title: xrn-2cd_xrn-2(xe31)_06h

description:
6 hour after temperature shift
xrn2cd_downstream_upstream_counts.tab
xrn2cd_gene_counts.tab

treatment_protocol: Worms were cultured from L1 to early L4 stage for 59 hours at 15°C, and temperature was shifted to 26°C. The worms were further cultured for 6 hours and harvested.


title: WT_06h (2)

status: Public on Feb 05 2018

type: SRA

city: Basel

first: Sarah

last: Carl

address: Maulbeerstrasse 66

department: Epigenetics

country: Switzerland

institute: Friedrich Miescher Institute

library_source: transcriptomic

data_processing:
Basecalling was performed using RTA v. 1.13.48.
Reads were aligned to the ce10 (WS220) genome assembly using the qAlign function from the QuasR R package (v. 3.2). ChIP-seq reads were aligned using the default parameters, while RNA-seq reads were aligned using the parameter “splicedAlignment=TRUE”, resulting in splice-aware alignments.
Gene expression was quantified using WS220 annotations downloaded from WormBase. The qCount function in the QuasR package was used to count reads overlapping all annotated exons for each gene.
Genome_build: ce10 (WS220)
Supplementary_files_format_and_content: Tab-delimited file: First column contains gene names (WormBase identifiers), following columns contain raw counts of reads overlapping each gene or the dowstream/upstream regions for each sample. Downstream regions extend 10kb from the 3’ end of the gene or until the next gene on the same strand; upstream regions extend 2kb from the 5’ end of the gene. BigWig: counts of the 5’-end of reads, summed in 50-bp bins across the genome. BigWig files from the same experiment are normalized for sequencing library depth within that experiment.

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: Whole worms

extract_protocol:
RNA was extracted using TRI Reagent (Molecular Research Center) and treated with DNase.
Library was prepared using the TruSeq Standard mRNA Library Prep Kit (Illumina).

tag: strain/genotype

value: N2 (wild-type)

tag: developmental stage


title: H3_cardioPE2_ChIPseq

status: Public on Feb 06 2018

city: Haifa

first: Izhak

last: Kehat

address: Efron St.

country: Israel

institute: Technion - Israel's Institute of Technology

library_source: genomic

data_processing:
Adapters were removed from all samples using the cutadapt tool
Reads that had a length less than 40 bases after the adapter trimming were discarded (cutadapt option –m 40).
Reads for each sample were mapped independently using Bowtie version (v 0.12.9) against the Rattus norvegicus genome.  Genome assembly: Rnor_6.0, Ensembl release 83
Peaks were called using Macs2 callpeak --nomodel --extsize 146.
Genome_build: Rn6
Supplementary_files_format_and_content: Bedgraph. In each file, peaks present in all biological replicates ('common peaks')

molecule: genomic DNA

organism: Rattus norvegicus

source_name: cardiomyocytes (heart tissue)

growth_protocol: Neonatal rat ventricular cardiomyocytes and cardiac fibroblasts were obtained from 1-3 days old rats using an enzymatic neonatal cardiomyocyte isolation system (Worthington Biochemical Corp). We used a Percoll (sigma) density centrifugation, to isolate cardiomyocytes and fibroblasts fractions. 1.5-2X106 live cardiomyocytes were plated on 10cm dishes, while fibroblasts were plated without counting.

extract_protocol:
according to MAGnify™ Chromatin Immunoprecipitation System (Invitrogen) protocol.
Libraries were prepared according to Blecher-Gonen et al.2013. Briefly, the ChIP product was subjected to end repair, A base addition, adapter ligation and PCR amplification to create libraries. The adaptors contain different barcodes to allow multiplexing of 12 samples in one pool.

treatment_protocol: Cell culture meduim was replaced 24h after plating to serum free medium for 'cardioSFM',or to serum free medium + phenylephrine for 'cardiacPE'

tag: cell type

value: neonatal rat ventricular myocytes

tag: passage

tag: growth medium

value: serum free medium with phenylephrine (10µM)

tag: chip antibody

value: anti H3K27ac antibody (abcam ab4729).


title: Control_input_rep2

description: input

extract_protocol:
Crosslinked and sonicated.
Library was prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB).

treatment_protocol: Worms were cultured from L1 to mid-L4 developmental stage at 20°C.

tag: replicate


title: Control_input_rep1

description: input


title: 0h_I

city: Ribeirão Preto

first: Pablo

middle: Rodrigo

last: Sanches

state: SP

address: Av. Bandeirantes, 3900

department: Genetics

country: Brazil

institute: University of São Paulo

description:
geneCounts_0h.txt
DESeq_3h_vs_0h.csv
DESeq_12h_vs_0h.csv

data_processing:
FastQC v0.11.2 was used to visualize the libraries quality before and after trimming.
FASTX-Tookit (fastq_quality_filter) was used to remove poor quality sequences, such that remaining sequences had a minimum quality score of 20 with a minimum of 50% of bases within a read meeting this quality score requirement.
Filtered reads were mapped onto the T. rubrum genome using the Bowtie2 v2.1.0.
Reads were assigned to annotated genes and counted using the "summarizeOverlaps" function from the GenomicRanges Bioconductor package.
The data were analyzed using the R package DESeq version 1.28.0. The samples were normalized, and the dispersions were estimated using the default DESeq settings. DESeq was then used to identify differentially expressed genes for each pairwise comparison of interest. Genes with an adjusted P value of < 0.05 and a log2(foldchange) > 1.5 (upregulation) or < -1.5 (downregulation) were called as differentially expressed.
Genome_build: Broad T. rubrum strain CBS118892 genome
Supplementary_files_format_and_content: tab-delimited text files include reads count values for each sample and DESeq output in CSV format containing mean expression, fold changes and p value.

molecule: total RNA

organism: Trichophyton rubrum

source_name: CBS 118892 - control, replicate I

growth_protocol: T. rubrum conidia (about 1x10^6 conidia per mL) were grown on Sabouraud medium for 96h, at 28ºC under shaking.

extract_protocol:
Approximately 100 mg of frozen mycelia were used for total RNA extraction using  Illustra RNAspin Mini Isolation Kit (GE, USA)  and treated with RNAse-free DNAse I. RNA concentrations were estimated through NanoDrop ND-1000 spectrophotometer, and RNA integrity was verified using  Agilent Bioanalyser platform 2100.
RNA libraries were prepared for sequencing according to Illumina guidelines.

treatment_protocol: The resulted mycelium  from pre inoculum of T. rubrum conidia was transferred to RPMI 1640 medium in the absence or presence UDA (17.25 μg/mL) for 3h and 12h under shaking.

tag: treatment


title: cardiacFibro1_ATACseq

data_processing:
Reads containing Nextera transposase or RNA PCR primer were trimmed using cutadapt
The reads were aligned uniquely to the rat genome (Rnor 6.0, from Ensembl) using bowtie (version 1.0.0)
Mitochondrial reads were filtered, and duplicated reads were removed using Picard tools
The two biological replicates were correlated and combined
Peaks were called using Macs2 callpeak --nomodel --extsize 100 --shift -46
Genome_build: Rn6
Supplementary_files_format_and_content: Bedgraph. In each file- peaks present in all biological replicates ('common peaks')

source_name: cardiac fibroblasts (heart tissue)

extract_protocol:
25000 cells from each sample were centrifugated and resuspended with lysis buffer, followed by transposition reaction using Tn5 transposase (Nextera kit).
Nextera DNA preparation kit  Illumina,Catalog number-FC-121-1030

treatment_protocol: Cell culture meduim was replaced 24h after plating to serum free medium for 'cardioSFM', serum free medium + phenylephrine for 'cardiacPE', serum free medium + infection with adenovirus expressing WT GATA4 gene for 'cardioGata4'

value: cardiac fibroblasts

value: serum containing medium


title: XRN2_input_rep2

description: input


title: 20140428_C04 E10.5 NR5A1-eGFP single-cell

city: Ramat Gan

first: Isabelle

last: Stévant

address: Institute of Nanotechnology and Advanced Materials, Building 206

institute: University of Bar Ilan

description:
20140428_C04
Poly-A RNA
Processed data file: XY_NR5A1-eGFP_single-cell_fetal_gonads.txt

data_processing:
Illumina Casava1.8.2 software used for basecalling.
FastQ files were mapped with GemTools (version 1.7.1) to the mouse reference genome (GRCm38.p3) and the genome annotation (version M4) downloaded from GENCODE, with an extra fake "Z" chromosome with the GFP sequence.
RPKM (Reads Per Kilobase of exon per Million reads mapped) were computed with an in-house pipeline.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: XY_NR5A1-eGFP_single-cell_fetal_gonads.txt: Tab-delimited text file includes RPKM values for each Sample.

organism: Mus musculus

source_name: XY gonad

extract_protocol:
XY gonads were collected in PBS at room temperature. PBS was removed and tissues were digested 10 minutes at 37°C with trypsin/EDTA 0.05% and filtered through a 40µm cell strainer to obtain single cell suspension. Nr5a1-eGFP+ cells were then sorted by fluorescent-active cell sorting (BD FACSARIA II) with Draq7TM dye to exclude dead cells and collected in PBS for the single-cell capture. Cells were centrifuged at low speed to be concentrated at an average of 400 million cells per mL prior cell capture. Single cells were captured on small size IFC microfluidic chips using the C1 Single-Cell Auto Prep System (Fluidigm) following the manufacturer recommended protocol. Reverse-transcription and pre-amplification of the single-cell cDNAs were achieved within the IFC chip using the SMARTer Ultra Low RNA kit for Illumina (Clontech) according to the C1 protocol.
RNA-sequencing libraries of the single-cell cDNA were prepared using the Illumina Nextera XT DNA Sample Preparation kit using the modified protocol described in the C1 documentation.

tag: strain/background

value: Mixed background

tag: genotype/variation

value: NR5A1-eGFP positive cells

tag: age

tag: c1 ifc size

value: small

tag: sequencing depth

value: 25M reads 100bp p-e


title: RNA-seq_PS_dKO_rep1

city: Cincinnati

first: So

last: Maezawa

address: 3333 Burnet Ave.

department: Reproductive Sciences

country: USA

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Data analysis was performed using the BioWardrobe (PMID: 26248465 )
For ChIP-Seq, Fastq files from Illumina pipeline were aligned by bowtie (version 1.1.1 PMID: 19261174) with maximum one allowed error in a sequence and no more than one number of hits was allowed. MACS2 (version 2.1.0.20140616 PMID: 18798982) were used to estimate fragment size and to find islands of enrichment. MACS2 were used with q-value threshold less than 0.2.
For RNA-seq, Fastq files from Illumina pipeline were aligned by STAR (version STAR_2.4.2a PMCID: PMC3530905) with ”--outFilterMultimapNmax 1 --outFilterMismatchNmax 2” (for the full manual see https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf?raw=true). RefSeq annotation from UCSC genome browser (11/2012 PMID: 23155063) for mm10 genome was used. The --outFilterMultimapNmax parameter is used to allow uniq alignment only and --outFilterMismatchNmax parameter is used to allow at max 2 errors. All reads from produced .bam files were split for related isoform with respect to RefSeq annotation. Then EM algorithm was used to estimate appropriate number of reads for each isoform.
Genome_build: mm10
Supplementary_files_format_and_content: csv file includes detected peaks for ChIP-seq or RPKM for RNA-seq

source_name: Pachyten spermatocytes

extract_protocol: ChIP-seq libraries were prepared through the ChIPmentation method (Schmidl et al., 2015). Briefly, beads were resuspended in 30 μl of the tagmentation reaction buffer (10 mM Tris-HCl pH 8.0 and 5 mM MgCl2) containing 1 μl Tagment DNA Enzyme from the Nextera DNA Sample Prep Kit (Illumina) and incubated at 37°C for 10 min in a thermocycler. The beads were washed twice with 150 μl cold wash buffer 1, incubated with elution buffer (as described above) at 42°C for 30 min, and then incubated at 65°C for another 5 h to reverse cross-linking. DNA was purified with the MinElute Reaction Cleanup Kit (Qiagen) and amplified with NEBNext High-Fidelity 2x PCR Master Mix (NEB). Amplified DNA was purified by Agencourt AMPure XP (Beckman Coulter). Afterward, DNA fragments in the 250- to 500-bp size range were prepared by agarose gel size selection. DNA libraries were adjusted to 5 nM in 10 mM Tris-HCl pH8.0 and sequenced with an Illumina HiSeq 2500. For RNA-seq libraries, total RNA was purified using an RNeasy micro kit (Qiagen) according to the manual provided. RNA quality and quantity were checked using, respectively, Bioanalyzer (Agilent) and Qubit (Life technologies). The initial amplification step was performed with the NuGEN Ovation RNA-Seq System v2. The assay was used to amplify RNA samples and create double stranded cDNA. Libraries were then created with the Nextera XT DNA Sample Preparation Kit (Illumina) and sequenced with an Illumina HiSeq 2500.

