title: mock_input_12

description: True_seq (Ilumina)

data_processing:
Trimming reads for adapters and light quality trimming was performed with cutadapt v1.10 using the parameters "--quality-cutoff 20 -a AGATCGGAAGAGC --minimum-length=25 --overlap=10". Two protocols were used for ChIP-seq library prep. For the libraries using the DNA SMART ChIP-seq kit (Clontech), the additional parameter "-u 3" was used to hard-clip the first three bases, which are added by the kit
Reads were aligned to dm6 using bowtie2 v2.2.8 with default parameters.
Multimapping reads were removed using the "view" program of samtools v1.3.1 with parameter "-q 20"
The Picard tools v2.5.0 program MarkDuplicates was used to remove PCR duplicates from mapped reads.
Peak calling methods depended on whether the binding of the protein is punctate (AGO2) or broad (all others, including histone modifications and all Pol II forms). In both cases we first used the MACS2 v2.1.1.20160309 callpeak program (Zhang et al. 2008 and https://github.com/taoliu/MACS) to call peaks on each replicate independently. For both punctate and broad marks we used the non-default parameters "--gsize dm --bdg --SPMR". Only for broad peaks we included the parameter "--broad". We then ran the same peak-calling steps but on the pooled set of replicates for each target protein, by providing all input and IP replicates to MACS2.
We selected final peaks for broad marks as those peaks in the pooled peak-calling run that were also found in at least one of the individual replicates. Specifically, using BEDTools v2.25.0 and pybedtools v0.7.9 we used "pooled.intersect([replicates], u=True).sort().merge()" where "pooled" points to the pooled peak calls and "[replicates]" is the list of individual peak calls for each replicate.
For the punctate AGO2 peaks, we used the Irreproducible Discovery Rate (IDR) method using IDR v2.0.3 (https://github.com/nboley/idr, and following recommendations from https://sites.google.com/site/anshulkundaje/projects/idr). Initial lenient peaks were called with MACS2 with the lenient parameters "-p 1e-3 --nomodel --to-large" on four versions of the IP data: replicates, pooled pseudoreplicates, self-pseudoreplicates and pooled replicates as recommended by IDR authors. Pooled input was always used as the control for these peak-calling runs. On each pair of replicate, self-pseudoreplicate, and pooled-pseudoreplicate called peaks, we ran IDR with parameters "--use-best-multisummit-IDR --soft-idr-threshold 0.05 --rank p.value --input-file-type narrowPeak --peak-list $POOLED" where "$POOLED" is the peaks called on all replicates pooled together. From the pooled peaks ranked by increasing p-value, we chose the final AGO2 peaks as the top N peaks were N was the number of peaks in the pooled-pseudoreplicate comparison passing an IDR threshold of 0.05, as recommended by the IDR authors.
Genome_build: dm6 (FlyBase r6.11)
Supplementary_files_format_and_content: BED files of called peaks

extract_protocol:
Approximately 1-2 X 107 cells were fixed by addition of 1% formaldehyde to cell media for 10 min at RT with gentle agitation. Formaldehyde was quenched by addition of glycine to 0.125 M with gentle agitation for 5 min at RT. Cells were pelleted at 2000xg, washed twice in PBS, and resuspended in 0.8 mL ice–cold cell lysis buffer (5 mM PIPES pH 8, 85 mM KCl, 0.5% NP-40) supplemented with Complete protease inhibitors (Roche), incubated on ice 10 min pelleted by centrifugation at 2000 xg for 5 min at 4°C. Next, the supernatant was removed and pellets were resuspended in 1 mL nuclear lysis buffer (50 mM Tris-HCl pH 8, 10 mM EDTA.Na2, 1% SDS) and incubated for 10 min at 4°C. Afterwards, 0.5 mL of IP dilution buffer was added (16.7 mM Tris-HCl pH 8, 1.2 mM EDTA, 167 mM NaCl, 1.1% Triton X-100, 0.01% SDS) and chromatin was fragmented to an average size of 300 bp by using PicoBioruptor (Diagenode) using 10 cycles of 30 s on plus 30 sec off, maximum output. Samples were centrifuged at max speed for 10 min at 4°C, and the supernatant (sheared chromatin) was saved at -80°C. Chromatin was diluted to 1:5 with IP buffer, and the assayed antibody in addition to 50 μL of prewashed protein A/G 50% slurry was added and rotated overnight at 4°C. The next day, beads were washed as follows:
--    3X Low salt IP dilution buffer (20 mM Tris-HCl pH 8, 2 mM EDTA.Na2, 150 mM NaCl, 1% Triton X-100, 0.1% SDS).
--     3X High salt IP dilution buffer (20 mM Tris-HCl pH 8, 2 mM EDTA.Na2, 500 mM NaCl, 1% Triton X-100, 0.1% SDS).
--     2X times  LiCl buffer (10 mM Tris-HCl pH 8, 1 mM EDTA.Na2, 0.25M LiCl, 1% NP-40, 1% DOC).
Chromatin was eluted twice with 200 μL of elution buffer (500 μL of 1M NaHCO3, 250μL of 20% SDS, 4.25 mL dH2O) for 30 min at 65°C each and further incubated overnight at 65°C with 38 μL of decrosslinking solution (20 μL of 5M NaCl, 8 μL of 0.5M EDTA, 10 μL of 1M Tris-HCl pH 8). After de-crosslinking, samples were treated with Proteinase K for 2 h at 50°C and then combined with 1 vol of phenol/chloroform/isoamyl alcohol (25:24:1), vortexed 15 s, and centrifuged for 5 min at 10,000 xg . The top layer was transferred to a new tube, and the procedure was repeated using 1 vol chloroform. The top layer was collected and subsequently precipitated with 0.1 vol of 3M NaOAc pH 5.2 and 2.5 vol of 100% ethanol supplemented with 2 μL of Glycoblue (Ambion). After incubating 30 min at -80°C, samples were centrifuged 20 min at 4°C at 10,000 xg. Pellets were washed with 70% ethanol and centrifuged 5 min at 4°C at 10,000 xg. Pellets were air dried at RT prior to resuspension in 10 μL of dH2O.
Samples for ChIP-seq were prepared according to the manufacturer’s protocol with Clontech or TruSeq adapters (Illumina).

tag: Sex

value: female

tag: input sample

value: input


title: mock_ago2_mueller_2

status: Public on Feb 27 2018

type: SRA

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

country: USA

institute: National Institutes of Health

description:
True_seq (Ilumina)
BED File: idr-macs2-mock_ago2_mueller.bed

library_source: genomic

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Kc167 cell line

tag: cell line

tag: treatment

value: mock

tag: antibody

value: AGO2 (A. Mueller)


title: mock_ago2_mueller_1


title: dslaminb_input_9

description: True_seq (Ilumina)

value: dslaminb


title: dslaminb_ago2_mueller_1

description:
True_seq (Ilumina)
BED File: idr-macs2-dslaminb_ago2_mueller.bed


title: NIH3T3-H3.3GFP-Infect48h-Input

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi, Higashi-ku, Fukuoka

department: Medical Institute of Bioregulation, Medical Institute of Bioregulation

country: Japan

institute: Kyushu University

description: countMatrix_GENCODEvM9_3T3ChIPseq.edit.txt.gz

data_processing:
The raw sequence reads were aligned to mouse genome (GRCm38) using HISAT2 (version 2.0.4), and the uniquely mapped reads were retained for ChIP-seq/ATAC-seq analysis.
The matrices of read counts on gencode genes (release M9) were generated using featureCounts (version 1.5.0-p3). For ATAC-seq, the option of featureCounts: -B -C -P -d 20 -D 150, were used to extract subnucleosomal fraction.
The coverage tracks of ATAC-seq (bigWig) were generated using bamCoverage command of deepTools (version 2.4.2) with the option: --smoothLength 60 --binSize 1 --extendReads.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: *.txt files include tab-delimited read count matrices
Supplementary_files_format_and_content: bigWig

organism: Mus musculus

source_name: Histone H3.3 overexpressing NIH3T3 cells

extract_protocol:
Cultured cells were cross-linked in 0.5% formaldehyde and suspended in ChIP buffer (5 mM PIPES, 200 mM KCl, 1 mM CaCl2, 1.5 mM MgCl2, 5% sucrose, 0.5% NP-40, and protease inhibitor cocktail; Nacalai Tesque Inc.).
ChIP libraries  were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: NIH3T3 cells were infected with retrovirus expressing MyoD.


title: NIH3T3-H3mm7GFP-UnInfect-GFP

source_name: Histone H3mm7 overexpressing NIH3T3 cells


title: dslaminb_input_10

description: True_seq (Ilumina)


title: mock_input_3


title: mock_pol2_8wg16_2

description:
True_seq (Ilumina)
BED File: mock_pol2_8wg16.bed

value: RNA Pol II 8WG16 Biolegend 920102


title: NIH3T3-H3.3GFP-UnInfect-Input


title: mock_pol2_8wg16_1


title: NIH3T3-H3mm7GFP-Infect48h-Input


title: T lymphocytes nucleofected with DEM Rep 3 (RNA-Seq)

city: Freiburg

first: Claudio

last: Mussolino

address: Breisacherstr. 115

country: Germany

institute: Institute for Transfusion Medicine and Gene Therapy

description:
normalized_counts.tsv
S442Nr8

library_source: transcriptomic

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina CASAVA (2.17).
Adapters were trimmed with Skewer (version 0.1.116) (Jiang et al. 2014)
Trimmed raw reads were aligned to the human reference genome (hg19) using STAR (version 2.5.1) (Dobin et al. 2013).
Reads were normalized with with DESeq2 (Love et al. 2014) in R (R Core Team 2015).
Genome_build: hg19
Supplementary_files_format_and_content: The data are provided in .tsv. This file can be opened in excel and contains a column with the gene identifier followed by 6 columns representing the 6 samples (3 controls and 3 samples)

molecule: total RNA

organism: Homo sapiens

source_name: T lymphocytes nucleofected with DEM

growth_protocol: Human CD4+ T cells were obtained from the peripheral  blood mononuclear cells (PBMCs) of healthy donors by Ficoll density gradient centrifugation followed by  human CD4+ T Cell Isolation Kit (Miltenyi Biotec) separation according to the manufacturer’s instructions.  The cells were activated for 3 days using magnetic beads conjugated with antibodies against CD2, CD3  and CD28 (Miltenyi Biotec) at a 2:1 cell to bead ratio and kept at a density of 1,3 x 106 cells/cm2 and  2,5x106 cells/ml in X-VIVO 15 Chemically Defined Serum-free Hematopoietic Cell Medium (Lonza). To  maintain the cells in culture long-term the activation was repeated every seven days and beads were  removed after 3 days of activation. After beads removal, growth medium was supplemented with 20 U/ml  interleukin 2 (Miltenyi Biotec).

extract_protocol:
Cells were harvested on the indicated days and total RNA isolated using the  RNeasy Mini kit (Qiagen) according to the manufacturer’s instructions
Library Preparation Kit: TruSeq Stranded mRNA Kit (Illumina)

treatment_protocol: Delivery in primary human  lymphocytes was achieved via nucleofection, 3 days post activation using the 4D Nucleofector X device  and the P3 Primary Cell 4D Nucleofector X kit (Lonza) following the manufacturer’s instructions

tag: cell type

value: Primary T lymphocytes

tag: agent

value: DEM

tag: day of analysis

value: Day 7 post thawing


title: T lymphocytes nucleofected with DEM Rep 2 (RNA-Seq)

description:
normalized_counts.tsv
S442Nr6


title: mock_input_11

description: True_seq (Ilumina)


title: NIH3T3-H3mm7GFP-UnInfect-Input


title: dslaminb_ago2_mueller_2


title: T lymphocytes nucleofected with DEM Rep 1 (RNA-Seq)

description:
normalized_counts.tsv
S442Nr5


title: NIH3T3-Control-UnInfect-Input

source_name: NIH3T3 cell line


title: Control T lymphocytes Rep 2 (RNA-Seq)

description:
normalized_counts.tsv
S442Nr2

source_name: Control T lymphocytes

value: control


title: Control T lymphocytes Rep 1 (RNA-Seq)

description:
normalized_counts.tsv
S442Nr1


title: NIH3T3-H3mm7GFP-Infect48h-GFP


title: SVA-ZN19

city: São Paulo

first: Murilo

last: Sena Amaral

state: SP

address: Avenida Prof Lineu Prestes

country: Brazil

institute: Universidade de São Paulo

data_processing:
RNA-seq was performed with hiPSCs-derived NPCs from 3 pairs of discordant twins (in each pair, one of the babies was affected by Congenital Zika syndrome and the other was not affected)
Raw reads were preprocessed using the standard Illumina pipeline to segregate multiplexed reads. Sequence quality was checked using the FastQC program (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).The data were preprocessed with the read trimming and cropping tool Trimmomatic v.0.30  and the command line: parameters: −phred33 ILLUMINACLIP: True_seq_PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Sequences were  aligned to the human reference genome GRCh38/hg38 using STAR (v. 2.5.0a) by using the command: STAR -- runThreadN 14 – genomeDir ENSEMBL.homo_sapiens.release-83/ --Homo_sapiens.GRCh38.89.chr_patch_hapl_scaff.gtf – readFilesIn fastafile_R1_001_fastq_gz_forward_paired.fq SVA- fastafile_R2_001_fastq_gz_reverse_paired.fq -- chimSegmentMin 20 – outSAMtype BAM SortedByCoordinate -- outWigType bedGraph -- outWigStrand Stranded
Uniquely mapped reads were counted using the Ensemble GRCh38.83 transcriptome reference through the R software package GenomicRanges, and the statistical tests for differential expression between samples were done using EdgeR (v. 3.16.5). Networks of related enriched GO terms were created and analyzed with Metascape.
Genome_build: hg38
Supplementary_files_format_and_content: Uniquely mapped reads counted using the Ensemble GRCh38.83 transcriptome reference through the R software package GenomicRanges

molecule: polyA RNA

growth_protocol: Human induced pluripotent stem-cells (hiPSCs) were generated from CD71+-cells which were isolated from three pairs of dizygotic discordant twins' peripheral blood samples. The reprogramming protocol was performed with episomal vectors systems. Three days after nucleoporation of plasmids, cells were seeded on irradiated murine embryonic fibroblasts in embryonic stem cell medium. The typical hiPSC colonies were transferred to matrigel and cultured in Essential 8 medium with 100μg/mL normocin. hiPSCs were maintained for three days with E8 media. On the fourth day, the medium was changed to 0.5x NB media (DMEM/F12 medium supplemented with 0.5x N2 and 0.5x B27 added with 1 μM dorsomorphin for 48 hours. Further, the colonies were detached from the plate and cultured in suspension as embryoid bodies (EBs) for 5 days in ultra- low attachment plates. The EBs were plated on matrigel-coated plates with NBF media (DMEM/F12 media supplemented with 0.5x N2, 0.5x B27 supplement, 20 ng/ml of FGF2, 20 ng/ml of EGF and 1% penicillin/streptomycin). The emerged rosettes were manually picked, dissociated and plated in a double-coated plate with poly-ornithine (10 μg ml−1) and laminin(2.5 μg ml−1) The NPC population was expanded using NBF media.

