title: Differentiated brown adipocyte (D7)

city: Daejeon

first: Lee

last: Sunwoo

address: #211, Next2Vill, 278-2, Jangdae-dong, Yuseong-gu

country: South Korea

institute: GenomicWorks

description: Fully differentiated adipocyte

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie2
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Interscapular brown adipose tissue of new born

growth_protocol: Primary brown preadipocytes were isolated from interscapular BATs of newborn C57BL/6 and cultured in DMEM plus 20% fetal bovine serum (FBS).

extract_protocol:
Total RNAs were isolated from brown preadipocyte at D0 and brown adipocyte at D7 using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For adipogenesis of brown preadipocytes, cells were plated at a density of 5 × 105 per 10 cm dish in differentiation medium (DMEM plus 10% FBS, 0.1 μM insulin and 1 nM T3) 4 days before induction of adipogenesis. At day 0, cells were treated with differentiation medium supplemented with inducing reagents 0.5 mM IBMX, 2 μg/ml dexamethasone, and 0.125 mM indomethacin.. Two days later, cells were changed to the differentiation medium alone and cultured for 7 days (D7).

value: Brown adipose tissue

value: New born


title: DMSO-in vitro US-1336733_PID20985_RNA-Seq_23Apr2014

status: Public on Sep 21 2016

type: SRA

city: Boston

first: Kenzie

last: MacIsaac

state: MA

address: 33 Avenue Louis Pasteur

department: Genetics and Pharmacogenomics

country: USA

institute: Merck Research Labs

description:
US-1336733_PID20985_RNA-Seq_23Apr2014
PID20985_23-04-2014.xlsx

library_source: transcriptomic

data_processing:
Reads were aligned to the mouse genome (mm10) and mRNA transcript abundance was quantified using the Omicsoft ArrayStudio software
Genome_build: mm10
Supplementary_files_format_and_content: Processed data is available in an Excel file containing five tabs; the first tab contains total read counts aligning to each gene; the second tab contains gene annotation information; the third tab contains FPKM values for each gene; the fourth tab contains an alignment report for each sample; the fifth tab contains a filtering report for each sample

molecule: total RNA

organism: Mus musculus

source_name: C57/BL6 thymocytes

growth_protocol: 1. Thymus were removed from C57BL/6 mice, were prepared in single cell suspension and cultured in vitro with MRL-871 or DMSO for 2hr; 2.C57BL/6 mice were treated with 20mg/kg MRL-871 or vehicle control. Thymus were removed at 2hr post-treatment, and single cell suspension was prepared; 3. Rorc KO thymic lymphoma cell line was derived from Rorc KO mice and maintained in RPMI. MIGR1-GFP or MIGR1-Rorc-GFP was used to transfect the cell line. GFP+ cells were FACS sorted on Aria.

extract_protocol:
RNA was extracted using QIAGEN RNeasy mini kit
Library construction and sequencing were performed using standard Illumina protocols by the Beijing Genomics Institute (BGI)

treatment_protocol: MRL-871 or DMSO in vitro; MRL-871 or vehicle in vivo; MIGR1-GFP or MIGR1-Rorc-GFP.

tag: sample type

value: in vitro

tag: treatment

value: DMSO


title: Primary cultured brown preadipocyte (D0)

description: Preadipocyte

tag: strain

tag: tissue

tag: age


title: Bmal1_KO_CT12_rep1

city: San Francisco

first: Zenghua

last: Fan

state: CA

address: 1550 4th Street

institute: University of California, San Francisco

data_processing:
Fastq files containing raw sequence reads were aligned to mouse genome (mm9) by Tophat2. Then bedtools (v2.19.1) were applied to calculate the number of reads of each transcript based on the gene annotations from Ensembl annotation(v69).  The reads numbers were normalized to reads per kilobase per million mapped reads (RPKM).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: liver

growth_protocol: The mice were housed under a 12-h light/12-h dark regimen with food and water available ad libitum for one week before being switched to complete darkness. The mice were switched to complete darkness two days before execution. ZT0 is defined as the time when the lights are turned on. All animal handing protocols have been approved by “Committee of Institute of Nutrition Science”.

extract_protocol:
Livers of all mice were quickly dissected and snap-frozen in liquid nitrogen and stored at −80 °C. Total RNA was extracted from each liver sample using Trizol.
The RNA samples of Bmal -/- and WT mice were converted into Illumina sequencing libraries by using Illumina TruSeq RNA Sample Prep Kit v2 as per manufacturer’s protocol.

treatment_protocol: Bmal1 liver-specific knock mice were obtained from the Jackson Lab(strain007668). Two Bmal1 -/- mice and two wildt-ype mice were sacrificed at ZT0 and ZT12 respectively after at least one week entrainment.

value: liver

value: 8 weeks


title: Bmal1_KO_CT12_rep3


title: Bmal1_KO_CT0_rep3


title: Bmal1_KO_CT12_rep2


title: Bmal1_KO_CT0_rep2


title: Bmal1_KO_CT0_rep1


title: Bmal1_WT_CT12_rep3


title: Ad_null_CT22_rep2

city: ShangHai

first: Haifang

last: Wang

address: NO 320, Yueyang Road

department: functional genomics group

country: China

institute: PICB

data_processing:
Fastq files containing raw sequence reads were aligned to mouse genome (mm9) by Tophat (default parameters). Then bedtools (v2.16.2) were applied to calculate the number of reads of each transcript based on the gene annotations from UCSC genome browser. The transcripts with summed reads number<20 in the samples were removed. The reads numbers were normalized to reads per kilobase per million tags (RPKM).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Livers of all mice were quickly dissected and snap-frozen in liquid nitrogen and stored at −80 °C. Total RNA was extracted from each liver sample using Trizol.
The RNA samples of ad-378 and ad-null mice were converted into Illumina sequencing libraries by using Illumina TruSeq RNA Sample Prep Kit v2 as per manufacturer’s protocol.

treatment_protocol: DNA fragments encoding miR-378 were introduced into pENTR/U6 vector under the control of the human U6 promoter. 5 × 108 plaque-forming unit viruses were administered to four ad-378 mice through tail vein injection for miR-378 over-expression. Control viruses were injected to four ad-null mice. Two ad-378 and two ad-null mice were sacrificed at CT10 and CT22 respectively eight days after injection.


title: Bmal1_WT_CT12_rep1


title: Bmal1_WT_CT0_rep2


title: control

city: Beijing

first: zi

last: ye

address: FuXing Road 28

institute: PLA General Hospital

data_processing:
The original mRNA sequencing reads were filtered according to three criteria: remove reads with sequence adaptors, reads with more than 2% “N” bases and low-quality reads.
Then clean reads were aligned to the human reference genome using TopHat. Reads per Kilobase of Transcript per Million Mapped Reads value was calculated to assess the transcript level in sample and control. According to the rigorous significance test for gene expression profiling, the differentially expressed mRNAs were determined by Cufflinks program based on the following criteria: fold change (FC) > 1.5 or FC < 0.67 and P value < 0.05.
Fastx was used to remove adaptor sequences and low quality sequences from the original small RNA reads. Then small RNA reads were aligned with miRBase, Rfam, UCSC and pirnabank databases for annotation. Moreover, the differentially expressed miRNAs were screened by comparing miRNA levels with the threshold |log2FC| > 1 and P < 0.05. The unannotated reads were used to predict novel miRNAs with miRCat program from sRNA Toolkit
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: expre.txt files include miRNA_ID, total_Count and Normalized_Value

organism: Homo sapiens

source_name: retinal pigment epithelial (RPE) cells

growth_protocol: Human D407 RPE cells were routinely maintained in DMEM supplemented with 10% fetal bovine serum (FBS), penicillin/streptomycin and glutamine at 37 °C in a 95% air/5% CO2 environment as described. The medium was replaced every 2 days and cells were subcutured by typsin treatment twice a week.

extract_protocol:
Total RNA was isolated from cells using Trizol (Invitrogen, USA) according to manufacturer’s instructions. RNA cleanup involved DNase I digestion step was performed using RAeasy spin colmna (Qiagen), followed by assessment of RNA purity using the ND-1000 Nanodrop. Purified RNA samples had an A260:A230 ratio above 2.2 and A260:A280 ratio above 1.8.
mRNA was purified from total RNA with oligo(dT) beads and fractionized for cDNA synthesis, followed by first-strand cDNA amplification using random hexamer-primers. The second-strand cDNA was synthesized using DNA polymerase I, RNase H, dNTPs and buffer. Short double-stranded cDNA fragments were purified, added “A” base and ligated to Illumina sequencing adaptors. Next, DNA fragments sized in 150-200 bp were gel-purified and amplified by PCR. Small RNA library was constructed according to the Illumina TruSeq Small RNA Sample Preparation protocol. Briefly, RNA 3’ and 5’ adaptors were ligated to total RNA followed by reverse transcription. cDNA and small RNA libraries were sequenced on Illumina HiSeq 2500 platform in RiboBio Co. Ltd,. (Guang zhou, China).

treatment_protocol: To study the effect of clusterin on the viability, D407 cells were treated with different concentrations of clusterin (0-10 μg/ml) as indicated, then the viability was determined by MTT assay.

tag: cell line

tag: agent


title: CLU group

value: clusterin


title: Sample_6-MB135_HDUX4CA_WITHdox_rep3

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

data_processing:
Illumina CASAVA software was used for basecalling and sample de-multiplexing.
Reads were mapped to the hg19 human genome assembly using Bowtie v1.0.0 and RSEM v1.2.4. RSEM was modified to call Bowtie  with the -v 2 mapping strategy. RSEM was then invoked with the arguments --bowtie-m 100 --bowtie-chunkmbs 500 --calc-ci --output-genome- bam on the gene annotation file.
Sample 1 to 6 are used to generate the processed csv files with EdgeR-based expression estimates and fold change values (with dox vs withoutdox) for coding genes.
Genome_build: hg19

molecule: polyA RNA

source_name: Cultured myoblasts

extract_protocol:
RNA was extracted from myoblasts using TRIzol reagent as per manufacturer's instructions and cleaned up using Qiagen Rneasy columns, including the optional, on-column DNAse digestion step.
The Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Samples were multiplexed using Illumina barcodes to run 2-6 samples per sequencing lane.