tag: strain

tag: tissue

value: testis

value: adult

tag: genotype

value: Rnf8- and Scml2-dKO

tag: biowardrobe ides


title: XRN2_input_rep1

description: input

tag: strain/genotype


title: K27ac_RS_WT_rep2

source_name: Round spermatides

value: wild type

tag: antibody


title: K27ac_RS_WT_rep1


title: Control_ChIP_rep2

description: ChIP

extract_protocol:
Crosslinked, sonicated and purified using (A-11122, Thermo Fisher Scientific)
Library was prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB).

tag: developmental stage


title: Control_ChIP_rep1

description: ChIP


title: K27ac_PS_WT_rep2


title: XRN2_ChIP_rep2

description: ChIP


title: K27ac_PS_WT_rep1


title: XRN2_ChIP_rep1

description: ChIP


title: AT1_P60

city: Beijing

first: huanwei

last: huang

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

country: China

institute: NIBS

data_processing:
The 10X scRNA-seq library were sequenced on Illumina HiSeq2500 platform using dual indexed sequencing protocol. The generated reads were de-multiplexed and mapped to mouse genome (mm10) using the 10X CellRanger pipeline (v1.3.1). For P60 AT2 cells, about 10% human A549 cells were added for checking the 10X droplet mixture rate (The human cells were identified using mm10_hg19 combined reference and only mouse cells were used in the studies).
The expressional datasets were further processed using R “Seurat” package (V2.0.0), The distribution of nGenes, nUMI, and mitochondrial reads ratio were plotted. The cells used in the study were extracted using cutoff for nGene<5000, nUMI<25000, percent.mito <0.1. The UMI count is normalized to 10,000 in each cell and log transformed.
Genome_build: mm10

source_name: alveolar type I (AT1)

extract_protocol:
Sftpc-CreER; Rosa26-Zsgreen; Hopx-RFP mice at various developmental stages were injected with 1-2 doses of tamoxifen. For AT1 cell isolation, lungs were inflated with an enzyme cocktail solution containing neutral protease (5U/ml,LS02111, Worthington), Elastase (4 U/ml, LS002294, Worthington), Type I collagenase (200 U/ml, 17100017, Gibco), and DNase I (0.33 U/ml, 10104159001, Roche) and incubated with the enzyme cocktail solution at room temperature for 45 minutes. Lungs were then cut into small pieces and filtered through 40μm cell strainers (BD Falcon). Cells were first incubated with red blood lysis buffer. After spinning down, cells were resuspended in DPBS+5% FBS (Gibco, 1767839). Cells were then stained with different antibodies. Antibodies used: PE-Cy™7 rat anti-CD45 (1:400, 552848, BD biosciences) and APC hamster anti-Pdpn (1:200, 127410, biolegend). For AT2 cell isolation, lungs were inflated with enzyme cocktail solution containing neutral protease (5U/ml, LS02111, Worthington) and DNase I (0.33 U/ml, 10104159001, Roche). DAPI was used to label dead cells. Sorting was performed on BD Aria2
RNA libraries were prepared for sequencing using 10X genomics single cell 3' standard protocols

tag: cell type

value: RFP+Pdpn+GFP-CD45- cells from tamoxifen treated Sftpc-CreER; Rosa26-Zsgreen; Hopx-RFP mice

value: postnatal day 60 (P60)

value: mixed FVB/C57BL6


title: AT2_P60

source_name: alveolar type II (AT2)

value: GFP+CD45- cells from tamoxifen treated Sftpc-CreER; Rosa26-Zsgreen; Hopx-RFP mice


title: xrn2(xe31)_10h_reseq

description:
xrn2_xe31_resequenced_gene_counts.tab
xrn2_xe31_resequenced_downstream_upstream_counts.tab

source_name: whole body

treatment_protocol: Worms were cultured from L1 to early L4 stage for 59 hours at 15°C, and temperature was shifted to 26°C. The worms were further cultured and harvested every hour for 10 hours until late L4 stage.

value: HW1660 (carrying the xrn-2(xe31) allele)


title: xrn2(xe31)_06h_reseq


title: RNA-seq_RS_dKO_rep2


title: WT_10h_reseq

value: N2 (wild-type)


title: AT1_P3

value: postnatal day 3 (P3)


title: WT_06h_reseq


title: 20140428_C17 E10.5 NR5A1-eGFP single-cell

description:
20140428_C17
Poly-A RNA
Processed data file: XY_NR5A1-eGFP_single-cell_fetal_gonads.txt


title: RNA-seq_RS_dKO_rep1


title: xrn2(xe31)_10h

description:
xrn2_xe31_timecourse_gene_counts.tab
xrn2_xe31_timecourse_downstream_upstream_counts.tab


title: xrn2(xe31)_09h


title: 93_DP_22157

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

country: United Kingdom

institute: Cancer Research UK Cambridge Institute

data_processing:
Single-end 50 bp reads generated on Illumina HiSeq were aligned to the human genome version GRCh37.64 using TopHat v2.0.4 (Trapnell et al., 2009). Read counts were obtained using HTSeq-count v0.5.3p9 (Anders et al., 2014), normalised and tested for differential gene expression using the Bioconductor package DESeq v1.10.1 (Anders and Huber, 2010).
Multiple testing corrections were applied using the Benjamini-Hochberg method (Benjamini and Hochberg, 1995). Genes were selected as differentially expressed such that FDR < 0.01.
Genome_build: GRCh38
Supplementary_files_format_and_content: HTSeq-count gene counts

source_name: Prostate

extract_protocol:
Prostates were removed, flash frozen on dry ice or immersed in RNA Later, homogenized by bead beating vortex and RNA was harvested using Allprep DNA/RNA/Protein Mini Kit Qiagen. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: FVB

tag: age in months

tag: prostate lobe

value: DP

tag: tumour stage

value: high-stage tumour


title: 94_DP_13


title: 92_DP_20994


title: 20140428_C38 E10.5 NR5A1-eGFP single-cell

description:
20140428_C38
Poly-A RNA
Processed data file: XY_NR5A1-eGFP_single-cell_fetal_gonads.txt

value: Mixed background

value: NR5A1-eGFP positive cells


title: 91_DP_52


title: xrn2(xe31)_06h


title: AT1_P15

value: postnatal day 15 (P15)


title: 90_LP_42101

value: LP


title: 89_LP_41299


title: 88_LP_37337


title: xrn2(xe31)_05h


title: xrn2(xe31)_04h


title: 87_LP_129


title: xrn2(xe31)_03h


title: 86_VP_38123

value: VP


title: xrn2(xe31)_02h


title: 85_VP_23422


title: 84_VP_71


title: xrn2(xe31)_01h


title: xrn2(xe31)_00h


title: WT_10h


title: WT_09h


title: 83_VP_6


title: WT_08h


title: xrn2(xe31)_07h


title: 80_AP_23422

value: AP


title: 81_AP_37718


title: WT_06h


title: 77_DP_1787

value: medium-stage tumour


title: 79_AP_22157


title: WT_04h


title: 82_AP_41229


title: 76_DP_41871


title: WT_02h


title: 78_DP_44251


title: WT_03h


title: 74__DP_39470


title: WT_01h


title: 73_LP_1787


title: WT_00h


title: 75_DP_40707


title: 71_LP_42331


title: 72_LP_1665


title: N2_mock(RNAi)_L1toL4_20°C_rRNA(-)

description:
rRNA(-)_xrn2_RNAi_gene_counts.tab
rRNA(-)_xrn2_RNAi_downstream_upstream_counts.tab

extract_protocol:
RNA was extracted using TRI Reagent (Molecular Research Center) and treated with DNase.
Library was prepared using the Ovation Universal RNA-Seq System (NuGEN).

treatment_protocol: Worms were treated with mock (empty vector) RNAi from L1 to mid-L4 developmental stage at 20°C.


title: 69_LP_15620


title: WT_07h


title: 70_LP_41871


title: WT_05h


title: PolII_ChIP_xrn-2(RNAi)_IP_rep2

description: ChIP

extract_protocol:
DNA-Pol II complexes were crosslinked, sonicated and purified using anti-Pol II antibody.
Library was prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB).

treatment_protocol: Worms were treated with xrn-2 RNAi from L1 to mid-L4 developmental stage at 20°C.

tag: replicate


title: PolII_ChIP_xrn-2(RNAi)_IP_rep1

description: ChIP


title: 65_VP_43668


title: 67_VP_1787


title: 68_VP_43578


title: PolII_ChIP_xrn-2(RNAi)_input_rep2

description: input

extract_protocol:
DNA-Pol II complexes were crosslinked and sonicated.
Library was prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB).


title: 64_VP_39740


title: PolII_ChIP_mock(RNAi)_IP_rep2

description: ChIP


title: PolII_ChIP_mock(RNAi)_IP_rep1

description: ChIP


title: 66_VP_176


title: 63_AP_41871


title: PolII_ChIP_mock(RNAi)_input_rep2

description: input


title: PolII_ChIP_xrn-2(RNAi)_input_rep1

description: input


title: PolII_ChIP_mock(RNAi)_input_rep1

description: input


title: 62_AP_40707


title: N2_mock(RNAi)_L1toL4_20°C_rep3

description:
polyA_xrn2_RNAi_gene_counts.tab
polyA_xrn2_RNAi_downstream_upstream_counts.tab


title: 61_AP_39470


title: N2_xrn2(RNAi)_L1toL4_20°C_rRNA(-)_rep2


title: N2_xrn2(RNAi)_L1toL4_20°C_rRNA(-)_rep1


title: 60_AP_37716


title: 59_AP_36848


title: 58_DP_1170

value: PIN


title: xrn2(xe31)_08h


title: 56_DP_1064


title: 55_DP_562


title: 57_DP_1065


title: 54_LP_1170


title: D2

city: Bergen

first: Eric

last: Thompson

address: Thormøhlensgt. 55

country: Norway

institute: Sars International Centre for Marine Molecular Biology

data_processing:
Reads were split by barcode using fastx_barcode_splitter.pl
Reads were trimmed using the fastx_trimmer, part of the FASTX Toolkit 0.0.13, and the following parameters: -f 10
Reads were mapped to the O. dioica reference genome using bowtie version 0.12.7.0 with the following parameters: -t -m 1 --trim5 1 --trim3 3
Unique 5' positions, and the number of aligned reads for each, were extracted using custom R code to define CTSSs within each sample. Tag counts were normalised to give tags per million (tpm)
1_Assembly_reference_unmasked_v3.0.fa
Genome_build: 1_Assembly_reference_unmasked_v3.0.fa/ASM20953v1/ASM20955v1 (e.g. scaffold_998 = locus FN654012.1)
Supplementary files format and content: Tab-delimited text files containing the location (scaffold, position, strand) and read count of each CTSS.

organism: Oikopleura dioica

source_name: Day 2 whole animals

extract_protocol:
Total RNA from each stage of development was isolated using RNAqueous Micro (Ambion) and treated by Terminator™ 5´-Phosphate-Dependent Exonuclease to deplete excess small RNAs.
Library was constructed by DNAFORM, Yokohama City, Japan. DNAFORM prepared CAGE libraries according to the CAGE standard protocol applying a random primer for the 1st strand cDNA synthesis (Kodzius R. et al., CAGE: cap analysis of gene expression, Nat. Methods. 2006 Mar;3(3):211-22). DNAFORM modified the protocol in such a way that it yields DNA fragments for direct sequencing on an Illumina GAII Genome Analyzer and they depleted each library of trans-spliced transcripts by first using a custom designed 5’ linker, specific to the 5’ spliced leader sequence, then using standard linkers for non-trans-spliced mRNAs. Barcodes were as follows: Tadpole ACA; D2 ATG; Tailbud GAT; Female_ D6 ACA; Oocyte ATG; Male_D6 GAT. DNA concentration and purity were confirmed using an Agilent Bioanalyzer.