extract_protocol:
Total RNA from NPCs was extracted using the RNeasy Micro Kit (Qiagen), treated with TURBO DNase (Ambion) for 1 h at 37 °C and then re-purified with the Qiagen RNeasy Micro Kit. RNA samples were quantified using the Qubit RNA HS Assay Kit (Thermo Fischer Scientific) their purity was evaluated on a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies) and the integrity was verified using the Agilent RNA 6000 Pico Kit (Agilent Technologies) in a 2100 Bioanalyzer Instrument (Agilent Technologies).
RNA samples from NPCs were used to prepare tagged sequencing libraries with the KAPA Stranded mRNA-Seq Kit (Illumina), according to the manufacturer’s instructions; then sequenced on the Illumina HiSeq4000 using 150 bp paired-end reads sequencing.

treatment_protocol: hiPSCs-derived NPCs were cultivated for 4 days, collected and flash frozen on dry ice before RNA extraction. No NPC treatment or infection was performed.

value: hiPSC-derived neural progenitor cells

tag: diagnosis

value: Congenital Zika syndrome


title: SVA-ZN17


title: NIH3T3-H3mm7GFP-Infect48h

description:
processed data file:
countMatrix_GENCODEvM9_3T3RNAseq.edit.txt.gz
countMatrix_GENCODEvM9_3T3RNAseq_inclMut.txt.gz

extract_protocol:
Total RNA was isolated and reversed-transcribed with PrimeScript Reverse Transcriptase (Takara Bio Inc.) and an oligo dT primer.
Library preparation and sequence analysis were performed according to the manufacturer's protocol (NEBNext Ultra Directional RNA Library Prep Kit for Illumina).


title: NIH3T3-H3.3GFP-UnInfect


title: SVA-ZN7


title: NIH3T3-H3mm7GFP-Infect24h


title: NIH3T3-Control-Infect48h


title: mock_input_4


title: SVA-ZN5


title: SVA-ZN3


title: NIH3T3-Control-Infect24h


title: C2C12-H3mm7KO-D72h-rep2

description: countMatrix_GENCODEvM9_C2C12RNAseq.edit.txt.gz

source_name: C2C12 cell line

growth_protocol: C2C12 cells were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 20% fetal bovine serum. Undifferentiated cells were harvested at 60%–70% confluence. Differentiated cells were transferred to DMEM containing 2% horse serum upon reaching confluence.


title: SVA-ZN1


title: NIH3T3-Control-Infect0h


title: NIH3T3-Control-UnInfect


title: NIH3T3-Control-Infect48h-Input


title: siGPBP1-BMN673-rep2

city: San Francisco

first: Sourav

last: Bandyopadhyay

state: California

address: 1450 3rd Street

department: Helen Diller Family Comprehensive Cancer Center

institute: University of California, San Francisco

data_processing:
Quality control checks on raw sequencing data was performed using FASTQC
Adapters in sequenced reads were removed using cutadapt and transcript abundance was calculated using Kallisto
Transcript abundance to gene level abundance was estimated using Tximport
Genome_build: GRC38 reference human transcriptome
Supplementary_files_format_and_content: Tab limited file with normalized TPM

growth_protocol: The human mammary epithelial cell line MCF10A was obtained from ATCC and maintained in DMEM/F12 medium supplemented with 5% horse serum, epidermal growth factor (20ng/ml), insulin (10µg/ml), hydrocortisone (0.5mg/ml), cholera toxin (100ng/ml), and penicillin/streptomycin. Cells were cultured in a humidified incubator with 5% CO2 at 37¡C.

extract_protocol:
RNA extraction from MCF10A cells was performed with RNeasy mini kit (Qiagen). The samples were treated sequentially with Baseline-ZERO DNase and Ribo-ZERO RNA removal kit (Epicentre) to deplete DNA and rRNA.
35ng of rRNA-depleted sample was used as input for library preparation using ScriptSeq v2 library preparation kit (Epicentre) according to the manufacturer's instructions. All libraries were indexed with Illumina barcodes for multiplexing.

treatment_protocol: MCF10A cells were transfected with siGPBP1 or siNT4 (non targeting control) using Lipofectamine RNAiMax transfection reagent (ThermoFisher) according to the manufacturer’s instruction. At 48hr post transfection, the cells were treated with BMN673 at 0.5uM or DMSO for 24 hrs before the total RNA is extracted.

value: siGPBP1 BMN673


title: siNT4-BMN673-rep2

value: siNT4 BMN673


title: siGPBP1-DMSO-rep2

value: siGPBP1 DMSO


title: C2C12-H3mm7KO-D48h-rep2


title: siGPBP1-BMN673-rep1


title: NIH3T3-H3.3GFP-Infect0h


title: Control T lymphocytes Rep 3 (RNA-Seq)

description:
normalized_counts.tsv
S442Nr4


title: siNT4-BMN673-rep1


title: C2C12-H3mm7KO-Growth-rep2


title: C2C12-H3mm7KO-D24h-rep2


title: C2C12-H3mm7KO-D72h-rep1


title: siNT4-DMSO-rep2

value: siNT4 DMSO


title: NIH3T3-H3mm7GFP-UnInfect


title: NIH3T3-H3mm7GFP-Infect0h


title: siNT4-DMSO-rep1


title: C2C12-H3mm7KO-D24h-rep1


title: C2C12-H3mm7KO-Growth-rep1


title: C2C12-H3mm7KO-D48h-rep1


title: C2C12-WT-D72h-rep2


title: C2C12-WT-D48h-rep2

growth_protocol: C2C12 cells were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 20% fetal bovine serum. Undifferentiated cells were harvested at 60%–70% confluence. Differentiated cells were transferred to DMEM containing 2% horse serum upon reachinn reachin

extract_protocol: Library preparation and sequence analysis were performed according to the manufacturer's protocol (NEBNext Ultra Directional RNA Library Prep Kit for Illumina).


title: C2C12-WT-D48h-rep1


title: C2C12-WT-Growth-rep2

growth_protocol: C2C12 cells were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 20% fetal bovine serum. Undifferentiated cells were harvested at 60%–70% confluence. Differentiated cells were transferred to DMEM containing 2% horse serum upon reachinonfluence.


title: C2C12-WT-D24h-rep2


title: siGPBP1-DMSO-rep1


title: C2C12-WT-D24h-rep1


title: C2C12-WT-D72h-rep1


title: WF6xKM6_EGK.X

city: Seoul

first: JAE

middle: YONG

last: HAN

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

country: South Korea

institute: Seoul National University

data_processing:
Trimmomatic was used for removing adapter sequences.
Such clean reads were mapped into reference genome derived from Ensembl database using HISAT2 aligner.
Finally, HTSeq-count was employed for quantification.
Genome_build: galGal4

organism: Gallus gallus

source_name: Embryonic cell

extract_protocol:
Removal of cytoplasmic and mitochondrial rRNA using Ribo-Zero
Libraries were prepared based on Illimina instruction

tag: developmental stage

tag: tissue

value: Embryonic cell


title: WF7xKM7_EGK.X


title: WF13xKM4_Zygote

value: Zygote


title: WF6xKM6_Zygote


title: WF13_Oocyte

value: Oocyte


title: WF7xKM7_Zygote


title: WF13xKM4_EGK.X


title: heart_1842_m_29wph

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

data_processing:
Sequence information were extracted in FastQ format using bcl2fastq v1.8.4
Reads were filtered for low quality and trimmed for 3' adaptor sequence.
Read length was filtered to be 18 to 33 nt
Reads were aligned to D. rerio mirBase v21.0 using Bowtie
Genome_build: D. rerio mirBase v21.0
Supplementary_files_format_and_content: Excel file includes read counts per sample

organism: Nothobranchius furzeri

source_name: heart

growth_protocol: N. furzeri was raised and maintained under standard laboratory conditions in fish Housing Systems (Aqua Schwarz, Goettingen, Germany).

extract_protocol:
Hearts were dissected and transferred into 2 ml tubes with 1 ml cooled QIAzol (Qiagen, Hilden, Germany) and one 5 mm stainless steel bead (Qiagen) was added. Homogenization was performed using a TissueLyzer II (Qiagen) at 20 Hz for 3x 1 min. After incubation for 5 min at room temperature 200 µl chloroform was added. The tube was shaken for 15 s and incubated for 3 min at room temperature. Phase separation was achieved by centrifugation at 12,000x g for 20 min at 4°C. The aqueous phase was transferred into a fresh cup and 10 µg of Glycogen (Invitrogen, Darmstadt, Germany), 0.16x volume NaAc (2 M; pH 4.0) and 1.1x volume isopropanol were added, mixed and incubated for 10 min at room temperature. The RNA was precipitated by a centrifugation step with 12,000x g at 4°C for 20 min. The supernatant was removed and the pellet was washed with 80% Ethanol twice and air dried for 10 min. The RNA was resuspended in 20 µl DEPC-treated water by pipetting up and down, followed by incubation at 65°C for 5 min. The RNA was quantified with a NanoDrop 1000 (PeqLab, Erlangen, Germany)
For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol (llumina Inc., San Diego, USA). cDNA was amplified with 11 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis (Invitrogen) and eluted into 300 µl elution buffer (Illumina) for at least 2 hours at room temperature, to enrich for molecules containing inserts in the range of 18–33 nt.

treatment_protocol: fish were sacrificed with MS222

tag: strain

tag: age group

value: old

value: heart


title: heart_1730_m_27wph


title: heart_1843_m_29wph


title: WF6_Oocyte


title: heart_1753_m_12wph

value: adult


title: heart_1728_m_27wph


title: heart_1752_m_12wph


title: heart_1751_m_12wph


title: heart_1721_m_5wph

value: young


title: heart_1719_m_5wph


title: heart_1749_m_12wph


title: heart_1718_m_5wph


title: C2C12-WT-Growth-rep1


title: 11-cnpB-3

city: Albany

first: Guangchun

last: Bai

state: NY

address: New Scotland Ave

department: DIMD

institute: Albany Medical College

data_processing:
trimmed using IDLE
uploaded in RNA-Rocket
Align and assemble transcript to Mycobacterium tuberculosis H37Rv  (Cole, et al. Nature 1998)
Differential expression analysis
Genome_build: complete genome sequence of Mycobacterium tuberculosis H37Rv (Cole, et al. Nature 1998)(Accession: AL123456.3; GI: 444893469)

organism: Mycobacterium tuberculosis

source_name: cnpB_M. tuberculosis

growth_protocol: Bacteria were grown in Middlebrook 7H9 broth supplement with 0.5% glycerol, 10% OADC and 0.05%Tween 80 in tissue cultural flasks (5 ml/flask) and were incubated at 37ºC for 7 d.

extract_protocol:
Bacteria were harvested by centrifugation and were disrupted using a beadbeater (BIoSpec). RNA was prepared using a trizol-based protocol and treated with DNase using Rnase-free Dnase Set (Qiagen).
Libraries were constructed using ScriptSeq complete kit (Bacteria)(Epicentre) following the manufacturer's mannual.

tag: genotype/variation

value: cnpB deletion


title: 7-cnpB-2


title: 5-wt-2

source_name: WT_M. tuberculosis

value: wild type


title: 3-cnpB-1


title: 9-wt-3


title: WF7_Oocyte


title: Myofibers-rep3

source_name: extensor digitorum longus muscle

extract_protocol:
Regenerating muscles were isolated 1 day after CTX injection. Mononuclear cells from uninjured or injured gastrocnemius muscles (quiescent satellite cells and activated satellite cells) were prepared using 0.2% collagenase type II (Worthington Biochemical, NJ, USA). The YFP-positive satellite cell population was sorted using a FACS Aria II flow cytometer (BD Immunocytometry Systems, CA, USA). Debris and dead cells were excluded by forward scatter, side scatter and PI gating. Data were collected using FACS Diva software (BD Biosciences, CA, USA). Individual MFs were isolated from the EDL muscle.
Libraries were prepared according to the protocol described in Hashimshony, T. et al. (Genome Biol. 2016).

treatment_protocol: Pax7-CreERT2; Rosa26-YFP mice were treated with tamoxifen to induce YFP in a Pax7-expressing satellite cell population. Tamoxifen dissolved in corn oil (5 µl/g of 20 mg/ml) was injected intraperitoneally into mice daily for 3 days prior to the induction of muscle injury. Muscle injury was induced by the intramuscular injection of 100 µl CTX (10 µM; (Sigma-Aldrich, St. Louis, MO) into the gastrocnemius muscles of anaesthetized mice using a 29 gauge 1/2 insulin syringe.

value: Pax7-CreERT2; Rosa26-YFP mice

value: extensor digitorum longus muscle


title: ActivatedSatelliteCells-rep2

source_name: gastrocnemius muscle

value: gastrocnemius muscle


title: Sibling 7

city: Madison

first: Oleg

last: Moskvin

state: WI

address: 1220 Capitol Court

institute: University of Wisconsin-Madison

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads filtered and trimmed to eliminate low-quality reads and adapter sequences
Gene expression estimates obtained using RSEM v 1.2.18, with Bowtie 1.1.1 for alignment. RSEM was run with option “--forward-prob 0” to take into account that the RNA-seq libraries were strand-specific
Genome_build: Zv9
Supplementary_files_format_and_content: tab-delimited files containing non-normalized "Expected Counts" and normalized "Transcripts Per Million" expression estimates calculated by RSEM.

organism: Danio rerio

source_name: sibling embryo

growth_protocol: embryos were produced from natural pair matings of double zic2 heterozygous carriers and allowed to develop in embryo medium at 29C until ~25 hours post fertilization.