tag: cell type

value: Facioscapulohumeral dystrophy (FSHD)

value: Immortalized primary myoblasts

value: Doxycyline


title: Sample_5-MB135_HDUX4CA_nodox_rep3


title: Sample_Ctrl-14h


title: Bmal1_WT_CT0_rep1


title: MRL871-in vivo US-1417473_PID20985_RNA-Seq_23Apr2014

description:
US-1417473_PID20985_RNA-Seq_23Apr2014
PID20985_23-04-2014.xlsx

value: in vivo


title: Sample_2-MB135_HDUX4CA_WITHdox_rep1


title: Sample_1-MB135_HDUX4CA_nodox_rep1


title: Sample_3-MB135_HDUX4CA_nodox_rep2


title: Wild-Type_2

city: Edinburgh

first: Hywel

last: Dunn-Davies

address: Max Born Crescent

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

description:
Sample 21
Wild type control

data_processing:
Reads were demultiplexed using pyCRAC
Reads were filtered and quality filtered using Flexbar 2.4
Reads were aligned to the EF4 Saccharomyces cerevisiae genome sequence (Ensembl release 74) by novoalign version 2.07.00
Reads were collapsed to remove PCR duplicates, reads mapped to the same start position in the genome and sharing the same 3-nucleotide random barcode sequence were collapsed (collapsing was done for U3 alignment analysis but not for 35S alignment)
Hits across genes were calculated using pyCRAC
Genome_build: EF4
Supplementary_files_format_and_content: Genomic coordinates of mapped reads in bedgraph file

organism: Saccharomyces cerevisiae

source_name: BY4741 (Wild type control)

growth_protocol: S.cerevisiae strains expressing C-terminal HTP tagged protein were grown at 30°C to A600 ∼ 0.5 in synthetic medium with glucose minus tryptophan.

extract_protocol:
UV stabilized protein-RNA interactions were purified under denaturing conditions and RNAs associated with the protein of interest were partially truncated.
Sequencing 3' adapter and 5' adapter were ligated while protein-RNA complexes were bound to Ni-NTA agarose, RNA library was reverse transcribed and PCR amplified.  3' adapter: 5' - TGGAATTCTCGGGTGCCAAGGC - 3'

treatment_protocol: Protein-RNA complexes were stabilized by in-vivo UV crosslinking.

tag: parent strain

tag: barcode

value: NNNTAAGC


title: UTP18_2

description:
Sample 19
UTP18 replicate 2

source_name: BY4741 UTP18-HTP

tag: expressing

value: HTP-tagged UTP18

tag: utp-a or utp-b complex

value: UTP-B

tag: purified protein

value: NNNTGGAGC


title: UTP15_2

description:
Sample 15
UTP15 replicate 2

source_name: BY4741 UTP15-HTP

value: HTP-tagged UTP15

value: UTP-A

value: NNNAGAGC


title: Wild-Type_1

description:
Sample 20
Wild type control


title: UTP15_1

description:
Sample 14
UTP15 replicate 1

value: NNNACTCAGC


title: Vehicle control-in vivo US-1417341_PID20985_RNA-Seq_23Apr2014

description:
US-1417341_PID20985_RNA-Seq_23Apr2014
PID20985_23-04-2014.xlsx

value: Vehicle


title: Sample_DUX4-14h


title: UTP17_1

description:
Sample 16
UTP17 replicate 1

source_name: BY4741 UTP17-HTP

value: HTP-tagged UTP17

value: NNNGACTTAGC


title: UTP13_1

description:
Sample 13
UTP13 replicate 1

source_name: BY4741 UTP13-HTP

value: HTP-tagged UTP13

value: NNNTCTCTAGC


title: Bmal1_WT_CT0_rep3

value: liver

value: 8 weeks


title: UTP17_2

description:
Sample 17
UTP17 replicate 2

value: NNNGTGAGC


title: UTP10_2

description:
Sample 12
UTP10 replicate 2

source_name: BY4741 UTP10-HTP

value: HTP-tagged UTP10


title: UTP9_2

description:
Sample 10
UTP9 replicate 2

source_name: BY4741 UTP9-HTP

value: HTP-tagged UTP9

value: NNNCTAGC


title: UTP9_1

description:
Sample 9
UTP9 replicate 1

value: NNNCACTAGC


title: UTP10_1

description:
Sample 11
UTP10 replicate 1


title: Sample_4-MB135_HDUX4CA_WITHdox_rep2

value: Facioscapulohumeral dystrophy (FSHD)

value: Immortalized primary myoblasts

value: Doxycyline


title: Bmal1_WT_CT12_rep2


title: Nkx2-1_IgG

city: Davis

first: Alex

last: Nord

address: 1544 Newton Court

department: Neurobiology, Physiology, and Behavior

institute: University of California Davis

description: Dissociated tissue

library_source: genomic

data_processing:
Base-calls were performed with CASAVA (v1.8.2) and bcl2fastq (v1.8.4).
ChIP-seq reads were filtered and aligned to whole mouse genome mm9 using BWA (v0.6.2).
Peak-calling was performed with MACS2 (v2.1.0).
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing coverage and txt files containing MACS2 peak-calls.

molecule: genomic DNA

source_name: Basal ganglia

extract_protocol:
Tissue was micro-dissected and prepared for TF or native ChIP, cross-linked, and sheared. Protein/antibody complexes were isolated with antibodies and collected using Dynabeads.
ChIP-seq libraries were generated using the Ovation Ultralow DR Multiplex System (NuGEN #0330).

tag: chip antibody

value: NKX2-1 polyclonal (Santa Cruz Biotechnology #sc-13040 RRID:AB_10015210)

tag: genotype

value: Wildtype

value: embryonic day 13.5

value: Basal ganglia


title: Nkx2-1_Input

description: Dissociated tissue


title: Lhx6_Input

description: Dissociated tissue

value: LHX6 polyclonal (Genscript)


title: Lhx6_IgG

description: Dissociated tissue


title: UTP8_2

description:
Sample 8
UTP8 replicate 2

source_name: BY4741 UTP8-HTP

value: HTP-tagged UTP8

value: UTP-A

value: NNNCGCTTAGC


title: Nkx2-1_ChIP

description: Dissociated tissue


title: Lhx6_ChIP

description: Dissociated tissue


title: UTP18_1

description:
Sample 18
UTP18 replicate 1

value: HTP-tagged UTP18

value: UTP-B


title: UTP5_2

description:
Sample 6
UTP5 replicate 2

source_name: BY4741 UTP5-HTP

value: HTP-tagged UTP5

value: NNNGCGCAGC


title: UTP5_1

description:
Sample 5
UTP5 replicate 1


title: UTP4_1

description:
Sample 3
UTP4 replicate 1

source_name: BY4741 UTP4-HTP

value: HTP-tagged UTP4

value: NNNGTGAGC


title: UTP1_2

description:
Sample 2
UTP1 replicate 2

source_name: BY4741 UTP1-HTP

value: HTP-tagged UTP1

value: NNNCACTAGC


title: LA11S9

status: Public on Sep 20 2016

city: Mississauga

first: Ingo

last: Ensminger

state: Ontario

address: 3359 Mississauga Road

department: Department of Biology

country: Canada

institute: University of Toronto, Mississauga

description: Last year (2009) needle tissue from southern sun exposed canopy 3m below top, height of 25-30m.

data_processing:
Base calling using CASAVA 1.7.
Alignment to putative unique transcript (PUT) set (PUT_set.fasta) using Bowtie 2 (V2.1) in local alignment mode (--local) and otherwise default settings.
Quantification of aligned reads per PUT: Non-uniquely mapped reads were retained. Only reads with min 95 sequence identity and alignment length > 80bp were retained. Quantification was performed using custom Python scripts and the HTSeq framework.
All PUTs with more than 1 read per million aligned reads (RPM) in at least four libraries were retained.
Genome_build: PUT_set.fasta: FASTA file used for alignment.
Supplementary_files_format_and_content: DataMatrix.txt: Includes the abundance measurements per PUT in each library, as well as functional annotation data. Gene Ontology indicates GO Terms inferred by the Blast2Go pipeline, TAIR_Id is the best hit in the Arabidopsis peptide database TAIR10, RefSeq is best hit in the NCBI RefSeq database, Blast2GO is the functional annotation inferred by the Blast2Go pipeline.
Supplementary_files_format_and_content: PUT_set.fasta: Includes the PUT set used for alignment.

organism: Pseudotsuga menziesii

source_name: Needle tissue, Cameron Lake provenance, Schluchsee site, September

extract_protocol:
Total RNA was extracted using a CTAB based extraction method modified after Chang, 1993. After precipitation, a DNase I digestion was performed using Qiagen's RNase-Free DNase Set (Cat. no. 79254). Afterwards, DNase was removed using silica columns (Qiagen RNeasy MinElute, Cat. no. 74204). RNA integrity was checked on a 2100 Bioanalyzer (Agilent, CA, USA)) using the RNA 6000 nano assay and the Plant total RNA protocol.
Sequence library was prepared using the TruSeq RNA Sample Preparation Kit v2 starting with 4ug total RNA.

