.
genome build: mm10
processed data files format and content: ChIP-seq and ATAC-Seq bigwigs were normalized to million mapped unique, non-duplicate reads.

tag: chip antibody

value: Mouse anti-Pol II (Abcam, ab817)


title: HET_SC_2

description:
transposed DNA
ATAC-seq

data_processing:
Library strategy: ATAC-seq
ChIP-seq and ATAC-seq: Raw reads were processed with cutadapt v1.8.1 to remove adapters and perform quality trimming. Trimmed reads were mapped to the UCSC mm10 assembly using Bowtie with default parameters and only uniquely aligned sequences were retained. ChIP-seq and ATAC-Seq peaks were called with MACS2 v2.1.0.
genome build: mm10
processed data files format and content: ChIP-seq and ATAC-Seq bigwigs were normalized to million mapped unique, non-duplicate reads.

source_name: spermatocytes

extract_protocol:
Spermatocytes were collected by Fluorescence-activated cell sorting (FACS).
Tn5 Transposase enzyme was used to generate transposed DNA for library preparation.

value: spermatocytes


title: HET_SC_3

description:
transposed DNA
ATAC-seq


title: KO_SC_1

description:
transposed DNA
ATAC-seq


title: KO_SC_3

description:
transposed DNA
ATAC-seq


title: IP_KO_POLII_1

description:
IP DNA
ChIP-seq


title: KO_SC_2

description:
transposed DNA
ATAC-seq


title: IP_KO_POLII_2

description:
IP DNA
ChIP-seq


title: IP_A-MYB_2

description:
IP DNA
ChIP-seq

value: Rabbit anti-A-MYB (Sigma-Aldrich, HPA008791)


title: IP_HET_POLII_1

description:
IP DNA
ChIP-seq


title: Input_KO_2

description:
Input DNA
ChIP-seq


title: Input_KO_1

description:
Input DNA
ChIP-seq


title: Input_HET_2

description:
Input DNA
ChIP-seq


title: Input_HET_1

description:
Input DNA
ChIP-seq


title: IP_mCherry-FLAG_1

description:
IP DNA
ChIP-seq


title: IP_FLAG_2

description:
IP DNA
ChIP-seq

value: Mouse anti-FLAG (Sigma-Aldrich, F3165)


title: IP_mCherry-FLAG_2

description:
IP DNA
ChIP-seq


title: IP_FLAG_1

description:
IP DNA
ChIP-seq


title: IP_mCherry_2

description:
IP DNA
ChIP-seq

value: Rat anti-mCherry (ThermoFisher Scientific, M11217)


title: Input_tag_3

description:
Input DNA
ChIP-seq


title: IP_mCherry_1

description:
IP DNA
ChIP-seq


title: Input_tag_2

description:
Input DNA
ChIP-seq


title: IP_mCherry-FLAG_3

description:
IP DNA
ChIP-seq


title: P18_KO_beta_s1

description:
small RNA with enriched piRNA
processed data file: sRNA-Seq-beta_counts.txt.gz
small RNA-seq


title: P18_KO_beta_s2


title: HET_SC_1

description:
transposed DNA
ATAC-seq


title: P18_Con_beta_s2


title: P18_Con_beta_s1


title: P14_Con_beta_s2

value: post natal day 14


title: P14_KO_beta_s1


title: P10_Con_beta_s1

value: post natal day 10


title: P10_KO_beta_s1


title: P14_Con_beta_s1


title: P10_Con_beta_s2


title: P14_KO_beta_s2


title: P14_Con_s2

description:
processed data file: sRNA-Seq_counts.txt.gz
small RNA-seq


title: IP_A-MYB_1

description:
IP DNA
ChIP-seq


title: P14_Con_s1


title: P10_KO_s2


title: P14_KO_s2


title: P10_KO_beta_s2


title: P14_KO_s1


title: Input_tag_1

description:
Input DNA
ChIP-seq


title: P10_Con_s2


title: RS_KO_2

description:
processed data file: RS_counts.txt.gz
RNA-seq

data_processing:
RNA-seq: Raw reads were processed with cutadapt v1.8.1 to remove adapters and perform quality trimming. Trimmed reads were mapped to the UCSC mm10 assembly using TopHat v2.1. Reads were counted in exons of the UCSC for mm10, using featureCounts from the Subread package V1.4.6-p3. Cufflinks was used to calculate FPKM.
genome build: mm10
processed data files format and content: counts table from featureCounts as tab-delimited text file

source_name: round spermatids

extract_protocol:
Total RNA was isolated using TRI Reagent and mRNA was purified by Dynabeads mRNA Purification Kit.
The libraries were constructed with Nextera DNA Sample Preparation Kit (testes) or NEBNext Ultra Directional RNA Library Prep Kit for Illumina (spermatocytes and round spermatids).

value: round spermatids


title: P10_Con_s1


title: RS_KO_1


title: RS_Con_2


title: RS_Con_3


title: SC_KO_1

description:
processed data file: SC_counts.txt.gz
RNA-seq


title: SC_Con_3


title: SC_KO_2


title: SC_Con_2


title: SC_Con_1


title: P28_KO_2

description:
processed data file: RNA-Seq_counts.txt.gz
RNA-seq

value: post natal day 28


title: P28_KO_1


title: P10_KO_s1


title: P28_Con_1


title: P18_KO_3


title: P18_KO_2


title: P14_KO_1


title: P28_Con_2


title: P14_Con_1


title: P18_Con_3


title: P18_KO_1


title: P14_Con_2


title: P14_KO_2


title: RS_KO_3


title: SC_KO_3


title: P10_KO_1


title: P18_Con_1


title: P10_Con_1


title: P10_Con_2


title: P18_Con_2


title: input DNA_KO_rep2

tag: passages


title: P10_Con_3


title: P10_KO_2


title: input DNA_WT_rep2


title: input DNA_KO_rep1


title: input DNA_WT_rep1


title: RS_Con_1


title: P10_KO_3


title: H3K27ac_KO_rep2

value: H3K27ac (Diagenode, pAb-196-050)