value: Day 2

value: Whole animal


title: Male_D6

source_name: Day 6 male whole animals

value: Day 6


title: Female_D6

source_name: Day 6 female whole animals


title: Oocyte

source_name: Oocytes

value: Oocytes


title: Tailbud

source_name: Tailbud stage whole animals

value: Tailbud


title: 52_LP_1064


title: CD11b MΦ bleomycin day 8 rep3_run2

city: Denver

first: Alexandra

middle: L

last: McCubbrey

state: CO

address: 1400 Jackson St

institute: National Jewish Health

data_processing:
Basecalling, barcode demultiplexing and adapter trimming was performed by Ion Torrent Suite 5.0.4.
Sequence reads of at least 30 nt length were mapped to the GRCm38 release of the mouse genome using STAR (version 2.4.1d) with splice site data from the Ensembl 84 annotation.
Reads mapping unambiguously to each gene in the Ensembl 84 annotation were quantified using the featureCounts program from the subread package (v1.5.0-p1).
Read counts from individual sequencing runs of the same sample were added together.
Statistical comparisons of the gene expression between the cell genotypes were performed with the DESeq2 package version 1.8.1 for the R statistical software version 3.2.0.
Genome_build: GRCm38
Supplementary_files_format_and_content: read counts assigned to each gene and sample, as tab-separated text tables: 1) output from subread featureCounts, 2) aggregated by adding different sequencing runs for each sample

source_name: lung macrophage

extract_protocol:
CD64+Mertk+ lung macrophages were sorted into SiglecF(high) and CD11b(high) subsets.  RNA was isolated from sorted cells using the RNeasy micro kit (QIAGEN).
A Clontech SMARTer® Ultra™ Low Input RNA Kit for Sequencing – v4 (Mountain View, CA, USA) and modified Kapa Biosystems KAPA Hyper Prep Kit (Wilmington, MA, USA) were used. Briefly, library construction started from isolation of total RNA species taking 3ng of total RNA into the protocol, followed by SMARTer 1st-strand cDNA synthesis, full length dscDNA amplification by LD-PCR, followed by purification and validation. After that, the samples were sheared using a Covaris system, vacuum concentrated and then processed through the Kapa protocol. The Kapa protocol consisted of end repair and A-tailing, adaptor ligation, amplification, and bead templating.  Libraries were sequenced as barcoded-pooled samples on a P1 Ion Proton chip.

treatment_protocol: 8 days prior to isolation of lung macrophages, 3 U/kg of bleomycin was administered intratracheally to mice to induce lung fibrosis

tag: Sex

value: female

value: 10 weeks

tag: treatment

value: bleomycin

value: CD11b(high) macrophage


title: N2_xrn-2(RNAi)_L1toL4_20°C_rep3

value: N2 (wild-type)


title: 53_LP_1065

value: FVB


title: CD11b MΦ bleomycin day 8 rep1_run1

tag: age


title: CD11b MΦ bleomycin day 8 rep2_run1


title: 49_VP_1065


title: 50_VP_1170


title: Tadpole

source_name: Tadpole stage whole animals

value: Tadpole


title: SiglecF MΦ bleomycin day 8 rep3_run2

value: SiglecF(high) macrophage


title: SiglecF MΦ bleomycin day 8 rep2_run2


title: SiglecF MΦ bleomycin day 8 rep2_run1


title: 51_LP_1063

value: LP


title: 48_VP_1063

value: VP


title: SiglecF MΦ bleomycin day 8 rep3_run1


title: SiglecF MΦ bleomycin day 8 rep1_run2


title: 47_VP_562


title: 46_AP_1170

value: AP


title: SiglecF MΦ naïve day 0 rep4_run1


title: SiglecF MΦ naïve day 0 rep3_run2


title: SiglecF MΦ naïve day 0 rep3_run1


title: CD11b MΦ bleomycin day 8 rep3_run1


title: CD11b MΦ bleomycin day 8 rep2_run2


title: 44_AP_49

value: PIN


title: 45_AP_12


title: SiglecF MΦ naïve day 0 rep1_run2


title: SiglecF MΦ naïve day 0 rep1_run1


title: 42_DP_57340

value: ARR2PB-Cre; Trp53flox/floxRb1flox/flox

value: proximal zone

value: Moderate and poorly differentiated adenocarcinoma


title: 43_AP_1457


title: RNA-Seq of mock-transfected HEK293TT cells mockco_3

city: Heidelberg

first: Sebastian

last: Eilebrecht

address: Im Neuenheimer Feld 280

department: Episomal-persistent DNA in Cancer and Chronic Diseases

country: Germany

institute: German Cancer Research Center

description: rRNA-depleted total RNA

data_processing:
RTA 1.18.64 software used for basecalling
Sequenced reads were mapped to the hg37 human genome or the corresponding BMMF genome using tophat2 (and STAR) with parameters --library-type fr-firststrand
hg37-mapped reads were counted for every gene using HT-SeqCount; for BMMF-mapped reads strand-specific reads were separated using samtools
Differential gene expression for hg37-mapped samples was analyzed using edgeR algorithm
Supplementary_files_format_and_content: .xls files containing read counts and normalized read counts (per million total reads) for each base and each strand; .tab files containing putative splice junctions; .Rinput files containing HT-Seq count data; .xls files containing normalized read data; .xls files containing log(2)-fold changes and p-values (edgeR output)

organism: Homo sapiens

source_name: HEK293TT cell line

growth_protocol: HEK293TT cells were maintained in Dulbeccos modified Eagles medium (DMEM) containing 10% fetal calf serum, 1% GLutamax, 1% non-essential amino acids (Invitrogen) and 400μg/ml hygromycin B (Roche Diagnostics).

extract_protocol:
Total RNA of transfected cells was isolated using the miRNeasy kit (Qiagen) according to the manufacturer’s instructions. The resulting RNA was digested with DNaseI and subsequently depleted for rRNAs using the the RiboZero kit (Illumina) according to the manufacturer’s instructions.
Strand-specific RNA libraries were prepared for sequencing using standard Illumina protocols using random primers.

treatment_protocol: HEK293TT cells were transfected with the corresponding BMMFs using Lipofectamine 2000 (Invitrogen) according to the manufacturer’s instructions.

tag: transfection

value: mock-transfected HEK293TT cells


title: 41_DP_57337


title: 40_DP_1880


title: 39_DP_883


title: 37_DP_1128

value: DP


title: CD11b MΦ bleomycin day 8 rep1_run2

value: female


title: Veh_8h_2

data_processing:
Single-end 50 bp reads generated on Illumina HiSeq were aligned to the human genome version GRCh37.64 using TopHat v2.0.4 (Trapnell et al., 2009). Read counts were obtained using HTSeq-count v0.5.3p9 (Anders et al., 2014), normalised and tested for differential gene expression using the Bioconductor package DESeq v1.10.1 (Anders and Huber, 2010).
Multiple testing corrections were applied using the Benjamini-Hochberg method (Benjamini and Hochberg, 1995). Genes were selected as differentially expressed such that FDR < 0.01.
Genome_build: GRCh37.64
Supplementary_files_format_and_content: HTSeq-count gene counts

source_name: Prostate cancer cell line

growth_protocol: Cells were grown at 37 °C and 5% CO2 in RPMI 1640 supplemented with 10% fetal bovine serum.

extract_protocol:
RNA was isolated using the RNeasy Plus Mini Kit according to the manufacturer’s instructions.
Library preparation was carried out using the Illumina® TruSeq Stranded mRNA Library Prep Kit (Life Technologies) according to standard Illumina protocols.

tag: cell line

tag: treatment type

value: Drug treatment

tag: treatment agent

value: DMSO

tag: treatment duration

value: 8 h


title: SiglecF MΦ bleomycin day 8 rep1_run1

tag: strain

value: 10 weeks

value: bleomycin


title: 38_DP_816

tag: genotype

value: FVB


title: Veh_8h_4


title: SiglecF MΦ naïve day 0 rep4_run2

value: SiglecF(high) macrophage


title: Veh_8h_1


title: RNA-Seq of mock-transfected HEK293TT cells mockco_2

description: rRNA-depleted total RNA


title: 36_DP_1127


title: 35_DP_1112


title: Veh_24h_4


title: 31_LP_1122

value: LP


title: 33_DP_1089


title: Veh_24h_3


title: Veh_24h_2


title: 29_LP_1089


title: 28_VP_1128

value: VP


title: 27_VP_1122


title: Veh_8h_3


title: RNA-Seq of mock-transfected HEK293TT cells mockco

description: rRNA-depleted total RNA


title: siMELK_C_2

value: Transient transfection

value: siMELK #3


title: siMELK_C_4


title: siMELK_C_3


title: 25_VP_1076

value: ARR2PB-Cre; Trp53flox/floxRb1flox/flox

value: PIN


title: 24_AP_1127

value: AP


title: 26_VP_1078


title: 23_AP_1122


title: 21_AP_1076


title: 22_AP_1096


title: RNA-seq_PS_dKO_rep2

tag: tissue

value: testis

value: adult

value: Rnf8- and Scml2-dKO

tag: biowardrobe ides


title: siMELK_C_1


title: siMELK_B_4

value: siMELK #2


title: siMELK_B_1


title: siMELK_B_2


title: siMELK_B_3


title: siCtrl_4

value: Negative control siRNA


title: 20_DP_1303

value: Ptenflox/flox

value: DP

value: Normal


title: 34_DP_1096

value: FVB


title: OrR_PB_6

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

data_processing:
Paired-end RNA-seq reads were mapped against the reference genome (FB2016_01 dmel_r6.09 with selected chromosomes) using STAR (version 2.5.0a) with quantMode GeneCounts for counting reads per gene.
Genome_build: FB2016_01 dmel_r6.09
Supplementary_files_format_and_content: Raw read counts per gene in csv format.

organism: Drosophila melanogaster

source_name: wild type_preblastoderm_embryo

extract_protocol:
Prior to RNA-seq, the AcfC flies were backrossed with the wild-type OrR strain for 8 generations. Embryos were collected 0-45 min AEL and allowed to develop at 25°C until approximately 30 min before the desired stage (around 1 h for Bownes Stage 3 and 4 h for Bownes Stage 8). Without prior dechorionation, embryos were hand-picked and submerged into a drop of Voltalef 10s halocarbon oil (Lehman and Voss Co.) placed on a microscope slide. After about 5 min, the embryonic structures become visible under the stereomicroscope. Embryos were allowed to develop further under the halocarbon oil until the desired stage. Single embryos were picked and crushed with a 26G needle into 200 µl of Lysis Buffer (supplemented with Proteinase K) from the Agencourt RNAdvance Tissue Kit (Beckman Coulter, Cat No A32645). After the addition of 10 µl of 1:100 ERCC Spike-in RNA mix (Ambion, Cat No 4456740), the samples were incubated at 37°C for 20 min, snap-frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted from the single-embryo homogenate using the same Agencourt RNAdvance Tissue Kit, following standard protocol but utilizing half of the volumes recommended. The RNA integrity was checked on a Bioanalyzer 2100 (Agilent).
Ribosomal RNA depletion was achieved using rRNA Depletion Kit (Human/Mouse/Rat) (New Englands Biolab, Cat No E6310) and the rRNA-depleted RNA was stored at -80°C until further processing. Non-directional libraries were prepared using NEBnext Ultra RNA Library Prep Kit for Illumina (New Englands Biolab, Cat No E7530S) following standard protocol. 6 replicates per genotype and stage were sequenced on an Illumina HiSeq1500 instrument.

tag: strain background

value: Oregon-R

tag: embryonic stage

value: preblastoderm (Bownes stage 3)

tag: genotype/variation

value: wild type

value: embryo

tag: molecule subtype

value: rRNA-depleted RNA


title: Veh_24h_1

value: Drug treatment

value: DMSO


title: siCtrl_3

value: Transient transfection


title: 19_DP_1205

tag: age in months

tag: prostate lobe

tag: tumour stage


title: siCtrl_2


title: OrR_PB_4


title: OrR_PB_5


title: 18_DP_1056b


title: siCtrl_1


title: OrR_PB_3


title: 17_DP_977


title: OrR_PB_2


title: 16_DP_1056a


title: MELKi_8h_3

value: 30 nM OTSSP167

value: 8 h


title: OrR_PB_1


title: 15_LP_1336

value: LP


title: MELKi_8h_4


title: 14_LP_1303


title: OrR_G_6

source_name: wild type_gastrula_embryo

value: gastrula (Bownes stage 8)


title: MELKi_8h_2


title: OrR_G_5


title: OrR_G_3


title: OrR_G_4


title: MELKI_24h_4


title: MELKI_24h_3


title: MELKI_24h_2


title: 10_VP_1336

value: VP


title: 12_LP_1058

value: Ptenflox/flox


title: OrR_G_2


title: 9_VP_978


title: RNA-Seq of MSBI1.176 and CMI1.252 co-transfected into HEK293TT cells MSBI1.176_CMI1.252co_3

description: rRNA-depleted total RNA

organism:
Homo sapiens
Sphinx1.76-related DNA


title: MELKi_8h_1


title: 8_VP_977


title: MELKI_24h_1


title: OrR_G_1


title: RNA-Seq of MSBI1.176 and CMI1.252 co-transfected into HEK293TT cells MSBI1.176_CMI1.252co_2