value: needle

tag: developmental stage

value: adult

tag: provenance

value: Cameron Lake

tag: tree

tag: site

value: Schluchsee

tag: month

value: noon


title: LA15S9

tag: tissue


title: LA10S9


title: YUMM2.1

city: Los Angeles

first: Jennifer

last: Tsoi

address: 570 Westwood Blvd, CNSI 4338

department: University of California, Los Angeles

institute: UCLA

data_processing:
Reads were mapped using TopHat2 v2.0.9 and aligned to the Mus musculus genome NCBI build 37.2
Expected counts were normalized to FPKM values using Cufflinks Cuffnorm program using the geometric library normalization method
Genome_build: Mus musculus genome NCBI build 37.2
Supplementary_files_format_and_content: Matrix of gene expression measurements in FPKM

source_name: Melanoma cell line

extract_protocol:
AllPrep DNA/RNA Mini kit from Qiagen
RNA libraries were prepared for sequencing using standard Illumina protocols


title: LA12S7

source_name: Needle tissue, Cameron Lake provenance, Schluchsee site, July


title: LA16S7


title: DMSO-in vitro US-1336705_PID20985_RNA-Seq_23Apr2014

description:
US-1336705_PID20985_RNA-Seq_23Apr2014
PID20985_23-04-2014.xlsx

source_name: C57/BL6 thymocytes

tag: sample type

value: in vitro

tag: treatment

value: DMSO


title: LA11S7


title: LA9S9


title: LA15S7


title: YUMM1.1

tag: cell line


title: UTP8_1

description:
Sample 7
UTP8 replicate 1

value: HTP-tagged UTP8

value: UTP-A


title: LA9S7


title: YUMM1.7


title: LA14S6

source_name: Needle tissue, Cameron Lake provenance, Schluchsee site, June


title: LA9S6


title: UTP4_2

description:
Sample 4
UTP4 replicate 2

value: NNNATTAGC


title: LA11S6


title: LA10S5

source_name: Needle tissue, Cameron Lake provenance, Schluchsee site, May


title: LA11S5


title: LA9S5


title: LA15S5


title: LA10S6


title: UTP1_1

description:
Sample 1
UTP1 replicate 1

value: UTP-B

value: NNNGACTTAGC


title: LA15S6


title: LA13P9

source_name: Needle tissue, Cameron Lake provenance, Wiesloch site, September

value: Wiesloch


title: LA15P9


title: LA14S5


title: LA16P9


title: LA9P9


title: LA12P7

source_name: Needle tissue, Cameron Lake provenance, Wiesloch site, July


title: LA16P6

source_name: Needle tissue, Cameron Lake provenance, Wiesloch site, June


title: LA12P9


title: LA15P7


title: LA16P7


title: LA13P7


title: LA12P6


title: LA9P7


title: LA13P5

source_name: Needle tissue, Cameron Lake provenance, Wiesloch site, May


title: LA15P6


title: LA9P6


title: LA9P5


title: AR14S9

source_name: Needle tissue, Salmon Arm provenance, Schluchsee site, September

value: Salmon Arm


title: LA12P5


title: LA16P5


title: AR13S9


title: AR15S7

source_name: Needle tissue, Salmon Arm provenance, Schluchsee site, July


title: AR12S7


title: AR9S9


title: AR15S9


title: AR14S7


title: AR13S7


title: AR16S6

source_name: Needle tissue, Salmon Arm provenance, Schluchsee site, June


title: AR9S7


title: AR13S6


title: AR9S6


title: LA15P5


title: AR13S5

source_name: Needle tissue, Salmon Arm provenance, Schluchsee site, May


title: AR12S5


title: AR16S5


title: AR9P9

source_name: Needle tissue, Salmon Arm provenance, Wiesloch site, September


title: AR12P7

source_name: Needle tissue, Salmon Arm provenance, Wiesloch site, July


title: AR14S5


title: AR13P9


title: AR14P7


title: AR15P7


title: AR11P7


title: AR13P6

source_name: Needle tissue, Salmon Arm provenance, Wiesloch site, June


title: AR9P7


title: AR9P6


title: AR14P5

source_name: Needle tissue, Salmon Arm provenance, Wiesloch site, May


title: AR15P5


title: AR12P5


title: AR12P6


title: AR15P6


title: AR12S6


title: AR9P5


title: mapping reads

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description:
mapping of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations by iPCR, paired-end reads
TRIP_HP1_D2, TRIP_HP1_D16

data_processing:
Basecalling and filtering was performed using standard software of the illumina HiSeq 2500 or MiSeq. Extraction of 21 nt barcode reads from fastq files and alignment of TRIP mapping reads was performed using the TRIP script available at http://trip.nki.nl. We set a Hamming distance of 2 for removing mutated barcodes, a maximum distance of 500 nt on the forward  read  and 20 nt on the reverse read to cluster the positions during mapping and a minimum read number of 1. Spike-in library gDNA was sequenced separately to determine the spike-in barcode sequences. A list of the most abundant spike-in barcodes with over 1000 counts in gDNA was used for extracting spike-in reads from the TRIP samples. For each TRIP experiment sample, cDNA read counts per barcode were divided by the sum of cDNA read counts for all spike-in barcodes to correct for sequencing depth and standardize expression between samples. gDNA read counts were transformed to counts per million (cpm) to correct for sequencing depth. Spike-in corrected cDNA counts were then divided by gDNA cpm counts which yields the normalized expression per barcode. We set a cutoff for barcodes that had at least 100 gDNA reads in all samples to ensure that each barcode was sufficiently represented in the pool. To ensure reliable allocation of barcode integrations, we worked with a total of 1093 barcodes that fit the following criteria: (1) more than 2 reads in both forward and reverse mapping (2) 80% of forward and reverse mapping reads matched with the first mapping location and less than 10% of forward and reverse mapping reads matched with the second mapping location (3) mapq score of 10 or higher for forward and reverse mapping.
Genome_build: dm3
Supplementary_files_format_and_content: CSV files containing barcode sequences, position of integration, read counts and normalized expression for each of the samples
Supplementary_files_format_and_content: space delimited list of spike-in barcode sequences

organism: Drosophila melanogaster

source_name: Kc167 cells

growth_protocol: Kc167 cells were cultured at 23.5°C in Shields and Sang M3 Insect Medium (Sigma-Aldrich) with 0.25% Bacto Peptone (BD), 0.1% Yeast Extract (BD), 5% heat-inactivated FBS (Thermo Scientific) and 1% Penicillin/Streptomycin (Thermo Scientific). For pMT induction, sterile-filtered CuSO4 (Sigma-Aldrich) dissolved in H2O was added to 0.5mM final concentration

extract_protocol: To map the reporter integrations, gDNA was extracted from 20*106 cells using ISOLATE II Genomic DNA Kit (Bioline) and digested with NlaIII (40 U, NEB) in buffer 4 supplemented with BSA in a total volume of 100 µl for 2 h at 37°C. The reaction was terminated by heat inactivation for 20 min at 65°C. Fragments were circularized over night at 12°C using T4 Ligase (100 U, NEB) in T4 Ligase buffer in a total volume of 1600 µl. Products were precipitated with ethanol and purified with ISOLATE II PCR and Gel kit (Bioline). Unligated fragments were removed by digestion with Plasmid-Safe DNase (20 U, Epicentre) with added ATP (final concentration 1 mM) in the manufacturer-supplied reaction buffer in a total volume of 100 µl for 5 h at 37°C. The reaction was terminated by heat-inactivation for 30 min at 70°C and purified using ISOLATE II PCR and Gel kit (Bioline). To eliminate any remaining unintegrated plasmid , products were digested with I-CeuI (5 U, NEB) in buffer 4 supplemented with BSA in s total volume of 60 µl for 2 h at 37°C. The reaction was terminated by heat-inactivation for 20 min at 65°C and purified using ISOLATE II PCR and Gel kit (Bioline). Products containing barcodes and flaking gDNA were amplified in two rounds by inverse PCR to add Illumina adapters for Illumina paired-end sequencing. For cDNA reads, RNA from 10*106 transfected cells isolated by FACS sorting was extracted with Chloroform from TRIsure-resuspended samples (Bioline). The polyadenylated fraction was isolated using the Oligotex kit (Qiagen). RNA samples were treated with RNase-free DNase I (2 U, Roche) in DNase buffer in a total volume of 20 µl for 30 min at 37°C. The reaction was terminated by adding 1 µl of 25 mM EDTA and incubation at 70°C  for 15 min. cDNA was generated using Tetro cDNA Synthesis Kit (Bioline) according to the manufacturer’s instructions with a GFP-specific primer instead of OligoDT. 1/4 of total cDNA was used in a PCR reaction to add adapters for Illumina single-end sequencing. The appropriate PCR cycle number was determined by qPCR to avoid overamplification. For gDNA reads, gDNA was isolated from 10*106 unsorted TRIP cells using ISOLATE II Genomic DNA Kit (Bioline). 500 ng were used in a PCR reaction to add adapters for Illumina single-end sequencing and amplified over 25 cycles.

treatment_protocol: To establish the pool of cells harboring reporter constructs, 1 million Kc167 cells were transfected with 1 µg barcoded 5xGal4UAS-pMT-GFP plasmid library and 1 µg plasmid encoding Sleeping Beauty transposase (Addgene #65487) by electroporation. Transposase expression was induced by four heat shock treatments of 2.5 h at 37°C distributed over 36 h. Transfected cells were expanded until Sleeping Beauty expression was lost. For the resulting TRIP pool, we determined the number of integrations to be 0.3 per cell based on qPCR on gDNA for GFP integrations compared to a cell line with a single integration. A subpool of 30,000 cells was taken from the TRIP pool and expanded to  limit the library complexity to a maximum of 10,000 integrations before gDNA was isolated for mapping of integrations. For assessing the effect of recruiting HP1a to integrated reporters, GFP expression was induced by adding 0.5 mM CuSO4 two days before the TRIP pool was transiently transfected with plasmids encoding either pAc5-Gal4DBD-V5-HP1a-T2A-mCherry or control plasmids encoding only Gal4DBD-V5 or V5-HP1a instead of Gal4DBD-V5-HP1. For assessing reporter expression by day two after transfection, cells were sorted for mCherry expression before gDNA and cDNA were isolated for further analysis. For determining reporter expression by day 16 after transfection, cells were kept unsorted before cDNA and gDNA isolation. To be able to compare bulk expression changes between cDNA samples, an independent TRIP pool with a complexity of approximately 200 barcodes was suspended in TRIsure (Bioline) and added to TRIP cells to an amount of 2.5% based on cell counts before RNA extraction.