extract_protocol:
Illustra RNA spin mini RNA isolation kit (GE healthcare).
Samples were then prepared for sequencing using the Illumina TruSeq RNA Sample Preparation Kit v2 (RS-122-2001), according to the manufacturer's protocol

value: control

value: embryo


title: Myofibers-rep1


title: Sibling 8


title: ActivatedSatelliteCells-rep3


title: Sibling 4


title: Sibling 3


title: QuiescentSatelliteCells-rep3


title: Mutant 7

source_name: mutant embryo

value: rfx4 mutant


title: Myofibers-rep2


title: Sibling 2


title: Mutant 6


title: QuiescentSatelliteCells-rep2


title: heart_1720_m_5wph


title: ActivatedSatelliteCells-rep1


title: 564 SCI Tam

city: Solna

first: Joakim

last: Lundeberg

address: Tomtebodavägen 23A

department: Gene Technology

country: Sweden

institute: KTH-Science for Life Laboratory

description:
Sample name: 108
Processed data file: All_count_table.txt
Processed data file: All_fpkm_table.txt

data_processing:
Aligned to the mouse genome reference mm9 with TopHat version 133.
Duplicates were removed using Picard Tools version 129.
Fragments per kilobase of exon per million mapped fragments (FPKM) values for features were calculated by Cufflinks version 130.
Raw read counts were generated using HTSeq version 051.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: All_count_tablet.xt contains read counts for all 12 samples.
Supplementary_files_format_and_content: All_fpkm_table.txt contains FPKM for all 12 samples.

source_name: Glast-Rasless-YFP mice, tamoxifen, SCI, spinal cord lesions

extract_protocol:
RNeasy kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: To induce recombination, Glast-Rasless-YFP mice received one daily intra-peritoneal injection of 2 mg of tamoxifen (Sigma, 20 mg/ml in 1:9 ethanol:corn oil) for 5 consecutive days. Vehicle animals (matched mice with the same genotype) received the same number of injections of the solvent (1:9 ethanol:corn oil) without tamoxifen. Dorsal hemisection spinal cord injuries were performed after a 7 days clearing period starting after the last tamoxifen injection. This ensures that all recombination occurs prior to the insult, so in case other cells than type A pericytes start expressing the Glast-CreERT2 transgene in response to the injury, it will not result in recombination. Fourteen days after injury, spinal cord injury sites were dissected out and snap frozen in liquid nitrogen.

tag: strain/background

value: Glast-CreERT2 x R26R-YFP x Rasless

tag: age

value: adult (>8 weeks old)

tag: injection

value: tamoxifen

value: spinal cord injury (SCI)

value: SCI site

tag: timepoint

value: 14 days after SCI


title: QuiescentSatelliteCells-rep1


title: NIH3T3-H3.3GFP-Infect24h


title: NIH3T3-H3.3GFP-Infect48h


title: Mutant 4


title: 513 SCI Tam

description:
Sample name: 106
Processed data file: All_count_table.txt
Processed data file: All_fpkm_table.txt


title: 1-wt-1


title: Single_Frz

city: Marselle

first: Emanuele

middle: G

last: Biondi

address: 31 chemin Joseph Aiguier

department: LCB

country: France

institute: CNRS

description: Immunoprecipitation using anti-GFP antibody

data_processing:
Cutadapt with default parameters used to remove remaining adapters
The software FLASH was used to merge together overlapping mates from paired end files
Alignment was performed with Bowtie1 with default parameters and the following additional commands -m 1 -v 0
Genome wide coverage was obtained by counting the number of reads overlapping to each nucleotide in the genome (GCF_000012685.1_ASM1268v1_genomic.fna). In case of paired end reads, only pairs aligning in the expected orientation were considered (i.e. the innies). All the region comprised among the most 5' nucleotide of the upstream read and the most 3' nucleotide of the downstream read was considered to be sequenced and coverage calculated accordingly.
Genome_build: GCF_000012685.1_ASM1268v1_genomic.fna
Supplementary_files_format_and_content: three columns file, col 1: genomic coordinate, col2: coverage PARB, col3: coverage FRZ expressed as rpkm. Header rows start with # and include the normalization factor for PARB and FRZ samples

organism: Myxococcus xanthus

source_name: Myxococcus xanthus cells

growth_protocol: Cells were grown up to mid-log phase cells (80 ml, OD600 of 0.6)

extract_protocol:
Anti-GFP antibodies were produced in rabbit, using a purified 6His-GFP (superfold) and purified. Antibodies were added to the remains of the supernatant (1:1,000 dilution), incubated overnight at 4°C with 80 μL of protein-A agarose beads pre-saturated with BSA, washed once with low salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 150 mM NaCl), high salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 500 mM NaCl) and LiCl buffer (0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl (pH 8.1) and twice with TE buffer (10 mM Tris-HCl (pH 8.1) and 1 mM EDTA). The protein-DNA complexes were eluted in 500 μL freshly prepared elution buffer (1% SDS, 0.1 M NaHCO3), supplemented with NaCl to a final concentration of 300 mM and incubated overnight at 65°C to reverse the crosslinks. The samples were treated with 2 μg of Proteinase K for 2 h at 45°C in 40 mM EDTA and 40 mM Tris-HCl (pH 6.5). DNA was extracted using QIAgen minelute kit and resuspended in 30 μl of Elution Buffer.
DNA libraries were prepared by The Biondi lab (Marseille France) using standard Illumina protocols

treatment_protocol: Cells were than were cross-linked in 10 mM sodium phosphate (pH 7.6) and 1% formaldehyde at room temperature for 10 min and on ice for 30 min thereafter, washed thrice in phosphate buffered saline (PBS) and lysed with lysozyme 2.2 mg ml-1 in TES (Tris-HCl 10 mM pH 7.5, EDTA 1 mM, NaCl 100 mM). Lysates (Final volume 1ml) were sonicated (Branson Digital Sonicator 450, Branson Sonic Power. Co., www.bransonic.com/) on ice using 10 bursts of 30 sec (50% duty) at 30% amplitude to shear DNA fragments to an average length of 0.3–0.5 kbp and cleared by centrifugation at 14,000 rpm for 2 min at 4°C. Lysates were normalized by protein content by measuring the absorbance at 280 nm; ca. 7.5 mg of protein was diluted in 1 mL of ChIP buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl [pH 8.1], 167 mM NaCl plus protease inhibitors (Euromedex, https://www.euromedex.com/) and pre-cleared with 80 μL of protein-A agarose (Sigma-Aldrich, www.sigmaaldrich.com) and 100 μg BSA.

value: DK 1622 FRXCD-GFP

tag: chip antibody

value: anti-GFP antibody


title: Mutant 5


title: Mutant 3


title: Mutant 1


title: 452 SCI Tam

description:
Sample name: 15
Processed data file: All_count_table.txt
Processed data file: All_fpkm_table.txt


title: Paired_ParB_original

value: DK 1622 ParB-YFP


title: 429 SCI Veh

description:
Sample name: 19
Processed data file: All_count_table.txt
Processed data file: All_fpkm_table.txt

source_name: Glast-Rasless-YFP mice, vehicle, SCI, spinal cord lesions

value: vehicle


title: 457 SCI Veh

description:
Sample name: 20
Processed data file: All_count_table.txt
Processed data file: All_fpkm_table.txt


title: 376 Uninjured

description:
Sample name: 1
Processed data file: All_count_table.txt
Processed data file: All_fpkm_table.txt

source_name: Glast-Rasless-YFP mice, uninjured spinal cord segment

value: spinal cord segment

value: 14 days


title: 402 SCI Veh

description:
Sample name: 17
Processed data file: All_count_table.txt
Processed data file: All_fpkm_table.txt


title: 467 Uninjured

description:
Sample name: 4
Processed data file: All_count_table.txt
Processed data file: All_fpkm_table.txt


title: 385 Uninjured

description:
Sample name: 3
Processed data file: All_count_table.txt
Processed data file: All_fpkm_table.txt


title: 377 Uninjured

description:
Sample name: 2
Processed data file: All_count_table.txt
Processed data file: All_fpkm_table.txt


title: CLIPseq_Pspc1

status: Public on Feb 26 2018

city: New York

first: Jianlong

last: Wang

state: New York

department: Department of Medicine

institute: Columbia University Irving Medical Center

data_processing:
CLIP-seq reads were trimmed by the 3' adaptor sequence: AGATCGGAAGAGCACACGTCT and cleaned by Trim Galore
CLIP-seq reads were aligned to the mouse genome (mm9) using TopHat (v2.0.10) and Bowtie2 (v2.1.0) with the default parameter settings
CLIP-seq peaks were determined using the Piranha tools (http://smithlabresearch.org/software/piranha/) with the parameters -s -b 200
Genome_build: mm9
Supplementary_files_format_and_content: Bed file of Piranha called peaks.

source_name: Embryonic stem cells

growth_protocol: mESCs were grown in DMEM (GIBCO) supplemented with 15% Serum (Corning), 10^3 units/ml recombinant murine Leukemia Inhibitory Factor (LIF) (ESGRO, Millipore), 2mM L- alanyl-L-glutamine dipeptide (Glutamax; Invitrogen), 1x non-essential amino acids (Invitrogen), and 0.1mM 2-mercaptoethanol (Sigma). mESCs were passaged every two day as a single cell suspension using 0.05% trypsin/EDTA and seeded at 3.0x10^4 cells/cm^2 for routine culture. All cells were grown on 0.1% (w/v) gelatin coated tissue culture dish.

extract_protocol:
Crosslinking immunoprecipitation and massive parallel sequencing (CLIP-seq) was performed as previously described (Mol Cell. 2009 Dec 25;36(6):996-1006. doi: 10.1016/j.molcel.2009.12.003.) by using a FLAG tag antibody (Sigma #F1804) targeting Pspc1.
CLIPed RNA was extracted with TRIzol and ligated with 5' RNA linker GUUCAGAGUUCUACAGUCCGACGAUC for 16 h at 16°C. Reverse transcription with RT primer AGACGTGTGCTCTTCCGATCT, followed by PCR for 25 cycles to generate and amplify the cDNA library. High-throughput sequencing of the resulting cDNA was performed on a Hiseq-2000 sequencer according to the manufacturer’s protocol.

treatment_protocol: J1 mESCs were transfected with a 3xFLAG tagged Pspc1 construct.

tag: cell line

tag: mouse strain

value: FLAG (Sigma #F1804)


title: Pto_KB_A83

city: Cologne

first: Tatsuya

last: Nobori

address: Carl-von-Linne Weg 10, Max-Planck Institute for Plant Breeding Research

data_processing:
Illumina CASAVA-1.8.2 software was used for basecalling and Illumina adapter matching reads were removed using cutadapt 1.5
Reads were mapped to the P. syringae pv. tomato DC3000 genome using Bowtie2 (version 2.2.8) with the parameters -p 20 -q --phred33 and transformed into a count per gene per library by using HTSeq (version 0.6.0).
Supplementary_files_format_and_content: Tab-delimited text file including raw read counts per gene for each sample.

organism: Pseudomonas syringae pv. tomato str. DC3000

source_name: Bacteria grown in King's B medium

growth_protocol: Arabidopsis plants were grown in a chamber at 22°C with a 10 h light period and 60% relative humidity for 3 weeks and then in another chamber at 22°C with a 12 h light period and 60% relative humidity.

extract_protocol:
For RNA extraction, the TriFast solution was mixed with 200 μl of chloroform and the aqueous phase was isolated by centrifugation (typically 400 μl). The aqueous phase was mixed with 200 μl (half volume) of ethanol and then applied to the column of RNAqueous kit (Ambion). RNA was eluted in 30 μl of RNase free water following the manufacture’s protocol and treated with 2 U of TURBO DNase (Ambion) for 30 min at 37 ºC. Plant rRNAs were removed using Ribo-Zero plant kit (Epicentre) following the manufacture’s protocol.
cDNA libraries were generated with Ovation Complete Prokaryotic RNA-Seq kit 1-8 (NuGEN)

value: Pto

tag: media

value: King's B Medium

tag: replicate


title: Pto-D36E_KB_A83

institute: Max-Planck Institute for Plant Breeding Research


title: Pto-AvrRpt2_KB_A83


title: Pto-AvrRps4_KB_A82


title: Pto-D36E_KB_A82


title: 549 SCI Tam

description:
Sample name: 107
Processed data file: All_count_table.txt
Processed data file: All_fpkm_table.txt

tag: treatment


title: Pto-AvrRpt2_KB_A82


title: Pto-D36E_KB_A81


title: Pto-AvrRps4_KB_A81


title: Pto_MM_A80_2

source_name: Bacteria grown in minimal medium

value: Minimal Medium


title: Pto-AvrRpt2_KB_A81


title: Pto_MM_A80_4


title: 428 SCI Veh

description:
Sample name: 18
Processed data file: All_count_table.txt
Processed data file: All_fpkm_table.txt