title: H3K27ac_KO_rep1


title: H3K27ac_WT_rep2


title: H3K27ac_WT_rep1


title: H3K27me3_KO_rep2

value: H3K27me3 (Diagenode, pAb-195-050)


title: H3K27me3_WT_rep1


title: H3K27me3_KO_rep1


title: H2Bub1_WT_rep1

value: H2Bub1 (Cell signaling, 5546)


title: H2Bub1_WT_rep2


title: Col_mock_rep3

first: Akira

last: Mine

state: Kyoto

address: Kitashirakawaoiwake-cho

department: Graduate School of Agriculture

institute: Kyoto university

description: replicate 3

data_processing:
Illumina CASAVA-1.8.2 software was used for basecalling and Illumina adapter matching reads were removed using cutadapt 1.5
Reads were mapped to the Arabidopsis genome using splice-aware read aligner TopHat (version 2.0.10) with the parameters -p 10 -a 10 -g 10 --library-type fr-firststrand -G TAIR10_GFF3_genes.gff and transformed into a count per gene per library by using HTSeq (version 0.6.1) with the parameters -s reverse -f bam -t exon.
Supplementary_files_format_and_content: Tab-delimited text file including raw read counts per gene for each sample.

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Arabidopsis seeds were sterilized and germinated in MGRL medium containing 0.2% agarose and 1% sucrose. Seedlings were grown for 8 days in a 16 hours light/ 8 hours dark cycle at 22°C (light) or 20°C (dark).

extract_protocol:
Total RNAs were extracted using TRIzol (Invitrogen), followed by Dnase I (Roche) treatment.
RNA libraries were prepared from 1 μg of total RNA. Poly A enrichment and library preparation were performed with NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: The seedlings were pre-incubated in liquid MGRL medium for 3 hours and then treated with 40 μM chitin.

value: Col-0 (WT)

value: mock


title: mapkkk5_mock_rep2

description: replicate 2


title: mapkkk5_chitin_rep2

description: replicate 2

value: chitin


title: Col_chitin_rep1

description: replicate 1


title: Col_chitin_rep2

description: replicate 2


title: Col_mock_rep2

description: replicate 2


title: mapkkk5_mock_rep1

description: replicate 1


title: Col_chitin_rep3

description: replicate 3


title: mapkkk5_chitin_rep1

description: replicate 1


title: Col_mock_rep1

description: replicate 1


title: WT rep3

city: Kansas City

first: Agne

last: Kozlovskaja-Gumbriene

state: MO

institute: Stowers Institute for Medical Research

data_processing:
Illumina CASAVA-1.8.2 software used for basecalling.
Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters -p 8 --transcriptome-index -G -o --no-coverage-search
The fragments per kilobase of transcript per million mapped reads (FPKM) values were generated using Cufflinks version 2.2.1 with parameters -p 4 -g -o.
Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters -m intersection-nonempty -s no -f bam.
Genome_build: danRer10 from UCSC
Supplementary_files_format_and_content: Two tab-delimited text files: one includes raw counts of sequencing reads for each Sample, one includes FPKM values for each Sample.

organism: Danio rerio

source_name: dissociated embryo tails

growth_protocol: Zebrafish embryos were raised for 36 hours post fertizilation in the 28.5C incubator.

extract_protocol:
Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2302) was used with 13 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Zebrafish embryos positive for GFP were selected.

value: dissociated embryo tails

value: 36 hours post fertilization

value: wild type


title: METTL21B-2

city: Muenster

first: Benedikt

middle: Sebastian

last: Nilges

address: Von-Esmarch-Straße 54

department: RNA Biology Group

institute: Max Planck Institute for Molecular Biomedicine

description: ribosome protected RNA

data_processing:
Basecalls performed using CASAVA
Adapters were clipped and reandomized nucleotides trimmed using the FASTx toolkit
Reads were aligned to human rRNA to remove rRNA derived reads and mapped to the hg19 transcriptome using bowtie
reads for each individual transcript were counted using a custom script
Genome_build: hg19
Supplementary_files_format_and_content: CSV file containing  raw counts per transcript for the four different samples.

source_name: Flp-In T-REx-293

growth_protocol: Cells were routinely cultured in Dulbecco’s modified Eagle’s medium, supplemented with 10% (v/v)  fetal bovine serum (FBS), 1× GlutaMAX™ and 100 units/ml of penicillin and streptomycin (P/S).

extract_protocol:
Cell lysates were incubated with RNAseI and subjected to sucrose gradient centrifugation. Monosomes were isolated and used for library preparation.
Libraries were prepared by isolating ribosome prorotected fragments, 3' linker ligation, reverse transcription with an RT primer complementary to the linker, cicularization of the resulting ssDNA and a final PCR to attach illumina index primers and amplify the library.

treatment_protocol: Cells were treated with cycloheximide for 1min, lyzed by scraping in a buffer containing 10 mM Tris-HCl pH 7.5, 100 mM NaCl, 10 mM MgCl2, 1% Triton X-100, 0.5 mM DTT, 100  g/ml CHX and flash-frozen in liquid nitrogen.

value: METTL21B knockout

value: Kidney

tag: cell line

value: Flp-In T-REx-293


title: NICD rep1

value: NICD


title: NICD rep2


title: METTL21B-1

description: ribosome protected RNA


title: WT rep2


title: NICD rep3


title: WT-1

description: ribosome protected RNA