tag: cell type

value: drosophila melanogaster dorsal closure stage embryonal cell line


title: AR16P9


title: MN_Spombe_KanSp_Rep2

city: Madrid

first: Enrique

last: Vazquez de Luis

state: Madrid

address: Melchor Fernandez Almagro, 3

country: Spain

institute: CNIC

description: Mononucleosomal DNA

data_processing:
Alignment: bowtie 0.12.7. Aligment against the proper replaced with the appropriate sequence for each mutant.
The smoothed signal is generated by using a modified version of NUCwave to normalize signal against repetitions.
Genome_build: S. pombe 2007 (ASM294v2)
Genome_build: S. cerevisiae (SacCer 3)

organism: Schizosaccharomyces pombe

source_name: Mononucleosomal DNA

growth_protocol: Yeast cultures were grown in YES medium (S. pombe) or YEPD (S. cerevisiae)

extract_protocol:
In S. pombe maps: 200 ml cultures at 0.8x10^7 cells/ml were collected  for preparation of mononucleosomal DNA. Cells were treated with 8 mg of Zymolyase  20T during 30 minutes at 30 ºC to induce spheroplasts formation. Mononucleosomal fragments were generated by digesting DNA with 150 units/ml  of micrococcal nuclease (MNAse) at 37 ºC during 45 minutes. The amount of MNase was optimized experimentally to generate a 80:20 ratio of mononucleosomes to dinucleosomes, as described (Lantermann et al. 2010). Mononucleosomal DNA was recovered from 1.5% agarose gels and sequenced in an Illumina NextSeq 500 using the pair-end sequencing protocol.
In S. cerevisiae maps: 200 ml cultures at 0.8x10^7 cells/ml were collected  for preparation of mononucleosomal DNA. Cells were treated with 10 mg of Zymolyase  20T during 5 minutes at 30 ºC to induce spheroplasts formation. Mononucleosomal fragments were generated by digesting DNA with 300 units/ml  of micrococcal nuclease (MNAse) at 37 ºC during 10 minutes. The amount of MNase was optimized experimentally to generate a 80:20 ratio of mononucleosomes to dinucleosomes, as described (Soriano et al. 2014). Mononucleosomal DNA was recovered from 1.5% agarose gels and sequenced in an Illumina NextSeq 500 using the pair-end sequencing protocol.
Mononucleosomal DNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: h- leu1-32 spbc16g5.03::KanMX_Sp


title: MN_Spombe_KanSc_Rep1

description: Mononucleosomal DNA

value: h- leu1-32 spbc16g5.03::KanMX_Sc


title: MN_Spombe_KanSc_Rep2

description: Mononucleosomal DNA


title: AR12P9

value: needle


title: AR11P9

value: adult


title: MN_Spombe_KanSp_Rep1

description: Mononucleosomal DNA


title: MN_Spombe_KanWT_Rep2

description: Mononucleosomal DNA

value: h- leu1-32 spbc16g5.03::KanMX_WT


title: MN_Spombe_Ura_japonicus_Rep2

description: Mononucleosomal DNA

value: h- leu1-32 ura4::ura4_japonicusWT


title: MN_Spombe_Ura_japonicus_Remastered_Rep1

description: Mononucleosomal DNA

value: h- leu1-32 ura4::ura4_japonicusModified


title: MN_Spombe_KanWT_Rep1

description: Mononucleosomal DNA


title: MN_Spombe_Ura_octosporus_Remastered_Rep2

description: Mononucleosomal DNA


title: MN_Spombe_Ura_japonicus_Rep1

description: Mononucleosomal DNA


title: MN_Spombe_Ura_octosporus_Rep2

description: Mononucleosomal DNA

value: h- leu1-32 ura4::ura4_octosporusWT


title: MN_Spombe_Ura_octosporus_Rep1

description: Mononucleosomal DNA


title: AR11P5

value: noon


title: AR9S5

value: Schluchsee


title: MN_Spombe_SeqSc-Sp_Rep1

description: Mononucleosomal DNA

value: h- KanMX-SeqSc in IGR SPAC6F6.11c-SPAC6F6.12


title: MN_Spombe_SeqSc-Sp_Rep2

description: Mononucleosomal DNA


title: MN_Spombe_UraInt_Rep1

description: Mononucleosomal DNA

value: h- leu1-32 ura4::ura4_int


title: MN_Spombe_UraDyad_Rep2

description: Mononucleosomal DNA

value: h- leu1-32 ura4::ura4_dyad


title: MN_Spombe_UraLinker_Rep2

description: Mononucleosomal DNA

value: h- leu1-32 ura4::ura4_linker


title: MN_Spombe_Ura_octosporus_Remastered_Rep1

description: Mononucleosomal DNA


title: MN_Spombe_UraInt_Rep2

description: Mononucleosomal DNA


title: MN_Spombe_UraLinker_Rep1

description: Mononucleosomal DNA


title: MN_Spombe_Figure2_Random_Rep2

description: Mononucleosomal DNA

value: h- KanMX-randomized sequence in IGR SPAC6F6.11c-SPAC6F6.12


title: MN_Spombe_SeqSp-Sp_Rep1

description: Mononucleosomal DNA

value: h- KanMX-SeqSp in IGR SPAC6F6.11c-SPAC6F6.12


title: MN_Spombe_Ura_japonicus_Remastered_Rep2

description: Mononucleosomal DNA


title: MN_Spombe_Figure2_Random_Rep1

description: Mononucleosomal DNA


title: MN_Spombe_Figure2_WT_Rep2

description: Mononucleosomal DNA

value: h- KanMX in IGR SPAC6F6.11c-SPAC6F6.12


title: MN_Spombe_UraCodonShuffled_Rep2

description: Mononucleosomal DNA

value: h- leu1-32 ura4::ura4_Shuffled


title: MN_Spombe_Figure2_WT_Rep1

description: Mononucleosomal DNA


title: MN_Spombe_UraCodonShuffled_Rep1

description: Mononucleosomal DNA


title: MN_Spombe_UraDyad_Rep1

description: Mononucleosomal DNA


title: MN_Spombe_Ura1-3_Rep1

description: Mononucleosomal DNA


title: MN_Spombe_Ura1-3_Rep2

description: Mononucleosomal DNA


title: MN_Spombe_Ura1-6_Rep2

description: Mononucleosomal DNA


title: MN_Spombe_Ura1-6_Rep1

description: Mononucleosomal DNA


title: MN_Spombe_972h-_Rep1

description: Mononucleosomal DNA


title: MN_Spombe_SeqSp-Sp_Rep2

description: Mononucleosomal DNA


title: MN_Spombe_972h-_Rep2

description: Mononucleosomal DNA


title: 1772071034_D03

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

data_processing:
Read processing was performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6), except that we removed any RNA molecule (i.e. Unique Molecular Identifier) supported only by a single read ("singleton molecules"). This removed a large number of false positive molecules, artefacts that can arise by sequencing error, PCR-induced mutations or translocations and cross-contamination.
The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA sythesis.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Tab-delimited table of total number of detected mRNA molecules from each gene in each cell

source_name: epidermis

growth_protocol: C57BL/6 mice (Charles River) were sacrificed at P56 +/-4 days and hair cycle stages were determined by staining dorsal skin sections for Ki67. Mice that showed signs of early anagen were excluded from this analysis. All animal experiments were performed in accordance with the Swedish legislation.

extract_protocol:
Clipped and disinfected dorsal skin was isolated, dermal and adipose tissue was removed and strips of skin were floated on trypsin (Sigma) for 2h at 32°C.  Epidermal tissue was subsequently scraped into S-MEM / 1% BSA and single cells were isolated by magnet stirring at 120 rpm for 25 min / RT. The resulting cell suspension was filtered through 70 µm and 40 µm cell strainers, resuspended in in Defined Keratinocyte Serum-free Medium (DK-SFM) without supplement (Life Technologies) and Sca1+ and Sca1- were separated using Anti-Sca1-FITC magnetic beads (Miltenyi Biotec) according to the manufacturer’s instructions. Cells were stored on ice in DK-SFM with 0.1 mg/ml DNase I (Stem Cell Technologies) until capturing. Before capturing, the cell suspension was carefully resuspended and two times passed through a 20 µm cell strainer. Epidermal cells were captured on a medium microfluidic chip (designed for cells from 10 µm – 17 µm) using the Fluidigm C1 Autoprep System. 14 µl filtered cell suspension (about 750 cells / µl in DK-SFM with DNase I) was mixed with 6 µl C1 Suspension Reagent and 14 µl were loaded onto the chip. Single-cells were then captured for 30 min at 4°C using the “Cell Load (1772x/1773x)” script.
Lysis mix, RT mix and PCR mix (described in Islam et al., Nat Methods. 2014 Feb;11(2):163-6) were added to the chip. The plate was placed in the Fluidigm C1 instrument and the 'mRNA Seq: RT + Amp (1772x/1773x)' script was executed, and included lysis, reverse transcription and 21 cycles of PCR. The amplified cDNA was harvested in a total of 13 μL C1 Harvesting Reagent. Amplified cDNA was simultaneously fragmented and barcoded by tagmentation using Tn5 DNA transposase to transfer adaptors to the target DNA as described (Ibid.). 100 µl Dynabeads MyOne Streptavidin C1 beads (Invitrogen) were washed in 2× BWT (10 mM Tris-HCl, pH 7.5, 1 mM EDTA, 2 M NaCl, 0.02% Tween-20) and resuspended in 2 ml 2× BWT. Twenty microliters of beads were added to each well and incubated at room temperature for 15 min. All fractions were pooled, the beads were immobilized and the supernatant removed. The beads were resuspended in 100 μL TNT (20 mM Tris, pH 7.5, 50 mM NaCl, 0.02% Tween), washed in 100 μL Qiagen Qiaquick PB, and twice in 100 μL TNT. The beads were resuspended in 100 μL restriction mix (1× NEB CutSmart, 0.4 U/μL PvuI-HF enzyme), designed to cleave 3′ fragments carrying a PvuI recognition site. The mix was incubated for 1 h at 37 °C, then washed three times in TNT. Finally, to elute DNA, beads were resuspend in 30 µL ddH2O and incubated 10 minutes at 70°C. Beads were then immediately bound to magnet and the supernatant was collected. To remove short fragments,  Ampure beads (Beckman Coulter) were used at 1.8× volume and eluted in 30 µL.