title: Pto-AvrRpt2_stp_A74

source_name: Bacteria isolated from Arabidopsis thaliana

tag: host genotype

value: stp1 stp13


title: Pto_KB_A81


title: Pto_MM_A80_1


title: Pto-AvrRpt2_stp_A71


title: Pto_stp_A71


title: Pto_Col_A74


title: Pto-AvrRpt2_Col_A74


title: Pto-AvrRpt2_Col_A71


title: Pto_stp_A74


title: Pto-AvrRpt2_col_A66


title: Pto_Col_A71


title: Pto-AvrRpt2_pad4sid2_A66

value: pad4-1 sid2-2


title: Pto_pad4sid2_A66


title: Pto_pad4_A66


title: Pto_col_A66


title: Pto-AvrRps4_col_A59


title: Pto-D36E_col_A59


title: Pto-AvrRpt2_col_A59


title: Pto_col_A59


title: Pto-AvrRpt2_col_A58


title: Pto_col_A58


title: Pto-D36E_col_A58


title: Pto_MM_A80_3


title: Pto-D36E_col_A57


title: Pto-AvrRps4_col_A57


title: Pto_col_A57


title: Pto-AvrRpt2_col_A57


title: Pto_col_SA_A54


title: Pto_col_chitin_A54


title: Pto_col_flg22_A54


title: Pto-AvrRpt2_pad4_A66


title: Pto_col_mock_A54


title: Pto_col_mock_A53


title: Pto_col_SA_A53


title: Pto_col_chitin_A53


title: Pto_col_flg22_A52


title: Pto_col_chitin_A52


title: Pto_col_flg22_A53


title: Pto-AvrRpt2_rr_A48


title: Pto-AvrRpt2_col_A48


title: Pto-AvrRpt2_rr_A47


title: Pto_col_mock_A52


title: Pto-AvrRpt2_col_A47


title: Pto-AvrRpt2_de_A44

value: dde2-2 ein2-1


title: Pto-AvrRpt2_npr1_A44


title: Pto-AvrRpt2_col_A44


title: Pto-AvrRpt2_deps_A44

value: dde2-2 ein2-1 pad4-1 sid2-2


title: Pto-AvrRpt2_pad4_A42


title: Pto-AvrRpt2_sid2_A42


title: Pto-AvrRpt2_col_A42


title: Pto_pad4_A42


title: Pto_sid2_A42


title: Pto_col_A42


title: Pto-AvrRpt2_b2b3_A26

value: cyp79b2 cyp79b3


title: Pto_col_SA_A52


title: Pto-AvrRpt2_sid2pmr4_A26

value: sid2-1 pmr4-1


title: Pto-AvrRpt2_col_A26


title: Pto-AvrRpt2_b2b3_A25


title: Pto_b2b3_A26


title: Pto_col_A26


title: Pto_sid2pmr4_A26


title: Pto-AvrRpt2_col_A25


title: Pto_b2b3_A25


title: Pto_sid2pmr4_A25


title: Pto-AvrRpt2_sid2pmr4_A25


title: Pto_col_mock_A23

value: Col-0 Mock treatment


title: Pto_col_flg22_A23

value: Col-0 flg22 treatment


title: Pto_col_flg22_A22


title: Pto-AvrRpt2_deps_A15


title: Pto-AvrRpt2_de_A15


title: Pto_de_A15


title: Pto-AvrRpt2_col_A15


title: Pto-AvrRpt2_npr1_A15


title: Pto_deps_A15


title: Pto_pad4sid2_A42


title: Pto_npr1_A15


title: Pto_col_A15


title: Pto-AvrRpt2_pad4sid2_A14


title: Pto-AvrRpt2_sid2_A14


title: Pto_col_A25


title: Pto_pad4_A14


title: Pto_pad4sid2_A14


title: skin_E9.5_embryo2

city: Beijing

first: Ji

last: Dong

address: Yiheyuan 5#

country: China

institute: Peking University

description: polyA RNA

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Raw reads were first organized by specific cell barcode information attached in the read 2 of pair-ended reads. Second, unique molecular identifier (UMI) information were added into the corresponding read 1 which were then trimmed to remove template switch oligo (TSO) sequence and polyA tails. Subsequently, we also removed reads with adapter contaminants and low-quality bases (N>10%).
Third, the cleaned reads were aligned to the mm10 mouse transcriptome (UCSC) using Tophat (version 2.0.12) (Trapnell et al., 2009). Fourth, uniquely mapped reads were counted using htseq-count of the HTSeq package and grouped by cell-specific barcode (Anders et al., 2014). Based on UMI information, duplicated transcripts of each gene were removed. Finally, within a given cell, distinct UMIs of each gene were counted as the transcript number of that gene.
The expression levels TPM, where TPM (transcript-per-million) was calculated by the number of UMIs of each gene divided by all the number of UMIs of a given cell, then multiplying by 1,000,000.
Genome_build: mm10
Supplementary_files_format_and_content: txt files which include theTPM values of RefSeq genes.

source_name: Mouse Fetal Cells

extract_protocol:
A modified Smart-seq2 protocol was applied for single-cell RNA-seq. Briefly, after MACS and FACS purification, a single PGC or gonadal somatic cell was picked into the lysis buffer by mouth pippete. The reverse transcription reaction was performed with 24 oligo (dT) primer anchored with the 8 bp cell specific barcode, and also with 8 bp unique molecular identifiers (UMIs).
After the first-strand reaction, the cDNA was amplified by 17 cycles. Then the amplified cDNA of the PGCs of the same fetal sample were pooled together and the amplified cDNA of the gonadal somatic cells of the same fetal sample were pooled together to proceed the following steps. Biotinylated pre-indexed primer was used to amplify the PCR product by additional 4 cycles to introduce biotin tags to the 3’ end of the amplified cDNA. About 300 ng DNA was sheared to around 300 bp by Covaris S2 and the 3’ ternimal of the DNA was captured by Dynabeads® MyOne™ Streptavidin C1 beads (Thermo Fisher). RNA seq library was constructed using Kapa Hyper Prep Kit (Kapabiosystems) and subjected to 150 bp paired-end sequencing on illumina HiSeq 2500 platform (sequenced by Novogene).

value: skin

tag: gender

value: female


title: somite_E9.5_embryo2

description: polyA RNA

value: somite

tag: developmental stage


title: Pto_col_A14


title: RNAseq_shPspc1_rep1

description: Pspc1 shRNA treatment

data_processing:
Reads were aligned to the genome using TopHat (v2.0.10) and Bowtie2 (v2.1.0) with the default parameter settings.
Transcript assembly and differential expression analysis were performed using Cufflinks (v2.1.1). Assembling of novel transcripts was not allowed (-G), other parameters of Cufflinks followed the default setting.
Genome_build: mm9
Supplementary_files_format_and_content: tsv files - tab-delimited files containing FPKM values for RefSeq genes in each sample generated using Cufflinks.

extract_protocol:
Total RNA was isolated using the RNeasy kit (#74136, Qiagen) according to manufacturer’s instructions.
Up to 1 μg of total RNA for each sample was taken for Ribo-Zero RNA-seq libraries preparation, and massively parallel sequencing was performed with the Illumina HiSeq 2500 Sequencing System. 100-bp paired-end reads were generated for each sample.

treatment_protocol: CCE mESCs were treated with control empty vector depletion (shEV) or Pspc1 depletion (shPspc1) shRNAs

value: CCE


title: lung_E9.5_embryo2

description: polyA RNA

tag: tissue

value: lung


title: hindbrain_E9.5_embryo2

description: polyA RNA

tag: strain

value: metencephalon


title: RNAseq_shEV_rep2

description: Empty vector treatment


title: RNAseq_shPspc1_rep2

description: Pspc1 shRNA treatment


title: Pto-AvrRpt2_col_A14


title: Pto_sid2_A14

value: Pto


title: Pto_col_mock_A22


title: liver_E9.5_embryo2

description: polyA RNA

value: liver


title: RNAseq_shEV_rep1

description: Empty vector treatment


title: Pto-AvrRpt2_sid2_A17


title: Pto-AvrRpt2_pad4_A17


title: intestine_E9.5_embryo2

description: polyA RNA

value: intestine


title: Pto-AvrRpt2_col_A17


title: Pto_pad4sid2_A17


title: Pto_pad4_A17


title: heart_E9.5_embryo2

description: polyA RNA

value: heart


title: Pto-AvrRpt2_pad4_A14


title: Pto_col_A17


title: Pto_sid2_A17


title: forebrain_E9.5_embryo2

description: polyA RNA

value: forebrain


title: Pto-AvrRpt2_deps_A13


title: somite_E9.5_embryo1

description: polyA RNA

value: male


title: Pto-AvrRpt2_pad4sid2_A17

value: pad4-1 sid2-2


title: hindbrain_E9.5_embryo1

description: polyA RNA


title: Pto-AvrRpt2_col_A13


title: Pto-AvrRpt2_npr1_A13


title: Pto-AvrRpt2_de_A13

value: dde2-2 ein2-1


title: Pto_deps_A13

value: dde2-2 ein2-1 pad4-1 sid2-2


title: Pto_npr1_A13


title: Pto_de_A13


title: heart_E9.5_embryo1

description: polyA RNA


title: FGF2 144h_2

city: Mölndal

first: Fabrice

last: CHIMIENTI

address: Pepparedsleden 1

institute: AstraZeneca

data_processing:
paired-end-end reads were generated using an Illumina NextSeq 500 and processed using the RNA-seq pipeline implemented in the bcbio-nextgen project [https://bcbio-nextgen.readthedocs.org/en/latest/]
Reads were aligned to the human genome version hg38 using the Hisat2 aligner (Nat Methods. 2015 Apr;12(4):357-60)
Counts of reads aligning to known genes are generated by featureCounts (Bioinformatics (Oxford, England) 30 (7). Oxford University Press: 923–30. doi:10.1093/bioinformatics/btt656)
Differential expression analysis was performed using DESeq2 (Genome Biol. 2014;15(12):550)
Genome_build: hg38
Supplementary_files_format_and_content: counts

source_name: FGF2 144h, EndoC-BH1

growth_protocol: Endo-BH1 cells were routinely cultured by passaging every week. Cells (2.106 cells per sample)were treated in triplicates with FGF2 (100 ng/mL) or vehicle alone for 0, 4, 24, 72 or 144h.

extract_protocol:
RNA was isolated using RNA Isolation Kit (Qiagen).The quality of the RNA was assessed by a Fragment Analyzer (Advanced Analytical Technologies).
One microgram of total RNA was used for each library. The RNA samples were processed with Illumina TruSeq Stranded mRNA Library prep kit following the manufacturer’s recommendations. Libraries were quantified with Qubit HS (ThermoFisher) and Fragment Analyzer (Advanced Analytical Technologies). Indexed libraries were pooled and sequenced on an Illumina NextSeq 500 high-output run using paired-end-end chemistry with 75 bp read length.

treatment_protocol: After teratment total mRNA has been isolated from cells and QC'd (RIN<7). Addintional quality control included qPCR with a few genes known to be differentially expressed from previous work. RNA weer then sent out for NGS sequencing (illumina NextSeq500)

tag: cell type

value: pancreatic beta cell

tag: agent

tag: time


title: forebrain_E9.5_embryo1

description: polyA RNA


title: intestine_E9.5_embryo1

description: polyA RNA


title: Pto_col_A13


title: FGF2 144h_1


title: FGF2 144h_3


title: FGF2 72h_2

source_name: FGF2 72h, EndoC-BH1


title: Ctrl 144h_2

source_name: Ctrl 144h, EndoC-BH1

value: Ctrl


title: FGF2 72h_1


title: FGF2 72h_3


title: Ctrl 144h_1


title: Ctrl 72h_1

source_name: Ctrl 72h, EndoC-BH1


title: FGF2 24h_3

source_name: FGF2 24h, EndoC-BH1


title: FGF2 24h_2


title: Ctrl 72h_3


title: FGF2 24h_1


title: Ctrl 144h_3


title: Ctrl 72h_2


title: liver_E9.5_embryo1

description: polyA RNA


title: Ctrl 24h_3

source_name: Ctrl 24h, EndoC-BH1


title: Pto_flg22_#3-3

data_processing:
Base calling was done by the Illumina Real Time Analysis software (RTA version 1.18.64).
Reads were mapped to the P. syringae pv. tomato DC3000 genome using Bowtie2 (version 2.2.8) with the parameters -p 20 -q --phred33 and transformed into a count per gene per library by using HTSeq (version 0.6.0).
Supplementary_files_format_and_content: Tab-delimited text file including raw read counts per gene for each sample.

source_name: Bacteria infected to Arabidopsis thaliana

growth_protocol: Plants were grown in a chamber with a 12-h light period, 23 °C temperature at day time and 21 °C at night time.

extract_protocol:
RNA was extracted using the TRIzolTM reagent (Thermo Fisher Scientific) and the Direct-zolTM RNA Miniprep kit (Zymo Research). Purified RNA was treated with 10 U of RNase-free DNase I (Roche Applied Science), after which RNA was purified a second time with the Direct-zolTM RNA Miniprep kit. Non-organellar 18S and 28S rRNAs, and poly(A) mRNAs were depleted using the MICROBEnrichTM kit (Thermo Fisher Scientific).
RNA-Seq libraries were prepared using the Ovation Arabidopsis RNA-Seq system 1–16 (NuGEN) with two modifications to the manufacturer’s protocol. First strand cDNA synthesis used only the first strand primer random mix (the oligo dT primer mix was omitted), while on strand selection II, custom insert dependent adapter cleavage probes (InDA-C; currently referred to as AnyDeplete) with specificity to highly abundant A. thaliana chloroplast and nuclear transcripts (361 probes) and Pto DC3000 rRNAs (65 probes) (1 µL of each 2 µM probe mixture was used) were added to the mixture of A. thaliana cytoplasmic, chloroplast, and mitochondrial rRNA custom probes that are included with the kit.

value: 500 nM flg22


title: Pto_flg22_#3-1


title: Pto_flg22_#3-2


title: Pto_mock_#3

value: DMSO


title: Ctrl 24h_1


title: FGF2 4h_3

source_name: FGF2 4h, EndoC-BH1


title: Ctrl 24h_2


title: Pto_flg22_#2-3


title: FGF2 4h_1


title: FGF2 4h_2


title: Pto_flg22_#2-2


title: Ctrl 4h_3

source_name: Ctrl 4h, EndoC-BH1


title: Pto_flg22_#2-1


title: hxk-glk mutant replicate 2

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

country: Netherlands

institute: Centre of fungal biodiversity

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequence reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the genome sequence of Aspergillus nidulans FGSC A4 whole genome using SOAPALIGNER/SOAP2. No more than 2 mismatches allowed in the alignment.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., 2008.
Genome_build: Aspergillus nidulans FGSC A4 genome version s10-m04-r01 from www.aspgd.org
Supplementary_files_format_and_content: Excel files include unique reads number, gene length, coverage, RPKM values, KEGG orthology, GO and Blast nr annotation of genes for each sample.

organism: Aspergillus nidulans

source_name: Liquid culture, hxk-glk mutant

growth_protocol: All the strains were pre-grown in 1-L Erlenmeyer flasks that contained 200 ml of CM + 2% D-xylose. Liquid cultures were inoculated with 10*6 spores/ml and shaken at 250 rpm in a rotary shaker. After 16 hours, the mycelium was harvested by filtration, washed twice with MM and transferred to 250 ml Erlenmeyer flaks containing 50 ml MM + 2% wheat bran and the appropriate supplements.

extract_protocol:
Total RNA was extracted from mycelium ground in a Tissue Lyser (QIAGEN) using TRIzol reagent (Invitrogen) according to the instructions of the manufacturer. RNA integrity and quantity were analyzed on a 1% agarose gel using gel electrophoresis and with the RNA6000 Nano Assay using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). cDNA library preparation and sequencing reactions were performed by BGI Tech Solutions Co., Ltd. (Hong Kong).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The mycelium was harvested from the liquid culture by vacuum filtration after 2 hours of incubation. The mycelium samples were dried between tissue paper, frozen in liquid nitrogen and processed according to the extraction protocol.

