title: P12 Mettl3 cKO mouse testis RNA-seq rep1

data_processing:
Basecalls performed by Casava using default settings
For RNA-Seq data, the clean reads were mapped to at mm9 genome assembly by HISAT2.  Default parameters of HISAT2 were used except with the options “--dta-cufflinks” and “--rna-strandness RF” opening.
Reads with unique genome location were retained for gene expression calculation using Cufflinks (version 2.0.2) with the option “--GTF”. And the genes with no less than 0.5 FPKM in at least one samples were used for the differential expressed genes analysis.
Fragments per Kilobase of exon per Megabase of library size (FPKM) was calculated using Cufflinks
Genome_build: mm9
Supplementary_files_format_and_content: FPKM files estimated by Cufflinks

extract_protocol:
RNA was isolated from control and Mettl3 cKO mouse testes using the TRIzol (Invitrogen) reagent by following the company's manual.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cKO mouse testes


title: BAT_DKO [GAR1112]

status: Public on Aug 16 2017

type: SRA

city: Garching

first: Martin

last: Jastroch

address: Parkring 13

department: Institute for Diabetes and Obesity

country: Germany

institute: Helmholtz Zentrum München

library_source: transcriptomic

data_processing:
STAR aligner was used for split-read alignment against the mouse genome assembly mm10 and UCSC known Gene annotation. To quantify the number of reads mapping to annotated genes we used HTseq-count
Genome_build: mm10
Supplementary_files_format_and_content: tsv files contain raw read count; they have two columns where the first column specifies the gene name and the second the actual read count

molecule: polyA RNA

organism: Mus musculus

source_name: BAT

extract_protocol:
Total RNA was extracted from inguinal WAT, BAT, muscle and hypothalamus of WT, FGF21 KO, UCP1 KO and dKO mice (n=5-6) using Qiazol according to the manufacturer’s instructions (Qiazol Lysis Reagent, Qiagen).
RNA molecules were poly(A) selected, fragmented, and reverse transcribed with the Elute, Prime, Fragment Mix (EPF, Illumina). End repair, A-tailing, adaptor ligation, and library enrichment were performed as described in the TruSeq Stranded mRNA Sample Preparation Guide (Illumina). RNA libraries were assessed for quality and quantity with the Agilent 2100 BioAnalyzer and the Quant-iT PicoGreen dsDNA Assay Kit (Life Technologies). Strand-specific RNA libraries were sequenced as 100 bp paired-end runs on an Illumina HiSeq2500 platform.

treatment_protocol: All mice were bred, born and weaned at 30°C. At the age of 10 to 12 weeks, mice were transferred to a temperature-controlled (+/- 0.5°C) climate chamber and kept for 12 days at 18°C followed by 3 weeks at 5°C. Afterwards, mice were euthanized after 2-3 hours food withdrawal, and serum and tissue samples were collected.

tag: tissue

value: BAT


title: BAT_DKO [GAR1116]


title: BAT_UCP [GAR1111]


title: iWAT_WT [GAR1126]

source_name: iWAT

value: iWAT


title: iWAT_UCP [GAR1129]


title: BAT_UCP [GAR1110]


title: P6 Mettl3 cKO mouse testis RNA-seq rep2

city: Beijing

first: Qi

last: Zhou

address: Datun Road, Chaoyang District

country: China

institute: Institute of Zoology,CAS

description: P6 Mettl3 cKO mouse testis RNA-seq rep2

molecule: total RNA

source_name: mouse testes

growth_protocol: The mice used in this study were B6D2F1 (C57BL/6×DBA2), DBA2 and C57BL6 strains.

value: mouse testes

tag: cell type

tag: passage

value: P6 (6 days post-partum)


title: BAT_UCP [GAR1109]


title: BAT_UCP [GAR1108]


title: P12 Mettl3 cKO mouse testis RNA-seq rep2

value: P12 (12 days post-partum)


title: P6 control mouse testis RNA-seq rep1

description: P6 control mouse testis RNA-seq rep1

value: control mouse testes


title: P6 control mouse testis RNA-seq rep2

description: P6 control mouse testis RNA-seq rep2


title: P6 Mettl3 cKO mouse testis RNA-seq rep1

description: P6 Mettl3 cKO mouse testis RNA-seq rep1


title: BAT_DKO [GAR1117]


title: BAT_FGF [GAR1118]


title: BAT_UCP [GAR1107]


title: miRNA_DC_31_S55_RACE-seq

city: Regensburg

first: Michael

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

institute: University Hospital Regensburg

description: amplicon sequencing of RACE products (RACE-seq)

data_processing:
Library strategy: RACE-seq
Use Nexalign version 1.3.5 to map the inner and outer primers to the human genome.
Use Blat version 34 to map sequenced reads to human genome.
Select transcripts for which both ends were sequenced.
Select transcripts for which the genomic location overlaps the genomic location of the inner primer.
Genome_build: Human genome hg19; including chr1-22, chrX, chrY, and chrM, excluding random, unplaced, and haplotype contigs.
Supplementary_files_format_and_content: Bed files, one for each cell type, with the mapped RACE sequences that overlapped one of the inner primers. The score number in the bed files represents the read count (column 5). The column headers are as follows: 1) chromosome, 2) Chromstart position, 3) chromEnd, 4) name 5) score (read count), 6) strand, 7) thickStart  = chromstart, 8) thickEnd = chromEnd, 9) itemRgb - Not used; always ".", 10) blockCount (The number of blocks in the transcript alignment), 11) blockSizes (A comma-separated list of the block sizes; the number of items in this list corresponds to blockCount, 12) blockStarts (A comma-separated list of block starts, relative to   chromStart; the number of items in this list corresponds to blockCount).

organism: Homo sapiens

source_name: monocyte-derived dendritic cells

extract_protocol:
Monocytes: Peripheral blood monocytes were separated by leukapheresis of healthy donors, followed by density gradient centrifugation over Ficoll/Hypaque and subsequent counter current centrifugal elutriation in a J6M-E centrifuge.
macrophages: Macrophages were generated by culturing monocytes in endotoxin-free RPMI 1640 medium (Biochrom) supplemented with 2% human pooled AB-group serum on Teflon foils for up to 7 days
DCs: To generate immature DCs, 1 × 10^6 monocytes/ml were cultured in RPMI 1640 medium (Thermo Scientific, Bonn, Germany) supplemented with 10% FCS (Biowhittaker, Verviers, Belgium), 20 U/ml IL-4 (Promokine, Heidelberg, Germany) and 280 U/ml granulocyte-macrophage colony-stimulating factor (Berlex, Seattle, WA, USA).  GmbH, Wiesbaden, Germany) and cultured on teflon foils.
Total cellular RNA was isolated using the RNeasy Mini Kit (Qiagen)
We mixed 4.0 μl 5X First-Strand Buffer, 0.5 μl DTT (100 mM; Invitrogen, catalog number 70726), 1.0 μl dNTP Mix (20 mM), spun briefly in a microcentrifuge, and kept at room temperature. We combined 1.0-10.0 μl with 1 μg total RNA from monocytes, macrophages, and dendritic cells, 1.0 μl Random Primer Mix (N-15) (20 μM), and 0-9 μl sterile water to reach a total volume of 11.0 μl in separate microcentrifuge tubes, mixed the contents and spun the tubes briefly. We incubated these tubes at 72 °C for 3 minutes, and then cooled to 42 °C for 2 minutes. After cooling, we spun the tubes for 10 seconds at 14,000 g to collect the contents at the bottom. Next, we added 1.0 μl of Smarter oligo (20 μM) per reaction, and mixed well by vortexing and spun the tube briefly in a microcentrifuge. We then added 0.5 μl RNase Inhibitor (40 U/μl; Invitrogen RNaseOUT™, catalog number 10777019) and 2.0 μl SMARTScribe Reverse Transcriptase (100 U; Clontech, catalog number 639537) to the buffer mix, and mixed these reagents at room temperature. Next, we added 8.0 μl of the master mix to the RNA solution, mixed the contents of the tubes by gently pipetting, and spun the tubes briefly. We incubated the tubes at 42 °C for 90 minutes and heated the tubes at 70 °C for 10 minutes in a hot-lid thermal cycler. We then added 90 μl Tricine-EDTA buffer to each tube. We prepared the master mix for the first PCR by combining 2.5 μl of the cDNA solution, 5.0 μl 10X Advantage 2 PCR buffer (Clontech, catalog number 639207), 1.0 μl dNTP Mix (10mM each) 50X Advantage 2 Polymerase Mix (Clontech), 1.0 μl of the smarterRACE_forward primer at 10 pmol/μl, 1.0 μl of the miRNA-specific outer primer (Table S20) at 10 pmol/μl, and added PCR-grade water to reach a volume of 50 μl. We ran a 2-step PCR program consisting of 1 minute at 95 °C, 25 cycles of 30 seconds at 95 °C followed by 70 seconds at 68 °C, 7 minutes at 68 °C, and finishing at 8 °C. We diluted 5 μl of the primary PCR product into 245 μl of Tricine-EDTA buffer. We prepared the master mix for the second PCR by combining 5.0 μl of the product of the first PCR after dilution with 5 μl of the 10X Advantage 2 PCR buffer, 1.0 μl dNTP Mix (10 mM), 1.0 μl of 50X Advantage 2 Polymerase Mix (Clontech), 2.0 μl of the Nextera_i7 primer, 2.0 μl of the miRNA-specific inner primer (Table S20), and 34 μl of PCR-grade water. We ran a 2-step PCR program consisting of 1 minute at 95 °C, 20 cycles of 30 seconds at 95 °C followed by 70 seconds at 68 °C, 7 minutes at 68 °C, and finishing at 8 °C. We diluted 5 μl of the PCR product into 245 μl of Tricine-EDTA buffer. We prepared the master mix for the third PCR by combining 5.0 μl of the PCR product of the second PCR with 5.0 μl of 10X Advantage 2 PCR buffer, 1.0 μl dNTP mix (10 mM), 1.0 μl of 40X Advantage 2 Polymerase Mix (Clontech), 2.0 μl of the Nextera_i7 primer, 2.0 μl of the Nextera_i5 primer, and 34 μl of PCR-grade water. We purified by AMPure at a 1.8 ratio, checked 2 μl of the second PCR product on a Tapestation, kept the libraries at -20 °C until sequencing, and pooled the PCR products, each with a different barcode combination before paired-end sequencing on a MiSeq sequencer (Illumina).

value: peripheral blood

value: monocyte-derived dendritic cells

tag: target mirna

tag: outer 5'race-primer

value: AGGTGAGGGCGTGAGAGGAACAG

tag: inner 5'race-primer with adapter


title: BAT_UCP [GAR1106]


title: miRNA_DC_27_S51_RACE-seq

value: AGTTCTTTCAGCCTGGACGCTGCTC


title: miRNA_DC_33_S57_RACE-seq

value: GTCTGTCCGTCGGCGTGTACTCTT


title: miRNA_DC_26_S50_RACE-seq

value: GTGAAGAGAACATCCAGGGTGAATGG


title: P12 control mouse testis RNA-seq rep1

description: P12 control mouse testis RNA-seq rep1


title: P12 control mouse testis RNA-seq rep2

description: P12 control mouse testis RNA-seq rep2


title: BAT_WT [GAR1105]


title: miRNA_DC_28_S52_RACE-seq

value: CGCCGCCCCTTCTTTTCCTTTGC


title: miRNA_DC_22_S46_RACE-seq

value: TTTCAGAGATGGTGCAAAGACCCCTCCT


title: miRNA_DC_21_S45_RACE-seq

value: GCATCCTTTCTGGTGGCTGCATTAC


title: BAT_WT [GAR1104]


title: BAT_WT [GAR1103]


title: miRNA_Mak_53_S77_RACE-seq

source_name: monocyte-derived macrophages

value: monocyte-derived macrophages


title: miRNA_Mak_51_S75_RACE-seq


title: miRNA_Mak_47_S71_RACE-seq


title: miRNA_Mak_46_S70_RACE-seq


title: BAT_WT [GAR1102]


title: miRNA_Mak_42_S66_RACE-seq


title: miRNA_Mak_48_S72_RACE-seq


title: miRNA_Mak_41_S65_RACE-seq


title: miRNA_MO_11_S35_RACE-seq

source_name: monocytes

value: monocytes


title: BAT_WT [GAR1101]

value: BAT


title: miRNA_MO_8_S32_RACE-seq


title: miRNA_MO_13_S37_RACE-seq


title: Gastrognemius_FGF [GAR1100]

source_name: Gastrognemius

value: Gastrognemius


title: miRNA_MO_7_S31_RACE-seq


title: miRNA_MO_2_S26_RACE-seq


title: miRNA_MO_6_S30_RACE-seq


title: Gastrognemius_FGF [GAR1096]


title: Gastrognemius_FGF [GAR1098]


title: Gastrognemius_FGF [GAR1097]


title: CPC H3K4me3 rep2

city: Box

first: Stuart

last: Shankland

state: WA

address: 1959 NE Pacific Avenue

department: Nephrology

country: USA

institute: University of Washington, Seattle

description:
H3K4me3_CPC_peaks.txt
CPC_H3K4me3.bw
Barcode: GTCCGC

library_source: genomic

data_processing:
ChIP-seq reads were aligned to hg19 using Bowtie 2.
RNA-seq reads were aligned to hg19 using Tophat-1.3.3
Peaks were called with MACS 1.4.2
Differential ChIP-seq regions were identified with DiffReps version 1.55.4
Differentially expressed genes were identified with DESeq
Genome_build: hg19
Supplementary_files_format_and_content: [ChIP-seq] peaks call were generated using MACS 1.4.2.  diff.txt files report differential ChIP-seq regions.
Supplementary_files_format_and_content: [RNA-seq] TPM values were generated with Isolator

molecule: genomic DNA

source_name: cardiac progenitor cells (CPCs)