tag: cell type level 1

value: IFE-DII

tag: Sex

value: female

tag: age

value: epidermis


title: 1772071034_C05

value: TC


title: 1772071034_C09


title: 1772071034_C06

value: OB


title: 1772071034_D04

value: uHF-III


title: 1772071034_D07

value: uHF-II


title: 1772071034_D02


title: 1772071034_D01

value: LH


title: 1772071034_B12


title: 1772071034_C03

value: IB


title: 1772071034_B06


title: 1772071034_A12

value: IFE-B


title: 1772071034_B05

value: uHF-I


title: 1772071034_A11


title: 1772071034_B01


title: 1772071034_A08

value: IFE-KI


title: 1772071034_A03

value: IFE-DI


title: 1772071034_A01


title: 1772071034_A02


title: 1772071032_H10


title: 1772071032_H12


title: 1772071032_H01


title: 1772071034_A05


title: 1772071032_G10


title: 1772071032_H05


title: 1772071032_E08


title: 1772071032_F09


title: 1772071032_F02


title: 1772071032_F05


title: 1772071032_F03


title: 1772071032_G04


title: 1772071032_F11


title: 1772071032_D12


title: 1772071032_G06


title: 1772071032_E10


title: 1772071032_E07


title: 1772071032_E02


title: 1772071032_E05


title: 1772071032_D07


title: 1772071032_D06


title: 1772071032_D10


title: 1772071032_D09


title: 1772071032_E04


title: 1772071032_E01


title: 1772071032_D04


title: 1772071032_D02


title: 1772071032_G08


title: 1772071032_C08


title: 1772071032_C05


title: 1772071032_C06


title: 1772071032_C03


title: 1772071032_D11


title: 1772071032_C02


title: 1772071032_B12


title: 1772071032_B10


title: 1772071032_B07


title: 1772071032_B09


title: 1772071032_B03


title: 1772071032_B01


title: 1772071032_A07


title: 1772071032_C09


title: 1772071032_A04


title: 1772071032_A08


title: 1772071032_A06


title: 1772071026_H06


title: 1772071034_A04


title: 1772071026_H05


title: 1772071032_A01


title: 1772071032_A02


title: 1772071026_H11


title: 1772071026_G05


title: 1772071026_G11


title: 1772071026_F12


title: 1772071026_G06


title: 1772071026_F07


title: 1772071026_F10


title: 1772071032_B02


title: 1772071032_B04


title: 1772071026_F05


title: 1772071026_E04


title: 1772071026_E10


title: 1772071026_D10


title: 1772071032_A12


title: 1772071026_E06


title: 1772071026_H04


title: 1772071026_D09


title: 1772071026_D08


title: 1772071026_D07


title: 1772071026_C05


title: 1772071026_C03


title: 1772071026_B09


title: 1772071026_C12


title: 1772071026_B04


title: 1772071026_B07


title: 1772071026_B05


title: 1772071026_B01


title: 1772071026_A11


title: 1772071026_B02


title: 1772071026_A07


title: 1772071026_A10


title: 1772071026_A02


title: 1772071026_A05


title: 1772071025_H10


title: 1772071026_B10


title: 1772071025_H07


title: 1772071025_H03


title: 1772071025_H01


title: 1772071025_G06


title: 1772071025_G12


title: 1772071026_F04


title: 1772071025_G10


title: 1772071026_B03


title: 1772071025_G04


title: 1772071025_E09


title: 1772071025_F06


title: 1772071025_F03


title: 1772071025_E03


title: 1772071025_D06


title: 1772071025_E07


title: 1772071025_E06


title: 1772071025_D08


title: 1772071025_E12


title: 1772071025_D04


title: 1772071025_D03


title: 1772071025_C09


title: 1772071025_C08


title: 1772071025_C10


title: 1772071025_C05


title: 1772071026_D12


title: 1772071025_D01


title: 1772071026_B08


title: 1772071025_C03


title: 1772071025_B07

value: IFE-KII


title: 1772071025_A10


title: 1772071025_A09


title: 1772071025_A07


title: 1772071025_A03


title: 1772071025_B06


title: 1772067095_H05


title: 1772071025_A01


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title: 1772071025_B12


title: 1772067095_G10


title: 1772067095_G05


title: 1772067095_H12


title: 1772071025_A12


title: 1772067095_H04


title: 1772067095_G04


title: 1772067095_F12


title: 1772067095_F10


title: 1772067095_F05


title: 1772067095_E11


title: 1772067095_E06


title: 1772067095_D08


title: 1772067095_D07


title: 1772067095_E05


title: 1772067095_D06


title: 1772067095_D05


title: 1772067095_D11


title: 1772067095_C09


title: 1772067095_B10


title: 1772067095_B07


title: 1772067095_B04


title: 1772071025_C02


title: 1772071025_A05


title: 1772067095_A11


title: 1772067095_B03


title: 1772067095_A01


title: 1772067095_A06


title: 1772067095_C01


title: 1772067090_H11


title: 1772067090_H06


title: 1772067090_H04


title: 1772067090_H05


title: 1772067090_H02


title: 1772067090_G12


title: 1772067095_D03


title: 1772067095_D01


title: 1772067095_C11


title: 1772067095_C06


title: 1772067090_G10


title: 1772067090_H10


title: 1772067090_G06


title: 1772067095_A04


title: 1772067090_G04


title: 1772067090_H12


title: 1772067095_A08


title: 1772067090_F12


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title: 1772067095_A02


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title: 1772067090_G05


title: 1772067090_F06


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title: 1772067090_D12


title: 1772067090_D11


title: 1772067090_E12


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title: 1772067090_D08


title: 1772067090_D09


title: 1772067090_D05


title: 1772067090_D06


title: 1772067090_G02


title: 1772067090_D04


title: 1772067090_F10


title: 1772067090_E10


title: 1772067090_C06


title: 1772067090_B11


title: 1772067090_C04


title: 1772067090_C05


title: 1772067090_C12


title: 1772067090_C02


title: 1772067090_C03


title: 1772067090_B04


title: 1772067090_B08


title: 1772067090_C11


title: 1772067090_B06


title: 1772067090_B01


title: 1772067090_C10


title: 1772067090_C01


title: 1772067090_A11


title: 1772067090_B02


title: 1772067090_A10


title: 1772067090_A08


title: 1772067090_A04


title: 1772067090_A07


title: 1772067090_A03


title: 1772067087_H11


title: 1772067087_H08


title: 1772067090_A02


title: 1772067087_H12


title: 1772067087_H05


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title: 1772067087_G11


title: 1772067090_A06


title: 1772067087_F10


title: 1772067087_G06


title: 1772067087_E06


title: 1772067087_F12


title: 1772067087_H02


title: 1772067087_D11

value: SG


title: 1772067087_G02


title: 1772067087_G05


title: 1772067087_E04


title: 1772067087_E08


title: 1772067087_F04


title: 1772067087_D12


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title: 1772067087_D10


title: 1772071034_A10


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title: 1772067087_F01


title: 1772067087_D03


title: 1772067087_E11


title: 1772067087_C10


title: 1772067087_E12


title: 1772067087_C08


title: 1772067087_C06


title: 1772067087_C04


title: 1772067087_C03


title: 1772067087_B12


title: 1772067087_B06


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title: 1772067087_A12


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title: 1772067095_D09


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title: 1772067086_D03


title: 1772067086_D01


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title: 1772067086_C10


title: 1772067086_C06


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title: 1772067086_C05


title: 1772067086_F05


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title: 1772067086_C12


title: 1772067086_B03


title: 1772067086_B11


title: 1772067086_C02


title: 1772067086_A06


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title: 1772067086_A03


title: 1772067085_H10


title: 1772067086_A05


title: 1772067085_H03


title: 1772067085_H07


title: 1772067086_A02


title: 1772067085_H01


title: 1772067085_G08


title: 1772067085_G10


title: 1772067085_E10


title: 1772067085_F08


title: 1772067085_F09


title: 1772067085_E09


title: 1772067086_B01


title: 1772067085_E03


title: 1772067085_E02


title: 1772067085_E12


title: 1772067085_D07


title: 1772067086_B04


title: 1772067085_D05


title: 1772067085_E01


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title: 1772067085_B07


title: 1772067085_H05


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title: 1772067085_B11


title: 1772067085_D01


title: 1772067085_B03


title: 1772067085_B05


title: 1772067085_B04


title: 1772067085_A10


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title: 1772067056_B06


title: 1772067056_A10


title: 1772067055_H11


title: 1772067055_H06


title: 1772067055_H08


title: 1772067055_G09


title: 1772067055_G10


title: 1772067055_G12


title: 1772067055_H12


title: 1772067055_H04


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title: GQF-7

city: Zurich

first: Bisrat

middle: Tewhibe

last: Woldemichael

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: Swiss Institute of Technology/University of Zurich

description:
total RNA (size fractionated)
processed data file: untrained_vs_trained_NIPP1.csv

data_processing:
Instrument: Hi-seq 2000, Number of sequencing cycles: 1 x 50 + 7 (index); Sequencing kit: TruSeq(TM) SBS v5; Tiles: 32; Data Analysis Pipeline: HiSeq Control Soft. v. 1.3.8, RTA 1.10.36, CASAVA 1.7.0; OLB-1.9.0
ncPro-seq pipeline was used for read alignment and profiling. Inserts of size 18 to 26 nt were aligned to reference genome using Bowtie, and BEDTools was used to find overlap between read alignments and miRNA families. Reads with 100% overlap with annotations are counted and normalized to total reads, and reads per million bases (RPM) were computed (Chen et al., 2012, Bioinformatics, Vol 28).
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: tab delimited csv files containing average read counts and adjusted p values for each pair of samples; bed files with mean read counts of annotated miRNA reads

source_name: trained NIPP1*

extract_protocol:
Mouse hippocampal tissue was homogenized using TissueLyser (Qiagen) in Trizol® reagent (Invitrogen). Total RNA was extracted by phenol-chlorofom precipitation.
The quality and quantity of RNA was determined by running the samples on a Bioanalyzer ® (Agilent) and Qubit® fluorometer (Invitrogen) respectively. Small RNA libraries were prepared from 1ug of total RNA using TruSeq® Small RNA Kit (Illumina) according to manufacturer’s instructions. Briefly, 3’ and 5’ adapters were ligated to small RNAs using T4 DNA ligase. Ligated RNA was reverse transcribed to cDNA using superscript II reverse transcriptase. The resulting cDNA template was amplified by PCR to generate a cDNA library. For each sample, a common forward primer (which binds to the 5’ adapter complement) and a unique reverse primer (which binds to the 3’ adapter complement and contains a unique sequence for each sample) were used.  The quality of the resulting amplicons was analyzed on a high sensitivity DNA ChIP (Bioanalyzer). Next, the cDNA construct was run on a 6% PAGE gel and amplicons corresponding to adapter ligated miRNA sequences (145-160nt) were excised out. DNA from excised gel was eluted and precipitated in Ethanol. The size, purity, and amount of cDNA was assessed on high sensitivity DNA ChIP (Bioanalzyer).  Then a titration run was done to check quality of the library and validate the amount.