tag: strain/background

tag: genotype/variation

value: hxk-glk mutant

tag: substrate

value: MM + wheat bran

tag: sampling time

value: 2 hours

value: mycelium


title: creA-hxk-glk mutant replicate 2

source_name: Liquid culture, creA-hxk-glk mutant

value: creA-hxk-glk mutant


title: Pto_mock_#2

value: Pto


title: Pto_flg22_#1-3


title: Ctrl 4h_2

tag: cell line


title: Ctrl 0h_3

source_name: Ctrl 0h, EndoC-BH1


title: creA mutant replicate 1

source_name: Liquid culture, creA mutant

value: creA mutant


title: creA mutant replicate 2


title: Ctrl 4h_1


title: Pto_flg22_#1-2


title: Ctrl 0h_1


title: AC606

status: Public on Feb 25 2018

first: Mariano

middle: Javier

last: Alvarez

address: 1130 St. Nicholas ave.

department: Systems Biology

institute: Columbia University

description: SI-NET

data_processing:
Sequencing was performed in a Hi-Seq 2500 sequencer (Illumina) and base calling was performed with Illumina HCS software.
Reads were mapped to human reference genome HG19 using Bowtie v0.12.8, using default parameters.
Reads mapping to known transcripts were counted with GenomicFeatures v1.22.13 (Bioconductor) for R-system v3.2.3.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *counts.txt: Matrix of raw counts for each known gene (Entrez Gene ID) in rows and sample in columns.

source_name: GEP-NET

extract_protocol:
212 GEP-NET samples with cellularity >70% were analyzed. Total RNA was isolated and RNA integrity assayed by a 2100 Bioanalyzer (Agilent Technologies). High-quality total RNA samples, with RIN (RNA integrity number) above 7, were processed by TruSeq library preparation for RNA-Seq profiling (Illumina). For each sample, a minimum of 30 million 100bp single-end reads or 90 million 100bp paired-end reads were sequenced on the Illumina HiSeq2500 platform.
Standard TruSeq protocols from Illumina.

tag: type

value: primary

tag: origin

value: small intestine


title: AC603

description: SI-NET


title: AC206

description: SI-NET


title: wild type replicate 1

source_name: Liquid culture, wild type

value: wild type


title: AC205

description: SI-NET


title: AC208

description: SI-NET


title: AC199

description: SI-NET


title: AC203

description: SI-NET


title: AC188

description: SI-NET


title: Pto_mock_#1

tag: replicate


title: AC196

description: SI-NET


title: AC542

description: SI-NET


title: hxk-glk mutant replicate 1


title: Pto_flg22_#1-1


title: AC541

description: SI-NET


title: AC497

description: SI-NET


title: AC540

description: SI-NET


title: AC490

description: SI-NET


title: AC539

description: SI-NET


title: wild type replicate 2


title: AC157

description: SI-NET


title: AC158

description: SI-NET


title: AC162

description: SI-NET


title: creA-hxk-glk mutant replicate 1


title: AC143

description: SI-NET


title: AC543

description: SI-NET


title: AC60

description: SI-NET


title: AC146

description: SI-NET


title: AC113

description: SI-NET


title: AC612

description: SI-NET


title: AC133

description: SI-NET


title: AC127

description: SI-NET


title: AC631

description: SI-NET


title: AC630

description: SI-NET


title: AC468

description: SI-NET


title: Ctrl 0h_2


title: AC430

description: SI-NET


title: AC496

description: SI-NET


title: AC111

description: SI-NET


title: AC392

description: SI-NET


title: AC389

description: SI-NET


title: AC383

description: SI-NET


title: AC609

description: SI-NET

value: mesenteric metastasis


title: AC99

description: SI-NET


title: AC417

description: SI-NET


title: AC611

description: SI-NET

value: lymph node metastasis


title: AC141

description: SI-NET


title: AC646

description: SI-NET


title: AC147

description: SI-NET


title: AC236

description: SI-NET


title: AC494

description: SI-NET


title: AC633

description: SI-NET


title: AC495

description: SI-NET


title: AC319

description: SI-NET

value: liver metastasis


title: AC480

description: SI-NET


title: AC314

description: SI-NET


title: AC315

description: SI-NET


title: AC576

description: SI-NET


title: AC395

description: SI-NET


title: AC632

description: SI-NET


title: AC288

description: SI-NET


title: AC79

description: SI-NET


title: AC301

description: SI-NET


title: AC610

description: SI-NET


title: AC283

description: SI-NET


title: AC300

description: SI-NET


title: AC281

description: SI-NET


title: AC316

description: SI-NET


title: AC271

description: SI-NET


title: AC75

description: SI-NET


title: AC270

description: SI-NET


title: AC268

description: SI-NET


title: AC273

description: SI-NET


title: AC388

description: SI-NET


title: AC267

description: SI-NET


title: AC263

description: SI-NET


title: AC498

description: SI-NET


title: AC262

description: SI-NET


title: AC248

description: SI-NET


title: AC244

description: SI-NET


title: AC384

description: SI-NET


title: AC577

description: RE-NET

value: rectum


title: AC259

description: SI-NET


title: AC261

description: SI-NET


title: AC252

description: SI-NET


title: AC286

description: SI-NET


title: AC578

description: RE-NET


title: AC274

description: SI-NET


title: AC277

description: SI-NET


title: AC535

description: RE-NET


title: AC534

description: RE-NET


title: AC61

description: SI-NET


title: AC47

description: RE-NET


title: AC579

description: RE-NET


title: AC241

description: RE-NET


title: AC16

description: RE-NET


title: AC246

description: RE-NET


title: AC509

description: RE-NET


title: AC510

description: RE-NET


title: AC508

description: RE-NET


title: AC636

description: RE-NET


title: AC652

description: RE-NET


title: AC219

description: P-NET

value: pancreas


title: AC452

description: RE-NET


title: AC243

description: RE-NET


title: AC218

description: P-NET


title: AC485

description: P-NET


title: AC484

description: P-NET


title: AC215

description: P-NET


title: AC214

description: P-NET


title: AC242

description: RE-NET


title: AC212

description: P-NET


title: AC211

description: P-NET


title: AC210

description: P-NET


title: AC489

description: P-NET


title: AC234

description: P-NET


title: AC607

description: P-NET


title: AC231

description: P-NET


title: AC488

description: P-NET


title: AC455

description: RE-NET


title: AC209

description: P-NET


title: AC233

description: P-NET


title: AC227

description: P-NET


title: AC224

description: P-NET


title: AC487

description: P-NET


title: AC221

description: P-NET


title: AC604

description: P-NET


title: AC350

description: P-NET


title: AC216

description: P-NET


title: AC348

description: P-NET


title: AC483

description: P-NET


title: AC486

description: P-NET


title: AC347

description: P-NET


title: AC346

description: P-NET


title: AC343

description: P-NET


title: AC608

description: P-NET


title: AC341

description: P-NET


title: AC339

description: P-NET


title: AC337

description: P-NET


title: AC333

description: P-NET


title: AC329

description: P-NET


title: AC213

description: P-NET


title: AC328

description: P-NET


title: AC139

description: P-NET


title: AC226

description: P-NET


title: AC153

description: P-NET


title: AC326

description: P-NET


title: AC126

description: P-NET


title: AC325

description: P-NET


title: AC137

description: P-NET


title: AC123

description: P-NET


title: AC125

description: P-NET


title: AC323

description: P-NET


title: AC322

description: P-NET


title: AC130

description: P-NET


title: AC116

description: P-NET


title: AC115

description: P-NET


title: AC474

description: P-NET


title: AC114

description: P-NET


title: AC106

description: P-NET


title: AC108

description: P-NET


title: AC473

description: P-NET


title: AC472

description: P-NET


title: AC110

description: P-NET


title: AC462

description: P-NET


title: AC422

description: P-NET


title: AC105

description: P-NET


title: AC412

description: P-NET


title: AC411

description: P-NET


title: AC408

description: P-NET


title: AC429

description: P-NET


title: AC405

description: P-NET


title: AC103

description: P-NET


title: AC403

description: P-NET


title: AC399

description: P-NET


title: AC393

description: P-NET


title: AC398

description: P-NET


title: AC400

description: P-NET


title: AC100

description: P-NET


title: AC397

description: P-NET


title: AC121

description: P-NET


title: AC365

description: P-NET


title: AC363

description: P-NET


title: AC361

description: P-NET


title: AC380

description: P-NET


title: AC355

description: P-NET


title: AC351

description: P-NET


title: AC500

description: P-NET


title: AC499

description: P-NET


title: AC235

description: P-NET


title: AC87

description: P-NET


title: AC89

description: P-NET


title: AC312

description: P-NET


title: AC305

description: P-NET


title: AC310

description: P-NET


title: AC292

description: P-NET


title: AC291

description: P-NET


title: AC302

description: P-NET


title: AC282

description: P-NET


title: AC279

description: P-NET


title: AC391

description: P-NET


title: AC73

description: P-NET


title: AC258

description: P-NET


title: AC256

description: P-NET


title: AC254

description: P-NET


title: AC255

description: P-NET


title: AC269

description: P-NET


title: AC257

description: P-NET


title: AC249

description: P-NET


title: AC425

description: P-NET


title: AC71

description: P-NET


title: AC409

description: P-NET


title: AC58

description: P-NET


title: AC318

description: P-NET


title: AC385

description: P-NET


title: AC431

description: P-NET


title: AC309

description: P-NET


title: AC276

description: P-NET


title: SU11274_1.52_24 [CR13D1]

data_processing:
Sequencing was performed in a Hi-Seq 2500 sequencer (Illumina) and base calling was performed with Illumina HCS software.
Single end reads were mapped to human reference genome HG19 using Bowtie v0.12.8, using default parameters.
Reads mapping to known transcripts were counted with GenomicFeatures v1.22.13 (Bioconductor) for R-system v3.2.3.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *txt: Tab-delimited matrix of raw counts for each known gene (EntrezID) in rows and sample in columns.

source_name: H-STS NET cell line, SU11274, 24h

growth_protocol: H-STS cells were maintained in 1:1 mix of M199 : Ham's F-12 containing 10% FBS and antibiotics (penicillin 100 IU/ml and streptomycin 100 ug/ml).

extract_protocol:
Cells were lysed and total RNA isolated. RNA integrity was evaluated with a 2100 Bioanalyzer.
Standard TruSeq protocols from Illumina.

treatment_protocol: Small molecule compounds were added to achieve a concentration corresponding to the ED20 and 1/10 of it, measured by cell viability at 60h after compound treatment. Vehicle control, including DMSO, ethanol and methanol were added in duplicate.

value: H-STS NET

tag: compound

tag: concentration (um)

tag: time-point

tag: batch


title: SU11274_1.52_24 [CR13C12]


title: PKC412_2.84_24 [CR13B3]

source_name: H-STS NET cell line, PKC412, 24h


title: Pluripotin_0.004_24 [CR13C6]

source_name: H-STS NET cell line, Pluripotin, 24h

value: Pluripotin


title: RAD001_5.88_24 [CR13D6]

source_name: H-STS NET cell line, RAD001, 24h


title: PKC412_2.84_24 [CR13B2]


title: PF-573228_2.08_24 [CR13C1]

source_name: H-STS NET cell line, PF-573228, 24h


title: RAD001_5.88_24 [CR13D7]


title: PF-573228_2.08_24 [CR13B12]


title: NIlotinib_7.68_24 [CR13C8]

source_name: H-STS NET cell line, NIlotinib, 24h

value: NIlotinib


title: NIlotinib_7.68_24 [CR13C9]


title: LY-2183240_0.64_24 [CR13B7]

source_name: H-STS NET cell line, LY-2183240, 24h


title: LY-2183240_0.64_24 [CR13B6]


title: Ethanol__24 [CR13B11]

source_name: H-STS NET cell line, Ethanol, 24h

value: Ethanol


title: AC410

description: P-NET


title: LEE011_26.32_24 [CR13C5]

source_name: H-STS NET cell line, LEE011, 24h


title: LEE011_26.32_24 [CR13C4]


title: LDK378_2.8_24 [CR13A8]

source_name: H-STS NET cell line, LDK378, 24h


title: Leptomycin B in Ethanol_0.00012_24 [CR13A11]

source_name: H-STS NET cell line, Leptomycin B in Ethanol, 24h

value: Leptomycin B in Ethanol


title: LDK378_2.8_24 [CR13A9]


title: INC280_20_24 [CR13C10]

source_name: H-STS NET cell line, INC280, 24h


title: DMSO__24 [CR13C3]

source_name: H-STS NET cell line, DMSO, 24h

value: DMSO


title: INC280_20_24 [CR13C11]


title: SCH-79797_0.06_24 [CR13C7]

source_name: H-STS NET cell line, SCH-79797, 24h


title: KU-0063794_0.04_24 [CR13A12]

source_name: H-STS NET cell line, KU-0063794, 24h


title: KU-0063794_0.04_24 [CR13B1]


title: DMSO__24 [CR13C2]


title: Leptomycin B in Ethanol_0.00012_24 [CR13A10]


title: Ethanol__24 [CR13B10]


title: CAY10618 in Methanol_7.4_24 [CR13A6]

source_name: H-STS NET cell line, CAY10618 in Methanol, 24h

value: CAY10618 in Methanol


title: Methanol__24 [CR13B5]

source_name: H-STS NET cell line, Methanol, 24h

value: Methanol


title: BKM120_1.2_24 [CR13A4]

source_name: H-STS NET cell line, BKM120, 24h


title: BIO_3_24 [CR13A2]

source_name: H-STS NET cell line, BIO, 24h

value: BIO


title: BIO_3_24 [CR13A1]


title: Methanol__24 [CR13B4]


title: CAY10618 in Methanol_7.4_24 [CR13A5]


title: BGJ398_4.56_24 [CR13B9]

source_name: H-STS NET cell line, BGJ398, 24h


title: BYL719_19.4_24 [CR13D3]

source_name: H-STS NET cell line, BYL719, 24h


title: Ciclopirox_3_24 [CR13A7]

source_name: H-STS NET cell line, Ciclopirox, 24h

value: Ciclopirox


title: BYL719_19.4_24 [CR13D2]


title: BGJ398_4.56_24 [CR13B8]


title: SU11274_1.52_6 [CR12B6]

source_name: H-STS NET cell line, SU11274, 6h


title: Y-27632_3.36_6 [CR12B1]