growth_protocol:
[Human ESC Cardiac Directed Differentiation] WT RUES2 human embryonic stem cells were used in this study. Undifferentiated cells were maintained in mouse embryonic fibroblast-conditioned media. Standard cardiomyocyte directed differentiation using a monolayer platform was performed with a modified protocol based on previous reports (Laflamme et al., 2007; Lian et al., 2012; Paige et al., 2010). The differentiation set up was initiated by plating undifferentiated hESCs as single cells as described previously (Gantz et al., 2012; Palpant et al., 2013).  The cultures were treated with CHIR-99021 (Cayman chemical, 13122) for 24 hours before reaching confluence. Cells were induced to differentiate (designated day 0) by replacing the culturing media with RPMI media (Invitrogen, 11875-119) containing 100 ng/mL activin A (R&D SYSTEMS, 338-AC-050), 1:60 diluted Matrigel (BD), and insulin-free B27 supplement (Invitrogen, 0050129SA). An RPMI media change the following day (17 hours) included BMP4 (R&D SYSTEMS, 314-BP-050), 1 µM CHIR-99021, and insulin-free B27 supplement. On day 3, media was changed to RPMI media with B27 minus insulin containing 1 µM XAV-939 (Tocris, 3748). RPMI containing insulin-free B27 supplement was utilized until differentiation day 7 in which the media is replaced with RPMI containing a B27 supplement that includes insulin (Invitrogen, 17504044).  Subsequent media changes included the insulin-containing supplement.
[ Human ESC Endothelial Differentiation] Endothelial differentiation involved initiation of differentiation with activin A and BMP4 as described above. Endocardial-like ECs are generated by induction with 100 ng/mL activin A on day 0 and 5 ng/mL BMP4 on day 1. Hemogenic endothelial cells are generated by induction with 50 ng/mL activin A on day 0 and 40 ng/mL BMP4 on day 1. For both EC populations, on day 2 media is changed to Stempro34 (Invitrogen, 10640019) backbone media containing 200 ng/mL VEGF (Peprotech, 100-20), 5 ng/mL bFGF (Peprotech, 100-18B), 10 ng/mL BMP4 (R&D SYSTEMS, 314-BP-050), 4x10-4 M monothioglycerol, 50 ug/mL Ascorbic Acid, 2mM L-Glutamine (Invitrogen, 25030-081), and pen-strep (Invitrogen, 15140-163)(Palpant et al., 2015b). Media was not changed until day 5. To determine HOPX worked through the Wnt/β-catenin pathway, we modified the protocol for H-EC differentiation to add 1µM XAV-939 from days 2-5. In some assays, day 5 C-ECs and H-ECs were passaged for maturation into CD31+ cells. This was performed by re-plating cells in gelatin coated tissue culture flasks with EGM media (Lonza, CC-3124) containing 20 ng/mL VEGF (Peprotech, 100-20), 20 ng/mL bFGF (Peprotech, 100-18B), and 1 µM CHIR-99021 (Cayman Chemical,13122). Cells were maintained until day 9 at which point cells were isolated, analyzed by flow cytometry for CD31 expression.

extract_protocol:
Day 5 cardiac progenitor cells, C-ECs, and H-ECs were fixed in 1% formaldehyde for 10 minutes at RT to crosslink the chromatin.  Following that glycine was added to a final concentration of 0.125 M. Cells were washed twice with cold PBS and frozen at -80ºC. Crosslinked samples were submitted to the University of Washington High Throughput Genomic Sequencing Center for ChIP-seq analysis for H3K4me3 and H3K27me3 histone modifications.
Total RNA from bulk cultures of cardiac progenitor cells, C-ECs, and H-ECs were isolated with RNALater (Qiagen, 76104). For each group, 2 biological replicates were submitted for analysis.
The chromatin was sonicated to small fragments (<500 bp) and histone bound chromatin was immunoprecipitated using antibiodies specific to H3K4me3 (Cat # 9751, Cell Signaling) or H3K27me3 (Cat # 07-449; Millipore). For each IP, Dynabeads (M-280, sheep anti-rabbit IgG, Invitrogen) were incubated with antibodies for 6 hr at 4°C and then incubated overnight with ∼100 μg sheared chromatin. The complexes were rinsed sequentially with IP wash buffer I (50 mMTris-HCl pH 8.0, 150 mM NaCl, 1 mM EDTA [pH8.0], 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate), high salt buffer (50 mMTris-HCl pH8.0, 0.5 M NaCl, 1 mM EDTA [pH8.0], 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate), IP wash buffer II (50 mMTris-HCl [pH8.0], 1 mM EDTA pH8.0, 1% NP-40, 0.7% sodium deoxycholate, 0.5 M LiCl), and TE buffer (10 mMTris-HCl [pH8.0], 1 mM EDTA pH8.0). The complexes were incubated with elution buffer (10 mMTris-HCl [pH 8.0], 0.3 M NaCl, 5 mM EDTA [pH8.0], 0.5% SDS) supplemented with RNase A (Ambion) at 65°C overnight. After separation, the DNA was treated with Proteinase K and purified by using PCR purification column (QIAGEN). The Illumina indexed sequencing libraries were prepared following a standard protocol using PE adapters (Illumina). The libraries were used to generate sequencing clusters on flowcells using cBot, and sequenced on Illumina HiSeq 2000 to generate PE 2X36 base pair reads.  Each library was on average sequenced to a depth of ∼18 million tags that mapped uniquely to the human genome (hg19).
Samples were submitted to University of Washington High Throughput Genomic Sequencing Center for isolation and analysis. RNA-seq was performed on poly-A enriched samples using Illumina TruSeq.

value: cardiac progenitor cells (CPCs)

tag: chip antibody

value: H3K4me3 (Cat # 9751, Cell Signaling)


title: miRNA_MO_1_S25_RACE-seq


title: Gastrognemius_FGF [GAR1099]


title: Gastrognemius_DKO [GAR1095]


title: CPC input rep2

description: Barcode: CCGTCC


title: CPC input rep1

description: Barcode: AGTCAA


title: CPC H3K27me3 rep2

description:
H3K27me3_CPC_peaks.txt
CPC_H3K27me3.bw
Barcode: GTGAAA

value: H3K27me3 (Cat # 07-449; Millipore)


title: Gastrognemius_DKO [GAR1092]


title: Gastrognemius_DKO [GAR1093]


title: Gastrognemius_DKO [GAR1094]


title: Sox9eGFP Sublow rep2

city: Ithica

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

data_processing:
Samples were processed using miRquant2.0 (https://github.com/Sethupathy-Lab/miRquant) using default settings
Genome_build: mm9
Supplementary_files_format_and_content: RPMMM_matrix is a comma separated value matrix containing the Reads Per Million miRs Mapped (RPMMM) for each of the samples

source_name: Intestine

extract_protocol: Libraries were prepared according to the TriLink CleanTag Small RNA Library Preparation Kit protocol

value: small intestine

tag: cell population

value: sublow

tag: strain


title: Sox9eGFP Sublow rep1


title: H-EC input rep2

description: Barcode: TAGCTT

source_name: hemogenic mesoderm (H-ECs)

value: hemogenic mesoderm (H-ECs)


title: Sox9eGFP Sublow rep3


title: Gastrognemius_DKO [GAR1091]


title: Sox9eGFP Non-sorted rep1

value: non-sorted


title: CPC H3K27me3 rep1

description:
H3K27me3_CPC_peaks.txt
CPC_H3K27me3.bw
Barcode: ATGTCA


title: Sox9eGFP Non-sorted rep2


title: Sox9eGFP Negative rep3

value: negative


title: Sox9eGFP Negative rep1


title: Gastrognemius_DKO [GAR1090]


title: Gastrognemius_UCP [GAR1089]


title: Sox9eGFP Low rep3

value: low


title: Sox9eGFP Low rep1


title: Gastrognemius_UCP [GAR1088]


title: Sox9eGFP High rep3

value: high


title: Sox9eGFP High rep2


title: H-EC H3K27me3 rep1

description:
H3K27me3_H-EC_peaks.txt
H-EC_H3K27me3.bw
Barcode: GATCAG


title: H-EC input rep1

description: Barcode: CAGATC


title: Sox9eGFP High rep1


title: Gastrognemius_UCP [GAR1087]


title: H-EC H3K4me3 rep1

description:
H3K4me3_H-EC_peaks.txt
H-EC_H3K4me3.bw
Barcode: ACTTGA


title: 4_hr_KO_CIP_C2

city: London

first: Christopher

middle: L

last: Pin

state: Ontario

address: 800 Commissioners Rd. E

department: Physiology and Pharmacology/Peadiatrics

country: Canada

institute: The University of Western Ontario/CHRI

data_processing:
[Alignment] STARv2.4.2a
[Read Counts] HTSeq (htseq-count)
[Annotations file] gencode M9 annotations
[Differential Expression] DESeq2
[Pathway & GO] Databases: Gene Ontology (GO), PANTHER, and KEGG
Genome_build: mm10 v6
Supplementary_files_format_and_content: raw count data files provided as .count files (raw text of read counts)

extract_protocol:
Modified Trizol extraction with Ambion PureLink kit (see Fazio et al, 2017 for details)
Illumina TruSeq Stranded Total RNA Library Prep Kit

treatment_protocol: 2-4 month old mice  were injected with 50 ug/kg of cerulein (experimental) or saline (control) 4 times over 4 hours. Pancreatic tissue was removed 4 hours into treatment and processed immediately for RNA

value: whole pancreas

tag: genotype/variation

tag: treatment

value: 4 hours cerulein


title: C-EC input rep2

description: Barcode: TGACCA

source_name: cardiogenic mesoderm (C-ECs)

value: cardiogenic mesoderm (C-ECs)


title: H-EC H3K4me3 rep2

description:
H3K4me3_H-EC_peaks.txt
H-EC_H3K4me3.bw
Barcode: GGCTAC


title: Gastrognemius_UCP [GAR1086]


title: Sox9eGFP Negative rep2


title: H-EC H3K27me3 rep2

description:
H3K27me3_H-EC_peaks.txt
H-EC_H3K27me3.bw
Barcode: CTTGTA


title: Gastrognemius_UCP [GAR1084]


title: 4_hr_KO_Sal_S1

value: 4 hours saline


title: 4_hr_KO_CIP_C3


title: C-EC H3K4me3 rep2

description:
H3K4me3_C-EC_peaks.txt
C-EC_H3K4me3.bw
Barcode: ACAGTG


title: Sox9eGFP Low rep2


title: Gastrognemius_WT [GAR1083]


title: C-EC H3K27me3 rep2

description:
H3K27me3_C-EC_peaks.txt
C-EC_H3K27me3.bw
Barcode: GCCAAT


title: 4_hr_WT_CIP_N3

value: control


title: 4_hr_KO_Sal_K4


title: C-EC input rep1

description: Barcode: ATCACG


title: 4_hr_WT_CIP_O1


title: Gastrognemius_WT [GAR1082]


title: C-EC H3K4me3 rep1

description:
H3K4me3_C-EC_peaks.txt
C-EC_H3K4me3.bw
Barcode: CGATGT


title: 4_hr_WT_CIP_O3


title: 4_hr_WT_Sal_R3


title: 4_hr_KO_CIP_L4


title: 4_hr_WT_Sal_K5


title: Gastrognemius_WT [GAR1081]


title: Gastrognemius_WT [GAR1080]


title: 4_hr_WT_Sal_W1


title: 4_hr_KO_Sal_Q1


title: C-EC H3K27me3 rep1

description:
H3K27me3_C-EC_peaks.txt
C-EC_H3K27me3.bw
Barcode: TTAGGC


title: Hypothalamus_FGF [GAR1077]

source_name: Hypothalamus

value: Hypothalamus


title: CPC RNA-seq rep2

description:
RNAseq_samples_TPM.txt
Barcode: GATCAG


title: Gastrognemius_WT [GAR1079]

value: Gastrognemius


title: Gastrognemius_WT [GAR1078]


title: Hypothalamus_FGF [GAR1076]


title: CPC RNA-seq rep1

description:
RNAseq_samples_TPM.txt
Barcode: ACAGTG

value: cardiac progenitor cells (CPCs)


title: H-EC RNAseq rep2

description:
RNAseq_samples_TPM.txt
Barcode: TGACCA


title: Hypothalamus_FGF [GAR1075]


title: Hypothalamus_FGF [GAR1074]


title: H-EC RNAseq rep1

description:
RNAseq_samples_TPM.txt
Barcode: TTAGGC


title: C-EC RNAseq rep2

description:
RNAseq_samples_TPM.txt
Barcode: CGATGT


title: CPC H3K4me3 rep1

description:
H3K4me3_CPC_peaks.txt
CPC_H3K4me3.bw
Barcode: AGTTCC

value: H3K4me3 (Cat # 9751, Cell Signaling)


title: D3

city: Toulouse

first: Beata

last: Jady

address: 118 route de Narbonne

country: France

institute: Laboratoire de Biologie Moléculaire Eucaryote

description:
depleted of Rio1p
Before cDNA preparation of ribosome-protected mRNA fragments, monosomes were further selected by immunoprecipitation to isolate monosomes containing pre-40S pre-ribosomal particles. For the immunoprecipitation reaction, the pre-40S pre-ribosomal particles were selected by tandem-affinity purification using the Flag-Pre-Scission protease cleavage site-Z sequence tag found on Nob1p protein. D3 is a replica of D2.

data_processing:
Reads were trimmed by Trim Galore! (Galaxy v0.4.2) in order to remove Illumina small RNA adapters.
Reads were aligned to the  reference genome by Hisat (Galaxy v2.0.3, k=5).
The aligned reads were filtered for MapQ>=30 by BamFilter (Galaxy v0.0.2).
Aligned and filtered reads were sorted with Samtools (Galaxy v2.0).
The genomic regions corresponding to the aligned reads were intersected with the regions of known yeast mRNA coding sequences (Bedtools v2.25.0; CDS intervals, positions of stop and start codons of SGD genes were downloaded from UCSC Genome Browser as a gtf file).
For each aligned read corresponding to an mRNA CDS, the middle position of the corresponding genomic interval was calculated using R (RStudio v0.99.896 with R v3.3.2). The corresponding script is deposited at https://github.com/jadybea/Rio1p.
Genome_build: S. cerevisiae sacCer3
Supplementary_files_format_and_content: For each read, the corresponding mRNA and the distance from either the translation start site (SampleNameDistanceFromTSS.csv) or  the stop codon (SamplenameDistanceFromStopCodon.csv) was documented.