description: rRNA-depleted total RNA


title: Acf_PB_6

value: AcfC


title: Acf_PB_5


title: 7_VP_665

value: Normal


title: 13_LP_1205

value: FVB


title: 6_VP_664


title: RNA-Seq of MSBI1.176 and CMI1.252 co-transfected into HEK293TT cells MSBI1.176_CMI1.252co

description: rRNA-depleted total RNA


title: RNA-Seq of MSBI1.176 alone transfected into HEK293TT cells MSBI1.176co_3

description: rRNA-depleted total RNA


title: 5_AP_1303

value: AP


title: Acf_PB_3

value: Oregon-R

value: preblastoderm (Bownes stage 3)


title: Acf_PB_4

value: embryo


title: Acf_PB_1

value: rRNA-depleted RNA


title: 2_AP_1058


title: RNA-Seq of MSBI1.176 alone transfected into HEK293TT cells MSBI1.176co

description: rRNA-depleted total RNA


title: RNA-Seq of MSBI1.176 alone transfected into HEK293TT cells MSBI1.176co_2

description: rRNA-depleted total RNA


title: 3_AP_1059


title: 1_AP_664


title: 11_LP_977


title: Acf_G_5


title: Acf_G_4


title: Acf_G_6


title: RNA-Seq of CMI1.252 alone transfected into HEK293TT cells CMI1.252co_2

description: rRNA-depleted total RNA


title: RNA-Seq of CMI1.252 alone transfected into HEK293TT cells CMI1.252co_3

description: rRNA-depleted total RNA


title: Acf_PB_2


title: RNA-Seq of MSBI2.176 transfected into HEK293TT cells MSBI2.176_3

description: rRNA-depleted total RNA


title: 2i-Jaki-BMP-Alk5i-day11 (II)

city: Toronto

first: Peter

last: Zandstra

state: Ontario

address: 160 College Street, University of Toronto

department: Institute of Biomaterials and Biomedical Engineering

country: Canada

institute: University of Toronto

data_processing:
bcl2fastq2 v2.17 software used for basecalling.
Reads were trimmed for adapters and a phred33 quality cutoff of 20 using TrimeGalore paired end mode with cutadapt
Genes were aligned to the mouse genome and the number of reads per gene were counted using STAR 2.4.2a with --quantMode GeneCounts
Genome_build: Ensembl NCBIM37
Supplementary_files_format_and_content: Tab delimited files of transcript counts as outputed by STAR
Column headers:
column 1:  gene ID
column 2:  counts for unstranded RNA-seq
column 3:  counts for the 1st read strand aligned with RNA
column 4:  counts for the 2nd read strand aligned with RNA
We used column 2 for unstranded RNA-seq

source_name: PSC

extract_protocol:
RNA was extracted using the PureLink RNA Mini Kit (Ambion, Life Technologies, Cat no. 12183018A and 12183025) according to the manufacturer’s instructions. Cells were homogenized using a QIAshredder (Qiagen, Cat no. 79654). Cell pellets were frozen at the treatment-specific time points and RNA was extracted from all pellets at the same time for each analysis.
Quality of total RNA samples were checked on an Agilent Bioanalyzer 2100 RNA Nano chip following Agilent Technologies’ recommendation. Concentration was measured by Qubit RNA HS Assay ona Qubit fluorometer (ThermoFisher). RNA library preparation was performed following the NEB NEBNext Ultra Directional Library Preparation protocol. Briefly, 250 ng of total RNA was used as the input material and enriched for poly-A mRNA, fragmented into the 200-300-bases range for 4 minutes at 94oC and converted to double stranded cDNA, end-repaired and adenylated at the 3’ to create an overhang A to allow for ligation of Illumina adapters with an overhang T; library fragments were amplified under the following conditions: initial denaturation at 98oC for 10 seconds, followed by 13 cycles of 98oC for 10 seconds, 60oC for 30 seconds and 72oC for 30 seconds, and finally an extension step for 5 minutes at 72oC; at the amplification step, each sample were amplified with a different barcoded adapters to allow for multiplex sequencing. One ul of the final RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems). Libraries were pooled in equimolar quantities and paired-end sequenced on an Illumina HiSeq 2500 platform using a High Throughput Run Mode flowcell and the V4 sequencing chemistry following Illumina’s recommended protocol to generate paired-end reads of 126-bases in length.

tag: treatment

tag: time


title: Acf_G_3


title: MTP2

city: Boston

first: Vandana

middle: A

last: Gupta

state: Massachusetts

address: 77 Avenue Louis pasteur, 168A

institute: Brigham and Women's Hospital

description: Polysomal RNA

data_processing:
Library strategy: Ribosome profiling
STAR was used to map sequencing reads to Mus musculus (mm10 build) reference genome
Gen expression counts were calculated using the program HTSeq for Mus musculus 10.0
R package edge R was used o make differential gene expression call.
Genome_build: mm10
Supplementary_files_format_and_content: text file with edgeR output

source_name: C2C12 myoblasts

extract_protocol:
Total RNA was purified by Trizol extractions. Polysomal RNA was isolated from purified polysomes by Trizol extraction
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: rna fraction

value: polysomal RNA

tag: cell line


title: RNA-Seq of CMI1.252 alone transfected into HEK293TT cells CMI1.252co

description: rRNA-depleted total RNA

tag: transfection


title: Acf_G_2


title: RNA-Seq of MSBI2.176 transfected into HEK293TT cells MSBI2.176_2

description: rRNA-depleted total RNA


title: 4_AP_1205


title: MTP3

description: Polysomal RNA


title: 2i-Jaki-BMP-Alk5i-day2 (II)


title: RNA-Seq of MSBI2.176 transfected into HEK293TT cells MSBI2.176

description: rRNA-depleted total RNA


title: MT3

description: Total RNA

data_processing:
STAR was used to map sequencing reads to Mus musculus (mm10 build) reference genome
Gen expression counts were calculated using the program HTSeq for Mus musculus 10.0
R package edge R was used o make differential gene expression call.
Genome_build: mm10
Supplementary_files_format_and_content: text file with edgeR output

value: Total cellular RNA


title: Acf_G_1


title: MNase-Seq Gal4DBD; N1(UAS-LacZ-mini-white) replicate 3

data_processing:
Paired-end reads were mapped to D. melanogaster genome assembly dm6. We used Bowtie v1.1.1 with “-X 750” parameter setting.
Dyad coverage vectors were obtained by size-selecting fragments of length >=120 and <=200 bp and resizing their length to 50 bp fixed at the fragment center
Genome_build: dm6
Supplementary_files_format_and_content: bedgraph files with dyad coverage

extract_protocol:
Eggs laid during a 6 hr period were collected and aged for a further two hours at 25°C. Subsequently, one gram embryos were dechorinated in 120 ml 1:5 diluted sodium hypochloride (VWR, Cat.no. 301696S) for 3 min, thoroughly washed and fixed in 10 ml fixing solution [0.1 M NaCl, 0.05 M HEPES pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1.8% Formaldehyde (FA; Sigma, Cat. No F1635) added to 30 ml n-Heptane (VWR, Cat. No. 8.22332.1000)] for 15 min at 16-18°C on a rotating wheel. Fixation was quenched by adding 125 mM glycine. The embryos were subsequently washed with PBS (including 0.01% Triton-X100) for 10 min and stored at -80°C. For nuclei isolation, embryos were slowly thawed and dounced using a glass homogenizer (Schubert, Cat.no. 9164693) with 20 strokes each of the A and B pestles in ice-cold NX-I buffer [15 mM HEPES pH 7.6, 10 mM KCl, 2 mM MgCl2, 0.5 mM EGTA, 0.1 mM EDTA, 350 mM sucrose, 1 mM DTT, 0.2 mM PMSF, Protease inhibitors Leupeptin, Pepstatin and Aprotinin (10 µg/ml)]. The lysate was filtered through Miracloth and nuclei were pelleted at 3,500 rpm, 10 min at 4°C. For MNase digestion, the nuclei were resuspended in the MNase digestion buffer. About 80 mg of nuclei were digested with 13 units of MNase (Sigma, Cat.no N5386) for 15 min, 37°C while shaking at 500 rpm. The reaction was stopped by adding 20 µl of 0.5 M EDTA, pH 8.0 and the tubes were quickly transferred to ice for 1 min. Nuclei were spun at 12,500 rpm, 10 min at 4°C. The supernatants containing most of the DNA were collected and the buffer composition was aDJ.gzusted to RIPA [1% Triton X-100, 0.1% Na deoxycholate, 140 mM NaCl, 10 mM Tris pH 8.0, 1 mM EDTA, 0.1% SDS, 1mM PMSF]. The digestion predominantly yielded mononucleosomes.
Recovered DNA was quantified using the Qubit® dsDNA HS Assay Kit (Life Technologies, Cat.no.Q32851) and sequencing libraries were prepared using the MicroPlex Library Preparation kit (Diagenode, Cat. No. C05010011) starting with 2 ng DNA whenever possible. PCR amplification was monitored by quantifying amplified libraries (maximum 19 cycles).

value: w1118; Gal4DBD; N1(UAS-LacZ-mini-white)

tag: developmental stage

value: 2-8 hour embryos

tag: replicate


title: 2i-Jaki-day5 (II)


title: MT2

description: Total RNA

tag: genotype


title: RNA-Seq of MSBI1.176 transfected into HEK293TT cells MSBI1.176_2

description: rRNA-depleted total RNA


title: CDX2-GFP-positive-sorted-ESCs-from-2i-Jaki-BMP-Alk5i-day2 (II)


title: MNase-Seq Acf-Gal4DBD; N1(UAS-LacZ-mini-white) replicate 3


title: MT1

description: Total RNA


title: 2i-Jaki-BMP-Alk5i-day5 (II)


title: 2i-day5 (II)


title: WTP3

description: Polysonal RNA

value: wildtype


title: MTP1

description: Polysomal RNA


title: RNA-Seq of CMI3.168 transfected into HEK293TT cells CMI3.168_3

description: rRNA-depleted total RNA


title: mesoderm-progenitor-day4 (II)


title: RNA-Seq of CMI3.168 transfected into HEK293TT cells CMI3.168_2

description: rRNA-depleted total RNA


title: MNase-Seq Acf-Gal4DBD; N1(UAS-LacZ-mini-white) replicate 2


title: MNase-Seq Gal4DBD; N1(UAS-LacZ-mini-white) replicate 2


title: mesoderm-progenitor-day3 (II)


title: WTP1

description: Polysomal RNA


title: TSC-day2 (I)

data_processing:
Illumina CASAVA v1.8.2 software used for basecalling.
Reads were trimmed for adapters and a phred33 quality cutoff of 20 using TrimeGalore paired end mode with cutadapt
Genes were aligned to the mouse genome and the number of reads per gene were counted using STAR 2.4.2a with --quantMode GeneCounts
Genome_build: Ensembl NCBIM37
Supplementary_files_format_and_content: Tab delimited files of transcript counts as outputed by STAR
Column headers:
column 1:  gene ID
column 2:  counts for unstranded RNA-seq
column 3:  counts for the 1st read strand aligned with RNA
column 4:  counts for the 2nd read strand aligned with RNA
We used column 2 for unstranded RNA-seq

source_name: TSC


title: MNase-Seq Gal4DBD-Acf; N1(UAS-LacZ-mini-white) replicate 3


title: RNA-Seq of CMI3.168 transfected into HEK293TT cells CMI3.168

description: rRNA-depleted total RNA


title: WT3

description: Total RNA


title: 2i-Jaki-BMP-Alk5i-day2 (I)


title: RNA-Seq of MSBI1.176 transfected into HEK293TT cells MSBI1.176_3

description: rRNA-depleted total RNA


title: MNase-Seq Gal4DBD-Acf; N1(UAS-LacZ-mini-white) replicate 2


title: 2i-Jaki-day2 (I)


title: MNase-Seq Gal4DBD; N1(UAS-LacZ-mini-white) replicate 1


title: RNA-Seq of CMI1.252 transfected into HEK293TT cells CMI1.252_3

description: rRNA-depleted total RNA


title: WT2

description: Total RNA


title: RNA-Seq of CMI1.252 transfected into HEK293TT cells CMI1.252_2

description: rRNA-depleted total RNA


title: MNase-Seq Acf-Gal4DBD; N1(UAS-LacZ-mini-white) replicate 1


title: RNA-Seq of MSBI1.176 transfected into HEK293TT cells MSBI1.176

description: rRNA-depleted total RNA


title: WT1

description: Total RNA


title: RNA-Seq of CMI1.252 transfected into HEK293TT cells CMI1.252

description: rRNA-depleted total RNA


title: WTP2

description: Polysomal RNA


title: MNase-Seq Gal4DBD-Acf; N1(UAS-LacZ-mini-white) replicate 1


title: 2i-day2 (I)


title: NF2.veh

status: Public on Feb 04 2018

city: St Louis

first: Susana

last: Gonzalo

state: MO

address: 1100 S Grand Blvd

department: Biochemistry and Molecular Biology

institute: Saint Louis University

description:
[processed data file:]
NF.vs.HGPS.xlsx

data_processing:
Basecalling and quality filtering was performed by Torrent Suite version 4 software using the default settings
Alignment to human genome sequence was performed using TMAP map4 algorithm with 5' and 3' softclipping and a minimum seed length of 20 nt
The strand specific total sequencing base pair coverage in all non-redundant exons was summed for all annotated genes in each sample and normalized to total coverage using bedtools, custom R code, and Microsoft Excel as described in Wu et al. 2015 PLoS Genetics Nov 6;11(11):e1005655.
Genome_build: Homo sapiens release hg19
Supplementary_files_format_and_content: Microsoft Excel files with normalized basepair coverage for annotated genes

source_name: cultured fibroblasts

growth_protocol: Normal human primary fibroblasts (NF) and HGPS fibroblasts were grown in culture in complete DMEM-HG media, containing 10% FBS, antibiotic, and antimycotics.