source_name: H-STS NET cell line, Y-27632, 6h


title: RAD001_5.88_6 [CR12B8]

source_name: H-STS NET cell line, RAD001, 6h


title: RAD001_5.88_6 [CR12B9]


title: SU11274_1.52_6 [CR12B7]


title: AUY922_0.02_24 [CR13D5]

source_name: H-STS NET cell line, AUY922, 24h


title: AUY922_0.02_24 [CR13D4]


title: PKC412_2.84_6 [CR12D01]

source_name: H-STS NET cell line, PKC412, 6h


title: PKC412_2.84_6 [CR12C12]


title: NIlotinib_7.68_6 [CR12A9]

source_name: H-STS NET cell line, NIlotinib, 6h


title: Ethanol__6 [CR12B11]

source_name: H-STS NET cell line, Ethanol, 6h


title: NIlotinib_7.68_6 [CR12A10]


title: Piperlongumine_1.04_6 [CR12A8]

source_name: H-STS NET cell line, Piperlongumine, 6h

value: Piperlongumine


title: Ethanol__6 [CR12B10]


title: Leptomycin B in Ethanol_0.00012_6 [CR12A12]

source_name: H-STS NET cell line, Leptomycin B in Ethanol, 6h


title: LEE011_26.32_6 [CR12C06]

source_name: H-STS NET cell line, LEE011, 6h


title: INC280_20_6 [CR12C11]

source_name: H-STS NET cell line, INC280, 6h


title: Methanol__6 [CR12B5]

source_name: H-STS NET cell line, Methanol, 6h


title: DMSO__6 [CR12C03]

source_name: H-STS NET cell line, DMSO, 6h


title: Leptomycin B in Ethanol_0.00012_6 [CR12A11]


title: CAY10618 in Methanol_7.4_6 [CR12A5]

source_name: H-STS NET cell line, CAY10618 in Methanol, 6h


title: LEE011_26.32_6 [CR12C07]


title: LDK378_2.8_6 [CR12C09]

source_name: H-STS NET cell line, LDK378, 6h


title: LDK378_2.8_6 [CR12C08]


title: DMSO__6 [CR12C02]


title: CAY10618 in Methanol_7.4_6 [CR12A6]


title: Methanol__6 [CR12B4]


title: Manumycin A_4.32_6 [CR12A2]

source_name: H-STS NET cell line, Manumycin A, 6h

value: Manumycin A


title: INC280_20_6 [CR12C10]


title: BYL719_19.4_6 [CR12B2]

source_name: H-STS NET cell line, BYL719, 6h


title: BKM120_1.2_6 [CR12C04]

source_name: H-STS NET cell line, BKM120, 6h


title: BGJ398_4.56_6 [CR12A4]

source_name: H-STS NET cell line, BGJ398, 6h


title: AUY922_0.02_6 [CR12C01]

source_name: H-STS NET cell line, AUY922, 6h


title: AUY922_0.02_6 [CR12B12]


title: BKM120_1.2_24 [CR13A3]

source_name: H-STS NET cell line, BKM120, 24h


title: BYL719_19.4_6 [CR12B3]


title: BKM120_1.2_6 [CR12C05]


title: BGJ398_4.56_6 [CR12A3]


title: PF-573228_2.08_6 [CR11B11]

source_name: H-STS NET cell line, PF-573228, 6h


title: LY-2183240_0.64_6 [CR11B6]

source_name: H-STS NET cell line, LY-2183240, 6h


title: PF-573228_2.08_6 [CR11B12]


title: LY-2183240_0.64_6 [CR11B5]


title: KU-0063794_0.04_6 [CR11A12]

source_name: H-STS NET cell line, KU-0063794, 6h


title: KU-0063794_0.04_6 [CR11A11]


title: BIO_3_6 [CR11A6]

source_name: H-STS NET cell line, BIO, 6h


title: Y-27632_3.36_24 [CR11C8]

source_name: H-STS NET cell line, Y-27632, 24h


title: DMSO__6 [CR11C6]


title: BIO_3_6 [CR12A1]


title: Rosiglitazone_20_24 [CR11C10]

source_name: H-STS NET cell line, Rosiglitazone, 24h

value: Rosiglitazone


title: Y-27632_3.36_24 [CR11C7]


title: Epigallocatechin gallate_15.12_24 [CR11D4]

source_name: H-STS NET cell line, Epigallocatechin gallate, 24h

value: Epigallocatechin gallate


title: Rosiglitazone_20_24 [CR11C9]


title: Parbendazole_0.054_24 [CR11C11]

source_name: H-STS NET cell line, Parbendazole, 24h

value: Parbendazole


title: Parbendazole_0.054_24 [CR11C12]


title: Vincristine_0.0008_24 [CR11D6]

source_name: H-STS NET cell line, Vincristine, 24h

value: Vincristine


title: Epigallocatechin gallate_15.12_24 [CR11D3]


title: Y-27632_3.36_6 [CR11A8]

source_name: H-STS NET cell line, Y-27632, 6h


title: DMSO__24 [CR11D1]

source_name: H-STS NET cell line, DMSO, 24h


title: Arachidonyl_7.44_24 [CR11C3]

source_name: H-STS NET cell line, Arachidonyl, 24h

value: Arachidonyl


title: DMSO__24 [CR11D2]

value: H-STS NET


title: Rosiglitazone_20_6 [CR11A10]

source_name: H-STS NET cell line, Rosiglitazone, 6h


title: Rosiglitazone_20_6 [CR11A9]


title: Arachidonyl_7.44_24 [CR11C4]


title: Vincristine_0.0008_6 [CR11B9]

source_name: H-STS NET cell line, Vincristine, 6h


title: DMSO__6 [CR11B4]

source_name: H-STS NET cell line, DMSO, 6h


title: Epigallocatechin gallate_15.12_6 [CR11B7]

source_name: H-STS NET cell line, Epigallocatechin gallate, 6h


title: Arachidonyl_7.44_6 [CR11A4]

source_name: H-STS NET cell line, Arachidonyl, 6h


title: Parbendazole_0.054_6 [CR11B1]

source_name: H-STS NET cell line, Parbendazole, 6h


title: Epigallocatechin gallate_15.12_6 [CR11B8]


title: Arachidonyl_7.44_6 [CR11A3]


title: DMSO__6 [CR11B3]


title: Vincristine_0.0008_24 [CR11D5]


title: Parbendazole_0.054_6 [CR11B2]


title: Vorinostat_0.2_24 [CR10D8]

source_name: H-STS NET cell line, Vorinostat, 24h

value: Vorinostat


title: Vorinostat_0.2_24 [CR10D7]


title: Pluripotin_0.005_24 [CR10C8]

source_name: H-STS NET cell line, Pluripotin, 24h

value: Pluripotin


title: TW-37_4_24 [CR10C1]

source_name: H-STS NET cell line, TW-37, 24h


title: Sorafenib_3.72_24 [CR10D2]

source_name: H-STS NET cell line, Sorafenib, 24h

value: Sorafenib


title: Sorafenib_3.72_24 [CR10D1]


title: Vincristine_0.0008_6 [CR11B10]


title: GSK461364_0.01_24 [CR10C9]

source_name: H-STS NET cell line, GSK461364, 24h


title: DMSO__24 [CR10D4]


title: Vorinostat_0.2_6 [CR10B7]

source_name: H-STS NET cell line, Vorinostat, 6h


title: DMSO__24 [CR10D3]


title: TW-37_4_6 [CR10A2]

source_name: H-STS NET cell line, TW-37, 6h


title: TW-37_4_6 [CR10A1]


title: Bortezomib_0.02_24 [CR10C3]

source_name: H-STS NET cell line, Bortezomib, 24h

value: Bortezomib


title: TW-37_4_24 [CR10C2]


title: Sorafenib_3.72_6 [CR10B2]

source_name: H-STS NET cell line, Sorafenib, 6h


title: Pluripotin_0.005_6 [CR10A7]

source_name: H-STS NET cell line, Pluripotin, 6h


title: Pluripotin_0.005_6 [CR10A8]


title: GSK461364_0.01_6 [CR10A9]

source_name: H-STS NET cell line, GSK461364, 6h


title: GSK461364_0.01_6 [CR10A10]


title: DMSO__6 [CR10B4]

value: DMSO


title: DMSO__6 [CR10B3]


title: GSK1210151A_0.88_24 [CR10C12]

source_name: H-STS NET cell line, GSK1210151A, 24h


title: Sorafenib_3.72_6 [CR10B1]


title: Bortezomib_0.02_6 [CR10A3]

source_name: H-STS NET cell line, Bortezomib, 6h


title: GSK1210151A_0.88_24 [CR10C11]


title: GSK461364_0.01_24 [CR10C10]


title: Pluripotin_0.005_24 [CR10C7]


title: Vorinostat_0.2_6 [CR10B8]


title: Bortezomib_0.02_24 [CR10C4]


title: Erastin_10_24 [CR10D6]

source_name: H-STS NET cell line, Erastin, 24h

value: Erastin


title: Gemcitabine_0.05_24 [CR10D12]

source_name: H-STS NET cell line, Gemcitabine, 24h

value: Gemcitabine


title: Erastin_10_24 [CR10D5]


title: Bortezomib_0.0088_24 [CR10C5]


title: GSK1210151A_0.88_6 [CR10A11]

source_name: H-STS NET cell line, GSK1210151A, 6h


title: DMSO__24 [CR10D9]

source_name: H-STS NET cell line, DMSO, 24h


title: GSK1210151A_0.88_6 [CR10A12]


title: Gemcitabine_0.05_6 [CR10B11]

source_name: H-STS NET cell line, Gemcitabine, 6h


title: Bortezomib_0.0088_24 [CR10C6]


title: Erastin_10_6 [CR10B6]

source_name: H-STS NET cell line, Erastin, 6h


title: DMSO__6 [CR10B10]

source_name: H-STS NET cell line, DMSO, 6h


title: DMSO__6 [CR10B9]


title: Bortezomib_0.02_6 [CR10A4]


title: SCH-79797_0.06_24 [CR09C12]

source_name: H-STS NET cell line, SCH-79797, 24h


title: Bortezomib_0.0088_6 [CR10A5]


title: SCH-529074_0.48_24 [CR09C5]

source_name: H-STS NET cell line, SCH-529074, 24h


title: SCH-79797_0.06_24 [CR09C11]


title: SB-743921_0.0004_24 [CR09D9]

source_name: H-STS NET cell line, SB-743921, 24h


title: SB-743921_0.0004_24 [CR09D10]


title: Bortezomib_0.0088_6 [CR10A6]


title: Gemcitabine_0.05_24 [CR10D11]


title: SB-225002_0.25_24 [CR09C9]

source_name: H-STS NET cell line, SB-225002, 24h


title: DMSO__24 [CR10D10]


title: Rigosertib_0.1_24 [CR09C4]

source_name: H-STS NET cell line, Rigosertib, 24h

value: Rigosertib


title: Rigosertib_0.1_24 [CR09C3]


title: PHA-665752_2.88_24 [CR09D7]

source_name: H-STS NET cell line, PHA-665752, 24h


title: PHA-665752_2.88_24 [CR09D8]


title: SB-225002_0.25_24 [CR09C10]


title: Paclitaxel_0.003_24 [CR09C8]

source_name: H-STS NET cell line, Paclitaxel, 24h

value: Paclitaxel


title: Gemcitabine_0.05_6 [CR10B12]


title: Paclitaxel_0.003_24 [CR09C7]


title: PAC-1_4_24 [CR09C1]

source_name: H-STS NET cell line, PAC-1, 24h


title: PF-3758309_0.008_24 [CR09D2]

source_name: H-STS NET cell line, PF-3758309, 24h


title: Erastin_10_6 [CR10B5]


title: PAC-1_4_24 [CR09C2]


title: Istradefylline_20_24 [CR09D11]

source_name: H-STS NET cell line, Istradefylline, 24h

value: Istradefylline


title: FK866_20_24 [CR09D5]

source_name: H-STS NET cell line, FK866, 24h


title: Istradefylline_20_24 [CR09D12]


title: DMSO__24 [CR09D4]


title: FK866_20_24 [CR09D6]


title: SCH-529074_0.48_24 [CR09C6]


title: DMSO__24 [CR09D3]


title: SCH-79797_0.06_6 [CR09A12]

source_name: H-STS NET cell line, SCH-79797, 6h


title: SB-743921_0.0004_6 [CR09B10]

source_name: H-STS NET cell line, SB-743921, 6h


title: SCH-529074_0.48_6 [CR09A5]

source_name: H-STS NET cell line, SCH-529074, 6h


title: SB-743921_0.0004_6 [CR09B9]


title: SCH-529074_0.48_6 [CR09A6]


title: SB-225002_0.25_6 [CR09A9]

source_name: H-STS NET cell line, SB-225002, 6h


title: SB-225002_0.25_6 [CR09A10]


title: PHA-665752_2.88_6 [CR09B7]

source_name: H-STS NET cell line, PHA-665752, 6h


title: PF-3758309_0.008_6 [CR09B1]

source_name: H-STS NET cell line, PF-3758309, 6h


title: PAC-1_4_6 [CR09A2]

source_name: H-STS NET cell line, PAC-1, 6h


title: Rigosertib_0.1_6 [CR09A3]

source_name: H-STS NET cell line, Rigosertib, 6h


title: Rigosertib_0.1_6 [CR09A4]


title: Paclitaxel_0.003_6 [CR09A7]

source_name: H-STS NET cell line, Paclitaxel, 6h


title: PHA-665752_2.88_6 [CR09B8]


title: Istradefylline_20_6 [CR09B12]

source_name: H-STS NET cell line, Istradefylline, 6h


title: PF-3758309_0.008_24 [CR09D1]


title: Paclitaxel_0.003_6 [CR09A8]


title: PAC-1_4_6 [CR09A1]


title: FK866_20_6 [CR09B6]

source_name: H-STS NET cell line, FK866, 6h


title: Istradefylline_20_6 [CR09B11]


title: PF-3758309_0.008_6 [CR09B2]


title: DMSO__6 [CR09B4]

source_name: H-STS NET cell line, DMSO, 6h


title: SCH-79797_0.06_6 [CR09A11]


title: DMSO__6 [CR09B3]


title: FK866_20_6 [CR09B5]


title: Nutlin-3_0.84_24 [CR08D11]

source_name: H-STS NET cell line, Nutlin-3, 24h


title: Necrosulfonamide_4_24 [CR08C11]