organism: Saccharomyces cerevisiae

source_name: Strain TetO7-RIO1, NOB1-FPZ depleted of Rio1p

growth_protocol: Yeast strains were grown in YP medium supplemented with 2% glucose.

extract_protocol:
Cells were were frozen and crushed in liquid nitrogen in a Retsch PM100 mixer mill. Lysates of about 1000 µg of proteins obtained after centrifugation of 5 min at 9300g were incubated with 750 units of RNase I for 1h at 20 °C. 100 units of SUPERase In RNase inhibitor was added to inhibit further digestion. Monosomes were separated on a 4.5%-45% sucrose gradient. The isolated mRNA fragments were extracted by phenol-extraction.
rRNAs were depleted with RiboZero Magnetic Gold solution and beads of Illumina. The remaining RNA fragments were 3' dephosphorylated and 5' phosphorylated using T4 Polynucleotide kinase. RNA fragments with size of about 30 nt were purified on a 15% denaturing acrylamide gel. Library of purified RNA fragments were prepared using TruSeq Small RNA kit of Illumina.
preparation of cDNA of small RNA fragments for Ribosome Profiling Analysis

treatment_protocol: 10 min before harvesting the cells, the medium was complemented with 100 µg/ml cycloheximide for all samples.

tag: tag

value: Nob1-Flag-Pre-Scission protease cleavage site-Z sequence tag

tag: culture condition

value: with 200 µg/ml doxycycline

tag: mrna

value: purified mRNAs bound by pre-40S pre-ribosomal particles that were immunoprecipitated using Nob1p as bait


title: C-EC RNAseq rep1

description:
RNAseq_samples_TPM.txt
Barcode: ATCACG


title: Hypothalamus_FGF [GAR1073]


title: Hypothalamus_DKO [GAR1070]


title: Lib2

description: expressing Rio1p

source_name: Strain TetO7-RIO1, NOB1-FPZ expressing Rio1p

value: without doxycycline

value: Total ribosome-associated mRNA


title: D2

description:
depleted of Rio1p
Before cDNA preparation of ribosome-protected mRNA fragments, monosomes were further selected by immunoprecipitation to isolate monosomes containing pre-40S pre-ribosomal particles. For the immunoprecipitation reaction, the pre-40S pre-ribosomal particles were selected by tandem-affinity purification using the Flag-Pre-Scission protease cleavage site-Z sequence tag found on Nob1p protein.


title: Hypothalamus_DKO [GAR1071]


title: Hypothalamus_DKO [GAR1068]


title: Hypothalamus_UCP [GAR1067]


title: Hypothalamus_DKO [GAR1069]


title: Hypothalamus_WT [GAR1061]


title: Hypothalamus_UCP [GAR1066]


title: Hypothalamus_UCP [GAR1065]


title: Hypothalamus_WT [GAR1057]


title: Hypothalamus_UCP [GAR1063]


title: Hypothalamus_UCP [GAR1062]


title: Hypothalamus_WT [GAR1060]


title: E2FL-1KO_C5

status: Public on Aug 15 2017

city: wuhan

first: Wei

last: Miao

state: hubei

address: donghu south road #7

institute: Institute of hydrobiology, CAS

data_processing:
Adaptors of raw reads were trimmed by Trim-Galore (version 0.4.0)
mRNA-Seq data processing: Trimmed-reads were mapped to the Tetrahymena themophila MAC genome (version 2014: http://ciliate.org/index.php/home/downloads) using TopHat (version 2.0.9).Genes expression values were quantify to the number of fragments per kilobase of exon per million fragments mapped (FPKM) using Cuffdiff (version 2.1.1).
Genome_build: Tetrahymena themophila MAC genome (version 2014: http://ciliate.org/index.php/home/downloads)
Supplementary_files_format_and_content: Reads counts table matrix

organism: Tetrahymena thermophila

source_name: Conjugation cells

growth_protocol: Tetrahymena thermophila cells were grown in SPP medium at 30 oC.  For conjugation, log-phase growing cells (~200k cells/ml) of two different mating types were washed, starved (~16 hrs) and mixed in Dryl’s buffer (2 mM sodium citrate, 1 mM NaH2PO4, 1 mM Na2HPO4, 1.5 mM CaCl2, pH 6.8) at 30°C.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols. First strand specific libraries were constructed using the Illumina TruSeq Stranded mRNA Sample Prep Kit (RS-122-2101). The Poly-A tailed mRNA as purified using the Sera‐Mag Magnetic Oligo(dT) Beads. The mRNA fragmentation, first strand cDNA synthesis, second strand cDNA synthesis, A tailing, adaptor ligation and PCR amplification were performed according to the stranded mRNA sample preparation guide of the kit.  Sequencing (Single-end (52X1) for C3 and C6, Paired-end (101x2) FOR C10) was performed using an Illumina HiSeq 2000 sequencer (DNA Sequencing Core of University of Michigan).

tag: genotype

value: E2FL-1 Knock out

tag: time point

value: Conjugation 5 hours


title: Hypothalamus_WT [GAR1059]


title: Hypothalamus_DKO [GAR1072]


title: Hypothalamus_WT [GAR1056]


title: WT-C3

value: WT

value: Conjugation 3 hours


title: WT-C2

value: Conjugation 2 hours


title: E2FL-1KO_C4

value: Conjugation 4 hours


title: Hypothalamus_WT [GAR1058]


title: WT-C7

value: Conjugation 7 hours


title: E2FL-1KO_C6

value: Conjugation 6 hours


title: WT_C3

growth_protocol: Tetrahymena thermophila cells were grown in SPP medium at 30°C.  For conjugation, log-phase growing cells (~200k cells/ml) of two different mating types were washed, starved (~16 hrs) and mixed in Dryl’s buffer (2 mM sodium citrate, 1 mM NaH2PO4, 1 mM Na2HPO4, 1.5 mM CaCl2, pH 6.8) at 30°C.

value: C3; Conjugation 3 hours


title: WT_C2

value: C2; Conjugation 2 hours


title: E2FL-1KO_C7


title: WT-C5


title: WT_C1

value: C1; Conjugation 1 hours


title: LibD2

description: depleted of Rio1p


title: WT-C4


title: Gastrognemius_UCP [GAR1085]

value: Gastrognemius


title: CYC17KO_C7

data_processing:
Adaptors of raw reads were trimmed by Trim-Galore (version 0.4.0)
mRNA-Seq data processing: RNA-Seq reads of each sample were firstly mapped to the MIC genome assembly of Tetrahymena thermophila (http://www.broadinstitute.org/annotation/genome/Tetrahymena/MultiHome.html) using TopHat allowing  2 edit distances (including mismatch and indels). To assemble the transcripts, the mapping results of all the samples were independently assembled in both strands using the Cufflinks program, and then merged the assemblies using cuffmerge.
Genome_build: Tetrahymena themophila MIC genome (http://www.broadinstitute.org/annotation/genome/Tetrahymena/MultiHome.html)
Supplementary_files_format_and_content: Reads counts table matrix

value: Cyc17 Knock out


title: E2FL-1KO_C3


title: WT_C6


title: Hypothalamus_UCP [GAR1064]

value: Hypothalamus


title: CDK3KO_C1

value: CDK3 Knock out


title: E2FL-1KO_C2


title: WT-C6


title: WT_C7


title: CYC17KO_C6


title: CYC17KO_C5


title: WT_C5


title: CDK3KO_C2


title: wt_Ler_chipseq_rep2

city: NORWICH

first: Robert

last: Sablowski

state: Norfolk

address: The John Innes Centre

department: CDB

country: United Kingdom

institute: JIC

data_processing:
Reads aligned against the TAIR10 Col-0 reference sequence with Bowtie2 (v2-2.1.0)
Data were sorted and indexed with Samtools to generate .bam files
MACS 2.0.10 was used to call peaks and calculate fold enrichments and q-values, comparing the combined replicates with combined controls.
Filtering: to select peaks that were consistently detected across replicates, peak calling with MACS 2.0.10 was applied to individual replicates and overlapping peak regions were accepted if they had q-values of 10-3 or lower in each RPL:RGA-GFP replicate, were not detected in any of the negative controls and the overlapping region was at least 50 nucleotides long.
Association with gene models: filtered peaks were attributed to gene models within 3 kb upstream or 1.5 kb downstream of the corresponding coding sequence, without intervening coding sequences.
Genome_build: TAIR10
Supplementary_files_format_and_content: Summary table RGA-GFP_overlapping_peaks_and_genes.txt is a tab-delimited text file that lists:  AGI name, Gene start, Gene end, Number of overlapping MACS peaks, Fold enrichment, log10 q-value, Type, Short_description, Computational_description. narrowPeak files and peaks.txt files were generated using MACS 2.0.10; files list chromosome number, nucleotide start, nucleotide end, pileup, -log10 p-value, -log10 q value and peak name.

organism: Arabidopsis thaliana

growth_protocol: Plants were grown in a controlled environment room at 20-22 °C, 16 h light (100 µE) until they produced approximately 10 mature flowers

extract_protocol:
ChIP was perfored as described in Schiessl et al. 2014, PNAS 111, 2830-2835, except that tissues were fixed with 2% formaldehyde in PBS 1x supplemented with 1 micromolar Di(N-succinimidyl) glutarate (DSG; Synchem) under vacuum for 20 min.
Illumina TruSeq ChIP-Seq libraries were constructed as described in Kaufmann et al, 2009, PLoS Biology 7, e90.
ChIP-seq: 50 bp single-end reads sequenced with Illumina HiSeq 2500 (Rapid-Run mode) as described by the manufacturer.

treatment_protocol: Three biological replicates were used for each treatment. Each replicate was prepared from 1-2 g of fresh inflorescence apices fixed immediately after harvesting.

tag: ecotype/accession background

value: Landsberg-erecta

value: wild-type; epitope-negatve control

value: inflorescence apices

value: anti-GFP µMACS Microbeads (Milteyi Biotec)


title: Blood_Platelets_NKI-NSCLC-2417-TR1857

city: Amsterdam

first: Myron

last: Best

address: De Boelelaan 1117

department: Neurosurgery

country: Netherlands

institute: VU University Medical Center

data_processing:
Single-end 100 bp reads were subjected to pre-aligment 5'-end quality trimming and sequence adapter clipping using Trimmomatic.
Cleaned-up reads were mapped to the hg19 reference genome using STAR (version 2.3.0), using splice aware alignments and allowing for 10 mismatches.
Intron-spanning read summarization was performed using a samtools-based filtering step and HTSeq (version 0.6.1) using union-mode, unstranded reads and minimal mapping quality of 35, all guided by the Ensembl gene annotation version 75.
Genome_build: hg19
Supplementary_files_format_and_content: Samples in the tab-delimited text file were processed according to the described protocol and data of all samples was merged in a comprehensive read count matrix.

source_name: Thrombocytes

extract_protocol:
Blood platelets were isolated from whole blood in purple-cap BD Vacutainers containing the EDTA anti-coagulant. The cells and aggregates were removed by centrifugation at room temperature for 20 minutes at 120g, resulting in platelet-rich plasma. The platelets were isolated from the platelet-rich plasma by centrifugation at room temperature for 20 minutes at 360g. The platelet pellet was collected in 30 μl RNAlater (Life Technologies), incubated overnight at 4°C and frozen at -80°C for further use. Frozen platelets were thawed on ice and total RNA was isolated using the mirVana RNA isolation kit (Life Technologies) according to the manufacturers’ protocol. Complementary purification of small RNAs was included in the isolation procedure by addition of miRNA homogenate (Life Technologies). Total RNA was dissolved in 30 μl Elution Buffer (Life Technologies) and RNA quality and quantity was measured using Bioanalyzer 2100 with RNA 6000 Picochip (Agilent).
100-500 pg of platelet total RNA diluted in nuclease free H2O was subjected to cDNA synthesis and amplification using the SMARTer Ultra Low RNA Kit for Illumina Sequencing v3 (Clontech, cat. nr. 634853) according to the manufacturers’ protocol. Conversion and efficient amplification of cDNA was quality-controlled using the Bioanalyzer 2100 with DNA High Sensitivity chip (Agilent). Samples with detectable fragments in the 300-7500 bp region were selected for further processing and Covaris shearing by sonication (Covaris Inc). Sample preparation for Illumina sequencing was performed using the Truseq DNA Sample Preparation Kit (Illumina, cat nr. FC-121-2001) or Truseq Nano DNA Sample Preparation Kit (Illumina, cat nr. FC-121-4001). Sample quality and quantity was measured using the DNA 7500 chip or DNA High Sensitivity chip (Agilent). High-quality samples with product sizes between 300-500 bp were pooled in equimolar concentrations (12-19 samples per Hiseq lane) and submitted for 100 bp Single Read sequencing on the Hiseq 2500 platform (Illumina).