value: transgenic NIPP1* (PP1 loss of function)

value: hippocampus

value: adult (3-5 months)


title: RNAse_T1-S7_mouse

first: Maxim

last: Gerashchenko

state: Massachusetts

address: 77 Louis Pasteur Ave, NRB 435

department: Medicine

institute: Brigham and Women's Hospital

description: Ribo-seq (Ribosome profiling, ART-seq)

data_processing:
adapter removal: cutadapt -u 1 -m 12 -a AGATCGGAAGAGCACACGTCT
mouse data mapping: tophat --transcriptome-index -T --library-type fr-firststrand -N 1 --read-gap-length 1 --read-edit-dist 1
yeast data mapping: bowtie1
mouse read count: HTseq-count
yeast read count: custom Perl script
Genome_build: yeast S288C (annotation 2012 SGD Saccharomyces cerevisiae.gff); mouse genome-build GRCm38.p3 (NCBI annotation 2015 Release 105)
Supplementary_files_format_and_content: mouse_expression.txt: htseq-count, containing ribosomal footprints per gene count
Supplementary_files_format_and_content: yeast_expression.txt: ribosomal footprints per gene count

source_name: mouse treated with RNases S7 and T1

extract_protocol:
3' adapter sequence, required for raw read trimming: AGATCGGAAGAGCACACGTCT
Libraries were prepared according to the protocol published in Gerashchenko MV, Gladyshev VN.,"Translation inhibitors cause abnormalities in ribosome profiling experiments", (2014), Nucleic Acids Res

value: liver


title: GQF-6

description: total RNA (size fractionated)


title: GQF-4

description:
total RNA (size fractionated)
processed data file: trained_wildtype_vs_trained_NIPP1.csv

source_name: trained wildtype

value: wildtype


title: GQF-1

description:
total RNA (size fractionated)
processed data file: untrained_vs_trained_wildtype.csv

source_name: untrained wildtype


title: GQF-2

description:
total RNA (size fractionated)
processed data file: untrained_wildtype_vs_untrained_NIPP1.csv

source_name: untrained NIPP1*


title: ESC_Sirt1KO_Otx2KD_rep2

city: Cambridge

first: Eric

last: Williams

state: Ma

department: Biology

institute: Massachusetts Institute of Technology

data_processing:
RNA seq libraries were sequenced with on an Illumina Hi Seq 2000 machine
FASTQ files were aligned to NCBI/mm9 reference genome using the Tophat aligner
Analysis of differential expression was performed using Cuffdiff from the Cufflinks package
Genome_build: mm9
Supplementary_files_format_and_content: comma-delimited files include FPKM values for each sample

growth_protocol:
ESCs were cultured on 0.1% gelatin coated plates in serum-free N2B27 medium composed of 1:1 Neurobasal (Invitrogen): DMEM/F12 (Invitrogen) media, 1% N2 supplement (Invitrogen), 1% B27 supplement (Invitrogen), 0.1 mM L-glutamine (Invitrogen), 1% penicillin/streptomycin (Invitrogen), 1% non-essential amino acids (Invitrogen), 0.033% BSA (Invitrogen), and 0.1 mM b-mercaptoethanol (Sigma). The naïve state was maintained by application of 2i+LIF which included the MEK inhibitor PD0325901 (1uM) (Sigma), GSK3b inhibitor (CHIR99021) (3uM) (Sigma) and mouse recombinant LIF.
Differentiation to EpiLCs was performed as previously described (Buecker et al., 2014; Hayashi et al., 2011). mESC were passaged 3-5 times in N2B27 2i+LIF and transferred to fibronectin coated plates. Differentiating cells were stimulated with 12 ng/ml Fgf2 (Invitrogen), 20ng/ml Activin A (Sigma), and 1% KOSR (Invitrogen) for 48 hours.

extract_protocol:
RNA was extracted with Trizol and purified using Direct-zol RNA miniprep kit (Zymo Research). RNA was subjected to oligo-dT purification and converted to cDNA using the Illumina Tru-Seq protocol.
Libraries were prepared using the automated Solid Phase Reversible Immbolization TE Nucleic Acid Extractor system.

value: C57 Bl/6J

value: ESC

tag: genotype/variation

value: Sirt1KO, Otx2KD


title: ESC_Sirt1KO_Otx2KD_rep3


title: 1772067055_H05

value: female

value: epidermis


title: 1772067055_H03


title: RNAse_S7_mouse

description: Ribo-seq (Ribosome profiling, ART-seq)

source_name: mouse treated with RNase S7


title: EpiLC_Wild Type_rep3

source_name: EpiLC_Wild Type

tag: differentiated cell type

value: EpiLC

value: wild type


title: ESC_Sirt1KO_rep2


title: ESC_Sirt1KO_rep3


title: RNAse_T1_mouse

description: Ribo-seq (Ribosome profiling, ART-seq)

source_name: mouse treated with RNase T1


title: EpiLC_Wild Type_rep1


title: 1772067055_G06

value: IFE-B


title: ESC_Wild_Type_rep2


title: ESC_Sirt1KO_Otx2KD_rep1


title: 1772067055_F08


title: ESC_Sirt1KO_rep1


title: ESC_Wild_Type_rep3


title: ESC_Wild_Type_rep1


title: GQF-5

description: total RNA (size fractionated)

tag: genotype


title: GQF-3

description: total RNA (size fractionated)

tag: developmental stage


title: ob4

city: Shanghai

first: Yuyao

last: Zhang

address: 320 Yueyang Road

institute: Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

data_processing:
Basecalling using Illumina Casava1.8.2 software
Map to mouse genome mm10 using Tophat(v 2.0.13)
Bam to Bedgraph using genomeCoverageBed,Bedgraph to bigwig using UCSC bedGraphToBigWig
Counted the mapping reads and normalized as FPKM values using Cufflinks.
Differential expression analysis was carried out using the R (v.3.1.1) package DEGseq (v.1.20.0)
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file (UCSC bigwig in an indexed binary format. http://genome.ucsc.edu/goldenPath/help/bigWig.html)

source_name: liver tissue

extract_protocol:
After snap-frozen, total RNA of livers was extracted using Trizol reagent.
Libraries were prepared for sequencing using standard Illumina protocols