extract_protocol:
NF and HGPS fibroblasts supplemented with 10-7 M 1,25D (1α,25-dihydroxyvitamin D3; Sigma-Aldrich) or FBS for 4 to 90 days were used to extract total RNA using Aurum Total RNA Mini Kit (Bio-Rad) with DNaseI treatment following the manufacturer’s protocol.
IonXpressRNA barcoded sequencing libraries were constructed using the Eukaryotic Ribominus and Ion Total RNA-seq v2 kits (Life Technologies) according to the manufacturer's directions.

treatment_protocol: Calcitriol, the most bioactive form of vitamin D (1,25D 100 nM) resuspended in FBS was added to cells growing in culture every 3 days for a total of 4 or 90 days.  Cells were collected, and RNA extracted.

value: Vehicle (FBS) treatment for 1-3 months

tag: cell type

value: cultured fibroblasts

tag: disease state

value: normal


title: NF4.veh.short.1

description:
[processed data file:]
NF.short.xlsx
NF.vs.HGPS.xlsx

value: Vehicle (FBS) treatment for 4 days


title: NF4.veh.short.3


title: NF4.veh

description:
[processed data file:]
NF.vs.HGPS.xlsx


title: NF4.calc.short.2

description:
[processed data file:]
NF.short.xlsx

value: Calcitrol (1,25D) treatment for 4 days


title: NF4.veh.short.2


title: HGPS5.veh.short.1

description:
[processed data file:]
HGPS5.short.xlsx
NF.vs.HGPS.xlsx

value: HGPS


title: HGPS5.calc.short.3

description:
[processed data file:]
HGPS5.short.xlsx


title: HGPS5.calc.short.2

description:
[processed data file:]
HGPS5.short.xlsx


title: NF4.calc.short.1

description:
[processed data file:]
NF.short.xlsx


title: HGPS5.calc.short.1

description:
[processed data file:]
HGPS5.short.xlsx


title: HGPS5.veh.short.3


title: HGPS9.veh.long

description:
[processed data file:]
HGPS.long.xlsx
NF.vs.HGPS.xlsx

value: Vehicle (FBS) treatment for 3 months


title: HGPS9.calc.long

description:
[processed data file:]
HGPS.long.xlsx

value: Calcitrol (1,25D) treatment for 3 months


title: HGPS3.veh.long


title: HGPS3.calc.long

description:
[processed data file:]
HGPS.long.xlsx


title: HGPS2.calc.long

description:
[processed data file:]
HGPS.long.xlsx


title: NF4.calc.short.3

description:
[processed data file:]
NF.short.xlsx


title: WT_3

city: Bethesda

first: Derek

last: Gildea

state: MD

address: 12 South Drive Rm 4009-24

institute: NHGRI/NIH

data_processing:
RNA from each sample was sequenced on two separate lanes, obtaining paired-end reads that were 101 bp in length. RNA-seq reads that passed the Illumina platform quality check were used for downstream analyses.
RNA-seq reads were aligned to the mouse mm9 reference genome sequence with the STAR (v. 2.3.0e) software using default parameters.
RNA-seq reads that mapped to genomic locations for known rRNAs (obtained from the UCSC genome browser) were filtered using split_bam.py included in the RSeQC package (v. 2.3.7).
RNA-seq read counts were calculated with the htseq_count (v. 0.5.3p3) software using annotations for protein coding genes obtained from Ensembl (release 67), thus obtaining counts for RNA-seq reads that mapped unambiguously to Ensembl gene models.
RNA-seq read counts were used for differential gene expression analysis performed with DESeq2.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file containing 2 columns: (1) Ensembl ID or other descriptor and (2) corresponding RNA-seq raw read count

source_name: WT, melanocyte stem cells

extract_protocol:
Melanocyte stem cells were isolated from dissociated dermis using flow cytometry, and subesquently harvested in TRIzol reagent. Total RNA was purified using the Directzol RNA MiniPrep Kit (Zymo), and quantified on a Qubit fluorometer. RNA quality for RNA sequencing was assessed by Bioanalyzer (Agilent), and only samples with RIN scores >7.5 were used.
mRNA libraries were constructed from ~200 ng total RNA using the Illumina TruSeq RNA Sample Prep Kits, version 2.  The resulting cDNA was fragmented using a Covaris E210. Library amplification was performed using 16 cycles.  Unique barcode adapters were applied to each library.

tag: age

tag: strain

value: melanocyte stem cells


title: Mitf_1

source_name: Mitf, melanocyte stem cells


title: WT_2


title: HGPS5.veh.short.2


title: WT_1


title: KO HSCs

city: hangzhou

first: Hu

last: Wang

address: wenyixi road 1378

institute: hangzhou normal university

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using MACS14

source_name: KO HSCs

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

value: LT-HSC

tag: genotype/variation

value: SIRT6 KO

tag: chip antibody

value: H3K56ac (Active motif)


title: WT HSCs

source_name: WT HSCs

value: control


title: Intact after 240 hours rep2

status: Public on Feb 03 2018

city: Würzburg

first: Alexander

last: Gabel

address: Josef-Schneider-Str. 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

description: 240B Intact

data_processing:
Sequenced reads were trimmed for adaptor sequences with cutadapt 1.8.1
Low quality regions of reads were removed using sickle 1.33 with pe -q 20 -l 50 -g
Reads were aligned to protein-coding gene sequences using Bowtie 2. The read assignment was performed by using the eXpress. Library scaling factors were inferred from the sum of the number of reads assigned to the genes in the lowest seventy-five percentiles of expressed genes for each library.
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: tab-delimited text files include library size and gene length normalized expression values and library size normalized expression values for each sample

organism: Arabidopsis thaliana

source_name: Hypocotyl tissue

growth_protocol: Seven day old Arabidopsis seedlings were grown vertically on Murashige and Skoog (MS) medium + 1% bacto agar (pH5.7; no sucrose) in short day conditions (8 hours of 80-100 µmol m-2 s-1 light) at 20°C.

extract_protocol:
RNA was extracted using an RNeasy Kit (Qiagen, UK) following the manufacturer’s instructions including on column DNase digestion. RNA was eluted from the column with 50ul of sterile water.
90-100ng of RNA was used to prepare RNA-seq libraries using the TruSeq® Stranded mRNA LT kit (Illumina, UK) according to the manufacturer’s instructions. The final PCR was for 15 cycles and samples were. Each sample had two libraries prepared from grafted tissues or separated tissues at different times so that independent biological replicates were made. Samples were diluted to 10nM and 11-12 barcoded samples randomly mixed to make a total of 7 mixes for 7 flow lanes, one mix per lane. resuspended in 23ul of distilled water

treatment_protocol: Seedlings were placed on one layer of 2.5x4cm sterile Hybond N membrane (GE Healthcare) on top of two 8.5cm circles of sterile 3 Chr Whatman paper (Scientific Laboratory Supplies) moisten with sterile distilled water in a 9cm petri dish. In a laminar flow hood using a dissecting microscope, one cotyledon was removed (intact treatment) and, in other treatments, a transverse cut was also made through the hypocotyl using a vascular dissecting knife. Plants were left separated (separated treatment) or they were assembled by aligning two cut halves of different plants and joining them together (grafted treatment), after which, petri dishes was sealed with parafilm and placed vertically under short day conditions at 20°C.

tag: hours after grafting

value: 240 hours

tag: condition

value: Intact

tag: ecotype


title: Separated bottom after 240 hours rep2

description: 240B Separated bottom

source_name: Hypocotyl tissue below graft junction

value: Separated bottom


title: Separated top after 240 hours rep2

description: 240B Separated top

source_name: Hypocotyl tissue above graft junction

value: Separated top


title: HGPS2.veh.long

tag: treatment


title: Separated top after 240 hours rep1

description: 240A Separated top


title: Mitf_3


title: Intact after 168 hours rep1

description: 168A Intact

value: 168 hours


title: Grafted top after 240 hours rep1

description: 240A Grafted top

value: Grafted top


title: Intact after 168 hours rep2

description: 168B Intact


title: Separated top after 168 hours rep1

description: 168A Separated top


title: Grafted top after 168 hours rep1

description: 168A Grafted top


title: Separated bottom after 168 hours rep1

description: 168A Separated bottom


title: Grafted top after 168 hours rep2

description: 168B Grafted top


title: Separated top after 168 hours rep2

description: 168B Separated top


title: Separated top after 120 hours rep2

description: 120B Separated top

value: 120 hours


title: Grafted bottom after 240 hours rep2

description: 240B Grafted bottom

value: Grafted bottom


title: Grafted top after 240 hours rep2

description: 240B Grafted top


title: Grafted bottom after 168 hours rep1

description: 168A Grafted bottom


title: Intact after 240 hours rep1

description: 240A Intact


title: Separated bottom after 120 hours rep2

description: 120B Separated bottom


title: Intact after 120 hours rep2

description: 120B Intact


title: Grafted bottom after 168 hours rep2

description: 168B Grafted bottom


title: Separated top after 120 hours rep1

description: 120A Separated top


title: Separated bottom after 240 hours rep1

description: 240A Separated bottom


title: Grafted bottom after 240 hours rep1

description: 240A Grafted bottom


title: Separated bottom after 168 hours rep2

description: 168B Separated bottom


title: Grafted top after 120 hours rep2

description: 120B Grafted top


title: Intact after 120 hours rep1

description: 120A Intact


title: Separated bottom after 120 hours rep1

description: 120A Separated bottom


title: Grafted top after 120 hours rep1

description: 120A Grafted top


title: Grafted bottom after 120 hours rep2

description: 120B Grafted bottom


title: Separated top after 72 hours rep2

description: 72B Separated top

value: 72 hours


title: Separated bottom after 72 hours rep2

description: 72B Separated bottom


title: Grafted bottom after 120 hours rep1

description: 120A Grafted bottom


title: Intact after 72 hours rep2

description: 72B Intact


title: Intact after 72 hours rep1

description: 72A Intact


title: Grafted top after 72 hours rep2

description: 72B Grafted top


title: Separated bottom after 48 hours rep1

description: 48A Separated bottom

value: 48 hours


title: Separated top after 48 hours rep2

description: 48B Separated top


title: Grafted top after 72 hours rep1

description: 72A Grafted top


title: Grafted bottom after 72 hours rep1

description: 72A Grafted bottom


title: Intact after 48 hours rep2

description: 48B Intact


title: Separated bottom after 48 hours rep2

description: 48B Separated bottom


title: Grafted bottom after 72 hours rep2

description: 72B Grafted bottom


title: Grafted top after 48 hours rep1

description: 48A Grafted top


title: Grafted bottom after 48 hours rep2

description: 48B Grafted bottom


title: Intact after 48 hours rep1

description: 48A Intact


title: Grafted top after 48 hours rep2

description: 48B Grafted top


title: Separated top after 24 hours rep2

description: 24B Separated top

value: 24 hours


title: Grafted bottom after 48 hours rep1

description: 48A Grafted bottom


title: Separated top after 24 hours rep1

description: 24A Separated top


title: Separated top after 72 hours rep1

description: 72A Separated top


title: Separated bottom after 24 hours rep2

description: 24B Separated bottom


title: Separated bottom after 72 hours rep1

description: 72A Separated bottom


title: Intact after 24 hours rep1

description: 24A Intact


title: Separated bottom after 24 hours rep1

description: 24A Separated bottom


title: Intact after 24 hours rep2

description: 24B Intact


title: Grafted top after 24 hours rep2

description: 24B Grafted top


title: Separated top after 48 hours rep1

description: 48A Separated top


title: Separated top after 12 hours rep2

description: 12B Separated top

value: 12 hours


title: Grafted bottom after 24 hours rep2

description: 24B Grafted bottom


title: Grafted top after 24 hours rep1

description: 24A Grafted top


title: Grafted bottom after 24 hours rep1

description: 24A Grafted bottom


title: Separated top after 12 hours rep1

description: 12A Separated top


title: Separated bottom after 12 hours rep1

description: 12A Separated bottom


title: Separated bottom after 12 hours rep2

description: 12B Separated bottom


title: naïve-1

city: New Haven

first: Anna

middle: Marie

last: Pyle

state: CT

address: 219 Prospect St.