tag: disease

value: NSCLC


title: Blood_Platelets_NKI-NSCLC-2194-TR1855


title: CDK3KO_C3


title: WT_C4

value: WT


title: wt_Ler_chipseq_rep3

tag: tissue


title: Blood_Platelets_UMCU-1-0009-AP-stable-TR942

value: nonCancer


title: Blood_Platelets_UMCU-NSAth-1-0145-TR828


title: wt_Ler_chipseq_rep1


title: RGA-GFP_chipseq_rep3

value: expressing a GFP-tagged, gibberellin-insensitive version of RGA (RGAp:GFP-rga-delta17)


title: Blood_Platelets_UMCU-HC-1-0210-TR819


title: Blood_Platelets_Vumc-HD-227-TR1716


title: Blood_Platelets_Vumc-ChronPan-29-TR1045


title: RGA-GFP_chipseq_rep1


title: Blood_Platelets_Vumc-NSCLC-539-TR2482


title: Blood_Platelets_Vumc-NSCLC-390-TR2479


title: CYC17KO_C4

value: Conjugation 4 hours


title: Blood_Platelets_Vumc-NSCLC-393-TR2478


title: Blood_Platelets_Vumc-NSCLC-441-TR2238


title: Blood_Platelets_Vumc-HD-148-TR931


title: Blood_Platelets_Vumc-NSCLC-1190-TR2199


title: Blood_Platelets_NKI-NSCLC-5465-TR2524


title: Blood_Platelets_Vumc-NSCLC-577-TR2483


title: Blood_Platelets_Vumc-NSCLC-859-TR2503


title: Blood_Platelets_Vumc-NSCLC-804-TR2502


title: Blood_Platelets_Vumc-NSCLC-782-TR2501


title: RGA-GFP_chipseq_rep2


title: Blood_Platelets_NKI-NSCLC-4888-TR2493


title: Blood_Platelets_NKI-NSCLC-4245-TR2521


title: Blood_Platelets_NKI-NSCLC-4649-TR2522


title: Blood_Platelets_Vumc-NSCLC-388-TR2477


title: Blood_Platelets_Vumc-NSCLC-459-TR2480


title: Blood_Platelets_NKI-NSCLC-2679-TR2492


title: Blood_Platelets_Vumc-NSCLC-928-TR2504


title: Blood_Platelets_NKI-NSCLC-2332-TR2513


title: Blood_Platelets_NKI-NSCLC-4202-TR2520


title: Blood_Platelets_NKI-NSCLC-2676-TR2515


title: Blood_Platelets_NKI-NSCLC-4067-TR2519


title: Blood_Platelets_NKI-NSCLC-3209-TR2517


title: Blood_Platelets_NKI-NSCLC-2381-TR2514


title: Blood_Platelets_NKI-NSCLC-0640-TR2509


title: Blood_Platelets_NKI-NSCLC-4780-TR2523


title: Blood_Platelets_NKI-NSCLC-1691-TR2491


title: Blood_Platelets_NKI-NSCLC-0527-TR2489


title: Blood_Platelets_NKI-NSCLC-0762-TR2511


title: Blood_Platelets_NKI-NSCLC-0818-TR2512


title: Blood_Platelets_NKI-NSCLC-0760-TR2490


title: Blood_Platelets_NKI-NSCLC-3211-TR2518


title: Blood_Platelets_MGH-NSCLC-L216-TR2498


title: Blood_Platelets_NKI-NSCLC-0193-TR2486


title: Blood_Platelets_NKI-NSCLC-0220-TR2487


title: Blood_Platelets_NKI-NSCLC-0649-TR2510


title: Blood_Platelets_MGH-NSCLC-L217-TR2499


title: Blood_Platelets_MGH-NSCLC-L195-TR2496


title: Blood_Platelets_NKI-NSCLC-0229-TR2488


title: Blood_Platelets_NKI-NSCLC-0470-TR2508


title: Blood_Platelets_NKI-NSCLC-0134-TR2485


title: Blood_Platelets_NKI-NSCLC-0423-TR2507


title: Blood_Platelets_NKI-NSCLC-0334-TR2506


title: Blood_Platelets_MGH-NSCLC-L190-TR2495


title: Blood_Platelets_NKI-NSCLC-0117-TR2484


title: Blood_Platelets_NKI-NSCLC-3147-TR2516


title: Blood_Platelets_Vumc-HD-4-TR1150

value: Healthy Control


title: Blood_Platelets_Vumc-HD-47-1-TR1167


title: Blood_Platelets_MGH-NSCLC-L189-TR2494


title: Blood_Platelets_Vumc-HD-54-1-TR1172


title: Blood_Platelets_NKI-NSCLC-2220-TR1807


title: Blood_Platelets_MGH-NSCLC-L206-TR2497


title: Blood_Platelets_NKI-NSCLC-2153-TR1839


title: Blood_Platelets_NKI-NSCLC-2403-TR1844


title: Blood_Platelets_NKI-NSCLC-2150-TR1847


title: Blood_Platelets_NKI-NSCLC-2149-TR1848


title: Blood_Platelets_NKI-NSCLC-2314-TR1854


title: Blood_Platelets_MGH-NSCLC-L194-TR2500


title: Blood_Platelets_NKI-NSCLC-2121-TR1900


title: Blood_Platelets_NKI-NSCLC-2205-TR1856


title: Blood_Platelets_NKI-NSCLC-2079-TR1897


title: Blood_Platelets_NKI-NSCLC-2006-TR1842


title: Blood_Platelets_NKI-NSCLC-2126-TR1843


title: Blood_Platelets_NKI-NSCLC-2062-TR1901


title: Blood_Platelets_NKI-NSCLC-2237-TR1853


title: Blood_Platelets_NKI-NSCLC-1931-TR1840


title: Blood_Platelets_NKI-NSCLC-1924-TR1892


title: Blood_Platelets_NKI-NSCLC-1844-TR1890


title: Blood_Platelets_NKI-NSCLC-1946-TR1898


title: Blood_Platelets_NKI-NSCLC-1671-TR1912


title: Blood_Platelets_NKI-NSCLC-1777-TR1788


title: Blood_Platelets_NKI-NSCLC-1665-TR1894


title: Blood_Platelets_NKI-NSCLC-1922-TR1841


title: Blood_Platelets_NKI-NSCLC-1593-TR1845


title: Blood_Platelets_NKI-NSCLC-1589-TR1895


title: Blood_Platelets_NKI-NSCLC-1663-TR1808


title: Blood_Platelets_NKI-NSCLC-1725-TR1896


title: Blood_Platelets_NKI-NSCLC-1544-TR1891


title: Blood_Platelets_NKI-NSCLC-1653-TR1893


title: Blood_Platelets_NKI-NSCLC-1574-TR1836


title: Blood_Platelets_NKI-NSCLC-642-TR1835


title: Blood_Platelets_NKI-NSCLC-1222-TR1837


title: Blood_Platelets_NKI-NSCLC-1114-TR1838


title: Blood_Platelets_NKI-NSCLC-281-TR1834


title: Blood_Platelets_NKI-NSCLC-1151-TR1899


title: Blood_Platelets_NKI-NSCLC-1292-TR1806


title: Blood_Platelets_NKI-NSCLC-1667-TR1341


title: Blood_Platelets_Vumc-NSCLC-251-TR1276


title: Blood_Platelets_NKI-NSCLC-1652-TR1344

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
NKI-NSCLC-1652-TR1344


title: Blood_Platelets_Vumc-NSCLC-313-TR1243


title: Blood_Platelets_NKI-NSCLC-689-TR1325

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
NKI-NSCLC-689-TR1325


title: Blood_Platelets_Vumc-NSCLC-258-TR1238


title: Blood_Platelets_NKI-NSCLC-1459-TR1339


title: Blood_Platelets_NKI-NSCLC-1565-TR1345

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
NKI-NSCLC-1565-TR1345


title: Blood_Platelets_NKI-NSCLC-1485-TR1340


title: Blood_Platelets_Vumc-NSCLC-391-TR1272


title: Blood_Platelets_NKI-NSCLC-1362-TR1381

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
NKI-NSCLC-1362-TR1381


title: Blood_Platelets_Vumc-NSCLC-470-TR1275


title: Blood_Platelets_NKI-NSCLC-1420-TR1338


title: Blood_Platelets_Vumc-NSCLC-253-TR1237


title: Blood_Platelets_NKI-NSCLC-895-TR1323

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
NKI-NSCLC-895-TR1323


title: Blood_Platelets_NKI-NSCLC-1059-TR1327


title: Blood_Platelets_NKI-NSCLC-1255-TR1321

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
NKI-NSCLC-1255-TR1321


title: Blood_Platelets_NKI-NSCLC-882-TR1319

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
NKI-NSCLC-882-TR1319


title: Blood_Platelets_NKI-NSCLC-975-TR1317


title: Blood_Platelets_NKI-NSCLC-1054-TR1324

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
NKI-NSCLC-1054-TR1324


title: Blood_Platelets_NKI-NSCLC-1041-TR1281


title: Blood_Platelets_NKI-NSCLC-1523-TR1846


title: Blood_Platelets_Vumc-NSCLC-404-TR1274


title: Blood_Platelets_NKI-NSCLC-1535-TR1308

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
NKI-NSCLC-1535-TR1308


title: Blood_Platelets_NKI-NSCLC-1409-TR1336

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
NKI-NSCLC-1409-TR1336


title: Blood_Platelets_Vumc-NSCLC-394-TR1273


title: Blood_Platelets_NKI-NSCLC-1587-TR1343

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
NKI-NSCLC-1587-TR1343


title: Blood_Platelets_NKI-NSCLC-1342-TR1334


title: Blood_Platelets_NKI-NSCLC-1349-TR1333


title: Blood_Platelets_NKI-NSCLC-1553-TR1331


title: Blood_Platelets_NKI-NSCLC-865-TR1312

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
NKI-NSCLC-865-TR1312


title: Blood_Platelets_NKI-NSCLC-1470-TR1384


title: Blood_Platelets_NKI-NSCLC-1379-TR1309

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
NKI-NSCLC-1379-TR1309


title: Blood_Platelets_NKI-NSCLC-1348-TR1332

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
NKI-NSCLC-1348-TR1332


title: Blood_Platelets_NKI-NSCLC-1613-TR1335


title: Blood_Platelets_NKI-NSCLC-1369-TR1311


title: Blood_Platelets_NKI-NSCLC-1109-TR1284


title: Blood_Platelets_Vumc-NSCLC-288-TR1268


title: Blood_Platelets_NKI-NSCLC-352-TR1330


title: Blood_Platelets_NKI-NSCLC-1016-TR1329


title: Blood_Platelets_NKI-NSCLC-1143-TR1282

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
NKI-NSCLC-1143-TR1282


title: Blood_Platelets_NKI-NSCLC-582-TR1279


title: Blood_Platelets_Vumc-NSCLC-513-TR1305


title: Blood_Platelets_Vumc-NSCLC-358-TR1310


title: Blood_Platelets_Vumc-NSCLC-323-TR1245


title: Blood_Platelets_Vumc-NSCLC-178-TR1255


title: Blood_Platelets_Vumc-NSCLC-257-TR1234


title: Blood_Platelets_NKI-NSCLC-1043-TR1283


title: Blood_Platelets_NKI-NSCLC-1244-TR1280


title: Blood_Platelets_NKI-NSCLC-879-TR1315


title: Blood_Platelets_Vumc-NSCLC-574-TR1307

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
Vumc-NSCLC-574-TR1307


title: Blood_Platelets_NKI-NSCLC-1019-TR1277


title: Blood_Platelets_NKI-NSCLC-1422-TR1337


title: Blood_Platelets_NKI-NSCLC-1128-TR1285


title: Blood_Platelets_NKI-NSCLC-1082-TR1322


title: Blood_Platelets_NKI-NSCLC-1205-TR1320


title: Blood_Platelets_NKI-NSCLC-868-TR1316


title: Blood_Platelets_Vumc-NSCLC-461-TR1303


title: Blood_Platelets_Vumc-NSCLC-335-TR1294


title: Blood_Platelets_NKI-NSCLC-1198-TR1318


title: Blood_Platelets_NKI-NSCLC-706-TR1314


title: Blood_Platelets_NKI-NSCLC-1528-TR1382

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
NKI-NSCLC-1528-TR1382


title: Blood_Platelets_Vumc-NSCLC-317-TR1244


title: Blood_Platelets_NKI-NSCLC-1034-TR1326

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
NKI-NSCLC-1034-TR1326


title: Blood_Platelets_NKI-NSCLC-1211-TR1286

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
NKI-NSCLC-1211-TR1286


title: Blood_Platelets_NKI-NSCLC-856-TR1313

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
NKI-NSCLC-856-TR1313


title: Blood_Platelets_Vumc-NSCLC-361-TR1036


title: Blood_Platelets_Vumc-NSCLC-348-TR1035


title: Blood_Platelets_Vumc-NSCLC-263-TR1239


title: Blood_Platelets_Vumc-NSCLC-282-TR1031


title: Blood_Platelets_Vumc-NSCLC-300-TR1034


title: Blood_Platelets_Vumc-NSCLC-298-TR1033


title: Blood_Platelets_Vumc-NSCLC-265-TR1019


title: Blood_Platelets_NKI-NSCLC-1530-TR1383

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
NKI-NSCLC-1530-TR1383


title: Blood_Platelets_Vumc-NSCLC-259-TR1007


title: Blood_Platelets_Vumc-NSCLC-260-TR1008


title: Blood_Platelets_Vumc-NSCLC-296-TR1032


title: Blood_Platelets_Vumc-NSCLC-267-TR1020


title: Blood_Platelets_Vumc-NSCLC-255-TR1006


title: Blood_Platelets_Vumc-NSCLC-248-TR1004


title: Blood_Platelets_NKI-NSCLC-1029-TR1328


title: Blood_Platelets_Vumc-NSCLC-278-TR1048


title: Blood_Platelets_Vumc-NSCLC-250-TR1005


title: Blood_Platelets_Vumc-NSCLC-241-TR1000


title: Blood_Platelets_Vumc-NSCLC-242-TR1001


title: Blood_Platelets_Vumc-NSCLC-243-TR1002


title: Blood_Platelets_Vumc-NSCLC-244-TR1003


title: Blood_Platelets_Vumc-NSCLC-226-TR997


title: Blood_Platelets_Vumc-NSCLC-232-TR998


title: Blood_Platelets_Vumc-NSCLC-240-TR999


title: Blood_Platelets_NKI-NSCLC-1476-TR1342


title: Blood_Platelets_Vumc-NSCLC-269-TR1021