value: FC-ob

value: 12-week old

tag: gender


title: ob3


title: ob1


title: ob2


title: DKO4

value: MRKO-ob


title: DKO3


title: DKO2


title: EpiLC_Wild Type_rep2


title: 1772072285_E06

value: OB


title: 1772072285_E02

value: IFE-KI


title: DKO1


title: 1772072285_G06


title: 1772072285_D12

value: uHF-I


title: 1772072285_D09


title: 1772072285_D05

value: IFE-DI


title: 1772072285_D01

value: IB


title: 1772072285_D06


title: 1772072285_C12

value: uHF-II


title: 1772072285_C08


title: 1772072285_D03


title: 1772072285_C10


title: 1772072285_C06


title: 1772072285_B12


title: 1772072285_C09


title: 1772072285_B07


title: 1772072285_C01

value: uHF-III


title: 1772072285_B10


title: 1772072285_B05


title: 1772072285_B11


title: 1772072285_B06


title: 1772072285_B04


title: 1772072285_B03


title: 1772072285_B02


title: 1772072285_B01


title: 1772072285_A11


title: 1772072285_A12


title: 1772072285_C11


title: 1772072284_H12

value: SG


title: 1772072284_G12

value: IFE-DII


title: 1772072285_A02

value: female


title: 1772072285_A03

value: epidermis


title: 1772072284_H11


title: 1772072284_H05


title: 1772072284_G06


title: 1772072284_F11


title: 1772072284_G11


title: 1772072284_F05


title: 1772072284_G02


title: 1772072284_F04


title: 1772072284_F09


title: 1772072284_F10

value: LH


title: 1772072285_A05


title: 1772072284_G05


title: 1772072284_G03


title: 1772072284_E11


title: 1772072284_E04


title: 1772072285_A09


title: 1772072284_D02


title: 1772072284_C11


title: 1772072284_D01


title: 1772072284_D05


title: 1772072284_C08


title: 1772072284_C06


title: 1772072284_C05


title: 1772072284_E10


title: 1772072284_C04


title: 1772072284_C02


title: 1772072284_B10


title: 1772072284_B02


title: 1772072284_B01


title: 1772072284_A10


title: 1772072284_A08


title: 1772072284_A05


title: 1772072284_A03


title: 1772072284_A01

value: IFE-KII


title: 1772072284_A02


title: 1772072283_G02


title: 1772072283_H01


title: 1772072283_H08


title: 1772072284_E01


title: 1772072283_G06


title: 1772072283_G03


title: 1772072283_G05


title: 1772072283_G04


title: 1772072283_F07


title: 1772072283_G11


title: 1772072283_F03


title: 1772072283_F01

value: TC


title: 1772072283_F06


title: 1772072283_F11


title: 1772072283_F08


title: 1772072283_E07


title: 1772072283_E10


title: 1772072283_E05


title: 1772072283_E06


title: 1772072283_E02


title: 1772072283_D08


title: 1772072283_D12

value: IFE-B


title: 1772072283_H09


title: 1772072283_D04


title: 1772072283_D03


title: 1772072283_C02


title: 1772072283_C08


title: 1772072283_D02


title: 1772072283_B09


title: 1772072283_C05


title: 1772072283_B08


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title: 1772072283_B01


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title: 1772072282_H10


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title: 1772072282_G12


title: 1772072283_D06


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title: 1772072283_C01


title: 1772072282_F01


title: 1772072282_E07


title: 1772072282_E09


title: 1772072282_D10


title: 1772072282_E03


title: 1772072283_A11


title: 1772072283_A01


title: 1772072282_D07


title: 1772072282_D04


title: 1772072282_D02


title: 1772072282_D05


title: 1772072282_H05


title: 1772072282_C10


title: 1772072282_C11


title: 1772072282_C02


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title: 1772072282_C01


title: 1772072282_F02


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title: 1772072282_B06


title: 1772072282_B08


title: 1772072282_B03


title: 1772072282_B04


title: 1772072282_A10


title: 1772072282_A12


title: 1772072282_A08


title: 1772072282_D06


title: 1772072282_A09


title: 1772072276_H09


title: 1772072282_A03


title: 1772072282_C08


title: 1772072276_G01


title: 1772072276_H05


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title: 1772072276_F10


title: 1772072276_F12


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title: 1772072276_E07


title: 1772072276_F09


title: 1772072276_E09


title: 1772072276_E02


title: 1772072276_E12


title: 1772072276_D12


title: 1772072276_D06


title: 1772072276_D08


title: 1772072276_D03


title: 1772072276_D02


title: 1772072276_C05


title: 1772072276_C08


title: 1772072276_C09


title: 1772072276_C02


title: 1772072276_C03


title: 1772072276_B11


title: 1772072276_B08


title: 1772072276_E05


title: 1772072276_B03


title: 1772072283_A09


title: 1772072276_A08


title: 1772072276_B05


title: 1772072276_B10


title: 1772072276_A12


title: 1772072276_A07


title: 1772072276_D10


title: 1772072276_A04


title: 1772072275_H08


title: 1772072275_H06


title: 1772072275_H12


title: 1772072276_A06


title: 1772072275_H05


title: 1772072275_H02


title: 1772072275_G07


title: 1772072275_G09


title: 1772072275_G04


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title: 1772071039_G05


title: 1772071051_A10


title: 1772071039_H06


title: 1772071051_A06


title: 1772071051_A05


title: 1772071039_F10


title: 1772071039_F12


title: 1772071039_F05


title: 1772071039_F06


title: 1772071039_D12


title: 1772071039_E08


title: 1772071039_F11


title: 1772071039_H12


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title: 1772071039_E10


title: 1772071039_D10


title: 1772071039_D01


title: pDC TG 4

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

data_processing:
FastQC v0.11.4 is used to check the quality of the samples
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic v0.35 with parameters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:35
Sequenced reads were then mapped to mm10 transcriptome using Tophat2 v2.1.0 with parameters --library-type fr-unstranded --min-intron-length 50 --no-coverage-search
The mapping files were then filtered using samtools v0.1.18 (samtools view with parameters -bq 20) and sorted using samtools sort
Reads were counted using HTSeqCount v0.6.1p1 with parameters -f bam -m intersection-strict -s no -a 10 -t exon -i gene_id
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including raw counts (output HTSeqCount) for each sample

source_name: pDCs from spleen Irf8fl/fl Itgax-cre mice 4

growth_protocol: Spleens were harvested from mice aged between 6 and 12 weeks

extract_protocol:
Spleens were digested in RMPI containing 20mg/ML Liberase and 10U/ml DNase (37oC for 30minutes). Single cell suspensions were filtered through a 70mM strainer and stained with antibodies to allow cDC1s and cDC2s to be isolated by FACS.
RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 4 ng of total RNA was used as input for the SMART-Seq v4 Ultra Low Input RNA protocol (version “040215”) from Clontech Laboratories, Inc. Subsequently, 1ng of purified cDNA was sheared to 300bp using the Covaris M220. From the sheared material, sequencing libraries were prepared with the NEBNext Ultra DNA Library Prep Kit for Illumina (version 3.0 -8/15), according to the manufacturer’s protocol including a size selection to 250bp insert size with the following minor modifications: only half of the library is subjected to a 15 cycle PCR in the final library amplification step. Sequence-libraries of each sample were equimolarly pooled and sequenced on 2 NextSeq500 flow-cells at 1x75 bp with a v2 high-output kit.

treatment_protocol: Steady state mice were used - no treatement

value: Spleen

tag: state

value: Irf8fl/fl Itgax-cre steady state

value: plasmacytoid dendritic cells


title: pDC TG 2

source_name: pDCs from spleen Irf8fl/fl Itgax-cre mice 2


title: pDC WT 8

source_name: pDCs from spleen Irf8fl/fl mice 8

value: Irf8fl/fl steady state


title: 1772071039_D07

value: IFE-KI


title: 1772071039_H11


title: 1772071039_C10


title: 1772071039_C03

value: uHF-I


title: pDC TG 3

source_name: pDCs from spleen Irf8fl/fl Itgax-cre mice 3


title: pDC TG 1

source_name: pDCs from spleen Irf8fl/fl Itgax-cre mice 1


title: 1772071039_C09


title: 1772071039_C07


title: pDC WT 2

source_name: pDCs from spleen Irf8fl/fl mice 2


title: 1772071039_B10


title: 1772071039_B02


title: pDC WT 6

source_name: pDCs from spleen Irf8fl/fl mice 6


title: pDC WT 4

source_name: pDCs from spleen Irf8fl/fl mice 4


title: pDC WT 5

source_name: pDCs from spleen Irf8fl/fl mice 5


title: 1772071039_C05

source_name: epidermis

value: IFE-DI


title: 1772071039_H10


title: 1772071039_A11


title: 1772071039_B09


title: 1772071039_A03


title: cDC2 WT 3

source_name: cDC2s from spleen Irf8fl/fl mice 3

value: CD172a+ conventional dendritic cells (cDC2s)


title: cDC2 WT 4

source_name: cDC2s from spleen Irf8fl/fl mice 4


title: cDC2 WT 2

source_name: cDC2s from spleen Irf8fl/fl mice 2


title: 1772071039_B03


title: 1772071051_B06


title: pDC WT 1

source_name: pDCs from spleen Irf8fl/fl mice 1


title: cDC2 WT 6

source_name: cDC2s from spleen Irf8fl/fl mice 6


title: cDC2 WT 8

source_name: cDC2s from spleen Irf8fl/fl mice 8


title: 1772071039_B01


title: 1772071037_H05


title: cDC1 WT 8

source_name: cDC1s from spleen Irf8fl/fl mice 8

value: CD24+ conventional dendritic cells (cDC1s)


title: cDC2 WT 7

source_name: cDC2s from spleen Irf8fl/fl mice 7


title: pDC WT 7

source_name: pDCs from spleen Irf8fl/fl mice 7


title: 1772071039_D03


title: 1772071039_A08

value: uHF-II


title: 1772071037_G07

value: IFE-DII


title: cDC2 WT 5

source_name: cDC2s from spleen Irf8fl/fl mice 5


title: 1772071037_H12

value: female


title: pDC WT 3

source_name: pDCs from spleen Irf8fl/fl mice 3


title: 1772071039_A02

value: epidermis


title: 1772071037_H10


title: cDC2 WT 1

source_name: cDC2s from spleen Irf8fl/fl mice 1


title: 1772071037_H02


title: cDC1 WT 7

source_name: cDC1s from spleen Irf8fl/fl mice 7


title: cDC1 WT 1

source_name: cDC1s from spleen Irf8fl/fl mice 1


title: 1772071037_G12


title: 1772071037_G11


title: cDC1 WT 5

source_name: cDC1s from spleen Irf8fl/fl mice 5


title: 1772071037_G06


title: cDC1 WT 6

source_name: cDC1s from spleen Irf8fl/fl mice 6


title: 1772071037_G10

source_name: epidermis


title: 1772071037_E12


title: 1772071037_F07


title: 1772071037_E10


title: cDC1 WT 4

source_name: cDC1s from spleen Irf8fl/fl mice 4


title: cDC1 WT 3

source_name: cDC1s from spleen Irf8fl/fl mice 3


title: 1772071037_G08


title: cDC1 WT 2

source_name: cDC1s from spleen Irf8fl/fl mice 2


title: 1772071037_E11


title: 1772071037_G05


title: 1772071037_G04


title: 1772071037_E06


title: 1772071037_E05


title: 1772071037_E04


title: 1772071037_D12


title: 1772071037_E03


title: 1772071037_E01


title: 1772071037_D03


title: 1772071037_D02


title: 1772071037_D05


title: 1772071037_D04


title: 1772071037_C10


title: 1772071037_C09


title: 1772071037_C12


title: 1772071037_C11


title: 1772071037_C04


title: 1772071037_C06


title: 1772071037_B12


title: 1772071037_C02


title: 1772071037_C03


title: 1772071037_B10


title: 1772071037_C08


title: 1772071037_B08


title: 1772071037_C01


title: 1772071037_B07


title: 1772071037_B03


title: 1772071037_B04


title: 1772071037_B09


title: 1772071037_B06


title: 1772071037_A09


title: 1772071037_B02


title: 1772071037_A08


title: 1772071037_A07


title: 1772071037_C05


title: 1772071037_A06


title: 1772071037_A02


title: 1772071037_A03


title: 1772071034_H12


title: 1772071037_A05


title: 1772071037_A01


title: 1772071034_H08


title: 1772071034_G08


title: 1772071034_G04

value: OB


title: 1772071034_G05


title: 1772071034_F12


title: 1772071034_G12


title: 1772071037_B05


title: 1772071034_F05

value: uHF-III


title: 1772071034_F04


title: 1772071034_E12


title: 1772071034_F03


title: 1772071034_E11


title: 1772071034_E07


title: 1772071034_E10


title: 1772071034_D10


title: 1772071034_E04


title: 1772071034_E01


title: 1772071034_D08


title: 1772067055_F05


title: 1772067055_F07


title: 1772067055_F06


title: 1772067055_E12


title: 1772067055_E07


title: 1772067055_E06


title: 1772067055_E09


title: 1772067055_E03


title: 1772067055_E05


title: 1772067055_E11


title: 1772067055_D10


title: 1772071034_F10


title: 1772067055_E02


title: 1772067055_D06


title: 1772067055_D05


title: 1772067055_D09


title: 1772067055_F04


title: 1772067055_D04


title: 1772067055_C10


title: 1772067055_C12


title: rRNA depletion US-1494958

city: Spartanburg

first: Bernard

last: Omolo

state: SC

address: 800 University Way

department: Mathematics and Computer Science

institute: University of South Carolina - Upstate

data_processing:
Libraries were normalized to 22 pM and subjected to cluster and single read sequencing was performed for 50 cycles on a HiSeq2500 instrument (Illumina, Inc. San Diego, CA, USA), according to the manufacturer's instructions. Base calling were done on the HiSeq instrument by RTA 1.17.21.3. FASTQ files were generated using CASAVA 1.8.2 (Illumina, Inc. San Diego, CA, USA).
FASTQ files were subjected to quality control with the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Raw reads from each capture library were aligned to the human reference genome (hg19). Reads were aligned by STAR_2.3.1 and processed with cufflinks.
Genome_build: human reference genome (hg19)
Supplementary_files_format_and_content: log2-transormed and z-score-normalized FPKM

extract_protocol:
RNA was isolated from FFPE samples using the QIAGEN RNA Purification Kit and quantified using ribogreen assay. Quality of RNA was assessed using using Agilent RNA 6000 Nano Kit on a 2100 Bioanalyzer instrument (Agilent Technologies, Santa Clara, CA, USA) and the percentages of fragments larger than 200 nucleotides were calculated.
RNA samples (100 ng total RNA) were fragmented at 94°C for 8 minutes on a thermal cycler. First strand cDNA syntheses were performed at 25°C for 10 minutes, 42°C for 15 minutes and 70°C for 15 minutes, using random hexameres and SuperScript II Reverse Transcriptase (Thermo Fisher Scientific Inc., Waltham, MA, USA). In a second strand cDNA synthesis the RNA templates were removed and a second replacement strand was generated by incorporation dUTP (in place of dTTP, to keep strand information) to generate ds cDNA. AMPure XP beads (Beckman Coulter, Inc., Indianapolis, IN, USA) were used to clean up the blunt-ended cDNA from the second strand reaction mix. The 3`ends of the cDNA were then adenylated to facilitate adaptor ligation in the next step. After ligation of indexing adaptors, AMPure XP beads were used to clean up the libraries. In a first PCR amplification step, PCR (15 cycles of 98°C for 10 seconds, 60°C for 30 seconds and 72°C for 30 seconds) were used to selectively enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. After validation of the libraries, using Agilent DNA 1000 kit on a 2100 Bioanalyzer instrument, the the libraries were quantitated by qPCR using KAPA Library Quantification Kit—Illumina/ABI Prism® (Kapa Biosystems, Inc., Wilmington, MA, USA) and validated using Agilent High Sensitivity DNA Kit on a Bioanalyzer. The size range of the DNA fragments were measured to be in the range of 200–650 bp and peaked around 250 bp.