institute: Yale University

data_processing:
Sequenced reads were checked for quality control using the FastQC tool (Babraham Bioinformatics, Babraham Institute, Cambridge, UK). Good quality reads were mapped to the reference genome (GRCm38/mm10) using the software package Tophat v 2.0.6. Default settings were used, except for the mean inner mate distance between the pairs that was set to 150bp. A maximum of two mismatches and a minimum length of 36 bp per segment were allowed.
The BAM files from Tophat were then converted to SAM format by Samtools (v 1.4) and raw counts estimated by the Python script HTSeq count. Reference GTF file for gene annotation was downloaded from iGenomes website.
EdgeR was used to calculate normalized gene expression levels, represented as counts per million (CPM).  CPMs were calculated for 39,169 transcripts from the Ensembl database.
Genome_build: GRCm38
Supplementary_files_format_and_content: CSV file contains CPM values for annotated transcripts for all samples

source_name: naïve, spleen

extract_protocol:
Tissues collected into RNAlater were blotted dry and transferred into Trizol (Thermo Fisher Scientific) in a Lysing Matrix D tube (MP Biomedical) for homogenization.  Supernatant was collected for chloroform phase separation and RNA was precipitated using isopropyl alcohol.  The RNA pellet was then washed with 75% ethanol and redissolved in water.
Libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500ng of purified total RNA according to the manufacturer’s protocol.

treatment_protocol: SLRs were complexed to in vivo-jetPEI® (Polyplus transfection) according to manufacturer’s instructions, with N/P ratio = 8.  25 µg of RNA in a 200 µl volume was injection per mouse intravenous

tag: agent

value: naïve

tag: tissue

value: spleen


title: naïve-2


title: naïve-3


title: vehicle-2

source_name: vehicle, spleen

value: vehicle


title: Grafted top after 12 hours rep2

description: 12B Grafted top


title: Grafted bottom after 12 hours rep2

description: 12B Grafted bottom


title: Grafted top after 12 hours rep1

description: 12A Grafted top


title: vehicle-1


title: Intact after 12 hours rep1

description: 12A Intact


title: Separated top after 6 hours rep2

description: 6B Separated top

value: 6 hours


title: pppNS-3

source_name: pppNS, spleen

value: pppNS


title: pppNS-2


title: Separated top after 6 hours rep1

description: 6A Separated top


title: pppNS-1


title: Separated bottom after 6 hours rep2

description: 6B Separated bottom


title: Intact after 6 hours rep2

description: 6B Intact


title: Separated bottom after 6 hours rep1

description: 6A Separated bottom


title: Intact after 6 hours rep1

description: 6A Intact


title: Intact after 12 hours rep2

description: 12B Intact


title: SLR14-3

source_name: SLR14, spleen


title: polyIC-1

source_name: polyIC, spleen

value: polyIC


title: polyIC-2


title: Grafted bottom after 12 hours rep1

description: 12A Grafted bottom


title: Grafted top after 6 hours rep2

description: 6B Grafted top


title: SLR14-2


title: delta_pSymAB_ETR+_1

city: Hamilton

first: Turlough

middle: M

last: Finan

address: 1280 Main St. W.

department: Department of Biology

institute: McMaster University

data_processing:
As a quality control step, FastQC was run on all sequencing samples.  Reads were trimmed with cutadapt with options to ensure quality of 25 from both ends, minimum size of 20 nts, and no Ns at the ends.  Each replicon of the S. meliloti Rm2011 genome were individually indexed with Burrows-Wheeler Aligner (bwa), bwa was then used to index and map the reads to each replicon, and htseq-count used to count the number of reads to each annotated gene.  Differential expression analysis was finally performed using DESeq2, with data the analysis run independently on each replicon.
Genome_build: Reads were mapped to the S. meliloti Rm2011 reference genome (NC_020528, NC_020527, NC_020560).
Supplementary_files_format_and_content: Three Excel files, one for each replicon in the S. meliloti genome.  Each file contains three providing the processed data for each sample.  Each line represents a distinct feature (CDS or RNA) of the genome.  The columns include: gene numerical ID, gene name, gene identifier, annotated protein function, log2(fold change) for each sample relative to the average of the wild-type (RmP3499) data, adjusted p-values for each comparison relative to wild-type (RmP3499).  In each file, one table provides the data for all features on the replicon, a second table provides the data for just the up-regulated genes (expression fold difference of at least two fold, adjusted p-value <= 0.01), and a third table provides the data for just the down-regulated genes (expression fold difference of at least two fold, adjusted p-value <= 0.01).

organism: Sinorhizobium meliloti

source_name: Bacterial cells

growth_protocol: S. meliloti strains were grown in M9-sucrose medium (41 mM Na2HPO4, 22 mM KH2PO4, 8.6 mM NaCl, 18.7 mM NH4Cl, 4.1 mM biotin, 42 nM CoCl2, 1 mM MgSO4, 0.25 mM CaCl2, 38 mM FeCl3, 5 µM thiamine-HCl, 10 mM sucrose) in duplicate.  Cultures were pelleted, washed once with M9-sucrose, and resuspended in M9-sucrose.  Cell suspensions were used to inoculate 100 mL cultures of M9-sucrose to a starting OD600 ~ 0.1.  Cultures were grown with shaking at 30°C and cells harvested when cultures reached an OD600 ~ 0.7.

extract_protocol:
Samples were kept on ice or at 4°C throughout the process except where indicated.  Each cell pellet was resuspended in 480 µL of resuspension solution (10 µL of 14.26 M β-mercaptoethanol per 1 mL of nuclease-free ddH2O) and transferred to a nuclease-free 1.5 mL centrifuge tube.  Cell suspensions were then mixed with 480 µL of room temperature hot phenol solution (per 6 mL: 5 mL of hot phenol buffer [20 mM Tris-HCl pH 7.5, 400 mM NaCl, 40 mM EDTA, 1% SDS, in nuclease-free ddH2O] and 1 mL unbuffered phenol), vigorously vortexed for 30 seconds, and incubated in a water bath at 95°C for 1 minute.  Samples were centrifuged at 16,000 g for 10 minutes at 4°C, and the supernatant was transferred to a fresh 1.5 mL nuclease-free centrifuge tube.  The supernatants were treated with two rounds of unbuffered-phenol:chloroform (1:1) extraction, followed by one round of chloroform extraction.  The nucleic acids were then precipitated by mixing the supernatant with one-tenth sample volume of 3 M sodium acetate and 2x sample volume of isopropanol, mixing, and the mixture was incubated on ice for 30 minutes.  The nucleic acids were pelleted by centrifugation at 16,000 g for 10 minutes, the pellet washed with ice cold 70% ethanol, and air dried.  The pellet was resuspended in 80 µL of nuclease-free ddH2O, mixed with 10 µL DNase I buffer and 10 µL DNase I (20 units; NEB catalog # M0303S), and incubated for 20 minutes at room temperature.  The 100 µL sample was then transferred to a fresh 1.5 mL nuclease-free centrifuge tube, extracted once with unbuffered-phenol:chloroform (1:1) and once with chloroform, and the RNA precipitated as before.  The RNA pellet was resuspended in 100 µL water, the integrity of the RNA confirmed as described below, and the remainder of the sample stored at -80°C until further use.
RNA libraries were prepared for sequencing using standard Illumina protocols by the Farncombe Family Digestive Health Research Institute located at McMaster University (Hamilton, Ontario, Canada). Ribosomal RNA was depleted using Ribo-Zero rRNA Removal kits (Illumina).

treatment_protocol: Cultures were harvested by immediately mixing 45 mL of culture with 5 mL of ice-cold cell stop solution (5% unbuffered phenol, 95% ethanol).  Cells were pelleted by centrifugation at 3,700 g at 4°C for 10 minutes, and the pellets flash frozen with liquid nitrogen.  Frozen pellets were stored at -80°C until use.

value: delta_pSymAB with the ETR region of S. fredii NGR234


title: Grafted top after 6 hours rep1

description: 6A Grafted top


title: Grafted bottom after 6 hours rep2

description: 6B Grafted bottom


title: SLR14-1


title: Grafted bottom after 6 hours rep1

description: 6A Grafted bottom


title: Wild_type_2

description:
Processed_chromosome_data.xlsx
Processed_pSymB_data.xlsx
Processed_pSymA_data.xlsx

value: delta_pSymAB with pSymAB re-introduced


title: delta_pSymA_2

description:
Processed_chromosome_data.xlsx
Processed_pSymB_data.xlsx

value: delta_pSymAB with pSymB re-introduced


title: Wild_type_1


title: SLR10-2

source_name: SLR10, spleen


title: Intact at 0 hours rep2

description: 0B Intact

value: 0 hours

value: Intact


title: SLR10-1


title: delta_pSymB_1

description:
Processed_chromosome_data.xlsx
Processed_pSymA_data.xlsx

value: delta_pSymAB with pSymA re-introduced


title: delta_pSymB_2


title: delta_pSymAB_2


title: delta_pSymA_1


title: delta_pSymAB_1


title: Intact at 0 hours rep1

description: 0A Intact


title: INPUT ChIP-seq Mixed_male

status: Public on Feb 02 2018

city: Amsterdam

first: Wilbert

last: Zwart

address: Plesmanlaan 121

country: Netherlands

institute: The Netherlands Cancer Institute

data_processing:
Sequences were generated by the Illumina Hiseq 2000 genome analyser (using 50bp reads) and were processed by the Illumina pipeline.
Reads were aligned to the Human Reference Genome (hg19) using BWA version 0.5.9. Reads with a BWA alignment quality score less than 20 were removed.
Peaks were called using DFilter (Kumar V et al. Nat Biotechnol 2013;31(7):615-22) and MACS peak caller version 1.4 (Zhang Y et al. Genome Biol 2008;9(9):R137). Only peaks called by both algorithms were used for the analysis. MACS was run with the default parameters, except p=10-7 for ChIP-seq data. DFilter was run with bs=100, ks=50 for FAIRE data and bs=50, ks=30, refine, nonzero for ChIP data.
Genome_build: hg19
Supplementary_files_format_and_content: peak.intersect files contain peaks called by both peak calling algorithms in bed format

source_name: Human breast tumor

extract_protocol:
Tissue was defrosted and crosslinked in solution A (50 mM Hepes, 100 mM NaCl, 1mM EDTA, 0.5 mM EGTA, pH= 7.4) containing 2 mM DSG, incubated for 25 minutes at room temperature while rotating. After 25 minutes formaldehyde was added to 1% final and incubated another 20 minutes at room temperature with rotation. Samples were quenched by adding a surplus of 0.2M glycine, pelleted by centrifugation (5'@4000rcf 4°C), washed with cold PBS and mechanically disrupted in cold PBS using a pellet pestle (Sigma). The PicoBioruptor (Diagenode) was used for sonication. For ChIP, antibodies were used to detect ERα (sc-543, Santa Cruz), AR (sc-816, Santa Cruz), FOXA1 (sc-6554, Santa Cruz), PR (sc-7208, Santa Cruz), GR (12041S lot 3, Cell Signaling Technology) and H3K4me1 (ab8895, AbCam). Immunoprecipitated DNA was prepared for Illumina multiplex-sequencing with 10 samples per lane at 65bp single end. For steroid hormone receptor ChIPs, 5µg of antibody and 50µl dynabeads (Invitrogen) were used, for FOXA1 and H3K4me1, 4µg of antibody and 40µl magnetic beads were used.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

tag: antibody

value: INPUT

tag: patient id

value: Human breast tumor

tag: Sex

value: male


title: INPUT ChIP-seq MCF7

tag: cell line

value: Human breast tumor, pleural effusion

value: female


title: H3K4me1 ChIP-seq Male_19

description: No quantified data produced for H3K4me1 ChIP-seq samples. Data were used for heatmap not included in the GEO records.