title: Blood_Platelets_Vumc-NSCLC-223-TR996


title: Blood_Platelets_Vumc-NSCLC-221-TR984


title: Blood_Platelets_Vumc-NSCLC-218-TR983


title: Blood_Platelets_Vumc-NSCLC-210-TR982


title: Blood_Platelets_Vumc-NSCLC-203-TR980


title: Blood_Platelets_Vumc-NSCLC-200-TR978


title: Blood_Platelets_Vumc-NSCLC-199-TR977


title: Blood_Platelets_Vumc-NSCLC-201-TR979


title: Blood_Platelets_Vumc-NSCLC-207-TR981


title: Blood_Platelets_Vumc-NSCLC-187-TR975


title: Blood_Platelets_Vumc-NSCLC-198-TR976


title: Blood_Platelets_Vumc-NSCLC-169-TR961


title: Blood_Platelets_Vumc-NSCLC-166-TR960


title: Blood_Platelets_Vumc-NSCLC-161-TR958


title: Blood_Platelets_Vumc-NSCLC-163-TR959


title: Blood_Platelets_Vumc-NSCLC-159-TR957


title: Blood_Platelets_Vumc-NSCLC-186-TR974


title: Blood_Platelets_Vumc-NSCLC-171-TR962


title: Blood_Platelets_Vumc-NSCLC-157-TR955


title: Blood_Platelets_Vumc-NSCLC-158-TR956


title: Blood_Platelets_Vumc-NSCLC-149-TR954

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
Vumc-NSCLC-149-TR954


title: Blood_Platelets_Vumc-NSCLC-148-TR953


title: Blood_Platelets_Vumc-NSCLC-130-TR952


title: Blood_Platelets_Vumc-NSCLC-105-TR950


title: Blood_Platelets_Vumc-NSCLC-230-TR882


title: Blood_Platelets_Vumc-NSCLC-229-TR881


title: Blood_Platelets_Vumc-NSCLC-231-TR906


title: Blood_Platelets_Vumc-NSCLC-239-TR940


title: Blood_Platelets_Vumc-NSCLC-225-TR905


title: Blood_Platelets_Vumc-NSCLC-224-TR879


title: Blood_Platelets_Vumc-NSCLC-214-TR873


title: Blood_Platelets_Vumc-NSCLC-209-TR871


title: Blood_Platelets_Vumc-NSCLC-208-TR902


title: Blood_Platelets_Vumc-NSCLC-211-TR903


title: Blood_Platelets_Vumc-NSCLC-202-TR900


title: Blood_Platelets_Vumc-NSCLC-205-TR870


title: Blood_Platelets_Vumc-NSCLC-191-TR898


title: Blood_Platelets_Vumc-NSCLC-194-TR899


title: Blood_Platelets_Vumc-NSCLC-212-TR878


title: Blood_Platelets_Vumc-NSCLC-236-TR939


title: Blood_Platelets_Vumc-NSCLC-167-TR693


title: Blood_Platelets_Vumc-NSCLC-165-TR692


title: Blood_Platelets_Vumc-NSCLC-168-TR694


title: Blood_Platelets_Vumc-NSCLC-204-TR901


title: Blood_Platelets_MGH-NSCLC-L180-TR919


title: Blood_Platelets_Vumc-NSCLC-181-TR876


title: Blood_Platelets_MGH-NSCLC-L158-TR913


title: Blood_Platelets_Vumc-NSCLC-219-TR916


title: Blood_Platelets_MGH-NSCLC-L145-TR912


title: Blood_Platelets_MGH-NSCLC-L134-TR911


title: Blood_Platelets_Vumc-NSCLC-164-TR691


title: Blood_Platelets_Vumc-NSCLC-213-TR872


title: Blood_Platelets_MGH-NSCLC-L178-TR918


title: Blood_Platelets_MGH-NSCLC-L131-TR909


title: Blood_Platelets_MGH-NSCLC-L173-TR915


title: Blood_Platelets_Vumc-NSCLC-217-TR904


title: Blood_Platelets_MGH-NSCLC-L126-TR917


title: Blood_Platelets_MGH-NSCLC-L149-TR883


title: Blood_Platelets_MGH-NSCLC-L119-TR688


title: Blood_Platelets_MGH-NSCLC-L117-TR686


title: Blood_Platelets_MGH-NSCLC-L118-TR687


title: Blood_Platelets_Vumc-NSCLC-216-TR874

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
Vumc-NSCLC-216-TR874


title: Blood_Platelets_MGH-NSCLC-L169-TR914


title: Blood_Platelets_Vumc-NSCLC-189-TR713


title: Blood_Platelets_MGH-NSCLC-L133-TR910


title: Blood_Platelets_Vumc-NSCLC-195-TR877


title: Blood_Platelets_Vumc-NSCLC-188-TR712


title: Blood_Platelets_MGH-NSCLC-L116-TR685


title: Blood_Platelets_MGH-NSCLC-L130-TR908


title: Blood_Platelets_MGH-NSCLC-L115-TR684


title: Blood_Platelets_Vumc-NSCLC-184-TR710


title: Blood_Platelets_Vumc-NSCLC-173-TR668


title: Blood_Platelets_Vumc-NSCLC-172-TR667


title: Blood_Platelets_Vumc-NSCLC-170-TR666


title: Blood_Platelets_Vumc-NSCLC-106-TR705


title: Blood_Platelets_Vumc-NSCLC-185-TR711


title: Blood_Platelets_Vumc-NSCLC-179-TR670


title: Blood_Platelets_Vumc-NSCLC-174-TR669


title: Blood_Platelets_Vumc-NSCLC-183-TR671


title: Blood_Platelets_NKI-NSCLC-107-705-TR727


title: Blood_Platelets_Vumc-NSCLC-131-TR709


title: Blood_Platelets_NKI-NSCLC-107-703-TR737

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
NKI-NSCLC-107-703-TR737


title: Blood_Platelets_NKI-NSCLC-107-642-TR726


title: Blood_Platelets_NKI-NSCLC-107-660-TR751


title: Blood_Platelets_Vumc-NSCLC-160-TR690


title: Blood_Platelets_NKI-NSCLC-107-673-TR736

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
NKI-NSCLC-107-673-TR736


title: Blood_Platelets_NKI-NSCLC-107-577-TR731


title: Blood_Platelets_Vumc-NSCLC-115-TR706


title: Blood_Platelets_MGH-NSCLC-L121-TR907


title: Blood_Platelets_NKI-NSCLC-107-572-TR722

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
NKI-NSCLC-107-572-TR722


title: Blood_Platelets_NKI-NSCLC-107-691-TR721

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
NKI-NSCLC-107-691-TR721


title: Blood_Platelets_NKI-NSCLC-107-546-TR741


title: Blood_Platelets_NKI-NSCLC-107-602-TR747


title: Blood_Platelets_NKI-NSCLC-107-663-TR733


title: Blood_Platelets_NKI-NSCLC-107-599-TR743

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
NKI-NSCLC-107-599-TR743


title: Blood_Platelets_NKI-NSCLC-107-558-TR739


title: Blood_Platelets_NKI-NSCLC-107-439-TR740


title: Blood_Platelets_NKI-NSCLC-107-419-TR745


title: Blood_Platelets_NKI-NSCLC-107-395-TR749


title: Blood_Platelets_NKI-NSCLC-107-288-TR732


title: Blood_Platelets_NKI-NSCLC-107-487-TR752

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
NKI-NSCLC-107-487-TR752


title: Blood_Platelets_NKI-NSCLC-107-466-TR738


title: Blood_Platelets_NKI-NSCLC-107-183-TR735


title: Blood_Platelets_NKI-NSCLC-107-455-TR742

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
NKI-NSCLC-107-455-TR742


title: Blood_Platelets_NKI-NSCLC-107-262-TR730


title: Blood_Platelets_NKI-NSCLC-107-162-TR723

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
NKI-NSCLC-107-162-TR723


title: Blood_Platelets_NKI-NSCLC-107-139-TR729

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
NKI-NSCLC-107-139-TR729


title: Blood_Platelets_NKI-NSCLC-107-245-TR744

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
NKI-NSCLC-107-245-TR744


title: Blood_Platelets_NKI-NSCLC-107-162-TR748


title: Blood_Platelets_NKI-NSCLC-107-081-TR728


title: Blood_Platelets_NKI-NSCLC-107-376-TR720


title: Blood_Platelets_MGH-NSCLC-L78-TR695


title: Blood_Platelets_NKI-NSCLC-107-270-TR725

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
NKI-NSCLC-107-270-TR725


title: Blood_Platelets_NKI-NSCLC-107-123-TR750


title: Blood_Platelets_MGH-NSCLC-L126-TR717


title: Blood_Platelets_NKI-NSCLC-107-533-TR746


title: Blood_Platelets_NKI-NSCLC-107-508-TR734


title: Blood_Platelets_MGH-NSCLC-L127-TR718


title: Blood_Platelets_MGH-NSCLC-L128-TR719


title: Blood_Platelets_NKI-NSCLC-107-518-TR724


title: Blood_Platelets_MGH-NSCLC-L125-TR716


title: Blood_Platelets_MGH-NSCLC-L122-TR715


title: Blood_Platelets_Vumc-NSCLC-VU079-TR631


title: Blood_Platelets_MGH-NSCLC-175-TR707


title: Blood_Platelets_Vumc-LGG-VU106-1-TR605


title: Blood_Platelets_Vumc-NSCLC-VU028-TR632


title: Blood_Platelets_Vumc-LGG-VU028-1-TR633


title: Blood_Platelets_MGH-NSCLC-L88-TR601


title: Blood_Platelets_MGH-NSCLC-L73-TR578


title: Blood_Platelets_MGH-NSCLC-L41-TR616


title: Blood_Platelets_MGH-NSCLC-L48-TR577


title: Blood_Platelets_Vumc-NSCLC-151-TR463


title: Blood_Platelets_MGH-NSCLC-L10-TR606


title: Blood_Platelets_Pang-NSCLC-B739-1-TR455


title: Blood_Platelets_Vumc-NSCLC-052-TR460


title: Blood_Platelets_Vumc-NSCLC-071-TR486


title: Blood_Platelets_Vumc-NSCLC-107-TR487


title: Blood_Platelets_MGH-NSCLC-L120-TR714


title: Blood_Platelets_MGH-NSCLC-L99-TR464


title: Blood_Platelets_Pang-NSCLC-B295-2-TR454


title: Blood_Platelets_MGH-NSCLC-L58-TR525


title: Blood_Platelets_MGH-NSCLC-L65-TR523


title: Blood_Platelets_MGH-NSCLC-L56-TR481


title: Blood_Platelets_Vumc-NSCLC-VU146-TR374


title: Blood_Platelets_MGH-NSCLC-L44-TR504


title: Blood_Platelets_Vumc-NSCLC-152-TR604


title: Blood_Platelets_NKI-NSCLC-107-348-TR753


title: Blood_Platelets_MGH-NSCLC-L37-TR503


title: Blood_Platelets_MGH-NSCLC-L40-TR520


title: Blood_Platelets_MGH-NSCLC-L36-TR502


title: Blood_Platelets_MGH-NSCLC-L39-TR519


title: Blood_Platelets_MGH-NSCLC-L22-TR462


title: Blood_Platelets_MGH-NSCLC-L32-TR501


title: Blood_Platelets_MGH-NSCLC-L23-TR524


title: Blood_Platelets_MGH-NSCLC-L18-TR479


title: Blood_Platelets_MGH-NSCLC-L51-TR521


title: Blood_Platelets_MGH-NSCLC-L20-TR500


title: Blood_Platelets_MGH-NSCLC-L12-TR478


title: Blood_Platelets_MGH-NSCLC-L11-TR477


title: Blood_Platelets_MGH-NSCLC-L33-TR600


title: Blood_Platelets_MGH-NSCLC-L114-TR527


title: Blood_Platelets_Vumc-NSCLC-66


title: Blood_Platelets_MGH-NSCLC-L100-TR526


title: Blood_Platelets_Vumc-NSCLC-154


title: Blood_Platelets_Vumc-NSCLC-59


title: Blood_Platelets_Vumc-NSCLC-57


title: Blood_Platelets_Vumc-NSCLC-155


title: Blood_Platelets_Vumc-NSCLC-49


title: Blood_Platelets_Vumc-NSCLC-145


title: Blood_Platelets_Vumc-NSCLC-147


title: Blood_Platelets_MGH-NSCLC-L07-TR459


title: Blood_Platelets_Vumc-NSCLC-150


title: Blood_Platelets_Vumc-NSCLC-69


title: Blood_Platelets_MGH-NSCLC-L03-TR488


title: Blood_Platelets_Vumc-NSCLC-142


title: Blood_Platelets_MGH-NSCLC-L19-TR461


title: Blood_Platelets_Vumc-NSCLC-139


title: Blood_Platelets_Vumc-NSCLC-140


title: Blood_Platelets_Vumc-NSCLC-143


title: Blood_Platelets_Vumc-NSCLC-141


title: Blood_Platelets_Vumc-NSCLC-138


title: Blood_Platelets_Vumc-NSCLC-133


title: Blood_Platelets_Vumc-NSCLC-132-1


title: Blood_Platelets_Vumc-NSCLC-137


title: Blood_Platelets_Vumc-NSCLC-134


title: Blood_Platelets_MGH-NSCLC-L01-TR458


title: Blood_Platelets_Vumc-NSCLC-129


title: Blood_Platelets_Vumc-NSCLC-128


title: Blood_Platelets_Vumc-NSCLC-124


title: Blood_Platelets_Vumc-NSCLC-127


title: Blood_Platelets_Vumc-NSCLC-121


title: Blood_Platelets_Vumc-NSCLC-125


title: Blood_Platelets_Vumc-NSCLC-122


title: Blood_Platelets_Vumc-NSCLC-117


title: Blood_Platelets_Vumc-NSCLC-123


title: Blood_Platelets_Vumc-NSCLC-144


title: Blood_Platelets_Vumc-NSCLC-120


title: Blood_Platelets_Vumc-NSCLC-118


title: Blood_Platelets_Vumc-NSCLC-114


title: Blood_Platelets_Vumc-NSCLC-109-1


title: Blood_Platelets_Vumc-NSCLC-103


title: Blood_Platelets_Vumc-NSCLC-113


title: Blood_Platelets_Vumc-NSCLC-093


title: Blood_Platelets_Vumc-NSCLC-092


title: Blood_Platelets_Vumc-NSCLC-089


title: Blood_Platelets_Vumc-NSCLC-088


title: Blood_Platelets_Vumc-NSCLC-084


title: Blood_Platelets_Vumc-NSCLC-086


title: Blood_Platelets_Vumc-NSCLC-080


title: Blood_Platelets_Vumc-NSCLC-081


title: Blood_Platelets_Vumc-NSCLC-083


title: Blood_Platelets_Vumc-NSCLC-063


title: Blood_Platelets_Vumc-NSCLC-068


title: Blood_Platelets_Vumc-NSCLC-070


title: Blood_Platelets_Vumc-NSCLC-054