source_name: H-STS NET cell line, Necrosulfonamide, 24h

value: Necrosulfonamide


title: Necrosulfonamide_4_24 [CR08C12]


title: Neratinib_0.25_24 [CR08D6]

source_name: H-STS NET cell line, Neratinib, 24h

value: Neratinib


title: Neratinib_0.25_24 [CR08D5]


title: ML210_0.04_24 [CR08C6]

source_name: H-STS NET cell line, ML210, 24h


title: MK-1775_0.08_24 [CR08D9]

source_name: H-STS NET cell line, MK-1775, 24h


title: MK-1775_0.08_24 [CR08D10]


title: Mithramycin A_0.024_24 [CR08C3]

source_name: H-STS NET cell line, Mithramycin A, 24h

value: Mithramycin A


title: MG-132_0.25_24 [CR08D7]

source_name: H-STS NET cell line, MG-132, 24h


title: Manumycin A_4.32_24 [CR08D2]

source_name: H-STS NET cell line, Manumycin A, 24h

value: Manumycin A


title: Manumycin A_4.32_24 [CR08D1]


title: Mitomycin C_0.44_24 [CR08C9]

source_name: H-STS NET cell line, Mitomycin C, 24h

value: Mitomycin C


title: Nutlin-3_0.84_24 [CR08D12]


title: Mitomycin C_0.44_24 [CR08C10]


title: Mithramycin A_0.024_24 [CR08C4]


title: Linifanib_5_24 [CR08C7]

source_name: H-STS NET cell line, Linifanib, 24h

value: Linifanib


title: DMSO__24 [CR08D4]

source_name: H-STS NET cell line, DMSO, 24h

value: H-STS NET


title: Linifanib_5_24 [CR08C8]


title: KX2-391_0.024_24 [CR08C1]

source_name: H-STS NET cell line, KX2-391, 24h


title: KX2-391_0.024_24 [CR08C2]


title: DMSO__24 [CR08D3]


title: MG-132_0.25_24 [CR08D8]


title: ML210_0.04_24 [CR08C5]


title: Necrosulfonamide_4_6 [CR08A12]

source_name: H-STS NET cell line, Necrosulfonamide, 6h


title: Nutlin-3_0.84_6 [CR08B11]

source_name: H-STS NET cell line, Nutlin-3, 6h


title: MK-1775_0.08_6 [CR08B9]

source_name: H-STS NET cell line, MK-1775, 6h


title: ML210_0.04_6 [CR08A6]

source_name: H-STS NET cell line, ML210, 6h


title: ML210_0.04_6 [CR08A5]


title: Necrosulfonamide_4_6 [CR08A11]


title: Mitomycin C_0.44_6 [CR08A9]

source_name: H-STS NET cell line, Mitomycin C, 6h


title: Neratinib_0.25_6 [CR08B5]

source_name: H-STS NET cell line, Neratinib, 6h


title: Mitomycin C_0.44_6 [CR08A10]


title: Mithramycin A_0.024_6 [CR08A3]

source_name: H-STS NET cell line, Mithramycin A, 6h


title: MG-132_0.25_6 [CR08B8]

source_name: H-STS NET cell line, MG-132, 6h


title: MG-132_0.25_6 [CR08B7]


title: Nutlin-3_0.84_6 [CR08B12]


title: Linifanib_5_6 [CR08A7]

source_name: H-STS NET cell line, Linifanib, 6h


title: KX2-391_0.024_6 [CR08A1]

source_name: H-STS NET cell line, KX2-391, 6h


title: Manumycin A_4.32_6 [CR08B1]

source_name: H-STS NET cell line, Manumycin A, 6h


title: Linifanib_5_6 [CR08A8]


title: DMSO__6 [CR08B4]

source_name: H-STS NET cell line, DMSO, 6h


title: DMSO__6 [CR08B3]


title: Manumycin A_4.32_6 [CR08B2]


title: HMN_214_0.1_24 [CR07D5]

source_name: H-STS NET cell line, HMN_214, 24h


title: Ibrutinib_2.4_24 [CR07D11]

source_name: H-STS NET cell line, Ibrutinib, 24h

value: Ibrutinib


title: GW-405833_5.4_24 [CR07C12]

source_name: H-STS NET cell line, GW-405833, 24h


title: KX2-391_0.024_6 [CR08A2]


title: Neratinib_0.25_6 [CR08B6]


title: MK-1775_0.08_6 [CR08B10]


title: Gossypol_4.44_24 [CR07C6]

source_name: H-STS NET cell line, Gossypol, 24h

value: Gossypol


title: GW-405833_5.4_24 [CR07C11]


title: Gemcitabine_0.15_24 [CR07D9]

source_name: H-STS NET cell line, Gemcitabine, 24h


title: Gemcitabine_0.15_24 [CR07D10]


title: Gossypol_4.44_24 [CR07C5]


title: Doxorubicin_0.008_24 [CR07C3]

source_name: H-STS NET cell line, Doxorubicin, 24h

value: Doxorubicin


title: Doxorubicin_0.008_24 [CR07C4]


title: Erastin_15_24 [CR07C10]

source_name: H-STS NET cell line, Erastin, 24h


title: DMSO__24 [CR07D3]

source_name: H-STS NET cell line, DMSO, 24h


title: Dinaciclib_0.009_24 [CR07D2]

source_name: H-STS NET cell line, Dinaciclib, 24h

value: Dinaciclib


title: DMSO__24 [CR07D4]

value: DMSO


title: Docetaxel_0.002_24 [CR07D8]

source_name: H-STS NET cell line, Docetaxel, 24h

value: Docetaxel


title: Dasatinib_0.004_24 [CR07C8]

source_name: H-STS NET cell line, Dasatinib, 24h

value: Dasatinib


title: Dasatinib_0.004_24 [CR07C7]


title: HMN_214_0.1_24 [CR07D6]


title: Dinaciclib_0.009_24 [CR07D1]


title: Erastin_15_24 [CR07C9]

value: Erastin


title: Crizotinib_0.48_24 [CR07C1]

source_name: H-STS NET cell line, Crizotinib, 24h

value: Crizotinib


title: Crizotinib_0.48_24 [CR07C2]


title: Ibrutinib_2.4_24 [CR07D12]


title: HMN_214_0.1_6 [CR07B5]

source_name: H-STS NET cell line, HMN_214, 6h


title: GW-405833_5.4_6 [CR07A11]

source_name: H-STS NET cell line, GW-405833, 6h


title: Gossypol_4.44_6 [CR07A5]

source_name: H-STS NET cell line, Gossypol, 6h


title: HMN_214_0.1_6 [CR07B6]


title: Gossypol_4.44_6 [CR07A6]


title: GW-405833_5.4_6 [CR07A12]


title: Mithramycin A_0.024_6 [CR08A4]

source_name: H-STS NET cell line, Mithramycin A, 6h


title: Gemcitabine_0.15_6 [CR07B9]

source_name: H-STS NET cell line, Gemcitabine, 6h

value: Gemcitabine


title: Gemcitabine_0.15_6 [CR07B10]


title: Docetaxel_0.002_24 [CR07D7]


title: Erastin_15_6 [CR07A9]

source_name: H-STS NET cell line, Erastin, 6h


title: Ibrutinib_2.4_6 [CR07B12]

source_name: H-STS NET cell line, Ibrutinib, 6h


title: Doxorubicin_0.008_6 [CR07A3]

source_name: H-STS NET cell line, Doxorubicin, 6h


title: Docetaxel_0.002_6 [CR07B8]

source_name: H-STS NET cell line, Docetaxel, 6h


title: Doxorubicin_0.008_6 [CR07A4]


title: Docetaxel_0.002_6 [CR07B7]


title: DMSO__6 [CR07B4]

source_name: H-STS NET cell line, DMSO, 6h


title: DMSO__6 [CR07B3]


title: Dinaciclib_0.009_6 [CR07B1]

source_name: H-STS NET cell line, Dinaciclib, 6h


title: Dinaciclib_0.009_6 [CR07B2]


title: Ibrutinib_2.4_6 [CR07B11]


title: Dasatinib_0.004_6 [CR07A8]

source_name: H-STS NET cell line, Dasatinib, 6h


title: Dasatinib_0.004_6 [CR07A7]


title: Crizotinib_0.48_6 [CR07A1]

source_name: H-STS NET cell line, Crizotinib, 6h


title: Crizotinib_0.48_6 [CR07A2]


title: Ciclopirox_5_24 [CR06D12]

source_name: H-STS NET cell line, Ciclopirox, 24h

value: Ciclopirox


title: DMSO__24 [CR06D3]

source_name: H-STS NET cell line, DMSO, 24h


title: Erastin_15_6 [CR07A10]


title: Cerulenin_0.68_24 [CR06C12]

source_name: H-STS NET cell line, Cerulenin, 24h

value: Cerulenin


title: Bexarotene_20_24 [CR06D9]

source_name: H-STS NET cell line, Bexarotene, 24h

value: Bexarotene


title: Cerulenin_0.68_24 [CR06C11]


title: CHM-1_0.084_24 [CR06D6]

source_name: H-STS NET cell line, CHM-1, 24h


title: CHM-1_0.084_24 [CR06D5]


title: Brivanib_7_24 [CR06C5]

source_name: H-STS NET cell line, Brivanib, 24h

value: Brivanib


title: Brivanib_7_24 [CR06C6]


title: Bardoxolone methyl_0.15_24 [CR06C9]

source_name: H-STS NET cell line, Bardoxolone methyl, 24h

value: Bardoxolone methyl


title: Bardoxolone methyl_0.15_24 [CR06C10]


title: Bafetinib_3.24_24 [CR06C4]

source_name: H-STS NET cell line, Bafetinib, 24h

value: Bafetinib


title: AZD7762_0.03_24 [CR06D7]

source_name: H-STS NET cell line, AZD7762, 24h

value: H-STS NET


title: AZD7762_0.03_24 [CR06D8]


title: AZD6482_0.322_24 [CR06D1]

source_name: H-STS NET cell line, AZD6482, 24h


title: (5Z)-7-Oxozeanol_0.22_24 [CR06C2]

source_name: H-STS NET cell line, (5Z)-7-Oxozeanol, 24h


title: Afatinib_1_24 [CR06C7]

source_name: H-STS NET cell line, Afatinib, 24h

value: Afatinib


title: Afatinib_1_24 [CR06C8]


title: DMSO__24 [CR06D4]


title: DMSO__6 [CR06B4]


title: (5Z)-7-Oxozeanol_0.22_24 [CR06C1]


title: DMSO__6 [CR06B3]


title: CHM-1_0.084_6 [CR06B6]

source_name: H-STS NET cell line, CHM-1, 6h


title: Ciclopirox_5_6 [CR06B11]

source_name: H-STS NET cell line, Ciclopirox, 6h


title: Cerulenin_0.68_6 [CR06A12]

source_name: H-STS NET cell line, Cerulenin, 6h


title: Bexarotene_20_24 [CR06D10]


title: Ciclopirox_5_24 [CR06D11]


title: Cerulenin_0.68_6 [CR06A11]


title: Bafetinib_3.24_24 [CR06C3]


title: AZD6482_0.322_24 [CR06D2]


title: Bexarotene_20_6 [CR06B9]

source_name: H-STS NET cell line, Bexarotene, 6h


title: Brivanib_7_6 [CR06A6]

source_name: H-STS NET cell line, Brivanib, 6h


title: Bexarotene_20_6 [CR06B10]


title: AZD7762_0.03_6 [CR06B7]

source_name: H-STS NET cell line, AZD7762, 6h


title: Bafetinib_3.24_6 [CR06A4]

source_name: H-STS NET cell line, Bafetinib, 6h


title: Brivanib_7_6 [CR06A5]


title: AZD7762_0.03_6 [CR06B8]


title: Bafetinib_3.24_6 [CR06A3]


title: Afatinib_1_6 [CR06A8]

source_name: H-STS NET cell line, Afatinib, 6h


title: AZD6482_0.322_6 [CR06B2]

source_name: H-STS NET cell line, AZD6482, 6h


title: AZD6482_0.322_6 [CR06B1]


title: Bardoxolone methyl_0.15_6 [CR06A9]

source_name: H-STS NET cell line, Bardoxolone methyl, 6h


title: Bardoxolone methyl_0.15_6 [CR06A10]


title: (5Z)-7-Oxozeanol_0.22_6 [CR06A2]

source_name: H-STS NET cell line, (5Z)-7-Oxozeanol, 6h


title: CHM-1_0.084_6 [CR06B5]


title: Piperlongumine_1.04_24 [CR05D12]

source_name: H-STS NET cell line, Piperlongumine, 24h

value: Piperlongumine


title: Piperlongumine_1.04_24 [CR05D11]


title: Panobinostat_0.005_24 [CR05D6]

source_name: H-STS NET cell line, Panobinostat, 24h

value: Panobinostat


title: Afatinib_1_6 [CR06A7]


title: MST-312_1.68_24 [CR05C6]

source_name: H-STS NET cell line, MST-312, 24h


title: Panobinostat_0.005_24 [CR05D5]


title: Ciclopirox_5_6 [CR06B12]


title: MST-312_1.68_24 [CR05C5]


title: (5Z)-7-Oxozeanol_0.22_6 [CR06A1]


title: KHS101_1.2_24 [CR05C9]

source_name: H-STS NET cell line, KHS101, 24h


title: KW 2449_5.52_24 [CR05D10]

source_name: H-STS NET cell line, KW 2449, 24h


title: KHS101_1.2_24 [CR05C10]


title: GSK1210151A_1.32_24 [CR05D2]

source_name: H-STS NET cell line, GSK1210151A, 24h


title: GSK461364_0.05_24 [CR05D7]

source_name: H-STS NET cell line, GSK461364, 24h


title: JNJ-26854165_0.6_24 [CR05C3]

source_name: H-STS NET cell line, JNJ-26854165, 24h


title: GSK461364_0.05_24 [CR05D8]


title: JNJ-26854165_0.6_24 [CR05C4]


title: GSK1210151A_1.32_24 [CR05D1]


title: GDC-0941_0.05_24 [CR05C8]

source_name: H-STS NET cell line, GDC-0941, 24h


title: Foretinib_0.214_24 [CR05C1]

source_name: H-STS NET cell line, Foretinib, 24h

value: Foretinib


title: Foretinib_0.214_24 [CR05C2]


title: DMSO__24 [CR05D4]