value: colon


title: rRNA depletion US-1493881


title: rRNA depletion US-1493868


title: 1772067055_C08

value: IFE-KII


title: 1772067055_C06

value: IFE-B


title: rRNA depletion US-1493853


title: rRNA depletion US-1493855


title: 1772067055_D02


title: 1772067055_C05


title: rRNA depletion US-1493850


title: rRNA depletion US-1493847


title: 1772067055_C03


title: rRNA depletion US-1493831


title: rRNA depletion US-1493221


title: rRNA depletion US-1493211


title: 1772067055_B12


title: rRNA depletion US-1493212


title: rRNA depletion US-1493215


title: rRNA depletion US-1493195


title: rRNA depletion US-1493193


title: rRNA depletion US-1493189


title: rRNA depletion US-1493188


title: 1772067055_B07


title: 1772067055_B06


title: rRNA depletion US-1493187


title: rRNA depletion US-1493184


title: rRNA depletion US-1493183


title: rRNA depletion US-1493181


title: 1772067055_B04


title: rRNA depletion US-1493179


title: 1772067055_C01


title: rRNA depletion US-1493173


title: rRNA depletion US-1493154


title: 1772067055_B02


title: rRNA depletion US-1492051


title: rRNA depletion US-1493200


title: 1772067055_B11


title: 1772067055_B01


title: 1772067055_B10


title: 1772067055_A09


title: rRNA depletion US-1493194


title: rRNA depletion US-1492043


title: rRNA depletion US-1492048


title: rRNA depletion US-1493191


title: rRNA depletion US-1492034


title: 1772067055_B09


title: rRNA depletion US-1492040


title: 1772067055_A07


title: 1772067055_A06


title: rRNA depletion US-1492032


title: 1772067055_B03


title: rRNA depletion US-1492026


title: rRNA depletion US-1492030


title: rRNA depletion US-1492025


title: 1772067055_A04


title: rRNA depletion US-1492083


title: 1772067055_A03


title: rRNA depletion US-1492016


title: rRNA depletion US-1492014


title: rRNA depletion US-1492013


title: 1772067055_A01


title: rRNA depletion US-1492011


title: rRNA depletion US-1492010


title: rRNA depletion US-1492004


title: rRNA depletion US-1492006


title: rRNA depletion US-1492007


title: rRNA depletion US-1492009


title: rRNA depletion US-1491997


title: rRNA depletion US-1491995


title: rRNA depletion US-1492019


title: rRNA depletion US-1492003


title: rRNA depletion US-1492020


title: rRNA depletion US-1491986


title: 1772067055_A05


title: rRNA depletion US-1493176


title: rRNA depletion US-1492012


title: rRNA depletion US-1491993


title: Targeted US-1553374 3

data_processing:
Libraries were normalized to 22 pM and subjected to cluster and single read sequencing was performed for 50 cycles on a HiSeq2500 instrument (Illumina, Inc. San Diego, CA, USA), according to the manufacturer's instructions. Base calling were done on the HiSeq instrument by RTA 1.17.21.3. FASTQ files were generated using CASAVA 1.8.2 (Illumina, Inc. San Diego, CA, USA).
FASTQ files were subjected to quality control with the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Raw reads from each capture library were aligned to the human reference genome (hg19). Reads were aligned by STAR_2.3.1 and processed with cufflinks.
For this targeted RNA data, we used median normalization. We obtained the median for each of the samples and subtracted this number from each of the gene counts for the sample.
Genome_build: human reference genome (hg19)
Supplementary_files_format_and_content: Hits per sample

extract_protocol:
RNA was isolated from FFPE samples using the QIAGEN RNA Purification Kit and quantified using ribogreen assay. Quality of RNA was assessed using using Agilent RNA 6000 Nano Kit on a 2100 Bioanalyzer instrument (Agilent Technologies, Santa Clara, CA, USA) and the percentages of fragments larger than 200 nucleotides were calculated.
RNA samples (100 ng total RNA) were fragmented at 94°C for 8 minutes on a thermal cycler. First strand cDNA syntheses were performed at 25°C for 10 minutes, 42°C for 15 minutes and 70°C for 15 minutes, using random hexameres and SuperScript II Reverse Transcriptase (Thermo Fisher Scientific Inc., Waltham, MA, USA). In a second strand cDNA synthesis the RNA templates were removed and a second replacement strand was generated by incorporation dUTP (in place of dTTP, to keep strand information) to generate ds cDNA. AMPure XP beads (Beckman Coulter, Inc., Indianapolis, IN, USA) were used to clean up the blunt-ended cDNA from the second strand reaction mix. The 3`ends of the cDNA were then adenylated to facilitate adaptor ligation in the next step. After ligation of indexing adaptors, AMPure XP beads were used to clean up the libraries. In a first PCR amplification step, PCR (15 cycles of 98°C for 10 seconds, 60°C for 30 seconds and 72°C for 30 seconds) were used to selectively enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. After validation of the libraries, using Agilent DNA 1000 kit on a 2100 Bioanalyzer instrument, the the libraries were quantitated by qPCR using KAPA Library Quantification Kit—Illumina/ABI Prism® (Kapa Biosystems, Inc., Wilmington, MA, USA) and validated using Agilent High Sensitivity DNA Kit on a Bioanalyzer. After validation of the libraries, using Agilent DNA 1000 kit on a 2100 Bioanalyzer instrument, the first hybridization step were performed using capture probes specific to genes of interest. Before hybridization a 4-plex pool of libraries were made, by combining 200 ng of each DNA library. The hybridization was performed by 18 cycles of 1 minute incubation, starting at 94°C, and then decreasing 2°C per cycle. Then streptavidin coated magnetic beads were used to capture probes hybridized to the target regions. The enriched libraries were then eluted from the beads and prepared for a second round of hybridization. This second hybridization (18 cycles of 1 minute incubation, starting at 94°C, and then decreasing 2°C per cycle) were required to ensure high specificity of the capture regions. A second capture with streptavidin coated beads were performed, followed by two heated wash procedures to remove non-specific binding form the beads. The enriched libraries where then eluted from the beads and cleaned up by AMPure XP beads prior to a second PCR amplification. The amplification step were performed by 10 cycles (98°C for 10 seconds, 60°C for 30 seconds and 72°C for 30 seconds) followed by a second PCR clean up using AMPure XP beads. Finally, the libraries were quantitated by qPCR using KAPA Library Quantification Kit—Illumina/ABI Prism® (Kapa Biosystems, Inc., Wilmington, MA, USA) and validated using Agilent High Sensitivity DNA Kit on a Bioanalyzer. The size range of the DNA fragments were measured to be in the range of 200–650 bp and peaked around 250 bp.


title: Targeted US-1553374 2


title: Targeted US-1494958


title: Targeted US-1493855


title: Targeted US-1493868


title: Targeted US-1553374 1


title: Targeted US-1493847


title: Targeted US-1493831


title: Targeted US-1493221


title: Targeted US-1493850


title: Targeted US-1493853


title: Targeted US-1493215


title: Targeted US-1493212


title: Targeted US-1493211


title: Targeted US-1493200


title: Targeted US-1493194


title: Targeted US-1493195


title: RNAse_S7_yeast

city: Boston

description: Ribo-seq (Ribosome profiling, ART-seq)

organism: Saccharomyces cerevisiae BY4741

source_name: yeast treated with RNase S7

value: whole cell culture


title: Targeted US-1493193


title: Targeted US-1493191


title: Targeted US-1493881


title: RNAse_A_yeast

description: Ribo-seq (Ribosome profiling, ART-seq)

source_name: yeast treated with RNase A


title: RNAse_I_yeast_replicate-2

description: Ribo-seq (Ribosome profiling, ART-seq)

source_name: yeast treated with RNase I


title: Targeted US-1493188


title: Targeted US-1493184


title: Targeted US-1493189


title: Targeted US-1493187


title: Targeted US-1493181


title: Targeted US-1493183


title: Targeted US-1493176


title: Targeted US-1493179


title: Targeted US-1493154


title: Targeted US-1492051


title: Targeted US-1492034


title: Targeted US-1492040


title: Targeted US-1492048


title: Targeted US-1492043


title: Targeted US-1492030


title: Targeted US-1492032


title: RNAse_T1_yeast

description: Ribo-seq (Ribosome profiling, ART-seq)

source_name: yeast treated with RNase T1


title: Targeted US-1492026


title: Targeted US-1492025


title: Targeted US-1492013


title: Targeted US-1492020


title: Targeted US-1492014


title: Targeted US-1492012


title: Targeted US-1492011


title: Targeted US-1492010


title: RNAse_I_yeast_replicate-1

description: Ribo-seq (Ribosome profiling, ART-seq)


title: Targeted US-1492009


title: Targeted US-1493173


title: Targeted US-1492083


title: Targeted US-1492007


title: Targeted US-1492003


title: Targeted US-1492004


title: Targeted US-1491995


title: Targeted US-1491997


title: Targeted US-1491986


title: Targeted US-1491993


title: Targeted US-1492006