title: Blood_Platelets_Vumc-NSCLC-027


title: Blood_Platelets_MGH-NSCLC-L-96


title: Blood_Platelets_MGH-NSCLC-L-74


title: Blood_Platelets_MGH-NSCLC-L-92


title: Blood_Platelets_MGH-NSCLC-L-42


title: Blood_Platelets_MGH-NSCLC-L-72


title: Blood_Platelets_MGH-NSCLC-L-89


title: Blood_Platelets_MGH-NSCLC-L-47


title: Blood_Platelets_Vumc-NSCLC-094


title: Blood_Platelets_UMCU-non-sign-athero-4-1696-TR1992

value: Non-significant Atherosclerosis


title: Blood_Platelets_MGH-NSCLC-L-09


title: Blood_Platelets_Vumc-ChronPan-1-2016584-TR1946

value: Chronic Pancreatitis


title: Blood_Platelets_Vumc-ChronPan-21-2016119-TR1947


title: Blood_Platelets_UMCU-non-sign-athero-4-1682-TR1990


title: Blood_Platelets_UMCU-non-sign-athero-4-1691-TR1990


title: Blood_Platelets_UMCU-non-sign-athero-4-1670-TR1988


title: Blood_Platelets_UMCU-non-sign-athero-4-1675-TR1989


title: Blood_Platelets_UMCU-non-sign-athero-4-1669-TR1987


title: Blood_Platelets_P-PH-001-013-TR1400

value: Pulmonary Hypertension


title: Blood_Platelets_UMCU-2-0570-AP-unstable-TR948

value: Unstable Angina Pectoris


title: Blood_Platelets_UMCU-2-0585-AP-unstable-TR949


title: Blood_Platelets_UMCU-1-0056-AP-stable-TR936

value: Stable Angina Pectoris


title: Blood_Platelets_UMCU-2-0533-AP-unstable-TR944


title: Blood_Platelets_UMCU-non-sign-athero-2-0657-TR1986


title: Blood_Platelets_UMCU-2-0566-AP-unstable-TR947


title: Blood_Platelets_UMCU-NSAth-1-0151-TR830


title: Blood_Platelets_UMCU-NSAth-1-0190-TR832


title: Blood_Platelets_UMCU-1-0006-AP-stable-TR938


title: Blood_Platelets_UMCU-NSAth-1-0147-TR829


title: Blood_Platelets_Vumc-EPI-018-TR1524

value: Epilepsy


title: Blood_Platelets_Vumc-EPI-009-TR1464


title: Blood_Platelets_Vumc-EPI-010-TR1426


title: Blood_Platelets_Vumc-EPI-019-TR1525


title: Blood_Platelets_Vumc-EPI-020-TR1526


title: Blood_Platelets_Vumc-EPI-016-TR1436


title: Blood_Platelets_UMCU-2-0540-AP-unstable-TR946


title: Blood_Platelets_UMCU-2-0536-AP-unstable-TR945


title: Blood_Platelets_Vumc-EPI-001-TR1425


title: Blood_Platelets_Vumc-EPI-012-TR1466


title: Blood_Platelets_Vumc-EPI-022-TR1438


title: Blood_Platelets_Vumc-EPI-013-TR1467


title: Blood_Platelets_UMCU-NSAth-1-0127-TR827

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
UMCU-NSAth-1-0127-TR827


title: Blood_Platelets_Vumc-EPI-014-TR1427


title: Blood_Platelets_Vumc-EPI-015-TR1435


title: Blood_Platelets_Vumc-EPI-002-TR1462


title: Blood_Platelets_UMCU-1-0024-AP-stable-TR943


title: Blood_Platelets_Vumc-EPI-016-TR1437


title: Blood_Platelets_Vumc-EPI-011-TR1465


title: Blood_Platelets_Pisa-ChronPan-2015VIT-TR972


title: Blood_Platelets_Vumc-EPI-007-TR1463

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
Vumc-EPI-007-TR1463


title: Blood_Platelets_Vumc-P-PH-001-050-TR1460


title: Blood_Platelets_UMCU-1-0018-AP-stable-TR942


title: Blood_Platelets_Vumc-EPI006-TR800


title: Blood_Platelets_Vumc-EPI008-TR802


title: Blood_Platelets_Vumc-P-PH-001-035-TR1418


title: Blood_Platelets_Vumc-P-PH-001-034-TR1512

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
Vumc-P-PH-001-034-TR1512


title: Blood_Platelets_Vumc-EPI005-TR799


title: Blood_Platelets_Vumc-EPI003-TR797


title: Blood_Platelets_UMCU-NSAth-1-0155-TR831


title: Blood_Platelets_Vumc-ChronPan-59-TR1046


title: Blood_Platelets_Vumc-EPI004-TR798


title: Blood_Platelets_Vumc-P-PH-001-039-TR1421


title: Blood_Platelets_Vumc-P-PH-001-053-TR1461


title: Blood_Platelets_Vumc-P-PH-001-027-TR1409


title: Blood_Platelets_Vumc-P-PH-001-014-TR1459


title: Blood_Platelets_Vumc-P-PH-001-010-TR1505

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
Vumc-P-PH-001-010-TR1505


title: Blood_Platelets_Vumc-ChronPan-61-TR1047


title: Blood_Platelets_Vumc-P-PH-001-005-TR1503


title: Blood_Platelets_Vumc-P-PH-001-003-TR1392


title: Blood_Platelets_Vumc-P-PH-001-013-TR1400


title: Blood_Platelets_Vumc-P-PH-001-054-TR1424

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
Vumc-P-PH-001-054-TR1424


title: Blood_Platelets_Vumc-P-PH-001-033-TR1417


title: Blood_Platelets_Vumc-P-PH-001-001-TR1502


title: Blood_Platelets_Vumc-P-PH-001-002-TR1391


title: Blood_Platelets_Vumc-P-PH-001-037-TR1420


title: Blood_Platelets_Vumc-P-PH-001-041-TR1422


title: Blood_Platelets_Vumc-P-PH-001-026-TR1408


title: Blood_Platelets_Vumc-P-PH-001-028-TR1410


title: Blood_Platelets_Vumc-P-PH-001-029-TR1434


title: Blood_Platelets_Vumc-P-PH-001-022-TR1511


title: Blood_Platelets_Vumc-P-PH-001-016-TR1404


title: Blood_Platelets_Vumc-P-PH-001-020-TR1509


title: Blood_Platelets_Vumc-P-PH-001-008-TR1504


title: Blood_Platelets_Vumc-P-PH-001-023-TR1407


title: Blood_Platelets_Vumc-P-PH-001-012-TR1506


title: Blood_Platelets_Vumc-P-PH-001-018-TR1413


title: Blood_Platelets_Vumc-P-PH-001-042-TR1423


title: Blood_Platelets_Vumc-P-PH-001-007-TR1395


title: Blood_Platelets_Vumc-MS-051-TR1532

value: Multiple Sclerosis


title: Blood_Platelets_Vumc-P-PH-001-006-TR1457


title: Blood_Platelets_Vumc-MS-061-TR1587


title: Blood_Platelets_Vumc-MS-054-TR1447


title: Blood_Platelets_Vumc-P-PH-001-011-TR1458


title: Blood_Platelets_Vumc-MS-028-TR1469


title: Blood_Platelets_Vumc-MS-058-TR1537


title: Blood_Platelets_Vumc-MS-053-TR1534


title: Blood_Platelets_Vumc-P-PH-001-017-TR1507


title: Blood_Platelets_Vumc-MS-Presto-035-TR1475


title: Blood_Platelets_Vumc-MS-050-TR1531


title: Blood_Platelets_Vumc-MS-057-TR1536


title: Blood_Platelets_Vumc-MS-033-TR1585


title: Blood_Platelets_Vumc-MS-056-TR1535


title: Blood_Platelets_Vumc-MS-062-TR1540


title: Blood_Platelets_Vumc-MS-Presto-026-TR1439

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
Vumc-MS-Presto-026-TR1439


title: Blood_Platelets_Vumc-MS-059-TR1538


title: Blood_Platelets_Vumc-MS-Presto-049-TR1530


title: Blood_Platelets_MGH-NSCLC-L25-TR480


title: Blood_Platelets_Vumc-P-PH-001-009-TR1397


title: Blood_Platelets_Vumc-MS-Presto-045-TR1446


title: Blood_Platelets_Vumc-MS-Presto-041-TR1442


title: Blood_Platelets_Vumc-MS-Presto-048-TR1529


title: Blood_Platelets_Vumc-MS-Presto-036-TR1476


title: Blood_Platelets_Vumc-MS-Presto-043-TR1444


title: Blood_Platelets_Vumc-MS-052-TR1533


title: Blood_Platelets_Vumc-MS-Presto-038-TR1478


title: Blood_Platelets_Vumc-MS-Presto-034-TR1474


title: Blood_Platelets_Vumc-MS-Presto-031-TR1472


title: Blood_Platelets_Vumc-MS-Presto-037-TR1477


title: Blood_Platelets_Vumc-MS-Presto-022-TR1430

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
Vumc-MS-Presto-022-TR1430


title: Blood_Platelets_Vumc-MS-Presto-029-TR1470


title: Blood_Platelets_Vumc-MS-Presto-044-TR1445


title: Blood_Platelets_Vumc-MS-Presto-024-TR1432

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
Vumc-MS-Presto-024-TR1432


title: Blood_Platelets_Vumc-MS-Presto-032-TR1473


title: Blood_Platelets_Vumc-MS-Presto-020-TR1428


title: Blood_Platelets_Vumc-MS-Presto-021-TR1429


title: Blood_Platelets_Vumc-MS-Presto-030-TR1471


title: Blood_Platelets_Vumc-MS-Presto-039-TR1440


title: Blood_Platelets_Vumc-MS-Presto-023-TR1431


title: Blood_Platelets_Vumc-MS-Presto-042-TR1443


title: Blood_Platelets_Vumc-MS-017-TR853


title: Blood_Platelets_Vumc-MS-Presto-025-TR1433


title: Blood_Platelets_Vumc-MS-018-TR854


title: Blood_Platelets_Vumc-MS-Presto-040-TR1441


title: Blood_Platelets_Vumc-MS-019-TR855


title: Blood_Platelets_Vumc-MS-014-TR673


title: Blood_Platelets_Vumc-MS-016-TR852


title: Blood_Platelets_Vumc-MS-012-TR850


title: Blood_Platelets_Vumc-MS-055-TR1586


title: Blood_Platelets_Vumc-MS-011-TR645


title: Blood_Platelets_Vumc-MS-009-TR643


title: Blood_Platelets_Vumc-MS-007-TR641


title: Blood_Platelets_Vumc-MS-010-TR644


title: Blood_Platelets_Vumc-MS-005-TR640


title: Blood_Platelets_Vumc-HD-217-TR1915


title: Blood_Platelets_Vumc-MS-Presto-027-TR1468

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
Vumc-MS-Presto-027-TR1468


title: Blood_Platelets_Vumc-HD-246-TR1916


title: Blood_Platelets_Vumc-MS-004-TR639


title: Blood_Platelets_Vumc-MS-008-TR642


title: Blood_Platelets_Vumc-MS-002-TR637


title: Blood_Platelets_Vumc-HD-199-TR1914


title: Blood_Platelets_Vumc-MS-001-TR636


title: Blood_Platelets_Vumc-HD-238-TR1878


title: Blood_Platelets_Vumc-MS-013-TR672


title: Blood_Platelets_Vumc-MS-003-TR638


title: Blood_Platelets_Vumc-HD-229-TR1882


title: Blood_Platelets_Vumc-HD-257-TR1865


title: Blood_Platelets_Vumc-HD-224-TR1885


title: Blood_Platelets_Vumc-HD-196-TR1852


title: Blood_Platelets_Vumc-HD-233-TR1879


title: Blood_Platelets_Vumc-HD-256-TR1864


title: Blood_Platelets_Vumc-HD-230-TR1881


title: Blood_Platelets_Vumc-MS-015-TR696


title: Blood_Platelets_Vumc-HD-175-TR1913


title: Blood_Platelets_Vumc-HD-189-TR1850


title: Blood_Platelets_Vumc-HD-244-TR1780


title: Blood_Platelets_Vumc-HD-239-TR1781


title: Blood_Platelets_Vumc-HD-264-TR1867


title: Blood_Platelets_Vumc-HD-188-TR1849


title: Blood_Platelets_Vumc-HD-266-TR1869


title: Blood_Platelets_Vumc-HD-195-TR1851


title: Blood_Platelets_Vumc-HD-280-TR1870


title: Blood_Platelets_Vumc-HD-236-TR1782


title: Blood_Platelets_Vumc-HD-220-TR1760


title: Blood_Platelets_Vumc-HD-225-TR1884


title: Blood_Platelets_Vumc-HD-283-TR1874


title: Blood_Platelets_Vumc-HD-186-TR1759


title: Blood_Platelets_Vumc-HD-33-1-TR1637


title: Blood_Platelets_Vumc-HD-228-TR1883


title: Blood_Platelets_Vumc-HD-253-TR1861


title: Blood_Platelets_Vumc-HD-163-TR1757


title: Blood_Platelets_Vumc-HD-247-TR1859


title: Blood_Platelets_Vumc-HD-250-TR1906


title: Blood_Platelets_Vumc-HD-272-TR1876


title: Blood_Platelets_Vumc-HD-231-TR1880


title: Blood_Platelets_Vumc-HD-169-TR1758


title: Blood_Platelets_Vumc-HD-263-TR1877


title: Blood_Platelets_Vumc-HD-162-TR1756


title: Blood_Platelets_Vumc-HD-282-TR1872


title: Blood_Platelets_Vumc-HD-198-TR1907


title: Blood_Platelets_Vumc-HD-255-TR1863


title: Blood_Platelets_Vumc-HD-262-TR1866


title: Blood_Platelets_Vumc-HD-254-TR1862


title: Blood_Platelets_Vumc-HD-1-TR1679


title: Blood_Platelets_Vumc-HD-45-2-TR1582


title: Blood_Platelets_Vumc-HD-34-1-TR1578


title: Blood_Platelets_Vumc-HD-235-TR1761


title: Blood_Platelets_Vumc-HD-252-TR1860


title: Blood_Platelets_Vumc-HD-265-TR1868


title: Blood_Platelets_Vumc-HD-38-2-TR1581


title: Blood_Platelets_Vumc-HD-13-2-TR1570


title: Blood_Platelets_Vumc-HD-218-TR1905


title: Blood_Platelets_Vumc-HD-25-2-TR1574


title: Blood_Platelets_Vumc-HD-37-2-TR1580


title: Blood_Platelets_Vumc-HD-234-TR1717


title: Blood_Platelets_Vumc-HD-31-2-TR1577


title: Blood_Platelets_Vumc-HD-6-2-TR1639


title: Blood_Platelets_Vumc-HD-29-2-TR1576