source_name: H-STS NET cell line, DMSO, 24h

value: DMSO


title: GDC-0941_0.05_24 [CR05C7]


title: Panobinostat_0.005_6 [CR05B5]

source_name: H-STS NET cell line, Panobinostat, 6h


title: Piperlongumine_1.04_6 [CR05B11]

source_name: H-STS NET cell line, Piperlongumine, 6h


title: DMSO__24 [CR05D3]


title: MST-312_1.68_6 [CR05A5]

source_name: H-STS NET cell line, MST-312, 6h


title: KHS101_1.2_6 [CR05A9]

source_name: H-STS NET cell line, KHS101, 6h


title: JNJ-26854165_0.6_6 [CR05A4]

source_name: H-STS NET cell line, JNJ-26854165, 6h


title: MST-312_1.68_6 [CR05A6]


title: Panobinostat_0.005_6 [CR05B6]


title: JNJ-26854165_0.6_6 [CR05A3]


title: GSK461364_0.05_6 [CR05B8]

source_name: H-STS NET cell line, GSK461364, 6h


title: KW 2449_5.52_6 [CR05B9]

source_name: H-STS NET cell line, KW 2449, 6h


title: GSK461364_0.05_6 [CR05B7]


title: KW 2449_5.52_6 [CR05B10]


title: KW 2449_5.52_24 [CR05D9]


title: GSK1210151A_1.32_6 [CR05B2]

source_name: H-STS NET cell line, GSK1210151A, 6h


title: KHS101_1.2_6 [CR05A10]


title: GSK1210151A_1.32_6 [CR05B1]


title: GDC-0941_0.05_6 [CR05A8]

source_name: H-STS NET cell line, GDC-0941, 6h


title: GDC-0941_0.05_6 [CR05A7]


title: DMSO__6 [CR05B4]

source_name: H-STS NET cell line, DMSO, 6h


title: Foretinib_0.214_6 [CR05A1]

source_name: H-STS NET cell line, Foretinib, 6h


title: Fluvastatin_0.76_24 [CR04D11]

source_name: H-STS NET cell line, Fluvastatin, 24h

value: Fluvastatin


title: DMSO__6 [CR05B3]


title: Foretinib_0.214_6 [CR05A2]


title: Fluvastatin_0.76_24 [CR04D12]


title: Flavopiridol_0.048_24 [CR04D09]

source_name: H-STS NET cell line, Flavopiridol, 24h

value: Flavopiridol


title: Fingolimod_4_24 [CR04D08]

source_name: H-STS NET cell line, Fingolimod, 24h

value: Fingolimod


title: Flavopiridol_0.048_24 [CR04D10]


title: Fingolimod_4_24 [CR04D07]


title: DBeQ_1.6_24 [CR04D06]

source_name: H-STS NET cell line, DBeQ, 24h

value: DBeQ


title: DBeQ_1.6_24 [CR04D05]


title: CD-437_0.236_24 [CR04D03]

source_name: H-STS NET cell line, CD-437, 24h


title: CD-437_0.236_24 [CR04D04]


title: Brefeldin A_0.042_24 [CR04C11]

source_name: H-STS NET cell line, Brefeldin A, 24h

value: Brefeldin A


title: DMSO__24 [CR04D01]

source_name: H-STS NET cell line, DMSO, 24h


title: DMSO__24 [CR04D02]


title: Brefeldin A_0.042_24 [CR04C12]


title: At13387_0.07_24 [CR04C03]

source_name: H-STS NET cell line, At13387, 24h


title: BMS-754807_0.72_24 [CR04C07]

source_name: H-STS NET cell line, BMS-754807, 24h


title: Flavopiridol_0.048_6 [CR04B10]

source_name: H-STS NET cell line, Flavopiridol, 6h


title: Fluvastatin_0.76_6 [CR04B11]

source_name: H-STS NET cell line, Fluvastatin, 6h


title: At13387_0.07_24 [CR04C04]


title: BI-2536_0.009_24 [CR04C05]

source_name: H-STS NET cell line, BI-2536, 24h


title: Parthenolide_0.8_24 [CR04C02]

source_name: H-STS NET cell line, Parthenolide, 24h

value: Parthenolide


title: BI-2536_0.009_24 [CR04C06]


title: Parthenolide_0.8_24 [CR04C01]


title: BMS-754807_0.72_24 [CR04C08]


title: Flavopiridol_0.048_6 [CR04B09]


title: Fingolimod_4_6 [CR04B07]

source_name: H-STS NET cell line, Fingolimod, 6h


title: DBeQ_1.6_6 [CR04B06]

source_name: H-STS NET cell line, DBeQ, 6h


title: CD-437_0.236_6 [CR04B04]

source_name: H-STS NET cell line, CD-437, 6h


title: CD-437_0.236_6 [CR04B03]


title: DMSO__6 [CR04B02]

source_name: H-STS NET cell line, DMSO, 6h


title: DBeQ_1.6_6 [CR04B05]


title: Brefeldin A_0.042_6 [CR04A12]

source_name: H-STS NET cell line, Brefeldin A, 6h


title: Bortezomib_0.05_6 [CR04A10]

source_name: H-STS NET cell line, Bortezomib, 6h

value: Bortezomib


title: DMSO__6 [CR04B01]


title: Bortezomib_0.05_6 [CR04A09]


title: BMS-754807_0.72_6 [CR04A07]

source_name: H-STS NET cell line, BMS-754807, 6h


title: BMS-754807_0.72_6 [CR04A08]


title: At13387_0.07_6 [CR04A04]

source_name: H-STS NET cell line, At13387, 6h


title: Fluvastatin_0.76_6 [CR04B12]


title: BI-2536_0.009_6 [CR04A06]

source_name: H-STS NET cell line, BI-2536, 6h


title: At13387_0.07_6 [CR04A03]


title: Parthenolide_0.8_6 [CR04A02]

source_name: H-STS NET cell line, Parthenolide, 6h


title: YM-155_0.00006_24 [CR03D09]

source_name: H-STS NET cell line, YM-155, 24h


title: YM-155_0.00006_24 [CR03D10]


title: Sunitinib_1.76_24 [CR03D03]

source_name: H-STS NET cell line, Sunitinib, 24h

value: Sunitinib


title: Sunitinib_0.176_24 [CR03D05]


title: YM-155_0.0007_24 [CR03D08]


title: Sunitinib_0.176_24 [CR03D06]


title: YM-155_0.0007_24 [CR03D07]


title: Brefeldin A_0.042_6 [CR04A11]


title: SNX-2112_0.006_24 [CR03D02]

source_name: H-STS NET cell line, SNX-2112, 24h


title: SNX-2112_0.006_24 [CR03D01]


title: Sunitinib_1.76_24 [CR03D04]


title: Fingolimod_4_6 [CR04B08]


title: Obatoclax_0.068_24 [CR03C06]

source_name: H-STS NET cell line, Obatoclax, 24h

value: Obatoclax


title: Obatoclax_0.068_24 [CR03C05]


title: DMSO_0_24 [CR03C02]

source_name: H-STS NET cell line, DMSO, 24h


title: DMSO_0_24 [CR03C01]


title: BI-2536_0.009_6 [CR04A05]


title: NVP-231_0.028_24 [CR03B12]

source_name: H-STS NET cell line, NVP-231, 24h


title: Obatoclax_0.68_24 [CR03C04]


title: NVP-231_0.028_24 [CR03B11]


title: NVP-231_0.27_24 [CR03B10]


title: Obatoclax_0.68_24 [CR03C03]


title: NVP-231_0.27_24 [CR03B09]


title: Parthenolide_0.8_6 [CR04A01]


title: Methylstat_0.072_24 [CR03B08]

source_name: H-STS NET cell line, Methylstat, 24h

value: Methylstat


title: Methylstat_0.72_24 [CR03B06]


title: Methylstat_0.072_24 [CR03B07]


title: SNX-2112_0.066_24 [CR03C12]


title: Alisertib_0.044_24 [CR03A02]

source_name: H-STS NET cell line, Alisertib, 24h

value: Alisertib


title: Alisertib_0.044_24 [CR03A01]

value: H-STS NET


title: YM-155_0.00006_6 [CR2D10]

source_name: H-STS NET cell line, YM-155, 6h


title: Methylstat_0.72_24 [CR03B05]


title: YM-155_0.0007_6 [CR2D07]


title: Sunitinib_0.176_6 [CR2D06]

source_name: H-STS NET cell line, Sunitinib, 6h


title: Alisertib_0.004_24 [CR03A04]


title: YM-155_0.0007_6 [CR2D08]


title: SNX-2112_0.006_6 [CR2D02]

source_name: H-STS NET cell line, SNX-2112, 6h


title: Sunitinib_1.76_6 [CR2D03]


title: Sunitinib_0.176_6 [CR2D05]


title: SNX-2112_0.006_6 [CR2D01]


title: Alisertib_0.004_24 [CR03A03]


title: SNX-2112_0.066_6 [CR2C11]


title: Obatoclax_0.068_6 [CR2C06]

source_name: H-STS NET cell line, Obatoclax, 6h


title: SNX-2112_0.066_6 [CR2C12]


title: SNX-2112_0.066_24 [CR03C11]


title: Obatoclax_0.68_6 [CR2C03]


title: DMSO_0_6 [CR2C01]

source_name: H-STS NET cell line, DMSO, 6h


title: NVP-231_0.028_6 [CR2B12]

source_name: H-STS NET cell line, NVP-231, 6h


title: NVP-231_0.028_6 [CR2B11]


title: YM-155_0.00006_6 [CR2D09]


title: NVP-231_0.27_6 [CR2B10]


title: NVP-231_0.27_6 [CR2B09]


title: Methylstat_0.072_6 [CR2B08]

source_name: H-STS NET cell line, Methylstat, 6h


title: Sunitinib_1.76_6 [CR2D04]


title: Methylstat_0.072_6 [CR2B07]


title: Methylstat_0.72_6 [CR2B05]


title: Alisertib_0.004_6 [CR2A03]

source_name: H-STS NET cell line, Alisertib, 6h


title: Alisertib_0.004_6 [CR2A04]


title: Obatoclax_0.068_6 [CR2C05]


title: Obatoclax_0.68_6 [CR2C04]


title: DMSO_0.2_6 [CR1F07]


title: Alisertib_0.044_6 [CR2A02]


title: Alisertib_0.044_6 [CR2A01]


title: DMSO_0.2_6 [CR1F08]


title: DMSO_0.2_24 [CR1F09]


title: DMSO_0.2_6 [CR1F06]


title: DMSO_0.2_24 [CR1F10]


title: DMSO_0_6 [CR2C02]


title: YK-4-279_0.065_24 [CR1F04]

source_name: H-STS NET cell line, YK-4-279, 24h


title: YK-4-279_0.65_24 [CR1F03]


title: Topotecan_0.0138_24 [CR1F01]

source_name: H-STS NET cell line, Topotecan, 24h

value: Topotecan


title: MK-2206_0.684_24 [CR1E10]

source_name: H-STS NET cell line, MK-2206, 24h


title: Topotecan_0.00138_24 [CR1F02]


title: Tivantinib_0.0709_24 [CR1E12]

source_name: H-STS NET cell line, Tivantinib, 24h

value: Tivantinib


title: MK-2206_6.84_24 [CR1E09]


title: Topotecan_0.00138_24 [CR1E06]


title: YK-4-279_0.065_24 [CR1E08]


title: YK-4-279_0.65_24 [CR1E07]


title: Tivantinib_0.0709_24 [CR1E04]


title: Methylstat_0.72_6 [CR2B06]


title: Tivantinib_0.709_24 [CR1E03]


title: DMSO_0.2_24 [CR1F11]


title: MK-2206_6.84_24 [CR1E01]


title: YK-4-279_0.065_6 [CR1D12]

source_name: H-STS NET cell line, YK-4-279, 6h


title: MK-2206_0.684_24 [CR1E02]


title: YK-4-279_0.65_6 [CR1D11]


title: Topotecan_0.00138_6 [CR1D10]

source_name: H-STS NET cell line, Topotecan, 6h


title: Topotecan_0.0138_6 [CR1D09]


title: Tivantinib_0.0709_6 [CR1D08]

source_name: H-STS NET cell line, Tivantinib, 6h


title: LoVo MEK inhibitor 1000 nM rep2

city: Fujisawa

first: Kanae

last: Gamo

state: Kanagawa

address: 26-1, Muraoka-higashi 2-chome

department: Immunology Unit, Research

institute: Takeda Pharmaceutical Company Limited

data_processing:
Base calling was performed using software provided with the Ion Torrent Proton sequencer (Torrent suite ver.5.0.4.0).
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence, then mapped to hg19_AmpliSeq_Transcriptome_ERCC_v1 using software provided with the Ion Torrent Proton sequencer (AmpliSeqRNA v5.0.4.0).
Count data were calculated using software provided with the Ion Torrent Proton sequencer (AmpliSeqRNA v5.0.4.0).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include gene symbol and gene expression (read count) for each sample.

source_name: LoVo treated with MEK inhibitor

growth_protocol: LoVo cells were cultured with F-12K in the presence of 10% FBS

extract_protocol:
Extraction of total RNA was performed according to the manufacturer's instructions (RNeasy, QIAGEN)
10 ng of total RNA from each dose and biological replicate were reverse transcribed to cDNA with SuperScript® VILO™ cDNA Synthesis Kit (Thermo Fisher Scientific). Then cDNA is amplified using Ion AmpliSeq™ technology (Thermo Fisher Scientific). After primer digestion, adapters and molecular barcodes were ligated to the amplicons followed by magnetic bead purification. Libraries were then diluted to 100 pM and pooled equally, with eighteen individual samples per pool.

treatment_protocol: Treatment with test article or DMSO for 24 hours

value: LoVo

tag: treatment

value: MEK inhibitor

tag: sample type

value: Colorectal cancer cell line


title: LoVo MEK inhibitor 1000 nM rep1


title: LoVo MEK inhibitor 300 nM rep3


title: Tivantinib_0.709_6 [CR1D07]


title: Topotecan_0.00138_6 [CR1D02]


title: MK-2206_0.684_6 [CR1D06]

source_name: H-STS NET cell line, MK-2206, 6h


title: Tivantinib_0.709_24 [CR1E11]


title: MK-2206_6.84_6 [CR1D05]


title: YK-4-279_0.65_6 [CR1D03]


title: Tivantinib_0.0709_6 [CR1C12]


title: LoVo MEK inhibitor 100 nM rep1