data_processing:
Sequences were generated by the Illumina Hiseq 2000 genome analyser (using 50bp reads) and were processed by the Illumina pipeline.
Reads were aligned to the Human Reference Genome (hg19) using BWA version 0.5.9. Reads with a BWA alignment quality score less than 20 were removed.
Peaks were called using DFilter (Kumar V et al. Nat Biotechnol 2013;31(7):615-22) and MACS peak caller version 1.4 (Zhang Y et al. Genome Biol 2008;9(9):R137). Only peaks called by both algorithms were used for the analysis. MACS was run with the default parameters, except p=10-7 for ChIP-seq data. DFilter was run with bs=100, ks=50 for FAIRE data and bs=50, ks=30, refine, nonzero for ChIP data.
Genome_build: hg19
Supplementary_files_format_and_content: no processed data for H3K4me1 ChIP-seq samples.


title: H3K4me1 ChIP-seq Male_24


title: INPUT ChIP-seq Mixed_female


title: H3K4me1 ChIP-seq Male_5


title: H3K4me1 ChIP-seq Male_14


title: SLR10-3


title: H3K4me1 ChIP-seq Male_6


title: polyIC-3


title: H3K4me1 ChIP-seq Male_3


title: H3K4me1 ChIP-seq Male_13


title: PR ChIP-seq Male_30

value: PR


title: GATA3 ChIP-seq Male_15


title: PR ChIP-seq Male_29


title: PR ChIP-seq Male_26


title: GR ChIP-seq Male_21

value: GR


title: GR ChIP-seq Male_26


title: GR ChIP-seq Male_15


title: GR ChIP-seq Male_9


title: GR ChIP-seq Male_10


title: GR ChIP-seq Male_12


title: GR ChIP-seq Male_1


title: FOXA1 ChIP-seq Male_19


title: FOXA1 ChIP-seq Male_14


title: FOXA1 ChIP-seq Male_13


title: FOXA1 ChIP-seq Male_1


title: GATA3 ChIP-seq Male_16


title: GATA3 ChIP-seq Male_21


title: ScOE 2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to BDGP6 genome using TopHat v2.0.10 with default parameters
Cufflinks v2.2.1 was run for relative quantitation of genes expression and differential expression analysis.
Genome_build: Ensemble Drosophila melanogaster BDGP6
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: intestinal stem cells

extract_protocol:
Drosophila midgut were removed and digested using Elastase (Sigma, cat. no. E0258). About 10000 ISCs labeled with green fluorescent protein (GFP) were sorted using FACSAria II cell sorter (Becton Dickinson) and RNA was harvested using the  Arcturus PicoPure RNA isolation kit (Applied Biosystems). The RNA was then amplified using Arcturus RiboAmp HS PLUS RNA ampliﬁcation kit (Applied Biosystems).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: midgut

value: adult stage day 2

tag: genotype

value: Sc overexpression


title: FOXA1 ChIP-seq Male_3


title: AR ChIP-seq Male_28

value: AR


title: ScOE 4


title: ScOE 1


title: ScOE 3


title: FOXA1 ChIP-seq Male_6


title: AR ChIP-seq Male_30


title: AR ChIP-seq Male_26


title: PR ChIP-seq Male_28


title: AR ChIP-seq Male_18


title: Ctrl 2

value: Wild type


title: AR ChIP-seq Male_17


title: AR ChIP-seq Male_10


title: Ctrl 1


title: m8_Dam

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

source_name: midgut

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

value: m8 overexpression


title: Mitf_2

tag: cell type

value: melanocyte stem cells


title: Ctrl_Dam


title: FOXA1 ChIP-seq Male_4


title: AR ChIP-seq Male_7


title: ER ChIP-seq Male_28

value: ER


title: ER ChIP-seq Male_29


title: AR ChIP-seq Male_20


title: Ctrl 3


title: ER ChIP-seq Male_27


title: ER ChIP-seq Male_26


title: ER ChIP-seq Male_24


title: ER ChIP-seq Male_22


title: ER ChIP-seq Male_20


title: ER ChIP-seq Male_19


title: ER ChIP-seq Male_21


title: ER ChIP-seq Male_25


title: ER ChIP-seq Male_16


title: ER ChIP-seq Male_23


title: ER ChIP-seq Male_17


title: ER ChIP-seq Male_18


title: AR ChIP-seq Male_8


title: ER ChIP-seq Male_14


title: RNA-seq Male_27

first: Tesa

last: Severson

address: 121 Plesmanlaan

department: Molecular Carcinogensis

institute: Netherlands Cancer Institute

data_processing:
Sequences were generated by the Illumina Hiseq 2500 genome analyser (using 100bp paired end reads) and were processed by the Illumina pipeline.
Reads were aligned to the Human Reference Transcriptome (Ensembl GRCh37.75, hg19) using STAR version 2.5.0a.
HTSeq was used to count reads for all genes using the htseq-count command. Normalization was carried out using the 'rlog' method. Only samples which had at least 5 reads across each gene were retained for further analysis (n=46)
Genome_build: GRCh37.75
Supplementary_files_format_and_content: gene expression matrix of samples (columns) by transcript (rows)

extract_protocol:
30µm sections of frozen tumor tissues was cut for RNA-isolation. Total RNA was extracted using the mirVana miRNA isolation kit according to the manufacterer's protocol up to the end of F1. Total RNA samples having RIN>8 were subjected to library generation.
Strand-specific libraries were prepared according to Illumina's instructions accompanying the mRNA Sample Kit (Part# RS-12221101/2).

tag: patient

value: primary breast tumor

tag: procedure

value: RNA-seq


title: RNA-seq Male_49


title: ER ChIP-seq Male_13


title: ER ChIP-seq Male_15


title: ER ChIP-seq Male_30


title: RNA-seq Male_26


title: ER ChIP-seq Male_12


title: ER ChIP-seq Male_11


title: RNA-seq Male_47


title: RNA-seq Male_25


title: ER ChIP-seq Male_8


title: ER ChIP-seq Male_9


title: RNA-seq Male_24


title: ER ChIP-seq Male_7


title: ER ChIP-seq Male_6


title: RNA-seq Male_23


title: DKK2_rep2

first: Weijia

address: 10 Amistad St

data_processing:
Images acquired from the HiSeq2000 are processed through the bundled Illumina image extraction pipeline (CASAVA) to get the sequence and quality score for each base.
Raw sequence reads were mapped to mm9 using TopHat (Galaxy Version 2.1.0).
The raw counts were then normalized using the trimmed mean of M values (TMM) method and compared using the Bioconductor package “edgeR”.
Reads per kilobase per million (RPKM) mapped reads were calculated by ENCODE annotation M1 using cuffdiff (Galaxy Version 2.1.0)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Natural killer cells

growth_protocol: Mouse primary NK cells were isolated from the spleens and cultured in the presence of 50 ng/ml recombinant murine IL-15 for 24 hours.

extract_protocol:
mRNA was isolated and purified by using RNeasy Plus Mini Kit (Qiagen).
RNA-Seq libraries were prepared using the TrueSeq Stranded Total RNA Library Prep Kit (Illumina).

treatment_protocol: Mouse primary NK cells were treated with mock or 200ng/ml DKK2 for another 24 hours.

value: Primary natural killer cells

tag: strain

value: 200ng/ml DKK2

tag: age

value: post natal day 56


title: RNA-seq Male_45


title: DKK2_rep1


title: ER ChIP-seq Male_3

value: Human breast tumor

value: male


title: RNA-seq Male_46


title: RNA-seq Male_48


title: RNA-seq Male_22


title: ER ChIP-seq Male_4


title: RNA-seq Male_21


title: Control_rep2

value: Mock


title: ER ChIP-seq Male_5


title: Control_rep1


title: ER ChIP-seq Male_10


title: ER ChIP-seq Male_2


title: ER ChIP-seq Male_1


title: sRNA_Ago2KO-AGO1dox_A [miRNA-seq]

city: Zurich

first: Constance

last: Ciaudo

email: cciaudo@ethz.ch, ciaudobeyer@gmail.com

address: Otto-Stern-Weg 7

department: D-BIOL

institute: ETH

description: Single stranded TrueSeq illumina small RNA library Protocol

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to mm10 and mature miRNAs (miRbase r21) using Bowtie allowing up to 2 mismatches, multiple mappers were randomly matched to single position
reads counts from bowtie alignement were parsed against mature miRNA index (miRbase r21)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw read count

source_name: Ago2KO1-AGO1_A with Dox cells

growth_protocol: mESCs were cultured in DMEM, 15% serum, 100 U/mL LIF, 01. mM Beta-mercaptoethanol, 1% Pen/Strep on0.2% gelatine coated plates. Stable cell lines expressing AGO1 were maintained in 2µg/mL of puromycin.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq Small RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina True-seq protocols by the Functional Genomic Center Zurich (Switzerland)

treatment_protocol: Cells were induced with 1µg/mL of doxycycline.

tag: strain background

tag: genotype/variation

value: Ago2KO1-AGO1; Ago2 knockout inducible ectopic expression AGO1

value: Blastocyst; mouse ES cells

tag: induced with

value: 1µg/mL of doxycycline

tag: molecule subtype

value: small RNA


title: RNA-seq Male_19


title: sRNA_Ago2KO-AGO1nodox_B [miRNA-seq]

source_name: Ago2KO1-AGO1_A cells


title: RNA-seq Male_18


title: GR ChIP-seq MCF-7

value: GR

value: Human breast tumor, pleural effusion

value: female


title: sRNA_Ago2KO-AGO1dox_B [miRNA-seq]


title: sRNA_Ago2KO-AGO1nodox_A [miRNA-seq]


title: RNA-seq Male_44


title: AR ChIP-seq Female_8

value: AR


title: AR ChIP-seq MCF-7


title: ER ChIP-seq Female_8

value: ER


title: sRNA_Ago2KO2 [miRNA-seq]

source_name: Ago2KO2 cells

value: Ago2KO; Ago2 knockout


title: RNA-seq Male_17

value: primary breast tumor

value: RNA-seq


title: RNA-seq Male_43


title: RNA-seq Male_20


title: RNA-seq Male_16


title: sRNA_E14_A [miRNA-seq]

source_name: E14 cells

value: wild type


title: sRNA_Ago2KO1 [miRNA-seq]

source_name: Ago2KO1 cells


title: sRNA_E14_B [miRNA-seq]


title: FOXA1 ChIP-seq Femlae_7


title: FOXA1 ChIP-seq Female_5


title: RNA-seq Male_42


title: RNA-seq Male_41


title: RNA-seq Male_40


title: ER ChIP-seq Female_6


title: RNA-seq Male_39


title: FOXA1 ChIP-seq Female_3


title: RNA-seq Male_38


title: RNA-seq Male_37


title: FOXA1 ChIP-seq Female_4


title: sRNA_Ago2KO1_XEN

source_name: Ago2KO1 XEN cells

growth_protocol: mESC were cultured in DMEM, 15% serum, 100 U/mL LIF, 01. mM Beta-mercaptoethanol, 1% Pen/Strep on gelatine coated plates.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq Small RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries and 20-100 ng for the IP libraries.
Small RNA libraries were prepared for sequencing using standard Illumina protocols by the Fasteris company (Switzerland).
small RNA-Seq

treatment_protocol: Cells were crosslinked with formaldehyde and AGO1/2 IP was performed.

value: E14 cells 129/Ola background

value: Blastocyst mouse ES cells

tag: treatment

value: not crosslinked

value: Ago2 knockout


title: sRNA_Ago1KO1_IP_Ago1

source_name: IP Ago1 in Ago1KO cells

value: Formaldehyde crosslink IP

value: Ago1 knockout


title: sRNA_E14_XEN_B

source_name: E14 XEN cells B

value: Wild Type


title: sRNA_E14_XEN_A

source_name: E14 XEN cells A


title: delta_pSymAB_ETR+_2

value: delta_pSymAB with the ETR region of S. fredii NGR234


title: FOXA1 ChIP-seq Female_6

value: Human breast tumor


title: FOXA1 ChIP-seq Female_2


title: RNA-seq Male_15


title: RNA-seq Male_36


title: RNA-seq Male_14


title: sRNA_Ago2KO1_IP_Ago1

source_name: IP Ago1 in Ago2KO cells


title: sRNA_Ago2KO2_XEN

source_name: Ago2KO2 XEN cells


title: FOXA1 ChIP-seq Female_1


title: sRNA_E14_IP_Ago1

source_name: IP Ago1 in E14 cells


title: sRNA_Ago2KO1_IP_Ago2

source_name: IP Ago2 in Ago2KO cells


title: ER ChIP-seq Female_3

source_name: Human breast tumor


title: sRNA_E14_IP_Ago2

source_name: IP Ago2 in E14 cells


title: ER ChIP-seq Female_2


title: RNA-seq Male_13


title: ER ChIP-seq Female_1


title: ER ChIP-seq Female_5


title: sRNA_Ago1KO2

source_name: IP input Ago1KO2 cells

value: Formaldehyde crosslink


title: sRNA_Ago1KO1

source_name: IP input Ago1KO1 cells


title: RNA-seq Male_9


title: SRpP55 KD (siSR#2) exposed 5

city: Brussels

first: Jonas

last: Juan Mateu

address: Route de Lennik 808 CP 618

department: Faculty of Medecine

country: Belgium

institute: Universite Libre de Bruxelles

data_processing:
Sequencing reads were mapped to the Homo sapiens genome (version GRCh37/hg19) using the program Tophat (http://ccb.jhu.edu/software/tophat/index.shtml) using default options the GENCODE 18 annotation of genes transcripts. The Tophat mapper reports all mappings and split-mappings.
GTF files: Mapped reads were used to quantify human transcripts from the GENCODE 18 annotation dataset, using the Flux Capacitor approach that deconvolves reads mapping to exonic regions shared by multiple transcripts by optimizing a system of linear equations and thus obtains a number of reads specifically assigned to each alternative spliceform (http://flux.sammeth.net). All genes and transcripts have been assigned a relative coverage rate as measured in RPKM units ("reads per kilobase per million mapped reads").
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: The processed data files are in standard transcript GTF format (for the full format description see http://www.ensembl.org/info/website/upload/gff.html). The attributes column contains informations on the transcript length, transcript abundance quantification RPKM (reads per kilobase per million mapped reads) and the number of read that mapped to it.