title: Blood_Platelets_Vumc-HD-10-2-TR1642


title: Blood_Platelets_Vumc-HD-26-2-TR1575


title: Blood_Platelets_Vumc-HD-226-TR1718


title: Blood_Platelets_Vumc-HD-48-1-TR1666


title: Blood_Platelets_Vumc-HD-35-2-TR1579


title: Blood_Platelets_Vumc-HD-18-2-TR1643


title: Blood_Platelets_Vumc-HD-180-TR1523


title: Blood_Platelets_Vumc-HD-241-TR1721


title: Blood_Platelets_Vumc-HD-52-TR1489


title: Blood_Platelets_Vumc-HD-24-2-TR1573


title: Blood_Platelets_Vumc-HD-242-TR1720


title: Blood_Platelets_Vumc-HD-8-TR1641


title: Blood_Platelets_Vumc-HD-46-2-TR1680


title: Blood_Platelets_Vumc-P-PH-001-024-TR1414


title: Blood_Platelets_Vumc-HD-14-1-TR1571


title: Blood_Platelets_Vumc-HD-159-TR1521


title: Blood_Platelets_G5-104N


title: Blood_Platelets_Vumc-HD-173-TR1488

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
Vumc-HD-173-TR1488


title: Blood_Platelets_Vumc-HD-161-TR1522


title: Blood_Platelets_G6-105N


title: Blood_Platelets_G2-101N


title: Blood_Platelets_Vumc-HD-237-TR1719


title: Blood_Platelets_G7-106N


title: Blood_Platelets_C3-12N


title: Blood_Platelets_Vumc-HDControl-8-TR1181


title: Blood_Platelets_Vumc-HDControl-9-TR1182


title: Blood_Platelets_Vumc-HD-9-TR1152


title: Blood_Platelets_Vumc-HDControl-10-TR1183


title: Blood_Platelets_Vumc-HDControl-6-TR1180


title: Blood_Platelets_B7-19N


title: Blood_Platelets_E12-24N


title: Blood_Platelets_G4-103N


title: Blood_Platelets_Vumc-HD-93-TR1085


title: Blood_Platelets_Vumc-HD-96-TR1088


title: Blood_Platelets_Vumc-HD-85-TR1084

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
Vumc-HD-85-TR1084


title: Blood_Platelets_Vumc-HD-94-TR1086


title: Blood_Platelets_Vumc-HD-82-TR1082


title: Blood_Platelets_Vumc-HD-95-TR1087


title: Blood_Platelets_Vumc-HD-78-TR1080


title: Blood_Platelets_Vumc-HD-77-TR1079


title: Blood_Platelets_Vumc-HD-72-TR1064


title: Blood_Platelets_E1-5N


title: Blood_Platelets_Vumc-HD-69-TR1061


title: Blood_Platelets_Vumc-HD-90-TR1083

description:
Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.
Vumc-HD-90-TR1083


title: Blood_Platelets_Vumc-HD-5-TR1151


title: Blood_Platelets_Vumc-HD-79-TR1081


title: Blood_Platelets_Vumc-HD-75-TR1065


title: Blood_Platelets_Vumc-HD-59-TR1093


title: Blood_Platelets_Vumc-HD-71-TR1063


title: Blood_Platelets_Vumc-HD-36-TR1165


title: Blood_Platelets_Vumc-HD-3-1-TR1149


title: Blood_Platelets_Vumc-HD-21-1-TR1161


title: Blood_Platelets_Vumc-HD-70-TR1062


title: Blood_Platelets_Vumc-HD-68-TR1060


title: Blood_Platelets_Vumc-HD-99-TR1094


title: Blood_Platelets_Vumc-HD-97-TR1089


title: Blood_Platelets_G3-102N


title: Blood_Platelets_Vumc-HD-76-TR1066


title: Blood_Platelets_Vumc-HD-158-TR1138


title: Blood_Platelets_Vumc-HD-53-1-TR1171


title: Blood_Platelets_Vumc-HD-50-1-TR1169


title: Blood_Platelets_Vumc-HD-49-1-TR1168


title: Blood_Platelets_Vumc-HD-51-1-TR1170


title: Blood_Platelets_Vumc-HD-157-TR1137


title: Blood_Platelets_Vumc-HD-154-TR1136


title: Blood_Platelets_Vumc-HD-44-2-TR1166


title: Blood_Platelets_Vumc-HD-152-TR1134


title: Blood_Platelets_Vumc-HD-39-1-TR1158


title: Blood_Platelets_Vumc-HD-40-1-TR1159


title: Blood_Platelets_Vumc-HD-15-1-TR1154


title: Blood_Platelets_Vumc-HD-32-2-TR1164


title: Blood_Platelets_Vumc-HD-30-2-TR1163


title: Blood_Platelets_Vumc-HD-2-1-TR1148


title: Blood_Platelets_Vumc-HD-22-1-TR1157


title: Blood_Platelets_Vumc-HD-67-TR1059


title: Blood_Platelets_Vumc-HD-27-2-TR1162


title: Blood_Platelets_Vumc-HD-141-TR1130


title: Blood_Platelets_Vumc-HD-66-TR1058


title: Blood_Platelets_Vumc-HD-20-1-TR1156


title: Blood_Platelets_Vumc-HD-17-1-TR1160


title: Blood_Platelets_Vumc-HD-136-TR1125


title: Blood_Platelets_Vumc-HD-132-TR1122


title: pan7_wt (TAM)

city: New Haven

first: Jun

last: Lu

state: CT

address: 10 Amistad St.

department: Yale Stem Cell Center

institute: Yale University

description:
pan7_wttam
Pan_7_AGTCAA
Pan_TAM_RNASeq.gct

data_processing:
Map to genome (mm9) with GenePattern's Tophat module
FPKM levels quantified with GenePattern's CuffDiff module by using GenePattern's standard UCSC genome browser's mm9 transcriptome definition
Genome_build: mm9
Supplementary_files_format_and_content: gct file format (tab delimited text file); contains gene level FPKM values

source_name: wt, TAMs

growth_protocol: YUMM1.7 melanoma cells (BrafV600EPten-/-Cdkn2a-/-)  were maintained in complete RPMI medium 1640 (Thermo Fisher), with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin/glutamine (PSG) at 37°C/5% CO2. For induction of tumor, YUMM1.7 melanoma cells were injected subcutaneously into the flanks of mice (2×10e5 cells per injection in 100μl PBS). Male C57BL/6J mice of 6 to 8 weeks of age were used. Tumors were harvested at 4 weeks, and TAMs were isolated by FACS-sorting of CD11b+F4/80+ cells.

extract_protocol:
Total RNA was extracted by TriZol
Standard Illumina protocol with polyA-based selection

treatment_protocol: No treatment

value: wildtype

tag: cell type

value: tumor associated macrophages (TAMs)


title: Blood_Platelets_Vumc-HD-16-1-TR1155


title: Blood_Platelets_Vumc-HD-131-TR1121


title: Blood_Platelets_Vumc-HD-129-TR1120


title: Blood_Platelets_Vumc-HD-153-TR1135


title: Blood_Platelets_Vumc-HD-126-TR1118


title: Blood_Platelets_Vumc-HD-146-TR1131


title: pan4_ko (TAM)

description:
pan4_kotam
Pan_4_GCCAAT
Pan_TAM_RNASeq.gct

source_name: ko, TAMs

value: Tet2 knockout


title: Blood_Platelets_Vumc-HD-147-TR1132


title: Blood_Platelets_Vumc-HD-138-TR1127


title: Blood_Platelets_Vumc-HD-135-TR1124


title: Blood_Platelets_Vumc-HD-139-TR1128


title: Blood_Platelets_Vumc-HD-150-TR1133


title: pan1_wt (TAM)

description:
pan1_wttam
Pan_1_CGATGT
Pan_TAM_RNASeq.gct


title: Blood_Platelets_Vumc-HD-140-TR1129


title: pan2_wt (TAM)

description:
pan2_wttam
Pan_2_TGACCA
Pan_TAM_RNASeq.gct


title: pan3_ko (TAM)

description:
pan3_kotam
Pan_3_ACAGTG
Pan_TAM_RNASeq.gct


title: pan6_ko (TAM)

description:
pan6_kotam
Pan_6_CTTGTA
Pan_TAM_RNASeq.gct


title: KO_M0 (5hmC)

data_processing:
Library strategy: DIP-seq
Raw reads were mapped to UCSC mouse mm9 assembly using bowtie2 with unique mapping option (-m 1). Peaks were called using the MACS14 algorithm.
Aligmed reads in .sam files were transferred to .bedGraph and then .bw format using UCSC file converters. Signals in .bw files were normalized by sequencing depth.
Genome_build: mm9
Supplementary_files_format_and_content: Processed files are in UCSC bigWig format (.bw)

source_name: KO_M0, BMDMs

growth_protocol: Total bone marrow cells were harvested from the long bones. ACK lysis buffer (Thermo Fisher, 5 ml) was then added to lyse the red blood cells for 2 minutes. To stop the lysis reaction, 20ml RPMI medium was added. The cells were washed and resuspended in BMDM medium (30% L929-conditioned medium, 20% FBS, 10 ng/ml recombinant murine M-CSF (Biolegend, cat#576402) in RPMI 1640 medium, with 1% penicillin/streptomycin/glutamine). The cells were then plated at 2.5×10e6 cells per well in a sterile six-well tissue culture plate, and cultured for 7 days. To activate BMDM cells, BMDM medium was changed into DMEM medium (DMEM, 10% FBS, 1% penicillin/streptomycin/glutamine) the night before the stimulation.

extract_protocol:
Genomic DNA was extracted by digesting cells with proteinase K, removal of protein by phenol/chloroform and ethanol precipitation.
Genomic DNA was sonicated to ~200bp fragments. Ten micrograms of sonicated genomic DNA were then used to ligate with the adaptor, provided in the NEBNext DNA Library Prep Master Mix Set for Illumina kit (E6040), following the manufacturer’s instructions. Sonicated and adaptor-ligated genomic DNA were incubated with 5 μl of 5hmC antibody (Active Motif, 39791) at 4°C overnight in a final volume of 500 μl in DIP buffer (10 mM sodium phosphate, pH 7.0, 140 mM NaCl, 0.05% Triton X-100). The immunoprecipitated DNA fragments were enriched with Dynabeads Protein G (Life Technologies) and amplified with the primers provided in the NEBNext Multiplex Oligos for Illumina preparation kit (E7335). The prepared libraries were sequenced on an Illumina HiSeq2000 machine at Yale Stem Cell Center.

treatment_protocol: 20 ng/ml IL4 was added

value: bone marrow derived macrophages (BMDMs)

value: none (untreated)

tag: dip antibody

value: anti-5hmC (Active Motif, 39791)


title: Blood_Platelets_Vumc-HD-125-TR1117


title: pan8_wt (TAM)

description:
pan8_wttam
Pan_8_AGTTCC
Pan_TAM_RNASeq.gct


title: Blood_Platelets_Vumc-HD-124-TR1116


title: Blood_Platelets_Vumc-HD-123-TR1115


title: pan5_ko (TAM)

description:
pan5_kotam
Pan_5_CAGATC
Pan_TAM_RNASeq.gct


title: Blood_Platelets_Vumc-HD-133-TR1123


title: Blood_Platelets_Vumc-HD-122-TR1114


title: Blood_Platelets_Vumc-HD-128-TR1119


title: KO_M2 (5hmC)

source_name: KO_M2, BMDMs

value: 20 ng/ml IL4 for 24 hrs


title: Blood_Platelets_Vumc-HD-121-TR1113


title: WT_M2 (5hmC)

source_name: WT_M2, BMDMs


title: WT_M0 (5hmC)

source_name: WT_M0, BMDMs


title: Blood_Platelets_Vumc-HD-119-TR1111


title: Blood_Platelets_Vumc-HD-118-TR1110


title: KO_H4K16_Ab_Rep1_ChIP_seq

city: Baton Rouge

first: Joomyeong

last: Kim

state: LA

address: 202 Life Sciences Bldg

department: Biological Sciences

institute: Louisiana State University

data_processing:
Basecalls performed using CASAVA version 1.4
The raw sequence reads derived from the libraries were mapped to the mouse reference genome sequence (mm10) using Bowtie2.2.
The sam files from the mapping were converted first into bed files and later into bigwig files using Samtools.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files

source_name: Mouse Embryonic Fbroblast

growth_protocol: Two litters of 14.5-dpc embryos were harvested through timed mating of the male mutant mice heterozygous for the KO allele with the female wild-type littermates.   The head portion and the red tissues were removed from the embryos, and the remaining portions were minced with razor blades.  These minced tissues were transferred to a 15 mL conical tubes containing 1 mL trypsin (Invitrogen, Cat. No. 25300062).  After 5 min incubation at 37°C, the cells were harvested with centrifugation, and later resuspended in 15 mL media (Life technologies, Cat. No.10566024).  Finally, the resuspended cells were plated onto a T-75 flask.  MEF from each embryo was first genotyped using the following primer set: Peg3-for (5’-ATGAGTCTCGATCCCAGGTATGCC-3’) and LoxR (5’-TGAACTGATGGCGAGCTCAGACC-3’).  The sex of each MEF was also determined using the following primer set: mSry-F (5’-GTCCCGTGGTGAGAGGCACAAG-3’) and mSry-R (5’-GCAGCTCTACTCCAGTCTTGCC-3’).

extract_protocol:
MEFs were first cross-linked with 1% formaldehyde for 20 mins, and then lysed with the buffer containing protease inhibitor cocktail (Millipore, Cat. No. 539131).  The released nuclei were fractionated with sonication to a pool of DNA fragments size-ranging from 300 to 1,000 bp in length.  The prepared chromatin was immunoprecipitated with the H4K16ac antibody.
The two pools of the immunoprecipitated DNA along with the two corresponding input DNA were used for constructing libraries for ChIP-seq experiments according to the manufacturers’ protocol (Illumina FC4014003).

value: Mouse Embryonic Fbroblast (MEF)

tag: passages

value: 3 to 5

value: H4K16ac (Millipore Cat No 07329)


title: Blood_Platelets_Vumc-HD-116-TR1108

value: Healthy Control


title: Treated-LPA-Set2-SSR

city: Kolkata

first: Sib

middle: Sankar

last: Roy

state: West Bengal

address: 4, Raja S. C. Mullick Road

department: Cell Biology and Physiology

country: India

institute: CSIR-Indian Institute of Chemical Biology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were checked for high quality reads and no adaptor contaminated sequence then mapped to GRC38 [Ensemble] whole genome using Tophat2 v2.1.0 with parameters -r 250 --mate-std-dev 50 --bowtie1
To assemble the mapped reads from RNA-seq against ENSEMBL gene structure annotation, Cufflinks (v2.2.1) was used and expression level for each transcript was estimated.
Cufflinks based probabilistic model of paired-end sequencing was used to evaluate abundances [FPKM]of isoforms, and detect ambiguous isoforms.
Genome_build: Human GRCh38
Supplementary_files_format_and_content: text file with FPKM values.

source_name: Human ovarian cancer PA-1 cell line

extract_protocol:
Total RNA was isolated from untreated and LPA treated PA-1 cells using TRI reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: Human ovarian cancer

tag: gender

value: female

value: LPA-Treated


title: Blood_Platelets_Vumc-HD-117-TR1109


title: KO_H4K16_Ab_Rep2_ChIP_seq

tag: chip antibody


title: KO_Input_ChIP_seq

tag: strain


title: Blood_Platelets_Vumc-HD-115-TR1107


title: Blood_Platelets_Vumc-HD-114-TR1106


title: WT_Input_ChIP_seq


title: wt_il424h_2 (BMDM)

data_processing:
Map to genome with GenePattern's Tophat module
FPKM levels quantified with GenePattern's CuffDiff module by using GenePattern's standard UCSC genome browser's mm9 transcriptome definition
Genome_build: mm9
Supplementary_files_format_and_content: gct file format (tab delimited text file); contains gene level FPKM values

source_name: wildtype_BMDMs_IL4_24 hrs

growth_protocol: Total bone marrow cells were harvested from the long bones. ACK lysis buffer (Thermo Fisher, 5 ml) was then added to lyse the red blood cells for 2 minutes. To stop the lysis reaction, 20ml RPMI was added. The cells were washed and resuspended in BMDM medium (30% L929-conditioned medium, 20% FBS, 10 ng/ml recombinant murine M-CSF (Biolegend, cat#576402) in 1640 medium, with 1% penicillin/streptomycin/glutamine). The cells were then plated at 2.5×106 cells per well in a sterile six-well tissue culture plate, and cultured for 7 days. To activate BMDM cells, BMDM medium was changed into DMEM medium (DMEM, 10% FBS, 1% penicillin/streptomycin/glutamine) the night before the stimulation.

extract_protocol:
Total RNA was extracted by TriZol
Standard Illumina protocol with ribozero-based ribosomal RNA depletion

tag: genotype/variation


title: ko_il424h_2 (BMDM)

source_name: Tet2 knockout_BMDMs_IL4_24 hrs

tag: treatment


title: ko_il424h_1 (BMDM)


title: Blood_Platelets_Vumc-HD-112-TR1104


title: WT_H4K16_Ab_Rep2_ChIP_seq


title: wt_il424h_1 (BMDM)


title: Blood_Platelets_Vumc-HD-120-TR1112


title: Blood_Platelets_Vumc-HD-11-1-TR1153


title: Pum2 global knockout Pum2 iClip rep2

first: Haifan

last: Lin

state: Connecticut

department: Cell Biology

institute: Yale Univeristy

data_processing:
Data were separated according to RT primer with random barcode/index. Procedure of peak calling is mentioned in the citation.
Genome_build: mm10
Supplementary_files_format_and_content: format: bed format
Supplementary_files_format_and_content: Content: binding sites of Pum

source_name: brain

extract_protocol:
0.5g neonatal mouse brain tissues were homogenized in PBS and crosslinked 400mj/cm2 at 254nm twice. 10 -7 dilution of RNase1 was used to trim RNA prior to IP with anti-Pum1/2 antibody. The other steps were performed as described in (Konig et al. 2011, Journal of visualized experiments: JoVE). The PCR cycle numbers were optimized for each sample to generate comparable amount of DNA. Please refer to Supplemental Figure S6 for the PCR cycle numbers for each individual sample.
RT primers are WT_P1_clip /5Phos/NNGCCANNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC; P1KO_P1_clip /5Phos/NNCGCCNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC; WT_P2_clip /5Phos/NNAACCNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC; P2KO_P2_clip /5Phos/NNATTGNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC

value: Pum2 global knockout Pum2


title: WT Pum1 iClip rep2

value: WT Pum1


title: Blood_Platelets_Vumc-HD-113-TR1105


title: ko_il410h_2 (BMDM)

source_name: Tet2 knockout_BMDMs_IL4_10 hrs

value: 20 ng/ml IL4 for 10 hrs


title: WT Pum2 iClip rep2

value: WT Pum2


title: WT_H4K16_Ab_Rep1_ChI_seq


title: Blood_Platelets_Vumc-HD-110-TR1102


title: SEN hADSC

city: San Francisco

first: Victoria

last: Lunyak

state: CA

address: 665 Third Street Suite 280

institute: Aelan Cell Technologies

description:
processed data file: SR_SEN_RNA-seq_gene_read_counts.xlsx
processed data file: SR_SEN_RNA-seq_normalized_gene_expression_RPKM.xlsx

data_processing:
Individual sequence reads were mapped to the human genome reference sequence (UCSC hg18; NCBI build 36.1) using the program BLAT.
BLAT was run with default settings with the exception that the minimal sequence identity was set to 99%
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al, Nature, 2008. The number of reads falling in the exons of each transcript were counted and normalized by the size of the total exome length and by the size of the library size.
Genome_build: hg18
Supplementary_files_format_and_content: Excel files include read counts and RPKM (normalized abundance) values for both samples

source_name: adipose derived mesenchymal stem cells

growth_protocol: Human adipose derived stem cells were isolated from human subcutaneous white adipose tissue collected during liposuction procedures. The lipoaspirate was suspended in Hank’s Buffered Salt Solution (HBSS, Life technology), 3.5% Bovine Serum Albumin (BSA, Sigma), 1% Collagenase Type II (Sigma) in 1:3 w/v ratio and shaken at 37°C for 50 min. The cells were filtered through a 70 μm mesh cell strainer (BD Falcon #352350), treated with Red Blood Cell Lysis buffer (150 mM NH4Cl, 10 mM KHCO3, 0.1 mM EDTA, pH 7.3), and expanded ex vivo in DMEM/F12 complete medium (DMEM/F12, 10% FBS, 100 U/ml penicillin, 100 μg/ml streptomycin; Life technology) in 10% CO2 at 37°C and passaged at 80% confluency, changing medium every 72–96 h. Cumulative population doublings were calculated by summing the population doublings (PD = log(N/N0) x 3.33, where N0 is the number of cells plated in the flask and N is the number of cells harvested at this passage) across multiple passages as a function of the number of days it was grown in culture. Five x 105 cells each were incubated for 30 min on ice in the dark with fluorochrome-conjugated antibodies (CD31, CD44, CD45 and CD105; Invitrogen) in PBS with 1% BSA (Sigma), washed and analyzed in a Guava  EasyCyte Mini System (Guava Technologies, Millipore). Data analysis was done with FlowJo software (Tree Star, Ashland, OR).  A senescence-associated β-galactosidase activity assay was done according to manufacturer’s instructions (BioVision). The cells were washed with PBS and fixed with fixation solution for 15 min at room temperature. The cells were washed with PBS twice and X-gal staining solution was added with a staining supplement per well and incubated overnight at 37°C. The cells were washed twice with PBS, and the images were captured using a microscope (Nikons, TE300, DXM1200 Digital Camera, Japan).

extract_protocol:
Cells were isolated from human subcutaneous white adipose tissue collected during liposuction procedures. Total RNA was extracted to construct RNA-seq library.
Total RNA was isolated from 3 different genetic lines of adipose derived stem cells in SR and SEN conditions. Samples were grouped together for SR and SEN. Total RNA preparation has been processed with RiboMinus kit to significantly reduce ribosomal RNA in the sample. All samples have been precipitated with Pellet-Paint and dissolved in depc-treated millipure water. SuperScript™ ds cDNA synthesis was performed with random-primers. GS FLX Titanium General Library Preparation Method was employed to incorporate Multiplex Identifier (MID)-containing adaptors for General (e.g.Shotgun) library preparation. Unidirectional Sequencing of Amplicon Libraries Using GS FLX Titanium emPCR Kits (Lib-L) according to Roche Protocol APP No.001-2009 GS FLX Titanium MID-1 ExST Primer1 5’-CCATCTCATCCCTGCGTGTCTCCGACTCAGACGAGTGCGTGAGCGGCCGCGAAGATCAGA-3’ GS FLX Titanium MID-3 ExST Primer1 5’-CCATCTCATCCCTGCGTGTCTCCGACTCAGAGACGCACTCGAGCGGCCGCGAAGATCAGA-3'

value: adipose derived mesenchymal stem cells (hADSCs)

tag: cell subtype

value: Senescent


title: Pum1 global knockout Pum1 iClip rep2

value: Pum1 global knockout Pum1


title: Control-Set2-SSR

value: Control


title: SR hADSC

value: Self-Replicating


title: WT Pum2 iClip rep1


title: wt_il410h_1 (BMDM)

source_name: wildtype_BMDMs_IL4_10 hrs

value: wildtype

value: bone marrow derived macrophages (BMDMs)


title: Blood_Platelets_Vumc-HD-107-TR1100


title: WT Pum1 iClip rep1


title: wt_il410h_2 (BMDM)


title: ko0h_2 (BMDM)

source_name: Tet2 knockout_BMDMs_untreated

value: Tet2 knockout

value: none (untreated)


title: Pum2 global knockout Pum2 iClip rep1


title: wt0h_1 (BMDM)


title: Blood_Platelets_Vumc-HD-105-TR1098

value: Healthy Control


title: Pum1 global knockout Pum1 iClip rep1


title: wild type Rep4

data_processing:
RNA-seq data are procssed via software tools including Tophat2 and Cufflinks. Differentially  expressed genes are identified by Cuffdiff program.
Genome_build: mm10
Supplementary_files_format_and_content: format: Cuffdiff output format of gene_expression.diff
Supplementary_files_format_and_content: content: differentially expressed genes among different comparisons

extract_protocol: Total RNA was extracted using RNeasy Plus Kit (QIAGEN Cat#74134) from half of a neonatal mouse brain. The libraries were constructed using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina, Cat #: RS-122-2101) and the sequencing was performed on an Illumina HiSeq 2000 platform.

value: WT


title: Blood_Platelets_Vumc-HD-111-TR1103


title: wt0h_2 (BMDM)


title: Blood_Platelets_Vumc-HD-104-TR1097


title: ko_il410h_1 (BMDM)


title: ko0h_1 (BMDM)


title: wild type Rep3


title: wild type Rep1


title: WT_normal_MCSF_no_LPS_rep4

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

data_processing:
Second mate was used for sample demultiplexing.
Individual single-end fastqs were aligned to mm10 genome using STAR with following options --outFilterMultimapNmax 15 --outFilterMismatchNmax 6 --outReadsUnmapped Fastx --outSAMstrandField All.
Gene expression was obtained via ht-seq and DESeq2 for differential expression.
Gene expression was obtained using in-house scripts bassed on MACS and HTSeq (https://github.com/ctlab/quant3p).
Genome_build: mm10
Supplementary_files_format_and_content: text file with read counts for genes

source_name: Bone marrow-derived macrophages

growth_protocol: Trem2–/– mice were originally generated by Turnbull et al. (J. Immunol. 177, 3520-3524 (2006).)

extract_protocol:
mRNA was extracted from cell lysates using oligo-dT beads (Invitrogen).
For cDNA synthesis, we used custom oligo-dT primer with a barcode and adaptor-linker sequence (CCTACACGACGCTCTTCCGATCT-XXXXXXXX-T15). After first-strand synthesis, samples were pooled together based on Actb qPCR values and RNA-DNA hybrids were degraded with consecutive acid-alkali treatment. Subsequently, a second sequencing linker (AGATCGGAAGAGCACACGTCTG) was ligated with T4 ligase (NEB) followed by SPRI-beads (Agencourt AMPure XP, BeckmanCoulter) clean-up. The mixture was enriched by PCR for 12 cycles and SPRI-beads (Agencourt AMPure XP, BeckmanCoulter) purified to yield final strand-specific RNA-seq libraries.

treatment_protocol: Bone marrow-derived macrophages (BMDMs) from WT and Trem2–/– mice were cultured in either 0.5% or 10% LCCM overnight in complete RPMI. Some samples cells were stimulated with 10 ng/ml LPS for 4 hours.

value: bone marrow

value: macrophages

tag: mcsf

value: normal

value: Ctrl


title: wild type Rep2


title: Blood_Platelets_AMC-HD-010-TR1147

source_name: Thrombocytes


title: Pum2 global knockout Rep4


title: WT_normal_MCSF_no_LPS_rep2


title: Blood_Platelets_Vumc-HD-109-TR1101


title: WT_normal_MCSF_no_LPS_rep1


title: Pum2 global knockout Rep3


title: Blood_Platelets_AMC-HD-008-TR1146


title: Blood_Platelets_AMC-HD-007-TR1145


title: WT_normal_MCSF_LPS_rep4

value: LPS


title: Blood_Platelets_AMC-HD-006-TR1144