source_name: EndoC-beta H1 human cell line

growth_protocol: Human insulin-producing EndoC-βH1 cells (Scharfmann et al., 2014) were grown on matrigel/fibronectin (100 and 2 μg/mL, respectively) coated plates and cultured in DMEM medium as previously described

extract_protocol:
Total RNA was isolated from Maria using the RNeasy Mini kit (Qiagen, Venlo, The Netherlands) which favours purification of RNA molecules longer than 200 nucleotides. mRNA was purified from 1 μg total RNA using oligo (dT) beads, before it was fragmented and randomly primed for reverse transcription followed by second-strand synthesis to create ds cDNA fragments.
mRNA was purified from 1 µg total RNA using oligo (dT) beads, before it was fragmented and randomly primed for reverse transcription followed by second-strand synthesis to create ds cDNA fragments. The generated cDNA had undergone paired-end repair to convert overhangs into blunt ends. After 39- monoadenylation and adaptor ligation, cDNAs were purified on a 2% agarose gel and 200 basepair (bp) products were excised from the gel. Following gel digestion, purified cDNA was amplified by PCR using primers specific for the ligated adaptors. The generated libraries were submitted to quality control with the Agilent bio- analyzer 2100 (Agilent Technologies, Wokingham, UK) before sequencing. The RNA integrity number (RIN) values for all samples were 7.5 and above. 1 µl cDNA was loaded on an Agilent DNA chip (DNA-1000) to verify cDNA quality and quantity. Only libraries reaching satisfactory conditions were used for sequencing, on an Illumina HiSeq 2000 system

value: SRpP55 KD (siSR#2)


title: SRpP55 KD (siSR#2) exposed 4


title: SRpP55 KD (siSR#2) exposed 2


title: RNA-seq Male_8


title: sRNA_Ago2KO2

source_name: IP input Ago2KO2 cells


title: SRpP55 KD (siSR#2) exposed 1


title: RNA-seq Male_35


title: RNA-seq Male_34


title: RNA-seq Male_12


title: sRNA_DicerKO

source_name: IP input DicerKO cells

value: Dicer knockout


title: SRpP55 KD (siSR#2) exposed 3


title: RNA-seq Male_7


title: control siRNA  exposed  5

value: control siRNA


title: control siRNA  exposed  3


title: control siRNA  exposed  4


title: sRNA_E14_B

source_name: IP Input E14 cells B


title: RNA-seq Male_33


title: sRNA_E14_A

source_name: IP Input E14 cells A


title: Ago2KO_C4_XEN

description: reverse-stranded protocol

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to mm10 whole genome using STAR v2.4.2a allowing up to 2 mismatches
FeatureCounts V1.4.5-p1 was used to summarize reads for each gene, using -s 2 (reversely stranded) and ignoring multiple-hit reads
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw read count

source_name: Ago2 knockout cells (C4)

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Differentiated cells were treated 5 days with : RPMI 1640 with 15% FBS, 1% Pen/Strep, 0.1 mM Beta-mercaptoethanol, 0.1µM all-trans retinioc acis and 10ng/mL od activine A  .

tag: differentiation status

value: 5 days XEN differentiation


title: Ago2KO_5-3_XEN

description: reverse-stranded protocol

source_name: Ago2 knockout cells (5-3)

tag: tissue


title: control siRNA  exposed  2


title: E14_XEN_B

description: reverse-stranded protocol

source_name: E14 XEN cells (B)


title: RNA-seq Male_10

value: primary breast tumor


title: RNA-seq Male_11

value: RNA-seq


title: RNA-seq Male_6


title: RNA-seq Male_5


title: E14_XEN_A

description: reverse-stranded protocol

source_name: E14 XEN cells (A)


title: RNA-seq Male_32


title: sRNA_Ago2KO1

source_name: IP input Ago2KO1 cells


title: control siRNA  exposed  1


title: Ago2KO_5-3_2

description: reverse-stranded protocol

source_name: Ago2 knockout cells (5-3_2)

value: Non differentiated


title: RNA-seq Male_4


title: Somatic cells female week 4

first: Sabine

last: Dietmann

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

data_processing:
Low quality bases (q < 20) from the 3' end and adapter sequences were removed with the TrimGalore wrapper scripts (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore).
Reads were mapped to the human (GRCh37/hg19) reference genome with Tophat 2.0.12 (http://ccb.jhu.edu/software/tophat)
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Processed data files contain read counts per ENSEMBL (release 74) transcripts generated by using the HTSeq 0.6.1 python package (http://www-huber.embl.de/users/anders/HTSeq)

source_name: Somatic cell isolated from developmental week 4 embryonic tissue

extract_protocol:
Total RNA was extracted with the PicoPure RNA Isolation Kit. Total RNA (0.5-2 ng) was reverse transcribed and amplified into cDNA using Ovation RNA-Seq System V2 (Nugen) according to manufacturer’s instructions.
Amplified cDNA was sonicated into 250 bp by Covaris S220 Focused-ultrasonicators. Subsequently, RNASeq library was generated with 500 ng of fragmented cDNA using Ovation Ultralow DR Multiplex System (Nugen). Library was quantified by KAPA Library Quantification Kit (Kapa Biosystems) using QuantStudio 6 Flex Real-Time PCR System (Applied Biosystems).

tag: facs

value: TNAP+, CD38+ and SSEA4+

tag: gender

value: female


title: RNA-seq Male_3


title: Ago2KO_5-3_1

description: reverse-stranded protocol

source_name: Ago2 knockout cells (5-3_1)

value: E14 cells 129/Ola background

value: Blastocyst mouse ES cells


title: RNA-seq Male_31

source_name: Human breast tumor


title: RNA-seq Male_2


title: Sample A

city: Taipei

first: HSI-Wen

last: Yeh

state: TAIWAN

address: Academia Sinica, No. 128

department: Institute of biomedical  science

country: Taiwan

institute: Academia Sinica

data_processing:
Sequenced reads were created by Illumina CASAVA_v1.8.2 software
BAM file was generated by TopHat (V2.0.7) tophat -o <output> -p 18 -r 0 human_glk_v37 <fastq.gz>
GTF file was generated by cufflinks ( 2.1.1.) cufflinks -q -p 18 -o <output> -u -g config/ncbi_annotation_104.gtf <accepted_hits.bam>
The ncbi_annotation_104 was original from ftp://ftp.ncbi.nih.gov/genomes/Homo_sapiens/ARCHIVE/ANNOTATION_RELEASE.104/mapview/seq_gene.md.gz
Supplementary_files_format_and_content: gtf format

source_name: A549, shLacZ

growth_protocol: A549 cells were cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin (Invitrogen).

extract_protocol:
Total RNA isolated from A549 shLac control cells and shpspc1 cells was extracted by Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Non-small cell lung cancer


title: Sample AI

source_name: A549, shPSPC1


title: hPGC female week 4

source_name: hPGC isolated from developmental week 4 embryonic tissue

value: TNAP-, CD38- and SSEA4-


title: RH41_HNRNPH1_sin3_rep1

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

data_processing:
Basecalling was performed using Illumina Casava 1.7
FASTQ sequences adapter trimmed (curtadapt) and mapped to the human hg19 genome by a pipeline that serially  employs STAR and BWA
Mapped reads were counted with HTSEQ
voom TMM normalized and contrasted using the empirical Bayes pipeline limma in R 3.2.3
Genome_build: hg19
Supplementary_files_format_and_content: count files are txt format files that contain raw read counts that map  to  transcripts for each defined gene.

source_name: Rhabdomyosarcoma cell line

growth_protocol: The RD, RH30 and RH41 cell lines were cultured in RPMI1640, 100 units/ml penicillin and 100 mg/ml streptomycin, and 10% fetal bovine serum (Sigma).

extract_protocol:
RNA was extracted with a Maxwell simplyRNA Tissue kit and Maxwell Instrument (Promega, Madison, WI).
The total RNA stranded library prepared from the final PCR products of indexed samples was subjected to 300 bp paired-end sequencing

treatment_protocol: All siRNAs were dissolved in Ultra-pure distilled water (Invitrogen) to 20 µM as stocks.  Lipofectamine RNAiMAX (Invitrogen) was used to transfect siRNA (siRNA stock to Lipofectamine at 1:1 v/v ratio) and medium was replaced with fresh one after 6 hours. For cells harvested 2 and 4 days post transfection, 2×105 (RD and RH30) or 2.4×105 (RH41) cells were seeded per well of 6-well plate, 2 µl RNAiMAX and 2 µl of 20 µM siRNA were used for transfection in 2 ml culture medium.

tag: expression modification

value: HNRNPH1 sin3


title: RH41_HNRNPH1_sin2_rep3

tag: cell line

value: HNRNPH1 sin2


title: RH41_HNRNPH1_sin2_rep2


title: arp5-5

city: Stanford

first: Sean

last: Beckwith

state: CA

address: 371 Serra Mall

department: Biology

institute: Stanford University

description: arp5KO Rap90 rep1

data_processing:
Reads were aligned using Bowtie2 and analysed using DESeq2. Replicates were combined for analysis and genes with low reads (< 5 FPKM across all samples) were removed.
Genome_build: sacCer3 (April 2011)
Supplementary_files_format_and_content: FPKM

organism: Saccharomyces cerevisiae

growth_protocol: Yeast were grown to mid-log-phase in YPD medium at 30C. (Asynchronous culture).

extract_protocol:
Pellets were collected, snap-frozen and then processed as per the RNA-seq protocol outlined. Two biological replicates were collected(-1,-2 or -3,-4 or -5,-6). RNA was prepared from samples (approximately 1.5 ODs) using the MasterPure™ Yeast RNA Purification Kit (Epicentre, MPY03100).
The sequencing libraries were prepared from 0.8 µg of RNA/sample using the Illumina TruSeq Stranded mRNA kit (Illumina, 15031047). The quality of the pooled library was checked using the Agilent Bioanalyser 2100 HS DNA assay. The library was sequenced on an Illumina HiSeq 2000 platform.

treatment_protocol: Asynchronous culture was treated with 30 nM rapamycin for 45 min, 90 min, or was untreated

tag: genotype

value: BY4741 arp5::LEU2

tag: growth protocol

value: Yeast liquid culture


title: RH41_HNRNPH1_sin3_rep3


title: arp5-6

description: arp5KO Rap90 rep2


title: RH41_HNRNPH1_sin2_rep1


title: RH30_HNRNPH1_sin3_rep1


title: RH41_siControl_rep3

value: siControl


title: RH41_siControl_rep1


title: ino80-6

description: ino80KO Rap90 rep2


title: RH30_HNRNPH1_sin3_rep2


title: RH41_siControl_rep2


title: RH30_HNRNPH1_sin3_rep3


title: RH41_HNRNPH1_sin3_rep2


title: RH30_HNRNPH1_sin2_rep3


title: ino80-5

description: ino80KO Rap90 rep1


title: Ago2KO_C4

description: reverse-stranded protocol

value: Ago2 knockout


title: wt-6

description: WT Rap90 rep2

source_name: wild type

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0


title: RNA-seq Male_1

tag: patient


title: RH30_HNRNPH1_sin2_rep2


title: RD_HNRNPH1_sin3_rep3

value: RD


title: arp5-4

description: arp5KO Rap45 rep2


title: RH30_siControl_rep3


title: wt-5

description: WT Rap90 rep1


title: RD_HNRNPH1_sin3_rep2


title: RH30_siControl_rep1


title: arp5-2

description: arp5KO Untreated rep2


title: RH30_siControl_rep2


title: wt-4

description: WT Rap45 rep2